def load_data_from_template(inps):
'''Load dataset for PySAR time series using input template'''
##------------------------------------ Read Input Path -------------------------------------##
# Initial value
inps.unw = None
inps.cor = None
#inps.int = None
inps.lut = None
inps.dem_radar = None
inps.dem_geo = None
# 1.1 Read template contents (support multiple template files input)
inps.template_file = [os.path.abspath(i) for i in inps.template_file]
# Move default template file pysarApp_template.txt to the end of list, so that it has highest priority
default_template_file = [i for i in inps.template_file if 'pysarApp' in i]
if default_template_file:
inps.template_file.remove(default_template_file[0])
inps.template_file.append(default_template_file[0])
template = dict()
# Read file by file
for File in inps.template_file:
temp_dict = readfile.read_template(File)
for key, value in temp_dict.iteritems():
temp_dict[key] = ut.check_variable_name(value)
template.update(temp_dict)
keyList = template.keys()
# Project Name
if not inps.project_name:
inps.template_filename = [
os.path.basename(i) for i in inps.template_file
]
try:
inps.template_filename.remove('pysarApp_template.txt')
except:
pass
if inps.template_filename:
inps.project_name = os.path.splitext(inps.template_filename[0])[0]
for key in [
'processor', 'processing_software', 'unavco.processing_software',
'pysar.insarProcessor'
]:
if key in keyList:
value = template[key]
if value == 'auto':
inps.insarProcessor = 'roipac'
else:
inps.insarProcessor = value
print '--------------------------------------------'
print 'InSAR processing software: ' + inps.insarProcessor
if 'pysar.unwrapFiles' in keyList: inps.unw = template['pysar.unwrapFiles']
if 'pysar.corFiles' in keyList: inps.cor = template['pysar.corFiles']
if 'pysar.lookupFile' in keyList: inps.lut = template['pysar.lookupFile']
if 'pysar.demFile.radarCoord' in keyList:
inps.dem_radar = template['pysar.demFile.radarCoord']
if 'pysar.demFile.geoCoord' in keyList:
inps.dem_geo = template['pysar.demFile.geoCoord']
# Check existed single dataset files
inps_tmp = argparse.Namespace()
inps_tmp = ut.check_loaded_dataset(inps.timeseries_dir,
inps_tmp,
print_msg=False)
if (not inps.lut or inps.lut == 'auto') and inps_tmp.lookup_file:
inps.lut = inps_tmp.lookup_file
if (not inps.dem_radar
or inps.dem_radar == 'auto') and inps_tmp.dem_radar_file:
inps.dem_radar = inps_tmp.dem_radar_file
if (not inps.dem_geo or inps.dem_geo == 'auto') and inps_tmp.dem_geo_file:
inps.dem_geo = inps_tmp.dem_geo_file
# 1.2 Auto Setting for Geodesy Lab - University of Miami
if pysar.miami_path and 'SCRATCHDIR' in os.environ and inps.project_name:
inps = auto_path_miami(inps, template)
# 1.3 get snap_connect.byt path if .unw is input
if inps.unw:
inps.snap_connect = inps.unw.split('.unw')[0] + '_snap_connect.byt'
else:
inps.snap_connect = None
# PYSAR directory
if not inps.timeseries_dir:
inps.timeseries_dir = os.getcwd()
if not os.path.isdir(inps.timeseries_dir):
os.makedirs(inps.timeseries_dir)
#print "PySAR working directory: "+inps.timeseries_dir
# TEMPLATE file directory (to support relative path input)
inps.template_dir = os.path.dirname(inps.template_file[-1])
os.chdir(inps.template_dir)
print 'Go to TEMPLATE directory: ' + inps.template_dir
print 'unwrapped interferograms to load: ' + str(inps.unw)
#print 'wrapped interferograms to load: '+str(inps.int)
print 'spatial coherence files to load: ' + str(inps.cor)
print 'lookup table file to load: ' + str(inps.lut)
print 'DEM file in radar coord to load: ' + str(inps.dem_radar)
print 'DEM file in geo coord to load: ' + str(inps.dem_geo)
##------------------------------------ Loading into HDF5 ---------------------------------------##
# required - unwrapped interferograms
inps.ifgram_file = load_file(inps.unw,
vars(inps),
file_type='interferograms')
inps.coherence_file = load_file(inps.cor,
vars(inps),
file_type='coherence')
#inps.wrap_ifgram_file = load_file(inps.int, vars(inps), file_type='wrapped')
if inps.snap_connect:
inps.snap_connect_file = load_file(inps.snap_connect, vars(inps))
# optional but recommend files - single_dataset file
inps.lookup_file = load_file(inps.lut, vars(inps), file_type='geometry')
inps.dem_radar_file = load_file(inps.dem_radar,
vars(inps),
file_type='dem')
inps.dem_geo_file = load_file(inps.dem_geo, vars(inps), file_type='dem')
os.chdir(inps.timeseries_dir)
print 'Go back to PYSAR directory: ' + inps.timeseries_dir
return inps
def main(argv):
try:
templateFile = argv[1]
except:
print '''
*******************************************
loading the processed data for PySAR:
interferograms (unwrapped and wrapped)
coherence files (generate Mask at the same time)
Usage: load_data.py TEMPLATEFILE
*******************************************
'''
sys.exit(1)
templateContents = readfile.read_template(templateFile)
projectName = os.path.basename(templateFile.partition('.')[0])
############# Assign workubf directory ##############################
try:
tssarProjectDir = os.getenv('TSSARDIR') +'/'+projectName # use TSSARDIR if environment variable exist
except:
tssarProjectDir = os.getenv('SCRATCHDIR') + '/' + projectName + "/TSSAR" # FA 7/2015: adopted for new directory structure
print "QQ " + tssarProjectDir
if not os.path.isdir(tssarProjectDir): os.mkdir(tssarProjectDir)
########### Use defaults if paths not given in template file #########
try:
igramPath=templateContents['pysar.inputdata']
igramPath=check_variable_name(igramPath)
except:
igramPath = os.getenv('SCRATCHDIR') + '/' + projectName + '/PROCESS/DONE/IFGRAM*/filt_*c10.unw'
try:
corPath=templateContents['pysar.CorFiles']
corPath=check_variable_name(corPath)
except:
corPath = os.getenv('SCRATCHDIR') + '/' + projectName + '/PROCESS/DONE/IFGRAM*/filt_*.cor'
try:
wrapPath=templateContents['pysar.wrapped']
wrapPath=check_variable_name(wrapPath)
except:
wrapPath = os.getenv('SCRATCHDIR') + '/' + projectName + '/PROCESS/DONE/I*/filt_*0*sim_HDR_*rlks.int'
######################### Unwrapped Interferograms ########################
try:
if os.path.isfile(tssarProjectDir+'/LoadedData.h5'):
print '\nLoadedData.h5'+ ' already exists.\n'
sys.exit(1)
print 'loading interferograms ...'
igramList = glob.glob(igramPath)
k = 'interferograms'
check_number(k,igramList) # number check
igramList,mode_width,mode_length = check_size(k,igramList) # size check
h5file = tssarProjectDir+'/LoadedData.h5'
f = h5py.File(h5file)
gg = f.create_group('interferograms')
MaskZero=np.ones([int(mode_length),int(mode_width)])
for igram in igramList:
if not os.path.basename(igram) in f:
print 'Adding ' + igram
group = gg.create_group(os.path.basename(igram))
amp,unw,unwrsc = readfile.read_float32(igram)
MaskZero=amp*MaskZero
dset = group.create_dataset(os.path.basename(igram), data=unw, compression='gzip')
for key,value in unwrsc.iteritems():
group.attrs[key] = value
d1,d2=unwrsc['DATE12'].split('-')
baseline_file=os.path.dirname(igram)+'/'+d1+'_'+d2+'_baseline.rsc'
baseline=readfile.read_rsc_file(baseline_file)
for key,value in baseline.iteritems():
group.attrs[key] = value
else:
print os.path.basename(h5file) + " already contains " + os.path.basename(igram)
Mask=np.ones([int(mode_length),int(mode_width)])
Mask[MaskZero==0]=0
gm = f.create_group('mask')
dset = gm.create_dataset('mask', data=Mask, compression='gzip')
f.close()
########################################################################
print 'writing to Mask.h5'
h5file = 'Mask.h5'
h5mask = h5py.File(h5file,'w')
group=h5mask.create_group('mask')
dset = group.create_dataset(os.path.basename('mask'), data=Mask, compression='gzip')
h5mask.close()
except:
print 'No unwrapped interferogram is loaded.\n'
############################# Coherence ################################
try:
if os.path.isfile(tssarProjectDir+'/Coherence.h5'):
print '\nCoherence.h5'+ ' already exists.\n'
sys.exit(1)
print 'loading corelation files ...'
corList = glob.glob(corPath)
k = 'coherence'
check_number(k,corList) # number check
corList,mode_width,mode_length = check_size(k,corList) # size check
h5file = tssarProjectDir+'/Coherence.h5'
fcor = h5py.File(h5file)
gg = fcor.create_group('coherence')
meanCoherence=np.zeros([int(mode_length),int(mode_width)])
for cor in corList:
if not os.path.basename(cor) in fcor:
print 'Adding ' + cor
group = gg.create_group(os.path.basename(cor))
amp,unw,unwrsc = readfile.read_float32(cor)
meanCoherence=meanCoherence+unw
dset = group.create_dataset(os.path.basename(cor), data=unw, compression='gzip')
for key,value in unwrsc.iteritems():
group.attrs[key] = value
d1,d2=unwrsc['DATE12'].split('-')
baseline_file=os.path.dirname(cor)+'/'+d1+'_'+d2+'_baseline.rsc'
baseline=readfile.read_rsc_file(baseline_file)
for key,value in baseline.iteritems():
group.attrs[key] = value
else:
print os.path.basename(h5file) + " already contains " + os.path.basename(cor)
meanCoherence=meanCoherence/(len(corList))
print '********************************'
print 'writing average_spatial_coherence.h5'
h5file_CorMean = tssarProjectDir+'/average_spatial_coherence.h5'
fcor_mean = h5py.File(h5file_CorMean,'w')
group=fcor_mean.create_group('mask')
dset = group.create_dataset(os.path.basename('mask'), data=meanCoherence, compression='gzip')
fcor_mean.close()
print '********************************'
print 'writing meanCoherence group to the interferogram file'
gc = fcor.create_group('meanCoherence')
dset = gc.create_dataset('meanCoherence', data=meanCoherence, compression='gzip')
print '********************************'
fcor.close()
except:
print 'No correlation file is loaded.\n'
########################## Wrapped Interferograms ############################
try:
if os.path.isfile(tssarProjectDir+'/Wrapped.h5'):
print '\nWrapped.h5'+ ' already exists.\n'
sys.exit(1)
print 'loading wrapped phase ...'
wrapList = glob.glob(wrapPath)
k = 'wrapped'
check_number(k,wrapList) # number check
wrapList,mode_width,mode_length = check_size(k,wrapList) # size check
h5file = tssarProjectDir+'/Wrapped.h5'
fw = h5py.File(h5file)
gg = fw.create_group('wrapped')
for wrap in wrapList:
if not os.path.basename(wrap) in fw:
print 'Adding ' + wrap
group = gg.create_group(os.path.basename(wrap))
amp,unw,unwrsc = readfile.read_complex64(wrap)
dset = group.create_dataset(os.path.basename(wrap), data=unw, compression='gzip')
for key,value in unwrsc.iteritems():
group.attrs[key] = value
d1,d2=unwrsc['DATE12'].split('-')
baseline_file=os.path.dirname(wrap)+'/'+d1+'_'+d2+'_baseline.rsc'
baseline=readfile.read_rsc_file(baseline_file)
for key,value in baseline.iteritems():
group.attrs[key] = value
else:
print os.path.basename(h5file) + " already contains " + os.path.basename(wrap)
fw.close()
print 'Writed '+str(len(wrapList))+' wrapped interferograms to '+h5file
except:
print 'No wrapped interferogram is loaded.\n'
try:
geomapFile=templateContents['pysar.geomap']
geomapFile=check_variable_name(geomapFile)
cpCmd="cp " + geomapFile + " " + tssarProjectDir
print cpCmd
os.system(cpCmd)
cpCmd="cp " + geomapFile + ".rsc " + tssarProjectDir
print cpCmd
os.system(cpCmd)
except:
print "*********************************"
print "Warning: no geomap file given"
print "*********************************"
def main(argv):
try:
templateFile = argv[1]
except:
print '''
*******************************************
loading the processed data for PySAR:
interferograms (unwrapped and wrapped)
coherence files (generate Mask at the same time)
Usage: load_data.py TEMPLATEFILE
*******************************************
'''
sys.exit(1)
templateContents = readfile.read_template(templateFile)
projectName = os.path.basename(templateFile.partition('.')[0])
############# Assign workubf directory ##############################
try:
tssarProjectDir = os.getenv(
'TSSARDIR'
) + '/' + projectName # use TSSARDIR if environment variable exist
except:
tssarProjectDir = os.getenv(
'SCRATCHDIR'
) + '/' + projectName + "/TSSAR" # FA 7/2015: adopted for new directory structure
print "QQ " + tssarProjectDir
if not os.path.isdir(tssarProjectDir): os.mkdir(tssarProjectDir)
########### Use defaults if paths not given in template file #########
try:
igramPath = templateContents['pysar.inputdata']
igramPath = check_variable_name(igramPath)
except:
igramPath = os.getenv(
'SCRATCHDIR'
) + '/' + projectName + '/PROCESS/DONE/IFGRAM*/filt_*c10.unw'
try:
corPath = templateContents['pysar.CorFiles']
corPath = check_variable_name(corPath)
except:
corPath = os.getenv(
'SCRATCHDIR'
) + '/' + projectName + '/PROCESS/DONE/IFGRAM*/filt_*.cor'
try:
wrapPath = templateContents['pysar.wrapped']
wrapPath = check_variable_name(wrapPath)
except:
wrapPath = os.getenv(
'SCRATCHDIR'
) + '/' + projectName + '/PROCESS/DONE/I*/filt_*0*sim_HDR_*rlks.int'
######################### Unwrapped Interferograms ########################
try:
if os.path.isfile(tssarProjectDir + '/LoadedData.h5'):
print '\nLoadedData.h5' + ' already exists.\n'
sys.exit(1)
print 'loading interferograms ...'
igramList = glob.glob(igramPath)
k = 'interferograms'
check_number(k, igramList) # number check
igramList, mode_width, mode_length = check_size(
k, igramList) # size check
h5file = tssarProjectDir + '/LoadedData.h5'
f = h5py.File(h5file)
gg = f.create_group('interferograms')
MaskZero = np.ones([int(mode_length), int(mode_width)])
for igram in igramList:
if not os.path.basename(igram) in f:
print 'Adding ' + igram
group = gg.create_group(os.path.basename(igram))
amp, unw, unwrsc = readfile.read_float32(igram)
MaskZero = amp * MaskZero
dset = group.create_dataset(os.path.basename(igram),
data=unw,
compression='gzip')
for key, value in unwrsc.iteritems():
group.attrs[key] = value
d1, d2 = unwrsc['DATE12'].split('-')
baseline_file = os.path.dirname(
igram) + '/' + d1 + '_' + d2 + '_baseline.rsc'
baseline = readfile.read_rsc_file(baseline_file)
for key, value in baseline.iteritems():
group.attrs[key] = value
else:
print os.path.basename(
h5file) + " already contains " + os.path.basename(igram)
Mask = np.ones([int(mode_length), int(mode_width)])
Mask[MaskZero == 0] = 0
gm = f.create_group('mask')
dset = gm.create_dataset('mask', data=Mask, compression='gzip')
f.close()
########################################################################
print 'writing to Mask.h5'
h5file = 'Mask.h5'
h5mask = h5py.File(h5file, 'w')
group = h5mask.create_group('mask')
dset = group.create_dataset(os.path.basename('mask'),
data=Mask,
compression='gzip')
h5mask.close()
except:
print 'No unwrapped interferogram is loaded.\n'
############################# Coherence ################################
try:
if os.path.isfile(tssarProjectDir + '/Coherence.h5'):
print '\nCoherence.h5' + ' already exists.\n'
sys.exit(1)
print 'loading corelation files ...'
corList = glob.glob(corPath)
k = 'coherence'
check_number(k, corList) # number check
corList, mode_width, mode_length = check_size(k, corList) # size check
h5file = tssarProjectDir + '/Coherence.h5'
fcor = h5py.File(h5file)
gg = fcor.create_group('coherence')
meanCoherence = np.zeros([int(mode_length), int(mode_width)])
for cor in corList:
if not os.path.basename(cor) in fcor:
print 'Adding ' + cor
group = gg.create_group(os.path.basename(cor))
amp, unw, unwrsc = readfile.read_float32(cor)
meanCoherence = meanCoherence + unw
dset = group.create_dataset(os.path.basename(cor),
data=unw,
compression='gzip')
for key, value in unwrsc.iteritems():
group.attrs[key] = value
d1, d2 = unwrsc['DATE12'].split('-')
baseline_file = os.path.dirname(
cor) + '/' + d1 + '_' + d2 + '_baseline.rsc'
baseline = readfile.read_rsc_file(baseline_file)
for key, value in baseline.iteritems():
group.attrs[key] = value
else:
print os.path.basename(
h5file) + " already contains " + os.path.basename(cor)
meanCoherence = meanCoherence / (len(corList))
print '********************************'
print 'writing average_spatial_coherence.h5'
h5file_CorMean = tssarProjectDir + '/average_spatial_coherence.h5'
fcor_mean = h5py.File(h5file_CorMean, 'w')
group = fcor_mean.create_group('mask')
dset = group.create_dataset(os.path.basename('mask'),
data=meanCoherence,
compression='gzip')
fcor_mean.close()
print '********************************'
print 'writing meanCoherence group to the interferogram file'
gc = fcor.create_group('meanCoherence')
dset = gc.create_dataset('meanCoherence',
data=meanCoherence,
compression='gzip')
print '********************************'
fcor.close()
except:
print 'No correlation file is loaded.\n'
########################## Wrapped Interferograms ############################
try:
if os.path.isfile(tssarProjectDir + '/Wrapped.h5'):
print '\nWrapped.h5' + ' already exists.\n'
sys.exit(1)
print 'loading wrapped phase ...'
wrapList = glob.glob(wrapPath)
k = 'wrapped'
check_number(k, wrapList) # number check
wrapList, mode_width, mode_length = check_size(k,
wrapList) # size check
h5file = tssarProjectDir + '/Wrapped.h5'
fw = h5py.File(h5file)
gg = fw.create_group('wrapped')
for wrap in wrapList:
if not os.path.basename(wrap) in fw:
print 'Adding ' + wrap
group = gg.create_group(os.path.basename(wrap))
amp, unw, unwrsc = readfile.read_complex64(wrap)
dset = group.create_dataset(os.path.basename(wrap),
data=unw,
compression='gzip')
for key, value in unwrsc.iteritems():
group.attrs[key] = value
d1, d2 = unwrsc['DATE12'].split('-')
baseline_file = os.path.dirname(
wrap) + '/' + d1 + '_' + d2 + '_baseline.rsc'
baseline = readfile.read_rsc_file(baseline_file)
for key, value in baseline.iteritems():
group.attrs[key] = value
else:
print os.path.basename(
h5file) + " already contains " + os.path.basename(wrap)
fw.close()
print 'Writed ' + str(
len(wrapList)) + ' wrapped interferograms to ' + h5file
except:
print 'No wrapped interferogram is loaded.\n'
try:
geomapFile = templateContents['pysar.geomap']
geomapFile = check_variable_name(geomapFile)
cpCmd = "cp " + geomapFile + " " + tssarProjectDir
print cpCmd
os.system(cpCmd)
cpCmd = "cp " + geomapFile + ".rsc " + tssarProjectDir
print cpCmd
os.system(cpCmd)
except:
print "*********************************"
print "Warning: no geomap file given"
print "*********************************"
def main(argv):
DelayType = 'comb'
try:
opts, args = getopt.getopt(argv, "f:d:s:h:D:i:")
except getopt.GetoptError:
Usage()
sys.exit(1)
for opt, arg in opts:
if opt == '-f': timeSeriesFile = arg
elif opt == '-d': demFile = arg
elif opt == '-s': atmSource = arg
elif opt == '-h': hr = arg
elif opt == '-D': DelayType = arg
elif opt == '-i': inc_angle = arg
try:
timeSeriesFile
demFile
except:
Usage()
sys.exit(1)
demFile = ut.check_variable_name(demFile)
demCoord = ut.radar_or_geo(demFile)
h5timeseries = h5py.File(timeSeriesFile)
yref = h5timeseries['timeseries'].attrs['ref_y']
xref = h5timeseries['timeseries'].attrs['ref_x']
###############################################################
#incidence angle to map the zenith delay to the slant delay
try:
inc_angle
except:
print '+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'
print 'WARNING:'
print 'incedence angle is not specified >>>> Average look angle is used ... '
print 'For more precise results use input option -i to introduce the incidence angle file or average incodence angle'
print '++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'
input_inc_angle = 'None'
wavelength = float(h5timeseries['timeseries'].attrs['WAVELENGTH'])
inc_angle1 = float(h5timeseries['timeseries'].attrs['LOOK_REF1'])
inc_angle2 = float(h5timeseries['timeseries'].attrs['LOOK_REF2'])
inc_angle = (inc_angle1 + inc_angle2) / 2.0
print '*******************************************************************************'
print 'Near Look Angle: ' + str(inc_angle1)
print 'Far Look Angle:' + str(inc_angle2)
print 'Average Look Angle (used in pyaps to calculate delay): ' + str(
inc_angle)
print 'Acquisition time is : ' + hr
print '*******************************************************************************'
inc_angle = str(inc_angle)
if os.path.isfile(inc_angle):
incidenceFile = inc_angle
h5incidence = h5py.File(incidenceFile, 'r')
iset = h5incidence['mask'].get('mask')
inc_angle = iset[0:iset.shape[0], 0:iset.shape[1]]
h5incidence.close()
else:
inc_angle = float(inc_angle)
print 'incidence angle = ' + str(inc_angle)
inc_angle = inc_angle * pi / 180.0
################################################################
dateList = h5timeseries['timeseries'].keys()
if atmSource in ['ecmwf', 'ECMWF']:
gribSource = 'ECMWF'
if not os.path.isdir('ECMWF'):
print 'making directory: ECMWF'
os.mkdir('ECMWF')
ecmwf_file = []
for d in dateList:
ecm = './ECMWF/ERA-Int_' + d + '_' + hr + '.grb'
ecmwf_file.append(ecm)
print[d]
if not os.path.isfile(ecm):
pa.ECMWFdload([d], hr, './ECMWF/')
else:
print ecm + ' already exists.'
elif atmSource in ['narr', 'NARR']:
gribSource = 'NARR'
if not os.path.isdir('NARR'):
print 'making directory: NARR'
os.mkdir('NARR')
ecmwf_file = []
for d in dateList:
ecm = './NARR/narr-a_221_' + d + '_' + hr + '00_000.grb'
ecmwf_file.append(ecm)
print[d]
if not os.path.isfile(ecm):
pa.NARRdload([d], hr, './NARR/')
else:
print ecm + ' already exists.'
elif atmSource in ['era', 'ERA']:
gribSource = 'ERA'
if not os.path.isdir('ERA'):
print 'making directory: ERA'
os.mkdir('ERA')
ecmwf_file = []
for d in dateList:
ecm = './ERA/ERA_' + d + '_' + hr + '.grb'
ecmwf_file.append(ecm)
print[d]
if not os.path.isfile(ecm):
pa.ERAdload([d], hr, './ERA/')
else:
print ecm + ' already exists.'
elif atmSource in ['merra', 'MERRA']:
gribSource = 'MERRA'
if not os.path.isdir('MERRA'):
print 'making directory: MERRA'
os.mkdir('MERRA')
ecmwf_file = []
for d in dateList:
ecm = './MERRA/merra-' + d + '-' + hr + '.hdf'
ecmwf_file.append(ecm)
print[d]
if not os.path.isfile(ecm):
pa.MERRAdload([d], hr, './MERRA/')
else:
print ecm + ' already exists.'
else:
Usage()
sys.exit(1)
print '*******************************************************************************'
print 'Calcualting delay for each epoch.'
h5phsName = atmSource + '.h5'
h5phs = h5py.File(h5phsName, 'w')
outName = timeSeriesFile.replace(
'.h5', '_') + atmSource + '.h5' #Yunjun, Feb 15, 2015
#outName=timeSeriesFile.replace('.h5','')+'_tropCorPyAPS.h5'
h5apsCor = h5py.File(outName, 'w')
group = h5apsCor.create_group('timeseries')
group_phs = h5phs.create_group('timeseries')
#if 'X_FIRST' in h5timeseries['timeseries'].attrs.keys():
# demCoord='geo'
# print 'The coordinate system is : Geo'
#else:
# demCoord='radar'
# print 'The coordinate system is : radar'
print ecmwf_file[0]
if demCoord == 'radar':
aps1 = pa.PyAPS_rdr(str(ecmwf_file[0]),
demFile,
grib=gribSource,
verb=True,
Del=DelayType)
else:
aps1 = pa.PyAPS_geo(str(ecmwf_file[0]),
demFile,
grib=gribSource,
verb=True,
Del=DelayType)
phs1 = zeros((aps1.ny, aps1.nx))
aps1.getdelay(phs1)
phs1 = (phs1 - phs1[yref, xref]) / cos(inc_angle)
dset = group.create_dataset(dateList[0],
data=phs1 - phs1,
compression='gzip')
for i in range(1, len(ecmwf_file)):
ecm = ecmwf_file[i]
print ecm
if demCoord == 'radar':
aps = pa.PyAPS_rdr(str(ecm),
demFile,
grib=gribSource,
verb=True,
Del=DelayType)
else:
aps = pa.PyAPS_geo(str(ecm),
demFile,
grib=gribSource,
verb=True,
Del=DelayType)
phs = zeros((aps.ny, aps.nx))
aps.getdelay(phs)
phs = (phs - phs[yref, xref]) / cos(inc_angle)
phs = phs - phs1
dset = group_phs.create_dataset(dateList[i],
data=phs,
compression='gzip')
dset1 = h5timeseries['timeseries'].get(dateList[i])
data1 = dset1[0:dset1.shape[0], 0:dset1.shape[1]]
dset = group.create_dataset(dateList[i],
data=data1 + phs,
compression='gzip')
for key, value in h5timeseries['timeseries'].attrs.iteritems():
group.attrs[key] = value
group_phs.attrs[key] = value
dset1 = h5timeseries['mask'].get('mask')
Mask = dset1[0:dset1.shape[0], 0:dset1.shape[1]]
group = h5apsCor.create_group('mask')
dset = group.create_dataset('mask', data=Mask, compression='gzip')
def main(argv):
DelayType='comb'
try:
opts, args = getopt.getopt(argv,"f:d:s:h:D:i:")
except getopt.GetoptError:
Usage() ; sys.exit(1)
for opt,arg in opts:
if opt == '-f':
timeSeriesFile = arg
elif opt == '-d':
demFile = arg
elif opt == '-s':
atmSource=arg
elif opt == '-h':
hr=arg
elif opt == '-D':
DelayType=arg
elif opt == '-i':
inc_angle=arg
try:
timeSeriesFile
demFile
except:
Usage() ; sys.exit(1)
demFile=check_variable_name(demFile)
h5timeseries = h5py.File(timeSeriesFile)
yref=h5timeseries['timeseries'].attrs['ref_y']
xref=h5timeseries['timeseries'].attrs['ref_x']
###############################################################
#incidence angle to map the zenith delay to the slant delay
try:
inc_angle
except:
print '+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'
print 'WARNING:'
print 'incedence angle is not specified >>>> Average look angle is used ... '
print 'For more precise results use input option -i to introduce the incidence angle file or average incodence angle'
print '++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'
input_inc_angle='None'
wavelength=float(h5timeseries['timeseries'].attrs['WAVELENGTH'])
inc_angle1=float(h5timeseries['timeseries'].attrs['LOOK_REF1'])
inc_angle2=float(h5timeseries['timeseries'].attrs['LOOK_REF2'])
inc_angle=(inc_angle1+inc_angle2)/2.0
print '*******************************************************************************'
print 'Near Look Angle: ' + str(inc_angle1)
print 'Far Look Angle:' + str(inc_angle2)
print 'Average Look Angle (used in pyaps to calculate delay): ' + str(inc_angle)
print 'Acquisition time is : '+ hr
print '*******************************************************************************'
inc_angle=str(inc_angle)
if os.path.isfile(inc_angle):
incidenceFile=inc_angle
h5incidence=h5py.File(incidenceFile,'r')
iset=h5incidence['mask'].get('mask')
inc_angle=iset[0:iset.shape[0],0:iset.shape[1]]
h5incidence.close()
else:
inc_angle=float(inc_angle)
print 'incidence angle = '+ str(inc_angle)
inc_angle=inc_angle*pi/180.0
################################################################
dateList = h5timeseries['timeseries'].keys()
if atmSource in ['ecmwf','ECMWF']:
gribSource='ECMWF'
if not os.path.isdir('ECMWF'):
print 'making directory: ECMWF'
os.mkdir('ECMWF')
ecmwf_file=[]
for d in dateList:
ecm='./ECMWF/ERA-Int_'+d+'_'+hr+'.grb'
ecmwf_file.append(ecm)
print [d]
if not os.path.isfile(ecm):
pa.ECMWFdload([d],hr,'./ECMWF/')
else:
print ecm + ' already exists.'
elif atmSource in ['narr','NARR']:
gribSource='NARR'
if not os.path.isdir('NARR'):
print 'making directory: NARR'
os.mkdir('NARR')
ecmwf_file=[]
for d in dateList:
ecm='./NARR/narr-a_221_'+d+'_'+hr+'00_000.grb'
ecmwf_file.append(ecm)
print [d]
if not os.path.isfile(ecm):
pa.NARRdload([d],hr,'./NARR/')
else:
print ecm + ' already exists.'
elif atmSource in ['era','ERA']:
gribSource='ERA'
if not os.path.isdir('ERA'):
print 'making directory: ERA'
os.mkdir('ERA')
ecmwf_file=[]
for d in dateList:
ecm='./ERA/ERA_'+d+'_'+hr+'.grb'
ecmwf_file.append(ecm)
print [d]
if not os.path.isfile(ecm):
pa.ERAdload([d],hr,'./ERA/')
else:
print ecm + ' already exists.'
elif atmSource in ['merra','MERRA']:
gribSource='MERRA'
if not os.path.isdir('MERRA'):
print 'making directory: MERRA'
os.mkdir('MERRA')
ecmwf_file=[]
for d in dateList:
ecm='./MERRA/merra-'+d+'-'+hr+'.hdf'
ecmwf_file.append(ecm)
print [d]
if not os.path.isfile(ecm):
pa.MERRAdload([d],hr,'./MERRA/')
else:
print ecm + ' already exists.'
else:
Usage();sys.exit(1)
print '*******************************************************************************'
print 'Calcualting delay for each epoch.'
h5phsName=atmSource + '.h5'
h5phs=h5py.File(h5phsName,'w')
outName=timeSeriesFile.replace('.h5','_') + atmSource + '.h5' #Yunjun, Feb 15, 2015
# outName=timeSeriesFile.replace('.h5','')+'_tropCorPyAPS.h5'
h5apsCor=h5py.File(outName,'w')
group=h5apsCor.create_group('timeseries')
group_phs=h5phs.create_group('timeseries')
if 'X_FIRST' in h5timeseries['timeseries'].attrs.keys():
demCoord='geo'
print 'The coordinate system is : Geo'
else:
demCoord='radar'
print 'The coordinate system is : radar'
print ecmwf_file[0]
if demCoord=='radar':
aps1 = pa.PyAPS_rdr(str(ecmwf_file[0]),demFile,grib=gribSource,verb=True,Del=DelayType)
else:
aps1 = pa.PyAPS_geo(ecmwf_file[0],demFile,grib=gribSource,verb=True,Del=DelayType)
phs1 = zeros((aps1.ny,aps1.nx))
aps1.getdelay(phs1)
phs1=(phs1 - phs1[yref,xref])/cos(inc_angle)
dset = group.create_dataset(dateList[0], data= phs1- phs1, compression='gzip')
for i in range(1,len(ecmwf_file)):
ecm=ecmwf_file[i]
print ecm
if demCoord=='radar':
aps = pa.PyAPS_rdr(str(ecm),demFile,grib=gribSource,verb=True,Del=DelayType)
else:
aps = pa.PyAPS_geo(str(ecm),demFile,grib=gribSource,verb=True,Del=DelayType)
phs = zeros((aps.ny,aps.nx))
aps.getdelay(phs)
phs=(phs - phs[yref,xref])/cos(inc_angle)
phs=phs-phs1
dset = group_phs.create_dataset(dateList[i], data= phs, compression='gzip')
dset1 = h5timeseries['timeseries'].get(dateList[i])
data1 = dset1[0:dset1.shape[0],0:dset1.shape[1]]
dset = group.create_dataset(dateList[i], data= data1+phs, compression='gzip')
for key,value in h5timeseries['timeseries'].attrs.iteritems():
group.attrs[key] = value
group_phs.attrs[key] = value
dset1 = h5timeseries['mask'].get('mask')
Mask = dset1[0:dset1.shape[0],0:dset1.shape[1]]
group = h5apsCor.create_group('mask')
dset = group.create_dataset('mask', data=Mask, compression='gzip')
def main(argv):
inps = cmdLineParse()
#print '\n*************** Loading ROI_PAC Data into PySAR ****************'
inps.project_name = os.path.splitext(os.path.basename(inps.template_file))[0]
print 'project: '+inps.project_name
##### 1. Read file path
# Priority: command line input > template > auto setting
# Read template contents into inps Namespace
inps.template_file = os.path.abspath(inps.template_file)
template_dict = readfile.read_template(inps.template_file)
for key, value in template_dict.iteritems():
template_dict[key] = ut.check_variable_name(value)
keyList = template_dict.keys()
if not inps.unw and 'pysar.unwrapFiles' in keyList: inps.unw = template_dict['pysar.unwrapFiles']
if not inps.cor and 'pysar.corFiles' in keyList: inps.cor = template_dict['pysar.corFiles']
if not inps.int and 'pysar.wrapFiles' in keyList: inps.int = template_dict['pysar.wrapFiles']
if not inps.geomap and 'pysar.geomap' in keyList: inps.geomap = template_dict['pysar.geomap']
if not inps.dem_radar and 'pysar.dem.radarCoord' in keyList: inps.dem_radar = template_dict['pysar.dem.radarCoord']
if not inps.dem_geo and 'pysar.dem.geoCoord' in keyList: inps.dem_geo = template_dict['pysar.dem.geoCoord']
# Auto Setting for Geodesy Lab - University of Miami
if pysar.miami_path and 'SCRATCHDIR' in os.environ:
inps = auto_path_miami(inps, template_dict)
# TIMESERIES directory for PySAR
if not inps.timeseries_dir:
inps.timeseries_dir = os.getcwd()
if not os.path.isdir(inps.timeseries_dir):
os.mkdir(inps.timeseries_dir)
print "PySAR working directory: "+inps.timeseries_dir
# TEMPLATE file directory (to support relative path input)
inps.template_dir = os.path.dirname(inps.template_file)
os.chdir(inps.template_dir)
print 'Go to TEMPLATE directory: '+inps.template_dir
# Get all file list
inps.snap_connect = []
if inps.unw:
print 'unwrapped interferograms: '+str(inps.unw)
inps.snap_connect = inps.unw.split('.unw')[0]+'_snap_connect.byt'
inps.snap_connect = sorted(glob.glob(inps.snap_connect))
inps.unw = sorted(glob.glob(inps.unw))
if inps.int:
print 'wrapped interferograms: '+str(inps.int)
inps.int = sorted(glob.glob(inps.int))
if inps.cor:
print 'coherence files: '+str(inps.cor)
inps.cor = sorted(glob.glob(inps.cor))
try: inps.geomap = glob.glob(inps.geomap)[0]
except: inps.geomap = None
try: inps.dem_radar = glob.glob(inps.dem_radar)[-1]
except: inps.dem_radar = None
try: inps.dem_geo = glob.glob(inps.dem_geo)[0]
except: inps.dem_geo = None
print 'geomap file: '+str(inps.geomap)
print 'DEM file in radar coord: '+str(inps.dem_radar)
print 'DEM file in geo coord: '+str(inps.dem_geo)
##### 2. Load data into hdf5 file
inps.ifgram_file = inps.timeseries_dir+'/unwrapIfgram.h5'
inps.coherence_file = inps.timeseries_dir+'/coherence.h5'
inps.wrapIfgram_file = inps.timeseries_dir+'/wrapIfgram.h5'
inps.snap_connect_file = inps.timeseries_dir+'/snaphuConnectComponent.h5'
inps.mask_file = inps.timeseries_dir+'/Mask.h5'
inps.spatial_coherence_file = inps.timeseries_dir+'/average_spatial_coherence.h5'
# 2.1 multi_group_hdf5_file
# Unwrapped Interferograms
if inps.unw:
unwList = load_roipac2multi_group_h5('interferograms', inps.unw, inps.ifgram_file, vars(inps))[1]
# Update mask only when update unwrapIfgram.h5
if unwList:
print 'Generate mask from amplitude of interferograms'
roipac_nonzero_mask(inps.unw, inps.mask_file)
elif os.path.isfile(inps.ifgram_file):
print os.path.basename(inps.ifgram_file)+' already exists, no need to re-load.'
else:
sys.exit('ERROR: Cannot load/find unwrapped interferograms!')
# Optional
if inps.snap_connect:
load_roipac2multi_group_h5('snaphu_connect_component', inps.snap_connect, inps.snap_connect_file, vars(inps))
# Coherence
if inps.cor:
cohFile,corList = load_roipac2multi_group_h5('coherence', inps.cor, inps.coherence_file, vars(inps))
if corList:
meanCohCmd = 'temporal_average.py '+cohFile+' '+inps.spatial_coherence_file
print meanCohCmd
os.system(meanCohCmd)
elif os.path.isfile(inps.coherence_file):
print os.path.basename(inps.coherence_file)+' already exists, no need to re-load.'
else:
print 'WARNING: Cannot load/find coherence.'
# Wrapped Interferograms
if inps.int:
load_roipac2multi_group_h5('wrapped', inps.int, inps.wrapIfgram_file, vars(inps))
elif os.path.isfile(inps.wrapIfgram_file):
print os.path.basename(inps.wrapIfgram_file)+' already exists, no need to re-load.'
else:
print "WARNING: Cannot load/find wrapped interferograms. It's okay, continue without it ..."
# 2.2 single dataset file
if inps.geomap:
copy_roipac_file(inps.geomap, inps.timeseries_dir)
if inps.dem_radar:
copy_roipac_file(inps.dem_radar, inps.timeseries_dir)
if inps.dem_geo:
copy_roipac_file(inps.dem_geo, inps.timeseries_dir)
def main(argv):
try:
templateFile = argv[1]
except:
Usage()
sys.exit(1)
projectName = os.path.basename(templateFile.partition('.')[0])
try:
tssarProjectDir = os.getenv('TSSARDIR') + '/' + projectName
except:
tssarProjectDir = os.getenv(
'SCRATCHDIR'
) + '/' + projectName + "/TSSAR" # FA 7/2015: adopted for new directory structure
print "QQ " + tssarProjectDir
if not os.path.isdir(tssarProjectDir): os.mkdir(tssarProjectDir)
os.chdir(tssarProjectDir)
igramFile = 'LoadedData.h5'
Modified_igramFile = 'Modified_LoadedData.h5'
if os.path.isfile(Modified_igramFile):
print Modified_igramFile + ' already exists.'
igramFile = Modified_igramFile
template = readfile.read_template(templateFile)
Rlooks = template['Rlooks_unw']
#########################################
# Loading interferograms
#########################################
print '******************************************'
print ''
if os.path.isfile(igramFile):
print igramFile + ' already exists.'
else:
loadCmd = 'load_data.py ' + templateFile
print loadCmd
os.system(loadCmd)
# copyDemCmd='copy_dem_trans.py ' + templateFile
# print copyDemCmd
# os.system(copyDemCmd)
print ''
print '******************************************'
#########################################
# Check the subset
#########################################
try:
subset = template['pysar.subset.yx'].split(',')
print subset
print subset[0]
subsetOutName = 'subset_' + igramFile
subsetCmd = 'subset.py -f ' + igramFile + ' -y ' + subset[
0] + ' -x ' + subset[1] + ' -o ' + subsetOutName
print '*****************************************'
print 'Subset the area ...'
print subsetCmd
os.system(subsetCmd)
igramFile = subsetOutName
print '*****************************************'
except:
print '*****************************************'
print 'No Subset selected. Processing the whole area'
print '*****************************************'
#########################################
#Referencing all interferograms to the same pixel
#########################################
rdr_or_geo = radar_Or_geo(igramFile)
print '******************************************'
print ''
if os.path.isfile('Seeded_' + igramFile):
igramFile = 'Seeded_' + igramFile
print igramFile + ' already exists.'
else:
print 'referncing all interferograms to the same pixel.'
if 'pysar.seed.ll' in template.keys():
'Checking the lat/lon refernce point'
lat = template['pysar.seed.ll'].split(',')[0]
lon = template['pysar.seed.ll'].split(',')[1]
seedCmd = 'SeedData.py -f ' + igramFile + ' -l ' + lat + ' -L ' + lon
elif 'pysar.seed.yx' in template.keys():
'Checking y/x reference point'
y = template['pysar.seed.yx'].split(',')[0]
x = template['pysar.seed.yx'].split(',')[1]
seedCmd = 'seed_data.py -f ' + igramFile + ' -y ' + y + ' -x ' + x
else:
seedCmd = 'seed_data.py -f ' + igramFile
igramFile = 'Seeded_' + igramFile
print seedCmd
os.system(seedCmd)
print ''
print '******************************************'
############################################
#unwrapping error correction based on the
# consistency of triplets of interferograms
############################################
print '******************************************'
print ''
try:
template['pysar.unwrap_error']
if template['pysar.unwrap_error'] in ('y', 'yes', 'Yes', 'YES'):
print 'unwrapping error correction might take a while depending on the size of your data set! '
unwCmd = 'unwrap_error.py ' + igramFile
os.system(unwCmd)
igramFile = igramFile.split('.')[0] + '_unwCor.h5'
else:
print 'No unwrapping error correction.'
except:
print 'No unwrapping error correction.'
print ''
print '******************************************'
#########################################
# inversion of interferograms
########################################
print '******************************************'
print ''
if os.path.isfile(igramFile.split('.')[0] + '_unwCor.h5'):
igramFile = igramFile.split('.')[0] + '_unwCor.h5'
print igramFile + ' exists.'
if os.path.isfile('timeseries.h5'):
print 'timeseries.h5 already exists, inversion is not needed.'
else:
invertCmd = 'igram_inversion.py ' + igramFile
print invertCmd
os.system(invertCmd)
timeseriesFile = 'timeseries.h5'
print ''
print '******************************************'
##############################################
#temporal coherence:
#A parameter to evaluate the consistency of
# timeseries with the interferograms
##############################################
print '******************************************'
print ''
# if os.path.isfile('temporal_coherence.h5'):
# print 'temporal_coherence.h5 already exists.'
# else:
# tempcohCmd='temporal_coherence.py '+igramFile+' '+timeseriesFile
# print tempcohCmd
# os.system(tempcohCmd)
tempcohCmd = 'temporal_coherence.py ' + igramFile + ' ' + timeseriesFile
print tempcohCmd
os.system(tempcohCmd)
print ''
print '******************************************'
##############################################
#update Mask based on temporal coherence
# add by Yunjun Feb 15, 2015
##############################################
print '******************************************'
print ''
try:
template['pysar.mask']
if template['pysar.mask'] in ('yes', 'Yes', 'YES', 'y'):
print 'Updating mask according to temporal coherence'
cohT = template['pysar.mask.threshold']
maskCmd = 'generate_mask.py -f temporal_coherence.h5 -m ' + cohT + ' -M 1.0 -o Mask.h5'
print maskCmd
os.system(maskCmd)
else:
print 'No update for mask.'
except:
print 'No update for mask.'
print ''
print '******************************************'
##############################################
# Generate incident angle
# add by Yunjun Feb 15, 2015
##############################################
print '******************************************'
print ''
inciCmd = 'incidence_angle.py -f timeseries.h5'
print inciCmd
os.system(inciCmd)
print ''
print '******************************************'
##############################################
#If Satellite is Envisat and if Coordinate
#system is radar then LOD correction
##############################################
print '******************************************'
print ''
h5file = h5py.File(timeseriesFile, 'r')
if rdr_or_geo == 'radar':
if h5file['timeseries'].attrs['PLATFORM'] == 'ENVISAT':
LODcmd = 'lod.py ' + timeseriesFile
print LODcmd
os.system(LODcmd)
timeseriesFile = timeseriesFile.split('.')[0] + '_LODcor.h5'
print ''
print '******************************************'
##############################################
# Tropospheric Correction
##############################################
print '******************************************'
print ''
try:
if (template['pysar.tropospheric_delay'] in ('y', 'yes', 'Yes', 'YES')
) and template['pysar.orbit_error.method'] == 'BaseTropCor':
print '''
+++++++++++++++++++++++++++++++++++++++++++++++++++
WARNING:
Orbital error correction was BaseTropCor.
Tropospheric correction was already applied simultaneous with baseline error correction.
Tropospheric correction can not be applied again.
To apply the tropospheric correction separate from baseline error correction, chhose other existing options for orbital error correction.
+++++++++++++++++++++++++++++++++++++++++++++++++++
'''
template['pysar.tropospheric_delay'] = 'no'
except:
print 'Checking the tropospheric delay correction ...'
if template['pysar.tropospheric_delay'] in ('y', 'yes', 'Yes', 'YES'):
# demFile='radar_'+Rlooks+'rlks.hgt'
demFile = template['pysar.dem']
demFile = check_variable_name(demFile)
# print 'DEM file: '+demFile
if not os.path.isfile(demFile):
print '++++++++++++++++++++++++++++++++++++++++++++++'
print 'Error:'
print 'DEM (radar_*rlks.hgt file) was not found!'
print 'Continue without tropospheric correction ...'
print '++++++++++++++++++++++++++++++++++++++++++++++'
else:
if template['pysar.tropospheric_delay.method'] in [
'height-correlation', 'height_correlation',
'Height-Correlation', 'Height_Correlation'
]:
print 'tropospheric delay correction with height-correlation approach'
try:
polyOrder = template['pysar.trop.polyOrder']
except:
print 'Deafult polynomial order for troposphreic correction = 1'
polyOrder = '1'
cmdTrop = 'tropospheric_correction.py' + ' -f ' + timeseriesFile + ' -d ' + demfile + ' -p ' + polyOrder
os.system(cmdTrop)
timeseriesFile = timeseriesFile.split('.')[0] + '_tropCor.h5'
elif template['pysar.tropospheric_delay.method'] == 'pyaps':
print 'Atmospheric correction using Numerical Weather Models (using PyAPS software)'
print 'reading DEM, source of NWM and acquisition time from template file'
source_of_NWM = template['pysar.Numerical_Weather_Model']
print 'Numerical Weather Model: ' + source_of_NWM
acquisition_time = template['pysar.acquisition_time']
print 'acquisition time: ' + acquisition_time
# cmdTrop = ["tropcor_pyaps.py -f ",timeseriesFile," -d ",demFile," -s ",source_of_NWM," -h ",acquisition_time," -i incidence_angle.h5"]
cmdTrop = 'tropcor_pyaps.py -f ' + timeseriesFile + ' -d ' + demFile + ' -s ' + source_of_NWM + ' -h ' + acquisition_time + ' -i incidence_angle.h5'
print cmdTrop
os.system(cmdTrop)
# subprocess.Popen(cmdTrop).wait()
timeseriesFile = timeseriesFile.split(
'.')[0] + '_' + source_of_NWM + '.h5'
else:
print 'Atmospheric correction method not recognized.'
else:
print 'No atmospheric delay correction.'
print ''
print '******************************************'
##############################################
#topographic residuals
##############################################
print '******************************************'
print ''
try:
template['pysar.topo_error']
if template['pysar.topo_error'] in ('yes', 'Yes', 'YES', 'y'):
print 'Correcting topographic residuals'
topoCmd = 'dem_error.py ' + timeseriesFile + ' ' + igramFile
print topoCmd
os.system(topoCmd)
timeseriesFile = timeseriesFile.split('.')[0] + '_demCor.h5'
else:
print 'No correction for topographic residuals.'
except:
print 'No correction for topographic residuals.'
print ''
print '******************************************'
##############################################
#Orbit correction
##############################################
print '******************************************'
print ''
try:
template['pysar.orbit_error']
if template['pysar.orbit_error'] in ('yes', 'Yes', 'YES', 'y'):
try:
orbit_error_method = template['pysar.orbit_error.method']
print 'orbit error correction method : ' + orbit_error_method
if orbit_error_method in [
'quadratic', 'plane', 'quardatic_range',
'quadratic_azimiuth', 'plane_range', 'plane_azimuth'
]:
orbitCmd = 'remove_plane.py ' + timeseriesFile + ' ' + template[
'pysar.orbit_error.method'] #+ ' Mask.h5'
timeseriesFile = timeseriesFile.split('.')[
0] + '_' + template['pysar.orbit_error.method'] + '.h5'
print orbitCmd
os.system(orbitCmd)
elif orbit_error_method == 'baselineCor':
orbitCmd = 'baseline_error.py ' + timeseriesFile #+ ' Mask.h5'
print orbitCmd
try:
h5file = h5py.File(timeseriesFile, 'r')
daz = float(
h5file['timeseries'].attrs['AZIMUTH_PIXEL_SIZE'])
os.system(orbitCmd)
timeseriesFile = timeseriesFile.split(
'.')[0] + '_' + template[
'pysar.orbit_error.method'] + '.h5'
except:
print 'WARNING!'
print 'Skipping orbital error correction.'
print 'baselineCor method can only be applied in radar coordinate'
elif orbit_error_method == 'BaseTropCor':
demfile = template['pysar.dem']
demfile = check_variable_name(demfile)
try:
polyOrder = template['pysar.trop.polyOrder']
except:
print 'Deafult polynomial order for troposphreic correction = 1'
polyOrder = 1
try:
h5file = h5py.File(timeseriesFile, 'r')
daz = float(
h5file['timeseries'].attrs['AZIMUTH_PIXEL_SIZE'])
orbitCmd = 'baseline_trop.py ' + timeseriesFile + ' ' + demfile + ' ' + polyOrder + 'range_and_azimuth'
print 'Joint estimation of Baseline error and tropospheric delay [height-correlation approach]'
print orbitCmd
os.system(orbitCmd)
timeseriesFile = timeseriesFile.split(
'.')[0] + '_' + template[
'pysar.orbit_error.method'] + '.h5'
except:
print 'WARNING!'
print 'Skipping orbital error correction.'
print 'baselineCor method can only be applied in radar coordinate'
else:
print '+++++++++++++++++++++++++++++++++++++++++++++++++++++++'
print 'WARNING!'
print 'Orbital error correction method was not recognized!'
print 'Possible options are:'
print 'quadratic, plane, quardatic_range, quadratic_azimiuth, plane_range, plane_azimuth,baselineCor,BaseTropCor'
print 'Continue without orbital errors correction...'
print '+++++++++++++++++++++++++++++++++++++++++++++++++++++++'
except:
print 'No orbital errors correction.'
else:
print 'No orbital errors correction.'
except:
print 'No orbital errors correction.'
print ''
print '******************************************'
#############################################
#Velocity and rmse maps
#############################################
print '******************************************'
print ''
velCmd = 'timeseries2velocity.py ' + timeseriesFile
print velCmd
os.system(velCmd)
print ''
print '******************************************'
#############################################
#Masking the velocity based on the temporal
#coherence or rmse if it's specified
#############################################
print '******************************************'
print ''
try:
template['pysar.mask']
if template['pysar.mask'] in ('yes', 'Yes', 'YES', 'y'):
try:
template['pysar.mask.threshold']
maskCmd = 'masking.py -f velocity.h5 -m temporal_coherence.h5 -t ' + template[
'pysar.mask.threshold']
print 'Masking the velocity file using the temporal coherence with the threshold of ' + template[
'pysar.mask.threshold']
except:
maskCmd = 'Masking.py -f velocity.h5 -m temporal_coherence.h5 -t 0.7'
print 'Masking the velocity file using the temporal coherence with the threshold of 0.7'
os.system(maskCmd)
# rmCmd='rm velocity.h5'
# os.system(rmCmd)
# mvCmd='mv velocity_masked.h5 velocity.h5'
# os.system(mvCmd)
else:
print 'No masking applied'
except:
print 'No masking applied'
print ''
print '******************************************'
############################################
#Geocoding
############################################
print '******************************************'
print ''
try:
template['pysar.geocode']
if template['pysar.geocode'] in ('y', 'yes', 'Yes', 'YES'):
geomapFile = 'geomap_' + Rlooks + 'rlks.trans'
# geoCmd = 'geocode.py '+timeseriesFile+' '+geomapFile
# print geoCmd
# os.system(geoCmd)
geoCmd = 'geocode.py velocity.h5 ' + geomapFile
print geoCmd
os.system(geoCmd)
geoCmd = 'geocode.py Mask.h5 ' + geomapFile
print geoCmd
os.system(geoCmd)
# maskCmd = 'Masking.py -f geo_'+timeseriesFile+' -m geo_Mask.h5'
# print maskCmd
# os.system(maskCmd)
maskCmd = 'masking.py -f geo_velocity.h5 -m geo_Mask.h5'
print maskCmd
os.system(maskCmd)
else:
print 'No geocoding applied'
except:
print 'No geocoding applied'
print ''
print '******************************************'
#############################################
# PySAR v1.0 #
#############################################
print ''
print '###############################################'
print ''
print 'End of PySAR processing.'
print ''
print '################################################'
def main(argv):
try:
templateFile = argv[1]
except:
Usage();sys.exit(1)
projectName = os.path.basename(templateFile.partition('.')[0])
try:
tssarProjectDir = os.getenv('TSSARDIR') +'/'+projectName
except:
tssarProjectDir = os.getenv('SCRATCHDIR') + '/' + projectName + "/TSSAR" # FA 7/2015: adopted for new directory structure
print "QQ " + tssarProjectDir
if not os.path.isdir(tssarProjectDir): os.mkdir(tssarProjectDir)
os.chdir(tssarProjectDir)
igramFile = 'LoadedData.h5'
Modified_igramFile = 'Modified_LoadedData.h5'
if os.path.isfile(Modified_igramFile):
print Modified_igramFile + ' already exists.'
igramFile=Modified_igramFile
template = readfile.read_template(templateFile)
Rlooks = template['Rlooks_unw']
#########################################
# Loading interferograms
#########################################
print '******************************************'
print''
if os.path.isfile(igramFile):
print igramFile + ' already exists.'
else:
loadCmd='load_data.py ' + templateFile
print loadCmd
os.system(loadCmd)
# copyDemCmd='copy_dem_trans.py ' + templateFile
# print copyDemCmd
# os.system(copyDemCmd)
print''
print '******************************************'
#########################################
# Check the subset
#########################################
try:
subset= template['pysar.subset.yx'].split(',')
print subset
print subset[0]
subsetOutName='subset_'+igramFile
subsetCmd='subset.py -f '+ igramFile + ' -y '+subset[0]+' -x '+subset[1] + ' -o ' + subsetOutName
print '*****************************************'
print 'Subset the area ...'
print subsetCmd
os.system(subsetCmd)
igramFile=subsetOutName
print '*****************************************'
except:
print '*****************************************'
print 'No Subset selected. Processing the whole area'
print '*****************************************'
#########################################
#Referencing all interferograms to the same pixel
#########################################
rdr_or_geo=radar_Or_geo(igramFile)
print '******************************************'
print''
if os.path.isfile('Seeded_'+igramFile):
igramFile = 'Seeded_'+igramFile
print igramFile + ' already exists.'
else:
print 'referncing all interferograms to the same pixel.'
if 'pysar.seed.ll' in template.keys():
'Checking the lat/lon refernce point'
lat= template['pysar.seed.ll'].split(',')[0]
lon= template['pysar.seed.ll'].split(',')[1]
seedCmd= 'SeedData.py -f ' + igramFile + ' -l ' +lat+ ' -L '+lon
elif 'pysar.seed.yx' in template.keys():
'Checking y/x reference point'
y= template['pysar.seed.yx'].split(',')[0]
x= template['pysar.seed.yx'].split(',')[1]
seedCmd= 'seed_data.py -f ' + igramFile + ' -y ' +y+ ' -x '+x
else:
seedCmd= 'seed_data.py -f ' + igramFile
igramFile = 'Seeded_'+igramFile
print seedCmd
os.system(seedCmd)
print''
print '******************************************'
############################################
#unwrapping error correction based on the
# consistency of triplets of interferograms
############################################
print '******************************************'
print''
try:
template['pysar.unwrap_error']
if template['pysar.unwrap_error'] in ('y','yes','Yes','YES'):
print 'unwrapping error correction might take a while depending on the size of your data set! '
unwCmd='unwrap_error.py '+igramFile
os.system(unwCmd)
igramFile=igramFile.split('.')[0]+'_unwCor.h5'
else:
print 'No unwrapping error correction.'
except:
print 'No unwrapping error correction.'
print''
print '******************************************'
#########################################
# inversion of interferograms
########################################
print '******************************************'
print''
if os.path.isfile(igramFile.split('.')[0]+'_unwCor.h5'):
igramFile = igramFile.split('.')[0]+'_unwCor.h5'
print igramFile + ' exists.'
if os.path.isfile('timeseries.h5'):
print 'timeseries.h5 already exists, inversion is not needed.'
else:
invertCmd = 'igram_inversion.py '+ igramFile
print invertCmd
os.system(invertCmd)
timeseriesFile='timeseries.h5'
print''
print '******************************************'
##############################################
#temporal coherence:
#A parameter to evaluate the consistency of
# timeseries with the interferograms
##############################################
print '******************************************'
print''
# if os.path.isfile('temporal_coherence.h5'):
# print 'temporal_coherence.h5 already exists.'
# else:
# tempcohCmd='temporal_coherence.py '+igramFile+' '+timeseriesFile
# print tempcohCmd
# os.system(tempcohCmd)
tempcohCmd='temporal_coherence.py '+igramFile+' '+timeseriesFile
print tempcohCmd
os.system(tempcohCmd)
print''
print '******************************************'
##############################################
#update Mask based on temporal coherence
# add by Yunjun Feb 15, 2015
##############################################
print '******************************************'
print''
try:
template['pysar.mask']
if template['pysar.mask'] in ('yes','Yes','YES','y'):
print 'Updating mask according to temporal coherence'
cohT=template['pysar.mask.threshold']
maskCmd='generate_mask.py -f temporal_coherence.h5 -m '+ cohT +' -M 1.0 -o Mask.h5'
print maskCmd
os.system(maskCmd)
else:
print 'No update for mask.'
except:
print 'No update for mask.'
print''
print '******************************************'
##############################################
# Generate incident angle
# add by Yunjun Feb 15, 2015
##############################################
print '******************************************'
print''
inciCmd='incidence_angle.py -f timeseries.h5'
print inciCmd
os.system(inciCmd)
print''
print '******************************************'
##############################################
#If Satellite is Envisat and if Coordinate
#system is radar then LOD correction
##############################################
print '******************************************'
print''
h5file=h5py.File(timeseriesFile,'r')
if rdr_or_geo =='radar':
if h5file['timeseries'].attrs['PLATFORM']=='ENVISAT':
LODcmd='lod.py '+timeseriesFile
print LODcmd
os.system(LODcmd)
timeseriesFile=timeseriesFile.split('.')[0]+'_LODcor.h5'
print''
print '******************************************'
##############################################
# Tropospheric Correction
##############################################
print '******************************************'
print''
try:
if (template['pysar.tropospheric_delay'] in ('y','yes','Yes','YES')) and template['pysar.orbit_error.method']=='BaseTropCor':
print '''
+++++++++++++++++++++++++++++++++++++++++++++++++++
WARNING:
Orbital error correction was BaseTropCor.
Tropospheric correction was already applied simultaneous with baseline error correction.
Tropospheric correction can not be applied again.
To apply the tropospheric correction separate from baseline error correction, chhose other existing options for orbital error correction.
+++++++++++++++++++++++++++++++++++++++++++++++++++
'''
template['pysar.tropospheric_delay']='no'
except:
print 'Checking the tropospheric delay correction ...'
if template['pysar.tropospheric_delay'] in ('y','yes','Yes','YES'):
# demFile='radar_'+Rlooks+'rlks.hgt'
demFile=template['pysar.dem']
demFile=check_variable_name(demFile)
# print 'DEM file: '+demFile
if not os.path.isfile(demFile):
print '++++++++++++++++++++++++++++++++++++++++++++++'
print 'Error:'
print 'DEM (radar_*rlks.hgt file) was not found!'
print 'Continue without tropospheric correction ...'
print '++++++++++++++++++++++++++++++++++++++++++++++'
else:
if template['pysar.tropospheric_delay.method'] in ['height-correlation','height_correlation','Height-Correlation','Height_Correlation']:
print 'tropospheric delay correction with height-correlation approach'
try:
polyOrder=template['pysar.trop.polyOrder']
except:
print 'Deafult polynomial order for troposphreic correction = 1'
polyOrder='1'
cmdTrop='tropospheric_correction.py'+ ' -f '+ timeseriesFile + ' -d '+ demfile + ' -p '+ polyOrder
os.system(cmdTrop)
timeseriesFile=timeseriesFile.split('.')[0]+'_tropCor.h5'
elif template['pysar.tropospheric_delay.method']=='pyaps':
print 'Atmospheric correction using Numerical Weather Models (using PyAPS software)'
print 'reading DEM, source of NWM and acquisition time from template file'
source_of_NWM=template['pysar.Numerical_Weather_Model']
print 'Numerical Weather Model: '+source_of_NWM
acquisition_time=template['pysar.acquisition_time']
print 'acquisition time: '+acquisition_time
# cmdTrop = ["tropcor_pyaps.py -f ",timeseriesFile," -d ",demFile," -s ",source_of_NWM," -h ",acquisition_time," -i incidence_angle.h5"]
cmdTrop = 'tropcor_pyaps.py -f '+timeseriesFile+ ' -d '+ demFile +' -s ' + source_of_NWM + ' -h '+ acquisition_time + ' -i incidence_angle.h5'
print cmdTrop
os.system(cmdTrop)
# subprocess.Popen(cmdTrop).wait()
timeseriesFile=timeseriesFile.split('.')[0]+'_'+source_of_NWM+'.h5'
else:
print 'Atmospheric correction method not recognized.'
else:
print 'No atmospheric delay correction.'
print''
print '******************************************'
##############################################
#topographic residuals
##############################################
print '******************************************'
print''
try:
template['pysar.topo_error']
if template['pysar.topo_error'] in ('yes','Yes','YES','y'):
print 'Correcting topographic residuals'
topoCmd='dem_error.py '+ timeseriesFile +' '+ igramFile
print topoCmd
os.system(topoCmd)
timeseriesFile=timeseriesFile.split('.')[0]+'_demCor.h5'
else:
print 'No correction for topographic residuals.'
except:
print 'No correction for topographic residuals.'
print''
print '******************************************'
##############################################
#Orbit correction
##############################################
print '******************************************'
print''
try:
template['pysar.orbit_error']
if template['pysar.orbit_error'] in ('yes','Yes','YES','y'):
try:
orbit_error_method=template['pysar.orbit_error.method']
print 'orbit error correction method : '+orbit_error_method
if orbit_error_method in ['quadratic', 'plane', 'quardatic_range', 'quadratic_azimiuth', 'plane_range', 'plane_azimuth']:
orbitCmd='remove_plane.py '+timeseriesFile+' '+template['pysar.orbit_error.method'] #+ ' Mask.h5'
timeseriesFile=timeseriesFile.split('.')[0]+'_'+template['pysar.orbit_error.method']+'.h5'
print orbitCmd
os.system(orbitCmd)
elif orbit_error_method == 'baselineCor':
orbitCmd='baseline_error.py ' +timeseriesFile #+ ' Mask.h5'
print orbitCmd
try:
h5file=h5py.File(timeseriesFile,'r')
daz=float(h5file['timeseries'].attrs['AZIMUTH_PIXEL_SIZE'])
os.system(orbitCmd)
timeseriesFile=timeseriesFile.split('.')[0]+'_'+template['pysar.orbit_error.method']+'.h5'
except:
print 'WARNING!'
print 'Skipping orbital error correction.'
print 'baselineCor method can only be applied in radar coordinate'
elif orbit_error_method =='BaseTropCor':
demfile=template['pysar.dem']
demfile=check_variable_name(demfile)
try:
polyOrder=template['pysar.trop.polyOrder']
except:
print 'Deafult polynomial order for troposphreic correction = 1'
polyOrder=1
try:
h5file=h5py.File(timeseriesFile,'r')
daz=float(h5file['timeseries'].attrs['AZIMUTH_PIXEL_SIZE'])
orbitCmd='baseline_trop.py '+timeseriesFile+' '+ demfile +' '+ polyOrder +'range_and_azimuth'
print 'Joint estimation of Baseline error and tropospheric delay [height-correlation approach]'
print orbitCmd
os.system(orbitCmd)
timeseriesFile=timeseriesFile.split('.')[0]+'_'+template['pysar.orbit_error.method']+'.h5'
except:
print 'WARNING!'
print 'Skipping orbital error correction.'
print 'baselineCor method can only be applied in radar coordinate'
else:
print '+++++++++++++++++++++++++++++++++++++++++++++++++++++++'
print 'WARNING!'
print 'Orbital error correction method was not recognized!'
print 'Possible options are:'
print 'quadratic, plane, quardatic_range, quadratic_azimiuth, plane_range, plane_azimuth,baselineCor,BaseTropCor'
print 'Continue without orbital errors correction...'
print '+++++++++++++++++++++++++++++++++++++++++++++++++++++++'
except:
print 'No orbital errors correction.'
else:
print 'No orbital errors correction.'
except:
print 'No orbital errors correction.'
print''
print '******************************************'
#############################################
#Velocity and rmse maps
#############################################
print '******************************************'
print''
velCmd='timeseries2velocity.py '+timeseriesFile
print velCmd
os.system(velCmd)
print''
print '******************************************'
#############################################
#Masking the velocity based on the temporal
#coherence or rmse if it's specified
#############################################
print '******************************************'
print''
try:
template['pysar.mask']
if template['pysar.mask'] in ('yes','Yes','YES','y'):
try:
template['pysar.mask.threshold']
maskCmd='masking.py -f velocity.h5 -m temporal_coherence.h5 -t '+template['pysar.mask.threshold']
print 'Masking the velocity file using the temporal coherence with the threshold of '+template['pysar.mask.threshold']
except:
maskCmd='Masking.py -f velocity.h5 -m temporal_coherence.h5 -t 0.7'
print 'Masking the velocity file using the temporal coherence with the threshold of 0.7'
os.system(maskCmd)
# rmCmd='rm velocity.h5'
# os.system(rmCmd)
# mvCmd='mv velocity_masked.h5 velocity.h5'
# os.system(mvCmd)
else:
print 'No masking applied'
except:
print 'No masking applied'
print''
print '******************************************'
############################################
#Geocoding
############################################
print '******************************************'
print''
try:
template['pysar.geocode']
if template['pysar.geocode'] in ('y','yes','Yes','YES'):
geomapFile='geomap_'+Rlooks+'rlks.trans'
# geoCmd = 'geocode.py '+timeseriesFile+' '+geomapFile
# print geoCmd
# os.system(geoCmd)
geoCmd = 'geocode.py velocity.h5 '+geomapFile
print geoCmd
os.system(geoCmd)
geoCmd = 'geocode.py Mask.h5 '+geomapFile
print geoCmd
os.system(geoCmd)
# maskCmd = 'Masking.py -f geo_'+timeseriesFile+' -m geo_Mask.h5'
# print maskCmd
# os.system(maskCmd)
maskCmd = 'masking.py -f geo_velocity.h5 -m geo_Mask.h5'
print maskCmd
os.system(maskCmd)
else:
print 'No geocoding applied'
except:
print 'No geocoding applied'
print''
print '******************************************'
#############################################
# PySAR v1.0 #
#############################################
print''
print '###############################################'
print ''
print 'End of PySAR processing.'
print ''
print '################################################'
def main(argv):
try:
templateFile = argv[1]
except:
Usage()
sys.exit(1)
from pysar._pysar_utilities import check_variable_name
templateContents = readfile.read_template(templateFile)
projectName = os.path.basename(templateFile).partition(".")[0]
try:
processProjectDir = argv[2]
tssarProjectDir = argv[3]
except:
if os.getenv("PARENTDIR"):
processProjectDir = os.getenv("SCRATCHDIR") + "/" + projectName + "/PROCESS"
tssarProjectDir = os.getenv("SCRATCHDIR") + "/" + projectName + "/TSSAR"
else:
processProjectDir = os.getenv("PROCESSDIR") + "/" + projectName
tssarProjectDir = os.getenv("TSSARDIR") + "/" + projectName
print "\n*************** Loading Data into PySAR ****************"
print "PROCESS directory: " + processProjectDir
print "TSSAR directory: " + tssarProjectDir
if not os.path.isdir(tssarProjectDir):
os.mkdir(tssarProjectDir)
########### Use defaults if paths not given in template file #########
import h5py
import numpy as np
optionName = {}
optionName["interferograms"] = "pysar.inputFiles"
optionName["coherence"] = "pysar.corFiles"
optionName["wrapped"] = "pysar.wrappedFiles"
optionName["geomap"] = "pysar.geomap"
optionName["demGeo"] = "pysar.dem.geoCoord"
optionName["demRdr"] = "pysar.dem.radarCoord"
try:
igramPath = templateContents["pysar.inputFiles"]
igramPath = check_variable_name(igramPath)
except:
igramPath = processProjectDir + "/DONE/IFGRAM*/filt_*.unw"
print "Path pattern for unwrapped interferogram: " + igramPath
# except: igramPath = os.getenv('SCRATCHDIR') + '/' + projectName + '/PROCESS/DONE/IFGRAM*/filt_*.unw'
try:
corPath = templateContents["pysar.corFiles"]
corPath = check_variable_name(corPath)
except:
corPath = processProjectDir + "/DONE/IFGRAM*/filt_*rlks.cor"
print "Path pattern for coherence: " + corPath
try:
wrapPath = templateContents["pysar.wrappedFiles"]
wrapPath = check_variable_name(wrapPath)
except:
wrapPath = processProjectDir + "/DONE/IFGRAM*/filt_*rlks.int"
print "Path pattern for wrapped interferogram: " + wrapPath
# try: demRdrPath = templateContents['pysar.dem.radarCoord']; demRdrPath = check_variable_name(demRdrPath)
# except:
# demRdrList=glob.glob(demRdrPath)
###########################################################################
######################### Unwrapped Interferograms ########################
try:
if os.path.isfile(tssarProjectDir + "/LoadedData.h5"):
print "\nLoadedData.h5" + " already exists."
sys.exit(1)
igramList = glob.glob(igramPath)
igramList = sorted(igramList)
k = "interferograms"
check_number(k, optionName[k], igramList) # number check
print "loading interferograms ..."
igramList, mode_width, mode_length = check_size(k, igramList) # size check
igramList = sorted(igramList)
h5file = tssarProjectDir + "/LoadedData.h5"
f = h5py.File(h5file, "w")
gg = f.create_group("interferograms")
MaskZero = np.ones([int(mode_length), int(mode_width)])
for igram in igramList:
if not os.path.basename(igram) in f:
print "Adding " + igram
group = gg.create_group(os.path.basename(igram))
amp, unw, unwrsc = readfile.read_float32(igram)
MaskZero *= amp
dset = group.create_dataset(os.path.basename(igram), data=unw, compression="gzip")
for key, value in unwrsc.iteritems():
group.attrs[key] = value
d1, d2 = unwrsc["DATE12"].split("-")
baseline_file = os.path.dirname(igram) + "/" + d1 + "_" + d2 + "_baseline.rsc"
baseline = readfile.read_roipac_rsc(baseline_file)
for key, value in baseline.iteritems():
group.attrs[key] = value
group.attrs["PROJECT_NAME"] = projectName
group.attrs["UNIT"] = "radian"
else:
print os.path.basename(h5file) + " already contains " + os.path.basename(igram)
Mask = np.ones([int(mode_length), int(mode_width)])
Mask[MaskZero == 0] = 0
# gm = f.create_group('mask')
# dset = gm.create_dataset('mask', data=Mask, compression='gzip')
f.close()
############## Mask file ###############
print "writing to Mask.h5\n"
# Mask=np.ones([int(mode_length),int(mode_width)])
# Mask[MaskZero==0]=0
h5file = tssarProjectDir + "/Mask.h5"
h5mask = h5py.File(h5file, "w")
group = h5mask.create_group("mask")
dset = group.create_dataset(os.path.basename("mask"), data=Mask, compression="gzip")
for key, value in unwrsc.iteritems():
group.attrs[key] = value
h5mask.close()
except:
print "No unwrapped interferogram is loaded.\n"
########################################################################
############################# Coherence ################################
try:
if os.path.isfile(tssarProjectDir + "/Coherence.h5"):
print "\nCoherence.h5" + " already exists."
sys.exit(1)
corList = glob.glob(corPath)
corList = sorted(corList)
k = "coherence"
check_number(k, optionName[k], corList) # number check
print "loading coherence files ..."
corList, mode_width, mode_length = check_size(k, corList) # size check
corList = sorted(corList)
h5file = tssarProjectDir + "/Coherence.h5"
fcor = h5py.File(h5file, "w")
gg = fcor.create_group("coherence")
meanCoherence = np.zeros([int(mode_length), int(mode_width)])
for cor in corList:
if not os.path.basename(cor) in fcor:
print "Adding " + cor
group = gg.create_group(os.path.basename(cor))
amp, unw, unwrsc = readfile.read_float32(cor)
meanCoherence += unw
dset = group.create_dataset(os.path.basename(cor), data=unw, compression="gzip")
for key, value in unwrsc.iteritems():
group.attrs[key] = value
d1, d2 = unwrsc["DATE12"].split("-")
baseline_file = os.path.dirname(cor) + "/" + d1 + "_" + d2 + "_baseline.rsc"
baseline = readfile.read_roipac_rsc(baseline_file)
for key, value in baseline.iteritems():
group.attrs[key] = value
group.attrs["PROJECT_NAME"] = projectName
group.attrs["UNIT"] = "1"
else:
print os.path.basename(h5file) + " already contains " + os.path.basename(cor)
# fcor.close()
########### mean coherence file ###############
meanCoherence = meanCoherence / (len(corList))
print "writing meanCoherence group to the coherence h5 file"
gc = fcor.create_group("meanCoherence")
dset = gc.create_dataset("meanCoherence", data=meanCoherence, compression="gzip")
print "writing average_spatial_coherence.h5\n"
h5file_CorMean = tssarProjectDir + "/average_spatial_coherence.h5"
fcor_mean = h5py.File(h5file_CorMean, "w")
group = fcor_mean.create_group("mask")
dset = group.create_dataset(os.path.basename("mask"), data=meanCoherence, compression="gzip")
for key, value in unwrsc.iteritems():
group.attrs[key] = value
fcor_mean.close()
fcor.close()
except:
print "No correlation file is loaded.\n"
##############################################################################
########################## Wrapped Interferograms ############################
try:
if os.path.isfile(tssarProjectDir + "/Wrapped.h5"):
print "\nWrapped.h5" + " already exists."
sys.exit(1)
wrapList = glob.glob(wrapPath)
wrapList = sorted(wrapList)
k = "wrapped"
check_number(k, optionName[k], wrapList) # number check
print "loading wrapped phase ..."
wrapList, mode_width, mode_length = check_size(k, wrapList) # size check
wrapList = sorted(wrapList)
h5file = tssarProjectDir + "/Wrapped.h5"
fw = h5py.File(h5file, "w")
gg = fw.create_group("wrapped")
for wrap in wrapList:
if not os.path.basename(wrap) in fw:
print "Adding " + wrap
group = gg.create_group(os.path.basename(wrap))
amp, unw, unwrsc = readfile.read_complex_float32(wrap)
dset = group.create_dataset(os.path.basename(wrap), data=unw, compression="gzip")
for key, value in unwrsc.iteritems():
group.attrs[key] = value
d1, d2 = unwrsc["DATE12"].split("-")
baseline_file = os.path.dirname(wrap) + "/" + d1 + "_" + d2 + "_baseline.rsc"
baseline = readfile.read_roipac_rsc(baseline_file)
for key, value in baseline.iteritems():
group.attrs[key] = value
group.attrs["PROJECT_NAME"] = projectName
group.attrs["UNIT"] = "radian"
else:
print os.path.basename(h5file) + " already contains " + os.path.basename(wrap)
fw.close()
print "Writed " + str(len(wrapList)) + " wrapped interferograms to " + h5file + "\n"
except:
print "No wrapped interferogram is loaded.\n"
##############################################################################
################################# geomap.trans ###############################
try:
geomapPath = tssarProjectDir + "/geomap*.trans"
geomapList = glob.glob(geomapPath)
if len(geomapList) > 0:
print "\ngeomap*.trans" + " already exists."
sys.exit(1)
geomapPath = templateContents["pysar.geomap"]
geomapPath = check_variable_name(geomapPath)
geomapList = glob.glob(geomapPath)
cpCmd = "cp " + geomapList[0] + " " + tssarProjectDir
print cpCmd
os.system(cpCmd)
cpCmd = "cp " + geomapList[0] + ".rsc " + tssarProjectDir
print cpCmd + "\n"
os.system(cpCmd)
except:
# print "*********************************"
print "no geomap file is loaded.\n"
# print "*********************************\n"
##############################################################################
################################## DEM #####################################
try:
demRdrPath = tssarProjectDir + "/radar*.hgt"
demRdrList = glob.glob(demRdrPath)
if len(demRdrList) > 0:
print "\nradar*.hgt" + " already exists."
sys.exit(1)
demRdrPath = templateContents["pysar.dem.radarCoord"]
demRdrPath = check_variable_name(demRdrPath)
demRdrList = glob.glob(demRdrPath)
cpCmd = "cp " + demRdrList[0] + " " + tssarProjectDir
print cpCmd
os.system(cpCmd)
cpCmd = "cp " + demRdrList[0] + ".rsc " + tssarProjectDir
print cpCmd + "\n"
os.system(cpCmd)
except:
# print "*********************************"
print "no DEM (radar coordinate) file is loaded.\n"
# print "*********************************"
try:
demGeoPath = tssarProjectDir + "/*.dem"
demGeoList = glob.glob(demGeoPath)
if len(demGeoList) > 0:
print "\n*.dem" + " already exists."
sys.exit(1)
demGeoPath = templateContents["pysar.dem.geoCoord"]
demGeoPath = check_variable_name(demGeoPath)
demGeoList = glob.glob(demGeoPath)
cpCmd = "cp " + demGeoList[0] + " " + tssarProjectDir
print cpCmd
os.system(cpCmd)
cpCmd = "cp " + demGeoList[0] + ".rsc " + tssarProjectDir
print cpCmd + "\n"
os.system(cpCmd)
except:
# print "*********************************"
print "no DEM (geo coordinate) file is loaded.\n"
