def main(argv):
try:
file = argv[0]
except:
usage()
sys.exit(1)
outfile = os.path.splitext(file)[0] + '_wrap' + os.path.splitext(file)[1]
one_cycle = 2 * np.pi
one_cycle = 0.05
atr = readfile.read_attribute(file)
k = atr['FILE_TYPE']
if k in ['interferograms', 'coherence', 'wrapped', 'timeseries']:
h5 = h5py.File(file, 'r')
epochList = sorted(h5[k].keys())
epoch_num = len(epochList)
prog_bar = ptime.progressBar(maxValue=epoch_num)
print('writing >>> ' + outfile)
h5out = h5py.File(outfile, 'w')
group = h5out.create_group(k)
if k in ['interferograms', 'coherence', 'wrapped']:
date12_list = ptime.list_ifgram2date12(epochList)
print('number of interferograms: ' + str(len(epochList)))
for i in range(epoch_num):
epoch = epochList[i]
data = h5[k][epoch].get(epoch)[:]
data_wrap = rewrap(data)
gg = group.create_group(epoch)
dset = gg.create_dataset(epoch, data=data_wrap)
for key, value in h5[k][epoch].attrs.items():
gg.attrs[key] = value
prog_bar.update(i + 1, suffix=date12_list[i])
elif k == 'timeseries':
print('number of acquisitions: ' + str(len(epochList)))
for i in range(epoch_num):
epoch = epochList[i]
data = h5[k].get(epoch)[:]
data_wrap = rewrap(data, one_cycle)
dset = group.create_dataset(epoch, data=data_wrap)
prog_bar.update(i + 1, suffix=epoch)
for key, value in h5[k].attrs.items():
group.attrs[key] = value
h5.close()
h5out.close()
prog_bar.close()
print('Done.')
return outfile
def main(argv):
# Inputs
try:
ifgram_file = argv[0]
timeseries_file = argv[1]
except:
usage()
sys.exit(1)
try:
outfile = argv[2]
except:
outfile = 'recon_'+ifgram_file
atr = readfile.read_attribute(timeseries_file)
length = int(atr['LENGTH'])
width = int(atr['WIDTH'])
# Read time-series file
print('loading timeseries ...')
h5ts = h5py.File(timeseries_file, 'r')
date_list = sorted(h5ts['timeseries'].keys())
date_num = len(date_list)
timeseries = np.zeros((date_num, length*width))
print('number of acquisitions: '+str(date_num))
prog_bar = ptime.progressBar(maxValue=date_num)
for i in range(date_num):
date = date_list[i]
d = h5ts['timeseries'].get(date)[:]
timeseries[i, :] = d.flatten(0)
prog_bar.update(i+1, suffix=date)
prog_bar.close()
h5ts.close()
del d
range2phase = -4*np.pi/float(atr['WAVELENGTH'])
timeseries = range2phase*timeseries
# Estimate interferograms from timeseries
print('estimating interferograms from timeseries using design matrix from input interferograms')
A, B = ut.design_matrix(ifgram_file)
p = -1*np.ones([A.shape[0], 1])
Ap = np.hstack((p, A))
estData = np.dot(Ap, timeseries)
del timeseries
# Write interferograms file
print('writing >>> '+outfile)
h5 = h5py.File(ifgram_file, 'r')
ifgram_list = sorted(h5['interferograms'].keys())
ifgram_num = len(ifgram_list)
date12_list = ptime.list_ifgram2date12(ifgram_list)
h5out = h5py.File(outfile, 'w')
group = h5out.create_group('interferograms')
print('number of interferograms: '+str(ifgram_num))
prog_bar = ptime.progressBar(maxValue=ifgram_num)
for i in range(ifgram_num):
ifgram = ifgram_list[i]
data = np.reshape(estData[i, :], (length, width))
gg = group.create_group(ifgram)
dset = gg.create_dataset(ifgram, data=data)
for key, value in h5['interferograms'][ifgram].attrs.items():
gg.attrs[key] = value
prog_bar.update(i+1, suffix=date12_list[i])
prog_bar.close()
h5.close()
h5out.close()
print('Done.')
return outfile
def main(iargs=None):
inps = cmd_line_parse(iargs)
atr = readfile.read_attribute(inps.velocity_file)
length = int(atr['LENGTH'])
width = int(atr['WIDTH'])
# Check subset input
if inps.subset_y:
inps.subset_y = sorted(inps.subset_y)
print('subset in y/azimuth direction: ' + str(inps.subset_y))
else:
inps.subset_y = [0, length]
if inps.subset_x:
inps.subset_x = sorted(inps.subset_x)
print('subset in x/range direction: ' + str(inps.subset_x))
else:
inps.subset_x = [0, width]
y0, y1 = inps.subset_y
x0, x1 = inps.subset_x
# Read velocity/rate
velocity = readfile.read(inps.velocity_file)[0]
print('read velocity file: ' + inps.velocity_file)
k = 'interferograms'
h5 = h5py.File(inps.ifgram_file, 'r')
ifgram_list = sorted(h5[k].keys())
ifgram_num = len(ifgram_list)
date12_list = ptime.list_ifgram2date12(ifgram_list)
print('number of interferograms: ' + str(ifgram_num))
# Select interferograms with unwrapping error
if inps.percentage > 0.0:
mask = readfile.read(inps.mask_file, datasetName='mask')[0]
print('read mask for pixels with unwrapping error from file: ' +
inps.mask_file)
unw_err_ifgram_num = int(np.rint(inps.percentage * ifgram_num))
unw_err_ifgram_idx = random.sample(list(range(ifgram_num)),
unw_err_ifgram_num)
unw_err_ifgram_list = [ifgram_list[i] for i in unw_err_ifgram_idx]
unw_err_date12_list = [date12_list[i] for i in unw_err_ifgram_idx]
print(
'randomly choose the following %d interferograms with unwrapping error'
% unw_err_ifgram_num)
print(unw_err_date12_list)
unit_unw_err = 2.0 * np.pi * mask
else:
unw_err_ifgram_list = []
# Generate simulated interferograms
m_dates = ptime.yyyymmdd([i.split('_')[0] for i in date12_list])
s_dates = ptime.yyyymmdd([i.split('_')[1] for i in date12_list])
range2phase = -4.0 * np.pi / float(atr['WAVELENGTH'])
print('writing simulated interferograms file: ' + inps.outfile)
h5out = h5py.File(inps.outfile, 'w')
group = h5out.create_group('interferograms')
for i in range(ifgram_num):
ifgram = ifgram_list[i]
# Get temporal baseline in years
t1 = datetime.datetime(*time.strptime(m_dates[i], "%Y%m%d")[0:5])
t2 = datetime.datetime(*time.strptime(s_dates[i], "%Y%m%d")[0:5])
dt = (t2 - t1)
dt = float(dt.days) / 365.25
# Simuated interferograms with unwrap error
unw = velocity * dt * range2phase
if ifgram in unw_err_ifgram_list:
rand_int = random.sample(list(range(1, 10)), 1)[0]
unw += rand_int * unit_unw_err
print(ifgram + ' - add unwrapping error of %d*2*pi' % rand_int)
else:
print(ifgram)
gg = group.create_group(ifgram)
dset = gg.create_dataset(ifgram, data=unw[y0:y1, x0:x1])
for key, value in h5[k][ifgram].attrs.items():
gg.attrs[key] = value
if ifgram in unw_err_ifgram_list:
gg.attrs['unwrap_error'] = 'yes'
else:
gg.attrs['unwrap_error'] = 'no'
gg.attrs['LENGTH'] = y1 - y0
gg.attrs['WIDTH'] = x1 - x0
h5.close()
h5out.close()
print('Done.')
return inps.outfile
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 unwrap_error_correction_bridging(ifgram_file, mask_file, y_list, x_list, ramp_type='plane',
ifgram_cor_file=None, save_cor_deramp_file=False):
"""Unwrapping error correction with bridging.
Inputs:
ifgram_file : string, name/path of interferogram(s) to be corrected
mask_file : string, name/path of mask file to mark different patches
y/x_list : list of int, bonding points in y/x
ifgram_cor_file : string, optional, output file name
save_cor_deramp_file : bool, optional
Output:
ifgram_cor_file
Example:
y_list = [235, 270, 350, 390]
x_list = [880, 890, 1200, 1270]
unwrap_error_correction_bridging('unwrapIfgram.h5', 'mask_all.h5', y_list, x_list, 'quadratic')
"""
##### Mask and Ramp
mask = readfile.read(mask_file, datasetName='mask')[0]
ramp_mask = mask == 1
print('estimate phase ramp during the correction')
print('ramp type: '+ramp_type)
# Bridge Info
# Check
for i in range(len(x_list)):
if mask[y_list[i], x_list[i]] == 0:
print('\nERROR: Connecting point (%d,%d) is out of masked area! Select them again!\n' % (y_list[i],
x_list[i]))
sys.exit(1)
print('Number of bridges: '+str(len(x_list)/2))
print('Bonding points coordinates:\nx: '+str(x_list)+'\ny: '+str(y_list))
# Plot Connecting Pair of Points
plot_bonding_points = False
if plot_bonding_points:
point_yx = ''
line_yx = ''
n_bridge = len(x)/2
for i in range(n_bridge):
pairs_yx = '{},{},{},{}'.format(y[2*i],
x[2*i],
y[2*i+1],
x[2*i+1])
if not i == n_bridge-1:
point_yx += pair_yx+','
line_yx += pair_yx+';'
else:
point_yx += pair_yx
line_yx += pair_yx
try:
plot_cmd = 'view.py --point-yx="'+point_yx+'" --line-yx="'+line_yx +\
'" --nodisplay -o bonding_points.png -f '+maskFile
print(plot_cmd)
os.system(plot_cmd)
except:
pass
# Basic info
ext = os.path.splitext(ifgram_file)[1]
atr = readfile.read_attribute(ifgram_file)
k = atr['FILE_TYPE']
try:
ref_y = int(atr['REF_Y'])
ref_x = int(atr['REF_X'])
print('reference pixel in y/x: %d/%d' % (ref_y, ref_x))
except:
sys.exit('ERROR: Can not find ref_y/x value, input file is not referenced in space!')
# output file name
if not ifgram_cor_file:
ifgram_cor_file = os.path.splitext(ifgram_file)[0]+'_unwCor'+ext
ifgram_cor_deramp_file = os.path.splitext(ifgram_cor_file)[0]+'_'+ramp_type+ext
# HDF5 file
if ext == '.h5':
# Read
h5 = h5py.File(ifgram_file, 'r')
ifgram_list = sorted(h5[k].keys())
ifgram_num = len(ifgram_list)
h5out = h5py.File(ifgram_cor_file, 'w')
group = h5out.create_group(k)
print('writing >>> '+ifgram_cor_file)
if save_cor_deramp_file:
h5out_deramp = h5py.File(ifgram_cor_deramp_file, 'w')
group_deramp = h5out_deramp.create_group(k)
print('writing >>> '+ifgram_cor_deramp_file)
# Loop
print('Number of interferograms: '+str(ifgram_num))
prog_bar = ptime.progressBar(maxValue=ifgram_num)
date12_list = ptime.list_ifgram2date12(ifgram_list)
for i in range(ifgram_num):
ifgram = ifgram_list[i]
data = h5[k][ifgram].get(ifgram)[:]
data -= data[ref_y, ref_x]
data_deramp, ramp = deramp.remove_data_surface(data, ramp_mask, ramp_type)
data_derampCor = bridging_data(data_deramp, mask, x_list, y_list)
ramp[data == 0.] = 0.
gg = group.create_group(ifgram)
dset = gg.create_dataset(ifgram, data=data_derampCor+ramp)
for key, value in h5[k][ifgram].attrs.items():
gg.attrs[key] = value
if save_cor_deramp_file:
gg_deramp = group_deramp.create_group(ifgram)
dset = gg_deramp.create_dataset(ifgram, data=data_derampCor)
for key, value in h5[k][ifgram].attrs.items():
gg_deramp.attrs[key] = value
prog_bar.update(i+1, suffix=date12_list[i])
prog_bar.close()
h5.close()
h5out.close()
try:
h5out_deramp.close()
except:
pass
# .unw file
elif ext == '.unw':
print('read '+ifgram_file)
data = readfile.read(ifgram_file)[0]
data -= data[ref_y, ref_x]
data_deramp, ramp = deramp.remove_data_surface(data, ramp_mask, ramp_type)
data_derampCor = bridging_data(data_deramp, mask, x_list, y_list)
print('writing >>> '+ifgram_cor_file)
ramp[data == 0.] = 0.
ifgram_cor_file = writefile.write(data_derampCor+ramp,
out_file=ifgram_cor_file,
metadata=atr)
if save_cor_deramp_file:
print('writing >>> '+ifgram_cor_deramp_file)
ifgram_cor_deramp_file = writefile.write(data_derampCor,
out_file=ifgram_cor_deramp_file,
metadata=atr)
else:
sys.exit('Un-supported file type: '+ext)
return ifgram_cor_file, ifgram_cor_deramp_file