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Merge pull request #113 from mirzaees/stack_runfiles 

Stack runfiles
LT1AB
Heresh Fattahi 2020-05-02 10:13:25 -07:00 committed by GitHub
parent 0b1b618363 a24f0e99bf
commit 9e7e090548
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GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 142 additions and 51 deletions
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106
contrib/stack/topsStack/Stack.py
View File

@ -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)
@ -389,16 +394,42 @@ 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)
configObj.overlapTrueOrFalse = 'True'
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.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')
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')
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')
def pairs_misregistration(self, dateList, safe_dict):
# generating overlap interferograms, estimate azimuth misregistration for each pair:
@ -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_igram_' + master + '_' + slave)
configName = os.path.join(self.config_path ,'config_generate_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
configObj.dirName = configObj.master
self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
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

35
contrib/stack/topsStack/stackSentinel.py
View File

@ -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.overlap_geo2rdr_resample(slaveDates)
runObj.configure(inps, 'run_' + str(i) + "_overlap_geo2rdr")
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.geo2rdr_resample(slaveDates)
runObj.configure(inps, 'run_' + str(i) + "_fullBurst_geo2rdr")
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

50
contrib/stack/topsStack/unwrap.py
View File

@ -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__':