def main(argv):
try:
file = argv[0]
except:
Usage()
sys.exit(1)
h5file = h5py.File(file)
curls, Triangles, C = ut.get_triangles(h5file)
try:
curlfile = argv[1]
except:
curlfile = "curls.h5"
if not os.path.isfile(curlfile):
ut.generate_curls(curlfile, h5file, Triangles, curls)
else:
print curlfile + " already exists!"
def main(argv):
try:
file = argv[0]
except:
Usage()
sys.exit(1)
h5file = h5py.File(file)
curls, Triangles, C = ut.get_triangles(h5file)
try:
curlfile = argv[1]
except:
curlfile = 'curls.h5'
if not os.path.isfile(curlfile):
ut.generate_curls(curlfile, h5file, Triangles, curls)
else:
print curlfile + " already exists!"
def main(argv):
try:
file = argv[0]
except:
Usage()
sys.exit(1)
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)
dataCor = data + EstUnwrap
unwCorFile = file.replace('.h5', '') + '_unwCor.h5'
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,:],[sy,sx]), compression='gzip')
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
MASK = h5file['mask'].get('mask')
gm = h5unwCor.create_group('mask')
dset = gm.create_dataset('mask', data=MASK, compression='gzip')
try:
Coh = h5file['meanCoherence'].get('meanCoherence')
gc = h5unwCor.create_group('meanCoherence')
dset = gc.create_dataset('meanCoherence', data=Coh, compression='gzip')
except:
print ''
h5unwCor.close()
h5file.close()
h5curl.close()
def unwrap_error_correction_phase_closure(ifgram_file, mask_file, ifgram_cor_file=None):
'''Correct unwrapping errors in network of interferograms using phase closure.
Inputs:
ifgram_file - string, name/path of interferograms file
mask_file - string, name/path of mask file to mask the pixels to be corrected
ifgram_cor_file - string, optional, name/path of corrected interferograms file
Output:
ifgram_cor_file
Example:
'unwrapIfgram_unwCor.h5' = unwrap_error_correction_phase_closure('Seeded_unwrapIfgram.h5','mask.h5')
'''
print('read mask from file: '+mask_file)
mask = readfile.read(mask_file)[0].flatten(1)
atr = readfile.read_attribute(ifgram_file)
length = int(atr['FILE_LENGTH'])
width = int(atr['WIDTH'])
k = atr['FILE_TYPE']
pixel_num = length*width
# Check reference pixel
try:
ref_y = int(atr['ref_y'])
ref_x = int(atr['ref_x'])
except:
sys.exit('ERROR: Can not find ref_y/x value, input file is not referenced in space!')
h5 = h5py.File(ifgram_file,'r')
ifgram_list = sorted(h5[k].keys())
ifgram_num = len(ifgram_list)
##### Prepare curls
curls, Triangles, C = ut.get_triangles(h5)
curl_num = np.shape(curls)[0]
print('Number of triangles: '+ str(curl_num))
curl_file='curls.h5'
if not os.path.isfile(curl_file):
print('writing >>> '+curl_file)
ut.generate_curls(curl_file, h5, Triangles, curls)
thr=0.50
curls = np.array(curls); n1=curls[:,0]; n2=curls[:,1]; n3=curls[:,2]
print('reading interferograms...')
print('Number of interferograms: '+ str(ifgram_num))
data = np.zeros((ifgram_num,pixel_num),np.float32)
prog_bar = ptime.progress_bar(maxValue=ifgram_num)
for ni in range(ifgram_num):
ifgram = ifgram_list[ni]
d = h5[k][ifgram].get(ifgram)[:].flatten(1)
data[ni,:] = d
prog_bar.update(ni+1)
prog_bar.close()
print('reading curls ...')
print('number of culrs: '+str(curl_num))
h5curl = h5py.File(curl_file,'r')
curl_list = sorted(h5curl[k].keys())
curl_data = np.zeros((curl_num, pixel_num),np.float32)
prog_bar = ptime.progress_bar(maxValue=curl_num)
for ni in range(curl_num):
d = h5curl[k][curl_list[ni]].get(curl_list[ni])[:].flatten(1)
curl_data[ni,:] = d.flatten(1)
prog_bar.update(ni+1)
prog_bar.close()
h5curl.close()
print('estimating unwrapping error pixel by pixel ...')
EstUnwrap = np.zeros((ifgram_num,pixel_num),np.float32)
prog_bar = ptime.progress_bar(maxValue=pixel_num)
for ni in range(pixel_num):
if mask[ni]==1:
dU = data[:,ni]
unwCurl = np.array(curl_data[:,ni])
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),ifgram_num])
for i in range(len(UniNc)):
D[i,UniNc[i]]=1
AAA = np.vstack([-2*np.pi*C,D])
AAAA = np.vstack([AAA,0.25*np.eye(ifgram_num)])
##########
# with Tikhonov regularization:
LLL = list(np.dot(C,dU)) + list(np.zeros(np.shape(UniNc)[0])) + list(np.zeros(ifgram_num))
ind = np.isnan(AAAA)
M1 = pinv(AAAA)
M = np.dot(M1,LLL)
EstUnwrap[:,ni] = np.round(M[0:ifgram_num])*2.0*np.pi
prog_bar.update(ni+1, suffix='%s/%d' % (ni,pixel_num))
prog_bar.close()
dataCor = data + EstUnwrap
##### Output
if not ifgram_cor_file:
ifgram_cor_file = os.path.splitext(ifgram_file)[0]+'_unwCor.h5'
print('writing >>> '+ifgram_cor_file)
h5unwCor = h5py.File(ifgram_cor_file,'w')
gg = h5unwCor.create_group(k)
prog_bar = ptime.progress_bar(maxValue=ifgram_num)
for i in range(ifgram_num):
ifgram = ifgram_list[i]
group = gg.create_group(ifgram)
dset = group.create_dataset(ifgram, data=np.reshape(dataCor[i,:],[width,length]).T, compression='gzip')
for key, value in h5[k][ifgram].attrs.items():
group.attrs[key] = value
prog_bar.update(i+1)
prog_bar.close()
h5unwCor.close()
h5.close()
return ifgram_cor_file
def main(argv):
try:
file = argv[0]
except:
Usage()
sys.exit(1)
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)
dataCor = data + EstUnwrap
unwCorFile = file.replace(".h5", "") + "_unwCor.h5"
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,:],[sy,sx]), compression='gzip')
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
MASK = h5file["mask"].get("mask")
gm = h5unwCor.create_group("mask")
dset = gm.create_dataset("mask", data=MASK, compression="gzip")
try:
Coh = h5file["meanCoherence"].get("meanCoherence")
gc = h5unwCor.create_group("meanCoherence")
dset = gc.create_dataset("meanCoherence", data=Coh, compression="gzip")
except:
print ""
h5unwCor.close()
h5file.close()
h5curl.close()
