Python tomopy.recon函数代码示例

def reconstruct(h5fname, sino, rot_center, binning, algorithm='gridrec'):

    sample_detector_distance = 8        # Propagation distance of the wavefront in cm
    detector_pixel_size_x = 2.247e-4    # Detector pixel size in cm (5x: 1.17e-4, 2X: 2.93e-4)
    monochromator_energy = 24.9         # Energy of incident wave in keV
    alpha = 1e-02                       # Phase retrieval coeff.
    zinger_level = 800                  # Zinger level for projections
    zinger_level_w = 1000               # Zinger level for white

    # Read APS 32-BM raw data.
    proj, flat, dark, theta = dxchange.read_aps_32id(h5fname, sino=sino)
        
    # zinger_removal
    # proj = tomopy.misc.corr.remove_outlier(proj, zinger_level, size=15, axis=0)
    # flat = tomopy.misc.corr.remove_outlier(flat, zinger_level_w, size=15, axis=0)

    # Flat-field correction of raw data.
    ##data = tomopy.normalize(proj, flat, dark, cutoff=0.8)
    data = tomopy.normalize(proj, flat, dark)

    # remove stripes
    data = tomopy.remove_stripe_fw(data,level=7,wname='sym16',sigma=1,pad=True)

    # data = tomopy.remove_stripe_ti(data, alpha=1.5)
    # data = tomopy.remove_stripe_sf(data, size=150)

    # phase retrieval
    #data = tomopy.prep.phase.retrieve_phase(data,pixel_size=detector_pixel_size_x,dist=sample_detector_distance,energy=monochromator_energy,alpha=alpha,pad=True)

    print("Raw data: ", h5fname)
    print("Center: ", rot_center)

    data = tomopy.minus_log(data)

    data = tomopy.remove_nan(data, val=0.0)
    data = tomopy.remove_neg(data, val=0.00)
    data[np.where(data == np.inf)] = 0.00

    rot_center = rot_center/np.power(2, float(binning))
    data = tomopy.downsample(data, level=binning) 
    data = tomopy.downsample(data, level=binning, axis=1)

    # Reconstruct object.
    if algorithm == 'sirtfbp':
        rec = rec_sirtfbp(data, theta, rot_center)
    elif algorithm == 'astrasirt':
        extra_options ={'MinConstraint':0}
        options = {'proj_type':'cuda', 'method':'SIRT_CUDA', 'num_iter':200, 'extra_options':extra_options}
        rec = tomopy.recon(data, theta, center=rot_center, algorithm=tomopy.astra, options=options)
    else:
        rec = tomopy.recon(data, theta, center=rot_center, algorithm=algorithm, filter_name='parzen')
        
    print("Algorithm: ", algorithm)

    # Mask each reconstructed slice with a circle.
    rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)
    
    return rec

def reconstruct(h5fname, sino, rot_center, binning, algorithm='gridrec'):

    sample_detector_distance = 30       # Propagation distance of the wavefront in cm
    detector_pixel_size_x = 1.17e-4     # Detector pixel size in cm (5x: 1.17e-4, 2X: 2.93e-4)
    monochromator_energy = 25.74        # Energy of incident wave in keV
    alpha = 1e-02                       # Phase retrieval coeff.
    zinger_level = 1000                 # Zinger level for projections
    zinger_level_w = 1000               # Zinger level for white

    miss_angles = [141,226]

    # Read APS 32-BM raw data.
    proj, flat, dark, theta = dxchange.read_aps_32id(h5fname, sino=sino)
        

    print (theta)
    # Manage the missing angles:
    #proj_size = np.shape(proj)
    #theta = np.linspace(0,180,proj_size[0])
    proj = np.concatenate((proj[0:miss_angles[0],:,:], proj[miss_angles[1]+1:-1,:,:]), axis=0)
    theta = np.concatenate((theta[0:miss_angles[0]], theta[miss_angles[1]+1:-1]))

    # zinger_removal
    #proj = tomopy.misc.corr.remove_outlier(proj, zinger_level, size=15, axis=0)
    #flat = tomopy.misc.corr.remove_outlier(flat, zinger_level_w, size=15, axis=0)

    # Flat-field correction of raw data.
    data = tomopy.normalize(proj, flat, dark, cutoff=0.8)

    # remove stripes
    data = tomopy.remove_stripe_fw(data,level=7,wname='sym16',sigma=1,pad=True)

    # phase retrieval
    # data = tomopy.prep.phase.retrieve_phase(data,pixel_size=detector_pixel_size_x,dist=sample_detector_distance,energy=monochromator_energy,alpha=alpha,pad=True)

    print("Raw data: ", h5fname)
    print("Center: ", rot_center)

    data = tomopy.minus_log(data)

    data = tomopy.remove_nan(data, val=0.0)
    data = tomopy.remove_neg(data, val=0.00)
    data[np.where(data == np.inf)] = 0.00

    rot_center = rot_center/np.power(2, float(binning))
    data = tomopy.downsample(data, level=binning) 
    data = tomopy.downsample(data, level=binning, axis=1)

    # Reconstruct object.
    if algorithm == 'sirtfbp':
        rec = rec_sirtfbp(data, theta, rot_center)
    else:
        rec = tomopy.recon(data, theta, center=rot_center, algorithm=algorithm, filter_name='parzen')
        
    print("Algorithm: ", algorithm)

    # Mask each reconstructed slice with a circle.
    ##rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)
    
    return rec

def reconstruct(proj_fn_template, layers, theta, console_out, outdir="recon"):
    """proj_fn_template: projection filename tempate
    layers: list of integers for layers to be reconstructed
    theta: sample rotation angle in radian
    """
    import tomopy
    proj = tomopy.read_tiff_stack(proj_fn_template % layers[0], layers, digit=5)
    proj = np.swapaxes(proj, 0,1)
    Y,X = proj[0].shape
    # reconstruct
    console_out.write("tomopy.reconstruct..."); console_out.flush()
    rec = tomopy.recon(
        proj,
        theta=theta, center=X/2.,
        algorithm='gridrec', emission=False,
        ncore = 1,
    )
    console_out.write("done\n"); console_out.flush()
    # output
    if not os.path.exists(outdir):
        os.makedirs(outdir)
    console_out.write("tomopy.write_tiff_stack..."); console_out.flush()
    tomopy.write_tiff_stack(
        rec, fname=os.path.join(outdir, 'recon'), axis=0, overwrite=True)
    console_out.write("done\n"); console_out.flush()
    return

def main(argv):
    try:
        opts, args = getopt.getopt(argv,"hc:s:",["core=","sino="])
    except getopt.GetoptError:
        print 'test.py -c <ncore> -s <nsino>'
        sys.exit(2)
    for opt, arg in opts:
        if opt == '-h':
            print 'test.py -c <ncore> -s <nsino>'
            sys.exit()
        elif opt in ("-c", "--core"):
            ncore = int(arg)
        elif opt in ("-s", "--sino"):
            nsino = int(arg)
    file_name = '/local/decarlo/data/proj_10.hdf'
    output_name = './recon/proj10_rec'
    sino_start = 200


    # Read HDF5 file.
    prj, flat, dark = tomopy.io.exchange.read_aps_32id(file_name, sino=(sino_start, sino_start+nsino))

    # Fix flats because sample did not move
    flat = np.full((flat.shape[0], flat.shape[1], flat.shape[2]), 1000)

    # Set angles
    theta  = tomopy.angles(prj.shape[0])

def recon_batch_singlenode(
        sinograms, theta, recon_series, center=None, algorithm=None):
    """reconstruct from a bunch of sinograms.
This is intended to be run on just one node.

    theta: sample rotation angle in radian
    """
    import tomopy, imars3d.io
    proj = [img.data for img in sinograms]
    proj = np.array(proj)
    proj = np.swapaxes(proj, 0, 1)
    Y,X = proj[0].shape
    if center is None:
        center = X/2.
    # reconstruct
    algorithm = algorithm or 'gridrec'
    # algorithm='fbp',
    # lgorithm='pml_hybrid',
    rec = tomopy.recon(
        proj,
        theta=theta, center=center,
        algorithm=algorithm, emission=False,
        ncore = 1,
    )
    # output
    for i, img in enumerate(recon_series):
        img.data = rec[i]
        img.save()
        continue
    return

def rec_try(h5fname, nsino, rot_center, center_search_width, algorithm, binning):
    zinger_level = 800                  # Zinger level for projections
    zinger_level_w = 1000               # Zinger level for white
    
    data_shape = get_dx_dims(h5fname, 'data')
    print(data_shape)
    ssino = int(data_shape[1] * nsino)

    center_range = (rot_center-center_search_width, rot_center+center_search_width, 0.5)
    #print(sino,ssino, center_range)
    #print(center_range[0], center_range[1], center_range[2])

    # Select sinogram range to reconstruct
    sino = None
        
    start = ssino
    end = start + 1
    sino = (start, end)

    # Read APS 32-BM raw data.
    proj, flat, dark, theta = dxchange.read_aps_32id(h5fname, sino=sino)

    # zinger_removal
    proj = tomopy.misc.corr.remove_outlier(proj, zinger_level, size=15, axis=0)
    flat = tomopy.misc.corr.remove_outlier(flat, zinger_level_w, size=15, axis=0)
        
    # Flat-field correction of raw data.
    data = tomopy.normalize(proj, flat, dark, cutoff=1.4)

    # remove stripes
    data = tomopy.remove_stripe_fw(data,level=7,wname='sym16',sigma=1,pad=True)


    print("Raw data: ", h5fname)
    print("Center: ", rot_center)

    data = tomopy.minus_log(data)

    stack = np.empty((len(np.arange(*center_range)), data_shape[0], data_shape[2]))

    index = 0
    for axis in np.arange(*center_range):
        stack[index] = data[:, 0, :]
        index = index + 1

    # Reconstruct the same slice with a range of centers.
    rec = tomopy.recon(stack, theta, center=np.arange(*center_range), sinogram_order=True, algorithm='gridrec', filter_name='parzen', nchunk=1)

    # Mask each reconstructed slice with a circle.
    rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)

    index = 0
    # Save images to a temporary folder.
    fname = os.path.dirname(h5fname) + '/' + 'try_rec/' + 'recon_' + os.path.splitext(os.path.basename(h5fname))[0]    
    for axis in np.arange(*center_range):
        rfname = fname + '_' + str('{0:.2f}'.format(axis) + '.tiff')
        dxchange.write_tiff(rec[index], fname=rfname, overwrite=True)
        index = index + 1

    print("Reconstructions: ", fname)

def recon(sinogram, theta, outpath, center=None):
    """Use tomopy to reconstruct from one sinogram
    
    theta: sample rotation angle in radian
    """
    import tomopy, imars3d.io
    proj = [sinogram.data]
    proj = np.array(proj)
    # tomopy.recon needs the shape to be
    # angles, Y, X
    proj = np.swapaxes(proj, 0, 1)
    Y,X = proj[0].shape
    if center is None:
        center = X/2.
    # reconstruct
    rec = tomopy.recon(
        proj,
        theta=theta, center=center,
        algorithm='gridrec',
        emission=False,
        ncore = 1,
    )
    rec = rec[0] # there is only one layer
    # output
    img = imars3d.io.ImageFile(path=outpath)
    img.data = rec
    img.save()
    return

def rec_test(file_name, sino_start, sino_end, astra_method, extra_options, num_iter=1):

    print '\n#### Processing '+ file_name
    sino_start = sino_start + 200
    sino_end = sino_start + 2
    print "Test reconstruction of slice [%d]" % sino_start
    # Read HDF5 file.
    prj, flat, dark = tomopy.io.exchange.read_aps_32id(file_name, sino=(sino_start, sino_end))

    # Manage the missing angles:
    theta  = tomopy.angles(prj.shape[0])
    prj = np.concatenate((prj[0:miss_angles[0],:,:], prj[miss_angles[1]+1:-1,:,:]), axis=0)
    theta = np.concatenate((theta[0:miss_angles[0]], theta[miss_angles[1]+1:-1]))

    # normalize the prj
    prj = tomopy.normalize(prj, flat, dark)
    
    # remove ring artefacts
    prjn = tomopy.remove_stripe_fw(prj)

    # reconstruct 
    rec = tomopy.recon(prj[:,::reduce_amount,::reduce_amount], theta, center=float(best_center)/reduce_amount, algorithm=tomopy.astra, options={'proj_type':proj_type,'method':astra_method,'extra_options':extra_options,'num_iter':num_iter}, emission=False)
        
    # Write data as stack of TIFs.
    tomopy.io.writer.write_tiff_stack(rec, fname=output_name)

    print "Slice saved as [%s_00000.tiff]" % output_name

def main():
    #****************************************************************************
    file_name = '/local/dataraid/databank/dataExchange/tmp/Australian_rank3.h5'
    output_name = '/local/dataraid/databank/dataExchange/tmp/rec/Australian_rank3'    
    sino_start = 290    
    sino_end = 294    

    # Read HDF5 file.
    exchange_rank = 3;
    prj, flat, dark = tomopy.io.exchange.read_aps_32id(file_name, exchange_rank, sino=(sino_start, sino_end))
    theta  = tomopy.angles(prj.shape[0])

    # normalize the data
    prj = tomopy.normalize(prj, flat, dark)

    best_center=1184
    print "Best Center: ", best_center
    calc_center = best_center
    #calc_center = tomopy.find_center(prj, theta, emission=False, ind=0, init=best_center, tol=0.8)
    print "Calculated Center:", calc_center
    
    # reconstruct 
    rec = tomopy.recon(prj, theta, center=calc_center, algorithm='gridrec', emission=False)
    #rec = tomopy.circ_mask(rec, axis=0)
    
    # Write data as stack of TIFs.
    tomopy.io.writer.write_tiff_stack(rec, fname=output_name)
    plt.gray()
    plt.axis('off')
    plt.imshow(rec[0])

def rec_test(file_name, sino_start, sino_end):

    print "\n#### Processing " + file_name
    sino_start = sino_start + 200
    sino_end = sino_start + 2
    print "Test reconstruction of slice [%d]" % sino_start
    # Read HDF5 file.
    prj, flat, dark = tomopy.io.exchange.read_aps_32id(file_name, sino=(sino_start, sino_end))

    # Manage the missing angles:
    theta = tomopy.angles(prj.shape[0])
    prj = np.concatenate((prj[0 : miss_angles[0], :, :], prj[miss_angles[1] + 1 : -1, :, :]), axis=0)
    theta = np.concatenate((theta[0 : miss_angles[0]], theta[miss_angles[1] + 1 : -1]))

    # normalize the prj
    prj = tomopy.normalize(prj, flat, dark)

    # reconstruct
    rec = tomopy.recon(prj, theta, center=best_center, algorithm="gridrec", emission=False)

    # Write data as stack of TIFs.
    tomopy.io.writer.write_tiff_stack(rec, fname=output_name)

    print "Slice saved as [%s_00000.tiff]" % output_name
    # show the reconstructed slice
    pl.gray()
    pl.axis("off")
    pl.imshow(rec[0])

def main(arg):

    parser = argparse.ArgumentParser()
    parser.add_argument("top", help="top directory where the tiff images are located: /data/")
    parser.add_argument("start", nargs='?', const=1, type=int, default=1, help="index of the first image: 1000 (default 1)")

    args = parser.parse_args()

    top = args.top
    index_start = int(args.start)

    template = os.listdir(top)[0]

    nfile = len(fnmatch.filter(os.listdir(top), '*.tif'))
    index_end = index_start + nfile
    ind_tomo = range(index_start, index_end)
    
    fname = top + template

    print (nfile, index_start, index_end, fname)


    # Select the sinogram range to reconstruct.
    start = 0
    end = 512
    sino=(start, end)

    # Read the tiff raw data.
    ndata = dxchange.read_tiff_stack(fname, ind=ind_tomo, slc=(sino, None))

    print(ndata.shape)
    binning = 8
    ndata = tomopy.downsample(ndata, level=binning, axis=1)
    print(ndata.shape)
    
    # Normalize to 1 using the air counts
    ndata = tomopy.normalize_bg(ndata, air=5)

    ## slider(ndata)

    # Set data collection angles as equally spaced between 0-180 degrees.
    theta = tomopy.angles(ndata.shape[0])
   
    rot_center = 960
    print("Center of rotation: ", rot_center)

    ndata = tomopy.minus_log(ndata)

    # Reconstruct object using Gridrec algorithm.
    rec = tomopy.recon(ndata, theta, center=rot_center, algorithm='gridrec')

    # Mask each reconstructed slice with a circle.
    rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)

    # Write data as stack of TIFs.
    dxchange.write_tiff_stack(rec, fname='/local/dataraid/mark/rec/recon')

def reconstruct(h5fname, sino, rot_center, binning, algorithm='gridrec'):

    sample_detector_distance = 8        # Propagation distance of the wavefront in cm
    detector_pixel_size_x = 2.247e-4    # Detector pixel size in cm (5x: 1.17e-4, 2X: 2.93e-4)
    monochromator_energy = 24.9         # Energy of incident wave in keV
    alpha = 1e-02                       # Phase retrieval coeff.
    zinger_level = 800                  # Zinger level for projections
    zinger_level_w = 1000               # Zinger level for white

    # h5fname_norm = '/local/data/2019-02/Burke/C47M_0015.h5'
    h5fname_norm = '/local/data/2019-02/Burke/kc78_Menardii_0003.h5'
    proj1, flat, dark, theta1 = dxchange.read_aps_32id(h5fname_norm, sino=sino)
    proj, dummy, dummy1, theta = dxchange.read_aps_32id(h5fname, sino=sino)
        
    # zinger_removal
    proj = tomopy.misc.corr.remove_outlier(proj, zinger_level, size=15, axis=0)
    flat = tomopy.misc.corr.remove_outlier(flat, zinger_level_w, size=15, axis=0)

    # Flat-field correction of raw data.
    ##data = tomopy.normalize(proj, flat, dark, cutoff=0.8)
    data = tomopy.normalize(proj, flat, dark)

    # remove stripes
    data = tomopy.remove_stripe_fw(data,level=7,wname='sym16',sigma=1,pad=True)

    #data = tomopy.remove_stripe_ti(data, alpha=1.5)
    data = tomopy.remove_stripe_sf(data, size=20)

    # phase retrieval
    #data = tomopy.prep.phase.retrieve_phase(data,pixel_size=detector_pixel_size_x,dist=sample_detector_distance,energy=monochromator_energy,alpha=alpha,pad=True)

    print("Raw data: ", h5fname)
    print("Center: ", rot_center)

    data = tomopy.minus_log(data)

    data = tomopy.remove_nan(data, val=0.0)
    data = tomopy.remove_neg(data, val=0.00)
    data[np.where(data == np.inf)] = 0.00

    rot_center = rot_center/np.power(2, float(binning))
    data = tomopy.downsample(data, level=binning) 
    data = tomopy.downsample(data, level=binning, axis=1)

    # Reconstruct object.
    if algorithm == 'sirtfbp':
        rec = rec_sirtfbp(data, theta, rot_center)
    else:
        rec = tomopy.recon(data, theta, center=rot_center, algorithm=algorithm, filter_name='parzen')
        
    print("Algorithm: ", algorithm)

    # Mask each reconstructed slice with a circle.
    rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)
    
    return rec

    def process_frames(self, data):
        self.sino = data[0]
        self.cors, angles, vol_shape, init = self.get_frame_params()

        if init:
            self.kwargs['init_recon'] = init

        recon = tomopy.recon(self.sino, np.deg2rad(angles),
                             center=self.cors[0], ncore=1, algorithm=self.alg,
                             **self.kwargs)
        return self._finalise_data(recon)

def run(phantom, algorithm, args, get_recon=False):

    global image_quality

    imgs = []
    bname = get_basepath(args, algorithm, phantom)
    oname = os.path.join(bname, "orig_{}_".format(algorithm))
    fname = os.path.join(bname, "stack_{}_".format(algorithm))
    dname = os.path.join(bname, "diff_{}_".format(algorithm))

    prj, ang, obj = generate(phantom, args.size, args.angles)

    # always add algorithm
    _kwargs = {"algorithm": algorithm}

    # assign number of cores
    _kwargs["ncore"] = ncores

    # don't assign "num_iter" if gridrec or fbp
    if algorithm not in ["fbp", "gridrec"]:
        _kwargs["num_iter"] = args.num_iter

    print("kwargs: {}".format(_kwargs))
    with timemory.util.auto_timer("[tomopy.recon(algorithm='{}')]".format(
                                  algorithm)):
        rec = tomopy.recon(prj, ang, **_kwargs)

    obj = normalize(obj)
    rec = normalize(rec)

    rec = trim_border(rec, rec.shape[0],
                      rec[0].shape[0] - obj[0].shape[0],
                      rec[0].shape[1] - obj[0].shape[1])

    label = "{} @ {}".format(algorithm.upper(), phantom.upper())

    quantify_difference(label, obj, rec)

    if "orig" not in image_quality:
        image_quality["orig"] = obj

    dif = obj - rec
    image_quality[algorithm] = dif

    if get_recon is True:
        return rec

    print("oname = {}, fname = {}, dname = {}".format(oname, fname, dname))
    imgs.extend(output_images(obj, oname, args.format, args.scale, args.ncol))
    imgs.extend(output_images(rec, fname, args.format, args.scale, args.ncol))
    imgs.extend(output_images(dif, dname, args.format, args.scale, args.ncol))

    return imgs

def reconstruct(h5fname, sino, rot_center, args, blocked_views=None):

    # Read APS 32-BM raw data.
    proj, flat, dark, theta = dxchange.read_aps_32id(h5fname, sino=sino)

    # Manage the missing angles:
    if blocked_views is not None:
        print("Blocked Views: ", blocked_views)
        proj = np.concatenate((proj[0:blocked_views[0], :, :],
                               proj[blocked_views[1]+1:-1, :, :]), axis=0)
        theta = np.concatenate((theta[0:blocked_views[0]],
                                theta[blocked_views[1]+1: -1]))

    # Flat-field correction of raw data.
    data = tomopy.normalize(proj, flat, dark, cutoff=1.4)

    # remove stripes
    data = tomopy.remove_stripe_fw(data, level=7, wname='sym16', sigma=1,
                                   pad=True)

    print("Raw data: ", h5fname)
    print("Center: ", rot_center)

    data = tomopy.minus_log(data)

    data = tomopy.remove_nan(data, val=0.0)
    data = tomopy.remove_neg(data, val=0.00)
    data[np.where(data == np.inf)] = 0.00

    algorithm = args.algorithm
    ncores = args.ncores
    nitr = args.num_iter

    # always add algorithm
    _kwargs = {"algorithm": algorithm}

    # assign number of cores
    _kwargs["ncore"] = ncores

    # don't assign "num_iter" if gridrec or fbp
    if algorithm not in ["fbp", "gridrec"]:
        _kwargs["num_iter"] = nitr

    # Reconstruct object.
    with timemory.util.auto_timer(
        "[tomopy.recon(algorithm='{}')]".format(algorithm)):
        rec = tomopy.recon(proj, theta, **_kwargs)

    # Mask each reconstructed slice with a circle.
    rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)

    return rec