def read_data(inps):
# metadata
atr = readfile.read_attribute(inps.file)
if 'WAVELENGTH' in atr.keys():
range2phase = -4 * np.pi / float(atr['WAVELENGTH'])
# change reference pixel
if inps.ref_yx:
atr['REF_Y'] = inps.ref_yx[0]
atr['REF_X'] = inps.ref_yx[1]
print('change reference point to y/x: {}'.format(inps.ref_yx))
# various file types
print('read {} from file {}'.format(inps.dset, inps.file))
k = atr['FILE_TYPE']
if k == 'velocity':
# read/prepare data
data = readfile.read(inps.file)[0] * range2phase
print(
"converting velocity to an interferogram with one year temporal baseline"
)
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
# metadata
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(
os.path.splitext(inps.file)[0], atr['FILE_TYPE'])
elif k == 'timeseries':
# date1 and date2
if '_' in inps.dset:
date1, date2 = ptime.yyyymmdd(inps.dset.split('_'))
else:
date1 = atr['REF_DATE']
date2 = ptime.yyyymmdd(inps.dset)
# read/prepare data
data = readfile.read(inps.file, datasetName=date2)[0]
data -= readfile.read(inps.file, datasetName=date1)[0]
print('converting range to phase')
data *= range2phase
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
# output filename
if not inps.outfile:
inps.outfile = '{}_{}.unw'.format(date1, date2)
if inps.file.startswith('geo_'):
inps.outfile = 'geo_' + inps.outfile
elif k == 'HDFEOS':
dname = inps.dset.split('-')[0]
# date1 and date2
if dname == 'displacement':
if '-' in inps.dset:
suffix = inps.dset.split('-')[1]
if '_' in suffix:
date1, date2 = ptime.yyyymmdd(suffix.split('_'))
else:
date1 = atr['REF_DATE']
date2 = ptime.yyyymmdd(suffix)
else:
raise ValueError(
"No '-' in input dataset! It is required for {}".format(
dname))
else:
date_list = HDFEOS(inps.file).get_date_list()
date1 = date_list[0]
date2 = date_list[-1]
date12 = '{}_{}'.format(date1, date2)
# read / prepare data
slice_list = readfile.get_slice_list(inps.file)
if 'displacement' in inps.dset:
# read/prepare data
slice_name1 = view.check_dataset_input(
slice_list, '{}-{}'.format(dname, date1))[0][0]
slice_name2 = view.check_dataset_input(
slice_list, '{}-{}'.format(dname, date2))[0][0]
data = readfile.read(inps.file, datasetName=slice_name1)[0]
data -= readfile.read(inps.file, datasetName=slice_name2)[0]
print('converting range to phase')
data *= range2phase
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
else:
slice_name = view.check_dataset_input(slice_list, inps.dset)[0][0]
data = readfile.read(inps.file, datasetName=slice_name)[0]
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
if dname == 'displacement':
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
elif 'coherence' in dname.lower():
atr['FILE_TYPE'] = '.cor'
atr['UNIT'] = '1'
elif dname == 'height':
atr['FILE_TYPE'] = '.dem'
atr['DATA_TYPE'] = 'int16'
else:
raise ValueError('unrecognized input dataset type: {}'.format(
inps.dset))
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(date12, atr['FILE_TYPE'])
elif k == 'ifgramStack':
dname, date12 = inps.dset.split('-')
date1, date2 = date12.split('_')
# read / prepare data
data = readfile.read(inps.file, datasetName=inps.dset)[0]
if dname.startswith('unwrapPhase'):
if 'REF_X' in atr.keys():
data -= data[int(atr['REF_Y']), int(atr['REF_X'])]
print('consider reference pixel in y/x: ({}, {})'.format(
atr['REF_Y'], atr['REF_X']))
else:
print('No REF_Y/X found.')
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
if dname.startswith('unwrapPhase'):
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
elif dname == 'coherence':
atr['FILE_TYPE'] = '.cor'
atr['UNIT'] = '1'
elif dname == 'wrapPhase':
atr['FILE_TYPE'] = '.int'
atr['UNIT'] = 'radian'
else:
raise ValueError('unrecognized dataset type: {}'.format(inps.dset))
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(date12, atr['FILE_TYPE'])
if inps.file.startswith('geo_'):
inps.outfile = 'geo_' + inps.outfile
else:
# read data
data = readfile.read(inps.file, datasetName=inps.dset)[0]
if inps.outfile:
fext = os.path.splitext(inps.outfile)[1]
atr['FILE_TYPE'] = fext
else:
# metadata
if 'coherence' in k.lower():
atr['FILE_TYPE'] = '.cor'
elif k in ['mask']:
atr['FILE_TYPE'] = '.msk'
elif k in ['geometry'] and inps.dset == 'height':
if 'Y_FIRST' in atr.keys():
atr['FILE_TYPE'] = '.dem'
else:
atr['FILE_TYPE'] = '.hgt'
atr['UNIT'] = 'm'
else:
atr['FILE_TYPE'] = '.unw'
inps.outfile = '{}{}'.format(
os.path.splitext(inps.file)[0], atr['FILE_TYPE'])
# get rid of starting . if output as hdf5 file
if inps.outfile.endswith('.h5'):
if atr['FILE_TYPE'].startswith('.'):
atr['FILE_TYPE'] = atr['FILE_TYPE'][1:]
atr['PROCESSOR'] = 'roipac'
return data, atr, inps.outfile
def read_data(inps):
# metadata
atr = readfile.read_attribute(inps.file)
range2phase = -4 * np.pi / float(atr['WAVELENGTH'])
# change reference pixel
if inps.ref_yx:
atr['REF_Y'] = inps.ref_yx[0]
atr['REF_X'] = inps.ref_yx[1]
print('change reference point to y/x: {}'.format(inps.ref_yx))
# various file types
print('read {} from file {}'.format(inps.dset, inps.file))
k = atr['FILE_TYPE']
if k == 'velocity':
# read/prepare data
data = readfile.read(inps.file)[0] * range2phase
print("converting velocity to an interferogram with one year temporal baseline")
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
# metadata
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(os.path.splitext(inps.file)[0], atr['FILE_TYPE'])
elif k == 'timeseries':
# date1 and date2
if '_' in inps.dset:
date1, date2 = ptime.yyyymmdd(inps.dset.split('_'))
else:
date1 = atr['REF_DATE']
date2 = ptime.yyyymmdd(inps.dset)
# read/prepare data
data = readfile.read(inps.file, datasetName=date2)[0]
data -= readfile.read(inps.file, datasetName=date1)[0]
print('converting range to phase')
data *= range2phase
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
# output filename
if not inps.outfile:
inps.outfile = '{}_{}.unw'.format(date1, date2)
if inps.file.startswith('geo_'):
inps.outfile = 'geo_'+inps.outfile
elif k == 'HDFEOS':
dname = inps.dset.split('-')[0]
# date1 and date2
if dname == 'displacement':
if '-' in inps.dset:
suffix = inps.dset.split('-')[1]
if '_' in suffix:
date1, date2 = ptime.yyyymmdd(suffix.split('_'))
else:
date1 = atr['REF_DATE']
date2 = ptime.yyyymmdd(suffix)
else:
raise ValueError("No '-' in input dataset! It is required for {}".format(dname))
else:
date_list = HDFEOS(inps.file).get_date_list()
date1 = date_list[0]
date2 = date_list[-1]
date12 = '{}_{}'.format(date1, date2)
# read / prepare data
slice_list = readfile.get_slice_list(inps.file)
if 'displacement' in inps.dset:
# read/prepare data
slice_name1 = view.check_dataset_input(slice_list, '{}-{}'.format(dname, date1))[0][0]
slice_name2 = view.check_dataset_input(slice_list, '{}-{}'.format(dname, date2))[0][0]
data = readfile.read(inps.file, datasetName=slice_name1)[0]
data -= readfile.read(inps.file, datasetName=slice_name2)[0]
print('converting range to phase')
data *= range2phase
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
else:
slice_name = view.check_dataset_input(slice_list, inps.dset)[0][0]
data = readfile.read(inps.file, datasetName=slice_name)[0]
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
if dname == 'displacement':
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
elif 'coherence' in dname.lower():
atr['FILE_TYPE'] = '.cor'
atr['UNIT'] = '1'
elif dname == 'height':
atr['FILE_TYPE'] = '.dem'
atr['DATA_TYPE'] = 'int16'
else:
raise ValueError('unrecognized input dataset type: {}'.format(inps.dset))
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(date12, atr['FILE_TYPE'])
elif k == 'ifgramStack':
dname, date12 = inps.dset.split('-')
date1, date2 = date12.split('_')
# read / prepare data
data = readfile.read(inps.file, datasetName=inps.dset)[0]
if dname.startswith('unwrapPhase'):
if 'REF_X' in atr.keys():
data -= data[int(atr['REF_Y']), int(atr['REF_X'])]
print('consider reference pixel in y/x: ({}, {})'.format(atr['REF_Y'], atr['REF_X']))
else:
print('No REF_Y/X found.')
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
if dname.startswith('unwrapPhase'):
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
elif dname == 'coherence':
atr['FILE_TYPE'] = '.cor'
atr['UNIT'] = '1'
elif dname == 'wrapPhase':
atr['FILE_TYPE'] = '.int'
atr['UNIT'] = 'radian'
else:
raise ValueError('unrecognized dataset type: {}'.format(inps.dset))
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(date12, atr['FILE_TYPE'])
if inps.file.startswith('geo_'):
inps.outfile = 'geo_'+inps.outfile
else:
# read data
data = readfile.read(inps.file, datasetName=inps.dset)[0]
# metadata
if 'coherence' in k.lower():
atr['FILE_TYPE'] = '.cor'
elif k in ['mask']:
atr['FILE_TYPE'] = '.msk'
atr['DATA_TYPE'] = 'byte'
elif k in ['geometry'] and inps.dset == 'height':
if 'Y_FIRST' in atr.keys():
atr['FILE_TYPE'] = '.dem'
atr['DATA_TYPE'] = 'int16'
else:
atr['FILE_TYPE'] = '.hgt'
atr['UNIT'] = 'm'
else:
atr['FILE_TYPE'] = '.unw'
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(os.path.splitext(inps.file)[0], atr['FILE_TYPE'])
atr['PROCESSOR'] = 'roipac'
return data, atr, inps.outfile
def read_data(inps):
# metadata
atr = readfile.read_attribute(inps.file)
if 'WAVELENGTH' in atr.keys():
range2phase = -4 * np.pi / float(atr['WAVELENGTH'])
# change reference pixel
if inps.ref_lalo:
if 'Y_FIRST' in atr.keys():
coord = ut.coordinate(atr)
ref_y, ref_x = coord.geo2radar(inps.ref_lalo[0],
inps.ref_lalo[1])[0:2]
inps.ref_yx = [ref_y, ref_x]
else:
raise ValueError(
"input file is not geocoded --> reference point in lat/lon is NOT support"
)
if inps.ref_yx:
atr['REF_Y'] = inps.ref_yx[0]
atr['REF_X'] = inps.ref_yx[1]
if 'Y_FIRST' in atr.keys():
coord = ut.coordinate(atr)
ref_lat, ref_lon = coord.radar2geo(inps.ref_yx[0],
inps.ref_yx[1])[0:2]
atr['REF_LAT'] = ref_lat
atr['REF_LON'] = ref_lon
print('change reference point to y/x: {}'.format(inps.ref_yx))
# various file types
print('read {} from file {}'.format(inps.dset, inps.file))
k = atr['FILE_TYPE']
if k == 'velocity':
# read/prepare data
data = readfile.read(inps.file)[0]
# velocity to displacement
print('convert velocity to displacement for {}'.format(atr['DATE12']))
date1, date2 = atr['DATE12'].split('_')
dt1, dt2 = ptime.date_list2vector([date1, date2])[0]
data *= (dt2 - dt1).days / 365.25
# displacement to phase
print('convert displacement to phase in radian')
data *= range2phase
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
# metadata
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
# output filename
if not inps.outfile:
inps.outfile = os.path.join(os.path.dirname(inps.file),
'{}.unw'.format(atr['DATE12']))
elif k == 'timeseries':
# date1 and date2
if '_' in inps.dset:
date1, date2 = ptime.yyyymmdd(inps.dset.split('_'))
else:
date1 = atr['REF_DATE']
date2 = ptime.yyyymmdd(inps.dset)
# read/prepare data
data = readfile.read(inps.file, datasetName=date2)[0]
data -= readfile.read(inps.file, datasetName=date1)[0]
print('converting range to phase')
data *= range2phase
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
# output filename
if not inps.outfile:
inps.outfile = '{}_{}.unw'.format(date1, date2)
if inps.file.startswith('geo_'):
inps.outfile = 'geo_' + inps.outfile
elif k == 'HDFEOS':
dname = inps.dset.split('-')[0]
# date1 and date2
if dname == 'displacement':
if '-' in inps.dset:
suffix = inps.dset.split('-')[1]
if '_' in suffix:
date1, date2 = ptime.yyyymmdd(suffix.split('_'))
else:
date1 = atr['REF_DATE']
date2 = ptime.yyyymmdd(suffix)
else:
raise ValueError(
"No '-' in input dataset! It is required for {}".format(
dname))
else:
date_list = HDFEOS(inps.file).get_date_list()
date1 = date_list[0]
date2 = date_list[-1]
date12 = '{}_{}'.format(date1, date2)
# read / prepare data
slice_list = readfile.get_slice_list(inps.file)
if 'displacement' in inps.dset:
# read/prepare data
slice_name1 = view.check_dataset_input(
slice_list, '{}-{}'.format(dname, date1))[0][0]
slice_name2 = view.check_dataset_input(
slice_list, '{}-{}'.format(dname, date2))[0][0]
data = readfile.read(inps.file, datasetName=slice_name1)[0]
data -= readfile.read(inps.file, datasetName=slice_name2)[0]
print('converting range to phase')
data *= range2phase
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
else:
slice_name = view.check_dataset_input(slice_list, inps.dset)[0][0]
data = readfile.read(inps.file, datasetName=slice_name)[0]
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
if dname == 'displacement':
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
elif 'coherence' in dname.lower():
atr['FILE_TYPE'] = '.cor'
atr['UNIT'] = '1'
elif dname == 'height':
atr['FILE_TYPE'] = '.dem'
atr['DATA_TYPE'] = 'int16'
else:
raise ValueError('unrecognized input dataset type: {}'.format(
inps.dset))
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(date12, atr['FILE_TYPE'])
elif k == 'ifgramStack':
dname, date12 = inps.dset.split('-')
date1, date2 = date12.split('_')
# read / prepare data
data = readfile.read(inps.file, datasetName=inps.dset)[0]
if dname.startswith('unwrapPhase'):
if 'REF_X' in atr.keys():
data -= data[int(atr['REF_Y']), int(atr['REF_X'])]
print('consider reference pixel in y/x: ({}, {})'.format(
atr['REF_Y'], atr['REF_X']))
else:
print('No REF_Y/X found.')
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
if dname.startswith('unwrapPhase'):
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
elif dname == 'coherence':
atr['FILE_TYPE'] = '.cor'
atr['UNIT'] = '1'
elif dname == 'wrapPhase':
atr['FILE_TYPE'] = '.int'
atr['UNIT'] = 'radian'
elif dname == 'connectComponent':
atr['FILE_TYPE'] = '.conncomp'
atr['UNIT'] = '1'
atr['DATA_TYPE'] = 'byte'
else:
raise ValueError('unrecognized dataset type: {}'.format(inps.dset))
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(date12, atr['FILE_TYPE'])
if inps.file.startswith('geo_'):
inps.outfile = 'geo_' + inps.outfile
else:
# read data
data = readfile.read(inps.file, datasetName=inps.dset)[0]
if inps.outfile:
fext = os.path.splitext(inps.outfile)[1]
atr['FILE_TYPE'] = fext
else:
# metadata
if 'coherence' in k.lower():
atr['FILE_TYPE'] = '.cor'
elif k in ['mask']:
atr['FILE_TYPE'] = '.msk'
elif k in ['geometry'] and inps.dset == 'height':
if 'Y_FIRST' in atr.keys():
atr['FILE_TYPE'] = '.dem'
else:
atr['FILE_TYPE'] = '.hgt'
atr['UNIT'] = 'm'
else:
atr['FILE_TYPE'] = '.unw'
inps.outfile = '{}{}'.format(
os.path.splitext(inps.file)[0], atr['FILE_TYPE'])
# mask
if inps.mask_file:
for m_file in inps.mask_file:
print('mask data based on input file: {}'.format(m_file))
mask = readfile.read(m_file)[0]
mask *= ~np.isnan(data)
data[mask == 0] = np.nan
# get rid of starting . if output as hdf5 file
if inps.outfile.endswith('.h5'):
if atr['FILE_TYPE'].startswith('.'):
atr['FILE_TYPE'] = atr['FILE_TYPE'][1:]
atr['PROCESSOR'] = 'roipac'
return data, atr, inps.outfile
def extract_data(inps, dataset, outdir):
"""extract data from HDFEOS file based on the given attribute"""
# read HDFEOS file
# metadata
atr = readfile.read_attribute("".join(inps.input_HDFEOS))
attr = "".join(inps.attribute)
# read 2d data
if attr == 'displacement' or attr == 'velocity':
if inps.date == None:
date1 = atr['START_DATE']
date2 = atr['END_DATE']
#raise Exception("ERROR! Date for displacement must be given!")
else:
# date1 and date2
if '_' in "".join(inps.date):
date1, date2 = ptime.yyyymmdd("".join(inps.date).split('_'))
else:
date1 = atr['START_DATE']
date2 = ptime.yyyymmdd("".join(inps.date))
#date12 = '{}_{}'.format(date1, date2)
if attr == 'displacement':
# read / prepare data
slice_list = readfile.get_slice_list("".join(inps.input_HDFEOS))
# read/prepare data
dname = 'displacement'
slice_name1 = view.check_dataset_input(
slice_list, '{}-{}'.format(dname, date1))[0][0]
slice_name2 = view.check_dataset_input(
slice_list, '{}-{}'.format(dname, date2))[0][1]
data = readfile.read("".join(inps.input_HDFEOS),
datasetName=slice_name1)[0]
data -= readfile.read("".join(inps.input_HDFEOS),
datasetName=slice_name2)[0]
data_name = '{}_{}_{}'.format(attr, date1, date2)
if inps.mask:
print("mask file")
maskfile = readfile.read(
"".join(inps.input_HDFEOS),
datasetName='/HDFEOS/GRIDS/timeseries/quality/mask')[0]
data[maskfile == 0] = np.nan
outfile = outdir + '/' + data_name + '.h5'
atr['FILE_TYPE'] = '.unw'
writefile.write(data, out_file=outfile, metadata=atr)
#print('converting range to phase')
#data *= range2phase
#if inps.ref_yx:
# data -= data[inps.ref_yx[0], inps.ref_yx[1]]
elif attr == 'velocity':
dname = 'displacement'
data_timeseries = readfile.read("".join(inps.input_HDFEOS),
datasetName=dataset + dname)[0]
if inps.mask:
print("mask file")
maskfile = readfile.read(
"".join(inps.input_HDFEOS),
datasetName='/HDFEOS/GRIDS/timeseries/quality/mask')[0]
data_timeseries[:, maskfile == 0] = np.nan
bperp_date = h5py.File("".join(inps.input_HDFEOS), 'r')
data_bperp = bperp_date[(dataset + 'bperp')]
data_date = bperp_date[(dataset + 'date')]
ts_data_name = 'timeseries_ERA_demErr.h5'
outfile = outdir + '/' + ts_data_name
# write to HDF5 file
dsDict = dict()
dsDict['bperp'] = data_bperp
dsDict['date'] = data_date
dsDict['timeseries'] = data_timeseries
atr['FILE_TYPE'] = attr
writefile.write(dsDict, out_file=outfile, metadata=atr)
# run timeseries2velocity.py
output_vel = 'velocity_' + date1 + '_' + date2 + '.h5'
data_name = output_vel.split('.')[0]
os.chdir(outdir)
completion_status = os.system(
multitrack_utilities.seperate_str_byspace([
'timeseries2velocity.py', outfile, '--start-date', date1,
'--end-date', date2, '--exclude', '../exclude_date.txt',
'--output', output_vel
]))
if completion_status == 1:
raise Exception('error when generate velocity!')
date_vel = readfile.read(output_vel, datasetName='velocity')[0]
data = date_vel
os.chdir('../')
else:
data = readfile.read("".join(inps.input_HDFEOS),
datasetName=dataset + attr)[0]
outfile = outdir + '/' + attr + '.h5'
data_name = attr
atr['FILE_TYPE'] = attr
if inps.mask:
print("mask file")
maskfile = readfile.read(
"".join(inps.input_HDFEOS),
datasetName='/HDFEOS/GRIDS/timeseries/quality/mask')[0]
data[maskfile == 0] = np.nan
writefile.write(data, out_file=outfile, metadata=atr)
# mask data
#if inps.mask:
# print("mask file")
# maskfile = readfile.read("".join(inps.input_HDFEOS),datasetName='/HDFEOS/GRIDS/timeseries/quality/mask')[0]
# data[maskfile == 0] = np.nan
return data, data_name, atr