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support for alosStack in ISCE #464

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Oct 22, 2020
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support for alosStack in ISCE #464

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f98e99e
support for alosStack in ISCE
CunrenLiang Oct 21, 2020
4c6eeef
example input file
CunrenLiang Oct 21, 2020
e3a8b12
update module_hierarchy
yunjunz Oct 22, 2020
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2 changes: 1 addition & 1 deletion docs/api/module_hierarchy.md
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ Hierarchy of sub-modules within MintPy. Level N modules depends on level N-1, N-
/utils
plot (objects/{stack, coord, colors}, utils/{ptime, utils0, utils1, readfile, network})
utils (objects/{stack, coord}, utils/{ptime, utils0, utils1, readfile})
isce_utils (utils/{readfile, writefile, utils1})
isce_utils (utils/{ptime, readfile, writefile, utils1})
------------------ level 6 --------------------
/objects
insar_vs_gps (objects/{stack, giant}, utils/{readfile, gps, plot, utils})
Expand Down
26 changes: 26 additions & 0 deletions docs/examples/input_files/NCalAlos2Scan.txt
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@@ -0,0 +1,26 @@
# vim: set filetype=cfg:
##-------------------------------- MintPy -----------------------------##
########## 1. Load Data (--load to exit after this step)
## load_data.py -H to check more details and example inputs.
mintpy.load.processor = isce
##NOTE: 150408 is the reference date of alosStack processing.
## (parameter "reference date of the stack" of alosStack input xml file)
##---------for ISCE only:
mintpy.load.metaFile = ../pairs/*-*/150408.track.xml
mintpy.load.baselineDir = ../baseline
##---------interferogram datasets:
mintpy.load.unwFile = ../pairs/*-*/insar/filt_*-*_5rlks_28alks.unw
mintpy.load.corFile = ../pairs/*-*/insar/*-*_5rlks_28alks.cor
mintpy.load.connCompFile = ../pairs/*-*/insar/filt_*-*_5rlks_28alks.unw.conncomp
##---------geometry datasets:
mintpy.load.demFile = ../dates_resampled/150408/insar/*_5rlks_28alks.hgt
mintpy.load.lookupYFile = ../dates_resampled/150408/insar/*_5rlks_28alks.lat
mintpy.load.lookupXFile = ../dates_resampled/150408/insar/*_5rlks_28alks.lon
mintpy.load.incAngleFile = ../dates_resampled/150408/insar/*_5rlks_28alks.los
mintpy.load.azAngleFile = ../dates_resampled/150408/insar/*_5rlks_28alks.los
mintpy.load.waterMaskFile = ../dates_resampled/150408/insar/*_5rlks_28alks.wbd

mintpy.reference.yx = 1500, 200
mintpy.networkInversion.weightFunc = no
mintpy.topographicResidual.pixelwiseGeometry = no

9 changes: 8 additions & 1 deletion mintpy/load_data.py
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Expand Up @@ -583,9 +583,12 @@ def prepare_metadata(inpsDict):

elif processor == 'isce':
from mintpy import prep_isce
from mintpy.utils.isce_utils import get_processor

meta_files = sorted(glob.glob(inpsDict['mintpy.load.metaFile']))
if len(meta_files) < 1:
warnings.warn('No input metadata file found: {}'.format(inpsDict['mintpy.load.metaFile']))

try:
# metadata and auxliary data
meta_file = meta_files[0]
Expand All @@ -597,7 +600,11 @@ def prepare_metadata(inpsDict):
obs_keys = [i for i in obs_keys if i in inpsDict.keys()]
obs_paths = [inpsDict[key] for key in obs_keys if inpsDict[key].lower() != 'auto']
if len(obs_paths) > 0:
obs_dir = os.path.dirname(os.path.dirname(obs_paths[0]))
processor = get_processor(meta_file)
if processor == 'alosStack':
obs_dir = os.path.dirname(obs_paths[0])
else:
obs_dir = os.path.dirname(os.path.dirname(obs_paths[0]))
obs_file = os.path.basename(obs_paths[0])
else:
obs_dir = None
Expand Down
12 changes: 12 additions & 0 deletions mintpy/objects/stackDict.py
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Expand Up @@ -287,6 +287,7 @@ class geometryDict:
'incidenceAngle':'$PROJECT_DIR/merged/geom_reference/los.rdr',
'heandingAngle' :'$PROJECT_DIR/merged/geom_reference/los.rdr',
'shadowMask' :'$PROJECT_DIR/merged/geom_reference/shadowMask.rdr',
'waterMask' :'$PROJECT_DIR/merged/geom_reference/waterMask.rdr',
'bperp' :bperpDict
...
}
Expand Down Expand Up @@ -507,7 +508,18 @@ def write2hdf5(self, outputFile='geometryRadar.h5', access_mode='w', box=None, c
t=str(dsDataType),
s=dsShape,
c=str(compression)))

# read
data = np.array(self.read(family=dsName, box=box)[0], dtype=dsDataType)
# water body: -1 for water and 0 for land
# water mask: 0 for water and 1 for land
fname = os.path.basename(self.datasetDict[dsName])
if fname.startswith('waterBody') or fname.endswith('.wbd'):
data = data > -0.5
print((' input file "{}" is water body (-1/0 for water/land), '
'convert to water mask (0/1 for water/land).'.format(fname)))

# write
ds = f.create_dataset(dsName,
data=data,
chunks=True,
Expand Down
102 changes: 71 additions & 31 deletions mintpy/prep_isce.py
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Expand Up @@ -20,9 +20,12 @@

EXAMPLE = """example:
# interferogram stack
prep_isce.py -d ./merged/interferograms -m ./reference/IW1.xml -b ./baselines -g ./merged/geom_reference #for topsStack
prep_isce.py -d ./Igrams -m ./referenceShelve/data.dat -b ./baselines -g ./geom_reference #for stripmapStack
prep_isce.py -m 20120507_slc_crop.xml -g ./geometry #for stripmapApp
prep_isce.py -d ./merged/interferograms -m ./reference/IW1.xml -b ./baselines -g ./merged/geom_reference #for topsStack
prep_isce.py -d ./Igrams -m ./referenceShelve/data.dat -b ./baselines -g ./geom_reference #for stripmapStack
prep_isce.py -m 20120507_slc_crop.xml -g ./geometry #for stripmapApp

# 150408 is the reference date of alosStack processing
prep_isce.py -d "pairs/*-*/insar" -m "pairs/*-*/150408.track.xml" -b baseline -g dates_resampled/150408/insar #for alosStack

# offset stack from topsStack
prep_isce.py -d ./merged/offsets -f filtAz*.off -m ./reference/IW1.xml -b ./baselines -g ./merged/offsets/geom_reference
Expand All @@ -33,22 +36,22 @@ def create_parser():
parser = argparse.ArgumentParser(description='Prepare ISCE metadata files.',
formatter_class=argparse.RawTextHelpFormatter,
epilog=EXAMPLE)
parser.add_argument('-d', '--ds-dir', '--dset-dir', dest='dsetDir', type=str, default=None,
parser.add_argument('-d', '--ds-dir', '--dset-dir', dest='dsetDir', type=str, default=None, required=True,
help='The directory which contains all pairs\n'
'e.g.: $PROJECT_DIR/merged/interferograms OR \n'
' $PROJECT_DIR/pairs/*-*/insar OR \n'
' $PROJECT_DIR/merged/offsets')
parser.add_argument('-f', '--file-pattern', nargs = '+', dest='dsetFiles', type=str,
default=['filt_*.unw'],
help='A list of files that will be used in mintpy\n'
'e.g.: filt_fine.unw filt_fine.cor OR\n'
' filtAz*.off filtRa*.off')
parser.add_argument('-m', '--meta-file', dest='metaFile', type=str, default=None,
parser.add_argument('-f', '--file-pattern', nargs = '+', dest='dsetFiles', type=str, default=['filt_*.unw'],
help='List of observation files, e.g.: filt_fine.unw OR filtAz*.off')
parser.add_argument('-m', '--meta-file', dest='metaFile', type=str, default=None, required=True,
help='Metadata file to extract common metada for the stack:\n'
'e.g.: for ISCE/topsStack: reference/IW3.xml;\n'
' for ISCE/stripmapStack: referenceShelve/data.dat')
'e.g.: for ISCE/topsStack : reference/IW3.xml;\n'
' for ISCE/stripmapStack: referenceShelve/data.dat;\n'
' for ISCE/alosStack : pairs/150408-150701/150408.track.xml\n'
' where 150408 is the reference date of stack processing')
parser.add_argument('-b', '--baseline-dir', dest='baselineDir', type=str, default=None,
help=' directory with baselines ')
parser.add_argument('-g', '--geometry-dir', dest='geometryDir', type=str, default=None,
parser.add_argument('-g', '--geometry-dir', dest='geometryDir', type=str, default=None, required=True,
help=' directory with geometry files ')
parser.add_argument('--force', dest='update_mode', action='store_false',
help='Force to overwrite all .rsc metadata files.')
Expand All @@ -58,9 +61,15 @@ def create_parser():
def cmd_line_parse(iargs = None):
parser = create_parser()
inps = parser.parse_args(args=iargs)
if all(not i for i in [inps.dsetDir, inps.geometryDir, inps.metaFile]):
parser.print_usage()
raise SystemExit('ERROR: at least one of the following arguments are required: -i, -g, -m')

# translate wildcard in metaFile
if "*" in inps.metaFile:
fnames = glob.glob(inps.metaFile)
if len(fnames) > 0:
inps.metaFile = fnames[0]
else:
raise FileNotFoundError(inps.metaFile)

return inps


Expand Down Expand Up @@ -89,17 +98,32 @@ def add_ifgram_metadata(metadata_in, dates=[], baseline_dict={}):
return metadata


def prepare_geometry(geom_dir, metadata=dict(), update_mode=True):
def prepare_geometry(geom_dir, metadata=dict(), processor='tops', update_mode=True):
"""Prepare and extract metadata from geometry files"""

print('prepare .rsc file for geometry files')
geom_dir = os.path.abspath(geom_dir)

# grab all existed files
isce_files = [os.path.join(os.path.abspath(geom_dir), '{}.rdr'.format(i))
for i in ['hgt','lat','lon','los','shadowMask','incLocal']]
isce_files = [i for i in isce_files if os.path.isfile(i)]
if len(isce_files) == 0:
isce_files = [os.path.join(os.path.abspath(geom_dir), '{}.rdr.full'.format(i))
for i in ['hgt','lat','lon','los','shadowMask','incLocal']]
if processor in ['tops', 'stripmap']:
fbases = ['hgt', 'lat', 'lon', 'los', 'shadowMask', 'incLocal']
isce_files = [os.path.join(geom_dir, '{}.rdr'.format(i)) for i in fbases]
isce_files = [i for i in isce_files if os.path.isfile(i)]
if len(isce_files) == 0:
isce_files = [os.path.join(geom_dir, '{}.rdr.full'.format(i)) for i in fbases]
isce_files = [i for i in isce_files if os.path.isfile(i)]

elif processor in ['alosStack']:
alooks = metadata['ALOOKS']
rlooks = metadata['RLOOKS']
isce_files = glob.glob(os.path.join(geom_dir, '*_{}rlks_{}alks.hgt'.format(rlooks, alooks)))+\
glob.glob(os.path.join(geom_dir, '*_{}rlks_{}alks.lat'.format(rlooks, alooks)))+\
glob.glob(os.path.join(geom_dir, '*_{}rlks_{}alks.lon'.format(rlooks, alooks)))+\
glob.glob(os.path.join(geom_dir, '*_{}rlks_{}alks.los'.format(rlooks, alooks)))+\
glob.glob(os.path.join(geom_dir, '*_{}rlks_{}alks.wbd'.format(rlooks, alooks)))

else:
raise Exception('unknown processor: {}'.format(processor))

# write rsc file for each file
for isce_file in isce_files:
Expand All @@ -115,12 +139,18 @@ def prepare_geometry(geom_dir, metadata=dict(), update_mode=True):
writefile.write_roipac_rsc(geom_metadata, rsc_file,
update_mode=update_mode,
print_msg=True)
return metadata
return


def prepare_stack(inputDir, filePattern, metadata=dict(), baseline_dict=dict(), update_mode=True):
def prepare_stack(inputDir, filePattern, metadata=dict(), baseline_dict=dict(), processor='tops', update_mode=True):
print('prepare .rsc file for ', filePattern)
isce_files = sorted(glob.glob(os.path.join(os.path.abspath(inputDir), '*', filePattern)))
if processor in ['tops', 'stripmap']:
isce_files = sorted(glob.glob(os.path.join(os.path.abspath(inputDir), '*', filePattern)))
elif processor == 'alosStack':
isce_files = sorted(glob.glob(os.path.join(os.path.abspath(inputDir), filePattern)))
else:
raise ValueError('Un-recognized ISCE stack processor: {}'.format(processor))

if len(isce_files) == 0:
raise FileNotFoundError('no file found in pattern: {}'.format(filePattern))

Expand All @@ -130,7 +160,14 @@ def prepare_stack(inputDir, filePattern, metadata=dict(), baseline_dict=dict(),
for i in range(num_file):
# prepare metadata for current file
isce_file = isce_files[i]
dates = os.path.basename(os.path.dirname(isce_file)).split('_') # to modify to YYYYMMDDTHHMMSS
if processor in ['tops', 'stripmap']:
dates = os.path.basename(os.path.dirname(isce_file)).split('_') # to modify to YYYYMMDDTHHMMSS
elif processor == 'alosStack':
dates = os.path.basename(os.path.dirname(os.path.dirname(isce_file))).split('-') # to modify to YYYYMMDDTHHMMSS
dates = ptime.yyyymmdd(dates)
else:
raise ValueError('Un-recognized ISCE stack processor: {}'.format(processor))

ifg_metadata = readfile.read_attribute(isce_file, metafile_ext='.xml')
ifg_metadata.update(metadata)
ifg_metadata = add_ifgram_metadata(ifg_metadata, dates, baseline_dict)
Expand Down Expand Up @@ -161,9 +198,10 @@ def main(iargs=None):

# prepare metadata for geometry file
if inps.geometryDir:
metadata = prepare_geometry(inps.geometryDir,
metadata=metadata,
update_mode=inps.update_mode)
prepare_geometry(inps.geometryDir,
metadata=metadata,
processor=inps.processor,
update_mode=inps.update_mode)

# read baseline info
baseline_dict = {}
Expand All @@ -174,9 +212,11 @@ def main(iargs=None):
# prepare metadata for ifgram file
if inps.dsetDir and inps.dsetFiles:
for namePattern in inps.dsetFiles:
prepare_stack(inps.dsetDir, namePattern,
prepare_stack(inps.dsetDir,
namePattern,
metadata=metadata,
baseline_dict=baseline_dict,
processor=inps.processor,
update_mode=inps.update_mode)
print('Done.')
return
Expand Down
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