def save_hdfeos5(inps, customTemplate=None):
if not inps.geocoded:
warnings.warn('Dataset is in radar coordinates, skip writting to HDF-EOS5 format.')
else:
# Add attributes from custom template to timeseries file
if customTemplate is not None:
ut.add_attribute(inps.timeseriesFile, customTemplate)
# Save to HDF-EOS5 format
print('--------------------------------------------')
hdfeos5Cmd = ('save_hdfeos5.py {t} -c {c} -m {m} -g {g}'
' -t {e}').format(t=inps.timeseriesFile,
c=inps.tempCohFile,
m=inps.maskFile,
g=inps.geomFile,
e=inps.templateFile)
print(hdfeos5Cmd)
atr = readfile.read_attribute(inps.timeseriesFile)
SAT = sensor.get_unavco_mission_name(atr)
try:
inps.hdfeos5File = ut.get_file_list('{}_*.he5'.format(SAT))[0]
except:
inps.hdfeos5File = None
if ut.run_or_skip(out_file=inps.hdfeos5File, in_file=[inps.timeseriesFile,
inps.tempCohFile,
inps.maskFile,
inps.geomFile]) == 'run':
status = subprocess.Popen(hdfeos5Cmd, shell=True).wait()
if status is not 0:
raise Exception('Error while generating HDF-EOS5 time-series file.\n')
return
def extract_metadata4lookup_table(fname):
"""Read/extract attribute for .UTM_TO_RDC file from Gamma to ROI_PAC
For example, it read input file, sim_150911-150922.UTM_TO_RDC,
find its associated par file, sim_150911-150922.utm.dem.par, read it, and
convert to ROI_PAC style and write it to an rsc file, sim_150911-150922.UTM_TO_RDC.rsc"""
# Check existed .rsc file
rsc_file_list = ut.get_file_list(fname+'.rsc')
if rsc_file_list:
rsc_file = rsc_file_list[0]
return rsc_file
atr = {}
atr['PROCESSOR'] = 'gamma'
atr['FILE_TYPE'] = os.path.splitext(fname)[1]
atr['Y_UNIT'] = 'degrees'
atr['X_UNIT'] = 'degrees'
par_file = os.path.splitext(fname)[0]+'.utm.dem.par'
par_dict = readfile.read_gamma_par(par_file)
atr.update(par_dict)
# Write to .rsc file
rsc_file = fname+'.rsc'
try:
atr_orig = readfile.read_roipac_rsc(rsc_file)
except:
atr_orig = dict()
if not set(atr.items()).issubset(set(atr_orig.items())):
atr_out = {**atr_orig, **atr}
print('writing >>> '+os.path.basename(rsc_file))
writefile.write_roipac_rsc(atr_out, out_file=rsc_file)
return rsc_file
def prepare_metadata(inps):
inps.file = ut.get_file_list(inps.file, abspath=True)
# check outfile and parallel option
if inps.parallel:
(num_cores,
inps.parallel,
Parallel,
delayed) = ut.check_parallel(len(inps.file), print_msg=False)
# multiple datasets files
ext = os.path.splitext(inps.file[0])[1]
if ext in ['.unw', '.cor', '.int']:
if len(inps.file) == 1:
extract_metadata4interferogram(inps.file[0])
elif inps.parallel:
Parallel(n_jobs=num_cores)(delayed(extract_metadata4interferogram)(file)
for file in inps.file)
else:
for File in inps.file:
extract_metadata4interferogram(File)
# Single dataset files
elif inps.file[0].endswith('.utm.dem'):
for File in inps.file:
atr_file = extract_metadata4dem_geo(File)
elif inps.file[0].endswith(('.rdc.dem', '.hgt_sim')):
for File in inps.file:
atr_file = extract_metadata4dem_radar(File)
elif ext in ['.UTM_TO_RDC']:
for File in inps.file:
atr_file = extract_metadata4lookup_table(File)
return
def _check_inps(inps):
inps.file = ut.get_file_list(inps.file)
if not inps.file:
raise Exception('ERROR: no input file found!')
elif len(inps.file) > 1:
inps.outfile = None
atr = readfile.read_attribute(inps.file[0])
if 'Y_FIRST' in atr.keys() and inps.radar2geo:
print('input file is already geocoded')
print('to resample geocoded files into radar coordinates, use --geo2radar option')
print('exit without doing anything.')
sys.exit(0)
elif 'Y_FIRST' not in atr.keys() and not inps.radar2geo:
print('input file is already in radar coordinates, exit without doing anything')
sys.exit(0)
inps.lookupFile = ut.get_lookup_file(inps.lookupFile)
if not inps.lookupFile:
raise FileNotFoundError('No lookup table found! Can not geocode without it.')
if inps.SNWE:
inps.SNWE = tuple(inps.SNWE)
inps.laloStep = [inps.latStep, inps.lonStep]
if None in inps.laloStep:
inps.laloStep = None
return inps
def cmd_line_parse(iargs=None):
parser = create_parser()
inps = parser.parse_args(args=iargs)
inps.file = ut.get_file_list(inps.file)
if inps.outfile or not inps.disp_fig:
inps.save_fig = True
return inps
def cmd_line_parse(iargs=None):
parser = create_parser()
inps = parser.parse_args(args=iargs)
inps.file = ut.get_file_list(inps.file)
if inps.ysub and not len(inps.ysub) % 2 == 0:
raise Exception('ERROR: -y input has to have even length!')
return inps
def cmd_line_parse(iargs=None):
parser = create_parser()
inps = parser.parse_args(args=iargs)
inps.file = ut.get_file_list(inps.file)
if len(inps.file) > 1 and inps.outfile:
inps.outfile = None
print('more than one file is input, disable custom output filename.')
return inps
def main(iargs=None):
inps = cmd_line_parse(iargs)
inps.file = ut.get_file_list(inps.file)[0]
inps = read_reference_input(inps)
if inps.go_reference:
reference_file(inps)
print('Done.')
return
def cmd_line_parse(iargs=None):
parser = create_parser()
inps = parser.parse_args(args=iargs)
inps.file = ut.get_file_list(inps.file)
#print('number of input files: ({})\n{}'.format(len(inps.file), inps.file))
if len(inps.file) > 1:
inps.outfile = None
return inps
def main(iargs=None):
inps = cmd_line_parse(iargs)
inps.file = ut.get_file_list(inps.file)
print('number of input files: ({})\n{}'.format(len(inps.file), inps.file))
inps = read_aux_subset2inps(inps)
subset_file_list(inps.file, inps)
print('Done.')
return
def cmd_line_parse(iargs=None):
parser = create_parser()
inps = parser.parse_args(args=iargs)
inps.file = ut.get_file_list(inps.file, abspath=True)
inps.file_ext = os.path.splitext(inps.file[0])[1]
# check input file extension
ext_list = ['.unw', '.cor', '.int', '.dem', '.hgt_sim', '.UTM_TO_RDC']
if inps.file_ext not in ext_list:
msg = 'unsupported input file extension: {}'.format(inps.file_ext)
msg += '\nsupported file extensions: {}'.format(ext_list)
raise ValueError()
return inps
def copy_aux_file(inps):
# for Univ of Miami
fileList = ['PROCESS/unavco_attributes.txt',
'PROCESS/bl_list.txt',
'SLC/summary*slc.jpg']
try:
projectDir = os.path.join(os.getenv('SCRATCHDIR'), inps.projectName)
fileList = ut.get_file_list([os.path.join(projectDir, i) for i in fileList],
abspath=True)
for file in fileList:
if ut.run_or_skip(out_file=os.path.basename(file),
in_file=file,
check_readable=False) == 'run':
shutil.copy2(file, inps.workDir)
print('copy {} to work directory'.format(os.path.basename(file)))
except:
pass
return inps
def check_exist_grib_file(gfile_list, print_msg=True):
"""Check input list of grib files, and return the existing ones with right size."""
gfile_exist = ut.get_file_list(gfile_list)
if gfile_exist:
file_sizes = [
os.path.getsize(i) for i in gfile_exist
if os.path.getsize(i) > 10e6
]
if file_sizes:
comm_size = ut.most_common([i for i in file_sizes])
if print_msg:
print('common file size: {} bytes'.format(comm_size))
print('number of grib files existed : {}'.format(
len(gfile_exist)))
gfile_corrupt = []
for gfile in gfile_exist:
if os.path.getsize(gfile) < comm_size * 0.9:
gfile_corrupt.append(gfile)
else:
gfile_corrupt = gfile_exist
if gfile_corrupt:
if print_msg:
print(
'------------------------------------------------------------------------------'
)
print(
'corrupted grib files detected! Delete them and re-download...'
)
print('number of grib files corrupted : {}'.format(
len(gfile_corrupt)))
for i in gfile_corrupt:
rmCmd = 'rm ' + i
print(rmCmd)
os.system(rmCmd)
gfile_exist.remove(i)
if print_msg:
print(
'------------------------------------------------------------------------------'
)
return gfile_exist
def set_mask():
global mask, inps, atr
if not inps.mask_file:
if os.path.basename(inps.timeseries_file).startswith('geo_'):
file_list = ['geo_maskTempCoh.h5']
else:
file_list = ['maskTempCoh.h5', 'mask.h5']
try:
inps.mask_file = ut.get_file_list(file_list)[0]
except:
inps.mask_file = None
try:
mask = readfile.read(inps.mask_file, datasetName='mask')[0]
mask[mask!=0] = 1
print(('load mask from file: '+inps.mask_file))
except:
mask = None
print('No mask used.')
def prepare_metadata(inps):
inps.file = ut.get_file_list(inps.file, abspath=True)
# Check input file type
ext = os.path.splitext(inps.file[0])[1]
if ext not in ['.unw', '.cor', '.int', '.byt']:
return
# check outfile and parallel option
if inps.parallel:
num_cores, inps.parallel, Parallel, delayed = ut.check_parallel(
len(inps.file), print_msg=False)
if len(inps.file) == 1:
extract_metadata(inps.file[0])
elif inps.parallel:
Parallel(n_jobs=num_cores)(delayed(extract_metadata)(fname)
for fname in inps.file)
else:
for fname in inps.file:
extract_metadata(fname)
return
def extract_metadata4lookup_table(fname):
"""Read/extract attribute for .UTM_TO_RDC file from Gamma to ROI_PAC
For example, it read input file, sim_150911-150922.UTM_TO_RDC,
find its associated par file, sim_150911-150922.utm.dem.par, read it, and
convert to ROI_PAC style and write it to an rsc file, sim_150911-150922.UTM_TO_RDC.rsc"""
# Check existed .rsc file
rsc_file_list = ut.get_file_list(fname + '.rsc')
if rsc_file_list:
rsc_file = rsc_file_list[0]
#print(rsc_file+' is existed, no need to re-extract.')
return rsc_file
atr = {}
atr['PROCESSOR'] = 'gamma'
atr['FILE_TYPE'] = os.path.splitext(fname)[1]
atr['Y_UNIT'] = 'degrees'
atr['X_UNIT'] = 'degrees'
par_file = os.path.splitext(fname)[0] + '.utm.dem.par'
#print('read '+os.path.basename(par_file))
par_dict = readfile.read_gamma_par(par_file)
atr.update(par_dict)
# Write to .rsc file
rsc_file = fname + '.rsc'
try:
atr_orig = readfile.read_roipac_rsc(rsc_file)
except:
atr_orig = None
#keyList = [i for i in atr_orig.keys() if i in atr.keys()]
if any((i not in atr_orig.keys() or atr_orig[i] != atr[i])
for i in atr.keys()):
print('writing >>> ' + os.path.basename(rsc_file))
writefile.write_roipac_rsc(atr, out_file=rsc_file)
return rsc_file
def dload_grib_pyaps(date_list, hour, trop_model='ECMWF', weather_dir='./'):
"""Download weather re-analysis grib files using PyAPS
Inputs:
date_list : list of string in YYYYMMDD format
hour : string in HH:MM or HH format
trop_model : string,
weather_dir : string,
Output:
grib_file_list : list of string
"""
print(
'*' * 50 +
'\nDownloading weather model data using PyAPS (Jolivet et al., 2011, GRL) ...'
)
# Grib data directory
grib_dir = weather_dir + '/' + trop_model
if not os.path.isdir(grib_dir):
os.makedirs(grib_dir)
print('making directory: ' + grib_dir)
# Date list to grib file list
grib_file_list = date_list2grib_file(date_list, hour, trop_model, grib_dir)
# Get date list to download (skip already downloaded files)
grib_file_existed = ut.get_file_list(grib_file_list)
if grib_file_existed:
grib_filesize_digit = ut.most_common(
[len(str(os.path.getsize(i))) for i in grib_file_existed])
grib_filesize_max2 = ut.most_common(
[str(os.path.getsize(i))[0:2] for i in grib_file_existed])
grib_file_corrupted = [
i for i in grib_file_existed
if (len(str(os.path.getsize(i))) != grib_filesize_digit
or str(os.path.getsize(i))[0:2] != grib_filesize_max2)
]
print('file size mode: %se%d bytes' %
(grib_filesize_max2, grib_filesize_digit - 2))
print('number of grib files existed : %d' % len(grib_file_existed))
if grib_file_corrupted:
print(
'------------------------------------------------------------------------------'
)
print(
'corrupted grib files detected! Delete them and re-download...'
)
print('number of grib files corrupted : %d' %
len(grib_file_corrupted))
for i in grib_file_corrupted:
rmCmd = 'rm ' + i
print(rmCmd)
os.system(rmCmd)
grib_file_existed.remove(i)
print(
'------------------------------------------------------------------------------'
)
grib_file2download = sorted(
list(set(grib_file_list) - set(grib_file_existed)))
date_list2download = [
str(re.findall('\d{8}', i)[0]) for i in grib_file2download
]
print('number of grib files to download: %d' % len(date_list2download))
print(
'------------------------------------------------------------------------------\n'
)
# Download grib file using PyAPS
if trop_model == 'ECMWF': pa.ECMWFdload(date_list2download, hour, grib_dir)
elif trop_model == 'MERRA':
pa.MERRAdload(date_list2download, hour, grib_dir)
elif trop_model == 'NARR':
pa.NARRdload(date_list2download, hour, grib_dir)
elif trop_model == 'ERA':
pa.ERAdload(date_list2download, hour, grib_dir)
elif trop_model == 'MERRA1':
pa.MERRA1dload(date_list2download, hour, grib_dir)
return grib_file_list
def read_template(inps):
print('\n********** Read Template File **********')
# default template
inps.templateFile = os.path.join(inps.workDir, 'pysarApp_template.txt')
if not os.path.isfile(inps.templateFile):
print('generate default template file: ' + inps.templateFile)
with open(inps.templateFile, 'w') as f:
f.write(TEMPLATE)
else:
inps.templateFile = check_obsolete_default_template(inps.templateFile)
# custom template
templateCustom = None
if inps.templateFileCustom:
# Copy custom template file to work directory
if ut.update_file(os.path.basename(inps.templateFileCustom),
inps.templateFileCustom,
check_readable=False):
shutil.copy2(inps.templateFileCustom, inps.workDir)
print('copy {} to work directory'.format(
os.path.basename(inps.templateFileCustom)))
# Read custom template
print('read custom template file: ' + inps.templateFileCustom)
templateCustom = readfile.read_template(inps.templateFileCustom)
# correct some loose type errors
for key in templateCustom.keys():
if templateCustom[key].lower() in ['default']:
templateCustom[key] = 'auto'
elif templateCustom[key].lower() in ['n', 'off', 'false']:
templateCustom[key] = 'no'
elif templateCustom[key].lower() in ['y', 'on', 'true']:
templateCustom[key] = 'yes'
for key in ['pysar.deramp', 'pysar.troposphericDelay.method']:
if key in templateCustom.keys():
templateCustom[key] = templateCustom[key].lower().replace(
'-', '_')
if 'processor' in templateCustom.keys():
templateCustom['pysar.load.processor'] = templateCustom[
'processor']
# Update default template with custom input template
print('update default template based on input custom template')
inps.templateFile = ut.update_template_file(inps.templateFile,
templateCustom)
if inps.generate_template:
raise SystemExit('Exit as planned after template file generation.')
print('read default template file: ' + inps.templateFile)
template = readfile.read_template(inps.templateFile)
template = ut.check_template_auto_value(template)
# Get existing files name: unavco_attributes.txt
try:
inps.unavcoMetadataFile = ut.get_file_list('unavco_attribute*txt',
abspath=True)[0]
except:
inps.unavcoMetadataFile = None
print('No UNAVCO attributes file found.')
return inps, template, templateCustom
def extract_metadata4interferogram(fname):
"""Read/extract attributes for PySAR from Gamma .unw, .cor and .int file
Parameters: fname : str, Gamma interferogram filename or path,
i.e. /PopoSLT143TsxD/diff_filt_HDR_130118-130129_4rlks.unw
Returns: atr : dict, Attributes dictionary
"""
file_dir = os.path.dirname(fname)
file_basename = os.path.basename(fname)
rsc_file = fname+'.rsc'
# if os.path.isfile(rsc_file):
# return rsc_file
atr = {}
atr['PROCESSOR'] = 'gamma'
atr['FILE_TYPE'] = os.path.splitext(fname)[1]
# Get info: date12, num of loooks
try:
date12 = str(re.findall('\d{8}[-_]\d{8}', file_basename)[0])
except:
date12 = str(re.findall('\d{6}[-_]\d{6}', file_basename)[0])
m_date, s_date = date12.replace('-', '_').split('_')
atr['DATE12'] = ptime.yymmdd(m_date)+'-'+ptime.yymmdd(s_date)
lks = os.path.splitext(file_basename.split(date12)[1])[0]
# Read .off and .par file
off_file = file_dir+'/*'+date12+lks+'.off'
m_par_file = [file_dir+'/*'+m_date+lks+i for i in ['.amp.par', '.ramp.par']]
s_par_file = [file_dir+'/*'+s_date+lks+i for i in ['.amp.par', '.ramp.par']]
try:
off_file = ut.get_file_list(off_file)[0]
except:
print('\nERROR: Can not find .off file, it supposed to be like: '+off_file)
try:
m_par_file = ut.get_file_list(m_par_file)[0]
except:
print('\nERROR: Can not find master date .par file, it supposed to be like: '+m_par_file)
try:
s_par_file = ut.get_file_list(s_par_file)[0]
except:
print('\nERROR: Can not find slave date .par file, it supposed to be like: '+s_par_file)
par_dict = readfile.read_gamma_par(m_par_file)
off_dict = readfile.read_gamma_par(off_file)
atr.update(par_dict)
atr.update(off_dict)
# Perp Baseline Info
atr = get_perp_baseline(m_par_file, s_par_file, off_file, atr)
# LAT/LON_REF1/2/3/4
atr = get_lalo_ref(m_par_file, atr)
# Write to .rsc file
try:
atr_orig = readfile.read_roipac_rsc(rsc_file)
except:
atr_orig = dict()
if not set(atr.items()).issubset(set(atr_orig.items())):
atr_out = {**atr_orig, **atr}
print('merge %s, %s and %s into %s' % (os.path.basename(m_par_file),
os.path.basename(s_par_file),
os.path.basename(off_file),
os.path.basename(rsc_file)))
writefile.write_roipac_rsc(atr_out, out_file=rsc_file)
return rsc_file
def main(iargs=None):
start_time = time.time()
inps = cmd_line_parse(iargs)
if inps.version:
raise SystemExit(version.version_description)
#########################################
# Initiation
#########################################
print(version.logo)
# Project Name
inps.projectName = None
if inps.templateFileCustom:
inps.templateFileCustom = os.path.abspath(inps.templateFileCustom)
inps.projectName = os.path.splitext(
os.path.basename(inps.templateFileCustom))[0]
print('Project name: ' + inps.projectName)
# Work directory
if not inps.workDir:
if autoPath and 'SCRATCHDIR' in os.environ and inps.projectName:
inps.workDir = os.path.join(os.getenv('SCRATCHDIR'),
inps.projectName, 'PYSAR')
else:
inps.workDir = os.getcwd()
inps.workDir = os.path.abspath(inps.workDir)
if not os.path.isdir(inps.workDir):
os.makedirs(inps.workDir)
os.chdir(inps.workDir)
print("Go to work directory: " + inps.workDir)
copy_aux_file(inps)
inps, template, templateCustom = read_template(inps)
#########################################
# Loading Data
#########################################
print('\n********** Load Data **********')
loadCmd = 'load_data.py --template {}'.format(inps.templateFile)
if inps.projectName:
loadCmd += ' --project {}'.format(inps.projectName)
print(loadCmd)
status = subprocess.Popen(loadCmd, shell=True).wait()
os.chdir(inps.workDir)
print('-' * 50)
inps, atr = ut.check_loaded_dataset(inps.workDir, inps)
# Add template options into HDF5 file metadata
# if inps.templateFileCustom:
# atrCmd = 'add_attribute.py {} {}'.format(inps.stackFile, inps.templateFileCustom)
# print(atrCmd)
# status = subprocess.Popen(atrCmd, shell=True).wait()
#ut.add_attribute(inps.stackFile, template)
if inps.load_dataset:
raise SystemExit('Exit as planned after loading/checking the dataset.')
if inps.reset:
print('Reset dataset attributtes for a fresh re-run.\n' + '-' * 50)
# Reset reference pixel
refPointCmd = 'reference_point.py {} --reset'.format(inps.stackFile)
print(refPointCmd)
status = subprocess.Popen(refPointCmd, shell=True).wait()
# Reset network modification
networkCmd = 'modify_network.py {} --reset'.format(inps.stackFile)
print(networkCmd)
status = subprocess.Popen(networkCmd, shell=True).wait()
#########################################
# Generating Aux files
#########################################
print('\n********** Generate Auxiliary Files **********')
# Initial mask (pixels with valid unwrapPhase or connectComponent in ALL interferograms)
inps.maskFile = 'mask.h5'
if ut.update_file(inps.maskFile, inps.stackFile):
maskCmd = 'generate_mask.py {} --nonzero -o {}'.format(
inps.stackFile, inps.maskFile)
print(maskCmd)
status = subprocess.Popen(maskCmd, shell=True).wait()
# Average spatial coherence
inps.avgSpatialCohFile = 'avgSpatialCoherence.h5'
if ut.update_file(inps.avgSpatialCohFile, inps.stackFile):
avgCmd = 'temporal_average.py {} --dataset coherence -o {}'.format(
inps.stackFile, inps.avgSpatialCohFile)
print(avgCmd)
status = subprocess.Popen(avgCmd, shell=True).wait()
#########################################
# Referencing Interferograms in Space
#########################################
print('\n********** Select Reference Point **********')
refPointCmd = 'reference_point.py {} -t {} -c {}'.format(
inps.stackFile, inps.templateFile, inps.avgSpatialCohFile)
print(refPointCmd)
status = subprocess.Popen(refPointCmd, shell=True).wait()
if status is not 0:
raise Exception('Error while finding reference pixel in space.\n')
############################################
# Unwrapping Error Correction (Optional)
# based on the consistency of triplets
# of interferograms
############################################
if template['pysar.unwrapError.method']:
print('\n********** Unwrapping Error Correction **********')
outName = '{}_unwCor.h5'.format(os.path.splitext(inps.stackFile)[0])
unwCmd = 'unwrap_error.py {} --mask {} --template {}'.format(
inps.stackFile, inps.maskFile, inps.templateFile)
print(unwCmd)
if ut.update_file(outName, inps.stackFile):
print(
'This might take a while depending on the size of your data set!'
)
status = subprocess.Popen(unwCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while correcting phase unwrapping errors.\n')
inps.stackFile = outName
#########################################
# Network Modification (Optional)
#########################################
print('\n********** Modify Network **********')
networkCmd = 'modify_network.py {} -t {}'.format(inps.stackFile,
inps.templateFile)
print(networkCmd)
status = subprocess.Popen(networkCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while modifying the network of interferograms.\n')
# Plot network colored in spatial coherence
print('--------------------------------------------------')
plotCmd = 'plot_network.py {} --template {} --nodisplay'.format(
inps.stackFile, inps.templateFile)
print(plotCmd)
inps.cohSpatialAvgFile = '{}_coherence_spatialAverage.txt'.format(
os.path.splitext(os.path.basename(inps.stackFile))[0])
if ut.update_file(
'Network.pdf',
check_readable=False,
inFile=[inps.stackFile, inps.cohSpatialAvgFile,
inps.templateFile]):
status = subprocess.Popen(plotCmd, shell=True).wait()
if inps.modify_network:
raise SystemExit('Exit as planned after network modification.')
#########################################
# Inversion of Interferograms
########################################
print(
'\n********** Invert Network of Interferograms into Time-series **********'
)
invCmd = 'ifgram_inversion.py {} --template {}'.format(
inps.stackFile, inps.templateFile)
print(invCmd)
inps.timeseriesFile = 'timeseries.h5'
inps.tempCohFile = 'temporalCoherence.h5'
if ut.update_file(inps.timeseriesFile, inps.stackFile):
status = subprocess.Popen(invCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while inverting network interferograms into timeseries')
print('\n--------------------------------------------')
print('Update Mask based on Temporal Coherence ...')
inps.maskFile = 'maskTempCoh.h5'
inps.minTempCoh = template['pysar.networkInversion.minTempCoh']
maskCmd = 'generate_mask.py {} -m {} -o {}'.format(inps.tempCohFile,
inps.minTempCoh,
inps.maskFile)
print(maskCmd)
if ut.update_file(inps.maskFile, inps.tempCohFile):
status = subprocess.Popen(maskCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while generating mask file from temporal coherence.')
if inps.invert_network:
raise SystemExit('Exit as planned after network inversion.')
# check number of pixels selected in mask file for following analysis
min_num_pixel = float(template['pysar.networkInversion.minNumPixel'])
msk = readfile.read(inps.maskFile)[0]
num_pixel = np.sum(msk != 0.)
print('number of pixels selected: {}'.format(num_pixel))
if num_pixel < min_num_pixel:
msg = "Not enought coherent pixels selected (minimum of {}). ".format(
int(min_num_pixel))
msg += "Try the following:\n"
msg += "1) Check the reference pixel and make sure it's not in areas with unwrapping errors\n"
msg += "2) Check the network and make sure it's fully connected without subsets"
raise RuntimeError(msg)
del msk
##############################################
# LOD (Local Oscillator Drift) Correction
# for Envisat data in radar coord only
##############################################
if atr['PLATFORM'].lower().startswith('env'):
print(
'\n********** Local Oscillator Drift Correction for Envisat **********'
)
outName = os.path.splitext(inps.timeseriesFile)[0] + '_LODcor.h5'
lodCmd = 'local_oscilator_drift.py {} {} -o {}'.format(
inps.timeseriesFile, inps.geomFile, outName)
print(lodCmd)
if ut.update_file(outName, [inps.timeseriesFile, inps.geomFile]):
status = subprocess.Popen(lodCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while correcting Local Oscillator Drift.\n')
inps.timeseriesFile = outName
##############################################
# Tropospheric Delay Correction (Optional)
##############################################
print('\n********** Tropospheric Delay Correction **********')
inps.tropPolyOrder = template['pysar.troposphericDelay.polyOrder']
inps.tropModel = template['pysar.troposphericDelay.weatherModel']
inps.tropMethod = template['pysar.troposphericDelay.method']
try:
fileList = [
os.path.join(inps.workDir, 'INPUTS/{}.h5'.format(inps.tropModel))
]
inps.tropFile = ut.get_file_list(fileList)[0]
except:
inps.tropFile = None
if inps.tropMethod:
# Check Conflict with base_trop_cor
if template['pysar.deramp'] == 'base_trop_cor':
msg = """
Method Conflict: base_trop_cor is in conflict with {} option!
base_trop_cor applies simultaneous ramp removal AND tropospheric correction.
IGNORE base_trop_cor input and continue pysarApp.py.
"""
warnings.warn(msg)
template['pysar.deramp'] = False
fbase = os.path.splitext(inps.timeseriesFile)[0]
# Call scripts
if inps.tropMethod == 'height_correlation':
outName = '{}_tropHgt.h5'.format(fbase)
print(
'tropospheric delay correction with height-correlation approach'
)
tropCmd = ('tropcor_phase_elevation.py {t} -d {d} -p {p}'
' -m {m} -o {o}').format(t=inps.timeseriesFile,
d=inps.geomFile,
p=inps.tropPolyOrder,
m=inps.maskFile,
o=outName)
print(tropCmd)
if ut.update_file(outName, inps.timeseriesFile):
status = subprocess.Popen(tropCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while correcting tropospheric delay.\n')
inps.timeseriesFile = outName
elif inps.tropMethod == 'pyaps':
inps.weatherDir = template['pysar.troposphericDelay.weatherDir']
outName = '{}_{}.h5'.format(fbase, inps.tropModel)
print(('Atmospheric correction using Weather Re-analysis dataset'
' (PyAPS, Jolivet et al., 2011)'))
print('Weather Re-analysis dataset: ' + inps.tropModel)
tropCmd = ('tropcor_pyaps.py -f {t} --model {m} --dem {d}'
' -i {i} -w {w}').format(t=inps.timeseriesFile,
m=inps.tropModel,
d=inps.geomFile,
i=inps.geomFile,
w=inps.weatherDir)
print(tropCmd)
if ut.update_file(outName, inps.timeseriesFile):
if inps.tropFile:
tropCmd = 'diff.py {} {} -o {}'.format(
inps.timeseriesFile, inps.tropFile, outName)
print('--------------------------------------------')
print('Use existed tropospheric delay file: {}'.format(
inps.tropFile))
print(tropCmd)
status = subprocess.Popen(tropCmd, shell=True).wait()
if status is not 0:
print(
'\nError while correcting tropospheric delay, try the following:'
)
print('1) Check the installation of PyAPS')
print(
' http://earthdef.caltech.edu/projects/pyaps/wiki/Main'
)
print(' Try in command line: python -c "import pyaps"')
print(
'2) Use other tropospheric correction method, height-correlation, for example'
)
print(
'3) or turn off the option by setting pysar.troposphericDelay.method = no.\n'
)
raise RuntimeError()
inps.timeseriesFile = outName
else:
print('No atmospheric delay correction.')
# Grab tropospheric delay file
try:
fileList = [
os.path.join(inps.workDir, 'INPUTS/{}.h5'.format(inps.tropModel))
]
inps.tropFile = ut.get_file_list(fileList)[0]
except:
inps.tropFile = None
##############################################
# Topographic (DEM) Residuals Correction (Optional)
##############################################
print(
'\n********** Topographic Residual (DEM error) Correction **********'
)
outName = os.path.splitext(inps.timeseriesFile)[0] + '_demErr.h5'
topoCmd = 'dem_error.py {} -g {} -t {} -o {}'.format(
inps.timeseriesFile, inps.geomFile, inps.templateFile, outName)
print(topoCmd)
inps.timeseriesResFile = None
if template['pysar.topographicResidual']:
if ut.update_file(outName, inps.timeseriesFile):
status = subprocess.Popen(topoCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while correcting topographic phase residual.\n')
inps.timeseriesFile = outName
inps.timeseriesResFile = 'timeseriesResidual.h5'
else:
print('No correction for topographic residuals.')
##############################################
# Timeseries Residual Standard Deviation
##############################################
print('\n********** Timeseries Residual Root Mean Square **********')
if inps.timeseriesResFile:
rmsCmd = 'timeseries_rms.py {} -t {}'.format(inps.timeseriesResFile,
inps.templateFile)
print(rmsCmd)
status = subprocess.Popen(rmsCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while calculating RMS of time series phase residual.\n')
else:
print('No timeseries residual file found! Skip residual RMS analysis.')
##############################################
# Reference in Time
##############################################
print('\n********** Select Reference Date **********')
if template['pysar.reference.date']:
outName = '{}_refDate.h5'.format(
os.path.splitext(inps.timeseriesFile)[0])
refCmd = 'reference_date.py {} -t {} -o {}'.format(
inps.timeseriesFile, inps.templateFile, outName)
print(refCmd)
if ut.update_file(outName, inps.timeseriesFile):
status = subprocess.Popen(refCmd, shell=True).wait()
if status is not 0:
raise Exception('Error while changing reference date.\n')
inps.timeseriesFile = outName
else:
print('No reference change in time.')
##############################################
# Phase Ramp Correction (Optional)
##############################################
print('\n********** Remove Phase Ramp **********')
inps.derampMaskFile = template['pysar.deramp.maskFile']
inps.derampMethod = template['pysar.deramp']
if inps.derampMethod:
print('Phase Ramp Removal method: {}'.format(inps.derampMethod))
if inps.geocoded and inps.derampMethod in [
'baseline_cor', 'base_trop_cor'
]:
warnings.warn(
('dataset is in geo coordinates,'
' can not apply {} method').format(inps.derampMethod))
print('skip deramping and continue.')
# Get executable command and output name
derampCmd = None
fbase = os.path.splitext(inps.timeseriesFile)[0]
if inps.derampMethod in [
'plane', 'quadratic', 'plane_range', 'quadratic_range',
'plane_azimuth', 'quadratic_azimuth'
]:
outName = '{}_{}.h5'.format(fbase, inps.derampMethod)
derampCmd = 'remove_ramp.py {} -s {} -m {} -o {}'.format(
inps.timeseriesFile, inps.derampMethod, inps.derampMaskFile,
outName)
elif inps.derampMethod == 'baseline_cor':
outName = '{}_baselineCor.h5'.format(fbase)
derampCmd = 'baseline_error.py {} {}'.format(
inps.timeseriesFile, inps.maskFile)
elif inps.derampMethod in [
'base_trop_cor', 'basetropcor', 'baselinetropcor'
]:
print('Joint estimation of Baseline error and tropospheric delay')
print('\t[height-correlation approach]')
outName = '{}_baseTropCor.h5'.format(fbase)
derampCmd = ('baseline_trop.py {t} {d} {p}'
' range_and_azimuth {m}').format(
t=inps.timeseriesFile,
d=inps.geomFile,
p=inps.tropPolyOrder,
m=inps.maskFile)
else:
warnings.warn('Unrecognized phase ramp method: {}'.format(
template['pysar.deramp']))
# Execute command
if derampCmd:
print(derampCmd)
if ut.update_file(outName, inps.timeseriesFile):
status = subprocess.Popen(derampCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while removing phase ramp for time-series.\n')
inps.timeseriesFile = outName
else:
print('No phase ramp removal.')
#############################################
# Velocity and rmse maps
#############################################
print('\n********** Estimate Velocity **********')
inps.velFile = 'velocity.h5'
velCmd = 'timeseries2velocity.py {} -t {} -o {}'.format(
inps.timeseriesFile, inps.templateFile, inps.velFile)
print(velCmd)
if ut.update_file(inps.velFile, [inps.timeseriesFile, inps.templateFile]):
status = subprocess.Popen(velCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while estimating linear velocity from time-series.\n')
# Velocity from Tropospheric delay
if inps.tropFile:
suffix = os.path.splitext(os.path.basename(inps.tropFile))[0].title()
inps.tropVelFile = '{}{}.h5'.format(
os.path.splitext(inps.velFile)[0], suffix)
velCmd = 'timeseries2velocity.py {} -t {} -o {}'.format(
inps.tropFile, inps.templateFile, inps.tropVelFile)
print(velCmd)
if ut.update_file(inps.tropVelFile,
[inps.tropFile, inps.templateFile]):
status = subprocess.Popen(velCmd, shell=True).wait()
############################################
# Post-processing
# Geocodeing --> Masking --> KMZ & HDF-EOS5
############################################
print('\n********** Post-processing **********')
if template['pysar.save.hdfEos5'] is True and template[
'pysar.geocode'] is False:
print('Turn ON pysar.geocode to be able to save to HDF-EOS5 format.')
template['pysar.geocode'] = True
# Geocoding
if not inps.geocoded:
if template['pysar.geocode'] is True:
print('\n--------------------------------------------')
geo_dir = os.path.abspath('./GEOCODE')
if not os.path.isdir(geo_dir):
os.makedirs(geo_dir)
print('create directory: {}'.format(geo_dir))
geoCmd = ('geocode.py {v} {c} {t} {g} -l {l} -t {e}'
' --outdir {d} --update').format(v=inps.velFile,
c=inps.tempCohFile,
t=inps.timeseriesFile,
g=inps.geomFile,
l=inps.lookupFile,
e=inps.templateFile,
d=geo_dir)
print(geoCmd)
status = subprocess.Popen(geoCmd, shell=True).wait()
if status is not 0:
raise Exception('Error while geocoding.\n')
else:
inps.velFile = os.path.join(
geo_dir, 'geo_' + os.path.basename(inps.velFile))
inps.tempCohFile = os.path.join(
geo_dir, 'geo_' + os.path.basename(inps.tempCohFile))
inps.timeseriesFile = os.path.join(
geo_dir, 'geo_' + os.path.basename(inps.timeseriesFile))
inps.geomFile = os.path.join(
geo_dir, 'geo_' + os.path.basename(inps.geomFile))
inps.geocoded = True
# generate mask based on geocoded temporal coherence
print('\n--------------------------------------------')
outName = os.path.join(geo_dir, 'geo_maskTempCoh.h5')
genCmd = 'generate_mask.py {} -m {} -o {}'.format(
inps.tempCohFile, inps.minTempCoh, outName)
print(genCmd)
if ut.update_file(outName, inps.tempCohFile):
status = subprocess.Popen(genCmd, shell=True).wait()
inps.maskFile = outName
# mask velocity file
if inps.velFile and inps.maskFile:
outName = '{}_masked.h5'.format(os.path.splitext(inps.velFile)[0])
maskCmd = 'mask.py {} -m {} -o {}'.format(inps.velFile, inps.maskFile,
outName)
print(maskCmd)
if ut.update_file(outName, [inps.velFile, inps.maskFile]):
status = subprocess.Popen(maskCmd, shell=True).wait()
try:
inps.velFile = glob.glob(outName)[0]
except:
inps.velFile = None
# Save to Google Earth KML file
if inps.geocoded and inps.velFile and template['pysar.save.kml'] is True:
print('\n--------------------------------------------')
print('creating Google Earth KMZ file for geocoded velocity file: ...')
outName = '{}.kmz'.format(
os.path.splitext(os.path.basename(inps.velFile))[0])
kmlCmd = 'save_kml.py {} -o {}'.format(inps.velFile, outName)
print(kmlCmd)
if ut.update_file(outName, inps.velFile, check_readable=False):
status = subprocess.Popen(kmlCmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while generating Google Earth KMZ file.')
#############################################
# Save Timeseries to HDF-EOS5 format
#############################################
if template['pysar.save.hdfEos5'] is True:
print('\n********** Save Time-series in HDF-EOS5 Format **********')
if not inps.geocoded:
warnings.warn(
'Dataset is in radar coordinates, skip saving to HDF-EOS5 format.'
)
else:
# Add attributes from custom template to timeseries file
if templateCustom is not None:
ut.add_attribute(inps.timeseriesFile, templateCustom)
# Save to HDF-EOS5 format
print('--------------------------------------------')
hdfeos5Cmd = ('save_hdfeos5.py {t} -c {c} -m {m} -g {g}'
' -t {e}').format(t=inps.timeseriesFile,
c=inps.tempCohFile,
m=inps.maskFile,
g=inps.geomFile,
e=inps.templateFile)
print(hdfeos5Cmd)
SAT = hdfeos5.get_mission_name(atr)
try:
inps.hdfeos5File = ut.get_file_list('{}_*.he5'.format(SAT))[0]
except:
inps.hdfeos5File = None
if ut.update_file(inps.hdfeos5File, [
inps.timeseriesFile, inps.tempCohFile, inps.maskFile,
inps.geomFile
]):
status = subprocess.Popen(hdfeos5Cmd, shell=True).wait()
if status is not 0:
raise Exception(
'Error while generating HDF-EOS5 time-series file.\n')
#############################################
# Plot Figures
#############################################
inps.plotShellFile = os.path.join(os.path.dirname(__file__),
'../sh/plot_pysarApp.sh')
plotCmd = './' + os.path.basename(inps.plotShellFile)
inps.plot = template['pysar.plot']
if inps.plot is True:
print('\n********** Plot Results / Save to PIC **********')
# Copy to workding directory if not existed yet.
if not os.path.isfile(plotCmd):
print('copy {} to work directory: {}'.format(
inps.plotShellFile, inps.workDir))
shutil.copy2(inps.plotShellFile, inps.workDir)
if inps.plot and os.path.isfile(plotCmd):
print(plotCmd)
status = subprocess.Popen(plotCmd, shell=True).wait()
print('\n' + '-' * 50)
print('For better figures:')
print(
' 1) Edit parameters in plot_pysarApp.sh and re-run this script.')
print(
' 2) Play with view.py, tsview.py and save_kml.py for more advanced/customized figures.'
)
if status is not 0:
raise Exception(
'Error while plotting data files using {}'.format(plotCmd))
#############################################
# Time #
#############################################
m, s = divmod(time.time() - start_time, 60)
print('\ntime used: {:02.0f} mins {:02.1f} secs'.format(m, s))
print('\n###############################################')
print('End of PySAR processing!')
print('################################################\n')
def cmd_line_parse(iargs=None):
parser = create_parser()
inps = parser.parse_args(args=iargs)
inps.file = ut.get_file_list(inps.file, abspath=True)
inps.outfile = os.path.abspath(inps.outfile)
return inps
def main(iargs=None):
# Actual code.
inps = cmd_line_parse(iargs)
# Time Series Info
atr = readfile.read_attribute(inps.timeseries_file)
k = atr['FILE_TYPE']
print('input file is ' + k + ': ' + inps.timeseries_file)
if not k in ['timeseries', 'GIANT_TS']:
raise ValueError('Only timeseries file is supported!')
obj = timeseries(inps.timeseries_file)
obj.open()
h5 = h5py.File(inps.timeseries_file, 'r')
if k in ['GIANT_TS']:
dateList = [
dt.fromordinal(int(i)).strftime('%Y%m%d')
for i in h5['dates'][:].tolist()
]
else:
dateList = obj.dateList
date_num = len(dateList)
inps.dates, inps.yearList = ptime.date_list2vector(dateList)
# Read exclude dates
if inps.ex_date_list:
input_ex_date = list(inps.ex_date_list)
inps.ex_date_list = []
if input_ex_date:
for ex_date in input_ex_date:
if os.path.isfile(ex_date):
ex_date = ptime.read_date_list(ex_date)
else:
ex_date = [ptime.yyyymmdd(ex_date)]
inps.ex_date_list += list(
set(ex_date) - set(inps.ex_date_list))
# delete dates not existed in input file
inps.ex_date_list = sorted(
list(set(inps.ex_date_list).intersection(dateList)))
inps.ex_dates = ptime.date_list2vector(inps.ex_date_list)[0]
inps.ex_idx_list = sorted(
[dateList.index(i) for i in inps.ex_date_list])
print('exclude date:' + str(inps.ex_date_list))
# Zero displacement for 1st acquisition
if inps.zero_first:
if inps.ex_date_list:
inps.zero_idx = min(
list(set(range(date_num)) - set(inps.ex_idx_list)))
else:
inps.zero_idx = 0
# File Size
length = int(atr['LENGTH'])
width = int(atr['WIDTH'])
print('data size in [y0,y1,x0,x1]: [%d, %d, %d, %d]' %
(0, length, 0, width))
try:
ullon = float(atr['X_FIRST'])
ullat = float(atr['Y_FIRST'])
lon_step = float(atr['X_STEP'])
lat_step = float(atr['Y_STEP'])
lrlon = ullon + width * lon_step
lrlat = ullat + length * lat_step
print('data size in [lat0,lat1,lon0,lon1]: [%.4f, %.4f, %.4f, %.4f]' %
(lrlat, ullat, ullon, lrlon))
except:
pass
# Initial Pixel Coord
if inps.lalo and 'Y_FIRST' in atr.keys():
y = int((inps.lalo[0] - ullat) / lat_step + 0.5)
x = int((inps.lalo[1] - ullon) / lon_step + 0.5)
inps.yx = [y, x]
if inps.ref_lalo and 'Y_FIRST' in atr.keys():
y = int((inps.ref_lalo[0] - ullat) / lat_step + 0.5)
x = int((inps.ref_lalo[1] - ullon) / lon_step + 0.5)
inps.ref_yx = [y, x]
# Display Unit
if inps.disp_unit == 'cm':
inps.unit_fac = 100.0
elif inps.disp_unit == 'm':
inps.unit_fac = 1.0
elif inps.disp_unit == 'dm':
inps.unit_fac = 10.0
elif inps.disp_unit == 'mm':
inps.unit_fac = 1000.0
elif inps.disp_unit == 'km':
inps.unit_fac = 0.001
else:
raise ValueError('Un-recognized unit: ' + inps.disp_unit)
if k in ['GIANT_TS']:
print('data unit: mm')
inps.unit_fac *= 0.001
else:
print('data unit: m')
print('display unit: ' + inps.disp_unit)
# Flip up-down / left-right
if inps.auto_flip:
inps.flip_lr, inps.flip_ud = pp.auto_flip_direction(atr)
else:
inps.flip_ud = False
inps.left_lr = False
# Mask file
if not inps.mask_file:
if os.path.basename(inps.timeseries_file).startswith('geo_'):
file_list = ['geo_maskTempCoh.h5']
else:
file_list = ['maskTempCoh.h5', 'mask.h5']
try:
inps.mask_file = ut.get_file_list(file_list)[0]
except:
inps.mask_file = None
try:
mask = readfile.read(inps.mask_file, datasetName='mask')[0]
mask[mask != 0] = 1
print('load mask from file: ' + inps.mask_file)
except:
mask = None
print('No mask used.')
# Initial Map
d_v = readfile.read(
inps.timeseries_file,
datasetName=dateList[inps.epoch_num])[0] * inps.unit_fac
if inps.ref_date:
inps.ref_d_v = readfile.read(
inps.timeseries_file, datasetName=inps.ref_date)[0] * inps.unit_fac
d_v -= inps.ref_d_v
if mask is not None:
d_v = mask_matrix(d_v, mask)
if inps.ref_yx:
d_v -= d_v[inps.ref_yx[0], inps.ref_yx[1]]
data_lim = [np.nanmin(d_v), np.nanmax(d_v)]
if not inps.ylim_mat:
inps.ylim_mat = data_lim
print('Initial data range: ' + str(data_lim))
print('Display data range: ' + str(inps.ylim_mat))
# Fig 1 - Cumulative Displacement Map
if not inps.disp_fig:
plt.switch_backend('Agg')
fig_v = plt.figure('Cumulative Displacement')
# Axes 1
#ax_v = fig_v.add_subplot(111)
# ax_v.set_position([0.125,0.25,0.75,0.65])
# This works on OSX. Original worked on Linux.
# rect[left, bottom, width, height]
ax_v = fig_v.add_axes([0.125, 0.25, 0.75, 0.65])
if inps.dem_file:
dem = readfile.read(inps.dem_file, datasetName='height')[0]
ax_v = pp.plot_dem_yx(ax_v, dem)
img = ax_v.imshow(d_v,
cmap=inps.colormap,
clim=inps.ylim_mat,
interpolation='nearest')
# Reference Pixel
if inps.ref_yx:
d_v -= d_v[inps.ref_yx[0], inps.ref_yx[1]]
ax_v.plot(inps.ref_yx[1], inps.ref_yx[0], 'ks', ms=6)
else:
try:
ax_v.plot(int(atr['REF_X']), int(atr['REF_Y']), 'ks', ms=6)
except:
pass
# Initial Pixel
if inps.yx:
ax_v.plot(inps.yx[1], inps.yx[0], 'ro', markeredgecolor='black')
ax_v.set_xlim(0, np.shape(d_v)[1])
ax_v.set_ylim(np.shape(d_v)[0], 0)
# Status Bar
def format_coord(x, y):
col = int(x + 0.5)
row = int(y + 0.5)
if 0 <= col < width and 0 <= row < length:
z = d_v[row, col]
try:
lon = ullon + x * lon_step
lat = ullat + y * lat_step
return 'x=%.0f, y=%.0f, value=%.4f, lon=%.4f, lat=%.4f' % (
x, y, z, lon, lat)
except:
return 'x=%.0f, y=%.0f, value=%.4f' % (x, y, z)
ax_v.format_coord = format_coord
# Title and Axis Label
ax_v.set_title(
'N = %d, Time = %s' %
(inps.epoch_num, inps.dates[inps.epoch_num].strftime('%Y-%m-%d')))
if not 'Y_FIRST' in atr.keys():
ax_v.set_xlabel('Range')
ax_v.set_ylabel('Azimuth')
# Flip axis
if inps.flip_lr:
ax_v.invert_xaxis()
print('flip map left and right')
if inps.flip_ud:
ax_v.invert_yaxis()
print('flip map up and down')
# Colorbar
cbar = fig_v.colorbar(img, orientation='vertical')
cbar.set_label('Displacement [%s]' % inps.disp_unit)
# Axes 2 - Time Slider
ax_time = fig_v.add_axes([0.125, 0.1, 0.6, 0.07],
facecolor='lightgoldenrodyellow',
yticks=[])
tslider = Slider(ax_time,
'Years',
inps.yearList[0],
inps.yearList[-1],
valinit=inps.yearList[inps.epoch_num])
tslider.ax.bar(inps.yearList,
np.ones(len(inps.yearList)),
facecolor='black',
width=0.01,
ecolor=None)
tslider.ax.set_xticks(
np.round(
np.linspace(inps.yearList[0], inps.yearList[-1], num=5) * 100) /
100)
def time_slider_update(val):
"""Update Displacement Map using Slider"""
timein = tslider.val
idx_nearest = np.argmin(np.abs(np.array(inps.yearList) - timein))
ax_v.set_title(
'N = %d, Time = %s' %
(idx_nearest, inps.dates[idx_nearest].strftime('%Y-%m-%d')))
d_v = h5[dateList[idx_nearest]][:] * inps.unit_fac
if inps.ref_date:
d_v -= inps.ref_d_v
if mask is not None:
d_v = mask_matrix(d_v, mask)
if inps.ref_yx:
d_v -= d_v[inps.ref_yx[0], inps.ref_yx[1]]
img.set_data(d_v)
fig_v.canvas.draw()
tslider.on_changed(time_slider_update)
# Fig 2 - Time Series Displacement - Point
fig_ts = plt.figure('Time series - point', figsize=inps.fig_size)
ax_ts = fig_ts.add_subplot(111)
# Read Error List
inps.error_ts = None
if inps.error_file:
error_fileContent = np.loadtxt(inps.error_file,
dtype=bytes).astype(str)
inps.error_ts = error_fileContent[:, 1].astype(
np.float) * inps.unit_fac
if inps.ex_date_list:
e_ts = inps.error_ts[:]
inps.ex_error_ts = np.array([e_ts[i] for i in inps.ex_idx_list])
inps.error_ts = np.array([
e_ts[i] for i in range(date_num) if i not in inps.ex_idx_list
])
def plot_timeseries_errorbar(ax, dis_ts, inps):
dates = list(inps.dates)
d_ts = dis_ts[:]
if inps.ex_date_list:
# Update displacement time-series
dates = sorted(list(set(inps.dates) - set(inps.ex_dates)))
ex_d_ts = np.array([dis_ts[i] for i in inps.ex_idx_list])
d_ts = np.array([
dis_ts[i] for i in range(date_num) if i not in inps.ex_idx_list
])
# Plot excluded dates
(_, caps, _) = ax.errorbar(inps.ex_dates,
ex_d_ts,
yerr=inps.ex_error_ts,
fmt='-o',
color='gray',
ms=inps.marker_size,
lw=0,
alpha=1,
mfc='gray',
elinewidth=inps.edge_width,
ecolor='black',
capsize=inps.marker_size * 0.5)
for cap in caps:
cap.set_markeredgewidth(inps.edge_width)
# Plot kept dates
(_, caps, _) = ax.errorbar(dates,
d_ts,
yerr=inps.error_ts,
fmt='-o',
ms=inps.marker_size,
lw=0,
alpha=1,
elinewidth=inps.edge_width,
ecolor='black',
capsize=inps.marker_size * 0.5)
for cap in caps:
cap.set_markeredgewidth(inps.edge_width)
return ax
def plot_timeseries_scatter(ax, dis_ts, inps):
dates = list(inps.dates)
d_ts = dis_ts[:]
if inps.ex_date_list:
# Update displacement time-series
dates = sorted(list(set(inps.dates) - set(inps.ex_dates)))
ex_d_ts = np.array([dis_ts[i] for i in inps.ex_idx_list])
d_ts = np.array([
dis_ts[i] for i in range(date_num) if i not in inps.ex_idx_list
])
# Plot excluded dates
ax.scatter(inps.ex_dates,
ex_d_ts,
s=inps.marker_size**2,
color='gray') # color='crimson'
# Plot kept dates
ax.scatter(dates, d_ts, s=inps.marker_size**2)
return ax
def update_timeseries(ax_ts, y, x):
"""Plot point time series displacement at pixel [y, x]"""
d_ts = read_timeseries_yx(
inps.timeseries_file, y, x, ref_yx=inps.ref_yx) * inps.unit_fac
# for date in dateList:
# d = h5[k].get(date)[y,x]
# if inps.ref_yx:
# d -= h5[k].get(date)[inps.ref_yx[0], inps.ref_yx[1]]
# d_ts.append(d*inps.unit_fac)
if inps.zero_first:
d_ts -= d_ts[inps.zero_idx]
ax_ts.cla()
if inps.error_file:
ax_ts = plot_timeseries_errorbar(ax_ts, d_ts, inps)
else:
ax_ts = plot_timeseries_scatter(ax_ts, d_ts, inps)
if inps.ylim:
ax_ts.set_ylim(inps.ylim)
for tick in ax_ts.yaxis.get_major_ticks():
tick.label.set_fontsize(inps.font_size)
# Title
title_ts = 'Y = %d, X = %d' % (y, x)
try:
lat = ullat + y * lat_step
lon = ullon + x * lon_step
title_ts += ', lat = %.4f, lon = %.4f' % (lat, lon)
except:
pass
if inps.disp_title:
ax_ts.set_title(title_ts)
ax_ts = pp.auto_adjust_xaxis_date(ax_ts,
inps.yearList,
fontSize=inps.font_size)[0]
ax_ts.set_xlabel('Time', fontsize=inps.font_size)
ax_ts.set_ylabel('Displacement [%s]' % inps.disp_unit,
fontsize=inps.font_size)
fig_ts.canvas.draw()
# Print to terminal
print('\n---------------------------------------')
print(title_ts)
print(d_ts)
# Slope estimation
if inps.ex_date_list:
inps.yearList_kept = [
inps.yearList[i] for i in range(date_num)
if i not in inps.ex_idx_list
]
d_ts_kept = [
d_ts[i] for i in range(date_num) if i not in inps.ex_idx_list
]
d_slope = stats.linregress(np.array(inps.yearList_kept),
np.array(d_ts_kept))
else:
d_slope = stats.linregress(np.array(inps.yearList), np.array(d_ts))
print('linear velocity: %.2f +/- %.2f [%s/yr]' %
(d_slope[0], d_slope[4], inps.disp_unit))
return d_ts
# Initial point time series plot
if inps.yx:
d_ts = update_timeseries(ax_ts, inps.yx[0], inps.yx[1])
else:
d_ts = np.zeros(len(inps.yearList))
ax_ts = plot_timeseries_scatter(ax_ts, d_ts, inps)
def plot_timeseries_event(event):
"""Event function to get y/x from button press"""
if event.inaxes != ax_v:
return
ii = int(event.ydata + 0.5)
jj = int(event.xdata + 0.5)
d_ts = update_timeseries(ax_ts, ii, jj)
# Output
if inps.save_fig and inps.yx:
print('save info for pixel ' + str(inps.yx))
if not inps.fig_base:
inps.fig_base = 'y%d_x%d' % (inps.yx[0], inps.yx[1])
# TXT - point time series
outName = inps.fig_base + '_ts.txt'
header_info = 'timeseries_file=' + inps.timeseries_file
header_info += '\ny=%d, x=%d' % (inps.yx[0], inps.yx[1])
try:
lat = ullat + inps.yx[0] * lat_step
lon = ullon + inps.yx[1] * lon_step
header_info += '\nlat=%.6f, lon=%.6f' % (lat, lon)
except:
pass
if inps.ref_yx:
header_info += '\nreference pixel: y=%d, x=%d' % (inps.ref_yx[0],
inps.ref_yx[1])
else:
header_info += '\nreference pixel: y=%s, x=%s' % (atr['REF_Y'],
atr['REF_X'])
header_info += '\nunit=m/yr'
np.savetxt(outName,
list(zip(np.array(dateList),
np.array(d_ts) / inps.unit_fac)),
fmt='%s',
delimiter=' ',
header=header_info)
print('save time series displacement in meter to ' + outName)
# Figure - point time series
outName = inps.fig_base + '_ts.pdf'
fig_ts.savefig(outName,
bbox_inches='tight',
transparent=True,
dpi=inps.fig_dpi)
print('save time series plot to ' + outName)
# Figure - map
outName = inps.fig_base + '_' + dateList[inps.epoch_num] + '.png'
fig_v.savefig(outName,
bbox_inches='tight',
transparent=True,
dpi=inps.fig_dpi)
print('save map plot to ' + outName)
# Final linking of the canvas to the plots.
cid = fig_v.canvas.mpl_connect('button_press_event', plot_timeseries_event)
if inps.disp_fig:
plt.show()
fig_v.canvas.mpl_disconnect(cid)
def cmd_line_parse(iargs=None):
parser = create_parser()
inps = parser.parse_args(args=iargs)
inps.file = ut.get_file_list(inps.file)
return inps
def write_kmz_file(data, metadata, out_file, inps=None):
""" Generate Google Earth KMZ file for input data matrix.
Inputs:
data - 2D np.array in int/float, data matrix to write
out_file - string, output file name
metadata - dict, containing the following attributes:
WIDTH/LENGTH : required, file size
X/Y_FIRST/STEP : required, for lat/lon spatial converage
ref_x/y : optional, column/row number of reference pixel
PROJECT_NAME : optional, for KMZ folder name
inps - Namespace, optional, input options for display
Output:
kmz_file - string, output KMZ filename
Example:
from pysar.utils import readfile, plot as pp
from pysar import save_kml
fname = 'geo_velocity_masked.h5'
data, atr = readfile.read(fname)
out_file = pp.auto_figure_title(fname, None)+'.kmz'
save_kml.write_kmz_file(data, atr, out_file)
"""
if not inps:
inps = cmd_line_parse()
if not inps.ylim:
inps.ylim = [np.nanmin(data), np.nanmax(data)]
west, east, south, north = ut.four_corners(metadata)
# 2.1 Make PNG file - Data
print('plotting data ...')
# Figure size
if not inps.fig_size:
plot_shape = [east - west, north - south]
fig_scale = min(pp.min_figsize_single / min(plot_shape),
pp.max_figsize_single / max(plot_shape),
pp.max_figsize_height / plot_shape[1])
inps.fig_size = [np.floor(i * fig_scale * 2) / 2 for i in plot_shape]
print('create figure in size: ' + str(inps.fig_size))
fig = plt.figure(figsize=inps.fig_size, frameon=False)
ax = fig.add_axes([0., 0., 1., 1.])
ax.set_axis_off()
print('colormap: ' + inps.colormap)
inps.colormap = plt.get_cmap(inps.colormap)
# Plot - data matrix
ax.imshow(data,
cmap=inps.colormap,
vmin=inps.ylim[0],
vmax=inps.ylim[1],
aspect='auto',
interpolation='nearest')
# Plot - reference pixel
if inps.disp_seed == 'yes':
try:
xref = int(metadata['REF_X'])
yref = int(metadata['REF_Y'])
ax.plot(xref, yref, 'ks', ms=inps.seed_size)
print('show reference point')
except:
inps.disp_seed = False
print('Cannot find reference point info!')
width = int(metadata['WIDTH'])
length = int(metadata['LENGTH'])
ax.set_xlim([0, width])
ax.set_ylim([length, 0])
out_name_base = os.path.splitext(out_file)[0]
data_png_file = out_name_base + '.png'
print('writing {} with dpi={}'.format(data_png_file, inps.fig_dpi))
plt.savefig(data_png_file,
pad_inches=0.0,
transparent=True,
dpi=inps.fig_dpi)
# 2.2 Making PNG file - colorbar
pc = plt.figure(figsize=(1, 8))
cax = pc.add_subplot(111)
norm = mpl.colors.Normalize(vmin=inps.ylim[0], vmax=inps.ylim[1])
cbar = mpl.colorbar.ColorbarBase(cax,
cmap=inps.colormap,
norm=norm,
orientation='vertical')
cbar.set_label('{} [{}]'.format(inps.cbar_label, inps.disp_unit))
cbar.locator = mpl.ticker.MaxNLocator(nbins=inps.cbar_bin_num)
cbar.update_ticks()
pc.subplots_adjust(left=0.2, bottom=0.3, right=0.4, top=0.7)
pc.patch.set_facecolor('white')
pc.patch.set_alpha(0.7)
cbar_png_file = '{}_cbar.png'.format(out_name_base)
print('writing ' + cbar_png_file)
pc.savefig(cbar_png_file,
bbox_inches='tight',
facecolor=pc.get_facecolor(),
dpi=inps.fig_dpi)
# 2.3 Generate KML file
print('generating kml file ...')
try:
doc = KML.kml(KML.Folder(KML.name(metadata['PROJECT_NAME'])))
except:
doc = KML.kml(KML.Folder(KML.name('PySAR product')))
# Add data png file
slc = KML.GroundOverlay(
KML.name(data_png_file), KML.Icon(KML.href(data_png_file)),
KML.altitudeMode('clampToGround'),
KML.LatLonBox(KML.north(str(north)), KML.east(str(east)),
KML.south(str(south)), KML.west(str(west))))
doc.Folder.append(slc)
# Add colorbar png file
cb_rg = min(north - south, east - west)
cb_N = (north + south) / 2.0 + 0.5 * 0.5 * cb_rg
cb_W = east + 0.1 * cb_rg
# Use mean height from existed DEM file
if not inps.cbar_height:
try:
fileList = [
'geo_geometry*.h5', 'INPUTS/geometry*.h5', 'dem*.h5', '*.dem',
'radar*.hgt'
]
dem_file = ut.get_file_list(fileList)[0]
print('use mean height from file: {} + 1000 m as colorbar height.'.
format(dem_file))
dem_data = readfile.read(dem_file, datasetName='height')[0]
inps.cbar_height = np.rint(np.nanmean(dem_data)) + 1000.0
except:
pass
elif str(inps.cbar_height).lower().endswith('ground'):
inps.cbar_height = None
if inps.cbar_height:
print('set colorbar in height: %.2f m' % inps.cbar_height)
slc1 = KML.GroundOverlay(
KML.name('colorbar'), KML.Icon(KML.href(cbar_png_file)),
KML.altitude(str(inps.cbar_height)), KML.altitudeMode('absolute'),
KML.LatLonBox(KML.north(str(cb_N)),
KML.south(str(cb_N - 0.5 * cb_rg)),
KML.west(str(cb_W)),
KML.east(str(cb_W + 0.14 * cb_rg))))
else:
print('set colorbar clampToGround')
slc1 = KML.GroundOverlay(
KML.name('colorbar'), KML.Icon(KML.href(cbar_png_file)),
KML.altitudeMode('clampToGround'),
KML.LatLonBox(KML.north(str(cb_N)),
KML.south(str(cb_N - 0.5 * cb_rg)),
KML.west(str(cb_W)),
KML.east(str(cb_W + 0.14 * cb_rg))))
doc.Folder.append(slc1)
kmlstr = etree.tostring(doc, pretty_print=True).decode('utf8')
# Write KML file
kml_file = '{}.kml'.format(out_name_base)
print('writing ' + kml_file)
with open(kml_file, 'w') as f:
f.write(kmlstr)
# 2.4 Generate KMZ file
kmz_file = '{}.kmz'.format(out_name_base)
cmdKMZ = 'zip {} {} {} {}'.format(kmz_file, kml_file, data_png_file,
cbar_png_file)
print('writing {}\n{}'.format(kmz_file, cmdKMZ))
os.system(cmdKMZ)
cmdClean = 'rm {} {} {}'.format(kml_file, data_png_file, cbar_png_file)
print(cmdClean)
os.system(cmdClean)
return kmz_file
def correct_tropospheric_delay(inps, template):
"""Correct tropospheric delay with options from template"""
inps.tropPolyOrder = template['pysar.troposphericDelay.polyOrder']
inps.tropModel = template['pysar.troposphericDelay.weatherModel']
inps.tropMethod = template['pysar.troposphericDelay.method']
# check existing tropospheric delay file
try:
fileList = [os.path.join(inps.workDir, 'INPUTS/{}.h5'.format(inps.tropModel))]
inps.tropFile = ut.get_file_list(fileList)[0]
except:
inps.tropFile = None
# run
if inps.tropMethod:
fbase = os.path.splitext(inps.timeseriesFile)[0]
# Phase/Elevation Ratio (Doin et al., 2009)
if inps.tropMethod == 'height_correlation':
outName = '{}_tropHgt.h5'.format(fbase)
print('tropospheric delay correction with height-correlation approach')
tropCmd = ('tropcor_phase_elevation.py {t} -g {d} -p {p}'
' -m {m} -o {o}').format(t=inps.timeseriesFile,
d=inps.geomFile,
p=inps.tropPolyOrder,
m=inps.maskFile,
o=outName)
print(tropCmd)
if ut.run_or_skip(out_file=outName, in_file=inps.timeseriesFile) == 'run':
status = subprocess.Popen(tropCmd, shell=True).wait()
if status is not 0:
raise Exception('Error while correcting tropospheric delay.\n')
inps.timeseriesFile = outName
inps.timeseriesFiles.append(outName)
# Weather Re-analysis Data (Jolivet et al., 2011;2014)
elif inps.tropMethod == 'pyaps':
inps.weatherDir = template['pysar.troposphericDelay.weatherDir']
outName = '{}_{}.h5'.format(fbase, inps.tropModel)
print(('Atmospheric correction using Weather Re-analysis dataset'
' (PyAPS, Jolivet et al., 2011)'))
print('Weather Re-analysis dataset:', inps.tropModel)
tropCmd = ('tropcor_pyaps.py -f {t} --model {m} -g {g}'
' -w {w}').format(t=inps.timeseriesFile,
m=inps.tropModel,
g=inps.geomFile,
w=inps.weatherDir)
print(tropCmd)
if ut.run_or_skip(out_file=outName, in_file=inps.timeseriesFile) == 'run':
if inps.tropFile:
tropCmd = 'diff.py {} {} -o {} --force'.format(inps.timeseriesFile,
inps.tropFile,
outName)
print('--------------------------------------------')
print('Use existed tropospheric delay file: {}'.format(inps.tropFile))
print(tropCmd)
status = subprocess.Popen(tropCmd, shell=True).wait()
if status is not 0:
print('\nError while correcting tropospheric delay, try the following:')
print('1) Check the installation of PyAPS')
print(' http://earthdef.caltech.edu/projects/pyaps/wiki/Main')
print(' Try in command line: python -c "import pyaps"')
print('2) Use other tropospheric correction method, height-correlation, for example')
print('3) or turn off the option by setting pysar.troposphericDelay.method = no.\n')
raise RuntimeError()
inps.timeseriesFile = outName
inps.timeseriesFiles.append(outName)
else:
print('Un-recognized atmospheric delay correction method: {}'.format(inps.tropMethod))
# Grab tropospheric delay file
try:
fileList = [os.path.join(inps.workDir, 'INPUTS/{}.h5'.format(inps.tropModel))]
inps.tropFile = ut.get_file_list(fileList)[0]
except:
inps.tropFile = None
return
def read_template(inps):
print('\n********** Read Template File **********')
# default template
inps.templateFile = os.path.join(inps.workDir, 'pysarApp_template.txt')
if not os.path.isfile(inps.templateFile):
print('generate default template file:', inps.templateFile)
shutil.copy2(inps.autoTemplateFile, inps.workDir)
else:
check_obsolete_default_template(inps)
# custom template
customTemplate = None
if inps.customTemplateFile:
# Copy custom template file to work directory
inputs_dir = os.path.join(inps.workDir, 'INPUTS')
if ut.run_or_skip(out_file=os.path.join(inputs_dir, os.path.basename(inps.customTemplateFile)),
in_file=inps.customTemplateFile,
check_readable=False) == 'run':
if not os.path.isdir(inputs_dir):
os.makedirs(inputs_dir)
print('create directory:', inputs_dir)
shutil.copy2(inps.customTemplateFile, inputs_dir)
print('copy {} to INPUTS directory'.format(os.path.basename(inps.customTemplateFile)))
# Read custom template
print('read custom template file:', inps.customTemplateFile)
customTemplate = readfile.read_template(inps.customTemplateFile)
# correct some loose type errors
standardValues = {'def':'auto', 'default':'auto',
'y':'yes', 'on':'yes', 'true':'yes',
'n':'no', 'off':'no', 'false':'no'
}
for key, value in customTemplate.items():
if value in standardValues.keys():
customTemplate[key] = standardValues[value]
for key in ['pysar.deramp', 'pysar.troposphericDelay.method']:
if key in customTemplate.keys():
customTemplate[key] = customTemplate[key].lower().replace('-', '_')
if 'processor' in customTemplate.keys():
customTemplate['pysar.load.processor'] = customTemplate['processor']
for key in ['SUBSET_XMIN', 'SUBSET_YMIN']:
if key in customTemplate.keys():
customTemplate.pop(key)
# Update default template with custom input template
print('update default template based on input custom template')
inps.templateFile = ut.update_template_file(inps.templateFile, customTemplate)
if inps.generate_template:
raise SystemExit('Exit as planned after template file generation.')
print('read default template file:', inps.templateFile)
template = readfile.read_template(inps.templateFile)
template = ut.check_template_auto_value(template)
# Get existing files name: unavco_attributes.txt
try:
inps.unavcoMetadataFile = ut.get_file_list('unavco_attribute*txt', abspath=True)[0]
except:
inps.unavcoMetadataFile = None
print('No UNAVCO attributes file found.')
return inps, template, customTemplate
def main(argv):
inps = cmdLineParse()
if inps.timeseries_file:
inps.timeseries_file = ut.get_file_list([inps.timeseries_file])[0]
atr = readfile.read_attribute(inps.timeseries_file)
k = atr['FILE_TYPE']
if 'ref_y' not in list(atr.keys()) and inps.ref_yx:
print('No reference info found in input file, use input ref_yx: ' +
str(inps.ref_yx))
atr['ref_y'] = inps.ref_yx[0]
atr['ref_x'] = inps.ref_yx[1]
#****reading incidence angle file***/
if os.path.isfile(inps.inc_angle):
inps.inc_angle = readfile.read(inps.inc_angle,
epoch='incidenceAngle')[0]
inps.inc_angle = np.nan_to_num(inps.inc_angle)
else:
inps.inps.inc_angle = float(inps.inc_angle)
print('incidence angle: ' + str(inps.inc_angle))
cinc = np.cos(inps.inc_angle * np.pi / 180.0)
#****look up file****/
if inps.lookup_file:
inps.lookup_file = ut.get_file_list(
[inps.lookup_file])[0] #'geomap_32rlks_tight.trans'
#****GACOS****/
delay_source = 'GACOS'
# Get weather directory
if not inps.GACOS_dir:
if inps.timeseries_file:
inps.GACOS_dir = os.path.dirname(
os.path.abspath(inps.timeseries_file)) + '/../WEATHER/GACOS'
elif inps.lookup_file:
inps.GACOS_dir = os.path.dirname(os.path.abspath(
inps.lookup_file)) + '/../WEATHER/GACOS'
else:
inps.GACOS_dir = os.path.abspath(os.getcwd())
print('Store weather data into directory: ' + inps.GACOS_dir)
#source_dir=os.path.dirname(os.path.abspath('timeseries_file'))+'/Agung/GACOS/data';print source_dir
#os.makedirs(GACOS_dir) -----------------------------------------------add part to copy/download weather data------#
#----get date list-----#
if not inps.date_list_file:
print('read date list info from: ' + inps.timeseries_file)
h5 = h5py.File(inps.timeseries_file, 'r')
if 'timeseries' in list(h5.keys()):
date_list = sorted(h5[k].keys())
elif k in ['interferograms', 'coherence', 'wrapped']:
ifgram_list = sorted(h5[k].keys())
date12_list = ptime.list_ifgram2date12(ifgram_list)
m_dates = [i.split('-')[0] for i in date12_list]
s_dates = [i.split('-')[1] for i in date12_list]
date_list = ptime.yyyymmdd(sorted(list(set(m_dates + s_dates))))
else:
raise ValueError('Un-support input file type:' + k)
h5.close()
else:
date_list = ptime.yyyymmdd(
np.loadtxt(inps.date_list_file, dtype=str, usecols=(0, )).tolist())
print('read date list info from: ' + inps.date_list_file)
#****cheacking availability of delays****/
print('checking availability of delays')
delay_file_list = []
for d in date_list:
if delay_source == 'GACOS':
delay_file = inps.GACOS_dir + '/' + d + '.ztd'
delay_file_list.append(delay_file)
delay_file_existed = ut.get_file_list(delay_file_list)
if len(delay_file_existed) == len(date_list):
print('no missing files')
else:
print('no. of date files found:', len(delay_file_existed))
print('no. of dates:', len(date_list))
#*****Calculating delays***/
print('calculating delays')
length = int(atr['FILE_LENGTH'])
width = int(atr['WIDTH'])
#initialise delay files
date_num = len(date_list)
trop_ts = np.zeros((date_num, length, width), np.float32)
#reading wrf files for each epoch and getting delay
for i in range(date_num):
delay_file = delay_file_existed[i]
date = date_list[i]
print('calculating delay for date', date)
trop_ts[i] = get_delay(delay_file, atr, inps.lookup_file, cinc)
print('Delays Calculated')
# Convert relative phase delay on reference date
try:
ref_date = atr['ref_date']
except:
ref_date = date_list[0]
print('convert to relative phase delay with reference date: ' + ref_date)
ref_idx = date_list.index(ref_date)
trop_ts -= np.tile(trop_ts[ref_idx, :, :], (date_num, 1, 1))
## Write tropospheric delay to HDF5
tropFile = 'GACOSdelays' + '.h5'
print('writing >>> %s' % (tropFile))
h5trop = h5py.File(tropFile, 'w')
group_trop = h5trop.create_group('timeseries')
print('number of acquisitions: ' + str(date_num))
prog_bar = ptime.progress_bar(maxValue=date_num)
for i in range(date_num):
date = date_list[i]
group_trop.create_dataset(date, data=trop_ts[i], compression='gzip')
prog_bar.update(i + 1, suffix=date)
prog_bar.close()
# Write Attributes
for key, value in atr.items():
group_trop.attrs[key] = value
h5trop.close()
## Write corrected Time series to HDF5
if k == 'timeseries':
if not inps.out_file:
inps.out_file = os.path.splitext(
inps.timeseries_file)[0] + '_' + 'GACOS' + '.h5'
print('writing trop corrected timeseries file %s' % (inps.out_file))
h5ts = h5py.File(inps.timeseries_file, 'r')
h5tsCor = h5py.File(inps.out_file, 'w')
group_tsCor = h5tsCor.create_group('timeseries')
print('number of acquisitions: ' + str(date_num))
prog_bar = ptime.progress_bar(maxValue=date_num)
for i in range(date_num):
date = date_list[i]
print(date)
ts = h5ts['timeseries'].get(date)[:]
group_tsCor.create_dataset(date,
data=ts - trop_ts[i],
compression='gzip')
prog_bar.update(i + 1, suffix=date)
prog_bar.close()
h5ts.close()
# Write Attributes
for key, value in atr.items():
group_tsCor.attrs[key] = value
h5tsCor.close()
print('delays written to %s' % (inps.out_file))
print('finished')
return inps.out_file
def extract_metadata4geometry_radar(fname):
"""Read/extract attribute for .hgt_sim file from Gamma to ROI_PAC
Input:
sim_20070813_20080310.hgt_sim
sim_20070813_20080310.rdc.dem
Search for:
sim_20070813_20080310.diff_par
Output:
sim_20070813_20080310.hgt_sim.rsc
sim_20070813_20080310.rdc.dem.rsc
"""
# Get/read GAMMA par file
# for loop to get rid of multiple dot in filename
fname_base = os.path.splitext(fname)[0]
for i in range(5):
fname_base = os.path.splitext(fname_base)[0]
par_file = fname_base + '.diff_par'
par_dict = readfile.read_gamma_par(par_file)
# Get/read LAT/LON_REF1/2/3/4
msg = 'grab LAT/LON_REF1/2/3/4 from par file: '
# get date of one acquisition
try:
m_date = str(re.findall('\d{8}', fname_base)[0])
except:
m_date = str(re.findall('\d{6}', fname_base)[0])
# search existing par file
geom_dir = os.path.dirname(fname) #PROJECT_DIR/geom_master
ifg_dir = os.path.join(geom_dir, '../*/{}_*'.format(
m_date)) #PROJECT_DIR/interferograms/{m_date}_20141225
m_par_files = [
os.path.join(geom_dir, '*{}*{}'.format(m_date, ext))
for ext in PAR_EXT_LIST
]
m_par_files += [
os.path.join(ifg_dir, '*{}*{}'.format(m_date, ext))
for ext in PAR_EXT_LIST
]
m_par_files = ut.get_file_list(m_par_files)
# read par file
if len(m_par_files) > 0:
m_par_file = m_par_files[0]
msg += m_par_file
par_dict = get_lalo_ref(m_par_file, par_dict)
else:
msg += ' no par file found with date: {}'.format(m_date)
print(msg)
# initiate ROIPAC dict
atr = {}
atr['PROCESSOR'] = 'gamma'
atr['FILE_TYPE'] = os.path.splitext(fname)[1]
atr.update(par_dict)
# Write to .rsc file
rsc_file = fname + '.rsc'
try:
atr_orig = readfile.read_roipac_rsc(rsc_file)
except:
atr_orig = dict()
if not set(atr.items()).issubset(set(atr_orig.items())):
atr_out = {**atr_orig, **atr}
print('writing >>> ' + os.path.basename(rsc_file))
writefile.write_roipac_rsc(atr_out, out_file=rsc_file)
return rsc_file