Merge commit 'f95a912' into cmake

applications/CMakeLists.txt

@@ -1,5 +1,7 @@
 set(files
     __init__.py
+    alos2App.py
+    alos2burstApp.py
     dataTileManager.py
     dem.py
     demdb.py
@@ -22,6 +24,7 @@ set(files
     upsampleDem.py
     waterMask.py
     wbd.py
+    wbd_with_correction.py
     wbdStitcher.py
     )
 

applications/SConscript

@@ -78,7 +78,10 @@ listFiles = ['mdx.py',
              'wbd.py',
 	     'downsampleDEM.py',
 	     'gdal2isce_xml.py',
-             'scansarApp.py']
+           'alos2App.py',
+           'alos2burstApp.py',
+             'scansarApp.py',
+             'wbd_with_correction.py']
 #             'isce2he5.py']
 
 envapplications.Install(install, listFiles)

applications/wbd_with_correction.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python3
+
+#
+# Author: Cunren Liang
+# Copyright 2020
+#
+
+
+import sys
+import isce
+from isceobj.Alos2Proc.runDownloadDem import download_wbd
+
+
+if __name__=="__main__":
+
+    if len(sys.argv) < 5:
+        print("usage: wbd_with_correction.py s n w e")
+        print("where s, n, w, e are latitude, longitude bounds in degrees")
+        sys.exit(0)
+
+    snwe = list(map(float,sys.argv[1:]))
+
+    download_wbd(snwe[0], snwe[1], snwe[2], snwe[3])

components/isceobj/Alos2Proc/Alos2Proc.py

@@ -0,0 +1,949 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import logging.config
+from iscesys.Component.Component import Component
+from iscesys.DateTimeUtil.DateTimeUtil import DateTimeUtil as DTU
+from iscesys.Compatibility import Compatibility
+
+
+MASTER_DATE = Component.Parameter('masterDate',
+                                public_name='master date',
+                                default=None,
+                                type=str,
+                                mandatory=True,
+                                doc='master acquistion date')
+
+SLAVE_DATE = Component.Parameter('slaveDate',
+                                public_name='slave date',
+                                default=None,
+                                type=str,
+                                mandatory=True,
+                                doc='slave acquistion date')
+
+MODE_COMBINATION = Component.Parameter('modeCombination',
+                                public_name='mode combination',
+                                default=None,
+                                type=int,
+                                mandatory=True,
+                                doc='mode combination')
+
+MASTER_FRAMES = Component.Parameter('masterFrames',
+                                public_name = 'master frames',
+                                default = None,
+                                type=str,
+                                container=list,
+                                mandatory=False,
+                                doc = 'master frames to process')
+
+SLAVE_FRAMES = Component.Parameter('slaveFrames',
+                                public_name = 'slave frames',
+                                default = None,
+                                type=str,
+                                container=list,
+                                mandatory=False,
+                                doc = 'slave frames to process')
+
+STARTING_SWATH = Component.Parameter('startingSwath',
+                                public_name='starting swath',
+                                default=1,
+                                type=int,
+                                mandatory=False,
+                                doc="starting swath to process")
+
+ENDING_SWATH = Component.Parameter('endingSwath',
+                                public_name='ending swath',
+                                default=5,
+                                type=int,
+                                mandatory=False,
+                                doc="ending swath to process")
+
+BURST_UNSYNCHRONIZED_TIME = Component.Parameter('burstUnsynchronizedTime',
+                                public_name = 'burst unsynchronized time',
+                                default = None,
+                                type = float,
+                                mandatory = False,
+                                doc = 'burst unsynchronized time in second')
+
+BURST_SYNCHRONIZATION = Component.Parameter('burstSynchronization',
+                                public_name = 'burst synchronization',
+                                default = None,
+                                type = float,
+                                mandatory = False,
+                                doc = 'average burst synchronization of all swaths and frames in percentage')
+
+SWATH_RANGE_OFFSET_GEOMETRICAL_MASTER = Component.Parameter('swathRangeOffsetGeometricalMaster',
+                                public_name = 'swath range offset from geometry master',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'swath range offset from geometry master')
+
+SWATH_AZIMUTH_OFFSET_GEOMETRICAL_MASTER = Component.Parameter('swathAzimuthOffsetGeometricalMaster',
+                                public_name = 'swath azimuth offset from geometry master',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'swath azimuth offset from geometry master')
+
+SWATH_RANGE_OFFSET_MATCHING_MASTER = Component.Parameter('swathRangeOffsetMatchingMaster',
+                                public_name = 'swath range offset from matching master',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'swath range offset from matching master')
+
+SWATH_AZIMUTH_OFFSET_MATCHING_MASTER = Component.Parameter('swathAzimuthOffsetMatchingMaster',
+                                public_name = 'swath azimuth offset from matching master',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'swath azimuth offset from matching master')
+
+SWATH_RANGE_OFFSET_GEOMETRICAL_SLAVE = Component.Parameter('swathRangeOffsetGeometricalSlave',
+                                public_name = 'swath range offset from geometry slave',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'swath range offset from geometry slave')
+
+SWATH_AZIMUTH_OFFSET_GEOMETRICAL_SLAVE = Component.Parameter('swathAzimuthOffsetGeometricalSlave',
+                                public_name = 'swath azimuth offset from geometry slave',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'swath azimuth offset from geometry slave')
+
+SWATH_RANGE_OFFSET_MATCHING_SLAVE = Component.Parameter('swathRangeOffsetMatchingSlave',
+                                public_name = 'swath range offset from matching slave',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'swath range offset from matching slave')
+
+SWATH_AZIMUTH_OFFSET_MATCHING_SLAVE = Component.Parameter('swathAzimuthOffsetMatchingSlave',
+                                public_name = 'swath azimuth offset from matching slave',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'swath azimuth offset from matching slave')
+
+
+
+FRAME_RANGE_OFFSET_GEOMETRICAL_MASTER = Component.Parameter('frameRangeOffsetGeometricalMaster',
+                                public_name = 'frame range offset from geometry master',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'frame range offset from geometry master')
+
+FRAME_AZIMUTH_OFFSET_GEOMETRICAL_MASTER = Component.Parameter('frameAzimuthOffsetGeometricalMaster',
+                                public_name = 'frame azimuth offset from geometry master',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'frame azimuth offset from geometry master')
+
+FRAME_RANGE_OFFSET_MATCHING_MASTER = Component.Parameter('frameRangeOffsetMatchingMaster',
+                                public_name = 'frame range offset from matching master',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'frame range offset from matching master')
+
+FRAME_AZIMUTH_OFFSET_MATCHING_MASTER = Component.Parameter('frameAzimuthOffsetMatchingMaster',
+                                public_name = 'frame azimuth offset from matching master',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'frame azimuth offset from matching master')
+
+FRAME_RANGE_OFFSET_GEOMETRICAL_SLAVE = Component.Parameter('frameRangeOffsetGeometricalSlave',
+                                public_name = 'frame range offset from geometry slave',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'frame range offset from geometry slave')
+
+FRAME_AZIMUTH_OFFSET_GEOMETRICAL_SLAVE = Component.Parameter('frameAzimuthOffsetGeometricalSlave',
+                                public_name = 'frame azimuth offset from geometry slave',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'frame azimuth offset from geometry slave')
+
+FRAME_RANGE_OFFSET_MATCHING_SLAVE = Component.Parameter('frameRangeOffsetMatchingSlave',
+                                public_name = 'frame range offset from matching slave',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'frame range offset from matching slave')
+
+FRAME_AZIMUTH_OFFSET_MATCHING_SLAVE = Component.Parameter('frameAzimuthOffsetMatchingSlave',
+                                public_name = 'frame azimuth offset from matching slave',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'frame azimuth offset from matching slave')
+
+NUMBER_RANGE_LOOKS1 = Component.Parameter('numberRangeLooks1',
+                                public_name='number of range looks 1',
+                                default=None,
+                                type=int,
+                                mandatory=False,
+                                doc="number of range looks when forming interferogram")
+
+NUMBER_AZIMUTH_LOOKS1 = Component.Parameter('numberAzimuthLooks1',
+                                public_name='number of azimuth looks 1',
+                                default=None,
+                                type=int,
+                                mandatory=False,
+                                doc="number of azimuth looks when forming interferogram")
+
+NUMBER_RANGE_LOOKS2 = Component.Parameter('numberRangeLooks2',
+                                public_name='number of range looks 2',
+                                default=None,
+                                type=int,
+                                mandatory=False,
+                                doc="number of range looks for further multiple looking")
+
+NUMBER_AZIMUTH_LOOKS2 = Component.Parameter('numberAzimuthLooks2',
+                                public_name='number of azimuth looks 2',
+                                default=None,
+                                type=int,
+                                mandatory=False,
+                                doc="number of azimuth looks for further multiple looking")
+
+NUMBER_RANGE_LOOKS_SIM = Component.Parameter('numberRangeLooksSim',
+                                public_name='number of range looks sim',
+                                default=None,
+                                type=int,
+                                mandatory=False,
+                                doc="number of range looks when simulating radar image")
+
+NUMBER_AZIMUTH_LOOKS_SIM = Component.Parameter('numberAzimuthLooksSim',
+                                public_name='number of azimuth looks sim',
+                                default=None,
+                                type=int,
+                                mandatory=False,
+                                doc="number of azimuth looks when simulating radar image")
+
+NUMBER_RANGE_LOOKS_ION = Component.Parameter('numberRangeLooksIon',
+                                public_name='number of range looks ion',
+                                default=None,
+                                type=int,
+                                mandatory=False,
+                                doc="number of range looks for ionospheric correction")
+
+NUMBER_AZIMUTH_LOOKS_ION = Component.Parameter('numberAzimuthLooksIon',
+                                public_name='number of azimuth looks ion',
+                                default=None,
+                                type=int,
+                                mandatory=False,
+                                doc="number of azimuth looks for ionospheric correction")
+
+SUBBAND_RADAR_WAVLENGTH = Component.Parameter('subbandRadarWavelength',
+                                public_name='lower and upper radar wavelength for ionosphere correction',
+                                default=None,
+                                type=float,
+                                mandatory=False,
+                                container = list,
+                                doc="lower and upper radar wavelength for ionosphere correction")
+
+RADAR_DEM_AFFINE_TRANSFORM = Component.Parameter('radarDemAffineTransform',
+                                public_name = 'radar dem affine transform parameters',
+                                default = None,
+                                type = float,
+                                mandatory = True,
+                                container = list,
+                                doc = 'radar dem affine transform parameters')
+
+
+MASTER_SLC = Component.Parameter('masterSlc',
+                                public_name='master slc',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='master slc file')
+
+SLAVE_SLC = Component.Parameter('slaveSlc',
+                                public_name='slave slc',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='slave slc file')
+
+MASTER_SWATH_OFFSET = Component.Parameter('masterSwathOffset',
+                                public_name='master swath offset',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='master swath offset file')
+
+SLAVE_SWATH_OFFSET = Component.Parameter('slaveSwathOffset',
+                                public_name='slave swath offset',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='slave swath offset file')
+
+MASTER_FRAME_OFFSET = Component.Parameter('masterFrameOffset',
+                                public_name='master frame offset',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='master frame offset file')
+
+SLAVE_FRAME_OFFSET = Component.Parameter('slaveFrameOffset',
+                                public_name='slave frame offset',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='slave frame offset file')
+
+MASTER_FRAME_PARAMETER = Component.Parameter('masterFrameParameter',
+                                public_name='master frame parameter',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='master frame parameter file')
+
+SLAVE_FRAME_PARAMETER = Component.Parameter('slaveFrameParameter',
+                                public_name='slave frame parameter',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='slave frame parameter file')
+
+MASTER_TRACK_PARAMETER = Component.Parameter('masterTrackParameter',
+                                public_name='master track parameter',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='master track parameter file')
+
+SLAVE_TRACK_PARAMETER = Component.Parameter('slaveTrackParameter',
+                                public_name='slave track parameter',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='slave track parameter file')
+
+DEM = Component.Parameter('dem',
+                                public_name='dem for coregistration',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='dem for coregistration file')
+
+DEM_GEO = Component.Parameter('demGeo',
+                                public_name='dem for geocoding',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='dem for geocoding file')
+
+WBD = Component.Parameter('wbd',
+                                public_name='water body',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='water body file')
+
+WBD_OUT = Component.Parameter('wbdOut',
+                                public_name='output water body',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='output water body file')
+
+INTERFEROGRAM = Component.Parameter('interferogram',
+                                public_name='interferogram',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='interferogram file')
+
+AMPLITUDE = Component.Parameter('amplitude',
+                                public_name='amplitude',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='amplitude file')
+
+DIFFERENTIAL_INTERFEROGRAM = Component.Parameter('differentialInterferogram',
+                                public_name='differential interferogram',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='differential interferogram file')
+
+MULTILOOK_DIFFERENTIAL_INTERFEROGRAM = Component.Parameter('multilookDifferentialInterferogram',
+                                public_name='multilook differential interferogram',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook differential interferogram file')
+
+MULTILOOK_DIFFERENTIAL_INTERFEROGRAM_ORIGINAL = Component.Parameter('multilookDifferentialInterferogramOriginal',
+                                public_name='original multilook differential interferogram',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='original multilook differential interferogram file')
+
+MULTILOOK_AMPLITUDE = Component.Parameter('multilookAmplitude',
+                                public_name='multilook amplitude',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook amplitude file')
+
+MULTILOOK_COHERENCE = Component.Parameter('multilookCoherence',
+                                public_name='multilook coherence',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook coherence file')
+
+MULTILOOK_PHSIG = Component.Parameter('multilookPhsig',
+                                public_name='multilook phase sigma',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook phase sigma file')
+
+FILTERED_INTERFEROGRAM = Component.Parameter('filteredInterferogram',
+                                public_name='filtered interferogram',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='filtered interferogram file')
+
+UNWRAPPED_INTERFEROGRAM = Component.Parameter('unwrappedInterferogram',
+                                public_name='unwrapped interferogram',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='unwrapped interferogram file')
+
+UNWRAPPED_MASKED_INTERFEROGRAM = Component.Parameter('unwrappedMaskedInterferogram',
+                                public_name='unwrapped masked interferogram',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='unwrapped masked interferogram file')
+
+LATITUDE = Component.Parameter('latitude',
+                                public_name='latitude',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='latitude file')
+
+LONGITUDE = Component.Parameter('longitude',
+                                public_name='longitude',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='longitude file')
+
+HEIGHT = Component.Parameter('height',
+                                public_name='height',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='height file')
+
+LOS = Component.Parameter('los',
+                                public_name='los',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='los file')
+
+SIM = Component.Parameter('sim',
+                                public_name='sim',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='sim file')
+
+MSK = Component.Parameter('msk',
+                                public_name='msk',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='msk file')
+
+RANGE_OFFSET = Component.Parameter('rangeOffset',
+                                public_name='range offset',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='range offset file')
+
+AZIMUTH_OFFSET = Component.Parameter('azimuthOffset',
+                                public_name='azimuth offset',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='azimuth offset file')
+
+
+MULTILOOK_LOS = Component.Parameter('multilookLos',
+                                public_name='multilook los',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook los file')
+
+MULTILOOK_MSK = Component.Parameter('multilookMsk',
+                                public_name='multilook msk',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook msk file')
+
+MULTILOOK_WBD_OUT = Component.Parameter('multilookWbdOut',
+                                public_name='multilook wbdOut',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook output water body file')
+
+MULTILOOK_LATITUDE = Component.Parameter('multilookLatitude',
+                                public_name='multilook latitude',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook latitude file')
+
+MULTILOOK_LONGITUDE = Component.Parameter('multilookLongitude',
+                                public_name='multilook longitude',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook longitude file')
+
+MULTILOOK_HEIGHT = Component.Parameter('multilookHeight',
+                                public_name='multilook height',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook height file')
+
+MULTILOOK_ION = Component.Parameter('multilookIon',
+                                public_name='multilook ionospheric phase',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='multilook ionospheric phase file')
+
+RECT_RANGE_OFFSET = Component.Parameter('rectRangeOffset',
+                                public_name='rectified range offset',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='rectified range offset file')
+
+GEO_INTERFEROGRAM = Component.Parameter('geoInterferogram',
+                                public_name='geocoded interferogram',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='geocoded interferogram file')
+
+GEO_MASKED_INTERFEROGRAM = Component.Parameter('geoMaskedInterferogram',
+                                public_name='geocoded masked interferogram',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='geocoded masked interferogram file')
+
+GEO_COHERENCE = Component.Parameter('geoCoherence',
+                                public_name='geocoded coherence',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='geocoded coherence file')
+
+GEO_LOS = Component.Parameter('geoLos',
+                                public_name='geocoded los',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='geocoded los file')
+
+GEO_ION = Component.Parameter('geoIon',
+                                public_name='geocoded ionospheric phase',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='geocoded ionospheric phase file')
+###################################################################
+
+#for dense offset
+OFFSET_IMAGE_TOPOFFSET = Component.Parameter('offsetImageTopoffset',
+                                public_name='offset image top offset',
+                                default=None,
+                                type=int,
+                                mandatory=False,
+                                doc="offset image top offset in samples")
+
+OFFSET_IMAGE_LEFTOFFSET = Component.Parameter('offsetImageLeftoffset',
+                                public_name='offset image left offset',
+                                default=None,
+                                type=int,
+                                mandatory=False,
+                                doc="offset image left offset in samples")
+
+SLAVE_SLC_COREGISTERED = Component.Parameter('slaveSlcCoregistered',
+                                public_name='coregistered slave slc',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='coregistered slave slc file')
+
+DENSE_OFFSET = Component.Parameter('denseOffset',
+                                public_name='dense offset',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='dense offset file')
+
+DENSE_OFFSET_SNR = Component.Parameter('denseOffsetSnr',
+                                public_name='dense offset snr',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='dense offset snr file')
+
+DENSE_OFFSET_COV = Component.Parameter('denseOffsetCov',
+                                public_name='dense offset covariance',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='dense offset covariance file')
+
+DENSE_OFFSET_FILT = Component.Parameter('denseOffsetFilt',
+                                public_name='filtered dense offset',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='filtered dense offset file')
+
+GEO_DENSE_OFFSET = Component.Parameter('GeoDenseOffset',
+                                public_name='geocoded dense offset',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='geocoded dense offset file')
+
+GEO_DENSE_OFFSET_SNR = Component.Parameter('GeoDenseOffsetSnr',
+                                public_name='geocoded dense offset snr',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='geocoded dense offset snr file')
+
+GEO_DENSE_OFFSET_FILT = Component.Parameter('GeoDenseOffsetFilt',
+                                public_name='geocoded dense offset with filtering',
+                                default=None,
+                                type=str,
+                                mandatory=False,
+                                doc='geocoded dense offset with filtering')
+###################################################################
+
+class Alos2Proc(Component):
+    """
+    This class holds the properties, along with methods (setters and getters)
+    to modify and return their values.
+    """
+
+    parameter_list = (MASTER_DATE,
+                      SLAVE_DATE,
+                      MODE_COMBINATION,
+                      MASTER_FRAMES,
+                      SLAVE_FRAMES,
+                      STARTING_SWATH,
+                      ENDING_SWATH,
+                      BURST_UNSYNCHRONIZED_TIME,
+                      BURST_SYNCHRONIZATION,
+                      SWATH_RANGE_OFFSET_GEOMETRICAL_MASTER,
+                      SWATH_AZIMUTH_OFFSET_GEOMETRICAL_MASTER,
+                      SWATH_RANGE_OFFSET_MATCHING_MASTER,
+                      SWATH_AZIMUTH_OFFSET_MATCHING_MASTER,
+                      SWATH_RANGE_OFFSET_GEOMETRICAL_SLAVE,
+                      SWATH_AZIMUTH_OFFSET_GEOMETRICAL_SLAVE,
+                      SWATH_RANGE_OFFSET_MATCHING_SLAVE,
+                      SWATH_AZIMUTH_OFFSET_MATCHING_SLAVE,
+                      FRAME_RANGE_OFFSET_GEOMETRICAL_MASTER,
+                      FRAME_AZIMUTH_OFFSET_GEOMETRICAL_MASTER,
+                      FRAME_RANGE_OFFSET_MATCHING_MASTER,
+                      FRAME_AZIMUTH_OFFSET_MATCHING_MASTER,
+                      FRAME_RANGE_OFFSET_GEOMETRICAL_SLAVE,
+                      FRAME_AZIMUTH_OFFSET_GEOMETRICAL_SLAVE,
+                      FRAME_RANGE_OFFSET_MATCHING_SLAVE,
+                      FRAME_AZIMUTH_OFFSET_MATCHING_SLAVE,
+                      NUMBER_RANGE_LOOKS1,
+                      NUMBER_AZIMUTH_LOOKS1,
+                      NUMBER_RANGE_LOOKS2,
+                      NUMBER_AZIMUTH_LOOKS2,
+                      NUMBER_RANGE_LOOKS_SIM,
+                      NUMBER_AZIMUTH_LOOKS_SIM,
+                      NUMBER_RANGE_LOOKS_ION,
+                      NUMBER_AZIMUTH_LOOKS_ION,
+                      SUBBAND_RADAR_WAVLENGTH,
+                      RADAR_DEM_AFFINE_TRANSFORM,
+                      MASTER_SLC,
+                      SLAVE_SLC,
+                      MASTER_SWATH_OFFSET,
+                      SLAVE_SWATH_OFFSET,
+                      MASTER_FRAME_OFFSET,
+                      SLAVE_FRAME_OFFSET,
+                      MASTER_FRAME_PARAMETER,
+                      SLAVE_FRAME_PARAMETER,
+                      MASTER_TRACK_PARAMETER,
+                      SLAVE_TRACK_PARAMETER,
+                      DEM,
+                      DEM_GEO,
+                      WBD,
+                      WBD_OUT,
+                      INTERFEROGRAM,
+                      AMPLITUDE,
+                      DIFFERENTIAL_INTERFEROGRAM,
+                      MULTILOOK_DIFFERENTIAL_INTERFEROGRAM,
+                      MULTILOOK_DIFFERENTIAL_INTERFEROGRAM_ORIGINAL,
+                      MULTILOOK_AMPLITUDE,
+                      MULTILOOK_COHERENCE,
+                      MULTILOOK_PHSIG,
+                      FILTERED_INTERFEROGRAM,
+                      UNWRAPPED_INTERFEROGRAM,
+                      UNWRAPPED_MASKED_INTERFEROGRAM,
+                      LATITUDE,
+                      LONGITUDE,
+                      HEIGHT,
+                      LOS,
+                      SIM,
+                      MSK,
+                      RANGE_OFFSET,
+                      AZIMUTH_OFFSET,
+                      MULTILOOK_LOS,
+                      MULTILOOK_MSK,
+                      MULTILOOK_WBD_OUT,
+                      MULTILOOK_LATITUDE,
+                      MULTILOOK_LONGITUDE,
+                      MULTILOOK_HEIGHT,
+                      MULTILOOK_ION,
+                      RECT_RANGE_OFFSET,
+                      GEO_INTERFEROGRAM,
+                      GEO_MASKED_INTERFEROGRAM,
+                      GEO_COHERENCE,
+                      GEO_LOS,
+                      GEO_ION,
+                      OFFSET_IMAGE_TOPOFFSET,
+                      OFFSET_IMAGE_LEFTOFFSET,
+                      SLAVE_SLC_COREGISTERED,
+                      DENSE_OFFSET,
+                      DENSE_OFFSET_SNR,
+                      DENSE_OFFSET_COV,
+                      DENSE_OFFSET_FILT,
+                      GEO_DENSE_OFFSET,
+                      GEO_DENSE_OFFSET_SNR,
+                      GEO_DENSE_OFFSET_FILT)
+
+    facility_list = ()
+
+
+    family='alos2context'
+
+    def __init__(self, name='', procDoc=None):
+        #self.updatePrivate()
+
+        super().__init__(family=self.__class__.family, name=name)
+        self.procDoc = procDoc
+        return None
+
+    def setFilename(self, masterDate, slaveDate, nrlks1, nalks1, nrlks2, nalks2):
+
+        # if masterDate == None:
+        #     masterDate = self.masterDate
+        # if slaveDate == None:
+        #     slaveDate = self.slaveDate
+        # if nrlks1 == None:
+        #     nrlks1 = self.numberRangeLooks1
+        # if nalks1 == None:
+        #     nalks1 = self.numberAzimuthLooks1
+        # if nrlks2 == None:
+        #     nrlks2 = self.numberRangeLooks2
+        # if nalks2 == None:
+        #     nalks2 = self.numberAzimuthLooks2
+
+        ms = masterDate + '-' + slaveDate
+        ml1 = '_{}rlks_{}alks'.format(nrlks1, nalks1)
+        ml2 = '_{}rlks_{}alks'.format(nrlks1*nrlks2, nalks1*nalks2)
+
+        self.masterSlc = masterDate + '.slc'
+        self.slaveSlc = slaveDate + '.slc'
+        self.masterSwathOffset = 'swath_offset_' + masterDate + '.txt'
+        self.slaveSwathOffset = 'swath_offset_' + slaveDate + '.txt'
+        self.masterFrameOffset = 'frame_offset_' + masterDate + '.txt'
+        self.slaveFrameOffset = 'frame_offset_' + slaveDate + '.txt'
+        self.masterFrameParameter = masterDate + '.frame.xml'
+        self.slaveFrameParameter = slaveDate + '.frame.xml'
+        self.masterTrackParameter = masterDate + '.track.xml'
+        self.slaveTrackParameter = slaveDate + '.track.xml'
+        #self.dem = 
+        #self.demGeo = 
+        #self.wbd = 
+        self.interferogram = ms + ml1 + '.int'
+        self.amplitude = ms + ml1 + '.amp'
+        self.differentialInterferogram = 'diff_' + ms + ml1 + '.int'
+        self.multilookDifferentialInterferogram = 'diff_' + ms + ml2 + '.int'
+        self.multilookDifferentialInterferogramOriginal = 'diff_' + ms + ml2 + '_ori.int'
+        self.multilookAmplitude = ms + ml2 + '.amp'
+        self.multilookCoherence = ms + ml2 + '.cor'
+        self.multilookPhsig = ms + ml2 + '.phsig'
+        self.filteredInterferogram = 'filt_' + ms + ml2 + '.int'
+        self.unwrappedInterferogram = 'filt_' + ms + ml2 + '.unw'
+        self.unwrappedMaskedInterferogram = 'filt_' + ms + ml2 + '_msk.unw'
+        self.latitude = ms + ml1 + '.lat'
+        self.longitude = ms + ml1 + '.lon'
+        self.height = ms + ml1 + '.hgt'
+        self.los = ms + ml1 + '.los'
+        self.sim = ms + ml1 + '.sim'
+        self.msk = ms + ml1 + '.msk'
+        self.wbdOut = ms + ml1 + '.wbd'
+        self.rangeOffset = ms + ml1 + '_rg.off'
+        self.azimuthOffset = ms + ml1 + '_az.off'
+        self.multilookLos = ms + ml2 + '.los'
+        self.multilookWbdOut = ms + ml2 + '.wbd'
+        self.multilookMsk = ms + ml2 + '.msk'
+        self.multilookLatitude = ms + ml2 + '.lat'
+        self.multilookLongitude = ms + ml2 + '.lon'
+        self.multilookHeight = ms + ml2 + '.hgt'
+        self.multilookIon = ms + ml2 + '.ion'
+        self.rectRangeOffset = ms + ml1 + '_rg_rect.off'
+        self.geoInterferogram = 'filt_' + ms + ml2 + '.unw.geo'
+        self.geoMaskedInterferogram = 'filt_' + ms + ml2 + '_msk.unw.geo'
+        self.geoCoherence = ms + ml2 + '.cor.geo'
+        self.geoLos = ms + ml2 + '.los.geo'
+        #dense offset field
+        self.slaveSlcCoregistered = slaveDate + '_coreg.slc'
+        self.denseOffset = ms + '_denseoffset.off'
+        self.denseOffsetSnr = ms + '_denseoffset.snr'
+        self.denseOffsetCov = ms + '_denseoffset.cov'
+        self.denseOffsetFilt = 'filt_' + ms + '_denseoffset.off'
+        self.GeoDenseOffset = ms + '_denseoffset.off.geo'
+        self.GeoDenseOffsetSnr = ms + '_denseoffset.snr.geo'
+        self.GeoDenseOffsetFilt = 'filt_' + ms + '_denseoffset.off.geo'
+        self.geoIon = ms + ml2 + '.ion.geo'
+
+
+    def loadProduct(self, xmlname):
+        '''
+        Load the product using Product Manager.
+        '''
+
+        from iscesys.Component.ProductManager import ProductManager as PM
+
+        pm = PM()
+        pm.configure()
+
+        obj = pm.loadProduct(xmlname)
+
+        return obj
+
+
+    def saveProduct(self, obj, xmlname):
+        '''
+        Save the product to an XML file using Product Manager.
+        '''
+        
+        from iscesys.Component.ProductManager import ProductManager as PM
+
+        pm = PM()
+        pm.configure()
+
+        pm.dumpProduct(obj, xmlname)
+        
+        return None
+
+
+    def loadTrack(self, master=True):
+        '''
+        Load the track using Product Manager.
+        '''
+        if master:
+            track = self.loadProduct(self.masterTrackParameter)
+        else:
+            track = self.loadProduct(self.slaveTrackParameter)
+
+        track.frames = []
+        for i, frameNumber in enumerate(self.masterFrames):
+            os.chdir('f{}_{}'.format(i+1, frameNumber))
+            if master:
+                track.frames.append(self.loadProduct(self.masterFrameParameter))
+            else:
+                track.frames.append(self.loadProduct(self.slaveFrameParameter))
+            os.chdir('../')
+
+        return track
+
+
+    def saveTrack(self, track, master=True):
+        '''
+        Save the track to XML files using Product Manager.
+        '''
+        if master:
+            self.saveProduct(track, self.masterTrackParameter)
+        else:
+            self.saveProduct(track, self.slaveTrackParameter)
+
+        for i, frameNumber in enumerate(self.masterFrames):
+            os.chdir('f{}_{}'.format(i+1, frameNumber))
+            if master:
+                self.saveProduct(track.frames[i], self.masterFrameParameter)
+            else:
+                self.saveProduct(track.frames[i], self.slaveFrameParameter)
+            os.chdir('../')
+
+        return None
+
+
+    def hasGPU(self):
+        '''
+        Determine if GPU modules are available.
+        '''
+
+        flag = False
+        try:
+            from zerodop.GPUtopozero.GPUtopozero import PyTopozero
+            from zerodop.GPUgeo2rdr.GPUgeo2rdr import PyGeo2rdr
+            flag = True
+        except:
+            pass
+
+        return flag
+

components/isceobj/Alos2Proc/CMakeLists.txt

@@ -0,0 +1,37 @@
+InstallSameDir(
+    __init__.py
+    Alos2Proc.py
+    Alos2ProcPublic.py
+    Factories.py
+    denseOffsetNote.txt
+    runCoherence.py
+    runDenseOffset.py
+    runDiffInterferogram.py
+    runDownloadDem.py
+    runFilt.py
+    runFiltOffset.py
+    runFormInterferogram.py
+    runFrameMosaic.py
+    runFrameOffset.py
+    runGeo2Rdr.py
+    runGeocode.py
+    runGeocodeOffset.py
+    runIonFilt.py
+    runIonSubband.py
+    runIonUwrap.py
+    runLook.py
+    runPrepareSlc.py
+    runPreprocessor.py
+    runRdr2Geo.py
+    runRdrDemOffset.py
+    runRectRangeOffset.py
+    runSlcMatch.py
+    runSlcMosaic.py
+    runSlcOffset.py
+    runSwathMosaic.py
+    runSwathOffset.py
+    runUnwrapSnaphu.py
+    srtm_no_swbd_tiles.txt
+    srtm_tiles.txt
+    swbd_tiles.txt
+    )

components/isceobj/Alos2Proc/Factories.py

@@ -0,0 +1,105 @@
+#
+# Author: Piyush Agram
+# Copyright 2016
+#
+
+# Path to the _RunWrapper factories
+_PATH = "isceobj.Alos2Proc."
+
+## A factory to make _RunWrapper factories
+def _factory(name, other_name=None):
+    """create_run_wrapper = _factory(name)
+    name is the module and class function name
+    """
+    other_name = other_name or name
+    module = __import__(
+        _PATH+name, fromlist=[""]
+        )
+    cls = getattr(module, other_name)
+    def creater(other, *args, **kwargs):
+        """_RunWrapper for object calling %s"""
+        return _RunWrapper(other, cls)
+    return creater
+
+## Put in "_" to prevernt import on "from Factorties import *"
+class _RunWrapper(object):
+    """_RunWrapper(other, func)(*args, **kwargs)
+
+    executes:
+
+    func(other, *args, **kwargs)
+
+    (like a method)
+    """
+    def __init__(self, other, func):
+        self.method = func
+        self.other = other
+        return None
+
+    def __call__(self, *args, **kwargs):
+        return self.method(self.other, *args, **kwargs)
+
+    pass
+
+def createUnwrapper(other, do_unwrap = None, unwrapperName = None,
+                    unwrap = None):
+    if not do_unwrap and not unwrap:
+        #if not defined create an empty method that does nothing
+        def runUnwrap(self):
+            return None
+    elif unwrapperName.lower() == 'snaphu':
+        from .runUnwrapSnaphu import runUnwrap
+    elif unwrapperName.lower() == 'snaphu_mcf':
+        from .runUnwrapSnaphu import runUnwrapMcf as runUnwrap
+    elif unwrapperName.lower() == 'downsample_snaphu':
+        from .run_downsample_unwrapper import runUnwrap
+    elif unwrapperName.lower() == 'icu':
+        from .runUnwrapIcu import runUnwrap
+    elif unwrapperName.lower() == 'grass':
+        from .runUnwrapGrass import runUnwrap
+    return _RunWrapper(other, runUnwrap)
+
+def createUnwrap2Stage(other, do_unwrap_2stage = None, unwrapperName = None):
+    if (not do_unwrap_2stage) or (unwrapperName.lower() == 'icu') or (unwrapperName.lower() == 'grass'):
+        #if not defined create an empty method that does nothing
+        def runUnwrap2Stage(*arg, **kwargs):
+            return None
+    else:
+      try:
+        import pulp
+        from .runUnwrap2Stage import runUnwrap2Stage
+      except ImportError:
+        raise Exception('Please install PuLP Linear Programming API to run 2stage unwrap')
+    return _RunWrapper(other, runUnwrap2Stage)
+
+
+createPreprocessor = _factory("runPreprocessor")
+createDownloadDem = _factory("runDownloadDem")
+createPrepareSlc = _factory("runPrepareSlc")
+createSlcOffset = _factory("runSlcOffset")
+createFormInterferogram = _factory("runFormInterferogram")
+createSwathOffset = _factory("runSwathOffset")
+createSwathMosaic = _factory("runSwathMosaic")
+createFrameOffset = _factory("runFrameOffset")
+createFrameMosaic = _factory("runFrameMosaic")
+createRdr2Geo = _factory("runRdr2Geo")
+createGeo2Rdr = _factory("runGeo2Rdr")
+createRdrDemOffset = _factory("runRdrDemOffset")
+createRectRangeOffset = _factory("runRectRangeOffset")
+createDiffInterferogram = _factory("runDiffInterferogram")
+createLook = _factory("runLook")
+createCoherence = _factory("runCoherence")
+createIonSubband = _factory("runIonSubband")
+createIonUwrap = _factory("runIonUwrap")
+createIonFilt = _factory("runIonFilt")
+createFilt = _factory("runFilt")
+createUnwrapSnaphu = _factory("runUnwrapSnaphu")
+createGeocode = _factory("runGeocode")
+
+createSlcMosaic = _factory("runSlcMosaic")
+createSlcMatch = _factory("runSlcMatch")
+createDenseOffset = _factory("runDenseOffset")
+createFiltOffset = _factory("runFiltOffset")
+createGeocodeOffset = _factory("runGeocodeOffset")
+
+

components/isceobj/Alos2Proc/SConscript

@@ -0,0 +1,45 @@
+#! /usr/bin/env python
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# Copyright 2012 California Institute of Technology. ALL RIGHTS RESERVED.
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# 
+# United States Government Sponsorship acknowledged. This software is subject to
+# U.S. export control laws and regulations and has been classified as 'EAR99 NLR'
+# (No [Export] License Required except when exporting to an embargoed country,
+# end user, or in support of a prohibited end use). By downloading this software,
+# the user agrees to comply with all applicable U.S. export laws and regulations.
+# The user has the responsibility to obtain export licenses, or other export
+# authority as may be required before exporting this software to any 'EAR99'
+# embargoed foreign country or citizen of those countries.
+#
+# Author: Eric Gurrola
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+
+
+
+
+#!/usr/bin/env python
+import os
+
+Import('envisceobj')
+package = envisceobj['PACKAGE']
+project = 'Alos2Proc'
+
+install = os.path.join(envisceobj['PRJ_SCONS_INSTALL'],package,project)
+
+listFiles = ['__init__.py', 'Factories.py', 'Alos2Proc.py', 'Alos2ProcPublic.py', 'runPreprocessor.py', 'runDownloadDem.py', 'runPrepareSlc.py', 'runSlcOffset.py', 'runFormInterferogram.py', 'runSwathOffset.py', 'runSwathMosaic.py', 'runFrameOffset.py', 'runFrameMosaic.py', 'runRdr2Geo.py', 'runGeo2Rdr.py', 'runRdrDemOffset.py', 'runRectRangeOffset.py', 'runDiffInterferogram.py', 'runLook.py', 'runCoherence.py', 'runIonSubband.py', 'runIonUwrap.py', 'runIonFilt.py', 'runFilt.py', 'runUnwrapSnaphu.py', 'runGeocode.py', 'srtm_no_swbd_tiles.txt', 'srtm_tiles.txt', 'swbd_tiles.txt', 'runSlcMosaic.py', 'runSlcMatch.py', 'runDenseOffset.py', 'runFiltOffset.py', 'runGeocodeOffset.py', 'denseOffsetNote.txt']
+envisceobj.Install(install,listFiles)
+envisceobj.Alias('install',install)

components/isceobj/Alos2Proc/__init__.py

@@ -0,0 +1,22 @@
+#
+# Author: Piyush Agram
+# Copyright 2016
+#
+
+from .Alos2Proc import *
+from .Factories import *
+
+def getFactoriesInfo():
+    return  {'Alos2Proc':
+                     {'args':
+                           {
+                            'procDoc':{'value':None,'type':'Catalog','optional':True}
+                            },
+                     'factory':'createAlos2Proc'                     
+                     }
+              
+              }
+
+def createAlos2Proc(name=None, procDoc= None):
+    from .Alos2Proc import Alos2Proc
+    return Alos2Proc(name = name,procDoc = procDoc)

components/isceobj/Alos2Proc/denseOffsetNote.txt

@@ -0,0 +1,31 @@
+on the following paramters might be changed in the denseoffset steps:
+=======================================================================
+        if self.frameOffsetMatching == False:
+            self._insar.frameRangeOffsetMatchingMaster = offsetMaster[2]
+            self._insar.frameAzimuthOffsetMatchingMaster = offsetMaster[3]
+        self._insar.frameRangeOffsetMatchingSlave = offsetSlave[2]
+        self._insar.frameAzimuthOffsetMatchingSlave = offsetSlave[3]
+
+
+Therefore these denseoffset steps could be moved to after 'frame_mosaic' step
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

components/isceobj/Alos2Proc/runCoherence.py

@@ -0,0 +1,131 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+
+logger = logging.getLogger('isce.alos2insar.runCoherence')
+
+def runCoherence(self):
+    '''Extract images.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    #masterTrack = self._insar.loadTrack(master=True)
+    #slaveTrack = self._insar.loadTrack(master=False)
+
+    insarDir = 'insar'
+    if not os.path.exists(insarDir):
+        os.makedirs(insarDir)
+    os.chdir(insarDir)
+
+    numberRangeLooks = self._insar.numberRangeLooks1 * self._insar.numberRangeLooks2
+    numberAzimuthLooks = self._insar.numberAzimuthLooks1 * self._insar.numberAzimuthLooks2
+
+    #here we choose not to scale interferogram and amplitude
+    #scaleAmplitudeInterferogram
+
+    #if (numberRangeLooks >= 5) and (numberAzimuthLooks >= 5):
+    if (numberRangeLooks * numberAzimuthLooks >= 9):
+        cmd = "imageMath.py -e='sqrt(b_0*b_1);abs(a)/(b_0+(b_0==0))/(b_1+(b_1==0))*(b_0!=0)*(b_1!=0)' --a={} --b={} -o {} -t float -s BIL".format(
+            self._insar.multilookDifferentialInterferogram,
+            self._insar.multilookAmplitude,
+            self._insar.multilookCoherence)
+        runCmd(cmd)
+    else:
+        #estimate coherence using a moving window
+        coherence(self._insar.multilookAmplitude, self._insar.multilookDifferentialInterferogram, self._insar.multilookCoherence, 
+            method="cchz_wave", windowSize=5)
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runCoherence")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+from isceobj.Util.decorators import use_api
+@use_api
+def coherence(amplitudeFile, interferogramFile, coherenceFile, method="cchz_wave", windowSize=5):
+    ''' 
+    compute coherence using a window
+    '''
+    import operator
+    from mroipac.correlation.correlation import Correlation
+
+    CORRELATION_METHOD = {
+        'phase_gradient' : operator.methodcaller('calculateEffectiveCorrelation'),
+        'cchz_wave' : operator.methodcaller('calculateCorrelation')
+        }
+
+    ampImage = isceobj.createAmpImage()
+    ampImage.load(amplitudeFile + '.xml')
+    ampImage.setAccessMode('read')
+    ampImage.createImage()
+
+    intImage = isceobj.createIntImage()
+    intImage.load(interferogramFile + '.xml')
+    intImage.setAccessMode('read')
+    intImage.createImage()
+
+    #there is no coherence image in the isceobj/Image
+    cohImage = isceobj.createOffsetImage()
+    cohImage.setFilename(coherenceFile)
+    cohImage.setWidth(ampImage.width)
+    cohImage.setAccessMode('write')
+    cohImage.createImage()
+
+    cor = Correlation()
+    cor.configure()
+    cor.wireInputPort(name='amplitude', object=ampImage)
+    cor.wireInputPort(name='interferogram', object=intImage)
+    cor.wireOutputPort(name='correlation', object=cohImage)
+    
+    cor.windowSize = windowSize
+
+    cohImage.finalizeImage()
+    intImage.finalizeImage()
+    ampImage.finalizeImage()
+
+    try:
+        CORRELATION_METHOD[method](cor)
+    except KeyError:
+        print("Unrecognized correlation method")
+        sys.exit(1)
+        pass
+    return None
+
+
+def scaleAmplitudeInterferogram(amplitudeFile, interferogramFile, ratio=100000.0):
+    '''
+    scale amplitude and interferogram, and balace the two channels of amplitude image
+    according to equation (2) in
+    Howard A. Zebker and Katherine Chen, Accurate Estimation of Correlation in InSAR Observations
+    IEEE GEOSCIENCE AND REMOTE SENSING LETTERS, VOL. 2, NO. 2, APRIL 2005.
+    the operation of the program does not affect coherence estimation
+    '''
+    ampObj = isceobj.createImage()
+    ampObj.load(amplitudeFile+'.xml')
+    width = ampObj.width
+    length = ampObj.length
+
+    inf = np.fromfile(interferogramFile, dtype=np.complex64).reshape(length, width)
+    amp = np.fromfile(amplitudeFile, dtype=np.complex64).reshape(length, width)
+
+    flag = (inf!=0)*(amp.real!=0)*(amp.imag!=0)
+    nvalid = np.sum(flag, dtype=np.float64)
+
+    mpwr1 =  np.sqrt(np.sum(amp.real * amp.real * flag, dtype=np.float64) / nvalid)
+    mpwr2 =  np.sqrt(np.sum(amp.imag * amp.imag * flag, dtype=np.float64) / nvalid)
+
+    amp.real = amp.real / ratio
+    amp.imag = amp.imag / ratio * mpwr1 / mpwr2
+    inf = inf / ratio / ratio * mpwr1 / mpwr2
+
+    amp.astype(np.complex64).tofile(inps.amp)
+    inf.astype(np.complex64).tofile(inps.inf)

components/isceobj/Alos2Proc/runDenseOffset.py

@@ -0,0 +1,327 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+from isceobj.Util.decorators import use_api
+
+logger = logging.getLogger('isce.alos2insar.runDenseOffset')
+
+def runDenseOffset(self):
+    '''estimate offset fied
+    '''
+    if not self.doDenseOffset:
+        return
+    if not ((self._insar.modeCombination == 0) or (self._insar.modeCombination == 1)):
+        return
+
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    denseOffsetDir = 'dense_offset'
+    if not os.path.exists(denseOffsetDir):
+        os.makedirs(denseOffsetDir)
+    os.chdir(denseOffsetDir)
+
+    #masterTrack = self._insar.loadProduct(self._insar.masterTrackParameter)
+    #slaveTrack = self._insar.loadProduct(self._insar.slaveTrackParameter)
+
+#########################################################################################
+
+    if self.useGPU and self._insar.hasGPU():
+        runDenseOffsetGPU(self)
+        #define null value. Lijun said there is actually no such null value in GPU ampcor.
+        nullValue = -10000.0
+    else:
+        runDenseOffsetCPU(self)
+        #define null value
+        nullValue = -10000.0
+
+    #null value set to zero
+    img = isceobj.createImage()
+    img.load(self._insar.denseOffset+'.xml')
+    width = img.width
+    length = img.length
+    offset=np.memmap(self._insar.denseOffset, dtype='float32', mode='r+', shape=(length*2, width))
+    snr=np.memmap(self._insar.denseOffsetSnr, dtype='float32', mode='r+', shape=(length, width))
+    offsetband1 = offset[0:length*2:2, :]
+    offsetband2 = offset[1:length*2:2, :]
+    index = np.nonzero(np.logical_or(offsetband1==nullValue, offsetband2==nullValue))
+    offsetband1[index] = 0
+    offsetband2[index] = 0
+    snr[index] = 0
+    del offset, offsetband1, offsetband2, snr
+
+    #areas covered by water body set to zero
+    if self.maskOffsetWithWbd:
+        img = isceobj.createImage()
+        img.load('wbd.rdr.xml')
+        width0 = img.width
+        length0 = img.length
+
+        img = isceobj.createImage()
+        img.load(self._insar.denseOffset+'.xml')
+        width = img.width
+        length = img.length
+
+        #get water body mask
+        wbd0=np.memmap('wbd.rdr', dtype=np.int8, mode='r', shape=(length0, width0))
+        wbd0=wbd0[0+self._insar.offsetImageTopoffset:length0:self.offsetSkipHeight, 
+                   0+self._insar.offsetImageLeftoffset:width0:self.offsetSkipWidth]
+        wbd = np.zeros((length+100, width+100), dtype=np.int8)
+        wbd[0:wbd0.shape[0], 0:wbd0.shape[1]]=wbd0
+
+        #mask offset and snr
+        offset=np.memmap(self._insar.denseOffset, dtype='float32', mode='r+', shape=(length*2, width))
+        snr=np.memmap(self._insar.denseOffsetSnr, dtype='float32', mode='r+', shape=(length, width))
+        (offset[0:length*2:2, :])[np.nonzero(wbd[0:length, 0:width]==-1)]=0
+        (offset[1:length*2:2, :])[np.nonzero(wbd[0:length, 0:width]==-1)]=0
+        snr[np.nonzero(wbd[0:length, 0:width]==-1)]=0
+
+        del wbd0, wbd, offset, snr
+
+
+#########################################################################################
+
+    os.chdir('../')
+    catalog.printToLog(logger, "runDenseOffset")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+#@use_api
+def runDenseOffsetCPU(self):
+    '''
+    Estimate dense offset field between a pair of SLCs.
+    '''
+    from mroipac.ampcor.DenseAmpcor import DenseAmpcor
+    from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+
+    ####For this module currently, we need to create an actual file on disk
+    for infile in [self._insar.masterSlc, self._insar.slaveSlcCoregistered]:
+        if os.path.isfile(infile):
+            continue
+        cmd = 'gdal_translate -of ENVI {0}.vrt {0}'.format(infile)
+        runCmd(cmd)
+
+    m = isceobj.createSlcImage()
+    m.load(self._insar.masterSlc + '.xml')
+    m.setAccessMode('READ')
+
+    s = isceobj.createSlcImage()
+    s.load(self._insar.slaveSlcCoregistered + '.xml')
+    s.setAccessMode('READ')
+
+    #objOffset.numberThreads = 1
+    print('\n************* dense offset estimation parameters *************')
+    print('master SLC: %s' % (self._insar.masterSlc))
+    print('slave SLC: %s' % (self._insar.slaveSlcCoregistered))
+    print('dense offset estimation window width: %d' % (self.offsetWindowWidth))
+    print('dense offset estimation window hight: %d' % (self.offsetWindowHeight))
+    print('dense offset search window width: %d' % (self.offsetSearchWindowWidth))
+    print('dense offset search window hight: %d' % (self.offsetSearchWindowHeight))
+    print('dense offset skip width: %d' % (self.offsetSkipWidth))
+    print('dense offset skip hight: %d' % (self.offsetSkipHeight))
+    print('dense offset covariance surface oversample factor: %d' % (self.offsetCovarianceOversamplingFactor))
+    print('dense offset covariance surface oversample window size: %d\n' % (self.offsetCovarianceOversamplingWindowsize))
+
+
+    objOffset = DenseAmpcor(name='dense')
+    objOffset.configure()
+
+    if m.dataType.startswith('C'):
+        objOffset.setImageDataType1('complex')
+    else:
+        objOffset.setImageDataType1('real')
+    if s.dataType.startswith('C'):
+        objOffset.setImageDataType2('complex')
+    else:
+        objOffset.setImageDataType2('real')
+
+    objOffset.offsetImageName = self._insar.denseOffset
+    objOffset.snrImageName = self._insar.denseOffsetSnr
+    objOffset.covImageName = self._insar.denseOffsetCov
+
+    objOffset.setWindowSizeWidth(self.offsetWindowWidth)
+    objOffset.setWindowSizeHeight(self.offsetWindowHeight)
+    #NOTE: actual number of resulting correlation pixels: self.offsetSearchWindowWidth*2+1
+    objOffset.setSearchWindowSizeWidth(self.offsetSearchWindowWidth)
+    objOffset.setSearchWindowSizeHeight(self.offsetSearchWindowHeight)
+    objOffset.setSkipSampleAcross(self.offsetSkipWidth)
+    objOffset.setSkipSampleDown(self.offsetSkipHeight)
+    objOffset.setOversamplingFactor(self.offsetCovarianceOversamplingFactor)
+    objOffset.setZoomWindowSize(self.offsetCovarianceOversamplingWindowsize)
+    objOffset.setAcrossGrossOffset(0)
+    objOffset.setDownGrossOffset(0)
+    #these are azimuth scaling factor
+    #Matching Scale for Sample/Line Directions (-) = 1.000000551500 1.000002373200
+    objOffset.setFirstPRF(1.0)
+    objOffset.setSecondPRF(1.0)
+
+    objOffset.denseampcor(m, s)
+
+    ### Store params for later
+    self._insar.offsetImageTopoffset = objOffset.locationDown[0][0]
+    self._insar.offsetImageLeftoffset = objOffset.locationAcross[0][0]
+
+    #change band order
+    width=objOffset.offsetCols
+    length=objOffset.offsetLines
+
+    offset1 = np.fromfile(self._insar.denseOffset, dtype=np.float32).reshape(length*2, width)
+    offset2 = np.zeros((length*2, width), dtype=np.float32)
+    offset2[0:length*2:2, :] = offset1[1:length*2:2, :]
+    offset2[1:length*2:2, :] = offset1[0:length*2:2, :]
+
+    os.remove(self._insar.denseOffset)
+    os.remove(self._insar.denseOffset+'.vrt')
+    os.remove(self._insar.denseOffset+'.xml')
+
+    offset2.astype(np.float32).tofile(self._insar.denseOffset)
+    outImg = isceobj.createImage()
+    outImg.setDataType('FLOAT')
+    outImg.setFilename(self._insar.denseOffset)
+    outImg.setBands(2)
+    outImg.scheme = 'BIL'
+    outImg.setWidth(width)
+    outImg.setLength(length)
+    outImg.addDescription('two-band pixel offset file. 1st band: range offset, 2nd band: azimuth offset')
+    outImg.setAccessMode('read')
+    outImg.renderHdr()
+
+    return (objOffset.offsetCols, objOffset.offsetLines)
+
+
+def runDenseOffsetGPU(self):
+    '''
+    Estimate dense offset field between a pair of SLCs.
+    '''
+    from contrib.PyCuAmpcor import PyCuAmpcor
+    from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+    ############################################################################################
+    # #different from minyan's script: cuDenseOffsets.py: deramp method (0: mag, 1: complex)
+    # objOffset.derampMethod = 2 #
+    # #varying-gross-offset parameters not set
+
+    # #not set in minyan's script: cuDenseOffsets.py
+    # objOffset.corrSurfaceZoomInWindow
+    # objOffset.grossOffsetAcrossStatic = 0
+    # objOffset.grossOffsetDownStatic = 0
+    ############################################################################################
+
+
+    ####For this module currently, we need to create an actual file on disk
+    for infile in [self._insar.masterSlc, self._insar.slaveSlcCoregistered]:
+        if os.path.isfile(infile):
+            continue
+        cmd = 'gdal_translate -of ENVI {0}.vrt {0}'.format(infile)
+        runCmd(cmd)
+
+    m = isceobj.createSlcImage()
+    m.load(self._insar.masterSlc + '.xml')
+    m.setAccessMode('READ')
+
+    s = isceobj.createSlcImage()
+    s.load(self._insar.slaveSlcCoregistered + '.xml')
+    s.setAccessMode('READ')
+
+    print('\n************* dense offset estimation parameters *************')
+    print('master SLC: %s' % (self._insar.masterSlc))
+    print('slave SLC: %s' % (self._insar.slaveSlcCoregistered))
+    print('dense offset estimation window width: %d' % (self.offsetWindowWidth))
+    print('dense offset estimation window hight: %d' % (self.offsetWindowHeight))
+    print('dense offset search window width: %d' % (self.offsetSearchWindowWidth))
+    print('dense offset search window hight: %d' % (self.offsetSearchWindowHeight))
+    print('dense offset skip width: %d' % (self.offsetSkipWidth))
+    print('dense offset skip hight: %d' % (self.offsetSkipHeight))
+    print('dense offset covariance surface oversample factor: %d' % (self.offsetCovarianceOversamplingFactor))
+    print('dense offset covariance surface oversample window size: %d\n' % (self.offsetCovarianceOversamplingWindowsize))
+
+
+    objOffset = PyCuAmpcor.PyCuAmpcor()
+    objOffset.algorithm = 0
+    objOffset.deviceID = -1
+    objOffset.nStreams = 2
+    #original ampcor program in roi_pac uses phase gradient to deramp
+    objOffset.derampMethod = 2
+    objOffset.masterImageName = self._insar.masterSlc
+    objOffset.masterImageHeight = m.length
+    objOffset.masterImageWidth = m.width
+    objOffset.slaveImageName = self._insar.slaveSlcCoregistered
+    objOffset.slaveImageHeight = s.length
+    objOffset.slaveImageWidth = s.width
+    objOffset.offsetImageName = self._insar.denseOffset
+    objOffset.snrImageName = self._insar.denseOffsetSnr
+
+    objOffset.windowSizeWidth = self.offsetWindowWidth
+    objOffset.windowSizeHeight = self.offsetWindowHeight
+    #objOffset.halfSearchRangeAcross = int(self.offsetSearchWindowWidth / 2 + 0.5)
+    #objOffset.halfSearchRangeDown = int(self.offsetSearchWindowHeight / 2 + 0.5)
+    objOffset.halfSearchRangeAcross = self.offsetSearchWindowWidth
+    objOffset.halfSearchRangeDown = self.offsetSearchWindowHeight
+    objOffset.skipSampleDown = self.offsetSkipHeight
+    objOffset.skipSampleAcross = self.offsetSkipWidth
+    #Oversampling method for correlation surface(0=fft,1=sinc)
+    objOffset.corrSufaceOverSamplingMethod = 0
+    objOffset.corrSurfaceOverSamplingFactor = self.offsetCovarianceOversamplingFactor
+    objOffset.corrSurfaceZoomInWindow = self.offsetCovarianceOversamplingWindowsize
+    objOffset.grossOffsetAcrossStatic = 0
+    objOffset.grossOffsetDownStatic = 0
+
+    objOffset.masterStartPixelDownStatic = self.offsetWindowHeight//2
+    objOffset.masterStartPixelAcrossStatic = self.offsetWindowWidth//2
+
+    objOffset.numberWindowDown = (m.length - 2*self.offsetSearchWindowHeight - self.offsetWindowHeight) // self.offsetSkipHeight
+    objOffset.numberWindowAcross = (m.width - 2*self.offsetSearchWindowWidth - self.offsetWindowWidth) // self.offsetSkipWidth
+
+    # generic control
+    objOffset.numberWindowDownInChunk = 8
+    objOffset.numberWindowAcrossInChunk = 8
+    objOffset.mmapSize = 16
+
+    objOffset.setupParams()
+    objOffset.setConstantGrossOffset(0, 0)
+    objOffset.checkPixelInImageRange()
+    objOffset.runAmpcor()
+
+    ### Store params for later
+    self._insar.offsetImageTopoffset = objOffset.halfSearchRangeDown
+    self._insar.offsetImageLeftoffset = objOffset.halfSearchRangeAcross
+
+    
+    width = objOffset.numberWindowAcross
+    length = objOffset.numberWindowDown
+    offsetBIP = np.fromfile(objOffset.offsetImageName.decode('utf-8'), dtype=np.float32).reshape(length, width*2)
+    offsetBIL = np.zeros((length*2, width), dtype=np.float32)
+    offsetBIL[0:length*2:2, :] = offsetBIP[:, 1:width*2:2]
+    offsetBIL[1:length*2:2, :] = offsetBIP[:, 0:width*2:2]
+    os.remove(objOffset.offsetImageName.decode('utf-8'))
+    offsetBIL.astype(np.float32).tofile(objOffset.offsetImageName.decode('utf-8'))
+
+    outImg = isceobj.createImage()
+    outImg.setDataType('FLOAT')
+    outImg.setFilename(objOffset.offsetImageName.decode('utf-8'))
+    outImg.setBands(2)
+    outImg.scheme = 'BIL'
+    outImg.setWidth(objOffset.numberWindowAcross)
+    outImg.setLength(objOffset.numberWindowDown)
+    outImg.addDescription('two-band pixel offset file. 1st band: range offset, 2nd band: azimuth offset')
+    outImg.setAccessMode('read')
+    outImg.renderHdr()
+
+    snrImg = isceobj.createImage()
+    snrImg.setFilename( objOffset.snrImageName.decode('utf8'))
+    snrImg.setDataType('FLOAT')
+    snrImg.setBands(1)
+    snrImg.setWidth(objOffset.numberWindowAcross)
+    snrImg.setLength(objOffset.numberWindowDown)
+    snrImg.setAccessMode('read')
+    snrImg.renderHdr()
+
+    return (objOffset.numberWindowAcross, objOffset.numberWindowDown)

components/isceobj/Alos2Proc/runDiffInterferogram.py

@@ -0,0 +1,41 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+
+logger = logging.getLogger('isce.alos2insar.runDiffInterferogram')
+
+def runDiffInterferogram(self):
+    '''Extract images.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+
+    insarDir = 'insar'
+    if not os.path.exists(insarDir):
+        os.makedirs(insarDir)
+    os.chdir(insarDir)
+
+
+    rangePixelSize = self._insar.numberRangeLooks1 * masterTrack.rangePixelSize
+    radarWavelength = masterTrack.radarWavelength
+
+    cmd = "imageMath.py -e='a*exp(-1.0*J*b*4.0*{}*{}/{}) * (b!=0)' --a={} --b={} -o {} -t cfloat".format(np.pi, rangePixelSize, radarWavelength, self._insar.interferogram, self._insar.rectRangeOffset, self._insar.differentialInterferogram)
+    runCmd(cmd)
+
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runDiffInterferogram")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+

components/isceobj/Alos2Proc/runDownloadDem.py

@@ -0,0 +1,204 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import glob
+import logging
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+from isceobj.Alos2Proc.Alos2ProcPublic import getBboxGeo
+
+logger = logging.getLogger('isce.alos2insar.runDownloadDem')
+
+def runDownloadDem(self):
+    '''download DEM and water body
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    bboxGeo = getBboxGeo(masterTrack)
+    bbox = np.array(bboxGeo)
+    bboxStr = '{} {} {} {}'.format(np.int(np.floor(bbox[0])), np.int(np.ceil(bbox[1])), np.int(np.floor(bbox[2])), np.int(np.ceil(bbox[3])))
+
+
+    #get 1 arcsecond dem for coregistration
+    if self.dem == None:
+        demDir = 'dem_1_arcsec'
+        if not os.path.exists(demDir):
+            os.makedirs(demDir)
+        os.chdir(demDir)
+
+        downloadUrl = 'http://e4ftl01.cr.usgs.gov/MEASURES/SRTMGL1.003/2000.02.11'
+        cmd = 'dem.py -a stitch -b {} -k -s 1 -c -f -u {}'.format(
+               bboxStr,
+               downloadUrl
+               )
+        runCmd(cmd)
+        cmd = 'fixImageXml.py -i demLat_*_*_Lon_*_*.dem.wgs84 -f'
+        runCmd(cmd)
+        cmd = 'rm *.hgt* *.log demLat_*_*_Lon_*_*.dem demLat_*_*_Lon_*_*.dem.vrt demLat_*_*_Lon_*_*.dem.xml'
+        runCmd(cmd)
+        os.chdir('../')
+
+        self.dem = glob.glob(os.path.join(demDir, 'demLat_*_*_Lon_*_*.dem.wgs84'))[0]
+
+    #get 3 arcsecond dem for geocoding
+    if self.demGeo == None:
+        demGeoDir = 'dem_3_arcsec'
+        if not os.path.exists(demGeoDir):
+            os.makedirs(demGeoDir)
+        os.chdir(demGeoDir)
+
+        downloadUrl = 'http://e4ftl01.cr.usgs.gov/MEASURES/SRTMGL3.003/2000.02.11'
+        cmd = 'dem.py -a stitch -b {} -k -s 3 -c -f -u {}'.format(
+               bboxStr,
+               downloadUrl
+               )
+        runCmd(cmd)
+        cmd = 'fixImageXml.py -i demLat_*_*_Lon_*_*.dem.wgs84 -f'
+        runCmd(cmd)
+        cmd = 'rm *.hgt* *.log demLat_*_*_Lon_*_*.dem demLat_*_*_Lon_*_*.dem.vrt demLat_*_*_Lon_*_*.dem.xml'
+        runCmd(cmd)
+        os.chdir('../')
+
+        self.demGeo = glob.glob(os.path.join(demGeoDir, 'demLat_*_*_Lon_*_*.dem.wgs84'))[0]
+
+    #get water body for masking interferogram
+    if self.wbd == None:
+        wbdDir = 'wbd_1_arcsec'
+        if not os.path.exists(wbdDir):
+            os.makedirs(wbdDir)
+        os.chdir(wbdDir)
+
+        #cmd = 'wbd.py {}'.format(bboxStr)
+        #runCmd(cmd)
+        download_wbd(np.int(np.floor(bbox[0])), np.int(np.ceil(bbox[1])), np.int(np.floor(bbox[2])), np.int(np.ceil(bbox[3])))
+        cmd = 'fixImageXml.py -i swbdLat_*_*_Lon_*_*.wbd -f'
+        runCmd(cmd)
+        cmd = 'rm *.log'
+        runCmd(cmd)
+        os.chdir('../')
+
+        self.wbd = glob.glob(os.path.join(wbdDir, 'swbdLat_*_*_Lon_*_*.wbd'))[0]
+
+    self._insar.dem = self.dem
+    self._insar.demGeo = self.demGeo
+    self._insar.wbd = self.wbd
+
+
+    catalog.printToLog(logger, "runDownloadDem")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+
+def download_wbd(s, n, w, e):
+    '''
+    download water body
+    water body. (0) --- land; (-1) --- water; (-2) --- no data.
+
+    set no-value pixel inside of latitude [-56, 60] to -1
+    set no-value pixel outside of latitidue [-56, 60] to -2
+
+    look at this figure for SRTM coverage:
+    https://www2.jpl.nasa.gov/srtm/images/SRTM_2-24-2016.gif
+    '''
+    import os
+    import numpy as np
+    import isceobj
+    from iscesys.DataManager import createManager
+
+    latMin = np.floor(s)
+    latMax = np.ceil(n)
+    lonMin = np.floor(w)
+    lonMax = np.ceil(e)
+
+    ############################################################
+    #1. download and stitch wbd
+    ############################################################
+    sw = createManager('wbd')
+    sw.configure()
+
+    outputFile = sw.defaultName([latMin,latMax,lonMin,lonMax])
+    if os.path.exists(outputFile) and os.path.exists(outputFile+'.xml'):
+        print('water body file: {}'.format(outputFile))
+        print('exists, do not download and correct')
+        return outputFile
+
+    #download and stitch the SWBD tiles
+    sw.noFilling = False
+    sw._fillingValue = -1
+    sw.stitch([latMin,latMax],[lonMin,lonMax])
+
+
+    ############################################################
+    #2. replace 'areas with SRTM but no SWBD' with zeros (land)
+    ############################################################
+    print('post-process water body file')
+
+    print('get SRTM tiles')
+    srtmListFile = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'srtm_tiles.txt')
+    with open(srtmListFile) as f:
+        srtmList = f.readlines()
+    srtmList = [x[0:7] for x in srtmList]
+
+    #get tiles that have SRTM DEM, but no SWBD, these are mostly tiles that do not have water body
+    print('get tiles with SRTM and without SWBD')
+    noSwbdListFile = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'srtm_no_swbd_tiles.txt')
+    with open(noSwbdListFile) as f:
+        noSwbdList = f.readlines()
+    noSwbdList = [x[0:7] for x in noSwbdList]
+
+    print('get SWBD tiles')
+    swbdListFile = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'swbd_tiles.txt')
+    with open(swbdListFile) as f:
+        swbdList = f.readlines()
+    swbdList = [x[0:7] for x in swbdList]
+
+
+    #read resulting mosaicked water body
+    wbdImage = isceobj.createDemImage()
+    wbdImage.load(outputFile+'.xml')
+    #using memmap instead, which should be faster, since we only have a few pixels to change
+    wbd=np.memmap(outputFile, dtype=np.int8, mode='r+', shape=(wbdImage.length, wbdImage.width))
+
+    #replace 'areas with SRTM but no SWBD' with zeros (land)
+    names, nlats, nlons = sw.createNameListFromBounds([latMin,latMax],[lonMin,lonMax])
+    sign={'S':-1, 'N':1, 'W':-1, 'E':1}
+    for tile in names:
+        print('checking tile: {}'.format(tile))
+        firstLatitude  = sign[tile[0].upper()]*int(tile[1:3])+1
+        firstLongitude = sign[tile[3].upper()]*int(tile[4:7])
+        lineOffset = np.int32((firstLatitude - wbdImage.firstLatitude) / wbdImage.deltaLatitude + 0.5)
+        sampleOffset = np.int32((firstLongitude - wbdImage.firstLongitude) / wbdImage.deltaLongitude + 0.5)
+
+        #first line/sample of mosaicked SWBD is integer lat/lon, but it does not include last integer lat/lon line/sample
+        #so here the size is 3600*3600 instead of 3601*3601
+
+        #assuming areas without swbd are water
+        if tile[0:7] not in swbdList:
+            wbd[0+lineOffset:3600+lineOffset, 0+sampleOffset:3600+sampleOffset] = -1
+        #assuming areas with srtm and without swbd are land
+        if tile[0:7] in noSwbdList:
+            wbd[0+lineOffset:3600+lineOffset, 0+sampleOffset:3600+sampleOffset] = 0
+
+
+    ############################################################
+    #3. set values outside of lat[-56, 60] to -2 (no data)
+    ############################################################
+    print('check water body file')
+    print('set areas outside of lat[-56, 60] to -2 (no data)')
+    for i in range(wbdImage.length):
+        lat = wbdImage.firstLatitude + wbdImage.deltaLatitude * i
+        if lat > 60.0 or lat < -56.0:
+            wbd[i, :] = -2
+    del wbd, wbdImage
+
+
+    return outputFile

components/isceobj/Alos2Proc/runFilt.py

@@ -0,0 +1,171 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import shutil
+import numpy as np
+
+import isceobj
+from mroipac.filter.Filter import Filter
+from contrib.alos2filter.alos2filter import psfilt1
+from mroipac.icu.Icu import Icu
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+from isceobj.Alos2Proc.Alos2ProcPublic import renameFile
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+logger = logging.getLogger('isce.alos2insar.runFilt')
+
+def runFilt(self):
+    '''filter interferogram
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    #masterTrack = self._insar.loadTrack(master=True)
+    #slaveTrack = self._insar.loadTrack(master=False)
+
+    insarDir = 'insar'
+    if not os.path.exists(insarDir):
+        os.makedirs(insarDir)
+    os.chdir(insarDir)
+
+
+    ############################################################
+    # STEP 1. filter interferogram
+    ############################################################
+    print('\nfilter interferogram: {}'.format(self._insar.multilookDifferentialInterferogram))
+
+    toBeFiltered = self._insar.multilookDifferentialInterferogram
+    if self.removeMagnitudeBeforeFiltering:
+        toBeFiltered = 'tmp.int'
+        cmd = "imageMath.py -e='a/(abs(a)+(a==0))' --a={} -o {} -t cfloat -s BSQ".format(self._insar.multilookDifferentialInterferogram, toBeFiltered)
+        runCmd(cmd)
+
+    #if shutil.which('psfilt1') != None:
+    if True:
+        intImage = isceobj.createIntImage()
+        intImage.load(toBeFiltered + '.xml')
+        width = intImage.width
+        length = intImage.length
+        # cmd = "psfilt1 {int} {filtint} {width} {filterstrength} 64 16".format(
+        #        int = toBeFiltered,
+        #        filtint = self._insar.filteredInterferogram,
+        #        width = width,
+        #        filterstrength = self.filterStrength
+        #        )
+        # runCmd(cmd)
+        windowSize = self.filterWinsize
+        stepSize = self.filterStepsize
+        psfilt1(toBeFiltered, self._insar.filteredInterferogram, width, self.filterStrength, windowSize, stepSize)
+        create_xml(self._insar.filteredInterferogram, width, length, 'int')
+    else:
+        #original
+        intImage = isceobj.createIntImage()
+        intImage.load(toBeFiltered + '.xml')
+        intImage.setAccessMode('read')
+        intImage.createImage()
+        width = intImage.width
+        length = intImage.length
+
+        #filtered
+        filtImage = isceobj.createIntImage()
+        filtImage.setFilename(self._insar.filteredInterferogram)
+        filtImage.setWidth(width)
+        filtImage.setAccessMode('write')
+        filtImage.createImage()
+
+        #looks like the ps filtering program keep the original interferogram magnitude, which is bad for phase unwrapping?
+        filters = Filter()
+        filters.wireInputPort(name='interferogram',object=intImage)
+        filters.wireOutputPort(name='filtered interferogram',object=filtImage)
+        filters.goldsteinWerner(alpha=self.filterStrength)
+        intImage.finalizeImage()
+        filtImage.finalizeImage()
+        del intImage, filtImage, filters
+
+    if self.removeMagnitudeBeforeFiltering:
+        os.remove(toBeFiltered)
+        os.remove(toBeFiltered + '.vrt')
+        os.remove(toBeFiltered + '.xml')
+
+    #restore original magnitude
+    tmpFile = 'tmp.int'
+    renameFile(self._insar.filteredInterferogram, tmpFile)
+    cmd = "imageMath.py -e='a*abs(b)' --a={} --b={} -o {} -t cfloat -s BSQ".format(tmpFile, self._insar.multilookDifferentialInterferogram, self._insar.filteredInterferogram)
+    runCmd(cmd)
+    os.remove(tmpFile)
+    os.remove(tmpFile + '.vrt')
+    os.remove(tmpFile + '.xml')
+
+
+    ############################################################
+    # STEP 2. create phase sigma using filtered interferogram
+    ############################################################
+    print('\ncreate phase sigma using: {}'.format(self._insar.filteredInterferogram))
+
+    #recreate filtered image
+    filtImage = isceobj.createIntImage()
+    filtImage.load(self._insar.filteredInterferogram + '.xml')
+    filtImage.setAccessMode('read')
+    filtImage.createImage()
+
+    #amplitude image
+    ampImage = isceobj.createAmpImage()
+    ampImage.load(self._insar.multilookAmplitude + '.xml')
+    ampImage.setAccessMode('read')
+    ampImage.createImage()
+
+    #phase sigma correlation image
+    phsigImage = isceobj.createImage()
+    phsigImage.setFilename(self._insar.multilookPhsig)
+    phsigImage.setWidth(width)
+    phsigImage.dataType='FLOAT'
+    phsigImage.bands = 1
+    phsigImage.setImageType('cor')
+    phsigImage.setAccessMode('write')
+    phsigImage.createImage()
+
+    icu = Icu(name='insarapp_filter_icu')
+    icu.configure()
+    icu.unwrappingFlag = False
+    icu.icu(intImage = filtImage, ampImage=ampImage, phsigImage=phsigImage)
+
+    phsigImage.renderHdr()
+
+    filtImage.finalizeImage()
+    ampImage.finalizeImage()
+    phsigImage.finalizeImage()
+
+    del filtImage
+    del ampImage
+    del phsigImage
+    del icu
+
+
+    ############################################################
+    # STEP 3. mask filtered interferogram using water body
+    ############################################################
+    print('\nmask filtered interferogram using: {}'.format(self._insar.multilookWbdOut))
+
+    if self.waterBodyMaskStartingStep=='filt':
+        if not os.path.exists(self._insar.multilookWbdOut):
+            catalog.addItem('warning message', 'requested masking interferogram with water body, but water body does not exist', 'runFilt')
+        else:
+            wbd = np.fromfile(self._insar.multilookWbdOut, dtype=np.int8).reshape(length, width)
+            phsig=np.memmap(self._insar.multilookPhsig, dtype='float32', mode='r+', shape=(length, width))
+            phsig[np.nonzero(wbd==-1)]=0
+            del phsig
+            filt=np.memmap(self._insar.filteredInterferogram, dtype='complex64', mode='r+', shape=(length, width))
+            filt[np.nonzero(wbd==-1)]=0
+            del filt
+            del wbd
+
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runFilt")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+

components/isceobj/Alos2Proc/runFiltOffset.py

@@ -0,0 +1,104 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import statistics
+import numpy as np
+from scipy.ndimage.filters import median_filter
+
+import isceobj
+
+logger = logging.getLogger('isce.alos2insar.runFiltOffset')
+
+def runFiltOffset(self):
+    '''filt offset fied
+    '''
+    if not self.doDenseOffset:
+        return
+    if not ((self._insar.modeCombination == 0) or (self._insar.modeCombination == 1)):
+        return
+
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    denseOffsetDir = 'dense_offset'
+    if not os.path.exists(denseOffsetDir):
+        os.makedirs(denseOffsetDir)
+    os.chdir(denseOffsetDir)
+
+    #masterTrack = self._insar.loadProduct(self._insar.masterTrackParameter)
+    #slaveTrack = self._insar.loadProduct(self._insar.slaveTrackParameter)
+
+#########################################################################################
+
+    if not self.doOffsetFiltering:
+        print('offset field filtering is not requested.')
+        os.chdir('../')
+        catalog.printToLog(logger, "runFiltOffset")
+        self._insar.procDoc.addAllFromCatalog(catalog)
+        return
+
+    windowSize = self.offsetFilterWindowsize
+    nullValue = 0
+    snrThreshold = self.offsetFilterSnrThreshold
+
+    if windowSize < 3:
+        raise Exception('dense offset field filter window size must >= 3')
+    if windowSize % 2 != 1:
+        windowSize += 1
+        print('dense offset field filter window size is not odd, changed to: {}'.format(windowSize))
+
+    print('\noffset filter parameters:')
+    print('**************************************')
+    print('filter window size: {}'.format(windowSize))
+    print('filter null value: {}'.format(nullValue))
+    print('filter snr threshold: {}\n'.format(snrThreshold))
+
+
+    img = isceobj.createImage()
+    img.load(self._insar.denseOffset+'.xml')
+    width = img.width
+    length = img.length
+
+    offset = np.fromfile(self._insar.denseOffset, dtype=np.float32).reshape(length*2, width)
+    snr = np.fromfile(self._insar.denseOffsetSnr, dtype=np.float32).reshape(length, width)
+    offsetFilt = np.zeros((length*2, width), dtype=np.float32)
+
+    edge = int((windowSize-1)/2+0.5)
+    for k in range(2):
+        print('filtering band {} of {}'.format(k+1, 2))
+        band = offset[k:length*2:2, :]
+        bandFilt = offsetFilt[k:length*2:2, :]
+        for i in range(0+edge, length-edge):
+            for j in range(0+edge, width-edge):
+                bandSub = band[i-edge:i+edge+1, j-edge:j+edge+1]
+                snrSub = snr[i-edge:i+edge+1, j-edge:j+edge+1]
+                #bandSubUsed is 1-d numpy array
+                bandSubUsed = bandSub[np.nonzero(np.logical_and(snrSub>snrThreshold, bandSub!=nullValue))]
+                if bandSubUsed.size == 0:
+                    bandFilt[i, j] = nullValue
+                else:
+                    bandFilt[i, j] = statistics.median(bandSubUsed)
+
+    offsetFilt.astype(np.float32).tofile(self._insar.denseOffsetFilt)
+    outImg = isceobj.createImage()
+    outImg.setDataType('FLOAT')
+    outImg.setFilename(self._insar.denseOffsetFilt)
+    outImg.setBands(2)
+    outImg.scheme = 'BIL'
+    outImg.setWidth(width)
+    outImg.setLength(length)
+    outImg.addDescription('two-band pixel offset file. 1st band: range offset, 2nd band: azimuth offset')
+    outImg.setAccessMode('read')
+    outImg.renderHdr()
+
+#########################################################################################
+
+    os.chdir('../')
+    catalog.printToLog(logger, "runFiltOffset")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+

components/isceobj/Alos2Proc/runFormInterferogram.py

@@ -0,0 +1,134 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+import stdproc
+from iscesys.StdOEL.StdOELPy import create_writer
+from isceobj.Alos2Proc.Alos2ProcPublic import readOffset
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+
+logger = logging.getLogger('isce.alos2insar.runFormInterferogram')
+
+def runFormInterferogram(self):
+    '''form interferograms.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            os.chdir(swathDir)
+
+            print('forming interferogram frame {}, swath {}'.format(frameNumber, swathNumber))
+
+            masterSwath = masterTrack.frames[i].swaths[j]
+            slaveSwath = slaveTrack.frames[i].swaths[j]
+
+
+            #############################################
+            #1. form interferogram
+            #############################################
+            refinedOffsets = readOffset('cull.off')
+            intWidth = int(masterSwath.numberOfSamples / self._insar.numberRangeLooks1)
+            intLength = int(masterSwath.numberOfLines / self._insar.numberAzimuthLooks1)
+            dopplerVsPixel = [i/slaveSwath.prf for i in slaveSwath.dopplerVsPixel]
+
+            #master slc
+            mSLC = isceobj.createSlcImage()
+            mSLC.load(self._insar.masterSlc+'.xml')
+            mSLC.setAccessMode('read')
+            mSLC.createImage()
+
+            #slave slc
+            sSLC = isceobj.createSlcImage()
+            sSLC.load(self._insar.slaveSlc+'.xml')
+            sSLC.setAccessMode('read')
+            sSLC.createImage()
+
+            #interferogram
+            interf = isceobj.createIntImage()
+            interf.setFilename(self._insar.interferogram)
+            interf.setWidth(intWidth)
+            interf.setAccessMode('write')
+            interf.createImage()
+
+            #amplitdue
+            amplitude = isceobj.createAmpImage()
+            amplitude.setFilename(self._insar.amplitude)
+            amplitude.setWidth(intWidth)
+            amplitude.setAccessMode('write')
+            amplitude.createImage()
+
+            #create a writer for resamp
+            stdWriter = create_writer("log", "", True, filename="resamp.log")
+            stdWriter.setFileTag("resamp", "log")
+            stdWriter.setFileTag("resamp", "err")
+            stdWriter.setFileTag("resamp", "out")
+
+
+            #set up resampling program now
+            #The setting has been compared with resamp_roi's setting in ROI_pac item by item.
+            #The two kinds of setting are exactly the same. The number of setting items are
+            #exactly the same
+            objResamp = stdproc.createResamp()
+            objResamp.wireInputPort(name='offsets', object=refinedOffsets)
+            objResamp.stdWriter = stdWriter
+            objResamp.setNumberFitCoefficients(6)
+            objResamp.setNumberRangeBin1(masterSwath.numberOfSamples)
+            objResamp.setNumberRangeBin2(slaveSwath.numberOfSamples)    
+            objResamp.setStartLine(1)
+            objResamp.setNumberLines(masterSwath.numberOfLines)
+            objResamp.setFirstLineOffset(1)
+            objResamp.setDopplerCentroidCoefficients(dopplerVsPixel)
+            objResamp.setRadarWavelength(slaveTrack.radarWavelength)
+            objResamp.setSlantRangePixelSpacing(slaveSwath.rangePixelSize)
+            objResamp.setNumberRangeLooks(self._insar.numberRangeLooks1)
+            objResamp.setNumberAzimuthLooks(self._insar.numberAzimuthLooks1)
+            objResamp.setFlattenWithOffsetFitFlag(0)
+            objResamp.resamp(mSLC, sSLC, interf, amplitude) 
+            
+            #finialize images
+            mSLC.finalizeImage()
+            sSLC.finalizeImage()
+            interf.finalizeImage()
+            amplitude.finalizeImage()
+            stdWriter.finalize()
+
+
+            #############################################
+            #2. trim amplitude
+            #############################################
+            # tmpAmplitude = 'tmp.amp'
+            # cmd = "imageMath.py -e='a_0*(a_1>0);a_1*(a_0>0)' --a={} -o={} -s BIP -t float".format(
+            #     self._insar.amplitude, 
+            #     tmpAmplitude
+            #     )
+            # runCmd(cmd)
+            # os.remove(self._insar.amplitude)
+            # os.remove(tmpAmplitude+'.xml')
+            # os.remove(tmpAmplitude+'.vrt')
+            # os.rename(tmpAmplitude, self._insar.amplitude)
+
+            #using memmap instead, which should be faster, since we only have a few pixels to change
+            amp=np.memmap(self._insar.amplitude, dtype='complex64', mode='r+', shape=(intLength, intWidth))
+            index = np.nonzero( (np.real(amp)==0) + (np.imag(amp)==0) )
+            amp[index]=0
+            del amp
+
+            os.chdir('../')
+        os.chdir('../')
+
+    catalog.printToLog(logger, "runFormInterferogram")
+    self._insar.procDoc.addAllFromCatalog(catalog)

components/isceobj/Alos2Proc/runFrameMosaic.py

@@ -0,0 +1,552 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import glob
+import logging
+import datetime
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+logger = logging.getLogger('isce.alos2insar.runFrameMosaic')
+
+def runFrameMosaic(self):
+    '''mosaic frames
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    mosaicDir = 'insar'
+    if not os.path.exists(mosaicDir):
+        os.makedirs(mosaicDir)
+    os.chdir(mosaicDir)
+
+    numberOfFrames = len(masterTrack.frames)
+    if numberOfFrames == 1:
+        import shutil
+        frameDir = os.path.join('f1_{}/mosaic'.format(self._insar.masterFrames[0]))
+        if not os.path.isfile(self._insar.interferogram):
+            os.symlink(os.path.join('../', frameDir, self._insar.interferogram), self._insar.interferogram)
+        #shutil.copy2() can overwrite
+        shutil.copy2(os.path.join('../', frameDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+        shutil.copy2(os.path.join('../', frameDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+        if not os.path.isfile(self._insar.amplitude):
+            os.symlink(os.path.join('../', frameDir, self._insar.amplitude), self._insar.amplitude)
+        shutil.copy2(os.path.join('../', frameDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+        shutil.copy2(os.path.join('../', frameDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+        # os.rename(os.path.join('../', frameDir, self._insar.interferogram), self._insar.interferogram)
+        # os.rename(os.path.join('../', frameDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+        # os.rename(os.path.join('../', frameDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+        # os.rename(os.path.join('../', frameDir, self._insar.amplitude), self._insar.amplitude)
+        # os.rename(os.path.join('../', frameDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+        # os.rename(os.path.join('../', frameDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+        #update track parameters
+        #########################################################
+        #mosaic size
+        masterTrack.numberOfSamples = masterTrack.frames[0].numberOfSamples
+        masterTrack.numberOfLines = masterTrack.frames[0].numberOfLines
+        #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+        #range parameters
+        masterTrack.startingRange = masterTrack.frames[0].startingRange
+        masterTrack.rangeSamplingRate = masterTrack.frames[0].rangeSamplingRate
+        masterTrack.rangePixelSize = masterTrack.frames[0].rangePixelSize
+        #azimuth parameters
+        masterTrack.sensingStart = masterTrack.frames[0].sensingStart
+        masterTrack.prf = masterTrack.frames[0].prf
+        masterTrack.azimuthPixelSize = masterTrack.frames[0].azimuthPixelSize
+        masterTrack.azimuthLineInterval = masterTrack.frames[0].azimuthLineInterval
+
+        #update track parameters, slave
+        #########################################################
+        #mosaic size
+        slaveTrack.numberOfSamples = slaveTrack.frames[0].numberOfSamples
+        slaveTrack.numberOfLines = slaveTrack.frames[0].numberOfLines
+        #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+        #range parameters
+        slaveTrack.startingRange = slaveTrack.frames[0].startingRange
+        slaveTrack.rangeSamplingRate = slaveTrack.frames[0].rangeSamplingRate
+        slaveTrack.rangePixelSize = slaveTrack.frames[0].rangePixelSize
+        #azimuth parameters
+        slaveTrack.sensingStart = slaveTrack.frames[0].sensingStart
+        slaveTrack.prf = slaveTrack.frames[0].prf
+        slaveTrack.azimuthPixelSize = slaveTrack.frames[0].azimuthPixelSize
+        slaveTrack.azimuthLineInterval = slaveTrack.frames[0].azimuthLineInterval
+
+    else:
+        #choose offsets
+        if self.frameOffsetMatching:
+            rangeOffsets = self._insar.frameRangeOffsetMatchingMaster
+            azimuthOffsets = self._insar.frameAzimuthOffsetMatchingMaster
+        else:
+            rangeOffsets = self._insar.frameRangeOffsetGeometricalMaster
+            azimuthOffsets = self._insar.frameAzimuthOffsetGeometricalMaster
+
+        #list of input files
+        inputInterferograms = []
+        inputAmplitudes = []
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            inputInterferograms.append(os.path.join('../', frameDir, 'mosaic', self._insar.interferogram))
+            inputAmplitudes.append(os.path.join('../', frameDir, 'mosaic', self._insar.amplitude))
+
+        #note that track parameters are updated after mosaicking
+        #mosaic amplitudes
+        frameMosaic(masterTrack, inputAmplitudes, self._insar.amplitude, 
+            rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+            updateTrack=False, phaseCompensation=False, resamplingMethod=0)
+        #mosaic interferograms
+        frameMosaic(masterTrack, inputInterferograms, self._insar.interferogram, 
+            rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+            updateTrack=True, phaseCompensation=True, resamplingMethod=1)
+
+        create_xml(self._insar.amplitude, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'amp')
+        create_xml(self._insar.interferogram, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'int')
+
+        #update slave parameters here
+        #do not match for slave, always use geometrical
+        rangeOffsets = self._insar.frameRangeOffsetGeometricalSlave
+        azimuthOffsets = self._insar.frameAzimuthOffsetGeometricalSlave
+        frameMosaicParameters(slaveTrack, rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1)
+
+    os.chdir('../')
+    #save parameter file
+    self._insar.saveProduct(masterTrack, self._insar.masterTrackParameter)
+    self._insar.saveProduct(slaveTrack, self._insar.slaveTrackParameter)
+
+    catalog.printToLog(logger, "runFrameMosaic")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def frameMosaic(track, inputFiles, outputfile, rangeOffsets, azimuthOffsets, numberOfRangeLooks, numberOfAzimuthLooks, updateTrack=False, phaseCompensation=False, resamplingMethod=0):
+    '''
+    mosaic frames
+    
+    track:                 track
+    inputFiles:            input file list
+    output file:           output mosaic file
+    rangeOffsets:          range offsets
+    azimuthOffsets:        azimuth offsets
+    numberOfRangeLooks:    number of range looks of the input files
+    numberOfAzimuthLooks:  number of azimuth looks of the input files
+    updateTrack:           whether update track parameters
+    phaseCompensation:     whether do phase compensation for each frame
+    resamplingMethod:      0: amp resampling. 1: int resampling. 2: slc resampling
+    '''
+    import numpy as np
+
+    from contrib.alos2proc_f.alos2proc_f import rect_with_looks
+    from contrib.alos2proc.alos2proc import resamp
+    from isceobj.Alos2Proc.runSwathMosaic import readImage
+    from isceobj.Alos2Proc.runSwathMosaic import findNonzero
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+    from isceobj.Alos2Proc.Alos2ProcPublic import find_vrt_file
+    from isceobj.Alos2Proc.Alos2ProcPublic import find_vrt_keyword
+
+    numberOfFrames = len(track.frames)
+    frames = track.frames
+
+    rectWidth = []
+    rectLength = []
+    for i in range(numberOfFrames):
+        infImg = isceobj.createImage()
+        infImg.load(inputFiles[i]+'.xml')
+        rectWidth.append(infImg.width)
+        rectLength.append(infImg.length)
+
+    #convert original offset to offset for images with looks
+    #use list instead of np.array to make it consistent with the rest of the code
+    rangeOffsets1 = [i/numberOfRangeLooks for i in rangeOffsets]
+    azimuthOffsets1 = [i/numberOfAzimuthLooks for i in azimuthOffsets]
+
+    #get offset relative to the first frame
+    rangeOffsets2 = [0.0]
+    azimuthOffsets2 = [0.0]
+    for i in range(1, numberOfFrames):
+        rangeOffsets2.append(0.0)
+        azimuthOffsets2.append(0.0)
+        for j in range(1, i+1):
+            rangeOffsets2[i] += rangeOffsets1[j]
+            azimuthOffsets2[i] += azimuthOffsets1[j]
+
+    #resample each frame
+    rinfs = []
+    for i, inf in enumerate(inputFiles):
+        rinfs.append("{}_{}{}".format(os.path.splitext(os.path.basename(inf))[0], i, os.path.splitext(os.path.basename(inf))[1]))
+        #do not resample first frame
+        if i == 0:
+            rinfs[i] = inf
+        else:
+            infImg = isceobj.createImage()
+            infImg.load(inf+'.xml')
+            rangeOffsets2Frac = rangeOffsets2[i] - int(rangeOffsets2[i])
+            azimuthOffsets2Frac = azimuthOffsets2[i] - int(azimuthOffsets2[i])
+
+            if resamplingMethod == 0:
+                rect_with_looks(inf,
+                                rinfs[i],
+                                infImg.width, infImg.length,
+                                infImg.width, infImg.length,
+                                1.0, 0.0,
+                                0.0, 1.0,
+                                rangeOffsets2Frac, azimuthOffsets2Frac,
+                                1,1,
+                                1,1,
+                                'COMPLEX',
+                                'Bilinear')
+                if infImg.getImageType() == 'amp':
+                    create_xml(rinfs[i], infImg.width, infImg.length, 'amp')
+                else:
+                    create_xml(rinfs[i], infImg.width, infImg.length, 'int')
+
+            elif resamplingMethod == 1:
+                #decompose amplitude and phase
+                phaseFile = 'phase'
+                amplitudeFile = 'amplitude'
+                data = np.fromfile(inf, dtype=np.complex64).reshape(infImg.length, infImg.width)
+                phase = np.exp(np.complex64(1j) * np.angle(data))
+                phase[np.nonzero(data==0)] = 0
+                phase.astype(np.complex64).tofile(phaseFile)
+                amplitude = np.absolute(data)
+                amplitude.astype(np.float32).tofile(amplitudeFile)
+
+                #resampling
+                phaseRectFile = 'phaseRect'
+                amplitudeRectFile = 'amplitudeRect'
+                rect_with_looks(phaseFile,
+                                phaseRectFile,
+                                infImg.width, infImg.length,
+                                infImg.width, infImg.length,
+                                1.0, 0.0,
+                                0.0, 1.0,
+                                rangeOffsets2Frac, azimuthOffsets2Frac,
+                                1,1,
+                                1,1,
+                                'COMPLEX',
+                                'Sinc')
+                rect_with_looks(amplitudeFile,
+                                amplitudeRectFile,
+                                infImg.width, infImg.length,
+                                infImg.width, infImg.length,
+                                1.0, 0.0,
+                                0.0, 1.0,
+                                rangeOffsets2Frac, azimuthOffsets2Frac,
+                                1,1,
+                                1,1,
+                                'REAL',
+                                'Bilinear')
+
+                #recombine amplitude and phase
+                phase = np.fromfile(phaseRectFile, dtype=np.complex64).reshape(infImg.length, infImg.width)
+                amplitude = np.fromfile(amplitudeRectFile, dtype=np.float32).reshape(infImg.length, infImg.width)
+                (phase*amplitude).astype(np.complex64).tofile(rinfs[i])
+
+                #tidy up
+                os.remove(phaseFile)
+                os.remove(amplitudeFile)
+                os.remove(phaseRectFile)
+                os.remove(amplitudeRectFile)
+                if infImg.getImageType() == 'amp':
+                    create_xml(rinfs[i], infImg.width, infImg.length, 'amp')
+                else:
+                    create_xml(rinfs[i], infImg.width, infImg.length, 'int')
+            else:
+                resamp(inf,
+                       rinfs[i],
+                       'fake',
+                       'fake',
+                       infImg.width, infImg.length,
+                       frames[i].swaths[0].prf,
+                       frames[i].swaths[0].dopplerVsPixel,
+                       [rangeOffsets2Frac, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+                       [azimuthOffsets2Frac, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0])
+                create_xml(rinfs[i], infImg.width, infImg.length, 'slc')
+
+    #determine output width and length
+    #actually no need to calculate in azimuth direction
+    xs = []
+    xe = []
+    ys = []
+    ye = []
+    for i in range(numberOfFrames):
+        if i == 0:
+            xs.append(0)
+            xe.append(rectWidth[i] - 1)
+            ys.append(0)
+            ye.append(rectLength[i] - 1)
+        else:
+            xs.append(0 - int(rangeOffsets2[i]))
+            xe.append(rectWidth[i] - 1 - int(rangeOffsets2[i]))
+            ys.append(0 - int(azimuthOffsets2[i]))
+            ye.append(rectLength[i] - 1 - int(azimuthOffsets2[i]))
+
+    (xmin, xminIndex) = min((v,i) for i,v in enumerate(xs))
+    (xmax, xmaxIndex) = max((v,i) for i,v in enumerate(xe))
+    (ymin, yminIndex) = min((v,i) for i,v in enumerate(ys))
+    (ymax, ymaxIndex) = max((v,i) for i,v in enumerate(ye))
+
+    outWidth = xmax - xmin + 1
+    outLength = ymax - ymin + 1
+
+
+    #prepare for mosaicing using numpy
+    xs = [x-xmin for x in xs]
+    xe = [x-xmin for x in xe]
+    ys = [y-ymin for y in ys]
+    ye = [y-ymin for y in ye]
+
+
+    #compute phase offset
+    if phaseCompensation:
+        phaseOffsetPolynomials = [np.array([0.0])]
+        for i in range(1, numberOfFrames):
+            upperframe = np.zeros((ye[i-1]-ys[i]+1, outWidth), dtype=np.complex128)
+            lowerframe = np.zeros((ye[i-1]-ys[i]+1, outWidth), dtype=np.complex128)
+            #upper frame
+            if os.path.isfile(rinfs[i-1]):
+                upperframe[:,xs[i-1]:xe[i-1]+1] = readImage(rinfs[i-1], rectWidth[i-1], rectLength[i-1], 0, rectWidth[i-1]-1, ys[i]-ys[i-1], ye[i-1]-ys[i-1])
+            else:
+                upperframe[:,xs[i-1]:xe[i-1]+1] = readImageFromVrt(rinfs[i-1], 0, rectWidth[i-1]-1, ys[i]-ys[i-1], ye[i-1]-ys[i-1])
+            #lower frame
+            if os.path.isfile(rinfs[i]):
+                lowerframe[:,xs[i]:xe[i]+1] = readImage(rinfs[i], rectWidth[i], rectLength[i], 0, rectWidth[i]-1, 0, ye[i-1]-ys[i])
+            else:
+                lowerframe[:,xs[i]:xe[i]+1] = readImageFromVrt(rinfs[i], 0, rectWidth[i]-1, 0, ye[i-1]-ys[i])
+            #get a polynomial
+            diff = np.sum(upperframe * np.conj(lowerframe), axis=0)
+            (firstLine, lastLine, firstSample, lastSample) = findNonzero(np.reshape(diff, (1, outWidth)))
+            #here i use mean value(deg=0) in case difference is around -pi or pi.
+            deg = 0
+            p = np.polyfit(np.arange(firstSample, lastSample+1), np.angle(diff[firstSample:lastSample+1]), deg)
+            phaseOffsetPolynomials.append(p)
+
+
+            #check fit result
+            DEBUG = False
+            if DEBUG:
+                #create a dir and work in this dir
+                diffDir = 'frame_mosaic'
+                if not os.path.exists(diffDir):
+                    os.makedirs(diffDir)
+                os.chdir(diffDir)
+
+                #dump phase difference
+                diffFilename = 'phase_difference_frame{}-frame{}.int'.format(i, i+1)
+                (upperframe * np.conj(lowerframe)).astype(np.complex64).tofile(diffFilename)
+                create_xml(diffFilename, outWidth, ye[i-1]-ys[i]+1, 'int')
+
+                #plot phase difference vs range
+                import matplotlib.pyplot as plt
+                x = np.arange(firstSample, lastSample+1)
+                y = np.angle(diff[firstSample:lastSample+1])
+                plt.plot(x, y, label='original phase difference')
+                plt.plot(x, np.polyval(p, x), label='fitted phase difference')
+                plt.legend()
+
+                plt.minorticks_on()
+                plt.tick_params('both', length=10, which='major')
+                plt.tick_params('both', length=5, which='minor')
+
+                plt.xlabel('Range Sample Number [Samples]')
+                plt.ylabel('Phase Difference [Rad]')
+                plt.savefig('phase_difference_frame{}-frame{}.pdf'.format(i, i+1))
+
+                os.chdir('../')
+
+
+    #mosaic file
+    outFp = open(outputfile,'wb')
+    for i in range(numberOfFrames):
+        print('adding frame: {}'.format(i+1))
+
+        #phase offset in the polynomials
+        if phaseCompensation:
+            cJ = np.complex64(1j)
+            phaseOffset = np.ones(outWidth, dtype=np.complex64)
+            for j in range(i+1):
+                phaseOffset *= np.exp(cJ*np.polyval(phaseOffsetPolynomials[j], np.arange(outWidth)))
+
+        #get start line number (starts with zero)
+        if i == 0:
+            ys1 = 0
+        else:
+            ys1 = int((ye[i-1]+ys[i])/2.0) + 1 - ys[i]
+        #get end line number (start with zero)
+        if i == numberOfFrames-1:
+            ye1 = rectLength[i] - 1
+        else:
+            ye1 = int((ye[i]+ys[i+1])/2.0) - ys[i]
+
+        #get image format
+        inputimage = find_vrt_file(rinfs[i]+'.vrt', 'SourceFilename', relative_path=True)
+        byteorder = find_vrt_keyword(rinfs[i]+'.vrt', 'ByteOrder')
+        if byteorder == 'LSB':
+            swapByte = False
+        else:
+            swapByte = True
+        imageoffset = int(find_vrt_keyword(rinfs[i]+'.vrt', 'ImageOffset'))
+        lineoffset = int(find_vrt_keyword(rinfs[i]+'.vrt', 'LineOffset'))
+
+        #read image
+        with open(inputimage,'rb') as fp:
+            for j in range(ys1, ye1+1):
+                fp.seek(imageoffset+j*lineoffset, 0)
+                data = np.zeros(outWidth, dtype=np.complex64)
+                if swapByte:
+                    tmp = np.fromfile(fp, dtype='>f', count=2*rectWidth[i])
+                    cJ = np.complex64(1j)
+                    data[xs[i]:xe[i]+1] = tmp[0::2] + cJ * tmp[1::2]
+                else:
+                    data[xs[i]:xe[i]+1] = np.fromfile(fp, dtype=np.complex64, count=rectWidth[i])
+                if phaseCompensation:
+                    data *= phaseOffset
+                data.astype(np.complex64).tofile(outFp)
+    outFp.close()
+
+
+    #delete files. DO NOT DELETE THE FIRST ONE!!!
+    for i in range(numberOfFrames):
+        if i == 0:
+            continue
+        os.remove(rinfs[i])
+        os.remove(rinfs[i]+'.vrt')
+        os.remove(rinfs[i]+'.xml')
+
+
+    #update frame parameters
+    if updateTrack:
+        #mosaic size
+        track.numberOfSamples = outWidth
+        track.numberOfLines = outLength
+        #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+        #range parameters
+        track.startingRange = frames[0].startingRange + (int(rangeOffsets2[0]) - int(rangeOffsets2[xminIndex])) * numberOfRangeLooks * frames[0].rangePixelSize
+        track.rangeSamplingRate = frames[0].rangeSamplingRate
+        track.rangePixelSize = frames[0].rangePixelSize
+        #azimuth parameters
+        track.sensingStart = frames[0].sensingStart
+        track.prf = frames[0].prf
+        track.azimuthPixelSize = frames[0].azimuthPixelSize
+        track.azimuthLineInterval = frames[0].azimuthLineInterval
+
+
+def frameMosaicParameters(track, rangeOffsets, azimuthOffsets, numberOfRangeLooks, numberOfAzimuthLooks):
+    '''
+    mosaic frames (this simplified version of frameMosaic to only update parameters)
+    
+    track:                 track
+    rangeOffsets:          range offsets
+    azimuthOffsets:        azimuth offsets
+    numberOfRangeLooks:    number of range looks of the input files
+    numberOfAzimuthLooks:  number of azimuth looks of the input files
+    '''
+
+    numberOfFrames = len(track.frames)
+    frames = track.frames
+
+    rectWidth = []
+    rectLength = []
+    for i in range(numberOfFrames):
+        rectWidth.append(frames[i].numberOfSamples)
+        rectLength.append(frames[i].numberOfLines)
+
+    #convert original offset to offset for images with looks
+    #use list instead of np.array to make it consistent with the rest of the code
+    rangeOffsets1 = [i/numberOfRangeLooks for i in rangeOffsets]
+    azimuthOffsets1 = [i/numberOfAzimuthLooks for i in azimuthOffsets]
+
+    #get offset relative to the first frame
+    rangeOffsets2 = [0.0]
+    azimuthOffsets2 = [0.0]
+    for i in range(1, numberOfFrames):
+        rangeOffsets2.append(0.0)
+        azimuthOffsets2.append(0.0)
+        for j in range(1, i+1):
+            rangeOffsets2[i] += rangeOffsets1[j]
+            azimuthOffsets2[i] += azimuthOffsets1[j]
+
+    #determine output width and length
+    #actually no need to calculate in azimuth direction
+    xs = []
+    xe = []
+    ys = []
+    ye = []
+    for i in range(numberOfFrames):
+        if i == 0:
+            xs.append(0)
+            xe.append(rectWidth[i] - 1)
+            ys.append(0)
+            ye.append(rectLength[i] - 1)
+        else:
+            xs.append(0 - int(rangeOffsets2[i]))
+            xe.append(rectWidth[i] - 1 - int(rangeOffsets2[i]))
+            ys.append(0 - int(azimuthOffsets2[i]))
+            ye.append(rectLength[i] - 1 - int(azimuthOffsets2[i]))
+
+    (xmin, xminIndex) = min((v,i) for i,v in enumerate(xs))
+    (xmax, xmaxIndex) = max((v,i) for i,v in enumerate(xe))
+    (ymin, yminIndex) = min((v,i) for i,v in enumerate(ys))
+    (ymax, ymaxIndex) = max((v,i) for i,v in enumerate(ye))
+
+    outWidth = xmax - xmin + 1
+    outLength = ymax - ymin + 1
+
+    #update frame parameters
+    #mosaic size
+    track.numberOfSamples = outWidth
+    track.numberOfLines = outLength
+    #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+    #range parameters
+    track.startingRange = frames[0].startingRange + (int(rangeOffsets2[0]) - int(rangeOffsets2[xminIndex])) * numberOfRangeLooks * frames[0].rangePixelSize
+    track.rangeSamplingRate = frames[0].rangeSamplingRate
+    track.rangePixelSize = frames[0].rangePixelSize
+    #azimuth parameters
+    track.sensingStart = frames[0].sensingStart
+    track.prf = frames[0].prf
+    track.azimuthPixelSize = frames[0].azimuthPixelSize
+    track.azimuthLineInterval = frames[0].azimuthLineInterval
+
+
+def readImageFromVrt(inputfile, startSample, endSample, startLine, endLine):
+    '''
+    read a chunk of image
+    the indexes (startSample, endSample, startLine, endLine) are included and start with zero
+
+    memmap is not used, because it is much slower
+
+    tested against readImage in runSwathMosaic.py
+    '''
+    import os
+    from isceobj.Alos2Proc.Alos2ProcPublic import find_vrt_keyword
+    from isceobj.Alos2Proc.Alos2ProcPublic import find_vrt_file
+
+    inputimage = find_vrt_file(inputfile+'.vrt', 'SourceFilename', relative_path=True)
+    byteorder = find_vrt_keyword(inputfile+'.vrt', 'ByteOrder')
+    if byteorder == 'LSB':
+        swapByte = False
+    else:
+        swapByte = True
+    imageoffset = int(find_vrt_keyword(inputfile+'.vrt', 'ImageOffset'))
+    lineoffset = int(find_vrt_keyword(inputfile+'.vrt', 'LineOffset'))
+
+    data = np.zeros((endLine-startLine+1, endSample-startSample+1), dtype=np.complex64)
+    with open(inputimage,'rb') as fp:
+        #fp.seek(imageoffset, 0)
+        #for i in range(endLine-startLine+1):
+        for i in range(startLine, endLine+1):
+            fp.seek(imageoffset+i*lineoffset+startSample*8, 0)
+            if swapByte:
+                tmp = np.fromfile(fp, dtype='>f', count=2*(endSample-startSample+1))
+                cJ = np.complex64(1j)
+                data[i-startLine] = tmp[0::2] + cJ * tmp[1::2]
+            else:
+                data[i-startLine] = np.fromfile(fp, dtype=np.complex64, count=endSample-startSample+1)
+    return data

components/isceobj/Alos2Proc/runFrameOffset.py

@@ -0,0 +1,287 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+
+logger = logging.getLogger('isce.alos2insar.runFrameOffset')
+
+def runFrameOffset(self):
+    '''estimate frame offsets.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    mosaicDir = 'insar'
+    if not os.path.exists(mosaicDir):
+        os.makedirs(mosaicDir)
+    os.chdir(mosaicDir)
+
+    if len(masterTrack.frames) > 1:
+        if (self._insar.modeCombination == 21) or \
+           (self._insar.modeCombination == 22) or \
+           (self._insar.modeCombination == 31) or \
+           (self._insar.modeCombination == 32):
+            matchingMode=0
+        else:
+            matchingMode=1
+
+        #compute swath offset
+        offsetMaster = frameOffset(masterTrack, self._insar.masterSlc, self._insar.masterFrameOffset, 
+                                   crossCorrelation=self.frameOffsetMatching, matchingMode=matchingMode)
+        #only use geometrical offset for slave
+        offsetSlave = frameOffset(slaveTrack, self._insar.slaveSlc, self._insar.slaveFrameOffset, 
+                                  crossCorrelation=False, matchingMode=matchingMode)
+
+        self._insar.frameRangeOffsetGeometricalMaster = offsetMaster[0]
+        self._insar.frameAzimuthOffsetGeometricalMaster = offsetMaster[1]
+        self._insar.frameRangeOffsetGeometricalSlave = offsetSlave[0]
+        self._insar.frameAzimuthOffsetGeometricalSlave = offsetSlave[1]
+        if self.frameOffsetMatching:
+            self._insar.frameRangeOffsetMatchingMaster = offsetMaster[2]
+            self._insar.frameAzimuthOffsetMatchingMaster = offsetMaster[3]
+            #self._insar.frameRangeOffsetMatchingSlave = offsetSlave[2]
+            #self._insar.frameAzimuthOffsetMatchingSlave = offsetSlave[3]
+
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runFrameOffset")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def frameOffset(track, image, outputfile, crossCorrelation=True, matchingMode=0):
+    '''
+    compute frame offset
+    track:                track object
+    image:                image for doing matching
+    outputfile:           output txt file for saving frame offset
+    crossCorrelation:     whether do matching
+    matchingMode:         how to match images. 0: ScanSAR full-aperture image, 1: regular image
+    '''
+
+    rangeOffsetGeometrical = []
+    azimuthOffsetGeometrical = []
+    rangeOffsetMatching = []
+    azimuthOffsetMatching = []
+
+    for j in range(len(track.frames)):
+        frameNumber = track.frames[j].frameNumber
+        swathNumber = track.frames[j].swaths[0].swathNumber
+        swathDir = 'f{}_{}/s{}'.format(j+1, frameNumber, swathNumber)
+
+        print('estimate offset frame {}'.format(frameNumber))
+
+        if j == 0:
+            rangeOffsetGeometrical.append(0.0)
+            azimuthOffsetGeometrical.append(0.0)
+            rangeOffsetMatching.append(0.0)
+            azimuthOffsetMatching.append(0.0)
+            swathDirLast = swathDir
+            continue
+
+        image1 = os.path.join('../', swathDirLast, image)
+        image2 = os.path.join('../', swathDir, image)
+        #swath1 = frame.swaths[j-1]
+        #swath2 = frame.swaths[j]
+        swath1 = track.frames[j-1].swaths[0]
+        swath2 = track.frames[j].swaths[0]
+
+
+        #offset from geometry
+        offsetGeometrical = computeFrameOffset(swath1, swath2)
+        rangeOffsetGeometrical.append(offsetGeometrical[0])
+        azimuthOffsetGeometrical.append(offsetGeometrical[1])
+
+        #offset from cross-correlation
+        if crossCorrelation:
+            offsetMatching = estimateFrameOffset(swath1, swath2, image1, image2, matchingMode=matchingMode)
+            if offsetMatching != None:
+                rangeOffsetMatching.append(offsetMatching[0])
+                azimuthOffsetMatching.append(offsetMatching[1])
+            else:
+                print('******************************************************************')
+                print('WARNING: bad matching offset, we are forced to use')
+                print('         geometrical offset for frame mosaicking')
+                print('******************************************************************')
+                rangeOffsetMatching.append(offsetGeometrical[0])
+                azimuthOffsetMatching.append(offsetGeometrical[1])
+
+        swathDirLast = swathDir
+
+
+    if crossCorrelation:
+        offsetComp = "\n\ncomparision of offsets:\n\n"
+        offsetComp += "offset type       i     geometrical           match      difference\n"
+        offsetComp += "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+        for i, (offset1, offset2) in enumerate(zip(rangeOffsetGeometrical, rangeOffsetMatching)):
+            offsetComp += "range offset     {:2d}   {:13.3f}   {:13.3f}   {:13.3f}\n".format(i, offset1, offset2, offset1 - offset2)
+        for i, (offset1, offset2) in enumerate(zip(azimuthOffsetGeometrical, azimuthOffsetMatching)):
+            offsetComp += "azimuth offset   {:2d}   {:13.3f}   {:13.3f}   {:13.3f}\n".format(i, offset1, offset2, offset1 - offset2)
+
+        #write and report offsets
+        with open(outputfile, 'w') as f:
+            f.write(offsetComp)
+        print("{}".format(offsetComp))
+
+
+    if crossCorrelation:
+        return (rangeOffsetGeometrical, azimuthOffsetGeometrical, rangeOffsetMatching, azimuthOffsetMatching)
+    else:
+        return (rangeOffsetGeometrical, azimuthOffsetGeometrical)
+
+
+def computeFrameOffset(swath1, swath2):
+
+    rangeOffset = -(swath2.startingRange - swath1.startingRange) / swath1.rangePixelSize
+    azimuthOffset = -((swath2.sensingStart - swath1.sensingStart).total_seconds()) / swath1.azimuthLineInterval
+
+    return (rangeOffset, azimuthOffset)
+
+
+def estimateFrameOffset(swath1, swath2, image1, image2, matchingMode=0):
+    '''
+    estimate offset of two adjacent frames using matching
+    matchingMode:  0: ScanSAR full-aperture image
+                   1: regular image
+    '''
+    import isceobj
+    from isceobj.Alos2Proc.Alos2ProcPublic import cullOffsets
+    from isceobj.Alos2Proc.Alos2ProcPublic import cullOffsetsRoipac
+    from isceobj.Alos2Proc.Alos2ProcPublic import meanOffset
+    from mroipac.ampcor.Ampcor import Ampcor
+
+    ##########################################
+    #2. match using ampcor
+    ##########################################
+    ampcor = Ampcor(name='insarapp_slcs_ampcor')
+    ampcor.configure()
+
+    #mSLC = isceobj.createSlcImage()
+    mSLC = isceobj.createImage()
+    mSLC.load(image1+'.xml')
+    mSLC.setFilename(image1)
+    #mSLC.extraFilename = image1 + '.vrt'
+    mSLC.setAccessMode('read')
+    mSLC.createImage()
+
+    #sSLC = isceobj.createSlcImage()
+    sSLC = isceobj.createImage()
+    sSLC.load(image2+'.xml')
+    sSLC.setFilename(image2)
+    #sSLC.extraFilename = image2 + '.vrt'
+    sSLC.setAccessMode('read')
+    sSLC.createImage()
+
+    if mSLC.dataType.upper() == 'CFLOAT':
+        ampcor.setImageDataType1('complex')
+        ampcor.setImageDataType2('complex')
+    elif mSLC.dataType.upper() == 'FLOAT':
+        ampcor.setImageDataType1('real')
+        ampcor.setImageDataType2('real')
+    else:
+        raise Exception('file type not supported yet.')
+
+    ampcor.setMasterSlcImage(mSLC)
+    ampcor.setSlaveSlcImage(sSLC)
+
+    #MATCH REGION
+    #compute an offset at image center to use
+    rgoff = -(swath2.startingRange - swath1.startingRange) / swath1.rangePixelSize
+    azoff = -((swath2.sensingStart - swath1.sensingStart).total_seconds()) / swath1.azimuthLineInterval
+    rgoff = int(rgoff)
+    azoff = int(azoff)
+    #it seems that we cannot use 0, haven't look into the problem
+    if rgoff == 0:
+        rgoff = 1
+    if azoff == 0:
+        azoff = 1
+    firstSample = 1
+    if rgoff < 0:
+        firstSample = int(35 - rgoff)
+    firstLine = 1
+    if azoff < 0:
+        firstLine = int(35 - azoff)
+    ampcor.setAcrossGrossOffset(rgoff)
+    ampcor.setDownGrossOffset(azoff)
+    ampcor.setFirstSampleAcross(firstSample)
+    ampcor.setLastSampleAcross(mSLC.width)
+    ampcor.setNumberLocationAcross(30)
+    ampcor.setFirstSampleDown(firstLine)
+    ampcor.setLastSampleDown(mSLC.length)
+    ampcor.setNumberLocationDown(10)
+
+    #MATCH PARAMETERS
+    #full-aperture mode
+    if matchingMode==0:
+        ampcor.setWindowSizeWidth(64)
+        ampcor.setWindowSizeHeight(512)
+        #note this is the half width/length of search area, number of resulting correlation samples: 32*2+1
+        ampcor.setSearchWindowSizeWidth(32)
+        ampcor.setSearchWindowSizeHeight(32)
+        #triggering full-aperture mode matching
+        ampcor.setWinsizeFilt(8)
+        ampcor.setOversamplingFactorFilt(64)
+    #regular mode
+    else:
+        ampcor.setWindowSizeWidth(64)
+        ampcor.setWindowSizeHeight(64)
+        ampcor.setSearchWindowSizeWidth(32)
+        ampcor.setSearchWindowSizeHeight(32)
+
+    #REST OF THE STUFF
+    ampcor.setAcrossLooks(1)
+    ampcor.setDownLooks(1)
+    ampcor.setOversamplingFactor(64)
+    ampcor.setZoomWindowSize(16)
+    #1. The following not set
+    #Matching Scale for Sample/Line Directions                       (-)    = 1. 1.
+    #should add the following in Ampcor.py?
+    #if not set, in this case, Ampcor.py'value is also 1. 1.
+    #ampcor.setScaleFactorX(1.)
+    #ampcor.setScaleFactorY(1.)
+
+    #MATCH THRESHOLDS AND DEBUG DATA
+    #2. The following not set
+    #in roi_pac the value is set to 0 1
+    #in isce the value is set to 0.001 1000.0
+    #SNR and Covariance Thresholds                                   (-)    =  {s1} {s2}
+    #should add the following in Ampcor?
+    #THIS SHOULD BE THE ONLY THING THAT IS DIFFERENT FROM THAT OF ROI_PAC
+    #ampcor.setThresholdSNR(0)
+    #ampcor.setThresholdCov(1)
+    ampcor.setDebugFlag(False)
+    ampcor.setDisplayFlag(False)
+
+    #in summary, only two things not set which are indicated by 'The following not set' above.
+
+    #run ampcor
+    ampcor.ampcor()
+    offsets = ampcor.getOffsetField()
+    #ampcorOffsetFile = 'ampcor.off'
+    #writeOffset(offsets, ampcorOffsetFile)
+
+    #finalize image, and re-create it
+    #otherwise the file pointer is still at the end of the image
+    mSLC.finalizeImage()
+    sSLC.finalizeImage()
+
+
+    #############################################
+    #3. cull offsets
+    #############################################
+    #refinedOffsets = cullOffsets(offsets)
+    refinedOffsets = cullOffsetsRoipac(offsets, numThreshold=50)
+
+    if refinedOffsets != None:
+        rangeOffset, azimuthOffset = meanOffset(refinedOffsets)
+        return (rangeOffset, azimuthOffset)
+    else:
+        return None

components/isceobj/Alos2Proc/runGeo2Rdr.py

@@ -0,0 +1,190 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+
+logger = logging.getLogger('isce.alos2insar.runGeo2Rdr')
+
+def runGeo2Rdr(self):
+    '''compute range and azimuth offsets
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    insarDir = 'insar'
+    if not os.path.exists(insarDir):
+        os.makedirs(insarDir)
+    os.chdir(insarDir)
+
+
+    hasGPU= self.useGPU and self._insar.hasGPU()
+    if hasGPU:
+        geo2RdrGPU(slaveTrack, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+            self._insar.latitude, self._insar.longitude, self._insar.height, self._insar.rangeOffset, self._insar.azimuthOffset)
+    else:
+        geo2RdrCPU(slaveTrack, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+            self._insar.latitude, self._insar.longitude, self._insar.height, self._insar.rangeOffset, self._insar.azimuthOffset)
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runGeo2Rdr")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def geo2RdrCPU(slaveTrack, numberRangeLooks, numberAzimuthLooks, latFile, lonFile, hgtFile, rangeOffsetFile, azimuthOffsetFile):
+    import datetime
+    from zerodop.geo2rdr import createGeo2rdr
+    from isceobj.Planet.Planet import Planet
+
+    pointingDirection = {'right': -1, 'left' :1}
+
+    latImage = isceobj.createImage()
+    latImage.load(latFile + '.xml')
+    latImage.setAccessMode('read')
+
+    lonImage = isceobj.createImage()
+    lonImage.load(lonFile + '.xml')
+    lonImage.setAccessMode('read')
+
+    demImage = isceobj.createDemImage()
+    demImage.load(hgtFile + '.xml')
+    demImage.setAccessMode('read')
+
+    planet = Planet(pname='Earth')
+
+    topo = createGeo2rdr()
+    topo.configure()
+    #set parameters
+    topo.slantRangePixelSpacing = numberRangeLooks * slaveTrack.rangePixelSize
+    topo.prf = 1.0 / (numberAzimuthLooks*slaveTrack.azimuthLineInterval)
+    topo.radarWavelength = slaveTrack.radarWavelength
+    topo.orbit = slaveTrack.orbit
+    topo.width = slaveTrack.numberOfSamples
+    topo.length = slaveTrack.numberOfLines
+    topo.demLength = demImage.length
+    topo.demWidth = demImage.width
+    topo.wireInputPort(name='planet', object=planet)
+    topo.numberRangeLooks = 1 #
+    topo.numberAzimuthLooks = 1 # must be set to be 1
+    topo.lookSide = pointingDirection[slaveTrack.pointingDirection]
+    topo.setSensingStart(slaveTrack.sensingStart + datetime.timedelta(seconds=(numberAzimuthLooks-1.0)/2.0*slaveTrack.azimuthLineInterval))
+    topo.rangeFirstSample = slaveTrack.startingRange + (numberRangeLooks-1.0)/2.0*slaveTrack.rangePixelSize
+    topo.dopplerCentroidCoeffs = [0.] # we are using zero doppler geometry
+    #set files
+    topo.latImage = latImage
+    topo.lonImage = lonImage
+    topo.demImage = demImage
+    topo.rangeOffsetImageName = rangeOffsetFile
+    topo.azimuthOffsetImageName = azimuthOffsetFile
+    #run it
+    topo.geo2rdr()
+
+    return
+
+
+def geo2RdrGPU(slaveTrack, numberRangeLooks, numberAzimuthLooks, latFile, lonFile, hgtFile, rangeOffsetFile, azimuthOffsetFile):
+    '''
+    currently we cannot set left/right looking.
+    works for right looking, but left looking probably not supported.
+    '''
+
+    import datetime
+    from zerodop.GPUgeo2rdr.GPUgeo2rdr import PyGeo2rdr
+    from isceobj.Planet.Planet import Planet
+    from iscesys import DateTimeUtil as DTU
+
+    latImage = isceobj.createImage()
+    latImage.load(latFile + '.xml')
+    latImage.setAccessMode('READ')
+    latImage.createImage()
+
+    lonImage = isceobj.createImage()
+    lonImage.load(lonFile + '.xml')
+    lonImage.setAccessMode('READ')
+    lonImage.createImage()
+
+    demImage = isceobj.createImage()
+    demImage.load(hgtFile + '.xml')
+    demImage.setAccessMode('READ')
+    demImage.createImage()
+
+    #####Run Geo2rdr
+    planet = Planet(pname='Earth')
+    grdr = PyGeo2rdr()
+
+    grdr.setRangePixelSpacing(numberRangeLooks * slaveTrack.rangePixelSize)
+    grdr.setPRF(1.0 / (numberAzimuthLooks*slaveTrack.azimuthLineInterval))
+    grdr.setRadarWavelength(slaveTrack.radarWavelength)
+
+    #CHECK IF THIS WORKS!!!
+    grdr.createOrbit(0, len(slaveTrack.orbit.stateVectors.list))
+    count = 0
+    for sv in slaveTrack.orbit.stateVectors.list:
+        td = DTU.seconds_since_midnight(sv.getTime())
+        pos = sv.getPosition()
+        vel = sv.getVelocity()
+
+        grdr.setOrbitVector(count, td, pos[0], pos[1], pos[2], vel[0], vel[1], vel[2])
+        count += 1
+
+    grdr.setOrbitMethod(0)
+    grdr.setWidth(slaveTrack.numberOfSamples)
+    grdr.setLength(slaveTrack.numberOfLines)
+    grdr.setSensingStart(DTU.seconds_since_midnight(slaveTrack.sensingStart + datetime.timedelta(seconds=(numberAzimuthLooks-1.0)/2.0*slaveTrack.azimuthLineInterval)))
+    grdr.setRangeFirstSample(slaveTrack.startingRange + (numberRangeLooks-1.0)/2.0*slaveTrack.rangePixelSize)
+    grdr.setNumberRangeLooks(1)
+    grdr.setNumberAzimuthLooks(1)
+    grdr.setEllipsoidMajorSemiAxis(planet.ellipsoid.a)
+    grdr.setEllipsoidEccentricitySquared(planet.ellipsoid.e2)
+
+
+    grdr.createPoly(0, 0., 1.)
+    grdr.setPolyCoeff(0, 0.)
+
+    grdr.setDemLength(demImage.getLength())
+    grdr.setDemWidth(demImage.getWidth())
+    grdr.setBistaticFlag(0)
+
+    rangeOffsetImage = isceobj.createImage()
+    rangeOffsetImage.setFilename(rangeOffsetFile)
+    rangeOffsetImage.setAccessMode('write')
+    rangeOffsetImage.setDataType('FLOAT')
+    rangeOffsetImage.setCaster('write', 'DOUBLE')
+    rangeOffsetImage.setWidth(demImage.width)
+    rangeOffsetImage.createImage()
+    
+    azimuthOffsetImage = isceobj.createImage()
+    azimuthOffsetImage.setFilename(azimuthOffsetFile)
+    azimuthOffsetImage.setAccessMode('write')
+    azimuthOffsetImage.setDataType('FLOAT')
+    azimuthOffsetImage.setCaster('write', 'DOUBLE')
+    azimuthOffsetImage.setWidth(demImage.width)
+    azimuthOffsetImage.createImage()
+    
+    grdr.setLatAccessor(latImage.getImagePointer())
+    grdr.setLonAccessor(lonImage.getImagePointer())
+    grdr.setHgtAccessor(demImage.getImagePointer())
+    grdr.setAzAccessor(0)
+    grdr.setRgAccessor(0)
+    grdr.setAzOffAccessor(azimuthOffsetImage.getImagePointer())
+    grdr.setRgOffAccessor(rangeOffsetImage.getImagePointer())
+
+    grdr.geo2rdr()
+
+    rangeOffsetImage.finalizeImage()
+    rangeOffsetImage.renderHdr()
+    
+    azimuthOffsetImage.finalizeImage()
+    azimuthOffsetImage.renderHdr()
+    latImage.finalizeImage()
+    lonImage.finalizeImage()
+    demImage.finalizeImage()
+
+    return

components/isceobj/Alos2Proc/runGeocode.py

@@ -0,0 +1,124 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import getBboxGeo
+
+logger = logging.getLogger('isce.alos2insar.runGeocode')
+
+def runGeocode(self):
+    '''geocode final products
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    #slaveTrack = self._insar.loadTrack(master=False)
+
+    demFile = os.path.abspath(self._insar.demGeo)
+
+    insarDir = 'insar'
+    if not os.path.exists(insarDir):
+        os.makedirs(insarDir)
+    os.chdir(insarDir)
+
+    #compute bounding box for geocoding
+    if self.bbox == None:
+        bbox = getBboxGeo(masterTrack)
+    else:
+        bbox = self.bbox
+    catalog.addItem('geocode bounding box', bbox, 'runGeocode')
+
+    if self.geocodeList == None:
+        geocodeList = [self._insar.unwrappedInterferogram,
+        self._insar.unwrappedMaskedInterferogram,
+        self._insar.multilookCoherence,
+        self._insar.multilookLos]
+        if self.doIon:
+            geocodeList.append(self._insar.multilookIon)
+    else:
+        geocodeList = self.geocodeList
+
+    numberRangeLooks = self._insar.numberRangeLooks1 * self._insar.numberRangeLooks2
+    numberAzimuthLooks = self._insar.numberAzimuthLooks1 * self._insar.numberAzimuthLooks2
+
+    for inputFile in geocodeList:
+        if self.geocodeInterpMethod == None:
+            img = isceobj.createImage()
+            img.load(inputFile + '.xml')
+            if img.dataType.upper() == 'CFLOAT':
+                interpMethod = 'sinc'
+            else:
+                interpMethod = 'bilinear'
+        else:
+            interpMethod = self.geocodeInterpMethod.lower()
+
+        geocode(masterTrack, demFile, inputFile, bbox, numberRangeLooks, numberAzimuthLooks, interpMethod, 0, 0)
+
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runGeocode")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def geocode(track, demFile, inputFile, bbox, numberRangeLooks, numberAzimuthLooks, interpMethod, topShift, leftShift, addMultilookOffset=True):
+    import datetime
+    from zerodop.geozero import createGeozero
+    from isceobj.Planet.Planet import Planet
+
+    pointingDirection = {'right': -1, 'left' :1}
+
+    demImage = isceobj.createDemImage()
+    demImage.load(demFile + '.xml')
+    demImage.setAccessMode('read')
+
+    inImage = isceobj.createImage()
+    inImage.load(inputFile + '.xml')
+    inImage.setAccessMode('read')
+
+    planet = Planet(pname='Earth')
+
+    topo = createGeozero()
+    topo.configure()
+    topo.slantRangePixelSpacing = numberRangeLooks * track.rangePixelSize
+    topo.prf = 1.0 / (numberAzimuthLooks*track.azimuthLineInterval)
+    topo.radarWavelength = track.radarWavelength
+    topo.orbit = track.orbit
+    topo.width = inImage.width
+    topo.length = inImage.length
+    topo.wireInputPort(name='dem', object=demImage)
+    topo.wireInputPort(name='planet', object=planet)
+    topo.wireInputPort(name='tobegeocoded', object=inImage)
+    topo.numberRangeLooks = 1
+    topo.numberAzimuthLooks = 1
+    topo.lookSide = pointingDirection[track.pointingDirection]
+    sensingStart = track.sensingStart + datetime.timedelta(seconds=topShift*track.azimuthLineInterval)
+    rangeFirstSample = track.startingRange + leftShift * track.rangePixelSize
+    if addMultilookOffset:
+        sensingStart += datetime.timedelta(seconds=(numberAzimuthLooks-1.0)/2.0*track.azimuthLineInterval)
+        rangeFirstSample += (numberRangeLooks-1.0)/2.0*track.rangePixelSize
+    topo.setSensingStart(sensingStart)
+    topo.rangeFirstSample = rangeFirstSample
+    topo.method=interpMethod
+    topo.demCropFilename = 'crop.dem'
+    #looks like this does not work
+    #topo.geoFilename = outputName
+    topo.dopplerCentroidCoeffs = [0.]
+    #snwe list <class 'list'>
+    topo.snwe = bbox
+
+    topo.geocode()
+
+    print('South: ', topo.minimumGeoLatitude)
+    print('North: ', topo.maximumGeoLatitude)
+    print('West:  ', topo.minimumGeoLongitude)
+    print('East:  ', topo.maximumGeoLongitude)
+    
+    return

components/isceobj/Alos2Proc/runGeocodeOffset.py

@@ -0,0 +1,64 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.runGeocode import geocode
+from isceobj.Alos2Proc.Alos2ProcPublic import getBboxGeo
+
+logger = logging.getLogger('isce.alos2insar.runGeocodeOffset')
+
+def runGeocodeOffset(self):
+    '''geocode offset fied
+    '''
+    if not self.doDenseOffset:
+        return
+    if not ((self._insar.modeCombination == 0) or (self._insar.modeCombination == 1)):
+        return
+
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    #use original track object to determine bbox
+    if self.bbox == None:
+        masterTrack = self._insar.loadTrack(master=True)
+        bbox = getBboxGeo(masterTrack)
+    else:
+        bbox = self.bbox
+    catalog.addItem('geocode bounding box', bbox, 'runGeocodeOffset')
+
+    demFile = os.path.abspath(self._insar.demGeo)
+
+    denseOffsetDir = 'dense_offset'
+    if not os.path.exists(denseOffsetDir):
+        os.makedirs(denseOffsetDir)
+    os.chdir(denseOffsetDir)
+
+    masterTrack = self._insar.loadProduct(self._insar.masterTrackParameter)
+    #slaveTrack = self._insar.loadProduct(self._insar.slaveTrackParameter)
+
+#########################################################################################
+    #compute bounding box for geocoding
+    #if self.bbox == None:
+    #    bbox = getBboxGeo(masterTrack)
+    #else:
+    #    bbox = self.bbox
+    #catalog.addItem('geocode bounding box', bbox, 'runGeocodeOffset')
+
+    geocodeList = [self._insar.denseOffset, self._insar.denseOffsetSnr]
+    if self.doOffsetFiltering:
+        geocodeList.append(self._insar.denseOffsetFilt)
+
+    for inputFile in geocodeList:
+        interpMethod = 'nearest'
+        geocode(masterTrack, demFile, inputFile, bbox, self.offsetSkipWidth, self.offsetSkipHeight, interpMethod, self._insar.offsetImageTopoffset, self._insar.offsetImageLeftoffset, addMultilookOffset=False)
+#########################################################################################
+
+    os.chdir('../')
+    catalog.printToLog(logger, "runGeocodeOffset")
+    self._insar.procDoc.addAllFromCatalog(catalog)

components/isceobj/Alos2Proc/runIonFilt.py

@@ -0,0 +1,599 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+import numpy.matlib
+
+import isceobj
+
+logger = logging.getLogger('isce.alos2insar.runIonFilt')
+
+def runIonFilt(self):
+    '''compute and filter ionospheric phase
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    if not self.doIon:
+        catalog.printToLog(logger, "runIonFilt")
+        self._insar.procDoc.addAllFromCatalog(catalog)
+        return
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    from isceobj.Alos2Proc.runIonSubband import defineIonDir
+    ionDir = defineIonDir()
+    subbandPrefix = ['lower', 'upper']
+
+    ionCalDir = os.path.join(ionDir['ion'], ionDir['ionCal'])
+    if not os.path.exists(ionCalDir):
+        os.makedirs(ionCalDir)
+    os.chdir(ionCalDir)
+
+
+    ############################################################
+    # STEP 1. compute ionospheric phase
+    ############################################################
+    from isceobj.Constants import SPEED_OF_LIGHT
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+    ###################################
+    #SET PARAMETERS HERE
+    #THESE SHOULD BE GOOD ENOUGH, NO NEED TO SET IN setup(self)
+    corThresholdAdj = 0.85
+    ###################################
+
+    print('\ncomputing ionosphere')
+    #get files
+    ml2 = '_{}rlks_{}alks'.format(self._insar.numberRangeLooks1*self._insar.numberRangeLooksIon, 
+                              self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksIon)
+
+    lowerUnwfile = subbandPrefix[0]+ml2+'.unw'
+    upperUnwfile = subbandPrefix[1]+ml2+'.unw'
+    corfile = 'diff'+ml2+'.cor'
+
+    #use image size from lower unwrapped interferogram
+    img = isceobj.createImage()
+    img.load(lowerUnwfile + '.xml')
+    width = img.width
+    length = img.length
+
+    lowerUnw = (np.fromfile(lowerUnwfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
+    upperUnw = (np.fromfile(upperUnwfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
+    cor = (np.fromfile(corfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
+    #amp = (np.fromfile(corfile, dtype=np.float32).reshape(length*2, width))[0:length*2:2, :]
+
+    #masked out user-specified areas
+    if self.maskedAreasIon != None:
+        maskedAreas = reformatMaskedAreas(self.maskedAreasIon, length, width)
+        for area in maskedAreas:
+            lowerUnw[area[0]:area[1], area[2]:area[3]] = 0
+            upperUnw[area[0]:area[1], area[2]:area[3]] = 0
+            cor[area[0]:area[1], area[2]:area[3]] = 0
+
+    #compute ionosphere
+    fl = SPEED_OF_LIGHT / self._insar.subbandRadarWavelength[0]
+    fu = SPEED_OF_LIGHT / self._insar.subbandRadarWavelength[1]
+    adjFlag = 1
+    ionos = computeIonosphere(lowerUnw, upperUnw, cor, fl, fu, adjFlag, corThresholdAdj, 0)
+
+    #dump ionosphere
+    ionfile = 'ion'+ml2+'.ion'
+    # ion = np.zeros((length*2, width), dtype=np.float32)
+    # ion[0:length*2:2, :] = amp
+    # ion[1:length*2:2, :] = ionos
+    # ion.astype(np.float32).tofile(ionfile)
+    # img.filename = ionfile
+    # img.extraFilename = ionfile + '.vrt'
+    # img.renderHdr()
+
+    ionos.astype(np.float32).tofile(ionfile)
+    create_xml(ionfile, width, length, 'float')
+
+
+    ############################################################
+    # STEP 2. filter ionospheric phase
+    ############################################################
+
+    #################################################
+    #SET PARAMETERS HERE
+    #if applying polynomial fitting
+    #False: no fitting, True: with fitting
+    fit = self.fitIon
+    #gaussian filtering window size
+    size_max = self.filteringWinsizeMaxIon
+    size_min = self.filteringWinsizeMinIon
+
+    #THESE SHOULD BE GOOD ENOUGH, NO NEED TO SET IN setup(self)
+    corThresholdIon = 0.85
+    #################################################
+
+    print('\nfiltering ionosphere')
+    ionfile = 'ion'+ml2+'.ion'
+    corfile = 'diff'+ml2+'.cor'
+    ionfiltfile = 'filt_ion'+ml2+'.ion'
+
+    img = isceobj.createImage()
+    img.load(ionfile + '.xml')
+    width = img.width
+    length = img.length
+    #ion = (np.fromfile(ionfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
+    ion = np.fromfile(ionfile, dtype=np.float32).reshape(length, width)
+    cor = (np.fromfile(corfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
+    #amp = (np.fromfile(ionfile, dtype=np.float32).reshape(length*2, width))[0:length*2:2, :]
+
+    #masked out user-specified areas
+    if self.maskedAreasIon != None:
+        maskedAreas = reformatMaskedAreas(self.maskedAreasIon, length, width)
+        for area in maskedAreas:
+            ion[area[0]:area[1], area[2]:area[3]] = 0
+            cor[area[0]:area[1], area[2]:area[3]] = 0
+
+    #remove possible wired values in coherence
+    cor[np.nonzero(cor<0)] = 0.0
+    cor[np.nonzero(cor>1)] = 0.0
+
+    # #applying water body mask here
+    # waterBodyFile = 'wbd'+ml2+'.wbd'
+    # if os.path.isfile(waterBodyFile):
+    #     print('applying water body mask to coherence used to compute ionospheric phase')
+    #     wbd = np.fromfile(waterBodyFile, dtype=np.int8).reshape(length, width)
+    #     cor[np.nonzero(wbd!=0)] = 0.00001
+
+    if fit:
+        ion_fit = weight_fitting(ion, cor, width, length, 1, 1, 1, 1, 2, corThresholdIon)
+        ion -= ion_fit * (ion!=0)
+
+    #minimize the effect of low coherence pixels
+    #cor[np.nonzero( (cor<0.85)*(cor!=0) )] = 0.00001
+    #filt = adaptive_gaussian(ion, cor, size_max, size_min)
+    #cor**14 should be a good weight to use. 22-APR-2018
+    filt = adaptive_gaussian(ion, cor**14, size_max, size_min)
+
+    if fit:
+        filt += ion_fit * (filt!=0)
+
+    # ion = np.zeros((length*2, width), dtype=np.float32)
+    # ion[0:length*2:2, :] = amp
+    # ion[1:length*2:2, :] = filt
+    # ion.astype(np.float32).tofile(ionfiltfile)
+    # img.filename = ionfiltfile
+    # img.extraFilename = ionfiltfile + '.vrt'
+    # img.renderHdr()
+
+    filt.astype(np.float32).tofile(ionfiltfile)
+    create_xml(ionfiltfile, width, length, 'float')
+
+
+    ############################################################
+    # STEP 3. resample ionospheric phase
+    ############################################################
+    from contrib.alos2proc_f.alos2proc_f import rect
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+    from scipy.interpolate import interp1d
+    import shutil
+
+    #################################################
+    #SET PARAMETERS HERE
+    #interpolation method
+    interpolationMethod = 1
+    #################################################
+
+    print('\ninterpolate ionosphere')
+
+    ml3 = '_{}rlks_{}alks'.format(self._insar.numberRangeLooks1*self._insar.numberRangeLooks2, 
+                              self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooks2)
+
+    ionfiltfile = 'filt_ion'+ml2+'.ion'
+    #ionrectfile = 'filt_ion'+ml3+'.ion'
+    ionrectfile = self._insar.multilookIon
+
+    img = isceobj.createImage()
+    img.load(ionfiltfile + '.xml')
+    width2 = img.width
+    length2 = img.length
+
+    img = isceobj.createImage()
+    img.load(os.path.join('../../', ionDir['insar'], self._insar.multilookDifferentialInterferogram) + '.xml')
+    width3 = img.width
+    length3 = img.length
+
+    #number of range looks output
+    nrlo = self._insar.numberRangeLooks1*self._insar.numberRangeLooks2
+    #number of range looks input
+    nrli = self._insar.numberRangeLooks1*self._insar.numberRangeLooksIon
+    #number of azimuth looks output
+    nalo = self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooks2
+    #number of azimuth looks input
+    nali = self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksIon
+
+    if (self._insar.numberRangeLooks2 != self._insar.numberRangeLooksIon) or \
+       (self._insar.numberAzimuthLooks2 != self._insar.numberAzimuthLooksIon):
+        #this should be faster using fortran
+        if interpolationMethod == 0:
+            rect(ionfiltfile, ionrectfile,
+                width2,length2,
+                width3,length3,
+                nrlo/nrli, 0.0,
+                0.0, nalo/nali,
+                (nrlo-nrli)/(2.0*nrli),
+                (nalo-nali)/(2.0*nali),
+                'REAL','Bilinear')
+        #finer, but slower method
+        else:
+            ionfilt = np.fromfile(ionfiltfile, dtype=np.float32).reshape(length2, width2)
+            index2 = np.linspace(0, width2-1, num=width2, endpoint=True)
+            index3 = np.linspace(0, width3-1, num=width3, endpoint=True) * nrlo/nrli + (nrlo-nrli)/(2.0*nrli)
+            ionrect = np.zeros((length3, width3), dtype=np.float32)
+            for i in range(length2):
+                f = interp1d(index2, ionfilt[i,:], kind='cubic', fill_value="extrapolate")
+                ionrect[i, :] = f(index3)
+            
+            index2 = np.linspace(0, length2-1, num=length2, endpoint=True)
+            index3 = np.linspace(0, length3-1, num=length3, endpoint=True) * nalo/nali + (nalo-nali)/(2.0*nali)
+            for j in range(width3):
+                f = interp1d(index2, ionrect[0:length2, j], kind='cubic', fill_value="extrapolate")
+                ionrect[:, j] = f(index3)
+            ionrect.astype(np.float32).tofile(ionrectfile)
+            del ionrect
+        create_xml(ionrectfile, width3, length3, 'float')
+
+        os.rename(ionrectfile, os.path.join('../../insar', ionrectfile))
+        os.rename(ionrectfile+'.vrt', os.path.join('../../insar', ionrectfile)+'.vrt')
+        os.rename(ionrectfile+'.xml', os.path.join('../../insar', ionrectfile)+'.xml')
+        os.chdir('../../insar')
+    else:
+        shutil.copyfile(ionfiltfile, os.path.join('../../insar', ionrectfile))
+        os.chdir('../../insar')
+        create_xml(ionrectfile, width3, length3, 'float')
+    #now we are in 'insar'
+
+
+    ############################################################
+    # STEP 4. correct interferogram
+    ############################################################
+    from isceobj.Alos2Proc.Alos2ProcPublic import renameFile
+    from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+
+    if self.applyIon:
+        print('\ncorrect interferogram')
+        if os.path.isfile(self._insar.multilookDifferentialInterferogramOriginal):
+            print('original interferogram: {} is already here, do not rename: {}'.format(self._insar.multilookDifferentialInterferogramOriginal, self._insar.multilookDifferentialInterferogram))
+        else:
+            print('renaming {} to {}'.format(self._insar.multilookDifferentialInterferogram, self._insar.multilookDifferentialInterferogramOriginal))
+            renameFile(self._insar.multilookDifferentialInterferogram, self._insar.multilookDifferentialInterferogramOriginal)
+
+        cmd = "imageMath.py -e='a*exp(-1.0*J*b)' --a={} --b={} -s BIP -t cfloat -o {}".format(
+            self._insar.multilookDifferentialInterferogramOriginal,
+            self._insar.multilookIon,
+            self._insar.multilookDifferentialInterferogram)
+        runCmd(cmd)
+    else:
+        print('\nionospheric phase estimation finished, but correction of interfeorgram not requested')
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runIonFilt")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+
+def computeIonosphere(lowerUnw, upperUnw, cor, fl, fu, adjFlag, corThresholdAdj, dispersive):
+    '''
+    This routine computes ionosphere and remove the relative phase unwrapping errors
+
+    lowerUnw:        lower band unwrapped interferogram
+    upperUnw:        upper band unwrapped interferogram
+    cor:             coherence
+    fl:              lower band center frequency
+    fu:              upper band center frequency
+    adjFlag:         method for removing relative phase unwrapping errors
+                       0: mean value
+                       1: polynomial
+    corThresholdAdj: coherence threshold of samples used in removing relative phase unwrapping errors
+    dispersive:      compute dispersive or non-dispersive
+                       0: dispersive
+                       1: non-dispersive
+    '''
+
+    #use image size from lower unwrapped interferogram
+    (length, width)=lowerUnw.shape
+
+##########################################################################################
+    # ADJUST PHASE USING MEAN VALUE
+    # #ajust phase of upper band to remove relative phase unwrapping errors
+    # flag = (lowerUnw!=0)*(cor>=ionParam.corThresholdAdj)
+    # index = np.nonzero(flag!=0)
+    # mv = np.mean((lowerUnw - upperUnw)[index], dtype=np.float64)
+    # print('mean value of phase difference: {}'.format(mv))
+    # flag2 = (lowerUnw!=0)
+    # index2 = np.nonzero(flag2)
+    # #phase for adjustment
+    # unwd = ((lowerUnw - upperUnw)[index2] - mv) / (2.0*np.pi)
+    # unw_adj = np.around(unwd) * (2.0*np.pi)
+    # #ajust phase of upper band
+    # upperUnw[index2] += unw_adj
+    # unw_diff = lowerUnw - upperUnw
+    # print('after adjustment:')
+    # print('max phase difference: {}'.format(np.amax(unw_diff)))
+    # print('min phase difference: {}'.format(np.amin(unw_diff)))
+##########################################################################################
+    #adjust phase using mean value
+    if adjFlag == 0:
+        flag = (lowerUnw!=0)*(cor>=corThresholdAdj)
+        index = np.nonzero(flag!=0)
+        mv = np.mean((lowerUnw - upperUnw)[index], dtype=np.float64)
+        print('mean value of phase difference: {}'.format(mv))
+        diff = mv
+    #adjust phase using a surface
+    else:
+        diff = weight_fitting(lowerUnw - upperUnw, cor, width, length, 1, 1, 1, 1, 2, corThresholdAdj)
+
+    flag2 = (lowerUnw!=0)
+    index2 = np.nonzero(flag2)
+    #phase for adjustment
+    unwd = ((lowerUnw - upperUnw) - diff)[index2] / (2.0*np.pi)
+    unw_adj = np.around(unwd) * (2.0*np.pi)
+    #ajust phase of upper band
+    upperUnw[index2] += unw_adj
+
+    unw_diff = (lowerUnw - upperUnw)[index2]
+    print('after adjustment:')
+    print('max phase difference: {}'.format(np.amax(unw_diff)))
+    print('min phase difference: {}'.format(np.amin(unw_diff)))
+    print('max-min: {}'.format(np.amax(unw_diff) - np.amin(unw_diff)    ))
+
+    #ionosphere
+    #fl = SPEED_OF_LIGHT / ionParam.radarWavelengthLower
+    #fu = SPEED_OF_LIGHT / ionParam.radarWavelengthUpper
+    f0 = (fl + fu) / 2.0
+    
+    #dispersive
+    if dispersive == 0:
+        ionos = fl * fu * (lowerUnw * fu - upperUnw * fl) / f0 / (fu**2 - fl**2)
+    #non-dispersive phase
+    else:
+        ionos = f0 * (upperUnw*fu - lowerUnw * fl) / (fu**2 - fl**2)
+
+    return ionos
+
+
+def fit_surface(x, y, z, wgt, order):
+    # x: x coordinate, a column vector
+    # y: y coordinate, a column vector
+    # z: z coordinate, a column vector
+    # wgt: weight of the data points, a column vector
+
+
+    #number of data points
+    m = x.shape[0]
+    l = np.ones((m,1), dtype=np.float64)
+
+#    #create polynomial
+#    if order == 1:
+#        #order of estimated coefficents: 1, x, y
+#        a1 = np.concatenate((l, x, y), axis=1)
+#    elif order == 2:
+#        #order of estimated coefficents: 1, x, y, x*y, x**2, y**2
+#        a1 = np.concatenate((l, x, y, x*y, x**2, y**2), axis=1)
+#    elif order == 3:
+#        #order of estimated coefficents: 1, x, y, x*y, x**2, y**2, x**2*y, y**2*x, x**3, y**3
+#        a1 = np.concatenate((l, x, y, x*y, x**2, y**2, x**2*y, y**2*x, x**3, y**3), axis=1)
+#    else:
+#        raise Exception('order not supported yet\n')
+
+    if order < 1:
+        raise Exception('order must be larger than 1.\n')
+
+    #create polynomial
+    a1 = l;
+    for i in range(1, order+1):
+        for j in range(i+1):
+            a1 = np.concatenate((a1, x**(i-j)*y**(j)), axis=1)
+
+    #number of variable to be estimated
+    n = a1.shape[1]
+
+    #do the least squares
+    a = a1 * np.matlib.repmat(np.sqrt(wgt), 1, n)
+    b = z * np.sqrt(wgt)
+    c = np.linalg.lstsq(a, b, rcond=-1)[0]
+    
+    #type: <class 'numpy.ndarray'>
+    return c
+
+
+def cal_surface(x, y, c, order):
+    #x: x coordinate, a row vector
+    #y: y coordinate, a column vector
+    #c: coefficients of polynomial from fit_surface
+    #order: order of polynomial
+
+    if order < 1:
+        raise Exception('order must be larger than 1.\n')
+
+    #number of lines
+    length = y.shape[0]
+    #number of columns, if row vector, only one element in the shape tuple
+    #width = x.shape[1]
+    width = x.shape[0]
+
+    x = np.matlib.repmat(x, length, 1)
+    y = np.matlib.repmat(y, 1, width)
+    z = c[0] * np.ones((length,width), dtype=np.float64)
+
+    index = 0
+    for i in range(1, order+1):
+        for j in range(i+1):
+            index += 1
+            z += c[index] * x**(i-j)*y**(j)
+
+    return z
+
+
+def weight_fitting(ionos, cor, width, length, nrli, nali, nrlo, nalo, order, coth):
+    '''
+    ionos:  input ionospheric phase
+    cor:    coherence of the interferogram
+    width:  file width
+    length: file length
+    nrli:   number of range looks of the input interferograms
+    nali:   number of azimuth looks of the input interferograms
+    nrlo:   number of range looks of the output ionosphere phase
+    nalo:   number of azimuth looks of the ioutput ionosphere phase
+    order:  the order of the polynomial for fitting ionosphere phase estimates
+    coth:   coherence threshhold for ionosphere phase estimation
+    '''
+
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_multi_index2
+
+    lengthi = int(length/nali)
+    widthi = int(width/nrli)
+    lengtho = int(length/nalo)
+    widtho = int(width/nrlo)
+
+    #calculate output index
+    rgindex = create_multi_index2(widtho, nrli, nrlo)
+    azindex = create_multi_index2(lengtho, nali, nalo)
+
+    #convert coherence to weight
+    cor = cor**2/(1.009-cor**2)
+
+    #look for data to use
+    flag = (cor>coth)*(ionos!=0)
+    point_index = np.nonzero(flag)
+    m = point_index[0].shape[0]
+
+    #calculate input index matrix
+    x0=np.matlib.repmat(np.arange(widthi), lengthi, 1)
+    y0=np.matlib.repmat(np.arange(lengthi).reshape(lengthi, 1), 1, widthi)
+
+    x = x0[point_index].reshape(m, 1)
+    y = y0[point_index].reshape(m, 1)
+    z = ionos[point_index].reshape(m, 1)
+    w = cor[point_index].reshape(m, 1)
+
+    #convert to higher precision type before use
+    x=np.asfarray(x,np.float64)
+    y=np.asfarray(y,np.float64)
+    z=np.asfarray(z,np.float64)
+    w=np.asfarray(w,np.float64)
+    coeff = fit_surface(x, y, z, w, order)
+
+    #convert to higher precision type before use
+    rgindex=np.asfarray(rgindex,np.float64)
+    azindex=np.asfarray(azindex,np.float64)
+    phase_fit = cal_surface(rgindex, azindex.reshape(lengtho, 1), coeff, order)
+
+    #format: widtho, lengtho, single band float32
+    return phase_fit
+
+
+def gaussian(size, sigma, scale = 1.0):
+
+    if size % 2 != 1:
+        raise Exception('size must be odd')
+    hsize = (size - 1) / 2
+    x = np.arange(-hsize, hsize + 1) * scale
+    f = np.exp(-x**2/(2.0*sigma**2)) / (sigma * np.sqrt(2.0*np.pi))
+    f2d=np.matlib.repmat(f, size, 1) * np.matlib.repmat(f.reshape(size, 1), 1, size)
+
+    return f2d/np.sum(f2d)
+
+
+def adaptive_gaussian(ionos, wgt, size_max, size_min):
+    '''
+    This program performs Gaussian filtering with adaptive window size.
+    ionos: ionosphere
+    wgt: weight
+    size_max: maximum window size
+    size_min: minimum window size
+    '''
+    import scipy.signal as ss
+
+    length = (ionos.shape)[0]
+    width = (ionos.shape)[1]
+    flag = (ionos!=0) * (wgt!=0)
+    ionos *= flag
+    wgt *= flag
+
+    size_num = 100
+    size = np.linspace(size_min, size_max, num=size_num, endpoint=True)
+    std = np.zeros((length, width, size_num))
+    flt = np.zeros((length, width, size_num))
+    out = np.zeros((length, width, 1))
+
+    #calculate filterd image and standard deviation
+    #sigma of window size: size_max
+    sigma = size_max / 2.0
+    for i in range(size_num):
+        size2 = np.int(np.around(size[i]))
+        if size2 % 2 == 0:
+            size2 += 1
+        if (i+1) % 10 == 0:
+            print('min win: %4d, max win: %4d, current win: %4d'%(np.int(np.around(size_min)), np.int(np.around(size_max)), size2))
+        g2d = gaussian(size2, sigma*size2/size_max, scale=1.0)
+        scale = ss.fftconvolve(wgt, g2d, mode='same')
+        flt[:, :, i] = ss.fftconvolve(ionos*wgt, g2d, mode='same') / (scale + (scale==0))
+        #variance of resulting filtered sample
+        scale = scale**2
+        var = ss.fftconvolve(wgt, g2d**2, mode='same') / (scale + (scale==0))
+        #in case there is a large area without data where scale is very small, which leads to wired values in variance
+        var[np.nonzero(var<0)] = 0
+        std[:, :, i] = np.sqrt(var)
+
+    std_mv = np.mean(std[np.nonzero(std!=0)], dtype=np.float64)
+    diff_max = np.amax(np.absolute(std - std_mv)) + std_mv + 1
+    std[np.nonzero(std==0)] = diff_max
+    
+    index = np.nonzero(np.ones((length, width))) + ((np.argmin(np.absolute(std - std_mv), axis=2)).reshape(length*width), )
+    out = flt[index]
+    out = out.reshape((length, width))
+
+    #remove artifacts due to varying wgt
+    size_smt = size_min
+    if size_smt % 2 == 0:
+        size_smt += 1
+    g2d = gaussian(size_smt, size_smt/2.0, scale=1.0)
+    scale = ss.fftconvolve((out!=0), g2d, mode='same')
+    out2 = ss.fftconvolve(out, g2d, mode='same') / (scale + (scale==0))
+
+    return out2
+
+
+def reformatMaskedAreas(maskedAreas, length, width):
+    '''
+    reformat masked areas coordinates that are ready to use
+    'maskedAreas' is a 2-D list. Each element in the 2-D list is a four-element list: [firstLine,
+    lastLine, firstColumn, lastColumn], with line/column numbers starting with 1. If one of the
+    four elements is specified with -1, the program will use firstLine/lastLine/firstColumn/
+    lastColumn instead.
+
+    output is a 2-D list containing the corresponding python-list/array-format indexes.
+    '''
+    numberOfAreas = len(maskedAreas)
+    maskedAreasReformated = [[0, length, 0, width] for i in range(numberOfAreas)]
+
+    for i in range(numberOfAreas):
+        if maskedAreas[i][0] != -1:
+            maskedAreasReformated[i][0] = maskedAreas[i][0] - 1
+        if maskedAreas[i][1] != -1:
+            maskedAreasReformated[i][1] = maskedAreas[i][1]
+        if maskedAreas[i][2] != -1:
+            maskedAreasReformated[i][2] = maskedAreas[i][2] - 1
+        if maskedAreas[i][3] != -1:
+            maskedAreasReformated[i][3] = maskedAreas[i][3]
+        if (not (0 <= maskedAreasReformated[i][0] <= length-1)) or \
+           (not (1 <= maskedAreasReformated[i][1] <= length)) or \
+           (not (0 <= maskedAreasReformated[i][2] <= width-1)) or \
+           (not (1 <= maskedAreasReformated[i][3] <= width)) or \
+           (not (maskedAreasReformated[i][1]-maskedAreasReformated[i][0]>=1)) or \
+           (not (maskedAreasReformated[i][3]-maskedAreasReformated[i][2]>=1)):
+            raise Exception('area {} masked out in ionospheric phase estimation not correct'.format(i+1))
+
+    return maskedAreasReformated

components/isceobj/Alos2Proc/runIonSubband.py

@@ -0,0 +1,457 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+from isceobj.Constants import SPEED_OF_LIGHT
+
+logger = logging.getLogger('isce.alos2insar.runIonSubband')
+
+def runIonSubband(self):
+    '''create subband interferograms
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    if not self.doIon:
+        catalog.printToLog(logger, "runIonSubband")
+        self._insar.procDoc.addAllFromCatalog(catalog)
+        return
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    #using 1/3, 1/3, 1/3 band split
+    radarWavelength = masterTrack.radarWavelength
+    rangeBandwidth = masterTrack.frames[0].swaths[0].rangeBandwidth
+    rangeSamplingRate = masterTrack.frames[0].swaths[0].rangeSamplingRate
+    radarWavelengthLower = SPEED_OF_LIGHT/(SPEED_OF_LIGHT / radarWavelength - rangeBandwidth / 3.0)
+    radarWavelengthUpper = SPEED_OF_LIGHT/(SPEED_OF_LIGHT / radarWavelength + rangeBandwidth / 3.0)
+    subbandRadarWavelength = [radarWavelengthLower, radarWavelengthUpper]
+    subbandBandWidth = [rangeBandwidth / 3.0 / rangeSamplingRate, rangeBandwidth / 3.0 / rangeSamplingRate]
+    subbandFrequencyCenter = [-rangeBandwidth / 3.0 / rangeSamplingRate, rangeBandwidth / 3.0 / rangeSamplingRate]
+
+    subbandPrefix = ['lower', 'upper']
+
+    '''
+    ionDir = {
+        ionDir['swathMosaic'] : 'mosaic',
+        ionDir['insar'] : 'insar',
+        ionDir['ion'] : 'ion',
+        ionDir['subband'] : ['lower', 'upper'],
+        ionDir['ionCal'] : 'ion_cal'
+        }
+    '''
+    #define upper level directory names
+    ionDir = defineIonDir()
+
+
+    self._insar.subbandRadarWavelength = subbandRadarWavelength
+
+
+    ############################################################
+    # STEP 1. create directories
+    ############################################################
+    #create and enter 'ion' directory
+    #after finishing each step, we are in this directory
+    if not os.path.exists(ionDir['ion']):
+        os.makedirs(ionDir['ion'])
+    os.chdir(ionDir['ion'])
+
+    #create insar processing directories
+    for k in range(2):
+        subbandDir = ionDir['subband'][k]
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+                swathDir = 's{}'.format(swathNumber)
+                fullDir = os.path.join(subbandDir, frameDir, swathDir)
+                if not os.path.exists(fullDir):
+                    os.makedirs(fullDir)
+
+    #create ionospheric phase directory
+    if not os.path.exists(ionDir['ionCal']):
+        os.makedirs(ionDir['ionCal'])
+
+
+    ############################################################
+    # STEP 2. create subband interferograms
+    ############################################################
+    import numpy as np
+    import stdproc
+    from iscesys.StdOEL.StdOELPy import create_writer
+    from isceobj.Alos2Proc.Alos2ProcPublic import readOffset
+    from contrib.alos2proc.alos2proc import rg_filter
+
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            #filter master and slave images
+            for slcx in [self._insar.masterSlc, self._insar.slaveSlc]:
+                slc = os.path.join('../', frameDir, swathDir, slcx)
+                slcLower = os.path.join(ionDir['subband'][0], frameDir, swathDir, slcx)
+                slcUpper = os.path.join(ionDir['subband'][1], frameDir, swathDir, slcx)
+                rg_filter(slc, 2, 
+                    [slcLower, slcUpper], 
+                    subbandBandWidth, 
+                    subbandFrequencyCenter, 
+                    257, 2048, 0.1, 0, 0.0)
+            #resample
+            for k in range(2):
+                os.chdir(os.path.join(ionDir['subband'][k], frameDir, swathDir))
+                #recreate xml file to remove the file path
+                #can also use fixImageXml.py?
+                for x in [self._insar.masterSlc, self._insar.slaveSlc]:
+                    img = isceobj.createSlcImage()
+                    img.load(x + '.xml')
+                    img.setFilename(x)
+                    img.extraFilename = x + '.vrt'
+                    img.setAccessMode('READ')
+                    img.renderHdr()
+
+                #############################################
+                #1. form interferogram
+                #############################################
+                masterSwath = masterTrack.frames[i].swaths[j]
+                slaveSwath = slaveTrack.frames[i].swaths[j]
+
+                refinedOffsets = readOffset(os.path.join('../../../../', frameDir, swathDir, 'cull.off'))
+                intWidth = int(masterSwath.numberOfSamples / self._insar.numberRangeLooks1)
+                intLength = int(masterSwath.numberOfLines / self._insar.numberAzimuthLooks1)
+                dopplerVsPixel = [i/slaveSwath.prf for i in slaveSwath.dopplerVsPixel]
+
+                #master slc
+                mSLC = isceobj.createSlcImage()
+                mSLC.load(self._insar.masterSlc+'.xml')
+                mSLC.setAccessMode('read')
+                mSLC.createImage()
+
+                #slave slc
+                sSLC = isceobj.createSlcImage()
+                sSLC.load(self._insar.slaveSlc+'.xml')
+                sSLC.setAccessMode('read')
+                sSLC.createImage()
+
+                #interferogram
+                interf = isceobj.createIntImage()
+                interf.setFilename(self._insar.interferogram)
+                interf.setWidth(intWidth)
+                interf.setAccessMode('write')
+                interf.createImage()
+
+                #amplitdue
+                amplitude = isceobj.createAmpImage()
+                amplitude.setFilename(self._insar.amplitude)
+                amplitude.setWidth(intWidth)
+                amplitude.setAccessMode('write')
+                amplitude.createImage()
+
+                #create a writer for resamp
+                stdWriter = create_writer("log", "", True, filename="resamp.log")
+                stdWriter.setFileTag("resamp", "log")
+                stdWriter.setFileTag("resamp", "err")
+                stdWriter.setFileTag("resamp", "out")
+
+
+                #set up resampling program now
+                #The setting has been compared with resamp_roi's setting in ROI_pac item by item.
+                #The two kinds of setting are exactly the same. The number of setting items are
+                #exactly the same
+                objResamp = stdproc.createResamp()
+                objResamp.wireInputPort(name='offsets', object=refinedOffsets)
+                objResamp.stdWriter = stdWriter
+                objResamp.setNumberFitCoefficients(6)
+                objResamp.setNumberRangeBin1(masterSwath.numberOfSamples)
+                objResamp.setNumberRangeBin2(slaveSwath.numberOfSamples)    
+                objResamp.setStartLine(1)
+                objResamp.setNumberLines(masterSwath.numberOfLines)
+                objResamp.setFirstLineOffset(1)
+                objResamp.setDopplerCentroidCoefficients(dopplerVsPixel)
+                objResamp.setRadarWavelength(subbandRadarWavelength[k])
+                objResamp.setSlantRangePixelSpacing(slaveSwath.rangePixelSize)
+                objResamp.setNumberRangeLooks(self._insar.numberRangeLooks1)
+                objResamp.setNumberAzimuthLooks(self._insar.numberAzimuthLooks1)
+                objResamp.setFlattenWithOffsetFitFlag(0)
+                objResamp.resamp(mSLC, sSLC, interf, amplitude) 
+                
+                #finialize images
+                mSLC.finalizeImage()
+                sSLC.finalizeImage()
+                interf.finalizeImage()
+                amplitude.finalizeImage()
+                stdWriter.finalize()
+
+                #############################################
+                #2. trim amplitude
+                #############################################
+                #using memmap instead, which should be faster, since we only have a few pixels to change
+                amp=np.memmap(self._insar.amplitude, dtype='complex64', mode='r+', shape=(intLength, intWidth))
+                index = np.nonzero( (np.real(amp)==0) + (np.imag(amp)==0) )
+                amp[index]=0
+
+                #Deletion flushes memory changes to disk before removing the object:
+                del amp
+
+                #############################################
+                #3. delete subband slcs
+                #############################################
+                os.remove(self._insar.masterSlc)
+                os.remove(self._insar.masterSlc + '.vrt')
+                os.remove(self._insar.masterSlc + '.xml')
+                os.remove(self._insar.slaveSlc)
+                os.remove(self._insar.slaveSlc + '.vrt')
+                os.remove(self._insar.slaveSlc + '.xml')
+
+                os.chdir('../../../')
+
+
+    ############################################################
+    # STEP 3. mosaic swaths
+    ############################################################
+    from isceobj.Alos2Proc.runSwathMosaic import swathMosaic
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+    for k in range(2):
+        os.chdir(ionDir['subband'][k])
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            os.chdir(frameDir)
+
+            mosaicDir = ionDir['swathMosaic']
+            if not os.path.exists(mosaicDir):
+                os.makedirs(mosaicDir)
+            os.chdir(mosaicDir)
+
+            if not (
+                   ((self._insar.modeCombination == 21) or \
+                    (self._insar.modeCombination == 22) or \
+                    (self._insar.modeCombination == 31) or \
+                    (self._insar.modeCombination == 32)) 
+                   and
+                   (self._insar.endingSwath-self._insar.startingSwath+1 > 1)
+                   ):
+                import shutil
+                swathDir = 's{}'.format(masterTrack.frames[i].swaths[0].swathNumber)
+                
+                # if not os.path.isfile(self._insar.interferogram):
+                #     os.symlink(os.path.join('../', swathDir, self._insar.interferogram), self._insar.interferogram)
+                # shutil.copy2(os.path.join('../', swathDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+                # shutil.copy2(os.path.join('../', swathDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+                # if not os.path.isfile(self._insar.amplitude):
+                #     os.symlink(os.path.join('../', swathDir, self._insar.amplitude), self._insar.amplitude)
+                # shutil.copy2(os.path.join('../', swathDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+                # shutil.copy2(os.path.join('../', swathDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+                os.rename(os.path.join('../', swathDir, self._insar.interferogram), self._insar.interferogram)
+                os.rename(os.path.join('../', swathDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+                os.rename(os.path.join('../', swathDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+                os.rename(os.path.join('../', swathDir, self._insar.amplitude), self._insar.amplitude)
+                os.rename(os.path.join('../', swathDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+                os.rename(os.path.join('../', swathDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+                #no need to update frame parameters here
+                os.chdir('../')
+                #no need to save parameter file here
+                os.chdir('../')
+
+                continue
+
+            #choose offsets
+            numberOfFrames = len(masterTrack.frames)
+            numberOfSwaths = len(masterTrack.frames[i].swaths)
+            if self.swathOffsetMatching:
+                #no need to do this as the API support 2-d list
+                #rangeOffsets = (np.array(self._insar.swathRangeOffsetMatchingMaster)).reshape(numberOfFrames, numberOfSwaths)
+                #azimuthOffsets = (np.array(self._insar.swathAzimuthOffsetMatchingMaster)).reshape(numberOfFrames, numberOfSwaths)
+                rangeOffsets = self._insar.swathRangeOffsetMatchingMaster
+                azimuthOffsets = self._insar.swathAzimuthOffsetMatchingMaster
+
+            else:
+                #rangeOffsets = (np.array(self._insar.swathRangeOffsetGeometricalMaster)).reshape(numberOfFrames, numberOfSwaths)
+                #azimuthOffsets = (np.array(self._insar.swathAzimuthOffsetGeometricalMaster)).reshape(numberOfFrames, numberOfSwaths)
+                rangeOffsets = self._insar.swathRangeOffsetGeometricalMaster
+                azimuthOffsets = self._insar.swathAzimuthOffsetGeometricalMaster
+
+            rangeOffsets = rangeOffsets[i]
+            azimuthOffsets = azimuthOffsets[i]
+
+            #list of input files
+            inputInterferograms = []
+            inputAmplitudes = []
+            for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+                swathDir = 's{}'.format(swathNumber)
+                inputInterferograms.append(os.path.join('../', swathDir, self._insar.interferogram))
+                inputAmplitudes.append(os.path.join('../', swathDir, self._insar.amplitude))
+
+            #note that frame parameters are updated after mosaicking, here no need to update parameters
+            #mosaic amplitudes
+            swathMosaic(masterTrack.frames[i], inputAmplitudes, self._insar.amplitude, 
+                rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, resamplingMethod=0)
+            #mosaic interferograms
+            swathMosaic(masterTrack.frames[i], inputInterferograms, self._insar.interferogram, 
+                rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, updateFrame=False, phaseCompensation=True, resamplingMethod=1)
+
+            create_xml(self._insar.amplitude, masterTrack.frames[i].numberOfSamples, masterTrack.frames[i].numberOfLines, 'amp')
+            create_xml(self._insar.interferogram, masterTrack.frames[i].numberOfSamples, masterTrack.frames[i].numberOfLines, 'int')
+
+            #update slave frame parameters here, here no need to update parameters
+            os.chdir('../')
+            #save parameter file, here no need to save parameter file
+            os.chdir('../')
+        os.chdir('../')
+
+
+    ############################################################
+    # STEP 4. mosaic frames
+    ############################################################
+    from isceobj.Alos2Proc.runFrameMosaic import frameMosaic
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+    for k in range(2):
+        os.chdir(ionDir['subband'][k])
+
+        mosaicDir = ionDir['insar']
+        if not os.path.exists(mosaicDir):
+            os.makedirs(mosaicDir)
+        os.chdir(mosaicDir)
+
+        numberOfFrames = len(masterTrack.frames)
+        if numberOfFrames == 1:
+            import shutil
+            frameDir = os.path.join('f1_{}/mosaic'.format(self._insar.masterFrames[0]))
+            # if not os.path.isfile(self._insar.interferogram):
+            #     os.symlink(os.path.join('../', frameDir, self._insar.interferogram), self._insar.interferogram)
+            # #shutil.copy2() can overwrite
+            # shutil.copy2(os.path.join('../', frameDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+            # shutil.copy2(os.path.join('../', frameDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+            # if not os.path.isfile(self._insar.amplitude):
+            #     os.symlink(os.path.join('../', frameDir, self._insar.amplitude), self._insar.amplitude)
+            # shutil.copy2(os.path.join('../', frameDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+            # shutil.copy2(os.path.join('../', frameDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+            os.rename(os.path.join('../', frameDir, self._insar.interferogram), self._insar.interferogram)
+            os.rename(os.path.join('../', frameDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+            os.rename(os.path.join('../', frameDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+            os.rename(os.path.join('../', frameDir, self._insar.amplitude), self._insar.amplitude)
+            os.rename(os.path.join('../', frameDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+            os.rename(os.path.join('../', frameDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+            #update track parameters, no need to update track parameters here
+
+        else:
+            #choose offsets
+            if self.frameOffsetMatching:
+                rangeOffsets = self._insar.frameRangeOffsetMatchingMaster
+                azimuthOffsets = self._insar.frameAzimuthOffsetMatchingMaster
+            else:
+                rangeOffsets = self._insar.frameRangeOffsetGeometricalMaster
+                azimuthOffsets = self._insar.frameAzimuthOffsetGeometricalMaster
+
+            #list of input files
+            inputInterferograms = []
+            inputAmplitudes = []
+            for i, frameNumber in enumerate(self._insar.masterFrames):
+                frameDir = 'f{}_{}'.format(i+1, frameNumber)
+                inputInterferograms.append(os.path.join('../', frameDir, 'mosaic', self._insar.interferogram))
+                inputAmplitudes.append(os.path.join('../', frameDir, 'mosaic', self._insar.amplitude))
+
+            #note that track parameters are updated after mosaicking
+            #mosaic amplitudes
+            frameMosaic(masterTrack, inputAmplitudes, self._insar.amplitude, 
+                rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+                updateTrack=False, phaseCompensation=False, resamplingMethod=0)
+            #mosaic interferograms
+            frameMosaic(masterTrack, inputInterferograms, self._insar.interferogram, 
+                rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+                updateTrack=False, phaseCompensation=True, resamplingMethod=1)
+
+            create_xml(self._insar.amplitude, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'amp')
+            create_xml(self._insar.interferogram, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'int')
+
+            #update slave parameters here, no need to update slave parameters here
+
+        os.chdir('../')
+        #save parameter file, no need to save parameter file here
+        os.chdir('../')
+
+
+    ############################################################
+    # STEP 5. clear frame processing files
+    ############################################################
+    import shutil
+    from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+
+    for k in range(2):
+        os.chdir(ionDir['subband'][k])
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            shutil.rmtree(frameDir)
+            #cmd = 'rm -rf {}'.format(frameDir)
+            #runCmd(cmd)
+        os.chdir('../')
+
+
+    ############################################################
+    # STEP 6. create differential interferograms
+    ############################################################
+    import numpy as np
+    from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+
+    for k in range(2):
+        os.chdir(ionDir['subband'][k])
+
+        insarDir = ionDir['insar']
+        if not os.path.exists(insarDir):
+            os.makedirs(insarDir)
+        os.chdir(insarDir)
+
+        rangePixelSize = self._insar.numberRangeLooks1 * masterTrack.rangePixelSize
+        radarWavelength = subbandRadarWavelength[k]
+        rectRangeOffset = os.path.join('../../../', insarDir, self._insar.rectRangeOffset)
+
+        cmd = "imageMath.py -e='a*exp(-1.0*J*b*4.0*{}*{}/{}) * (b!=0)' --a={} --b={} -o {} -t cfloat".format(np.pi, rangePixelSize, radarWavelength, self._insar.interferogram, rectRangeOffset, self._insar.differentialInterferogram)
+        runCmd(cmd)
+
+        os.chdir('../../')
+
+
+    os.chdir('../')
+    catalog.printToLog(logger, "runIonSubband")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def defineIonDir():
+    '''
+    define directory names for ionospheric correction
+    '''
+
+    ionDir = {
+        #swath mosaicking directory
+        'swathMosaic' : 'mosaic',
+        #final insar processing directory
+        'insar' : 'insar',
+        #ionospheric correction directory
+        'ion' : 'ion',
+        #subband directory
+        'subband' : ['lower', 'upper'],
+        #final ionospheric phase calculation directory
+        'ionCal' : 'ion_cal'
+        }
+
+    return ionDir
+
+
+def defineIonFilenames():
+    pass
+
+
+
+
+
+
+

components/isceobj/Alos2Proc/runIonUwrap.py

@@ -0,0 +1,213 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import datetime
+import numpy as np
+
+import isceobj
+
+logger = logging.getLogger('isce.alos2insar.runIonUwrap')
+
+def runIonUwrap(self):
+    '''unwrap subband interferograms
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    if not self.doIon:
+        catalog.printToLog(logger, "runIonUwrap")
+        self._insar.procDoc.addAllFromCatalog(catalog)
+        return
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    from isceobj.Alos2Proc.runIonSubband import defineIonDir
+    ionDir = defineIonDir()
+    subbandPrefix = ['lower', 'upper']
+
+    ionCalDir = os.path.join(ionDir['ion'], ionDir['ionCal'])
+    if not os.path.exists(ionCalDir):
+        os.makedirs(ionCalDir)
+    os.chdir(ionCalDir)
+
+
+    ############################################################
+    # STEP 1. take looks
+    ############################################################
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+    from contrib.alos2proc.alos2proc import look
+
+    ml2 = '_{}rlks_{}alks'.format(self._insar.numberRangeLooks1*self._insar.numberRangeLooksIon, 
+                              self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksIon)
+
+    for k in range(2):
+        fullbandDir = os.path.join('../../', ionDir['insar'])
+        subbandDir = os.path.join('../', ionDir['subband'][k], ionDir['insar'])
+        prefix = subbandPrefix[k]
+
+        amp = isceobj.createImage()
+        amp.load(os.path.join(subbandDir, self._insar.amplitude)+'.xml')
+        width = amp.width
+        length = amp.length
+        width2 = int(width / self._insar.numberRangeLooksIon)
+        length2 = int(length / self._insar.numberAzimuthLooksIon)
+
+        #take looks
+        look(os.path.join(subbandDir, self._insar.differentialInterferogram), prefix+ml2+'.int', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 4, 0, 1)
+        create_xml(prefix+ml2+'.int', width2, length2, 'int')
+        look(os.path.join(subbandDir, self._insar.amplitude), prefix+ml2+'.amp', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 4, 1, 1)
+        create_xml(prefix+ml2+'.amp', width2, length2, 'amp')
+
+        # #water body
+        # if k == 0:
+        #     wbdOutFile = os.path.join(fullbandDir, self._insar.wbdOut)
+        #     if os.path.isfile(wbdOutFile):
+        #         look(wbdOutFile, 'wbd'+ml2+'.wbd', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 0, 0, 1)
+        #         create_xml('wbd'+ml2+'.wbd', width2, length2, 'byte')
+
+
+    ############################################################
+    # STEP 2. compute coherence
+    ############################################################
+    from isceobj.Alos2Proc.Alos2ProcPublic import cal_coherence
+
+    lowerbandInterferogramFile = subbandPrefix[0]+ml2+'.int'
+    upperbandInterferogramFile = subbandPrefix[1]+ml2+'.int'
+    lowerbandAmplitudeFile = subbandPrefix[0]+ml2+'.amp'
+    upperbandAmplitudeFile = subbandPrefix[1]+ml2+'.amp'
+    lowerbandCoherenceFile = subbandPrefix[0]+ml2+'.cor'
+    upperbandCoherenceFile = subbandPrefix[1]+ml2+'.cor'
+    coherenceFile = 'diff'+ml2+'.cor'
+
+    lowerint = np.fromfile(lowerbandInterferogramFile, dtype=np.complex64).reshape(length2, width2)
+    upperint = np.fromfile(upperbandInterferogramFile, dtype=np.complex64).reshape(length2, width2)
+    loweramp = np.fromfile(lowerbandAmplitudeFile, dtype=np.float32).reshape(length2, width2*2)
+    upperamp = np.fromfile(upperbandAmplitudeFile, dtype=np.float32).reshape(length2, width2*2)
+
+    #compute coherence only using interferogram
+    #here I use differential interferogram of lower and upper band interferograms
+    #so that coherence is not affected by fringes
+    cord = cal_coherence(lowerint*np.conjugate(upperint), win=3, edge=4)
+    cor = np.zeros((length2*2, width2), dtype=np.float32)
+    cor[0:length2*2:2, :] = np.sqrt( (np.absolute(lowerint)+np.absolute(upperint))/2.0 )
+    cor[1:length2*2:2, :] = cord
+    cor.astype(np.float32).tofile(coherenceFile)
+    create_xml(coherenceFile, width2, length2, 'cor')
+
+    #create lower and upper band coherence files
+    #lower
+    amp1 = loweramp[:, 0:width2*2:2]
+    amp2 = loweramp[:, 1:width2*2:2]
+    cor[1:length2*2:2, :] = np.absolute(lowerint)/(amp1+(amp1==0))/(amp2+(amp2==0))*(amp1!=0)*(amp2!=0)
+    cor.astype(np.float32).tofile(lowerbandCoherenceFile)
+    create_xml(lowerbandCoherenceFile, width2, length2, 'cor')
+
+    #upper
+    amp1 = upperamp[:, 0:width2*2:2]
+    amp2 = upperamp[:, 1:width2*2:2]
+    cor[1:length2*2:2, :] = np.absolute(upperint)/(amp1+(amp1==0))/(amp2+(amp2==0))*(amp1!=0)*(amp2!=0)
+    cor.astype(np.float32).tofile(upperbandCoherenceFile)
+    create_xml(upperbandCoherenceFile, width2, length2, 'cor')
+
+
+    ############################################################
+    # STEP 3. filtering subband interferograms
+    ############################################################
+    from contrib.alos2filter.alos2filter import psfilt1
+    from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+    from mroipac.icu.Icu import Icu
+
+    if self.filterSubbandInt:
+        for k in range(2):
+            toBeFiltered = 'tmp.int'
+            if self.removeMagnitudeBeforeFilteringSubbandInt:
+                cmd = "imageMath.py -e='a/(abs(a)+(a==0))' --a={} -o {} -t cfloat -s BSQ".format(subbandPrefix[k]+ml2+'.int', toBeFiltered)
+            else:
+                #scale the inteferogram, otherwise its magnitude is too large for filtering
+                cmd = "imageMath.py -e='a/100000.0' --a={} -o {} -t cfloat -s BSQ".format(subbandPrefix[k]+ml2+'.int', toBeFiltered)
+            runCmd(cmd)
+
+            intImage = isceobj.createIntImage()
+            intImage.load(toBeFiltered + '.xml')
+            width = intImage.width
+            length = intImage.length
+
+            windowSize = self.filterWinsizeSubbandInt
+            stepSize = self.filterStepsizeSubbandInt
+            psfilt1(toBeFiltered, 'filt_'+subbandPrefix[k]+ml2+'.int', width, self.filterStrengthSubbandInt, windowSize, stepSize)
+            create_xml('filt_'+subbandPrefix[k]+ml2+'.int', width, length, 'int')
+
+            os.remove(toBeFiltered)
+            os.remove(toBeFiltered + '.vrt')
+            os.remove(toBeFiltered + '.xml')
+
+            #create phase sigma for phase unwrapping
+            #recreate filtered image
+            filtImage = isceobj.createIntImage()
+            filtImage.load('filt_'+subbandPrefix[k]+ml2+'.int' + '.xml')
+            filtImage.setAccessMode('read')
+            filtImage.createImage()
+
+            #amplitude image
+            ampImage = isceobj.createAmpImage()
+            ampImage.load(subbandPrefix[k]+ml2+'.amp' + '.xml')
+            ampImage.setAccessMode('read')
+            ampImage.createImage()
+
+            #phase sigma correlation image
+            phsigImage = isceobj.createImage()
+            phsigImage.setFilename(subbandPrefix[k]+ml2+'.phsig')
+            phsigImage.setWidth(width)
+            phsigImage.dataType='FLOAT'
+            phsigImage.bands = 1
+            phsigImage.setImageType('cor')
+            phsigImage.setAccessMode('write')
+            phsigImage.createImage()
+
+            icu = Icu(name='insarapp_filter_icu')
+            icu.configure()
+            icu.unwrappingFlag = False
+            icu.icu(intImage = filtImage, ampImage=ampImage, phsigImage=phsigImage)
+
+            phsigImage.renderHdr()
+
+            filtImage.finalizeImage()
+            ampImage.finalizeImage()
+            phsigImage.finalizeImage()
+
+
+    ############################################################
+    # STEP 4. phase unwrapping
+    ############################################################
+    from isceobj.Alos2Proc.Alos2ProcPublic import snaphuUnwrap
+
+    for k in range(2):
+        tmid = masterTrack.sensingStart + datetime.timedelta(seconds=(self._insar.numberAzimuthLooks1-1.0)/2.0*masterTrack.azimuthLineInterval+
+               masterTrack.numberOfLines/2.0*self._insar.numberAzimuthLooks1*masterTrack.azimuthLineInterval)
+
+        if self.filterSubbandInt:
+            toBeUnwrapped = 'filt_'+subbandPrefix[k]+ml2+'.int'
+            coherenceFile = subbandPrefix[k]+ml2+'.phsig'
+        else:
+            toBeUnwrapped = subbandPrefix[k]+ml2+'.int'
+            coherenceFile = 'diff'+ml2+'.cor'
+
+        snaphuUnwrap(masterTrack, tmid, 
+            toBeUnwrapped, 
+            coherenceFile, 
+            subbandPrefix[k]+ml2+'.unw', 
+            self._insar.numberRangeLooks1*self._insar.numberRangeLooksIon, 
+            self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksIon, 
+            costMode = 'SMOOTH',initMethod = 'MCF', defomax = 2, initOnly = True)
+
+
+    os.chdir('../../')
+    catalog.printToLog(logger, "runIonUwrap")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+

components/isceobj/Alos2Proc/runLook.py

@@ -0,0 +1,70 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+from contrib.alos2proc.alos2proc import look
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+from isceobj.Alos2Proc.Alos2ProcPublic import waterBodyRadar
+
+logger = logging.getLogger('isce.alos2insar.runLook')
+
+def runLook(self):
+    '''take looks
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    #masterTrack = self._insar.loadTrack(master=True)
+    #slaveTrack = self._insar.loadTrack(master=False)
+    wbdFile = os.path.abspath(self._insar.wbd)
+
+    insarDir = 'insar'
+    if not os.path.exists(insarDir):
+        os.makedirs(insarDir)
+    os.chdir(insarDir)
+
+
+    amp = isceobj.createImage()
+    amp.load(self._insar.amplitude+'.xml')
+    width = amp.width
+    length = amp.length
+    width2 = int(width / self._insar.numberRangeLooks2)
+    length2 = int(length / self._insar.numberAzimuthLooks2)
+
+    if not ((self._insar.numberRangeLooks2 == 1) and (self._insar.numberAzimuthLooks2 == 1)):
+        #take looks
+        look(self._insar.differentialInterferogram, self._insar.multilookDifferentialInterferogram, width, self._insar.numberRangeLooks2, self._insar.numberAzimuthLooks2, 4, 0, 1)
+        look(self._insar.amplitude, self._insar.multilookAmplitude, width, self._insar.numberRangeLooks2, self._insar.numberAzimuthLooks2, 4, 1, 1)
+        look(self._insar.latitude, self._insar.multilookLatitude, width, self._insar.numberRangeLooks2, self._insar.numberAzimuthLooks2, 3, 0, 1)
+        look(self._insar.longitude, self._insar.multilookLongitude, width, self._insar.numberRangeLooks2, self._insar.numberAzimuthLooks2, 3, 0, 1)
+        look(self._insar.height, self._insar.multilookHeight, width, self._insar.numberRangeLooks2, self._insar.numberAzimuthLooks2, 3, 0, 1)
+        #creat xml
+        create_xml(self._insar.multilookDifferentialInterferogram, width2, length2, 'int')
+        create_xml(self._insar.multilookAmplitude, width2, length2, 'amp')
+        create_xml(self._insar.multilookLatitude, width2, length2, 'double')
+        create_xml(self._insar.multilookLongitude, width2, length2, 'double')
+        create_xml(self._insar.multilookHeight, width2, length2, 'double')
+        #los has two bands, use look program in isce instead
+        cmd = "looks.py -i {} -o {} -r {} -a {}".format(self._insar.los, self._insar.multilookLos, self._insar.numberRangeLooks2, self._insar.numberAzimuthLooks2)
+        runCmd(cmd)
+
+        #water body
+        #this looking operation has no problems where there is only water and land, but there is also possible no-data area
+        #look(self._insar.wbdOut, self._insar.multilookWbdOut, width, self._insar.numberRangeLooks2, self._insar.numberAzimuthLooks2, 0, 0, 1)
+        #create_xml(self._insar.multilookWbdOut, width2, length2, 'byte')
+        #use waterBodyRadar instead to avoid the problems of no-data pixels in water body
+        waterBodyRadar(self._insar.multilookLatitude, self._insar.multilookLongitude, wbdFile, self._insar.multilookWbdOut)
+
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runLook")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+

components/isceobj/Alos2Proc/runPrepareSlc.py

@@ -0,0 +1,466 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import datetime
+import numpy as np
+
+import isceobj
+from isceobj.Constants import SPEED_OF_LIGHT
+from isceobj.Alos2Proc.Alos2ProcPublic import overlapFrequency
+from contrib.alos2proc.alos2proc import rg_filter
+from contrib.alos2proc.alos2proc import resamp
+from contrib.alos2proc.alos2proc import mbf
+
+logger = logging.getLogger('isce.alos2insar.runPrepareSlc')
+
+def runPrepareSlc(self):
+    '''Extract images.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+
+    ####################################################
+    #1. crop slc
+    ####################################################
+    #for ScanSAR-stripmap interferometry, we always crop slcs
+    #for other cases, up to users
+    if ((self._insar.modeCombination == 31) or (self._insar.modeCombination == 32)) or (self.cropSlc):
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            os.chdir(frameDir)
+            for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+                swathDir = 's{}'.format(swathNumber)
+                os.chdir(swathDir)
+
+                print('cropping frame {}, swath {}'.format(frameNumber, swathNumber))
+
+                masterSwath = masterTrack.frames[i].swaths[j]
+                slaveSwath = slaveTrack.frames[i].swaths[j]
+                
+                #crop master
+                cropSlc(masterTrack.orbit, masterSwath, self._insar.masterSlc, slaveTrack.orbit, slaveSwath, edge=0, useVirtualFile=self.useVirtualFile)
+                #crop slave, since slave may go through resampling, we set edge=9
+                #cropSlc(slaveTrack.orbit, slaveSwath, self._insar.slaveSlc, masterTrack.orbit, masterSwath, edge=9, useVirtualFile=self.useVirtualFile)
+                cropSlc(slaveTrack.orbit, slaveSwath, self._insar.slaveSlc, masterTrack.orbit, masterSwath, edge=0, useVirtualFile=self.useVirtualFile)
+
+                os.chdir('../')
+            os.chdir('../')
+
+
+    ####################################################
+    #2. range-filter slc
+    ####################################################
+    #compute filtering parameters, radarwavelength and range bandwidth should be the same across all swaths and frames
+    centerfreq1 = SPEED_OF_LIGHT / masterTrack.radarWavelength
+    bandwidth1 = masterTrack.frames[0].swaths[0].rangeBandwidth
+    centerfreq2 = SPEED_OF_LIGHT / slaveTrack.radarWavelength
+    bandwidth2 = slaveTrack.frames[0].swaths[0].rangeBandwidth
+    overlapfreq = overlapFrequency(centerfreq1, bandwidth1, centerfreq2, bandwidth2)
+
+    if overlapfreq == None:
+        raise Exception('there is no overlap bandwidth in range')
+    overlapbandwidth = overlapfreq[1] - overlapfreq[0]
+    if overlapbandwidth < 3e6:
+        print('overlap bandwidth: {}, percentage: {}%'.format(overlapbandwidth, 100.0*overlapbandwidth/bandwidth1))
+        raise Exception('there is not enough overlap bandwidth in range')
+    centerfreq = (overlapfreq[1] + overlapfreq[0]) / 2.0
+
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            os.chdir(swathDir)
+
+            print('range filtering frame {}, swath {}'.format(frameNumber, swathNumber))
+
+            masterSwath = masterTrack.frames[i].swaths[j]
+            slaveSwath = slaveTrack.frames[i].swaths[j]
+
+            # #compute filtering parameters
+            # centerfreq1 = SPEED_OF_LIGHT / masterTrack.radarWavelength
+            # bandwidth1 = masterSwath.rangeBandwidth
+            # centerfreq2 = SPEED_OF_LIGHT / slaveTrack.radarWavelength
+            # bandwidth2 = slaveSwath.rangeBandwidth
+            # overlapfreq = overlapFrequency(centerfreq1, bandwidth1, centerfreq2, bandwidth2)
+
+            # if overlapfreq == None:
+            #     raise Exception('there is no overlap bandwidth in range')
+            # overlapbandwidth = overlapfreq[1] - overlapfreq[0]
+            # if overlapbandwidth < 3e6:
+            #     print('overlap bandwidth: {}, percentage: {}%'.format(overlapbandwidth, 100.0*overlapbandwidth/bandwidth1))
+            #     raise Exception('there is not enough overlap bandwidth in range')
+            # centerfreq = (overlapfreq[1] + overlapfreq[0]) / 2.0
+
+            #filter master
+            if abs(centerfreq1 - centerfreq) < 1.0 and (bandwidth1 - 1.0) < overlapbandwidth:
+                print('no need to range filter {}'.format(self._insar.masterSlc))
+            else:
+                print('range filter {}'.format(self._insar.masterSlc))
+                tmpSlc = 'tmp.slc'
+                rg_filter(self._insar.masterSlc, 1, [tmpSlc], [overlapbandwidth / masterSwath.rangeSamplingRate], 
+                    [(centerfreq - centerfreq1) / masterSwath.rangeSamplingRate], 
+                    257, 2048, 0.1, 0, 0.0)
+
+                if os.path.isfile(self._insar.masterSlc):
+                    os.remove(self._insar.masterSlc)
+                os.remove(self._insar.masterSlc+'.vrt')
+                os.remove(self._insar.masterSlc+'.xml')
+
+                img = isceobj.createSlcImage()
+                img.load(tmpSlc + '.xml')
+                #remove original
+                os.remove(tmpSlc + '.vrt')
+                os.remove(tmpSlc + '.xml')
+                os.rename(tmpSlc, self._insar.masterSlc)
+                #creat new
+                img.setFilename(self._insar.masterSlc)
+                img.extraFilename = self._insar.masterSlc + '.vrt'
+                img.setAccessMode('READ')
+                img.renderHdr()
+
+                masterTrack.radarWavelength = SPEED_OF_LIGHT/centerfreq
+                masterSwath.rangeBandwidth = overlapbandwidth
+
+            #filter slave
+            if abs(centerfreq2 - centerfreq) < 1.0 and (bandwidth2 - 1.0) < overlapbandwidth:
+                print('no need to range filter {}'.format(self._insar.slaveSlc))
+            else:
+                print('range filter {}'.format(self._insar.slaveSlc))
+                tmpSlc = 'tmp.slc'
+                rg_filter(self._insar.slaveSlc, 1, [tmpSlc], [overlapbandwidth / slaveSwath.rangeSamplingRate], 
+                    [(centerfreq - centerfreq2) / slaveSwath.rangeSamplingRate], 
+                    257, 2048, 0.1, 0, 0.0)
+
+                if os.path.isfile(self._insar.slaveSlc):
+                    os.remove(self._insar.slaveSlc)
+                os.remove(self._insar.slaveSlc+'.vrt')
+                os.remove(self._insar.slaveSlc+'.xml')
+
+                img = isceobj.createSlcImage()
+                img.load(tmpSlc + '.xml')
+                #remove original
+                os.remove(tmpSlc + '.vrt')
+                os.remove(tmpSlc + '.xml')
+                os.rename(tmpSlc, self._insar.slaveSlc)
+                #creat new
+                img.setFilename(self._insar.slaveSlc)
+                img.extraFilename = self._insar.slaveSlc + '.vrt'
+                img.setAccessMode('READ')
+                img.renderHdr()
+
+                slaveTrack.radarWavelength = SPEED_OF_LIGHT/centerfreq
+                slaveSwath.rangeBandwidth = overlapbandwidth
+
+            os.chdir('../')
+        os.chdir('../')
+
+    
+    ####################################################
+    #3. equalize sample size
+    ####################################################
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            os.chdir(swathDir)
+
+            print('equalize sample size frame {}, swath {}'.format(frameNumber, swathNumber))
+
+            masterSwath = masterTrack.frames[i].swaths[j]
+            slaveSwath = slaveTrack.frames[i].swaths[j]
+
+            if abs(masterSwath.rangeSamplingRate - slaveSwath.rangeSamplingRate) < 1.0 and abs(masterSwath.prf - slaveSwath.prf) < 1.0:
+                print('no need to resample {}.'.format(self._insar.slaveSlc))
+            else:
+                outWidth  = round(slaveSwath.numberOfSamples / slaveSwath.rangeSamplingRate * masterSwath.rangeSamplingRate)
+                outLength = round(slaveSwath.numberOfLines / slaveSwath.prf * masterSwath.prf)
+                
+                tmpSlc = 'tmp.slc'
+                resamp(self._insar.slaveSlc, tmpSlc, 'fake', 'fake', outWidth, outLength, slaveSwath.prf, slaveSwath.dopplerVsPixel, 
+                    rgcoef=[0.0, (1.0/masterSwath.rangeSamplingRate) / (1.0/slaveSwath.rangeSamplingRate) - 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 
+                    azcoef=[0.0, 0.0, (1.0/masterSwath.prf) / (1.0/slaveSwath.prf) - 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 
+                    azpos_off=0.0)
+
+                if os.path.isfile(self._insar.slaveSlc):
+                    os.remove(self._insar.slaveSlc)
+                os.remove(self._insar.slaveSlc+'.vrt')
+                os.remove(self._insar.slaveSlc+'.xml')
+
+                img = isceobj.createSlcImage()
+                img.load(tmpSlc + '.xml')
+                #remove original
+                os.remove(tmpSlc + '.vrt')
+                os.remove(tmpSlc + '.xml')
+                os.rename(tmpSlc, self._insar.slaveSlc)
+                #creat new
+                img.setFilename(self._insar.slaveSlc)
+                img.extraFilename = self._insar.slaveSlc + '.vrt'
+                img.setAccessMode('READ')
+                img.renderHdr()
+
+                #update parameters
+                #update doppler and azfmrate first
+                index2  = np.arange(outWidth)
+                index = np.arange(outWidth) * (1.0/masterSwath.rangeSamplingRate) / (1.0/slaveSwath.rangeSamplingRate)
+                dop = np.polyval(slaveSwath.dopplerVsPixel[::-1], index)
+                p = np.polyfit(index2, dop, 3)
+                slaveSwath.dopplerVsPixel = [p[3], p[2], p[1], p[0]]
+
+                azfmrate = np.polyval(slaveSwath.azimuthFmrateVsPixel[::-1], index)
+                p = np.polyfit(index2, azfmrate, 3)
+                slaveSwath.azimuthFmrateVsPixel = [p[3], p[2], p[1], p[0]]
+
+                slaveSwath.numberOfSamples = outWidth
+                slaveSwath.numberOfLines = outLength
+
+                slaveSwath.prf = masterSwath.prf
+                slaveSwath.rangeSamplingRate = masterSwath.rangeSamplingRate
+                slaveSwath.rangePixelSize = masterSwath.rangePixelSize
+                slaveSwath.azimuthPixelSize = masterSwath.azimuthPixelSize
+                slaveSwath.azimuthLineInterval = masterSwath.azimuthLineInterval
+                slaveSwath.prfFraction = masterSwath.prfFraction
+
+            os.chdir('../')
+        os.chdir('../')
+
+
+    ####################################################
+    #4. mbf
+    ####################################################
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            os.chdir(swathDir)
+
+            print('azimuth filter frame {}, swath {}'.format(frameNumber, swathNumber))
+
+            masterSwath = masterTrack.frames[i].swaths[j]
+            slaveSwath = slaveTrack.frames[i].swaths[j]
+
+            #using Piyush's code for computing range and azimuth offsets
+            midRange = masterSwath.startingRange + masterSwath.rangePixelSize * masterSwath.numberOfSamples * 0.5
+            midSensingStart = masterSwath.sensingStart + datetime.timedelta(seconds = masterSwath.numberOfLines * 0.5 / masterSwath.prf)
+            llh = masterTrack.orbit.rdr2geo(midSensingStart, midRange)
+            slvaz, slvrng = slaveTrack.orbit.geo2rdr(llh)
+            ###Translate to offsets
+            #at this point, slave range pixel size and prf should be the same as those of master
+            rgoff = ((slvrng - slaveSwath.startingRange) / masterSwath.rangePixelSize) - masterSwath.numberOfSamples * 0.5
+            azoff = ((slvaz - slaveSwath.sensingStart).total_seconds() * masterSwath.prf) - masterSwath.numberOfLines * 0.5
+
+            #filter master
+            if not ((self._insar.modeCombination == 21) and (self._insar.burstSynchronization <= self.burstSynchronizationThreshold)):
+                print('no need to azimuth filter {}.'.format(self._insar.masterSlc))
+            else:
+                index = np.arange(masterSwath.numberOfSamples) + rgoff
+                dop = np.polyval(slaveSwath.dopplerVsPixel[::-1], index)
+                p = np.polyfit(index-rgoff, dop, 3)
+                dopplerVsPixelSlave = [p[3], p[2], p[1], p[0]]
+
+                tmpSlc = 'tmp.slc'
+                mbf(self._insar.masterSlc, tmpSlc, masterSwath.prf, 1.0, 
+                    masterSwath.burstLength, masterSwath.burstCycleLength-masterSwath.burstLength, 
+                    self._insar.burstUnsynchronizedTime * masterSwath.prf, 
+                    (masterSwath.burstStartTime - masterSwath.sensingStart).total_seconds() * masterSwath.prf, 
+                    masterSwath.azimuthFmrateVsPixel, masterSwath.dopplerVsPixel, dopplerVsPixelSlave)
+
+                if os.path.isfile(self._insar.masterSlc):
+                    os.remove(self._insar.masterSlc)
+                os.remove(self._insar.masterSlc+'.vrt')
+                os.remove(self._insar.masterSlc+'.xml')
+
+                img = isceobj.createSlcImage()
+                img.load(tmpSlc + '.xml')
+                #remove original
+                os.remove(tmpSlc + '.vrt')
+                os.remove(tmpSlc + '.xml')
+                os.rename(tmpSlc, self._insar.masterSlc)
+                #creat new
+                img.setFilename(self._insar.masterSlc)
+                img.extraFilename = self._insar.masterSlc + '.vrt'
+                img.setAccessMode('READ')
+                img.renderHdr()
+
+            #filter slave
+            if not(
+                ((self._insar.modeCombination == 21) and (self._insar.burstSynchronization <= self.burstSynchronizationThreshold)) or \
+                (self._insar.modeCombination == 31)
+                ):
+                print('no need to azimuth filter {}.'.format(self._insar.slaveSlc))
+            else:
+                index = np.arange(slaveSwath.numberOfSamples) - rgoff
+                dop = np.polyval(masterSwath.dopplerVsPixel[::-1], index)
+                p = np.polyfit(index+rgoff, dop, 3)
+                dopplerVsPixelMaster = [p[3], p[2], p[1], p[0]]
+
+                tmpSlc = 'tmp.slc'
+                mbf(self._insar.slaveSlc, tmpSlc, slaveSwath.prf, 1.0, 
+                    slaveSwath.burstLength, slaveSwath.burstCycleLength-slaveSwath.burstLength, 
+                    -self._insar.burstUnsynchronizedTime * slaveSwath.prf, 
+                    (slaveSwath.burstStartTime - slaveSwath.sensingStart).total_seconds() * slaveSwath.prf, 
+                    slaveSwath.azimuthFmrateVsPixel, slaveSwath.dopplerVsPixel, dopplerVsPixelMaster)
+
+                if os.path.isfile(self._insar.slaveSlc):
+                    os.remove(self._insar.slaveSlc)
+                os.remove(self._insar.slaveSlc+'.vrt')
+                os.remove(self._insar.slaveSlc+'.xml')
+
+                img = isceobj.createSlcImage()
+                img.load(tmpSlc + '.xml')
+                #remove original
+                os.remove(tmpSlc + '.vrt')
+                os.remove(tmpSlc + '.xml')
+                os.rename(tmpSlc, self._insar.slaveSlc)
+                #creat new
+                img.setFilename(self._insar.slaveSlc)
+                img.extraFilename = self._insar.slaveSlc + '.vrt'
+                img.setAccessMode('READ')
+                img.renderHdr()
+
+            os.chdir('../')
+        os.chdir('../')
+
+    #in case parameters changed
+    self._insar.saveTrack(masterTrack, master=True)
+    self._insar.saveTrack(slaveTrack, master=False)
+
+    catalog.printToLog(logger, "runPrepareSlc")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def cropSlc(orbit, swath, slc, orbit2, swath2, edge=0, useVirtualFile=True):
+    from isceobj.Alos2Proc.Alos2ProcPublic import find_vrt_keyword
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+    '''
+    orbit:  orbit of the image to be cropped
+    swath:  swath of the image to be cropped
+    slc:    image to be cropped
+    orbit2: orbit of the other image
+    swath2: swath of the other image
+    '''
+
+    #find topleft and lowerright corners
+    #all indices start with 0
+    corner = []
+    for x in [[0, 0], [swath2.numberOfLines -1, swath2.numberOfSamples-1]]:
+        line2 = x[0]
+        sample2 = x[1]
+        rg2 = swath2.startingRange + swath2.rangePixelSize * sample2
+        az2 = swath2.sensingStart + datetime.timedelta(seconds = line2 / swath2.prf)
+        llh2 = orbit2.rdr2geo(az2, rg2)
+        az, rg = orbit.geo2rdr(llh2)
+        line = (az - swath.sensingStart).total_seconds() * swath.prf
+        sample = (rg - swath.startingRange) / swath.rangePixelSize
+        corner.append([line, sample])
+
+    #image (to be cropped) bounds
+    firstLine   = 0
+    lastLine    = swath.numberOfLines-1
+    firstSample = 0
+    lastSample  = swath.numberOfSamples-1
+
+    #the othe image bounds in image (to be cropped)
+    #add edge
+    #edge = 9
+    firstLine2   = int(corner[0][0] - edge)
+    lastLine2    = int(corner[1][0] + edge)
+    firstSample2 = int(corner[0][1] - edge)
+    lastSample2  = int(corner[1][1] + edge)
+
+    #image (to be cropped) output bounds
+    firstLine3   = max(firstLine, firstLine2)
+    lastLine3    = min(lastLine, lastLine2)
+    firstSample3 = max(firstSample, firstSample2)
+    lastSample3  = min(lastSample, lastSample2)
+    numberOfSamples3 = lastSample3-firstSample3+1
+    numberOfLines3 = lastLine3-firstLine3+1
+
+    #check if there is overlap
+    if lastLine3 - firstLine3 +1 < 1000:
+        raise Exception('azimuth overlap < 1000 lines, not enough area for InSAR\n')
+    if lastSample3 - firstSample3 +1 < 1000:
+        raise Exception('range overlap < 1000 samples, not enough area for InSAR\n')
+
+    #check if there is a need to crop image
+    if abs(firstLine3-firstLine) < 100 and abs(lastLine3-lastLine) < 100 and \
+       abs(firstSample3-firstSample) < 100 and abs(lastSample3-lastSample) < 100:
+        print('no need to crop {}. nothing is done by crop.'.format(slc))
+        return
+
+    #crop image
+    if useVirtualFile:
+        #vrt
+        SourceFilename = find_vrt_keyword(slc+'.vrt', 'SourceFilename')
+        ImageOffset    = int(find_vrt_keyword(slc+'.vrt', 'ImageOffset'))
+        PixelOffset    = int(find_vrt_keyword(slc+'.vrt', 'PixelOffset'))
+        LineOffset     = int(find_vrt_keyword(slc+'.vrt', 'LineOffset'))
+
+        #overwrite vrt and xml
+        img = isceobj.createImage()
+        img.load(slc+'.xml')
+        img.width = numberOfSamples3
+        img.length = numberOfLines3
+        img.renderHdr()
+
+        #overrite vrt
+        with open(slc+'.vrt', 'w') as fid:
+                fid.write('''<VRTDataset rasterXSize="{0}" rasterYSize="{1}">
+    <VRTRasterBand band="1" dataType="CFloat32" subClass="VRTRawRasterBand">
+        <SourceFilename relativeToVRT="0">{2}</SourceFilename>
+        <ByteOrder>MSB</ByteOrder>
+        <ImageOffset>{3}</ImageOffset>
+        <PixelOffset>8</PixelOffset>
+        <LineOffset>{4}</LineOffset>
+    </VRTRasterBand>
+</VRTDataset>'''.format(numberOfSamples3, 
+                        numberOfLines3,
+                       SourceFilename,
+                       ImageOffset + firstLine3*LineOffset + firstSample3*8,
+                       LineOffset))
+    else:
+        #read and crop data
+        with open(slc, 'rb') as f:
+            f.seek(firstLine3 * swath.numberOfSamples * np.dtype(np.complex64).itemsize, 0)
+            data = np.fromfile(f, dtype=np.complex64, count=numberOfLines3 * swath.numberOfSamples)\
+                               .reshape(numberOfLines3,swath.numberOfSamples)
+            data2 = data[:, firstSample3:lastSample3+1]
+        #overwrite original
+        data2.astype(np.complex64).tofile(slc)
+        
+        #creat new vrt and xml
+        os.remove(slc + '.xml')
+        os.remove(slc + '.vrt')
+        create_xml(slc, numberOfSamples3, numberOfLines3, 'slc')
+
+    #update parameters
+    #update doppler and azfmrate first
+    dop = np.polyval(swath.dopplerVsPixel[::-1], np.arange(swath.numberOfSamples))
+    dop3 = dop[firstSample3:lastSample3+1]
+    p = np.polyfit(np.arange(numberOfSamples3), dop3, 3)
+    swath.dopplerVsPixel = [p[3], p[2], p[1], p[0]]
+
+    azfmrate = np.polyval(swath.azimuthFmrateVsPixel[::-1], np.arange(swath.numberOfSamples))
+    azfmrate3 = azfmrate[firstSample3:lastSample3+1]
+    p = np.polyfit(np.arange(numberOfSamples3), azfmrate3, 3)
+    swath.azimuthFmrateVsPixel = [p[3], p[2], p[1], p[0]]
+
+    swath.numberOfSamples = numberOfSamples3
+    swath.numberOfLines = numberOfLines3
+
+    swath.startingRange += firstSample3 * swath.rangePixelSize
+    swath.sensingStart  += datetime.timedelta(seconds = firstLine3 / swath.prf)
+
+    #no need to update frame and track, as parameters requiring changes are determined
+    #in swath and frame mosaicking, which is not yet done at this point.
+

components/isceobj/Alos2Proc/runPreprocessor.py

@@ -0,0 +1,598 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import glob
+import logging
+import datetime
+import numpy as np
+
+import isceobj
+import isceobj.Sensor.MultiMode as MultiMode
+from isceobj.Planet.Planet import Planet
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+from isceobj.Alos2Proc.Alos2ProcPublic import getBboxRdr
+from isceobj.Alos2Proc.Alos2ProcPublic import getBboxGeo
+
+logger = logging.getLogger('isce.alos2insar.runPreprocessor')
+
+def runPreprocessor(self):
+    '''Extract images.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+
+
+    #find files
+    #actually no need to use absolute path any longer, since we are able to find file from vrt now. 27-JAN-2020, CRL.
+    #denseoffset may still need absolute path when making links
+    self.masterDir = os.path.abspath(self.masterDir)
+    self.slaveDir = os.path.abspath(self.slaveDir)
+
+    ledFilesMaster = sorted(glob.glob(os.path.join(self.masterDir, 'LED-ALOS2*-*-*')))
+    imgFilesMaster = sorted(glob.glob(os.path.join(self.masterDir, 'IMG-{}-ALOS2*-*-*'.format(self.masterPolarization.upper()))))
+
+    ledFilesSlave = sorted(glob.glob(os.path.join(self.slaveDir, 'LED-ALOS2*-*-*')))
+    imgFilesSlave = sorted(glob.glob(os.path.join(self.slaveDir, 'IMG-{}-ALOS2*-*-*'.format(self.slavePolarization.upper()))))
+
+    firstFrameMaster = ledFilesMaster[0].split('-')[-3][-4:]
+    firstFrameSlave = ledFilesSlave[0].split('-')[-3][-4:]
+    firstFrameImagesMaster = sorted(glob.glob(os.path.join(self.masterDir, 'IMG-{}-ALOS2*{}-*-*'.format(self.masterPolarization.upper(), firstFrameMaster))))
+    firstFrameImagesSlave = sorted(glob.glob(os.path.join(self.slaveDir, 'IMG-{}-ALOS2*{}-*-*'.format(self.slavePolarization.upper(), firstFrameSlave))))
+
+
+    #determin operation mode
+    masterMode = os.path.basename(ledFilesMaster[0]).split('-')[-1][0:3]
+    slaveMode = os.path.basename(ledFilesSlave[0]).split('-')[-1][0:3]
+    spotlightModes = ['SBS']
+    stripmapModes = ['UBS', 'UBD', 'HBS', 'HBD', 'HBQ', 'FBS', 'FBD', 'FBQ']
+    scansarNominalModes = ['WBS', 'WBD', 'WWS', 'WWD']
+    scansarWideModes = ['VBS', 'VBD']
+    scansarModes = ['WBS', 'WBD', 'WWS', 'WWD', 'VBS', 'VBD']
+
+    #usable combinations
+    if (masterMode in spotlightModes) and (slaveMode in spotlightModes):
+        self._insar.modeCombination = 0
+    elif (masterMode in stripmapModes) and (slaveMode in stripmapModes):
+        self._insar.modeCombination = 1
+    elif (masterMode in scansarNominalModes) and (slaveMode in scansarNominalModes):
+        self._insar.modeCombination = 21
+    elif (masterMode in scansarWideModes) and (slaveMode in scansarWideModes):
+        self._insar.modeCombination = 22
+    elif (masterMode in scansarNominalModes) and (slaveMode in stripmapModes):
+        self._insar.modeCombination = 31
+    elif (masterMode in scansarWideModes) and (slaveMode in stripmapModes):
+        self._insar.modeCombination = 32
+    else:
+        print('\n\nthis mode combination is not possible')
+        print('note that for ScanSAR-stripmap, ScanSAR must be master\n\n')
+        raise Exception('mode combination not supported')
+
+# pixel size from real data processing. azimuth pixel size may change a bit as
+# the antenna points to a different swath and therefore uses a different PRF.
+
+#   MODE  RANGE PIXEL SIZE (LOOKS)       AZIMUTH PIXEL SIZE (LOOKS)
+# -------------------------------------------------------------------
+#   SPT    [SBS]
+#          1.4304222392897463 (2)         0.9351804642158579 (4)
+#   SM1    [UBS,UBD]
+#          1.4304222392897463 (2)         1.8291988125114438 (2)
+#   SM2    [HBS,HBD,HBQ]
+#          2.8608444785794984 (2)         3.0672373839847196 (2)
+#   SM3    [FBS,FBD,FBQ]
+#          4.291266717869248  (2)         3.2462615913656667 (4)
+
+#   WD1    [WBS,WBD] [WWS,WWD]
+#          8.582533435738496  (1)         2.6053935830031887 (14)
+#          8.582533435738496  (1)         2.092362043327227  (14)
+#          8.582533435738496  (1)         2.8817632034495717 (14)
+#          8.582533435738496  (1)         3.054362492601842  (14)
+#          8.582533435738496  (1)         2.4582084463356977 (14)
+
+#   WD2    [VBS,VBD]
+#          8.582533435738496  (1)         2.9215796012950728 (14)
+#          8.582533435738496  (1)         3.088859074497863  (14)
+#          8.582533435738496  (1)         2.8792293071133073 (14)
+#          8.582533435738496  (1)         3.0592146044234854 (14)
+#          8.582533435738496  (1)         2.8818767752199137 (14)
+#          8.582533435738496  (1)         3.047038521027477  (14)
+#          8.582533435738496  (1)         2.898816222039108  (14)
+
+    #determine default number of looks:
+    self._insar.numberRangeLooks1 = self.numberRangeLooks1
+    self._insar.numberAzimuthLooks1 = self.numberAzimuthLooks1
+    self._insar.numberRangeLooks2 = self.numberRangeLooks2
+    self._insar.numberAzimuthLooks2 = self.numberAzimuthLooks2
+    #the following two will be automatically determined by runRdrDemOffset.py
+    self._insar.numberRangeLooksSim = self.numberRangeLooksSim
+    self._insar.numberAzimuthLooksSim = self.numberAzimuthLooksSim
+    self._insar.numberRangeLooksIon = self.numberRangeLooksIon
+    self._insar.numberAzimuthLooksIon = self.numberAzimuthLooksIon
+
+    if self._insar.numberRangeLooks1 == None:
+        if masterMode in ['SBS']:
+            self._insar.numberRangeLooks1 = 2
+        elif masterMode in ['UBS', 'UBD']:
+            self._insar.numberRangeLooks1 = 2
+        elif masterMode in ['HBS', 'HBD', 'HBQ']:
+            self._insar.numberRangeLooks1 = 2
+        elif masterMode in ['FBS', 'FBD', 'FBQ']:
+            self._insar.numberRangeLooks1 = 2
+        elif masterMode in ['WBS', 'WBD']:
+            self._insar.numberRangeLooks1 = 1
+        elif masterMode in ['WWS', 'WWD']:
+            self._insar.numberRangeLooks1 = 2
+        elif masterMode in ['VBS', 'VBD']:
+            self._insar.numberRangeLooks1 = 1
+        else:
+            raise Exception('unknow acquisition mode')
+
+    if self._insar.numberAzimuthLooks1 == None:
+        if masterMode in ['SBS']:
+            self._insar.numberAzimuthLooks1 = 4
+        elif masterMode in ['UBS', 'UBD']:
+            self._insar.numberAzimuthLooks1 = 2
+        elif masterMode in ['HBS', 'HBD', 'HBQ']:
+            self._insar.numberAzimuthLooks1 = 2
+        elif masterMode in ['FBS', 'FBD', 'FBQ']:
+            self._insar.numberAzimuthLooks1 = 4
+        elif masterMode in ['WBS', 'WBD']:
+            self._insar.numberAzimuthLooks1 = 14
+        elif masterMode in ['WWS', 'WWD']:
+            self._insar.numberAzimuthLooks1 = 14
+        elif masterMode in ['VBS', 'VBD']:
+            self._insar.numberAzimuthLooks1 = 14
+        else:
+            raise Exception('unknow acquisition mode')
+
+    if self._insar.numberRangeLooks2 == None:
+        if masterMode in spotlightModes:
+            self._insar.numberRangeLooks2 = 4
+        elif masterMode in stripmapModes:
+            self._insar.numberRangeLooks2 = 4
+        elif masterMode in scansarModes:
+            self._insar.numberRangeLooks2 = 5
+        else:
+            raise Exception('unknow acquisition mode')
+
+    if self._insar.numberAzimuthLooks2 == None:
+        if masterMode in spotlightModes:
+            self._insar.numberAzimuthLooks2 = 4
+        elif masterMode in stripmapModes:
+            self._insar.numberAzimuthLooks2 = 4
+        elif masterMode in scansarModes:
+            self._insar.numberAzimuthLooks2 = 2
+        else:
+            raise Exception('unknow acquisition mode')
+
+    if self._insar.numberRangeLooksIon == None:
+        if masterMode in spotlightModes:
+            self._insar.numberRangeLooksIon = 16
+        elif masterMode in stripmapModes:
+            self._insar.numberRangeLooksIon = 16
+        elif masterMode in scansarModes:
+            self._insar.numberRangeLooksIon = 40
+        else:
+            raise Exception('unknow acquisition mode')
+
+    if self._insar.numberAzimuthLooksIon == None:
+        if masterMode in spotlightModes:
+            self._insar.numberAzimuthLooksIon = 16
+        elif masterMode in stripmapModes:
+            self._insar.numberAzimuthLooksIon = 16
+        elif masterMode in scansarModes:
+            self._insar.numberAzimuthLooksIon = 16
+        else:
+            raise Exception('unknow acquisition mode')
+
+
+    #define processing file names
+    self._insar.masterDate = os.path.basename(ledFilesMaster[0]).split('-')[2]
+    self._insar.slaveDate = os.path.basename(ledFilesSlave[0]).split('-')[2]
+    self._insar.setFilename(masterDate=self._insar.masterDate, slaveDate=self._insar.slaveDate, nrlks1=self._insar.numberRangeLooks1, nalks1=self._insar.numberAzimuthLooks1, nrlks2=self._insar.numberRangeLooks2, nalks2=self._insar.numberAzimuthLooks2)
+
+
+    #find frame numbers
+    if (self._insar.modeCombination == 31) or (self._insar.modeCombination == 32):
+        if (self.masterFrames == None) or (self.slaveFrames == None):
+            raise Exception('for ScanSAR-stripmap inteferometry, you must set master and slave frame numbers')
+    #if not set, find frames automatically
+    if self.masterFrames == None:
+        self.masterFrames = []
+        for led in ledFilesMaster:
+            frameNumber = os.path.basename(led).split('-')[1][-4:]
+            if frameNumber not in self.masterFrames:
+                self.masterFrames.append(frameNumber)
+    if self.slaveFrames == None:
+        self.slaveFrames = []
+        for led in ledFilesSlave:
+            frameNumber = os.path.basename(led).split('-')[1][-4:]
+            if frameNumber not in self.slaveFrames:
+                self.slaveFrames.append(frameNumber)
+    #sort frames
+    self.masterFrames = sorted(self.masterFrames)
+    self.slaveFrames = sorted(self.slaveFrames)
+    #check number of frames
+    if len(self.masterFrames) != len(self.slaveFrames):
+        raise Exception('number of frames in master dir is not equal to number of frames \
+            in slave dir. please set frame number manually')
+
+
+    #find swath numbers (if not ScanSAR-ScanSAR, compute valid swaths)
+    if (self._insar.modeCombination == 0) or (self._insar.modeCombination == 1):
+        self.startingSwath = 1
+        self.endingSwath = 1
+
+    if self._insar.modeCombination == 21:
+        if self.startingSwath == None:
+            self.startingSwath = 1
+        if self.endingSwath == None:
+            self.endingSwath = 5
+
+    if self._insar.modeCombination == 22:
+        if self.startingSwath == None:
+            self.startingSwath = 1
+        if self.endingSwath == None:
+            self.endingSwath = 7
+
+    #determine starting and ending swaths for ScanSAR-stripmap, user's settings are overwritten
+    #use first frame to check overlap
+    if (self._insar.modeCombination == 31) or (self._insar.modeCombination == 32):
+        if self._insar.modeCombination == 31:
+            numberOfSwaths = 5
+        else:
+            numberOfSwaths = 7
+        overlapSubswaths = []
+        for i in range(numberOfSwaths):
+            overlapRatio = check_overlap(ledFilesMaster[0], firstFrameImagesMaster[i], ledFilesSlave[0], firstFrameImagesSlave[0])
+            if overlapRatio > 1.0 / 4.0:
+                overlapSubswaths.append(i+1)
+        if overlapSubswaths == []:
+            raise Exception('There is no overlap area between the ScanSAR-stripmap pair')
+        self.startingSwath = int(overlapSubswaths[0])
+        self.endingSwath = int(overlapSubswaths[-1])
+
+    #save the valid frames and swaths for future processing
+    self._insar.masterFrames = self.masterFrames
+    self._insar.slaveFrames = self.slaveFrames
+    self._insar.startingSwath = self.startingSwath
+    self._insar.endingSwath = self.endingSwath
+
+
+    ##################################################
+    #1. create directories and read data
+    ##################################################
+    self.master.configure()
+    self.slave.configure()
+    self.master.track.configure()
+    self.slave.track.configure()
+    for i, (masterFrame, slaveFrame) in enumerate(zip(self._insar.masterFrames, self._insar.slaveFrames)):
+        #frame number starts with 1
+        frameDir = 'f{}_{}'.format(i+1, masterFrame)
+        if not os.path.exists(frameDir):
+            os.makedirs(frameDir)
+        os.chdir(frameDir)
+
+        #attach a frame to master and slave
+        frameObjMaster = MultiMode.createFrame()
+        frameObjSlave = MultiMode.createFrame()
+        frameObjMaster.configure()
+        frameObjSlave.configure()
+        self.master.track.frames.append(frameObjMaster)
+        self.slave.track.frames.append(frameObjSlave)
+
+        #swath number starts with 1
+        for j in range(self._insar.startingSwath, self._insar.endingSwath+1):
+            print('processing frame {} swath {}'.format(masterFrame, j))
+
+            swathDir = 's{}'.format(j)
+            if not os.path.exists(swathDir):
+                os.makedirs(swathDir)
+            os.chdir(swathDir)
+
+            #attach a swath to master and slave
+            swathObjMaster = MultiMode.createSwath()
+            swathObjSlave = MultiMode.createSwath()
+            swathObjMaster.configure()
+            swathObjSlave.configure()
+            self.master.track.frames[-1].swaths.append(swathObjMaster)
+            self.slave.track.frames[-1].swaths.append(swathObjSlave)
+
+            #setup master
+            self.master.leaderFile = sorted(glob.glob(os.path.join(self.masterDir, 'LED-ALOS2*{}-*-*'.format(masterFrame))))[0]
+            if masterMode in scansarModes:
+                self.master.imageFile = sorted(glob.glob(os.path.join(self.masterDir, 'IMG-{}-ALOS2*{}-*-*-F{}'.format(self.masterPolarization.upper(), masterFrame, j))))[0]
+            else:
+                self.master.imageFile = sorted(glob.glob(os.path.join(self.masterDir, 'IMG-{}-ALOS2*{}-*-*'.format(self.masterPolarization.upper(), masterFrame))))[0]
+            self.master.outputFile = self._insar.masterSlc
+            self.master.useVirtualFile = self.useVirtualFile
+            #read master
+            (imageFDR, imageData)=self.master.readImage()
+            (leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord)=self.master.readLeader()
+            self.master.setSwath(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+            self.master.setFrame(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+            self.master.setTrack(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+
+            #setup slave
+            self.slave.leaderFile = sorted(glob.glob(os.path.join(self.slaveDir, 'LED-ALOS2*{}-*-*'.format(slaveFrame))))[0]
+            if slaveMode in scansarModes:
+                self.slave.imageFile = sorted(glob.glob(os.path.join(self.slaveDir, 'IMG-{}-ALOS2*{}-*-*-F{}'.format(self.slavePolarization.upper(), slaveFrame, j))))[0]
+            else:
+                self.slave.imageFile = sorted(glob.glob(os.path.join(self.slaveDir, 'IMG-{}-ALOS2*{}-*-*'.format(self.slavePolarization.upper(), slaveFrame))))[0]
+            self.slave.outputFile = self._insar.slaveSlc
+            self.slave.useVirtualFile = self.useVirtualFile
+            #read slave
+            (imageFDR, imageData)=self.slave.readImage()
+            (leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord)=self.slave.readLeader()
+            self.slave.setSwath(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+            self.slave.setFrame(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+            self.slave.setTrack(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+
+            os.chdir('../')
+        self._insar.saveProduct(self.master.track.frames[-1], self._insar.masterFrameParameter)
+        self._insar.saveProduct(self.slave.track.frames[-1], self._insar.slaveFrameParameter)
+        os.chdir('../')
+    self._insar.saveProduct(self.master.track, self._insar.masterTrackParameter)
+    self._insar.saveProduct(self.slave.track, self._insar.slaveTrackParameter)
+
+
+    ##################################################
+    #2. compute burst synchronization
+    ##################################################
+    #burst synchronization may slowly change along a track as a result of the changing relative speed of the two flights
+    #in one frame, real unsynchronized time is the same for all swaths
+    unsynTime = 0
+    #real synchronized time/percentage depends on the swath burst length (synTime = burstlength - abs(unsynTime))
+    #synTime = 0
+    synPercentage = 0
+
+    numberOfFrames = len(self._insar.masterFrames)
+    numberOfSwaths = self._insar.endingSwath - self._insar.startingSwath + 1
+    
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            masterSwath = self.master.track.frames[i].swaths[j]
+            slaveSwath = self.slave.track.frames[i].swaths[j]
+            #using Piyush's code for computing range and azimuth offsets
+            midRange = masterSwath.startingRange + masterSwath.rangePixelSize * masterSwath.numberOfSamples * 0.5
+            midSensingStart = masterSwath.sensingStart + datetime.timedelta(seconds = masterSwath.numberOfLines * 0.5 / masterSwath.prf)
+            llh = self.master.track.orbit.rdr2geo(midSensingStart, midRange)
+            slvaz, slvrng = self.slave.track.orbit.geo2rdr(llh)
+            ###Translate to offsets
+            #note that slave range pixel size and prf might be different from master, here we assume there is a virtual slave with same
+            #range pixel size and prf
+            rgoff = ((slvrng - slaveSwath.startingRange) / masterSwath.rangePixelSize) - masterSwath.numberOfSamples * 0.5
+            azoff = ((slvaz - slaveSwath.sensingStart).total_seconds() * masterSwath.prf) - masterSwath.numberOfLines * 0.5
+
+            #compute burst synchronization
+            #burst parameters for ScanSAR wide mode not estimed yet
+            if self._insar.modeCombination == 21:
+                scburstStartLine = (masterSwath.burstStartTime - masterSwath.sensingStart).total_seconds() * masterSwath.prf + azoff
+                #slave burst start times corresponding to master burst start times (100% synchronization)
+                scburstStartLines = np.arange(scburstStartLine - 100000*masterSwath.burstCycleLength, \
+                                              scburstStartLine + 100000*masterSwath.burstCycleLength, \
+                                              masterSwath.burstCycleLength)
+                dscburstStartLines = -((slaveSwath.burstStartTime - slaveSwath.sensingStart).total_seconds() * slaveSwath.prf - scburstStartLines)
+                #find the difference with minimum absolute value
+                unsynLines = dscburstStartLines[np.argmin(np.absolute(dscburstStartLines))]
+                if np.absolute(unsynLines) >= slaveSwath.burstLength:
+                    synLines = 0
+                    if unsynLines > 0:
+                        unsynLines = slaveSwath.burstLength
+                    else:
+                        unsynLines = -slaveSwath.burstLength
+                else:
+                    synLines = slaveSwath.burstLength - np.absolute(unsynLines)
+
+                unsynTime += unsynLines / masterSwath.prf
+                synPercentage += synLines / masterSwath.burstLength * 100.0
+
+                catalog.addItem('burst synchronization of frame {} swath {}'.format(frameNumber, swathNumber), '%.1f%%'%(synLines / masterSwath.burstLength * 100.0), 'runPreprocessor')
+
+            ############################################################################################
+            #illustration of the sign of the number of unsynchronized lines (unsynLines)     
+            #The convention is the same as ampcor offset, that is,
+            #              slaveLineNumber = masterLineNumber + unsynLines
+            #
+            # |-----------------------|     ------------
+            # |                       |        ^
+            # |                       |        |
+            # |                       |        |   unsynLines < 0
+            # |                       |        |
+            # |                       |       \ /
+            # |                       |    |-----------------------|
+            # |                       |    |                       |
+            # |                       |    |                       |
+            # |-----------------------|    |                       |
+            #        Master Burst          |                       |
+            #                              |                       |
+            #                              |                       |
+            #                              |                       |
+            #                              |                       |
+            #                              |-----------------------|
+            #                                     Slave Burst
+            #
+            #
+            ############################################################################################
+ 
+            ##burst parameters for ScanSAR wide mode not estimed yet
+            elif self._insar.modeCombination == 31:
+                #scansar is master
+                scburstStartLine = (masterSwath.burstStartTime - masterSwath.sensingStart).total_seconds() * masterSwath.prf + azoff
+                #slave burst start times corresponding to master burst start times (100% synchronization)
+                for k in range(-100000, 100000):
+                    saz_burstx = scburstStartLine + masterSwath.burstCycleLength * k
+                    st_burstx = slaveSwath.sensingStart + datetime.timedelta(seconds=saz_burstx / masterSwath.prf)
+                    if saz_burstx >= 0.0 and saz_burstx <= slaveSwath.numberOfLines -1:
+                        slaveSwath.burstStartTime = st_burstx
+                        slaveSwath.burstLength = masterSwath.burstLength
+                        slaveSwath.burstCycleLength = masterSwath.burstCycleLength
+                        slaveSwath.swathNumber = masterSwath.swathNumber
+                        break
+                #unsynLines = 0
+                #synLines = masterSwath.burstLength
+                #unsynTime += unsynLines / masterSwath.prf
+                #synPercentage += synLines / masterSwath.burstLength * 100.0
+                catalog.addItem('burst synchronization of frame {} swath {}'.format(frameNumber, swathNumber), '%.1f%%'%(100.0), 'runPreprocessor')
+            else:
+                pass
+
+        #overwrite original frame parameter file
+        if self._insar.modeCombination == 31:
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            self._insar.saveProduct(self.slave.track.frames[i], os.path.join(frameDir, self._insar.slaveFrameParameter))
+
+    #getting average
+    if self._insar.modeCombination == 21:
+        unsynTime /= numberOfFrames*numberOfSwaths
+        synPercentage /= numberOfFrames*numberOfSwaths
+    elif self._insar.modeCombination == 31:
+        unsynTime = 0.
+        synPercentage = 100.
+    else:
+        pass
+
+    #record results
+    if (self._insar.modeCombination == 21) or (self._insar.modeCombination == 31):
+        self._insar.burstUnsynchronizedTime = unsynTime
+        self._insar.burstSynchronization = synPercentage
+        catalog.addItem('burst synchronization averaged', '%.1f%%'%(synPercentage), 'runPreprocessor')
+
+
+    ##################################################
+    #3. compute baseline
+    ##################################################
+    #only compute baseline at four corners and center of the master track
+    bboxRdr = getBboxRdr(self.master.track)
+
+    rangeMin = bboxRdr[0]
+    rangeMax = bboxRdr[1]
+    azimuthTimeMin = bboxRdr[2]
+    azimuthTimeMax = bboxRdr[3]
+
+    azimuthTimeMid = azimuthTimeMin+datetime.timedelta(seconds=(azimuthTimeMax-azimuthTimeMin).total_seconds()/2.0)
+    rangeMid = (rangeMin + rangeMax) / 2.0
+
+    points = [[azimuthTimeMin, rangeMin],
+              [azimuthTimeMin, rangeMax],
+              [azimuthTimeMax, rangeMin],
+              [azimuthTimeMax, rangeMax],
+              [azimuthTimeMid, rangeMid]]
+
+    Bpar = []
+    Bperp = []
+    #modify Piyush's code for computing baslines
+    refElp = Planet(pname='Earth').ellipsoid
+    for x in points:
+        masterSV = self.master.track.orbit.interpolate(x[0], method='hermite')
+        target = self.master.track.orbit.rdr2geo(x[0], x[1])
+
+        slvTime, slvrng = self.slave.track.orbit.geo2rdr(target)
+        slaveSV = self.slave.track.orbit.interpolateOrbit(slvTime, method='hermite')
+
+        targxyz = np.array(refElp.LLH(target[0], target[1], target[2]).ecef().tolist())
+        mxyz = np.array(masterSV.getPosition())
+        mvel = np.array(masterSV.getVelocity())
+        sxyz = np.array(slaveSV.getPosition())
+
+        aa = np.linalg.norm(sxyz-mxyz)
+        costheta = (x[1]*x[1] + aa*aa - slvrng*slvrng)/(2.*x[1]*aa)
+
+        Bpar.append(aa*costheta)
+
+        perp = aa * np.sqrt(1 - costheta*costheta)
+        direction = np.sign(np.dot( np.cross(targxyz-mxyz, sxyz-mxyz), mvel))
+        Bperp.append(direction*perp)    
+
+    catalog.addItem('parallel baseline at upperleft of master track', Bpar[0], 'runPreprocessor')
+    catalog.addItem('parallel baseline at upperright of master track', Bpar[1], 'runPreprocessor')
+    catalog.addItem('parallel baseline at lowerleft of master track', Bpar[2], 'runPreprocessor')
+    catalog.addItem('parallel baseline at lowerright of master track', Bpar[3], 'runPreprocessor')
+    catalog.addItem('parallel baseline at center of master track', Bpar[4], 'runPreprocessor')
+
+    catalog.addItem('perpendicular baseline at upperleft of master track', Bperp[0], 'runPreprocessor')
+    catalog.addItem('perpendicular baseline at upperright of master track', Bperp[1], 'runPreprocessor')
+    catalog.addItem('perpendicular baseline at lowerleft of master track', Bperp[2], 'runPreprocessor')
+    catalog.addItem('perpendicular baseline at lowerright of master track', Bperp[3], 'runPreprocessor')
+    catalog.addItem('perpendicular baseline at center of master track', Bperp[4], 'runPreprocessor')
+
+
+    ##################################################
+    #4. compute bounding box
+    ##################################################
+    masterBbox = getBboxGeo(self.master.track)
+    slaveBbox = getBboxGeo(self.slave.track)
+
+    catalog.addItem('master bounding box', masterBbox, 'runPreprocessor')
+    catalog.addItem('slave bounding box', slaveBbox, 'runPreprocessor')
+
+
+    catalog.printToLog(logger, "runPreprocessor")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+
+def check_overlap(ldr_m, img_m, ldr_s, img_s):
+    from isceobj.Constants import SPEED_OF_LIGHT
+
+    rangeSamplingRateMaster, widthMaster, nearRangeMaster = read_param_for_checking_overlap(ldr_m, img_m)
+    rangeSamplingRateSlave, widthSlave, nearRangeSlave = read_param_for_checking_overlap(ldr_s, img_s)
+
+    farRangeMaster = nearRangeMaster + (widthMaster-1) * 0.5 * SPEED_OF_LIGHT / rangeSamplingRateMaster
+    farRangeSlave = nearRangeSlave + (widthSlave-1) * 0.5 * SPEED_OF_LIGHT / rangeSamplingRateSlave
+
+    #This should be good enough, although precise image offsets are not used.
+    if farRangeMaster <= nearRangeSlave:
+        overlapRatio = 0.0
+    elif farRangeSlave <= nearRangeMaster:
+        overlapRatio = 0.0
+    else:
+        #                     0                  1               2               3
+        ranges = np.array([nearRangeMaster, farRangeMaster, nearRangeSlave, farRangeSlave])
+        rangesIndex = np.argsort(ranges)
+        overlapRatio = ranges[rangesIndex[2]]-ranges[rangesIndex[1]] / (farRangeMaster-nearRangeMaster)
+
+    return overlapRatio
+
+
+def read_param_for_checking_overlap(leader_file, image_file):
+    from isceobj.Sensor import xmlPrefix
+    import isceobj.Sensor.CEOS as CEOS
+
+    #read from leader file
+    fsampConst = { 104: 1.047915957140240E+08,
+                   52: 5.239579785701190E+07,
+                   34: 3.493053190467460E+07,
+                   17: 1.746526595233730E+07 }
+
+    fp = open(leader_file,'rb')
+    leaderFDR = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/leader_file.xml'),dataFile=fp)
+    leaderFDR.parse()
+    fp.seek(leaderFDR.getEndOfRecordPosition())
+    sceneHeaderRecord = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/scene_record.xml'),dataFile=fp)
+    sceneHeaderRecord.parse()
+    fp.seek(sceneHeaderRecord.getEndOfRecordPosition())
+
+    fsamplookup = int(sceneHeaderRecord.metadata['Range sampling rate in MHz'])
+    rangeSamplingRate = fsampConst[fsamplookup]
+    fp.close()
+    #print('{}'.format(rangeSamplingRate))
+
+    #read from image file
+    fp = open(image_file, 'rb')
+    imageFDR = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/image_file.xml'), dataFile=fp)
+    imageFDR.parse()
+    fp.seek(imageFDR.getEndOfRecordPosition())
+    imageData = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/image_record.xml'), dataFile=fp)
+    imageData.parseFast()
+
+    width = imageFDR.metadata['Number of pixels per line per SAR channel']
+    near_range = imageData.metadata['Slant range to 1st data sample']
+    fp.close()
+    #print('{}'.format(width))
+    #print('{}'.format(near_range))
+
+    return (rangeSamplingRate, width, near_range)
+
+

components/isceobj/Alos2Proc/runRdr2Geo.py

@@ -0,0 +1,230 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import waterBodyRadar
+
+logger = logging.getLogger('isce.alos2insar.runRdr2Geo')
+
+def runRdr2Geo(self):
+    '''compute lat/lon/hgt
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    demFile = os.path.abspath(self._insar.dem)
+    wbdFile = os.path.abspath(self._insar.wbd)
+
+    insarDir = 'insar'
+    if not os.path.exists(insarDir):
+        os.makedirs(insarDir)
+    os.chdir(insarDir)
+
+
+    if self.useGPU and self._insar.hasGPU():
+        topoGPU(masterTrack, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, demFile, 
+                       self._insar.latitude, self._insar.longitude, self._insar.height, self._insar.los)
+    else:
+        snwe = topoCPU(masterTrack, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, demFile, 
+                       self._insar.latitude, self._insar.longitude, self._insar.height, self._insar.los)
+    waterBodyRadar(self._insar.latitude, self._insar.longitude, wbdFile, self._insar.wbdOut)
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runRdr2Geo")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def topoCPU(masterTrack, numberRangeLooks, numberAzimuthLooks, demFile, latFile, lonFile, hgtFile, losFile):
+    import datetime
+    import isceobj
+    from zerodop.topozero import createTopozero
+    from isceobj.Planet.Planet import Planet
+
+    pointingDirection = {'right': -1, 'left' :1}
+
+    demImage = isceobj.createDemImage()
+    demImage.load(demFile + '.xml')
+    demImage.setAccessMode('read')
+
+    planet = Planet(pname='Earth')
+
+    topo = createTopozero()
+    topo.slantRangePixelSpacing = numberRangeLooks * masterTrack.rangePixelSize
+    topo.prf = 1.0 / (numberAzimuthLooks*masterTrack.azimuthLineInterval)
+    topo.radarWavelength = masterTrack.radarWavelength
+    topo.orbit = masterTrack.orbit
+    topo.width = masterTrack.numberOfSamples
+    topo.length = masterTrack.numberOfLines
+    topo.wireInputPort(name='dem', object=demImage)
+    topo.wireInputPort(name='planet', object=planet)
+    topo.numberRangeLooks = 1 #must be set as 1
+    topo.numberAzimuthLooks = 1 #must be set as 1 Cunren
+    topo.lookSide = pointingDirection[masterTrack.pointingDirection]
+    topo.sensingStart = masterTrack.sensingStart + datetime.timedelta(seconds=(numberAzimuthLooks-1.0)/2.0*masterTrack.azimuthLineInterval)
+    topo.rangeFirstSample = masterTrack.startingRange + (numberRangeLooks-1.0)/2.0*masterTrack.rangePixelSize
+    topo.demInterpolationMethod='BIQUINTIC'
+
+    topo.latFilename = latFile
+    topo.lonFilename = lonFile
+    topo.heightFilename = hgtFile
+    topo.losFilename = losFile
+    #topo.incFilename = incName
+    #topo.maskFilename = mskName
+
+    topo.topo()
+
+    return list(topo.snwe)
+
+
+def topoGPU(masterTrack, numberRangeLooks, numberAzimuthLooks, demFile, latFile, lonFile, hgtFile, losFile):
+    '''
+    Try with GPU module.
+    '''
+    import datetime
+    import numpy as np
+    from isceobj.Planet.Planet import Planet
+    from zerodop.GPUtopozero.GPUtopozero import PyTopozero
+    from isceobj.Util.Poly2D import Poly2D
+    from iscesys import DateTimeUtil as DTU
+
+    pointingDirection = {'right': -1, 'left' :1}
+
+    #creat poynomials
+    polyDoppler = Poly2D(name='topsApp_dopplerPoly')
+    polyDoppler.setWidth(masterTrack.numberOfSamples)
+    polyDoppler.setLength(masterTrack.numberOfLines)
+    polyDoppler.setNormRange(1.0)
+    polyDoppler.setNormAzimuth(1.0)
+    polyDoppler.setMeanRange(0.0)
+    polyDoppler.setMeanAzimuth(0.0)
+    polyDoppler.initPoly(rangeOrder=0,azimuthOrder=0, coeffs=[[0.]])
+    polyDoppler.createPoly2D()
+
+    slantRangeImage = Poly2D()
+    slantRangeImage.setWidth(masterTrack.numberOfSamples)
+    slantRangeImage.setLength(masterTrack.numberOfLines)
+    slantRangeImage.setNormRange(1.0)
+    slantRangeImage.setNormAzimuth(1.0)
+    slantRangeImage.setMeanRange(0.)
+    slantRangeImage.setMeanAzimuth(0.)
+    slantRangeImage.initPoly(rangeOrder=1,azimuthOrder=0,
+        coeffs=[[masterTrack.startingRange + (numberRangeLooks-1.0)/2.0*masterTrack.rangePixelSize,numberRangeLooks * masterTrack.rangePixelSize]])
+    slantRangeImage.createPoly2D()
+
+    #creat images
+    latImage = isceobj.createImage()
+    latImage.initImage(latFile, 'write', masterTrack.numberOfSamples, 'DOUBLE')
+    latImage.createImage()
+
+    lonImage = isceobj.createImage()
+    lonImage.initImage(lonFile, 'write', masterTrack.numberOfSamples, 'DOUBLE')
+    lonImage.createImage()
+
+    losImage = isceobj.createImage()
+    losImage.initImage(losFile, 'write', masterTrack.numberOfSamples, 'FLOAT', bands=2, scheme='BIL')
+    losImage.setCaster('write', 'DOUBLE')
+    losImage.createImage()
+
+    heightImage = isceobj.createImage()
+    heightImage.initImage(hgtFile, 'write', masterTrack.numberOfSamples, 'DOUBLE')
+    heightImage.createImage()
+
+    demImage = isceobj.createDemImage()
+    demImage.load(demFile + '.xml')
+    demImage.setCaster('read', 'FLOAT')
+    demImage.createImage()
+
+    #compute a few things
+    t0 = masterTrack.sensingStart + datetime.timedelta(seconds=(numberAzimuthLooks-1.0)/2.0*masterTrack.azimuthLineInterval)
+    orb = masterTrack.orbit
+    pegHdg = np.radians( orb.getENUHeading(t0))
+    elp = Planet(pname='Earth').ellipsoid
+
+    #call gpu topo
+    topo = PyTopozero()
+    topo.set_firstlat(demImage.getFirstLatitude())
+    topo.set_firstlon(demImage.getFirstLongitude())
+    topo.set_deltalat(demImage.getDeltaLatitude())
+    topo.set_deltalon(demImage.getDeltaLongitude())
+    topo.set_major(elp.a)
+    topo.set_eccentricitySquared(elp.e2)
+    topo.set_rSpace(numberRangeLooks * masterTrack.rangePixelSize)
+    topo.set_r0(masterTrack.startingRange + (numberRangeLooks-1.0)/2.0*masterTrack.rangePixelSize)
+    topo.set_pegHdg(pegHdg)
+    topo.set_prf(1.0 / (numberAzimuthLooks*masterTrack.azimuthLineInterval))
+    topo.set_t0(DTU.seconds_since_midnight(t0))
+    topo.set_wvl(masterTrack.radarWavelength)
+    topo.set_thresh(.05)
+    topo.set_demAccessor(demImage.getImagePointer())
+    topo.set_dopAccessor(polyDoppler.getPointer())
+    topo.set_slrngAccessor(slantRangeImage.getPointer())
+    topo.set_latAccessor(latImage.getImagePointer())
+    topo.set_lonAccessor(lonImage.getImagePointer())
+    topo.set_losAccessor(losImage.getImagePointer())
+    topo.set_heightAccessor(heightImage.getImagePointer())
+    topo.set_incAccessor(0)
+    topo.set_maskAccessor(0)
+    topo.set_numIter(25)
+    topo.set_idemWidth(demImage.getWidth())
+    topo.set_idemLength(demImage.getLength())
+    topo.set_ilrl(pointingDirection[masterTrack.pointingDirection])
+    topo.set_extraIter(10)
+    topo.set_length(masterTrack.numberOfLines)
+    topo.set_width(masterTrack.numberOfSamples)
+    topo.set_nRngLooks(1)
+    topo.set_nAzLooks(1)
+    topo.set_demMethod(5) # BIQUINTIC METHOD
+    topo.set_orbitMethod(0) # HERMITE
+
+    # Need to simplify orbit stuff later
+    nvecs = len(orb._stateVectors)
+    topo.set_orbitNvecs(nvecs)
+    topo.set_orbitBasis(1) # Is this ever different?
+    topo.createOrbit() # Initializes the empty orbit to the right allocated size
+    count = 0
+    for sv in orb._stateVectors:
+        td = DTU.seconds_since_midnight(sv.getTime())
+        pos = sv.getPosition()
+        vel = sv.getVelocity()
+        topo.set_orbitVector(count,td,pos[0],pos[1],pos[2],vel[0],vel[1],vel[2])
+        count += 1
+
+    topo.runTopo()
+
+    #tidy up
+    latImage.addDescription('Pixel-by-pixel latitude in degrees.')
+    latImage.finalizeImage()
+    latImage.renderHdr()
+
+    lonImage.addDescription('Pixel-by-pixel longitude in degrees.')
+    lonImage.finalizeImage()
+    lonImage.renderHdr()
+
+    heightImage.addDescription('Pixel-by-pixel height in meters.')
+    heightImage.finalizeImage()
+    heightImage.renderHdr()
+
+    descr = '''Two channel Line-Of-Sight geometry image (all angles in degrees). Represents vector drawn from target to platform.
+            Channel 1: Incidence angle measured from vertical at target (always +ve).
+            Channel 2: Azimuth angle measured from North in Anti-clockwise direction.'''
+    losImage.setImageType('bil')
+    losImage.addDescription(descr)
+    losImage.finalizeImage()
+    losImage.renderHdr()
+
+    demImage.finalizeImage()
+
+    if slantRangeImage:
+        try:
+            slantRangeImage.finalizeImage()
+        except:
+            pass
+
+

components/isceobj/Alos2Proc/runRdrDemOffset.py

@@ -0,0 +1,322 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+from mroipac.ampcor.Ampcor import Ampcor
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+from contrib.alos2proc.alos2proc import look
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+from isceobj.Alos2Proc.Alos2ProcPublic import writeOffset
+from contrib.alos2proc_f.alos2proc_f import fitoff
+
+logger = logging.getLogger('isce.alos2insar.runRdrDemOffset')
+
+def runRdrDemOffset(self):
+    '''estimate between radar image and dem
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    demFile = os.path.abspath(self._insar.dem)
+
+    insarDir = 'insar'
+    if not os.path.exists(insarDir):
+        os.makedirs(insarDir)
+    os.chdir(insarDir)
+
+    rdrDemDir = 'rdr_dem_offset'
+    if not os.path.exists(rdrDemDir):
+        os.makedirs(rdrDemDir)
+    os.chdir(rdrDemDir)
+
+    ##################################################################################################
+    #compute dem pixel size
+    demImage = isceobj.createDemImage()
+    demImage.load(demFile + '.xml')
+    #DEM pixel size in meters (appoximate value)
+    demDeltaLon = abs(demImage.getDeltaLongitude()) / 0.0002777777777777778 * 30.0
+    demDeltaLat = abs(demImage.getDeltaLatitude())  / 0.0002777777777777778 * 30.0
+
+    #number of looks to take in range
+    if self._insar.numberRangeLooksSim == None:
+        if self._insar.numberRangeLooks1 * masterTrack.rangePixelSize > demDeltaLon:
+            self._insar.numberRangeLooksSim = 1
+        else:
+            self._insar.numberRangeLooksSim = int(demDeltaLon / (self._insar.numberRangeLooks1 * masterTrack.rangePixelSize) + 0.5)
+    #number of looks to take in azimuth
+    if self._insar.numberAzimuthLooksSim == None:
+        if self._insar.numberAzimuthLooks1 * masterTrack.azimuthPixelSize > demDeltaLat:
+            self._insar.numberAzimuthLooksSim = 1
+        else:
+            self._insar.numberAzimuthLooksSim = int(demDeltaLat / (self._insar.numberAzimuthLooks1 * masterTrack.azimuthPixelSize) + 0.5)
+
+    #simulate a radar image using dem
+    simulateRadar(os.path.join('../', self._insar.height), self._insar.sim, scale=3.0, offset=100.0)
+    sim = isceobj.createImage()
+    sim.load(self._insar.sim+'.xml')
+
+    #take looks
+    if (self._insar.numberRangeLooksSim == 1) and (self._insar.numberAzimuthLooksSim == 1):
+        simLookFile = self._insar.sim
+        ampLookFile = 'amp_{}rlks_{}alks.float'.format(self._insar.numberRangeLooksSim*self._insar.numberRangeLooks1, 
+                                                       self._insar.numberAzimuthLooksSim*self._insar.numberAzimuthLooks1)
+        cmd = "imageMath.py -e='sqrt(a_0*a_0+a_1*a_1)' --a={} -o {} -t float".format(os.path.join('../', self._insar.amplitude), ampLookFile)
+        runCmd(cmd)
+    else:
+        simLookFile = 'sim_{}rlks_{}alks.float'.format(self._insar.numberRangeLooksSim*self._insar.numberRangeLooks1, 
+                                                       self._insar.numberAzimuthLooksSim*self._insar.numberAzimuthLooks1)
+        ampLookFile = 'amp_{}rlks_{}alks.float'.format(self._insar.numberRangeLooksSim*self._insar.numberRangeLooks1, 
+                                                       self._insar.numberAzimuthLooksSim*self._insar.numberAzimuthLooks1)
+        ampTmpFile = 'amp_tmp.float'
+        look(self._insar.sim, simLookFile, sim.width, self._insar.numberRangeLooksSim, self._insar.numberAzimuthLooksSim, 2, 0, 1)
+        look(os.path.join('../', self._insar.amplitude), ampTmpFile, sim.width, self._insar.numberRangeLooksSim, self._insar.numberAzimuthLooksSim, 4, 1, 1)
+ 
+        width = int(sim.width/self._insar.numberRangeLooksSim)
+        length = int(sim.length/self._insar.numberAzimuthLooksSim)
+        create_xml(simLookFile, width, length, 'float')
+        create_xml(ampTmpFile, width, length, 'amp')
+
+        cmd = "imageMath.py -e='sqrt(a_0*a_0+a_1*a_1)' --a={} -o {} -t float".format(ampTmpFile, ampLookFile)
+        runCmd(cmd)
+        os.remove(ampTmpFile)
+        os.remove(ampTmpFile+'.vrt')
+        os.remove(ampTmpFile+'.xml')
+
+    #initial number of offsets to use
+    numberOfOffsets = 800
+    #compute land ratio to further determine the number of offsets to use
+    wbd=np.memmap(os.path.join('../', self._insar.wbdOut), dtype='byte', mode='r', shape=(sim.length, sim.width))
+    landRatio = np.sum(wbd[0:sim.length:10, 0:sim.width:10]!=-1) / int(sim.length/10) / int(sim.width/10)
+    del wbd
+    if (landRatio <= 0.00125):
+        print('\n\nWARNING: land area too small for estimating offsets between radar and dem')
+        print('do not estimate offsets between radar and dem\n\n')
+        self._insar.radarDemAffineTransform = [1.0, 0.0, 0.0, 1.0, 0.0, 0.0]
+        catalog.addItem('warning message', 'land area too small for estimating offsets between radar and dem', 'runRdrDemOffset')
+
+        catalog.printToLog(logger, "runRdrDemOffset")
+        self._insar.procDoc.addAllFromCatalog(catalog)
+
+        return
+
+    #total number of offsets to use
+    numberOfOffsets /= landRatio
+    #allocate number of offsets in range/azimuth according to image width/length
+    width = int(sim.width/self._insar.numberRangeLooksSim)
+    length = int(sim.length/self._insar.numberAzimuthLooksSim)
+    #number of offsets to use in range/azimuth
+    numberOfOffsetsRange = int(np.sqrt(numberOfOffsets * width / length))
+    numberOfOffsetsAzimuth = int(length / width * np.sqrt(numberOfOffsets * width / length))
+
+    #this should be better?
+    numberOfOffsetsRange = int(np.sqrt(numberOfOffsets))
+    numberOfOffsetsAzimuth = int(np.sqrt(numberOfOffsets))
+
+
+    if numberOfOffsetsRange > int(width/2):
+        numberOfOffsetsRange = int(width/2)
+    if numberOfOffsetsAzimuth > int(length/2):
+        numberOfOffsetsAzimuth = int(length/2)
+
+    if numberOfOffsetsRange < 10:
+        numberOfOffsetsRange = 10
+    if numberOfOffsetsAzimuth < 10:
+        numberOfOffsetsAzimuth = 10
+
+    catalog.addItem('number of range offsets', '{}'.format(numberOfOffsetsRange), 'runRdrDemOffset')
+    catalog.addItem('number of azimuth offsets', '{}'.format(numberOfOffsetsAzimuth), 'runRdrDemOffset')
+
+    #matching
+    ampcor = Ampcor(name='insarapp_slcs_ampcor')
+    ampcor.configure()
+
+    mMag = isceobj.createImage()
+    mMag.load(ampLookFile+'.xml')
+    mMag.setAccessMode('read')
+    mMag.createImage()
+
+    sMag = isceobj.createImage()
+    sMag.load(simLookFile+'.xml')
+    sMag.setAccessMode('read')
+    sMag.createImage()
+
+    ampcor.setImageDataType1('real')
+    ampcor.setImageDataType2('real')
+
+    ampcor.setMasterSlcImage(mMag)
+    ampcor.setSlaveSlcImage(sMag)
+
+    #MATCH REGION
+    rgoff = 0
+    azoff = 0
+    #it seems that we cannot use 0, haven't look into the problem
+    if rgoff == 0:
+        rgoff = 1
+    if azoff == 0:
+        azoff = 1
+    firstSample = 1
+    if rgoff < 0:
+        firstSample = int(35 - rgoff)
+    firstLine = 1
+    if azoff < 0:
+        firstLine = int(35 - azoff)
+    ampcor.setAcrossGrossOffset(rgoff)
+    ampcor.setDownGrossOffset(azoff)
+    ampcor.setFirstSampleAcross(firstSample)
+    ampcor.setLastSampleAcross(width)
+    ampcor.setNumberLocationAcross(numberOfOffsetsRange)
+    ampcor.setFirstSampleDown(firstLine)
+    ampcor.setLastSampleDown(length)
+    ampcor.setNumberLocationDown(numberOfOffsetsAzimuth)
+
+    #MATCH PARAMETERS
+    ampcor.setWindowSizeWidth(64)
+    ampcor.setWindowSizeHeight(64)
+    #note this is the half width/length of search area, so number of resulting correlation samples: 8*2+1
+    ampcor.setSearchWindowSizeWidth(16)
+    ampcor.setSearchWindowSizeHeight(16)
+
+    #REST OF THE STUFF
+    ampcor.setAcrossLooks(1)
+    ampcor.setDownLooks(1)
+    ampcor.setOversamplingFactor(64)
+    ampcor.setZoomWindowSize(16)
+    #1. The following not set
+    #Matching Scale for Sample/Line Directions                       (-)    = 1. 1.
+    #should add the following in Ampcor.py?
+    #if not set, in this case, Ampcor.py'value is also 1. 1.
+    #ampcor.setScaleFactorX(1.)
+    #ampcor.setScaleFactorY(1.)
+
+    #MATCH THRESHOLDS AND DEBUG DATA
+    #2. The following not set
+    #in roi_pac the value is set to 0 1
+    #in isce the value is set to 0.001 1000.0
+    #SNR and Covariance Thresholds                                   (-)    =  {s1} {s2}
+    #should add the following in Ampcor?
+    #THIS SHOULD BE THE ONLY THING THAT IS DIFFERENT FROM THAT OF ROI_PAC
+    #ampcor.setThresholdSNR(0)
+    #ampcor.setThresholdCov(1)
+    ampcor.setDebugFlag(False)
+    ampcor.setDisplayFlag(False)
+
+    #in summary, only two things not set which are indicated by 'The following not set' above.
+
+    #run ampcor
+    ampcor.ampcor()
+    offsets = ampcor.getOffsetField()
+    ampcorOffsetFile = 'ampcor.off'
+    cullOffsetFile = 'cull.off'
+    affineTransformFile = 'affine_transform.txt'
+    writeOffset(offsets, ampcorOffsetFile)
+
+    #finalize image, and re-create it
+    #otherwise the file pointer is still at the end of the image
+    mMag.finalizeImage()
+    sMag.finalizeImage()
+
+    # #cull offsets
+    # import io
+    # from contextlib import redirect_stdout
+    # f = io.StringIO()
+    # with redirect_stdout(f):
+    #     fitoff(ampcorOffsetFile, cullOffsetFile, 1.5, .5, 50)
+    # s = f.getvalue()
+    # #print(s)
+    # with open(affineTransformFile, 'w') as f:
+    #     f.write(s)
+
+    #cull offsets
+    import subprocess
+    proc = subprocess.Popen(["python3", "-c", "import isce; from contrib.alos2proc_f.alos2proc_f import fitoff; fitoff('ampcor.off', 'cull.off', 1.5, .5, 50)"], stdout=subprocess.PIPE)
+    out = proc.communicate()[0]
+    with open(affineTransformFile, 'w') as f:
+        f.write(out.decode('utf-8'))
+
+    #check number of offsets left
+    with open(cullOffsetFile, 'r') as f:
+        numCullOffsets = sum(1 for linex in f)
+    if numCullOffsets < 50:
+        print('\n\nWARNING: too few points left after culling, {} left'.format(numCullOffsets))
+        print('do not estimate offsets between radar and dem\n\n')
+        self._insar.radarDemAffineTransform = [1.0, 0.0, 0.0, 1.0, 0.0, 0.0]
+        catalog.addItem('warning message', 'too few points left after culling, {} left'.format(numCullOffsets), 'runRdrDemOffset')
+
+        catalog.printToLog(logger, "runRdrDemOffset")
+        self._insar.procDoc.addAllFromCatalog(catalog)
+
+        return
+
+    #read affine transform parameters
+    with open(affineTransformFile) as f:
+        lines = f.readlines()
+    i = 0
+    for linex in lines:
+        if 'Affine Matrix ' in linex:
+            m11 = float(lines[i + 2].split()[0])
+            m12 = float(lines[i + 2].split()[1])
+            m21 = float(lines[i + 3].split()[0])
+            m22 = float(lines[i + 3].split()[1])
+            t1  = float(lines[i + 7].split()[0])
+            t2  = float(lines[i + 7].split()[1])
+            break
+        i += 1    
+
+    self._insar.radarDemAffineTransform = [m11, m12, m21, m22, t1, t2]
+    ##################################################################################################
+
+    os.chdir('../../')
+
+
+    catalog.printToLog(logger, "runRdrDemOffset")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def simulateRadar(hgtfile, simfile, scale=3.0, offset=100.0):
+    '''
+    simulate a radar image by computing gradient of a dem image.
+    '''
+    import numpy as np
+    import isceobj
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+    #set chunk length here for efficient processing
+    ###############################################
+    chunk_length = 1000
+    ###############################################
+
+    hgt = isceobj.createImage()
+    hgt.load(hgtfile+'.xml')
+
+    chunk_width = hgt.width
+    num_chunk = int(hgt.length/chunk_length)
+    chunk_length_last = hgt.length - num_chunk * chunk_length
+
+    simData = np.zeros((chunk_length, chunk_width), dtype=np.float32)
+
+    hgtfp = open(hgtfile,'rb')
+    simfp = open(simfile,'wb')
+
+    print("simulating a radar image using topography")
+    for i in range(num_chunk):
+        print("processing chunk %6d of %6d" % (i+1, num_chunk), end='\r', flush=True)
+        hgtData = np.fromfile(hgtfp, dtype=np.float64, count=chunk_length*chunk_width).reshape(chunk_length, chunk_width)
+        simData[:, 0:chunk_width-1] = scale * np.diff(hgtData, axis=1) + offset
+        simData.astype(np.float32).tofile(simfp)
+
+    print("processing chunk %6d of %6d" % (num_chunk, num_chunk))
+    if chunk_length_last != 0:
+        hgtData = np.fromfile(hgtfp, dtype=np.float64, count=chunk_length_last*chunk_width).reshape(chunk_length_last, chunk_width)
+        simData[0:chunk_length_last, 0:chunk_width-1] = scale * np.diff(hgtData, axis=1) + offset
+        (simData[0:chunk_length_last, :]).astype(np.float32).tofile(simfp)
+
+    hgtfp.close()
+    simfp.close()
+    create_xml(simfile, hgt.width, hgt.length, 'float')

components/isceobj/Alos2Proc/runRectRangeOffset.py

@@ -0,0 +1,57 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+from contrib.alos2proc_f.alos2proc_f import rect_with_looks
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+logger = logging.getLogger('isce.alos2insar.runRectRangeOffset')
+
+def runRectRangeOffset(self):
+    '''rectify range offset
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    insarDir = 'insar'
+    if not os.path.exists(insarDir):
+        os.makedirs(insarDir)
+    os.chdir(insarDir)
+
+
+    #rectify
+    rgoff = isceobj.createImage()
+    rgoff.load(self._insar.rangeOffset+'.xml')
+
+    if self._insar.radarDemAffineTransform == [1.0, 0.0, 0.0, 1.0, 0.0, 0.0]:
+        if not os.path.isfile(self._insar.rectRangeOffset):
+            os.symlink(self._insar.rangeOffset, self._insar.rectRangeOffset)
+            create_xml(self._insar.rectRangeOffset, rgoff.width, rgoff.length, 'float')
+    else:
+        rect_with_looks(self._insar.rangeOffset,
+                        self._insar.rectRangeOffset,
+                        rgoff.width, rgoff.length,
+                        rgoff.width, rgoff.length,
+                        self._insar.radarDemAffineTransform[0], self._insar.radarDemAffineTransform[1],
+                        self._insar.radarDemAffineTransform[2], self._insar.radarDemAffineTransform[3],
+                        self._insar.radarDemAffineTransform[4], self._insar.radarDemAffineTransform[5],
+                        self._insar.numberRangeLooksSim*self._insar.numberRangeLooks1, self._insar.numberAzimuthLooksSim*self._insar.numberAzimuthLooks1,
+                        self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1,
+                        'REAL',
+                        'Bilinear')
+        create_xml(self._insar.rectRangeOffset, rgoff.width, rgoff.length, 'float')
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runRectRangeOffset")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+

components/isceobj/Alos2Proc/runSlcMatch.py

@@ -0,0 +1,273 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.runRdr2Geo import topoCPU
+from isceobj.Alos2Proc.runRdr2Geo import topoGPU
+from isceobj.Alos2Proc.runGeo2Rdr import geo2RdrCPU
+from isceobj.Alos2Proc.runGeo2Rdr import geo2RdrGPU
+from contrib.alos2proc.alos2proc import resamp
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+from isceobj.Alos2Proc.Alos2ProcPublic import renameFile
+from isceobj.Alos2Proc.Alos2ProcPublic import waterBodyRadar
+from mroipac.ampcor.Ampcor import Ampcor
+from isceobj.Alos2Proc.Alos2ProcPublic import meanOffset
+from isceobj.Alos2Proc.Alos2ProcPublic import cullOffsetsRoipac
+
+logger = logging.getLogger('isce.alos2insar.runSlcMatch')
+
+def runSlcMatch(self):
+    '''match a pair of SLCs
+    '''
+    if not self.doDenseOffset:
+        return
+    if not ((self._insar.modeCombination == 0) or (self._insar.modeCombination == 1)):
+        return
+
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    demFile = os.path.abspath(self._insar.dem)
+    wbdFile = os.path.abspath(self._insar.wbd)
+
+    denseOffsetDir = 'dense_offset'
+    if not os.path.exists(denseOffsetDir):
+        os.makedirs(denseOffsetDir)
+    os.chdir(denseOffsetDir)
+
+    masterTrack = self._insar.loadProduct(self._insar.masterTrackParameter)
+    slaveTrack = self._insar.loadProduct(self._insar.slaveTrackParameter)
+
+#########################################################################################
+
+
+    ##################################################
+    # compute geometric offsets
+    ##################################################
+    if self.useGPU and self._insar.hasGPU():
+        topoGPU(masterTrack, 1, 1, demFile, 
+                       'lat.rdr', 'lon.rdr', 'hgt.rdr', 'los.rdr')
+        geo2RdrGPU(slaveTrack, 1, 1, 
+            'lat.rdr', 'lon.rdr', 'hgt.rdr', 'rg.off', 'az.off')
+    else:
+        topoCPU(masterTrack, 1, 1, demFile, 
+                       'lat.rdr', 'lon.rdr', 'hgt.rdr', 'los.rdr')
+        geo2RdrCPU(slaveTrack, 1, 1, 
+            'lat.rdr', 'lon.rdr', 'hgt.rdr', 'rg.off', 'az.off')
+
+
+    ##################################################
+    # resample SLC
+    ##################################################
+    #SlaveSlcResampled = os.path.splitext(self._insar.slaveSlc)[0]+'_resamp'+os.path.splitext(self._insar.slaveSlc)[1]
+    SlaveSlcResampled = self._insar.slaveSlcCoregistered
+    rangeOffsets2Frac = 0.0
+    azimuthOffsets2Frac = 0.0
+    resamp(self._insar.slaveSlc,
+           SlaveSlcResampled,
+           'rg.off',
+           'az.off',
+           masterTrack.numberOfSamples, masterTrack.numberOfLines,
+           slaveTrack.prf,
+           slaveTrack.dopplerVsPixel,
+           [rangeOffsets2Frac, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+           [azimuthOffsets2Frac, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0])
+    create_xml(SlaveSlcResampled, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'slc')
+
+
+    if self.estimateResidualOffset:
+
+        numberOfOffsets = 800
+        rangeStep = 50
+
+        length = masterTrack.numberOfLines
+        width = masterTrack.numberOfSamples
+        waterBodyRadar('lat.rdr', 'lon.rdr', wbdFile, 'wbd.rdr')
+        wbd=np.memmap('wbd.rdr', dtype=np.int8, mode='r', shape=(length, width))
+        azimuthStep = int(length/width*rangeStep+0.5)
+        landRatio = np.sum(wbd[0:length:azimuthStep,0:width:rangeStep]!=-1)/(int(length/azimuthStep)*int(width/rangeStep))
+        del wbd
+
+        if (landRatio <= 0.00125):
+            print('\n\nWARNING: land area too small for estimating residual slc offsets')
+            print('do not estimate residual offsets\n\n')
+            catalog.addItem('warning message', 'land area too small for estimating residual slc offsets', 'runSlcMatch')
+        else:
+            numberOfOffsets /= landRatio
+            #we use equal number of offsets in range and azimuth here
+            numberOfOffsetsRange = int(np.sqrt(numberOfOffsets)+0.5)
+            numberOfOffsetsAzimuth = int(np.sqrt(numberOfOffsets)+0.5)
+            if numberOfOffsetsRange > int(width/2):
+                numberOfOffsetsRange = int(width/2)
+            if numberOfOffsetsAzimuth > int(length/2):
+                numberOfOffsetsAzimuth = int(length/2)
+            if numberOfOffsetsRange < 10:
+                numberOfOffsetsRange = 10
+            if numberOfOffsetsAzimuth < 10:
+                numberOfOffsetsAzimuth = 10
+
+
+            ##########################################
+            #2. match using ampcor
+            ##########################################
+            ampcor = Ampcor(name='insarapp_slcs_ampcor')
+            ampcor.configure()
+
+            mSLC = isceobj.createSlcImage()
+            mSLC.load(self._insar.masterSlc+'.xml')
+            mSLC.setAccessMode('read')
+            mSLC.createImage()
+
+            sSLC = isceobj.createSlcImage()
+            sSLC.load(SlaveSlcResampled+'.xml')
+            sSLC.setAccessMode('read')
+            sSLC.createImage()
+
+            ampcor.setImageDataType1('complex')
+            ampcor.setImageDataType2('complex')
+
+            ampcor.setMasterSlcImage(mSLC)
+            ampcor.setSlaveSlcImage(sSLC)
+
+            #MATCH REGION
+            #compute an offset at image center to use
+            rgoff = 0.0
+            azoff = 0.0
+            #it seems that we cannot use 0, haven't look into the problem
+            if rgoff == 0:
+                rgoff = 1
+            if azoff == 0:
+                azoff = 1
+            firstSample = 1
+            if rgoff < 0:
+                firstSample = int(35 - rgoff)
+            firstLine = 1
+            if azoff < 0:
+                firstLine = int(35 - azoff)
+            ampcor.setAcrossGrossOffset(rgoff)
+            ampcor.setDownGrossOffset(azoff)
+            ampcor.setFirstSampleAcross(firstSample)
+            ampcor.setLastSampleAcross(mSLC.width)
+            ampcor.setNumberLocationAcross(numberOfOffsetsRange)
+            ampcor.setFirstSampleDown(firstLine)
+            ampcor.setLastSampleDown(mSLC.length)
+            ampcor.setNumberLocationDown(numberOfOffsetsAzimuth)
+
+            #MATCH PARAMETERS
+            #full-aperture mode
+            if (self._insar.modeCombination == 21) or \
+               (self._insar.modeCombination == 22) or \
+               (self._insar.modeCombination == 31) or \
+               (self._insar.modeCombination == 32):
+                ampcor.setWindowSizeWidth(64)
+                ampcor.setWindowSizeHeight(512)
+                #note this is the half width/length of search area, number of resulting correlation samples: 32*2+1
+                ampcor.setSearchWindowSizeWidth(32)
+                ampcor.setSearchWindowSizeHeight(32)
+                #triggering full-aperture mode matching
+                ampcor.setWinsizeFilt(8)
+                ampcor.setOversamplingFactorFilt(64)
+            #regular mode
+            else:
+                ampcor.setWindowSizeWidth(64)
+                ampcor.setWindowSizeHeight(64)
+                ampcor.setSearchWindowSizeWidth(16)
+                ampcor.setSearchWindowSizeHeight(16)
+
+            #REST OF THE STUFF
+            ampcor.setAcrossLooks(1)
+            ampcor.setDownLooks(1)
+            ampcor.setOversamplingFactor(64)
+            ampcor.setZoomWindowSize(16)
+            #1. The following not set
+            #Matching Scale for Sample/Line Directions                       (-)    = 1. 1.
+            #should add the following in Ampcor.py?
+            #if not set, in this case, Ampcor.py'value is also 1. 1.
+            #ampcor.setScaleFactorX(1.)
+            #ampcor.setScaleFactorY(1.)
+
+            #MATCH THRESHOLDS AND DEBUG DATA
+            #2. The following not set
+            #in roi_pac the value is set to 0 1
+            #in isce the value is set to 0.001 1000.0
+            #SNR and Covariance Thresholds                                   (-)    =  {s1} {s2}
+            #should add the following in Ampcor?
+            #THIS SHOULD BE THE ONLY THING THAT IS DIFFERENT FROM THAT OF ROI_PAC
+            #ampcor.setThresholdSNR(0)
+            #ampcor.setThresholdCov(1)
+            ampcor.setDebugFlag(False)
+            ampcor.setDisplayFlag(False)
+
+            #in summary, only two things not set which are indicated by 'The following not set' above.
+
+            #run ampcor
+            ampcor.ampcor()
+            offsets = ampcor.getOffsetField()
+            mSLC.finalizeImage()
+            sSLC.finalizeImage()
+
+
+            #3. cull offsets
+            refinedOffsets = cullOffsetsRoipac(offsets, numThreshold=50)
+            if refinedOffsets == None:
+                print('\n\nWARNING: too few offsets left for slc residual offset estimation')
+                print('do not estimate residual offsets\n\n')
+                catalog.addItem('warning message', 'too few offsets left for slc residual offset estimation', 'runSlcMatch')
+            else:
+                rangeOffset, azimuthOffset = meanOffset(refinedOffsets)
+                os.remove(SlaveSlcResampled)
+                os.remove(SlaveSlcResampled+'.vrt')
+                os.remove(SlaveSlcResampled+'.xml')
+                
+                rangeOffsets2Frac = rangeOffset
+                azimuthOffsets2Frac = azimuthOffset
+                resamp(self._insar.slaveSlc,
+                       SlaveSlcResampled,
+                       'rg.off',
+                       'az.off',
+                       masterTrack.numberOfSamples, masterTrack.numberOfLines,
+                       slaveTrack.prf,
+                       slaveTrack.dopplerVsPixel,
+                       [rangeOffsets2Frac, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+                       [azimuthOffsets2Frac, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0])
+                create_xml(SlaveSlcResampled, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'slc')
+
+                catalog.addItem('number of offsets range', numberOfOffsetsRange, 'runSlcMatch')
+                catalog.addItem('number of offsets azimuth', numberOfOffsetsAzimuth, 'runSlcMatch')
+                catalog.addItem('range residual offset after geometric coregistration', rangeOffset, 'runSlcMatch')
+                catalog.addItem('azimuth residual offset after geometric coregistration', azimuthOffset, 'runSlcMatch')
+
+
+
+
+    if self.deleteGeometryFiles:
+        os.remove('lat.rdr')
+        os.remove('lat.rdr.vrt')
+        os.remove('lat.rdr.xml')
+        os.remove('lon.rdr')
+        os.remove('lon.rdr.vrt')
+        os.remove('lon.rdr.xml')
+        os.remove('hgt.rdr')
+        os.remove('hgt.rdr.vrt')
+        os.remove('hgt.rdr.xml')
+        os.remove('los.rdr')
+        os.remove('los.rdr.vrt')
+        os.remove('los.rdr.xml')
+        # if os.path.isfile('wbd.rdr'):
+        #     os.remove('wbd.rdr')
+        #     os.remove('wbd.rdr.vrt')
+        #     os.remove('wbd.rdr.xml')
+
+#########################################################################################
+
+    os.chdir('../')
+    catalog.printToLog(logger, "runSlcMatch")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+

components/isceobj/Alos2Proc/runSlcMosaic.py

@@ -0,0 +1,182 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.runFrameOffset import frameOffset
+from isceobj.Alos2Proc.runFrameMosaic import frameMosaic
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+logger = logging.getLogger('isce.alos2insar.runSlcMosaic')
+
+def runSlcMosaic(self):
+    '''mosaic SLCs
+    '''
+    if not self.doDenseOffset:
+        print('\ndense offset not requested, skip this and the remaining steps...')
+        return
+    if not ((self._insar.modeCombination == 0) or (self._insar.modeCombination == 1)):
+        print('dense offset only support spotligh-spotlight and stripmap-stripmap pairs')
+        return
+
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    denseOffsetDir = 'dense_offset'
+    if not os.path.exists(denseOffsetDir):
+        os.makedirs(denseOffsetDir)
+    os.chdir(denseOffsetDir)
+
+
+    ##################################################
+    # estimate master and slave frame offsets
+    ##################################################
+    if len(masterTrack.frames) > 1:
+        matchingMode=1
+
+        #if master offsets from matching are not already computed
+        if self.frameOffsetMatching == False:
+            offsetMaster = frameOffset(masterTrack, self._insar.masterSlc, self._insar.masterFrameOffset, 
+                                       crossCorrelation=True, matchingMode=matchingMode)
+        offsetSlave = frameOffset(slaveTrack, self._insar.slaveSlc, self._insar.slaveFrameOffset, 
+                                  crossCorrelation=True, matchingMode=matchingMode)
+        if self.frameOffsetMatching == False:
+            self._insar.frameRangeOffsetMatchingMaster = offsetMaster[2]
+            self._insar.frameAzimuthOffsetMatchingMaster = offsetMaster[3]
+        self._insar.frameRangeOffsetMatchingSlave = offsetSlave[2]
+        self._insar.frameAzimuthOffsetMatchingSlave = offsetSlave[3]
+
+
+    ##################################################
+    # mosaic slc
+    ##################################################
+    numberOfFrames = len(masterTrack.frames)
+    if numberOfFrames == 1:
+        import shutil
+        #frameDir = os.path.join('f1_{}/mosaic'.format(self._insar.masterFrames[0]))
+        frameDir = os.path.join('f1_{}/s{}'.format(self._insar.masterFrames[0], self._insar.startingSwath))
+        if not os.path.isfile(self._insar.masterSlc):
+            if os.path.isfile(os.path.join('../', frameDir, self._insar.masterSlc)):
+                os.symlink(os.path.join('../', frameDir, self._insar.masterSlc), self._insar.masterSlc)
+        #shutil.copy2() can overwrite
+        shutil.copy2(os.path.join('../', frameDir, self._insar.masterSlc+'.vrt'), self._insar.masterSlc+'.vrt')
+        shutil.copy2(os.path.join('../', frameDir, self._insar.masterSlc+'.xml'), self._insar.masterSlc+'.xml')
+        if not os.path.isfile(self._insar.slaveSlc):
+            if os.path.isfile(os.path.join('../', frameDir, self._insar.slaveSlc)):
+                os.symlink(os.path.join('../', frameDir, self._insar.slaveSlc), self._insar.slaveSlc)
+        shutil.copy2(os.path.join('../', frameDir, self._insar.slaveSlc+'.vrt'), self._insar.slaveSlc+'.vrt')
+        shutil.copy2(os.path.join('../', frameDir, self._insar.slaveSlc+'.xml'), self._insar.slaveSlc+'.xml')
+
+        #update track parameters
+        #########################################################
+        #mosaic size
+        masterTrack.numberOfSamples = masterTrack.frames[0].swaths[0].numberOfSamples
+        masterTrack.numberOfLines = masterTrack.frames[0].swaths[0].numberOfLines
+        #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+        #range parameters
+        masterTrack.startingRange = masterTrack.frames[0].swaths[0].startingRange
+        masterTrack.rangeSamplingRate = masterTrack.frames[0].swaths[0].rangeSamplingRate
+        masterTrack.rangePixelSize = masterTrack.frames[0].swaths[0].rangePixelSize
+        #azimuth parameters
+        masterTrack.sensingStart = masterTrack.frames[0].swaths[0].sensingStart
+        masterTrack.prf = masterTrack.frames[0].swaths[0].prf
+        masterTrack.azimuthPixelSize = masterTrack.frames[0].swaths[0].azimuthPixelSize
+        masterTrack.azimuthLineInterval = masterTrack.frames[0].swaths[0].azimuthLineInterval
+
+        masterTrack.dopplerVsPixel = masterTrack.frames[0].swaths[0].dopplerVsPixel
+
+        #update track parameters, slave
+        #########################################################
+        #mosaic size
+        slaveTrack.numberOfSamples = slaveTrack.frames[0].swaths[0].numberOfSamples
+        slaveTrack.numberOfLines = slaveTrack.frames[0].swaths[0].numberOfLines
+        #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+        #range parameters
+        slaveTrack.startingRange = slaveTrack.frames[0].swaths[0].startingRange
+        slaveTrack.rangeSamplingRate = slaveTrack.frames[0].swaths[0].rangeSamplingRate
+        slaveTrack.rangePixelSize = slaveTrack.frames[0].swaths[0].rangePixelSize
+        #azimuth parameters
+        slaveTrack.sensingStart = slaveTrack.frames[0].swaths[0].sensingStart
+        slaveTrack.prf = slaveTrack.frames[0].swaths[0].prf
+        slaveTrack.azimuthPixelSize = slaveTrack.frames[0].swaths[0].azimuthPixelSize
+        slaveTrack.azimuthLineInterval = slaveTrack.frames[0].swaths[0].azimuthLineInterval
+
+        slaveTrack.dopplerVsPixel = slaveTrack.frames[0].swaths[0].dopplerVsPixel
+
+    else:
+        #mosaic master slc
+        #########################################################
+        #choose offsets
+        rangeOffsets = self._insar.frameRangeOffsetMatchingMaster
+        azimuthOffsets = self._insar.frameAzimuthOffsetMatchingMaster
+
+        #list of input files
+        slcs = []
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            swathDir = 's{}'.format(self._insar.startingSwath)
+            slcs.append(os.path.join('../', frameDir, swathDir, self._insar.masterSlc))
+
+        #note that track parameters are updated after mosaicking
+        #parameters update is checked, it is OK.
+        frameMosaic(masterTrack, slcs, self._insar.masterSlc, 
+            rangeOffsets, azimuthOffsets, 1, 1, 
+            updateTrack=True, phaseCompensation=True, resamplingMethod=2)
+        create_xml(self._insar.masterSlc, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'slc')
+        masterTrack.dopplerVsPixel = computeTrackDoppler(masterTrack)
+
+        #mosaic slave slc
+        #########################################################
+        #choose offsets
+        rangeOffsets = self._insar.frameRangeOffsetMatchingSlave
+        azimuthOffsets = self._insar.frameAzimuthOffsetMatchingSlave
+
+        #list of input files
+        slcs = []
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            swathDir = 's{}'.format(self._insar.startingSwath)
+            slcs.append(os.path.join('../', frameDir, swathDir, self._insar.slaveSlc))
+
+        #note that track parameters are updated after mosaicking
+        #parameters update is checked, it is OK.
+        frameMosaic(slaveTrack, slcs, self._insar.slaveSlc, 
+            rangeOffsets, azimuthOffsets, 1, 1, 
+            updateTrack=True, phaseCompensation=True, resamplingMethod=2)
+        create_xml(self._insar.slaveSlc, slaveTrack.numberOfSamples, slaveTrack.numberOfLines, 'slc')
+        slaveTrack.dopplerVsPixel = computeTrackDoppler(slaveTrack)
+
+
+    #save parameter file inside denseoffset directory
+    self._insar.saveProduct(masterTrack, self._insar.masterTrackParameter)
+    self._insar.saveProduct(slaveTrack, self._insar.slaveTrackParameter)
+
+
+    os.chdir('../')
+    catalog.printToLog(logger, "runSlcMosaic")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def computeTrackDoppler(track):
+    '''
+    compute doppler for a track
+    '''
+    numberOfFrames = len(track.frames)
+    dop = np.zeros(track.numberOfSamples)
+    for i in range(numberOfFrames):
+        index = track.startingRange + np.arange(track.numberOfSamples) * track.rangePixelSize
+        index = (index - track.frames[i].swaths[0].startingRange) / track.frames[i].swaths[0].rangePixelSize
+        dop = dop + np.polyval(track.frames[i].swaths[0].dopplerVsPixel[::-1], index)
+    
+    index1 = np.arange(track.numberOfSamples)
+    dop1 = dop/numberOfFrames
+    p = np.polyfit(index1, dop1, 3)
+
+    return [p[3], p[2], p[1], p[0]]

components/isceobj/Alos2Proc/runSlcOffset.py

@@ -0,0 +1,275 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import glob
+import logging
+import datetime
+import numpy as np
+
+import isceobj
+import mroipac
+from mroipac.ampcor.Ampcor import Ampcor
+from isceobj.Alos2Proc.Alos2ProcPublic import topo
+from isceobj.Alos2Proc.Alos2ProcPublic import geo2rdr
+from isceobj.Alos2Proc.Alos2ProcPublic import waterBodyRadar
+from isceobj.Alos2Proc.Alos2ProcPublic import reformatGeometricalOffset
+from isceobj.Alos2Proc.Alos2ProcPublic import writeOffset
+from isceobj.Alos2Proc.Alos2ProcPublic import cullOffsets
+from isceobj.Alos2Proc.Alos2ProcPublic import computeOffsetFromOrbit
+
+logger = logging.getLogger('isce.alos2insar.runSlcOffset')
+
+def runSlcOffset(self):
+    '''estimate SLC offsets
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    demFile = os.path.abspath(self._insar.dem)
+    wbdFile = os.path.abspath(self._insar.wbd)
+
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            os.chdir(swathDir)
+
+            print('estimating offset frame {}, swath {}'.format(frameNumber, swathNumber))
+
+            masterSwath = masterTrack.frames[i].swaths[j]
+            slaveSwath = slaveTrack.frames[i].swaths[j]
+
+            ##########################################
+            #1. set number of matching points
+            ##########################################
+            #set initinial numbers
+            if (self._insar.modeCombination == 21) or (self._insar.modeCombination == 22):
+                numberOfOffsetsRange = 10
+                numberOfOffsetsAzimuth = 40
+            else:
+                numberOfOffsetsRange = 20
+                numberOfOffsetsAzimuth = 20
+
+            #change the initial numbers using water body
+            if self.useWbdForNumberOffsets and (self._insar.wbd != None):
+                numberRangeLooks=100
+                numberAzimuthLooks=100
+                #compute land ratio using topo module
+                topo(masterSwath, masterTrack, demFile, 'lat.rdr', 'lon.rdr', 'hgt.rdr', losFile='los.rdr', 
+                    incFile=None, mskFile=None, 
+                    numberRangeLooks=numberRangeLooks, numberAzimuthLooks=numberAzimuthLooks, multilookTimeOffset=False)
+                waterBodyRadar('lat.rdr', 'lon.rdr', wbdFile, 'wbd.rdr')
+
+                wbdImg = isceobj.createImage()
+                wbdImg.load('wbd.rdr.xml')
+                width = wbdImg.width
+                length = wbdImg.length
+
+                wbd = np.fromfile('wbd.rdr', dtype=np.byte).reshape(length, width)
+                landRatio = np.sum(wbd==0) / (length*width)
+
+                if (landRatio <= 0.00125):
+                    print('\n\nWARNING: land too small for estimating slc offsets at frame {}, swath {}'.format(frameNumber, swathNumber))
+                    print('proceed to use geometric offsets for forming interferogram')
+                    print('but please consider not using this swath\n\n')
+                    catalog.addItem('warning message', 'land too small for estimating slc offsets at frame {}, swath {}, use geometric offsets'.format(frameNumber, swathNumber), 'runSlcOffset')
+                    
+                    #compute geomtricla offsets
+                    geo2rdr(slaveSwath, slaveTrack, 'lat.rdr', 'lon.rdr', 'hgt.rdr', 'rg.rdr', 'az.rdr', numberRangeLooks=numberRangeLooks, numberAzimuthLooks=numberAzimuthLooks, multilookTimeOffset=False)
+                    reformatGeometricalOffset('rg.rdr', 'az.rdr', 'cull.off', rangeStep=numberRangeLooks, azimuthStep=numberAzimuthLooks, maximumNumberOfOffsets=2000)
+
+                    os.remove('lat.rdr')
+                    os.remove('lat.rdr.vrt')
+                    os.remove('lat.rdr.xml')
+                    os.remove('lon.rdr')
+                    os.remove('lon.rdr.vrt')
+                    os.remove('lon.rdr.xml')
+                    os.remove('hgt.rdr')
+                    os.remove('hgt.rdr.vrt')
+                    os.remove('hgt.rdr.xml')
+                    os.remove('los.rdr')
+                    os.remove('los.rdr.vrt')
+                    os.remove('los.rdr.xml')
+                    os.remove('wbd.rdr')
+                    os.remove('wbd.rdr.vrt')
+                    os.remove('wbd.rdr.xml')
+
+                    os.remove('rg.rdr')
+                    os.remove('rg.rdr.vrt')
+                    os.remove('rg.rdr.xml')
+                    os.remove('az.rdr')
+                    os.remove('az.rdr.vrt')
+                    os.remove('az.rdr.xml')
+
+                    os.chdir('../')
+                    continue
+
+
+                os.remove('lat.rdr')
+                os.remove('lat.rdr.vrt')
+                os.remove('lat.rdr.xml')
+                os.remove('lon.rdr')
+                os.remove('lon.rdr.vrt')
+                os.remove('lon.rdr.xml')
+                os.remove('hgt.rdr')
+                os.remove('hgt.rdr.vrt')
+                os.remove('hgt.rdr.xml')
+                os.remove('los.rdr')
+                os.remove('los.rdr.vrt')
+                os.remove('los.rdr.xml')
+                os.remove('wbd.rdr')
+                os.remove('wbd.rdr.vrt')
+                os.remove('wbd.rdr.xml')
+
+                #put the results on a grid with a specified interval
+                interval = 0.2
+                axisRatio = int(np.sqrt(landRatio)/interval)*interval + interval
+                if axisRatio > 1:
+                    axisRatio = 1
+
+                numberOfOffsetsRange = int(numberOfOffsetsRange/axisRatio)
+                numberOfOffsetsAzimuth = int(numberOfOffsetsAzimuth/axisRatio)
+            else:
+                catalog.addItem('warning message', 'no water mask used to determine number of matching points. frame {} swath {}'.format(frameNumber, swathNumber), 'runSlcOffset')
+
+            #user's settings
+            if self.numberRangeOffsets != None:
+                numberOfOffsetsRange = self.numberRangeOffsets[i][j]
+            if self.numberAzimuthOffsets != None:
+                numberOfOffsetsAzimuth = self.numberAzimuthOffsets[i][j]
+
+            catalog.addItem('number of offsets range frame {} swath {}'.format(frameNumber, swathNumber), numberOfOffsetsRange, 'runSlcOffset')
+            catalog.addItem('number of offsets azimuth frame {} swath {}'.format(frameNumber, swathNumber), numberOfOffsetsAzimuth, 'runSlcOffset')
+
+            ##########################################
+            #2. match using ampcor
+            ##########################################
+            ampcor = Ampcor(name='insarapp_slcs_ampcor')
+            ampcor.configure()
+
+            mSLC = isceobj.createSlcImage()
+            mSLC.load(self._insar.masterSlc+'.xml')
+            mSLC.setAccessMode('read')
+            mSLC.createImage()
+
+            sSLC = isceobj.createSlcImage()
+            sSLC.load(self._insar.slaveSlc+'.xml')
+            sSLC.setAccessMode('read')
+            sSLC.createImage()
+
+            ampcor.setImageDataType1('complex')
+            ampcor.setImageDataType2('complex')
+
+            ampcor.setMasterSlcImage(mSLC)
+            ampcor.setSlaveSlcImage(sSLC)
+
+            #MATCH REGION
+            #compute an offset at image center to use
+            rgoff, azoff = computeOffsetFromOrbit(masterSwath, masterTrack, slaveSwath, slaveTrack, 
+                masterSwath.numberOfSamples * 0.5, 
+                masterSwath.numberOfLines * 0.5)
+            #it seems that we cannot use 0, haven't look into the problem
+            if rgoff == 0:
+                rgoff = 1
+            if azoff == 0:
+                azoff = 1
+            firstSample = 1
+            if rgoff < 0:
+                firstSample = int(35 - rgoff)
+            firstLine = 1
+            if azoff < 0:
+                firstLine = int(35 - azoff)
+            ampcor.setAcrossGrossOffset(rgoff)
+            ampcor.setDownGrossOffset(azoff)
+            ampcor.setFirstSampleAcross(firstSample)
+            ampcor.setLastSampleAcross(mSLC.width)
+            ampcor.setNumberLocationAcross(numberOfOffsetsRange)
+            ampcor.setFirstSampleDown(firstLine)
+            ampcor.setLastSampleDown(mSLC.length)
+            ampcor.setNumberLocationDown(numberOfOffsetsAzimuth)
+
+            #MATCH PARAMETERS
+            #full-aperture mode
+            if (self._insar.modeCombination == 21) or \
+               (self._insar.modeCombination == 22) or \
+               (self._insar.modeCombination == 31) or \
+               (self._insar.modeCombination == 32):
+                ampcor.setWindowSizeWidth(64)
+                ampcor.setWindowSizeHeight(512)
+                #note this is the half width/length of search area, number of resulting correlation samples: 32*2+1
+                ampcor.setSearchWindowSizeWidth(32)
+                ampcor.setSearchWindowSizeHeight(32)
+                #triggering full-aperture mode matching
+                ampcor.setWinsizeFilt(8)
+                ampcor.setOversamplingFactorFilt(64)
+            #regular mode
+            else:
+                ampcor.setWindowSizeWidth(64)
+                ampcor.setWindowSizeHeight(64)
+                ampcor.setSearchWindowSizeWidth(32)
+                ampcor.setSearchWindowSizeHeight(32)
+
+            #REST OF THE STUFF
+            ampcor.setAcrossLooks(1)
+            ampcor.setDownLooks(1)
+            ampcor.setOversamplingFactor(64)
+            ampcor.setZoomWindowSize(16)
+            #1. The following not set
+            #Matching Scale for Sample/Line Directions                       (-)    = 1. 1.
+            #should add the following in Ampcor.py?
+            #if not set, in this case, Ampcor.py'value is also 1. 1.
+            #ampcor.setScaleFactorX(1.)
+            #ampcor.setScaleFactorY(1.)
+
+            #MATCH THRESHOLDS AND DEBUG DATA
+            #2. The following not set
+            #in roi_pac the value is set to 0 1
+            #in isce the value is set to 0.001 1000.0
+            #SNR and Covariance Thresholds                                   (-)    =  {s1} {s2}
+            #should add the following in Ampcor?
+            #THIS SHOULD BE THE ONLY THING THAT IS DIFFERENT FROM THAT OF ROI_PAC
+            #ampcor.setThresholdSNR(0)
+            #ampcor.setThresholdCov(1)
+            ampcor.setDebugFlag(False)
+            ampcor.setDisplayFlag(False)
+
+            #in summary, only two things not set which are indicated by 'The following not set' above.
+
+            #run ampcor
+            ampcor.ampcor()
+            offsets = ampcor.getOffsetField()
+            ampcorOffsetFile = 'ampcor.off'
+            writeOffset(offsets, ampcorOffsetFile)
+
+            #finalize image, and re-create it
+            #otherwise the file pointer is still at the end of the image
+            mSLC.finalizeImage()
+            sSLC.finalizeImage()
+
+            ##########################################
+            #3. cull offsets
+            ##########################################
+            refinedOffsets = cullOffsets(offsets)
+            if refinedOffsets == None:
+                print('******************************************************************')
+                print('WARNING: There are not enough offsets left, so we are forced to')
+                print('         use offset without culling. frame {}, swath {}'.format(frameNumber, swathNumber))
+                print('******************************************************************')
+                catalog.addItem('warning message', 'not enough offsets left, use offset without culling. frame {} swath {}'.format(frameNumber, swathNumber), 'runSlcOffset')
+                refinedOffsets = offsets
+
+            cullOffsetFile = 'cull.off'
+            writeOffset(refinedOffsets, cullOffsetFile)
+
+            os.chdir('../')
+        os.chdir('../')
+
+    catalog.printToLog(logger, "runSlcOffset")
+    self._insar.procDoc.addAllFromCatalog(catalog)

components/isceobj/Alos2Proc/runSwathMosaic.py

@@ -0,0 +1,574 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import glob
+import logging
+import datetime
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+logger = logging.getLogger('isce.alos2insar.runSwathMosaic')
+
+def runSwathMosaic(self):
+    '''mosaic subswaths
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+
+        mosaicDir = 'mosaic'
+        if not os.path.exists(mosaicDir):
+            os.makedirs(mosaicDir)
+        os.chdir(mosaicDir)
+
+        if not (
+               ((self._insar.modeCombination == 21) or \
+                (self._insar.modeCombination == 22) or \
+                (self._insar.modeCombination == 31) or \
+                (self._insar.modeCombination == 32)) 
+               and
+               (self._insar.endingSwath-self._insar.startingSwath+1 > 1)
+               ):
+            import shutil
+            swathDir = 's{}'.format(masterTrack.frames[i].swaths[0].swathNumber)
+            
+            if not os.path.isfile(self._insar.interferogram):
+                os.symlink(os.path.join('../', swathDir, self._insar.interferogram), self._insar.interferogram)
+            shutil.copy2(os.path.join('../', swathDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+            shutil.copy2(os.path.join('../', swathDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+            if not os.path.isfile(self._insar.amplitude):
+                os.symlink(os.path.join('../', swathDir, self._insar.amplitude), self._insar.amplitude)
+            shutil.copy2(os.path.join('../', swathDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+            shutil.copy2(os.path.join('../', swathDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+            # os.rename(os.path.join('../', swathDir, self._insar.interferogram), self._insar.interferogram)
+            # os.rename(os.path.join('../', swathDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+            # os.rename(os.path.join('../', swathDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+            # os.rename(os.path.join('../', swathDir, self._insar.amplitude), self._insar.amplitude)
+            # os.rename(os.path.join('../', swathDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+            # os.rename(os.path.join('../', swathDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+            #update frame parameters
+            #########################################################
+            frame = masterTrack.frames[i]
+            infImg = isceobj.createImage()
+            infImg.load(self._insar.interferogram+'.xml')
+            #mosaic size
+            frame.numberOfSamples = infImg.width
+            frame.numberOfLines = infImg.length
+            #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+            #range parameters
+            frame.startingRange = frame.swaths[0].startingRange
+            frame.rangeSamplingRate = frame.swaths[0].rangeSamplingRate
+            frame.rangePixelSize = frame.swaths[0].rangePixelSize
+            #azimuth parameters
+            frame.sensingStart = frame.swaths[0].sensingStart
+            frame.prf = frame.swaths[0].prf
+            frame.azimuthPixelSize = frame.swaths[0].azimuthPixelSize
+            frame.azimuthLineInterval = frame.swaths[0].azimuthLineInterval
+
+            #update frame parameters, slave
+            #########################################################
+            frame = slaveTrack.frames[i]
+            #mosaic size
+            frame.numberOfSamples = int(frame.swaths[0].numberOfSamples/self._insar.numberRangeLooks1)
+            frame.numberOfLines = int(frame.swaths[0].numberOfLines/self._insar.numberAzimuthLooks1)
+            #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+            #range parameters
+            frame.startingRange = frame.swaths[0].startingRange
+            frame.rangeSamplingRate = frame.swaths[0].rangeSamplingRate
+            frame.rangePixelSize = frame.swaths[0].rangePixelSize
+            #azimuth parameters
+            frame.sensingStart = frame.swaths[0].sensingStart
+            frame.prf = frame.swaths[0].prf
+            frame.azimuthPixelSize = frame.swaths[0].azimuthPixelSize
+            frame.azimuthLineInterval = frame.swaths[0].azimuthLineInterval
+
+            os.chdir('../')
+
+            #save parameter file
+            self._insar.saveProduct(masterTrack.frames[i], self._insar.masterFrameParameter)
+            self._insar.saveProduct(slaveTrack.frames[i], self._insar.slaveFrameParameter)
+
+            os.chdir('../')
+
+            continue
+
+        #choose offsets
+        numberOfFrames = len(masterTrack.frames)
+        numberOfSwaths = len(masterTrack.frames[i].swaths)
+        if self.swathOffsetMatching:
+            #no need to do this as the API support 2-d list
+            #rangeOffsets = (np.array(self._insar.swathRangeOffsetMatchingMaster)).reshape(numberOfFrames, numberOfSwaths)
+            #azimuthOffsets = (np.array(self._insar.swathAzimuthOffsetMatchingMaster)).reshape(numberOfFrames, numberOfSwaths)
+            rangeOffsets = self._insar.swathRangeOffsetMatchingMaster
+            azimuthOffsets = self._insar.swathAzimuthOffsetMatchingMaster
+
+        else:
+            #rangeOffsets = (np.array(self._insar.swathRangeOffsetGeometricalMaster)).reshape(numberOfFrames, numberOfSwaths)
+            #azimuthOffsets = (np.array(self._insar.swathAzimuthOffsetGeometricalMaster)).reshape(numberOfFrames, numberOfSwaths)
+            rangeOffsets = self._insar.swathRangeOffsetGeometricalMaster
+            azimuthOffsets = self._insar.swathAzimuthOffsetGeometricalMaster
+
+        rangeOffsets = rangeOffsets[i]
+        azimuthOffsets = azimuthOffsets[i]
+
+        #list of input files
+        inputInterferograms = []
+        inputAmplitudes = []
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            inputInterferograms.append(os.path.join('../', swathDir, self._insar.interferogram))
+            inputAmplitudes.append(os.path.join('../', swathDir, self._insar.amplitude))
+
+        #note that frame parameters are updated after mosaicking
+        #mosaic amplitudes
+        swathMosaic(masterTrack.frames[i], inputAmplitudes, self._insar.amplitude, 
+            rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, resamplingMethod=0)
+        #mosaic interferograms
+        swathMosaic(masterTrack.frames[i], inputInterferograms, self._insar.interferogram, 
+            rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, updateFrame=True, resamplingMethod=1)
+
+        create_xml(self._insar.amplitude, masterTrack.frames[i].numberOfSamples, masterTrack.frames[i].numberOfLines, 'amp')
+        create_xml(self._insar.interferogram, masterTrack.frames[i].numberOfSamples, masterTrack.frames[i].numberOfLines, 'int')
+
+        #update slave frame parameters here
+        #no matching for slave, always use geometry
+        rangeOffsets = self._insar.swathRangeOffsetGeometricalSlave
+        azimuthOffsets = self._insar.swathAzimuthOffsetGeometricalSlave
+        rangeOffsets = rangeOffsets[i]
+        azimuthOffsets = azimuthOffsets[i]
+        swathMosaicParameters(slaveTrack.frames[i], rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1)
+
+        os.chdir('../')
+
+        #save parameter file
+        self._insar.saveProduct(masterTrack.frames[i], self._insar.masterFrameParameter)
+        self._insar.saveProduct(slaveTrack.frames[i], self._insar.slaveFrameParameter)
+
+        os.chdir('../')
+
+    catalog.printToLog(logger, "runSwathMosaic")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def swathMosaic(frame, inputFiles, outputfile, rangeOffsets, azimuthOffsets, numberOfRangeLooks, numberOfAzimuthLooks, updateFrame=False, phaseCompensation=False, pcRangeLooks=1, pcAzimuthLooks=4, filt=False, resamplingMethod=0):
+    '''
+    mosaic swaths
+    
+    frame:                 frame
+    inputFiles:            input file list
+    output file:           output mosaic file
+    rangeOffsets:          range offsets
+    azimuthOffsets:        azimuth offsets
+    numberOfRangeLooks:    number of range looks of the input files
+    numberOfAzimuthLooks:  number of azimuth looks of the input files
+    phaseCompensation:     whether do phase compensation for each swath
+    pcRangeLooks:          number of range looks to take when compute swath phase difference
+    pcAzimuthLooks:        number of azimuth looks to take when compute swath phase difference
+    filt:                  whether do filtering when compute swath phase difference
+    resamplingMethod:      0: amp resampling. 1: int resampling.
+    '''
+    from contrib.alos2proc_f.alos2proc_f import rect_with_looks
+    from contrib.alos2proc.alos2proc import mosaicsubswath
+    from isceobj.Alos2Proc.Alos2ProcPublic import multilook
+    from isceobj.Alos2Proc.Alos2ProcPublic import cal_coherence_1
+    from isceobj.Alos2Proc.Alos2ProcPublic import filterInterferogram
+
+    numberOfSwaths = len(frame.swaths)
+    swaths = frame.swaths
+
+    rangeScale = []
+    azimuthScale = []
+    rectWidth = []
+    rectLength = []
+    for i in range(numberOfSwaths):
+        rangeScale.append(swaths[0].rangePixelSize / swaths[i].rangePixelSize)
+        azimuthScale.append(swaths[0].azimuthLineInterval / swaths[i].azimuthLineInterval)
+        if i == 0:
+            rectWidth.append( int(swaths[i].numberOfSamples / numberOfRangeLooks) )
+            rectLength.append( int(swaths[i].numberOfLines / numberOfAzimuthLooks) )
+        else:
+            rectWidth.append( int(1.0 / rangeScale[i] * int(swaths[i].numberOfSamples / numberOfRangeLooks)) )
+            rectLength.append( int(1.0 / azimuthScale[i] * int(swaths[i].numberOfLines / numberOfAzimuthLooks)) )
+
+    #convert original offset to offset for images with looks
+    #use list instead of np.array to make it consistent with the rest of the code
+    rangeOffsets1 = [i/numberOfRangeLooks for i in rangeOffsets]
+    azimuthOffsets1 = [i/numberOfAzimuthLooks for i in azimuthOffsets]
+
+    #get offset relative to the first frame
+    rangeOffsets2 = [0.0]
+    azimuthOffsets2 = [0.0]
+    for i in range(1, numberOfSwaths):
+        rangeOffsets2.append(0.0)
+        azimuthOffsets2.append(0.0)
+        for j in range(1, i+1):
+            rangeOffsets2[i] += rangeOffsets1[j]
+            azimuthOffsets2[i] += azimuthOffsets1[j]
+
+    #resample each swath
+    rinfs = []
+    for i, inf in enumerate(inputFiles):
+        rinfs.append("{}_{}{}".format(os.path.splitext(os.path.basename(inf))[0], i, os.path.splitext(os.path.basename(inf))[1]))
+        #do not resample first swath
+        if i == 0:
+            if os.path.isfile(rinfs[i]):
+                os.remove(rinfs[i])
+            os.symlink(inf, rinfs[i])
+        else:
+            infImg = isceobj.createImage()
+            infImg.load(inf+'.xml')
+            rangeOffsets2Frac = rangeOffsets2[i] - int(rangeOffsets2[i])
+            azimuthOffsets2Frac = azimuthOffsets2[i] - int(azimuthOffsets2[i])
+
+
+            if resamplingMethod == 0:
+                rect_with_looks(inf,
+                                rinfs[i],
+                                infImg.width, infImg.length,
+                                rectWidth[i], rectLength[i],
+                                rangeScale[i], 0.0,
+                                0.0,azimuthScale[i],
+                                rangeOffsets2Frac * rangeScale[i], azimuthOffsets2Frac * azimuthScale[i],
+                                1,1,
+                                1,1,
+                                'COMPLEX',
+                                'Bilinear')
+            elif resamplingMethod == 1:
+                #decompose amplitude and phase
+                phaseFile = 'phase'
+                amplitudeFile = 'amplitude'
+                data = np.fromfile(inf, dtype=np.complex64).reshape(infImg.length, infImg.width)
+                phase = np.exp(np.complex64(1j) * np.angle(data))
+                phase[np.nonzero(data==0)] = 0
+                phase.astype(np.complex64).tofile(phaseFile)
+                amplitude = np.absolute(data)
+                amplitude.astype(np.float32).tofile(amplitudeFile)
+
+                #resampling
+                phaseRectFile = 'phaseRect'
+                amplitudeRectFile = 'amplitudeRect'
+                rect_with_looks(phaseFile,
+                                phaseRectFile,
+                                infImg.width, infImg.length,
+                                rectWidth[i], rectLength[i],
+                                rangeScale[i], 0.0,
+                                0.0,azimuthScale[i],
+                                rangeOffsets2Frac * rangeScale[i], azimuthOffsets2Frac * azimuthScale[i],
+                                1,1,
+                                1,1,
+                                'COMPLEX',
+                                'Sinc')
+                rect_with_looks(amplitudeFile,
+                                amplitudeRectFile,
+                                infImg.width, infImg.length,
+                                rectWidth[i], rectLength[i],
+                                rangeScale[i], 0.0,
+                                0.0,azimuthScale[i],
+                                rangeOffsets2Frac * rangeScale[i], azimuthOffsets2Frac * azimuthScale[i],
+                                1,1,
+                                1,1,
+                                'REAL',
+                                'Bilinear')
+
+                #recombine amplitude and phase
+                phase = np.fromfile(phaseRectFile, dtype=np.complex64).reshape(rectLength[i], rectWidth[i])
+                amplitude = np.fromfile(amplitudeRectFile, dtype=np.float32).reshape(rectLength[i], rectWidth[i])
+                (phase*amplitude).astype(np.complex64).tofile(rinfs[i])
+
+                #tidy up
+                os.remove(phaseFile)
+                os.remove(amplitudeFile)
+                os.remove(phaseRectFile)
+                os.remove(amplitudeRectFile)
+
+
+    #determine output width and length
+    #actually no need to calculate in range direction
+    xs = []
+    xe = []
+    ys = []
+    ye = []
+    for i in range(numberOfSwaths):
+        if i == 0:
+            xs.append(0)
+            xe.append(rectWidth[i] - 1)
+            ys.append(0)
+            ye.append(rectLength[i] - 1)
+        else:
+            xs.append(0 - int(rangeOffsets2[i]))
+            xe.append(rectWidth[i] - 1 - int(rangeOffsets2[i]))
+            ys.append(0 - int(azimuthOffsets2[i]))
+            ye.append(rectLength[i] - 1 - int(azimuthOffsets2[i]))
+
+    (xmin, xminIndex) = min((v,i) for i,v in enumerate(xs))
+    (xmax, xmaxIndex) = max((v,i) for i,v in enumerate(xe))
+    (ymin, yminIndex) = min((v,i) for i,v in enumerate(ys))
+    (ymax, ymaxIndex) = max((v,i) for i,v in enumerate(ye))
+
+    outWidth = xmax - xmin + 1
+    outLength = ymax - ymin + 1
+
+    #prepare offset for mosaicing
+    rangeOffsets3 = []
+    azimuthOffsets3 = []
+    for i in range(numberOfSwaths):
+        azimuthOffsets3.append(int(azimuthOffsets2[i]) - int(azimuthOffsets2[yminIndex]))
+        if i != 0:
+            rangeOffsets3.append(int(rangeOffsets2[i]) - int(rangeOffsets2[i-1]))
+        else:
+            rangeOffsets3.append(0)
+
+
+    delta = int(30 / numberOfRangeLooks)
+
+    #compute compensation phase for each swath
+    diffMean2 = [0.0 for i in range(numberOfSwaths)]
+    if phaseCompensation:
+        #compute swath phase offset
+        diffMean = [0.0]
+        for i in range(1, numberOfSwaths):
+            #all indexes start with zero, all the computed start/end sample/line indexes are included.
+            
+            #no need to add edge here, as we are going to find first/last nonzero sample/lines later
+            #edge = delta
+            edge = 0
+
+            #image i-1
+            startSample1 =  edge + 0 - int(rangeOffsets2[i]) + int(rangeOffsets2[i-1])
+            endSample1   = -edge + rectWidth[i-1]-1
+            startLine1   =  edge + max(0 - int(azimuthOffsets2[i]) + int(azimuthOffsets2[i-1]), 0)
+            endLine1     = -edge + min(rectLength[i]-1 - int(azimuthOffsets2[i]) + int(azimuthOffsets2[i-1]), rectLength[i-1]-1)
+            data1 = readImage(rinfs[i-1], rectWidth[i-1], rectLength[i-1], startSample1, endSample1, startLine1, endLine1)
+
+            #image i
+            startSample2 =  edge + 0
+            endSample2   = -edge + rectWidth[i-1]-1 - int(rangeOffsets2[i-1]) + int(rangeOffsets2[i])
+            startLine2   =  edge + max(0 - int(azimuthOffsets2[i-1]) + int(azimuthOffsets2[i]), 0)
+            endLine2     = -edge + min(rectLength[i-1]-1 - int(azimuthOffsets2[i-1]) + int(azimuthOffsets2[i]), rectLength[i]-1)
+            data2 = readImage(rinfs[i], rectWidth[i], rectLength[i], startSample2, endSample2, startLine2, endLine2)
+
+            #remove edge due to incomplete covolution in resampling
+            edge = 9
+            (startLine0, endLine0, startSample0, endSample0) = findNonzero( np.logical_and((data1!=0), (data2!=0)) )
+            data1 = data1[startLine0+edge:endLine0+1-edge, startSample0+edge:endSample0+1-edge]
+            data2 = data2[startLine0+edge:endLine0+1-edge, startSample0+edge:endSample0+1-edge]
+
+            #take looks
+            data1 = multilook(data1, pcAzimuthLooks, pcRangeLooks)
+            data2 = multilook(data2, pcAzimuthLooks, pcRangeLooks)
+
+            #filter
+            if filt:
+                data1 /= (np.absolute(data1)+(data1==0))
+                data2 /= (np.absolute(data2)+(data2==0))
+                data1 = filterInterferogram(data1, 3.0, 64, 1)
+                data2 = filterInterferogram(data2, 3.0, 64, 1)
+
+
+            #get difference
+            corth = 0.87
+            if filt:
+                corth = 0.90
+            diffMean0 = 0.0
+            for k in range(5):
+                dataDiff = data1 * np.conj(data2)
+                cor = cal_coherence_1(dataDiff, win=3)
+                index = np.nonzero(np.logical_and(cor>corth, dataDiff!=0))
+                if index[0].size < 100:
+                    diffMean0 = 0.0
+                    print('\n\nWARNING: too few high coherence pixels for swath phase difference estimation between swath {} and {}'.format(i-1, i))
+                    print('       : first swath swath number: 0\n\n')
+                    break
+                angle = np.mean(np.angle(dataDiff[index]), dtype=np.float64)
+                diffMean0 += angle
+                data2 *= np.exp(np.complex64(1j) * angle)
+                print('phase offset: %15.12f rad after loop: %3d'%(diffMean0, k))
+
+                DEBUG=False
+                if DEBUG and (k==0):
+                    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+                    (lengthxx, widthxx)=dataDiff.shape
+                    filtnamePrefix = 'subswath{}_subswath{}_loop{}'.format(frame.swaths[i-1].swathNumber, frame.swaths[i].swathNumber, k)
+                    cor.astype(np.float32).tofile(filtnamePrefix+'.cor')
+                    create_xml(filtnamePrefix+'.cor', widthxx, lengthxx, 'float')
+                    dataDiff.astype(np.complex64).tofile(filtnamePrefix+'.int')
+                    create_xml(filtnamePrefix+'.int', widthxx, lengthxx, 'int')
+
+            diffMean.append(diffMean0)
+            print('phase offset: subswath{} - subswath{}: {}'.format(frame.swaths[i-1].swathNumber, frame.swaths[i].swathNumber, diffMean0))
+
+        for i in range(1, numberOfSwaths):
+            for j in range(1, i+1):
+                diffMean2[i] += diffMean[j]
+
+
+    #mosaic swaths
+    diffflag = 1
+    oflag = [0 for i in range(numberOfSwaths)]
+    mosaicsubswath(outputfile, outWidth, outLength, delta, diffflag, numberOfSwaths, 
+        rinfs, rectWidth, rangeOffsets3, azimuthOffsets3, diffMean2, oflag)
+    #remove tmp files
+    for x in rinfs:
+        os.remove(x)
+
+
+    #update frame parameters
+    if updateFrame:
+        #mosaic size
+        frame.numberOfSamples = outWidth
+        frame.numberOfLines = outLength
+        #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+        #range parameters
+        frame.startingRange = frame.swaths[0].startingRange
+        frame.rangeSamplingRate = frame.swaths[0].rangeSamplingRate
+        frame.rangePixelSize = frame.swaths[0].rangePixelSize
+        #azimuth parameters
+        azimuthTimeOffset = - max([int(x) for x in azimuthOffsets2]) * numberOfAzimuthLooks * frame.swaths[0].azimuthLineInterval
+        frame.sensingStart = frame.swaths[0].sensingStart + datetime.timedelta(seconds = azimuthTimeOffset)
+        frame.prf = frame.swaths[0].prf
+        frame.azimuthPixelSize = frame.swaths[0].azimuthPixelSize
+        frame.azimuthLineInterval = frame.swaths[0].azimuthLineInterval
+
+
+def swathMosaicParameters(frame, rangeOffsets, azimuthOffsets, numberOfRangeLooks, numberOfAzimuthLooks):
+    '''
+    mosaic swaths (this is simplified version of swathMosaic to update parameters only)
+    
+    frame:                 frame
+    rangeOffsets:          range offsets
+    azimuthOffsets:        azimuth offsets
+    numberOfRangeLooks:    number of range looks of the input files
+    numberOfAzimuthLooks:  number of azimuth looks of the input files
+    '''
+
+    numberOfSwaths = len(frame.swaths)
+    swaths = frame.swaths
+
+    rangeScale = []
+    azimuthScale = []
+    rectWidth = []
+    rectLength = []
+    for i in range(numberOfSwaths):
+        rangeScale.append(swaths[0].rangePixelSize / swaths[i].rangePixelSize)
+        azimuthScale.append(swaths[0].azimuthLineInterval / swaths[i].azimuthLineInterval)
+        if i == 0:
+            rectWidth.append( int(swaths[i].numberOfSamples / numberOfRangeLooks) )
+            rectLength.append( int(swaths[i].numberOfLines / numberOfAzimuthLooks) )
+        else:
+            rectWidth.append( int(1.0 / rangeScale[i] * int(swaths[i].numberOfSamples / numberOfRangeLooks)) )
+            rectLength.append( int(1.0 / azimuthScale[i] * int(swaths[i].numberOfLines / numberOfAzimuthLooks)) )
+
+    #convert original offset to offset for images with looks
+    #use list instead of np.array to make it consistent with the rest of the code
+    rangeOffsets1 = [i/numberOfRangeLooks for i in rangeOffsets]
+    azimuthOffsets1 = [i/numberOfAzimuthLooks for i in azimuthOffsets]
+
+    #get offset relative to the first frame
+    rangeOffsets2 = [0.0]
+    azimuthOffsets2 = [0.0]
+    for i in range(1, numberOfSwaths):
+        rangeOffsets2.append(0.0)
+        azimuthOffsets2.append(0.0)
+        for j in range(1, i+1):
+            rangeOffsets2[i] += rangeOffsets1[j]
+            azimuthOffsets2[i] += azimuthOffsets1[j]
+
+    #determine output width and length
+    #actually no need to calculate in range direction
+    xs = []
+    xe = []
+    ys = []
+    ye = []
+    for i in range(numberOfSwaths):
+        if i == 0:
+            xs.append(0)
+            xe.append(rectWidth[i] - 1)
+            ys.append(0)
+            ye.append(rectLength[i] - 1)
+        else:
+            xs.append(0 - int(rangeOffsets2[i]))
+            xe.append(rectWidth[i] - 1 - int(rangeOffsets2[i]))
+            ys.append(0 - int(azimuthOffsets2[i]))
+            ye.append(rectLength[i] - 1 - int(azimuthOffsets2[i]))
+
+    (xmin, xminIndex) = min((v,i) for i,v in enumerate(xs))
+    (xmax, xmaxIndex) = max((v,i) for i,v in enumerate(xe))
+    (ymin, yminIndex) = min((v,i) for i,v in enumerate(ys))
+    (ymax, ymaxIndex) = max((v,i) for i,v in enumerate(ye))
+
+    outWidth = xmax - xmin + 1
+    outLength = ymax - ymin + 1
+
+    #update frame parameters
+    #mosaic size
+    frame.numberOfSamples = outWidth
+    frame.numberOfLines = outLength
+    #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+    #range parameters
+    frame.startingRange = frame.swaths[0].startingRange
+    frame.rangeSamplingRate = frame.swaths[0].rangeSamplingRate
+    frame.rangePixelSize = frame.swaths[0].rangePixelSize
+    #azimuth parameters
+    azimuthTimeOffset = - max([int(x) for x in azimuthOffsets2]) * numberOfAzimuthLooks * frame.swaths[0].azimuthLineInterval
+    frame.sensingStart = frame.swaths[0].sensingStart + datetime.timedelta(seconds = azimuthTimeOffset)
+    frame.prf = frame.swaths[0].prf
+    frame.azimuthPixelSize = frame.swaths[0].azimuthPixelSize
+    frame.azimuthLineInterval = frame.swaths[0].azimuthLineInterval
+
+
+def readImage(inputfile, numberOfSamples, numberOfLines, startSample, endSample, startLine, endLine):
+    '''
+    read a chunk of image
+    the indexes (startSample, endSample, startLine, endLine) are included and start with zero
+
+    memmap is not used, because it is much slower
+    '''
+    data = np.zeros((endLine-startLine+1, endSample-startSample+1), dtype=np.complex64)
+    with open(inputfile,'rb') as fp:
+        #for i in range(endLine-startLine+1):
+        for i in range(startLine, endLine+1):
+            fp.seek((i*numberOfSamples+startSample)*8, 0)
+            data[i-startLine] = np.fromfile(fp, dtype=np.complex64, count=endSample-startSample+1)
+    return data
+
+
+def findNonzero_v1(data):
+    '''
+    find the first/last non-zero line/sample
+    all indexes start from zero
+    '''
+    indexes = np.nonzero(data)
+
+           #first line     last line       first sample    last sample
+    return (indexes[0][0], indexes[0][-1], indexes[1][0], indexes[1][-1])
+
+
+def findNonzero(data, lineRatio=0.5, sampleRatio=0.5):
+    '''
+    find the first/last non-zero line/sample
+    all indexes start from zero
+    '''
+    import numpy as np
+    
+    (length, width)=data.shape
+
+    lineIndex = (np.nonzero(np.sum((data!=0), axis=1) > width*lineRatio))[0]
+    sampleIndex = (np.nonzero(np.sum((data!=0), axis=0) > length*sampleRatio))[0]
+
+           #first line     last line       first sample    last sample
+    return (lineIndex[0], lineIndex[-1], sampleIndex[0], sampleIndex[-1])
+
+

components/isceobj/Alos2Proc/runSwathOffset.py

@@ -0,0 +1,390 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import glob
+import logging
+import datetime
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import multilook
+
+
+logger = logging.getLogger('isce.alos2insar.runSwathOffset')
+
+def runSwathOffset(self):
+    '''estimate swath offsets.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+
+        mosaicDir = 'mosaic'
+        if not os.path.exists(mosaicDir):
+            os.makedirs(mosaicDir)
+        os.chdir(mosaicDir)
+
+        if not (
+               ((self._insar.modeCombination == 21) or \
+                (self._insar.modeCombination == 22) or \
+                (self._insar.modeCombination == 31) or \
+                (self._insar.modeCombination == 32)) 
+               and
+               (self._insar.endingSwath-self._insar.startingSwath+1 > 1)
+               ):
+
+            os.chdir('../../')
+
+            continue
+
+        #compute swath offset
+        offsetMaster = swathOffset(masterTrack.frames[i], self._insar.masterSlc, self._insar.masterSwathOffset, 
+                                   crossCorrelation=self.swathOffsetMatching, numberOfAzimuthLooks=10)
+        #only use geometrical offset for slave
+        offsetSlave = swathOffset(slaveTrack.frames[i], self._insar.slaveSlc, self._insar.slaveSwathOffset, 
+                                  crossCorrelation=False, numberOfAzimuthLooks=10)
+
+        #initialization
+        if i == 0:
+            self._insar.swathRangeOffsetGeometricalMaster = []
+            self._insar.swathAzimuthOffsetGeometricalMaster = []
+            self._insar.swathRangeOffsetGeometricalSlave = []
+            self._insar.swathAzimuthOffsetGeometricalSlave = []
+            if self.swathOffsetMatching:
+                self._insar.swathRangeOffsetMatchingMaster = []
+                self._insar.swathAzimuthOffsetMatchingMaster = []
+                #self._insar.swathRangeOffsetMatchingSlave = []
+                #self._insar.swathAzimuthOffsetMatchingSlave = []
+
+        #append list directly, as the API support 2-d list
+        self._insar.swathRangeOffsetGeometricalMaster.append(offsetMaster[0])
+        self._insar.swathAzimuthOffsetGeometricalMaster.append(offsetMaster[1])
+        self._insar.swathRangeOffsetGeometricalSlave.append(offsetSlave[0])
+        self._insar.swathAzimuthOffsetGeometricalSlave.append(offsetSlave[1])
+        if self.swathOffsetMatching:
+            self._insar.swathRangeOffsetMatchingMaster.append(offsetMaster[2])
+            self._insar.swathAzimuthOffsetMatchingMaster.append(offsetMaster[3])
+            #self._insar.swathRangeOffsetMatchingSlave.append(offsetSlave[2])
+            #self._insar.swathAzimuthOffsetMatchingSlave.append(offsetSlave[3])
+
+        os.chdir('../../')
+
+    catalog.printToLog(logger, "runSwathOffset")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def swathOffset(frame, image, outputfile, crossCorrelation=True, numberOfAzimuthLooks=10):
+    '''
+    compute swath offset
+    frame:                frame object
+    image:                image for doing matching
+    outputfile:           output txt file for saving swath offset
+    crossCorrelation:     whether do matching
+    numberOfAzimuthLooks: number of looks to take in azimuth before matching
+    '''
+
+    rangeOffsetGeometrical = []
+    azimuthOffsetGeometrical = []
+    rangeOffsetMatching = []
+    azimuthOffsetMatching = []
+
+    for j in range(len(frame.swaths)):
+        frameNumber = frame.frameNumber
+        swathNumber = frame.swaths[j].swathNumber
+        swathDir = 's{}'.format(swathNumber)
+
+        print('estimate offset frame {}, swath {}'.format(frameNumber, swathNumber))
+
+        if j == 0:
+            rangeOffsetGeometrical.append(0.0)
+            azimuthOffsetGeometrical.append(0.0)
+            rangeOffsetMatching.append(0.0)
+            azimuthOffsetMatching.append(0.0)
+            swathDirLast = swathDir
+            continue
+
+        image1 = os.path.join('../', swathDirLast, image)
+        image2 = os.path.join('../', swathDir, image)
+        swath0 = frame.swaths[0]
+        swath1 = frame.swaths[j-1]
+        swath2 = frame.swaths[j]
+
+        rangeScale1   = swath0.rangePixelSize / swath1.rangePixelSize
+        azimuthScale1 = swath0.azimuthLineInterval / swath1.azimuthLineInterval
+        rangeScale2   = swath0.rangePixelSize / swath2.rangePixelSize
+        azimuthScale2 = swath0.azimuthLineInterval / swath2.azimuthLineInterval
+
+        #offset from geometry
+        offsetGeometrical = computeSwathOffset(swath1, swath2, rangeScale1, azimuthScale1)
+        rangeOffsetGeometrical.append(offsetGeometrical[0])
+        azimuthOffsetGeometrical.append(offsetGeometrical[1])
+
+        #offset from cross-correlation
+        if crossCorrelation:
+            offsetMatching = estimateSwathOffset(swath1, swath2, image1, image2, rangeScale1, 
+                                                 azimuthScale1, rangeScale2, azimuthScale2, numberOfAzimuthLooks)
+            if offsetMatching != None:
+                rangeOffsetMatching.append(offsetMatching[0])
+                azimuthOffsetMatching.append(offsetMatching[1])
+            else:
+                print('******************************************************************')
+                print('WARNING: bad matching offset, we are forced to use')
+                print('         geometrical offset for swath mosaicking')
+                print('******************************************************************')
+                rangeOffsetMatching.append(offsetGeometrical[0])
+                azimuthOffsetMatching.append(offsetGeometrical[1])
+
+        swathDirLast = swathDir
+
+
+    if crossCorrelation:
+        offsetComp = "\n\ncomparision of offsets:\n\n"
+        offsetComp += "offset type       i     geometrical           match      difference\n"
+        offsetComp += "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+        for i, (offset1, offset2) in enumerate(zip(rangeOffsetGeometrical, rangeOffsetMatching)):
+            offsetComp += "range offset     {:2d}   {:13.3f}   {:13.3f}   {:13.3f}\n".format(i, offset1, offset2, offset1 - offset2)
+        for i, (offset1, offset2) in enumerate(zip(azimuthOffsetGeometrical, azimuthOffsetMatching)):
+            offsetComp += "azimuth offset   {:2d}   {:13.3f}   {:13.3f}   {:13.3f}\n".format(i, offset1, offset2, offset1 - offset2)
+
+        #write and report offsets
+        with open(outputfile, 'w') as f:
+            f.write(offsetComp)
+        print("{}".format(offsetComp))
+
+
+    if crossCorrelation:
+        return (rangeOffsetGeometrical, azimuthOffsetGeometrical, rangeOffsetMatching, azimuthOffsetMatching)
+    else:
+        return (rangeOffsetGeometrical, azimuthOffsetGeometrical)
+
+
+def computeSwathOffset(swath1, swath2, rangeScale1=1, azimuthScale1=1):
+
+    rangeOffset = -(swath2.startingRange - swath1.startingRange) / swath1.rangePixelSize
+    azimuthOffset = -((swath2.sensingStart - swath1.sensingStart).total_seconds()) / swath1.azimuthLineInterval
+
+    rangeOffset /= rangeScale1
+    azimuthOffset /= azimuthScale1
+
+    return (rangeOffset, azimuthOffset)
+
+
+def estimateSwathOffset(swath1, swath2, image1, image2, rangeScale1=1, azimuthScale1=1, rangeScale2=1, azimuthScale2=1, numberOfAzimuthLooks=10):
+    '''
+    estimate offset of two adjacent swaths using matching
+    '''
+    from osgeo import gdal
+    import isceobj
+    from contrib.alos2proc_f.alos2proc_f import rect_with_looks
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+    from isceobj.Alos2Proc.Alos2ProcPublic import cullOffsets
+    from isceobj.Alos2Proc.Alos2ProcPublic import meanOffset
+    from mroipac.ampcor.Ampcor import Ampcor
+
+    
+    #processing image 1
+    rangeOff1 = int((swath2.startingRange - swath1.startingRange) / swath1.rangePixelSize)
+    if rangeOff1 < 0:
+        rangeOff1 = 0
+    numberOfSamples1 = swath1.numberOfSamples - rangeOff1
+
+    numberOfSamplesRect1 = int(numberOfSamples1/rangeScale1)
+    numberOfLinesRect1 = int(swath1.numberOfLines/azimuthScale1)
+
+    numberOfSamplesLook1 = int(numberOfSamplesRect1/1)
+    numberOfLinesLook1 = int(numberOfLinesRect1/numberOfAzimuthLooks)
+
+    #get magnitude image whether complex or not
+    #ReadAsArray: https://pcjericks.github.io/py-gdalogr-cookbook/raster_layers.html
+    ds = gdal.Open(image1 + '.vrt', gdal.GA_ReadOnly)
+    data = ds.ReadAsArray(rangeOff1, 0, numberOfSamples1, swath1.numberOfLines)
+    ds = None
+    (np.absolute(data)).astype(np.float32).tofile('image1.float')
+
+    #rectify
+    if rangeScale1 == 1 and azimuthScale1 == 1:
+        os.rename('image1.float', 'image1_rect.float')
+    else:
+        rect_with_looks('image1.float',
+                        'image1_rect.float',
+                        numberOfSamples1, swath1.numberOfLines,
+                        numberOfSamplesRect1, numberOfLinesRect1,
+                        rangeScale1, 0.0,
+                        0.0,azimuthScale1,
+                        0.0,0.0,
+                        1,1,
+                        1,1,
+                        'REAL',
+                        'Bilinear')
+        os.remove('image1.float')
+
+    #take looks
+    if numberOfAzimuthLooks == 1:
+        os.rename('image1_rect.float', 'image1_look.float')
+    else:
+        data1 = np.fromfile('image1_rect.float', dtype=np.float32).reshape(numberOfLinesRect1, numberOfSamplesRect1)
+        data1 = np.sqrt(multilook(data1**2, numberOfAzimuthLooks, 1))
+        data1.astype(np.float32).tofile('image1_look.float')
+        os.remove('image1_rect.float')
+    create_xml('image1_look.float', numberOfSamplesLook1, numberOfLinesLook1, 'float')
+
+
+    #processing image 2
+    rangeOff2 = 0
+    numberOfSamples2 = int((swath1.startingRange + swath1.rangePixelSize * (swath1.numberOfSamples - 1) - swath2.startingRange) / swath2.rangePixelSize) + 1
+    if numberOfSamples2 > swath2.numberOfSamples:
+        numberOfSamples2 = swath2.numberOfSamples
+
+    numberOfSamplesRect2 = int(numberOfSamples2/rangeScale2)
+    numberOfLinesRect2 = int(swath2.numberOfLines/azimuthScale2)
+
+    numberOfSamplesLook2 = int(numberOfSamplesRect2/1)
+    numberOfLinesLook2 = int(numberOfLinesRect2/numberOfAzimuthLooks)
+
+    #get magnitude image whether complex or not
+    ds = gdal.Open(image2 + '.vrt', gdal.GA_ReadOnly)
+    data = ds.ReadAsArray(rangeOff2, 0, numberOfSamples2, swath2.numberOfLines)
+    ds = None
+    (np.absolute(data)).astype(np.float32).tofile('image2.float')
+
+    #rectify
+    if rangeScale2 == 1 and azimuthScale2 == 1:
+        os.rename('image2.float', 'image2_rect.float')
+    else:
+        rect_with_looks('image2.float',
+                        'image2_rect.float',
+                        numberOfSamples2, swath2.numberOfLines,
+                        numberOfSamplesRect2, numberOfLinesRect2,
+                        rangeScale2, 0.0,
+                        0.0,azimuthScale2,
+                        0.0,0.0,
+                        1,1,
+                        1,1,
+                        'REAL',
+                        'Bilinear')
+        os.remove('image2.float')
+
+    #take looks
+    if numberOfAzimuthLooks == 1:
+        os.rename('image2_rect.float', 'image2_look.float')
+    else:
+        data2 = np.fromfile('image2_rect.float', dtype=np.float32).reshape(numberOfLinesRect2, numberOfSamplesRect2)
+        data2 = np.sqrt(multilook(data2**2, numberOfAzimuthLooks, 1))
+        data2.astype(np.float32).tofile('image2_look.float')
+        os.remove('image2_rect.float')
+    create_xml('image2_look.float', numberOfSamplesLook2, numberOfLinesLook2, 'float')
+
+
+    #matching
+    ampcor = Ampcor(name='insarapp_slcs_ampcor')
+    ampcor.configure()
+
+    mMag = isceobj.createImage()
+    mMag.load('image1_look.float.xml')
+    mMag.setAccessMode('read')
+    mMag.createImage()
+
+    sMag = isceobj.createImage()
+    sMag.load('image2_look.float.xml')
+    sMag.setAccessMode('read')
+    sMag.createImage()
+
+    ampcor.setImageDataType1('real')
+    ampcor.setImageDataType2('real')
+
+    ampcor.setMasterSlcImage(mMag)
+    ampcor.setSlaveSlcImage(sMag)
+
+    #MATCH REGION
+    rgoff = 0
+    azoff = int((swath1.sensingStart - swath2.sensingStart).total_seconds() / swath1.azimuthLineInterval / azimuthScale1 / numberOfAzimuthLooks)
+    #it seems that we cannot use 0, haven't look into the problem
+    if rgoff == 0:
+        rgoff = 1
+    if azoff == 0:
+        azoff = 1
+    firstSample = 1
+    if rgoff < 0:
+        firstSample = int(35 - rgoff)
+    firstLine = 1
+    if azoff < 0:
+        firstLine = int(35 - azoff)
+    ampcor.setAcrossGrossOffset(rgoff)
+    ampcor.setDownGrossOffset(azoff)
+    ampcor.setFirstSampleAcross(firstSample)
+    ampcor.setLastSampleAcross(numberOfSamplesLook1)
+    ampcor.setNumberLocationAcross(20)
+    ampcor.setFirstSampleDown(firstLine)
+    ampcor.setLastSampleDown(numberOfLinesLook1)
+    ampcor.setNumberLocationDown(100)
+
+    #MATCH PARAMETERS
+    ampcor.setWindowSizeWidth(32)
+    ampcor.setWindowSizeHeight(32)
+    #note this is the half width/length of search area, so number of resulting correlation samples: 8*2+1
+    ampcor.setSearchWindowSizeWidth(8)
+    ampcor.setSearchWindowSizeHeight(8)
+
+    #REST OF THE STUFF
+    ampcor.setAcrossLooks(1)
+    ampcor.setDownLooks(1)
+    ampcor.setOversamplingFactor(64)
+    ampcor.setZoomWindowSize(16)
+    #1. The following not set
+    #Matching Scale for Sample/Line Directions                       (-)    = 1. 1.
+    #should add the following in Ampcor.py?
+    #if not set, in this case, Ampcor.py'value is also 1. 1.
+    #ampcor.setScaleFactorX(1.)
+    #ampcor.setScaleFactorY(1.)
+
+    #MATCH THRESHOLDS AND DEBUG DATA
+    #2. The following not set
+    #in roi_pac the value is set to 0 1
+    #in isce the value is set to 0.001 1000.0
+    #SNR and Covariance Thresholds                                   (-)    =  {s1} {s2}
+    #should add the following in Ampcor?
+    #THIS SHOULD BE THE ONLY THING THAT IS DIFFERENT FROM THAT OF ROI_PAC
+    #ampcor.setThresholdSNR(0)
+    #ampcor.setThresholdCov(1)
+    ampcor.setDebugFlag(False)
+    ampcor.setDisplayFlag(False)
+
+    #in summary, only two things not set which are indicated by 'The following not set' above.
+
+    #run ampcor
+    ampcor.ampcor()
+    offsets = ampcor.getOffsetField()
+    refinedOffsets = cullOffsets(offsets)
+
+    #finalize image, and re-create it
+    #otherwise the file pointer is still at the end of the image
+    mMag.finalizeImage()
+    sMag.finalizeImage()
+
+    os.remove('image1_look.float')
+    os.remove('image1_look.float.vrt')
+    os.remove('image1_look.float.xml')
+    os.remove('image2_look.float')
+    os.remove('image2_look.float.vrt')
+    os.remove('image2_look.float.xml')
+
+    if refinedOffsets != None:
+        rangeOffset, azimuthOffset = meanOffset(refinedOffsets)
+        rangeOffset   -= rangeOff1/rangeScale1
+        azimuthOffset *= numberOfAzimuthLooks
+        return (rangeOffset, azimuthOffset)
+    else:
+        return None
+
+
+
+

components/isceobj/Alos2Proc/runUnwrapSnaphu.py

@@ -0,0 +1,91 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import shutil
+import logging
+import datetime
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import snaphuUnwrap
+from isceobj.Alos2Proc.Alos2ProcPublic import snaphuUnwrapOriginal
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+
+logger = logging.getLogger('isce.alos2insar.runUnwrapSnaphu')
+
+def runUnwrapSnaphu(self):
+    '''unwrap filtered interferogram
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    #slaveTrack = self._insar.loadTrack(master=False)
+
+    insarDir = 'insar'
+    if not os.path.exists(insarDir):
+        os.makedirs(insarDir)
+    os.chdir(insarDir)
+
+
+    ############################################################
+    # STEP 1. unwrap interferogram
+    ############################################################
+    if shutil.which('snaphu') != None:
+        print('\noriginal snaphu program found')
+        print('unwrap {} using original snaphu, rather than that in ISCE'.format(self._insar.filteredInterferogram))
+        snaphuUnwrapOriginal(self._insar.filteredInterferogram, 
+            self._insar.multilookPhsig, 
+            self._insar.multilookAmplitude, 
+            self._insar.unwrappedInterferogram, 
+            costMode = 's', 
+            initMethod = 'mcf')
+    else:
+        tmid = masterTrack.sensingStart + datetime.timedelta(seconds=(self._insar.numberAzimuthLooks1-1.0)/2.0*masterTrack.azimuthLineInterval+
+               masterTrack.numberOfLines/2.0*self._insar.numberAzimuthLooks1*masterTrack.azimuthLineInterval)
+        snaphuUnwrap(masterTrack, tmid, 
+            self._insar.filteredInterferogram, 
+            self._insar.multilookPhsig, 
+            self._insar.unwrappedInterferogram, 
+            self._insar.numberRangeLooks1*self._insar.numberRangeLooks2, 
+            self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooks2, 
+            costMode = 'SMOOTH',initMethod = 'MCF', defomax = 2, initOnly = True)
+
+
+    ############################################################
+    # STEP 2. mask using connected components
+    ############################################################
+    cmd = "imageMath.py -e='a_0*(b>0);a_1*(b>0)' --a={} --b={} -s BIL -t float -o={}".format(self._insar.unwrappedInterferogram, self._insar.unwrappedInterferogram+'.conncomp', self._insar.unwrappedMaskedInterferogram)
+    runCmd(cmd)
+
+
+    ############################################################
+    # STEP 3. mask using water body
+    ############################################################
+
+    if self.waterBodyMaskStartingStep=='unwrap':
+        wbdImage = isceobj.createImage()
+        wbdImage.load(self._insar.multilookWbdOut+'.xml')
+        width = wbdImage.width
+        length = wbdImage.length
+        if not os.path.exists(self._insar.multilookWbdOut):
+            catalog.addItem('warning message', 'requested masking interferogram with water body, but water body does not exist', 'runUnwrapSnaphu')
+        else:
+            wbd = np.fromfile(self._insar.multilookWbdOut, dtype=np.int8).reshape(length, width)
+            unw=np.memmap(self._insar.unwrappedInterferogram, dtype='float32', mode='r+', shape=(length*2, width))
+            (unw[0:length*2:2, :])[np.nonzero(wbd==-1)]=0
+            (unw[1:length*2:2, :])[np.nonzero(wbd==-1)]=0
+            del unw
+            unw=np.memmap(self._insar.unwrappedMaskedInterferogram, dtype='float32', mode='r+', shape=(length*2, width))
+            (unw[0:length*2:2, :])[np.nonzero(wbd==-1)]=0
+            (unw[1:length*2:2, :])[np.nonzero(wbd==-1)]=0
+            del unw, wbd
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runUnwrapSnaphu")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+

components/isceobj/Alos2burstProc/CMakeLists.txt

@@ -0,0 +1,19 @@
+InstallSameDir(
+    __init__.py
+    Factories.py
+    Alos2burstProc.py
+    runPreprocessor.py
+    runExtractBurst.py
+    runCoregGeom.py
+    runCoregCc.py
+    runCoregSd.py
+    runSwathOffset.py
+    runSwathMosaic.py
+    runFrameOffset.py
+    runFrameMosaic.py
+    runIonSubband.py
+    runLookSd.py
+    runFiltSd.py
+    runUnwrapSnaphuSd.py
+    runGeocodeSd.py
+    )

components/isceobj/Alos2burstProc/Factories.py

@@ -0,0 +1,114 @@
+#
+# Author: Piyush Agram
+# Copyright 2016
+#
+
+# Path to the _RunWrapper factories
+_PATH = "isceobj.Alos2burstProc."
+
+## A factory to make _RunWrapper factories
+def _factory(name, other_name=None, path=_PATH):
+    """create_run_wrapper = _factory(name)
+    name is the module and class function name
+    """
+    other_name = other_name or name
+    module = __import__(
+        path+name, fromlist=[""]
+        )
+    cls = getattr(module, other_name)
+    def creater(other, *args, **kwargs):
+        """_RunWrapper for object calling %s"""
+        return _RunWrapper(other, cls)
+    return creater
+
+## Put in "_" to prevernt import on "from Factorties import *"
+class _RunWrapper(object):
+    """_RunWrapper(other, func)(*args, **kwargs)
+
+    executes:
+
+    func(other, *args, **kwargs)
+
+    (like a method)
+    """
+    def __init__(self, other, func):
+        self.method = func
+        self.other = other
+        return None
+
+    def __call__(self, *args, **kwargs):
+        return self.method(self.other, *args, **kwargs)
+
+    pass
+
+def createUnwrapper(other, do_unwrap = None, unwrapperName = None,
+                    unwrap = None):
+    if not do_unwrap and not unwrap:
+        #if not defined create an empty method that does nothing
+        def runUnwrap(self):
+            return None
+    elif unwrapperName.lower() == 'snaphu':
+        from .runUnwrapSnaphu import runUnwrap
+    elif unwrapperName.lower() == 'snaphu_mcf':
+        from .runUnwrapSnaphu import runUnwrapMcf as runUnwrap
+    elif unwrapperName.lower() == 'downsample_snaphu':
+        from .run_downsample_unwrapper import runUnwrap
+    elif unwrapperName.lower() == 'icu':
+        from .runUnwrapIcu import runUnwrap
+    elif unwrapperName.lower() == 'grass':
+        from .runUnwrapGrass import runUnwrap
+    return _RunWrapper(other, runUnwrap)
+
+def createUnwrap2Stage(other, do_unwrap_2stage = None, unwrapperName = None):
+    if (not do_unwrap_2stage) or (unwrapperName.lower() == 'icu') or (unwrapperName.lower() == 'grass'):
+        #if not defined create an empty method that does nothing
+        def runUnwrap2Stage(*arg, **kwargs):
+            return None
+    else:
+      try:
+        import pulp
+        from .runUnwrap2Stage import runUnwrap2Stage
+      except ImportError:
+        raise Exception('Please install PuLP Linear Programming API to run 2stage unwrap')
+    return _RunWrapper(other, runUnwrap2Stage)
+
+
+createPreprocessor = _factory("runPreprocessor")
+createExtractBurst = _factory("runExtractBurst")
+createDownloadDem = _factory("runDownloadDem", path = "isceobj.Alos2Proc.")
+createCoregGeom = _factory("runCoregGeom")
+createCoregCc = _factory("runCoregCc")
+createCoregSd = _factory("runCoregSd")
+createSwathOffset = _factory("runSwathOffset")
+createSwathMosaic = _factory("runSwathMosaic")
+createFrameOffset = _factory("runFrameOffset")
+createFrameMosaic = _factory("runFrameMosaic")
+createRdr2Geo = _factory("runRdr2Geo", path = "isceobj.Alos2Proc.")
+createGeo2Rdr = _factory("runGeo2Rdr", path = "isceobj.Alos2Proc.")
+createRdrDemOffset = _factory("runRdrDemOffset", path = "isceobj.Alos2Proc.")
+createRectRangeOffset = _factory("runRectRangeOffset", path = "isceobj.Alos2Proc.")
+createDiffInterferogram = _factory("runDiffInterferogram", path = "isceobj.Alos2Proc.")
+createLook = _factory("runLook", path = "isceobj.Alos2Proc.")
+createCoherence = _factory("runCoherence", path = "isceobj.Alos2Proc.")
+createIonSubband = _factory("runIonSubband")
+createIonUwrap = _factory("runIonUwrap", path = "isceobj.Alos2Proc.")
+createIonFilt = _factory("runIonFilt", path = "isceobj.Alos2Proc.")
+createFilt = _factory("runFilt", path = "isceobj.Alos2Proc.")
+createUnwrapSnaphu = _factory("runUnwrapSnaphu", path = "isceobj.Alos2Proc.")
+createGeocode = _factory("runGeocode", path = "isceobj.Alos2Proc.")
+
+createLookSd = _factory("runLookSd")
+createFiltSd = _factory("runFiltSd")
+createUnwrapSnaphuSd = _factory("runUnwrapSnaphuSd")
+createGeocodeSd = _factory("runGeocodeSd")
+
+
+# steps imported from: Alos2Proc
+# ##############################################################
+# there is only problem with (at start of script):
+# logger = logging.getLogger('isce.alos2insar.runDownloadDem')
+# but it looks like OK.
+
+
+
+

components/isceobj/Alos2burstProc/SConscript

@@ -0,0 +1,45 @@
+#! /usr/bin/env python
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# Copyright 2012 California Institute of Technology. ALL RIGHTS RESERVED.
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# 
+# United States Government Sponsorship acknowledged. This software is subject to
+# U.S. export control laws and regulations and has been classified as 'EAR99 NLR'
+# (No [Export] License Required except when exporting to an embargoed country,
+# end user, or in support of a prohibited end use). By downloading this software,
+# the user agrees to comply with all applicable U.S. export laws and regulations.
+# The user has the responsibility to obtain export licenses, or other export
+# authority as may be required before exporting this software to any 'EAR99'
+# embargoed foreign country or citizen of those countries.
+#
+# Author: Eric Gurrola
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+
+
+
+
+#!/usr/bin/env python
+import os
+
+Import('envisceobj')
+package = envisceobj['PACKAGE']
+project = 'Alos2burstProc'
+
+install = os.path.join(envisceobj['PRJ_SCONS_INSTALL'],package,project)
+
+listFiles = ['__init__.py', 'Factories.py', 'Alos2burstProc.py', 'runPreprocessor.py', 'runExtractBurst.py', 'runCoregGeom.py', 'runCoregCc.py', 'runCoregSd.py', 'runSwathOffset.py', 'runSwathMosaic.py', 'runFrameOffset.py', 'runFrameMosaic.py', 'runIonSubband.py', 'runLookSd.py', 'runFiltSd.py', 'runUnwrapSnaphuSd.py', 'runGeocodeSd.py']
+envisceobj.Install(install,listFiles)
+envisceobj.Alias('install',install)

components/isceobj/Alos2burstProc/__init__.py

@@ -0,0 +1,22 @@
+#
+# Author: Piyush Agram
+# Copyright 2016
+#
+
+from .Alos2burstProc import *
+from .Factories import *
+
+def getFactoriesInfo():
+    return  {'Alos2burstProc':
+                     {'args':
+                           {
+                            'procDoc':{'value':None,'type':'Catalog','optional':True}
+                            },
+                     'factory':'createAlos2burstProc'                     
+                     }
+              
+              }
+
+def createAlos2burstProc(name=None, procDoc= None):
+    from .Alos2burstProc import Alos2burstProc
+    return Alos2burstProc(name = name,procDoc = procDoc)

components/isceobj/Alos2burstProc/readme.txt

@@ -0,0 +1,13 @@
+order of Doppler and azimuth FM rate polynomials
+##############################################################
+while Doppler and azimuth FM rate polynomials support 3rd order, try to use smaller order,
+because (range sample number)^3 can be very large. There may be float point error that is too
+large?
+
+
+
+
+
+
+
+

components/isceobj/Alos2burstProc/runCoregCc.py

@@ -0,0 +1,306 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import copy
+import shutil
+import logging
+import numpy as np
+
+import isceobj
+from mroipac.ampcor.Ampcor import Ampcor
+from isceobj.Alos2Proc.Alos2ProcPublic import cullOffsetsRoipac
+from isceobj.Alos2Proc.Alos2ProcPublic import meanOffset
+from isceobj.Alos2Proc.Alos2ProcPublic import resampleBursts
+from isceobj.Alos2Proc.Alos2ProcPublic import mosaicBurstAmplitude
+from isceobj.Alos2Proc.Alos2ProcPublic import mosaicBurstInterferogram
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+logger = logging.getLogger('isce.alos2burstinsar.runCoregCc')
+
+def runCoregCc(self):
+    '''coregister bursts by cross correlation
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    #demFile = os.path.abspath(self._insar.dem)
+    #wbdFile = os.path.abspath(self._insar.wbd)
+###############################################################################
+    self._insar.rangeResidualOffsetCc = [[] for i in range(len(masterTrack.frames))]
+    self._insar.azimuthResidualOffsetCc = [[] for i in range(len(masterTrack.frames))]
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            os.chdir(swathDir)
+
+            print('processing frame {}, swath {}'.format(frameNumber, swathNumber))
+
+            masterSwath = masterTrack.frames[i].swaths[j]
+            slaveSwath = slaveTrack.frames[i].swaths[j]
+
+            ##################################################
+            # estimate cross-correlation offsets
+            ##################################################
+            #compute number of offsets to use
+            wbdImg = isceobj.createImage()
+            wbdImg.load(self._insar.wbdOut+'.xml')
+            width = wbdImg.width
+            length = wbdImg.length
+
+            #initial number of offsets to use
+            numberOfOffsets = 800
+
+            #compute land ratio to further determine the number of offsets to use
+            if self.useWbdForNumberOffsets:
+                wbd=np.memmap(self._insar.wbdOut, dtype='byte', mode='r', shape=(length, width))
+                landRatio = np.sum(wbd==0) / length / width
+                del wbd
+                if (landRatio <= 0.00125):
+                    print('\n\nWARNING: land area too small for estimating offsets between master and slave magnitudes at frame {}, swath {}'.format(frameNumber, swathNumber))
+                    print('set offsets to zero\n\n')
+                    self._insar.rangeResidualOffsetCc[i].append(0.0)
+                    self._insar.azimuthResidualOffsetCc[i].append(0.0)
+                    catalog.addItem('warning message', 'land area too small for estimating offsets between master and slave magnitudes at frame {}, swath {}'.format(frameNumber, swathNumber), 'runCoregCc')
+                    continue
+                #total number of offsets to use
+                numberOfOffsets /= landRatio
+
+            #allocate number of offsets in range/azimuth according to image width/length
+            #number of offsets to use in range/azimuth
+            numberOfOffsetsRange = int(np.sqrt(numberOfOffsets * width / length))
+            numberOfOffsetsAzimuth = int(length / width * np.sqrt(numberOfOffsets * width / length))
+
+            #this should be better?
+            numberOfOffsetsRange = int(np.sqrt(numberOfOffsets))
+            numberOfOffsetsAzimuth = int(np.sqrt(numberOfOffsets))
+
+            if numberOfOffsetsRange > int(width/2):
+                numberOfOffsetsRange = int(width/2)
+            if numberOfOffsetsAzimuth > int(length/2):
+                numberOfOffsetsAzimuth = int(length/2)
+
+            if numberOfOffsetsRange < 10:
+                numberOfOffsetsRange = 10
+            if numberOfOffsetsAzimuth < 10:
+                numberOfOffsetsAzimuth = 10
+
+            #user's settings
+            if self.numberRangeOffsets != None:
+                numberOfOffsetsRange = self.numberRangeOffsets[i][j]
+            if self.numberAzimuthOffsets != None:
+                numberOfOffsetsAzimuth = self.numberAzimuthOffsets[i][j]
+
+            catalog.addItem('number of range offsets at frame {}, swath {}'.format(frameNumber, swathNumber), '{}'.format(numberOfOffsetsRange), 'runCoregCc')
+            catalog.addItem('number of azimuth offsets at frame {}, swath {}'.format(frameNumber, swathNumber), '{}'.format(numberOfOffsetsAzimuth), 'runCoregCc')
+
+            #need to cp to current directory to make it (gdal) work
+            if not os.path.isfile(self._insar.masterMagnitude):
+                os.symlink(os.path.join(self._insar.masterBurstPrefix, self._insar.masterMagnitude), self._insar.masterMagnitude)
+            #shutil.copy2() can overwrite
+            shutil.copy2(os.path.join(self._insar.masterBurstPrefix, self._insar.masterMagnitude+'.vrt'), self._insar.masterMagnitude+'.vrt')
+            shutil.copy2(os.path.join(self._insar.masterBurstPrefix, self._insar.masterMagnitude+'.xml'), self._insar.masterMagnitude+'.xml')
+
+            if not os.path.isfile(self._insar.slaveMagnitude):
+                os.symlink(os.path.join(self._insar.slaveBurstPrefix + '_1_coreg_geom', self._insar.slaveMagnitude), self._insar.slaveMagnitude)
+            #shutil.copy2() can overwrite
+            shutil.copy2(os.path.join(self._insar.slaveBurstPrefix + '_1_coreg_geom', self._insar.slaveMagnitude+'.vrt'), self._insar.slaveMagnitude+'.vrt')
+            shutil.copy2(os.path.join(self._insar.slaveBurstPrefix + '_1_coreg_geom', self._insar.slaveMagnitude+'.xml'), self._insar.slaveMagnitude+'.xml')
+
+            #matching
+            ampcor = Ampcor(name='insarapp_slcs_ampcor')
+            ampcor.configure()
+
+            mMag = isceobj.createImage()
+            mMag.load(self._insar.masterMagnitude+'.xml')
+            mMag.setAccessMode('read')
+            mMag.createImage()
+
+            sMag = isceobj.createImage()
+            sMag.load(self._insar.slaveMagnitude+'.xml')
+            sMag.setAccessMode('read')
+            sMag.createImage()
+
+            ampcor.setImageDataType1('real')
+            ampcor.setImageDataType2('real')
+
+            ampcor.setMasterSlcImage(mMag)
+            ampcor.setSlaveSlcImage(sMag)
+
+            #MATCH REGION
+            rgoff = 0
+            azoff = 0
+            #it seems that we cannot use 0, haven't look into the problem
+            if rgoff == 0:
+                rgoff = 1
+            if azoff == 0:
+                azoff = 1
+            firstSample = 1
+            if rgoff < 0:
+                firstSample = int(35 - rgoff)
+            firstLine = 1
+            if azoff < 0:
+                firstLine = int(35 - azoff)
+            ampcor.setAcrossGrossOffset(rgoff)
+            ampcor.setDownGrossOffset(azoff)
+            ampcor.setFirstSampleAcross(firstSample)
+            ampcor.setLastSampleAcross(mMag.width)
+            ampcor.setNumberLocationAcross(numberOfOffsetsRange)
+            ampcor.setFirstSampleDown(firstLine)
+            ampcor.setLastSampleDown(mMag.length)
+            ampcor.setNumberLocationDown(numberOfOffsetsAzimuth)
+
+            #MATCH PARAMETERS
+            ampcor.setWindowSizeWidth(64)
+            ampcor.setWindowSizeHeight(64)
+            #note this is the half width/length of search area, so number of resulting correlation samples: 8*2+1
+            ampcor.setSearchWindowSizeWidth(8)
+            ampcor.setSearchWindowSizeHeight(8)
+
+            #REST OF THE STUFF
+            ampcor.setAcrossLooks(1)
+            ampcor.setDownLooks(1)
+            ampcor.setOversamplingFactor(64)
+            ampcor.setZoomWindowSize(16)
+            #1. The following not set
+            #Matching Scale for Sample/Line Directions                       (-)    = 1. 1.
+            #should add the following in Ampcor.py?
+            #if not set, in this case, Ampcor.py'value is also 1. 1.
+            #ampcor.setScaleFactorX(1.)
+            #ampcor.setScaleFactorY(1.)
+
+            #MATCH THRESHOLDS AND DEBUG DATA
+            #2. The following not set
+            #in roi_pac the value is set to 0 1
+            #in isce the value is set to 0.001 1000.0
+            #SNR and Covariance Thresholds                                   (-)    =  {s1} {s2}
+            #should add the following in Ampcor?
+            #THIS SHOULD BE THE ONLY THING THAT IS DIFFERENT FROM THAT OF ROI_PAC
+            #ampcor.setThresholdSNR(0)
+            #ampcor.setThresholdCov(1)
+            ampcor.setDebugFlag(False)
+            ampcor.setDisplayFlag(False)
+
+            #in summary, only two things not set which are indicated by 'The following not set' above.
+
+            #run ampcor
+            ampcor.ampcor()
+            offsets = ampcor.getOffsetField()
+            refinedOffsets = cullOffsetsRoipac(offsets, numThreshold=50)
+
+            #finalize image, and re-create it
+            #otherwise the file pointer is still at the end of the image
+            mMag.finalizeImage()
+            sMag.finalizeImage()
+
+            #clear up
+            os.remove(self._insar.masterMagnitude)
+            os.remove(self._insar.masterMagnitude+'.vrt')
+            os.remove(self._insar.masterMagnitude+'.xml')
+            os.remove(self._insar.slaveMagnitude)
+            os.remove(self._insar.slaveMagnitude+'.vrt')
+            os.remove(self._insar.slaveMagnitude+'.xml')
+
+            #compute average offsets to use in resampling
+            if refinedOffsets == None:
+                rangeOffset = 0
+                azimuthOffset = 0
+                self._insar.rangeResidualOffsetCc[i].append(rangeOffset)
+                self._insar.azimuthResidualOffsetCc[i].append(azimuthOffset)
+                print('\n\nWARNING: too few offsets left in matching master and slave magnitudes at frame {}, swath {}'.format(frameNumber, swathNumber))
+                print('set offsets to zero\n\n')
+                catalog.addItem('warning message', 'too few offsets left in matching master and slave magnitudes at frame {}, swath {}'.format(frameNumber, swathNumber), 'runCoregCc')
+            else:
+                rangeOffset, azimuthOffset = meanOffset(refinedOffsets)
+                #for range offset, need to compute from a polynomial
+                #see components/isceobj/Location/Offset.py and components/isceobj/Util/Library/python/Poly2D.py for definations
+                (azimuthPoly, rangePoly) = refinedOffsets.getFitPolynomials(rangeOrder=2,azimuthOrder=2)
+                #make a deep copy, otherwise it also changes original coefficient list of rangePoly, which affects following rangePoly(*, *) computation
+                polyCoeff = copy.deepcopy(rangePoly.getCoeffs())
+                rgIndex = (np.arange(width)-rangePoly.getMeanRange())/rangePoly.getNormRange()
+                azIndex = (np.arange(length)-rangePoly.getMeanAzimuth())/rangePoly.getNormAzimuth()
+                rangeOffset =  polyCoeff[0][0] + polyCoeff[0][1]*rgIndex[None,:] + polyCoeff[0][2]*rgIndex[None,:]**2 + \
+                              (polyCoeff[1][0] + polyCoeff[1][1]*rgIndex[None,:]) * azIndex[:, None] + \
+                               polyCoeff[2][0] * azIndex[:, None]**2
+                polyCoeff.append([rangePoly.getMeanRange(), rangePoly.getNormRange(), rangePoly.getMeanAzimuth(), rangePoly.getNormAzimuth()])
+                self._insar.rangeResidualOffsetCc[i].append(polyCoeff)
+                self._insar.azimuthResidualOffsetCc[i].append(azimuthOffset)
+
+                catalog.addItem('range residual offset at {} {} at frame {}, swath {}'.format(0, 0, frameNumber, swathNumber), 
+                    '{}'.format(rangePoly(0, 0)), 'runCoregCc')
+                catalog.addItem('range residual offset at {} {} at frame {}, swath {}'.format(0, width-1, frameNumber, swathNumber), 
+                    '{}'.format(rangePoly(0, width-1)), 'runCoregCc')
+                catalog.addItem('range residual offset at {} {} at frame {}, swath {}'.format(length-1, 0, frameNumber, swathNumber), 
+                    '{}'.format(rangePoly(length-1, 0)), 'runCoregCc')
+                catalog.addItem('range residual offset at {} {} at frame {}, swath {}'.format(length-1,width-1, frameNumber, swathNumber), 
+                    '{}'.format(rangePoly(length-1,width-1)), 'runCoregCc')
+                catalog.addItem('azimuth residual offset at frame {}, swath {}'.format(frameNumber, swathNumber), 
+                    '{}'.format(azimuthOffset), 'runCoregCc')
+
+                DEBUG=False
+                if DEBUG:
+                    print('+++++++++++++++++++++++++++++')
+                    print(rangeOffset[0,0], rangePoly(0, 0))
+                    print(rangeOffset[0,width-1], rangePoly(0, width-1))
+                    print(rangeOffset[length-1,0], rangePoly(length-1, 0))
+                    print(rangeOffset[length-1,width-1], rangePoly(length-1,width-1))
+                    print(rangeOffset[int((length-1)/2),int((width-1)/2)], rangePoly(int((length-1)/2),int((width-1)/2)))
+                    print('+++++++++++++++++++++++++++++')
+                
+
+            ##################################################
+            # resample bursts
+            ##################################################
+            slaveBurstResampledDir = self._insar.slaveBurstPrefix + '_2_coreg_cc'
+            #interferogramDir = self._insar.masterBurstPrefix + '-' + self._insar.slaveBurstPrefix + '_coreg_geom'
+            interferogramDir = 'burst_interf_2_coreg_cc'
+            interferogramPrefix = self._insar.masterBurstPrefix + '-' + self._insar.slaveBurstPrefix
+            resampleBursts(masterSwath, slaveSwath, 
+                self._insar.masterBurstPrefix, self._insar.slaveBurstPrefix, slaveBurstResampledDir, interferogramDir,
+                self._insar.masterBurstPrefix, self._insar.slaveBurstPrefix, self._insar.slaveBurstPrefix, interferogramPrefix, 
+                self._insar.rangeOffset, self._insar.azimuthOffset, rangeOffsetResidual=rangeOffset, azimuthOffsetResidual=azimuthOffset)
+
+
+            ##################################################
+            # mosaic burst amplitudes and interferograms
+            ##################################################
+            os.chdir(slaveBurstResampledDir)
+            mosaicBurstAmplitude(masterSwath, self._insar.slaveBurstPrefix, self._insar.slaveMagnitude, numberOfLooksThreshold=4)
+            os.chdir('../')
+
+            os.chdir(interferogramDir)
+            mosaicBurstInterferogram(masterSwath, interferogramPrefix, self._insar.interferogram, numberOfLooksThreshold=4)
+            os.chdir('../')
+
+
+            ##################################################
+            # final amplitude and interferogram
+            ##################################################
+            amp = np.zeros((masterSwath.numberOfLines, 2*masterSwath.numberOfSamples), dtype=np.float32)
+            amp[0:, 1:masterSwath.numberOfSamples*2:2] = np.fromfile(os.path.join(slaveBurstResampledDir, self._insar.slaveMagnitude), \
+                dtype=np.float32).reshape(masterSwath.numberOfLines, masterSwath.numberOfSamples)
+            amp[0:, 0:masterSwath.numberOfSamples*2:2] = np.fromfile(os.path.join(self._insar.masterBurstPrefix, self._insar.masterMagnitude), \
+                dtype=np.float32).reshape(masterSwath.numberOfLines, masterSwath.numberOfSamples)
+            amp.astype(np.float32).tofile(self._insar.amplitude)
+            create_xml(self._insar.amplitude, masterSwath.numberOfSamples, masterSwath.numberOfLines, 'amp')
+
+            os.rename(os.path.join(interferogramDir, self._insar.interferogram), self._insar.interferogram)
+            os.rename(os.path.join(interferogramDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+            os.rename(os.path.join(interferogramDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+
+            os.chdir('../')
+        os.chdir('../')
+
+###############################################################################
+    catalog.printToLog(logger, "runCoregCc")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+

components/isceobj/Alos2burstProc/runCoregGeom.py

@@ -0,0 +1,142 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+from isceobj.Alos2Proc.runRdr2Geo import topoCPU
+from isceobj.Alos2Proc.runRdr2Geo import topoGPU
+from isceobj.Alos2Proc.runGeo2Rdr import geo2RdrCPU
+from isceobj.Alos2Proc.runGeo2Rdr import geo2RdrGPU
+from isceobj.Alos2Proc.Alos2ProcPublic import waterBodyRadar
+from isceobj.Alos2Proc.Alos2ProcPublic import resampleBursts
+from isceobj.Alos2Proc.Alos2ProcPublic import mosaicBurstAmplitude
+from isceobj.Alos2Proc.Alos2ProcPublic import mosaicBurstInterferogram
+
+logger = logging.getLogger('isce.alos2burstinsar.runCoregGeom')
+
+def runCoregGeom(self):
+    '''compute geometric offset
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    demFile = os.path.abspath(self._insar.dem)
+    wbdFile = os.path.abspath(self._insar.wbd)
+###############################################################################
+
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            os.chdir(swathDir)
+
+            print('processing frame {}, swath {}'.format(frameNumber, swathNumber))
+
+            masterSwath = masterTrack.frames[i].swaths[j]
+            slaveSwath = slaveTrack.frames[i].swaths[j]
+
+
+            ##################################################
+            # compute geometric offsets
+            ##################################################
+            #set up track parameters just for computing offsets
+            #ALL track parameters are listed here
+            #master
+            #masterTrack.passDirection = 
+            #masterTrack.pointingDirection = 
+            #masterTrack.operationMode = 
+            #masterTrack.radarWavelength = 
+            masterTrack.numberOfSamples = masterSwath.numberOfSamples
+            masterTrack.numberOfLines = masterSwath.numberOfLines
+            masterTrack.startingRange = masterSwath.startingRange
+            #masterTrack.rangeSamplingRate = 
+            masterTrack.rangePixelSize = masterSwath.rangePixelSize
+            masterTrack.sensingStart = masterSwath.sensingStart
+            #masterTrack.prf = 
+            #masterTrack.azimuthPixelSize = 
+            masterTrack.azimuthLineInterval = masterSwath.azimuthLineInterval
+            #masterTrack.dopplerVsPixel = 
+            #masterTrack.frames = 
+            #masterTrack.orbit = 
+
+            #slave
+            slaveTrack.numberOfSamples = slaveSwath.numberOfSamples
+            slaveTrack.numberOfLines = slaveSwath.numberOfLines
+            slaveTrack.startingRange = slaveSwath.startingRange
+            slaveTrack.rangePixelSize = slaveSwath.rangePixelSize
+            slaveTrack.sensingStart = slaveSwath.sensingStart
+            slaveTrack.azimuthLineInterval = slaveSwath.azimuthLineInterval
+
+            if self.useGPU and self._insar.hasGPU():
+                topoGPU(masterTrack, 1, 1, demFile, 
+                               self._insar.latitude, self._insar.longitude, self._insar.height, self._insar.los)
+                geo2RdrGPU(slaveTrack, 1, 1, 
+                    self._insar.latitude, self._insar.longitude, self._insar.height, self._insar.rangeOffset, self._insar.azimuthOffset)
+            else:
+                topoCPU(masterTrack, 1, 1, demFile, 
+                               self._insar.latitude, self._insar.longitude, self._insar.height, self._insar.los)
+                geo2RdrCPU(slaveTrack, 1, 1, 
+                    self._insar.latitude, self._insar.longitude, self._insar.height, self._insar.rangeOffset, self._insar.azimuthOffset)
+
+            waterBodyRadar(self._insar.latitude, self._insar.longitude, wbdFile, self._insar.wbdOut)
+
+            #clear up, leaving only range/azimuth offsets
+            os.remove(self._insar.latitude)
+            os.remove(self._insar.latitude+'.vrt')
+            os.remove(self._insar.latitude+'.xml')
+            os.remove(self._insar.longitude)
+            os.remove(self._insar.longitude+'.vrt')
+            os.remove(self._insar.longitude+'.xml')
+            os.remove(self._insar.height)
+            os.remove(self._insar.height+'.vrt')
+            os.remove(self._insar.height+'.xml')
+            os.remove(self._insar.los)
+            os.remove(self._insar.los+'.vrt')
+            os.remove(self._insar.los+'.xml')
+
+
+            ##################################################
+            # resample bursts
+            ##################################################
+            slaveBurstResampledDir = self._insar.slaveBurstPrefix + '_1_coreg_geom'
+            #interferogramDir = self._insar.masterBurstPrefix + '-' + self._insar.slaveBurstPrefix + '_coreg_geom'
+            interferogramDir = 'burst_interf_1_coreg_geom'
+            interferogramPrefix = self._insar.masterBurstPrefix + '-' + self._insar.slaveBurstPrefix
+            resampleBursts(masterSwath, slaveSwath, 
+                self._insar.masterBurstPrefix, self._insar.slaveBurstPrefix, slaveBurstResampledDir, interferogramDir,
+                self._insar.masterBurstPrefix, self._insar.slaveBurstPrefix, self._insar.slaveBurstPrefix, interferogramPrefix, 
+                self._insar.rangeOffset, self._insar.azimuthOffset, rangeOffsetResidual=0, azimuthOffsetResidual=0)
+
+
+            ##################################################
+            # mosaic burst amplitudes and interferograms
+            ##################################################
+            os.chdir(slaveBurstResampledDir)
+            mosaicBurstAmplitude(masterSwath, self._insar.slaveBurstPrefix, self._insar.slaveMagnitude, numberOfLooksThreshold=4)
+            os.chdir('../')
+
+            #the interferogram is not good enough, do not mosaic
+            mosaic=False
+            if mosaic:
+                os.chdir(interferogramDir)
+                mosaicBurstInterferogram(masterSwath, interferogramPrefix, self._insar.interferogram, numberOfLooksThreshold=4)
+                os.chdir('../')
+
+
+            os.chdir('../')
+        os.chdir('../')
+
+###############################################################################
+    catalog.printToLog(logger, "runCoregGeom")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+

components/isceobj/Alos2burstProc/runCoregSd.py

@@ -0,0 +1,236 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import resampleBursts
+from isceobj.Alos2Proc.Alos2ProcPublic import mosaicBurstAmplitude
+from isceobj.Alos2Proc.Alos2ProcPublic import mosaicBurstInterferogram
+
+logger = logging.getLogger('isce.alos2burstinsar.runCoregSd')
+
+def runCoregSd(self):
+    '''coregister bursts by spectral diversity
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    #demFile = os.path.abspath(self._insar.dem)
+    #wbdFile = os.path.abspath(self._insar.wbd)
+###############################################################################
+    #self._insar.rangeResidualOffsetSd = [[] for i in range(len(masterTrack.frames))]
+    self._insar.azimuthResidualOffsetSd = [[] for i in range(len(masterTrack.frames))]
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            os.chdir(swathDir)
+
+            print('processing frame {}, swath {}'.format(frameNumber, swathNumber))
+
+            masterSwath = masterTrack.frames[i].swaths[j]
+            slaveSwath = slaveTrack.frames[i].swaths[j]
+
+            ##################################################
+            # spectral diversity or mai
+            ##################################################
+            sdDir = 'spectral_diversity'
+            if not os.path.exists(sdDir):
+                os.makedirs(sdDir)
+            os.chdir(sdDir)
+
+            interferogramDir = 'burst_interf_2_coreg_cc'
+            interferogramPrefix = self._insar.masterBurstPrefix + '-' + self._insar.slaveBurstPrefix
+            offsetSd = spectralDiversity(masterSwath, os.path.join('../', interferogramDir), interferogramPrefix, self._insar.interferogramSd,
+                numberLooksScanSAR=4, numberRangeLooks=28, numberAzimuthLooks=8, coherenceThreshold=0.85, 
+                keep=True, filt=True, filtWinSizeRange=5, filtWinSizeAzimuth=5)
+            #here use the number of looks for sd as filtWinSizeRange and filtWinSizeAzimuth to get the best filtering result?
+
+            os.chdir('../')
+
+            self._insar.azimuthResidualOffsetSd[i].append(offsetSd)
+            catalog.addItem('azimuth residual offset at frame {}, swath {}'.format(frameNumber, swathNumber), '{}'.format(offsetSd), 'runCoregSd')
+            
+
+            #this small residual azimuth offset has small impact, it's not worth the time to resample slave bursts again.
+            formInterferogram=False
+            if formInterferogram:
+                ##################################################
+                # resample bursts
+                ##################################################
+                slaveBurstResampledDir = self._insar.slaveBurstPrefix + '_3_coreg_sd'
+                #interferogramDir = self._insar.masterBurstPrefix + '-' + self._insar.slaveBurstPrefix + '_coreg_geom'
+                interferogramDir = 'burst_interf_3_coreg_sd'
+                interferogramPrefix = self._insar.masterBurstPrefix + '-' + self._insar.slaveBurstPrefix
+                resampleBursts(masterSwath, slaveSwath, 
+                    self._insar.masterBurstPrefix, self._insar.slaveBurstPrefix, slaveBurstResampledDir, interferogramDir,
+                    self._insar.masterBurstPrefix, self._insar.slaveBurstPrefix, self._insar.slaveBurstPrefix, interferogramPrefix, 
+                    self._insar.rangeOffset, self._insar.azimuthOffset, rangeOffsetResidual=self._insar.rangeResidualOffsetCc[i][j], azimuthOffsetResidual=self._insar.azimuthResidualOffsetCc[i][j]+offsetSd)
+
+
+                ##################################################
+                # mosaic burst amplitudes and interferograms
+                ##################################################
+                os.chdir(slaveBurstResampledDir)
+                mosaicBurstAmplitude(masterSwath, self._insar.slaveBurstPrefix, self._insar.slaveMagnitude, numberOfLooksThreshold=4)
+                os.chdir('../')
+
+                os.chdir(interferogramDir)
+                mosaicBurstInterferogram(masterSwath, interferogramPrefix, self._insar.interferogram, numberOfLooksThreshold=4)
+                os.chdir('../')
+
+
+            os.chdir('../')
+        os.chdir('../')
+
+###############################################################################
+    catalog.printToLog(logger, "runCoregSd")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def spectralDiversity(masterSwath, interferogramDir, interferogramPrefix, outputList, numberLooksScanSAR=None, numberRangeLooks=20, numberAzimuthLooks=10, coherenceThreshold=0.85, keep=False, filt=False, filtWinSizeRange=5, filtWinSizeAzimuth=5):
+    '''
+    numberLooksScanSAR: number of looks of the ScanSAR system
+    numberRangeLooks:   number of range looks to take
+    numberAzimuthLooks: number of azimuth looks to take
+    keep:               whether keep intermediate files
+    '''
+    import os
+    import numpy as np
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_multi_index
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+    from isceobj.Alos2Proc.Alos2ProcPublic import multilook
+    from isceobj.Alos2Proc.Alos2ProcPublic import cal_coherence_1
+
+    width  = masterSwath.numberOfSamples
+    length = masterSwath.numberOfLines
+    lengthBurst = masterSwath.burstSlcNumberOfLines
+    nBurst = masterSwath.numberOfBursts
+    azsi = masterSwath.azimuthLineInterval
+    tc = masterSwath.burstCycleLength / masterSwath.prf
+
+    bursts = [os.path.join(interferogramDir, interferogramPrefix+'_%02d.int'%(i+1)) for i in range(masterSwath.numberOfBursts)]
+
+    ####################################################
+    #input parameters
+    rgl = numberRangeLooks
+    azl = numberAzimuthLooks
+    cor_th = coherenceThreshold
+    nls0 = lengthBurst / (masterSwath.burstSlcFirstLineOffsets[nBurst-1] / (nBurst-1.0))
+    print('number of looks of the ScanSAR system: {}'.format(nls0))
+    if numberLooksScanSAR != None:
+        nls = numberLooksScanSAR
+    else:
+        nls = int(nls0)
+    print('number of looks to be used: {}'.format(nls))
+    ####################################################
+
+    #read burst interferograms
+    inf = np.zeros((length, width, nls), dtype=np.complex64)
+    cnt = np.zeros((length, width), dtype=np.int8)
+    for i in range(nBurst):
+        if (i+1)%5 == 0 or (i+1) == nBurst:
+            print('reading burst %02d' % (i+1))
+
+        burst = np.fromfile(bursts[i], dtype=np.complex64).reshape(lengthBurst, width)
+
+        #subset for the burst
+        cntBurst = cnt[0+masterSwath.burstSlcFirstLineOffsets[i]:lengthBurst+masterSwath.burstSlcFirstLineOffsets[i], :]
+        infBurst = inf[0+masterSwath.burstSlcFirstLineOffsets[i]:lengthBurst+masterSwath.burstSlcFirstLineOffsets[i], :, :]
+        
+        #set number of non-zero pixels
+        cntBurst[np.nonzero(burst)] += 1
+
+        #get index
+        index1 = np.nonzero(np.logical_and(burst!=0, cntBurst<=nls))
+        index2 = index1 + (cntBurst[index1]-1,)
+
+        #set values
+        infBurst[index2] = burst[index1]
+    
+    #number of looks for each sample
+    if keep:
+        nlFile = 'number_of_looks.nl'
+        cnt.astype(np.int8).tofile(nlFile)
+        create_xml(nlFile, width, length, 'byte')        
+
+    if filt:
+        import scipy.signal as ss
+        filterKernel = np.ones((filtWinSizeAzimuth,filtWinSizeRange), dtype=np.float64)
+        for i in range(nls):
+            print('filtering look {}'.format(i+1))
+            flag = (inf[:,:,i]!=0)
+            #scale = ss.fftconvolve(flag, filterKernel, mode='same')
+            #inf[:,:,i] = flag*ss.fftconvolve(inf[:,:,i], filterKernel, mode='same') / (scale + (scale==0))
+            #this should be faster?
+            scale = ss.convolve2d(flag, filterKernel, mode='same')
+            inf[:,:,i] = flag*ss.convolve2d(inf[:,:,i], filterKernel, mode='same') / (scale + (scale==0))
+ 
+    #width and length after multilooking
+    widthm = int(width/rgl)
+    lengthm = int(length/azl)
+    #use the convention that ka > 0
+    ka = -np.polyval(masterSwath.azimuthFmrateVsPixel[::-1], create_multi_index(width, rgl))
+
+    #get spectral diversity inteferogram
+    offset_sd=[]
+    for i in range(1, nls):
+        print('ouput spectral diversity inteferogram %d' % i)
+        #original spectral diversity inteferogram
+        sd = inf[:,:,0] * np.conj(inf[:,:,i])
+
+        #replace original amplitude with its square root
+        index = np.nonzero(sd!=0)
+        sd[index] /= np.sqrt(np.absolute(sd[index]))
+
+        sdFile = outputList[i-1]
+        sd.astype(np.complex64).tofile(sdFile)
+        create_xml(sdFile, width, length, 'int')
+
+        #multi look
+        sdm = multilook(sd, azl, rgl)
+        cor = cal_coherence_1(sdm)
+
+        #convert phase to offset
+        offset = np.angle(sdm)/(2.0 * np.pi * ka * tc * i)[None,:] / azsi
+
+        #compute offset using good samples
+        point_index = np.nonzero(np.logical_and(cor>=cor_th, np.angle(sdm)!=0))
+        npoint = round(np.size(point_index)/2)
+        if npoint < 20:
+            print('WARNING: too few good samples for spectral diversity at look {}: {}'.format(i, npoint))
+            offset_sd.append(0)
+        else:
+            offset_sd.append(  np.sum(offset[point_index]*cor[point_index])/np.sum(cor[point_index])  )
+
+        if keep:
+            sdmFile = 'sd_%d_%drlks_%dalks.int' % (i, rgl, azl)
+            sdm.astype(np.complex64).tofile(sdmFile)
+            create_xml(sdmFile, widthm, lengthm, 'int')
+            corFile = 'sd_%d_%drlks_%dalks.cor' % (i, rgl, azl)
+            cor.astype(np.float32).tofile(corFile)
+            create_xml(corFile, widthm, lengthm, 'float')
+            offsetFile = 'sd_%d_%drlks_%dalks.off' % (i, rgl, azl)
+            offset.astype(np.float32).tofile(offsetFile)
+            create_xml(offsetFile, widthm, lengthm, 'float')
+
+    offset_mean = np.sum(np.array(offset_sd) * np.arange(1, nls)) / np.sum(np.arange(1, nls))
+
+    return offset_mean
+
+
+
+
+
+
+
+

components/isceobj/Alos2burstProc/runExtractBurst.py

@@ -0,0 +1,136 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import glob
+import logging
+import datetime
+#import subprocess
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+from isceobj.Alos2Proc.Alos2ProcPublic import mosaicBurstAmplitude
+from contrib.alos2proc.alos2proc import extract_burst
+
+logger = logging.getLogger('isce.alos2burstinsar.runExtractBurst')
+
+def runExtractBurst(self):
+    '''extract bursts.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    #demFile = os.path.abspath(self._insar.dem)
+    #wbdFile = os.path.abspath(self._insar.wbd)
+###############################################################################
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            os.chdir(swathDir)
+
+            print('extracting bursts frame {}, swath {}'.format(frameNumber, swathNumber))
+
+            az_ratio1 = 20.0
+            for k in range(2):
+                if k==0:
+                    #master
+                    swath = masterTrack.frames[i].swaths[j]
+                    unsynLines = self._insar.burstUnsynchronizedTime * swath.prf
+                    extractDir = self._insar.masterBurstPrefix
+                    burstPrefix = self._insar.masterBurstPrefix
+                    fullApertureSlc = self._insar.masterSlc
+                    magnitude = self._insar.masterMagnitude
+                else:
+                    #slave
+                    swath = slaveTrack.frames[i].swaths[j]
+                    unsynLines = -self._insar.burstUnsynchronizedTime * swath.prf
+                    extractDir = self._insar.slaveBurstPrefix
+                    burstPrefix = self._insar.slaveBurstPrefix
+                    fullApertureSlc = self._insar.slaveSlc
+                    magnitude = self._insar.slaveMagnitude
+
+                #UPDATE SWATH PARAMETERS 1
+                #########################################################################################
+                if self._insar.burstSynchronization <= self.burstSynchronizationThreshold:
+                    swath.burstLength -= abs(unsynLines)
+                    if unsynLines < 0:
+                        swath.burstStartTime += datetime.timedelta(seconds=abs(unsynLines)/swath.prf)
+                #########################################################################################
+
+                #extract burst
+                if not os.path.exists(extractDir):
+                    os.makedirs(extractDir)
+                os.chdir(extractDir)
+                if os.path.isfile(os.path.join('../', fullApertureSlc)):
+                    os.rename(os.path.join('../', fullApertureSlc), fullApertureSlc)
+                os.rename(os.path.join('../', fullApertureSlc+'.vrt'), fullApertureSlc+'.vrt')
+                os.rename(os.path.join('../', fullApertureSlc+'.xml'), fullApertureSlc+'.xml')
+
+                extract_burst(fullApertureSlc, burstPrefix, swath.prf, swath.prfFraction, swath.burstLength, swath.burstCycleLength-swath.burstLength, \
+                (swath.burstStartTime - swath.sensingStart).total_seconds() * swath.prf, swath.azimuthFmrateVsPixel, swath.dopplerVsPixel, az_ratio1, 0.0)
+
+                #read output parameters
+                with open('extract_burst.txt', 'r') as f:
+                    lines = f.readlines()
+                offsetFromFirstBurst = []
+                for linex in lines:
+                    if 'total number of bursts extracted' in linex:
+                        numberOfBursts = int(linex.split(':')[1])
+                    if 'output burst length' in linex:
+                        burstSlcNumberOfLines = int(linex.split(':')[1])
+                    if 'line number of first line of first output burst in original SLC (1.0/prf)' in linex:
+                        fb_ln = float(linex.split(':')[1])
+                    if 'bsl of first output burst' in linex:
+                        bsl_firstburst = float(linex.split(':')[1])
+                    if 'offset from first burst' in linex:
+                        offsetFromFirstBurst.append(int(linex.split(',')[0].split(':')[1]))
+
+                #time of first line of first burst raw
+                firstBurstRawStartTime = swath.sensingStart + datetime.timedelta(seconds=bsl_firstburst/swath.prf)
+
+                #time of first line of first burst slc
+                #original time is at the upper edge of first line, we change it to center of first line. 
+                sensingStart = swath.sensingStart + datetime.timedelta(seconds=fb_ln/swath.prf+(az_ratio1-1.0)/2.0/swath.prf)
+                numberOfLines = offsetFromFirstBurst[numberOfBursts-1] + burstSlcNumberOfLines
+
+                for ii in range(numberOfBursts):
+                    burstFile = burstPrefix + '_%02d.slc'%(ii+1)
+                    create_xml(burstFile, swath.numberOfSamples, burstSlcNumberOfLines, 'slc')
+
+                #UPDATE SWATH PARAMETERS 2
+                #########################################################################################
+                swath.numberOfLines = numberOfLines
+                #this is also the time of the first line of the first burst slc
+                swath.sensingStart = sensingStart
+                swath.azimuthPixelSize = az_ratio1 * swath.azimuthPixelSize
+                swath.azimuthLineInterval = az_ratio1 * swath.azimuthLineInterval
+
+                swath.numberOfBursts = numberOfBursts
+                swath.firstBurstRawStartTime = firstBurstRawStartTime
+                swath.firstBurstSlcStartTime = sensingStart
+                swath.burstSlcFirstLineOffsets = offsetFromFirstBurst
+                swath.burstSlcNumberOfSamples = swath.numberOfSamples
+                swath.burstSlcNumberOfLines = burstSlcNumberOfLines
+                #########################################################################################
+
+                #create a magnitude image
+                mosaicBurstAmplitude(swath, burstPrefix, magnitude, numberOfLooksThreshold=4)
+
+                os.chdir('../')
+            os.chdir('../')
+        self._insar.saveProduct(masterTrack.frames[i], self._insar.masterFrameParameter)
+        self._insar.saveProduct(slaveTrack.frames[i], self._insar.slaveFrameParameter)
+        os.chdir('../')
+
+###############################################################################
+    catalog.printToLog(logger, "runExtractBurst")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+

components/isceobj/Alos2burstProc/runFiltSd.py

@@ -0,0 +1,94 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import shutil
+import logging
+import numpy as np
+
+import isceobj
+from mroipac.filter.Filter import Filter
+from mroipac.icu.Icu import Icu
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+from isceobj.Alos2Proc.Alos2ProcPublic import renameFile
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+from contrib.alos2filter.alos2filter import psfilt1
+from isceobj.Alos2Proc.Alos2ProcPublic import cal_coherence
+
+logger = logging.getLogger('isce.alos2burstinsar.runFiltSd')
+
+def runFiltSd(self):
+    '''filter interferogram
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    #masterTrack = self._insar.loadTrack(master=True)
+    #slaveTrack = self._insar.loadTrack(master=False)
+
+    sdDir = 'sd'
+    if not os.path.exists(sdDir):
+        os.makedirs(sdDir)
+    os.chdir(sdDir)
+
+    sd = isceobj.createImage()
+    sd.load(self._insar.multilookInterferogramSd[0]+'.xml')
+    width = sd.width
+    length = sd.length
+
+    ############################################################
+    # STEP 1. filter interferogram
+    ############################################################
+    for sdInterferogram, sdInterferogramFilt, sdCoherence in zip(self._insar.multilookInterferogramSd, self._insar.filteredInterferogramSd, self._insar.multilookCoherenceSd):
+        print('filter interferogram: {}'.format(sdInterferogram))
+        #remove mangnitude
+        data = np.fromfile(sdInterferogram, dtype=np.complex64).reshape(length, width)
+        index = np.nonzero(data!=0)
+        data[index] /= np.absolute(data[index])
+        data.astype(np.complex64).tofile('tmp.int')
+
+        #filter
+        windowSize = self.filterWinsizeSd
+        stepSize = self.filterStepsizeSd
+        psfilt1('tmp.int', sdInterferogramFilt, width, self.filterStrengthSd, windowSize, stepSize)
+        create_xml(sdInterferogramFilt, width, length, 'int')
+        os.remove('tmp.int')
+
+        #restore magnitude
+        data = np.fromfile(sdInterferogram, dtype=np.complex64).reshape(length, width)
+        dataFilt = np.fromfile(sdInterferogramFilt, dtype=np.complex64).reshape(length, width)
+        index = np.nonzero(dataFilt!=0)
+        dataFilt[index] = dataFilt[index] / np.absolute(dataFilt[index]) * np.absolute(data[index])
+        dataFilt.astype(np.complex64).tofile(sdInterferogramFilt)
+
+        # #create a coherence using an interferogram with most sparse fringes
+        # if sdInterferogramFilt == self._insar.filteredInterferogramSd[0]:
+        #     print('create coherence using: {}'.format(sdInterferogramFilt))
+        #     cor = cal_coherence(dataFilt, win=3, edge=2)
+        #     cor.astype(np.float32).tofile(self._insar.multilookCoherenceSd)
+        #     create_xml(self._insar.multilookCoherenceSd, width, length, 'float')
+
+        cor = cal_coherence(dataFilt, win=3, edge=2)
+        cor.astype(np.float32).tofile(sdCoherence)
+        create_xml(sdCoherence, width, length, 'float')
+
+
+    ############################################################
+    # STEP 3. mask filtered interferogram using water body
+    ############################################################
+    if self.waterBodyMaskStartingStepSd=='filt':
+        print('mask filtered interferogram using: {}'.format(self._insar.multilookWbdOutSd))
+        wbd = np.fromfile(self._insar.multilookWbdOutSd, dtype=np.int8).reshape(length, width)
+        cor=np.memmap(self._insar.multilookCoherenceSd, dtype='float32', mode='r+', shape=(length, width))
+        cor[np.nonzero(wbd==-1)]=0
+        for sdInterferogramFilt in self._insar.filteredInterferogramSd:
+            filt=np.memmap(sdInterferogramFilt, dtype='complex64', mode='r+', shape=(length, width))
+            filt[np.nonzero(wbd==-1)]=0
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runFiltSd")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+

components/isceobj/Alos2burstProc/runFrameMosaic.py

@@ -0,0 +1,172 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+from isceobj.Alos2Proc.runFrameMosaic import frameMosaic
+from isceobj.Alos2Proc.runFrameMosaic import frameMosaicParameters
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+logger = logging.getLogger('isce.alos2burstinsar.runFrameMosaic')
+
+def runFrameMosaic(self):
+    '''mosaic frames
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    mosaicDir = 'insar'
+    if not os.path.exists(mosaicDir):
+        os.makedirs(mosaicDir)
+    os.chdir(mosaicDir)
+
+    numberOfFrames = len(masterTrack.frames)
+    if numberOfFrames == 1:
+        import shutil
+        frameDir = os.path.join('f1_{}/mosaic'.format(self._insar.masterFrames[0]))
+        if not os.path.isfile(self._insar.interferogram):
+            os.symlink(os.path.join('../', frameDir, self._insar.interferogram), self._insar.interferogram)
+        #shutil.copy2() can overwrite
+        shutil.copy2(os.path.join('../', frameDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+        shutil.copy2(os.path.join('../', frameDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+        if not os.path.isfile(self._insar.amplitude):
+            os.symlink(os.path.join('../', frameDir, self._insar.amplitude), self._insar.amplitude)
+        shutil.copy2(os.path.join('../', frameDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+        shutil.copy2(os.path.join('../', frameDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+        # os.rename(os.path.join('../', frameDir, self._insar.interferogram), self._insar.interferogram)
+        # os.rename(os.path.join('../', frameDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+        # os.rename(os.path.join('../', frameDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+        # os.rename(os.path.join('../', frameDir, self._insar.amplitude), self._insar.amplitude)
+        # os.rename(os.path.join('../', frameDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+        # os.rename(os.path.join('../', frameDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+        #update track parameters
+        #########################################################
+        #mosaic size
+        masterTrack.numberOfSamples = masterTrack.frames[0].numberOfSamples
+        masterTrack.numberOfLines = masterTrack.frames[0].numberOfLines
+        #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+        #range parameters
+        masterTrack.startingRange = masterTrack.frames[0].startingRange
+        masterTrack.rangeSamplingRate = masterTrack.frames[0].rangeSamplingRate
+        masterTrack.rangePixelSize = masterTrack.frames[0].rangePixelSize
+        #azimuth parameters
+        masterTrack.sensingStart = masterTrack.frames[0].sensingStart
+        masterTrack.prf = masterTrack.frames[0].prf
+        masterTrack.azimuthPixelSize = masterTrack.frames[0].azimuthPixelSize
+        masterTrack.azimuthLineInterval = masterTrack.frames[0].azimuthLineInterval
+
+        #update track parameters, slave
+        #########################################################
+        #mosaic size
+        slaveTrack.numberOfSamples = slaveTrack.frames[0].numberOfSamples
+        slaveTrack.numberOfLines = slaveTrack.frames[0].numberOfLines
+        #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+        #range parameters
+        slaveTrack.startingRange = slaveTrack.frames[0].startingRange
+        slaveTrack.rangeSamplingRate = slaveTrack.frames[0].rangeSamplingRate
+        slaveTrack.rangePixelSize = slaveTrack.frames[0].rangePixelSize
+        #azimuth parameters
+        slaveTrack.sensingStart = slaveTrack.frames[0].sensingStart
+        slaveTrack.prf = slaveTrack.frames[0].prf
+        slaveTrack.azimuthPixelSize = slaveTrack.frames[0].azimuthPixelSize
+        slaveTrack.azimuthLineInterval = slaveTrack.frames[0].azimuthLineInterval
+
+    else:
+        #choose offsets
+        if self.frameOffsetMatching:
+            rangeOffsets = self._insar.frameRangeOffsetMatchingMaster
+            azimuthOffsets = self._insar.frameAzimuthOffsetMatchingMaster
+        else:
+            rangeOffsets = self._insar.frameRangeOffsetGeometricalMaster
+            azimuthOffsets = self._insar.frameAzimuthOffsetGeometricalMaster
+
+        #list of input files
+        inputInterferograms = []
+        inputAmplitudes = []
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            inputInterferograms.append(os.path.join('../', frameDir, 'mosaic', self._insar.interferogram))
+            inputAmplitudes.append(os.path.join('../', frameDir, 'mosaic', self._insar.amplitude))
+
+        #note that track parameters are updated after mosaicking
+        #mosaic amplitudes
+        frameMosaic(masterTrack, inputAmplitudes, self._insar.amplitude, 
+            rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+            updateTrack=False, phaseCompensation=False, resamplingMethod=0)
+        #mosaic interferograms
+        frameMosaic(masterTrack, inputInterferograms, self._insar.interferogram, 
+            rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+            updateTrack=True, phaseCompensation=True, resamplingMethod=1)
+
+        create_xml(self._insar.amplitude, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'amp')
+        create_xml(self._insar.interferogram, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'int')
+
+        #update slave parameters here
+        #do not match for slave, always use geometrical
+        rangeOffsets = self._insar.frameRangeOffsetGeometricalSlave
+        azimuthOffsets = self._insar.frameAzimuthOffsetGeometricalSlave
+        frameMosaicParameters(slaveTrack, rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1)
+
+    os.chdir('../')
+    #save parameter file
+    self._insar.saveProduct(masterTrack, self._insar.masterTrackParameter)
+    self._insar.saveProduct(slaveTrack, self._insar.slaveTrackParameter)
+
+
+
+    #mosaic spectral diversity inteferograms
+    mosaicDir = 'sd'
+    if not os.path.exists(mosaicDir):
+        os.makedirs(mosaicDir)
+    os.chdir(mosaicDir)
+
+    numberOfFrames = len(masterTrack.frames)
+    if numberOfFrames == 1:
+        import shutil
+        frameDir = os.path.join('f1_{}/mosaic'.format(self._insar.masterFrames[0]))
+        for sdFile in self._insar.interferogramSd:
+            if not os.path.isfile(sdFile):
+                os.symlink(os.path.join('../', frameDir, sdFile), sdFile)
+            shutil.copy2(os.path.join('../', frameDir, sdFile+'.vrt'), sdFile+'.vrt')
+            shutil.copy2(os.path.join('../', frameDir, sdFile+'.xml'), sdFile+'.xml')
+    else:
+        #choose offsets
+        if self.frameOffsetMatching:
+            rangeOffsets = self._insar.frameRangeOffsetMatchingMaster
+            azimuthOffsets = self._insar.frameAzimuthOffsetMatchingMaster
+        else:
+            rangeOffsets = self._insar.frameRangeOffsetGeometricalMaster
+            azimuthOffsets = self._insar.frameAzimuthOffsetGeometricalMaster
+
+        #list of input files
+        inputSd = [[], [], []]
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            for k, sdFile in enumerate(self._insar.interferogramSd):
+                inputSd[k].append(os.path.join('../', frameDir, 'mosaic', sdFile))
+
+        #mosaic spectral diversity interferograms
+        for inputSdList, outputSdFile in zip(inputSd, self._insar.interferogramSd):
+            frameMosaic(masterTrack, inputSdList, outputSdFile, 
+                rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+                updateTrack=False, phaseCompensation=True, resamplingMethod=1)
+
+        for sdFile in self._insar.interferogramSd:
+            create_xml(sdFile, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'int')
+
+    os.chdir('../')
+
+
+    catalog.printToLog(logger, "runFrameMosaic")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+

components/isceobj/Alos2burstProc/runFrameOffset.py

@@ -0,0 +1,55 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+from isceobj.Alos2Proc.runFrameOffset import frameOffset
+
+logger = logging.getLogger('isce.alos2burstinsar.runFrameOffset')
+
+def runFrameOffset(self):
+    '''estimate frame offsets.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    mosaicDir = 'insar'
+    if not os.path.exists(mosaicDir):
+        os.makedirs(mosaicDir)
+    os.chdir(mosaicDir)
+
+    if len(masterTrack.frames) > 1:
+        #here we use master amplitude image mosaicked from extracted bursts.
+        matchingMode=1
+
+        #compute swath offset
+        offsetMaster = frameOffset(masterTrack, os.path.join(self._insar.masterBurstPrefix, self._insar.masterMagnitude), self._insar.masterFrameOffset, 
+                                   crossCorrelation=self.frameOffsetMatching, matchingMode=matchingMode)
+        #only use geometrical offset for slave
+        offsetSlave = frameOffset(slaveTrack, os.path.join(self._insar.slaveBurstPrefix, self._insar.slaveMagnitude), self._insar.slaveFrameOffset, 
+                                  crossCorrelation=False, matchingMode=matchingMode)
+
+        self._insar.frameRangeOffsetGeometricalMaster = offsetMaster[0]
+        self._insar.frameAzimuthOffsetGeometricalMaster = offsetMaster[1]
+        self._insar.frameRangeOffsetGeometricalSlave = offsetSlave[0]
+        self._insar.frameAzimuthOffsetGeometricalSlave = offsetSlave[1]
+        if self.frameOffsetMatching:
+            self._insar.frameRangeOffsetMatchingMaster = offsetMaster[2]
+            self._insar.frameAzimuthOffsetMatchingMaster = offsetMaster[3]
+            #self._insar.frameRangeOffsetMatchingSlave = offsetSlave[2]
+            #self._insar.frameAzimuthOffsetMatchingSlave = offsetSlave[3]
+
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runFrameOffset")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+

components/isceobj/Alos2burstProc/runGeocodeSd.py

@@ -0,0 +1,64 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.runGeocode import geocode
+from isceobj.Alos2Proc.Alos2ProcPublic import getBboxGeo
+
+logger = logging.getLogger('isce.alos2insar.runGeocodeSd')
+
+def runGeocodeSd(self):
+    '''geocode final products
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    #slaveTrack = self._insar.loadTrack(master=False)
+
+    demFile = os.path.abspath(self._insar.demGeo)
+
+    sdDir = 'sd'
+    if not os.path.exists(sdDir):
+        os.makedirs(sdDir)
+    os.chdir(sdDir)
+
+    if self.geocodeListSd == None:
+        geocodeList = self._insar.multilookCoherenceSd + self._insar.azimuthDeformationSd + self._insar.maskedAzimuthDeformationSd
+    else:
+        geocodeList = self.geocodeListSd
+
+    if self.bbox == None:
+        bbox = getBboxGeo(masterTrack)
+    else:
+        bbox = self.bbox
+    catalog.addItem('geocode bounding box', bbox, 'runGeocodeSd')
+
+    numberRangeLooks = self._insar.numberRangeLooks1 * self._insar.numberRangeLooksSd
+    numberAzimuthLooks = self._insar.numberAzimuthLooks1 * self._insar.numberAzimuthLooksSd
+
+    for inputFile in geocodeList:
+        if self.geocodeInterpMethodSd == None:
+            img = isceobj.createImage()
+            img.load(inputFile + '.xml')
+            if img.dataType.upper() == 'CFLOAT':
+                interpMethod = 'sinc'
+            else:
+                interpMethod = 'bilinear'
+        else:
+            interpMethod = self.geocodeInterpMethodSd.lower()
+
+        geocode(masterTrack, demFile, inputFile, bbox, numberRangeLooks, numberAzimuthLooks, interpMethod, 0, 0)
+
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runGeocodeSd")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+

components/isceobj/Alos2burstProc/runIonSubband.py

@@ -0,0 +1,425 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import shutil
+import logging
+
+import isceobj
+from isceobj.Constants import SPEED_OF_LIGHT
+
+logger = logging.getLogger('isce.alos2burstinsar.runIonSubband')
+
+def runIonSubband(self):
+    '''create subband interferograms
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    if not self.doIon:
+        catalog.printToLog(logger, "runIonSubband")
+        self._insar.procDoc.addAllFromCatalog(catalog)
+        return
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+    #using 1/3, 1/3, 1/3 band split
+    radarWavelength = masterTrack.radarWavelength
+    rangeBandwidth = masterTrack.frames[0].swaths[0].rangeBandwidth
+    rangeSamplingRate = masterTrack.frames[0].swaths[0].rangeSamplingRate
+    radarWavelengthLower = SPEED_OF_LIGHT/(SPEED_OF_LIGHT / radarWavelength - rangeBandwidth / 3.0)
+    radarWavelengthUpper = SPEED_OF_LIGHT/(SPEED_OF_LIGHT / radarWavelength + rangeBandwidth / 3.0)
+    subbandRadarWavelength = [radarWavelengthLower, radarWavelengthUpper]
+    subbandBandWidth = [rangeBandwidth / 3.0 / rangeSamplingRate, rangeBandwidth / 3.0 / rangeSamplingRate]
+    subbandFrequencyCenter = [-rangeBandwidth / 3.0 / rangeSamplingRate, rangeBandwidth / 3.0 / rangeSamplingRate]
+
+    subbandPrefix = ['lower', 'upper']
+
+    '''
+    ionDir = {
+        ionDir['swathMosaic'] : 'mosaic',
+        ionDir['insar'] : 'insar',
+        ionDir['ion'] : 'ion',
+        ionDir['subband'] : ['lower', 'upper'],
+        ionDir['ionCal'] : 'ion_cal'
+        }
+    '''
+    #define upper level directory names
+    ionDir = defineIonDir()
+
+
+    self._insar.subbandRadarWavelength = subbandRadarWavelength
+
+
+    ############################################################
+    # STEP 1. create directories
+    ############################################################
+    #create and enter 'ion' directory
+    #after finishing each step, we are in this directory
+    if not os.path.exists(ionDir['ion']):
+        os.makedirs(ionDir['ion'])
+    os.chdir(ionDir['ion'])
+
+    #create insar processing directories
+    for k in range(2):
+        subbandDir = ionDir['subband'][k]
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+                swathDir = 's{}'.format(swathNumber)
+                fullDir = os.path.join(subbandDir, frameDir, swathDir)
+                if not os.path.exists(fullDir):
+                    os.makedirs(fullDir)
+
+    #create ionospheric phase directory
+    if not os.path.exists(ionDir['ionCal']):
+        os.makedirs(ionDir['ionCal'])
+
+
+    ############################################################
+    # STEP 2. create subband interferograms
+    ############################################################
+    import shutil
+    import numpy as np
+    from contrib.alos2proc.alos2proc import rg_filter
+    from isceobj.Alos2Proc.Alos2ProcPublic import resampleBursts
+    from isceobj.Alos2Proc.Alos2ProcPublic import mosaicBurstAmplitude
+    from isceobj.Alos2Proc.Alos2ProcPublic import mosaicBurstInterferogram
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            #filter master and slave images
+            for burstPrefix, swath in zip([self._insar.masterBurstPrefix, self._insar.slaveBurstPrefix], 
+                                   [masterTrack.frames[i].swaths[j], slaveTrack.frames[i].swaths[j]]):
+                slcDir = os.path.join('../', frameDir, swathDir, burstPrefix)
+                slcLowerDir = os.path.join(ionDir['subband'][0], frameDir, swathDir, burstPrefix)
+                slcUpperDir = os.path.join(ionDir['subband'][1], frameDir, swathDir, burstPrefix)
+                if not os.path.exists(slcLowerDir):
+                    os.makedirs(slcLowerDir)
+                if not os.path.exists(slcUpperDir):
+                    os.makedirs(slcUpperDir)
+                for k in range(swath.numberOfBursts):
+                    print('processing burst: %02d'%(k+1))
+                    slc = os.path.join(slcDir, burstPrefix+'_%02d.slc'%(k+1))
+                    slcLower = os.path.join(slcLowerDir, burstPrefix+'_%02d.slc'%(k+1))
+                    slcUpper = os.path.join(slcUpperDir, burstPrefix+'_%02d.slc'%(k+1))
+                    rg_filter(slc, 2, 
+                        [slcLower, slcUpper], 
+                        subbandBandWidth, 
+                        subbandFrequencyCenter, 
+                        257, 2048, 0.1, 0, 0.0)
+            #resample
+            for l in range(2):
+                os.chdir(os.path.join(ionDir['subband'][l], frameDir, swathDir))
+                #recreate xml file to remove the file path
+                #can also use fixImageXml.py?
+                for burstPrefix, swath in zip([self._insar.masterBurstPrefix, self._insar.slaveBurstPrefix], 
+                                       [masterTrack.frames[i].swaths[j], slaveTrack.frames[i].swaths[j]]):
+                    os.chdir(burstPrefix)
+                    for k in range(swath.numberOfBursts):
+                        slc = burstPrefix+'_%02d.slc'%(k+1)
+                        img = isceobj.createSlcImage()
+                        img.load(slc + '.xml')
+                        img.setFilename(slc)
+                        img.extraFilename = slc + '.vrt'
+                        img.setAccessMode('READ')
+                        img.renderHdr()
+                    os.chdir('../')
+
+                #############################################
+                #1. form interferogram
+                #############################################
+                masterSwath = masterTrack.frames[i].swaths[j]
+                slaveSwath = slaveTrack.frames[i].swaths[j]
+
+                #set up resampling parameters
+                width = masterSwath.numberOfSamples
+                length = masterSwath.numberOfLines
+                polyCoeff = self._insar.rangeResidualOffsetCc[i][j]
+                rgIndex = (np.arange(width)-polyCoeff[-1][0])/polyCoeff[-1][1]
+                azIndex = (np.arange(length)-polyCoeff[-1][2])/polyCoeff[-1][3]
+                rangeOffset =  polyCoeff[0][0] + polyCoeff[0][1]*rgIndex[None,:] + polyCoeff[0][2]*rgIndex[None,:]**2 + \
+                              (polyCoeff[1][0] + polyCoeff[1][1]*rgIndex[None,:]) * azIndex[:, None] + \
+                               polyCoeff[2][0] * azIndex[:, None]**2
+                azimuthOffset = self._insar.azimuthResidualOffsetCc[i][j]
+
+                slaveBurstResampledDir = self._insar.slaveBurstPrefix + '_2_coreg_cc'
+                interferogramDir = 'burst_interf_2_coreg_cc'
+                interferogramPrefix = self._insar.masterBurstPrefix + '-' + self._insar.slaveBurstPrefix
+                resampleBursts(masterSwath, slaveSwath, 
+                    self._insar.masterBurstPrefix, self._insar.slaveBurstPrefix, slaveBurstResampledDir, interferogramDir,
+                    self._insar.masterBurstPrefix, self._insar.slaveBurstPrefix, self._insar.slaveBurstPrefix, interferogramPrefix, 
+                    os.path.join('../../../../{}/{}'.format(frameDir, swathDir), self._insar.rangeOffset), 
+                    os.path.join('../../../../{}/{}'.format(frameDir, swathDir), self._insar.azimuthOffset), 
+                    rangeOffsetResidual=rangeOffset, azimuthOffsetResidual=azimuthOffset)
+
+                os.chdir(self._insar.masterBurstPrefix)
+                mosaicBurstAmplitude(masterSwath, self._insar.masterBurstPrefix, self._insar.masterMagnitude, numberOfLooksThreshold=4)
+                os.chdir('../')
+
+                os.chdir(slaveBurstResampledDir)
+                mosaicBurstAmplitude(masterSwath, self._insar.slaveBurstPrefix, self._insar.slaveMagnitude, numberOfLooksThreshold=4)
+                os.chdir('../')
+
+                os.chdir(interferogramDir)
+                mosaicBurstInterferogram(masterSwath, interferogramPrefix, self._insar.interferogram, numberOfLooksThreshold=4)
+                os.chdir('../')
+
+
+                amp = np.zeros((masterSwath.numberOfLines, 2*masterSwath.numberOfSamples), dtype=np.float32)
+                amp[0:, 1:masterSwath.numberOfSamples*2:2] = np.fromfile(os.path.join(slaveBurstResampledDir, self._insar.slaveMagnitude), \
+                    dtype=np.float32).reshape(masterSwath.numberOfLines, masterSwath.numberOfSamples)
+                amp[0:, 0:masterSwath.numberOfSamples*2:2] = np.fromfile(os.path.join(self._insar.masterBurstPrefix, self._insar.masterMagnitude), \
+                    dtype=np.float32).reshape(masterSwath.numberOfLines, masterSwath.numberOfSamples)
+                amp.astype(np.float32).tofile(self._insar.amplitude)
+                create_xml(self._insar.amplitude, masterSwath.numberOfSamples, masterSwath.numberOfLines, 'amp')
+
+                os.rename(os.path.join(interferogramDir, self._insar.interferogram), self._insar.interferogram)
+                os.rename(os.path.join(interferogramDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+                os.rename(os.path.join(interferogramDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+
+                #############################################
+                #2. delete subband slcs
+                #############################################
+                shutil.rmtree(self._insar.masterBurstPrefix)
+                shutil.rmtree(self._insar.slaveBurstPrefix)
+                shutil.rmtree(slaveBurstResampledDir)
+                shutil.rmtree(interferogramDir)
+
+                os.chdir('../../../')
+
+
+    ############################################################
+    # STEP 3. mosaic swaths
+    ############################################################
+    from isceobj.Alos2Proc.runSwathMosaic import swathMosaic
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+    for k in range(2):
+        os.chdir(ionDir['subband'][k])
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            os.chdir(frameDir)
+
+            mosaicDir = 'mosaic'
+            if not os.path.exists(mosaicDir):
+                os.makedirs(mosaicDir)
+            os.chdir(mosaicDir)
+
+            if self._insar.endingSwath-self._insar.startingSwath+1 == 1:
+                import shutil
+                swathDir = 's{}'.format(masterTrack.frames[i].swaths[0].swathNumber)
+                
+                # if not os.path.isfile(self._insar.interferogram):
+                #     os.symlink(os.path.join('../', swathDir, self._insar.interferogram), self._insar.interferogram)
+                # shutil.copy2(os.path.join('../', swathDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+                # shutil.copy2(os.path.join('../', swathDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+                # if not os.path.isfile(self._insar.amplitude):
+                #     os.symlink(os.path.join('../', swathDir, self._insar.amplitude), self._insar.amplitude)
+                # shutil.copy2(os.path.join('../', swathDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+                # shutil.copy2(os.path.join('../', swathDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+                os.rename(os.path.join('../', swathDir, self._insar.interferogram), self._insar.interferogram)
+                os.rename(os.path.join('../', swathDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+                os.rename(os.path.join('../', swathDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+                os.rename(os.path.join('../', swathDir, self._insar.amplitude), self._insar.amplitude)
+                os.rename(os.path.join('../', swathDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+                os.rename(os.path.join('../', swathDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+                os.chdir('../')
+                os.chdir('../')
+                continue
+
+            #choose offsets
+            numberOfFrames = len(masterTrack.frames)
+            numberOfSwaths = len(masterTrack.frames[i].swaths)
+            if self.swathOffsetMatching:
+                #no need to do this as the API support 2-d list
+                #rangeOffsets = (np.array(self._insar.swathRangeOffsetMatchingMaster)).reshape(numberOfFrames, numberOfSwaths)
+                #azimuthOffsets = (np.array(self._insar.swathAzimuthOffsetMatchingMaster)).reshape(numberOfFrames, numberOfSwaths)
+                rangeOffsets = self._insar.swathRangeOffsetMatchingMaster
+                azimuthOffsets = self._insar.swathAzimuthOffsetMatchingMaster
+
+            else:
+                #rangeOffsets = (np.array(self._insar.swathRangeOffsetGeometricalMaster)).reshape(numberOfFrames, numberOfSwaths)
+                #azimuthOffsets = (np.array(self._insar.swathAzimuthOffsetGeometricalMaster)).reshape(numberOfFrames, numberOfSwaths)
+                rangeOffsets = self._insar.swathRangeOffsetGeometricalMaster
+                azimuthOffsets = self._insar.swathAzimuthOffsetGeometricalMaster
+
+            rangeOffsets = rangeOffsets[i]
+            azimuthOffsets = azimuthOffsets[i]
+
+            #list of input files
+            inputInterferograms = []
+            inputAmplitudes = []
+            for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+                swathDir = 's{}'.format(swathNumber)
+                inputInterferograms.append(os.path.join('../', swathDir, self._insar.interferogram))
+                inputAmplitudes.append(os.path.join('../', swathDir, self._insar.amplitude))
+
+            #note that frame parameters are updated after mosaicking
+            #mosaic amplitudes
+            swathMosaic(masterTrack.frames[i], inputAmplitudes, self._insar.amplitude, 
+                rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, resamplingMethod=0)
+            #mosaic interferograms
+            swathMosaic(masterTrack.frames[i], inputInterferograms, self._insar.interferogram, 
+                rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, updateFrame=False, phaseCompensation=True, resamplingMethod=1)
+
+            create_xml(self._insar.amplitude, masterTrack.frames[i].numberOfSamples, masterTrack.frames[i].numberOfLines, 'amp')
+            create_xml(self._insar.interferogram, masterTrack.frames[i].numberOfSamples, masterTrack.frames[i].numberOfLines, 'int')
+
+            os.chdir('../')
+            os.chdir('../')
+        os.chdir('../')
+
+
+    ############################################################
+    # STEP 4. mosaic frames
+    ############################################################
+    from isceobj.Alos2Proc.runFrameMosaic import frameMosaic
+    from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+    for k in range(2):
+        os.chdir(ionDir['subband'][k])
+
+        mosaicDir = 'insar'
+        if not os.path.exists(mosaicDir):
+            os.makedirs(mosaicDir)
+        os.chdir(mosaicDir)
+
+        numberOfFrames = len(masterTrack.frames)
+        if numberOfFrames == 1:
+            import shutil
+            frameDir = os.path.join('f1_{}/mosaic'.format(self._insar.masterFrames[0]))
+            # if not os.path.isfile(self._insar.interferogram):
+            #     os.symlink(os.path.join('../', frameDir, self._insar.interferogram), self._insar.interferogram)
+            # #shutil.copy2() can overwrite
+            # shutil.copy2(os.path.join('../', frameDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+            # shutil.copy2(os.path.join('../', frameDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+            # if not os.path.isfile(self._insar.amplitude):
+            #     os.symlink(os.path.join('../', frameDir, self._insar.amplitude), self._insar.amplitude)
+            # shutil.copy2(os.path.join('../', frameDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+            # shutil.copy2(os.path.join('../', frameDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+            os.rename(os.path.join('../', frameDir, self._insar.interferogram), self._insar.interferogram)
+            os.rename(os.path.join('../', frameDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+            os.rename(os.path.join('../', frameDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+            os.rename(os.path.join('../', frameDir, self._insar.amplitude), self._insar.amplitude)
+            os.rename(os.path.join('../', frameDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+            os.rename(os.path.join('../', frameDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+        else:
+            #choose offsets
+            if self.frameOffsetMatching:
+                rangeOffsets = self._insar.frameRangeOffsetMatchingMaster
+                azimuthOffsets = self._insar.frameAzimuthOffsetMatchingMaster
+            else:
+                rangeOffsets = self._insar.frameRangeOffsetGeometricalMaster
+                azimuthOffsets = self._insar.frameAzimuthOffsetGeometricalMaster
+
+            #list of input files
+            inputInterferograms = []
+            inputAmplitudes = []
+            for i, frameNumber in enumerate(self._insar.masterFrames):
+                frameDir = 'f{}_{}'.format(i+1, frameNumber)
+                inputInterferograms.append(os.path.join('../', frameDir, 'mosaic', self._insar.interferogram))
+                inputAmplitudes.append(os.path.join('../', frameDir, 'mosaic', self._insar.amplitude))
+
+            #note that track parameters are updated after mosaicking
+            #mosaic amplitudes
+            frameMosaic(masterTrack, inputAmplitudes, self._insar.amplitude, 
+                rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+                updateTrack=False, phaseCompensation=False, resamplingMethod=0)
+            #mosaic interferograms
+            frameMosaic(masterTrack, inputInterferograms, self._insar.interferogram, 
+                rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, 
+                updateTrack=False, phaseCompensation=True, resamplingMethod=1)
+
+            create_xml(self._insar.amplitude, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'amp')
+            create_xml(self._insar.interferogram, masterTrack.numberOfSamples, masterTrack.numberOfLines, 'int')
+
+        os.chdir('../')
+        os.chdir('../')
+
+
+    ############################################################
+    # STEP 5. clear frame processing files
+    ############################################################
+    import shutil
+    from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+
+    for k in range(2):
+        os.chdir(ionDir['subband'][k])
+        for i, frameNumber in enumerate(self._insar.masterFrames):
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            shutil.rmtree(frameDir)
+            #cmd = 'rm -rf {}'.format(frameDir)
+            #runCmd(cmd)
+        os.chdir('../')
+
+
+    ############################################################
+    # STEP 6. create differential interferograms
+    ############################################################
+    import numpy as np
+    from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+
+    for k in range(2):
+        os.chdir(ionDir['subband'][k])
+
+        insarDir = ionDir['insar']
+        if not os.path.exists(insarDir):
+            os.makedirs(insarDir)
+        os.chdir(insarDir)
+
+        rangePixelSize = self._insar.numberRangeLooks1 * masterTrack.rangePixelSize
+        radarWavelength = subbandRadarWavelength[k]
+        rectRangeOffset = os.path.join('../../../', insarDir, self._insar.rectRangeOffset)
+
+        cmd = "imageMath.py -e='a*exp(-1.0*J*b*4.0*{}*{}/{}) * (b!=0)' --a={} --b={} -o {} -t cfloat".format(np.pi, rangePixelSize, radarWavelength, self._insar.interferogram, rectRangeOffset, self._insar.differentialInterferogram)
+        runCmd(cmd)
+
+        os.chdir('../../')
+
+
+    os.chdir('../')
+    catalog.printToLog(logger, "runIonSubband")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+def defineIonDir():
+    '''
+    define directory names for ionospheric correction
+    '''
+
+    ionDir = {
+        #swath mosaicking directory
+        'swathMosaic' : 'mosaic',
+        #final insar processing directory
+        'insar' : 'insar',
+        #ionospheric correction directory
+        'ion' : 'ion',
+        #subband directory
+        'subband' : ['lower', 'upper'],
+        #final ionospheric phase calculation directory
+        'ionCal' : 'ion_cal'
+        }
+
+    return ionDir
+
+
+def defineIonFilenames():
+    pass
+
+
+
+
+
+
+

components/isceobj/Alos2burstProc/runLookSd.py

@@ -0,0 +1,57 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+from contrib.alos2proc.alos2proc import look
+from isceobj.Alos2Proc.Alos2ProcPublic import waterBodyRadar
+
+logger = logging.getLogger('isce.alos2burstinsar.runLookSd')
+
+def runLookSd(self):
+    '''take looks
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    #masterTrack = self._insar.loadTrack(master=True)
+    #slaveTrack = self._insar.loadTrack(master=False)
+    wbdFile = os.path.abspath(self._insar.wbd)
+
+    sdDir = 'sd'
+    if not os.path.exists(sdDir):
+        os.makedirs(sdDir)
+    os.chdir(sdDir)
+
+    sd = isceobj.createImage()
+    sd.load(self._insar.interferogramSd[0]+'.xml')
+    width = sd.width
+    length = sd.length
+    width2 = int(width / self._insar.numberRangeLooksSd)
+    length2 = int(length / self._insar.numberAzimuthLooksSd)
+
+    if not ((self._insar.numberRangeLooksSd == 1) and (self._insar.numberAzimuthLooksSd == 1)):
+        #take looks
+        for sd, sdMultilook in zip(self._insar.interferogramSd, self._insar.multilookInterferogramSd):
+            look(sd, sdMultilook, width, self._insar.numberRangeLooksSd, self._insar.numberAzimuthLooksSd, 4, 0, 1)
+            create_xml(sdMultilook, width2, length2, 'int')
+        look(os.path.join('../insar', self._insar.latitude), self._insar.multilookLatitudeSd, width, 
+            self._insar.numberRangeLooksSd, self._insar.numberAzimuthLooksSd, 3, 0, 1)
+        look(os.path.join('../insar', self._insar.longitude), self._insar.multilookLongitudeSd, width, 
+            self._insar.numberRangeLooksSd, self._insar.numberAzimuthLooksSd, 3, 0, 1)
+        create_xml(self._insar.multilookLatitudeSd, width2, length2, 'double')
+        create_xml(self._insar.multilookLongitudeSd, width2, length2, 'double')
+        #water body
+        waterBodyRadar(self._insar.multilookLatitudeSd, self._insar.multilookLongitudeSd, wbdFile, self._insar.multilookWbdOutSd)
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runLookSd")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+

components/isceobj/Alos2burstProc/runPreprocessor.py

@@ -0,0 +1,521 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import glob
+import logging
+import datetime
+import numpy as np
+
+import isceobj
+import isceobj.Sensor.MultiMode as MultiMode
+from isceobj.Planet.Planet import Planet
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+from isceobj.Alos2Proc.Alos2ProcPublic import getBboxRdr
+from isceobj.Alos2Proc.Alos2ProcPublic import getBboxGeo
+
+logger = logging.getLogger('isce.alos2burstinsar.runPreprocessor')
+
+def runPreprocessor(self):
+    '''Extract images.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+
+
+    #find files
+    #actually no need to use absolute path any longer, since we are able to find file from vrt now. 27-JAN-2020, CRL.
+    #denseoffset may still need absolute path when making links
+    self.masterDir = os.path.abspath(self.masterDir)
+    self.slaveDir = os.path.abspath(self.slaveDir)
+
+    ledFilesMaster = sorted(glob.glob(os.path.join(self.masterDir, 'LED-ALOS2*-*-*')))
+    imgFilesMaster = sorted(glob.glob(os.path.join(self.masterDir, 'IMG-{}-ALOS2*-*-*'.format(self.masterPolarization.upper()))))
+
+    ledFilesSlave = sorted(glob.glob(os.path.join(self.slaveDir, 'LED-ALOS2*-*-*')))
+    imgFilesSlave = sorted(glob.glob(os.path.join(self.slaveDir, 'IMG-{}-ALOS2*-*-*'.format(self.slavePolarization.upper()))))
+
+    firstFrameMaster = ledFilesMaster[0].split('-')[-3][-4:]
+    firstFrameSlave = ledFilesSlave[0].split('-')[-3][-4:]
+    firstFrameImagesMaster = sorted(glob.glob(os.path.join(self.masterDir, 'IMG-{}-ALOS2*{}-*-*'.format(self.masterPolarization.upper(), firstFrameMaster))))
+    firstFrameImagesSlave = sorted(glob.glob(os.path.join(self.slaveDir, 'IMG-{}-ALOS2*{}-*-*'.format(self.slavePolarization.upper(), firstFrameSlave))))
+
+
+    #determin operation mode
+    masterMode = os.path.basename(ledFilesMaster[0]).split('-')[-1][0:3]
+    slaveMode = os.path.basename(ledFilesSlave[0]).split('-')[-1][0:3]
+    spotlightModes = ['SBS']
+    stripmapModes = ['UBS', 'UBD', 'HBS', 'HBD', 'HBQ', 'FBS', 'FBD', 'FBQ']
+    scansarNominalModes = ['WBS', 'WBD', 'WWS', 'WWD']
+    scansarWideModes = ['VBS', 'VBD']
+    scansarModes = ['WBS', 'WBD', 'WWS', 'WWD', 'VBS', 'VBD']
+
+    #usable combinations
+    if (masterMode in spotlightModes) and (slaveMode in spotlightModes):
+        self._insar.modeCombination = 0
+    elif (masterMode in stripmapModes) and (slaveMode in stripmapModes):
+        self._insar.modeCombination = 1
+    elif (masterMode in scansarNominalModes) and (slaveMode in scansarNominalModes):
+        self._insar.modeCombination = 21
+    elif (masterMode in scansarWideModes) and (slaveMode in scansarWideModes):
+        self._insar.modeCombination = 22
+    elif (masterMode in scansarNominalModes) and (slaveMode in stripmapModes):
+        self._insar.modeCombination = 31
+    elif (masterMode in scansarWideModes) and (slaveMode in stripmapModes):
+        self._insar.modeCombination = 32
+    else:
+        print('\n\nthis mode combination is not possible')
+        print('note that for ScanSAR-stripmap, ScanSAR must be master\n\n')
+        raise Exception('mode combination not supported')
+
+
+    if self._insar.modeCombination != 21:
+        print('\n\nburst processing only support {}\n\n'.format(scansarNominalModes))
+        raise Exception('mode combination not supported')
+
+
+    #determine default number of looks:
+    self._insar.numberRangeLooks1 = self.numberRangeLooks1
+    self._insar.numberAzimuthLooks1 = self.numberAzimuthLooks1
+    self._insar.numberRangeLooks2 = self.numberRangeLooks2
+    self._insar.numberAzimuthLooks2 = self.numberAzimuthLooks2
+    #the following two will be automatically determined by runRdrDemOffset.py
+    self._insar.numberRangeLooksSim = self.numberRangeLooksSim
+    self._insar.numberAzimuthLooksSim = self.numberAzimuthLooksSim
+    self._insar.numberRangeLooksIon = self.numberRangeLooksIon
+    self._insar.numberAzimuthLooksIon = self.numberAzimuthLooksIon
+    self._insar.numberRangeLooksSd = self.numberRangeLooksSd
+    self._insar.numberAzimuthLooksSd = self.numberAzimuthLooksSd
+
+    #force number of looks 1 to 1
+    self.numberRangeLooks1 = 1
+    self.numberAzimuthLooks1 = 1
+    self._insar.numberRangeLooks1 = 1
+    self._insar.numberAzimuthLooks1 = 1
+    if self._insar.numberRangeLooks2 == None:
+        self._insar.numberRangeLooks2 = 7
+    if self._insar.numberAzimuthLooks2 == None:
+        self._insar.numberAzimuthLooks2 = 2
+    if self._insar.numberRangeLooksIon == None:
+        self._insar.numberRangeLooksIon = 42
+    if self._insar.numberAzimuthLooksIon == None:
+        self._insar.numberAzimuthLooksIon = 12
+    if self._insar.numberRangeLooksSd == None:
+        self._insar.numberRangeLooksSd = 14
+    if self._insar.numberAzimuthLooksSd == None:
+        self._insar.numberAzimuthLooksSd = 4
+
+    #define processing file names
+    self._insar.masterDate = os.path.basename(ledFilesMaster[0]).split('-')[2]
+    self._insar.slaveDate = os.path.basename(ledFilesSlave[0]).split('-')[2]
+    self._insar.setFilename(masterDate=self._insar.masterDate, slaveDate=self._insar.slaveDate, 
+        nrlks1=self._insar.numberRangeLooks1, nalks1=self._insar.numberAzimuthLooks1, 
+        nrlks2=self._insar.numberRangeLooks2, nalks2=self._insar.numberAzimuthLooks2)
+    self._insar.setFilenameSd(masterDate=self._insar.masterDate, slaveDate=self._insar.slaveDate, 
+        nrlks1=self._insar.numberRangeLooks1, nalks1=self._insar.numberAzimuthLooks1, 
+        nrlks_sd=self._insar.numberRangeLooksSd, nalks_sd=self._insar.numberAzimuthLooksSd, nsd=3)
+
+    #find frame numbers
+    if (self._insar.modeCombination == 31) or (self._insar.modeCombination == 32):
+        if (self.masterFrames == None) or (self.slaveFrames == None):
+            raise Exception('for ScanSAR-stripmap inteferometry, you must set master and slave frame numbers')
+    #if not set, find frames automatically
+    if self.masterFrames == None:
+        self.masterFrames = []
+        for led in ledFilesMaster:
+            frameNumber = os.path.basename(led).split('-')[1][-4:]
+            if frameNumber not in self.masterFrames:
+                self.masterFrames.append(frameNumber)
+    if self.slaveFrames == None:
+        self.slaveFrames = []
+        for led in ledFilesSlave:
+            frameNumber = os.path.basename(led).split('-')[1][-4:]
+            if frameNumber not in self.slaveFrames:
+                self.slaveFrames.append(frameNumber)
+    #sort frames
+    self.masterFrames = sorted(self.masterFrames)
+    self.slaveFrames = sorted(self.slaveFrames)
+    #check number of frames
+    if len(self.masterFrames) != len(self.slaveFrames):
+        raise Exception('number of frames in master dir is not equal to number of frames \
+            in slave dir. please set frame number manually')
+
+
+    #find swath numbers (if not ScanSAR-ScanSAR, compute valid swaths)
+    if (self._insar.modeCombination == 0) or (self._insar.modeCombination == 1):
+        self.startingSwath = 1
+        self.endingSwath = 1
+
+    if self._insar.modeCombination == 21:
+        if self.startingSwath == None:
+            self.startingSwath = 1
+        if self.endingSwath == None:
+            self.endingSwath = 5
+
+    if self._insar.modeCombination == 22:
+        if self.startingSwath == None:
+            self.startingSwath = 1
+        if self.endingSwath == None:
+            self.endingSwath = 7
+
+    #determine starting and ending swaths for ScanSAR-stripmap, user's settings are overwritten
+    #use first frame to check overlap
+    if (self._insar.modeCombination == 31) or (self._insar.modeCombination == 32):
+        if self._insar.modeCombination == 31:
+            numberOfSwaths = 5
+        else:
+            numberOfSwaths = 7
+        overlapSubswaths = []
+        for i in range(numberOfSwaths):
+            overlapRatio = check_overlap(ledFilesMaster[0], firstFrameImagesMaster[i], ledFilesSlave[0], firstFrameImagesSlave[0])
+            if overlapRatio > 1.0 / 4.0:
+                overlapSubswaths.append(i+1)
+        if overlapSubswaths == []:
+            raise Exception('There is no overlap area between the ScanSAR-stripmap pair')
+        self.startingSwath = int(overlapSubswaths[0])
+        self.endingSwath = int(overlapSubswaths[-1])
+
+    #save the valid frames and swaths for future processing
+    self._insar.masterFrames = self.masterFrames
+    self._insar.slaveFrames = self.slaveFrames
+    self._insar.startingSwath = self.startingSwath
+    self._insar.endingSwath = self.endingSwath
+
+
+    ##################################################
+    #1. create directories and read data
+    ##################################################
+    self.master.configure()
+    self.slave.configure()
+    self.master.track.configure()
+    self.slave.track.configure()
+    for i, (masterFrame, slaveFrame) in enumerate(zip(self._insar.masterFrames, self._insar.slaveFrames)):
+        #frame number starts with 1
+        frameDir = 'f{}_{}'.format(i+1, masterFrame)
+        if not os.path.exists(frameDir):
+            os.makedirs(frameDir)
+        os.chdir(frameDir)
+
+        #attach a frame to master and slave
+        frameObjMaster = MultiMode.createFrame()
+        frameObjSlave = MultiMode.createFrame()
+        frameObjMaster.configure()
+        frameObjSlave.configure()
+        self.master.track.frames.append(frameObjMaster)
+        self.slave.track.frames.append(frameObjSlave)
+
+        #swath number starts with 1
+        for j in range(self._insar.startingSwath, self._insar.endingSwath+1):
+            print('processing frame {} swath {}'.format(masterFrame, j))
+
+            swathDir = 's{}'.format(j)
+            if not os.path.exists(swathDir):
+                os.makedirs(swathDir)
+            os.chdir(swathDir)
+
+            #attach a swath to master and slave
+            swathObjMaster = MultiMode.createSwath()
+            swathObjSlave = MultiMode.createSwath()
+            swathObjMaster.configure()
+            swathObjSlave.configure()
+            self.master.track.frames[-1].swaths.append(swathObjMaster)
+            self.slave.track.frames[-1].swaths.append(swathObjSlave)
+
+            #setup master
+            self.master.leaderFile = sorted(glob.glob(os.path.join(self.masterDir, 'LED-ALOS2*{}-*-*'.format(masterFrame))))[0]
+            if masterMode in scansarModes:
+                self.master.imageFile = sorted(glob.glob(os.path.join(self.masterDir, 'IMG-{}-ALOS2*{}-*-*-F{}'.format(self.masterPolarization.upper(), masterFrame, j))))[0]
+            else:
+                self.master.imageFile = sorted(glob.glob(os.path.join(self.masterDir, 'IMG-{}-ALOS2*{}-*-*'.format(self.masterPolarization.upper(), masterFrame))))[0]
+            self.master.outputFile = self._insar.masterSlc
+            self.master.useVirtualFile = self.useVirtualFile
+            #read master
+            (imageFDR, imageData)=self.master.readImage()
+            (leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord)=self.master.readLeader()
+            self.master.setSwath(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+            self.master.setFrame(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+            self.master.setTrack(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+
+            #setup slave
+            self.slave.leaderFile = sorted(glob.glob(os.path.join(self.slaveDir, 'LED-ALOS2*{}-*-*'.format(slaveFrame))))[0]
+            if slaveMode in scansarModes:
+                self.slave.imageFile = sorted(glob.glob(os.path.join(self.slaveDir, 'IMG-{}-ALOS2*{}-*-*-F{}'.format(self.slavePolarization.upper(), slaveFrame, j))))[0]
+            else:
+                self.slave.imageFile = sorted(glob.glob(os.path.join(self.slaveDir, 'IMG-{}-ALOS2*{}-*-*'.format(self.slavePolarization.upper(), slaveFrame))))[0]
+            self.slave.outputFile = self._insar.slaveSlc
+            self.slave.useVirtualFile = self.useVirtualFile
+            #read slave
+            (imageFDR, imageData)=self.slave.readImage()
+            (leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord)=self.slave.readLeader()
+            self.slave.setSwath(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+            self.slave.setFrame(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+            self.slave.setTrack(leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData)
+
+            os.chdir('../')
+        self._insar.saveProduct(self.master.track.frames[-1], self._insar.masterFrameParameter)
+        self._insar.saveProduct(self.slave.track.frames[-1], self._insar.slaveFrameParameter)
+        os.chdir('../')
+    self._insar.saveProduct(self.master.track, self._insar.masterTrackParameter)
+    self._insar.saveProduct(self.slave.track, self._insar.slaveTrackParameter)
+
+
+    ##################################################
+    #2. compute burst synchronization
+    ##################################################
+    #burst synchronization may slowly change along a track as a result of the changing relative speed of the two flights
+    #in one frame, real unsynchronized time is the same for all swaths
+    unsynTime = 0
+    #real synchronized time/percentage depends on the swath burst length (synTime = burstlength - abs(unsynTime))
+    #synTime = 0
+    synPercentage = 0
+
+    numberOfFrames = len(self._insar.masterFrames)
+    numberOfSwaths = self._insar.endingSwath - self._insar.startingSwath + 1
+    
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            masterSwath = self.master.track.frames[i].swaths[j]
+            slaveSwath = self.slave.track.frames[i].swaths[j]
+            #using Piyush's code for computing range and azimuth offsets
+            midRange = masterSwath.startingRange + masterSwath.rangePixelSize * masterSwath.numberOfSamples * 0.5
+            midSensingStart = masterSwath.sensingStart + datetime.timedelta(seconds = masterSwath.numberOfLines * 0.5 / masterSwath.prf)
+            llh = self.master.track.orbit.rdr2geo(midSensingStart, midRange)
+            slvaz, slvrng = self.slave.track.orbit.geo2rdr(llh)
+            ###Translate to offsets
+            #note that slave range pixel size and prf might be different from master, here we assume there is a virtual slave with same
+            #range pixel size and prf
+            rgoff = ((slvrng - slaveSwath.startingRange) / masterSwath.rangePixelSize) - masterSwath.numberOfSamples * 0.5
+            azoff = ((slvaz - slaveSwath.sensingStart).total_seconds() * masterSwath.prf) - masterSwath.numberOfLines * 0.5
+
+            #compute burst synchronization
+            #burst parameters for ScanSAR wide mode not estimed yet
+            if self._insar.modeCombination == 21:
+                scburstStartLine = (masterSwath.burstStartTime - masterSwath.sensingStart).total_seconds() * masterSwath.prf + azoff
+                #slave burst start times corresponding to master burst start times (100% synchronization)
+                scburstStartLines = np.arange(scburstStartLine - 100000*masterSwath.burstCycleLength, \
+                                              scburstStartLine + 100000*masterSwath.burstCycleLength, \
+                                              masterSwath.burstCycleLength)
+                dscburstStartLines = -((slaveSwath.burstStartTime - slaveSwath.sensingStart).total_seconds() * slaveSwath.prf - scburstStartLines)
+                #find the difference with minimum absolute value
+                unsynLines = dscburstStartLines[np.argmin(np.absolute(dscburstStartLines))]
+                if np.absolute(unsynLines) >= slaveSwath.burstLength:
+                    synLines = 0
+                    if unsynLines > 0:
+                        unsynLines = slaveSwath.burstLength
+                    else:
+                        unsynLines = -slaveSwath.burstLength
+                else:
+                    synLines = slaveSwath.burstLength - np.absolute(unsynLines)
+
+                unsynTime += unsynLines / masterSwath.prf
+                synPercentage += synLines / masterSwath.burstLength * 100.0
+
+                catalog.addItem('burst synchronization of frame {} swath {}'.format(frameNumber, swathNumber), '%.1f%%'%(synLines / masterSwath.burstLength * 100.0), 'runPreprocessor')
+
+            ############################################################################################
+            #illustration of the sign of the number of unsynchronized lines (unsynLines)     
+            #The convention is the same as ampcor offset, that is,
+            #              slaveLineNumber = masterLineNumber + unsynLines
+            #
+            # |-----------------------|     ------------
+            # |                       |        ^
+            # |                       |        |
+            # |                       |        |   unsynLines < 0
+            # |                       |        |
+            # |                       |       \ /
+            # |                       |    |-----------------------|
+            # |                       |    |                       |
+            # |                       |    |                       |
+            # |-----------------------|    |                       |
+            #        Master Burst          |                       |
+            #                              |                       |
+            #                              |                       |
+            #                              |                       |
+            #                              |                       |
+            #                              |-----------------------|
+            #                                     Slave Burst
+            #
+            #
+            ############################################################################################
+ 
+            ##burst parameters for ScanSAR wide mode not estimed yet
+            elif self._insar.modeCombination == 31:
+                #scansar is master
+                scburstStartLine = (masterSwath.burstStartTime - masterSwath.sensingStart).total_seconds() * masterSwath.prf + azoff
+                #slave burst start times corresponding to master burst start times (100% synchronization)
+                for k in range(-100000, 100000):
+                    saz_burstx = scburstStartLine + masterSwath.burstCycleLength * k
+                    st_burstx = slaveSwath.sensingStart + datetime.timedelta(seconds=saz_burstx / masterSwath.prf)
+                    if saz_burstx >= 0.0 and saz_burstx <= slaveSwath.numberOfLines -1:
+                        slaveSwath.burstStartTime = st_burstx
+                        slaveSwath.burstLength = masterSwath.burstLength
+                        slaveSwath.burstCycleLength = masterSwath.burstCycleLength
+                        slaveSwath.swathNumber = masterSwath.swathNumber
+                        break
+                #unsynLines = 0
+                #synLines = masterSwath.burstLength
+                #unsynTime += unsynLines / masterSwath.prf
+                #synPercentage += synLines / masterSwath.burstLength * 100.0
+                catalog.addItem('burst synchronization of frame {} swath {}'.format(frameNumber, swathNumber), '%.1f%%'%(100.0), 'runPreprocessor')
+            else:
+                pass
+
+        #overwrite original frame parameter file
+        if self._insar.modeCombination == 31:
+            frameDir = 'f{}_{}'.format(i+1, frameNumber)
+            self._insar.saveProduct(self.slave.track.frames[i], os.path.join(frameDir, self._insar.slaveFrameParameter))
+
+    #getting average
+    if self._insar.modeCombination == 21:
+        unsynTime /= numberOfFrames*numberOfSwaths
+        synPercentage /= numberOfFrames*numberOfSwaths
+    elif self._insar.modeCombination == 31:
+        unsynTime = 0.
+        synPercentage = 100.
+    else:
+        pass
+
+    #record results
+    if (self._insar.modeCombination == 21) or (self._insar.modeCombination == 31):
+        self._insar.burstUnsynchronizedTime = unsynTime
+        self._insar.burstSynchronization = synPercentage
+        catalog.addItem('burst synchronization averaged', '%.1f%%'%(synPercentage), 'runPreprocessor')
+
+
+    ##################################################
+    #3. compute baseline
+    ##################################################
+    #only compute baseline at four corners and center of the master track
+    bboxRdr = getBboxRdr(self.master.track)
+
+    rangeMin = bboxRdr[0]
+    rangeMax = bboxRdr[1]
+    azimuthTimeMin = bboxRdr[2]
+    azimuthTimeMax = bboxRdr[3]
+
+    azimuthTimeMid = azimuthTimeMin+datetime.timedelta(seconds=(azimuthTimeMax-azimuthTimeMin).total_seconds()/2.0)
+    rangeMid = (rangeMin + rangeMax) / 2.0
+
+    points = [[azimuthTimeMin, rangeMin],
+              [azimuthTimeMin, rangeMax],
+              [azimuthTimeMax, rangeMin],
+              [azimuthTimeMax, rangeMax],
+              [azimuthTimeMid, rangeMid]]
+
+    Bpar = []
+    Bperp = []
+    #modify Piyush's code for computing baslines
+    refElp = Planet(pname='Earth').ellipsoid
+    for x in points:
+        masterSV = self.master.track.orbit.interpolate(x[0], method='hermite')
+        target = self.master.track.orbit.rdr2geo(x[0], x[1])
+
+        slvTime, slvrng = self.slave.track.orbit.geo2rdr(target)
+        slaveSV = self.slave.track.orbit.interpolateOrbit(slvTime, method='hermite')
+
+        targxyz = np.array(refElp.LLH(target[0], target[1], target[2]).ecef().tolist())
+        mxyz = np.array(masterSV.getPosition())
+        mvel = np.array(masterSV.getVelocity())
+        sxyz = np.array(slaveSV.getPosition())
+
+        aa = np.linalg.norm(sxyz-mxyz)
+        costheta = (x[1]*x[1] + aa*aa - slvrng*slvrng)/(2.*x[1]*aa)
+
+        Bpar.append(aa*costheta)
+
+        perp = aa * np.sqrt(1 - costheta*costheta)
+        direction = np.sign(np.dot( np.cross(targxyz-mxyz, sxyz-mxyz), mvel))
+        Bperp.append(direction*perp)    
+
+    catalog.addItem('parallel baseline at upperleft of master track', Bpar[0], 'runPreprocessor')
+    catalog.addItem('parallel baseline at upperright of master track', Bpar[1], 'runPreprocessor')
+    catalog.addItem('parallel baseline at lowerleft of master track', Bpar[2], 'runPreprocessor')
+    catalog.addItem('parallel baseline at lowerright of master track', Bpar[3], 'runPreprocessor')
+    catalog.addItem('parallel baseline at center of master track', Bpar[4], 'runPreprocessor')
+
+    catalog.addItem('perpendicular baseline at upperleft of master track', Bperp[0], 'runPreprocessor')
+    catalog.addItem('perpendicular baseline at upperright of master track', Bperp[1], 'runPreprocessor')
+    catalog.addItem('perpendicular baseline at lowerleft of master track', Bperp[2], 'runPreprocessor')
+    catalog.addItem('perpendicular baseline at lowerright of master track', Bperp[3], 'runPreprocessor')
+    catalog.addItem('perpendicular baseline at center of master track', Bperp[4], 'runPreprocessor')
+
+
+    ##################################################
+    #4. compute bounding box
+    ##################################################
+    masterBbox = getBboxGeo(self.master.track)
+    slaveBbox = getBboxGeo(self.slave.track)
+
+    catalog.addItem('master bounding box', masterBbox, 'runPreprocessor')
+    catalog.addItem('slave bounding box', slaveBbox, 'runPreprocessor')
+
+
+    catalog.printToLog(logger, "runPreprocessor")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+
+
+def check_overlap(ldr_m, img_m, ldr_s, img_s):
+    from isceobj.Constants import SPEED_OF_LIGHT
+
+    rangeSamplingRateMaster, widthMaster, nearRangeMaster = read_param_for_checking_overlap(ldr_m, img_m)
+    rangeSamplingRateSlave, widthSlave, nearRangeSlave = read_param_for_checking_overlap(ldr_s, img_s)
+
+    farRangeMaster = nearRangeMaster + (widthMaster-1) * 0.5 * SPEED_OF_LIGHT / rangeSamplingRateMaster
+    farRangeSlave = nearRangeSlave + (widthSlave-1) * 0.5 * SPEED_OF_LIGHT / rangeSamplingRateSlave
+
+    #This should be good enough, although precise image offsets are not used.
+    if farRangeMaster <= nearRangeSlave:
+        overlapRatio = 0.0
+    elif farRangeSlave <= nearRangeMaster:
+        overlapRatio = 0.0
+    else:
+        #                     0                  1               2               3
+        ranges = np.array([nearRangeMaster, farRangeMaster, nearRangeSlave, farRangeSlave])
+        rangesIndex = np.argsort(ranges)
+        overlapRatio = ranges[rangesIndex[2]]-ranges[rangesIndex[1]] / (farRangeMaster-nearRangeMaster)
+
+    return overlapRatio
+
+
+def read_param_for_checking_overlap(leader_file, image_file):
+    from isceobj.Sensor import xmlPrefix
+    import isceobj.Sensor.CEOS as CEOS
+
+    #read from leader file
+    fsampConst = { 104: 1.047915957140240E+08,
+                   52: 5.239579785701190E+07,
+                   34: 3.493053190467460E+07,
+                   17: 1.746526595233730E+07 }
+
+    fp = open(leader_file,'rb')
+    leaderFDR = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/leader_file.xml'),dataFile=fp)
+    leaderFDR.parse()
+    fp.seek(leaderFDR.getEndOfRecordPosition())
+    sceneHeaderRecord = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/scene_record.xml'),dataFile=fp)
+    sceneHeaderRecord.parse()
+    fp.seek(sceneHeaderRecord.getEndOfRecordPosition())
+
+    fsamplookup = int(sceneHeaderRecord.metadata['Range sampling rate in MHz'])
+    rangeSamplingRate = fsampConst[fsamplookup]
+    fp.close()
+    #print('{}'.format(rangeSamplingRate))
+
+    #read from image file
+    fp = open(image_file, 'rb')
+    imageFDR = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/image_file.xml'), dataFile=fp)
+    imageFDR.parse()
+    fp.seek(imageFDR.getEndOfRecordPosition())
+    imageData = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/image_record.xml'), dataFile=fp)
+    imageData.parseFast()
+
+    width = imageFDR.metadata['Number of pixels per line per SAR channel']
+    near_range = imageData.metadata['Slant range to 1st data sample']
+    fp.close()
+    #print('{}'.format(width))
+    #print('{}'.format(near_range))
+
+    return (rangeSamplingRate, width, near_range)
+
+

components/isceobj/Alos2burstProc/runSwathMosaic.py

@@ -0,0 +1,221 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+from isceobj.Alos2Proc.runSwathMosaic import swathMosaic
+from isceobj.Alos2Proc.runSwathMosaic import swathMosaicParameters
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+logger = logging.getLogger('isce.alos2burstinsar.runSwathMosaic')
+
+def runSwathMosaic(self):
+    '''mosaic subswaths
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+
+        mosaicDir = 'mosaic'
+        if not os.path.exists(mosaicDir):
+            os.makedirs(mosaicDir)
+        os.chdir(mosaicDir)
+
+        if self._insar.endingSwath-self._insar.startingSwath+1 == 1:
+            import shutil
+            swathDir = 's{}'.format(masterTrack.frames[i].swaths[0].swathNumber)
+            
+            if not os.path.isfile(self._insar.interferogram):
+                os.symlink(os.path.join('../', swathDir, self._insar.interferogram), self._insar.interferogram)
+            shutil.copy2(os.path.join('../', swathDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+            shutil.copy2(os.path.join('../', swathDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+            if not os.path.isfile(self._insar.amplitude):
+                os.symlink(os.path.join('../', swathDir, self._insar.amplitude), self._insar.amplitude)
+            shutil.copy2(os.path.join('../', swathDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+            shutil.copy2(os.path.join('../', swathDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+            # os.rename(os.path.join('../', swathDir, self._insar.interferogram), self._insar.interferogram)
+            # os.rename(os.path.join('../', swathDir, self._insar.interferogram+'.vrt'), self._insar.interferogram+'.vrt')
+            # os.rename(os.path.join('../', swathDir, self._insar.interferogram+'.xml'), self._insar.interferogram+'.xml')
+            # os.rename(os.path.join('../', swathDir, self._insar.amplitude), self._insar.amplitude)
+            # os.rename(os.path.join('../', swathDir, self._insar.amplitude+'.vrt'), self._insar.amplitude+'.vrt')
+            # os.rename(os.path.join('../', swathDir, self._insar.amplitude+'.xml'), self._insar.amplitude+'.xml')
+
+            #update frame parameters
+            #########################################################
+            frame = masterTrack.frames[i]
+            infImg = isceobj.createImage()
+            infImg.load(self._insar.interferogram+'.xml')
+            #mosaic size
+            frame.numberOfSamples = infImg.width
+            frame.numberOfLines = infImg.length
+            #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+            #range parameters
+            frame.startingRange = frame.swaths[0].startingRange
+            frame.rangeSamplingRate = frame.swaths[0].rangeSamplingRate
+            frame.rangePixelSize = frame.swaths[0].rangePixelSize
+            #azimuth parameters
+            frame.sensingStart = frame.swaths[0].sensingStart
+            frame.prf = frame.swaths[0].prf
+            frame.azimuthPixelSize = frame.swaths[0].azimuthPixelSize
+            frame.azimuthLineInterval = frame.swaths[0].azimuthLineInterval
+
+            #update frame parameters, slave
+            #########################################################
+            frame = slaveTrack.frames[i]
+            #mosaic size
+            frame.numberOfSamples = int(frame.swaths[0].numberOfSamples/self._insar.numberRangeLooks1)
+            frame.numberOfLines = int(frame.swaths[0].numberOfLines/self._insar.numberAzimuthLooks1)
+            #NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
+            #range parameters
+            frame.startingRange = frame.swaths[0].startingRange
+            frame.rangeSamplingRate = frame.swaths[0].rangeSamplingRate
+            frame.rangePixelSize = frame.swaths[0].rangePixelSize
+            #azimuth parameters
+            frame.sensingStart = frame.swaths[0].sensingStart
+            frame.prf = frame.swaths[0].prf
+            frame.azimuthPixelSize = frame.swaths[0].azimuthPixelSize
+            frame.azimuthLineInterval = frame.swaths[0].azimuthLineInterval
+
+            os.chdir('../')
+
+            #save parameter file
+            self._insar.saveProduct(masterTrack.frames[i], self._insar.masterFrameParameter)
+            self._insar.saveProduct(slaveTrack.frames[i], self._insar.slaveFrameParameter)
+
+            os.chdir('../')
+
+            continue
+
+        #choose offsets
+        numberOfFrames = len(masterTrack.frames)
+        numberOfSwaths = len(masterTrack.frames[i].swaths)
+        if self.swathOffsetMatching:
+            #no need to do this as the API support 2-d list
+            #rangeOffsets = (np.array(self._insar.swathRangeOffsetMatchingMaster)).reshape(numberOfFrames, numberOfSwaths)
+            #azimuthOffsets = (np.array(self._insar.swathAzimuthOffsetMatchingMaster)).reshape(numberOfFrames, numberOfSwaths)
+            rangeOffsets = self._insar.swathRangeOffsetMatchingMaster
+            azimuthOffsets = self._insar.swathAzimuthOffsetMatchingMaster
+
+        else:
+            #rangeOffsets = (np.array(self._insar.swathRangeOffsetGeometricalMaster)).reshape(numberOfFrames, numberOfSwaths)
+            #azimuthOffsets = (np.array(self._insar.swathAzimuthOffsetGeometricalMaster)).reshape(numberOfFrames, numberOfSwaths)
+            rangeOffsets = self._insar.swathRangeOffsetGeometricalMaster
+            azimuthOffsets = self._insar.swathAzimuthOffsetGeometricalMaster
+
+        rangeOffsets = rangeOffsets[i]
+        azimuthOffsets = azimuthOffsets[i]
+
+        #list of input files
+        inputInterferograms = []
+        inputAmplitudes = []
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            inputInterferograms.append(os.path.join('../', swathDir, self._insar.interferogram))
+            inputAmplitudes.append(os.path.join('../', swathDir, self._insar.amplitude))
+
+        #note that frame parameters are updated after mosaicking
+        #mosaic amplitudes
+        swathMosaic(masterTrack.frames[i], inputAmplitudes, self._insar.amplitude, 
+            rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, resamplingMethod=0)
+        #mosaic interferograms
+        swathMosaic(masterTrack.frames[i], inputInterferograms, self._insar.interferogram, 
+            rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, updateFrame=True, resamplingMethod=1)
+
+        create_xml(self._insar.amplitude, masterTrack.frames[i].numberOfSamples, masterTrack.frames[i].numberOfLines, 'amp')
+        create_xml(self._insar.interferogram, masterTrack.frames[i].numberOfSamples, masterTrack.frames[i].numberOfLines, 'int')
+
+        #update slave frame parameters here
+        #no matching for slave, always use geometry
+        rangeOffsets = self._insar.swathRangeOffsetGeometricalSlave
+        azimuthOffsets = self._insar.swathAzimuthOffsetGeometricalSlave
+        rangeOffsets = rangeOffsets[i]
+        azimuthOffsets = azimuthOffsets[i]
+        swathMosaicParameters(slaveTrack.frames[i], rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1)
+
+        os.chdir('../')
+
+        #save parameter file
+        self._insar.saveProduct(masterTrack.frames[i], self._insar.masterFrameParameter)
+        self._insar.saveProduct(slaveTrack.frames[i], self._insar.slaveFrameParameter)
+
+        os.chdir('../')
+
+
+    #mosaic spectral diversity interferograms
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+
+        mosaicDir = 'mosaic'
+        if not os.path.exists(mosaicDir):
+            os.makedirs(mosaicDir)
+        os.chdir(mosaicDir)
+
+        if self._insar.endingSwath-self._insar.startingSwath+1 == 1:
+            import shutil
+            swathDir = 's{}'.format(masterTrack.frames[i].swaths[0].swathNumber)
+            
+            for sdFile in self._insar.interferogramSd:
+                if not os.path.isfile(sdFile):
+                    os.symlink(os.path.join('../', swathDir, 'spectral_diversity', sdFile), sdFile)
+                shutil.copy2(os.path.join('../', swathDir, 'spectral_diversity', sdFile+'.vrt'), sdFile+'.vrt')
+                shutil.copy2(os.path.join('../', swathDir, 'spectral_diversity', sdFile+'.xml'), sdFile+'.xml')
+
+            os.chdir('../')
+            os.chdir('../')
+            continue
+
+        #choose offsets
+        numberOfFrames = len(masterTrack.frames)
+        numberOfSwaths = len(masterTrack.frames[i].swaths)
+        if self.swathOffsetMatching:
+            #no need to do this as the API support 2-d list
+            #rangeOffsets = (np.array(self._insar.swathRangeOffsetMatchingMaster)).reshape(numberOfFrames, numberOfSwaths)
+            #azimuthOffsets = (np.array(self._insar.swathAzimuthOffsetMatchingMaster)).reshape(numberOfFrames, numberOfSwaths)
+            rangeOffsets = self._insar.swathRangeOffsetMatchingMaster
+            azimuthOffsets = self._insar.swathAzimuthOffsetMatchingMaster
+
+        else:
+            #rangeOffsets = (np.array(self._insar.swathRangeOffsetGeometricalMaster)).reshape(numberOfFrames, numberOfSwaths)
+            #azimuthOffsets = (np.array(self._insar.swathAzimuthOffsetGeometricalMaster)).reshape(numberOfFrames, numberOfSwaths)
+            rangeOffsets = self._insar.swathRangeOffsetGeometricalMaster
+            azimuthOffsets = self._insar.swathAzimuthOffsetGeometricalMaster
+
+        rangeOffsets = rangeOffsets[i]
+        azimuthOffsets = azimuthOffsets[i]
+
+        #list of input files
+        inputSd = [[], [], []]
+        for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
+            swathDir = 's{}'.format(swathNumber)
+            for k, sdFile in enumerate(self._insar.interferogramSd):
+                inputSd[k].append(os.path.join('../', swathDir, 'spectral_diversity', sdFile))
+
+        #mosaic spectral diversity interferograms
+        for inputSdList, outputSdFile in zip(inputSd, self._insar.interferogramSd):
+            swathMosaic(masterTrack.frames[i], inputSdList, outputSdFile, 
+                rangeOffsets, azimuthOffsets, self._insar.numberRangeLooks1, self._insar.numberAzimuthLooks1, updateFrame=False, phaseCompensation=True, pcRangeLooks=5, pcAzimuthLooks=5, filt=True, resamplingMethod=1)
+
+        for sdFile in self._insar.interferogramSd:
+            create_xml(sdFile, masterTrack.frames[i].numberOfSamples, masterTrack.frames[i].numberOfLines, 'int')
+
+        os.chdir('../')
+        os.chdir('../')
+
+
+    catalog.printToLog(logger, "runSwathMosaic")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+

components/isceobj/Alos2burstProc/runSwathOffset.py

@@ -0,0 +1,73 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import logging
+
+import isceobj
+from isceobj.Alos2Proc.runSwathOffset import swathOffset
+
+logger = logging.getLogger('isce.alos2burstinsar.runSwathOffset')
+
+def runSwathOffset(self):
+    '''estimate swath offsets.
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    slaveTrack = self._insar.loadTrack(master=False)
+
+
+
+    for i, frameNumber in enumerate(self._insar.masterFrames):
+        frameDir = 'f{}_{}'.format(i+1, frameNumber)
+        os.chdir(frameDir)
+
+        mosaicDir = 'mosaic'
+        if not os.path.exists(mosaicDir):
+            os.makedirs(mosaicDir)
+        os.chdir(mosaicDir)
+
+        if self._insar.endingSwath-self._insar.startingSwath+1 == 1:
+            os.chdir('../../')
+            continue
+
+        #compute swath offset
+        offsetMaster = swathOffset(masterTrack.frames[i], os.path.join(self._insar.masterBurstPrefix, self._insar.masterMagnitude), self._insar.masterSwathOffset, 
+                                   crossCorrelation=self.swathOffsetMatching, numberOfAzimuthLooks=1)
+        #only use geometrical offset for slave
+        offsetSlave = swathOffset(slaveTrack.frames[i], os.path.join(self._insar.slaveBurstPrefix, self._insar.slaveMagnitude), self._insar.slaveSwathOffset, 
+                                  crossCorrelation=False, numberOfAzimuthLooks=1)
+
+        #initialization
+        if i == 0:
+            self._insar.swathRangeOffsetGeometricalMaster = []
+            self._insar.swathAzimuthOffsetGeometricalMaster = []
+            self._insar.swathRangeOffsetGeometricalSlave = []
+            self._insar.swathAzimuthOffsetGeometricalSlave = []
+            if self.swathOffsetMatching:
+                self._insar.swathRangeOffsetMatchingMaster = []
+                self._insar.swathAzimuthOffsetMatchingMaster = []
+                #self._insar.swathRangeOffsetMatchingSlave = []
+                #self._insar.swathAzimuthOffsetMatchingSlave = []
+
+        #append list directly, as the API support 2-d list
+        self._insar.swathRangeOffsetGeometricalMaster.append(offsetMaster[0])
+        self._insar.swathAzimuthOffsetGeometricalMaster.append(offsetMaster[1])
+        self._insar.swathRangeOffsetGeometricalSlave.append(offsetSlave[0])
+        self._insar.swathAzimuthOffsetGeometricalSlave.append(offsetSlave[1])
+        if self.swathOffsetMatching:
+            self._insar.swathRangeOffsetMatchingMaster.append(offsetMaster[2])
+            self._insar.swathAzimuthOffsetMatchingMaster.append(offsetMaster[3])
+            #self._insar.swathRangeOffsetMatchingSlave.append(offsetSlave[2])
+            #self._insar.swathAzimuthOffsetMatchingSlave.append(offsetSlave[3])
+
+        os.chdir('../../')
+
+    catalog.printToLog(logger, "runSwathOffset")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+
+

components/isceobj/Alos2burstProc/runUnwrapSnaphuSd.py

@@ -0,0 +1,199 @@
+#
+# Author: Cunren Liang
+# Copyright 2015-present, NASA-JPL/Caltech
+#
+
+import os
+import shutil
+import logging
+import datetime
+import numpy as np
+
+import isceobj
+from isceobj.Alos2Proc.Alos2ProcPublic import snaphuUnwrap
+from isceobj.Alos2Proc.Alos2ProcPublic import snaphuUnwrapOriginal
+from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
+from contrib.alos2proc.alos2proc import look
+from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
+
+logger = logging.getLogger('isce.alos2burstinsar.runUnwrapSnaphuSd')
+
+def runUnwrapSnaphuSd(self):
+    '''unwrap filtered interferogram
+    '''
+    catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
+    self.updateParamemetersFromUser()
+
+    masterTrack = self._insar.loadTrack(master=True)
+    #slaveTrack = self._insar.loadTrack(master=False)
+
+    sdDir = 'sd'
+    if not os.path.exists(sdDir):
+        os.makedirs(sdDir)
+    os.chdir(sdDir)
+
+
+    ############################################################
+    # STEP 1. unwrap interferogram
+    ############################################################
+    nsd = len(self._insar.filteredInterferogramSd)
+    img = isceobj.createImage()
+    img.load(self._insar.filteredInterferogramSd[0]+'.xml')
+    width = img.width
+    length = img.length
+
+    if shutil.which('snaphu') != None:
+        print('\noriginal snaphu program found, use it for unwrapping interferograms')
+        useOriginalSnaphu = True
+        #create an amplitude for use
+        # amplitude = os.path.join('../insar', self._insar.amplitude)
+        # amplitudeMultilook = 'tmp.amp'
+        # img = isceobj.createImage()
+        # img.load(amplitude+'.xml')
+        # look(amplitude, amplitudeMultilook, img.width, self._insar.numberRangeLooksSd, self._insar.numberAzimuthLooksSd, 4, 1, 1)
+    else:
+        useOriginalSnaphu = False
+
+    for sdCoherence, sdInterferogramFilt, sdInterferogramUnwrap in zip(self._insar.multilookCoherenceSd, self._insar.filteredInterferogramSd, self._insar.unwrappedInterferogramSd):
+        if useOriginalSnaphu:
+            amplitudeMultilook = 'tmp.amp'
+            cmd = "imageMath.py -e='sqrt(abs(a));sqrt(abs(a))' --a={} -o {} -t float -s BSQ".format(sdInterferogramFilt, amplitudeMultilook)
+            runCmd(cmd)
+            snaphuUnwrapOriginal(sdInterferogramFilt, 
+                sdCoherence, 
+                amplitudeMultilook, 
+                sdInterferogramUnwrap, 
+                costMode = 's', 
+                initMethod = 'mcf')
+            os.remove(amplitudeMultilook)
+            os.remove(amplitudeMultilook+'.vrt')
+            os.remove(amplitudeMultilook+'.xml')
+        else:
+            tmid = masterTrack.sensingStart + datetime.timedelta(seconds=(self._insar.numberAzimuthLooks1-1.0)/2.0*masterTrack.azimuthLineInterval+
+                   masterTrack.numberOfLines/2.0*self._insar.numberAzimuthLooks1*masterTrack.azimuthLineInterval)
+            snaphuUnwrap(masterTrack, tmid, 
+                sdInterferogramFilt, 
+                sdCoherence, 
+                sdInterferogramUnwrap, 
+                self._insar.numberRangeLooks1*self._insar.numberRangeLooksSd, 
+                self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksSd, 
+                costMode = 'SMOOTH',initMethod = 'MCF', defomax = 2, initOnly = True)
+
+    #if useOriginalSnaphu:
+    #    os.remove(amplitudeMultilook)
+
+
+    ############################################################
+    # STEP 2. mask using connected components
+    ############################################################
+    for sdInterferogramUnwrap, sdInterferogramUnwrapMasked in zip(self._insar.unwrappedInterferogramSd, self._insar.unwrappedMaskedInterferogramSd):
+        cmd = "imageMath.py -e='a_0*(b>0);a_1*(b>0)' --a={} --b={} -s BIL -t float -o={}".format(sdInterferogramUnwrap, sdInterferogramUnwrap+'.conncomp', sdInterferogramUnwrapMasked)
+        runCmd(cmd)
+
+
+    ############################################################
+    # STEP 3. mask using water body
+    ############################################################
+    if self.waterBodyMaskStartingStepSd=='unwrap':
+        wbd = np.fromfile(self._insar.multilookWbdOutSd, dtype=np.int8).reshape(length, width)
+
+        for sdInterferogramUnwrap, sdInterferogramUnwrapMasked in zip(self._insar.unwrappedInterferogramSd, self._insar.unwrappedMaskedInterferogramSd):
+            unw=np.memmap(sdInterferogramUnwrap, dtype='float32', mode='r+', shape=(length*2, width))
+            (unw[0:length*2:2, :])[np.nonzero(wbd==-1)] = 0
+            (unw[1:length*2:2, :])[np.nonzero(wbd==-1)] = 0
+            unw=np.memmap(sdInterferogramUnwrapMasked, dtype='float32', mode='r+', shape=(length*2, width))
+            (unw[0:length*2:2, :])[np.nonzero(wbd==-1)] = 0
+            (unw[1:length*2:2, :])[np.nonzero(wbd==-1)] = 0
+
+
+    ############################################################
+    # STEP 4. convert to azimuth deformation
+    ############################################################
+    #burst cycle in s
+    burstCycleLength = masterTrack.frames[0].swaths[0].burstCycleLength / masterTrack.frames[0].swaths[0].prf
+
+    #compute azimuth fmrate
+    #stack all azimuth fmrates
+    index = np.array([], dtype=np.float64)
+    ka = np.array([], dtype=np.float64)
+    for frame in masterTrack.frames:
+        for swath in frame.swaths:
+            startingRangeMultilook = masterTrack.frames[0].swaths[0].startingRange + \
+                                    (self._insar.numberRangeLooks1*self._insar.numberRangeLooksSd-1.0)/2.0*masterTrack.frames[0].swaths[0].rangePixelSize
+            rangePixelSizeMultilook = self._insar.numberRangeLooks1 * self._insar.numberRangeLooksSd * masterTrack.frames[0].swaths[0].rangePixelSize
+            index0 = (swath.startingRange + np.arange(swath.numberOfSamples) * swath.rangePixelSize - startingRangeMultilook) / rangePixelSizeMultilook
+            ka0 = np.polyval(swath.azimuthFmrateVsPixel[::-1], np.arange(swath.numberOfSamples))
+            index = np.concatenate((index, index0))
+            ka = np.concatenate((ka, ka0))
+    p = np.polyfit(index, ka, 3)
+    #new ka
+    ka = np.polyval(p, np.arange(width))
+
+    #compute radar beam footprint velocity at middle track
+    tmid = masterTrack.sensingStart + datetime.timedelta(seconds=(self._insar.numberAzimuthLooks1-1.0)/2.0*masterTrack.azimuthLineInterval+
+           masterTrack.numberOfLines/2.0*self._insar.numberAzimuthLooks1*masterTrack.azimuthLineInterval)
+    svmid = masterTrack.orbit.interpolateOrbit(tmid, method='hermite')
+    #earth radius in meters
+    r = 6371 * 1000.0
+    #radar footprint velocity
+    veln = np.linalg.norm(svmid.getVelocity()) * r / np.linalg.norm(svmid.getPosition())
+    print('radar beam footprint velocity at middle track: %8.2f m/s'%veln)
+
+    #phase to defo factor
+    factor = -1.0* veln / (2.0 * np.pi * ka * burstCycleLength)
+
+    #process unwrapped without mask
+    sdunw_out = np.zeros((length*2, width))
+    flag = np.zeros((length, width))
+    wgt = np.zeros((length, width))
+    for i in range(nsd):
+        sdunw = np.fromfile(self._insar.unwrappedInterferogramSd[i], dtype=np.float32).reshape(length*2, width)
+        sdunw[1:length*2:2, :] *= factor[None, :] / (i+1.0)
+        sdunw.astype(np.float32).tofile(self._insar.azimuthDeformationSd[i])
+        create_xml(self._insar.azimuthDeformationSd[i], width, length, 'rmg')
+        flag += (sdunw[1:length*2:2, :]!=0)
+        #since the interferogram is filtered, we only use this light weight
+        wgt0 = (i+1)**2
+        wgt += wgt0 * (sdunw[1:length*2:2, :]!=0)
+        sdunw_out[0:length*2:2, :] += (sdunw[0:length*2:2, :])**2
+        sdunw_out[1:length*2:2, :] += wgt0 * sdunw[1:length*2:2, :]
+    #output weighting average
+    index = np.nonzero(flag!=0)
+    (sdunw_out[0:length*2:2, :])[index] = np.sqrt((sdunw_out[0:length*2:2, :])[index] / flag[index])
+    (sdunw_out[1:length*2:2, :])[index] = (sdunw_out[1:length*2:2, :])[index] / wgt[index]
+    if not self.unionSd:
+        (sdunw_out[0:length*2:2, :])[np.nonzero(flag<nsd)] = 0
+        (sdunw_out[1:length*2:2, :])[np.nonzero(flag<nsd)] = 0
+    sdunw_out.astype(np.float32).tofile(self._insar.azimuthDeformationSd[-1])
+    create_xml(self._insar.azimuthDeformationSd[-1], width, length, 'rmg')
+
+    #process unwrapped with mask
+    sdunw_out = np.zeros((length*2, width))
+    flag = np.zeros((length, width))
+    wgt = np.zeros((length, width))
+    for i in range(nsd):
+        sdunw = np.fromfile(self._insar.unwrappedMaskedInterferogramSd[i], dtype=np.float32).reshape(length*2, width)
+        sdunw[1:length*2:2, :] *= factor[None, :] / (i+1.0)
+        sdunw.astype(np.float32).tofile(self._insar.maskedAzimuthDeformationSd[i])
+        create_xml(self._insar.maskedAzimuthDeformationSd[i], width, length, 'rmg')
+        flag += (sdunw[1:length*2:2, :]!=0)
+        #since the interferogram is filtered, we only use this light weight
+        wgt0 = (i+1)**2
+        wgt += wgt0 * (sdunw[1:length*2:2, :]!=0)
+        sdunw_out[0:length*2:2, :] += (sdunw[0:length*2:2, :])**2
+        sdunw_out[1:length*2:2, :] += wgt0 * sdunw[1:length*2:2, :]
+    #output weighting average
+    index = np.nonzero(flag!=0)
+    (sdunw_out[0:length*2:2, :])[index] = np.sqrt((sdunw_out[0:length*2:2, :])[index] / flag[index])
+    (sdunw_out[1:length*2:2, :])[index] = (sdunw_out[1:length*2:2, :])[index] / wgt[index]
+    if not self.unionSd:
+        (sdunw_out[0:length*2:2, :])[np.nonzero(flag<nsd)] = 0
+        (sdunw_out[1:length*2:2, :])[np.nonzero(flag<nsd)] = 0
+    sdunw_out.astype(np.float32).tofile(self._insar.maskedAzimuthDeformationSd[-1])
+    create_xml(self._insar.maskedAzimuthDeformationSd[-1], width, length, 'rmg')
+
+    os.chdir('../')
+
+    catalog.printToLog(logger, "runUnwrapSnaphuSd")
+    self._insar.procDoc.addAllFromCatalog(catalog)
+

components/isceobj/CMakeLists.txt

@@ -1,6 +1,8 @@
 add_subdirectory(Util)
 add_subdirectory(Sensor)
 
+add_subdirectory(Alos2Proc)
+add_subdirectory(Alos2burstProc)
 add_subdirectory(Attitude)
 add_subdirectory(Catalog)
 add_subdirectory(Constants)

components/isceobj/SConscript

@@ -71,3 +71,5 @@ SConscript('StripmapProc/SConscript')
 SConscript('TopsProc/SConscript')
 SConscript('RtcProc/SConscript')
 SConscript('ScansarProc/SConscript')
+SConscript('Alos2Proc/SConscript')
+SConscript('Alos2burstProc/SConscript')

components/isceobj/Sensor/CMakeLists.txt

@@ -1,6 +1,7 @@
 add_subdirectory(db)
 add_subdirectory(TOPS)
 add_subdirectory(ScanSAR)
+add_subdirectory(MultiMode)
 
 set(installfiles
     alos

components/isceobj/Sensor/MultiMode/ALOS2.py

@@ -0,0 +1,831 @@
+#!/usr/bin/env python3
+
+#Author: Cunren Liang, 2015-
+
+import os
+import datetime
+import isceobj.Sensor.CEOS as CEOS
+import logging
+from isceobj.Orbit.Orbit import StateVector,Orbit
+from isceobj.Planet.AstronomicalHandbook import Const
+from isceobj.Planet.Planet import Planet
+from iscesys.Component.Component import Component
+from isceobj.Sensor import xmlPrefix
+from isceobj.Util import Polynomial
+from iscesys.DateTimeUtil import secondsSinceMidnight
+import numpy as np
+import struct
+
+import isceobj
+
+#changed to use the following parameters
+IMAGE_FILE = Component.Parameter('imageFile',
+        public_name='image file',
+        type = str,
+        default=None,
+        mandatory = True,
+        doc = 'ALOS-2 CEOS image file')
+
+LEADER_FILE = Component.Parameter('leaderFile',
+        public_name='leader file',
+        type = str,
+        default=None,
+        mandatory = True,
+        doc = 'ALOS-2 CEOS leader file')
+
+OUTPUT_FILE = Component.Parameter('outputFile',
+        public_name='output file',
+        type = str,
+        default=None,
+        mandatory = True,
+        doc = 'output file')
+
+USE_VIRTUAL_FILE = Component.Parameter('useVirtualFile',
+        public_name='use virtual file',
+        type=bool,
+        default=True,
+        mandatory=False,
+        doc='use virtual files instead of using disk space')
+
+####List of facilities
+TRACK = Component.Facility('track',
+        public_name='track',
+        module = 'isceobj.Sensor.MultiMode',
+        factory='createTrack',
+        args = (),
+        mandatory = True,
+        doc = 'A track of ALOS-2 SLCs populated by the reader')
+
+
+class ALOS2(Component):
+    """
+    ALOS-2 multi-mode reader
+    """
+    family = 'alos2multimode'
+    logging = 'isce.sensor.alos2multimode'
+
+    parameter_list = (IMAGE_FILE,
+                      LEADER_FILE,
+                      OUTPUT_FILE,
+                      USE_VIRTUAL_FILE)
+
+    facility_list = (TRACK,)
+
+    # Range sampling rate
+    fsampConst = { 104: 1.047915957140240E+08,
+                   52: 5.239579785701190E+07,
+                   34: 3.493053190467460E+07,
+                   17: 1.746526595233730E+07 }
+    # Orbital Elements (Quality) Designator, data format P68
+    orbitElementsDesignator = {'0':'0: preliminary',
+                               '1':'1: decision',
+                               '2':'2: high precision'}
+    # Operation mode, data format P50
+    operationModeDesignator = {'00': '00: Spotlight mode',
+                               '01': '01: Ultra-fine mode',
+                               '02': '02: High-sensitive mode',
+                               '03': '03: Fine mode',
+                               '04': '04: spare',
+                               '05': '05: spare',
+                               '08': '08: ScanSAR nominal mode',
+                               '09': '09: ScanSAR wide mode',
+                               '18': '18: Full (Quad.) pol./High-sensitive mode',
+                               '19': '19: Full (Quad.) pol./Fine mode',
+                               '64': '64: Manual observation'}
+
+    def __init__(self, name=''):
+        super().__init__(family=self.__class__.family, name=name) 
+
+        return
+
+
+    def readImage(self):
+        '''
+        read image and get parameters
+        '''
+        try:
+            fp = open(self.imageFile,'rb')
+        except IOError as errs:
+            errno,strerr = errs
+            print("IOError: %s" % strerr)
+            return
+
+        #read meta data
+        imageFDR = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/image_file.xml'), dataFile=fp)
+        imageFDR.parse()
+        fp.seek(imageFDR.getEndOfRecordPosition())
+
+        #record length: header (544 bytes) + SAR data (width*8 bytes)
+        recordlength = imageFDR.metadata['SAR DATA record length']
+        width =  imageFDR.metadata['Number of pixels per line per SAR channel']
+        length = imageFDR.metadata['Number of SAR DATA records']
+
+        #line header
+        imageData = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/image_record.xml'), dataFile=fp)
+        imageData.parseFast()
+
+        #creat vrt and xml files for sar data
+        image = isceobj.createSlcImage()
+        image.setFilename(self.outputFile)
+        image.setWidth(width)
+        image.setLength(length)
+        image.renderHdr()
+
+        #sar data
+        fileHeaderBytes = 720
+        lineHeaderBytes = 544
+        if self.useVirtualFile:
+            #this overwrites the previous vrt
+            with open(self.outputFile+'.vrt', 'w') as fid:
+                fid.write('''<VRTDataset rasterXSize="{0}" rasterYSize="{1}">
+    <VRTRasterBand band="1" dataType="CFloat32" subClass="VRTRawRasterBand">
+        <SourceFilename relativeToVRT="0">{2}</SourceFilename>
+        <ByteOrder>MSB</ByteOrder>
+        <ImageOffset>{3}</ImageOffset>
+        <PixelOffset>8</PixelOffset>
+        <LineOffset>{4}</LineOffset>
+    </VRTRasterBand>
+</VRTDataset>'''.format(width, length,
+                       self.imageFile,
+                       fileHeaderBytes + lineHeaderBytes,
+                       width*8 + lineHeaderBytes))
+        else:
+            #read sar data line by line
+            try:
+                fp2 = open(self.outputFile,'wb')
+            except IOError as errs:
+                errno,strerr = errs
+                print("IOError: %s" % strerr)
+                return
+            fp.seek(-lineHeaderBytes, 1)
+            for line in range(length):
+                if (((line+1)%1000) == 0):
+                    print("extracting line %6d of %6d" % (line+1, length), end='\r', flush=True)
+                fp.seek(lineHeaderBytes, 1)
+                IQLine = np.fromfile(fp, dtype='>f', count=2*width)
+                self.writeRawData(fp2, IQLine)
+                #IQLine.tofile(fp2)
+            print("extracting line %6d of %6d" % (length, length))
+            fp2.close()
+
+        #close input image file
+        fp.close()
+
+        return (imageFDR, imageData)
+
+
+    def readLeader(self):
+        '''
+        read meta data from leader
+        '''
+        try:
+            fp = open(self.leaderFile,'rb')
+        except IOError as errs:
+            errno,strerr = errs
+            print("IOError: %s" % strerr)
+            return
+        
+        # Leader record
+        leaderFDR = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/leader_file.xml'),dataFile=fp)
+        leaderFDR.parse()
+        fp.seek(leaderFDR.getEndOfRecordPosition())
+
+        # Scene Header
+        sceneHeaderRecord = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/scene_record.xml'),dataFile=fp)
+        sceneHeaderRecord.parse()
+        fp.seek(sceneHeaderRecord.getEndOfRecordPosition())
+
+        # Platform Position
+        platformPositionRecord = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/platform_position_record.xml'),dataFile=fp)
+        platformPositionRecord.parse()
+        fp.seek(platformPositionRecord.getEndOfRecordPosition())
+
+        #####Skip attitude information
+        fp.seek(16384,1)
+        #####Skip radiometric information
+        fp.seek(9860,1)
+        ####Skip the data quality information
+        fp.seek(1620,1)
+        ####Skip facility 1-4
+        fp.seek(325000 + 511000 + 3072 + 728000, 1)
+
+        ####Read facility 5
+        facilityRecord = CEOS.CEOSDB(xml=os.path.join(xmlPrefix,'alos2_slc/facility_record.xml'), dataFile=fp)
+        facilityRecord.parse()
+
+        ###close file
+        fp.close()
+
+        return (leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord)
+
+
+    def setTrack(self, leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData):
+        '''
+        set track parameters
+        '''
+        track = self.track
+
+        #passDirection
+        passDirection = sceneHeaderRecord.metadata['Time direction indicator along line direction']
+        if passDirection == 'ASCEND':
+            track.passDirection = 'ascending'
+        elif passDirection == 'DESCEND':
+            track.passDirection = 'descending'
+        else:
+            raise Exception('Unknown passDirection. passDirection = {0}'.format(passDirection))
+
+        #pointingDirection
+        ######ALOS-2 includes this information in clock angle
+        clockAngle = sceneHeaderRecord.metadata['Sensor clock angle']
+        if clockAngle == 90.0:
+            track.pointingDirection = 'right'
+        elif clockAngle == -90.0:
+            track.pointingDirection = 'left'
+        else:
+            raise Exception('Unknown look side. Clock Angle = {0}'.format(clockAngle))
+
+        #operation mode
+        track.operationMode = self.operationModeDesignator[
+                              (sceneHeaderRecord.metadata['Sensor ID and mode of operation for this channel'])[10:12]
+                              ]
+
+        #use this instead. 30-JAN-2020
+        track.operationMode = os.path.basename(self.leaderFile).split('-')[-1][0:3]
+
+        #radarWavelength
+        track.radarWavelength = sceneHeaderRecord.metadata['Radar wavelength']
+
+        #orbit
+        orb = self.readOrbit(platformPositionRecord)
+        track.orbit.setOrbitSource(orb.getOrbitSource())
+        track.orbit.setOrbitQuality(orb.getOrbitQuality())
+        #add orbit from frame
+        for sv in orb:
+            addOrbit = True
+            #Orbit class does not check this
+            for x in track.orbit:
+                if x.getTime() == sv.getTime():
+                    addOrbit = False
+                    break
+            if addOrbit:
+                track.orbit.addStateVector(sv)
+
+        # the following are to be set when mosaicking frames.
+        # 'numberOfSamples',
+        # 'numberOfLines',
+        # 'startingRange',
+        # 'rangeSamplingRate',
+        # 'rangePixelSize',
+        # 'sensingStart',
+        # 'prf',
+        # 'azimuthPixelSize'
+
+
+    def setFrame(self, leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData):
+        '''
+        set frame parameters
+        '''
+        frame = self.track.frames[-1]
+
+        #get frame number from file name
+        frame.frameNumber = os.path.basename(self.imageFile).split('-')[2][-4:]
+        frame.processingFacility = sceneHeaderRecord.metadata['Processing facility identifier']
+        frame.processingSystem = sceneHeaderRecord.metadata['Processing system identifier']
+        frame.processingSoftwareVersion = sceneHeaderRecord.metadata['Processing version identifier']
+        #orbit quality
+        orb = self.readOrbit(platformPositionRecord)
+        frame.orbitQuality = orb.getOrbitQuality()
+
+        # the following are to be set when mosaicking swaths
+        # 'numberOfSamples',
+        # 'numberOfLines',
+        # 'startingRange',
+        # 'rangeSamplingRate',
+        # 'rangePixelSize',
+        # 'sensingStart',
+        # 'prf',
+        # 'azimuthPixelSize'
+
+
+    def setSwath(self, leaderFDR, sceneHeaderRecord, platformPositionRecord, facilityRecord, imageFDR, imageData):
+        '''
+        set swath parameters
+        '''
+        swath = self.track.frames[-1].swaths[-1]
+        operationMode = (sceneHeaderRecord.metadata['Sensor ID and mode of operation for this channel'])[10:12]
+        
+        #set swath number here regardless of operation mode, will be updated for ScanSAR later
+        swath.swathNumber = 1
+
+        #polarization
+        polDesignator = {0: 'H',
+                         1: 'V'}
+        swath.polarization = '{}{}'.format(polDesignator[imageData.metadata['Transmitted polarization']],
+                             polDesignator[imageData.metadata['Received polarization']])
+
+        #image dimensions
+        swath.numberOfSamples = imageFDR.metadata['Number of pixels per line per SAR channel']
+        swath.numberOfLines = imageFDR.metadata['Number of SAR DATA records']
+
+        #range
+        swath.startingRange = imageData.metadata['Slant range to 1st data sample']
+        swath.rangeSamplingRate = self.fsampConst[int(sceneHeaderRecord.metadata['Range sampling rate in MHz'])]
+        swath.rangePixelSize = Const.c/(2.0*swath.rangeSamplingRate)
+        swath.rangeBandwidth =abs((sceneHeaderRecord.metadata['Nominal range pulse (chirp) amplitude coefficient linear term']) *
+                               (sceneHeaderRecord.metadata['Range pulse length in microsec']*1.0e-6))
+
+        #sensingStart
+        yr = imageData.metadata['Sensor acquisition year']
+        dys = imageData.metadata['Sensor acquisition day of year']
+        msecs = imageData.metadata['Sensor acquisition milliseconds of day']
+        usecs = imageData.metadata['Sensor acquisition micro-seconds of day']
+        swath.sensingStart = datetime.datetime(yr,1,1) + datetime.timedelta(days=(dys-1)) + datetime.timedelta(seconds = usecs*1e-6)
+
+        #prf
+        if operationMode == '08' or operationMode == '09':
+            # Operation mode
+            # '00': 'Spotlight mode',
+            # '01': 'Ultra-fine mode',
+            # '02': 'High-sensitive mode',
+            # '03': 'Fine mode',
+            # '04': 'spare',
+            # '05': 'spare',
+            # '08': 'ScanSAR nominal mode',
+            # '09': 'ScanSAR wide mode',
+            # '18': 'Full (Quad.) pol./High-sensitive mode',
+            # '19': 'Full (Quad.) pol./Fine mode',
+            # '64': 'Manual observation'
+            #print('ScanSAR mode, using PRF from the line header')
+            swath.prf = imageData.metadata['PRF'] * 1.0e-3
+        else:
+            #print('not ScanSAR mode, using PRF from leader file')
+            swath.prf = sceneHeaderRecord.metadata['Pulse Repetition Frequency in mHz']*1.0e-3
+
+        #azimuth pixel size at swath center on ground
+        azimuthTime = swath.sensingStart + datetime.timedelta(seconds=swath.numberOfLines/swath.prf/2.0)
+        orbit = self.readOrbit(platformPositionRecord)
+        svmid = orbit.interpolateOrbit(azimuthTime, method='hermite')
+        height = np.linalg.norm(svmid.getPosition())
+        velocity = np.linalg.norm(svmid.getVelocity())
+        #earth radius in meters
+        r = 6371 * 1000.0
+        swath.azimuthPixelSize = velocity / swath.prf * r / height
+        swath.azimuthLineInterval = 1.0 / swath.prf
+
+        #doppler
+        swath.dopplerVsPixel = self.reformatDoppler(sceneHeaderRecord, imageFDR, imageData)
+
+        #azimuth FM rate
+        azimuthTime = swath.sensingStart + datetime.timedelta(seconds=swath.numberOfLines/swath.prf/2.0)
+        swath.azimuthFmrateVsPixel = self.computeAzimuthFmrate(sceneHeaderRecord, platformPositionRecord, imageFDR, imageData, azimuthTime)
+
+
+        #burst information estimated from azimuth spectrum. Cunren, 14-DEC-2015
+        if operationMode == '08' or operationMode == '09':
+            sceneCenterIncidenceAngle = sceneHeaderRecord.metadata['Incidence angle at scene centre']
+            sarChannelId = imageData.metadata['SAR channel indicator']
+            #Scan ID starts with 1, ScanSAR = 1 to 7, Except ScanSAR = 0
+            scanId = imageData.metadata['Scan ID']
+            swath.swathNumber = scanId
+
+            #looks like all ScanSAR nominal modes (WBS,WBD,WWS,WWD) have same burst parameters, so remove the limitation here
+            #if (sceneCenterIncidenceAngle > 39.032 - 5.0 and sceneCenterIncidenceAngle < 39.032 + 5.0) and (sarChannelId == 2):
+            if operationMode == '08':
+                #burst parameters, currently only for the second, dual polarization, ScanSAR nominal mode
+                #that is the second WBD mode
+                #p.25 and p.115 of ALOS-2/PALSAR-2 Level 1.1/1.5/2.1/3.1 CEOS SAR Product Format Description
+                #for the definations of wide swath mode
+                nbraw = [358,        470,        358,        355,        487]
+                ncraw = [2086.26,    2597.80,    1886.18,    1779.60,    2211.17]
+
+                swath.burstLength = nbraw[scanId-1]
+                swath.burstCycleLength = ncraw[scanId-1]
+
+                #this is the prf fraction (total azimuth bandwith) used in extracting burst
+                #here the total bandwith is 0.93 * prfs[3] for all subswaths, which is the following values:
+                #[0.7933, 0.6371, 0.8774, 0.9300, 0.7485] 
+                prfs=[2661.847, 3314.512, 2406.568, 2270.575, 2821.225]
+                swath.prfFraction = 0.93 * prfs[3]/prfs[scanId-1]
+
+        #compute burst start time
+        if operationMode == '08':
+            (burstStartTime, burstCycleLengthNew) = self.burstTimeRefining(self.outputFile, 
+                swath.numberOfSamples, 
+                swath.numberOfLines, 
+                swath.prf, 
+                swath.burstLength, 
+                swath.burstCycleLength, 
+                swath.azimuthFmrateVsPixel, 
+                swath.sensingStart, 
+                self.useVirtualFile)
+            swath.burstStartTime = burstStartTime
+            swath.burstCycleLength = burstCycleLengthNew
+
+
+    def computeAzimuthFmrate(self, sceneHeaderRecord, platformPositionRecord, imageFDR, imageData, azimuthTime):
+        import copy
+        '''
+        compute azimuth FM rate, copied from Piyush's code.
+        azimuthTime: middle of the scene should be a good time
+        '''
+        #parameters required
+        orbit = self.readOrbit(platformPositionRecord)
+        dopplerVsPixel = self.reformatDoppler(sceneHeaderRecord, imageFDR, imageData)
+        width = imageFDR.metadata['Number of pixels per line per SAR channel']
+
+        startingRange = imageData.metadata['Slant range to 1st data sample']
+        rangeSamplingRate = self.fsampConst[int(sceneHeaderRecord.metadata['Range sampling rate in MHz'])]
+        radarWavelength = sceneHeaderRecord.metadata['Radar wavelength']
+
+        clockAngle = sceneHeaderRecord.metadata['Sensor clock angle']
+        if clockAngle == 90.0:
+            #right
+            pointingDirection = -1
+        elif clockAngle == -90.0:
+            #left
+            pointingDirection = 1
+        else:
+            raise Exception('Unknown look side. Clock Angle = {0}'.format(clockAngle))
+
+        ##We have to compute FM rate here.
+        ##Cunren's observation that this is all set to zero in CEOS file.
+        ##Simplification from Cunren's fmrate.py script
+        ##Should be the same as the one in focus.py
+        planet = Planet(pname='Earth')
+        elp = copy.copy(planet.ellipsoid)
+        svmid = orbit.interpolateOrbit(azimuthTime, method='hermite')
+        xyz = svmid.getPosition()
+        vxyz = svmid.getVelocity()
+        llh = elp.xyz_to_llh(xyz)
+        hdg = orbit.getENUHeading(azimuthTime)
+
+        elp.setSCH(llh[0], llh[1], hdg)
+        sch, schvel = elp.xyzdot_to_schdot(xyz, vxyz)
+
+        ##Computeation of acceleration
+        dist= np.linalg.norm(xyz)
+        r_spinvec = np.array([0., 0., planet.spin])
+        r_tempv = np.cross(r_spinvec, xyz)
+        inert_acc = np.array([-planet.GM*x/(dist**3) for x in xyz])
+        r_tempa = np.cross(r_spinvec, vxyz)
+        r_tempvec = np.cross(r_spinvec, r_tempv)
+        axyz = inert_acc - 2 * r_tempa - r_tempvec
+        
+        schbasis = elp.schbasis(sch)
+        schacc = np.dot(schbasis.xyz_to_sch, axyz).tolist()[0]
+
+        ##Jumping back straight into Cunren's script here
+        centerVel = schvel
+        centerAcc = schacc
+        avghgt = llh[2]
+        radiusOfCurvature = elp.pegRadCur
+
+        fmrate = []
+        lookSide = pointingDirection
+        centerVelNorm = np.linalg.norm(centerVel)
+
+        ##Retaining Cunren's code for computing at every pixel.
+        ##Can be done every 10th pixel since we only fit a quadratic/ cubic.
+        ##Also can be vectorized for speed.
+
+        for ii in range(width):
+            rg = startingRange + ii * 0.5 * Const.c / rangeSamplingRate
+            #don't forget to flip coefficients
+            dop = np.polyval(dopplerVsPixel[::-1], ii)
+
+            th = np.arccos(((avghgt+radiusOfCurvature)**2 + rg**2 -radiusOfCurvature**2)/(2.0 * (avghgt + radiusOfCurvature) * rg))
+            thaz = np.arcsin(((radarWavelength*dop/(2.0*np.sin(th))) + (centerVel[2] / np.tan(th))) / np.sqrt(centerVel[0]**2 + centerVel[1]**2)) - lookSide * np.arctan(centerVel[1]/centerVel[0])
+
+            lookVec = [ np.sin(th) * np.sin(thaz),
+                        np.sin(th) * np.cos(thaz) * lookSide,
+                        -np.cos(th)]
+
+            vdotl = np.dot(lookVec, centerVel)
+            adotl = np.dot(lookVec, centerAcc)
+            fmratex = 2.0*(adotl + (vdotl**2 - centerVelNorm**2)/rg)/(radarWavelength)
+            fmrate.append(fmratex)
+
+        ##Fitting order 2 polynomial to FM rate
+        p = np.polyfit(np.arange(width), fmrate, 2)
+        azimuthFmrateVsPixel = [p[2], p[1], p[0], 0.]
+
+        return azimuthFmrateVsPixel
+
+
+    def reformatDoppler(self, sceneHeaderRecord, imageFDR, imageData):
+        '''
+        reformat Doppler coefficients
+        '''
+        dopplerCoeff = [sceneHeaderRecord.metadata['Doppler center frequency constant term'],
+        sceneHeaderRecord.metadata['Doppler center frequency linear term']]
+
+        width = imageFDR.metadata['Number of pixels per line per SAR channel']
+        startingRange = imageData.metadata['Slant range to 1st data sample']
+        rangeSamplingRate = self.fsampConst[int(sceneHeaderRecord.metadata['Range sampling rate in MHz'])]
+        
+        rng = startingRange + np.arange(0,width,100) * 0.5 * Const.c / rangeSamplingRate
+        doppler = dopplerCoeff[0] + dopplerCoeff[1] * rng / 1000.
+        dfit = np.polyfit(np.arange(0, width, 100), doppler, 1)
+        dopplerVsPixel = [dfit[1], dfit[0], 0., 0.]
+
+        return dopplerVsPixel
+
+
+    def readOrbit(self, platformPositionRecord):
+        '''
+        reformat orbit from platformPositionRecord
+        '''
+        orb=Orbit()
+        orb.setOrbitSource('leaderfile')
+        orb.setOrbitQuality(self.orbitElementsDesignator[platformPositionRecord.metadata['Orbital elements designator']])
+
+        t0 = datetime.datetime(year=platformPositionRecord.metadata['Year of data point'],
+                               month=platformPositionRecord.metadata['Month of data point'],
+                               day=platformPositionRecord.metadata['Day of data point'])
+        t0 = t0 + datetime.timedelta(seconds=platformPositionRecord.metadata['Seconds of day'])
+
+        #####Read in orbit in inertial coordinates
+        deltaT = platformPositionRecord.metadata['Time interval between data points']
+        numPts = platformPositionRecord.metadata['Number of data points']
+        for i in range(numPts):
+            vec = StateVector()
+            t = t0 + datetime.timedelta(seconds=i*deltaT)
+            vec.setTime(t)
+
+            dataPoints = platformPositionRecord.metadata['Positional Data Points'][i]
+            pos = [dataPoints['Position vector X'], dataPoints['Position vector Y'], dataPoints['Position vector Z']]
+            vel = [dataPoints['Velocity vector X'], dataPoints['Velocity vector Y'], dataPoints['Velocity vector Z']]
+            vec.setPosition(pos)
+            vec.setVelocity(vel)
+            orb.addStateVector(vec)
+
+        return orb
+
+
+    def burstTimeRefining(self, slcFile, numberOfSamples, numberOfLines, pulseRepetitionFrequency, burstLength, burstCycleLength, azimuthFmrateVsPixel, sensingStart, useVirtualFile=True):
+        '''
+        compute start time of raw burst
+        '''
+        #number of lines from start and end of file
+        #this mainly considers ALOS-2 full-aperture length, should be updated for ALOS-4?
+        delta_line = 15000
+
+        #first estimate at file start
+        start_line1 = delta_line
+        (burstStartLine1, burstStartTime1, burstStartLineEstimated1) = self.burstTime(slcFile, 
+            numberOfSamples, 
+            numberOfLines, 
+            pulseRepetitionFrequency, 
+            burstLength, 
+            burstCycleLength, 
+            azimuthFmrateVsPixel, 
+            sensingStart, 
+            start_line1, 
+            1000, 
+            1, 
+            useVirtualFile)
+
+        #estimate again at file end
+        #number of burst cycles
+        num_nc = np.around((numberOfLines - delta_line*2) / burstCycleLength)
+        start_line2 = int(np.around(start_line1 + num_nc * burstCycleLength))
+        (burstStartLine2, burstStartTime2, burstStartLineEstimated2) = self.burstTime(slcFile, 
+            numberOfSamples, 
+            numberOfLines, 
+            pulseRepetitionFrequency, 
+            burstLength, 
+            burstCycleLength, 
+            azimuthFmrateVsPixel, 
+            sensingStart, 
+            start_line2, 
+            1000, 
+            1, 
+            useVirtualFile)
+
+        #correct burst cycle value
+        LineDiffIndex = 0
+        LineDiffMin = np.fabs(burstStartLineEstimated1 + burstCycleLength * LineDiffIndex - burstStartLineEstimated2)
+        for i in range(0, 100000):
+            LineDiffMinx = np.fabs(burstStartLineEstimated1 + burstCycleLength * i - burstStartLineEstimated2)
+            if LineDiffMinx <= LineDiffMin:
+                LineDiffMin = LineDiffMinx
+                LineDiffIndex = i
+        burstCycleLengthNew = burstCycleLength - (burstStartLineEstimated1 + burstCycleLength * LineDiffIndex - burstStartLineEstimated2) / LineDiffIndex
+
+        #use correct burstCycleLength to do final estimation
+        start_line = int(np.around(numberOfLines/2.0))
+        (burstStartLine, burstStartTime, burstStartLineEstimated) = self.burstTime(slcFile, 
+            numberOfSamples, 
+            numberOfLines, 
+            pulseRepetitionFrequency, 
+            burstLength, 
+            burstCycleLengthNew, 
+            azimuthFmrateVsPixel, 
+            sensingStart, 
+            start_line, 
+            1000, 
+            1, 
+            useVirtualFile)
+        
+        #return burstStartTime and refined burstCycleLength
+        return (burstStartTime, burstCycleLengthNew)
+
+
+    def burstTime(self, slcFile, numberOfSamples, numberOfLines, pulseRepetitionFrequency, burstLength, burstCycleLength, azimuthFmrateVsPixel, sensingStart, startLine=500, startColumn=500, pow2=1, useVirtualFile=True):
+        '''
+        compute start time of raw burst
+        '''
+        #######################################################
+        #set these parameters
+        width         = numberOfSamples
+        length        = numberOfLines
+        prf           = pulseRepetitionFrequency
+        nb            = burstLength
+        nc            = burstCycleLength
+        fmrateCoeff   = azimuthFmrateVsPixel
+        sensing_start = sensingStart
+        saz           = startLine #start line to be used (included, index start with 0. default: 500)
+        srg           = startColumn #start column to be used (included, index start with 0. default: 500)
+        p2            = pow2 #must be 1(default) or power of 2. azimuth fft length = THIS ARGUMENT * next of power of 2 of full-aperture length.
+        #######################################################  
+
+        def create_lfm(ns, it, offset, k):
+            '''
+            # create linear FM signal
+            # ns: number of samples
+            # it: time interval of the samples
+            # offset: offset
+            # k: linear FM rate
+            #offset-centered, this applies to both odd and even cases
+            '''
+            ht = (ns - 1) / 2.0
+            t = np.arange(-ht, ht+1.0, 1)
+            t = (t + offset) * it
+            cj = np.complex64(1j)
+            lfm = np.exp(cj * np.pi * k * t**2)
+
+            return lfm
+
+
+        def next_pow2(a):
+            x=2
+            while x < a:
+                x *= 2
+            return x
+
+
+        def is_power2(num):
+            '''states if a number is a power of two'''
+            return num != 0 and ((num & (num - 1)) == 0)
+
+
+        if not (p2 == 1 or is_power2(p2)):
+            raise Exception('pow2 must be 1 or power of 2\n')
+
+        #fmrate, use the convention that ka > 0
+        ka = -np.polyval(fmrateCoeff[::-1], np.arange(width))
+
+        #area to be used for estimation
+        naz = int(np.round(nc))            #number of lines to be used.
+        eaz = saz+naz-1                    #ending line to be used (included)
+        caz = int(np.round((saz+eaz)/2.0)) #central line of the lines used.
+        caz_deramp = (saz+eaz)/2.0         #center of deramp signal (may be fractional line number)
+
+        nrg = 400                          #number of columns to be used
+        erg = srg+nrg-1                    #ending column to be used (included)
+        crg = int(np.round((srg+erg)/2.0)) #central column of the columns used.
+
+        #check parameters
+        if not (saz >=0 and saz <= length - 1):
+            raise Exception('wrong starting line\n')
+        if not (eaz >=0 and eaz <= length - 1):
+            raise Exception('wrong ending line\n')
+        if not (srg >=0 and srg <= width - 1):
+            raise Exception('wrong starting column\n')
+        if not (erg >=0 and erg <= width - 1):
+            raise Exception('wrong ending column\n')
+
+        #number of lines of a full-aperture
+        nfa = int(np.round(prf / ka[crg] / (1.0 / prf)))
+        #use nfa to determine fft size. fft size can be larger than this
+        nazfft = next_pow2(nfa) * p2
+
+        #deramp signal
+        deramp = np.zeros((naz, nrg), dtype=np.complex64)
+        for i in range(nrg):
+            deramp[:, i] = create_lfm(naz, 1.0/prf, 0, -ka[i+srg])
+
+        #read data, python should be faster
+        useGdal = False
+        if useGdal:
+            from osgeo import gdal
+            ###Read in chunk of data
+            ds = gdal.Open(slcFile + '.vrt', gdal.GA_ReadOnly)
+            data = ds.ReadAsArray(srg, saz, nrg, naz)
+            ds = None
+        else:
+            #!!!hard-coded: ALOS-2 image file header 720 bytes, line header 544 bytes
+            if useVirtualFile == True:
+                fileHeader = 720
+                lineHeader = 544
+                #lineHeader is just integer multiples of complex pixle size, so it's good
+                lineHeaderSamples = int(lineHeader/np.dtype(np.complex64).itemsize)
+                slcFile = self.find_keyword(slcFile+'.vrt', 'SourceFilename')
+            else:
+                fileHeader = 0
+                lineHeader = 0
+                lineHeaderSamples = 0
+            data = np.memmap(slcFile, np.complex64,'r', offset = fileHeader, shape=(numberOfLines,lineHeaderSamples+numberOfSamples))
+            data = data[saz:eaz+1, lineHeaderSamples+srg:lineHeaderSamples+erg+1]
+            if useVirtualFile == True:
+                data = data.byteswap()
+
+        #deramp data
+        datadr = deramp * data
+
+        #spectrum
+        spec = np.fft.fft(datadr, n=nazfft, axis=0)
+
+        #shift zero-frequency component to center of spectrum
+        spec = np.fft.fftshift(spec, axes=0)
+
+        specm=np.mean(np.absolute(spec), axis=1)
+
+        #number of samples of the burst in frequncy domain
+        nbs  = int(np.round(nb*(1.0/prf)*ka[crg]/prf*nazfft));
+        #number of samples of the burst cycle in frequncy domain
+        ncs  = int(np.round(nc*(1.0/prf)*ka[crg]/prf*nazfft));
+        rect = np.ones(nbs, dtype=np.float32)
+
+        #make sure orders of specm and rect are correct, so that peaks
+        #happen in the same order as their corresponding bursts
+        corr=np.correlate(specm, rect,'same')
+
+        #find burst spectrum center
+        ncs_rh = int(np.round((nazfft - ncs) / 2.0))
+        #corr_bc = corr[ncs_rh: ncs_rh+ncs]
+        #offset between spectrum center and center
+        offset_spec = np.argmax(corr[ncs_rh: ncs_rh+ncs])+ncs_rh - (nazfft - 1.0) / 2.0
+        #offset in number of azimuth lines
+        offset_naz  = offset_spec / nazfft * prf / ka[crg] / (1.0/prf)
+
+        #start line of burst (fractional line number)
+        saz_burst = -offset_naz + caz_deramp - (nb - 1.0) / 2.0
+
+        #find out the start line of all bursts (fractional line number,
+        #line index start with 0, line 0 is the first SLC line)
+        #now only find first burst
+        for i in range(-100000, 100000):
+            saz_burstx = saz_burst + nc * i
+            st_burstx = sensing_start + datetime.timedelta(seconds=saz_burstx * (1.0/prf))
+            if saz_burstx >= 0.0 and saz_burstx <= length:
+                burstStartLine = saz_burstx
+                burstStartTime = st_burstx
+                break
+        burstStartLineEstimated = saz_burst
+
+        #dump spectrum and correlation
+        debug = False
+        if debug:
+            specm_corr = ''
+            for i in range(nazfft):
+                specm_corr += '{:6d}     {:f}     {:6d}     {:f}\n'.format(i, specm[i], i, corr[i])
+            specm_corr_name = str(sensingStart.year)[2:] + '%02d' % sensingStart.month + '%02d' % sensingStart.day + '_spec_corr.txt'
+            with open(specm_corr_name, 'w') as f:
+                f.write(specm_corr)
+
+        return (burstStartLine, burstStartTime, burstStartLineEstimated)
+
+
+    def find_keyword(self, xmlfile, keyword):
+        from xml.etree.ElementTree import ElementTree
+
+        value = None
+        xmlx = ElementTree(file=open(xmlfile,'r')).getroot()
+        #try 10 times
+        for i in range(10):
+            path=''
+            for j in range(i):
+                path += '*/'
+            value0 = xmlx.find(path+keyword)
+            if value0 != None:
+                value = value0.text
+                break
+
+        return value
+
+
+    def writeRawData(self, fp, line):
+        '''
+        Convert complex integer to complex64 format.
+        '''
+        cJ = np.complex64(1j)
+        data = line[0::2] + cJ * line[1::2]
+        data.tofile(fp)
+
+
+
+if __name__ == '__main__':
+
+    main()
+

components/isceobj/Sensor/MultiMode/CMakeLists.txt

@@ -0,0 +1,7 @@
+InstallSameDir(
+    __init__.py
+    ALOS2.py
+    Frame.py
+    Swath.py
+    Track.py
+    )

components/isceobj/Sensor/MultiMode/Frame.py

@@ -0,0 +1,164 @@
+#!/usr/bin/env python3
+
+#Author: Cunren Liang, 2015-
+
+import isce
+import datetime
+import isceobj
+import numpy as np
+from iscesys.Component.Component import Component
+from iscesys.Traits import datetimeType
+
+
+####List of parameters
+FRAME_NUMBER = Component.Parameter('frameNumber',
+        public_name = 'frame number',
+        default = None,
+        type = str,
+        mandatory = True,
+        doc = 'frame number in unpacked file names (not in zip file name!)')
+
+PROCESSING_FACILITY = Component.Parameter('processingFacility',
+    public_name='processing facility',
+    default=None,
+    type = str,
+    mandatory = False,
+    doc = 'processing facility information')
+
+PROCESSING_SYSTEM = Component.Parameter('processingSystem',
+    public_name='processing system',
+    default=None,
+    type = str,
+    mandatory = False,
+    doc = 'processing system information')
+
+PROCESSING_SYSTEM_VERSION = Component.Parameter('processingSoftwareVersion',
+    public_name='processing software version',
+    default=None,
+    type = str,
+    mandatory = False,
+    doc = 'processing system software version')
+
+ORBIT_QUALITY = Component.Parameter('orbitQuality',
+    public_name='orbit quality',
+    default=None,
+    type = str,
+    mandatory = False,
+    doc = 'orbit quality. 0: preliminary, 1: decision, 2: high precision')
+
+#note that following parameters consider range/azimuth number of looks in interferogram formation
+#except: rangeSamplingRate, prf
+
+NUMBER_OF_SAMPLES = Component.Parameter('numberOfSamples',
+        public_name='number of samples',
+        default=None,
+        type=int,
+        mandatory=True,
+        doc='width of the burst slc')
+
+NUMBER_OF_LINES = Component.Parameter('numberOfLines',
+        public_name='number of lines',
+        default=None,
+        type=int,
+        mandatory=True,
+        doc='length of the burst slc')
+
+STARTING_RANGE = Component.Parameter('startingRange',
+        public_name='starting range',
+        default=None,
+        type=float,
+        mandatory=True,
+        doc='slant range to first pixel in m')
+
+RANGE_SAMPLING_RATE = Component.Parameter('rangeSamplingRate',
+        public_name = 'range sampling rate',
+        default = None,
+        type = float,
+         mandatory = True,
+         doc = 'range sampling rate in Hz')
+
+RANGE_PIXEL_SIZE = Component.Parameter('rangePixelSize',
+        public_name = 'range pixel size',
+        default = None,
+        type=float,
+        mandatory = True,
+        doc = 'slant range pixel size in m')
+
+SENSING_START = Component.Parameter('sensingStart',
+        public_name='sensing start',
+        default=None,
+        type=datetimeType,
+        mandatory=True,
+        doc='UTC time corresponding to first line of swath SLC')
+
+PRF = Component.Parameter('prf',
+        public_name = 'pulse repetition frequency',
+        default = None,
+        type = float,
+        mandatory = True,
+        doc = 'pulse repetition frequency in Hz')
+
+AZIMUTH_PIXEL_SIZE = Component.Parameter('azimuthPixelSize',
+        public_name = 'azimuth pixel size',
+        default = None,
+        type=float,
+        mandatory = True,
+        doc = 'azimuth pixel size on ground in m')
+
+AZIMUTH_LINE_INTERVAL = Component.Parameter('azimuthLineInterval',
+        public_name = 'azimuth line interval',
+        default = None,
+        type=float,
+        mandatory = True,
+        doc = 'azimuth line interval in s')
+
+####List of facilities
+SWATHS = Component.Facility('swaths',
+        public_name='swaths',
+        module = 'iscesys.Component',
+        factory = 'createTraitSeq',
+        args=('swath',),
+        mandatory = False,
+        doc = 'trait sequence of swath SLCs')
+
+class Frame(Component):
+    """A class to represent a frame"""
+    
+    family = 'frame'
+    logging_name = 'isce.frame'
+
+
+
+
+    parameter_list = (FRAME_NUMBER,
+                      PROCESSING_FACILITY,
+                      PROCESSING_SYSTEM,
+                      PROCESSING_SYSTEM_VERSION,
+                      ORBIT_QUALITY,
+                      NUMBER_OF_SAMPLES,
+                      NUMBER_OF_LINES,
+                      STARTING_RANGE,
+                      RANGE_SAMPLING_RATE,
+                      RANGE_PIXEL_SIZE,
+                      SENSING_START,
+                      PRF,
+                      AZIMUTH_PIXEL_SIZE,
+                      AZIMUTH_LINE_INTERVAL
+                      )
+
+
+    facility_list = (SWATHS,)
+
+
+    def __init__(self,name=''):
+        super(Frame, self).__init__(family=self.__class__.family, name=name)
+        return None
+
+
+    def clone(self):
+        import copy
+        res = copy.deepcopy(self)
+        res.image._accessor = None
+        res.image._factory = None
+
+        return res

components/isceobj/Sensor/MultiMode/SConscript

@@ -0,0 +1,31 @@
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+#                                 Walter Szeliga
+#                        NASA Jet Propulsion Laboratory
+#                      California Institute of Technology
+#                        (c) 2010  All Rights Reserved
+#
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+
+#!/usr/bin/env python
+import os
+
+Import('envSensor')
+envMultiMode = envSensor.Clone()
+project = 'MultiMode'
+package = envMultiMode['PACKAGE']
+envMultiMode['PROJECT'] = project
+envMultiMode['SENSOR_SCONS_INSTALL'] = os.path.join(
+    envMultiMode['PRJ_SCONS_INSTALL'], package, 'Sensor',project)
+install = envMultiMode['SENSOR_SCONS_INSTALL']
+
+listFiles = ['__init__.py','ALOS2.py','Frame.py','Swath.py','Track.py']
+
+helpList,installHelp = envMultiMode['HELP_BUILDER'](envMultiMode,'__init__.py',install)
+
+envMultiMode.Install(installHelp,helpList)
+envMultiMode.Alias('install',installHelp)
+
+envMultiMode.Install(install,listFiles)
+envMultiMode.Alias('install',install)

components/isceobj/Sensor/MultiMode/Swath.py

@@ -0,0 +1,236 @@
+#!/usr/bin/env python3
+
+#Author: Cunren Liang, 2015-
+
+import isce
+import datetime
+import isceobj
+import numpy as np
+from iscesys.Component.Component import Component
+from isceobj.Image.Image import Image
+from isceobj.Orbit.Orbit import Orbit
+from isceobj.Util.decorators import type_check
+from iscesys.Traits import datetimeType
+
+
+####List of parameters
+SWATH_NUMBER = Component.Parameter('swathNumber',
+        public_name = 'swath number',
+        default = None,
+        type = int,
+        mandatory = True,
+        doc = 'swath number for bookkeeping')
+
+POLARIZATION = Component.Parameter('polarization',
+        public_name = 'polarization',
+        default = None,
+        type = str,
+        mandatory = True,
+        doc = 'polarization')
+
+NUMBER_OF_SAMPLES = Component.Parameter('numberOfSamples',
+        public_name='number of samples',
+        default=None,
+        type=int,
+        mandatory=True,
+        doc='width of the burst slc')
+
+NUMBER_OF_LINES = Component.Parameter('numberOfLines',
+        public_name='number of lines',
+        default=None,
+        type=int,
+        mandatory=True,
+        doc='length of the burst slc')
+
+STARTING_RANGE = Component.Parameter('startingRange',
+        public_name='starting range',
+        default=None,
+        type=float,
+        mandatory=True,
+        doc='slant range to first pixel in m')
+
+RANGE_SAMPLING_RATE = Component.Parameter('rangeSamplingRate',
+        public_name = 'range sampling rate',
+        default = None,
+        type = float,
+         mandatory = True,
+         doc = 'range sampling rate in Hz')
+
+RANGE_PIXEL_SIZE = Component.Parameter('rangePixelSize',
+        public_name = 'range pixel size',
+        default = None,
+        type=float,
+        mandatory = True,
+        doc = 'slant range pixel size in m')
+
+RANGE_BANDWIDTH = Component.Parameter('rangeBandwidth',
+        public_name = 'range bandwidth',
+        default = None,
+        type=float,
+        mandatory = True,
+        doc = 'range bandwidth in Hz')
+
+SENSING_START = Component.Parameter('sensingStart',
+        public_name='sensing start',
+        default=None,
+        type=datetimeType,
+        mandatory=True,
+        doc='UTC time corresponding to first line of swath SLC')
+
+PRF = Component.Parameter('prf',
+        public_name = 'pulse repetition frequency',
+        default = None,
+        type = float,
+        mandatory = True,
+        doc = 'pulse repetition frequency in Hz')
+
+AZIMUTH_PIXEL_SIZE = Component.Parameter('azimuthPixelSize',
+        public_name = 'azimuth pixel size',
+        default = None,
+        type=float,
+        mandatory = True,
+        doc = 'azimuth pixel size on ground in m')
+
+AZIMUTH_LINE_INTERVAL = Component.Parameter('azimuthLineInterval',
+        public_name = 'azimuth line interval',
+        default = None,
+        type=float,
+        mandatory = True,
+        doc = 'azimuth line interval in s')
+
+DOPPLER_VS_PIXEL = Component.Parameter('dopplerVsPixel',
+        public_name = 'doppler vs pixel',
+        default = None,
+        type = float,
+        mandatory = True,
+        container = list,
+        doc = 'Doppler (Hz) polynomial coefficients vs range pixel number')
+
+AZIMUTH_FMRATE_VS_PIXEL = Component.Parameter('azimuthFmrateVsPixel',
+        public_name = 'azimuth fm rate vs pixel',
+        default = [],
+        type = float,
+        mandatory = True,
+        container = list,
+        doc = 'azimuth FM rate (Hz/s) polynomial coefficients vs range pixel number')
+
+#for ScanSAR full-aperture product
+BURST_LENGTH = Component.Parameter('burstLength',
+        public_name = 'Burst Length',
+        default = None,
+        type = float,
+#        type = int,
+        mandatory = False,
+        doc = 'number of pulses in a raw burst')
+
+BURST_CYCLE_LENGTH = Component.Parameter('burstCycleLength',
+        public_name = 'Burst cycle length',
+        default = None,
+        type = float,
+        mandatory = False,
+        doc = 'number of pulses in a raw burst cycle')
+
+BURST_START_TIME = Component.Parameter('burstStartTime',
+        public_name='Burst start time',
+        default=None,
+        type=datetimeType,
+        mandatory=False,
+        doc='start time of a raw burst')
+
+#for ScanSAR burst-by-burst processing
+PRF_FRACTION = Component.Parameter('prfFraction',
+        public_name = 'prf fraction',
+        default = None,
+        type = float,
+        mandatory = False,
+        doc = 'fraction of PRF for extracting bursts for bookkeeping')
+
+NUMBER_OF_BURSTS = Component.Parameter('numberOfBursts',
+        public_name='number of bursts',
+        default=None,
+        type=int,
+        mandatory=False,
+        doc='number of bursts in a swath')
+
+FIRST_BURST_RAW_START_TIME = Component.Parameter('firstBurstRawStartTime',
+        public_name='start time of first raw burst',
+        default=None,
+        type=datetimeType,
+        mandatory=False,
+        doc='start time of first raw burst')
+
+FIRST_BURST_SLC_START_TIME = Component.Parameter('firstBurstSlcStartTime',
+        public_name='start time of first burst slc',
+        default=None,
+        type=datetimeType,
+        mandatory=False,
+        doc='start time of first burst slc')
+
+BURST_SLC_FIRST_LINE_OFFSETS = Component.Parameter('burstSlcFirstLineOffsets',
+                                public_name = 'burst SLC first line offsets',
+                                default = None,
+                                type = int,
+                                mandatory = False,
+                                container = list,
+                                doc = 'burst SLC first line offsets')
+
+BURST_SLC_NUMBER_OF_SAMPLES = Component.Parameter('burstSlcNumberOfSamples',
+        public_name='burst slc number of samples',
+        default=None,
+        type=int,
+        mandatory=False,
+        doc='burst slc width of the burst slc')
+
+BURST_SLC_NUMBER_OF_LINES = Component.Parameter('burstSlcNumberOfLines',
+        public_name='burst slc number of lines',
+        default=None,
+        type=int,
+        mandatory=False,
+        doc='burst slc length of the burst slc')
+
+
+class Swath(Component):
+    """A class to represent a swath SLC"""
+    
+    family = 'swath'
+    logging_name = 'isce.swath'
+
+    parameter_list = (SWATH_NUMBER,
+                      POLARIZATION,
+                      NUMBER_OF_SAMPLES,
+                      NUMBER_OF_LINES,
+                      STARTING_RANGE,
+                      RANGE_SAMPLING_RATE,
+                      RANGE_PIXEL_SIZE,
+                      RANGE_BANDWIDTH,
+                      SENSING_START,
+                      PRF,
+                      AZIMUTH_PIXEL_SIZE,
+                      AZIMUTH_LINE_INTERVAL,
+                      DOPPLER_VS_PIXEL,
+                      AZIMUTH_FMRATE_VS_PIXEL,
+                      BURST_LENGTH,
+                      BURST_CYCLE_LENGTH,
+                      BURST_START_TIME,
+                      PRF_FRACTION,
+                      NUMBER_OF_BURSTS,
+                      FIRST_BURST_RAW_START_TIME,
+                      FIRST_BURST_SLC_START_TIME,
+                      BURST_SLC_FIRST_LINE_OFFSETS,
+                      BURST_SLC_NUMBER_OF_SAMPLES,
+                      BURST_SLC_NUMBER_OF_LINES
+                    )
+
+
+    def __init__(self,name=''):
+        super(Swath, self).__init__(family=self.__class__.family, name=name)
+        return None
+
+
+    def clone(self):
+        import copy
+        res = copy.deepcopy(self)
+        res.image._accessor = None
+        res.image._factory = None
+
+        return res

components/isceobj/Sensor/MultiMode/Track.py

@@ -0,0 +1,186 @@
+#!/usr/bin/env python3
+
+#Author: Cunren Liang, 2015-
+
+import isce
+import datetime
+import isceobj
+import numpy as np
+from iscesys.Component.Component import Component
+from isceobj.Image.Image import Image
+from isceobj.Orbit.Orbit import Orbit
+from isceobj.Util.decorators import type_check
+from iscesys.Traits import datetimeType
+
+
+####List of parameters
+PASS_DIRECTION = Component.Parameter('passDirection',
+        public_name='pass direction',
+        default = None,
+        type=str,
+        mandatory=True,
+        doc = 'satellite flying direction, ascending/descending')
+
+POINTING_DIRECTION = Component.Parameter('pointingDirection',
+        public_name='pointing direction',
+        default=None,
+        type = str,
+        mandatory = True,
+        doc = 'antenna point direction: right/left')
+
+OPERATION_MODE = Component.Parameter('operationMode',
+        public_name='operation mode',
+        default=None,
+        type = str,
+        mandatory = True,
+        doc = 'JAXA ALOS-2 operation mode code')
+
+RADAR_WAVELENGTH = Component.Parameter('radarWavelength',
+        public_name = 'radarWavelength',
+        default = None,
+        type = float,
+        mandatory = True,
+        doc = 'radar wavelength in m')
+
+NUMBER_OF_SAMPLES = Component.Parameter('numberOfSamples',
+        public_name='number of samples',
+        default=None,
+        type=int,
+        mandatory=True,
+        doc='width of the burst slc')
+
+NUMBER_OF_LINES = Component.Parameter('numberOfLines',
+        public_name='number of lines',
+        default=None,
+        type=int,
+        mandatory=True,
+        doc='length of the burst slc')
+
+STARTING_RANGE = Component.Parameter('startingRange',
+        public_name='starting range',
+        default=None,
+        type=float,
+        mandatory=True,
+        doc='slant range to first pixel in m')
+
+RANGE_SAMPLING_RATE = Component.Parameter('rangeSamplingRate',
+        public_name = 'range sampling rate',
+        default = None,
+        type = float,
+         mandatory = True,
+         doc = 'range sampling rate in Hz')
+
+RANGE_PIXEL_SIZE = Component.Parameter('rangePixelSize',
+        public_name = 'range pixel size',
+        default = None,
+        type=float,
+        mandatory = True,
+        doc = 'slant range pixel size in m')
+
+SENSING_START = Component.Parameter('sensingStart',
+        public_name='sensing start',
+        default=None,
+        type=datetimeType,
+        mandatory=True,
+        doc='UTC time corresponding to first line of swath SLC')
+
+PRF = Component.Parameter('prf',
+        public_name = 'pulse repetition frequency',
+        default = None,
+        type = float,
+        mandatory = True,
+        doc = 'pulse repetition frequency in Hz')
+
+AZIMUTH_PIXEL_SIZE = Component.Parameter('azimuthPixelSize',
+        public_name = 'azimuth pixel size',
+        default = None,
+        type=float,
+        mandatory = True,
+        doc = 'azimuth pixel size on ground in m')
+
+AZIMUTH_LINE_INTERVAL = Component.Parameter('azimuthLineInterval',
+        public_name = 'azimuth line interval',
+        default = None,
+        type=float,
+        mandatory = True,
+        doc = 'azimuth line interval in s')
+
+#########################################################################################################
+#for dense offset
+DOPPLER_VS_PIXEL = Component.Parameter('dopplerVsPixel',
+        public_name = 'doppler vs pixel',
+        default = None,
+        type = float,
+        mandatory = True,
+        container = list,
+        doc = 'Doppler (Hz) polynomial coefficients vs range pixel number')
+#########################################################################################################
+
+
+#ProductManager cannot handle two or more layers of createTraitSeq
+#use list instead for bookkeeping
+#can creat a class Frames(Component) and wrap trait sequence, but it
+#leads to more complicated output xml file, which is not good for viewing
+FRAMES = Component.Parameter('frames',
+        public_name = 'frames',
+        default = [],
+        #type = float,
+        mandatory = True,
+        container = list,
+        doc = 'sequence of frames')
+
+
+####List of facilities
+ORBIT = Component.Facility('orbit',
+    public_name='orbit',
+    module='isceobj.Orbit.Orbit',
+    factory='createOrbit',
+    args=(),
+    doc = 'orbit state vectors')
+
+# FRAMES = Component.Facility('frames',
+#         public_name='frames',
+#         module = 'iscesys.Component',
+#         factory = 'createTraitSeq',
+#         args=('frame',),
+#         mandatory = False,
+#         doc = 'trait sequence of frames')
+
+class Track(Component):
+    """A class to represent a track"""
+    
+    family = 'track'
+    logging_name = 'isce.track'
+##############################################################################
+    parameter_list = (PASS_DIRECTION,
+                      POINTING_DIRECTION,
+                      OPERATION_MODE,
+                      RADAR_WAVELENGTH,
+                      NUMBER_OF_SAMPLES,
+                      NUMBER_OF_LINES,
+                      STARTING_RANGE,
+                      RANGE_SAMPLING_RATE,
+                      RANGE_PIXEL_SIZE,
+                      SENSING_START,
+                      PRF,
+                      AZIMUTH_PIXEL_SIZE,
+                      AZIMUTH_LINE_INTERVAL,
+                      DOPPLER_VS_PIXEL,
+                      FRAMES
+                    )
+
+    facility_list = (ORBIT,
+                    )
+
+    def __init__(self,name=''):
+        super(Track, self).__init__(family=self.__class__.family, name=name)
+        return None
+
+
+    def clone(self):
+        import copy
+        res = copy.deepcopy(self)
+        res.image._accessor = None
+        res.image._factory = None
+
+        return res

components/isceobj/Sensor/MultiMode/__init__.py

@@ -0,0 +1,55 @@
+#Author: Cunren Liang, 2015-
+
+def createSwath():
+    from .Swath import Swath
+    return Swath()
+
+def createFrame():
+    from .Frame import Frame
+    return Frame()
+
+def createTrack():
+    from .Track import Track
+    return Track()
+
+
+def createALOS2(name=None):
+    from .ALOS2 import ALOS2
+    return ALOS2()
+
+
+SENSORS = {
+             'ALOS2' : createALOS2,
+          }
+
+def getFactoriesInfo():
+    """
+    Returns a dictionary with information on how to create an object Sensor from its factory
+    """
+    return  {'MultiModeSensor':
+                     {'args':
+                           {
+                            'sensor':{'value':list(SENSORS.keys()),'type':'str','optional':False}
+                            },
+                     'factory':'createSensor'
+                     }
+              }
+
+
+
+def createSensor(sensor='', name=None):
+    
+    try:
+        cls = SENSORS[str(sensor).upper()]
+        try:
+            instance = cls(name)
+        except AttributeError:
+            raise TypeError("'sensor name'=%s  cannot be interpreted" %
+                            str(sensor))
+        pass
+    except:
+        print("Sensor type not recognized. Valid Sensor types:\n",
+              SENSORS.keys())
+        instance = None
+        pass
+    return instance

components/isceobj/Sensor/SConscript

@@ -57,3 +57,4 @@ SConscript(os.path.join('src', 'SConscript'),
 SConscript(os.path.join('TOPS','SConscript'))
 SConscript(os.path.join('GRD', 'SConscript'))
 SConscript(os.path.join('ScanSAR', 'SConscript'))
+SConscript(os.path.join('MultiMode', 'SConscript'))

components/isceobj/TopsProc/runIon.py

@@ -473,7 +473,7 @@ def subband(self, ionParam):
                 
                 #subband
                 rg_filter(tmpFilename,
-                          burst.numberOfSamples,
+                          #burst.numberOfSamples,
                           2,
                           [os.path.join(lowerDir, tmpFilename2), os.path.join(upperDir, tmpFilename2)],
                           [ionParam.rgBandwidthSub / rangeSamplingRate, ionParam.rgBandwidthSub / rangeSamplingRate],

components/mroipac/ampcor/Ampcor.py

@@ -1,28 +1,20 @@
 #!/usr/bin/env python3 
 
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# Copyright 2012 California Institute of Technology. ALL RIGHTS RESERVED.
+# copyright: 2012 to the present, california institute of technology.
+# all rights reserved. united states government sponsorship acknowledged.
+# any commercial use must be negotiated with the office of technology transfer
+# at the california institute of technology.
 # 
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
+# this software may be subject to u.s. export control laws. by accepting this
+# software, the user agrees to comply with all applicable u.s. export laws and
+# regulations. user has the responsibility to obtain export licenses,  or other
+# export authority as may be required before exporting such information to
+# foreign countries or providing access to foreign persons.
 # 
-# http://www.apache.org/licenses/LICENSE-2.0
-# 
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-# 
-# United States Government Sponsorship acknowledged. This software is subject to
-# U.S. export control laws and regulations and has been classified as 'EAR99 NLR'
-# (No [Export] License Required except when exporting to an embargoed country,
-# end user, or in support of a prohibited end use). By downloading this software,
-# the user agrees to comply with all applicable U.S. export laws and regulations.
-# The user has the responsibility to obtain export licenses, or other export
-# authority as may be required before exporting this software to any 'EAR99'
-# embargoed foreign country or citizen of those countries.
+# installation and use of this software is restricted by a license agreement
+# between the licensee and the california institute of technology. it is the
+# user's responsibility to abide by the terms of the license agreement.
 #
 # Author: Giangi Sacco
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -41,7 +33,7 @@ from iscesys.Compatibility import Compatibility
 Compatibility.checkPythonVersion()
 from mroipac.ampcor import ampcor
 from isceobj.Util.mathModule import is_power2
-from isceobj.Util.decorators import use_api
+#from isceobj.Util.decorators import use_api
 
 WINDOW_SIZE_WIDTH = Component.Parameter('windowSizeWidth',
         public_name='WINDOW_SIZE_WIDTH',
@@ -297,7 +289,7 @@ class Ampcor(Component):
                       DEBUG_FLAG,
                       DISPLAY_FLAG)
 
-    @use_api
+#    @use_api
     def ampcor(self,slcImage1 = None,slcImage2 = None, band1=None, band2=None):
         if not (slcImage1 == None):
             self.slcImage1 = slcImage1
@@ -396,8 +388,8 @@ class Ampcor(Component):
         #if self.searchWindowSizeHeight >= 2*self.windowSizeHeight :
         #    raise ValueError('Search Window Size Height should be < 2 * Window Size Height')
 
-        if self.zoomWindowSize >= min(self.searchWindowSizeWidth, self.searchWindowSizeHeight):
-            raise ValueError('Zoom window size should be <= Search window size')
+        #if self.zoomWindowSize >= min(self.searchWindowSizeWidth, self.searchWindowSizeHeight):
+        #    raise ValueError('Zoom window size should be <= Search window size')
 
 
     def checkSkip(self):
@@ -519,6 +511,12 @@ class Ampcor(Component):
         ampcor.setAcrossLooks_Py(self.acrossLooks)
         ampcor.setDownLooks_Py(self.downLooks)
 
+        #reference values
+        #self.winsizeFilt = 8
+        #self.oversamplingFactorFilt = 64
+        ampcor.setWinsizeFilt_Py(self.winsizeFilt)
+        ampcor.setOversamplingFactorFilt_Py(self.oversamplingFactorFilt)
+
         return
 
     def setImageDataType1(self, var):
@@ -641,6 +639,14 @@ class Ampcor(Component):
             raise ValueError('Oversampling factor needs to be a power of 2.')
         self.oversamplingFactor = temp
 
+    def setWinsizeFilt(self, var):
+        temp = int(var)
+        self.winsizeFilt = temp
+
+    def setOversamplingFactorFilt(self, var):
+        temp = int(var)
+        self.oversamplingFactorFilt = temp
+
     def setSearchWindowSizeWidth(self, var):
         self.searchWindowSizeWidth = int(var)
         return
@@ -822,6 +828,8 @@ class Ampcor(Component):
         self.scaleFactorX = None
         self.scaleFactorY = None
         self.numRows = None
+        self.winsizeFilt = 1
+        self.oversamplingFactorFilt = 64
         self.dictionaryOfVariables = { \
                                       'IMAGETYPE1' : ['imageDataType1', 'str', 'optional'], \
                                       'IMAGETYPE2' : ['imageDataType2', 'str', 'optional'], \

components/mroipac/ampcor/DenseAmpcor.py

@@ -632,8 +632,8 @@ class DenseAmpcor(Component):
         if self.searchWindowSizeHeight >= 2*self.windowSizeHeight :
             raise ValueError('Search Window Size Height should be < 2 * Window Size Height')
 
-        if self.zoomWindowSize >= min(self.searchWindowSizeWidth, self.searchWindowSizeHeight):
-            raise ValueError('Zoom window size should be <= Search window size')
+        if self.zoomWindowSize > min(self.searchWindowSizeWidth*2+1, self.searchWindowSizeHeight*2+1):
+            raise ValueError('Zoom window size should be <= Search window size * 2 + 1')
 
         if self._stdWriter is None:
             self._stdWriter = create_writer("log", "", True, filename="denseampcor.log")

components/mroipac/ampcor/bindings/ampcormodule.cpp

@@ -724,3 +724,27 @@ PyObject * getCov3_C(PyObject* self, PyObject* args)
         delete [] vectorV;
         return Py_BuildValue("N",list);
 }
+
+
+
+PyObject* setWinsizeFilt_C(PyObject* self, PyObject* args)
+{
+  int factor;
+  if( !PyArg_ParseTuple(args,"i",&factor) )
+  {
+    return NULL;
+  }
+  setWinsizeFilt_f(&factor);
+  return Py_BuildValue("i",0);
+}
+
+PyObject* setOversamplingFactorFilt_C(PyObject* self, PyObject* args)
+{
+  int factor;
+  if( !PyArg_ParseTuple(args,"i",&factor) )
+  {
+    return NULL;
+  }
+  setOversamplingFactorFilt_f(&factor);
+  return Py_BuildValue("i",0);
+}

components/mroipac/ampcor/include/ampcormodule.h

@@ -152,6 +152,10 @@ extern "C"
   PyObject * setScaleFactorX_C(PyObject*, PyObject*);
   PyObject * setScaleFactorY_C(PyObject*, PyObject*);
 
+  void setOversamplingFactorFilt_f(int*);
+  PyObject* setOversamplingFactorFilt_C(PyObject*, PyObject*);
+  void setWinsizeFilt_f(int*);
+  PyObject* setWinsizeFilt_C(PyObject*, PyObject*);
 }
 
 
@@ -226,6 +230,9 @@ static PyMethodDef ampcor_methods[] =
  { "deallocate_cov2Ret_Py", deallocate_cov2Ret_C, METH_VARARGS, " "},
  { "deallocate_cov3Ret_Py", deallocate_cov3Ret_C, METH_VARARGS, " "},
 
+ { "setWinsizeFilt_Py", setWinsizeFilt_C, METH_VARARGS, " "},
+ { "setOversamplingFactorFilt_Py", setOversamplingFactorFilt_C, METH_VARARGS, " "},
+
  {NULL, NULL, 0 , NULL}
 };
 

components/mroipac/ampcor/include/ampcormoduleFortTrans.h

@@ -67,6 +67,8 @@
               #define deallocate_cov2Ret_f deallocate_cov2ret_
               #define deallocate_cov3Ret_f deallocate_cov3ret_
 
+              #define setWinsizeFilt_f setwinsizefilt_
+              #define setOversamplingFactorFilt_f setoversamplingfactorfilt_
 
         #else
             #error Unknown translation for FORTRAN external symbols

components/mroipac/ampcor/src/ampcor.F

@@ -1,3 +1,14 @@
+!c This program has been upgraded for matching ScanSAR full-aperture images.
+!c 1. setting the following two parameters to use:
+!c      winsize_filt = 8
+!c      i_covs_filt = 64
+!c 2. use same original parameter values as you use in the original program for
+!c    ScanSAR full-aperture image matching.
+!c 3. Original matching method is still available by setting winsize_filt to 1.
+!c    In this case, i_covs_filt has no effects.
+
+!c Cunren Liang, 25-DEC-2019, Caltech
+
 !c****************************************************************
 
       subroutine ampcor(imgAccessor1, imgAccessor2, band1, band2)
@@ -126,6 +137,24 @@
       external seconds
       integer count
 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!c    for ScanSAR full-aperture mode matching
+      real*4 r_shfty_filt,r_shftx_filt
+      integer i_shiftx_filt,i_shifty_filt
+      !integer winsize_filt
+      integer i_wsyi_filt
+      integer i_wsyj_filt
+      integer iii, num_pixel
+      !integer i_covs_filt, i_cw_filt
+      integer i_cw_filt
+      real, dimension(:,:), allocatable :: r_imgi_filt, r_imgj_filt, r_imgc_filt
+      complex, dimension(:), allocatable :: c_corr_filt, c_corrt_filt
+      real tmp_corr
+      integer continue_fine_matching
+
+!c    added to avoid accessing indexes out of bounds (segmentation fault) 02-FEB-2020
+      integer x_index
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
       write(6,*) 'Input Bands: ', band1, band2
 
@@ -204,6 +233,48 @@
       i_n2wsxj = 2**(nextpower(i_wsxjp))
       i_n2wsyj = 2**(nextpower(i_wsyjp))
 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!c    for ScanSAR full-aperture mode matching
+      !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+      !input parameter reference values:
+      !winsize_filt should be power of 2 to faciliate subsequent processing
+      !winsize_filt = 8
+      !i_covs_filt = i_covs
+      !i_covs_filt = 64
+      !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+      
+      !better be power of 2 for fft
+      i_cw_filt = (i_wsyj - i_wsyi) / winsize_filt
+      i_wsyi_filt = i_wsyi / winsize_filt
+      i_wsyj_filt = i_wsyj / winsize_filt
+
+      if(winsize_filt .ne. 1)then
+        write(6,*) ''
+        write(6,*) '   *** using ScanSAR full-aperture mode for gross offset estimation ***'
+        write(6,*) 'azimuth multi-looking window size: ', winsize_filt
+        write(6,*) 'number of azimuth samples before and after multi-looking (master): ', i_wsyi, i_wsyi_filt
+        write(6,*) 'number of azimuth samples before and after multi-looking (slave): ', i_wsyj, i_wsyj_filt
+        write(6,*) 'azimuth covariance surface oversampling factor: ', i_covs_filt
+        write(6,*) 'total number of azimuth samples to be oversampled', i_cw_filt
+        write(6,*) ''
+      endif
+
+      if(i_cw_filt .lt. 4)then
+        write(6,*) 'ERROR - number of samples availabe for estating gross offset is too small:', i_cw_filt
+        write(6,*) '        the value is computed as 2*i_srchy/winsize_filt'
+        write(6,*) '        current i_srchy (azimuth search window size):', i_srchy
+        write(6,*) '        current winsize_filt (azimuth filtering window size):', winsize_filt
+        return
+      endif
+
+      if(i_cw_filt .ne. 2**nextpower(i_cw_filt))then
+        write(6,*) 'WARNING - number of samples availabe for estating gross offset is NOT power of 2:', i_cw_filt
+        write(6,*) '          the value is computed as 2*i_srchy/winsize_filt'
+        write(6,*) '          better to make it power of 2 for FFT'
+        write(6,*) '          current i_srchy (azimuth search window size):', i_srchy
+        write(6,*) '          current winsize_filt (azimuth filtering window size):', winsize_filt
+      endif
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
       !c Set max width to largest of the width
       i_maxsamp = max(i_samples(1), i_samples(2))
@@ -230,6 +301,15 @@
        allocate( c_ossch(i_ovs*i_n2wsxj*i_ovs*i_n2wsyj) )
        allocate( c_osref(i_ovs*i_n2wsxi*i_ovs*i_n2wsyi) )
 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!c    for ScanSAR full-aperture mode matching
+      allocate( r_imgi_filt(i_wsxi,i_wsyi_filt))
+      allocate( r_imgj_filt(i_wsxj,i_wsyj_filt))
+      allocate( r_imgc_filt(i_wsxj,i_wsyj_filt))
+      allocate( c_corr_filt(i_covs_filt*i_cw_filt*i_covs_filt*i_cw_filt) )
+      allocate( c_corrt_filt(i_cw_filt*i_cw_filt) )
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
 !c-------------------------------
 !c        begin ruggedize ... a bunch of input checking
 
@@ -485,13 +565,27 @@
 
             do i_yy = 1,i_wsyi
                do i_xx = 1,i_wsxi
-                  r_imgi(i_xx,i_yy) = cabs(c_refimg(i_x+i_xx-1,i_yy))
+
+                  x_index = i_x+i_xx-1
+                  if ((x_index .lt. 1).or.(x_index .gt. i_maxsamp)) then
+                     r_imgi(i_xx,i_yy) = 0.0
+                  else
+                     r_imgi(i_xx,i_yy) = cabs(c_refimg(x_index,i_yy))
+                  endif
+
                end do
             end do
 
             do i_yy = 1, i_wsyj
                do i_xx = 1 , i_wsxj
-                  r_imgj(i_xx,i_yy) = cabs(c_srchimg(i_xlu+i_xx-1-i_srchx+i_grossx,i_yy))
+
+                  x_index = i_xlu+i_xx-1-i_srchx+i_grossx
+                  if ((x_index .lt. 1).or.(x_index .gt. i_maxsamp)) then
+                     r_imgj(i_xx,i_yy) = 0.0
+                  else
+                     r_imgj(i_xx,i_yy) = cabs(c_srchimg(x_index,i_yy))
+                  endif
+
                end do
             end do
 
@@ -504,8 +598,201 @@
                call dump_chip_r4(a_debugfile,r_imgj,1,i_wsxj,1,i_wsyj,i_wsxj,i_wsyj)
             endif
 
-!c     correlate the subimages
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!c    for ScanSAR full-aperture mode matching
 
+!c          correlate azimuth-multiple-looked images
+            if (winsize_filt .ne. 1) then
+!c          get azimuth-multiple-looked images
+              do i_yy = 1,i_wsyi_filt
+                 do i_xx = 1,i_wsxi
+                    r_imgi_filt(i_xx,i_yy) = 0.
+                    num_pixel = 0
+                    do iii = 1,winsize_filt
+                      if(r_imgi(i_xx,(i_yy-1)*winsize_filt+iii) .ne. 0) then
+                        num_pixel = num_pixel + 1
+                        r_imgi_filt(i_xx,i_yy) = r_imgi_filt(i_xx,i_yy) + r_imgi(i_xx,(i_yy-1)*winsize_filt+iii)**2
+                      endif
+                    end do
+                    if(num_pixel .ne. 0) then
+                      r_imgi_filt(i_xx,i_yy) = sqrt(r_imgi_filt(i_xx,i_yy)/num_pixel)
+                    endif
+                 end do
+              end do
+
+
+              do i_yy = 1, i_wsyj_filt
+                 do i_xx = 1 , i_wsxj
+                    r_imgj_filt(i_xx,i_yy) = 0.
+                    num_pixel = 0
+                    do iii = 1,winsize_filt
+                      if(r_imgj(i_xx,(i_yy-1)*winsize_filt+iii) .ne. 0) then
+                        num_pixel = num_pixel + 1
+                        r_imgj_filt(i_xx,i_yy) = r_imgj_filt(i_xx,i_yy) + r_imgj(i_xx,(i_yy-1)*winsize_filt+iii)**2
+                      endif
+                    end do
+                    if(num_pixel .ne. 0) then
+                      r_imgj_filt(i_xx,i_yy) = sqrt(r_imgj_filt(i_xx,i_yy)/num_pixel)
+                    endif
+                 end do
+              end do
+
+!c            correlate images
+!c            i_avgx = i_avgy = 1 
+              call correlate(r_imgi_filt,r_imgj_filt,i_wsxi,i_wsyi_filt,i_wsxj,
+     &           i_wsyj_filt,1,1,1,r_meani,r_stdvi,r_meanj,
+     &           r_stdvj,r_peak,r_noise,r_cov,r_eval1,
+     &           r_eval2,r_evec1,r_evec2,r_imgc_filt,i_shiftx_filt,i_shifty_filt,i_edge,
+     &           i_flag,l_debug)
+
+              r_shftx_filt=float(i_shiftx_filt) - i_srchx + i_grossx
+              r_shfty_filt=float(i_shifty_filt) - float(i_srchy)/winsize_filt + float(i_grossy)/winsize_filt
+              r_shfty_filt=r_shfty_filt*winsize_filt
+
+              if(i_flag .eq. 0 .and. i_edge(1) .eq. 0 .and.
+     &           i_edge(2) .eq. 0)then !found a potentially good data point
+
+                r_outside = 0.0
+                i_cnta = 0
+                do l=max(i_shifty_filt-9,1),min(i_shifty_filt+11,i_wsyj_filt-i_wsyi_filt)
+                  do k=max(i_shiftx_filt-9,1),min(i_shiftx_filt+11,i_wsxj-i_wsxi)
+                    i_cnta = i_cnta + 1
+                    r_outside = r_outside + r_imgc_filt(k,l)**2
+                  enddo
+                enddo
+                r_outside = r_outside - r_peak**2
+                r_outside = r_outside/(i_cnta-1)
+
+                r_snr = r_peak**2/max(r_outside,1.e-10)
+
+                if(r_snr .gt. r_snrth .and. r_cov(1) .lt. r_covth .and. r_cov(2) .lt. r_covth)then
+                  continue_fine_matching = 1
+                else
+                  continue_fine_matching = 0
+                endif
+
+              else
+                continue_fine_matching = 0
+              endif
+
+!c            compute finer offset by oversampling covariance surface
+              if(continue_fine_matching .ne. 0)then
+                r_max = 0.0
+                r_mean_cor = 0.0
+                i_cnta = 0
+                i_px = i_shiftx_filt+1
+                i_py = i_shifty_filt+1
+
+                do i_yy=-i_cw_filt/2,i_cw_filt/2-1
+
+                    do i_xx=-i_cw_filt/2,i_cw_filt/2-1
+
+                      i_index = (i_yy+i_cw_filt/2)*i_cw_filt + i_xx + i_cw_filt/2 + 1
+
+                      if (i_xx+i_px .ge. 1 .and. i_xx+i_px .le. (2*i_srchx+1)*1 .and.
+     &                         i_yy+i_py .ge. 1 .and. i_yy+i_py .le. (2*i_srchy+1)*1 )then
+                        c_corrt_filt(i_index) = cmplx(abs(r_imgc_filt(i_xx+i_px,i_yy+i_py)/r_peak),0.)
+                        r_mean_cor = r_mean_cor + cabs(c_corrt_filt(i_index))
+                        i_cnta = i_cnta + 1
+                      else
+                        c_corrt_filt(i_index) = cmplx(0.0, 0.0)
+                      endif
+
+                      if(cabs(c_corrt_filt(i_index)) .gt. r_max)then
+                        r_max = cabs(c_corrt_filt(i_index))
+                        i_p1 = i_xx
+                        i_p2 = i_yy
+                      endif
+
+                  enddo
+
+                enddo
+
+!c              substract off the mean
+!c              looks like it does not do anything, so can comment out these
+!c                r_mean_cor = r_mean_cor/max(i_cnta,1)
+!c                r_mean_cor = 0.0
+!c                do i_yy=-i_cw_filt/2,i_cw_filt/2-1
+!c                  do i_xx=-i_cw_filt/2,i_cw_filt/2-1
+!c                    i_index = (i_yy+i_cw_filt/2)*i_cw_filt + i_xx + i_cw_filt/2 + 1
+!c                    c_corrt_filt(i_index) = c_corrt_filt(i_index) - cmplx(r_mean_cor,0.0)
+!c                  enddo
+!c                enddo
+
+!c              oversample via Fourier transforms
+!c              forward fft the data
+                i_nn(1) = i_cw_filt
+                i_nn(2) = i_cw_filt
+                i_dir = 1
+                call fourn2d(c_corrt_filt,i_nn,i_dir)
+
+!c              spread the spectral data out for inverse transforms
+                i_nn(1) = i_cw_filt*i_covs_filt
+                i_nn(2) = i_cw_filt*i_covs_filt
+                i_dir = -1
+
+                do k=1,i_nn(2)
+                   do l=1,i_nn(1)
+                      i_index = (k-1)*i_nn(1) + l
+                      c_corr_filt(i_index) = 0.0
+                   enddo
+                enddo
+
+                do l=1,i_cw_filt/2
+                   do k=1,i_cw_filt/2
+                      i_index = (k-1)*i_nn(1) + l
+                      i_indexi = (k-1)*i_cw_filt + l
+                      c_corr_filt(i_index) = c_corrt_filt(i_indexi)
+                      i_index = l + (i_nn(2)-i_cw_filt/2+k-1)*i_nn(1)
+                      i_indexi = l + (k+i_cw_filt/2-1)*i_cw_filt
+                      c_corr_filt(i_index) = c_corrt_filt(i_indexi)
+                      i_index = i_nn(1)-i_cw_filt/2+l + (k-1)*i_nn(2)
+                      i_indexi = l+i_cw_filt/2 + (k-1)*i_cw_filt
+                      c_corr_filt(i_index) = c_corrt_filt(i_indexi)
+                      i_index = i_nn(1)-i_cw_filt/2+l + (i_nn(2)-i_cw_filt/2+k-1)*i_nn(1)
+                      i_indexi = l+i_cw_filt/2 + (k+i_cw_filt/2-1)*i_cw_filt
+                      c_corr_filt(i_index) = c_corrt_filt(i_indexi)
+                   enddo
+                enddo
+
+!c              inverse transform
+                call fourn2d(c_corr_filt,i_nn,i_dir)
+
+
+!c              detect the peak
+                 r_max=0.
+                 do i_yy=1,i_cw_filt*i_covs_filt
+                    do i_xx=1,i_cw_filt*i_covs_filt
+                       i_index = (i_yy-1)*i_cw_filt*i_covs_filt + i_xx
+                       tmp_corr = cabs(c_corr_filt(i_index))/((i_cw_filt**2)*(i_cw_filt*i_covs_filt)**2)
+                       if (abs(i_xx-i_cw_filt*i_covs_filt/2) .le. i_covs_filt .and.
+     &                          abs(i_yy-i_cw_filt*i_covs_filt/2) .le. i_covs_filt) then
+                          if (tmp_corr .ge. r_max) then
+                             r_max = tmp_corr
+                             i_cpeak(1) = i_xx - i_cw_filt/2*i_covs_filt
+                             i_cpeak(2) = i_yy - i_cw_filt/2*i_covs_filt
+                          endif
+                       endif
+                    enddo
+                 enddo
+
+                 r_oscoroff(1) = float(i_cpeak(1)-1)/float(i_covs_filt)
+                 r_oscoroff(2) = float(i_cpeak(2)-1)/float(i_covs_filt)
+                 r_oscoroff(2) = r_oscoroff(2) * winsize_filt
+
+                 r_shftx = r_oscoroff(1)/1 + r_shftx_filt + i_xlu - i_x
+                 r_shfty = r_oscoroff(2)/1 + r_shfty_filt + i_ylu - i_y
+
+                 !get integer values for subsequent use. note that all four variables
+                 !are used, so they need to be consistent
+                 r_shftx = nint(r_shftx)
+                 r_shfty = nint(r_shfty)
+                 i_shiftx = nint(r_shftx) + i_srchx - i_grossx
+                 i_shifty = nint(r_shfty) + i_srchy - i_grossy
+              endif
+            else
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!c          correlate original images
             call correlate(r_imgi,r_imgj,i_wsxi,i_wsyi,i_wsxj,
      &           i_wsyj,i_avgx,i_avgy,1,r_meani,r_stdvi,r_meanj,
      &           r_stdvj,r_peak,r_noise,r_cov,r_eval1,
@@ -546,9 +833,21 @@
 
                r_snr = r_peak**2/max(r_outside,1.e-10)
 !ccccc               write(6,'(a,1x,2(f20.10,1x))') 'Peak/SNR = ',r_peak,r_snr
-
                if(r_snr .gt. r_snrth .and. r_cov(1) .lt. r_covth .and. r_cov(2) .lt. r_covth)then
+                continue_fine_matching = 1
+               else
+                continue_fine_matching = 0
+               endif
+            else
+              continue_fine_matching = 0
+            endif
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+            endif
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
+!c          this is just used to keep the original indentation level
+            if(1 .eq. 1)then
+               if(continue_fine_matching .ne. 0)then
 !c     oversample the region around the peak 2 to 1 to estimate the fractional offset
 
 !c     write the reference image and search image around the peak into arrays
@@ -1138,6 +1437,16 @@
          deallocate( c_chipsch)
          deallocate( c_ossch)
          deallocate( c_osref)
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!c    for ScanSAR full-aperture mode matching
+         deallocate( r_imgi_filt)
+         deallocate( r_imgj_filt)
+         deallocate( r_imgc_filt)
+         deallocate( c_corr_filt)
+         deallocate( c_corrt_filt)
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
       close(13)
       close(14)
 !c     close(15)

components/mroipac/ampcor/src/ampcorPrintState.F

@@ -26,7 +26,9 @@
          write(6,*) "r_covth       = ",r_covth
          write(6,*) "l_debug       = ",l_debug
          write(6,*) "l_display     = ",l_display
-   
+
+         write(6,*) "winsize_filt  = ",winsize_filt
+         write(6,*) "i_covs_filt   = ",i_covs_filt
          return
        end
          

components/mroipac/ampcor/src/ampcorSetState.F

@@ -198,3 +198,16 @@
           r_scaley = var
        end
       
+       subroutine setWinsizeFilt(winsize_filt_val)
+          use ampcorState
+          implicit none
+          integer winsize_filt_val
+          winsize_filt = winsize_filt_val
+       end
+
+       subroutine setOversamplingFactorFilt(i_covs_filt_val)
+          use ampcorState
+          implicit none
+          integer i_covs_filt_val
+          i_covs_filt = i_covs_filt_val
+       end

components/mroipac/ampcor/src/ampcorState.F

@@ -33,4 +33,7 @@
 !c we only know the max number of rows. at the end of the ampcor we can get it        
         integer numRowTable
         
+        integer winsize_filt
+        integer i_covs_filt
+
       end module ampcorState

contrib/CMakeLists.txt

@@ -7,7 +7,9 @@ add_subdirectory(downsample_unwrapper)
 
 #add_subdirectory(PyCuAmpcor)
 add_subdirectory(splitSpectrum)
+add_subdirectory(alos2filter)
 add_subdirectory(alos2proc)
+add_subdirectory(alos2proc_f)
 add_subdirectory(rfi)
 add_subdirectory(mdx)
 

contrib/SConscript

@@ -77,7 +77,9 @@ SConscript(rfi)
 
 SConscript('PyCuAmpcor/SConscript')
 SConscript('splitSpectrum/SConscript')
+SConscript('alos2filter/SConscript')
 SConscript('alos2proc/SConscript')
+SConscript('alos2proc_f/SConscript')
 
 if os.path.exists('geo_autoRIFT'):
     SConscript('geo_autoRIFT/SConscript')

contrib/alos2filter/CMakeLists.txt

@@ -0,0 +1,6 @@
+add_library(alos2filter SHARED src/psfilt1.c)
+InstallSameDir(
+    alos2filter
+    __init__.py
+    alos2filter.py
+    )

contrib/alos2filter/SConscript

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+
+#Cunren Liang, 2015-2018
+
+import os
+
+Import('envcontrib')
+envalos2filter = envcontrib.Clone()
+package = envcontrib['PACKAGE']
+project = 'alos2filter'
+Export('envalos2filter')
+
+
+
+
+srcScons = os.path.join('src','SConscript')
+varDir = os.path.join(envalos2filter['PRJ_SCONS_BUILD'],package,project,'src')
+SConscript(srcScons, variant_dir = varDir)
+
+
+install = os.path.join(envcontrib['PRJ_SCONS_INSTALL'],package,project)
+listFiles = ['__init__.py','alos2filter.py']
+envcontrib.Install(install,listFiles)
+envcontrib.Alias('install',install)
+

contrib/alos2filter/__init__.py

@@ -0,0 +1 @@
+#!/usr/bin/env python3

contrib/alos2filter/alos2filter.py

@@ -0,0 +1,17 @@
+import os
+import copy
+import ctypes
+import logging
+import isceobj
+from xml.etree.ElementTree import ElementTree
+
+def psfilt1(inputfile, outputfile, width, alpha, fftw, step):
+    filters = ctypes.cdll.LoadLibrary(os.path.join(os.path.dirname(__file__),'libalos2filter.so'))
+    filters.psfilt1(
+        ctypes.c_char_p(bytes(inputfile,'utf-8')),
+        ctypes.c_char_p(bytes(outputfile,'utf-8')),
+        ctypes.c_int(width),
+        ctypes.c_double(alpha),
+        ctypes.c_int(fftw),
+        ctypes.c_int(step)
+        )

contrib/alos2filter/src/SConscript

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+
+import os
+
+Import('envalos2filter')
+
+install = os.path.join(envalos2filter['PRJ_SCONS_INSTALL'], envalos2filter['PACKAGE'], 'alos2filter')
+listFiles = ['psfilt1.c']
+
+# -shared
+# -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -lm
+# -lfftw3f_threads -lfftw3f -lpthread -fopenmp -O3 
+
+#envalos2proc.Append(CFLAGS=['-D_LARGEFILE64_SOURCE', '-D_FILE_OFFSET_BITS=64', '-lm', '-shared', '-fopenmp', '-O3'])
+#envalos2proc.Append(LIBS=['fftw3f', 'fftw3f_threads', 'pthread'])
+
+lib = envalos2filter.LoadableModule(target = 'libalos2filter.so', source = listFiles, parse_flags='-fopenmp')
+envalos2filter.Install(install,lib)
+envalos2filter.Alias('install',install)
+
+
+
+

contrib/alos2filter/src/psfilt1.c

@@ -0,0 +1,496 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <math.h>
+
+#define PLUS 1
+#define MINU 2
+#define CHG  3
+#define GUID 4
+#define LSNR 8
+#define VIST 16
+#define BRPT 32
+#define CUT  64
+#define LAWN 128
+#define TREE 128
+
+#define NFFT 	32	/* size of FFT */
+#define STEP	NFFT/2	/* stepsize in range and azimuth for filter */
+#define ALPHA	0.5	/* default exponent for weighting of the spectrum */
+
+#define REL_BEGIN 0	/* fseek relative to beginning of file */
+#define REL_CUR   1	/* fseek relative to current position in the file */
+#define REL_EOF   2	/* fseek relative to end of file */
+
+#define SQR(a)    ( (a)*(a) )
+#define PI	3.14159265359 
+#define TWO_PI  6.28318530718
+#define SQRT2   1.41421356237 	/* square root of 2 */
+#define RTD	57.2957795131	/* radians to degrees */
+#define DTR	.0174532925199	/* degrees to radians */
+#define C	2.99792458e8
+
+#define NR_END 1
+#define FREE_ARG char*
+
+typedef struct{float re,im;} fcomplex;
+
+void fourn(float *, unsigned int *, int ndim, int isign); 
+void psd_wgt(fcomplex **cmp, fcomplex **seg_fft, double, int, int, int);
+
+void start_timing();					/* timing routines */
+void stop_timing();
+	
+unsigned int nfft[3];
+int xmin=0;						/* window column minima */
+int ymin=0;						/* window row minima */
+int ymax, xmax;          /* interferogram width, window maxima */
+
+fcomplex **cmatrix(int nrl, int nrh, int ncl, int nch);
+void free_cmatrix(fcomplex **m, int nrl, int nrh, int ncl, int nch);
+void nrerror(char error_text[]);
+signed char IsFinite(double d);
+
+int psfilt1(char *inputfile, char *outputfile, int width, double alpha, int fftw, int step)
+{
+   fcomplex *bufcz, **cmp;		/* interferogram line buffer, complex input data, row pointers */
+   fcomplex **sm, **seg_fft, *seg_fftb;	/* smoothed interferogram, 2d fft of segment */
+   fcomplex **tmp, **tmp1;		/* arrays of pointers for temp storage of line pointers in circular buffers */
+   double **wf, *wfb;			/* 2-D weights */
+
+   float *data;				/* pointer to floats for FFT, union with seg_fft */
+   //double alpha;			/* exponent used to to determine spectal weighting function */
+   double rw,azw;			/* range and azimuth weights used in window function */
+ 
+   int nlines=0;			/* number of lines in the file */
+   int offs;				/* width and height of file segment*/
+   //int fftw;       /* fft window size*/
+   //int step;				/* step size in range and azimuth for filtering of interferogram */
+   int xw,yh;				/* width, height of processed region */
+   int i,j,i1,j1;			/* loop counters */
+   int ndim;				/* number of dimensions of FFT */
+   int isign;				/* direction of FFT */     
+   int nlc;				/* number of guides, number of low correlation pixels */
+   int lc;				/* line counter */
+    
+   FILE *int_file, *sm_file;
+
+   int k;
+   float sf; // scale factor for FFT, otherwise FFT will magnify the data by FFT length
+             // usually the magnitude of the interferogram is very large, so the data are
+             // multiplied by this factor before FFT, rather than after FFT in this program.
+   float sf0; // an extra factor to scale the data
+   sf0  = 1.0;
+
+   
+   fprintf(stderr,"*** Weighted power spectrum interferogram filter v1.0 clw 19-Feb-97 ***\n");
+    if(0){
+     //fprintf(stderr,"\nUsage: %s <interferogram> <smoothed interferogram> <width> [alpha] [fftw] [step] [xmin] [xmax] [ymin] [ymax]\n\n",argv[0]) ;
+    
+     fprintf(stderr,"input parameters: \n");
+     fprintf(stderr,"  interferogram      complex interferogram image filename\n");
+     fprintf(stderr,"  smoothed interf.   smoothed interferogram filename\n");
+     fprintf(stderr,"  width              number of samples/row\n");
+     fprintf(stderr,"  alpha              spectrum amplitude scale factor (default=.5)\n");  
+     fprintf(stderr,"  fftw               fft window size in both range and azimuth directions \n");
+     fprintf(stderr,"  step               moving step size in both range and azimuth directions (default = fftw/2)\n");
+     fprintf(stderr,"  xmin               offset to starting range pixel (default = 0)\n");    
+     fprintf(stderr,"  xmax               offset last range pixel (default = width-1)\n");    
+     fprintf(stderr,"  ymin               offset to starting azimuth row (default = 0)\n");    
+     fprintf(stderr,"  ymax               offset to last azimuth row (default = nlines-1)\n\n");    
+     exit(-1);
+   }
+
+   start_timing();
+   int_file = fopen(inputfile,"rb"); 
+   if (int_file == NULL){fprintf(stderr,"cannot open interferogram file: %s\n",inputfile); exit(-1);}
+
+   sm_file = fopen(outputfile,"wb"); 
+   if (sm_file == NULL){fprintf(stderr,"cannot create smoothed interferogram file: %s\n",outputfile); exit(-1);}
+
+   //sscanf(argv[3],"%d",&width);  
+   xmax = width-1;	 
+ 
+   fseeko(int_file, 0L, REL_EOF);		/* determine # lines in the file */
+   nlines=(int)(ftello(int_file)/(width*2*sizeof(float)));
+   fprintf(stderr,"#lines in the interferogram file: %d\n",nlines); 
+   rewind(int_file);
+
+   
+   //alpha = ALPHA;
+   //if(argc >= 4)sscanf(argv[4],"%lf",&alpha);
+   fprintf(stdout,"spectrum weighting exponent: %8.4f\n",alpha);
+
+   //fftw = NFFT;
+   //if (argc >5)sscanf(argv[5],"%d",&fftw);
+   fprintf(stdout,"FFT window size: %5d\n",fftw);
+
+   sf = fftw * fftw * sf0;
+
+   //step = fftw/2;
+   //if (argc >6)sscanf(argv[6],"%d",&step);
+   if (step <= 0 || step > fftw){
+     fprintf(stdout,"WARNING: wrong step size: %5d, using %5d instead\n",step, fftw/2);
+     step = fftw/2;
+   }
+   fprintf(stdout,"range and azimuth step size (pixels): %5d\n",step); 
+   
+   ymax=nlines-1;				/* default value of ymax */
+   //if(argc > 7)sscanf(argv[7],"%d",&xmin);	/* window to process */
+   //if(argc > 8)sscanf(argv[8],"%d",&xmax);
+   //if(argc > 9)sscanf(argv[9],"%d",&ymin);
+   //if(argc > 10)sscanf(argv[10],"%d",&ymax);
+ 
+   if (ymax > nlines-1){
+     ymax = nlines-1; 
+    fprintf(stderr,"WARNING: insufficient #lines in the file for given input range: ymax: %d\n",ymax);     
+   }
+
+   if (xmax > width-1) xmax=width-1;	/* check to see if xmax within bounds */
+   xw=xmax-xmin+1;			/* width of array */
+   yh=ymax-ymin+1;			/* height of array */ 
+   offs=ymin;				/* first line of file to start reading/writing */
+   fprintf(stdout,"array width, height, offset: %5d %5d %5d\n",xw,yh,offs);
+ 
+   cmp = cmatrix(0, fftw-1, -fftw,width+fftw);			/* add space around the arrays */ 
+   sm = cmatrix(0,fftw-1,-fftw,width+fftw);
+
+   tmp = (fcomplex **)malloc(sizeof(fcomplex *)*step);
+   tmp1 = (fcomplex **)malloc(sizeof(fcomplex *)*step);
+   if (tmp == NULL || tmp1==NULL){fprintf(stderr,"ERROR: failure to allocate space for circular buffer pointers\n"); exit(-1);}
+
+   bufcz = (fcomplex *)malloc(sizeof(fcomplex)*width);
+   if(bufcz == NULL){fprintf(stderr,"ERROR: failure to allocate space for input line buffer\n"); exit(-1);}
+
+   seg_fftb = (fcomplex *)malloc(sizeof(fcomplex)*fftw*fftw);
+   if(seg_fftb == NULL){fprintf(stderr,"ERROR: failure to allocate space for FFT data\n"); exit(-1);}
+   seg_fft = (fcomplex **)malloc(sizeof(fcomplex *)*fftw);
+   if(seg_fft == NULL){fprintf(stderr,"ERROR: failure to allocate space for FFT data pointers\n"); exit(-1);}
+
+   wfb = (double *)malloc(sizeof(double)*fftw*fftw);
+   if (wfb == NULL){fprintf(stderr,"ERROR: weight memory allocation failure...\n"); exit(-1);}
+   wf = (double **)malloc(sizeof(double *)*fftw);
+   if (wf == NULL){fprintf(stderr,"ERROR: weight pointers memory allocation failure...\n"); exit(-1);}
+
+   for(i=0; i < fftw; i++) seg_fft[i] = seg_fftb  + i*fftw;
+   for(j=0; j < fftw; j++) wf[j] = wfb + j*fftw;
+
+   for(j=0; j < width; j++){bufcz[j].re=0.; bufcz[j].im=0.;}
+
+   for(i=0; i < fftw; i++){				/* initialize circular data buffers */
+     for(j= -fftw; j < width+fftw; j++){
+       cmp[i][j].re = 0.0; cmp[i][j].im = 0.0;
+       sm[i][j].re = 0.0; sm[i][j].im = 0.0;   
+     }
+   }
+ 
+   for (i=0; i < fftw; i++){
+     for (j=0; j < fftw; j++){
+       azw = 1.0 - fabs(2.0*(double)(i-fftw/2)/(fftw+1));  
+       rw  = 1.0 - fabs(2.0*(double)(j-fftw/2)/(fftw+1));  
+       wf[i][j]=azw*rw/(double)(fftw*fftw);
+#ifdef DEBUG
+       fprintf(stderr,"i,j,wf: %5d %5d %12.4e\n",i,j,wf[i][j]);
+#endif
+     }
+   }
+ 
+   nfft[1] = fftw;
+   nfft[2] = nfft[1];
+   nfft[0] = 0;
+   ndim = 2;
+   isign = 1;				/* initialize FFT parameter values, inverse FFT */
+
+   
+   fseek(int_file, offs*width*sizeof(fcomplex), REL_BEGIN); 	/* seek offset to start line of interferogram */
+   for (i=0; i < fftw - step; i++){
+    fread((char *)cmp[i], sizeof(fcomplex), width, int_file);
+    for(k = 0; k < width; k++){
+      cmp[i][k].re /= sf;
+      cmp[i][k].im /= sf;
+    }
+   }
+   lc=0;
+
+   for (i=0; i < yh; i += step){
+     for(i1=fftw - step; i1 < fftw; i1++){
+       fread((char *)cmp[i1], sizeof(fcomplex), width, int_file);
+       for(k = 0; k < width; k++){
+        cmp[i1][k].re /= sf;
+        cmp[i1][k].im /= sf;
+       }
+       if (feof(int_file) != 0){				/* fill with zero if at end of file */
+         for(j1= -fftw; j1 < width+fftw; j1++){cmp[i1][j1].re=0.0; cmp[i1][j1].im=0.0;}
+       }
+       for(j1= -fftw; j1 < width+fftw; j1++){
+         sm[i1][j1].re=0.0; sm[i1][j1].im=0.0; 			/* clear out area for new sum */
+       }     
+     }
+     if(i%(2*step) == 0)fprintf(stderr,"\rprogress: %3d%%", (int)(i*100/yh + 0.5));
+  
+     for (j=0; j < width; j += step){
+       psd_wgt(cmp, seg_fft, alpha, j, i, fftw);	
+       fourn((float *)seg_fft[0]-1,nfft,ndim,isign);	/* 2D inverse FFT of region, get back filtered fringes */
+
+       for (i1=0; i1 < fftw; i1++){			/* save filtered output values */
+         for (j1=0; j1 < fftw; j1++){
+           if(cmp[i1][j+j1].re !=0.0){
+             sm[i1][j+j1].re += wf[i1][j1]*seg_fft[i1][j1].re; 
+             sm[i1][j+j1].im += wf[i1][j1]*seg_fft[i1][j1].im;
+           }
+           else{
+             sm[i1][j+j1].re=0.0; 
+             sm[i1][j+j1].im=0.0;
+           }
+         }
+       }
+     }         
+     for (i1=0; i1 < step; i1++){	
+       if (lc < yh){
+        for(k = 0; k < width; k++){
+          if(!IsFinite(sm[i1][k].re))
+            sm[i1][k].re = 0.0;
+          if(!IsFinite(sm[i1][k].im))
+            sm[i1][k].im = 0.0;
+          if(!IsFinite(sqrt(sm[i1][k].re*sm[i1][k].re + sm[i1][k].im*sm[i1][k].im))){
+            sm[i1][k].re = 0.0;
+            sm[i1][k].im = 0.0;
+          }
+        }
+        fwrite((char *)sm[i1], sizeof(fcomplex), width, sm_file); 
+       }
+       lc++;
+     }
+     for (i1=0; i1 < step; i1++){tmp[i1] = cmp[i1]; tmp1[i1] = sm[i1];}		/* save pointers to lines just written out */
+     for (i1=0; i1 < fftw - step; i1++){cmp[i1] = cmp[i1+step]; sm[i1] = sm[i1+step];}	/* shift the data just processed  */
+     for (i1=0; i1 < step; i1++){cmp[fftw - step+i1] = tmp[i1]; sm[fftw - step+i1]=tmp1[i1];} /* copy pointers back */
+   }
+   fprintf(stderr,"\rprogress: %3d%%", 100);
+   
+   for(i=lc; i < yh; i++){				/* write null lines of filtered complex data */	
+     for(k = 0; k < width; k++){
+      if(!IsFinite(bufcz[k].re))
+        bufcz[k].re = 0.0;
+      if(!IsFinite(bufcz[k].im))
+        bufcz[k].im = 0.0;  
+      if(!IsFinite(sqrt(bufcz[k].re*bufcz[k].re + bufcz[k].im*bufcz[k].im))){
+        bufcz[k].re = 0.0;
+        bufcz[k].im = 0.0;
+      }
+     }
+     fwrite((char *)bufcz, sizeof(fcomplex), width, sm_file);
+     lc++;
+   } 
+
+   fprintf(stdout,"\nnumber of lines written to file: %d\n",lc);
+   stop_timing();
+
+   free(bufcz);
+   //free_cmatrix(cmp, 0, fftw-1, -fftw,width+fftw);
+   //free_cmatrix(sm, 0,fftw-1,-fftw,width+fftw);
+   free(seg_fft);
+   free(seg_fftb);
+   free(tmp);
+   free(tmp1);
+   free(wf);
+   free(wfb);
+   fclose(int_file); 
+   fclose(sm_file);
+
+   return(0);  
+} 
+ 
+void psd_wgt(fcomplex **cmp, fcomplex **seg_fft, double alpha, int ix, int iy, int fftw)
+/* 
+  subroutine to perform non-linear spectral filtering  17-Feb-97 clw
+*/
+
+{
+  double psd,psd_sc;	/* power spectrum, scale factor */
+  int i,j;		/* loop counters */
+  int ndim,isign;	/* number of dimensions in fft */
+  
+  int ic;
+ 
+  unsigned int nfft[3];
+  ic = 0;
+   
+  ndim=2, isign = -1, nfft[1]=fftw, nfft[2]=fftw, nfft[0]=0; /* fft initialization */
+  
+  for (i=0; i < fftw; i++){  					/* load up data array */
+    for (j=ix; j < ix+fftw; j++){
+      seg_fft[i][j-ix].re = cmp[i][j].re;
+      seg_fft[i][j-ix].im = cmp[i][j].im;
+    }
+  }
+
+  fourn((float *)seg_fft[0]-1, nfft, ndim, isign);		/* 2D forward FFT of region */
+
+  for (i=0; i < fftw; i++){
+    for (j=0; j < fftw; j++){
+      psd = seg_fft[i][j].re * seg_fft[i][j].re + seg_fft[i][j].im * seg_fft[i][j].im;
+      psd_sc = pow(psd,alpha/2.);
+      seg_fft[i][j].re *= psd_sc;
+      seg_fft[i][j].im *= psd_sc;    
+    }
+  }
+}
+
+
+#define SWAP(a,b) tempr=(a);(a)=(b);(b)=tempr
+void fourn(float data[], unsigned int nn[], int ndim, int isign)
+{
+	int idim;
+	unsigned long i1,i2,i3,i2rev,i3rev,ip1,ip2,ip3,ifp1,ifp2;
+	unsigned long ibit,k1,k2,n,nprev,nrem,ntot;
+	float tempi,tempr;
+	double theta,wi,wpi,wpr,wr,wtemp;
+
+	for (ntot=1,idim=1;idim<=ndim;idim++)
+		ntot *= nn[idim];
+	nprev=1;
+	for (idim=ndim;idim>=1;idim--) {
+		n=nn[idim];
+		nrem=ntot/(n*nprev);
+		ip1=nprev << 1;
+		ip2=ip1*n;
+		ip3=ip2*nrem;
+		i2rev=1;
+		for (i2=1;i2<=ip2;i2+=ip1) {
+			if (i2 < i2rev) {
+				for (i1=i2;i1<=i2+ip1-2;i1+=2) {
+					for (i3=i1;i3<=ip3;i3+=ip2) {
+						i3rev=i2rev+i3-i2;
+						SWAP(data[i3],data[i3rev]);
+						SWAP(data[i3+1],data[i3rev+1]);
+					}
+				}
+			}
+			ibit=ip2 >> 1;
+			while (ibit >= ip1 && i2rev > ibit) {
+				i2rev -= ibit;
+				ibit >>= 1;
+			}
+			i2rev += ibit;
+		}
+		ifp1=ip1;
+		while (ifp1 < ip2) {
+			ifp2=ifp1 << 1;
+			theta=isign*6.28318530717959/(ifp2/ip1);
+			wtemp=sin(0.5*theta);
+			wpr = -2.0*wtemp*wtemp;
+			wpi=sin(theta);
+			wr=1.0;
+			wi=0.0;
+			for (i3=1;i3<=ifp1;i3+=ip1) {
+				for (i1=i3;i1<=i3+ip1-2;i1+=2) {
+					for (i2=i1;i2<=ip3;i2+=ifp2) {
+						k1=i2;
+						k2=k1+ifp1;
+						tempr=(float)wr*data[k2]-(float)wi*data[k2+1];
+						tempi=(float)wr*data[k2+1]+(float)wi*data[k2];
+						data[k2]=data[k1]-tempr;
+						data[k2+1]=data[k1+1]-tempi;
+						data[k1] += tempr;
+						data[k1+1] += tempi;
+					}
+				}
+				wr=(wtemp=wr)*wpr-wi*wpi+wr;
+				wi=wi*wpr+wtemp*wpi+wi;
+			}
+			ifp1=ifp2;
+		}
+		nprev *= n;
+	}
+}
+
+#undef SWAP
+
+fcomplex **cmatrix(int nrl, int nrh, int ncl, int nch)
+/* allocate a fcomplex matrix with subscript range m[nrl..nrh][ncl..nch] */
+{
+	int i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+	fcomplex **m;
+
+	/* allocate pointers to rows */
+	m=(fcomplex **)malloc((size_t)((nrow+NR_END)*sizeof(fcomplex*)));
+	if (!m) nrerror("ERROR: allocation failure 1 in cmatrix()");
+	m += NR_END;
+	m -= nrl;
+
+	/* allocate rows and set pointers to them */
+	m[nrl]=(fcomplex *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(fcomplex)));
+	if (!m[nrl]) nrerror("ERROR: allocation failure 2 in cmatrix()");
+	m[nrl] += NR_END;
+	m[nrl] -= ncl;
+
+	for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+
+	/* return pointer to array of pointers to rows */
+	return m;
+}
+
+void free_cmatrix(fcomplex **m, int nrl, int nrh, int ncl, int nch)
+/* free a float matrix allocated by matrix() */
+{
+	free((FREE_ARG) (m[nrl]+ncl-NR_END));
+	free((FREE_ARG) (m+nrl-NR_END));
+}
+
+void nrerror(char error_text[])
+/* Numerical Recipes standard error handler */
+{
+	fprintf(stdout,"Numerical Recipes run-time error...\n");
+	fprintf(stdout,"%s\n",error_text);
+	fprintf(stdout,"...now exiting to system...\n");
+	exit(1);
+}
+
+#include <sys/types.h>
+#include <sys/time.h>
+#include <sys/times.h>
+#include <unistd.h>
+#include <limits.h>
+
+struct tms buffer;
+int user_time, system_time, start_time;
+
+void start_timing()
+{
+  start_time = (int) times(&buffer);
+  user_time = (int) buffer.tms_utime;
+  system_time = (int) buffer.tms_stime;
+}
+
+void stop_timing()
+{
+  int  end_time,elapsed_time;
+  int clk_tck;
+
+  clk_tck = (int)sysconf(_SC_CLK_TCK);
+
+  end_time = (int) times(&buffer);
+  user_time = (int) (buffer.tms_utime - user_time);
+  system_time = (int) (buffer.tms_stime - system_time);
+  elapsed_time = (end_time - start_time);
+
+  fprintf(stdout,"\n\nuser time    (s):  %10.3f\n", (double)user_time/clk_tck);
+  fprintf(stdout,"system time  (s):  %10.3f\n", (double)system_time/clk_tck); 
+  fprintf(stdout,"elapsed time (s):  %10.3f\n\n", (double) elapsed_time/clk_tck);
+}
+
+/* function: IsFinite()
+ * --------------------
+ * This function takes a double and returns a nonzero value if 
+ * the arguemnt is finite (not NaN and not infinite), and zero otherwise.
+ * Different implementations are given here since not all machines have
+ * these functions available.
+ */
+signed char IsFinite(double d){
+
+  return(finite(d));
+  /* return(isfinite(d)); */
+  /* return(!(isnan(d) || isinf(d))); */
+  /* return(TRUE) */
+}
+

contrib/alos2proc/CMakeLists.txt

@@ -5,6 +5,10 @@ Python_add_library(libalos2proc MODULE
     src/mbf.c
     src/lib_array.c
     src/lib_func.c
+    src/resamp.c
+    src/mosaicsubswath.c
+    src/look.c
+    src/extract_burst.c
     )
 target_include_directories(libalos2proc PUBLIC include)
 target_link_libraries(libalos2proc PUBLIC

contrib/alos2proc/alos2proc.py

@@ -6,13 +6,12 @@ import copy
 import ctypes
 import logging
 import isceobj
+from xml.etree.ElementTree import ElementTree
 
-
-def mbf(inputfile, outputfile, nrg, prf, prf_frac, nb, nbg, nboff, bsl, kacoeff, dopcoeff1, dopcoeff2):
+def mbf(inputfile, outputfile, prf, prf_frac, nb, nbg, nboff, bsl, kacoeff, dopcoeff1, dopcoeff2):
     #############################
     # inputfile:       input file
     # outputfile:      output file
-    # nrg:             file width
     # prf:             PRF
     # prf_frac:        fraction of PRF processed
     #                     (represents azimuth bandwidth)
@@ -27,8 +26,8 @@ def mbf(inputfile, outputfile, nrg, prf, prf_frac, nb, nbg, nboff, bsl, kacoeff,
     #                     (float, the line number of the first line of the full-aperture SLC is zero)
     #                     (no need to be first burst, any one is OK)
 
-    # kacoeff[0-2]:    FM rate coefficients
-    #                     (three coefficients of a quadratic polynomial with regard to)
+    # kacoeff[0-3]:    FM rate coefficients
+    #                     (four coefficients of a third order polynomial with regard to)
     #                     (range sample number. range sample number starts with zero)
 
     # dopcoeff1[0-3]:  Doppler centroid frequency coefficients of this image
@@ -41,18 +40,34 @@ def mbf(inputfile, outputfile, nrg, prf, prf_frac, nb, nbg, nboff, bsl, kacoeff,
     #############################
 
     #examples:
-    # kacoeff = [-625.771055784221, 0.007887946763383646, -9.10142814131697e-08]
+    # kacoeff = [-625.771055784221, 0.007887946763383646, -9.10142814131697e-08, 0.0]
     # dopcoeff1 = [-0.013424025141940908, -6.820475445542178e-08, 0.0, 0.0]
     # dopcoeff2 = [-0.013408164465406417, -7.216577938502655e-08, 3.187158113584236e-24, -9.081842749918244e-28]
 
-    inputfile2 = copy.deepcopy(inputfile)
-    outputfile2 = copy.deepcopy(outputfile)
-    inputfile = bytes(inputfile,'utf-8')
-    outputfile = bytes(outputfile,'utf-8')
+    img = isceobj.createSlcImage()
+    img.load(inputfile + '.xml')
+
+    width = img.getWidth()
+    length = img.getLength()
+
+    inputimage = find_vrt_file(inputfile+'.vrt', 'SourceFilename')
+    byteorder = find_vrt_keyword(inputfile+'.vrt', 'ByteOrder')
+    if byteorder == 'LSB':
+        byteorder = 0
+    else:
+        byteorder = 1
+    imageoffset = find_vrt_keyword(inputfile+'.vrt', 'ImageOffset')
+    imageoffset = int(imageoffset)
+    lineoffset = find_vrt_keyword(inputfile+'.vrt', 'LineOffset')
+    lineoffset = int(lineoffset)
+
+    #lineoffset = lineoffset - width * 8
+    #imageoffset = imageoffset - lineoffset
+
     if type(kacoeff) != list:
         raise Exception('kacoeff must be a python list.\n')
-        if len(kacoeff) != 3:
-            raise Exception('kacoeff must have three elements.\n')
+        if len(kacoeff) != 4:
+            raise Exception('kacoeff must have four elements.\n')
     if type(dopcoeff1) != list:
         raise Exception('dopcoeff1 must be a python list.\n')
         if len(dopcoeff1) != 4:
@@ -64,9 +79,10 @@ def mbf(inputfile, outputfile, nrg, prf, prf_frac, nb, nbg, nboff, bsl, kacoeff,
 
     filters = ctypes.cdll.LoadLibrary(os.path.join(os.path.dirname(__file__),'libalos2proc.so'))
     filters.mbf(
-        ctypes.c_char_p(inputfile),
-        ctypes.c_char_p(outputfile),
-        ctypes.c_int(nrg),
+        ctypes.c_char_p(bytes(inputimage,'utf-8')),
+        ctypes.c_char_p(bytes(outputfile,'utf-8')),
+        ctypes.c_int(width),
+        ctypes.c_int(length),
         ctypes.c_float(prf),
         ctypes.c_float(prf_frac),
         ctypes.c_float(nb),
@@ -76,24 +92,26 @@ def mbf(inputfile, outputfile, nrg, prf, prf_frac, nb, nbg, nboff, bsl, kacoeff,
         (ctypes.c_float * len(kacoeff))(*kacoeff),
         (ctypes.c_float * len(dopcoeff1))(*dopcoeff1),
         (ctypes.c_float * len(dopcoeff2))(*dopcoeff2),
+        ctypes.c_int(byteorder),
+        ctypes.c_long(imageoffset),
+        ctypes.c_long(lineoffset)
         )
 
-    img = isceobj.createSlcImage()
-    img.load(inputfile2 + '.xml')
-    img.setFilename(outputfile2)
-    img.extraFilename = outputfile2 + '.vrt'
+    #img = isceobj.createSlcImage()
+    #img.load(inputfile + '.xml')
+    img.setFilename(outputfile)
+    img.extraFilename = outputfile + '.vrt'
     img.setAccessMode('READ')
     img.renderHdr()
 
 
-def rg_filter(inputfile, nrg, nout, outputfile, bw, bc, nfilter, nfft, beta, zero_cf, offset):
+def rg_filter(inputfile, nout, outputfile, bw, bc, nfilter, nfft, beta, zero_cf, offset):
     #############################
     # inputfile:  input file
-    # nrg         file width
     # nout:       number of output files
-    # outputfile: (value_of_out_1, value_of_out_2, value_of_out_3...) output files
-    # bw:         (value_of_out_1, value_of_out_2, value_of_out_3...) filter bandwidth divided by sampling frequency [0, 1]
-    # bc:         (value_of_out_1, value_of_out_2, value_of_out_3...) filter center frequency divided by sampling frequency
+    # outputfile: [value_of_out_1, value_of_out_2, value_of_out_3...] output files
+    # bw:         [value_of_out_1, value_of_out_2, value_of_out_3...] filter bandwidth divided by sampling frequency [0, 1]
+    # bc:         [value_of_out_1, value_of_out_2, value_of_out_3...] filter center frequency divided by sampling frequency
 
     # nfilter:    number samples of the filter (odd). Reference Value: 65
     # nfft:       number of samples of the FFT. Reference Value: 1024
@@ -103,19 +121,35 @@ def rg_filter(inputfile, nrg, nout, outputfile, bw, bc, nfilter, nfft, beta, zer
     #############################
 
     #examples
-    #outputfile = [bytes('result/crop_filt_1.slc','utf-8'), bytes('result/crop_filt_2.slc','utf-8')]
+    #outputfile = ['result/crop_filt_1.slc', 'result/crop_filt_2.slc']
     #bw = [0.3, 0.3]
     #bc = [0.1, -0.1]
 
-    inputfile2 = copy.deepcopy(inputfile)
+    img = isceobj.createSlcImage()
+    img.load(inputfile + '.xml')
+
+    width = img.getWidth()
+    length = img.getLength()
+
+    inputimage = find_vrt_file(inputfile+'.vrt', 'SourceFilename')
+    byteorder = find_vrt_keyword(inputfile+'.vrt', 'ByteOrder')
+    if byteorder == 'LSB':
+        byteorder = 0
+    else:
+        byteorder = 1
+    imageoffset = find_vrt_keyword(inputfile+'.vrt', 'ImageOffset')
+    imageoffset = int(imageoffset)
+    lineoffset = find_vrt_keyword(inputfile+'.vrt', 'LineOffset')
+    lineoffset = int(lineoffset)
+
+    #lineoffset = lineoffset - width * 8
+    #imageoffset = imageoffset - lineoffset
+
     outputfile2 = copy.deepcopy(outputfile)
-
-    inputfile = bytes(inputfile,'utf-8')
-
     if type(outputfile) != list:
         raise Exception('outputfile must be a python list.\n')
         if len(outputfile) != nout:
-            raise Exception('number of output files is not equal to list length.\n')
+            raise Exception('number of output files is not equal to outputfile list length.\n')
     else:
         tmp = []
         for x in outputfile:
@@ -125,17 +159,18 @@ def rg_filter(inputfile, nrg, nout, outputfile, bw, bc, nfilter, nfft, beta, zer
     if type(bw) != list:
         raise Exception('bw must be a python list.\n')
         if len(bw) != nout:
-            raise Exception('number of output files is not equal to list length.\n')
+            raise Exception('number of output files is not equal to bw list length.\n')
 
     if type(bc) != list:
         raise Exception('bc must be a python list.\n')
         if len(bc) != nout:
-            raise Exception('number of output files is not equal to list length.\n')
+            raise Exception('number of output files is not equal to bc list length.\n')
 
     filters = ctypes.cdll.LoadLibrary(os.path.join(os.path.dirname(__file__),'libalos2proc.so'))
     filters.rg_filter(
-        ctypes.c_char_p(inputfile),
-        ctypes.c_int(nrg),
+        ctypes.c_char_p(bytes(inputimage,'utf-8')),
+        ctypes.c_int(width),
+        ctypes.c_int(length),
         ctypes.c_int(nout),
         (ctypes.c_char_p * len(outputfile))(*outputfile),
         (ctypes.c_float * len(bw))(*bw),
@@ -144,13 +179,286 @@ def rg_filter(inputfile, nrg, nout, outputfile, bw, bc, nfilter, nfft, beta, zer
         ctypes.c_int(nfft),
         ctypes.c_float(beta),
         ctypes.c_int(zero_cf),
-        ctypes.c_float(offset)
+        ctypes.c_float(offset),
+        ctypes.c_int(byteorder),
+        ctypes.c_long(imageoffset),
+        ctypes.c_long(lineoffset)
         )
 
-    img = isceobj.createSlcImage()
-    img.load(inputfile2 + '.xml')
+    #img = isceobj.createSlcImage()
+    #img.load(inputfile + '.xml')
     for x in outputfile2:
         img.setFilename(x)
         img.extraFilename = x + '.vrt'
         img.setAccessMode('READ')
         img.renderHdr()
+
+
+def resamp(slc2, rslc2, rgoff_file, azoff_file, nrg1, naz1, prf, dopcoeff, rgcoef=[0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0], azcoef=[0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0], azpos_off=0.0, verbose=0):
+    #############################
+    # mandatory:
+    # slc2:             slave image
+    # rslc2:            resampled slave image
+    # rgoff_file:       range offset file. if no range offset file, specify 'fake'
+    # azoff_file:       azimuth offset file. if no azimuth offset file, specify 'fake'
+    # nrg1:             number of columns in master image
+    # naz1:             number of lines in master image
+    # prf:              PRF of slave image
+    # dopcoeff[0]-[3]:  Doppler centroid frequency coefficents
+    # optional:
+    # rgcoef[0]-[9]:    range offset polynomial coefficents. First of two fit results of resamp_roi
+    # azcoef[0]-[9]:    azimuth offset polynomial coefficents. First of two fit results of resamp_roi
+    # azpos_off:        azimuth position offset. Azimuth line number (column 3) of first offset in culled offset file
+    # verbose:          if not zero, print resampling info
+    #############################
+
+    #examples:
+    # dopcoeff = [-0.013424025141940908, -6.820475445542178e-08, 0.0, 0.0]
+
+    img = isceobj.createSlcImage()
+    img.load(slc2 + '.xml')
+
+    width = img.getWidth()
+    length = img.getLength()
+
+    inputimage = find_vrt_file(slc2+'.vrt', 'SourceFilename')
+    byteorder = find_vrt_keyword(slc2+'.vrt', 'ByteOrder')
+    if byteorder == 'LSB':
+        byteorder = 0
+    else:
+        byteorder = 1
+    imageoffset = find_vrt_keyword(slc2+'.vrt', 'ImageOffset')
+    imageoffset = int(imageoffset)
+    lineoffset = find_vrt_keyword(slc2+'.vrt', 'LineOffset')
+    lineoffset = int(lineoffset)
+
+    #lineoffset = lineoffset - width * 8
+    #imageoffset = imageoffset - lineoffset
+
+    if type(dopcoeff) != list:
+        raise Exception('dopcoeff must be a python list.\n')
+        if len(dopcoeff) != 4:
+            raise Exception('dopcoeff must have four elements.\n')
+    if type(rgcoef) != list:
+        raise Exception('rgcoef must be a python list.\n')
+        if len(rgcoef) != 10:
+            raise Exception('rgcoef must have 10 elements.\n')
+    if type(azcoef) != list:
+        raise Exception('azcoef must be a python list.\n')
+        if len(azcoef) != 10:
+            raise Exception('azcoef must have 10 elements.\n')
+
+    filters = ctypes.cdll.LoadLibrary(os.path.join(os.path.dirname(__file__),'libalos2proc.so'))
+    filters.resamp(
+        ctypes.c_char_p(bytes(inputimage,'utf-8')),
+        ctypes.c_char_p(bytes(rslc2,'utf-8')),
+        ctypes.c_char_p(bytes(rgoff_file,'utf-8')),
+        ctypes.c_char_p(bytes(azoff_file,'utf-8')),
+        ctypes.c_int(nrg1),
+        ctypes.c_int(naz1),
+        ctypes.c_int(width),
+        ctypes.c_int(length),
+        ctypes.c_float(prf),
+        (ctypes.c_float * len(dopcoeff))(*dopcoeff),
+        (ctypes.c_float * len(rgcoef))(*rgcoef),
+        (ctypes.c_float * len(azcoef))(*azcoef),
+        ctypes.c_float(azpos_off),
+        ctypes.c_int(byteorder),
+        ctypes.c_long(imageoffset),
+        ctypes.c_long(lineoffset),
+        ctypes.c_int(verbose)
+        )
+
+    #img = isceobj.createSlcImage()
+    #img.load(inputfile + '.xml')
+    img.setFilename(rslc2)
+    img.extraFilename = rslc2 + '.vrt'
+    img.setWidth(nrg1)
+    img.setLength(naz1)
+    img.setAccessMode('READ')
+    img.renderHdr()
+
+
+def mosaicsubswath(outputfile, nrgout, nazout, delta, diffflag, n, inputfile, nrgin, nrgoff, nazoff, phc, oflag):
+    '''
+    outputfile: (char) output file
+    nrgout:     (int)  number of output samples
+    nazout:     (int)  number of output lines
+    delta:      (int)  edge to be removed of the overlap area (number of samples)
+    diffflag:   (int)  whether output the overlap area as two-band BIL image. 0: yes, otherwise: no
+    n:          (int)  number of input file
+    inputfile:  (char list) [value_of_out_1, value_of_out_2, value_of_out_3...] input files to mosaic
+    nrgin:      (int list)  [value_of_out_1, value_of_out_2, value_of_out_3...] input file widths
+    nrgoff:     (int list)  [value_of_out_1, value_of_out_2, value_of_out_3...] input file range offsets
+    nazoff:     (int list)  [value_of_out_1, value_of_out_2, value_of_out_3...] input file azimuth offsets
+    phc:        (float list) [value_of_out_1, value_of_out_2, value_of_out_3...] input file compensation phase
+    oflag:      (int list)  [value_of_out_1, value_of_out_2, value_of_out_3...] overlap area mosaicking flag 
+
+    for each frame
+    range offset is relative to the first sample of last subswath
+    azimuth offset is relative to the uppermost line
+    '''
+
+    if type(inputfile) != list:
+        raise Exception('inputfile must be a python list.\n')
+        if len(inputfile) != n:
+            raise Exception('number of input files is not equal to inputfile list length.\n')
+    else:
+        inputfile = [bytes(x,'utf-8') for x in inputfile]
+
+    filters = ctypes.cdll.LoadLibrary(os.path.join(os.path.dirname(__file__),'libalos2proc.so'))
+    filters.mosaicsubswath(
+        ctypes.c_char_p(bytes(outputfile,'utf-8')),
+        ctypes.c_int(nrgout),
+        ctypes.c_int(nazout),
+        ctypes.c_int(delta),
+        ctypes.c_int(diffflag),
+        ctypes.c_int(n),
+        (ctypes.c_char_p * len(inputfile))(*inputfile),
+        (ctypes.c_int * len(nrgin))(*nrgin),
+        (ctypes.c_int * len(nrgoff))(*nrgoff),
+        (ctypes.c_int * len(nazoff))(*nazoff),
+        (ctypes.c_float * len(phc))(*phc),
+        (ctypes.c_int * len(oflag))(*oflag)
+        )
+
+
+def look(inputfile, outputfile, nrg, nrlks, nalks, ft=0, sum=0, avg=0):
+    '''
+    inputfile:  input file
+    outputfile: output file
+    nrg:     file width
+    nrlks:   number of looks in range (default: 4)
+    nalks:   number of looks in azimuth (default: 4)
+    ft:      file type (default: 0)
+               0: signed char
+               1: int
+               2: float
+               3: double
+               4: complex (real and imagery: float)
+               5: complex (real and imagery: double)
+    sum:     sum method (default: 0)
+               0: simple sum
+               1: power sum (if complex, do this for each channel seperately)
+    avg:     take average (default: 0)
+               0: no
+               1: yes
+    '''
+
+    filters = ctypes.cdll.LoadLibrary(os.path.join(os.path.dirname(__file__),'libalos2proc.so'))
+    filters.look(
+        ctypes.c_char_p(bytes(inputfile,'utf-8')),
+        ctypes.c_char_p(bytes(outputfile,'utf-8')),
+        ctypes.c_long(nrg),
+        ctypes.c_int(nrlks),
+        ctypes.c_int(nalks),
+        ctypes.c_int(ft),
+        ctypes.c_int(sum),
+        ctypes.c_int(avg)
+        )
+
+
+def extract_burst(inputf, outputf, prf, prf_frac, nb, nbg, bsl, kacoeff, dopcoeff, az_ratio, min_line_offset):
+    '''
+    see extract_burst.c for usage
+    '''
+
+    img = isceobj.createSlcImage()
+    img.load(inputf + '.xml')
+
+    width = img.getWidth()
+    length = img.getLength()
+
+    inputimage = find_vrt_file(inputf+'.vrt', 'SourceFilename')
+    byteorder = find_vrt_keyword(inputf+'.vrt', 'ByteOrder')
+    if byteorder == 'LSB':
+        byteorder = 0
+    else:
+        byteorder = 1
+    imageoffset = find_vrt_keyword(inputf+'.vrt', 'ImageOffset')
+    imageoffset = int(imageoffset)
+    lineoffset = find_vrt_keyword(inputf+'.vrt', 'LineOffset')
+    lineoffset = int(lineoffset)
+
+    if type(kacoeff) != list:
+        raise Exception('kacoeff must be a python list.\n')
+        if len(kacoeff) != 4:
+            raise Exception('kacoeff must have four elements.\n')
+    if type(dopcoeff) != list:
+        raise Exception('dopcoeff must be a python list.\n')
+        if len(dopcoeff) != 4:
+            raise Exception('dopcoeff must have four elements.\n')
+
+    filters = ctypes.cdll.LoadLibrary(os.path.join(os.path.dirname(__file__),'libalos2proc.so'))
+    filters.extract_burst(
+        ctypes.c_char_p(bytes(inputimage,'utf-8')),
+        ctypes.c_char_p(bytes(outputf,'utf-8')),
+        ctypes.c_int(width),
+        ctypes.c_int(length),
+        ctypes.c_float(prf),
+        ctypes.c_float(prf_frac),
+        ctypes.c_float(nb),
+        ctypes.c_float(nbg),
+        ctypes.c_float(bsl),
+        (ctypes.c_float * len(kacoeff))(*kacoeff),
+        (ctypes.c_float * len(dopcoeff))(*dopcoeff),
+        ctypes.c_float(az_ratio),
+        ctypes.c_float(min_line_offset),
+        ctypes.c_int(byteorder),
+        ctypes.c_long(imageoffset),
+        ctypes.c_long(lineoffset)
+        )
+
+    #img = isceobj.createSlcImage()
+    #img.load(inputfile + '.xml')
+    #img.setFilename(outputfile)
+    #img.extraFilename = outputfile + '.vrt'
+    #img.setAccessMode('READ')
+    #img.renderHdr()
+
+
+def find_vrt_keyword(xmlfile, keyword):
+    from xml.etree.ElementTree import ElementTree
+
+    value = None
+    xmlx = ElementTree(file=open(xmlfile,'r')).getroot()
+    #try 10 times
+    for i in range(10):
+        path=''
+        for j in range(i):
+            path += '*/'
+        value0 = xmlx.find(path+keyword)
+        if value0 != None:
+            value = value0.text
+            break
+
+    return value
+
+
+
+def find_vrt_file(xmlfile, keyword, relative_path=True):
+    '''
+    find file in vrt in another directory
+    xmlfile: vrt file
+    relative_path: True: return relative (to current directory) path of the file
+                   False: return absolute path of the file
+    '''
+    import os
+    #get absolute directory of xmlfile
+    xmlfile_dir = os.path.dirname(os.path.abspath(xmlfile))
+    #find source file path
+    file = find_vrt_keyword(xmlfile, keyword)
+    #get absolute path of source file
+    file = os.path.abspath(os.path.join(xmlfile_dir, file))
+    #get relative path of source file
+    if relative_path:
+        file = os.path.relpath(file, './')
+    return file
+
+
+
+
+
+
+
+

contrib/alos2proc/src/SConscript

@@ -5,7 +5,7 @@ import os
 Import('envalos2proc')
 
 install = os.path.join(envalos2proc['PRJ_SCONS_INSTALL'], envalos2proc['PACKAGE'], 'alos2proc')
-listFiles = ['lib_array.c', 'lib_cpx.c', 'lib_file.c', 'lib_func.c', 'mbf.c', 'rg_filter.c']
+listFiles = ['lib_array.c', 'lib_cpx.c', 'lib_file.c', 'lib_func.c', 'mbf.c', 'rg_filter.c', 'resamp.c', 'mosaicsubswath.c', 'look.c', 'extract_burst.c']
 
 # -shared
 # -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -lm
@@ -14,7 +14,7 @@ listFiles = ['lib_array.c', 'lib_cpx.c', 'lib_file.c', 'lib_func.c', 'mbf.c', 'r
 #envalos2proc.Append(CFLAGS=['-D_LARGEFILE64_SOURCE', '-D_FILE_OFFSET_BITS=64', '-lm', '-shared', '-fopenmp', '-O3'])
 #envalos2proc.Append(LIBS=['fftw3f', 'fftw3f_threads', 'pthread'])
 
-lib = envalos2proc.LoadableModule(target = 'libalos2proc.so', source = listFiles)
+lib = envalos2proc.LoadableModule(target = 'libalos2proc.so', source = listFiles, parse_flags='-fopenmp')
 envalos2proc.Install(install,lib)
 envalos2proc.Alias('install',install)
 

contrib/alos2proc/src/extract_burst.c

@@ -0,0 +1,576 @@
+//////////////////////////////////////
+// Cunren Liang, NASA JPL/Caltech
+// Copyright 2017
+//////////////////////////////////////
+
+
+#include "resamp.h"
+#include <fftw3.h>
+
+#define SWAP4(a) (*(unsigned int *)&(a) = (((*(unsigned int *)&(a) & 0x000000ff) << 24) | ((*(unsigned int *)&(a) & 0x0000ff00) << 8) | ((*(unsigned int *)&(a) >> 8) & 0x0000ff00) | ((*(unsigned int *)&(a) >> 24) & 0x000000ff)))
+
+
+int extract_burst(char *inputf, char *outputf, int nrg, int naz, float prf, float prf_frac, float nb, float nbg, float bsl, float *kacoeff, float *dopcoeff, float az_ratio, float min_line_offset, int byteorder, long imageoffset, long lineoffset){
+  FILE *infp;
+  FILE *outfp;
+  FILE *infofp;
+
+  char output_filename[512];
+  char burst_num[512];
+
+  fcomplex **in; //data read in
+  fcomplex **out; //data written to output file
+  fcomplex **filter; //multi-band bandpass filter
+  fcomplex **deramp; //deramp signal
+
+  fcomplex *data; //data to be filtered.
+
+  //int nrg; //file width
+  //int naz; //file length
+  int naz_burst_in; //number of lines of the input burst
+  int naz_burst_out; //number of lines of the output burst
+
+  //float prf;
+  float pri; // 1.0/prf
+  //float prf_frac; // azimuth bandwidth used for burst extraction = prf_frac * prf
+  //float kacoeff[3]; //FM rate along range (experessed by quadratic polynomial
+                    //as a function of range sample number)
+  //float dopcoeff[4]; //doppler centroid frequency along range (expressed by quadratic polynomial
+                      //as a function of range sample number). this image
+
+  //float nb; //burst length in terms of pri. number of lines
+  //float nbg; //burst gap length in terms of pri. number of lines
+  //float bsl; //burst start line, input float
+  float bcl; //burst center line, float
+  float bfw; //burst bandwidth
+  //float az_ratio; //azimuth sampling interval of output burst: az_ratio * pri;
+
+  float *ka; //azimuth fm rate
+  float *dop; //doppler centroid frequency
+  float *nfa;
+
+  float *start_line; //burst imaged area start line number for each column
+  float *end_line; //burst imaged area ending line number for each column
+
+  float min_line; //minimum of start_line
+  float max_line; //maximum of end_line
+  int min_line_column; //column of minimum
+  int max_line_column; //column of maximum
+
+  int *output_start; //relative start line in the output burst for each column
+  int *output_end; //relative end line in the output burst for each column
+
+  int min_line_in; //first line of input burst
+  float min_line_out; //first line of output burst
+  float min_line_out_first; //first line of first output burst
+  int offset_from_first_burst; //offset between first burst and this burst in az_ratio * pri
+  int offset_from_first_burst0; //offset between first burst and last burst in az_ratio * pri
+
+  //float min_line_offset; // the offset of first line of output burst in pri, compared with roundfi(min_line)
+                         // this is mainly used to adjust the output burst location. so usually can be set to 0 
+
+  int burst_index;
+  int burst_index_tmp;
+  int burst_index_first;
+
+  int nfft; //fft length
+  int nfilter; //filter length, MUST BE ODD
+  int hnfilter; //half filter length
+  float beta; //kaiser window beta of filter
+  float sc; //constant to scale the data read in to avoid large values during fft and ifft
+
+  //resampling parameters
+  float beta_resamp; //beta of kaiser window of resampling kernal
+  int n; //number of samples to be used in the resampling(odd)
+  int m; //multiples of n, so that a lookup table can be generated(even)
+
+  int hn;  //half of n
+  int hnm; //half of n*m
+  float *sincc; //sinc coefficents
+  float *kaiserc; // kaiser window coefficents
+  float *kernel; // sincc*kaiserc
+  
+  float tmpa, tmpb, tmpc; //temperal variables effective for a longer time
+  float tmp1, tmp2, tmp3; //temperal variables effective for a shorter time
+  fcomplex reramp;
+  int index;
+
+  int i, j, k;
+
+  fftwf_plan p_forward;
+  fftwf_plan p_backward;
+
+/*****************************************************************************/
+//I just put these parametes which can be set here. These can also be set via
+//arguments before running the programs if modifying the code to accept these
+//arguments.
+  //min_line_offset = 0.0;
+
+  //filtering parameters
+  beta = 1.0;
+  nfilter = 257; //MUST BE ODD
+  sc = 10000.0;
+
+  //resampling parameters
+  beta_resamp = 2.5;
+  n = 9; //MUST BE ODD
+  m = 10000; //MUST BE EVEN
+
+/*****************************************************************************/
+
+  if(0){
+  //if(argc != 18){
+    fprintf(stderr, "\nusage: %s inputf outputf nrg naz prf prf_frac nb nbg bsl kacoeff[0-3] dopcoeff[0-3] az_ratio min_line_offset byteorder imageoffset lineoffset\n");
+    fprintf(stderr, "\nmandatory:\n");
+    fprintf(stderr, "  inputf:          input file\n");
+    fprintf(stderr, "  outputf:         prefix of output files\n");
+    fprintf(stderr, "  nrg:             file width\n");
+    fprintf(stderr, "  naz:             file length\n");
+    fprintf(stderr, "  prf:             PRF\n");
+    fprintf(stderr, "  prf_frac:        fraction of PRF used for burst generation\n");
+    fprintf(stderr, "                      (represents azimuth bandwidth)\n");
+    fprintf(stderr, "  nb:              number of lines in a burst\n");
+    fprintf(stderr, "                      (float, in terms of 1/PRF)\n");
+    fprintf(stderr, "  nbg:             number of lines in a burst gap\n");
+    fprintf(stderr, "                      (float, in terms of 1/PRF)\n");
+    fprintf(stderr, "  bsl:             start line number of a burst\n");
+    fprintf(stderr, "                      (float, the line number of the first line of the full-aperture SLC is zero)\n");
+    fprintf(stderr, "                      (no need to be first burst, any one is OK)\n");
+
+    fprintf(stderr, "  kacoeff[0-3]:    FM rate coefficients\n");
+    fprintf(stderr, "                      (four coefficients of a third order polynomial with regard to)\n");
+    fprintf(stderr, "                      (range sample number. range sample number starts with zero)\n");
+
+    fprintf(stderr, "  dopcoeff[0-3]:   Doppler centroid frequency coefficients of this image\n");
+    fprintf(stderr, "                      (four coefficients of a third order polynomial with regard to)\n");
+    fprintf(stderr, "                      (range sample number. range sample number starts with zero)\n");
+    fprintf(stderr, "  az_ratio:        line interval of output burst: az_ratio * (1/PRF)\n");
+    fprintf(stderr, "  min_line_offset: adjust output line location by this offset\n");
+    fprintf(stderr, "                      (in terms of 1/PRF, within [-50/PRF, 50/PRF])\n");
+    fprintf(stderr, "                      (offset < 0, start earlier than original)\n");
+    fprintf(stderr, "                      (offset = 0, original)\n");
+    fprintf(stderr, "                      (offset > 0, start later than original)\n");
+
+    fprintf(stderr, "byteorder:            (0) LSB, little endian; (1) MSB, big endian of intput file\n");
+    fprintf(stderr, "imageoffset:          offset from start of the image of input file\n");
+    fprintf(stderr, "lineoffset:           length of each line of input file\n\n");
+
+    exit(1);
+  }
+
+  infofp  = openfile("extract_burst.txt", "w");
+
+  //open files
+  infp  = openfile(inputf, "rb");
+  //nrg  = atoi(argv[3]);
+  //prf = atof(argv[4]);
+  //prf_frac = atof(argv[5]);
+  //nb = atof(argv[6]);
+  //nbg = atof(argv[7]);
+  //bsl = atof(argv[8]);
+
+  //kacoeff[0] = atof(argv[9]);
+  //kacoeff[1] = atof(argv[10]);
+  //kacoeff[2] = atof(argv[11]);
+
+  //dopcoeff[0] = atof(argv[12]);
+  //dopcoeff[1] = atof(argv[13]);
+  //dopcoeff[2] = atof(argv[14]);
+  //dopcoeff[3] = atof(argv[15]);
+
+  //az_ratio = atof(argv[16]);
+  //min_line_offset = atof(argv[17]);
+
+
+  fprintf(infofp, "\n\ninput parameters:\n");
+  fprintf(infofp, "input file: %s\n", inputf);
+  fprintf(infofp, "prefix of output files: %s\n", outputf);
+  fprintf(infofp, "nrg: %d\n", nrg);
+  fprintf(infofp, "prf: %f\n", prf);
+  fprintf(infofp, "prf_frac: %f\n", prf_frac);
+  fprintf(infofp, "nb: %f\n", nb);
+  fprintf(infofp, "nbg: %f\n", nbg);
+  fprintf(infofp, "bsl: %f\n", bsl);
+
+  fprintf(infofp, "kacoeff: %f, %f, %f, %f\n", kacoeff[0], kacoeff[1], kacoeff[2], kacoeff[3]);
+  fprintf(infofp, "dopcoeff1: %f, %f, %f, %f\n", dopcoeff[0], dopcoeff[1], dopcoeff[2], dopcoeff[3]);
+
+  fprintf(infofp, "az_ratio: %f\n", az_ratio);
+  fprintf(infofp, "offset: %f\n\n", min_line_offset);
+
+  if(fabs(min_line_offset) > 50.0){
+    fprintf(stderr, "offset too big!\n");
+    exit(1);
+  }
+
+  if(nfilter % 2 != 1){
+    fprintf(stderr, "filter length must be odd!\n");
+    exit(1);
+  }
+
+  if(n % 2 != 1){
+    fprintf(stderr, "resample kernal length must be odd!\n");
+    exit(1);
+  }
+  if(n < 7){
+    fprintf(stderr, "resample kernal length too small!\n");
+    exit(1);
+  }
+
+  if(m % 2 != 0){
+    fprintf(stderr, "m must be even!\n");
+    exit(1);
+  }
+  if(m < 1000){
+    fprintf(stderr, "m too small!\n");
+    exit(1);
+  }
+
+  pri = 1.0/prf;
+  hnfilter = (nfilter - 1) / 2;
+
+  hn = n / 2;
+  hnm = n * m / 2;
+
+
+  //naz  = file_length(infp, nrg, sizeof(fcomplex));
+  fprintf(infofp, "file width: %d, file length: %d\n\n", nrg, naz);
+
+  ka = array1d_float(nrg);
+  dop = array1d_float(nrg);
+  nfa = array1d_float(nrg);
+
+  start_line = array1d_float(nrg);
+  end_line = array1d_float(nrg);
+  output_start = array1d_int(nrg);
+  output_end = array1d_int(nrg);
+
+  sincc = vector_float(-hnm, hnm);
+  kaiserc = vector_float(-hnm, hnm);
+  kernel = vector_float(-hnm, hnm);
+
+  //initialize sinc coefficents
+  sinc(n, m, sincc);
+  kaiser(n, m, kaiserc, beta_resamp);
+  for(i = -hnm; i <= hnm; i++)
+    kernel[i] = kaiserc[i] * sincc[i];
+
+  //calculate some range variant variables
+  for(i = 0; i < nrg; i++){
+    //azimuth FM rate. we follow the convention ka > 0
+    ka[i] = kacoeff[3] * i * i * i + kacoeff[2] * i * i + kacoeff[1] * i + kacoeff[0];
+    ka[i] = -ka[i];
+    
+    //doppler centroid frequency
+    dop[i] = dopcoeff[0] + dopcoeff[1] * i + dopcoeff[2] * i * i + dopcoeff[3] * i * i * i;
+    //dop[i] *= prf;
+
+    //full-aperture length
+    nfa[i] = prf * prf_frac / ka[i] / pri;
+  }
+
+  tmp1 = -1.0; //maximum oversampling ratio
+  tmp2 = 10000000000.0; //minimum oversampling ratio
+  for(i = 0; i < nrg; i++){
+    tmp3 = 1.0 / (az_ratio * pri) / (nb * pri * ka[i]);
+    if(tmp3 > tmp1)
+      tmp1 = tmp3;
+    if(tmp3 < tmp2)
+      tmp2 = tmp3;
+  }
+
+  fprintf(infofp, "azimuth oversampling ratio of output burst, minimum: %6.2f, maximum: %6.2f\n\n", tmp2, tmp1);
+
+
+  //find burst starting line closest to first line and after first line
+  //to make sure the bsl used in the following is not too big to avoid overflow
+  //bsl is defined by 0 = first line of input SLC, this defines the absolute line numbers used in the following
+  //here we stop at burst_index_tmp
+  for(i = -100000; i < 100000; i++){
+    tmp1 = bsl + (nb + nbg) * i;
+    if(tmp1 >= 0){
+      bsl = tmp1;
+      burst_index_tmp = i;
+      break;
+    }
+  }
+
+  //starting and ending lines for each column
+  for(i = 0; i < nrg; i++){
+    //starting index
+    start_line[i] = bsl + (nb - 1.0) / 2.0 + dop[i] / ka[i] / pri - (nfa[i] - nb - 1.0) / 2.0;
+    //ending index
+    end_line[i] = bsl + (nb - 1.0) / 2.0 + dop[i] / ka[i] / pri + (nfa[i] - nb - 1.0) / 2.0;
+  }
+
+  //starting and ending lines for the whole block
+  min_line = start_line[0];
+  max_line = end_line[0];
+  for(i = 0; i < nrg; i++){
+  	if(start_line[i] <= min_line){
+  	  min_line = start_line[i];
+  	  min_line_column = i;
+  	}
+  	if(end_line[i] >= max_line){
+  	  max_line = end_line[i];
+  	  max_line_column = i;
+  	}
+  }
+
+  //number of lines of the input burst
+  naz_burst_in = roundfi((max_line - min_line) + 2 * hnfilter);
+  //number of lines of the output burst
+  naz_burst_out = roundfi((max_line - min_line) / az_ratio);
+  //to make circular convolution equivalent to linear convolution
+  nfft = next_pow2(naz_burst_in + nfilter - 1);
+
+  fprintf(infofp, "for all the output bursts:\n");
+  fprintf(infofp, "input data block length: %d\n", naz_burst_in);
+  fprintf(infofp, "output burst length: %d\n", naz_burst_out);
+  fprintf(infofp, "fft length: %d\n\n", nfft);
+
+  //calculate relative start and end lines in the output burst
+  for(i = 0; i < nrg; i++){
+    output_start[i] = roundfi((start_line[i] - min_line) / az_ratio); //made sure: first line has output. Include this start line
+    output_end[i] = naz_burst_out - 1 + roundfi((end_line[i] - max_line) / az_ratio); //made sure: last line has output. Include this end line
+  }
+
+  in  = array2d_fcomplex(naz_burst_in, nrg);
+  out = array2d_fcomplex(naz_burst_out, nrg);
+  deramp  = array2d_fcomplex(naz_burst_in, nrg);
+  filter = array2d_fcomplex(nrg, nfft);
+  data = array1d_fcomplex(nfft);
+
+  fprintf(infofp, "calculating filter...\n\n");
+
+  //create plans before initializing data, because FFTW_MEASURE overwrites the in/out arrays.
+  p_forward = fftwf_plan_dft_1d(nfft, (fftwf_complex*)data, (fftwf_complex*)data, FFTW_FORWARD, FFTW_ESTIMATE);
+  p_backward = fftwf_plan_dft_1d(nfft, (fftwf_complex*)data, (fftwf_complex*)data, FFTW_BACKWARD, FFTW_ESTIMATE);
+
+  //create filter, ZERO center frequency for all columns
+  for(i = 0; i < nrg; i++){
+    bfw = nb * pri * ka[i];
+    //create filter: first sample corresponding to first fully convolution sample
+    bandpass_filter(bfw/prf, 0.0/prf, nfilter, nfft, (nfilter-1)/2, beta, filter[i]);
+    //forward fft
+    //four1((float *)filter[i] - 1, nfft, -1);
+    //data = filter[i];
+    memcpy((void *) data, (const void *) filter[i], (size_t) nfft * sizeof(fcomplex));
+    fftwf_execute(p_forward);
+    //filter[i] = data;
+    memcpy((void *) filter[i], (const void *) data, (size_t) nfft * sizeof(fcomplex));
+  }
+
+
+  //let's extract burst now, start from burst_index_tmp where we stop last time
+  burst_index_first = burst_index_tmp - 1;
+  tmpa = min_line; //save min_line caculated last time
+  offset_from_first_burst0 = 0;
+  for(burst_index = burst_index_tmp; burst_index < 100000; burst_index++){
+    
+    //burst first line number
+    tmpb = bsl + (burst_index - burst_index_tmp) * (nb + nbg);  
+    //burst center line number
+    bcl = tmpb + (nb - 1.0) / 2.0;
+    //minimum line of imaged area of the burst
+  	min_line = tmpa + (burst_index - burst_index_tmp) * (nb + nbg);
+    //minimum line of input burst
+  	min_line_in = roundfi(min_line) - hnfilter;
+
+    //skip bursts that are not or partly in the image
+    if(min_line_in < 0)
+      continue;
+    //stop at last burst that is fully in the image
+    if(min_line_in + naz_burst_in - 1 > naz - 1)
+      break;
+    
+
+/*********************************************************
+                   (int)
+                 min_line_in
+                   ------
+    (float)        |    |          (float)
+   min_line        |    |         min_line_out
+    ------         |    |           ------           
+    |    |         |    |           |    |
+    |    |  ====>  |    |   ====>   |    |
+    |    |         |    |           |    |
+    ------         |    |           ------  
+ burst imaged      |    |         output burst
+     area          ------
+                burst read in
+*********************************************************/
+
+    //first burst
+    if(burst_index_first == burst_index_tmp - 1){
+      burst_index_first = burst_index;
+
+      min_line_out = roundfi(min_line) + min_line_offset;
+      
+      min_line_out_first = min_line_out;
+      offset_from_first_burst = 0;
+
+      fprintf(infofp, "line number of first line of original SLC is 0.\n");
+      fprintf(infofp, "line number of first line of first output burst in original SLC (1.0/prf): %f\n", min_line_out);
+      fprintf(infofp, "bsl of first output burst: %f\n\n", tmpb);
+    }
+    //adjust starting line of following bursts
+    else{
+      min_line_out = min_line + min_line_offset;
+      offset_from_first_burst = roundfi((min_line_out - min_line_out_first) / az_ratio);
+      tmp1 = offset_from_first_burst - (min_line_out - min_line_out_first) / az_ratio;
+      min_line_out = min_line_out + tmp1 * az_ratio;
+    }
+   
+    fprintf(infofp, "extracting burst %3d\n", burst_index - burst_index_first + 1);
+    fprintf(infofp, "offset from first burst: %5d, offset from last burst: %5d (az_ratio/prf)\n\n", offset_from_first_burst, offset_from_first_burst - offset_from_first_burst0);
+    offset_from_first_burst0 = offset_from_first_burst;
+
+    //read data block
+    //fseeko(infp, (size_t)min_line_in * (size_t)nrg * sizeof(fcomplex), SEEK_SET);
+    //readdata((fcomplex *)in[0], (size_t)naz_burst_in * (size_t)nrg * sizeof(fcomplex), infp);
+
+    fseeko(infp, (size_t)imageoffset + (size_t)min_line_in * (size_t)lineoffset, SEEK_SET);
+    for(i = 0; i < naz_burst_in; i++){
+      if(i!=0)
+        fseek(infp, lineoffset-(size_t)nrg*sizeof(fcomplex), SEEK_CUR);
+      readdata((fcomplex *)in[i], (size_t)nrg * sizeof(fcomplex), infp);
+    }
+
+    if(byteorder!=0){
+      //printf("swapping bytes...\n");
+      for(i = 0; i < naz_burst_in; i++)
+        for(j = 0; j < nrg; j++){
+          SWAP4(in[i][j].re);
+          SWAP4(in[i][j].im);
+        }
+    }
+
+    //create deramping signal: make center of azimuth spectrum ZERO
+    for(i = 0; i < nrg; i++){
+      for(j = 0; j < naz_burst_in; j++){
+        //distance from raw burst center in number of lines
+        tmp1 = j + min_line_in - bcl;
+        tmp2 = - PI * ka[i] * (tmp1 * pri) * (tmp1 * pri);
+        deramp[j][i].re = cos(tmp2);
+        deramp[j][i].im = sin(tmp2);
+      }
+    }
+
+    //do the filtering column by column
+    for(i = 0; i < nrg; i++){
+      //prepare data
+      for(j = 0; j < nfft; j++){
+        if(j < naz_burst_in){
+          data[j].re = in[j][i].re / sc;
+          data[j].im = in[j][i].im / sc;
+        }
+        else{
+          data[j].re = 0.0;
+          data[j].im = 0.0;
+        }
+      }
+      
+      //deramp the data
+      for(j = 0; j < naz_burst_in; j++){
+        data[j] = cmul(data[j], deramp[j][i]);
+      }
+
+      //forward fft
+      //four1((float *)data - 1, nfft, -1);
+      fftwf_execute(p_forward);
+
+      //multiplication in the frequency domain
+      for(j = 0; j < nfft; j++)
+        data[j] = cmul(data[j], filter[i][j]);
+
+      //backward fft
+      //four1((float *)data - 1, nfft, 1);
+      fftwf_execute(p_backward);
+
+      //put filtered data back
+      for(j = 0; j < naz_burst_in; j++){
+        in[j][i].re = data[j].re * sc / nfft;
+        in[j][i].im = data[j].im * sc / nfft;
+      }
+    }
+
+    //zero output
+    for(i = 0; i < naz_burst_out; i++){
+      for(j = 0; j < nrg; j++){
+        out[i][j].re = 0.0;
+        out[i][j].im = 0.0;
+      }
+    }
+    
+    //do the resampling column by column
+    for(i = 0; i < nrg; i++){
+      //resampling to output grid
+      for(j = 0; j < naz_burst_out; j++){
+        if((j < output_start[i]) || (j > output_end[i]))
+          continue;
+        
+        //location of output line in the data block read in
+        tmp1 = min_line_out + j * az_ratio - min_line_in;
+
+        //interpolation
+        for(k = -hn; k <= hn; k++){
+          index = roundfi(tmp1) + k;
+          tmp2 = index - tmp1;
+
+          if( (index < 0) || (index > naz_burst_in - 1) )
+            continue;
+          //verified: roundfi(tmp2*m) won't be out of [-hnm, hnm], if no computation error of floating point
+          out[j][i].re += in[index][i].re * kernel[roundfi(tmp2*m)];
+          out[j][i].im += in[index][i].im * kernel[roundfi(tmp2*m)];
+        }
+        
+        //reramp
+        tmp1 = j * az_ratio + min_line_out - bcl;
+        tmp2 = PI * ka[i] * (tmp1 * pri) * (tmp1 * pri);
+        reramp.re = cos(tmp2);
+        reramp.im = sin(tmp2);
+        
+        out[j][i] = cmul(out[j][i], reramp);
+
+      }
+    }
+
+    //write to file
+    strcpy(output_filename, outputf);
+    sprintf(burst_num, "_%02d.slc", burst_index - burst_index_first + 1);
+    strcat(output_filename, burst_num);
+    
+    outfp = openfile(output_filename, "wb");
+    writedata((fcomplex *)out[0], (size_t)naz_burst_out * (size_t)nrg * sizeof(fcomplex), outfp);
+    fclose(outfp);
+  }
+
+  fprintf(infofp, "total number of bursts extracted: %3d\n\n", burst_index - burst_index_first);
+
+  fftwf_destroy_plan(p_forward);
+  fftwf_destroy_plan(p_backward);
+
+  free_array1d_float(ka);
+  free_array1d_float(dop);
+  free_array1d_float(nfa);
+
+  free_array1d_float(start_line);
+  free_array1d_float(end_line);
+  free_array1d_int(output_start);
+  free_array1d_int(output_end);
+
+  free_vector_float(sincc, -hnm, hnm);
+  free_vector_float(kaiserc, -hnm, hnm);
+  free_vector_float(kernel, -hnm, hnm);
+
+  free_array2d_fcomplex(in);
+  free_array2d_fcomplex(out);
+  free_array2d_fcomplex(deramp);
+  free_array2d_fcomplex(filter);
+  free_array1d_fcomplex(data);
+
+  //close files
+  fclose(infp);
+  fclose(infofp);
+}

contrib/alos2proc/src/look.c

@@ -0,0 +1,327 @@
+//////////////////////////////////////
+// Cunren Liang, NASA JPL/Caltech
+// Copyright 2017
+//////////////////////////////////////
+
+
+//a program for taking looks for single band file
+
+#include "resamp.h"
+
+int look(char *inputfile, char *outputfile, long nrg, int nrlks, int nalks, int ft, int sum, int avg){
+
+  FILE *infp;
+  FILE *outfp;
+  
+  signed char *in0;
+  int *in1;
+  float *in2;
+  double *in3;
+  fcomplex *in4;
+  dcomplex *in5;
+
+  signed char *out0;
+  int *out1;
+  float *out2;
+  double *out3;
+  fcomplex *out4;
+  dcomplex *out5;
+
+  int sum_nz;
+  double sum1, sum2;
+
+  long index;
+
+  long naz;
+  long nrg1, naz1;
+  //int nrlks, nalks;
+
+  //int ft, sum, avg;
+
+  int i, j;
+  int ii, jj;
+
+
+  // if(argc < 4){
+  //   fprintf(stderr, "\nUsage: %s infile outfile nrg [nrlks] [nalks] [ft] [sum] [avg]\n", argv[0]);
+  //   fprintf(stderr, "  infile:  input file\n");
+  //   fprintf(stderr, "  outfile: output file\n");
+  //   fprintf(stderr, "  nrg:     file width\n");
+  //   fprintf(stderr, "  nrlks:   number of looks in range (default: 4)\n");
+  //   fprintf(stderr, "  nalks:   number of looks in azimuth (default: 4)\n");
+  //   fprintf(stderr, "  ft:      file type (default: 0)\n");
+  //   fprintf(stderr, "             0: signed char\n");
+  //   fprintf(stderr, "             1: int\n");
+  //   fprintf(stderr, "             2: float\n");
+  //   fprintf(stderr, "             3: double\n");
+  //   fprintf(stderr, "             4: complex (real and imagery: float)\n");
+  //   fprintf(stderr, "             5: complex (real and imagery: double)\n");
+  //   fprintf(stderr, "  sum:     sum method (default: 0)\n");
+  //   fprintf(stderr, "             0: simple sum\n");
+  //   fprintf(stderr, "             1: power sum (if complex, do this for each channel seperately)\n");
+  //   fprintf(stderr, "  avg:     take average (default: 0)\n");
+  //   fprintf(stderr, "             0: no\n");
+  //   fprintf(stderr, "             1: yes\n\n");
+
+  //   exit(1);
+  // }
+
+  infp  = openfile(inputfile, "rb");
+  outfp = openfile(outputfile, "wb");
+
+  //nrg = atoi(argv[3]);
+
+  //if(argc > 4)
+  //  nrlks = atoi(argv[4]);
+  //else
+  //  nrlks = 4;
+
+  //if(argc > 5)
+  //  nalks = atoi(argv[5]);
+  //else
+  //  nalks = 4;
+  
+  //if(argc > 6)
+  //  ft = atoi(argv[6]);
+  //else
+  //  ft = 0;
+
+  //if(argc > 7)
+  //  sum = atoi(argv[7]);
+  //else
+  //  sum = 0;
+
+  //if(argc > 8)
+  //  avg = atoi(argv[8]);
+  //else
+  //  avg = 0;
+
+  nrg1 = nrg / nrlks;
+
+  if(ft == 0){
+    in0 = array1d_char(nrg*nalks);
+    out0 = array1d_char(nrg1);
+    naz = file_length(infp, nrg, sizeof(signed char));
+  }
+  else if(ft == 1){
+    in1 = array1d_int(nrg*nalks);
+    out1 = array1d_int(nrg1);
+    naz = file_length(infp, nrg, sizeof(int));
+  }
+  else if(ft == 2){
+    in2 = array1d_float(nrg*nalks);
+    out2 = array1d_float(nrg1);
+    naz = file_length(infp, nrg, sizeof(float));
+  }
+  else if(ft == 3){
+    in3 = array1d_double(nrg*nalks);
+    out3 = array1d_double(nrg1);
+    naz = file_length(infp, nrg, sizeof(double));
+  }
+  else if(ft == 4){
+    in4 = array1d_fcomplex(nrg*nalks);
+    out4 = array1d_fcomplex(nrg1);
+    naz = file_length(infp, nrg, sizeof(fcomplex));
+  }
+  else if(ft == 5){
+    in5 = array1d_dcomplex(nrg*nalks);
+    out5 = array1d_dcomplex(nrg1);
+    naz = file_length(infp, nrg, sizeof(dcomplex));
+  }
+  else{
+    fprintf(stderr, "Error: file type not supported.\n\n");
+    exit(1);
+  }
+
+  naz1 = naz / nalks;
+
+  for(i = 0; i < naz1; i++){
+
+    if((i + 1) % 100 == 0)
+      fprintf(stderr,"processing line: %6d of %6d\r", i+1, naz1);
+
+    //read data
+    if(ft == 0){
+      readdata((signed char *)in0, (size_t)nalks * (size_t)nrg * sizeof(signed char), infp);
+    }
+    else if(ft == 1){
+      readdata((int *)in1, (size_t)nalks * (size_t)nrg * sizeof(int), infp);
+    }
+    else if(ft == 2){
+      readdata((float *)in2, (size_t)nalks * (size_t)nrg * sizeof(float), infp);
+    }
+    else if(ft == 3){
+      readdata((double *)in3, (size_t)nalks * (size_t)nrg * sizeof(double), infp);
+    }
+    else if(ft == 4){
+      readdata((fcomplex *)in4, (size_t)nalks * (size_t)nrg * sizeof(fcomplex), infp);
+    }
+    else if(ft == 5){
+      readdata((dcomplex *)in5, (size_t)nalks * (size_t)nrg * sizeof(dcomplex), infp);
+    }
+
+    //process data
+    for(j = 0; j < nrg1; j++){
+      //get sum
+      sum_nz = 0;
+      sum1 = 0.0;
+      sum2 = 0.0;
+      for(ii = 0; ii < nalks; ii++){
+        for(jj = 0; jj < nrlks; jj++){
+          index = ii * nrg + j * nrlks + jj;
+          if(ft == 0){
+            if(in0[index] != 0){
+              if(sum == 0)
+                sum1 += in0[index];
+              else
+                sum1 += in0[index] * in0[index];
+              sum_nz += 1;
+            }
+          }
+          else if(ft == 1){
+            if(in1[index] != 0){
+              if(sum == 0)
+                sum1 += in1[index];
+              else
+                sum1 += in1[index] * in1[index];
+              sum_nz += 1;
+            }
+          }
+          else if(ft == 2){
+            if(in2[index] != 0){
+              if(sum == 0)
+                sum1 += in2[index];
+              else
+                sum1 += in2[index] * in2[index];
+              sum_nz += 1;
+            }
+          }
+          else if(ft == 3){
+            if(in3[index] != 0){
+              if(sum == 0)
+                sum1 += in3[index];
+              else
+                sum1 += in3[index] * in3[index];
+              sum_nz += 1;
+            }
+          }
+          else if(ft == 4){
+            if(in4[index].re != 0 || in4[index].im != 0){
+              if(sum ==0){
+                sum1 += in4[index].re;
+                sum2 += in4[index].im;
+              }
+              else{
+                sum1 += in4[index].re * in4[index].re;
+                sum2 += in4[index].im * in4[index].im;
+              }
+              sum_nz += 1;
+            }
+          }
+          else if(ft == 5){
+            if(in5[index].re != 0 || in5[index].im != 0){
+              if(sum == 0){
+                sum1 += in5[index].re;
+                sum2 += in5[index].im;
+              }
+              else{
+                sum1 += in5[index].re * in5[index].re;
+                sum2 += in5[index].im * in5[index].im;
+              }
+              sum_nz += 1;
+            }
+          }
+        }
+      }
+
+      //preprocessing
+      if(avg == 1){
+        if(sum_nz != 0){
+          sum1 /= sum_nz;
+          if(ft == 4 || ft == 5)
+            sum2 /= sum_nz;
+        }
+      }
+      if(sum == 1){
+        if(sum_nz != 0){
+          sum1 = sqrt(sum1);
+          if(ft == 4 || ft ==5)
+            sum2 = sqrt(sum2);
+        }
+      }
+
+      //get data
+      if(ft == 0){
+        out0[j] = (signed char)(roundfi(sum1));
+      }
+      else if(ft == 1){
+        out1[j] = (int)(roundfi(sum1));
+      }
+      else if(ft == 2){
+        out2[j] = sum1;
+      }
+      else if(ft == 3){
+        out3[j] = sum1;
+      }
+      else if(ft == 4){
+        out4[j].re = sum1;
+        out4[j].im = sum2;
+      }
+      else if(ft == 5){
+        out5[j].re = sum1;
+        out5[j].im = sum2;
+      }
+    }
+
+    //write data
+    if(ft == 0){
+      writedata((signed char *)out0, nrg1 * sizeof(signed char), outfp);
+    }
+    else if(ft == 1){
+      writedata((int *)out1, nrg1 * sizeof(int), outfp);
+    }
+    else if(ft == 2){
+      writedata((float *)out2, nrg1 * sizeof(float), outfp);
+    }
+    else if(ft == 3){
+      writedata((double *)out3, nrg1 * sizeof(double), outfp);
+    }
+    else if(ft == 4){
+      writedata((fcomplex *)out4, nrg1 * sizeof(fcomplex), outfp);
+    }
+    else if(ft == 5){
+      writedata((dcomplex *)out5, nrg1 * sizeof(dcomplex), outfp);
+    }
+  }
+  fprintf(stderr,"processing line: %6d of %6d\n", naz1, naz1);
+
+  //clear up
+  if(ft == 0){
+    free_array1d_char(in0);
+    free_array1d_char(out0);
+  }
+  else if(ft == 1){
+    free_array1d_int(in1);
+    free_array1d_int(out1);
+  }
+  else if(ft == 2){
+    free_array1d_float(in2);
+    free_array1d_float(out2);
+  }
+  else if(ft == 3){
+    free_array1d_double(in3);
+    free_array1d_double(out3);
+  }
+  else if(ft == 4){
+    free_array1d_fcomplex(in4);
+    free_array1d_fcomplex(out4);
+  }
+  else if(ft == 5){
+    free_array1d_dcomplex(in5);
+    free_array1d_dcomplex(out5);
+  }
+  fclose(infp);
+  fclose(outfp);
+
+  return 0;
+}

contrib/alos2proc/src/mbf.c

@@ -6,14 +6,17 @@
 
 #include "resamp.h"
 #include <fftw3.h>
+#include <omp.h>
 
+#define SWAP4(a) (*(unsigned int *)&(a) = (((*(unsigned int *)&(a) & 0x000000ff) << 24) | ((*(unsigned int *)&(a) & 0x0000ff00) << 8) | ((*(unsigned int *)&(a) >> 8) & 0x0000ff00) | ((*(unsigned int *)&(a) >> 24) & 0x000000ff)))
 
-int mbf(char *inputfile, char *outputfile, int nrg, float prf, float prf_frac, float nb, float nbg, float nboff, float bsl, float *kacoeff, float *dopcoeff1, float *dopcoeff2){
+int mbf(char *inputfile, char *outputfile, int nrg, int naz, float prf, float prf_frac, float nb, float nbg, float nboff, float bsl, float *kacoeff, float *dopcoeff1, float *dopcoeff2, int byteorder, long imageoffset, long lineoffset){
   /*
 
   inputfile:       input file
   outputfile:      output file
   nrg:             file width
+  naz:             file length
   prf:             PRF
   prf_frac:        fraction of PRF processed
                       (represents azimuth bandwidth)
@@ -28,8 +31,8 @@ int mbf(char *inputfile, char *outputfile, int nrg, float prf, float prf_frac, f
                       (float, the line number of the first line of the full-aperture SLC is zero)
                       (no need to be first burst, any one is OK)
 
-  kacoeff[0-2]:    FM rate coefficients
-                      (three coefficients of a quadratic polynomial with regard to)
+  kacoeff[0-3]:    FM rate coefficients
+                      (four coefficients of a third order polynomial with regard to)
                       (range sample number. range sample number starts with zero)
 
   dopcoeff1[0-3]:  Doppler centroid frequency coefficients of this image
@@ -40,6 +43,9 @@ int mbf(char *inputfile, char *outputfile, int nrg, float prf, float prf_frac, f
                       (four coefficients of a third order polynomial with regard to)
                       (range sample number. range sample number starts with zero)
 
+  byteorder:      (0) LSB, little endian; (1) MSB, big endian of intput file
+  imageoffset:    offset from start of the image of input file
+  lineoffset:     length of each line of input file
   */
 
   FILE *infp;
@@ -54,7 +60,7 @@ int mbf(char *inputfile, char *outputfile, int nrg, float prf, float prf_frac, f
   fcomplex *data; //data to be filtered.
 
   //int nrg; //file width
-  int naz; //file length
+  //int naz; //file length
   //float prf; //assume prf are the same
   //float prf_frac; // azimuth processed bandwidth = prf_frac * prf
   //float nb; //burst length in terms of pri. number of lines
@@ -168,17 +174,36 @@ int mbf(char *inputfile, char *outputfile, int nrg, float prf, float prf_frac, f
   printf("nboff: %f\n", nboff);
   printf("bsl: %f\n", bsl);
 
-  printf("kacoeff: %f, %f, %f\n", kacoeff[0], kacoeff[1], kacoeff[2]);
+  printf("kacoeff: %f, %f, %f, %f\n", kacoeff[0], kacoeff[1], kacoeff[2], kacoeff[3]);
   printf("dopcoeff1: %f, %f, %f, %f\n", dopcoeff1[0], dopcoeff1[1], dopcoeff1[2], dopcoeff1[3]);
   printf("dopcoeff2: %f, %f, %f, %f\n", dopcoeff2[0], dopcoeff2[1], dopcoeff2[2], dopcoeff2[3]);
 
+  if(byteorder == 0){
+    printf("inputfile byte order: little endian\n");
+  }
+  else{
+    printf("inputfile byte order: big endian\n");
+  }
+  printf("input file image offset [byte]: %ld\n", imageoffset);
+  printf("input file line offset [byte]: %ld\n", lineoffset);
+  if(imageoffset < 0){
+    fprintf(stderr, "image offset must be >= 0\n");
+    exit(1);
+  }
+  if(lineoffset < 0){
+    fprintf(stderr, "lineoffset offset must be >= 0\n");
+    exit(1);
+  }
 
   if(nfilter % 2 != 1){
     fprintf(stderr, "filter length must be odd!\n");
     exit(1);
   }
 
-  naz  = file_length(infp, nrg, sizeof(fcomplex));
+  //naz  = file_length(infp, nrg, sizeof(fcomplex));
+  //fseeko(infp,0L,SEEK_END);
+  //naz = (ftello(infp) - imageoffset) / (lineoffset + nrg*sizeof(fcomplex));
+  //rewind(infp);
   printf("file width: %d, file length: %d\n\n", nrg, naz);
 
 
@@ -216,14 +241,14 @@ int mbf(char *inputfile, char *outputfile, int nrg, float prf, float prf_frac, f
   for(i = 0; i < nrg; i++){
     
     //azimuth FM rate. we follow the convention ka > 0
-    ka[i] = kacoeff[2] * i * i + kacoeff[1] * i + kacoeff[0];
+    ka[i] = kacoeff[3] * i * i * i + kacoeff[2] * i * i + kacoeff[1] * i + kacoeff[0];
     ka[i] = -ka[i];
 
     //doppler centroid frequency
     dop1[i] = dopcoeff1[0] + dopcoeff1[1] * i + dopcoeff1[2] * i * i + dopcoeff1[3] * i * i * i;
-    dop1[i] *= prf;
+    //dop1[i] *= prf;
     dop2[i] = dopcoeff2[0] + dopcoeff2[1] * i + dopcoeff2[2] * i * i + dopcoeff2[3] * i * i * i;
-    dop2[i] *= prf;
+    //dop2[i] *= prf;
 
     //full aperture length
     nfa[i] = prf * prf_frac / ka[i] / pri;
@@ -299,9 +324,47 @@ int mbf(char *inputfile, char *outputfile, int nrg, float prf, float prf_frac, f
     }
   }
 
-  
-  //read in data
-  readdata((fcomplex *)in[0], (size_t)naz * (size_t)nrg * sizeof(fcomplex), infp);
+///////////////////////////////////////////////////////////////////////////////////////
+  //This section is for reading data
+  printf("reading data...\n");
+
+  //skip image header
+  fseek(infp, imageoffset, SEEK_SET);
+
+  for(i = 0; i < naz; i++){
+    if(i!=0)
+      fseek(infp, lineoffset-(size_t)nrg*sizeof(fcomplex), SEEK_CUR);
+    readdata((fcomplex *)in[i], (size_t)nrg * sizeof(fcomplex), infp);
+  }
+
+  //read image data
+  //if(lineoffset == 0){
+  //  readdata((fcomplex *)in[0], (size_t)naz * (size_t)nrg * sizeof(fcomplex), infp);
+  //}
+  //else{
+  //  for(i = 0; i < naz; i++){
+  //    fseek(infp, lineoffset, SEEK_CUR);
+  //    readdata((fcomplex *)in[i], (size_t)nrg * sizeof(fcomplex), infp);
+  //  }
+  //}
+
+  //swap bytes
+  if(byteorder!=0){
+    printf("swapping bytes...\n");
+    for(i = 0; i < naz; i++)
+      for(j = 0; j < nrg; j++){
+        SWAP4(in[i][j].re);
+        SWAP4(in[i][j].im);
+      }
+  }
+
+  int debug=0;
+  if(debug){
+    printf("%f, %f\n", in[0][0].re, in[0][0].im);
+    printf("%f, %f\n", in[100][100].re, in[100][100].im);
+    printf("%f, %f\n", in[naz-1][nrg-1].re, in[naz-1][nrg-1].im);
+  }
+///////////////////////////////////////////////////////////////////////////////////////
 
   //initialize output data
   //for(j = 0; j < naz; j++){
@@ -311,7 +374,7 @@ int mbf(char *inputfile, char *outputfile, int nrg, float prf, float prf_frac, f
   //  }
   //}
 
-
+  printf("filtering image...\n");
   for(i = 0; i < nrg; i++){
 
     if((i + 1) % 100 == 0 || (i+1) == nrg)
@@ -566,6 +629,7 @@ int mbf(char *inputfile, char *outputfile, int nrg, float prf, float prf_frac, f
 
   }//i: each column
 
+  printf("writing filtering result...\n");
   writedata((fcomplex *)in[0], (size_t)naz * (size_t)nrg * sizeof(fcomplex), outfp);
 
   //free arrays
@@ -590,9 +654,3 @@ int mbf(char *inputfile, char *outputfile, int nrg, float prf, float prf_frac, f
 
   return 0;
 }//end main()
-
-
-//////////////////////////////////////////////////////////////////////////////////////////////////////
-
-
-

contrib/alos2proc/src/mosaicsubswath.c

@@ -0,0 +1,386 @@
+//////////////////////////////////////
+// Cunren Liang, NASA JPL/Caltech
+// Copyright 2017
+//////////////////////////////////////
+
+
+// program for mosaicking multiple consecutive subswaths
+// Cunren Liang, 03-JUN-2015
+// JPL/Caltech
+
+//////////////////////////////////////////////////////////////////
+//update history
+//12-APR-2016, CL. output data of both adjacent subswaths as BIL
+//                 file, instead of output the difference.
+//////////////////////////////////////////////////////////////////
+
+
+#include "resamp.h"
+
+//int main(int argc, char *argv[]){
+int mosaicsubswath(char *outputfile, int nrgout, int nazout, int delta, int diffflag, int n, char **inputfile, int *nrgin, int *nrgoff, int *nazoff, float *phc, int *oflag){
+
+  FILE **infp;
+  FILE *outfp;
+  
+  fcomplex **in;
+  fcomplex *out, out1, out2;
+  //fcomplex *leftoverlap;
+  //fcomplex *rightoverlap;
+  fcomplex tmp;
+  int cnt;
+  
+  //int n;
+  //int *nrgin;
+  int *nazin;
+  //int *nrgoff;
+  //int *nazoff;
+  //int *oflag;
+  //int nrgout;
+  //int nazout;
+  int nrginmax;
+
+  int los, loe, low; //start, end and width of left overlap area
+  int ros, roe, row; //start, end and width of right overlap area
+  int cnw; //width of center area
+
+  int paroff;
+  int parcyc;
+
+  char diffname[256][256];
+  FILE **difffp;
+  fcomplex **diff;
+  fcomplex **diff2;
+  //int diffflag;
+  //diffflag = 0;
+
+  int ns;
+  float r;
+
+  int i, j, k, l;
+
+  //int delta; //edge to be removed of the overlap area (number of samples)
+  //delta = 20;
+
+
+  // if(argc < 5){
+  //   fprintf(stderr, "\nUsage: %s outputfile nrgout nazout delta diffflag n [inputfile0] [nrgin0] [nrgoff0] [nazoff0] [oflag0] (repeat...)\n\n", argv[0]);
+  //   fprintf(stderr, "  for each frame\n");
+  //   fprintf(stderr, "  range offset is relative to the first sample of last subswath\n");
+  //   fprintf(stderr, "  azimuth offset is relative to the uppermost line\n\n");
+  //   exit(1);
+  // }
+
+
+  //read mandatory parameters
+  outfp    = openfile(outputfile, "wb");
+  //nrgout   = atoi(argv[2]);
+  //nazout   = atoi(argv[3]);
+  //delta    = atoi(argv[4]);
+  //diffflag = atoi(argv[5]);
+  //n        = atoi(argv[6]);
+
+
+  //allocate memory
+  infp   = array1d_FILE(n);
+  //nrgin  = array1d_int(n);
+  nazin  = array1d_int(n);
+  //nrgoff = array1d_int(n); //nrgoff must be <= 0
+  //nazoff = array1d_int(n); //nazoff must be <= 0
+  //oflag  = array1d_int(n);
+
+  difffp = array1d_FILE(n - 1);
+
+  //read optional parameters
+  paroff = 6;
+  parcyc = 5;
+  for(i = 0; i < n; i++){
+    infp[i] = openfile(inputfile[i], "rb");
+    //nrgin[i] = atoi(argv[paroff + parcyc*i + 2]);
+    //nrgoff[i] = atoi(argv[paroff + parcyc*i + 3]);
+    //nazoff[i] = atoi(argv[paroff + parcyc*i + 4]);
+    //oflag[i] = atoi(argv[paroff + parcyc*i + 5]);
+    nazin[i] = file_length(infp[i], nrgin[i], sizeof(fcomplex));
+    if(nrgoff[i] > 0){
+      fprintf(stderr,"Error: positive range offset: %d\n\n", nrgoff[i]);
+      exit(1);
+    }
+    if(nazoff[i] > 0){
+      fprintf(stderr,"Error: positive azimuth offset: %d\n\n", nazoff[i]);
+      exit(1);
+    }
+    if(nazout < nazin[i] - nazoff[i]){
+      fprintf(stderr,"Error: ouput length < nazin[%d] - nazoff[%d], %d, %d\n\n", i, i, nazout, nazin[i] - nazoff[i]);
+      exit(1);
+    }
+  }
+
+  //find max width
+  nrginmax = nrgin[0];
+  for(i = 0; i < n; i++)
+    if(nrgin[i] > nrginmax)
+      nrginmax = nrgin[i];
+
+  in   = array2d_fcomplex(n, nrginmax);
+  out  = array1d_fcomplex(nrgout);
+  //out1 = array1d_fcomplex(nrginmax);
+  //out2 = array1d_fcomplex(nrginmax);
+  diff = array2d_fcomplex(n-1, nrginmax);
+  diff2 = array2d_fcomplex(n-1, nrginmax);
+
+  if(diffflag == 0)
+    for(i = 0; i < n - 1; i++){
+      sprintf(diffname[i], "%d-%d.int", i, i+1);
+      difffp[i] = openfile(diffname[i], "wb");
+    }
+
+
+  for(i = 0; i < nazout; i++){
+
+    if((i + 1) % 1000 == 0)
+      fprintf(stderr,"processing line: %6d of %6d\r", i + 1, nazout);
+    if(i + 1 == nazout)
+      fprintf(stderr,"processing line: %6d of %6d\n\n", i + 1, nazout);
+
+    //prepare for writing data
+    for(j = 0; j < nrgout; j++){
+      out[j].re = 0.0;
+      out[j].im = 0.0;
+    }
+
+    //prepare for reading data
+    for(j = 0; j < n; j++){
+      for(k = 0; k < nrginmax; k++){
+        in[j][k].re = 0.0;
+        in[j][k].im = 0.0;
+      }
+    }
+
+    for(j = 0; j < n; j++){
+      if(i + nazoff[j] >= 0 && i + nazoff[j] <= nazin[j] - 1)
+        readdata((fcomplex *)in[j], nrgin[j] * sizeof(fcomplex), infp[j]);
+      
+      if(phc[j]!=0.0){
+        tmp.re = cos(phc[j]);
+        tmp.im = sin(phc[j]);
+        for(k = 0; k < nrgin[j]; k++)
+          in[j][k] = cmul(in[j][k], tmp);
+      }
+    }
+
+
+    cnt = 0;
+    for(j = 0; j < n; j++){
+
+      //we follow the following convention: line and column number start with 0.
+      //left overlap area of subswath j
+      if(j != 0){
+        los = - nrgoff[j];
+        loe = nrgin[j-1] - 1;
+        low = loe - los + 1;
+        if(low < delta * 2){
+          fprintf(stderr,"Error: not enough overlap area between subswath: %d and %d\n\n", j-1, j);
+          exit(1);
+        }
+      }
+      else{
+        los = 0;
+        loe = 0;
+        low = 0;
+      }
+
+      //right overlap area of subswath j
+      if(j != n - 1){
+        ros = - nrgoff[j+1];
+        roe = nrgin[j] - 1;
+        row = roe - ros + 1;
+        if(row < delta * 2){
+          fprintf(stderr,"Error: not enough overlap area between subswath: %d and %d\n\n", j, j+1);
+          exit(1);
+        }
+      }
+      else{
+        ros = 0;
+        roe = 0;
+        row = 0;
+      }
+
+      //center non-overlap area of subswath j
+      //should add a check here?
+      cnw = nrgin[j] - low - row;
+
+      //deal with center non-overlap area.
+      //this only excludes the right overlap area for the first subswath
+      //this only excludes the left overlap area for the last subswath
+      for(k = 0; k < cnw; k++){
+        out[cnt + k].re = in[j][low + k].re;
+        out[cnt + k].im = in[j][low + k].im;
+      }
+      cnt += cnw;
+
+      //deal with right overlap area of subswath j, which is also the left overlap area
+      //of subswath j + 1 (next subswath)
+      
+      //for last subswath, just skip
+      if(j == n - 1){
+        break;
+      }
+
+
+      for(k = 0; k < nrginmax; k++){
+        diff[j][k].re = 0.0;
+        diff[j][k].im = 0.0;
+        diff2[j][k].re = 0.0;
+        diff2[j][k].im = 0.0;
+      }
+
+      for(k = 0; k < row; k++){
+
+        
+        out1.re = in[j][low + cnw + k].re;
+        out1.im = in[j][low + cnw + k].im;
+        out2.re = in[j+1][k].re;
+        out2.im = in[j+1][k].im;
+
+        //left edge of overlap area
+        //use current subswath: subswath j
+        if(k < delta){
+          out[cnt + k].re = out1.re;
+          out[cnt + k].im = out1.im;
+        }
+        else if(k >= delta && k < row - delta){
+
+          //output difference of overlap area
+          //diffflag 0: subswath j phase - subswath j+1 phase
+          if(diffflag == 0){
+            if(out1.re != 0.0 && out1.im != 0.0 && out2.re != 0.0 && out2.im != 0.0){
+              //diff[j][k - delta] = cmul(out1, cconj(out2));
+              diff[j][k - delta] = out1;
+              diff2[j][k - delta] = out2;
+            }
+          }
+          //diffflag 1: subswath j - subswath j+1
+          //else if(diffflag == 1){
+          //  if(out1.re != 0.0 && out1.im != 0.0 && out2.re != 0.0 && out2.im != 0.0){
+          //    diff[j][k - delta].re = out1.re - out2.re;
+          //    diff[j][k - delta].im = out1.im - out2.im;
+          //  }
+          //}
+          else{
+            ;
+          }
+
+          //mosaic overlap area
+          //case 0: mosaic at the center of overlap area
+          if(oflag[j] == 0){
+            if(k < row / 2){
+              //avoid holes, Cunren Liang, Dec. 18, 2015.
+              if(out1.re != 0.0 && out1.im != 0.0){
+                out[cnt + k].re = out1.re;
+                out[cnt + k].im = out1.im;
+              }
+              else{
+                out[cnt + k].re = out2.re;
+                out[cnt + k].im = out2.im;                
+              }
+            }
+            else{
+              //avoid holes, Cunren Liang, Dec. 18, 2015.
+              if(out2.re != 0.0 && out2.im != 0.0){
+                out[cnt + k].re = out2.re;
+                out[cnt + k].im = out2.im;
+              }
+              else{
+                out[cnt + k].re = out1.re;
+                out[cnt + k].im = out1.im;                
+              }
+            }
+          }
+          //case 1: mosaic at the right egde of overlap area
+          else if(oflag[j] == 1){
+            out[cnt + k].re = out1.re;
+            out[cnt + k].im = out1.im;
+          }
+          //case 2: mosaic at the left edge of overlap area
+          else if(oflag[j] == 2){
+            out[cnt + k].re = out2.re;
+            out[cnt + k].im = out2.im;
+          }
+          //case 3: add overlap area
+          else if(oflag[j] == 3){
+            out[cnt + k].re = out1.re + out2.re;
+            out[cnt + k].im = out1.im + out2.im;
+
+            if(out1.re != 0.0 && out1.im != 0.0 && out2.re != 0.0 && out2.im != 0.0){
+              out[cnt + k].re /= 2.0;
+              out[cnt + k].im /= 2.0;
+            }
+
+          }
+          //case 4: add by weight determined by distance to overlap center
+          //perform overlapp area smoothing using a method discribed in:
+          //C. Liang, Q. Zeng, J. Jia, J. Jiao, and X. Cui, ScanSAR interferometric processing
+          //using existing standard InSAR software for measuring large scale land deformation
+          //Computers & Geosciences, 2013.
+          else{
+            l = k - delta + 1; // l start with 1
+            ns = row - 2 * delta;
+            
+            if(out1.re != 0.0 && out1.im != 0.0 && out2.re != 0.0 && out2.im != 0.0){
+              r = sqrt((out1.re * out1.re + out1.im * out1.im) / (out2.re * out2.re + out2.im * out2.im));
+              out[cnt + k].re = ((ns - l + 0.5) * out1.re + r * (l - 0.5) * out2.re) / ns;
+              out[cnt + k].im = ((ns - l + 0.5) * out1.im + r * (l - 0.5) * out2.im) / ns;
+            }
+            else{
+              out[cnt + k].re = out1.re + out2.re;
+              out[cnt + k].im = out1.im + out2.im;
+            }
+          }
+          //cnt += row - 2 * delta;
+        }
+        //right edge of overlap area
+        //use next subswath: subswath j+1
+        //else if(k >= row - delta){
+        else{
+          out[cnt + k].re = out2.re;
+          out[cnt + k].im = out2.im;
+        }
+        //cnt += 1;
+      }
+      cnt += row;
+
+      if(diffflag == 0){
+        writedata((fcomplex *)diff[j], (row - 2 * delta) * sizeof(fcomplex), difffp[j]);
+        writedata((fcomplex *)diff2[j], (row - 2 * delta) * sizeof(fcomplex), difffp[j]);
+      }
+
+    } //loop of j, subswath
+    writedata((fcomplex *)out, nrgout * sizeof(fcomplex), outfp);
+  } //loop of i, output line
+
+  for(i = 0; i < n; i++)
+    fclose(infp[i]);
+  fclose(outfp);
+
+  if(diffflag == 0)
+    for(i = 0; i < n - 1; i++)
+      fclose(difffp[i]);
+
+  free_array1d_FILE(infp);
+  free_array1d_FILE(difffp);
+
+  free_array2d_fcomplex(in);
+  free_array1d_fcomplex(out);
+
+  //free_array1d_int(nrgin);
+  free_array1d_int(nazin);
+  //free_array1d_int(nrgoff); //nrgoff must be <= 0
+  //free_array1d_int(nazoff); //nazoff must be <= 0
+  //free_array1d_int(oflag);
+
+  free_array2d_fcomplex(diff);
+  free_array2d_fcomplex(diff2);
+
+  return 0;
+
+}

contrib/alos2proc/src/resamp.c

@@ -0,0 +1,401 @@
+//////////////////////////////////////
+// Cunren Liang, NASA JPL/Caltech
+// Copyright 2017
+//////////////////////////////////////
+//update: add default value azpos_off = 0.0; 12-DEC-2019
+//update: normalization of resampling kernals. 12-DEC-2019
+
+
+#include "resamp.h"
+
+#define SWAP4(a) (*(unsigned int *)&(a) = (((*(unsigned int *)&(a) & 0x000000ff) << 24) | ((*(unsigned int *)&(a) & 0x0000ff00) << 8) | ((*(unsigned int *)&(a) >> 8) & 0x0000ff00) | ((*(unsigned int *)&(a) >> 24) & 0x000000ff)))
+
+void normalize_kernel(float *kernel, long start_index, long end_index);
+
+int resamp(char *slc2, char *rslc2, char *rgoff_file, char *azoff_file, int nrg1, int naz1, int nrg2, int naz2, float prf, float *dopcoeff, float *rgcoef, float *azcoef, float azpos_off, int byteorder, long imageoffset, long lineoffset, int verbose){
+  /*
+    mandatory:
+    slc2:  slave image
+    rslc2: resampled slave image
+    rgoff_file: range offset file. if no range offset file, specify fake
+    azoff_file: azimuth offset file. if no azimuth offset file, specify fake
+    nrg1:  number of columns in master image
+    naz1:  number of lines in master image
+    nrg2:  number of columns in slave image
+    naz2:  number of lines in slave image
+    prf:   PRF of slave image
+    dopcoeff[0]-[3]: Doppler centroid frequency coefficents
+    optional:
+    rgcoef[0]-[9]:   range offset polynomial coefficents. First of two fit results of resamp_roi
+    azcoef[0]-[9]:   azimuth offset polynomial coefficents. First of two fit results of resamp_roi
+    azpos_off:       azimuth position offset. Azimuth line number (column 3) of first offset in culled offset file
+
+    byteorder:      (0) LSB, little endian; (1) MSB, big endian of intput file
+    imageoffset:    offset from start of the image of input file
+    lineoffset:     length of each line of input file
+  */
+
+  FILE *slc2fp;
+  FILE *rslc2fp;
+  FILE *rgoffp;
+  FILE *azoffp;
+  int rgflag;
+  int azflag;
+  //int nrg1;
+  //int naz1;
+  //int nrg2;
+  //int naz2;
+  //float prf;
+  //float dopcoeff[4];
+  //float rgcoef[10];
+  //float azcoef[10];
+  //float azpos_off;
+  float beta;
+  int n;
+  int m;
+  int interp_method;
+  int edge_method;
+  float rgpos;
+  float azpos;
+  float rgoff;
+  float azoff;
+  float rgoff1;
+  float azoff1;
+  float *rgoff2;
+  float *azoff2;
+  float rg2;
+  float az2;
+  int rgi2;
+  int azi2;
+  float rgf;
+  float azf;
+  int rgfn;
+  int azfn;
+  int hnm;
+  int hn;
+  float *sincc;
+  float *kaiserc;
+  float *kernel;
+  float *rgkernel;
+  float *azkernel;
+  fcomplex *azkernel_fc;
+  fcomplex *rgrs;
+  fcomplex *azca;
+  fcomplex *rgrsb;
+  fcomplex *azrs;
+  float *dop;
+  float dopx;
+  fcomplex **inb;
+  int i, j, k, k1, k2;
+  int tmp1, tmp2;
+  int zero_flag;
+  float ftmp1, ftmp2;
+  fcomplex fctmp1, fctmp2;
+  beta = 2.5;
+  n = 9;
+  m = 10000;
+  interp_method = 0;
+  edge_method = 0;
+
+
+  slc2fp = openfile(slc2, "rb");
+  rslc2fp = openfile(rslc2, "wb");
+  rgflag = 0;
+  azflag = 0;
+  if (strcmp(rgoff_file, "fake") == 0){
+    rgflag = 0;
+    printf("range offset file not provided\n");
+  }
+  else{
+    rgflag = 1;
+    rgoffp = openfile(rgoff_file, "rb");
+  }
+  if (strcmp(azoff_file, "fake") == 0){
+    azflag = 0;
+    printf("azimuth offset file not provided\n");
+  }
+  else{
+    azflag = 1;
+    azoffp = openfile(azoff_file, "rb");
+  }
+  //nrg1 = atoi(argv[5]);
+  //naz1 = atoi(argv[6]);
+  //nrg2 = atoi(argv[7]);
+  //naz2 = atoi(argv[8]);
+  //prf = atof(argv[9]);
+  //for(i = 0; i < 4; i++){
+  //  dopcoeff[i] = atof(argv[10+i]);
+  //}
+  //for(i = 0; i < 10; i++){
+  //  if(argc > 14 + i)
+  //    rgcoef[i] = atof(argv[14+i]);
+  //  else
+  //    rgcoef[i] = 0.0;
+  //}
+  //for(i = 0; i < 10; i++){
+  //  if(argc > 24 + i)
+  //    azcoef[i] = atof(argv[24+i]);
+  //  else
+  //    azcoef[i] = 0.0;
+  //}
+  //if(argc > 34)
+  //  azpos_off = atof(argv[34]);
+  //else
+  //  azpos_off = 0.0;
+  if(verbose != 0){
+  printf("\n\ninput parameters:\n");
+  printf("slc2: %s\n", slc2);
+  printf("rslc2: %s\n", rslc2);
+  printf("rgoff_file: %s\n", rgoff_file);
+  printf("azoff_file: %s\n\n", azoff_file);
+  printf("nrg1: %d\n", nrg1);
+  printf("naz1: %d\n", naz1);
+  printf("nrg2: %d\n", nrg2);
+  printf("naz2: %d\n\n", naz2);
+  printf("prf: %f\n\n", prf);
+  for(i = 0; i < 4; i++){
+    printf("dopcoeff[%d]: %e\n", i, dopcoeff[i]);
+  }
+  printf("\n");
+  for(i = 0; i < 10; i++){
+    printf("rgcoef[%d]: %e\n", i, rgcoef[i]);
+  }
+  printf("\n");
+  for(i = 0; i < 10; i++){
+    printf("azcoef[%d]: %e\n", i, azcoef[i]);
+  }
+  printf("\n");
+  printf("azpos_off: %f\n\n", azpos_off);
+
+  if(byteorder == 0){
+    printf("inputfile byte order: little endian\n");
+  }
+  else{
+    printf("inputfile byte order: big endian\n");
+  }
+  printf("input file image offset [byte]: %ld\n", imageoffset);
+  printf("input file line offset [byte]: %ld\n", lineoffset);
+  }
+
+  if(imageoffset < 0){
+    fprintf(stderr, "image offset must be >= 0\n");
+    exit(1);
+  }
+  if(lineoffset < 0){
+    fprintf(stderr, "lineoffset offset must be >= 0\n");
+    exit(1);
+  }
+
+hn = n / 2;
+hnm = n * m / 2;
+rgoff2 = array1d_float(nrg1);
+azoff2 = array1d_float(nrg1);
+sincc = vector_float(-hnm, hnm);
+kaiserc = vector_float(-hnm, hnm);
+kernel = vector_float(-hnm, hnm);
+rgkernel = vector_float(-hn, hn);
+azkernel = vector_float(-hn, hn);
+azkernel_fc = vector_fcomplex(-hn, hn);
+rgrs = vector_fcomplex(-hn, hn);
+azca = vector_fcomplex(-hn, hn);
+rgrsb = vector_fcomplex(-hn, hn);
+azrs = array1d_fcomplex(nrg1);
+dop = array1d_float(nrg2);
+inb = array2d_fcomplex(naz2, nrg2);
+sinc(n, m, sincc);
+kaiser(n, m, kaiserc, beta);
+for(i = -hnm; i <= hnm; i++)
+  kernel[i] = kaiserc[i] * sincc[i];
+if(verbose != 0)
+printf("\n");
+for(i = 0; i < nrg2; i++){
+  dop[i] = dopcoeff[0] + dopcoeff[1] * i + dopcoeff[2] * i * i + dopcoeff[3] * i * i * i;
+  //get rid of this bad convention from roi_pac
+  //dop[i] *= prf;
+  if(verbose != 0)
+  if(i % 500 == 0)
+    printf("range sample: %5d, doppler centroid frequency: %8.2f Hz\n", i, dop[i]);
+}
+if(verbose != 0)
+printf("\n");
+
+//////////////////////////////////////////////////////////////////////////////////////////////
+//skip image header
+fseek(slc2fp, imageoffset, SEEK_SET);
+
+for(i = 0; i < naz2; i++){
+  if(i!=0)
+    fseek(slc2fp, lineoffset - (size_t)nrg2 * sizeof(fcomplex), SEEK_CUR);
+  readdata((fcomplex *)inb[i], (size_t)nrg2 * sizeof(fcomplex), slc2fp);
+}
+
+//read image data
+//if(lineoffset == 0){
+//  readdata((fcomplex *)inb[0], (size_t)naz2 * (size_t)nrg2 * sizeof(fcomplex), slc2fp);
+//}
+//else{
+//  for(i = 0; i < naz2; i++){
+//    fseek(slc2fp, lineoffset, SEEK_CUR);
+//    readdata((fcomplex *)inb[i], (size_t)nrg2 * sizeof(fcomplex), slc2fp);
+//  }
+//}
+//swap bytes
+if(byteorder!=0){
+  printf("swapping bytes...\n");
+  for(i = 0; i < naz2; i++)
+    for(j = 0; j < nrg2; j++){
+      SWAP4(inb[i][j].re);
+      SWAP4(inb[i][j].im);
+    }
+}
+//////////////////////////////////////////////////////////////////////////////////////////////
+
+for(i = 0; i < naz1; i++){
+  if((i + 1) % 100 == 0)
+    fprintf(stderr,"processing line: %6d of %6d\r", i+1, naz1);
+    if (rgflag == 1){
+      readdata((float *)rgoff2, nrg1 * sizeof(float), rgoffp);
+    }
+    if (azflag == 1){
+      readdata((float *)azoff2, nrg1 * sizeof(float), azoffp);
+    }
+  for(j = 0; j < nrg1; j++){
+    azrs[j].re = 0.0;
+    azrs[j].im = 0.0;
+  }
+  for(j = 0; j < nrg1; j++){
+    rgpos = j;
+    azpos = i - azpos_off;
+    rgoff1 = rgcoef[0] + azpos*(rgcoef[2] + \
+             azpos*(rgcoef[5] + azpos*rgcoef[9])) + \
+             rgpos*(rgcoef[1] + rgpos*(rgcoef[4] + \
+             rgpos*rgcoef[8])) + \
+             rgpos*azpos*(rgcoef[3] + azpos*rgcoef[6] + \
+             rgpos*rgcoef[7]);
+    azoff1 = azcoef[0] + azpos*(azcoef[2] + \
+             azpos*(azcoef[5] + azpos*azcoef[9])) + \
+             rgpos*(azcoef[1] + rgpos*(azcoef[4] + \
+             rgpos*azcoef[8])) + \
+             rgpos*azpos*(azcoef[3] + azpos*azcoef[6] + \
+             rgpos*azcoef[7]);
+    if (rgflag == 1){
+      rgoff = rgoff1 + rgoff2[j];
+    }
+    else{
+      rgoff = rgoff1;
+    }
+    if (azflag == 1){
+      azoff = azoff1 + azoff2[j];
+    }
+    else{
+      azoff = azoff1;
+    }
+    rg2 = j + rgoff;
+    az2 = i + azoff;
+    rgi2 = roundfi(rg2);
+    azi2 = roundfi(az2);
+    rgf = rg2 - rgi2;
+    azf = az2 - azi2;
+    rgfn = roundfi(rgf * m);
+    azfn = roundfi(azf * m);
+    for(k = -hn; k <= hn; k++){
+      tmp1 = k * m - rgfn;
+      tmp2 = k * m - azfn;
+      if(tmp1 > hnm) tmp1 = hnm;
+      if(tmp2 > hnm) tmp2 = hnm;
+      if(tmp1 < -hnm) tmp1 = -hnm;
+      if(tmp2 < -hnm) tmp2 = -hnm;
+      rgkernel[k] = kernel[tmp1];
+      azkernel[k] = kernel[tmp2];
+    }
+    normalize_kernel(rgkernel, -hn, hn);
+    normalize_kernel(azkernel, -hn, hn);
+    for(k1 = -hn; k1 <= hn; k1++){
+      rgrs[k1].re = 0.0;
+      rgrs[k1].im = 0.0;
+      if(edge_method == 0){
+        if(azi2 < hn || azi2 > naz2 - 1 - hn || rgi2 < hn || rgi2 > nrg2 - 1 - hn){
+          continue;
+        }
+      }
+      else if(edge_method == 1){
+        if(azi2 < 0 || azi2 > naz2 - 1 || rgi2 < 0 || rgi2 > nrg2 - 1){
+          continue;
+        }
+      }
+      else{
+        if(azi2 < -hn || azi2 > naz2 - 1 + hn || rgi2 < -hn || rgi2 > nrg2 - 1 + hn){
+          continue;
+        }
+      }
+      for(k2 = -hn; k2 <= hn; k2++){
+        if(azi2 + k1 < 0 || azi2 + k1 > naz2 - 1 || rgi2 + k2 < 0 || rgi2 + k2 > nrg2 - 1)
+          continue;
+        rgrs[k1].re += inb[azi2 + k1][rgi2 + k2].re * rgkernel[k2];
+        rgrs[k1].im += inb[azi2 + k1][rgi2 + k2].im * rgkernel[k2];
+      }
+    }
+    for(k = -hn; k <= hn; k++){
+      if(rgrs[k].re == 0.0 && rgrs[k].im == 0.0)
+        continue;
+      dopx = dopcoeff[0] + dopcoeff[1] * rg2 + dopcoeff[2] * rg2 * rg2 + dopcoeff[3] * rg2 * rg2 * rg2;
+      //get rid of this bad convention from roi_pac
+      //dopx *= prf;
+      ftmp1 = 2.0 * PI * dopx * k / prf;
+      azca[k].re = cos(ftmp1);
+      azca[k].im = sin(ftmp1);
+      if(interp_method == 0){
+       rgrsb[k] = cmul(rgrs[k], cconj(azca[k]));
+        azrs[j].re += rgrsb[k].re * azkernel[k];
+        azrs[j].im += rgrsb[k].im * azkernel[k];
+      }
+      else{
+        azkernel_fc[k].re = azca[k].re * azkernel[k];
+        azkernel_fc[k].im = azca[k].im * azkernel[k];
+        azrs[j] = cadd(azrs[j], cmul(rgrs[k], azkernel_fc[k]));
+      }
+    }
+    if(interp_method == 0){
+      ftmp1 = 2.0 * PI * dopx * azf / prf;
+      fctmp1.re = cos(ftmp1);
+      fctmp1.im = sin(ftmp1);
+      azrs[j] = cmul(azrs[j], fctmp1);
+    }
+  }
+  writedata((fcomplex *)azrs, nrg1 * sizeof(fcomplex), rslc2fp);
+}
+fprintf(stderr,"processing line: %6d of %6d\n", naz1, naz1);
+free_array1d_float(rgoff2);
+free_array1d_float(azoff2);
+free_vector_float(sincc, -hnm, hnm);
+free_vector_float(kaiserc, -hnm, hnm);
+free_vector_float(kernel, -hnm, hnm);
+free_vector_float(rgkernel, -hn, hn);
+free_vector_float(azkernel, -hn, hn);
+free_vector_fcomplex(azkernel_fc, -hn, hn);
+free_vector_fcomplex(rgrs, -hn, hn);
+free_vector_fcomplex(azca, -hn, hn);
+free_vector_fcomplex(rgrsb, -hn, hn);
+free_array1d_fcomplex(azrs);
+free_array1d_float(dop);
+free_array2d_fcomplex(inb);
+fclose(slc2fp);
+fclose(rslc2fp);
+if (rgflag == 1){
+  fclose(rgoffp);
+}
+if (azflag == 1){
+  fclose(azoffp);
+}
+return 0;
+}
+void normalize_kernel(float *kernel, long start_index, long end_index){
+  double sum;
+  long i;
+  sum = 0.0;
+  for(i = start_index; i <= end_index; i++)
+    sum += kernel[i];
+  if(sum!=0)
+    for(i = start_index; i <= end_index; i++)
+      kernel[i] /= sum;
+}

contrib/alos2proc/src/rg_filter.c

@@ -8,8 +8,9 @@
 #include <fftw3.h>
 #include <omp.h>
 
+#define SWAP4(a) (*(unsigned int *)&(a) = (((*(unsigned int *)&(a) & 0x000000ff) << 24) | ((*(unsigned int *)&(a) & 0x0000ff00) << 8) | ((*(unsigned int *)&(a) >> 8) & 0x0000ff00) | ((*(unsigned int *)&(a) >> 24) & 0x000000ff)))
 
-int rg_filter(char *inputfile, int nrg, int nout, char **outputfile, float *bw, float *bc, int nfilter, int nfft, float beta, int zero_cf, float offset){
+int rg_filter(char *inputfile, int nrg, int naz, int nout, char **outputfile, float *bw, float *bc, int nfilter, int nfft, float beta, int zero_cf, float offset, int byteorder, long imageoffset, long lineoffset){
   /*
   inputfile:  input file
   nrg         file width
@@ -23,6 +24,10 @@ int rg_filter(char *inputfile, int nrg, int nout, char **outputfile, float *bw,
   beta:       kaiser window beta. Reference Value: 1.0
   zero_cf:    if bc != 0.0, move center frequency to zero? 0: Yes (Reference Value). 1: No.
   offset:     offset (in samples) of linear phase for moving center frequency. Reference Value: 0.0
+
+  byteorder:      (0) LSB, little endian; (1) MSB, big endian of intput file
+  imageoffset:    offset from start of the image of input file
+  lineoffset:     length of each line of input file
   */
 
 ///////////////////////////////
@@ -64,7 +69,7 @@ int rg_filter(char *inputfile, int nrg, int nout, char **outputfile, float *bw,
 
   //int nout; //number of output files
   //int nrg; //file width
-  int naz; //file length
+  //int naz; //file length
 
   //int nfft; //fft length
   //int nfilter; //filter length
@@ -107,7 +112,10 @@ int rg_filter(char *inputfile, int nrg, int nout, char **outputfile, float *bw,
 /*****************************************************************************/
 
   infp  = openfile(inputfile, "rb");
-  naz  = file_length(infp, nrg, sizeof(fcomplex));
+  //naz  = file_length(infp, nrg, sizeof(fcomplex));
+  //fseeko(infp,0L,SEEK_END);
+  //naz = (ftello(infp) - imageoffset) / (lineoffset + nrg*sizeof(fcomplex));
+  //rewind(infp);
   printf("file width: %d, file length: %d\n\n", nrg, naz);
   if(nout < 1){
     fprintf(stderr, "there should be at least one output file!\n");
@@ -128,6 +136,23 @@ int rg_filter(char *inputfile, int nrg, int nout, char **outputfile, float *bw,
     exit(1);
   }
 
+  if(byteorder == 0){
+    printf("inputfile byte order: little endian\n");
+  }
+  else{
+    printf("inputfile byte order: big endian\n");
+  }
+  printf("input file image offset [byte]: %ld\n", imageoffset);
+  printf("input file line offset [byte]: %ld\n", lineoffset);
+  if(imageoffset < 0){
+    fprintf(stderr, "image offset must be >= 0\n");
+    exit(1);
+  }
+  if(lineoffset < 0){
+    fprintf(stderr, "lineoffset offset must be >= 0\n");
+    exit(1);
+  }
+
   //compute block processing parameters
   hnfilter = (nfilter - 1) / 2;
   nblock_in = nfft - nfilter + 1;
@@ -211,6 +236,11 @@ int rg_filter(char *inputfile, int nrg, int nout, char **outputfile, float *bw,
   }
   fftwf_destroy_plan(p_forward_filter);  
 
+
+  //skip image header
+  if(imageoffset != 0)
+    fseek(infp, imageoffset, SEEK_SET);
+
   //process data
   for(i = 0; i < naz; i++){
     //progress report
@@ -220,7 +250,17 @@ int rg_filter(char *inputfile, int nrg, int nout, char **outputfile, float *bw,
       fprintf(stderr,"\n\n");
   
     //read data
+    if(i != 0)
+      fseek(infp, lineoffset-(size_t)nrg * sizeof(fcomplex), SEEK_CUR);
     readdata((fcomplex *)in, (size_t)nrg * sizeof(fcomplex), infp);
+    //swap bytes
+    if(byteorder!=0){
+      for(j = 0; j < nrg; j++){
+        SWAP4(in[j].re);
+        SWAP4(in[j].im);
+      }
+    }
+
     #pragma omp parallel for private(j) shared(nrg,in, zeroflag, sc)
     for(j = 0; j < nrg; j++){
       if(in[j].re != 0.0 || in[j].im != 0.0){