Esempio n. 1
0
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!"
Esempio n. 2
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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!"
Esempio n. 3
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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()
Esempio n. 4
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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
Esempio n. 5
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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()