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Merge pull request #276 from yunjunz/offset 

cuDenseOffsets.prep*Geom*: supp. full-reso file w/o .full in the name
LT1AB
Ryan Burns 2021-06-14 15:48:21 -07:00 committed by GitHub
parent cd66b264e3 a5891a8ac0
commit a976d12c51
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2 changed files with 125 additions and 110 deletions
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33
contrib/PyCuAmpcor/examples/cuDenseOffsets.py
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@ -40,6 +40,8 @@ def createParser():
help='Reference image') help='Reference image')
parser.add_argument('-s', '--secondary',type=str, dest='secondary', required=True, parser.add_argument('-s', '--secondary',type=str, dest='secondary', required=True,
help='Secondary image') help='Secondary image')
parser.add_argument('--fix-xml','--fix-image-xml', dest='fixImageXml', action='store_true',
help='Fix the image file path in the XML file. Enable this if input files havee been moved.')
parser.add_argument('--op','--outprefix','--output-prefix', type=str, dest='outprefix', parser.add_argument('--op','--outprefix','--output-prefix', type=str, dest='outprefix',
default='offset', required=True, default='offset', required=True,
@ -166,12 +168,13 @@ def estimateOffsetField(reference, secondary, inps=None):
return 0 return 0
# update file path in xml file # update file path in xml file
for fname in [reference, secondary]: if inps.fixImageXml:
fname = os.path.abspath(fname) for fname in [reference, secondary]:
img = IML.loadImage(fname)[0] fname = os.path.abspath(fname)
img.filename = fname img = IML.loadImage(fname)[0]
img.setAccessMode('READ') img.filename = fname
img.renderHdr() img.setAccessMode('READ')
img.renderHdr()
###Loading the secondary image object ###Loading the secondary image object
sim = isceobj.createSlcImage() sim = isceobj.createSlcImage()
@ -382,14 +385,24 @@ def prepareGeometry(full_dir, out_dir, x_start, y_start, x_step, y_step, num_win
x/y_step - int, output pixel step in column/row direction x/y_step - int, output pixel step in column/row direction
num_win_x/y - int, number of columns/rows num_win_x/y - int, number of columns/rows
""" """
full_dir = os.path.abspath(full_dir)
out_dir = os.path.abspath(out_dir)
# grab the file extension for full resolution file
full_exts = ['.rdr.full','.rdr'] if full_dir != out_dir else ['.rdr.full']
full_exts = [e for e in full_exts if os.path.isfile(os.path.join(full_dir, '{f}{e}'.format(f=fbases[0], e=e)))]
if len(full_exts) == 0:
raise ValueError('No full resolution {}.rdr* file found in: {}'.format(fbases[0], full_dir))
full_ext = full_exts[0]
print('-'*50) print('-'*50)
print('generate the corresponding multi-looked geometry datasets using gdal ...') print('generate the corresponding multi-looked geometry datasets using gdal ...')
in_files = [os.path.join(full_dir, '{}.rdr.full'.format(i)) for i in fbases] # input files
in_files = [os.path.join(full_dir, '{f}{e}'.format(f=f, e=full_ext)) for f in fbases]
in_files = [i for i in in_files if os.path.isfile(i)] in_files = [i for i in in_files if os.path.isfile(i)]
if len(in_files) == 0:
raise ValueError('No full resolution geometry file found in: {}'.format(full_dir))
fbases = [os.path.basename(i).split('.')[0] for i in in_files] fbases = [os.path.basename(i).split('.')[0] for i in in_files]
# output files
out_files = [os.path.join(out_dir, '{}.rdr'.format(i)) for i in fbases] out_files = [os.path.join(out_dir, '{}.rdr'.format(i)) for i in fbases]
os.makedirs(out_dir, exist_ok=True) os.makedirs(out_dir, exist_ok=True)

202
contrib/stack/stripmapStack/stackStripMap.py
View File

@ -26,6 +26,7 @@ noMCF = 'False'
defoMax = '2' defoMax = '2'
maxNodes = 72 maxNodes = 72
def createParser(): def createParser():
parser = argparse.ArgumentParser( description='Preparing the directory structure and config files for stack processing of StripMap data') parser = argparse.ArgumentParser( description='Preparing the directory structure and config files for stack processing of StripMap data')
@ -42,7 +43,7 @@ def createParser():
parser.add_argument('-m', '--reference_date', dest='referenceDate', type=str, default=None, parser.add_argument('-m', '--reference_date', dest='referenceDate', type=str, default=None,
help='Directory with reference acquisition') help='Directory with reference acquisition')
parser.add_argument('-t', '--time_threshold', dest='dtThr', type=float, default=10000.0, parser.add_argument('-t', '--time_threshold', dest='dtThr', type=float, default=10000.0,
help='Time threshold (max temporal baseline in days)') help='Time threshold (max temporal baseline in days)')
@ -57,7 +58,7 @@ def createParser():
parser.add_argument('-S', '--sensor', dest='sensor', type=str, required=False, parser.add_argument('-S', '--sensor', dest='sensor', type=str, required=False,
help='SAR sensor used to define square multi-look pixels') help='SAR sensor used to define square multi-look pixels')
parser.add_argument('-u', '--unw_method', dest='unwMethod', type=str, default='snaphu', parser.add_argument('-u', '--unw_method', dest='unwMethod', type=str, default='snaphu',
help='unwrapping method (icu, snaphu, or snaphu2stage), no to skip phase unwrapping.') help='unwrapping method (icu, snaphu, or snaphu2stage), no to skip phase unwrapping.')
parser.add_argument('-f','--filter_strength', dest='filtStrength', type=str, default=filtStrength, parser.add_argument('-f','--filter_strength', dest='filtStrength', type=str, default=filtStrength,
@ -72,7 +73,7 @@ def createParser():
iono.add_argument('-B', '--subband_bandwidth ', dest='bandWidth', type=str, default=None, iono.add_argument('-B', '--subband_bandwidth ', dest='bandWidth', type=str, default=None,
help='sub-band band width') help='sub-band band width')
iono.add_argument('--filter_sigma_x', dest='filterSigmaX', type=str, default='100', iono.add_argument('--filter_sigma_x', dest='filterSigmaX', type=str, default='100',
help='filter sigma for gaussian filtering the dispersive and nonDispersive phase') help='filter sigma for gaussian filtering the dispersive and nonDispersive phase')
iono.add_argument('--filter_sigma_y', dest='filterSigmaY', type=str, default='100.0', iono.add_argument('--filter_sigma_y', dest='filterSigmaY', type=str, default='100.0',
@ -87,14 +88,14 @@ def createParser():
iono.add_argument('--filter_kernel_rotation', dest='filterKernelRotation', type=str, default='0.0', iono.add_argument('--filter_kernel_rotation', dest='filterKernelRotation', type=str, default='0.0',
help='rotation angle of the filter kernel in degrees (default = 0.0)') help='rotation angle of the filter kernel in degrees (default = 0.0)')
parser.add_argument('-W', '--workflow', dest='workflow', type=str, default='slc', parser.add_argument('-W', '--workflow', dest='workflow', type=str, default='slc',
help='The InSAR processing workflow : (slc, interferogram, ionosphere)') help='The InSAR processing workflow : (slc, interferogram, ionosphere)')
parser.add_argument('-z', '--zero', dest='zerodop', action='store_true', default=False, parser.add_argument('-z', '--zero', dest='zerodop', action='store_true', default=False,
help='Use zero doppler geometry for processing - Default : No') help='Use zero doppler geometry for processing - Default : No')
parser.add_argument('--nofocus', dest='nofocus', action='store_true', default=False, parser.add_argument('--nofocus', dest='nofocus', action='store_true', default=False,
help='If input data is already focused to SLCs - Default : do focus') help='If input data is already focused to SLCs - Default : do focus')
parser.add_argument('-c', '--text_cmd', dest='text_cmd', type=str, default='', parser.add_argument('-c', '--text_cmd', dest='text_cmd', type=str, default='',
help='text command to be added to the beginning of each line of the run files. Example : 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('-useGPU', '--useGPU', dest='useGPU',action='store_true', default=False, parser.add_argument('-useGPU', '--useGPU', dest='useGPU',action='store_true', default=False,
help='Allow App to use GPU when available') help='Allow App to use GPU when available')
@ -102,18 +103,19 @@ def createParser():
parser.add_argument('--summary', dest='summary', action='store_true', default=False, help='Show summary only') parser.add_argument('--summary', dest='summary', action='store_true', default=False, help='Show summary only')
return parser return parser
def cmdLineParse(iargs = None): def cmdLineParse(iargs = None):
parser = createParser() parser = createParser()
inps = parser.parse_args(args=iargs) inps = parser.parse_args(args=iargs)
inps.slcDir = os.path.abspath(inps.slcDir) inps.slcDir = os.path.abspath(inps.slcDir)
inps.workDir = os.path.abspath(inps.workDir) inps.workDir = os.path.abspath(inps.workDir)
inps.dem = os.path.abspath(inps.dem) inps.dem = os.path.abspath(inps.dem)
return inps return inps
def get_dates(inps): def get_dates(inps):
dirs = glob.glob(inps.slcDir+'/*') dirs = glob.glob(inps.slcDir+'/*')
acuisitionDates = [] acuisitionDates = []
for dirf in dirs: for dirf in dirs:
@ -134,13 +136,13 @@ def get_dates(inps):
inps.referenceDate = acuisitionDates[0] inps.referenceDate = acuisitionDates[0]
secondaryDates = acuisitionDates.copy() secondaryDates = acuisitionDates.copy()
secondaryDates.remove(inps.referenceDate) secondaryDates.remove(inps.referenceDate)
return acuisitionDates, inps.referenceDate, secondaryDates return acuisitionDates, inps.referenceDate, secondaryDates
def slcStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs, splitFlag=False, rubberSheet=False): def slcStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs, splitFlag=False, rubberSheet=False):
# A coregistered stack of SLCs # A coregistered stack of SLCs
i=0 i=0
if inps.bbox: if inps.bbox:
i+=1 i+=1
runObj = run() runObj = run()
@ -149,7 +151,6 @@ def slcStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs,
runObj.crop(acquisitionDates, config_prefix, native=not inps.zerodop, israw=not inps.nofocus) runObj.crop(acquisitionDates, config_prefix, native=not inps.zerodop, israw=not inps.nofocus)
runObj.finalize() runObj.finalize()
i+=1 i+=1
runObj = run() runObj = run()
runObj.configure(inps, 'run_{:02d}_reference'.format(i)) runObj.configure(inps, 'run_{:02d}_reference'.format(i))
@ -190,40 +191,40 @@ def slcStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs,
config_prefix = 'config_fineResamp_' config_prefix = 'config_fineResamp_'
runObj.secondarys_fine_resampleSlc(stackReferenceDate, secondaryDates, config_prefix, split=splitFlag) runObj.secondarys_fine_resampleSlc(stackReferenceDate, secondaryDates, config_prefix, split=splitFlag)
runObj.finalize() runObj.finalize()
if rubberSheet: if rubberSheet:
i+=1 i+=1
runObj = run() runObj = run()
runObj.configure(inps, 'run_{:02d}_denseOffset'.format(i)) runObj.configure(inps, 'run_{:02d}_denseOffset'.format(i))
config_prefix = 'config_denseOffset_' config_prefix = 'config_denseOffset_'
runObj.denseOffsets_Network(pairs, stackReferenceDate, secondaryDates, config_prefix) runObj.denseOffsets_Network(pairs, stackReferenceDate, secondaryDates, config_prefix)
runObj.finalize() runObj.finalize()
i+=1 i+=1
runObj = run() runObj = run()
runObj.configure(inps, 'run_{:02d}_invertDenseOffsets'.format(i)) runObj.configure(inps, 'run_{:02d}_invertDenseOffsets'.format(i))
runObj.invertDenseOffsets() runObj.invertDenseOffsets()
runObj.finalize() runObj.finalize()
i+=1
runObj = run()
runObj.configure(inps, 'run_{:02d}_resampleOffset'.format(i))
config_prefix = 'config_resampOffsets_'
runObj.resampleOffset(secondaryDates, config_prefix)
runObj.finalize()
i+=1 i+=1
runObj = run() runObj = run()
runObj.configure(inps, 'run_{:02d}_replaceOffsets'.format(i)) runObj.configure(inps, 'run_{:02d}_resampleOffset'.format(i))
runObj.replaceOffsets(secondaryDates) config_prefix = 'config_resampOffsets_'
runObj.finalize() runObj.resampleOffset(secondaryDates, config_prefix)
runObj.finalize()
i+=1 i+=1
runObj = run() runObj = run()
runObj.configure(inps, 'run_{:02d}_fineResamp'.format(i)) runObj.configure(inps, 'run_{:02d}_replaceOffsets'.format(i))
config_prefix = 'config_fineResamp_' runObj.replaceOffsets(secondaryDates)
runObj.secondarys_fine_resampleSlc(stackReferenceDate, secondaryDates, config_prefix, split=splitFlag) runObj.finalize()
runObj.finalize()
i+=1
runObj = run()
runObj.configure(inps, 'run_{:02d}_fineResamp'.format(i))
config_prefix = 'config_fineResamp_'
runObj.secondarys_fine_resampleSlc(stackReferenceDate, secondaryDates, config_prefix, split=splitFlag)
runObj.finalize()
# adding the baseline grid generation # adding the baseline grid generation
i+=1 i+=1
@ -235,20 +236,22 @@ def slcStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs,
return i return i
def interferogramStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs): def interferogramStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs):
# an interferogram stack without ionosphere correction. # an interferogram stack without ionosphere correction.
# coregistration is with geometry + const offset # coregistration is with geometry + const offset
i = slcStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs, splitFlag=False, rubberSheet=False) i = slcStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs, splitFlag=False, rubberSheet=False)
i+=1 i+=1
runObj = run() runObj = run()
runObj.configure(inps, 'run_{:02d}_igram'.format(i)) runObj.configure(inps, 'run_{:02d}_igram'.format(i))
config_prefix = 'config_igram_' config_prefix = 'config_igram_'
low_or_high = "/" low_or_high = "/"
runObj.igrams_network(pairs, acquisitionDates, stackReferenceDate, low_or_high, config_prefix) runObj.igrams_network(pairs, acquisitionDates, stackReferenceDate, low_or_high, config_prefix)
runObj.finalize() runObj.finalize()
return
def interferogramIonoStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs): def interferogramIonoStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs):
@ -273,7 +276,7 @@ def interferogramIonoStack(inps, acquisitionDates, stackReferenceDate, secondary
config_prefix = 'config_igram_' config_prefix = 'config_igram_'
low_or_high = "/" low_or_high = "/"
runObj.igrams_network(pairs, acquisitionDates, stackReferenceDate, low_or_high, config_prefix) runObj.igrams_network(pairs, acquisitionDates, stackReferenceDate, low_or_high, config_prefix)
runObj.finalize() runObj.finalize()
i+=1 i+=1
runObj = run() runObj = run()
@ -297,69 +300,68 @@ def interferogramIonoStack(inps, acquisitionDates, stackReferenceDate, secondary
config_prefix = 'config_iono_' config_prefix = 'config_iono_'
lowBand = '/LowBand/' lowBand = '/LowBand/'
highBand = '/HighBand/' highBand = '/HighBand/'
runObj.dispersive_nonDispersive(pairs, acquisitionDates, stackReferenceDate, runObj.dispersive_nonDispersive(pairs, acquisitionDates, stackReferenceDate, lowBand, highBand, config_prefix)
lowBand, highBand, config_prefix)
runObj.finalize() runObj.finalize()
return
def main(iargs=None): def main(iargs=None):
inps = cmdLineParse(iargs) inps = cmdLineParse(iargs)
# name of the folder of the coreg SLCs including baselines, SLC, geom_reference subfolders # name of the folder of the coreg SLCs including baselines, SLC, geom_reference subfolders
inps.stack_folder = 'merged' inps.stack_folder = 'merged'
inps.dense_offsets_folder = 'dense_offsets' inps.dense_offsets_folder = 'dense_offsets'
# check if a sensor is defined and update if needed azimuth looks to give square pixels # check if a sensor is defined and update if needed azimuth looks to give square pixels
ar=1 ar=1
if inps.sensor: if inps.sensor:
if inps.sensor.lower() == "alos": if inps.sensor.lower() == "alos":
ar=4 ar=4
print("Looks like " + inps.sensor.lower() + ", multi-look AR=" + str(ar)) print("Looks like " + inps.sensor.lower() + ", multi-look AR=" + str(ar))
elif inps.sensor.lower() == "envisat" or inps.sensor.lower() == "ers": elif inps.sensor.lower() == "envisat" or inps.sensor.lower() == "ers":
ar=5 ar=5
print("Looks like " + inps.sensor.lower() + ", multi-look AR=" + str(ar)) print("Looks like " + inps.sensor.lower() + ", multi-look AR=" + str(ar))
else: else:
print("Sensor is not hard-coded (ers, envisat, alos), will keep default alks") print("Sensor is not hard-coded (ers, envisat, alos), will keep default alks")
# sensor is not recognised, report to user and state default # sensor is not recognised, report to user and state default
inps.alks = str(int(inps.alks)*int(ar)) inps.alks = str(int(inps.alks)*int(ar))
# getting the acquisitions
acquisitionDates, stackReferenceDate, secondaryDates = get_dates(inps)
configDir = os.path.join(inps.workDir,'configs')
os.makedirs(configDir, exist_ok=True)
runDir = os.path.join(inps.workDir,'run_files')
os.makedirs(runDir, exist_ok=True)
if inps.sensor.lower() == 'uavsar_stack': # don't try to calculate baselines for UAVSAR_STACK data # getting the acquisitions
pairs = selectPairs(inps,stackReferenceDate, secondaryDates, acquisitionDates,doBaselines=False) acquisitionDates, stackReferenceDate, secondaryDates = get_dates(inps)
else: configDir = os.path.join(inps.workDir,'configs')
pairs = selectPairs(inps,stackReferenceDate, secondaryDates, acquisitionDates,doBaselines=True) os.makedirs(configDir, exist_ok=True)
print ('number of pairs: ', len(pairs)) runDir = os.path.join(inps.workDir,'run_files')
os.makedirs(runDir, exist_ok=True)
###If only a summary is requested quit after this if inps.sensor and inps.sensor.lower() == 'uavsar_stack': # don't try to calculate baselines for UAVSAR_STACK data
if inps.summary: pairs = selectPairs(inps,stackReferenceDate, secondaryDates, acquisitionDates,doBaselines=False)
return else:
pairs = selectPairs(inps,stackReferenceDate, secondaryDates, acquisitionDates,doBaselines=True)
print ('number of pairs: ', len(pairs))
#if cropping is requested, then change the slc directory: ###If only a summary is requested quit after this
inps.fullFrameSlcDir = inps.slcDir if inps.summary:
return
if inps.bbox: #if cropping is requested, then change the slc directory:
inps.slcDir = inps.slcDir + "_crop" inps.fullFrameSlcDir = inps.slcDir
#############################
if inps.workflow == 'slc': if inps.bbox:
slcStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs, splitFlag=False, rubberSheet=False) inps.slcDir = inps.slcDir + "_crop"
#############################
elif inps.workflow == 'interferogram': if inps.workflow == 'slc':
interferogramStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs) slcStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs, splitFlag=False, rubberSheet=False)
elif inps.workflow == 'interferogram':
interferogramStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs)
elif inps.workflow == 'ionosphere':
interferogramIonoStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs)
return
elif inps.workflow == 'ionosphere':
interferogramIonoStack(inps, acquisitionDates, stackReferenceDate, secondaryDates, pairs)
if __name__ == "__main__": if __name__ == "__main__":
# Main engine
# Main engine main(sys.argv[1:])
main()