def main(argv):
parser = build_parser()
parseArgs = parser.parse_args()
username = parseArgs.user
password = parseArgs.password
host = parseArgs.host
db = parseArgs.db
working_dir = parseArgs.folder
# make sure we have a final / so the below code doesn't break
if working_dir[-1] != "/":
working_dir += "/"
unavco_name = parseArgs.unavco_name
attributes_file = working_dir + "add_Attribute.txt"
attributes = readfile.read_template(attributes_file)
dbController = InsarDatabaseController(username, password, host, db)
dbController.connect()
for key in attributes:
print("Setting attribute " + key + " to " + attributes[key])
if key == "plotAttributes":
dbController.add_plot_attribute(unavco_name, key, attributes[key])
else:
dbController.add_attribute(unavco_name, key, attributes[key])
dbController.index_table_on("extra_attributes", "area_id", "area_id_idx")
dbController.close()
def read_template2inps(template_file, inps=None):
'''Read input template file into inps.ex_date'''
if not inps:
inps = cmdLineParse()
template = readfile.read_template(template_file)
key_list = list(template.keys())
# Read template option
prefix = 'pysar.velocity.'
key = prefix + 'excludeDate'
if key in key_list:
value = template[key]
if value == 'auto':
inps.ex_date = ['exclude_date.txt']
elif value == 'no':
inps.ex_date = []
else:
inps.ex_date = value.replace(',', ' ').split()
key = prefix + 'startDate'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.min_date = ptime.yyyymmdd(value)
key = prefix + 'endDate'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.max_date = ptime.yyyymmdd(value)
return inps
def read_template2inps(templateFile, inps=None):
'''Update inps with options from templateFile'''
if not inps:
inps = cmdLineParse()
template = readfile.read_template(templateFile)
key_list = list(template.keys())
key = 'pysar.reference.date'
if key in key_list:
inps.ref_date = template[key]
prefix = 'pysar.residualStd.'
key = prefix+'maskFile'
if key in key_list:
value = template[key]
if value == 'auto':
inps.mask_file = 'maskTempCoh.h5'
elif value == 'no':
inps.mask_file = None
else:
inps.mask_file = value
key = prefix+'ramp'
if key in key_list:
value = template[key]
if value == 'auto':
inps.ramp_type = 'quadratic'
else:
inps.ramp_type = 'no'
return inps
def main(argv):
inps = cmdLineParse()
# output filename
ext = os.path.splitext(inps.ifgram_file)[1]
if not inps.outfile:
inps.outfile = os.path.splitext(inps.ifgram_file)[0]+'_unwCor'+ext
# read template file
if inps.template_file:
template = readfile.read_template(inps.template_file)
key = 'pysar.unwrapError.yx'
if key in list(template.keys()):
print('read '+key+' option from template file: '+inps.template_file)
yx = template[key].replace(';',' ').replace(',',' ').split()
yx = [int(i) for i in yx]
inps.y = yx[0::2]
inps.x = yx[1::2]
# Memthod
if inps.y and inps.x:
inps.method = 'bridging'
else:
inps.method = 'phase_closure'
print('unwrapping error correction using method: '+inps.method)
#####
if inps.method == 'phase_closure':
inps.outfile = unwrap_error_correction_phase_closure(inps.ifgram_file, inps.mask_file, inps.outfile)
elif inps.method == 'bridging':
inps.outfile = unwrap_error_correction_bridging(inps.ifgram_file, inps.mask_file, inps.y, inps.x,\
inps.ramp_type, inps.outfile)[0]
print('Done.')
return inps.outfile
def read_template2inps(template_file, inps=None):
'''Read input template file into inps.ex_date'''
if not inps:
inps = cmdLineParse()
template = readfile.read_template(template_file)
key_list = list(template.keys())
# Read template option
prefix = 'pysar.topoError.'
key = prefix + 'polyOrder'
if key in key_list:
value = template[key]
if value == 'auto':
inps.poly_order = 2
else:
inps.poly_order = int(value)
key = prefix + 'excludeDate'
if key in key_list:
value = template[key]
if value in ['auto', 'no']:
inps.ex_date = []
else:
inps.ex_date = value.replace(',', ' ').split()
key = prefix + 'stepFuncDate'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.step_date = ptime.yyyymmdd(value)
else:
inps.step_date = None
return inps
def main(argv):
##### Check Inputs
if not argv or argv[0] in ['-h', '--help']:
usage()
sys.exit(1)
if len(argv) < 2 or not argv[1]:
raise Exception('\nAt lease 2 inputs are needed.\n')
##### Read Original Attributes
#print '************ Add / Update HDF5 File Attributes *************'
File = argv[0]
atr = readfile.read_attribute(File)
print('Input file is ' + atr['PROCESSOR'] + ' ' + atr['FILE_TYPE'] + ': ' +
File)
##### Read New Attributes
atr_new = dict()
for i in range(1, len(argv)):
if os.path.isfile(argv[i]):
atr_tmp = readfile.read_template(argv[i])
atr_new.update(atr_tmp)
else:
atr_tmp = argv[i].split('=')
atr_new[atr_tmp[0].strip()] = atr_tmp[1].strip()
print(
"The following attributes will be added/updated, or removed if new value is 'None':"
)
info.print_attributes(atr_new)
ext = os.path.splitext(File)[1]
##### Update h5 File
if ext in ['.h5', '.he5']:
File = ut.add_attribute(File, atr_new)
else:
if not ut.update_attribute_or_not(atr_new, atr):
print(
'All updated (removed) attributes already exists (do not exists) and have the same value, skip update.'
)
else:
for key, value in atr_new.items():
# delete the item is new value is None
if value == 'None':
try:
atr.pop(key)
except:
pass
else:
atr[key] = value
if atr['PROCESSOR'] == 'roipac':
print('writing >>> ' + File + '.rsc')
writefile.write_roipac_rsc(atr, File + '.rsc')
return File
def read_template2inps(templateFile, inps=None):
'''Update inps with pysar.residualRms.* option from templateFile'''
if not inps:
inps = cmdLineParse()
template = readfile.read_template(templateFile)
key_list = list(template.keys())
prefix = 'pysar.residualRms.'
key = prefix + 'maskFile'
if key in key_list:
value = template[key]
if value == 'auto':
inps.mask_file = 'maskTempCoh.h5'
elif value == 'no':
inps.mask_file = None
else:
inps.mask_file = value
key = prefix + 'ramp'
if key in key_list:
value = template[key]
if value == 'auto':
inps.ramp_type = 'quadratic'
else:
inps.ramp_type = value
key = prefix + 'threshold'
if key in key_list:
value = template[key]
if value == 'auto':
inps.min_rms = 0.02
else:
inps.min_rms = float(value)
key = prefix + 'saveRefDate'
if key in key_list:
value = template[key]
if value in ['auto', 'yes']:
inps.save_reference_date = True
else:
inps.save_reference_date = False
key = prefix + 'saveExcludeDate'
if key in key_list:
value = template[key]
if value in ['auto', 'yes']:
inps.save_exclude_date = True
else:
inps.save_exclude_date = False
return inps
def read_seed_template2inps(template_file, inps=None):
'''Read seed/reference info from template file and update input namespace'''
if not inps:
inps = cmdLineParse([''])
template = readfile.read_template(template_file)
key_list = list(template.keys())
prefix = 'pysar.reference.'
key = prefix + 'yx'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.ref_y, inps.ref_x = [int(i) for i in value.split(',')]
key = prefix + 'lalo'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.ref_lat, inps.ref_lon = [float(i) for i in value.split(',')]
key = prefix + 'maskFile'
if key in key_list:
value = template[key]
if value == 'auto':
inps.mask_file = None
elif value == 'no':
inps.mask_file = None
else:
inps.mask_file = value
key = prefix + 'coherenceFile'
if key in key_list:
value = template[key]
if value == 'auto':
inps.coherence_file = 'averageSpatialCoherence.h5'
else:
inps.coherence_file = value
key = prefix + 'minCoherence'
if key in key_list:
value = template[key]
if value == 'auto':
inps.min_coherence = 0.85
else:
inps.min_coherence = float(value)
return inps
def main(argv):
# import pdb; pdb.set_trace()
messageRsmas.log(' '.join(argv))
inps = command_line_parse()
# moved below to parse methods
# parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
# epilog=EXAMPLE)
# parser.add_argument('custom_template_file', nargs='?',
# help='custom template with option settings.\n')
# inps = parser.parse_args()
custom_template = readfile.read_template(inps.custom_template_file)
# import pdb;
# pdb.set_trace()
if os.path.isdir('DEM'):
shutil.rmtree('DEM')
os.mkdir('DEM')
os.chdir('DEM')
# cwd = os.getcwd()
if 'sentinelStack.demMethod' not in custom_template.keys():
custom_template['sentinelStack.demMethod'] = 'bbox'
if custom_template['sentinelStack.demMethod'] == 'bbox' and inps.ssara:
call_ssara_dem()
if inps.new:
print('nice job kawan! You aren\' dumb!')
if custom_template['sentinelStack.demMethod'] == 'bbox' and inps.isce:
print('you started isce')
call_isce_dem(custom_template)
print('you finished isce')
else:
sys.exit('Error unspported demMethod option: ' +
custom_template['sentinelStack.demMethod'])
print('\n###############################################')
print('End of dem_rsmas.py')
print('################################################\n')
def read_subset_template2box(templateFile):
'''Read pysar.subset.lalo/yx option from template file into box type
Return None if not specified.
'''
tmpl = readfile.read_template(templateFile)
try:
sub = [i.strip() for i in tmpl['pysar.subset.lalo'].split(',')]
sub_lat = sorted([float(i.strip()) for i in sub[0].split(':')])
sub_lon = sorted([float(i.strip()) for i in sub[1].split(':')])
geo_box = (sub_lon[0], sub_lat[1], sub_lon[1], sub_lat[0])
except:
geo_box = None
try:
sub = [i.strip() for i in tmpl['pysar.subset.yx'].split(',')]
sub_y = sorted([int(i.strip()) for i in sub[0].split(':')])
sub_x = sorted([int(i.strip()) for i in sub[1].split(':')])
pix_box = (sub_x[0], sub_y[0], sub_x[1], sub_y[1])
except:
pix_box = None
return pix_box, geo_box
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:
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]
print templateFile
except:
print '''
*******************************************
Copy DEM (radar and geo coordinate) and
geomap*.trans file from PROCESS folder
to TSSAR folder
Usage: copy_dem_trans.py TEMPLATEFILE
*******************************************
'''
sys.exit(1)
templateContents = readfile.read_template(templateFile)
projectName = os.path.basename(templateFile.partition('.')[0])
masterDate = templateContents['masterDate']
Rlooks = templateContents['Rlooks_unw']
try:
processDir = os.getenv('PROCESSDIR') + '/' + projectName
tssarDir = os.getenv('TSSARDIR') + '/' + projectName
except:
processDir = os.getenv(
'SCRATCHDIR'
) + '/' + projectName + '/PROCESS' # FA 7/2015: adopted for new directory structure
tssarDir = os.getenv(
'SCRATCHDIR'
) + '/' + projectName + '/TSSAR' # FA 7/2015: adopted for new directory structure
#tssarDir = scratchDirectory + '/' + projectName + "/TSSAR"
print "QQ: AFTER: " + processDir
print "QQ: AFTER: " + tssarDir
sys.exit(1)
"""copy geomap_*rlks.trans"""
geomapPath = processDir + '/GEO/geo_' + masterDate + '*'
geomapList = glob.glob(geomapPath)
numGeomap = len(geomapList)
if numGeomap > 0:
geomapDir = geomapList[0]
geomapFile = geomapDir + '/geomap_' + Rlooks + 'rlks.trans'
geomapRscFile = geomapFile + '.rsc'
# print geomapFile
# print geomapRscFile
geomapCmd = 'cp ' + geomapFile + ' ' + geomapRscFile + ' ' + tssarDir
print geomapCmd
os.system(geomapCmd)
else:
print 'WARNING: no geomap file of master interferograms found!'
print 'Check the PROCESS/Project/GEO folder.'
sys.exit(1)
"""copy radar_*rlks.hgt"""
doneIgramPath = processDir + '/DONE/IFGRAM_*'
doneIgramList = glob.glob(doneIgramPath)
numDoneIgram = len(doneIgramList)
if numDoneIgram > 0:
doneIgramDir = doneIgramList[0]
radarHgt = doneIgramDir + '/radar_' + Rlooks + 'rlks.hgt'
radarHgtRsc = radarHgt + '.rsc'
# print radarHgt
# print radarHgtRsc
radarCmd = 'cp ' + radarHgt + ' ' + radarHgtRsc + ' ' + tssarDir
print radarCmd
os.system(radarCmd)
else:
print 'WARNING: no radar_*rlks.hgt file found!'
print 'Check the PROCESS/Project/DONE folder.'
sys.exit(1)
"""copy DEM file from $DEMDIR"""
demPath = templateContents['DEM']
demRscPath = demPath + '.rsc'
demCmd = 'cp ' + demPath + ' ' + demRscPath + ' ' + tssarDir
print demCmd
os.system(demCmd)
def main(argv):
try:
templateFile = argv[1]
print templateFile
except:
print '''
*******************************************
Copy DEM (radar and geo coordinate) and
geomap*.trans file from PROCESS folder
to TSSAR folder
Usage: copy_dem_trans.py TEMPLATEFILE
*******************************************
'''
sys.exit(1)
templateContents = readfile.read_template(templateFile)
projectName = os.path.basename(templateFile.partition('.')[0])
masterDate = templateContents['masterDate']
Rlooks = templateContents['Rlooks_unw']
try:
processDir = os.getenv('PROCESSDIR') +'/'+ projectName
tssarDir = os.getenv('TSSARDIR') +'/'+projectName
except:
processDir = os.getenv('SCRATCHDIR') + '/' + projectName + '/PROCESS' # FA 7/2015: adopted for new directory structure
tssarDir = os.getenv('SCRATCHDIR') + '/' + projectName + '/TSSAR' # FA 7/2015: adopted for new directory structure
#tssarDir = scratchDirectory + '/' + projectName + "/TSSAR"
print "QQ: AFTER: " + processDir
print "QQ: AFTER: " + tssarDir
sys.exit(1)
"""copy geomap_*rlks.trans"""
geomapPath = processDir+'/GEO/geo_'+masterDate+'*'
geomapList = glob.glob(geomapPath)
numGeomap = len(geomapList)
if numGeomap>0:
geomapDir = geomapList[0]
geomapFile = geomapDir+'/geomap_'+Rlooks+'rlks.trans'
geomapRscFile = geomapFile+'.rsc'
# print geomapFile
# print geomapRscFile
geomapCmd = 'cp '+geomapFile+' '+geomapRscFile+' '+tssarDir
print geomapCmd
os.system(geomapCmd)
else:
print 'WARNING: no geomap file of master interferograms found!'
print 'Check the PROCESS/Project/GEO folder.'
sys.exit(1)
"""copy radar_*rlks.hgt"""
doneIgramPath = processDir+'/DONE/IFGRAM_*'
doneIgramList = glob.glob(doneIgramPath)
numDoneIgram = len(doneIgramList)
if numDoneIgram>0:
doneIgramDir = doneIgramList[0]
radarHgt = doneIgramDir+'/radar_'+Rlooks+'rlks.hgt'
radarHgtRsc = radarHgt + '.rsc'
# print radarHgt
# print radarHgtRsc
radarCmd = 'cp '+radarHgt+' '+radarHgtRsc+' '+tssarDir
print radarCmd
os.system(radarCmd)
else:
print 'WARNING: no radar_*rlks.hgt file found!'
print 'Check the PROCESS/Project/DONE folder.'
sys.exit(1)
"""copy DEM file from $DEMDIR"""
demPath=templateContents['DEM']
demRscPath=demPath+'.rsc'
demCmd = 'cp '+demPath+' '+demRscPath+' '+tssarDir
print demCmd
os.system(demCmd)
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 read_template2inps(templateFile, inps=None):
'''Read network options from template file into Namespace variable inps'''
template_dict = readfile.read_template(templateFile)
if not template_dict:
print('Empty template: '+templateFile)
return None
keyList = list(template_dict.keys())
if not inps:
inps = cmdLineParse([''])
# Read network option regardless of prefix
for key in keyList:
if 'selectPairs.' in key: template_dict[key.split('selectPairs.')[1]] = template_dict[key]
if 'pysar.network.' in key: template_dict[key.split('pysar.network.')[1]] = template_dict[key]
if 'select.network.' in key: template_dict[key.split('select.network.')[1]] = template_dict[key]
keyList = list(template_dict.keys())
for key, value in template_dict.items():
if value.lower() in ['off','false','n']: template_dict[key] = 'no'
if value.lower() in ['on', 'true', 'y']: template_dict[key] = 'yes'
# Update inps value if not existed
if not inps.method:
if 'selectMethod' in keyList: inps.method = template_dict['selectMethod']
elif 'method' in keyList: inps.method = template_dict['method']
else: inps.method = 'all'
if not inps.perp_base_max:
if 'perpBaseMax' in keyList: inps.perp_base_max = float(template_dict['perpBaseMax'])
else: inps.perp_base_max = 500.0
if not inps.temp_base_max:
if 'lengthDayMax' in keyList: inps.temp_base_max = float(template_dict['lengthDayMax'])
elif 'tempBaseMax' in keyList: inps.temp_base_max = float(template_dict['tempBaseMax'])
else: inps.temp_base_max = 1800.0
if not inps.temp_base_min:
if 'lengthDayMin' in keyList: inps.temp_base_min = float(template_dict['lengthDayMin'])
elif 'tempBaseMin' in keyList: inps.temp_base_min = float(template_dict['tempBaseMin'])
else: inps.temp_base_min = 0.0
if 'seasonal' in keyList and template_dict['seasonal'].lower() == 'no': inps.keep_seasonal = False
if 'keepSeasonal' in keyList and template_dict['keepSeasonal'].lower() == 'no': inps.keep_seasonal = False
if not inps.dop_overlap_min:
if 'DopOverlapThresh' in keyList: inps.dop_overlap_min = float(template_dict['DopOverlapThresh'])
elif 'dopOverlapThresh' in keyList: inps.dop_overlap_min = float(template_dict['dopOverlapThresh'])
elif 'dopOverlapMin' in keyList: inps.dop_overlap_min = float(template_dict['dopOverlapMin'])
else: inps.dop_overlap_min = 15.0
if not inps.reference_file and 'referenceFile' in keyList: inps.reference_file = template_dict['referenceFile']
if not inps.increment_num:
if 'incrementNum' in keyList: inps.increment_num = int(template_dict['incrementNum'])
else: inps.increment_num = 3
if not inps.temp_perp_list:
if 'dayPerpList' in keyList: inps.temp_perp_list = template_dict['dayPerpList']
elif 'tempPerpList' in keyList: inps.temp_perp_list = template_dict['tempPerpList']
else: inps.temp_perp_list = '16,1600;32,800;48,600;64,200'
inps.temp_perp_list = [[float(j) for j in i.split(',')] for i in inps.temp_perp_list.split(';')]
if not inps.exclude_date and 'excludeDate' in keyList:
ex_date_list = [i for i in template_dict['excludeDate'].split(',')]
inps.exclude_date = ptime.yymmdd(ex_date_list)
if not inps.start_date and 'startDate' in keyList:
inps.start_date = ptime.yyyymmdd(template_dict['startDate'])
if not inps.end_date and 'endDate' in keyList:
inps.end_date = ptime.yyyymmdd(template_dict['endDate'])
if not inps.m_date and 'masterDate' in keyList:
inps.m_date = ptime.yymmdd(template_dict['masterDate'])
return inps
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.trans = 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.items():
temp_dict[key] = ut.check_variable_name(value)
template.update(temp_dict)
keyList = list(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.insar_processor = 'roipac'
else:
inps.insar_processor = value
print('--------------------------------------------')
print('InSAR processing software: '+inps.insar_processor)
if 'pysar.unwrapFiles' in keyList: inps.unw = template['pysar.unwrapFiles']
if 'pysar.corFiles' in keyList: inps.cor = template['pysar.corFiles']
if 'pysar.transFile' in keyList: inps.trans = template['pysar.transFile']
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.trans or inps.trans == 'auto') and inps_tmp.trans_file : inps.trans = inps_tmp.trans_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('transformation file to load: '+str(inps.trans))
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))
# optional but recommended files - multi_group_hdf5_file
inps.coherence_file = load_file(inps.cor, vars(inps))
#inps.wrap_ifgram_file = load_file(inps.int, vars(inps))
if inps.snap_connect:
inps.snap_connect_file = load_file(inps.snap_connect, vars(inps))
# optional but recommend files - single_dataset file
inps.trans_file = load_file(inps.trans, vars(inps))
inps.dem_radar_file = load_file(inps.dem_radar, vars(inps))
inps.dem_geo_file = load_file(inps.dem_geo, vars(inps))
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 read_template2inps(template_file, inps=None):
'''Read input template options into Namespace inps'''
if not inps:
inps = cmdLineParse()
template = readfile.read_template(inps.template_file)
key_list = list(template.keys())
# Coherence-based network modification
prefix = 'pysar.network.'
key = prefix + 'coherenceBased'
if key in key_list and template[key] in ['auto', 'yes']:
inps.coherence_based = True
key = prefix + 'keepMinSpanTree'
if key in key_list and template[key] in ['no']:
inps.keep_mst = False
key = prefix + 'coherenceFile'
if key in key_list:
if template[key] == 'auto':
inps.coherence_file = 'coherence.h5'
else:
inps.coherence_file = template[key]
# find coherence file from input files if inps.coherence_file does not exists.
if inps.coherence_based and not os.path.isfile(inps.coherence_file):
k_list = [readfile.read_attribute(f)['FILE_TYPE'] for f in inps.file]
try:
coh_file_idx = k_list.index('coherence')
except ValueError:
print(
'No coherence file found! Can not use coherence-based method without it.'
)
inps.coherence_file = inps.file[coh_file_idx]
key = prefix + 'minCoherence'
if key in key_list:
if template[key] == 'auto':
inps.min_coherence = 0.7
else:
inps.min_coherence = float(template[key])
key = prefix + 'maskFile'
if key in key_list:
value = template[key]
if value == 'auto':
inps.mask_file = 'mask.h5'
elif value == 'no':
inps.mask_file = None
else:
inps.mask_file = value
key = prefix + 'maskAoi.yx'
if key in key_list:
value = template[key]
if value in ['auto', 'no']:
inps.aoi_pix_box = None
else:
tmp = [i.strip() for i in value.split(',')]
sub_y = sorted([int(i.strip()) for i in tmp[0].split(':')])
sub_x = sorted([int(i.strip()) for i in tmp[1].split(':')])
inps.aoi_pix_box = (sub_x[0], sub_y[0], sub_x[1], sub_y[1])
key = prefix + 'maskAoi.lalo'
if key in key_list:
value = template[key]
if value in ['auto', 'no']:
inps.aoi_geo_box = None
else:
tmp = [i.strip() for i in value.split(',')]
sub_lat = sorted([float(i.strip()) for i in tmp[0].split(':')])
sub_lon = sorted([float(i.strip()) for i in tmp[1].split(':')])
inps.aoi_geo_box = (sub_lon[0], sub_lat[1], sub_lon[1], sub_lat[0])
# Check trans file
try:
inps.trans_file = ut.get_file_list(inps.trans_file)[0]
except:
inps.trans_file = None
print(
'Warning: no mapping transformation file found! Can not use '
+ key + ' option without it.')
print('skip this option.')
inps.aoi_pix_box = None
## Network Modification based on thresholds
key = prefix + 'tempBaseMax'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.max_temp_baseline = float(value)
key = prefix + 'perpBaseMax'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.max_perp_baseline = float(value)
key = prefix + 'referenceFile'
if key in key_list:
value = template[key]
if value in ['auto', 'no']:
inps.reference_file = None
else:
inps.reference_file = value
key = prefix + 'excludeDate'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.exclude_date = [i for i in value.replace(',', ' ').split()]
key = prefix + 'excludeIfgIndex'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.exclude_ifg_index = [
i for i in value.replace(',', ' ').split()
]
key = prefix + 'startDate'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.start_date = ptime.yymmdd(value)
key = prefix + 'endDate'
if key in key_list:
value = template[key]
if value not in ['auto', 'no']:
inps.end_date = ptime.yymmdd(value)
return inps
