various bugfix for topsStack (#500)

* stackSentinel: add compute arg group and simplify main()

+ createParser(): add compute sub group for more organized print out msg

+ main():
   - remove the unsed inps.workflow value checking, as it's covered in the argparse
   - move the update stack date list checking insidie selectNeighborPairs()

* topsStack/mergeBursts: bugfix for float outY/XSize and gdal

+ mergeBursts.py: bugfix for the gdal call when outY/XSize is not integer by
   - set width/height to integer
   - add srcWin argument

+ mergeBursts.py: repeat gdal.Translate call as a workaround solution to the following gdal issue:
   - ERROR 1: Input and output dataset sizes or band counts do not match in GDALDatasetCopyWholeRaster()
   - the issue happens to version 3.3.3 and 3.4, but not in 2.3

+ unwrap: bugfix for intendation inconsistency

+ invertIon: print out num of pairs/dates

+ stackSentinel:
   - sort orbit date for downloading
   - add missing stackReferenceDate arg to selectNeighborPairs() for update mode

+ README: add link to stack processor readme for quick navigation.

* bugfix by removing existing *.hdr files

+ remove existing *.hdr files, to avoid gdal error, instead of repeat the gdal func call

+ replace the gdal_translate cmd call with gdal.Translate() in python.

+ add progress_cb() from stack overflow to printout progress bar in gdal.Translate() call

README.md

@@ -42,6 +42,7 @@ TERRASARX, UAVSAR and SAOCOM1A.
    - [Running ISCE from the command line](#running-isce-from-the-command-line)
    - [Running ISCE in the Python interpreter](#running-isce-in-the-python-interpreter)
    - [Running ISCE with steps](#running-isce-with-steps)
+   - [Running ISCE stack processors](./contrib/stack/README.md)
    - [Notes on Digital Elevation Models (DEMs)](#notes-on-digital-elevation-models)
 4. [Input Files](#input-files)
 5. [Component Configurability](#component-configurability)
@@ -515,6 +516,8 @@ this mode of interacting with the pickle object to discover much about
 the workflow states and also to edit the state to see its effect
 on a subsequent run with \-\-dostep or \-\-start.
 
+### Running [ISCE stack processors](./contrib/stack/README.md)
+
 ### Notes on Digital Elevation Models
 
 - ISCE will automatically download SRTM Digital Elevation Models when you run an

contrib/stack/topsStack/invertIon.py

@@ -192,10 +192,10 @@ if __name__ == '__main__':
     else:
         dateZero = dates[0]
 
-    print('all pairs:\n{}'.format(' '.join(pairsAll)))
+    print(f'all pairs ({len(pairsAll)}):\n{pairsAll}')
-    print('all dates:\n{}'.format(' '.join(datesAll)))
+    print(f'all dates ({len(datesAll)}):\n{datesAll}')
-    print('used pairs:\n{}'.format(' '.join(pairs)))
+    print(f'used pairs ({len(pairs)}):\n{pairs}')
-    print('used dates:\n{}'.format(' '.join(dates)))
+    print(f'used dates ({len(dates)}):\n{dates}')
 
 
 ####################################################################################

contrib/stack/topsStack/mergeBursts.py

@@ -11,6 +11,7 @@ import datetime
 import logging
 import argparse
 import numpy as np
+from osgeo import gdal
 
 import isce
 import isceobj
@@ -283,51 +284,43 @@ def multilook(infile, outname=None, alks=5, rlks=15, multilook_tool="isce", no_d
     Take looks.
     '''
 
+    # default output filename
+    if outname is None:
+        spl = os.path.splitext(infile)
+        ext = '.{0}alks_{1}rlks'.format(alks, rlks)
+        outname = spl[0] + ext + spl[1]
+
     if multilook_tool=="gdal":
+        # remove existing *.hdr files, to avoid the following gdal error:
+        # ERROR 1: Input and output dataset sizes or band counts do not match in GDALDatasetCopyWholeRaster()
+        fbase = os.path.splitext(outname)[0]
+        print(f'remove {fbase}*.hdr')
+        for fname in glob.glob(f'{fbase}*.hdr'):
+            os.remove(fname)
 
-        from osgeo import gdal
+        print(f"multilooking {rlks} x {alks} using gdal for {infile} ...")
-
+        ds = gdal.Open(infile+'.vrt', gdal.GA_ReadOnly)
-        print("multi looking using gdal ...")
-        if outname is None:
-            spl = os.path.splitext(infile)
-            ext = '.{0}alks_{1}rlks'.format(alks, rlks)
-            outname = spl[0] + ext + spl[1]
-        
-        print(infile)
-        ds = gdal.Open(infile + ".vrt", gdal.GA_ReadOnly)
 
         xSize = ds.RasterXSize
         ySize = ds.RasterYSize
+        outXSize = int(xSize / int(rlks))
+        outYSize = int(ySize / int(alks))
+        srcXSize = outXSize * int(rlks)
+        srcYSize = outYSize * int(alks)
 
-        outXSize = xSize/int(rlks)
+        options_str = f'-of ENVI -outsize {outXSize} {outYSize} -srcwin 0 0 {srcXSize} {srcYSize} '
-        outYSize = ySize/int(alks)
+        options_str += f'-a_nodata {no_data}' if no_data else ''
-
+        gdal.Translate(outname, ds, options=options_str)
-        if no_data:
+        # generate VRT file
-            gdalTranslateOpts = gdal.TranslateOptions(format="ENVI", width=outXSize, height=outYSize, noData=no_data)
+        gdal.Translate(outname+".vrt", outname, options='-of VRT')
-        else:
-            gdalTranslateOpts = gdal.TranslateOptions(format="ENVI", width=outXSize, height=outYSize)
-
-        gdal.Translate(outname, ds, options=gdalTranslateOpts)       
-        ds = None
-
-        
-        ds = gdal.Open(outname, gdal.GA_ReadOnly)
-        gdal.Translate(outname+".vrt", ds, options=gdal.TranslateOptions(format="VRT"))
-        ds = None
 
     else:
         from mroipac.looks.Looks import Looks
-
+        print(f'multilooking {rlks} x {alks} using isce2 for {infile} ...')
-        print('Multilooking {0} ...'.format(infile))
 
         inimg = isceobj.createImage()
         inimg.load(infile + '.xml')
 
-        if outname is None:
-            spl = os.path.splitext(inimg.filename)
-            ext = '.{0}alks_{1}rlks'.format(alks, rlks)
-            outname = spl[0] + ext + spl[1]
-
         lkObj = Looks()
         lkObj.setDownLooks(alks)
         lkObj.setAcrossLooks(rlks)
@@ -338,6 +331,20 @@ def multilook(infile, outname=None, alks=5, rlks=15, multilook_tool="isce", no_d
     return outname
 
 
+def progress_cb(complete, message, cb_data):
+    '''Emit progress report in numbers for 10% intervals and dots for 3%
+    Link: https://stackoverflow.com/questions/68025043/adding-a-progress-bar-to-gdal-translate
+    '''
+    if int(complete*100) % 10 == 0:
+        msg = f'{complete*100:.0f}'
+        print(msg, end='', flush=True)
+        if msg == '100':
+            print(' ')
+    elif int(complete*100) % 3 == 0:
+        print(f'{cb_data}', end='', flush=True)
+
+    return
+
 
 def main(iargs=None):
     '''
@@ -408,11 +415,12 @@ def main(iargs=None):
     mergeBurstsVirtual(frames, referenceFrames, fileList, inps.outfile+suffix, validOnly=inps.validOnly)
 
     if (not virtual):
-        print('writing merged file to disk ...')
+        print('writing merged file to disk via gdal.Translate ...')
-        cmd = 'gdal_translate -of ENVI -co INTERLEAVE=BIL ' + inps.outfile + suffix + '.vrt ' + inps.outfile + suffix 
+        gdal.Translate(inps.outfile+suffix, inps.outfile+suffix+'.vrt',
-        os.system(cmd)
+                       options='-of ENVI -co INTERLEAVE=BIL',
+                       callback=progress_cb,
+                       callback_data='.')
 
-    print(inps.multilook)
     if inps.multilook:
         multilook(inps.outfile+suffix,
                   outname=inps.outfile, 

contrib/stack/topsStack/stackSentinel.py

@@ -17,7 +17,7 @@ from isceobj.Sensor.TOPS.Sentinel1 import Sentinel1
 from Stack import config, run, sentinelSLC
 
 
-helpstr= '''
+helpstr = """
 
 Stack processor for Sentinel-1 data using ISCE software.
 
@@ -73,7 +73,7 @@ stackSentinel.py -s ../SLC/ -d ../../MexicoCity/demLat_N18_N20_Lon_W100_W097.dem
 For all workflows, coregistration can be done using only geometry or with geometry plus refined azimuth offsets through NESD approach.
 Existing workflows: slc, interferogram, correlation, offset
 
-'''
+"""
 
 class customArgparseAction(argparse.Action):
     def __call__(self, parser, args, values, option_string=None):
@@ -85,7 +85,7 @@ class customArgparseAction(argparse.Action):
 
 
 def createParser():
-    parser = argparse.ArgumentParser( description='Preparing the directory structure and config files for stack processing of Sentinel data')
+    parser = argparse.ArgumentParser(description='Preparing the directory structure and config files for stack processing of Sentinel data')
 
     parser.add_argument('-H','--hh', nargs=0, action=customArgparseAction,
                         help='Display detailed help information.')
@@ -117,37 +117,33 @@ def createParser():
     parser.add_argument('-b', '--bbox', dest='bbox', type=str, default=None,
                         help="Lat/Lon Bounding SNWE. -- Example : '19 20 -99.5 -98.5' -- Default : common overlap between stack")
 
-    parser.add_argument('-t', '--text_cmd', dest='text_cmd', type=str, default='', 
+    parser.add_argument('-x', '--exclude_dates', dest='exclude_dates', type=str, default=None,
-                        help="text command to be added to the beginning of each line of the run files (default: '%(default)s'). "
-                             "Example : 'source ~/.bash_profile;'")
-
-    parser.add_argument('-x', '--exclude_dates', dest='exclude_dates', type=str, default=None, 
                         help="List of the dates to be excluded for processing. -- Example : '20141007,20141031' (default: %(default)s).")
 
-    parser.add_argument('-i', '--include_dates', dest='include_dates', type=str, default=None, 
+    parser.add_argument('-i', '--include_dates', dest='include_dates', type=str, default=None,
                         help="List of the dates to be included for processing. -- Example : '20141007,20141031' (default: %(default)s).")
 
-    parser.add_argument('--start_date', dest='startDate', type=str, default=None, 
+    parser.add_argument('--start_date', dest='startDate', type=str, default=None,
                         help='Start date for stack processing. Acquisitions before start date are ignored. '
                              'format should be YYYY-MM-DD e.g., 2015-01-23')
 
-    parser.add_argument('--stop_date', dest='stopDate', type=str, default=None, 
+    parser.add_argument('--stop_date', dest='stopDate', type=str, default=None,
                         help='Stop date for stack processing. Acquisitions after stop date are ignored. '
                              'format should be YYYY-MM-DD e.g., 2017-02-26')
 
-    parser.add_argument('-z', '--azimuth_looks', dest='azimuthLooks', type=str, default='3', 
+    parser.add_argument('-z', '--azimuth_looks', dest='azimuthLooks', type=str, default='3',
                         help='Number of looks in azimuth for interferogram multi-looking (default: %(default)s).')
 
-    parser.add_argument('-r', '--range_looks', dest='rangeLooks', type=str, default='9', 
+    parser.add_argument('-r', '--range_looks', dest='rangeLooks', type=str, default='9',
                         help='Number of looks in range for interferogram multi-looking (default: %(default)s).')
 
-    parser.add_argument('-f', '--filter_strength', dest='filtStrength', type=str, default='0.5', 
+    parser.add_argument('-f', '--filter_strength', dest='filtStrength', type=str, default='0.5',
                         help='Filter strength for interferogram filtering (default: %(default)s).')
 
-    parser.add_argument('--snr_misreg_threshold', dest='snrThreshold', type=str, default='10', 
+    parser.add_argument('--snr_misreg_threshold', dest='snrThreshold', type=str, default='10',
                         help='SNR threshold for estimating range misregistration using cross correlation (default: %(default)s).')
 
-    parser.add_argument('-p', '--polarization', dest='polarization', type=str, default='vv', 
+    parser.add_argument('-p', '--polarization', dest='polarization', type=str, default='vv',
                         help='SAR data polarization (default: %(default)s).')
 
     parser.add_argument('-C', '--coregistration', dest='coregistration', type=str, default='NESD', choices=['geometry', 'NESD'],
@@ -157,39 +153,46 @@ def createParser():
                         help='number of overlap interferograms between each date and subsequent dates used for NESD computation '
                              '(for azimuth offsets misregistration) (default: %(default)s).')
 
-    parser.add_argument('-e', '--esd_coherence_threshold', dest='esdCoherenceThreshold', type=str, default='0.85', 
+    parser.add_argument('-e', '--esd_coherence_threshold', dest='esdCoherenceThreshold', type=str, default='0.85',
                         help='Coherence threshold for estimating azimuth misregistration using enhanced spectral diversity (default: %(default)s).')
 
     parser.add_argument('-W', '--workflow', dest='workflow', type=str, default='interferogram',
                         choices=['slc', 'correlation', 'interferogram', 'offset'],
                         help='The InSAR processing workflow (default: %(default)s).')
 
-    parser.add_argument('-V', '--virtual_merge', dest='virtualMerge', type=str, default=None, choices=['True', 'False'],
+    # unwrap
-                        help='Use virtual files for the merged SLCs and geometry files.\n'
-                             'Default: True  for correlation / interferogram workflow\n'
-                             '         False for slc / offset workflow')
-
-    parser.add_argument('-useGPU', '--useGPU', dest='useGPU',action='store_true', default=False,
-                        help='Allow App to use GPU when available')
-
-    parser.add_argument('--num_proc', '--num_process', dest='numProcess', type=int, default=1,
-                        help='number of tasks running in parallel in each run file (default: %(default)s).')
-
-    parser.add_argument('--num_proc4topo', '--num_process4topo', dest='numProcess4topo', type=int, default=1,
-                        help='number of parallel processes (for topo only) (default: %(default)s).')
-
     parser.add_argument('-u', '--unw_method', dest='unwMethod', type=str, default='snaphu', choices=['icu', 'snaphu'],
                         help='Unwrapping method (default: %(default)s).')
 
     parser.add_argument('-rmFilter', '--rmFilter', dest='rmFilter', action='store_true', default=False,
                         help='Make an extra unwrap file in which filtering effect is removed')
 
-    parser.add_argument('--param_ion', dest='param_ion', type=str, default=None, 
+    # ionospheric correction
+    parser.add_argument('--param_ion', dest='param_ion', type=str, default=None,
                         help='ionosphere estimation parameter file. if provided, will do ionosphere estimation.')
 
     parser.add_argument('--num_connections_ion', dest='num_connections_ion', type=str, default = '3',
                         help='number of interferograms between each date and subsequent dates for ionosphere estimation (default: %(default)s).')
 
+    # computing
+    compute = parser.add_argument_group('Computing options')
+    compute.add_argument('-useGPU', '--useGPU', dest='useGPU',action='store_true', default=False,
+                         help='Allow App to use GPU when available')
+
+    compute.add_argument('--num_proc', '--num_process', dest='numProcess', type=int, default=1,
+                         help='number of tasks running in parallel in each run file (default: %(default)s).')
+
+    compute.add_argument('--num_proc4topo', '--num_process4topo', dest='numProcess4topo', type=int, default=1,
+                         help='number of parallel processes (for topo only) (default: %(default)s).')
+
+    compute.add_argument('-t', '--text_cmd', dest='text_cmd', type=str, default='',
+                         help="text command to be added to the beginning of each line of the run files (default: '%(default)s'). "
+                              "Example : 'source ~/.bash_profile;'")
+
+    compute.add_argument('-V', '--virtual_merge', dest='virtualMerge', type=str, default=None, choices=['True', 'False'],
+                         help='Use virtual files for the merged SLCs and geometry files.\n'
+                              'Default: True  for correlation / interferogram workflow\n'
+                              '         False for slc / offset workflow')
 
     return parser
 
@@ -213,7 +216,7 @@ def cmdLineParse(iargs = None):
 def generate_geopolygon(bbox):
     """generate shapely Polygon"""
     from shapely.geometry import Point, Polygon
-    
+
     # convert pnts to shapely polygon format
     # the order of pnts is conter-clockwise, starting from the lower ldft corner
     # the order for Point is lon,lat
@@ -221,6 +224,7 @@ def generate_geopolygon(bbox):
 
     return Polygon([(p.coords.xy[0][0], p.coords.xy[1][0]) for p in points])
 
+
 ####################################
 def get_dates(inps):
     # Given the SLC directory This function extracts the acquisition dates
@@ -249,9 +253,9 @@ def get_dates(inps):
             SAFE_files.append(str.replace(line,'\n','').strip())
 
     else:
-        SAFE_files = glob.glob(os.path.join(inps.slc_dirname,'S1*_IW_SLC*zip')) # changed to zip file by Minyan Zhong
+        SAFE_files = sorted(glob.glob(os.path.join(inps.slc_dirname, 'S1*_IW_SLC*zip'))) # changed to zip file by Minyan Zhong
         if SAFE_files == []:
-            SAFE_files = glob.glob(os.path.join(inps.slc_dirname,'S1*_IW_SLC*SAFE'))
+            SAFE_files = sorted(glob.glob(os.path.join(inps.slc_dirname, 'S1*_IW_SLC*SAFE')))
 
     if len(SAFE_files) == 0:
         raise Exception('No SAFE file found')
@@ -429,19 +433,32 @@ def get_dates(inps):
 
     return dateList, inps.reference_date, secondaryList, safe_dict
 
-def selectNeighborPairs(dateList, num_connections, updateStack=False):  # should be changed to able to account for the existed aquisitions -- Minyan Zhong
+
+def selectNeighborPairs(dateList, stackReferenceDate, secondaryDates, num_connections, updateStack=False):
+    """Select nearest neighbor acquisitions to form seqential pairs."""
 
     pairs = []
+
+    if updateStack:
+        # use the secondaryDates (new acquisitions), instead of the entire list of dates
+        print('\nUpdating an existing stack ...\n')
+        # include the reference date for pairing if it is among the most recent acquisitions
+        dateList = sorted(secondaryDates + [stackReferenceDate])[1:]
+    num_date = len(dateList)
+
+    # translate num_connections input
     if num_connections == 'all':
         num_connections = len(dateList) - 1
     else:
         num_connections = int(num_connections)
 
+    # selecting nearest pairs based on dateList and num_connections
     num_connections = num_connections + 1
-    for i in range(len(dateList)-1):
+    for i in range(num_date-1):
-        for j in range(i+1,i + num_connections):
+        for j in range(i+1, i+num_connections):
-            if j<len(dateList):
+            if j < num_date:
-                pairs.append((dateList[i],dateList[j]))
+                pairs.append((dateList[i], dateList[j]))
+    print('selecting pairs with {} nearest neighbor connections: {}'.format(num_connections-1, len(pairs)))
 
     return pairs
 
@@ -474,7 +491,7 @@ def selectNeighborPairsIonosphere(safe_dict, num_connections):
         if starting_ranges[i] not in starting_ranges_unique:
             starting_ranges_unique.append(starting_ranges[i])
     ndate_unique = len(starting_ranges_unique)
- 
+
     #put dates of same starting ranges in a list
     #result is a 2-D list, each D is sorted by date
     starting_ranges_unique_dates = [[] for i in range(ndate_unique)]
@@ -850,12 +867,9 @@ def checkCurrentStatus(inps):
         coregSLC.sort()
         if len(coregSLC)>0:
             print('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
-            print('')
+            print('\nAn existing stack with following coregistered SLCs was found:')
-            print('An existing stack with following coregistered SLCs was found:')
             print(coregSLC)
-            print('')
+            print('\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
-            print('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
-
         else:
             pass
 
@@ -863,11 +877,9 @@ def checkCurrentStatus(inps):
         newAcquisitions.sort()
         if len(newAcquisitions)>0:
             print('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
-            print('')
+            print('\nNew acquisitions was found: ')
-            print('New acquisitions was found: ')
             print(newAcquisitions)
-            print('')
+            print('\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
-            print('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
         else:
             print('         *********************************           ')
             print('                 *****************           ')
@@ -883,7 +895,6 @@ def checkCurrentStatus(inps):
 
 
         if inps.coregistration in ['NESD','nesd']:
-
             numSLCReprocess = 2*int(inps.num_overlap_connections)
             if numSLCReprocess > len(secondaryDates):
                 numSLCReprocess = len(secondaryDates)
@@ -894,7 +905,6 @@ def checkCurrentStatus(inps):
                 raise Exception('The original SAFE files for latest {0} coregistered SLCs is needed'.format(numSLCReprocess))
 
         else:  # add by Minyan Zhong, should be changed later as numSLCReprocess should be 0
-
             numSLCReprocess = int(inps.num_connections)
             if numSLCReprocess > len(secondaryDates):
                 numSLCReprocess = len(secondaryDates)
@@ -905,7 +915,6 @@ def checkCurrentStatus(inps):
                 raise Exception('The original SAFE files for latest {0} coregistered SLCs is needed'.format(numSLCReprocess))
 
         print ('Last {0} coregistred SLCs to be updated: '.format(numSLCReprocess), latestCoregSLCs)
-
         secondaryDates = latestCoregSLCs + newAcquisitions
         secondaryDates.sort()
 
@@ -941,6 +950,7 @@ def checkCurrentStatus(inps):
 
     return acquisitionDates, stackReferenceDate, secondaryDates, safe_dict, stackUpdate
 
+
 def main(iargs=None):
 
     inps = cmdLineParse(iargs)
@@ -955,29 +965,11 @@ def main(iargs=None):
         print('**************************')
         sys.exit(1)
 
-    if inps.workflow not in ['interferogram', 'offset', 'correlation', 'slc']:
-        print('')
-        print('**************************')
-        print('Error: workflow ', inps.workflow, ' is not valid.')
-        print('Please choose one of these workflows: interferogram, offset, correlation, slc')
-        print('Use argument "-W" or "--workflow" to choose a specific workflow.')
-        print('**************************')
-        print('')
-        sys.exit(1)
-
     acquisitionDates, stackReferenceDate, secondaryDates, safe_dict, updateStack = checkCurrentStatus(inps)
 
-
+    # selecting pairs for interferograms / correlation / offset workflows
-
+    if inps.workflow != 'slc':
-    if updateStack:
+        pairs = selectNeighborPairs(acquisitionDates, stackReferenceDate, secondaryDates, inps.num_connections, updateStack)
-        print('')
-        print('Updating an existing stack ...')
-        print('')
-        dates4NewPairs = sorted(secondaryDates + [stackReferenceDate])[1:]
-        pairs = selectNeighborPairs(dates4NewPairs, inps.num_connections,updateStack)   # will be change later
-    else:
-        pairs = selectNeighborPairs(acquisitionDates, inps.num_connections,updateStack)
-
 
     print ('*****************************************')
     print ('Coregistration method: ', inps.coregistration )
@@ -1007,6 +999,5 @@ def main(iargs=None):
 
 
 if __name__ == "__main__":
-
   # Main engine
   main(sys.argv[1:])

contrib/stack/topsStack/unwrap.py

@@ -211,7 +211,7 @@ def runUnwrap(infile, outfile, corfile, config, costMode = None,initMethod = Non
     outImage.setWidth(width)
     outImage.setLength(length)
     outImage.setAccessMode('read')
-   # outImage.createImage()
+    # outImage.createImage()
     outImage.renderHdr()
     outImage.renderVRT()
     #outImage.finalizeImage()
@@ -225,10 +225,10 @@ def runUnwrap(infile, outfile, corfile, config, costMode = None,initMethod = Non
         connImage.setLength(length)
         connImage.setAccessMode('read')
         connImage.setDataType('BYTE')
-    #    connImage.createImage()
+        # connImage.createImage()
         connImage.renderHdr()
         connImage.renderVRT()
-     #   connImage.finalizeImage()
+        # connImage.finalizeImage()
 
     return
 
@@ -241,15 +241,9 @@ def runUnwrapMcf(infile, outfile, corfile, config, defomax=2):
 def runUnwrapIcu(infile, outfile):
     from mroipac.icu.Icu import Icu
     #Setup images
-    #ampImage
-   # ampImage = obj.insar.resampAmpImage.copy(access_mode='read')
-   # width = self.ampImage.getWidth()
-
     img = isceobj.createImage()
     img.load(infile + '.xml')
-
+    width = img.getWidth()
-
-    width      = img.getWidth()
 
     #intImage
     intImage = isceobj.createIntImage()
@@ -329,21 +323,20 @@ def main(iargs=None):
         else:
             fncall = runUnwrapMcf
         swathList = ut.getSwathList(inps.reference) 
-        #metadata = extractInfo(inps.reference+'.xml', inps)
         xmlFile = os.path.join(inps.reference , 'IW{0}.xml'.format(swathList[0]))
         metadata = extractInfo(xmlFile, inps)
         fncall(inps.intfile, inps.unwfile, inps.cohfile, metadata, defomax=inps.defomax)
 
-       #mask out wired values from snaphu
+        #mask out wired values from snaphu
-       intImage = isceobj.createImage()
+        intImage = isceobj.createImage()
-       intImage.load(inps.intfile+'.xml')
+        intImage.load(inps.intfile+'.xml')
-       width = intImage.width
+        width = intImage.width
-       length = intImage.length
+        length = intImage.length
 
-       flag = np.fromfile(inps.intfile, dtype=np.complex64).reshape(length, width)
+        flag = np.fromfile(inps.intfile, dtype=np.complex64).reshape(length, width)
-       unw=np.memmap(inps.unwfile, dtype='float32', mode='r+', shape=(length*2, width))
+        unw=np.memmap(inps.unwfile, dtype='float32', mode='r+', shape=(length*2, width))
-       (unw[0:length*2:2, :])[np.nonzero(flag==0)]=0
+        (unw[0:length*2:2, :])[np.nonzero(flag==0)]=0
-       (unw[1:length*2:2, :])[np.nonzero(flag==0)]=0
+        (unw[1:length*2:2, :])[np.nonzero(flag==0)]=0
 
     elif inps.method == 'icu':
         runUnwrapIcu(inps.intfile, inps.unwfile)