def main(iargs=None):
inps = cmd_line_parse(iargs)
if inps.reset:
print('--------------------------------------------------')
reset_network(inps.file)
return inps.file
inps.date12_to_drop = get_date12_to_drop(inps)
if inps.date12_to_drop is not None:
ifgramStack(inps.file).update_drop_ifgram(date12List_to_drop=inps.date12_to_drop)
#print('--------------------------------------------------')
#ut.nonzero_mask(inps.file)
#print('--------------------------------------------------')
#ut.temporal_average(inps.file, datasetName='coherence', updateMode=True)
# Touch spatial average txt file of coherence if it's existed
ut.touch(os.path.splitext(os.path.basename(inps.file))[0]+'_coherence_spatialAvg.txt')
# Plot result
if inps.plot:
print('\nplot modified network and save to file.')
plotCmd = 'plot_network.py {} --nodisplay'.format(inps.file)
if inps.template_file:
plotCmd += ' --template {}'.format(inps.template_file)
print(plotCmd)
os.system(plotCmd)
print('Done.')
return
def reset_network(stackFile):
"""Reset/restore all pairs within the input file by set all DROP_IFGRAM=no"""
print("reset dataset 'dropIfgram' to True for all interferograms for file: "+stackFile)
obj = ifgramStack(stackFile)
obj.open(print_msg=False)
if np.all(obj.dropIfgram):
print('All dropIfgram are already True, no need to reset.')
else:
with h5py.File(stackFile, 'r+') as f:
f['dropIfgram'][:] = True
ut.touch(os.path.splitext(os.path.basename(stackFile))[0]+'_coherence_spatialAvg.txt')
return stackFile
def main(iargs=None):
inps = cmd_line_parse(iargs)
if inps.reset:
print('--------------------------------------------------')
reset_network(inps.file)
return inps.file
inps.date12_to_drop = get_date12_to_drop(inps)
if inps.date12_to_drop is not None:
ifgramStack(inps.file).update_drop_ifgram(date12List_to_drop=inps.date12_to_drop)
ut.touch('coherenceSpatialAvg.txt')
print('Done.')
return
def reference_file(inps):
"""Seed input file with option from input namespace
Return output file name if succeed; otherwise, return None
"""
if not inps:
inps = cmd_line_parse([''])
atr = readfile.read_attribute(inps.file)
# update_mode
if (not inps.force and inps.ref_y is not None
and inps.ref_y == int(atr.get('REF_Y', -999))
and inps.ref_x is not None
and inps.ref_x == int(atr.get('REF_X', -999))):
print(
'SAME reference pixel is already selected/saved in file, skip updating.'
)
return inps.file
# Check 1 - stack and its non-nan mask pixel coverage
stack = ut.temporal_average(inps.file,
datasetName='unwrapPhase',
updateMode=True,
outFile=False)[0]
mask = np.multiply(~np.isnan(stack), stack != 0.)
if np.nansum(mask) == 0.0:
raise ValueError(
'no pixel found with valid phase value in all datasets.')
# Check 2 - input ref_y/x: location and validity
if inps.ref_y is not None and inps.ref_x is not None:
if mask[inps.ref_y, inps.ref_x] == 0.:
raise ValueError(
'reference y/x have nan value in some dataset. Please re-select.'
)
else:
# Find reference y/x
if inps.method == 'maxCoherence':
inps.ref_y, inps.ref_x = select_max_coherence_yx(
coh_file=inps.coherenceFile,
mask=mask,
min_coh=inps.minCoherence)
elif inps.method == 'random':
inps.ref_y, inps.ref_x = random_select_reference_yx(mask)
elif inps.method == 'manual':
inps = manual_select_reference_yx(stack, inps, mask)
# Check ref_y/x from auto method
if inps.ref_y is None or inps.ref_x is None:
raise ValueError('ERROR: no reference y/x found.')
# Seeding file with reference y/x
atrNew = reference_point_attribute(atr, y=inps.ref_y, x=inps.ref_x)
if not inps.write_data:
print('Add/update ref_x/y attribute to file: ' + inps.file)
print(atrNew)
inps.outfile = ut.add_attribute(inps.file, atrNew)
else:
if not inps.outfile:
inps.outfile = inps.file
k = atr['FILE_TYPE']
fext = os.path.splitext(inps.file)[1]
if fext == '.h5':
if inps.outfile == inps.file:
print('updating data value without re-writing to a new file')
if k == 'ifgramStack':
with h5py.File(inps.file, 'r+') as f:
ds = f['unwrapPhase']
for i in range(ds.shape[0]):
ds[i, :, :] -= ds[i, inps.ref_y, inps.ref_x]
print('update metadata')
f.attrs.update(atrNew)
else:
with h5py.File(inps.file, 'r+') as f:
ds = f[k]
if len(ds.shape) == 3:
# 3D matrix
for i in range(ds.shape[0]):
ds[i, :, :] -= ds[i, inps.ref_y, inps.ref_x]
else:
# 2D matrix
ds[:] -= ds[inps.ref_y, inps.ref_x]
print('update metadata')
f.attrs.update(atrNew)
else:
## write to a new file
print('writing the referenced data into file: {}'.format(
inps.outfile))
# 1. read and update data value
data, atr = readfile.read(inps.file)
if len(data.shape) == 3:
# 3D matrix
for i in range(data.shape[0]):
data[i, :, :] -= data[i, inps.ref_y, inps.ref_x]
else:
# 2D matrix
data -= data[inps.ref_y, inps.ref_x]
# 2. update metadata
atr.update(atrNew)
# 3. write to file
writefile.write(data,
inps.outfile,
metadata=atr,
ref_file=inps.file)
else:
# for binary file, over-write directly
data = readfile.read(inps.file)[0]
data -= data[inps.ref_y, inps.ref_x]
atr.update(atrNew)
writefile.write(data, out_file=inps.outfile, metadata=atr)
ut.touch([inps.coherenceFile, inps.maskFile])
return inps.outfile
def reference_file(inps):
"""Seed input file with option from input namespace
Return output file name if succeed; otherwise, return None
"""
if not inps:
inps = cmd_line_parse([''])
atr = readfile.read_attribute(inps.file)
if (inps.ref_y and inps.ref_x and 'REF_Y' in atr.keys()
and inps.ref_y == int(atr['REF_Y'])
and inps.ref_x == int(atr['REF_X']) and not inps.force):
print(
'Same reference pixel is already selected/saved in file, skip updating.'
)
return inps.file
# Get stack and mask
stack = ut.temporal_average(inps.file,
datasetName='unwrapPhase',
updateMode=True,
outFile=False)[0]
mask = np.multiply(~np.isnan(stack), stack != 0.)
if np.nansum(mask) == 0.0:
raise ValueError(
'no pixel found with valid phase value in all datasets.')
if inps.ref_y and inps.ref_x and mask[inps.ref_y, inps.ref_x] == 0.:
raise ValueError(
'reference y/x have nan value in some dataset. Please re-select.')
# Find reference y/x
if not inps.ref_y or not inps.ref_x:
if inps.method == 'maxCoherence':
inps.ref_y, inps.ref_x = select_max_coherence_yx(
coh_file=inps.coherenceFile,
mask=mask,
min_coh=inps.minCoherence)
elif inps.method == 'random':
inps.ref_y, inps.ref_x = random_select_reference_yx(mask)
elif inps.method == 'manual':
inps = manual_select_reference_yx(stack, inps, mask)
if not inps.ref_y or not inps.ref_x:
raise ValueError('ERROR: no reference y/x found.')
# Seeding file with reference y/x
atrNew = reference_point_attribute(atr, y=inps.ref_y, x=inps.ref_x)
if not inps.write_data:
print('Add/update ref_x/y attribute to file: ' + inps.file)
print(atrNew)
inps.outfile = ut.add_attribute(inps.file, atrNew)
else:
if not inps.outfile:
inps.outfile = '{}_seeded{}'.format(
os.path.splitext(inps.file)[0],
os.path.splitext(inps.file)[1])
k = atr['FILE_TYPE']
# For ifgramStack file, update data value directly, do not write to new file
if k == 'ifgramStack':
f = h5py.File(inps.file, 'r+')
ds = f[k].get('unwrapPhase')
for i in range(ds.shape[0]):
ds[i, :, :] -= ds[i, inps.ref_y, inps.ref_x]
f[k].attrs.update(atrNew)
f.close()
inps.outfile = inps.file
elif k == 'timeseries':
data = timeseries(inps.file).read()
for i in range(data.shape[0]):
data[i, :, :] -= data[i, inps.ref_y, inps.ref_x]
obj = timeseries(inps.outfile)
atr.update(atrNew)
obj.write2hdf5(data=data, metadata=atr, refFile=inps.file)
obj.close()
else:
print('writing >>> ' + inps.outfile)
data = readfile.read(inps.file)[0]
data -= data[inps.ref_y, inps.ref_x]
atr.update(atrNew)
writefile.write(data, out_file=inps.outfile, metadata=atr)
ut.touch([inps.coherenceFile, inps.maskFile])
return inps.outfile
def reference_file(inps):
"""Seed input file with option from input namespace
Return output file name if succeed; otherwise, return None
"""
if not inps:
inps = cmd_line_parse([''])
atr = readfile.read_attribute(inps.file)
if (inps.ref_y and inps.ref_x and 'REF_Y' in atr.keys()
and inps.ref_y == int(atr['REF_Y']) and inps.ref_x == int(atr['REF_X'])
and not inps.force):
print('Same reference pixel is already selected/saved in file, skip updating.')
return inps.file
# Get stack and mask
stack = ut.temporal_average(inps.file, datasetName='unwrapPhase', updateMode=True, outFile=False)[0]
mask = np.multiply(~np.isnan(stack), stack != 0.)
if np.nansum(mask) == 0.0:
raise ValueError('no pixel found with valid phase value in all datasets.')
if inps.ref_y and inps.ref_x and mask[inps.ref_y, inps.ref_x] == 0.:
raise ValueError('reference y/x have nan value in some dataset. Please re-select.')
# Find reference y/x
if not inps.ref_y or not inps.ref_x:
if inps.method == 'maxCoherence':
inps.ref_y, inps.ref_x = select_max_coherence_yx(coh_file=inps.coherenceFile,
mask=mask,
min_coh=inps.minCoherence)
elif inps.method == 'random':
inps.ref_y, inps.ref_x = random_select_reference_yx(mask)
elif inps.method == 'manual':
inps = manual_select_reference_yx(stack, inps, mask)
if not inps.ref_y or not inps.ref_x:
raise ValueError('ERROR: no reference y/x found.')
# Seeding file with reference y/x
atrNew = reference_point_attribute(atr, y=inps.ref_y, x=inps.ref_x)
if not inps.write_data:
print('Add/update ref_x/y attribute to file: '+inps.file)
print(atrNew)
inps.outfile = ut.add_attribute(inps.file, atrNew)
else:
if not inps.outfile:
inps.outfile = '{}_seeded{}'.format(os.path.splitext(inps.file)[0],
os.path.splitext(inps.file)[1])
k = atr['FILE_TYPE']
# For ifgramStack file, update data value directly, do not write to new file
if k == 'ifgramStack':
f = h5py.File(inps.file, 'r+')
ds = f[k].get('unwrapPhase')
for i in range(ds.shape[0]):
ds[i, :, :] -= ds[i, inps.ref_y, inps.ref_x]
f[k].attrs.update(atrNew)
f.close()
inps.outfile = inps.file
elif k == 'timeseries':
data = timeseries(inps.file).read()
for i in range(data.shape[0]):
data[i, :, :] -= data[i, inps.ref_y, inps.ref_x]
obj = timeseries(inps.outfile)
atr.update(atrNew)
obj.write2hdf5(data=data, metadata=atr, refFile=inps.file)
obj.close()
else:
print('writing >>> '+inps.outfile)
data = readfile.read(inps.file)[0]
data -= data[inps.ref_y, inps.ref_x]
atr.update(atrNew)
writefile.write(data, out_file=inps.outfile, metadata=atr)
ut.touch([inps.coherenceFile, inps.maskFile])
return inps.outfile
