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)[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):
pair_yx = str(y[2 * i]) + ',' + str(x[2 * i]) + ',' + str(
y[2 * i + 1]) + ',' + str(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.progress_bar(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 = rm.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,
compression='gzip')
for key, value in h5[k][ifgram].attrs.iteritems():
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,
compression='gzip')
for key, value in h5[k][ifgram].attrs.iteritems():
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 = rm.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, atr,
ifgram_cor_file)
if save_cor_deramp_file:
print 'writing >>> ' + ifgram_cor_deramp_file
ifgram_cor_deramp_file = writefile.write(data_derampCor, atr,
ifgram_cor_deramp_file)
else:
sys.exit('Un-supported file type: ' + ext)
return ifgram_cor_file, ifgram_cor_deramp_file
def main(argv):
method = 'triangular_consistency' ## or 'bonding_point'
ramp_type = 'plane'
save_rampCor = 'yes'
plot_bonding_points = 'yes'
##### Check Inputs
if len(sys.argv) > 2:
try:
opts, args = getopt.getopt(argv, 'h:f:m:x:y:o:t:',
['ramp=', 'no-ramp-save'])
except getopt.GetoptError:
print 'Error while getting args'
usage()
sys.exit(1)
for opt, arg in opts:
if opt in ['-h', '--help']:
usage()
sys.exit()
elif opt in '-f':
File = arg
elif opt in '-m':
maskFile = arg
elif opt in '-o':
outName = arg
elif opt in '-x':
x = [int(i) for i in arg.split(',')]
method = 'bonding_point'
elif opt in '-y':
y = [int(i) for i in arg.split(',')]
method = 'bonding_point'
elif opt in '-t':
templateFile = arg
elif opt in '--ramp':
ramp_type = arg.lower()
elif opt in '--no-ramp-save':
save_rampCor = 'no'
elif len(sys.argv) == 2:
if argv[0] in ['-h', '--help']:
usage()
sys.exit()
elif os.path.isfile(argv[0]):
File = argv[0]
maskFile = argv[1]
else:
print 'Input file does not existed: ' + argv[0]
sys.exit(1)
else:
usage()
sys.exit(1)
##### Check template file
try:
templateFile
templateContents = readfile.read_template(templateFile)
except:
pass
try:
yx = [
int(i) for i in templateContents['pysar.unwrapError.yx'].split(',')
]
x = yx[1::2]
y = yx[0::2]
method = 'bonding_point'
except:
pass
##### Read Mask File
## Priority:
## Input mask file > pysar.mask.file > existed Modified_Mask.h5 > existed Mask.h5
try:
maskFile
except:
try:
maskFile = templateContents['pysar.mask.file']
except:
if os.path.isfile('Modified_Mask.h5'):
maskFile = 'Modified_Mask.h5'
elif os.path.isfile('Mask.h5'):
maskFile = 'Mask.h5'
else:
print 'No mask found!'
sys.exit(1)
try:
Mask, Matr = readfile.read(maskFile)
print 'mask: ' + maskFile
except:
print 'Can not open mask file: ' + maskFile
sys.exit(1)
##### Output file name
ext = os.path.splitext(File)[1]
try:
outName
except:
outName = File.split('.')[0] + '_unwCor' + ext
print '\n**************** Unwrapping Error Correction ******************'
#################### Triangular Consistency (Phase Closure) ####################
if method == 'triangular_consistency':
print 'Phase unwrapping error correction using Triangular Consistency / Phase Closure'
h5file = h5py.File(File)
ifgramList = h5file['interferograms'].keys()
sx = int(h5file['interferograms'][ifgramList[0]].attrs['WIDTH'])
sy = int(h5file['interferograms'][ifgramList[0]].attrs['FILE_LENGTH'])
curls, Triangles, C = ut.get_triangles(h5file)
A, B = ut.design_matrix(h5file)
ligram, lv = np.shape(B)
lcurls = np.shape(curls)[0]
print 'Number of all triangles: ' + str(lcurls)
print 'Number of interferograms: ' + str(ligram)
#print curls
curlfile = 'curls.h5'
if not os.path.isfile(curlfile):
ut.generate_curls(curlfile, h5file, Triangles, curls)
thr = 0.50
curls = np.array(curls)
n1 = curls[:, 0]
n2 = curls[:, 1]
n3 = curls[:, 2]
numPixels = sy * sx
print 'reading interferograms...'
data = np.zeros((ligram, numPixels), np.float32)
for ni in range(ligram):
dset = h5file['interferograms'][ifgramList[ni]].get(ifgramList[ni])
d = dset[0:dset.shape[0], 0:dset.shape[1]]
data[ni] = d.flatten(1)
print np.shape(data)
print 'reading curls ...'
h5curl = h5py.File(curlfile)
curlList = h5curl['interferograms'].keys()
curlData = np.zeros((lcurls, numPixels), np.float32)
for ni in range(lcurls):
dset = h5curl['interferograms'][curlList[ni]].get(curlList[ni])
d = dset[0:dset.shape[0], 0:dset.shape[1]]
curlData[ni] = d.flatten(1)
pi = np.pi
EstUnwrap = np.zeros((ligram, numPixels), np.float32)
#try:
# maskFile=argv[1]
# h5Mask=h5py.File(maskFile)
# dset = h5Mask['mask'].get('mask')
# Mask=dset[0:dset.shape[0],0:dset.shape[1]]
#except:
# dset = h5file['mask'].get('mask')
# Mask=dset[0:dset.shape[0],0:dset.shape[1]]
Mask = Mask.flatten(1)
for ni in range(numPixels):
#dU = np.zeros([ligram,1])
#print np.shape(dU)
#print np.shape(data[:,ni])
if Mask[ni] == 1:
dU = data[:, ni]
#nan_ndx = dataPoint == 0.
unwCurl = np.array(curlData[:, ni])
#print unwCurl
ind = np.abs(unwCurl) >= thr
N1 = n1[ind]
N2 = n2[ind]
N3 = n3[ind]
indC = np.abs(unwCurl) < thr
Nc1 = n1[indC]
Nc2 = n2[indC]
Nc3 = n3[indC]
N = np.hstack([N1, N2, N3])
UniN = np.unique(N)
Nc = np.hstack([Nc1, Nc2, Nc3])
UniNc = np.unique(Nc)
inter = list(set(UniNc) & set(UniN)) # intersetion
UniNc = list(UniNc)
for x in inter:
UniNc.remove(x)
D = np.zeros([len(UniNc), ligram])
for i in range(len(UniNc)):
D[i, UniNc[i]] = 1
AAA = np.vstack([-2 * pi * C, D])
#AAA1=np.hstack([AAA,np.zeros([AAA.shape[0],lv])])
#AAA2=np.hstack([-2*pi*np.eye(ligram),B])
#AAAA=np.vstack([AAA1,AAA2])
AAAA = np.vstack([AAA, 0.25 * np.eye(ligram)])
#print '************************'
#print np.linalg.matrix_rank(C)
#print np.linalg.matrix_rank(AAA)
#print np.linalg.matrix_rank(AAAA)
#print '************************'
#LLL=list(np.dot(C,dU)) + list(np.zeros(np.shape(UniNc)[0]))# + list(dU)
#ind=np.isnan(AAA)
#M1=pinv(AAA)
#M=np.dot(M1,LLL)
#EstUnwrap[:,ni]=np.round(M[0:ligram])*2.0*np.pi
##########
# with Tikhonov regularization:
AAAA = np.vstack([AAA, 0.25 * np.eye(ligram)])
LLL = list(np.dot(C, dU)) + list(np.zeros(
np.shape(UniNc)[0])) + list(np.zeros(ligram))
ind = np.isnan(AAAA)
M1 = pinv(AAAA)
M = np.dot(M1, LLL)
EstUnwrap[:, ni] = np.round(M[0:ligram]) * 2.0 * np.pi
#print M[0:ligram]
#print np.round(M[0:ligram])
else:
EstUnwrap[:, ni] = np.zeros([ligram])
if not np.remainder(ni, 10000):
print 'Processing point: %7d of %7d ' % (ni, numPixels)
##### Output
dataCor = data + EstUnwrap
unwCorFile = File.replace('.h5', '') + '_unwCor.h5'
print 'writing >>> ' + unwCorFile
h5unwCor = h5py.File(unwCorFile, 'w')
gg = h5unwCor.create_group('interferograms')
for i in range(ligram):
group = gg.create_group(ifgramList[i])
dset = group.create_dataset(ifgramList[i],
data=np.reshape(
dataCor[i, :], [sx, sy]).T,
compression='gzip')
for key, value in h5file['interferograms'][
ifgramList[i]].attrs.iteritems():
group.attrs[key] = value
try:
MASK = h5file['mask'].get('mask')
gm = h5unwCor.create_group('mask')
dset = gm.create_dataset('mask', data=MASK, compression='gzip')
except:
pass
h5unwCor.close()
h5file.close()
h5curl.close()
#################### Bonding Points (Spatial Continuity) ####################
elif method == 'bonding_point':
print 'Phase unwrapping error correction using Bonding Points / Spatial Continuity'
##### Read Bridge Points Info
try:
x
y
if len(x) != len(y) or np.mod(len(x), 2) != 0:
print 'Wrong number of bridge points input: ' + str(
len(x)) + ' for x, ' + str(len(y)) + ' for y'
usage()
sys.exit(1)
except:
print 'Error in reading bridge points info!'
usage()
sys.exit(1)
for i in range(0, len(x)):
if Mask[y[i], x[i]] == 0:
print '\nERROR: Connecting point (' + str(y[i]) + ',' + str(
x[i]) + ') is out of masked area! Select them again!\n'
sys.exit(1)
print 'Number of bonding point pairs: ' + str(len(x) / 2)
print 'Bonding points coordinates:\nx: ' + str(x) + '\ny: ' + str(y)
## Plot Connecting Pair of Points
if plot_bonding_points == 'yes':
point_yx = ''
line_yx = ''
n_bridge = len(x) / 2
for i in range(n_bridge):
pair_yx = str(y[2 * i]) + ',' + str(x[2 * i]) + ',' + str(
y[2 * i + 1]) + ',' + str(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
##### Ramp Info
ramp_mask = Mask == 1
print 'estimate phase ramp during the correction'
print 'ramp type: ' + ramp_type
if save_rampCor == 'yes':
outName_ramp = os.path.basename(outName).split(
ext)[0] + '_' + ramp_type + ext
########## PySAR ##########
if ext == '.h5':
##### Read
try:
h5file = h5py.File(File, 'r')
except:
print 'ERROR: Cannot open input file: ' + File
sys.exit(1)
k = h5file.keys()
if 'interferograms' in k:
k[0] = 'interferograms'
print 'Input file is ' + k[0]
else:
print 'Input file - ' + File + ' - is not interferograms.'
usage()
sys.exit(1)
igramList = sorted(h5file[k[0]].keys())
#### Write
h5out = h5py.File(outName, 'w')
gg = h5out.create_group(k[0])
print 'writing >>> ' + outName
if save_rampCor == 'yes':
h5out_ramp = h5py.File(outName_ramp, 'w')
gg_ramp = h5out_ramp.create_group(k[0])
print 'writing >>> ' + outName_ramp
##### Loop
print 'Number of interferograms: ' + str(len(igramList))
for igram in igramList:
print igram
data = h5file[k[0]][igram].get(igram)[:]
data_ramp, ramp = rm.remove_data_surface(
data, ramp_mask, ramp_type)
#ramp = data_ramp - data
data_rampCor = phase_bonding(data_ramp, Mask, x, y)
dataCor = data_rampCor - ramp
group = gg.create_group(igram)
dset = group.create_dataset(igram,
data=dataCor,
compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group.attrs[key] = value
if save_rampCor == 'yes':
group_ramp = gg_ramp.create_group(igram)
dset = group_ramp.create_dataset(igram,
data=data_rampCor,
compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group_ramp.attrs[key] = value
try:
mask = h5file['mask'].get('mask')
gm = h5out.create_group('mask')
dset = gm.create_dataset('mask',
data=mask[0:mask.shape[0],
0:mask.shape[1]],
compression='gzip')
except:
print 'no mask group found.'
h5file.close()
h5out.close()
if save_rampCor == 'yes':
h5out_ramp.close()
########## ROI_PAC ##########
elif ext == '.unw':
print 'Input file is ' + ext
a, data, atr = readfile.read_float32(File)
data_ramp, ramp = rm.remove_data_surface(data, ramp_mask,
ramp_type)
#ramp = data_ramp - data
data_rampCor = phase_bonding(data_ramp, Mask, x, y)
dataCor = data_rampCor - ramp
writefile.write(dataCor, atr, outName)
if save_rampCor == 'yes':
writefile.write(data_rampCor, atr, outName_ramp)
else:
print 'Un-supported file type: ' + ext
usage()
sys.exit(1)
def main(argv):
method = 'triangular_consistency' ## or 'bonding_point'
ramp_type = 'plane'
save_rampCor = 'yes'
plot_bonding_points = 'yes'
##### Check Inputs
if len(sys.argv)>2:
try: opts, args = getopt.getopt(argv,'h:f:m:x:y:o:t:',['ramp=','no-ramp-save'])
except getopt.GetoptError: print 'Error while getting args'; Usage(); sys.exit(1)
for opt,arg in opts:
if opt in ['-h','--help']: Usage(); sys.exit()
elif opt in '-f': File = arg
elif opt in '-m': maskFile = arg
elif opt in '-o': outName = arg
elif opt in '-x': x = [int(i) for i in arg.split(',')]; method = 'bonding_point'
elif opt in '-y': y = [int(i) for i in arg.split(',')]; method = 'bonding_point'
elif opt in '-t': templateFile = arg
elif opt in '--ramp' : ramp_type = arg.lower()
elif opt in '--no-ramp-save' : save_rampCor = 'no'
elif len(sys.argv)==2:
if argv[0] in ['-h','--help']: Usage(); sys.exit()
elif os.path.isfile(argv[0]): File = argv[0]; maskFile = argv[1]
else: print 'Input file does not existed: '+argv[0]; sys.exit(1)
else: Usage(); sys.exit(1)
##### Check template file
try:
templateFile
templateContents = readfile.read_template(templateFile)
except: pass
try:
yx = [int(i) for i in templateContents['pysar.unwrapError.yx'].split(',')]
x = yx[1::2]
y = yx[0::2]
method = 'bonding_point'
except: pass
##### Read Mask File
## Priority:
## Input mask file > pysar.mask.file > existed Modified_Mask.h5 > existed Mask.h5
try: maskFile
except:
try: maskFile = templateContents['pysar.mask.file']
except:
if os.path.isfile('Modified_Mask.h5'): maskFile = 'Modified_Mask.h5'
elif os.path.isfile('Mask.h5'): maskFile = 'Mask.h5'
else: print 'No mask found!'; sys.exit(1)
try: Mask,Matr = readfile.read(maskFile); print 'mask: '+maskFile
except: print 'Can not open mask file: '+maskFile; sys.exit(1)
##### Output file name
ext = os.path.splitext(File)[1]
try: outName
except: outName = File.split('.')[0]+'_unwCor'+ext
print '\n**************** Unwrapping Error Correction ******************'
#################### Triangular Consistency (Phase Closure) ####################
if method == 'triangular_consistency':
print 'Phase unwrapping error correction using Triangular Consistency / Phase Closure'
h5file=h5py.File(File)
ifgramList = h5file['interferograms'].keys()
sx = int(h5file['interferograms'][ifgramList[0]].attrs['WIDTH'])
sy = int(h5file['interferograms'][ifgramList[0]].attrs['FILE_LENGTH'])
curls,Triangles,C=ut.get_triangles(h5file)
A,B = ut.design_matrix(h5file)
ligram,lv=np.shape(B)
lcurls=np.shape(curls)[0]
print 'Number of all triangles: '+ str(lcurls)
print 'Number of interferograms: '+ str(ligram)
#print curls
curlfile='curls.h5'
if not os.path.isfile(curlfile):
ut.generate_curls(curlfile,h5file,Triangles,curls)
thr=0.50
curls=np.array(curls); n1=curls[:,0]; n2=curls[:,1]; n3=curls[:,2]
numPixels=sy*sx
print 'reading interferograms...'
data = np.zeros((ligram,numPixels),np.float32)
for ni in range(ligram):
dset=h5file['interferograms'][ifgramList[ni]].get(ifgramList[ni])
d = dset[0:dset.shape[0],0:dset.shape[1]]
data[ni] = d.flatten(1)
print np.shape(data)
print 'reading curls ...'
h5curl=h5py.File(curlfile)
curlList=h5curl['interferograms'].keys()
curlData = np.zeros((lcurls,numPixels),np.float32)
for ni in range(lcurls):
dset=h5curl['interferograms'][curlList[ni]].get(curlList[ni])
d = dset[0:dset.shape[0],0:dset.shape[1]]
curlData[ni] = d.flatten(1)
pi=np.pi
EstUnwrap=np.zeros((ligram,numPixels),np.float32)
#try:
# maskFile=argv[1]
# h5Mask=h5py.File(maskFile)
# dset = h5Mask['mask'].get('mask')
# Mask=dset[0:dset.shape[0],0:dset.shape[1]]
#except:
# dset = h5file['mask'].get('mask')
# Mask=dset[0:dset.shape[0],0:dset.shape[1]]
Mask=Mask.flatten(1)
from scipy.linalg import pinv as pinv
for ni in range(numPixels):
#dU = np.zeros([ligram,1])
#print np.shape(dU)
#print np.shape(data[:,ni])
if Mask[ni]==1:
dU = data[:,ni]
#nan_ndx = dataPoint == 0.
unwCurl = np.array(curlData[:,ni])
#print unwCurl
ind = np.abs(unwCurl)>=thr; N1 =n1[ind]; N2 =n2[ind]; N3 =n3[ind]
indC = np.abs(unwCurl)< thr; Nc1=n1[indC]; Nc2=n2[indC]; Nc3=n3[indC]
N =np.hstack([N1, N2, N3]); UniN =np.unique(N)
Nc=np.hstack([Nc1,Nc2,Nc3]); UniNc=np.unique(Nc)
inter=list(set(UniNc) & set(UniN)) # intersetion
UniNc= list(UniNc)
for x in inter:
UniNc.remove(x)
D=np.zeros([len(UniNc),ligram])
for i in range(len(UniNc)):
D[i,UniNc[i]]=1
AAA=np.vstack([-2*pi*C,D])
#AAA1=np.hstack([AAA,np.zeros([AAA.shape[0],lv])])
#AAA2=np.hstack([-2*pi*np.eye(ligram),B])
#AAAA=np.vstack([AAA1,AAA2])
AAAA=np.vstack([AAA,0.25*np.eye(ligram)])
#print '************************'
#print np.linalg.matrix_rank(C)
#print np.linalg.matrix_rank(AAA)
#print np.linalg.matrix_rank(AAAA)
#print '************************'
#LLL=list(np.dot(C,dU)) + list(np.zeros(np.shape(UniNc)[0]))# + list(dU)
#ind=np.isnan(AAA)
#M1=pinv(AAA)
#M=np.dot(M1,LLL)
#EstUnwrap[:,ni]=np.round(M[0:ligram])*2.0*np.pi
##########
# with Tikhonov regularization:
AAAA=np.vstack([AAA,0.25*np.eye(ligram)])
LLL=list(np.dot(C,dU)) + list(np.zeros(np.shape(UniNc)[0])) + list(np.zeros(ligram))
ind=np.isnan(AAAA)
M1=pinv(AAAA)
M=np.dot(M1,LLL)
EstUnwrap[:,ni]=np.round(M[0:ligram])*2.0*np.pi
#print M[0:ligram]
#print np.round(M[0:ligram])
else:
EstUnwrap[:,ni]=np.zeros([ligram])
if not np.remainder(ni,10000): print 'Processing point: %7d of %7d ' % (ni,numPixels)
##### Output
dataCor = data+EstUnwrap
unwCorFile=File.replace('.h5','')+'_unwCor.h5'; print 'writing >>> '+unwCorFile
h5unwCor=h5py.File(unwCorFile,'w')
gg = h5unwCor.create_group('interferograms')
for i in range(ligram):
group = gg.create_group(ifgramList[i])
dset = group.create_dataset(ifgramList[i], data=np.reshape(dataCor[i,:],[sx,sy]).T, compression='gzip')
for key, value in h5file['interferograms'][ifgramList[i]].attrs.iteritems():
group.attrs[key] = value
try:
MASK=h5file['mask'].get('mask')
gm = h5unwCor.create_group('mask')
dset = gm.create_dataset('mask', data=MASK, compression='gzip')
except: pass
h5unwCor.close()
h5file.close()
h5curl.close()
#################### Bonding Points (Spatial Continuity) ####################
elif method == 'bonding_point':
print 'Phase unwrapping error correction using Bonding Points / Spatial Continuity'
##### Read Bridge Points Info
try:
x
y
if len(x) != len(y) or np.mod(len(x),2) != 0:
print 'Wrong number of bridge points input: '+str(len(x))+' for x, '+str(len(y))+' for y'
Usage(); sys.exit(1)
except: print 'Error in reading bridge points info!'; Usage(); sys.exit(1)
for i in range(0,len(x)):
if Mask[y[i],x[i]] == 0:
print '\nERROR: Connecting point ('+str(y[i])+','+str(x[i])+') is out of masked area! Select them again!\n'
sys.exit(1)
print 'Number of bonding point pairs: '+str(len(x)/2)
print 'Bonding points coordinates:\nx: '+str(x)+'\ny: '+str(y)
## Plot Connecting Pair of Points
if plot_bonding_points == 'yes':
point_yx = ''
line_yx = ''
n_bridge = len(x)/2
for i in range(n_bridge):
pair_yx = str(y[2*i])+','+str(x[2*i])+','+str(y[2*i+1])+','+str(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
##### Ramp Info
ramp_mask = Mask==1
print 'estimate phase ramp during the correction'
print 'ramp type: '+ramp_type
if save_rampCor == 'yes':
outName_ramp = os.path.basename(outName).split(ext)[0]+'_'+ramp_type+ext
########## PySAR ##########
if ext == '.h5':
##### Read
try: h5file=h5py.File(File,'r')
except: print 'ERROR: Cannot open input file: '+File; sys.exit(1)
k=h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'; print 'Input file is '+k[0]
else: print 'Input file - '+File+' - is not interferograms.'; Usage(); sys.exit(1)
igramList = h5file[k[0]].keys()
igramList = sorted(igramList)
#### Write
h5out = h5py.File(outName,'w')
gg = h5out.create_group(k[0])
print 'writing >>> '+outName
if save_rampCor == 'yes':
h5out_ramp = h5py.File(outName_ramp,'w')
gg_ramp = h5out_ramp.create_group(k[0])
print 'writing >>> '+outName_ramp
##### Loop
print 'Number of interferograms: '+str(len(igramList))
for igram in igramList:
print igram
data = h5file[k[0]][igram].get(igram)[:]
data_ramp,ramp = rm.remove_data_surface(data,ramp_mask,ramp_type)
#ramp = data_ramp - data
data_rampCor = phase_bonding(data_ramp,Mask,x,y)
dataCor = data_rampCor - ramp
group = gg.create_group(igram)
dset = group.create_dataset(igram, data=dataCor, compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group.attrs[key]=value
if save_rampCor == 'yes':
group_ramp = gg_ramp.create_group(igram)
dset = group_ramp.create_dataset(igram, data=data_rampCor, compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group_ramp.attrs[key]=value
try:
mask = h5file['mask'].get('mask');
gm = h5out.create_group('mask')
dset = gm.create_dataset('mask', data=mask[0:mask.shape[0],0:mask.shape[1]], compression='gzip')
except: print 'no mask group found.'
h5file.close()
h5out.close()
if save_rampCor == 'yes':
h5out_ramp.close()
########## ROI_PAC ##########
elif ext == '.unw':
print 'Input file is '+ext
a,data,atr = readfile.read_float32(File);
data_ramp,ramp = rm.remove_data_surface(data,ramp_mask,ramp_type)
#ramp = data_ramp - data
data_rampCor = phase_bonding(data_ramp,Mask,x,y)
dataCor = data_rampCor - ramp
writefile.write(dataCor, atr, outName)
if save_rampCor == 'yes':
writefile.write(data_rampCor,atr,outName_ramp)
else: print 'Un-supported file type: '+ext; Usage(); sys.exit(1)