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): 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 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']) 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!' ) 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.iteritems(): group.attrs[key] = value prog_bar.update(i + 1) prog_bar.close() h5unwCor.close() h5.close() return ifgram_cor_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) 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)