def update_attribute_geo_lut(atr_rdr, atr_lut, print_msg=True):
'''Get attributes in geo coord from atr_rdr dict and atr_lut dict
Inputs:
atr_rdr : dict, attributes of file in radar coord
atr_lut : dict, attributes of mapping transformation file
print_msg : bool, print out message or not
Output:
atr : dict, attributes of output file in geo coord.
'''
# copy atr_rdr
atr = dict()
for key, value in atr_rdr.iteritems():
atr[key] = str(value)
atr['FILE_LENGTH'] = atr_lut['FILE_LENGTH']
atr['WIDTH'] = atr_lut['WIDTH']
atr['Y_FIRST'] = atr_lut['Y_FIRST']
atr['X_FIRST'] = atr_lut['X_FIRST']
atr['Y_STEP'] = atr_lut['Y_STEP']
atr['X_STEP'] = atr_lut['X_STEP']
try: atr['Y_UNIT'] = atr_lut['Y_UNIT']
except: atr['Y_UNIT'] = 'degrees'
try: atr['X_UNIT'] = atr_lut['X_UNIT']
except: atr['X_UNIT'] = 'degrees'
# Reference point from y/x to lat/lon
if 'ref_y' in atr_rdr.keys() and 'ref_x' in atr_rdr.keys():
ref_x_rdr = np.array(int(atr_rdr['ref_x']))
ref_y_rdr = np.array(int(atr_rdr['ref_y']))
trans_file = atr_lut['FILE_PATH']
ref_lat, ref_lon = ut.radar2glob(ref_y_rdr, ref_x_rdr, trans_file, atr_rdr, print_msg=False)[0:2]
if ~np.isnan(ref_lat) and ~np.isnan(ref_lon):
ref_y = np.rint((ref_lat - float(atr['Y_FIRST'])) / float(atr['Y_STEP']))
ref_x = np.rint((ref_lon - float(atr['X_FIRST'])) / float(atr['X_STEP']))
atr['ref_lat'] = str(ref_lat)
atr['ref_lon'] = str(ref_lon)
atr['ref_y'] = str(int(ref_y))
atr['ref_x'] = str(int(ref_x))
if print_msg:
print 'update ref_lat/lon/y/x'
else:
warnings.warn("original reference pixel is out of .trans file's coverage. Continue.")
try: atr.pop('ref_y')
except: pass
try: atr.pop('ref_x')
except: pass
try: atr.pop('ref_lat')
except: pass
try: atr.pop('ref_lon')
except: pass
return atr
def bbox_radar2geo(pix_box, atr_rdr=dict(), transFile='geomap*.trans'):
'''Calculate bounding box in lat/lon for file in geo coord, based on input radar/pixel box
Inputs:
pix_box - tuple of 4 int, indicating the UL/LR x/y
atr_rdr - dict, attributes of file in radar coord
transFile - string, path of transformation file, i.e. geomap_4rlks.trans
Output:
geo_box - tuple of 4 float, indicating the UL/LR lon/lat of the bounding box
'''
x = np.array([pix_box[0], pix_box[2], pix_box[0], pix_box[2]])
y = np.array([pix_box[1], pix_box[1], pix_box[3], pix_box[3]])
lat, lon, lat_res, lon_res = ut.radar2glob(y, x, transFile, atr_rdr)
buf = 10 * (np.max([lat_res, lon_res]))
geo_box = (np.min(lon) - buf, np.max(lat) + buf, np.max(lon) + buf,
np.min(lat) - buf)
return geo_box
def geocode_attribute(atr_rdr, atr_geo, transFile=None):
'''Update attributes after geocoding'''
atr = dict()
for key, value in atr_geo.iteritems():
atr[key] = str(value)
for key, value in atr_rdr.iteritems():
atr[key] = value
atr['WIDTH'] = atr_geo['WIDTH']
atr['FILE_LENGTH'] = atr_geo['FILE_LENGTH']
# Reference point from y/x to lat/lon
if transFile and ('ref_x' and 'ref_y' in atr_rdr.keys()):
ref_x = np.array(int(atr_rdr['ref_x']))
ref_y = np.array(int(atr_rdr['ref_y']))
ref_lat, ref_lon = ut.radar2glob(ref_y, ref_x, transFile, atr_rdr)[0:2]
atr['ref_lat'] = ref_lat
atr['ref_lon'] = ref_lon
return atr
def main(argv):
if len(sys.argv) < 3:
usage(); sys.exit(1)
y = int(argv[0])
x = int(argv[1])
print 'input radar coord: y/azimuth=%d, x/range=%d' % (y, x)
try: trans_file = argv[2]
except: trans_file = ut.get_lookup_file()
try: radar_file = argv[3]
except: radar_file = 'unwrapIfgram.h5'
atr_rdr = readfile.read_attribute(radar_file)
lat, lon = ut.radar2glob(np.array(y), np.array(x), trans_file, atr_rdr)[0:2]
print 'corresponding geo coord: lat=%.4f, lon=%.4f' % (lat, lon)
return
def bbox_radar2geo(pix_box, atr_rdr=dict(), lookupFile=None):
'''Calculate bounding box in lat/lon for file in geo coord, based on input radar/pixel box
Inputs:
pix_box - tuple of 4 int, indicating the UL/LR x/y
atr_rdr - dict, attributes of file in radar coord
lookupFile - string, path of transformation file, i.e. geomap_4rlks.trans
Output:
geo_box - tuple of 4 float, indicating the UL/LR lon/lat of the bounding box
'''
x = np.array([pix_box[0], pix_box[2], pix_box[0], pix_box[2]])
y = np.array([pix_box[1], pix_box[1], pix_box[3], pix_box[3]])
if 'Y_FIRST' in atr_rdr.keys():
lat = coord_radar2geo(y, atr_rdr, 'y')
lon = coord_radar2geo(x, atr_rdr, 'x')
geo_box = (lon[0], lat[0], lon[1], lat[2])
else:
lat, lon, lat_res, lon_res = ut.radar2glob(y, x, lookupFile, atr_rdr)
buf = 2 * (np.max(np.abs([lat_res, lon_res])))
geo_box = (np.min(lon) - buf, np.max(lat) + buf, np.max(lon) + buf,
np.min(lat) - buf)
return geo_box
def main(argv):
start = time.time()
try: templateFile = argv[1]
except: Usage(); sys.exit(1)
########### Path ############
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 "\nprojectName: ", projectName
print "QQ " + tssarProjectDir
if not os.path.isdir(tssarProjectDir): os.mkdir(tssarProjectDir)
os.chdir(tssarProjectDir)
########## Initial File Name ########
import h5py
import pysar._pysar_utilities as ut
import pysar._readfile as readfile
template = readfile.read_template(templateFile)
igramFile = 'LoadedData.h5'
if os.path.isfile('Modified_'+igramFile): igramFile = 'Modified_'+igramFile
corFile = 'Coherence.h5'
if os.path.isfile('Modified_'+corFile): corFile = 'Modified_'+corFile
maskFile = 'Mask.h5'
if os.path.isfile('Modified_'+maskFile): maskFile = 'Modified_'+maskFile
#########################################
# Loading Data
#########################################
print '\n********** Loading Data *****************************'
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)
if not os.path.isfile(igramFile): sys.exit('\nERROR: No interferograms file found!\n')
########## Initial File Name - 2 ####
try: demGeoFile = find_filename(template, 'pysar.dem.geoCoord')
except: print '\nWARNING:\n No geo coded DEM found! Might be a problem in tropospheric delay / orbital error correction!\n'
try: demRdrFile = find_filename(template, 'pysar.dem.radarCoord')
except: print '\nWARNING:\n No radar coded DEM found! Will be a problem in tropospheric delay / orbital error correction!\n'
try: geomapFile = find_filename(template, 'pysar.geomap')
except: print '\nWARNING:\n No geomap*.trans file found! Will be a problem in geocoding!\n'
#########################################
# Check the subset (Optional)
#########################################
print '\n********** Subseting ********************************'
if 'pysar.subset.yx' in template.keys():
print 'subseting data with y/x input...'
subset = template['pysar.subset.yx'].split(',')
print 'calculating bounding box in geo coordinate.'
import numpy as np
ysub = [float(i) for i in subset[0].split(':')]; ysub.sort()
xsub = [float(i) for i in subset[1].split(':')]; xsub.sort()
x = np.array([xsub[0],xsub[1],xsub[0],xsub[1]])
y = np.array([ysub[0],ysub[0],ysub[1],ysub[1]])
lat,lon,lat_res,lon_res = ut.radar2glob(x,y,igramFile,1)
buf = 10*(np.max([lat_res,lon_res]))
latsub = str(np.min(lat)-buf)+':'+str(np.max(lat)+buf)
lonsub = str(np.min(lon)-buf)+':'+str(np.max(lon)+buf)
print ' subset in y - '+subset[0]+'\n subset in x - '+subset[1]
print ' subset in lat - '+latsub +'\n subset in lon - '+lonsub
## subset radar coded file
igramFile = check_subset(igramFile, subset, option='yx')
maskFile = check_subset(maskFile, subset, option='yx')
try: demRdrFile = check_subset(demRdrFile,subset, option='yx')
except: pass
## subset geo coded file
try: demGeoFile = check_subset(demGeoFile,[latsub,lonsub], option='lalo')
except: pass
try: geomapFile = check_subset(geomapFile,[latsub,lonsub], option='lalo')
except: pass
elif 'pysar.subset.lalo' in template.keys():
print 'subseting data with lat/lon input...'
subset= template['pysar.subset.lalo'].split(',')
print 'calculate bounding box in radar coordinate.'
import numpy as np
latsub = [float(i) for i in subset[0].split(':')]; latsub.sort()
lonsub = [float(i) for i in subset[1].split(':')]; lonsub.sort()
lat = np.array([latsub[0],latsub[0],latsub[1],latsub[1]])
lon = np.array([lonsub[0],lonsub[1],lonsub[0],lonsub[1]])
x,y,x_res,y_res = ut.glob2radar(lat,lon)
buf = 10*(np.max([x_res,y_res]))
xsub = str(np.min(x)-buf)+':'+str(np.max(x)+buf)
ysub = str(np.min(y)-buf)+':'+str(np.max(y)+buf)
print ' subset in lat - '+subset[0]+'\n subset in lon - '+subset[1]
print ' subset in y - ' +ysub +'\n subset in x - '+xsub
## subset geo coded files
try: demGeoFile = check_subset(demGeoFile, subset, option='lalo')
except: pass
try: geomapFile = check_subset(geomapFile, subset, option='lalo')
except: pass
## subset radar coded files
igramFile = check_subset(igramFile, [ysub,xsub], option='yx')
maskFile = check_subset(maskFile, [ysub,xsub], option='yx')
try: demRdrFile = check_subset(demRdrFile,[ysub,xsub], option='yx')
except: pass
else: print 'No Subset selected. Processing the whole area'
#try:
# subset= template['pysar.subset.yx'].split(',')
# print 'subset in y - '+str(subset[0])
# print 'subset in x - '+str(subset[1])
# igramFile = check_subset(igramFile, subset)
# corFile = check_subset(corFile, subset)
# maskFile = check_subset(maskFile, subset)
# demRdrFile = check_subset(demRdrFile,subset)
# demGeoFile = check_subset(demGeoFile,subset)
# #geomapFile = check_subset(geomapFile,subset)
#except: print 'No Subset selected. Processing the whole area'
#########################################
# Referencing Interferograms
#########################################
print '\n********** Referencing Interferograms ***************'
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.lalo' in template.keys():
'Checking lat/lon refernce point'
lat= template['pysar.seed.lalo'].split(',')[0]
lon= template['pysar.seed.lalo'].split(',')[1]
seedCmd= 'seed_data.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)
############################################
# Unwrapping Error Correction (Optional)
# based on the consistency of triplets
# of interferograms
############################################
print '\n********** Unwrapping Error Correction **************'
outName = igramFile.split('.')[0]+'_unwCor.h5'
try:
template['pysar.unwrapError']
if template['pysar.unwrapError'] in ('Y','y','yes','Yes','YES'):
if os.path.isfile(outName):
igramFile = outName
print igramFile+' exists.'
else:
print 'This might take a while depending on the size of your data set!'
unwCmd='unwrap_error.py '+igramFile
os.system(unwCmd)
igramFile = outName
else: print 'No unwrapping error correction.'
except: print 'No unwrapping error correction.'
#########################################
# Inversion of Interferograms
########################################
print '\n********** Time Series Inversion ********************'
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'
##############################################
# Temporal Coherence:
# A parameter to evaluate the consistency
# of timeseries with the interferograms
##############################################
print '\n********** Generate Temporal Coherence file *********'
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)
tempCohFile = 'temporal_coherence.h5'
##############################################
# Update Mask based on temporal coherence (Optional)
##############################################
print '\n********** Update Mask based on Temporal Coherence **'
outName = maskFile.split('.')[0]+'_tempCoh.h5'
try:
template['pysar.mask']
if template['pysar.mask'] in ('Y','yes','Yes','YES','y'):
if os.path.isfile(outName):
maskFile = outName
print maskFile+' already exists.'
else:
try: cohT = template['pysar.mask.threshold']
except: cohT = '0.7'
maskCmd='generate_mask.py -f '+tempCohFile+' -m '+ cohT +' -M 1.0 -o '+outName
print maskCmd
os.system(maskCmd)
maskFile = outName
else: print 'No mask update from temporal coherence'
except: print 'No mask update from temporal coherence'
##############################################
# Incident Angle
##############################################
print '\n********** Generate Incident Angle file *************'
if os.path.isfile('incidence_angle.h5'):
print 'incidence_angle.h5 already exists.'
else:
inciCmd = 'incidence_angle.py -f '+timeseriesFile
print inciCmd
os.system(inciCmd)
##############################################
# LOD (Local Oscillator Drift) Correction
# when Satellite is Envisat and
# Coordinate system is radar
##############################################
print '\n********** Local Oscillator Drift correction ********'
rdr_or_geo = ut.radar_or_geo(timeseriesFile)
outName = timeseriesFile.split('.')[0]+'_LODcor.h5'
if os.path.isfile(outName):
timeseriesFile = outName
print timeseriesFile+' already exists.'
else:
h5file = h5py.File(timeseriesFile,'r')
platform = h5file['timeseries'].attrs['PLATFORM']
if platform == 'ENVISAT':
if rdr_or_geo == 'radar':
LODcmd='lod.py '+timeseriesFile
print LODcmd
os.system(LODcmd)
timeseriesFile = outName
else: print 'Cannot correct LOD for geocoded data.'
else: print 'No need of LOD correction for '+platform
h5file.close()
##############################################
# Tropospheric Delay Correction (Optional)
##############################################
print '\n********** Tropospheric Correction ******************'
try:
if (template['pysar.troposphericDelay'] in ('Y','y','yes','Yes','YES')) and\
template['pysar.orbitError.method'] in ['BaseTropCor','basetropcor','base_trop_cor']:
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 separated from baseline error correction, \
choose other existing options for orbital error correction.
+++++++++++++++++++++++++++++++++++++++++++++++++++
'''
template['pysar.troposphericDelay']='no'
except: print 'Checking the tropospheric delay correction ...'
if template['pysar.troposphericDelay'] in ('Y','y','yes','Yes','YES'):
if rdr_or_geo == 'radar': demFile = demRdrFile
elif rdr_or_geo == 'geo': demFile = demGeoFile
if not os.path.isfile(demFile):
print '++++++++++++++++++++++++++++++++++++++++++++++'
print 'ERROR:'
print ' DEM file was not found!'
print ' Continue without tropospheric correction ...'
print '++++++++++++++++++++++++++++++++++++++++++++++'
else:
if template['pysar.troposphericDelay.method'] in ['height-correlation','height_correlation',\
'Height-Correlation','Height_Correlation']:
print 'tropospheric delay correction with height-correlation approach'
outName = timeseriesFile.split('.')[0]+'_tropCor.h5'
if os.path.isfile(outName):
timeseriesFile = outName
print timeseriesFile+' already exists.'
else:
try: poly_order = template['pysar.troposphericDelay.polyOrder']
except: poly_order = '1'; print 'Deafult polynomial order for troposphreic correction = 1'
cmdTrop = 'tropcor_phase_elevation.py'+' -f '+timeseriesFile+' -d '+demFile+' -p '+str(poly_order)
print cmdTrop
os.system(cmdTrop)
timeseriesFile = outName
elif template['pysar.troposphericDelay.method'] in ['pyaps','PyAPS','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.troposphericDelay.weatherModel']
print 'Numerical Weather Model: '+source_of_NWM
outName = timeseriesFile.split('.')[0]+'_'+source_of_NWM+'.h5'
if os.path.isfile(outName):
timeseriesFile = outName
print timeseriesFile+' already exists.'
else:
acquisition_time = template['pysar.acquisitionTime']
print 'acquisition time: '+acquisition_time
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 = outName
else: print 'ERROR: Unrecognized atmospheric correction method: '+template['pysar.trop.method']
else: print 'No atmospheric delay correction.'
##############################################
# Topographic (DEM) Residuals Correction (Optional)
##############################################
print '\n********** Topographic (DEM) Error correction *******'
outName = timeseriesFile.split('.')[0]+'_demCor.h5'
try:
template['pysar.topoError']
if template['pysar.topoError'] in ('Y','yes','Yes','YES','y'):
if os.path.isfile(outName):
timeseriesFile = outName
print timeseriesFile+' already exists.'
else:
print 'Correcting topographic residuals'
topoCmd='dem_error.py '+ timeseriesFile +' '+ igramFile
print topoCmd
os.system(topoCmd)
timeseriesFile = outName
else: print 'No correction for topographic residuals.'
except: print 'No correction for topographic residuals.'
##############################################
# Orbit Correction (Optional)
##############################################
print '\n********** Orbital Correction ***********************'
try:
template['pysar.orbitError']
if template['pysar.orbitError'] in ('Y','yes','Yes','YES','y'):
try:
orbit_error_method=template['pysar.orbitError.method']
print 'orbit error correction method : '+orbit_error_method
outName = timeseriesFile.split('.')[0]+'_'+orbit_error_method+'.h5'
if os.path.isfile(outName):
timeseriesFile = outName
print timeseriesFile+' already exists.'
else:
if orbit_error_method in [ 'plane', 'plane_range', 'plane_azimuth',\
'quadratic', 'quadratic_range', 'quadratic_azimuth']:
orbitCmd='remove_plane.py '+timeseriesFile+' '+orbit_error_method #+ ' Mask.h5'
print orbitCmd
os.system(orbitCmd)
timeseriesFile = outName
elif orbit_error_method in ['baselineCor','BaselineCor']:
try:
h5file=h5py.File(timeseriesFile,'r')
daz=float(h5file['timeseries'].attrs['AZIMUTH_PIXEL_SIZE'])
orbitCmd='baseline_error.py ' +timeseriesFile #+ ' Mask.h5'
print orbitCmd
os.system(orbitCmd)
timeseriesFile = outName
except:
print 'WARNING!'
print 'Skipping orbital error correction.'
print 'baselineCor method can only be applied in radar coordinate'
elif orbit_error_method in ['BaseTropCor','basetropcor','base_trop_cor']:
try:
h5file=h5py.File(timeseriesFile,'r')
daz=float(h5file['timeseries'].attrs['AZIMUTH_PIXEL_SIZE'])
print 'Joint estimation of Baseline error and tropospheric delay [height-correlation approach]'
if rdr_or_geo == 'radar': demFile = demRdrFile
elif rdr_or_geo == 'geo': demFile = demGeoFile
try: poly_order = template['pysar.trop.poly_order']
except: poly_order = 1; print 'Deafult polynomial order for troposphreic correction = 1'
orbitCmd='baseline_trop.py '+timeseriesFile+' '+ demFile +' '+ str(poly_order) +' range_and_azimuth'
print orbitCmd
os.system(orbitCmd)
timeseriesFile = outName
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'
print ' 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.'
#############################################
# Velocity and rmse maps
#############################################
print '\n********** Velocity estimation **********************'
if os.path.isfile('velocity.h5'):
print 'velocity.h5 file already exists.'
else:
velCmd='timeseries2velocity.py '+timeseriesFile
print velCmd
os.system(velCmd)
velocityFile = 'velocity.h5'
############################################
# Geocoding (Optional)
############################################
print '\n********** Geocoding ********************************'
try:
template['pysar.geocode']
if template['pysar.geocode'] in ('Y','y','yes','Yes','YES'):
#geoTsFile = check_geocode(timeseriesFile,geomapFile)
geoVelocityFile = check_geocode(velocityFile, geomapFile)
geoMaskFile = check_geocode(maskFile, geomapFile)
else: print 'No geocoding applied'
except: print 'No geocoding applied'
#############################################
# Masking (Optional)
#############################################
print '\n********** Masking Velocity *************************'
velocityFile = check_mask( velocityFile, maskFile)
try: geoVelocityFile = check_mask(geoVelocityFile, geoMaskFile)
except: pass
#############################################
# PySAR v1.0 #
#############################################
s = time.time()-start; m, s = divmod(s, 60); h, m = divmod(m, 60)
print '\nTime used: %02d hours %02d mins %02d secs' % (h, m, s)
print '\n###############################################'
print 'End of PySAR processing!'
print '################################################\n'
def main(argv):
start = time.time()
try:
templateFile = argv[1]
except:
Usage()
sys.exit(1)
########### Path ############
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 "\nprojectName: ", projectName
print "QQ " + tssarProjectDir
if not os.path.isdir(tssarProjectDir): os.mkdir(tssarProjectDir)
os.chdir(tssarProjectDir)
########## Initial File Name ########
import h5py
import pysar._pysar_utilities as ut
import pysar._readfile as readfile
template = readfile.read_template(templateFile)
igramFile = 'LoadedData.h5'
if os.path.isfile('Modified_' + igramFile):
igramFile = 'Modified_' + igramFile
corFile = 'Coherence.h5'
if os.path.isfile('Modified_' + corFile): corFile = 'Modified_' + corFile
maskFile = 'Mask.h5'
if os.path.isfile('Modified_' + maskFile):
maskFile = 'Modified_' + maskFile
#########################################
# Loading Data
#########################################
print '\n********** Loading Data *****************************'
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)
if not os.path.isfile(igramFile):
sys.exit('\nERROR: No interferograms file found!\n')
########## Initial File Name - 2 ####
try:
demGeoFile = find_filename(template, 'pysar.dem.geoCoord')
except:
print '\nWARNING:\n No geo coded DEM found! Might be a problem in tropospheric delay / orbital error correction!\n'
try:
demRdrFile = find_filename(template, 'pysar.dem.radarCoord')
except:
print '\nWARNING:\n No radar coded DEM found! Will be a problem in tropospheric delay / orbital error correction!\n'
try:
geomapFile = find_filename(template, 'pysar.geomap')
except:
print '\nWARNING:\n No geomap*.trans file found! Will be a problem in geocoding!\n'
#########################################
# Check the subset (Optional)
#########################################
print '\n********** Subseting ********************************'
if 'pysar.subset.yx' in template.keys():
print 'subseting data with y/x input...'
subset = template['pysar.subset.yx'].split(',')
print 'calculating bounding box in geo coordinate.'
import numpy as np
ysub = [float(i) for i in subset[0].split(':')]
ysub.sort()
xsub = [float(i) for i in subset[1].split(':')]
xsub.sort()
x = np.array([xsub[0], xsub[1], xsub[0], xsub[1]])
y = np.array([ysub[0], ysub[0], ysub[1], ysub[1]])
lat, lon, lat_res, lon_res = ut.radar2glob(x, y, igramFile, 1)
buf = 10 * (np.max([lat_res, lon_res]))
latsub = str(np.min(lat) - buf) + ':' + str(np.max(lat) + buf)
lonsub = str(np.min(lon) - buf) + ':' + str(np.max(lon) + buf)
print ' subset in y - ' + subset[
0] + '\n subset in x - ' + subset[1]
print ' subset in lat - ' + latsub + '\n subset in lon - ' + lonsub
## subset radar coded file
igramFile = check_subset(igramFile, subset, option='yx')
maskFile = check_subset(maskFile, subset, option='yx')
try:
demRdrFile = check_subset(demRdrFile, subset, option='yx')
except:
pass
## subset geo coded file
try:
demGeoFile = check_subset(demGeoFile, [latsub, lonsub],
option='lalo')
except:
pass
try:
geomapFile = check_subset(geomapFile, [latsub, lonsub],
option='lalo')
except:
pass
elif 'pysar.subset.lalo' in template.keys():
print 'subseting data with lat/lon input...'
subset = template['pysar.subset.lalo'].split(',')
print 'calculate bounding box in radar coordinate.'
import numpy as np
latsub = [float(i) for i in subset[0].split(':')]
latsub.sort()
lonsub = [float(i) for i in subset[1].split(':')]
lonsub.sort()
lat = np.array([latsub[0], latsub[0], latsub[1], latsub[1]])
lon = np.array([lonsub[0], lonsub[1], lonsub[0], lonsub[1]])
x, y, x_res, y_res = ut.glob2radar(lat, lon)
buf = 10 * (np.max([x_res, y_res]))
xsub = str(np.min(x) - buf) + ':' + str(np.max(x) + buf)
ysub = str(np.min(y) - buf) + ':' + str(np.max(y) + buf)
print ' subset in lat - ' + subset[
0] + '\n subset in lon - ' + subset[1]
print ' subset in y - ' + ysub + '\n subset in x - ' + xsub
## subset geo coded files
try:
demGeoFile = check_subset(demGeoFile, subset, option='lalo')
except:
pass
try:
geomapFile = check_subset(geomapFile, subset, option='lalo')
except:
pass
## subset radar coded files
igramFile = check_subset(igramFile, [ysub, xsub], option='yx')
maskFile = check_subset(maskFile, [ysub, xsub], option='yx')
try:
demRdrFile = check_subset(demRdrFile, [ysub, xsub], option='yx')
except:
pass
else:
print 'No Subset selected. Processing the whole area'
#try:
# subset= template['pysar.subset.yx'].split(',')
# print 'subset in y - '+str(subset[0])
# print 'subset in x - '+str(subset[1])
# igramFile = check_subset(igramFile, subset)
# corFile = check_subset(corFile, subset)
# maskFile = check_subset(maskFile, subset)
# demRdrFile = check_subset(demRdrFile,subset)
# demGeoFile = check_subset(demGeoFile,subset)
# #geomapFile = check_subset(geomapFile,subset)
#except: print 'No Subset selected. Processing the whole area'
#########################################
# Referencing Interferograms
#########################################
print '\n********** Referencing Interferograms ***************'
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.lalo' in template.keys():
'Checking lat/lon refernce point'
lat = template['pysar.seed.lalo'].split(',')[0]
lon = template['pysar.seed.lalo'].split(',')[1]
seedCmd = 'seed_data.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)
############################################
# Unwrapping Error Correction (Optional)
# based on the consistency of triplets
# of interferograms
############################################
print '\n********** Unwrapping Error Correction **************'
outName = igramFile.split('.')[0] + '_unwCor.h5'
try:
template['pysar.unwrapError']
if template['pysar.unwrapError'] in ('Y', 'y', 'yes', 'Yes', 'YES'):
if os.path.isfile(outName):
igramFile = outName
print igramFile + ' exists.'
else:
print 'This might take a while depending on the size of your data set!'
unwCmd = 'unwrap_error.py ' + igramFile
os.system(unwCmd)
igramFile = outName
else:
print 'No unwrapping error correction.'
except:
print 'No unwrapping error correction.'
#########################################
# Inversion of Interferograms
########################################
print '\n********** Time Series Inversion ********************'
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'
##############################################
# Temporal Coherence:
# A parameter to evaluate the consistency
# of timeseries with the interferograms
##############################################
print '\n********** Generate Temporal Coherence file *********'
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)
tempCohFile = 'temporal_coherence.h5'
##############################################
# Update Mask based on temporal coherence (Optional)
##############################################
print '\n********** Update Mask based on Temporal Coherence **'
outName = maskFile.split('.')[0] + '_tempCoh.h5'
try:
template['pysar.mask']
if template['pysar.mask'] in ('Y', 'yes', 'Yes', 'YES', 'y'):
if os.path.isfile(outName):
maskFile = outName
print maskFile + ' already exists.'
else:
try:
cohT = template['pysar.mask.threshold']
except:
cohT = '0.7'
maskCmd = 'generate_mask.py -f ' + tempCohFile + ' -m ' + cohT + ' -M 1.0 -o ' + outName
print maskCmd
os.system(maskCmd)
maskFile = outName
else:
print 'No mask update from temporal coherence'
except:
print 'No mask update from temporal coherence'
##############################################
# Incident Angle
##############################################
print '\n********** Generate Incident Angle file *************'
if os.path.isfile('incidence_angle.h5'):
print 'incidence_angle.h5 already exists.'
else:
inciCmd = 'incidence_angle.py -f ' + timeseriesFile
print inciCmd
os.system(inciCmd)
##############################################
# LOD (Local Oscillator Drift) Correction
# when Satellite is Envisat and
# Coordinate system is radar
##############################################
print '\n********** Local Oscillator Drift correction ********'
rdr_or_geo = ut.radar_or_geo(timeseriesFile)
outName = timeseriesFile.split('.')[0] + '_LODcor.h5'
if os.path.isfile(outName):
timeseriesFile = outName
print timeseriesFile + ' already exists.'
else:
h5file = h5py.File(timeseriesFile, 'r')
platform = h5file['timeseries'].attrs['PLATFORM']
if platform == 'ENVISAT':
if rdr_or_geo == 'radar':
LODcmd = 'lod.py ' + timeseriesFile
print LODcmd
os.system(LODcmd)
timeseriesFile = outName
else:
print 'Cannot correct LOD for geocoded data.'
else:
print 'No need of LOD correction for ' + platform
h5file.close()
##############################################
# Tropospheric Delay Correction (Optional)
##############################################
print '\n********** Tropospheric Correction ******************'
try:
if (template['pysar.troposphericDelay'] in ('Y','y','yes','Yes','YES')) and\
template['pysar.orbitError.method'] in ['BaseTropCor','basetropcor','base_trop_cor']:
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 separated from baseline error correction, \
choose other existing options for orbital error correction.
+++++++++++++++++++++++++++++++++++++++++++++++++++
'''
template['pysar.troposphericDelay'] = 'no'
except:
print 'Checking the tropospheric delay correction ...'
if template['pysar.troposphericDelay'] in ('Y', 'y', 'yes', 'Yes', 'YES'):
if rdr_or_geo == 'radar': demFile = demRdrFile
elif rdr_or_geo == 'geo': demFile = demGeoFile
if not os.path.isfile(demFile):
print '++++++++++++++++++++++++++++++++++++++++++++++'
print 'ERROR:'
print ' DEM file was not found!'
print ' Continue without tropospheric correction ...'
print '++++++++++++++++++++++++++++++++++++++++++++++'
else:
if template['pysar.troposphericDelay.method'] in ['height-correlation','height_correlation',\
'Height-Correlation','Height_Correlation']:
print 'tropospheric delay correction with height-correlation approach'
outName = timeseriesFile.split('.')[0] + '_tropCor.h5'
if os.path.isfile(outName):
timeseriesFile = outName
print timeseriesFile + ' already exists.'
else:
try:
poly_order = template[
'pysar.troposphericDelay.polyOrder']
except:
poly_order = '1'
print 'Deafult polynomial order for troposphreic correction = 1'
cmdTrop = 'tropcor_phase_elevation.py' + ' -f ' + timeseriesFile + ' -d ' + demFile + ' -p ' + str(
poly_order)
print cmdTrop
os.system(cmdTrop)
timeseriesFile = outName
elif template['pysar.troposphericDelay.method'] in [
'pyaps', 'PyAPS', '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.troposphericDelay.weatherModel']
print 'Numerical Weather Model: ' + source_of_NWM
outName = timeseriesFile.split(
'.')[0] + '_' + source_of_NWM + '.h5'
if os.path.isfile(outName):
timeseriesFile = outName
print timeseriesFile + ' already exists.'
else:
acquisition_time = template['pysar.acquisitionTime']
print 'acquisition time: ' + acquisition_time
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 = outName
else:
print 'ERROR: Unrecognized atmospheric correction method: ' + template[
'pysar.trop.method']
else:
print 'No atmospheric delay correction.'
##############################################
# Topographic (DEM) Residuals Correction (Optional)
##############################################
print '\n********** Topographic (DEM) Error correction *******'
outName = timeseriesFile.split('.')[0] + '_demCor.h5'
try:
template['pysar.topoError']
if template['pysar.topoError'] in ('Y', 'yes', 'Yes', 'YES', 'y'):
if os.path.isfile(outName):
timeseriesFile = outName
print timeseriesFile + ' already exists.'
else:
print 'Correcting topographic residuals'
topoCmd = 'dem_error.py ' + timeseriesFile + ' ' + igramFile
print topoCmd
os.system(topoCmd)
timeseriesFile = outName
else:
print 'No correction for topographic residuals.'
except:
print 'No correction for topographic residuals.'
##############################################
# Orbit Correction (Optional)
##############################################
print '\n********** Orbital Correction ***********************'
try:
template['pysar.orbitError']
if template['pysar.orbitError'] in ('Y', 'yes', 'Yes', 'YES', 'y'):
try:
orbit_error_method = template['pysar.orbitError.method']
print 'orbit error correction method : ' + orbit_error_method
outName = timeseriesFile.split(
'.')[0] + '_' + orbit_error_method + '.h5'
if os.path.isfile(outName):
timeseriesFile = outName
print timeseriesFile + ' already exists.'
else:
if orbit_error_method in [ 'plane', 'plane_range', 'plane_azimuth',\
'quadratic', 'quadratic_range', 'quadratic_azimuth']:
orbitCmd = 'remove_plane.py ' + timeseriesFile + ' ' + orbit_error_method #+ ' Mask.h5'
print orbitCmd
os.system(orbitCmd)
timeseriesFile = outName
elif orbit_error_method in ['baselineCor', 'BaselineCor']:
try:
h5file = h5py.File(timeseriesFile, 'r')
daz = float(h5file['timeseries'].
attrs['AZIMUTH_PIXEL_SIZE'])
orbitCmd = 'baseline_error.py ' + timeseriesFile #+ ' Mask.h5'
print orbitCmd
os.system(orbitCmd)
timeseriesFile = outName
except:
print 'WARNING!'
print 'Skipping orbital error correction.'
print 'baselineCor method can only be applied in radar coordinate'
elif orbit_error_method in [
'BaseTropCor', 'basetropcor', 'base_trop_cor'
]:
try:
h5file = h5py.File(timeseriesFile, 'r')
daz = float(h5file['timeseries'].
attrs['AZIMUTH_PIXEL_SIZE'])
print 'Joint estimation of Baseline error and tropospheric delay [height-correlation approach]'
if rdr_or_geo == 'radar': demFile = demRdrFile
elif rdr_or_geo == 'geo': demFile = demGeoFile
try:
poly_order = template['pysar.trop.poly_order']
except:
poly_order = 1
print 'Deafult polynomial order for troposphreic correction = 1'
orbitCmd = 'baseline_trop.py ' + timeseriesFile + ' ' + demFile + ' ' + str(
poly_order) + ' range_and_azimuth'
print orbitCmd
os.system(orbitCmd)
timeseriesFile = outName
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'
print ' 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.'
#############################################
# Velocity and rmse maps
#############################################
print '\n********** Velocity estimation **********************'
if os.path.isfile('velocity.h5'):
print 'velocity.h5 file already exists.'
else:
velCmd = 'timeseries2velocity.py ' + timeseriesFile
print velCmd
os.system(velCmd)
velocityFile = 'velocity.h5'
############################################
# Geocoding (Optional)
############################################
print '\n********** Geocoding ********************************'
try:
template['pysar.geocode']
if template['pysar.geocode'] in ('Y', 'y', 'yes', 'Yes', 'YES'):
#geoTsFile = check_geocode(timeseriesFile,geomapFile)
geoVelocityFile = check_geocode(velocityFile, geomapFile)
geoMaskFile = check_geocode(maskFile, geomapFile)
else:
print 'No geocoding applied'
except:
print 'No geocoding applied'
#############################################
# Masking (Optional)
#############################################
print '\n********** Masking Velocity *************************'
velocityFile = check_mask(velocityFile, maskFile)
try:
geoVelocityFile = check_mask(geoVelocityFile, geoMaskFile)
except:
pass
#############################################
# PySAR v1.0 #
#############################################
s = time.time() - start
m, s = divmod(s, 60)
h, m = divmod(m, 60)
print '\nTime used: %02d hours %02d mins %02d secs' % (h, m, s)
print '\n###############################################'
print 'End of PySAR processing!'
print '################################################\n'
