Merge pull request #113 from mirzaees/stack_runfiles

Stack runfiles

contrib/stack/topsStack/Stack.py

@@ -223,6 +223,7 @@ class config(object):
         self.f.write('defomax : ' + self.defoMax + '\n')
         self.f.write('rlks : ' + self.rangeLooks + '\n')
         self.f.write('alks : ' + self.azimuthLooks + '\n')
+        self.f.write('rmfilter : ' + self.rmFilter + '\n')
         self.f.write('method : ' + self.unwMethod + '\n')
 
     def unwrapSnaphu(self, function):
@@ -282,7 +283,7 @@ class run(object):
         os.makedirs(self.config_path, exist_ok=True)
 
         for slcdate in acquisitionDates:
-            configName = os.path.join(self.config_path,'config_'+slcdate)
+            configName = os.path.join(self.config_path,'config_unpack_'+slcdate)
             configObj = config(configName)
             configObj.configure(self)
             configObj.dirName = safe_dict[slcdate].safe_file
@@ -377,11 +378,15 @@ class run(object):
 
         self.runf.write(self.text_cmd + 'subsetMaster.py -m ' + os.path.join(self.work_dir, 'master') + ' -g ' + os.path.join(self.work_dir, 'geom_master') + '\n')
 
-    def overlap_geo2rdr_resample(self, slaveList):
+
+    def geo2rdr_offset(self, slaveList, fullBurst='False'):
 
         for slave in slaveList:
             master = self.master_date
-            configName = os.path.join(self.config_path ,'config_resamp_overlap_'+slave)
+            if fullBurst == 'True':
+                configName = os.path.join(self.config_path, 'config_fullBurst_geo2rdr_' + slave)
+            else:
+                configName = os.path.join(self.config_path, 'config_overlap_geo2rdr_'+slave)
             ###########
             configObj = config(configName)
             configObj.configure(self)
@@ -389,13 +394,39 @@ class run(object):
             configObj.masterDir = os.path.join(self.work_dir, 'master')
             configObj.geom_master = os.path.join(self.work_dir, 'geom_master')
             configObj.coregSlaveDir = os.path.join(self.work_dir, 'coreg_slaves/'+slave)
+            if fullBurst == 'True':
+                configObj.misreg_az = os.path.join(self.work_dir, 'misreg/azimuth/dates/' + slave + '.txt')
+                configObj.misreg_rng = os.path.join(self.work_dir, 'misreg/range/dates/' + slave + '.txt')
+                configObj.overlapTrueOrFalse = 'False'
+            else:
                 configObj.overlapTrueOrFalse = 'True'
             configObj.geo2rdr('[Function-1]')
+            configObj.finalize()
+            del configObj
+            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
+
+    def resample_with_carrier(self, slaveList, fullBurst='False'):
+        for slave in slaveList:
+            master = self.master_date
+            if fullBurst == 'True':
+                configName = os.path.join(self.config_path, 'config_fullBurst_resample_' + slave)
+            else:
+                configName = os.path.join(self.config_path, 'config_overlap_resample_' + slave)
             ###########
+            configObj = config(configName)
+            configObj.configure(self)
+            configObj.slaveDir = os.path.join(self.work_dir, 'slaves/' + slave)
+            configObj.masterDir = os.path.join(self.work_dir, 'master')
+            configObj.coregSlaveDir = os.path.join(self.work_dir, 'coreg_slaves/' + slave)
             configObj.interferogram_prefix = 'coarse'
-            configObj.masterDir = os.path.join(self.work_dir,'master')
+            configObj.masterDir = os.path.join(self.work_dir, 'master')
-            configObj.resamp_withCarrier('[Function-2]')
+            if fullBurst == 'True':
-            ###########
+                configObj.misreg_az = os.path.join(self.work_dir, 'misreg/azimuth/dates/' + slave + '.txt')
+                configObj.misreg_rng = os.path.join(self.work_dir, 'misreg/range/dates/' + slave + '.txt')
+                configObj.overlapTrueOrFalse = 'False'
+            else:
+                configObj.overlapTrueOrFalse = 'True'
+            configObj.resamp_withCarrier('[Function-1]')
             configObj.finalize()
             del configObj
             self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
@@ -453,37 +484,13 @@ class run(object):
         self.runf.write(self.text_cmd + 'invertMisreg.py -i ' + os.path.join(self.work_dir,'misreg/azimuth/pairs/') + ' -o ' + os.path.join(self.work_dir,'misreg/azimuth/dates/') + '\n')
         self.runf.write(self.text_cmd + 'invertMisreg.py -i ' + os.path.join(self.work_dir,'misreg/range/pairs/') + ' -o ' + os.path.join(self.work_dir,'misreg/range/dates/') + '\n')
 
-    def geo2rdr_resample(self, slaveList):
-        # geometry offsets and resampling each full burst slave SLC
-        for slave in slaveList:
-            master = self.master_date
-            configName = os.path.join(self.config_path , 'config_resamp_' + slave)
-            ###########
-            configObj = config(configName)
-            configObj.configure(self)
-            configObj.slaveDir = os.path.join(self.work_dir, 'slaves/' + slave)
-            configObj.masterDir = os.path.join(self.work_dir, 'master')
-            configObj.geom_master = os.path.join(self.work_dir, 'geom_master')
-            configObj.coregSlaveDir = os.path.join(self.work_dir, 'coreg_slaves/' + slave)
-            configObj.misreg_az = os.path.join(self.work_dir, 'misreg/azimuth/dates/' + slave + '.txt')
-            configObj.misreg_rng = os.path.join(self.work_dir, 'misreg/range/dates/' + slave + '.txt')
-            configObj.overlapTrueOrFalse = 'False'
-            configObj.geo2rdr('[Function-1]')
-            ###########
-            configObj.interferogram_prefix = 'coarse'
-            configObj.masterDir = os.path.join(self.work_dir, 'master')
-            configObj.resamp_withCarrier('[Function-2]')
-            ###########
-            configObj.finalize()
-            del configObj
-            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
-
     def extractStackValidRegion(self):
         masterDir = os.path.join(self.work_dir, 'master')
         coregSlaveDir = os.path.join(self.work_dir, 'coreg_slaves')
         self.runf.write(self.text_cmd + 'extractCommonValidRegion.py -m ' + masterDir + ' -s ' + coregSlaveDir + '\n')
 
-    def burstIgram_mergeBurst(self, dateList, safe_dict, pairs):
+    def generate_burstIgram(self, dateList, safe_dict, pairs):
+
         for date in dateList:
             safe_dict[date].slc = os.path.join(self.work_dir, 'coreg_slaves/'+date)
         safe_dict[self.master_date].slc = os.path.join(self.work_dir , 'master')
@@ -491,8 +498,7 @@ class run(object):
             master = pair[0]
             slave = pair[1]
             interferogramDir = os.path.join(self.work_dir, 'interferograms/' + master + '_' + slave)
-            mergedDir = os.path.join(self.work_dir, 'merged/interferograms/' + master + '_' + slave)
+            configName = os.path.join(self.config_path ,'config_generate_igram_' + master + '_' + slave)
-            configName = os.path.join(self.config_path ,'config_igram_' + master + '_' + slave)
             configObj = config(configName)
             configObj.configure(self)
             configObj.masterDir = safe_dict[master].slc
@@ -502,9 +508,26 @@ class run(object):
             configObj.flatten = 'False'
             configObj.overlapTrueOrFalse = 'False'
             configObj.generateIgram('[Function-1]')
+            configObj.finalize()
+            del configObj
 
-            configObj.master = configObj.interferogramDir
+            self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
-            configObj.dirName = configObj.master
+
+    def igram_mergeBurst(self, dateList, safe_dict, pairs):
+        for date in dateList:
+            safe_dict[date].slc = os.path.join(self.work_dir, 'coreg_slaves/'+date)
+        safe_dict[self.master_date].slc = os.path.join(self.work_dir , 'master')
+        for pair in pairs:
+            master = pair[0]
+            slave = pair[1]
+            interferogramDir = os.path.join(self.work_dir, 'interferograms/' + master + '_' + slave)
+            mergedDir = os.path.join(self.work_dir, 'merged/interferograms/' + master + '_' + slave)
+            configName = os.path.join(self.config_path ,'config_merge_igram_' + master + '_' + slave)
+            configObj = config(configName)
+            configObj.configure(self)
+            configObj.interferogram_prefix = 'fine'
+            configObj.master = interferogramDir
+            configObj.dirName = interferogramDir
             configObj.namePattern = 'fine*int'
             configObj.mergedFile = mergedDir + '/' + configObj.interferogram_prefix + '.int'
             configObj.mergeBurstsMethod = 'top'
@@ -513,7 +536,7 @@ class run(object):
             configObj.useVirtualFiles = 'True'
             configObj.multiLook = 'True'
             configObj.stack = os.path.join(self.work_dir, 'stack')
-            configObj.mergeBurst('[Function-2]')
+            configObj.mergeBurst('[Function-1]')
             configObj.finalize()
             del configObj
 
@@ -657,6 +680,7 @@ class run(object):
             configObj.cohName = os.path.join(mergedDir,'filt_fine.cor')
             configObj.unwName = os.path.join(mergedDir,'filt_fine.unw')
             configObj.noMCF = noMCF
+            configObj.rmFilter = self.rmFilter
             configObj.master = os.path.join(self.work_dir,'master')
             configObj.defoMax = defoMax
             configObj.unwMethod = self.unwMethod

contrib/stack/topsStack/stackSentinel.py

@@ -162,6 +162,9 @@ def createParser():
     parser.add_argument('-useGPU', '--useGPU', dest='useGPU',action='store_true', default=False,
         help='Allow App to use GPU when available')
 
+    parser.add_argument('-rmFilter', '--rmFilter', dest='rmFilter', action='store_true', default=False,
+                        help='Make an extra unwrap file in which filtering effect is removed')
+
     return parser
 
 def cmdLineParse(iargs = None):
@@ -457,10 +460,16 @@ def slcStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe_dict, upd
             runObj.extractOverlaps()
             runObj.finalize()
 
-        i+=1
+        i += 1
         runObj = run()
-        runObj.configure(inps, 'run_' + str(i) + "_overlap_geo2rdr_resample")
+        runObj.configure(inps, 'run_' + str(i) + "_overlap_geo2rdr")
-        runObj.overlap_geo2rdr_resample(slaveDates)
+        runObj.geo2rdr_offset(slaveDates)
+        runObj.finalize()
+
+        i += 1
+        runObj = run()
+        runObj.configure(inps, 'run_' + str(i) + "_overlap_resample")
+        runObj.resample_with_carrier(slaveDates)
         runObj.finalize()
 
         i+=1
@@ -478,10 +487,16 @@ def slcStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe_dict, upd
         runObj.timeseries_misregistration()
         runObj.finalize()
 
-    i+=1
+    i += 1
     runObj = run()
-    runObj.configure(inps, 'run_' + str(i) + "_geo2rdr_resample")
+    runObj.configure(inps, 'run_' + str(i) + "_fullBurst_geo2rdr")
-    runObj.geo2rdr_resample(slaveDates)
+    runObj.geo2rdr_offset(slaveDates, fullBurst='True')
+    runObj.finalize()
+
+    i += 1
+    runObj = run()
+    runObj.configure(inps, 'run_' + str(i) + "_fullBurst_resample")
+    runObj.resample_with_carrier(slaveDates, fullBurst='True')
     runObj.finalize()
 
     i+=1
@@ -546,8 +561,14 @@ def interferogramStack(inps, acquisitionDates, stackMasterDate, slaveDates, safe
 
     i+=1
     runObj = run()
+    runObj.configure(inps, 'run_' + str(i) + "_generate_burst_igram")
+    runObj.generate_burstIgram(acquisitionDates, safe_dict, pairs)
+    runObj.finalize()
+
+    i += 1
+    runObj = run()
     runObj.configure(inps, 'run_' + str(i) + "_merge_burst_igram")
-    runObj.burstIgram_mergeBurst(acquisitionDates, safe_dict, pairs)
+    runObj.igram_mergeBurst(acquisitionDates, safe_dict, pairs)
     runObj.finalize()
 
     i+=1

contrib/stack/topsStack/unwrap.py

@@ -38,9 +38,11 @@ from isceobj.Constants import SPEED_OF_LIGHT
 import argparse
 import os
 import pickle
-import sys
+import gdal
+import numpy as np
 #import shelve
 import s1a_isce_utils as ut
+from isceobj.Util.ImageUtil import ImageLib as IML
 
 def createParser():
     '''
@@ -70,6 +72,9 @@ def createParser():
     parser.add_argument('-m', '--method', dest='method', type=str, default='icu',
             help='unwrapping method')
 
+    parser.add_argument('--rmfilter', action='store_true', default=False,
+            help='remove the effect of filtering from final unwrapped interferograms')
+
     return parser
 
 
@@ -276,14 +281,48 @@ def runUnwrapIcu(infile, outfile):
     #unwImage.finalizeImage()
     unwImage.renderHdr()
 
+
+def remove_filter(intfile, filtfile, unwfile):
+
+    outunw = os.path.abspath(unwfile).split('filt_')
+    outunw = outunw[0] + outunw[1]
+
+    ds_unw = gdal.Open(unwfile + ".vrt", gdal.GA_ReadOnly)
+    width = ds_unw.RasterXSize
+    length = ds_unw.RasterYSize
+
+    unw_phase = np.memmap(unwfile, dtype='f', mode='r', shape=(2, length, width))
+    filt_phase = np.memmap(filtfile, dtype='f', mode='r', shape=(length, width))
+    int_phase = np.memmap(intfile, dtype='f', mode='r', shape=(length, width))
+
+    outfile = np.memmap(outunw, dtype='f', mode='w+', shape=(2, length, width))
+
+    for line in range(length):
+        integer_jumps = unw_phase[1, line, :] - np.angle(filt_phase[line, :])
+        outfile[1, line, :] = integer_jumps + np.angle(int_phase[line, :])
+        outfile[0, line, :] = unw_phase[0, line, :]
+    
+    unwImage = isceobj.Image.createImage()
+    unwImage.setFilename(outunw)
+    unwImage.setWidth(width)
+    unwImage.setLength(length)
+    unwImage.imageType = 'unw'
+    unwImage.bands = 2
+    unwImage.scheme = 'BIL'
+    unwImage.dataType = 'FLOAT'
+    unwImage.setAccessMode('read')
+    unwImage.renderHdr()
+
+    return
+
 def main(iargs=None):
     '''
     The main driver.
     '''
 
     inps = cmdLineParse(iargs)
-    interferogramDir = os.path.dirname(inps.intfile)
     print ('unwrapping method : ' , inps.method)
+    
     if inps.method == 'snaphu':
        if inps.nomcf: 
            fncall =  runUnwrap
@@ -298,6 +337,13 @@ def main(iargs=None):
     elif inps.method == 'icu':
        runUnwrapIcu(inps.intfile, inps.unwfile)
 
+    if inps.rmfilter:
+        filtfile = os.path.abspath(inps.intfile)
+        intfile = filtfile.split('filt_')
+        intfile = intfile[0] + intfile[1]
+
+        remove_filter(intfile, filtfile, inps.unwfile)
+
 
 if __name__ == '__main__':