Merge commit '64768d4' into cmake

2020-04-08 11:05:14 -07:00 · 2020-04-08 11:05:14 -07:00 · 4057a645a2
parent de0ea75272 64768d4f36
commit 4057a645a2
51 changed files with 516 additions and 571 deletions
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@ -72,7 +72,7 @@ jobs:
              set -ex
              pwd
              . /opt/conda/bin/activate root
-              export ISCE_HOME=/root/project/install/isce
+              ISCE_HOME=/root/project/install/isce
              export PATH="$ISCE_HOME/bin:$ISCE_HOME/applications:/opt/conda/bin:$PATH"
              export PYTHONPATH="/root/project/install:$PYTHONPATH"
              export LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH"
--- a/init.py
+++ b/init.py
@ -32,7 +32,12 @@ version = release_history # compatibility alias
 __version__ = release_version

 import sys, os
-isce_path = os.path.split(os.path.abspath(__file__))[0]
+isce_path = os.path.dirname(os.path.abspath(__file__))
+
+import logging
+from logging.config import fileConfig as _fc
+_fc(os.path.join(isce_path, 'defaults', 'logging', 'logging.conf'))
+
 sys.path.insert(1,isce_path)
 sys.path.insert(1,os.path.join(isce_path,'applications'))
 sys.path.insert(1,os.path.join(isce_path,'components'))
--- a/applications/CalculatePegPoint.py
+++ b/applications/CalculatePegPoint.py
@ -31,12 +31,8 @@



-import os
 import math
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
+from isce import logging
 from iscesys.Compatibility import Compatibility
 Compatibility.checkPythonVersion()
 from isceobj.Location.Peg import Peg
--- a/applications/calculateBaseline.py
+++ b/applications/calculateBaseline.py
@ -30,11 +30,7 @@



-import os
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
+from isce import logging
 from iscesys.Compatibility import Compatibility
 Compatibility.checkPythonVersion()
 from iscesys.Component.FactoryInit import FactoryInit
--- a/applications/createGeneric.py
+++ b/applications/createGeneric.py
@ -30,11 +30,7 @@



-import os
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
+from isce import logging
 import isceobj
 from iscesys.Component.FactoryInit import FactoryInit

--- a/applications/dem.py
+++ b/applications/dem.py
@ -34,6 +34,8 @@ import sys
 import os
 import argparse
 from contrib.demUtils import createDemStitcher
+
+
 def main():
    #if not argument provided force the --help flag
    if(len(sys.argv) == 1):
@ -132,8 +134,12 @@ def main():
                print('Could not create a stitched DEM. Some tiles are missing')
            else:
                if(args.correct):
-                    ds.correct()
                    #ds.correct(args.output,args.source,width,min(lat[0],lat[1]),min(lon[0],lon[1]))
+                    demImg = ds.correct()
+                    # replace filename with full path including dir in which file is located
+                    demImg.filename = os.path.abspath(os.path.join(args.dir, demImg.filename))
+                    demImg.setAccessMode('READ')
+                    demImg.renderHdr()
        else:
            print('Error. The --bbox (or -b) option must be specified when --action stitch is used')
            raise ValueError
--- a/applications/extractHDROrbit.py
+++ b/applications/extractHDROrbit.py
@ -30,12 +30,8 @@



-import os
 import datetime
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
+from isce import logging
 from iscesys.Compatibility import Compatibility
 Compatibility.checkPythonVersion()
 from iscesys.Component.FactoryInit import FactoryInit
--- a/applications/fixImageXml.py
+++ b/applications/fixImageXml.py
@ -1,9 +1,12 @@
 #!/usr/bin/env python3

+
+import os
+import argparse
 import isce
 import isceobj
-import argparse
-import os
+from isceobj.Util.ImageUtil import ImageLib as IML
+

 def cmdLineParse():
    '''
@ -13,19 +16,14 @@ def cmdLineParse():
    parser = argparse.ArgumentParser(description='Fixes pathnames in ISCE image XML files. Can be used to do more things in the future.')
    parser.add_argument('-i', '--input', type=str, required=True, dest='infile',
            help = 'Input image for which the XML file needs to be fixed.')
-    parser.add_argument('-f', '--full', action='store_true', default=False, dest='full',
+
+    fname = parser.add_mutually_exclusive_group(required=True)
+    fname.add_argument('-f', '--full', action='store_false',
            help = 'Replace filename with full path including dir in which file is located')
-    parser.add_argument('-b', '--base', action='store_true', default=False, dest='base',
+    fname.add_argument('-b', '--base', action='store_true',
            help = 'Replace filename with basename to use in current directory')

    inps = parser.parse_args()
-
-    if (inps.full and inps.base):
-        raise Exception('User requested to use both full path and basename')
-
-    if (not inps.full) and (not inps.base):
-        raise Exception('User did not request any change')
-
    return inps


@ -33,8 +31,6 @@ if __name__ == '__main__':
    '''
    Main driver.
    '''
-    from imageMath import IML
-
    inps = cmdLineParse()

    if inps.infile.endswith('.xml'):
@ -42,15 +38,15 @@ if __name__ == '__main__':

    dirname  = os.path.dirname(inps.infile)

-    img, dataname, metaName = IML.loadImage(inps.infile)
+    img = IML.loadImage(inps.infile)[0]

    if inps.full:
        fname = os.path.abspath( os.path.join(dirname, os.path.basename(inps.infile)))
-    elif inps.base:
-        fname = os.path.basename( os.path.basename(inps.infile))
    else:
-        raise Exception('Unknown state in {0}'.format(os.path.basename(__file__)))
+        fname = os.path.basename( os.path.basename(inps.infile))

    img.filename = fname
    img.setAccessMode('READ')
    img.renderHdr()
+
+
--- a/applications/focus.py
+++ b/applications/focus.py
@ -30,12 +30,8 @@



-import os
 import math
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
+from isce import logging
 import isceobj
 from iscesys.Component.FactoryInit import FactoryInit
 from iscesys.DateTimeUtil.DateTimeUtil import DateTimeUtil as DTU
--- a/applications/insarApp.py
+++ b/applications/insarApp.py
@ -34,8 +34,7 @@ from __future__ import print_function
 import time
 import os
 import sys
-import logging
-import logging.config
+from isce import logging

 import isce
 import isceobj
@ -46,11 +45,6 @@ from iscesys.Component.Configurable import SELF
 import isceobj.InsarProc as InsarProc
 from isceobj.Scene.Frame import FrameMixin

-logging.config.fileConfig(
-    os.path.join(os.environ['ISCE_HOME'], 'defaults', 'logging',
-        'logging.conf')
-)
-
 logger = logging.getLogger('isce.insar')


--- a/applications/isceApp.py
+++ b/applications/isceApp.py
@ -41,8 +41,7 @@ import datetime
 import os
 import sys
 import math
-import logging
-import logging.config
+from isce import logging

 import isce
 import isceobj
@ -1438,11 +1437,6 @@ class IsceApp(Application, FrameMixin):
            sys.exit("Could not find the output directory: %s" % self.outputDir)
        os.chdir(self.outputDir) ##change working directory to given output directory

-        ##read configfile only here so that log path is in output directory
-        logging.config.fileConfig(
-            os.path.join(os.environ['ISCE_HOME'], 'defaults', 'logging',
-                'logging.conf')
-        )
        logger = logging.getLogger('isce.isceProc')
        logger.info(self.intromsg)
        self._isce.dataDirectory = self.outputDir
--- a/applications/make_raw.py
+++ b/applications/make_raw.py
@ -27,16 +27,8 @@
 # Author: Walter Szeliga
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-
-
-
-import os
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
-
 import isce
+from isce import logging
 from iscesys.Compatibility import Compatibility
 from iscesys.Component.Component import Component, Port
 from isceobj.Planet.Ellipsoid import Ellipsoid
--- a/applications/rtcApp.py
+++ b/applications/rtcApp.py
@ -30,10 +30,8 @@


 import time
-import os
 import sys
-import logging
-import logging.config
+from isce import logging

 import isce
 import isceobj
@ -44,11 +42,6 @@ from iscesys.Component.Configurable import SELF
 from isceobj import RtcProc
 from isceobj.Util.decorators import use_api

-logging.config.fileConfig(
-    os.path.join(os.environ['ISCE_HOME'], 'defaults', 'logging',
-        'logging.conf')
-)
-
 logger = logging.getLogger('isce.grdsar')


--- a/applications/scansarApp.py
+++ b/applications/scansarApp.py
@ -27,13 +27,9 @@
 # Authors: Giangi Sacco, Eric Gurrola
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-
-
 import time
-import os
 import sys
-import logging
-import logging.config
+from isce import logging

 import isce
 import isceobj
@ -43,11 +39,6 @@ from iscesys.Compatibility import Compatibility
 from iscesys.Component.Configurable import SELF
 from isceobj import ScansarProc

-logging.config.fileConfig(
-    os.path.join(os.environ['ISCE_HOME'], 'defaults', 'logging',
-        'logging.conf')
-)
-
 logger = logging.getLogger('isce.insar')


--- a/applications/stripmapApp.py
+++ b/applications/stripmapApp.py
@ -35,10 +35,8 @@

 from __future__ import print_function
 import time
-import os
 import sys
-import logging
-import logging.config
+from isce import logging

 import isce
 import isceobj
@ -50,11 +48,6 @@ import isceobj.StripmapProc as StripmapProc
 from isceobj.Scene.Frame import FrameMixin
 from isceobj.Util.decorators import use_api

-logging.config.fileConfig(
-    os.path.join(os.environ['ISCE_HOME'], 'defaults', 'logging',
-        'logging.conf')
-)
-
 logger = logging.getLogger('isce.insar')


@ -391,6 +384,13 @@ RENDERER = Application.Parameter(
    )
                                        )

+DISPERSIVE_FILTER_FILLING_METHOD = Application.Parameter('dispersive_filling_method',
+                                            public_name = 'dispersive filter filling method',
+                                            default='nearest_neighbour',
+                                            type=str,
+                                            mandatory=False,
+                                            doc='method to fill the holes left by masking the ionospheric phase estimate')
+					    
 DISPERSIVE_FILTER_KERNEL_XSIZE = Application.Parameter('kernel_x_size',
                                      public_name='dispersive filter kernel x-size',
                                      default=800,
@ -446,7 +446,6 @@ DISPERSIVE_FILTER_COHERENCE_THRESHOLD = Application.Parameter('dispersive_filter
                                      type=float,
                                      mandatory=False,
                                      doc='Coherence threshold to generate a mask file which gets used in the iterative filtering of the dispersive and non-disperive phase')
-
 #Facility declarations

 MASTER = Application.Facility(
@ -555,6 +554,7 @@ class _RoiBase(Application, FrameMixin):
                      PICKLE_LOAD_DIR,
                      RENDERER,
                      DO_DISPERSIVE,
+                      DISPERSIVE_FILTER_FILLING_METHOD,
                      DISPERSIVE_FILTER_KERNEL_XSIZE,
                      DISPERSIVE_FILTER_KERNEL_YSIZE,
                      DISPERSIVE_FILTER_KERNEL_SIGMA_X,
--- a/applications/topsApp.py
+++ b/applications/topsApp.py
@ -34,10 +34,8 @@


 import time
-import os
 import sys
-import logging
-import logging.config
+from isce import logging

 import isce
 import isceobj
@ -47,11 +45,6 @@ from iscesys.Compatibility import Compatibility
 from iscesys.Component.Configurable import SELF
 from isceobj import TopsProc

-logging.config.fileConfig(
-    os.path.join(os.environ['ISCE_HOME'], 'defaults', 'logging',
-        'logging.conf')
-)
-
 logger = logging.getLogger('isce.insar')


--- a/applications/topsOffsetApp.py
+++ b/applications/topsOffsetApp.py
@ -30,10 +30,8 @@


 import time
-import os
 import sys
-import logging
-import logging.config
+from isce import logging

 import isce
 import isceobj
@ -42,11 +40,6 @@ from isce.applications.topsApp import TopsInSAR
 from iscesys.Component.Application import Application
 from isceobj.Util.decorators import use_api

-logging.config.fileConfig(
-    os.path.join(os.environ['ISCE_HOME'], 'defaults', 'logging',
-        'logging.conf')
-)
-
 logger = logging.getLogger('isce.insar')

 WINDOW_SIZE_WIDTH = Application.Parameter(
--- a/applications/viewMetadata.py
+++ b/applications/viewMetadata.py
@ -27,14 +27,7 @@
 # Author: Walter Szeliga
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-
-
-
-import os
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
+from isce import logging
 from iscesys.Compatibility import Compatibility
 Compatibility.checkPythonVersion()
 from iscesys.Component.FactoryInit import FactoryInit
--- a/components/isceobj/Location/Offset.py
+++ b/components/isceobj/Location/Offset.py
@ -29,11 +29,7 @@


 import math
-import os
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
+from isce import logging

 from isceobj.Util.decorators import type_check, force, pickled, logged
 import numpy as np
--- a/components/isceobj/Scene/test/testTrack.py
+++ b/components/isceobj/Scene/test/testTrack.py
@ -27,14 +27,7 @@
 # Author: Walter Szeliga
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-
-
-
-import os
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
+from isce import logging
 from isceobj.Sensor.ERS import ERS
 from isceobj.Scene.Track import Track
 logger = logging.getLogger("testTrack")
--- a/components/isceobj/Sensor/TOPS/Sentinel1.py
+++ b/components/isceobj/Sensor/TOPS/Sentinel1.py
@ -493,15 +493,9 @@ class Sentinel1(Component):
            offset = np.int(np.rint((aslice.product.bursts[0].burstStartUTC - t0).total_seconds() / burstStartInterval.total_seconds()))

            for kk in range(aslice.product.numberOfBursts):
-                #####Overwrite previous copy if one exists
+                #####Skip appending if burst also exists from previous scene
                if (offset+kk) < len(self.product.bursts):
-                    self.product.bursts[offset+kk] = aslice.product.bursts[kk]
-
-                    ####Keep track of tiff src files
-                    if len(self.tiff):
-                        self._tiffSrc[offset+kk] = aslice.tiff[0]
-
-                    self._elevationAngleVsTau[offset+kk] = aslice._elevationAngleVsTau[kk]
+                    continue

                elif (offset+kk) == len(self.product.bursts):
                    self.product.bursts.append(aslice.product.bursts[kk])
--- a/components/isceobj/StripmapProc/runDispersive.py
+++ b/components/isceobj/StripmapProc/runDispersive.py
@ -3,17 +3,12 @@
 #
 #
 import logging
-import os
+import os,gdal
 import isceobj
 from isceobj.Constants import SPEED_OF_LIGHT
 import numpy as np
-import gdal

-try:
-    import cv2
-except ImportError:
-    print('OpenCV2 does not appear to be installed / is not importable.')
-    print('OpenCV2 is needed for this step. You may experience failures ...')
+


 logger = logging.getLogger('isce.insar.runDispersive')
@ -29,19 +24,8 @@ def getValue(dataFile, band, y_ref, x_ref):
    ds = None
    return ref[0][0]

-def check_consistency(lowBandIgram, highBandIgram, outputDir):

-
-    jumpFile = os.path.join(outputDir , "jumps.bil")
-    cmd = 'imageMath.py -e="round((a_1-b_1)/(2.0*PI))" --a={0}  --b={1} -o {2} -t float  -s BIL'.format(lowBandIgram, highBandIgram, jumpFile)
-    print(cmd)
-    os.system(cmd)
-
-    return jumpFile
-
-
-
-def dispersive_nonDispersive(lowBandIgram, highBandIgram, f0, fL, fH, outDispersive, outNonDispersive, jumpFile, y_ref=None, x_ref=None, m=None , d=None):
+def dispersive_nonDispersive(lowBandIgram, highBandIgram, f0, fL, fH, outDispersive, outNonDispersive, y_ref=None, x_ref=None, m=None , d=None):
    
    if y_ref and x_ref:
        refL = getValue(lowBandIgram, 2, y_ref, x_ref)
@ -57,100 +41,80 @@ def dispersive_nonDispersive(lowBandIgram, highBandIgram, f0, fL, fH, outDispers
    if m and d:

        coef = (fL*fH)/(f0*(fH**2 - fL**2))
-        #cmd = 'imageMath.py -e="{0}*((a_1-{8}-2*PI*c)*{1}-(b_1-{9}-2*PI*(c+f))*{2})" --a={3} --b={4} --c={5} --f={6} -o {7} -t float32 -s BIL'.format(coef,fH, fL, lowBandIgram, highBandIgram, m , d, outDispersive, refL, refH)
-        cmd = 'imageMath.py -e="{0}*((a_1-2*PI*c)*{1}-(b_1+(2.0*PI*g)-2*PI*(c+f))*{2})" --a={3} --b={4} --c={5} --f={6} --g={7} -o {8} -t float32 -s BIL'.format(coef,fH, fL, lowBandIgram, highBandIgram, m , d, jumpFile, outDispersive)
+        cmd = 'imageMath.py -e="{0}*((a_1-2*PI*c)*{1}-(b_1+(2.0*PI)-2*PI*(c+f))*{2})" --a={3} --b={4} --c={5} --f={6} -o {7} -t float32 -s BIL'.format(coef,fH, fL, lowBandIgram, highBandIgram, m , d, outDispersive)
        print(cmd)
        os.system(cmd)

        coefn = f0/(fH**2-fL**2)
-        #cmd = 'imageMath.py -e="{0}*((a_1-{8}-2*PI*c)*{1}-(b_1-{9}-2*PI*(c+f))*{2})" --a={3} --b={4} --c={5} --f={6} -o {7} -t float32 -s BIL'.format(coefn,fH, fL, highBandIgram, lowBandIgram, m , d, outNonDispersive, refH, refL)
-        cmd = 'imageMath.py -e="{0}*((a_1+(2.0*PI*g)-2*PI*c)*{1}-(b_1-2*PI*(c+f))*{2})" --a={3} --b={4} --c={5} --f={6} --g={7} -o {8} -t float32 -s BIL'.format(coefn,fH, fL, highBandIgram, lowBandIgram, m , d, jumpFile, outNonDispersive)
+        cmd = 'imageMath.py -e="{0}*((a_1+(2.0*PI)-2*PI*c)*{1}-(b_1-2*PI*(c+f))*{2})" --a={3} --b={4} --c={5} --f={6} -o {7} -t float32 -s BIL'.format(coefn,fH, fL, highBandIgram, lowBandIgram, m , d, outNonDispersive)
        print(cmd)
        os.system(cmd)

    else:
        
        coef = (fL*fH)/(f0*(fH**2 - fL**2))
-        #cmd = 'imageMath.py -e="{0}*((a_1-{6})*{1}-(b_1-{7})*{2})" --a={3} --b={4} -o {5} -t float32 -s BIL'.format(coef,fH, fL, lowBandIgram, highBandIgram, outDispersive, refL, refH)
-        cmd = 'imageMath.py -e="{0}*(a_1*{1}-(b_1+2.0*PI*c)*{2})" --a={3} --b={4} --c={5}  -o {6} -t float32 -s BIL'.format(coef,fH, fL, lowBandIgram, highBandIgram, jumpFile, outDispersive)
+        cmd = 'imageMath.py -e="{0}*(a_1*{1}-(b_1+2.0*PI)*{2})" --a={3} --b={4} -o {5} -t float32 -s BIL'.format(coef,fH, fL, lowBandIgram, highBandIgram, outDispersive)

        print(cmd)
        os.system(cmd)

        coefn = f0/(fH**2-fL**2)
-        #cmd = 'imageMath.py -e="{0}*((a_1-{6})*{1}-(b_1-{7})*{2})" --a={3} --b={4} -o {5} -t float32 -s BIL'.format(coefn,fH, fL, highBandIgram, lowBandIgram, outNonDispersive, refH, refL) 
-        cmd = 'imageMath.py -e="{0}*((a_1+2.0*PI*c)*{1}-(b_1)*{2})" --a={3} --b={4} --c={5} -o {6} -t float32 -s BIL'.format(coefn,fH, fL, highBandIgram, lowBandIgram, jumpFile, outNonDispersive)
+        cmd = 'imageMath.py -e="{0}*((a_1+2.0*PI)*{1}-(b_1)*{2})" --a={3} --b={4} -o {5} -t float32 -s BIL'.format(coefn,fH, fL, highBandIgram, lowBandIgram, outNonDispersive)
        print(cmd)
        os.system(cmd)


    return None

+def std_iono_mean_coh(f0,fL,fH,coh_mean,rgLooks,azLooks):
+    
+    # From Liao et al., Remote Sensing of Environment 2018
+    
+    # STD sub-band at average coherence value (Eq. 8)
+    Nb = (rgLooks*azLooks)/3.0
+    coeffA = (np.sqrt(2.0*Nb))**(-1)
+    coeffB = np.sqrt(1-coh_mean**2)/coh_mean
+    std_subbands = coeffA * coeffB
+    
+    # STD Ionosphere (Eq. 7)
+    coeffC = np.sqrt(1+(fL/fH)**2)
+    coeffD = (fH*fL*fH)/(f0*(fH**2-fL**2))
+    std_iono = coeffC*coeffD*std_subbands
+    
+    return std_iono
+    
 def theoretical_variance_fromSubBands(self, f0, fL, fH, B, Sig_phi_iono, Sig_phi_nonDisp,N):
-    # Calculating the theoretical variance of the 
-    # ionospheric phase based on the coherence of
-    # the sub-band interferograns 
+    
+    # Calculating the theoretical variance of the ionospheric phase based on the coherence of the sub-band interferograns 
    ifgDirname = os.path.join(self.insar.ifgDirname, self.insar.lowBandSlcDirname)
    lowBandCoherence = os.path.join(ifgDirname , self.insar.coherenceFilename)
    Sig_phi_L = os.path.join(ifgDirname , 'filt_' + self.insar.ifgFilename + ".sig")

    ifgDirname = os.path.join(self.insar.ifgDirname, self.insar.highBandSlcDirname)
-    #highBandIgram = os.path.join(ifgDirname , 'filt_' + self.insar.ifgFilename + ".unw")
-
-    #ifgDirname = os.path.dirname(self.insar.lowBandIgram)
-    #lowBandCoherence = os.path.join(ifgDirname , self.insar.coherenceFilename)
-    #Sig_phi_L = os.path.join(ifgDirname , 'filt_' + self.insar.ifgFilename + ".sig")
-
-    #ifgDirname = os.path.dirname(self.insar.highBandIgram)
    highBandCoherence = os.path.join(ifgDirname , self.insar.coherenceFilename)
    Sig_phi_H = os.path.join(ifgDirname , 'filt_' + self.insar.ifgFilename + ".sig")
-
-    #N = self.numberAzimuthLooks*self.numberRangeLooks
-    #PI = np.pi
-    #fL,f0,fH,B = getBandFrequencies(inps)
-    #cL = read(inps.lowBandCoherence,bands=[1])
-    #cL = cL[0,:,:]
-    #cL[cL==0.0]=0.001
    
    cmd = 'imageMath.py -e="sqrt(1-a**2)/a/sqrt(2.0*{0})" --a={1} -o {2} -t float -s BIL'.format(N, lowBandCoherence, Sig_phi_L)
+   
    print(cmd)
    os.system(cmd)
-    #Sig_phi_L = np.sqrt(1-cL**2)/cL/np.sqrt(2.*N)
-
-    #cH = read(inps.highBandCoherence,bands=[1])
-    #cH = cH[0,:,:]
-    #cH[cH==0.0]=0.001
-
    cmd = 'imageMath.py -e="sqrt(1-a**2)/a/sqrt(2.0*{0})" --a={1} -o {2} -t float -s BIL'.format(N, highBandCoherence, Sig_phi_H)
    print(cmd)
    os.system(cmd)
-    #Sig_phi_H = np.sqrt(1-cH**2)/cH/np.sqrt(2.0*N)

    coef = (fL*fH)/(f0*(fH**2 - fL**2))

    cmd = 'imageMath.py -e="sqrt(({0}**2)*({1}**2)*(a**2) + ({0}**2)*({2}**2)*(b**2))" --a={3} --b={4} -o {5} -t float -s BIL'.format(coef, fL, fH, Sig_phi_L, Sig_phi_H, Sig_phi_iono)
    os.system(cmd)

-    #Sig_phi_iono = np.sqrt((coef**2)*(fH**2)*Sig_phi_H**2 + (coef**2)*(fL**2)*Sig_phi_L**2)
-    #length, width = Sig_phi_iono.shape
-
-    #outFileIono = os.path.join(inps.outDir, 'Sig_iono.bil')
-    #write(Sig_phi_iono, outFileIono, 1, 6)
-    #write_xml(outFileIono, length, width)
-
    coef_non = f0/(fH**2 - fL**2)
    cmd = 'imageMath.py -e="sqrt(({0}**2)*({1}**2)*(a**2) + ({0}**2)*({2}**2)*(b**2))" --a={3} --b={4} -o {5} -t float -s BIL'.format(coef_non, fL, fH, Sig_phi_L, Sig_phi_H, Sig_phi_nonDisp)
    os.system(cmd)

-    #Sig_phi_non_dis = np.sqrt((coef_non**2) * (fH**2) * Sig_phi_H**2 + (coef_non**2) * (fL**2) * Sig_phi_L**2)
-
-    #outFileNonDis = os.path.join(inps.outDir, 'Sig_nonDis.bil')
-    #write(Sig_phi_non_dis, outFileNonDis, 1, 6)
-    #write_xml(outFileNonDis, length, width)
-
+  
    return None #Sig_phi_iono, Sig_phi_nonDisp

-def lowPassFilter(dataFile, sigDataFile, maskFile, Sx, Sy, sig_x, sig_y, iteration=5, theta=0.0):
+def lowPassFilter(self,dataFile, sigDataFile, maskFile, Sx, Sy, sig_x, sig_y, iteration=5, theta=0.0):
    ds = gdal.Open(dataFile + '.vrt', gdal.GA_ReadOnly)
    length = ds.RasterYSize
    width = ds.RasterXSize
@ -159,7 +123,7 @@ def lowPassFilter(dataFile, sigDataFile, maskFile, Sx, Sy, sig_x, sig_y, iterati
    sigData = np.memmap(sigDataFile, dtype=np.float32, mode='r', shape=(length,width))
    mask = np.memmap(maskFile, dtype=np.byte, mode='r', shape=(length,width))

-    dataF, sig_dataF = iterativeFilter(dataIn[:,:], mask[:,:], sigData[:,:], iteration, Sx, Sy, sig_x, sig_y, theta)
+    dataF, sig_dataF = iterativeFilter(self,dataIn[:,:], mask[:,:], sigData[:,:], iteration, Sx, Sy, sig_x, sig_y, theta)

    filtDataFile = dataFile + ".filt"
    sigFiltDataFile  = sigDataFile + ".filt"
@ -192,7 +156,7 @@ def write_xml(fileName,width,length,bands,dataType,scheme):
    
    return None

-def iterativeFilter(dataIn, mask, Sig_dataIn, iteration, Sx, Sy, sig_x, sig_y, theta=0.0):
+def iterativeFilter(self,dataIn, mask, Sig_dataIn, iteration, Sx, Sy, sig_x, sig_y, theta=0.0):
    data = np.zeros(dataIn.shape)
    data[:,:] = dataIn[:,:]
    Sig_data = np.zeros(dataIn.shape)
@ -201,17 +165,30 @@ def iterativeFilter(dataIn, mask, Sig_dataIn, iteration, Sx, Sy, sig_x, sig_y, t
    print ('masking the data')
    data[mask==0]=np.nan
    Sig_data[mask==0]=np.nan
-    print ('Filling the holes with nearest neighbor interpolation')
-    dataF = fill(data)
-    Sig_data = fill(Sig_data)
+    
+    if self.dispersive_filling_method == "smoothed":
+       print('Filling the holes with smoothed values')
+       dataF = fill_with_smoothed(data,3)
+       Sig_data = fill_with_smoothed(Sig_data,3) 
+    else:
+       print ('Filling the holes with nearest neighbor interpolation')
+       dataF = fill(data)
+       Sig_data = fill(Sig_data)
+       
    print ('Low pass Gaussian filtering the interpolated data')
    dataF, Sig_dataF = Filter(dataF, Sig_data, Sx, Sy, sig_x, sig_y, theta=0.0)
    for i in range(iteration):
       print ('iteration: ', i , ' of ',iteration)
       print ('masking the interpolated and filtered data')
       dataF[mask==0]=np.nan
-       print('Filling the holes with nearest neighbor interpolation of the filtered data from previous step')
-       dataF = fill(dataF)
+       
+       if self.dispersive_filling_method == "smoothed":
+          print("Fill the holes with smoothed values")
+          dataF = fill_with_smoothed(dataF,3)
+       else:
+          print('Filling the holes with nearest neighbor interpolation of the filtered data from previous step')
+          dataF = fill(dataF)
+
       print('Replace the valid pixels with original unfiltered data')
       dataF[mask==1]=data[mask==1]
       dataF, Sig_dataF = Filter(dataF, Sig_data, Sx, Sy, sig_x, sig_y, theta=0.0)
@ -219,6 +196,9 @@ def iterativeFilter(dataIn, mask, Sig_dataIn, iteration, Sx, Sy, sig_x, sig_y, t
    return dataF, Sig_dataF

 def Filter(data, Sig_data, Sx, Sy, sig_x, sig_y, theta=0.0):
+    
+    import cv2
+
    kernel = Gaussian_kernel(Sx, Sy, sig_x, sig_y) #(800, 800, 15.0, 100.0)
    kernel = rotate(kernel , theta)

@ -227,11 +207,6 @@ def Filter(data, Sig_data, Sx, Sy, sig_x, sig_y, theta=0.0):
    W1 = cv2.filter2D(1.0/Sig_data**2,-1,kernel)
    W2 = cv2.filter2D(1.0/Sig_data**2,-1,kernel**2)

-    #data = ndimage.convolve(data,kernel, mode='nearest')
-    #W1 = ndimage.convolve(1.0/Sig_data**2,kernel, mode='nearest')
-    #W2 = ndimage.convolve(1.0/Sig_data**2,kernel**2, mode='nearest')
-
-
    return data/W1, np.sqrt(W2/(W1**2))

 def Gaussian_kernel(Sx, Sy, sig_x,sig_y):
@ -281,7 +256,34 @@ def rotate(k , theta):
        k = a*k
    return k

+def fill_with_smoothed(off,filterSize):
+    
+    from astropy.convolution import convolve
+    
+    off_2filt=np.copy(off)
+    kernel = np.ones((filterSize,filterSize),np.float32)/(filterSize*filterSize)
+    loop = 0
+    cnt2=1
+    
+    while (cnt2!=0 & loop<100):
+       loop += 1
+       idx2= np.isnan(off_2filt)
+       cnt2 = np.sum(np.count_nonzero(np.isnan(off_2filt)))
+       print(cnt2)
+       if cnt2 != 0:
+          off_filt= convolve(off_2filt,kernel,boundary='extend',nan_treatment='interpolate')
+          off_2filt[idx2]=off_filt[idx2]
+          idx3 = np.where(off_filt == 0)
+          off_2filt[idx3]=np.nan
+          off_filt=None
+          
+    return off_2filt
+    
+
+
 def fill(data, invalid=None):
+    
+    from scipy import ndimage
    """
    Replace the value of invalid 'data' cells (indicated by 'invalid')
    by the value of the nearest valid data cell
@ -295,8 +297,6 @@ def fill(data, invalid=None):
    Output:
        Return a filled array.
    """
-    from scipy import ndimage
-
    if invalid is None: invalid = np.isnan(data)

    ind = ndimage.distance_transform_edt(invalid,
@ -305,8 +305,10 @@ def fill(data, invalid=None):
    return data[tuple(ind)]


-def getMask(self, maskFile):
-   
+def getMask(self, maskFile,std_iono):
+    
+    from scipy.ndimage import median_filter
+    
    ifgDirname = os.path.join(self.insar.ifgDirname, self.insar.lowBandSlcDirname)
    lowBandIgram = os.path.join(ifgDirname , 'filt_' + self.insar.ifgFilename )
    lowBandCor = os.path.join(ifgDirname ,self.insar.coherenceFilename)
@ -329,7 +331,7 @@ def getMask(self, maskFile):
    else:
        highBandIgram += '.unw'

-    if self.dispersive_filter_mask_type == "coherence":
+    if (self.dispersive_filter_mask_type == "coherence") and (not self.dispersive_filter_mask_type == "median_filter"):
        print ('generating a mask based on coherence files of sub-band interferograms with a threshold of {0}'.format(self.dispersive_filter_coherence_threshold))
        cmd = 'imageMath.py -e="(a>{0})*(b>{0})" --a={1} --b={2} -t byte -s BIL -o {3}'.format(self.dispersive_filter_coherence_threshold, lowBandCor, highBandCor, maskFile)
        os.system(cmd)
@ -339,28 +341,31 @@ def getMask(self, maskFile):
        print ('generating a mask based on .conncomp files')
        cmd = 'imageMath.py -e="(a>0)*(b>0)" --a={0} --b={1} -t byte -s BIL -o {2}'.format(lowBandIgram + '.conncomp', highBandIgram + '.conncomp', maskFile)
        os.system(cmd)
-        #m = read(lowBandIgram + '.conncomp')
-        #m = m[0,:,:]
-        #m = thresholdConnectedComponents(m,minPixelConnComp)
-        #mask = np.ones_like((m))
-        #mask[m==0] = 0.0

-        #m = read(highBandIgram + '.conncomp')
-        #m = m[0,:,:]
-        #m = thresholdConnectedComponents(m,minPixelConnComp)
-        #mask[m==0] = 0.0
+    elif self.dispersive_filter_mask_type == "median_filter":
+        print('Generating mask based on median filtering of the raw dispersive component')
+	
+	# Open raw dispersive component (non-filtered, no unwrapping-error corrected)
+        dispFilename = os.path.join(self.insar.ionosphereDirname,self.insar.dispersiveFilename)
+        sigFilename = os.path.join(self.insar.ionosphereDirname,self.insar.dispersiveFilename+'.sig')
+	
+        ds = gdal.Open(dispFilename+'.vrt',gdal.GA_ReadOnly)
+        disp = ds.GetRasterBand(1).ReadAsArray()
+        ds=None

-        #outName = os.path.join(inps.outDir, 'mask0.bil')
-        #length, width = mask.shape
-        #write(mask, outName, 1, 6)
-        #write_xml(outName, length, width)
+        mask = (np.abs(disp-median_filter(disp,15))<3*std_iono) 
+        
+        mask = mask.astype(np.float32)
+        mask.tofile(maskFile)
+        dims=np.shape(mask)
+        write_xml(maskFile,dims[1],dims[0],1,"FLOAT","BIL")

    else:
        print ('generating a mask based on unwrapped files. Pixels with phase = 0 are masked out.')
        cmd = 'imageMath.py -e="(a_1!=0)*(b_1!=0)" --a={0} --b={1} -t byte -s BIL -o {2}'.format(lowBandIgram , highBandIgram , maskFile)
        os.system(cmd)

-def unwrapp_error_correction(f0, B, dispFile, nonDispFile,lowBandIgram, highBandIgram, jumpsFile, y_ref=None, x_ref=None):
+def unwrapp_error_correction(f0, B, dispFile, nonDispFile,lowBandIgram, highBandIgram, y_ref=None, x_ref=None):

    dFile = os.path.join(os.path.dirname(dispFile) , "dJumps.bil")
    mFile = os.path.join(os.path.dirname(dispFile) , "mJumps.bil")
@ -373,28 +378,14 @@ def unwrapp_error_correction(f0, B, dispFile, nonDispFile,lowBandIgram, highBand
        refL = 0.0
        refH = 0.0

-    #cmd = 'imageMath.py -e="round(((a_1-{7}) - (b_1-{8}) - (2.0*{0}/3.0/{1})*c + (2.0*{0}/3.0/{1})*f )/2.0/PI)" --a={2} --b={3} --c={4} --f={5}  -o {6} -t float32 -s BIL'.format(B, f0, highBandIgram, lowBandIgram, nonDispFile, dispFile, dFile, refH, refL)
-
-    cmd = 'imageMath.py -e="round(((a_1+(2.0*PI*g)) - (b_1) - (2.0*{0}/3.0/{1})*c + (2.0*{0}/3.0/{1})*f )/2.0/PI)" --a={2} --b={3} --c={4} --f={5} --g={6}  -o {7} -t float32 -s BIL'.format(B, f0, highBandIgram, lowBandIgram, nonDispFile, dispFile, jumpsFile, dFile)
-
+    cmd = 'imageMath.py -e="round(((a_1+(2.0*PI)) - (b_1) - (2.0*{0}/3.0/{1})*c + (2.0*{0}/3.0/{1})*f )/2.0/PI)" --a={2} --b={3} --c={4} --f={5}  -o {6} -t float32 -s BIL'.format(B, f0, highBandIgram, lowBandIgram, nonDispFile, dispFile, dFile)
    print(cmd)
-
    os.system(cmd)
-    #d = (phH - phL - (2.*B/3./f0)*ph_nondis + (2.*B/3./f0)*ph_iono )/2./PI
-    #d = np.round(d)
-
-    #cmd = 'imageMath.py -e="round(((a_1 - {6}) + (b_1-{7}) - 2.0*c - 2.0*f )/4.0/PI - g/2)" --a={0} --b={1} --c={2} --f={3} --g={4} -o {5} -t float32 -s BIL'.format(lowBandIgram, highBandIgram, nonDispFile, dispFile, dFile, mFile, refL, refH)
-
-    cmd = 'imageMath.py -e="round(((a_1 ) + (b_1+(2.0*PI*k)) - 2.0*c - 2.0*f )/4.0/PI - g/2)" --a={0} --b={1} --c={2} --f={3} --g={4} --k={5} -o {6} -t float32 -s BIL'.format(lowBandIgram, highBandIgram, nonDispFile, dispFile, dFile, jumpsFile, mFile)
-
+    
+    cmd = 'imageMath.py -e="round(((a_1 ) + (b_1+(2.0*PI)) - 2.0*c - 2.0*f )/4.0/PI - g/2)" --a={0} --b={1} --c={2} --f={3} --g={4} -o {5} -t float32 -s BIL'.format(lowBandIgram, highBandIgram, nonDispFile, dispFile, dFile, mFile)
    print(cmd)
-
    os.system(cmd)

-
-    #m = (phL + phH - 2*ph_nondis - 2*ph_iono)/4./PI - d/2.
-    #m = np.round(m)
-
    return mFile , dFile


@ -451,33 +442,33 @@ def runDispersive(self):

    pulseLength = masterFrame.instrument.pulseLength
    chirpSlope = masterFrame.instrument.chirpSlope
+   
    # Total Bandwidth
    B = np.abs(chirpSlope)*pulseLength
-
+    
+    
    ###Determine looks
    azLooks, rgLooks = self.insar.numberOfLooks( masterFrame, self.posting,
                                        self.numberAzimuthLooks, self.numberRangeLooks)

-
-    #########################################################
-    # make sure the low-band and high-band interferograms have consistent unwrapping errors. 
-    # For this we estimate jumps as the difference of lowBand and highBand phases divided by 2PI
-    # The assumprion is that bothe interferograms are flattened and the phase difference between them
-    # is less than 2PI. This assumprion is valid for current sensors. It needs to be evaluated for
-    # future sensors like NISAR.
-    jumpsFile = check_consistency(lowBandIgram, highBandIgram, outputDir)
-
-    #########################################################
    # estimating the dispersive and non-dispersive components
-    dispersive_nonDispersive(lowBandIgram, highBandIgram, f0, fL, fH, outDispersive, outNonDispersive, jumpsFile)
+    dispersive_nonDispersive(lowBandIgram, highBandIgram, f0, fL, fH, outDispersive, outNonDispersive)

+    # If median filter is selected, compute the ionosphere phase standard deviation at a mean coherence value defined by the user
+    if self.dispersive_filter_mask_type == "median_filter":
+       coh_thres = self.dispersive_filter_coherence_threshold
+       std_iono = std_iono_mean_coh(f0,fL,fH,coh_thres,rgLooks,azLooks)
+    else:
+       std_iono = None
+    
    # generating a mask which will help filtering the estimated dispersive and non-dispersive phase
-    getMask(self, maskFile)
+    getMask(self, maskFile,std_iono)
+    
    # Calculating the theoretical standard deviation of the estimation based on the coherence of the interferograms
    theoretical_variance_fromSubBands(self, f0, fL, fH, B, sigmaDispersive, sigmaNonDispersive, azLooks * rgLooks) 
-
+    
    # low pass filtering the dispersive phase
-    lowPassFilter(outDispersive, sigmaDispersive, maskFile, 
+    lowPassFilter(self,outDispersive, sigmaDispersive, maskFile, 
                    self.kernel_x_size, self.kernel_y_size, 
                    self.kernel_sigma_x, self.kernel_sigma_y, 
                    iteration = self.dispersive_filter_iterations, 
@ -485,7 +476,7 @@ def runDispersive(self):


    # low pass filtering the  non-dispersive phase
-    lowPassFilter(outNonDispersive, sigmaNonDispersive, maskFile, 
+    lowPassFilter(self,outNonDispersive, sigmaNonDispersive, maskFile, 
                    self.kernel_x_size, self.kernel_y_size,
                    self.kernel_sigma_x, self.kernel_sigma_y,
                    iteration = self.dispersive_filter_iterations,
@ -494,21 +485,21 @@ def runDispersive(self):
            
    # Estimating phase unwrapping errors
    mFile , dFile = unwrapp_error_correction(f0, B, outDispersive+".filt", outNonDispersive+".filt", 
-                                                    lowBandIgram, highBandIgram, jumpsFile)
+                                                    lowBandIgram, highBandIgram)

    # re-estimate the dispersive and non-dispersive phase components by taking into account the unwrapping errors
    outDispersive = outDispersive + ".unwCor"
    outNonDispersive = outNonDispersive + ".unwCor"
-    dispersive_nonDispersive(lowBandIgram, highBandIgram, f0, fL, fH, outDispersive, outNonDispersive, jumpsFile, m=mFile , d=dFile)
+    dispersive_nonDispersive(lowBandIgram, highBandIgram, f0, fL, fH, outDispersive, outNonDispersive, m=mFile , d=dFile)

    # low pass filtering the new estimations 
-    lowPassFilter(outDispersive, sigmaDispersive, maskFile, 
+    lowPassFilter(self,outDispersive, sigmaDispersive, maskFile, 
                    self.kernel_x_size, self.kernel_y_size,
                    self.kernel_sigma_x, self.kernel_sigma_y,
                    iteration = self.dispersive_filter_iterations,
                    theta = self.kernel_rotation)

-    lowPassFilter(outNonDispersive, sigmaNonDispersive, maskFile,
+    lowPassFilter(self,outNonDispersive, sigmaNonDispersive, maskFile,
                    self.kernel_x_size, self.kernel_y_size,
                    self.kernel_sigma_x, self.kernel_sigma_y,
                    iteration = self.dispersive_filter_iterations,
--- a/components/isceobj/TopsProc/runESD.py
+++ b/components/isceobj/TopsProc/runESD.py
@ -24,6 +24,8 @@ def runESD(self, debugPlot=True):

    extraOffset = self.extraESDCycles * np.pi * 2

+    val = np.array([])
+
    for swath in swathList:

        if self._insar.numberOfCommonBursts[swath-1] < 2:
@ -53,7 +55,6 @@ def runESD(self, debugPlot=True):
                os.remove(ff)


-        val = []
        lineCount = 0
        for ii in range(minBurst, maxBurst):
            intname = os.path.join(esddir, 'overlap_IW%d_%02d.%dalks_%drlks.int'%(swath,ii+1, alks,rlks))
--- a/components/isceobj/Util/ImageUtil/ImageLib.py
+++ b/components/isceobj/Util/ImageUtil/ImageLib.py
@ -470,7 +470,7 @@ def mmapFromISCE(fname, logger=None):
            isceFile=False
            dataName = fname
        except:
-            raise Exception('Input file: {0} should either be an ISCE image / GDAL image. Appears to be neither')
+            raise Exception('Input file: {0} should either be an ISCE image / GDAL image. Appears to be neither'.format(fname))

    if logger is not None:
        logger.debug('Creating readonly ISCE mmap with \n' +
--- a/components/isceobj/Util/geo/init.py
+++ b/components/isceobj/Util/geo/init.py
@ -45,10 +45,6 @@ ellipsoid        oblate ellipsoid of revolution (e.g, WGS84) with all the
  See mainpage.txt for a complete dump of geo's philosophy-- otherwise,
  use the docstrings.
 """
-import os
-isce_path  = os.getenv("ISCE_HOME")

 ## \namespace geo  Vector- and Affine-spaces, on Earth
 __all__ = ['euclid', 'coordinates', 'ellipsoid', 'charts', 'affine', 'motion']
-
-
--- a/components/iscesys/Component/Application.py
+++ b/components/iscesys/Component/Application.py
@ -297,7 +297,7 @@ class Application(Component, StepHelper):
                        (self._pickleObj, os.path.join(self.pickleLoadDir, name))
                        )
        except IOError:
-            print("Cannot open %s", os.path.join(self.pickleLoadDir, name))
+            print("Cannot open %s" % (os.path.join(self.pickleLoadDir, name)))
        return None


--- a/components/iscesys/Component/Configurable.py
+++ b/components/iscesys/Component/Configurable.py
@ -32,10 +32,7 @@ from __future__ import print_function
 import os
 import sys
 import operator
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
+from isce import logging
 from iscesys.DictUtils.DictUtils import DictUtils as DU
 from iscesys.Compatibility import Compatibility
 Compatibility.checkPythonVersion()
--- a/components/iscesys/DataRetriever/DataRetriever.py
+++ b/components/iscesys/DataRetriever/DataRetriever.py
@ -37,8 +37,7 @@ import isce
 import zipfile
 import os
 import sys
-import logging
-import logging.config
+from isce import logging
 from iscesys.Component.Component import Component
 import shutil
 from urllib import request
@ -325,8 +324,4 @@ class DataRetriever(Component):
        # logger not defined until baseclass is called

        if not self.logger:
-            logging.config.fileConfig(
-                os.path.join(os.environ['ISCE_HOME'], 'defaults',
-                'logging', 'logging.conf')
-            )
            self.logger = logging.getLogger('isce.iscesys.DataRetriever')
--- a/components/iscesys/DictUtils/DictUtils.py
+++ b/components/iscesys/DictUtils/DictUtils.py
@ -81,7 +81,7 @@ class DictUtils:
            spare = []
       
        # dict1 is the one to update
-        for k2,v2 in dict2.items():
+        for k2,v2 in dict(dict2).items():
            if DictUtils.keyIsIn(k2,dict1):
                if isinstance(v2,dict):#if is a dict keep going down the node
                    DictUtils.updateDictionary(dict1[k2],v2,replace,spare)
--- a/components/mroipac/looks/bindings/looksmodule.cpp
+++ b/components/mroipac/looks/bindings/looksmodule.cpp
@ -250,7 +250,7 @@ int takeLookscpx(DataAccessor *IAIn, DataAccessor* IAout, int ld, int la)

            for(int j = 0; j < nfull; j++)
            {
-                bdbl[j] += ain[j];
+                bdbl[j] += complex<double>(ain[j].real(), ain[j].imag());
            }

        }
--- a/components/stdproc/orbit/orbitLib/CalcSchHeightVel.py
+++ b/components/stdproc/orbit/orbitLib/CalcSchHeightVel.py
@ -29,10 +29,8 @@



-import os
 import logging
 import math
-import logging.config

 from iscesys.Compatibility import Compatibility

@ -40,9 +38,6 @@ from isceobj.Planet import Planet
 from isceobj import Constants as CN
 from iscesys.Component.Component import Component, Port

-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
-
 RANGE_SAMPLING_RATE = Component.Parameter('rangeSamplingRate',
                                          public_name='range sampling rate',
                                          type=float,
--- a/contrib/demUtils/demstitcher/DemStitcher.py
+++ b/contrib/demUtils/demstitcher/DemStitcher.py
@ -43,8 +43,7 @@ import os
 import sys
 import math
 import urllib.request, urllib.parse, urllib.error
-import logging
-import logging.config
+from isce import logging
 from iscesys.Component.Component import Component

 import xml.etree.ElementTree as ET
@ -1013,10 +1012,6 @@ class DemStitcher(Component):
        # logger not defined until baseclass is called

        if not self.logger:
-            logging.config.fileConfig(
-                os.path.join(os.environ['ISCE_HOME'], 'defaults',
-                'logging', 'logging.conf')
-            )
            self.logger = logging.getLogger('isce.contrib.demUtils.DemStitcher')

    url = property(getUrl,setUrl)
--- a/contrib/demUtils/demstitcher/DemStitcherV3.py
+++ b/contrib/demUtils/demstitcher/DemStitcherV3.py
@ -39,8 +39,7 @@ from ctypes import cdll
 import os
 import sys
 import urllib.request, urllib.error, urllib.parse
-import logging
-import logging.config
+from isce import logging
 from iscesys.Component.Component import Component
 from contrib.demUtils.DemStitcher import DemStitcher as DS
 #Parameters definitions
@ -291,7 +290,4 @@ class DemStitcher(DS):
        #it's /srtm/version2_1/SRTM(1,3)
        self._remove = ['.jpg','.xml']
        if not self.logger:
-            logging.config.fileConfig(
-            os.environ['ISCE_HOME'] + '/library/applications/logging.conf'
-            )
            self.logger = logging.getLogger('isce.contrib.demUtils.DemStitcherV3')
--- a/contrib/demUtils/swbdstitcher/SWBDStitcher.py
+++ b/contrib/demUtils/swbdstitcher/SWBDStitcher.py
@ -39,9 +39,8 @@ from ctypes import cdll
 import numpy as np
 import os
 import sys
-import logging
+from isce import logging
 import math
-import logging.config
 import urllib.request, urllib.parse, urllib.error
 from iscesys.Component.Component import Component
 from contrib.demUtils.DemStitcher import DemStitcher
@ -315,9 +314,6 @@ class SWBDStitcher(DemStitcher):
        #it's /srtm/version2_1/SRTM(1,3)
        self._remove = ['.jpg','.xml']
        if not self.logger:
-            logging.config.fileConfig(
-            os.environ['ISCE_HOME'] + '/library/applications/logging.conf'
-            )
            self.logger = logging.getLogger('isce.contrib.demUtils.SWBDStitcher')

        self.parameter_list = self.parameter_list + super(DemStitcher,self).parameter_list
--- a/contrib/demUtils/watermask/WaterMask.py
+++ b/contrib/demUtils/watermask/WaterMask.py
@ -35,8 +35,7 @@ import sys
 import math
 from html.parser import HTMLParser
 import urllib.request, urllib.parse, urllib.error
-import logging
-import logging.config
+from isce import logging
 from iscesys.Component.Component import Component
 import zipfile
 import os
@ -979,10 +978,6 @@ class MaskStitcher(Component):
        # logger not defined until baseclass is called

        if not self.logger:
-            logging.config.fileConfig(
-                os.path.join(os.environ['ISCE_HOME'], 'defaults',
-                'logging', 'logging.conf')
-            )
            self.logger = logging.getLogger('isce.contrib.demUtils.MaskStitcher')

    utl = property(getUrl,setUrl)
--- a/contrib/issi/applications/ISSI.py
+++ b/contrib/issi/applications/ISSI.py
@ -32,10 +32,7 @@

 import os
 import math
-import logging
-import logging.config
-logging.config.fileConfig(os.path.join(os.environ['ISCE_HOME'], 'defaults',
-    'logging', 'logging.conf'))
+from isce import logging

 import isce
 from iscesys.Component.FactoryInit import FactoryInit
--- a/contrib/mdx/src/SConscript
+++ b/contrib/mdx/src/SConscript
@ -35,7 +35,7 @@ import os
 Import('envmdx')
 envmdx.Append( CCFLAGS=['-DSUN','-DIO64','-I'+envmdx['MOTIFINCPATH'],'-I'+envmdx['X11INCPATH']] )
 envmdx.PrependUnique( LIBPATH=[envmdx['MOTIFLIBPATH'],envmdx['X11LIBPATH']] )
-envmdx.Append( FORTRANFLAGS=['-DSUN','-DIO64','-DGFORTRAN'] )
+envmdx.Append( FORTRANFLAGS=['-DSUN','-DIO64'] )

 listFiles = ['graphx_mdx.c','rdf_reader_subs.f','mdx_subs.F']
 build = envmdx['PRJ_LIB_DIR']
--- a/contrib/mdx/src/mdx_main.F
+++ b/contrib/mdx/src/mdx_main.F
@ -74,12 +74,6 @@ c*****************************************************************
          integer i_arg
          integer i_inarg

-          integer iargc
-#ifdef GFORTRAN
-c          external iargc
-#else
-           external iargc
-#endif
          integer rdflen
          external rdflen

@ -110,7 +104,7 @@ c          external iargc
          equivalence(b_data,r_data)

          a_cmd = '-V'
-          i_inarg = iargc()
+          i_inarg = command_argument_count()
          if (i_inarg .eq. 0) then
            write(6,*) '  '
            write(6,'(1x,a,a18,a)'     ) '   <<  mdx    Version  ',version_mdx(),        '  >>   '
--- a/contrib/stack/stripmapStack/MaskAndFilter.py
+++ b/contrib/stack/stripmapStack/MaskAndFilter.py
@ -4,52 +4,80 @@
 # Copyright 2016
 #
            
-import numpy as np
-import argparse
 import os   
-import isce
-import isceobj
+import argparse
+import numpy as np
+from scipy import ndimage
+import matplotlib.pyplot as plt
 import gdal
 from gdalconst import GA_ReadOnly
-from scipy import ndimage
+
+# suppress the DEBUG message
+import logging
+mpl_logger = logging.getLogger('matplotlib')
+mpl_logger.setLevel(logging.WARNING)
+
+import isce
+import isceobj
+from isceobj.Util.ImageUtil import ImageLib as IML


 GDAL2NUMPY_DATATYPE = {
-    
-1 : np.uint8,
-2 : np.uint16,
-3 : np.int16,
-4 : np.uint32,
-5 : np.int32,
-6 : np.float32,
-7 : np.float64,
-10: np.complex64,
-11: np.complex128,
-
+    1 : np.uint8,
+    2 : np.uint16,
+    3 : np.int16,
+    4 : np.uint32,
+    5 : np.int32,
+    6 : np.float32,
+    7 : np.float64,
+    10: np.complex64,
+    11: np.complex128,
 }   

+
+EXAMPLE = '''example:
+  MaskAndFilter.py -d offset.bip -s offset_snr.bip
+  MaskAndFilter.py -d offset.bip -s offset_snr.bip --plot
+'''
+
+
 def createParser():
    '''     
    Command line parser.
    '''
           
-    parser = argparse.ArgumentParser( description='filters the densOffset, oversamples it and adds back to the geometry offset')
+    parser = argparse.ArgumentParser(description='Mask and filter the densOffset',
+                                     formatter_class=argparse.RawTextHelpFormatter,
+                                     epilog=EXAMPLE)
    parser.add_argument('-d', '--dense_offset', dest='denseOffset', type=str, required=True,
            help='The dense offsets file obtained from cross correlation or any other approach')
    parser.add_argument('-s', '--snr', dest='snr', type=str, required=True,
            help='The SNR of the dense offsets obtained from cross correlation or any other approach')
    parser.add_argument('-n', '--filter_size', dest='filterSize', type=int, default=8,
-            help='The size of the median filter')
+            help='Size of the median filter (default: %(default)s).')
    parser.add_argument('-t', '--snr_threshold', dest='snrThreshold', type=float, default=5,
-            help='The snr threshold used to mask the offset')
+            help='Min SNR used in the offset (default: %(default)s).')
+
+    # output
    parser.add_argument('-A', '--output_azimuth_offset', dest='outAzimuth', type=str, default='filtAzimuth.off',
-            help='The azimuth offsets after rubber sheeting')
+            help='File name of the azimuth offsets after rubber sheeting (default: %(default)s).')
    parser.add_argument('-R', '--output_range_offset', dest='outRange', type=str, default='filtRange.off',
-            help='The range offsets after rubber sheeting')
+            help='File name of the range offsets after rubber sheeting (default: %(default)s).')
    parser.add_argument('-o', '--output_directory', dest='outDir', type=str, default='./',
-            help='Output directory')
-    parser.add_argument('-p', '--plot', dest='plot', action='store_true', default=False,
-            help='plot the offsets before and after masking and filtering')
+            help='Output directory (default: %(default)s).')
+
+    # plot
+    plot = parser.add_argument_group('plot')
+    plot.add_argument('-p', '--plot', dest='plot', action='store_true', default=False,
+                      help='plot the offsets before and after masking and filtering')
+    plot.add_argument('-v', dest='vlim', nargs=2, type=float, default=(-0.05, 0.05),
+                      help='display range for offset (default: %(default)s).')
+    plot.add_argument('--v-snr', dest='vlim_snr', nargs=2, type=float, default=(0, 100),
+                      help='display range for offset SNR (default: %(default)s).')
+    plot.add_argument('--figsize', dest='figsize', nargs=2, type=float, default=(18, 5),
+                      help='figure size in inch (default: %(default)s).')
+    plot.add_argument('--save', dest='fig_name', type=str, default=None,
+                      help='save figure as file')

    return parser

@ -58,7 +86,7 @@ def cmdLineParse(iargs = None):
    return parser.parse_args(args=iargs)


-def read(file, processor='ISCE' , bands=None , dataType=None):
+def read(file, processor='ISCE', bands=None, dataType=None):
    ''' raeder based on GDAL.
       
    Args:
@ -73,10 +101,13 @@ def read(file, processor='ISCE' , bands=None , dataType=None):
    Returns:
        * data : A numpy array with dimensions : number_of_bands * length * width
    '''
-
+    # generate ENVI hdr file and fix the file path in xml
+    file = os.path.abspath(file)
    if processor == 'ISCE':
-        cmd = 'isce2gis.py envi -i ' + file
-        os.system(cmd)
+        img, dataname, metaname = IML.loadImage(file)
+        img.filename = file
+        img.setAccessMode('READ')
+        img.renderHdr()

    dataset = gdal.Open(file,GA_ReadOnly)

@ -97,23 +128,22 @@ def read(file, processor='ISCE' , bands=None , dataType=None):
    # Fill the array with the Raster bands
    idx=0
    for i in bands:
-       band=dataset.GetRasterBand(i)
-       data[idx,:,:] = band.ReadAsArray()
-       idx+=1
+        band=dataset.GetRasterBand(i)
+        data[idx,:,:] = band.ReadAsArray()
+        idx+=1

    dataset = None
    return data


 def write(raster, fileName, nbands, bandType):
-
-    ############
    # Create the file
    driver = gdal.GetDriverByName( 'ENVI' )
    dst_ds = driver.Create(fileName, raster.shape[1], raster.shape[0], nbands, bandType )
    dst_ds.GetRasterBand(1).WriteArray( raster, 0 ,0 )
-    
    dst_ds = None
+    return
+

 def fill(data, invalid=None):
    """
@ -132,40 +162,46 @@ def fill(data, invalid=None):
    if invalid is None: invalid = np.isnan(data)

    ind = ndimage.distance_transform_edt(invalid,
-                                    return_distances=False,
-                                    return_indices=True)
+                                         return_distances=False,
+                                         return_indices=True)
    return data[tuple(ind)]

-def mask_filter(inps, band, outName, plot=False):
-    #masking and Filtering
-    Offset = read(inps.denseOffset, bands=band) 
-    Offset = Offset[0,:,:]

+def mask_filter(inps, band, outName):
+    """masking and Filtering"""
+
+    # read offset
+    offset = read(inps.denseOffset, bands=band) 
+    offset = offset[0,:,:]
+
+    # read SNR
    snr = read(inps.snr, bands=[1])
    snr = snr[0,:,:]
+    snr[np.isnan(snr)] = 0

-    # Masking the dense offsets based on SNR
-    print ('masking the dense offsets with SNR threshold: ', inps.snrThreshold)
-    Offset[snr<inps.snrThreshold] = 0
+    # mask the offset based on SNR
+    print('masking the dense offsets with SNR threshold: {}'.format(inps.snrThreshold))
+    offset1 = np.array(offset)
+    offset1[snr < inps.snrThreshold] = np.nan

-    ############
-    Offset[snr<inps.snrThreshold]=np.nan
-    Offset = fill(Offset)
-    ############
+    # fill the hole in offset with nearest data
+    print('fill the masked out region with nearest data')
+    offset2 = fill(offset1)

-    # Median filtering the masked offsets
-    print ('Filtering with median filter with size : ', inps.filterSize)
-    Offset = ndimage.median_filter(Offset, size=inps.filterSize)
-    length, width = Offset.shape
+    # median filtering
+    print('filtering with median filter with size : ', inps.filterSize)
+    offset3 = ndimage.median_filter(offset2, size=inps.filterSize)
+    length, width = offset3.shape

-    # writing the masked and filtered offsets to a file
-    print ('writing masked and filtered offsets to: ', outName)
-    write(Offset, outName, 1, 6)
+    # write data to file
+    print('writing masked and filtered offsets to: ', outName)
+    write(offset3, outName, 1, 6)

-    # write the xml file
+    # write the xml/vrt/hdr file
    img = isceobj.createImage()
    img.setFilename(outName)
    img.setWidth(width)
+    img.setLength(length)
    img.setAccessMode('READ')
    img.bands = 1
    img.dataType = 'FLOAT'
@ -175,103 +211,72 @@ def mask_filter(inps, band, outName, plot=False):
    img.renderVRT()
    #img.finalizeImage()

-    ################################
-    if plot:
-       import matplotlib.pyplot as plt
-       fig = plt.figure()
+    return [snr, offset, offset1, offset2, offset3]

-       ax=fig.add_subplot(1,2,1)
-       # cax=ax.imshow(azOffset[800:,:], vmin=-2, vmax=4)
-       cax=ax.imshow(Offset, vmin=-2, vmax=4)
-       ax.set_title('''Offset''')
-    
-       ax=fig.add_subplot(1,2,2)
-    #ax.imshow(azOffset_filt[800:,:], vmin=-2, vmax=4)
-       ax.imshow(Offset_filt, vmin=-2, vmax=4)
-       ax.set_title('''Offset filt''')
-       plt.show()

-def getShape(file):
-    
-    dataset = gdal.Open(file,GA_ReadOnly) 
-    return dataset.RasterYSize, dataset.RasterXSize
+def plot_mask_and_filtering(az_list, rg_list, inps=None):

-def resampleOffset(maskedFiltOffset, geometryOffset, resampledOffset, outName):
-    
-    length, width = getShape(geometryOffset)
-    print('oversampling the filtered and masked offsets to the width and length:', width, ' ', length ) 
-    cmd = 'gdal_translate -of ENVI  -outsize  ' + str(width) + ' ' + str(length) + ' ' + maskedFiltOffset + ' ' + resampledOffset
-    os.system(cmd)
+    fig, axs = plt.subplots(nrows=2, ncols=5, figsize=inps.figsize, sharex=True, sharey=True)
+    titles = ['SNR', 'offset', 'offset (mask)', 'offset (mask/fill)', 'offset (mask/fill/filter)']

-    img = isceobj.createImage()
-    img.setFilename(resampledOffset)
-    img.setWidth(width)
-    img.setAccessMode('READ')
-    img.bands = 1
-    img.dataType = 'FLOAT'
-    img.scheme = 'BIP'
-    #img.createImage()
-    img.renderHdr()
-    img.renderVRT()
-    #img.finalizeImage()
+    # plot SNR
+    im0 = axs[0,0].imshow(az_list[0], vmin=inps.vlim_snr[0], vmax=inps.vlim_snr[1], cmap='RdBu')
+    im0 = axs[1,0].imshow(rg_list[0], vmin=inps.vlim_snr[0], vmax=inps.vlim_snr[1], cmap='RdBu')
+    axs[0,0].set_title('SNR', fontsize=12)

-    print ('Adding the dense offsets to the geometry offsets. Output: ', outName)
-    cmd = "imageMath.py -e='a+b' -o " + outName + " -t float  --a=" + geometryOffset + " --b=" + resampledOffset
-    os.system(cmd)
+    # label
+    axs[0,0].set_ylabel('azimuth', fontsize=12)
+    axs[1,0].set_ylabel('range', fontsize=12)
+
+    # plot offset
+    for i in range(1,len(az_list)):
+        im1 = axs[0,i].imshow(az_list[i], vmin=inps.vlim[0], vmax=inps.vlim[1], cmap='jet')
+        im1 = axs[1,i].imshow(rg_list[i], vmin=inps.vlim[0], vmax=inps.vlim[1], cmap='jet')
+        axs[0,i].set_title(titles[i], fontsize=12)
+    fig.tight_layout()
+
+    # colorbar
+    fig.subplots_adjust(bottom=0.15)
+    cax0 = fig.add_axes([0.09, 0.1, 0.08, 0.015])
+    cbar0 = plt.colorbar(im0, cax=cax0, orientation='horizontal')
+    cax0.yaxis.set_ticks_position('left')
+
+    #fig.subplots_adjust(right=0.93)
+    cax1 = fig.add_axes([0.57, 0.1, 0.08, 0.015])
+    cbar1 = plt.colorbar(im1, cax=cax1,  orientation='horizontal')
+    cbar1.set_label('pixel', fontsize=12)
+
+    # save figure to file
+    if inps.fig_name is not None:
+        inps.fig_name = os.path.abspath(inps.fig_name)
+        print('save figure to file {}'.format(inps.fig_name))
+        plt.savefig(inps.fig_name, bbox_inches='tight', transparent=True, dpi=300)
+    plt.show()
+    return


 def main(iargs=None):

-        inps = cmdLineParse(iargs)
-        #######################
-        # working on the azimuth offsets
-        #######################
-        #cmd = 'isce2gis.py envi -i ' + inps.geometryAzimuthOffset
-        #os.system(cmd)
-        
-        if not os.path.exists(inps.outDir):
-            os.makedirs(inps.outDir)
+    inps = cmdLineParse(iargs)

-        #######################
-        # masking the dense offsets based on SNR and median filter the masked offsets
-        maskedFiltOffset = os.path.join(inps.outDir, inps.outAzimuth)
-        mask_filter(inps, band=[1], outName = maskedFiltOffset, plot=inps.plot)
+    if not os.path.exists(inps.outDir):
+        os.makedirs(inps.outD)

-        cmd = 'isce2gis.py envi -i ' + maskedFiltOffset
-        os.system(cmd)
-        #######################
-        # resampling the masked and filtered dense offsets to the same 
-        # grid size of the geometry offsets and adding back to the 
-        # geometry offsets
-      #  outAzimuth = os.path.join(inps.outDir, inps.outAzimuth) 
+    #######################
+    # masking the dense offsets based on SNR and median filter the masked offs

-      #  resampledDenseOffset = os.path.join(inps.outDir, 'filtAzOff_resampled.bil')
-      #  resampleOffset(maskedFiltOffset, inps.geometryAzimuthOffset, resampledDenseOffset, outAzimuth)
-        
-        #######################
-           
-        #######################
-        # working on the range offsets
-        #######################
-        #cmd = 'isce2gis.py envi -i ' + inps.geometryRangeOffset
-        #os.system(cmd)
-        
-        if not os.path.exists(inps.outDir):
-            os.makedirs(inps.outDir)
-        #######################
-        # masking the dense offsets based on SNR and median filter the masked offsets
+    # azimuth offsets
+    inps.outAzimuth = os.path.join(inps.outDir, inps.outAzimuth)
+    az_list = mask_filter(inps, band=[1], outName=inps.outAzimuth)

-        maskedFiltOffset = os.path.join(inps.outDir, inps.outRange)
-        mask_filter(inps, band=[2], outName = maskedFiltOffset, plot=inps.plot)
+    # range offsets
+    inps.outRange = os.path.join(inps.outDir, inps.outRange)
+    rg_list = mask_filter(inps, band=[2], outName=inps.outRange)

-        cmd = 'isce2gis.py envi -i ' + maskedFiltOffset
-        os.system(cmd)
-        #######################
-        # resampling the masked and filtered dense offsets to the same grid size of the geometry offsets
-        #outRange = os.path.join(inps.outDir, inps.outRange)
-
-        #resampledDenseOffset = os.path.join(inps.outDir, 'filtRngOff_resampled.bil')
-        #resampleOffset(maskedFiltOffset, inps.geometryRangeOffset, resampledDenseOffset, outRange)
+    # plot result
+    if inps.plot:
+        plot_mask_and_filtering(az_list, rg_list, inps)
+    return


 if __name__ == '__main__':
--- a/contrib/stack/stripmapStack/README.md
+++ b/contrib/stack/stripmapStack/README.md
@ -29,7 +29,6 @@ d) fix the path of the file in the xml file of the DEM by using fixImageXml.py.
 mkdir DEM; cd DEM
 dem.py -a stitch -b -37 -31 -72 -69 -r -s 1 -c
 rm demLat*.dem demLat*.dem.xml demLat*.dem.vrt
-fixImageXml.py -f -i demLat*.dem.wgs84
 cd ..
 ```

--- a/contrib/stack/stripmapStack/Stack.py
+++ b/contrib/stack/stripmapStack/Stack.py
@ -654,33 +654,40 @@ class workflow(object):

 ##############################

-def baselinePair(baselineDir, master, slave):
+def baselinePair(baselineDir, master, slave,doBaselines=True):
    
-    try:
-        mdb = shelve.open( os.path.join(master, 'raw'), flag='r')
-        sdb = shelve.open( os.path.join(slave, 'raw'), flag='r')
-    except:
-        mdb = shelve.open( os.path.join(master, 'data'), flag='r')
-        sdb = shelve.open( os.path.join(slave, 'data'), flag='r')
+    if doBaselines: # open files to calculate baselines
+        try:
+            mdb = shelve.open( os.path.join(master, 'raw'), flag='r')
+            sdb = shelve.open( os.path.join(slave, 'raw'), flag='r')
+        except:
+            mdb = shelve.open( os.path.join(master, 'data'), flag='r')
+            sdb = shelve.open( os.path.join(slave, 'data'), flag='r')

-    mFrame = mdb['frame']
-    sFrame = sdb['frame']
+        mFrame = mdb['frame']
+        sFrame = sdb['frame']


-    bObj = Baseline()
-    bObj.configure()
-    bObj.wireInputPort(name='masterFrame', object=mFrame)
-    bObj.wireInputPort(name='slaveFrame', object=sFrame)
-    bObj.baseline()    
+        bObj = Baseline()
+        bObj.configure()
+        bObj.wireInputPort(name='masterFrame', object=mFrame)
+        bObj.wireInputPort(name='slaveFrame', object=sFrame)
+        bObj.baseline()    # calculate baseline from orbits
+        pBaselineBottom = bObj.pBaselineBottom
+        pBaselineTop = bObj.pBaselineTop
+    else:       # set baselines to zero if not calculated
+        pBaselineBottom = 0.0
+        pBaselineTop = 0.0
+        
    baselineOutName = os.path.basename(master) + "_" + os.path.basename(slave) + ".txt"
    f = open(os.path.join(baselineDir, baselineOutName) , 'w')
-    f.write("PERP_BASELINE_BOTTOM " + str(bObj.pBaselineBottom) + '\n')
-    f.write("PERP_BASELINE_TOP " + str(bObj.pBaselineTop) + '\n')
+    f.write("PERP_BASELINE_BOTTOM " + str(pBaselineBottom) + '\n')
+    f.write("PERP_BASELINE_TOP " + str(pBaselineTop) + '\n')
    f.close()
-    print('Baseline at top/bottom: %f %f'%(bObj.pBaselineTop,bObj.pBaselineBottom))
-    return (bObj.pBaselineTop+bObj.pBaselineBottom)/2.
+    print('Baseline at top/bottom: %f %f'%(pBaselineTop,pBaselineBottom))
+    return (pBaselineTop+pBaselineBottom)/2.

-def baselineStack(inps,stackMaster,acqDates):
+def baselineStack(inps,stackMaster,acqDates,doBaselines=True):
    from collections import OrderedDict
    baselineDir = os.path.join(inps.workDir,'baselines')
    if not os.path.exists(baselineDir):
@ -693,7 +700,7 @@ def baselineStack(inps,stackMaster,acqDates):
    for slv in acqDates:
        if slv != stackMaster:
            slave = os.path.join(inps.slcDir, slv)
-            baselineDict[slv]=baselinePair(baselineDir, master, slave)
+            baselineDict[slv]=baselinePair(baselineDir, master, slave, doBaselines)
            t = datetime.datetime.strptime(slv, datefmt)
            timeDict[slv] = t - t0
        else:
@ -702,11 +709,11 @@ def baselineStack(inps,stackMaster,acqDates):

    return baselineDict, timeDict

-def selectPairs(inps,stackMaster, slaveDates, acuisitionDates):
-    baselineDict, timeDict = baselineStack(inps, stackMaster, acuisitionDates)
+def selectPairs(inps,stackMaster, slaveDates, acuisitionDates,doBaselines=True):
+
+    baselineDict, timeDict = baselineStack(inps, stackMaster, acuisitionDates,doBaselines)
    for slave in slaveDates:
       print (slave,' : ' , baselineDict[slave])
-
    numDates = len(acuisitionDates)
    pairs = []
    for i in range(numDates-1):
--- a/contrib/stack/stripmapStack/createWaterMask.py
+++ b/contrib/stack/stripmapStack/createWaterMask.py
@ -32,10 +32,16 @@ def createParser():
                             'and (0,360) or (-180,180) for longitudes.')
    parser.add_argument('-d','--dem_file', dest='demName', type=str, default=None,
                      help='DEM file in geo coordinates, i.e. demLat*.dem.wgs84.')
+
    parser.add_argument('-l', '--lat_file', dest='latName', type=str, default=None, 
                      help='pixel by pixel lat file in radar coordinate')
    parser.add_argument('-L', '--lon_file', dest='lonName', type=str, default=None, 
                      help='pixel by pixel lat file in radar coordinate')
+
+    parser.add_argument('--fill', dest='fillValue', type=int, default=-1, choices={-1,0},
+                      help='fill value for pixels with missing data. Default: -1.\n'
+                           '-1 for water body\n'
+                           ' 0 for land')
    parser.add_argument('-o', '--output', dest='outfile', type=str,
                      help='output filename of water mask in radar coordinates')
    return parser
@ -73,7 +79,7 @@ def dem2bbox(dem_file):
    return bbox


-def download_waterMask(bbox, dem_file):
+def download_waterMask(bbox, dem_file, fill_value=-1):
    out_dir = os.getcwd()
    # update out_dir and/or bbox if dem_file is input
    if dem_file:
@ -86,8 +92,7 @@ def download_waterMask(bbox, dem_file):
    #inps.waterBodyGeo = sw.defaultName(inps.bbox)
    sw.outputFile = os.path.join(out_dir, sw.defaultName(bbox))
    sw._noFilling = False
-    sw._fillingValue = -1.0    #fill pixels without DEM data with value of -1, same as water body
-    #sw._fillingValue = 0.0
+    sw._fillingValue = fill_value
    sw.stitch(bbox[0:2], bbox[2:])
    return sw.outputFile

@ -106,7 +111,7 @@ def geo2radar(geo_file, rdr_file, lat_file, lon_file):
 def main(iargs=None):

    inps = cmdLineParse(iargs)
-    geo_file = download_waterMask(inps.bbox, inps.demName)    
+    geo_file = download_waterMask(inps.bbox, inps.demName, inps.fillValue)
    if inps.latName and inps.lonName:
        geo2radar(geo_file, inps.outfile, inps.latName, inps.lonName)
    return
--- a/contrib/stack/stripmapStack/prepareUAVSAR_coregStack.py
+++ b/contrib/stack/stripmapStack/prepareUAVSAR_coregStack.py
@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+# modified to work for different UAVSAR stack segments EJF 2019/05/04

 import os
 import glob
@ -14,15 +15,17 @@ def createParser():
    Create command line parser.
    '''

-    parser = argparse.ArgumentParser(description='Unzip Alos zip files.')
+    parser = argparse.ArgumentParser(description='Prepare UAVSAR SLC Stack files.')
    parser.add_argument('-i', '--input', dest='input', type=str, required=True,
-            help='directory which has all dates as directories. Inside each date, zip files are expected.')
+            help='directory which has all dates.')
    parser.add_argument('-d', '--dop_file', dest='dopFile', type=str, required=True,
-            help='Doppler file for the stack.')
+            help='Doppler file for the stack. Needs to be in directory where command is run.')
    parser.add_argument('-o', '--output', dest='output', type=str, required=True,
            help='output directory which will be used for unpacking.')
-    parser.add_argument('-t', '--text_cmd', dest='text_cmd', type=str, default='source ~/.bash_profile;'
-       , help='text command to be added to the beginning of each line of the run files. Example : source ~/.bash_profile;')
+    parser.add_argument('-s', '--segment', dest='segment', type=str, default='1',
+            help='segment of the UAVSAR stack to prepare. For "s2" use "2", etc. Default is "1" ')
+    parser.add_argument('-t', '--text_cmd', dest='text_cmd', type=str, default='source ~/.bash_profile;', 
+            help='text command to be added to the beginning of each line of the run files. Default: source ~/.bash_profile;')

    return parser

@ -64,14 +67,13 @@ def main(iargs=None):
    inps = cmdLineParse(iargs)
    
    outputDir = os.path.abspath(inps.output)
-    run_unPack = 'run_unPackAlos'

    #######################################
-    slc_files = glob.glob(os.path.join(inps.input, '*_s5_1x1.slc'))
+    slc_files = glob.glob(os.path.join(inps.input, '*_s'+inps.segment+'_1x1.slc'))
    for file in slc_files:
        imgDate = get_Date(file)
        print (imgDate)
-        annFile = file.replace('_s5_1x1.slc','')+'.ann'
+        annFile = file.replace('_s'+inps.segment+'_1x1.slc','')+'.ann'
        print (annFile)
        imgDir = os.path.join(outputDir,imgDate)
        if not os.path.exists(imgDir):
@ -81,7 +83,8 @@ def main(iargs=None):
        print (cmd)
        os.system(cmd)
        
-        cmd = 'mv ' + file + ' ' + imgDir
+        slcFile = os.path.join(imgDir, imgDate+'.slc')
+        cmd = 'mv ' + file + ' ' + slcFile
        print(cmd)
        os.system(cmd)

@ -90,7 +93,6 @@ def main(iargs=None):
        os.system(cmd)

        shelveFile = os.path.join(imgDir, 'data')
-        slcFile = os.path.join(imgDir, os.path.basename(file))
        write_xml(shelveFile, slcFile)

 if __name__ == '__main__':
--- a/contrib/stack/stripmapStack/stackStripMap.py
+++ b/contrib/stack/stripmapStack/stackStripMap.py
@ -325,7 +325,10 @@ def main(iargs=None):
  if not os.path.exists(runDir):
       os.makedirs(runDir)

-  pairs = selectPairs(inps,stackMasterDate, slaveDates, acquisitionDates)
+  if inps.sensor.lower() == 'uavsar_stack':    # don't try to calculate baselines for UAVSAR_STACK data
+    pairs = selectPairs(inps,stackMasterDate, slaveDates, acquisitionDates,doBaselines=False)
+  else:
+    pairs = selectPairs(inps,stackMasterDate, slaveDates, acquisitionDates,doBaselines=True)  
  print ('number of pairs: ', len(pairs))

  ###If only a summary is requested quit after this
--- a/contrib/stack/stripmapStack/topo.py
+++ b/contrib/stack/stripmapStack/topo.py
@ -401,7 +401,8 @@ def runMultilook(in_dir, out_dir, alks, rlks):
    return out_dir


-def runMultilookGdal(in_dir, out_dir, alks, rlks):
+def runMultilookGdal(in_dir, out_dir, alks, rlks, in_ext='.rdr', out_ext='.rdr',
+                     fbase_list=['hgt', 'incLocal', 'lat', 'lon', 'los', 'shadowMask', 'waterMask']):
    print('generate multilooked geometry files with alks={} and rlks={}'.format(alks, rlks))
    import gdal

@ -411,10 +412,9 @@ def runMultilookGdal(in_dir, out_dir, alks, rlks):
        print('create directory: {}'.format(out_dir))

    # multilook files one by one
-    for fbase in ['hgt', 'incLocal', 'lat', 'lon', 'los', 'shadowMask', 'waterMask']:
-        fname = '{}.rdr'.format(fbase)
-        in_file = os.path.join(in_dir, fname)
-        out_file = os.path.join(out_dir, fname)
+    for fbase in fbase_list:
+        in_file = os.path.join(in_dir, '{}{}'.format(fbase, in_ext))
+        out_file = os.path.join(out_dir, '{}{}'.format(fbase, out_ext))

        if os.path.isfile(in_file):
            ds = gdal.Open(in_file, gdal.GA_ReadOnly)
@ -434,8 +434,9 @@ def runMultilookGdal(in_dir, out_dir, alks, rlks):
            # copy the full resolution xml/vrt file from ./merged/geom_master to ./geom_master
            # to facilitate the number of looks extraction
            # the file path inside .xml file is not, but should, updated
-            shutil.copy(in_file+'.xml', out_file+'.full.xml')
-            shutil.copy(in_file+'.vrt', out_file+'.full.vrt')
+            if in_file != out_file+'.full':
+                shutil.copy(in_file+'.xml', out_file+'.full.xml')
+                shutil.copy(in_file+'.vrt', out_file+'.full.vrt')

    return out_dir

--- a/contrib/stack/topsStack/FilterAndCoherence.py
+++ b/contrib/stack/topsStack/FilterAndCoherence.py
@ -30,10 +30,12 @@


 import logging
-import isce
-import isceobj
 import argparse
 import os
+
+import isce
+import isceobj
+from isceobj.TopsProc.runBurstIfg import computeCoherence
 logger = logging.getLogger('isce.tops.runFilter')

 def runFilter(infile, outfile, filterStrength):
@ -135,7 +137,11 @@ def createParser():
            dest='cohfile')
    parser.add_argument('-s', '--strength', type=float, default=0.5, help='Filter strength',
            dest='filterstrength')
-
+    parser.add_argument('--slc1', type=str, help="SLC 1", dest='slc1')
+    parser.add_argument('--slc2', type=str, help="SLC 2", dest='slc2')
+    parser.add_argument('--cc','--complex_coh',type=str, default='fine.cori.full',help='complex coherence file',dest='cpx_cohfile')
+    parser.add_argument('-r','--range_looks',type=int, default=9, help= 'range looks', dest='numberRangelooks')
+    parser.add_argument('-z','--azimuth_looks',type=int, default=3, help= 'azimuth looks', dest='numberAzlooks')
    return parser

 def cmdLineParse(iargs=None):
@ -152,7 +158,31 @@ def main(iargs=None):
    runFilter(inps.infile, inps.filtfile, inps.filterstrength)

    estCoherence(inps.filtfile, inps.cohfile)
+    if inps.slc1 and inps.slc2:
+        computeCoherence(inps.slc1,inps.slc2,inps.cpx_cohfile)
+        from mroipac.looks.Looks import Looks

+        print('Multilooking {0} ...'.format(inps.cpx_cohfile))
+        
+        infile=inps.cpx_cohfile
+        inimg = isceobj.createImage()
+        inimg.load(infile + '.xml')
+
+        alks=inps.numberAzlooks
+        rlks=inps.numberRangelooks
+        
+        spl = os.path.splitext(inimg.filename)
+        #ext = '.{0}alks_{1}rlks'.format(alks, rlks)
+        #outname = spl[0] + ext + spl[1]
+        outname=spl[0]
+        lkObj = Looks()
+        lkObj.setDownLooks(alks)
+        lkObj.setAcrossLooks(rlks)
+        lkObj.setInputImage(inimg)
+        lkObj.setOutputFilename(outname)
+        lkObj.looks()
+        fullfilename=inps.cpx_cohfile
+        ret=os.system('rm '+fullfilename)
 if __name__ == '__main__':
    
    main()
--- a/contrib/stack/topsStack/README.md
+++ b/contrib/stack/topsStack/README.md
@ -57,7 +57,6 @@ Download of DEM (need to use wgs84 version) using the ISCE DEM download script.
 mkdir DEM; cd DEM
 dem.py -a stitch -b 18 20 -100 -97 -r -s 1 –c
 rm demLat*.dem demLat*.dem.xml demLat*.dem.vrt
-fixImageXml.py -f -i demLat*.dem.wgs84             #Updating DEM’s wgs84 xml to include full path to the DEM
 cd ..
 ```

--- a/contrib/stack/topsStack/Stack.py
+++ b/contrib/stack/topsStack/Stack.py
@ -205,7 +205,12 @@ class config(object):
        self.f.write('filt : ' + self.filtName + '\n')
        self.f.write('coh : ' + self.cohName + '\n')
        self.f.write('strength : ' + self.filtStrength + '\n')
-
+        self.f.write('slc1 : ' + self.slc1 + '\n')
+        self.f.write('slc2 : ' + self.slc2 + '\n')
+        self.f.write('complex_coh : '+ self.cpxcor + '\n')
+        self.f.write('range_looks : ' + self.rangeLooks + '\n')
+        self.f.write('azimuth_looks : ' + self.azimuthLooks + '\n')
+	
    def unwrap(self, function):
        self.f.write('###################################'+'\n')
        self.f.write(function + '\n')
@ -629,12 +634,16 @@ class run(object):
            master = pair[0]
            slave = pair[1]
            mergedDir = os.path.join(self.work_dir, 'merged/interferograms/' + master + '_' + slave)
+            mergedSLCDir = os.path.join(self.work_dir, 'merged/SLC')        
            configName = os.path.join(self.config_path ,'config_igram_filt_coh_' + master + '_' + slave)
            configObj = config(configName)
            configObj.configure(self)
            configObj.input = os.path.join(mergedDir,'fine.int')
            configObj.filtName = os.path.join(mergedDir,'filt_fine.int')
            configObj.cohName = os.path.join(mergedDir,'filt_fine.cor')
+            configObj.slc1=os.path.join(mergedSLCDir, '{}/{}.slc.full'.format(master, master))
+            configObj.slc2=os.path.join(mergedSLCDir, '{}/{}.slc.full'.format(slave, slave))
+            configObj.cpxcor=os.path.join(mergedDir,'fine.cor.full')
            #configObj.filtStrength = str(self.filtStrength)
            configObj.FilterAndCoherence('[Function-1]')
            configObj.finalize()
--- a/contrib/stack/topsStack/mergeBursts.py
+++ b/contrib/stack/topsStack/mergeBursts.py
@ -390,8 +390,7 @@ def main(iargs=None):
        fileList.append([os.path.join(inps.dirname, 'IW{0}'.format(swath), namePattern[0] + '_%02d.%s'%(x,namePattern[1])) for x in range(minBurst, maxBurst+1)])

    mergedir = os.path.dirname(inps.outfile)
-    if not os.path.isdir(mergedir):
-        os.makedirs(mergedir)
+    os.makedirs(mergedir, exist_ok=True)
    
    suffix = '.full'
    if (inps.numberRangeLooks == 1) and (inps.numberAzimuthLooks==1):
--- a/contrib/stack/topsStack/stackSentinel.py
+++ b/contrib/stack/topsStack/stackSentinel.py
@ -430,11 +430,16 @@ def slcStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe_dict, upd
    #############################
    i=0

+    if not updateStack:
+        i += 1
+        runObj = run()
+        runObj.configure(inps, 'run_' + str(i) + "_unpack_topo_master")
+        runObj.unpackStackMasterSLC(safe_dict)
+        runObj.finalize()
+
    i+=1
    runObj = run()
-    runObj.configure(inps, 'run_' + str(i) + "_unpack_slc_topo_master")
-    if not updateStack:
-        runObj.unpackStackMasterSLC(safe_dict)
+    runObj.configure(inps, 'run_' + str(i) + "_unpack_slave_slc")
    runObj.unpackSlavesSLC(stackMasterDate, slaveDates, safe_dict)
    runObj.finalize()
   
@ -505,12 +510,14 @@ def slcStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe_dict, upd
 def correlationStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe_dict, pairs, updateStack):

    #############################
-    i = slcStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe_dict, updateStack)
+    i = slcStack(inps, acquisitionDates,stackMasterDate, slaveDates, safe_dict, updateStack)
+

    i+=1
    runObj = run()
-    runObj.configure(inps, 'run_' + str(i) + "_merge_master")
-    runObj.mergeMaster(stackMasterDate, virtual = 'False')
+    runObj.configure(inps, 'run_' + str(i) + "_merge_master_slave_slc")
+    runObj.mergeMaster(stackMasterDate, virtual = 'True')
+    runObj.mergeSlaveSLC(slaveDates, virtual = 'True')
    runObj.finalize()

    i+=1
@ -530,6 +537,13 @@ def interferogramStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe

    i = slcStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe_dict, updateStack)

+    i+=1
+    runObj = run()
+    runObj.configure(inps, 'run_' + str(i) + "_merge_master_slave_slc")
+    runObj.mergeMaster(stackMasterDate, virtual = 'True')
+    runObj.mergeSlaveSLC(slaveDates, virtual = 'True')
+    runObj.finalize()
+
    i+=1
    runObj = run()
    runObj.configure(inps, 'run_' + str(i) + "_merge_burst_igram") 
@ -548,12 +562,6 @@ def interferogramStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe
    runObj.unwrap(pairs)
    runObj.finalize()

-    i+=1
-    runObj = run()
-    runObj.configure(inps, 'run_' + str(i) + "_merge_master_slave_slc")
-    runObj.mergeMaster(stackMasterDate, virtual = 'True')
-    runObj.mergeSlaveSLC(slaveDates, virtual = 'True')
-    runObj.finalize()

 def offsetStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe_dict, pairs, updateStack):

--- a/contrib/stack/topsStack/topo.py
+++ b/contrib/stack/topsStack/topo.py
@ -10,6 +10,8 @@ import sys
 import s1a_isce_utils as ut
 from isceobj.Planet.Planet import Planet
 from zerodop.topozero import createTopozero
+import multiprocessing as mp
+

 def createParser():
    parser = argparse.ArgumentParser( description='Generates lat/lon/h and los for each pixel')
@ -30,6 +32,49 @@ def cmdLineParse(iargs=None):
    return parser.parse_args(args=iargs)


+def call_topo(input):
+
+    (dirname, demImage, master, ind) = input
+
+    burst = master.bursts[ind]
+    latname = os.path.join(dirname, 'lat_%02d.rdr' % (ind + 1))
+    lonname = os.path.join(dirname, 'lon_%02d.rdr' % (ind + 1))
+    hgtname = os.path.join(dirname, 'hgt_%02d.rdr' % (ind + 1))
+    losname = os.path.join(dirname, 'los_%02d.rdr' % (ind + 1))
+    maskname = os.path.join(dirname, 'shadowMask_%02d.rdr' % (ind + 1))
+    incname = os.path.join(dirname, 'incLocal_%02d.rdr' % (ind + 1))
+    #####Run Topo
+    planet = Planet(pname='Earth')
+    topo = createTopozero()
+    topo.slantRangePixelSpacing = burst.rangePixelSize
+    topo.prf = 1.0 / burst.azimuthTimeInterval
+    topo.radarWavelength = burst.radarWavelength
+    topo.orbit = burst.orbit
+    topo.width = burst.numberOfSamples
+    topo.length = burst.numberOfLines
+    topo.wireInputPort(name='dem', object=demImage)
+    topo.wireInputPort(name='planet', object=planet)
+    topo.numberRangeLooks = 1
+    topo.numberAzimuthLooks = 1
+    topo.lookSide = -1
+    topo.sensingStart = burst.sensingStart
+    topo.rangeFirstSample = burst.startingRange
+    topo.demInterpolationMethod = 'BIQUINTIC'
+    topo.latFilename = latname
+    topo.lonFilename = lonname
+    topo.heightFilename = hgtname
+    topo.losFilename = losname
+    topo.maskFilename = maskname
+    topo.incFilename = incname
+    topo.topo()
+
+    bbox = [topo.minimumLatitude, topo.maximumLatitude, topo.minimumLongitude, topo.maximumLongitude]
+
+    topo = None
+
+    return bbox
+
+
 def main(iargs=None):

    inps = cmdLineParse(iargs)
@ -40,6 +85,8 @@ def main(iargs=None):
    demImage.load(inps.dem + '.xml')

    boxes = []
+    inputs = []
+
    for swath in swathList:
        master =  ut.loadProduct(os.path.join(inps.master , 'IW{0}.xml'.format(swath)))
    
@ -51,50 +98,20 @@ def main(iargs=None):
        else:
            os.makedirs(dirname)

-
-    ###For each burst
        for ind in range(master.numberOfBursts):
-            burst = master.bursts[ind]
+            inputs.append((dirname, demImage, master, ind))

-            latname = os.path.join(dirname, 'lat_%02d.rdr'%(ind+1))
-            lonname = os.path.join(dirname, 'lon_%02d.rdr'%(ind+1))
-            hgtname = os.path.join(dirname, 'hgt_%02d.rdr'%(ind+1))
-            losname = os.path.join(dirname, 'los_%02d.rdr'%(ind+1))
-            maskname = os.path.join(dirname, 'shadowMask_%02d.rdr'%(ind+1))
-            incname = os.path.join(dirname, 'incLocal_%02d.rdr'%(ind+1))
-        #####Run Topo
-            planet = Planet(pname='Earth')
-            topo = createTopozero()
-            topo.slantRangePixelSpacing = burst.rangePixelSize
-            topo.prf = 1.0/burst.azimuthTimeInterval
-            topo.radarWavelength = burst.radarWavelength
-            topo.orbit = burst.orbit
-            topo.width = burst.numberOfSamples
-            topo.length = burst.numberOfLines
-            topo.wireInputPort(name='dem', object=demImage)
-            topo.wireInputPort(name='planet', object=planet)
-            topo.numberRangeLooks = 1
-            topo.numberAzimuthLooks = 1
-            topo.lookSide = -1
-            topo.sensingStart = burst.sensingStart
-            topo.rangeFirstSample = burst.startingRange
-            topo.demInterpolationMethod='BIQUINTIC'
-            topo.latFilename = latname
-            topo.lonFilename = lonname
-            topo.heightFilename = hgtname
-            topo.losFilename = losname
-            topo.maskFilename = maskname
-            topo.incFilename = incname
-            topo.topo()
+    pool = mp.Pool(mp.cpu_count())
+    results = pool.map(call_topo, inputs)
+    pool.close()

-            bbox = [topo.minimumLatitude, topo.maximumLatitude, topo.minimumLongitude, topo.maximumLongitude]
-            boxes.append(bbox)
-
-            topo = None
+    for bbox in results:
+        boxes.append(bbox)

    boxes = np.array(boxes)
    bbox = [np.min(boxes[:,0]), np.max(boxes[:,1]), np.min(boxes[:,2]), np.max(boxes[:,3])]
    print ('bbox : ',bbox)
+    

 if __name__ == '__main__':