Merge branch 'master' of https://github.com/isce-framework/isce2 into UAVSAR

SConstruct

@@ -216,43 +216,12 @@ else:
 ### End of GPU branch-specific modifications
 
 
-file = '__init__.py'
-if not os.path.exists(file):
-    fout = open(file,"w")
-    fout.write("#!/usr/bin/env python3")
-    fout.close()
-
-env.Install(inst,file)
-try:
-    from subprocess import check_output
-    svn_revision = check_output('svnversion').strip() or 'Unknown'
-    if sys.version_info[0] == 3:
-        svn_revision = svn_revision.decode('utf-8')
-except ImportError:
-    try:
-        import popen2
-        stdout, stdin, stderr = popen2.popen3('svnversion')
-        svn_revision = stdout.read().strip()
-        if stderr.read():
-            raise Exception
-    except Exception:
-        svn_revision = 'Unknown'
-except OSError:
-    svn_revision = 'Unknown'
+env.Install(inst, '__init__.py')
+env.Install(inst, 'release_history.py')
 
 if not os.path.exists(inst):
     os.makedirs(inst)
 
-fvers = open(os.path.join(inst,'version.py'),'w')
-
-from release_history import release_version, release_svn_revision, release_date
-fvers_lines = ["release_version = '"+release_version+"'\n",
-               "release_svn_revision = '"+release_svn_revision+"'\n",
-               "release_date = '"+release_date+"'\n",
-               "svn_revision = '"+svn_revision+"'\n\n"]
-
-fvers.write(''.join(fvers_lines))
-fvers.close()
 v = 0
 if isrerun == 'no':
     cmd = 'scons -Q install --isrerun=yes'

__init__.py

@@ -25,13 +25,9 @@
 # Author: Giangi Sacco
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-
-
-
-from __future__ import print_function
-
-from .version import release_version, release_svn_revision, release_date
-from .version import svn_revision
+from .release_history import release_version, release_svn_revision, release_date
+svn_revision = release_svn_revision
+version = release_history # compatibility alias
 
 __version__ = release_version
 

components/isceobj/StripmapProc/runDispersive.py

@@ -9,7 +9,6 @@ from isceobj.Constants import SPEED_OF_LIGHT
 import numpy as np
 import gdal
 
-from scipy import ndimage
 try:
     import cv2
 except ImportError:
@@ -296,6 +295,8 @@ 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,

components/isceobj/StripmapProc/runResampleSlc.py

@@ -75,6 +75,7 @@ def runResampleSlc(self, kind='coarse'):
     if kind in ['coarse', 'refined']:
         azname = os.path.join(offsetsDir, self.insar.azimuthOffsetFilename)
         rgname = os.path.join(offsetsDir, self.insar.rangeOffsetFilename)
+        flatten = True
     else:
         azname = os.path.join(offsetsDir, self.insar.azimuthRubbersheetFilename)
         if self.doRubbersheetingRange:

components/isceobj/StripmapProc/runRubbersheet.py

@@ -6,7 +6,6 @@
 import isce
 import isceobj
 from osgeo import gdal
-from scipy import ndimage
 import numpy as np
 import os
 
@@ -24,6 +23,9 @@ 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,
@@ -35,6 +37,8 @@ def fill(data, invalid=None):
 def mask_filter(denseOffsetFile, snrFile, band, snrThreshold, filterSize, outName):
     #masking and Filtering
 
+    from scipy import ndimage
+
     ##Read in the offset file
     ds = gdal.Open(denseOffsetFile + '.vrt', gdal.GA_ReadOnly)
     Offset = ds.GetRasterBand(1).ReadAsArray()

components/isceobj/StripmapProc/runRubbersheetAzimuth.py

@@ -9,14 +9,14 @@
 import isce
 import isceobj
 from osgeo import gdal
-from scipy import ndimage
-from astropy.convolution import convolve
 import numpy as np
 import os
 
 def mask_filterNoSNR(denseOffsetFile,filterSize,outName):
     # Masking the offsets with a data-based approach
-    
+
+    from scipy import ndimage
+
     # Open the offsets
     ds = gdal.Open(denseOffsetFile+'.vrt',gdal.GA_ReadOnly)
     off_az = ds.GetRasterBand(1).ReadAsArray()
@@ -79,6 +79,9 @@ def mask_filterNoSNR(denseOffsetFile,filterSize,outName):
 
 
 def off_masking(off,filterSize,thre=2):
+
+    from scipy import ndimage
+
     # Define the mask to fill the offsets
     vram = ndimage.median_filter(off.real, filterSize)
     vazm = ndimage.median_filter(off.imag, filterSize)
@@ -112,6 +115,8 @@ def fill(data, invalid=None):
 def mask_filter(denseOffsetFile, snrFile, band, snrThreshold, filterSize, outName):
     #masking and Filtering
 
+    from scipy import ndimage
+
     ##Read in the offset file
     ds = gdal.Open(denseOffsetFile + '.vrt', gdal.GA_ReadOnly)
     Offset = ds.GetRasterBand(band).ReadAsArray()
@@ -154,7 +159,9 @@ def mask_filter(denseOffsetFile, snrFile, band, snrThreshold, filterSize, outNam
     return None
 
 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

components/isceobj/StripmapProc/runRubbersheetRange.py

@@ -9,15 +9,14 @@
 import isce
 import isceobj
 from osgeo import gdal
-from scipy import ndimage
 import numpy as np
 import os
-from astropy.convolution import convolve
-
 
 def mask_filterNoSNR(denseOffsetFile,filterSize,outName):
     # Masking the offsets with a data-based approach
-    
+
+    from scipy import ndimage
+
     # Open the offsets
     ds = gdal.Open(denseOffsetFile+'.vrt',gdal.GA_ReadOnly)
     off_az = ds.GetRasterBand(1).ReadAsArray()
@@ -78,6 +77,9 @@ def mask_filterNoSNR(denseOffsetFile,filterSize,outName):
     return 
 
 def off_masking(off,filterSize,thre=2):
+
+    from scipy import ndimage
+
     vram = ndimage.median_filter(off.real, filterSize)
     vazm = ndimage.median_filter(off.imag, filterSize)
 
@@ -100,6 +102,8 @@ 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,
@@ -108,7 +112,9 @@ def fill(data, invalid=None):
     return data[tuple(ind)]
 
 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
@@ -131,6 +137,8 @@ def fill_with_smoothed(off,filterSize):
 def mask_filter(denseOffsetFile, snrFile, band, snrThreshold, filterSize, outName):
     #masking and Filtering
 
+    from scipy import ndimage
+
     ##Read in the offset file
     ds = gdal.Open(denseOffsetFile + '.vrt', gdal.GA_ReadOnly)
     Offset = ds.GetRasterBand(band).ReadAsArray()
@@ -236,6 +244,8 @@ def resampleOffset(maskedFiltOffset, geometryOffset, outName):
 
 def runRubbersheetRange(self):
 
+    from scipy import ndimage
+
     if not self.doRubbersheetingRange:
         print('Rubber sheeting in azimuth not requested ... skipping')
         return

components/isceobj/TopsProc/runIon.py

@@ -9,9 +9,6 @@ import shutil
 import datetime
 import numpy as np
 import numpy.matlib
-import scipy.signal as ss
-from scipy import interpolate
-from scipy.interpolate import interp1d
 
 import isceobj
 import logging
@@ -638,6 +635,7 @@ def cal_coherence(inf, win=5, edge=0):
 
           4: keep all samples
     '''
+    import scipy.signal as ss
 
     if win % 2 != 1:
         raise Exception('window size must be odd!')
@@ -1682,6 +1680,9 @@ def computeDopplerOffset(burst, firstline, lastline, firstcolumn, lastcolumn, nr
 
     output: first lines > 0, last lines < 0
     '''
+    from scipy import interpolate
+    from scipy.interpolate import interp1d
+
     Vs = np.linalg.norm(burst.orbit.interpolateOrbit(burst.sensingMid, method='hermite').getVelocity())
     Ks =   2 * Vs * burst.azimuthSteeringRate / burst.radarWavelength 
 
@@ -1830,6 +1831,7 @@ def adaptive_gaussian(ionos, wgt, size_max, size_min):
     size_max: maximum window size
     size_min: minimum window size
     '''
+    import scipy.signal as ss
 
     length = (ionos.shape)[0]
     width = (ionos.shape)[1]
@@ -1892,6 +1894,8 @@ def filt_gaussian(self, ionParam):
     currently not implemented.
     a less accurate method is to use ionsphere without any projection
     '''
+    from scipy import interpolate
+    from scipy.interpolate import interp1d
 
     #################################################
     #SET PARAMETERS HERE
@@ -2659,5 +2663,3 @@ def runIon(self):
     #esd_noion(self, ionParam)
 
     return
-
-    

components/isceobj/TopsProc/runOffsetFilter.py

@@ -3,7 +3,6 @@
 # Copyright 2016
 #
 
-from scipy.ndimage.filters import median_filter
 import numpy as np
 import isce
 import isceobj
@@ -20,6 +19,8 @@ def runOffsetFilter(self):
     if not self.doDenseOffsets:
         return
 
+    from scipy.ndimage.filters import median_filter
+
     offsetfile = os.path.join(self._insar.mergedDirname, self._insar.offsetfile) 
     snrfile = os.path.join(self._insar.mergedDirname, self._insar.snrfile)
     print('\n======================================')

components/isceobj/TopsProc/runPrepESD.py

@@ -8,7 +8,6 @@ import numpy as np
 import os
 import isceobj
 import logging
-import scipy.signal as SS
 from isceobj.Util.ImageUtil import ImageLib as IML
 import datetime
 import pprint
@@ -177,6 +176,7 @@ def createCoherence(intfile, win=5):
     '''
     Compute coherence using scipy convolve 2D.
     '''
+    import scipy.signal as SS
 
     corfile = os.path.splitext(intfile)[0] + '.cor'
     filt = np.ones((win,win))/ (1.0*win*win)

contrib/stack/stripmapStack/Stack.py

@@ -197,6 +197,8 @@ class config(object):
         self.f.write('nomcf : ' + self.noMCF + '\n')
         self.f.write('master : ' + self.master + '\n')
         self.f.write('defomax : ' + self.defoMax + '\n')
+        self.f.write('alks : ' + self.alks + '\n')
+        self.f.write('rlks : ' + self.rlks + '\n')
         self.f.write('method : ' + self.unwMethod + '\n')
         self.f.write('##########################'+'\n')
 

contrib/stack/stripmapStack/unwrap.py

@@ -113,9 +113,19 @@ def extractInfoFromPickle(pckfile, inps):
     data['earthRadius'] = elp.local_radius_of_curvature(llh.lat, hdg)
     
     #azspacing  = burst.azimuthTimeInterval * sv.getScalarVelocity()
-    azres = 20.0 
+    #azres = 20.0 
+    azspacing = sv.getScalarVelocity() / burst.PRF
+    azres = burst.platform.antennaLength / 2.0
+    azfact = azres / azspacing
+
+    burst.getInstrument()
+    rgBandwidth = burst.instrument.pulseLength * burst.instrument.chirpSlope
+    rgres = abs(SPEED_OF_LIGHT / (2.0 * rgBandwidth))
+    rgspacing = burst.instrument.rangePixelSize
+    rgfact = rgres / rgspacing
 
     #data['corrlooks'] = inps.rglooks * inps.azlooks * azspacing / azres
+    data['corrlooks'] = inps.rglooks * inps.azlooks / (azfact * rgfact)
     data['rglooks'] = inps.rglooks
     data['azlooks'] = inps.azlooks
 
@@ -149,7 +159,7 @@ def runUnwrap(infile, outfile, corfile, config, costMode = None,initMethod = Non
     altitude   = config['altitude']
     rangeLooks = config['rglooks']
     azimuthLooks = config['azlooks']
-    #corrLooks = config['corrlooks']
+    corrLooks = config['corrlooks']
     maxComponents = 20
 
     snp = Snaphu()
@@ -163,7 +173,7 @@ def runUnwrap(infile, outfile, corfile, config, costMode = None,initMethod = Non
     snp.setAltitude(altitude)
     snp.setCorrfile(corfile)
     snp.setInitMethod(initMethod)
-   # snp.setCorrLooks(corrLooks)
+    snp.setCorrLooks(corrLooks)
     snp.setMaxComponents(maxComponents)
     snp.setDefoMaxCycles(defomax)
     snp.setRangeLooks(rangeLooks)
@@ -248,33 +258,34 @@ def runUnwrapIcu(infile, outfile):
     unwImage.finalizeImage()
     unwImage.renderHdr()
 
-def runUnwrap2Stage(unwrappedIntFilename,connectedComponentsFilename,unwrapped2StageFilename, unwrapper_2stage_name=None, solver_2stage=None):                                                                                            
+def runUnwrap2Stage(unwrappedIntFilename,connectedComponentsFilename,unwrapped2StageFilename,
+                    unwrapper_2stage_name=None, solver_2stage=None):
   
-      if unwrapper_2stage_name is None:
-          unwrapper_2stage_name = 'REDARC0'
-  
-      if solver_2stage is None:
-          # If unwrapper_2state_name is MCF then solver is ignored
-          # and relaxIV MCF solver is used by default
-          solver_2stage = 'pulp'
-  
-      print('Unwrap 2 Stage Settings:')
-      print('Name: %s'%unwrapper_2stage_name)
-      print('Solver: %s'%solver_2stage)
-  
-      inpFile = unwrappedIntFilename
-      ccFile  = connectedComponentsFilename
-      outFile = unwrapped2StageFilename
-  
-      # Hand over to 2Stage unwrap
-      unw = UnwrapComponents()
-      unw.setInpFile(inpFile)
-      unw.setConnCompFile(ccFile)
-      unw.setOutFile(outFile)
-      unw.setSolver(solver_2stage)
-      unw.setRedArcs(unwrapper_2stage_name)
-      unw.unwrapComponents()
-      return
+    if unwrapper_2stage_name is None:
+        unwrapper_2stage_name = 'REDARC0'
+
+    if solver_2stage is None:
+        # If unwrapper_2state_name is MCF then solver is ignored
+        # and relaxIV MCF solver is used by default
+        solver_2stage = 'pulp'
+
+    print('Unwrap 2 Stage Settings:')
+    print('Name: %s'%unwrapper_2stage_name)
+    print('Solver: %s'%solver_2stage)
+
+    inpFile = unwrappedIntFilename
+    ccFile  = connectedComponentsFilename
+    outFile = unwrapped2StageFilename
+
+    # Hand over to 2Stage unwrap
+    unw = UnwrapComponents()
+    unw.setInpFile(inpFile)
+    unw.setConnCompFile(ccFile)
+    unw.setOutFile(outFile)
+    unw.setSolver(solver_2stage)
+    unw.setRedArcs(unwrapper_2stage_name)
+    unw.unwrapComponents()
+    return
 
 
 def main(iargs=None):
@@ -293,24 +304,26 @@ def main(iargs=None):
 
     if inps.method != 'icu':
     
-       masterShelveDir = os.path.join(interferogramDir , 'masterShelve')
-       if not os.path.exists(masterShelveDir):
-          os.makedirs(masterShelveDir)
+        masterShelveDir = os.path.join(interferogramDir , 'masterShelve')
+        if not os.path.exists(masterShelveDir):
+            os.makedirs(masterShelveDir)
+
+        inps.master = os.path.dirname(inps.master)
+        cpCmd='cp ' + os.path.join(inps.master, 'data*') +' '+masterShelveDir
+        os.system(cpCmd)
+        pckfile = os.path.join(masterShelveDir,'data')
+        print(pckfile)
+        metadata = extractInfoFromPickle(pckfile, inps)
 
-       inps.master = os.path.dirname(inps.master)
-       cpCmd='cp ' + os.path.join(inps.master, 'data*') +' '+masterShelveDir
-       os.system(cpCmd)
-       pckfile = os.path.join(masterShelveDir,'data')
-       print(pckfile)
-       metadata = extractInfoFromPickle(pckfile, inps)
     ########
     print ('unwrapping method : ' , inps.method)
     if inps.method == 'snaphu':
-       if inps.nomcf: 
-           fncall =  runUnwrap
-       else:
-           fncall = runUnwrapMcf
-       fncall(inps.intfile, inps.unwprefix + '_snaphu.unw', inps.cohfile, metadata, defomax=inps.defomax)
+        if inps.nomcf: 
+            fncall =  runUnwrap
+        else:
+            fncall = runUnwrapMcf
+        fncall(inps.intfile, inps.unwprefix + '_snaphu.unw', inps.cohfile, metadata, defomax=inps.defomax)
+
     elif inps.method == 'snaphu2stage':
         if inps.nomcf: 
             fncall =  runUnwrap
@@ -319,11 +332,12 @@ def main(iargs=None):
         fncall(inps.intfile, inps.unwprefix + '_snaphu.unw', inps.cohfile, metadata, defomax=inps.defomax)
 
         # adding in the two-stage
-        runUnwrap2Stage(inps.unwprefix + '_snaphu.unw', inps.unwprefix + '_snaphu.unw.conncomp',inps.unwprefix + '_snaphu2stage.unw')
-
+        runUnwrap2Stage(inps.unwprefix + '_snaphu.unw',
+                        inps.unwprefix + '_snaphu.unw.conncomp',
+                        inps.unwprefix + '_snaphu2stage.unw')
 
     elif inps.method == 'icu':
-       runUnwrapIcu(inps.intfile, inps.unwprefix + '_icu.unw')
+        runUnwrapIcu(inps.intfile, inps.unwprefix + '_icu.unw')
 
 
 if __name__ == '__main__':

examples/input_files/stripmapApp.xml

@@ -12,7 +12,8 @@
         <value>/Users/fattahi/process/test_roiApp/Alos_Maule_T116/demLat_S39_S35_Lon_W074_W071.dem.wgs84</value>
     </property>
     <!--
-    <property name="do rubbersheeting">True</property>
+      <property name="do rubbersheetingAzimuth">True</property>
+      <property name="do rubbersheetingRange">False</property>
     -->
     <property name="do denseoffsets">True</property>
     <property name="do split spectrum">True</property>