def _process (lock, int_from, int_to, infile, outfile, outshape, outtype, skipflat, plan, norm_sx, norm_dx, flat_end, half_half, half_half_line, ext_fov, ext_fov_rot_right, ext_fov_overlap, ext_fov_normalize, ext_fov_average, ringrem, dynamic_ff, EFF, filtEFF, im_dark, logfilename): # Process the required subset of images: for i in range(int_from, int_to + 1): # Read input image: t0 = time() f_in = getHDF5(infile, 'r') if "/tomo" in f_in: dset = f_in['tomo'] else: dset = f_in['exchange/data'] im = tdf.read_sino(dset,i).astype(float32) f_in.close() t1 = time() # Perform pre-processing (flat fielding, extended FOV, ring removal): if not skipflat: if dynamic_ff: # Dynamic flat fielding with downsampling = 2: im = dynamic_flat_fielding(im, i, EFF, filtEFF, 2, im_dark, norm_sx, norm_dx) else: im = flat_fielding(im, i, plan, flat_end, half_half, half_half_line, norm_sx, norm_dx) if ext_fov: im = extfov_correction(im, ext_fov_rot_right, ext_fov_overlap, ext_fov_normalize, ext_fov_average) if not skipflat and not dynamic_ff: im = ring_correction (im, ringrem, flat_end, plan['skip_flat_after'], half_half, half_half_line, ext_fov) else: im = ring_correction (im, ringrem, False, False, half_half, half_half_line, ext_fov) t2 = time() # Save processed image to HDF5 file (atomic procedure - lock used): _write_data(lock, im, i, outfile, outshape, outtype, logfilename, t2 - t1, t1 - t0)
def _process(lock, int_from, int_to, infile, outfile, outshape, outtype, skipflat, plan, flat_end, half_half, half_half_line, dynamic_ff, EFF, filtEFF, im_dark, rotation, interp, border, rescale_factor, logfilename): # Process the required subset of images: for i in range(int_from, int_to + 1): # Read input image: t0 = time() f_in = getHDF5(infile, 'r') if "/tomo" in f_in: dset = f_in['tomo'] else: dset = f_in['exchange/data'] im = tdf.read_tomo(dset,i).astype(float32) f_in.close() t1 = time() # Perform pre-processing (flat fielding, extended FOV, ring removal): if not skipflat: if dynamic_ff: # Dynamic flat fielding with downsampling = 2: im = dynamic_flat_fielding(im, EFF, filtEFF, 2, im_dark) else: im = flat_fielding(im, i, plan, flat_end, half_half, half_half_line, norm_sx, norm_dx) t2 = time() # Rotate: rows, cols = im.shape #if (cols > rows): # angle = - arctan(2.0 / cols) * (rows / 2.0) / 2.0 #else: # angle = - arctan(2.0 / rows) * (cols / 2.0) / 2.0 #print(angle) M = cv2.getRotationMatrix2D((cols / 2, rows / 2), rotation, 1) if interp == 'nearest': interpflag = cv2.INTER_NEAREST elif interp == 'cubic': interpflag = cv2.INTER_CUBIC elif interp == 'lanczos': interpflag = cv2.INTER_LANCZOS4 else: interpflag = cv2.INTER_LINEAR if border == 'constant': borderflag = cv2.BORDER_CONSTANT else: borderflag = cv2.BORDER_REPLICATE im = cv2.warpAffine(im, M, (cols, rows), flags = interpflag, borderMode = borderflag) # Save processed image to HDF5 file (atomic procedure - lock used): _write_data(lock, im, i, outfile, outshape, outtype, rescale_factor, logfilename, t2 - t1, t1 - t0)
def _process(lock, int_from, int_to, infile, outfile, outshape, outtype,
skipflat, plan, norm_sx, norm_dx, flat_end, half_half,
half_half_line, ext_fov, ext_fov_rot_right, ext_fov_overlap,
ext_fov_normalize, ext_fov_average, ringrem, dynamic_ff, EFF,
filtEFF, im_dark, logfilename):
# Process the required subset of images:
for i in range(int_from, int_to + 1):
# Read input image:
t0 = time()
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
im = tdf.read_sino(dset, i).astype(float32)
f_in.close()
t1 = time()
# Perform pre-processing (flat fielding, extended FOV, ring removal):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im = dynamic_flat_fielding(im, i, EFF, filtEFF, 2, im_dark,
norm_sx, norm_dx)
else:
im = flat_fielding(im, i, plan, flat_end, half_half,
half_half_line, norm_sx, norm_dx)
if ext_fov:
im = extfov_correction(im, ext_fov_rot_right, ext_fov_overlap,
ext_fov_normalize, ext_fov_average)
if not skipflat and not dynamic_ff:
im = ring_correction(im, ringrem, flat_end,
plan['skip_flat_after'], half_half,
half_half_line, ext_fov)
else:
im = ring_correction(im, ringrem, False, False, half_half,
half_half_line, ext_fov)
t2 = time()
# Save processed image to HDF5 file (atomic procedure - lock used):
_write_data(lock, im, i, outfile, outshape, outtype, logfilename,
t2 - t1, t1 - t0)
def _process(lock, int_from, int_to, infile, outfile, outshape, outtype,
skipflat, plan, flat_end, half_half, half_half_line, dynamic_ff,
EFF, filtEFF, im_dark, rotation, interp, border, rescale_factor,
logfilename):
# Process the required subset of images:
for i in range(int_from, int_to + 1):
# Read input image:
t0 = time()
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
im = tdf.read_tomo(dset, i).astype(float32)
f_in.close()
t1 = time()
# Perform pre-processing (flat fielding, extended FOV, ring removal):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im = dynamic_flat_fielding(im, EFF, filtEFF, 2, im_dark)
else:
im = flat_fielding(im, i, plan, flat_end, half_half,
half_half_line, norm_sx, norm_dx)
t2 = time()
# Rotate:
rows, cols = im.shape
#if (cols > rows):
# angle = - arctan(2.0 / cols) * (rows / 2.0) / 2.0
#else:
# angle = - arctan(2.0 / rows) * (cols / 2.0) / 2.0
#print(angle)
M = cv2.getRotationMatrix2D((cols / 2, rows / 2), rotation, 1)
if interp == 'nearest':
interpflag = cv2.INTER_NEAREST
elif interp == 'cubic':
interpflag = cv2.INTER_CUBIC
elif interp == 'lanczos':
interpflag = cv2.INTER_LANCZOS4
else:
interpflag = cv2.INTER_LINEAR
if border == 'constant':
borderflag = cv2.BORDER_CONSTANT
else:
borderflag = cv2.BORDER_REPLICATE
im = cv2.warpAffine(im,
M, (cols, rows),
flags=interpflag,
borderMode=borderflag)
# Save processed image to HDF5 file (atomic procedure - lock used):
_write_data(lock, im, i, outfile, outshape, outtype, rescale_factor,
logfilename, t2 - t1, t1 - t0)
def process(sino_idx, num_sinos, infile, outfile, preprocessing_required, corr_plan, skipflat, norm_sx, norm_dx, flat_end, half_half,
half_half_line, ext_fov, ext_fov_rot_right, ext_fov_overlap, ext_fov_normalize, ext_fov_average,
ringrem, phaseretrieval_required, phrtmethod, phrt_param1,
phrt_param2, energy, distance, pixsize, phrtpad, approx_win, angles, angles_projfrom, angles_projto,
offset, logtransform, recpar, circle, scale, pad, method, rolling, roll_shift,
zerone_mode, dset_min, dset_max, decim_factor, downsc_factor, corr_offset, postprocess_required,
polarfilt_opt, convert_opt, crop_opt, dynamic_ff, EFF, filtEFF, im_dark, nr_threads, logfilename, tmppath):
"""To do...
"""
# Perform reconstruction (on-the-fly preprocessing and phase retrieval, if
# required):
if (phaseretrieval_required):
# In this case a bunch of sinograms is loaded into memory:
#
# Load the temporary data structure reading the input TDF file.
# To know the right dimension the first sinogram is pre-processed.
#
# Open the TDF file and get the dataset:
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
# Downscaling and decimation factors considered when determining the
# approximation window:
zrange = arange(sino_idx - approx_win * downsc_factor / 2, sino_idx + approx_win * downsc_factor / 2, downsc_factor)
zrange = zrange[(zrange >= 0)]
zrange = zrange[(zrange < num_sinos)]
approx_win = zrange.shape[0]
# Approximation window cannot be odd:
if (approx_win % 2 == 1):
approx_win = approx_win - 1
zrange = zrange[0:approx_win]
# Read one sinogram to get the proper dimensions:
test_im = tdf.read_sino(dset, zrange[0]*downsc_factor).astype(float32)
# Apply projection removal (if required):
test_im = test_im[angles_projfrom:angles_projto, :]
# Apply decimation and downscaling (if required):
test_im = test_im[::decim_factor, ::downsc_factor]
# Perform the pre-processing of the first sinogram to get the right
# dimension:
if (preprocessing_required):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
#test_im = dynamic_flat_fielding(test_im, zrange[0] / downsc_factor, EFF, filtEFF, 2, im_dark, norm_sx, norm_dx)
test_im = dynamic_flat_fielding(test_im, zrange[0] , EFF, filtEFF, 2, im_dark, norm_sx, norm_dx)
else:
#test_im = flat_fielding(test_im, zrange[0] / downsc_factor, corr_plan, flat_end, half_half,
# half_half_line / decim_factor, norm_sx, norm_dx).astype(float32)
test_im = flat_fielding(test_im, zrange[0], corr_plan, flat_end, half_half,
half_half_line / decim_factor, norm_sx, norm_dx).astype(float32)
if ext_fov:
test_im = extfov_correction(test_im, ext_fov_rot_right, ext_fov_overlap / downsc_factor, ext_fov_normalize, ext_fov_average).astype(float32)
if not skipflat and not dynamic_ff:
test_im = ring_correction(test_im, ringrem, flat_end, corr_plan['skip_flat_after'], half_half,
half_half_line / decim_factor, ext_fov).astype(float32)
else:
test_im = ring_correction(test_im, ringrem, False, False, half_half,
half_half_line / decim_factor, ext_fov).astype(float32)
# Now we can allocate memory for the bunch of slices:
tmp_im = empty((approx_win, test_im.shape[0], test_im.shape[1]), dtype=float32)
tmp_im[0,:,:] = test_im
# Reading all the the sinos from TDF file and close:
for ct in range(1, approx_win):
# Read the sinogram:
test_im = tdf.read_sino(dset, zrange[ct]*downsc_factor).astype(float32)
# Apply projection removal (if required):
test_im = test_im[angles_projfrom:angles_projto, :]
# Apply decimation and downscaling (if required):
test_im = test_im[::decim_factor, ::downsc_factor]
# Perform the pre-processing for each sinogram of the bunch:
if (preprocessing_required):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
#test_im = dynamic_flat_fielding(test_im, zrange[ct] / downsc_factor, EFF, filtEFF, 2, im_dark, norm_sx, norm_dx)
test_im = dynamic_flat_fielding(test_im, zrange[ct], EFF, filtEFF, 2, im_dark, norm_sx, norm_dx)
else:
#test_im = flat_fielding(test_im, zrange[ct] / downsc_factor, corr_plan, flat_end, half_half,
# half_half_line / decim_factor, norm_sx, norm_dx).astype(float32)
test_im = flat_fielding(test_im, zrange[ct], corr_plan, flat_end, half_half,
half_half_line / decim_factor, norm_sx, norm_dx).astype(float32)
if ext_fov:
test_im = extfov_correction(test_im, ext_fov_rot_right, ext_fov_overlap / downsc_factor, ext_fov_normalize, ext_fov_average).astype(float32)
if not skipflat and not dynamic_ff:
test_im = ring_correction(test_im, ringrem, flat_end, corr_plan['skip_flat_after'], half_half,
half_half_line / decim_factor, ext_fov).astype(float32)
else:
test_im = ring_correction(test_im, ringrem, False, False, half_half,
half_half_line / decim_factor, ext_fov).astype(float32)
tmp_im[ct,:,:] = test_im
f_in.close()
# Now everything has to refer to a downscaled dataset:
sino_idx = ((zrange == sino_idx).nonzero())
#
# Perform phase retrieval:
#
# Prepare the plan:
if (phrtmethod == 0):
# Paganin's:
phrtplan = tiehom_plan(tmp_im[:,0,:], phrt_param1, phrt_param2, energy, distance, pixsize * downsc_factor, phrtpad)
else:
phrtplan = phrt_plan(tmp_im[:,0,:], energy, distance, pixsize * downsc_factor, phrt_param2, phrt_param1, phrtmethod, phrtpad)
#phrtplan = prepare_plan (tmp_im[:,0,:], beta, delta, energy, distance,
#pixsize*downsc_factor, padding=phrtpad)
# Process each projection (whose height depends on the size of the bunch):
for ct in range(0, tmp_im.shape[1]):
#tmp_im[:,ct,:] = phase_retrieval(tmp_im[:,ct,:], phrtplan).astype(float32)
if (phrtmethod == 0):
tmp_im[:,ct,:] = tiehom(tmp_im[:,ct,:], phrtplan).astype(float32)
else:
tmp_im[:,ct,:] = phrt(tmp_im[:,ct,:], phrtplan, phrtmethod).astype(float32)
# Extract the requested sinogram:
im = tmp_im[sino_idx[0],:,:].squeeze()
else:
# Read only one sinogram:
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
im = tdf.read_sino(dset,sino_idx * downsc_factor).astype(float32)
f_in.close()
# Apply projection removal (if required):
im = im[angles_projfrom:angles_projto, :]
# Apply decimation and downscaling (if required):
im = im[::decim_factor,::downsc_factor]
#sino_idx = sino_idx / downsc_factor # Downscaling for the index already applied
# Perform the preprocessing of the sinogram (if required):
if (preprocessing_required):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im = dynamic_flat_fielding(im, sino_idx, EFF, filtEFF, 2, im_dark, norm_sx, norm_dx)
else:
im = flat_fielding(im, sino_idx, corr_plan, flat_end, half_half, half_half_line / decim_factor,
norm_sx, norm_dx).astype(float32)
if ext_fov:
im = extfov_correction(im, ext_fov_rot_right, ext_fov_overlap / downsc_factor, ext_fov_normalize, ext_fov_average)
if not skipflat and not dynamic_ff:
im = ring_correction(im, ringrem, flat_end, corr_plan['skip_flat_after'], half_half,
half_half_line / decim_factor, ext_fov)
else:
im = ring_correction(im, ringrem, False, False, half_half,
half_half_line / decim_factor, ext_fov)
# Additional ring removal before reconstruction:
#im = boinhaibel(im, '11;')
#im = munchetal(im, '5;1.8')
#im = rivers(im, '13;')
#im = raven(im, '11;0.8')
#im = oimoen(im, '51;51')
# Actual reconstruction:
im = reconstruct(im, angles, offset / downsc_factor, logtransform, recpar, circle, scale, pad, method,
zerone_mode, dset_min, dset_max, corr_offset, rolling, roll_shift, tmppath).astype(float32)
# Apply post-processing (if required):
if postprocess_required:
im = polarfilter(im, polarfilt_opt)
im = croprescale(im, convert_opt, crop_opt)
else:
# Create the circle mask for fancy output:
if (circle == True):
siz = im.shape[1]
if siz % 2:
rang = arange(-siz / 2 + 1, siz / 2 + 1)
else:
rang = arange(-siz / 2,siz / 2)
x,y = meshgrid(rang,rang)
z = x ** 2 + y ** 2
a = (z < (siz / 2 - int(round(abs(offset) / downsc_factor))) ** 2)
im = im * a
# Write down reconstructed preview file (file name modified with metadata):
im = im.astype(float32)
outfile = outfile + '_' + str(im.shape[1]) + 'x' + str(im.shape[0]) + '_' + str(amin(im)) + '$' + str(amax(im))
im.tofile(outfile)
def process(sino_idx, num_sinos, infile, outpath, preprocessing_required, corr_plan, norm_sx, norm_dx, flat_end, half_half, half_half_line, ext_fov, ext_fov_rot_right, ext_fov_overlap, ext_fov_normalize, ext_fov_average, ringrem, phaseretrieval_required, phrtmethod, phrt_param1, phrt_param2, energy, distance, pixsize, phrtpad, approx_win, angles, offset, logtransform, param1, circle, scale, pad, method, zerone_mode, dset_min, dset_max, decim_factor, downsc_factor, corr_offset, postprocess_required, convert_opt, crop_opt, nr_threads, angles_from, angles_to, logfilename, lock, slice_prefix): """To do... """ slice_nr = sino_idx # Perform reconstruction (on-the-fly preprocessing and phase retrieval, if required): if (phaseretrieval_required): # In this case a bunch of sinograms is loaded into memory: # # Load the temporary data structure reading the input TDF file. # To know the right dimension the first sinogram is pre-processed. # # Open the TDF file and get the dataset: f_in = getHDF5(infile, 'r') if "/tomo" in f_in: dset = f_in['tomo'] else: dset = f_in['exchange/data'] # Downscaling and decimation factors considered when determining the approximation window: zrange = arange(sino_idx - approx_win*downsc_factor/2, sino_idx + approx_win*downsc_factor/2, downsc_factor) zrange = zrange[ (zrange >= 0) ] zrange = zrange[ (zrange < num_sinos) ] approx_win = zrange.shape[0] # Approximation window cannot be odd: if (approx_win % 2 == 1): approx_win = approx_win-1 zrange = zrange[0:approx_win] # Read one sinogram to get the proper dimensions: test_im = tdf.read_sino(dset, zrange[0]*downsc_factor).astype(float32) # Apply decimation and downscaling (if required): test_im = test_im[::decim_factor, ::downsc_factor] # Perform the pre-processing of the first sinogram to get the right dimension: if (preprocessing_required): test_im = flat_fielding (test_im, zrange[0], corr_plan, flat_end, half_half, half_half_line/decim_factor, norm_sx, norm_dx).astype(float32) if ext_fov: test_im = extfov_correction (test_im, ext_fov_rot_right, ext_fov_overlap/downsc_factor, ext_fov_normalize, ext_fov_average).astype(float32) test_im = ring_correction (test_im, ringrem, flat_end, corr_plan['skip_flat_after'], half_half, half_half_line/decim_factor, ext_fov).astype(float32) # Now we can allocate memory for the bunch of slices: tmp_im = empty((approx_win, test_im.shape[0], test_im.shape[1]), dtype=float32) tmp_im[0,:,:] = test_im # Reading all the the sinos from TDF file and close: for ct in range(1, approx_win): test_im = tdf.read_sino(dset, zrange[ct]*downsc_factor).astype(float32) test_im = test_im[::decim_factor, ::downsc_factor] # Perform the pre-processing for each sinogram of the bunch: if (preprocessing_required): test_im = flat_fielding (test_im, zrange[ct], corr_plan, flat_end, half_half, half_half_line/decim_factor, norm_sx, norm_dx).astype(float32) if ext_fov: test_im = extfov_correction (test_im, ext_fov_rot_right, ext_fov_overlap/downsc_factor, ext_fov_normalize, ext_fov_average).astype(float32) test_im = ring_correction (test_im, ringrem, flat_end, corr_plan['skip_flat_after'], half_half, half_half_line/decim_factor, ext_fov).astype(float32) tmp_im[ct,:,:] = test_im f_in.close() # Now everything has to refer to a downscaled dataset: sino_idx = ((zrange == sino_idx).nonzero()) # # Perform phase retrieval: # # Prepare the plan: if (phrtmethod == 0): # Paganin's: phrtplan = tiehom_plan (tmp_im[:,0,:], phrt_param1, phrt_param2, energy, distance, pixsize*downsc_factor, padding=phrtpad) else: phrtplan = phrt_plan (tmp_im[:,0,:], energy, distance, pixsize*downsc_factor, phrt_param2, phrt_param1, phrtmethod, padding=phrtpad) # Process each projection (whose height depends on the size of the bunch): for ct in range(0, tmp_im.shape[1]): if (phrtmethod == 0): tmp_im[:,ct,:] = tiehom(tmp_im[:,ct,:], phrtplan).astype(float32) else: tmp_im[:,ct,:] = phrt(tmp_im[:,ct,:], phrtplan, phrtmethod).astype(float32) # Extract the requested sinogram: im = tmp_im[sino_idx[0],:,:].squeeze() else: # Read only one sinogram: f_in = getHDF5(infile, 'r') if "/tomo" in f_in: dset = f_in['tomo'] else: dset = f_in['exchange/data'] im = tdf.read_sino(dset,sino_idx * downsc_factor).astype(float32) f_in.close() # Downscale and decimate the sinogram: im = im[::decim_factor,::downsc_factor] #sino_idx = sino_idx/downsc_factor # Perform the preprocessing of the sinogram (if required): if (preprocessing_required): im = flat_fielding (im, sino_idx, corr_plan, flat_end, half_half, half_half_line/decim_factor, norm_sx, norm_dx).astype(float32) if ext_fov: test_im = extfov_correction (test_im, ext_fov_rot_right, ext_fov_overlap/downsc_factor, ext_fov_normalize, ext_fov_average).astype(float32) im = ring_correction (im, ringrem, flat_end, corr_plan['skip_flat_after'], half_half, half_half_line/decim_factor, ext_fov) # Log infos: log = open(logfilename,"a") log.write(linesep + "\tPerforming reconstruction with multiple centers of rotation...") log.write(linesep + "\t--------------") log.close() # Split the computation into multiple processes: for num in range(nr_threads): start = ( (angles_to - angles_from + 1) / nr_threads)*num + angles_from if (num == nr_threads - 1): end = angles_to else: end = ( (angles_to - angles_from + 1) / nr_threads)*(num + 1) + angles_from - 1 Process(target=reconstruct, args=(im, angles, offset/downsc_factor, logtransform, param1, circle, scale, pad, method, zerone_mode, dset_min, dset_max, corr_offset, postprocess_required, convert_opt, crop_opt, start, end, outpath, slice_nr, downsc_factor, decim_factor, logfilename, lock, slice_prefix)).start()
def process(lock, int_from, int_to, num_sinos, infile, outpath,
preprocessing_required, skipflat, corr_plan, norm_sx, norm_dx,
flat_end, half_half, half_half_line, ext_fov, ext_fov_rot_right,
ext_fov_overlap, ext_fov_normalize, ext_fov_average, ringrem,
angles, angles_projfrom, angles_projto, offset, logtransform,
param1, circle, scale, pad, method, rolling, roll_shift,
zerone_mode, dset_min, dset_max, decim_factor, downsc_factor,
corr_offset, postprocess_required, polarfilt_opt, convert_opt,
crop_opt, dynamic_ff, EFF, filtEFF, im_dark, outprefix,
logfilename):
"""To do...
"""
# Process the required subset of images:
for i in range(int_from, int_to + 1):
# Perform reconstruction (on-the-fly preprocessing and phase retrieval, if
# required):
#if (phaseretrieval_required):
# # Load into memory a bunch of sinograms:
# t0 = time()
# # Open the TDF file for reading:
# f_in = getHDF5(infile, 'r')
# if "/tomo" in f_in:
# dset = f_in['tomo']
# else:
# dset = f_in['exchange/data']
# # Prepare the data structure according to the approximation window:
# tmp_im = numpy.empty((tdf.get_nr_projs(dset),tdf.get_det_size(dset),
# approx_win), dtype=float32)
# # Load the temporary data structure reading the input TDF file:
# # (It can be parallelized Open-MP style)
# ct = 0
# for j in range(i - approx_win/2, i + approx_win/2 + 1):
# if (j < 0):
# j = 0
# if (j >= num_sinos):
# j = num_sinos - 1
# a = tdf.read_sino(dset,j).astype(float32)
# tmp_im[:,:,ct] = a
# ct = ct + 1
# # Close the TDF file:
# f_in.close()
# t1 = time()
# # Perform the processing:
# if (preprocessing_required):
# ct = 0
# # (It can be parallelized Open-MP style)
# for j in range(i - approx_win/2, i + approx_win/2 + 1):
# if (j < 0):
# j = 0
# if (j >= num_sinos):
# j = num_sinos - 1
# tmp_im[:,:,ct] = flat_fielding (tmp_im[:,:,ct], j, corr_plan, flat_end,
# half_half, half_half_line, norm_sx, norm_dx).astype(float32)
# tmp_im[:,:,ct] = extfov_correction (tmp_im[:,:,ct], ext_fov,
# ext_fov_rot_right, ext_fov_overlap).astype(float32)
# tmp_im[:,:,ct] = ring_correction (tmp_im[:,:,ct], ringrem, flat_end,
# corr_plan['skip_flat_after'], half_half, half_half_line,
# ext_fov).astype(float32)
# ct = ct + 1
# # Perform phase retrieval:
# # (It can be parallelized Open-MP style)
# for ct in range(0, tmp_im.shape[0]):
# tmp_im[ct,:,:] = phase_retrieval(tmp_im[ct,:,:].T,
# phrt_plan).astype(float32).T
# ct = ct + 1
# # Extract the central processed sinogram:
# im = tmp_im[:,:,approx_win/2]
#else:
# Read only one sinogram:
t0 = time()
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
im = tdf.read_sino(dset, i * downsc_factor).astype(float32)
f_in.close()
t1 = time()
# Apply projection removal (if required):
im = im[angles_projfrom:angles_projto, :]
# Apply decimation and downscaling (if required):
im = im[::decim_factor, ::downsc_factor]
#i = i / downsc_factor
# Perform the preprocessing of the sinogram (if required):
if (preprocessing_required):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im = dynamic_flat_fielding(im, i, EFF, filtEFF, 2, im_dark,
norm_sx,
norm_dx).astype(float32)
else:
im = flat_fielding(im, i, corr_plan, flat_end, half_half,
half_half_line / decim_factor, norm_sx,
norm_dx).astype(float32)
if ext_fov:
im = extfov_correction(im, ext_fov_rot_right,
ext_fov_overlap / downsc_factor,
ext_fov_normalize, ext_fov_average)
if not skipflat and not dynamic_ff:
im = ring_correction(im, ringrem, flat_end,
corr_plan['skip_flat_after'], half_half,
half_half_line / decim_factor, ext_fov)
else:
im = ring_correction(im, ringrem, False, False, half_half,
half_half_line, ext_fov)
# Actual reconstruction:
im = reconstruct(im, angles, offset / downsc_factor, logtransform,
param1, circle, scale, pad, method, rolling,
roll_shift, zerone_mode, dset_min, dset_max,
decim_factor, downsc_factor,
corr_offset).astype(float32)
# Apply post-processing (if required):
if postprocess_required:
im = polarfilter(im, polarfilt_opt)
im = croprescale(im, convert_opt, crop_opt)
else:
# Create the circle mask for fancy output:
if (circle == True):
siz = im.shape[1]
if siz % 2:
rang = arange(-siz / 2 + 1, siz / 2 + 1)
else:
rang = arange(-siz / 2, siz / 2)
x, y = meshgrid(rang, rang)
z = x**2 + y**2
a = (z < (siz / 2 - abs(offset))**2)
im = im * a
# Write down reconstructed slice:
t2 = time()
fname = outpath + outprefix + '_' + str(i).zfill(4) + '.tif'
imsave(fname, im)
t3 = time()
# Write log (atomic procedure - lock used):
write_log(lock, fname, logfilename, t2 - t1, (t3 - t2) + (t1 - t0))
def process(lock, int_from, int_to, num_sinos, infile, outpath, preprocessing_required, corr_plan, norm_sx, norm_dx, flat_end, half_half, half_half_line, ext_fov, ext_fov_rot_right, ext_fov_overlap, ringrem, angles, offset, logtransform, param1, circle, scale, pad, method, zerone_mode, dset_min, dset_max, decim_factor, downsc_factor, corr_offset, postprocess_required, convert_opt, crop_opt, outprefix, logfilename): """To do... """ # Process the required subset of images: for i in range(int_from, int_to + 1): # Perform reconstruction (on-the-fly preprocessing and phase retrieval, if required): #if (phaseretrieval_required): # # Load into memory a bunch of sinograms: # t0 = time() # # Open the TDF file for reading: # f_in = getHDF5(infile, 'r') # if "/tomo" in f_in: # dset = f_in['tomo'] # else: # dset = f_in['exchange/data'] # # Prepare the data structure according to the approximation window: # tmp_im = numpy.empty((tdf.get_nr_projs(dset),tdf.get_det_size(dset), approx_win), dtype=float32) # # Load the temporary data structure reading the input TDF file: # # (It can be parallelized Open-MP style) # ct = 0 # for j in range(i - approx_win/2, i + approx_win/2 + 1): # if (j < 0): # j = 0 # if (j >= num_sinos): # j = num_sinos - 1 # a = tdf.read_sino(dset,j).astype(float32) # tmp_im[:,:,ct] = a # ct = ct + 1 # # Close the TDF file: # f_in.close() # t1 = time() # # Perform the processing: # if (preprocessing_required): # ct = 0 # # (It can be parallelized Open-MP style) # for j in range(i - approx_win/2, i + approx_win/2 + 1): # if (j < 0): # j = 0 # if (j >= num_sinos): # j = num_sinos - 1 # tmp_im[:,:,ct] = flat_fielding (tmp_im[:,:,ct], j, corr_plan, flat_end, half_half, half_half_line, norm_sx, norm_dx).astype(float32) # tmp_im[:,:,ct] = extfov_correction (tmp_im[:,:,ct], ext_fov, ext_fov_rot_right, ext_fov_overlap).astype(float32) # tmp_im[:,:,ct] = ring_correction (tmp_im[:,:,ct], ringrem, flat_end, corr_plan['skip_flat_after'], half_half, half_half_line, ext_fov).astype(float32) # ct = ct + 1 # # Perform phase retrieval: # # (It can be parallelized Open-MP style) # for ct in range(0, tmp_im.shape[0]): # tmp_im[ct,:,:] = phase_retrieval(tmp_im[ct,:,:].T, phrt_plan).astype(float32).T # ct = ct + 1 # # Extract the central processed sinogram: # im = tmp_im[:,:,approx_win/2] #else: # Read only one sinogram: t0 = time() f_in = getHDF5(infile, 'r') if "/tomo" in f_in: dset = f_in['tomo'] else: dset = f_in['exchange/data'] im = tdf.read_sino(dset,i).astype(float32) f_in.close() t1 = time() # Perform the preprocessing of the sinogram (if required): if (preprocessing_required): im = flat_fielding (im, i, corr_plan, flat_end, half_half, half_half_line, norm_sx, norm_dx).astype(float32) im = extfov_correction (im, ext_fov, ext_fov_rot_right, ext_fov_overlap) im = ring_correction (im, ringrem, flat_end, corr_plan['skip_flat_after'], half_half, half_half_line, ext_fov) # Actual reconstruction: im = reconstruct(im, angles, offset, logtransform, param1, circle, scale, pad, method, zerone_mode, dset_min, dset_max, decim_factor, downsc_factor, corr_offset).astype(float32) # Appy post-processing (if required): if postprocess_required: im = postprocess(im, convert_opt, crop_opt) else: # Create the circle mask for fancy output: if (circle == True): siz = im.shape[1] if siz % 2: rang = arange(-siz / 2 + 1, siz / 2 + 1) else: rang = arange(-siz / 2,siz / 2) x,y = meshgrid(rang,rang) z = x ** 2 + y ** 2 a = (z < (siz / 2 - abs(offset) ) ** 2) im = im * a # Write down reconstructed slice: t2 = time() fname = outpath + outprefix + '_' + str(i).zfill(4) + '.tif' imsave(fname, im) t3 = time() # Write log (atomic procedure - lock used): write_log(lock, fname, logfilename, t2 - t1, (t3 - t2) + (t1 - t0) )
def process(sino_idx, num_sinos, infile, outfile, preprocessing_required, corr_plan, norm_sx, norm_dx, flat_end, half_half,
half_half_line, ext_fov, ext_fov_rot_right, ext_fov_overlap, ringrem, phaseretrieval_required, beta, delta,
energy, distance, pixsize, phrtpad, approx_win, angles, offset, logtransform, param1, circle, scale, pad, method,
zerone_mode, dset_min, dset_max, decim_factor, downsc_factor, corr_offset, postprocess_required, convert_opt,
crop_opt, nr_threads, logfilename):
"""To do...
"""
# Perform reconstruction (on-the-fly preprocessing and phase retrieval, if required):
if (phaseretrieval_required):
# In this case a bunch of sinograms is loaded into memory:
#
# Load the temporary data structure reading the input TDF file.
# To know the right dimension the first sinogram is pre-processed.
#
# Open the TDF file and get the dataset:
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
# Downscaling and decimation factors considered when determining the approximation window:
zrange = arange(sino_idx - approx_win*downsc_factor/2, sino_idx + approx_win*downsc_factor/2, downsc_factor)
zrange = zrange[ (zrange >= 0) ]
zrange = zrange[ (zrange < num_sinos) ]
approx_win = zrange.shape[0]
# Approximation window cannot be odd:
if (approx_win % 2 == 1):
approx_win = approx_win-1
zrange = zrange[0:approx_win]
# Read one sinogram to get the proper dimensions:
test_im = tdf.read_sino(dset, zrange[0]).astype(float32)
test_im = test_im[::decim_factor, ::downsc_factor]
# Perform the pre-processing of the first sinogram to get the right dimension:
if (preprocessing_required):
test_im = flat_fielding (test_im, zrange[0]/downsc_factor, corr_plan, flat_end, half_half,
half_half_line/decim_factor, norm_sx, norm_dx).astype(float32)
test_im = extfov_correction (test_im, ext_fov, ext_fov_rot_right, ext_fov_overlap/downsc_factor).astype(float32)
test_im = ring_correction (test_im, ringrem, flat_end, corr_plan['skip_flat_after'], half_half,
half_half_line/decim_factor, ext_fov).astype(float32)
# Now we can allocate memory for the bunch of slices:
tmp_im = empty((approx_win, test_im.shape[0], test_im.shape[1]), dtype=float32)
tmp_im[0,:,:] = test_im
# Reading all the the sinos from TDF file and close:
for ct in range(1, approx_win):
test_im = tdf.read_sino(dset, zrange[ct]).astype(float32)
test_im = test_im[::decim_factor, ::downsc_factor]
# Perform the pre-processing for each sinogram of the bunch:
if (preprocessing_required):
test_im = flat_fielding (test_im, zrange[ct]/downsc_factor, corr_plan, flat_end, half_half,
half_half_line/decim_factor, norm_sx, norm_dx).astype(float32)
test_im = extfov_correction (test_im, ext_fov, ext_fov_rot_right, ext_fov_overlap/downsc_factor).astype(float32)
test_im = ring_correction (test_im, ringrem, flat_end, corr_plan['skip_flat_after'], half_half,
half_half_line/decim_factor, ext_fov).astype(float32)
tmp_im[ct,:,:] = test_im
f_in.close()
# Now everything has to refer to a downscaled dataset:
sino_idx = ((zrange == sino_idx).nonzero())
#
# Perform phase retrieval:
#
# Prepare the plan:
phrtplan = prepare_plan (tmp_im[:,0,:], beta, delta, energy, distance, pixsize*downsc_factor, padding=phrtpad)
# Process each projection (whose height depends on the size of the bunch):
for ct in range(0, tmp_im.shape[1]):
tmp_im[:,ct,:] = phase_retrieval(tmp_im[:,ct,:], phrtplan).astype(float32)
# Extract the requested sinogram:
im = tmp_im[sino_idx[0],:,:].squeeze()
else:
# Read only one sinogram:
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
im = tdf.read_sino(dset,sino_idx).astype(float32)
f_in.close()
# Downscale and decimate the sinogram:
im = im[::decim_factor,::downsc_factor]
sino_idx = sino_idx/downsc_factor
# Perform the preprocessing of the sinogram (if required):
if (preprocessing_required):
im = flat_fielding (im, sino_idx, corr_plan, flat_end, half_half, half_half_line/decim_factor,
norm_sx, norm_dx).astype(float32)
im = extfov_correction (im, ext_fov, ext_fov_rot_right, ext_fov_overlap)
#imsave('C:\\Temp\\StupidFolder\\sinoprimaringrem.tif', im.astype(float32))
im = ring_correction (im, ringrem, flat_end, corr_plan['skip_flat_after'], half_half,
half_half_line/decim_factor, ext_fov)
#imsave('C:\\Temp\\StupidFolder\\sinodoporingrem.tif', im.astype(float32))
# Actual reconstruction:
im = reconstruct(im, angles, offset/downsc_factor, logtransform, param1, circle, scale, pad, method,
zerone_mode, dset_min, dset_max, corr_offset).astype(float32)
# Apply post-processing (if required):
if postprocess_required:
im = postprocess(im, convert_opt, crop_opt)
else:
# Create the circle mask for fancy output:
if (circle == True):
siz = im.shape[1]
if siz % 2:
rang = arange(-siz / 2 + 1, siz / 2 + 1)
else:
rang = arange(-siz / 2,siz / 2)
x,y = meshgrid(rang,rang)
z = x ** 2 + y ** 2
a = (z < (siz / 2 - int(round(abs(offset)/downsc_factor)) ) ** 2)
im = im * a
# Write down reconstructed preview file (file name modified with metadata):
im = im.astype(float32)
outfile = outfile + '_' + str(im.shape[1]) + 'x' + str(im.shape[0]) + '_' + str( amin(im)) + '$' + str( amax(im) )
im.tofile(outfile)
def main(argv):
"""To do...
"""
# Get the zero-order index of the sinogram to pre-process:
idx = int(argv[0])
# Get paths:
infile = argv[1]
outfile = argv[2]
# Normalization parameters:
norm_sx = int(argv[3])
norm_dx = int(argv[4])
# Params for flat fielding with post flats/darks:
flat_end = True if argv[5] == "True" else False
half_half = True if argv[6] == "True" else False
half_half_line = int(argv[7])
# Flat fielding method (conventional or dynamic):
dynamic_ff = True if argv[8] == "True" else False
# Parameters for rotation:
rotation = float(argv[9])
interp = argv[10]
border = argv[11]
# Tmp path and log file:
tmppath = argv[12]
if not tmppath.endswith(sep): tmppath += sep
logfilename = argv[13]
# Open the HDF5 file:
f_in = getHDF5(infile, 'r')
try:
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
except:
log = open(logfilename, "a")
log.write(linesep + "\tError reading input dataset. Process will end.")
log.close()
exit()
num_proj = tdf.get_nr_projs(dset)
num_sinos = tdf.get_nr_sinos(dset)
# Check if the HDF5 makes sense:
if (num_sinos == 0):
log = open(logfilename, "a")
log.write(linesep + "\tNo projections found. Process will end.")
log.close()
exit()
# Get flat and darks from cache or from file:
skipflat = False
skipdark = False
if not dynamic_ff:
try:
corrplan = cache2plan(infile, tmppath)
except Exception as e:
#print "Error(s) when reading from cache"
corrplan = extract_flatdark(f_in, flat_end, logfilename)
if (isscalar(corrplan['im_flat'])
and isscalar(corrplan['im_flat_after'])):
skipflat = True
else:
plan2cache(corrplan, infile, tmppath)
else:
# Dynamic flat fielding:
if "/tomo" in f_in:
if "/flat" in f_in:
flat_dset = f_in['flat']
if "/dark" in f_in:
im_dark = _medianize(f_in['dark'])
else:
skipdark = True
else:
skipflat = True # Nothing to do in this case
else:
if "/exchange/data_white" in f_in:
flat_dset = f_in['/exchange/data_white']
if "/exchange/data_dark" in f_in:
im_dark = _medianize(f_in['/exchange/data_dark'])
else:
skipdark = True
else:
skipflat = True # Nothing to do in this case
# Prepare plan for dynamic flat fielding with 16 repetitions:
if not skipflat:
EFF, filtEFF = dff_prepare_plan(flat_dset, 16, im_dark)
# Read input image:
im = tdf.read_tomo(dset, idx).astype(float32)
f_in.close()
# Perform pre-processing (flat fielding, extended FOV, ring removal):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im = dynamic_flat_fielding(im, EFF, filtEFF, 2, im_dark)
else:
im = flat_fielding(im, idx, corrplan, flat_end, half_half,
half_half_line, norm_sx, norm_dx)
# Rotate:
rows, cols = im.shape
M = cv2.getRotationMatrix2D((cols / 2, rows / 2), rotation, 1)
if interp == 'nearest':
interpflag = cv2.INTER_NEAREST
elif interp == 'cubic':
interpflag = cv2.INTER_CUBIC
elif interp == 'lanczos':
interpflag = cv2.INTER_LANCZOS4
else:
interpflag = cv2.INTER_LINEAR
if border == 'constant':
borderflag = cv2.BORDER_CONSTANT
else:
borderflag = cv2.BORDER_REPLICATE
im = cv2.warpAffine(im,
M, (cols, rows),
flags=interpflag,
borderMode=borderflag)
# Write down reconstructed preview file (file name modified with metadata):
im = im.astype(float32)
outfile2 = outfile + '_' + str(im.shape[1]) + 'x' + str(
im.shape[0]) + '_' + str(nanmin(im)) + '$' + str(
nanmax(im)) + '_after.raw'
im.tofile(outfile2)
def _process(lock, int_from, int_to, num_sinos, infile_1, infile_2, infile_3,
outfile_abs, outfile_ref, outfile_sca, r1, r2, r3, d1, d2, d3,
dd1, dd2, dd3, shiftVert_1, shiftHoriz_1, shiftVert_2,
shiftHoriz_2, shiftVert_3, shiftHoriz_3, outshape, outtype,
skipflat_1, skipflat_2, skipflat_3, plan_1, plan_2, plan_3,
norm_sx, norm_dx, flat_end, half_half, half_half_line, ext_fov,
ext_fov_rot_right, ext_fov_overlap, ext_fov_normalize,
ext_fov_average, ringrem, dynamic_ff, EFF_1, EFF_2, EFF_3,
filtEFF_1, filtEFF_2, filtEFF_3, im_dark_1, im_dark_2, im_dark_3,
logfilename):
# Process the required subset of images:
for i in range(int_from, int_to + 1):
# Read input image for top, left and right:
t0 = time()
f_in = getHDF5(infile_1, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
flat_avg1 = float(f_in['flat'].attrs['avg'])
dark_avg1 = float(f_in['dark'].attrs['avg'])
else:
dset = f_in['exchange/data']
flat_avg1 = float(f_in['exchange/data_white'].attrs['avg'])
dark_avg1 = float(f_in['exchange/data_dark'].attrs['avg'])
# Processing in the sinogram domain so a vertical shift of the
# projection requires loading a different sinogram:
idx1 = min(max(0, i - shiftVert_1), num_sinos - 1)
im_1 = tdf.read_sino(dset, idx1).astype(float32)
f_in.close()
f_in = getHDF5(infile_2, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
flat_avg2 = float(f_in['flat'].attrs['avg'])
dark_avg2 = float(f_in['dark'].attrs['avg'])
else:
dset = f_in['exchange/data']
flat_avg2 = float(f_in['exchange/data_white'].attrs['avg'])
dark_avg2 = float(f_in['exchange/data_dark'].attrs['avg'])
# Processing in the sinogram domain so a vertical shift of the
# projection requires loading a different sinogram:
idx2 = min(max(0, i - shiftVert_2), num_sinos - 1)
im_2 = tdf.read_sino(dset, idx2).astype(float32)
f_in.close()
f_in = getHDF5(infile_3, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
flat_avg3 = float(f_in['flat'].attrs['avg'])
dark_avg3 = float(f_in['dark'].attrs['avg'])
else:
dset = f_in['exchange/data']
flat_avg3 = float(f_in['exchange/data_white'].attrs['avg'])
dark_avg3 = float(f_in['exchange/data_dark'].attrs['avg'])
# Processing in the sinogram domain so a vertical shift of the projection
# requires loading a different sinogram:
idx3 = min(max(0, i - shiftVert_3), num_sinos - 1)
im_3 = tdf.read_sino(dset, idx3).astype(float32)
f_in.close()
t1 = time()
# Perform pre-processing (flat fielding, extended FOV, ring removal):
if not skipflat_1:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im_1 = dynamic_flat_fielding(im_1, idx1, EFF_1, filtEFF_1, 2,
im_dark_1, norm_sx, norm_dx)
else:
im_1 = flat_fielding(im_1, idx1, plan_1, flat_end, half_half,
half_half_line, norm_sx, norm_dx)
if ext_fov:
im_1 = extfov_correction(im_1, ext_fov_rot_right, ext_fov_overlap,
ext_fov_normalize, ext_fov_average)
if not skipflat_1 and not dynamic_ff:
im_1 = ring_correction(im_1, ringrem, flat_end,
plan_1['skip_flat_after'], half_half,
half_half_line, ext_fov)
else:
im_1 = ring_correction(im_1, ringrem, False, False, half_half,
half_half_line, ext_fov)
# Perform pre-processing (flat fielding, extended FOV, ring removal):
if not skipflat_2:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im_2 = dynamic_flat_fielding(im_2, idx2, EFF_2, filtEFF_2, 2,
im_dark_2, norm_sx, norm_dx)
else:
im_2 = flat_fielding(im_2, idx2, plan_2, flat_end, half_half,
half_half_line, norm_sx, norm_dx)
if ext_fov:
im_2 = extfov_correction(im_2, ext_fov_rot_right, ext_fov_overlap,
ext_fov_normalize, ext_fov_average)
if not skipflat_2 and not dynamic_ff:
im_2 = ring_correction(im_2, ringrem, flat_end,
plan_2['skip_flat_after'], half_half,
half_half_line, ext_fov)
else:
im_2 = ring_correction(im_2, ringrem, False, False, half_half,
half_half_line, ext_fov)
# Perform pre-processing (flat fielding, extended FOV, ring removal):
if not skipflat_3:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im_3 = dynamic_flat_fielding(im_3, idx3, EFF_3, filtEFF_3, 2,
im_dark_3, norm_sx, norm_dx)
else:
im_3 = flat_fielding(im_3, idx3, plan_3, flat_end, half_half,
half_half_line, norm_sx, norm_dx)
if ext_fov:
im_3 = extfov_correction(im_3, ext_fov_rot_right, ext_fov_overlap,
ext_fov_normalize, ext_fov_average)
if not skipflat_3 and not dynamic_ff:
im_3 = ring_correction(im_3, ringrem, flat_end,
plan_3['skip_flat_after'], half_half,
half_half_line, ext_fov)
else:
im_3 = ring_correction(im_3, ringrem, False, False, half_half,
half_half_line, ext_fov)
t2 = time()
# Processing in the sinogram domain so a vertical shift of the
# projection requires loading a different sinogram:
# Only horizontal shift can be considered at a sinogram level:
if (shiftHoriz_1 != 0):
im_1 = _shift_horiz(im_1, shiftHoriz_1)
if (shiftHoriz_2 != 0):
im_2 = _shift_horiz(im_2, shiftHoriz_2)
if (shiftHoriz_3 != 0):
im_3 = _shift_horiz(im_3, shiftHoriz_3)
# Re-normalize with average of the flat-field images:
max_val = amax(
array([
mean(flat_avg1 - dark_avg1),
mean(flat_avg2 - dark_avg2),
mean(flat_avg3 - dark_avg3)
]))
im_1 = im_1 * (flat_avg1 - dark_avg1) / max_val
im_2 = im_2 * (flat_avg2 - dark_avg2) / max_val
im_3 = im_3 * (flat_avg3 - dark_avg3) / max_val
# Apply GDEI:
(im_abs, im_ref, im_sca) = gdei(im_1, im_2, im_3, r1, r2, r3, d1, d2,
d3, dd1, dd2, dd3)
# Save processed image to HDF5 file (atomic procedure - lock used):
lock.acquire()
try:
t3 = time()
_write_data(im_abs, i, outfile_abs, outshape, outtype)
_write_data(im_ref, i, outfile_ref, outshape, outtype)
_write_data(im_sca, i, outfile_sca, outshape, outtype)
t4 = time()
# Print out execution time:
log = open(logfilename, "a")
log.write(
linesep +
"\tsino_%s processed (CPU: %0.3f sec - I/O: %0.3f sec)." %
(str(i).zfill(4), t2 - t1, (t1 - t0) + (t4 - t3)))
log.close()
finally:
lock.release()
def main(argv):
"""To do...
"""
# Get the zero-order index of the sinogram to pre-process:
idx = int(argv[0])
# Get paths:
infile = argv[1]
outfile = argv[2]
# Normalization parameters:
norm_sx = int(argv[3])
norm_dx = int(argv[4])
# Params for flat fielding with post flats/darks:
flat_end = True if argv[5] == "True" else False
half_half = True if argv[6] == "True" else False
half_half_line = int(argv[7])
# Params for extended FOV:
ext_fov = True if argv[8] == "True" else False
ext_fov_rot_right = argv[9]
if ext_fov_rot_right == "True":
ext_fov_rot_right = True
if (ext_fov):
norm_sx = 0
else:
ext_fov_rot_right = False
if (ext_fov):
norm_dx = 0
ext_fov_overlap = int(argv[10])
ext_fov_normalize = True if argv[11] == "True" else False
ext_fov_average = True if argv[12] == "True" else False
# Method and parameters coded into a string:
ringrem = argv[13]
# Flat fielding method (conventional or dynamic):
dynamic_ff = True if argv[14] == "True" else False
# Tmp path and log file:
tmppath = argv[15]
if not tmppath.endswith(sep): tmppath += sep
logfilename = argv[16]
# Open the HDF5 file:
f_in = getHDF5(infile, 'r')
try:
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
except:
log = open(logfilename, "a")
log.write(linesep + "\tError reading input dataset. Process will end.")
log.close()
exit()
num_proj = tdf.get_nr_projs(dset)
num_sinos = tdf.get_nr_sinos(dset)
# Check if the HDF5 makes sense:
if (num_sinos == 0):
log = open(logfilename, "a")
log.write(linesep + "\tNo projections found. Process will end.")
log.close()
exit()
# Get flat and darks from cache or from file:
skipflat = False
skipdark = False
if not dynamic_ff:
try:
corrplan = cache2plan(infile, tmppath)
except Exception as e:
#print "Error(s) when reading from cache"
corrplan = extract_flatdark(f_in, flat_end, logfilename)
if (isscalar(corrplan['im_flat'])
and isscalar(corrplan['im_flat_after'])):
skipflat = True
else:
plan2cache(corrplan, infile, tmppath)
else:
# Dynamic flat fielding:
if "/tomo" in f_in:
if "/flat" in f_in:
flat_dset = f_in['flat']
if "/dark" in f_in:
im_dark = _medianize(f_in['dark'])
else:
skipdark = True
else:
skipflat = True # Nothing to do in this case
else:
if "/exchange/data_white" in f_in:
flat_dset = f_in['/exchange/data_white']
if "/exchange/data_dark" in f_in:
im_dark = _medianize(f_in['/exchange/data_dark'])
else:
skipdark = True
else:
skipflat = True # Nothing to do in this case
# Prepare plan for dynamic flat fielding with 16 repetitions:
if not skipflat:
EFF, filtEFF = dff_prepare_plan(flat_dset, 16, im_dark)
# Read input image:
im = tdf.read_sino(dset, idx).astype(float32)
f_in.close()
# Perform pre-processing (flat fielding, extended FOV, ring removal):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im = dynamic_flat_fielding(im, idx, EFF, filtEFF, 2, im_dark,
norm_sx, norm_dx)
else:
im = flat_fielding(im, idx, corrplan, flat_end, half_half,
half_half_line, norm_sx, norm_dx)
if ext_fov:
im = extfov_correction(im, ext_fov_rot_right, ext_fov_overlap,
ext_fov_normalize, ext_fov_average)
if not skipflat and not dynamic_ff:
im = ring_correction(im, ringrem, flat_end,
corrplan['skip_flat_after'], half_half,
half_half_line, ext_fov)
else:
im = ring_correction(im, ringrem, False, False, half_half,
half_half_line, ext_fov)
# Write down reconstructed preview file (file name modified with metadata):
im = im.astype(float32)
outfile = outfile + '_' + str(im.shape[1]) + 'x' + str(
im.shape[0]) + '_' + str(nanmin(im)) + '$' + str(nanmax(im))
im.tofile(outfile)
def process(sino_idx, num_sinos, infile, outfile, preprocessing_required,
corr_plan, skipflat, norm_sx, norm_dx, flat_end, half_half,
half_half_line, ext_fov, ext_fov_rot_right, ext_fov_overlap,
ext_fov_normalize, ext_fov_average, ringrem,
phaseretrieval_required, phrtmethod, phrt_param1, phrt_param2,
energy, distance, pixsize, phrtpad, approx_win, angles,
angles_projfrom, angles_projto, offset, logtransform, recpar,
circle, scale, pad, method, rolling, roll_shift, zerone_mode,
dset_min, dset_max, decim_factor, downsc_factor, corr_offset,
postprocess_required, polarfilt_opt, convert_opt, crop_opt,
dynamic_ff, EFF, filtEFF, im_dark, nr_threads, logfilename,
tmppath):
"""To do...
"""
# Perform reconstruction (on-the-fly preprocessing and phase retrieval, if
# required):
if (phaseretrieval_required):
# In this case a bunch of sinograms is loaded into memory:
#
# Load the temporary data structure reading the input TDF file.
# To know the right dimension the first sinogram is pre-processed.
#
# Open the TDF file and get the dataset:
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
# Downscaling and decimation factors considered when determining the
# approximation window:
zrange = arange(sino_idx - approx_win * downsc_factor / 2,
sino_idx + approx_win * downsc_factor / 2,
downsc_factor)
zrange = zrange[(zrange >= 0)]
zrange = zrange[(zrange < num_sinos)]
approx_win = zrange.shape[0]
# Approximation window cannot be odd:
if (approx_win % 2 == 1):
approx_win = approx_win - 1
zrange = zrange[0:approx_win]
# Read one sinogram to get the proper dimensions:
test_im = tdf.read_sino(dset,
zrange[0] * downsc_factor).astype(float32)
# Apply projection removal (if required):
test_im = test_im[angles_projfrom:angles_projto, :]
# Apply decimation and downscaling (if required):
test_im = test_im[::decim_factor, ::downsc_factor]
# Perform the pre-processing of the first sinogram to get the right
# dimension:
if (preprocessing_required):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
#test_im = dynamic_flat_fielding(test_im, zrange[0] / downsc_factor, EFF, filtEFF, 2, im_dark, norm_sx, norm_dx)
test_im = dynamic_flat_fielding(test_im, zrange[0], EFF,
filtEFF, 2, im_dark,
norm_sx, norm_dx)
else:
#test_im = flat_fielding(test_im, zrange[0] / downsc_factor, corr_plan, flat_end, half_half,
# half_half_line / decim_factor, norm_sx, norm_dx).astype(float32)
test_im = flat_fielding(test_im, zrange[0], corr_plan,
flat_end, half_half,
half_half_line / decim_factor,
norm_sx, norm_dx).astype(float32)
if ext_fov:
test_im = extfov_correction(test_im, ext_fov_rot_right,
ext_fov_overlap / downsc_factor,
ext_fov_normalize,
ext_fov_average).astype(float32)
if not skipflat and not dynamic_ff:
test_im = ring_correction(test_im, ringrem, flat_end,
corr_plan['skip_flat_after'],
half_half,
half_half_line / decim_factor,
ext_fov).astype(float32)
else:
test_im = ring_correction(test_im, ringrem, False, False,
half_half,
half_half_line / decim_factor,
ext_fov).astype(float32)
# Now we can allocate memory for the bunch of slices:
tmp_im = empty((approx_win, test_im.shape[0], test_im.shape[1]),
dtype=float32)
tmp_im[0, :, :] = test_im
# Reading all the the sinos from TDF file and close:
for ct in range(1, approx_win):
# Read the sinogram:
test_im = tdf.read_sino(dset,
zrange[ct] * downsc_factor).astype(float32)
# Apply projection removal (if required):
test_im = test_im[angles_projfrom:angles_projto, :]
# Apply decimation and downscaling (if required):
test_im = test_im[::decim_factor, ::downsc_factor]
# Perform the pre-processing for each sinogram of the bunch:
if (preprocessing_required):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
#test_im = dynamic_flat_fielding(test_im, zrange[ct] / downsc_factor, EFF, filtEFF, 2, im_dark, norm_sx, norm_dx)
test_im = dynamic_flat_fielding(
test_im, zrange[ct], EFF, filtEFF, 2, im_dark,
norm_sx, norm_dx)
else:
#test_im = flat_fielding(test_im, zrange[ct] / downsc_factor, corr_plan, flat_end, half_half,
# half_half_line / decim_factor, norm_sx, norm_dx).astype(float32)
test_im = flat_fielding(test_im, zrange[ct], corr_plan,
flat_end, half_half,
half_half_line / decim_factor,
norm_sx,
norm_dx).astype(float32)
if ext_fov:
test_im = extfov_correction(
test_im, ext_fov_rot_right,
ext_fov_overlap / downsc_factor, ext_fov_normalize,
ext_fov_average).astype(float32)
if not skipflat and not dynamic_ff:
test_im = ring_correction(test_im, ringrem, flat_end,
corr_plan['skip_flat_after'],
half_half,
half_half_line / decim_factor,
ext_fov).astype(float32)
else:
test_im = ring_correction(test_im, ringrem, False, False,
half_half,
half_half_line / decim_factor,
ext_fov).astype(float32)
tmp_im[ct, :, :] = test_im
f_in.close()
# Now everything has to refer to a downscaled dataset:
sino_idx = ((zrange == sino_idx).nonzero())
#
# Perform phase retrieval:
#
# Prepare the plan:
if (phrtmethod == 0):
# Paganin 2002:
phrtplan = tiehom_plan(tmp_im[:, 0, :], phrt_param1, phrt_param2,
energy, distance, pixsize * downsc_factor,
phrtpad)
elif (phrtmethod == 1):
# Paganin 2020:
phrtplan = tiehom_plan2020(tmp_im[:, 0, :], phrt_param1,
phrt_param2, energy, distance,
pixsize * downsc_factor, phrtpad)
else:
phrtplan = phrt_plan(tmp_im[:, 0, :], energy, distance,
pixsize * downsc_factor, phrt_param2,
phrt_param1, phrtmethod, phrtpad)
#phrtplan = prepare_plan (tmp_im[:,0,:], beta, delta, energy, distance,
#pixsize*downsc_factor, padding=phrtpad)
# Process each projection (whose height depends on the size of the bunch):
for ct in range(0, tmp_im.shape[1]):
#tmp_im[:,ct,:] = phase_retrieval(tmp_im[:,ct,:], phrtplan).astype(float32)
if (phrtmethod == 0):
tmp_im[:, ct, :] = tiehom(tmp_im[:, ct, :],
phrtplan).astype(float32)
elif (phrtmethod == 1):
tmp_im[:, ct, :] = tiehom2020(tmp_im[:, ct, :],
phrtplan).astype(float32)
else:
tmp_im[:, ct, :] = phrt(tmp_im[:, ct, :], phrtplan,
phrtmethod).astype(float32)
# Extract the requested sinogram:
im = tmp_im[sino_idx[0], :, :].squeeze()
else:
# Read only one sinogram:
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
im = tdf.read_sino(dset, sino_idx * downsc_factor).astype(float32)
f_in.close()
# Apply projection removal (if required):
im = im[angles_projfrom:angles_projto, :]
# Apply decimation and downscaling (if required):
im = im[::decim_factor, ::downsc_factor]
#sino_idx = sino_idx / downsc_factor # Downscaling for the index already applied
# Perform the preprocessing of the sinogram (if required):
if (preprocessing_required):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im = dynamic_flat_fielding(im, sino_idx, EFF, filtEFF, 2,
im_dark, norm_sx, norm_dx)
else:
im = flat_fielding(im, sino_idx, corr_plan, flat_end,
half_half,
half_half_line / decim_factor, norm_sx,
norm_dx).astype(float32)
if ext_fov:
im = extfov_correction(im, ext_fov_rot_right,
ext_fov_overlap / downsc_factor,
ext_fov_normalize, ext_fov_average)
if not skipflat and not dynamic_ff:
im = ring_correction(im, ringrem, flat_end,
corr_plan['skip_flat_after'], half_half,
half_half_line / decim_factor, ext_fov)
else:
im = ring_correction(im, ringrem, False, False, half_half,
half_half_line / decim_factor, ext_fov)
# Additional ring removal before reconstruction:
#im = boinhaibel(im, '11;')
#im = munchetal(im, '5;1.8')
#im = rivers(im, '13;')
#im = raven(im, '11;0.8')
#im = oimoen(im, '51;51')
# Actual reconstruction:
im = reconstruct(im, angles, offset / downsc_factor, logtransform, recpar,
circle, scale, pad, method, zerone_mode, dset_min,
dset_max, corr_offset, rolling, roll_shift,
tmppath).astype(float32)
# Apply post-processing (if required):
if postprocess_required:
im = polarfilter(im, polarfilt_opt)
im = croprescale(im, convert_opt, crop_opt)
else:
# Create the circle mask for fancy output:
if (circle == True):
siz = im.shape[1]
if siz % 2:
rang = arange(-siz / 2 + 1, siz / 2 + 1)
else:
rang = arange(-siz / 2, siz / 2)
x, y = meshgrid(rang, rang)
z = x**2 + y**2
a = (z < (siz / 2 - int(round(abs(offset) / downsc_factor)))**2)
im = im * a
# Write down reconstructed preview file (file name modified with metadata):
im = im.astype(float32)
outfile = outfile + '_' + str(im.shape[1]) + 'x' + str(
im.shape[0]) + '_' + str(amin(im)) + '$' + str(amax(im))
im.tofile(outfile)
def process_gridrec(lock, int_from, int_to, num_sinos, infile, outpath, preprocessing_required, skipflat, corr_plan, norm_sx, norm_dx, flat_end, half_half, half_half_line, ext_fov, ext_fov_rot_right, ext_fov_overlap, ext_fov_normalize, ext_fov_average, ringrem, angles, angles_projfrom, angles_projto, offset, logtransform, param1, circle, scale, pad, rolling, roll_shift, zerone_mode, dset_min, dset_max, decim_factor, downsc_factor, corr_offset, postprocess_required, polarfilt_opt, convert_opt, crop_opt, dynamic_ff, EFF, filtEFF, im_dark, outprefix, logfilename): """To do... """ # Process the required subset of images: for i in range(int_from, int_to + 1, 2): # Read two sinograms: t0 = time() f_in = getHDF5(infile, 'r') if "/tomo" in f_in: dset = f_in['tomo'] else: dset = f_in['exchange/data'] im1 = tdf.read_sino(dset,i*downsc_factor).astype(float32) if ( (i + downsc_factor) <= (int_to + 1) ): im2 = tdf.read_sino(dset,i*downsc_factor + downsc_factor).astype(float32) else: im2 = im1 f_in.close() t1 = time() # Apply projection removal (if required): im1 = im1[angles_projfrom:angles_projto, :] im2 = im2[angles_projfrom:angles_projto, :] # Apply decimation and downscaling (if required): im1 = im1[::decim_factor,::downsc_factor] im2 = im2[::decim_factor,::downsc_factor] #i = i / downsc_factor # Perform the preprocessing of the sinograms (if required): if (preprocessing_required): if not skipflat: if dynamic_ff: # Dynamic flat fielding with downsampling = 2: im1 = dynamic_flat_fielding(im1, i, EFF, filtEFF, 2, im_dark, norm_sx, norm_dx) else: im1 = flat_fielding (im1, i, corr_plan, flat_end, half_half, half_half_line / decim_factor, norm_sx, norm_dx).astype(float32) if ext_fov: im1 = extfov_correction (im1, ext_fov_rot_right, ext_fov_overlap / downsc_factor, ext_fov_normalize, ext_fov_average) if not skipflat: im1 = ring_correction (im1, ringrem, flat_end, corr_plan['skip_flat_after'], half_half, half_half_line / decim_factor, ext_fov) else: im1 = ring_correction (im1, ringrem, False, False, half_half, half_half_line / decim_factor, ext_fov) if not skipflat: if dynamic_ff: # Dynamic flat fielding with downsampling = 2: im2 = dynamic_flat_fielding(im2, i + 1, EFF, filtEFF, 2, im_dark, norm_sx, norm_dx) else: im2 = flat_fielding (im2, i + 1, corr_plan, flat_end, half_half, half_half_line / decim_factor, norm_sx, norm_dx).astype(float32) if ext_fov: im2 = extfov_correction (im2, ext_fov_rot_right, ext_fov_overlap / downsc_factor, ext_fov_normalize, ext_fov_average) if not skipflat and not dynamic_ff: im2 = ring_correction (im2, ringrem, flat_end, corr_plan['skip_flat_after'], half_half, half_half_line / decim_factor, ext_fov) else: im2 = ring_correction (im2, ringrem, False, False, half_half, half_half_line, ext_fov) # Actual reconstruction: [im1, im2] = reconstruct_gridrec(im1, im2, angles, offset / downsc_factor, logtransform, param1, circle, scale, pad, rolling, roll_shift, zerone_mode, dset_min, dset_max, decim_factor, downsc_factor, corr_offset) # Appy post-processing (if required): if postprocess_required: # Filter (if required): im1 = polarfilter(im1, polarfilt_opt) im2 = polarfilter(im2, polarfilt_opt) im1 = croprescale(im1, convert_opt, crop_opt, circle) im2 = croprescale(im2, convert_opt, crop_opt, circle) else: # Create the circle mask for fancy output: if (circle == True): siz = im1.shape[1] if siz % 2: rang = arange(-siz / 2 + 1, siz / 2 + 1) else: rang = arange(-siz / 2,siz / 2) x,y = meshgrid(rang,rang) z = x ** 2 + y ** 2 a = (z < (siz / 2 - int(round(abs(offset)/downsc_factor)) ) ** 2) im1 = im1 * a im2 = im2 * a # Write down reconstructed slices: t2 = time() fname1 = outpath + outprefix + '_' + str(i).zfill(4) + '.tif' imsave(fname1, im1) fname2 = outpath + outprefix + '_' + str(i + 1).zfill(4) + '.tif' imsave(fname2, im2) t3 = time() # Write log (atomic procedure - lock used): write_log_gridrec(lock, fname1, fname2, logfilename, t2 - t1, (t3 - t2) + (t1 - t0) )
def main(argv): """To do... """ # Get the zero-order index of the sinogram to pre-process: idx = int(argv[0]) # Get paths: infile = argv[1] outfile = argv[2] # Normalization parameters: norm_sx = int(argv[3]) norm_dx = int(argv[4]) # Params for flat fielding with post flats/darks: flat_end = True if argv[5] == "True" else False half_half = True if argv[6] == "True" else False half_half_line = int(argv[7]) # Params for extended FOV: ext_fov = True if argv[8] == "True" else False ext_fov_rot_right = argv[9] if ext_fov_rot_right == "True": ext_fov_rot_right = True if (ext_fov): norm_sx = 0 else: ext_fov_rot_right = False if (ext_fov): norm_dx = 0 ext_fov_overlap = int(argv[10]) ext_fov_normalize = True if argv[11] == "True" else False ext_fov_average = True if argv[12] == "True" else False # Method and parameters coded into a string: ringrem = argv[13] # Flat fielding method (conventional or dynamic): dynamic_ff = True if argv[14] == "True" else False # Tmp path and log file: tmppath = argv[15] if not tmppath.endswith(sep): tmppath += sep logfilename = argv[16] # Open the HDF5 file: f_in = getHDF5(infile, 'r') try: if "/tomo" in f_in: dset = f_in['tomo'] else: dset = f_in['exchange/data'] except: log = open(logfilename,"a") log.write(linesep + "\tError reading input dataset. Process will end.") log.close() exit() num_proj = tdf.get_nr_projs(dset) num_sinos = tdf.get_nr_sinos(dset) # Check if the HDF5 makes sense: if (num_sinos == 0): log = open(logfilename,"a") log.write(linesep + "\tNo projections found. Process will end.") log.close() exit() # Get flat and darks from cache or from file: skipflat = False skipdark = False if not dynamic_ff: try: corrplan = cache2plan(infile, tmppath) except Exception as e: #print "Error(s) when reading from cache" corrplan = extract_flatdark(f_in, flat_end, logfilename) if (isscalar(corrplan['im_flat']) and isscalar(corrplan['im_flat_after']) ): skipflat = True else: plan2cache(corrplan, infile, tmppath) else: # Dynamic flat fielding: if "/tomo" in f_in: if "/flat" in f_in: flat_dset = f_in['flat'] if "/dark" in f_in: im_dark = _medianize(f_in['dark']) else: skipdark = True else: skipflat = True # Nothing to do in this case else: if "/exchange/data_white" in f_in: flat_dset = f_in['/exchange/data_white'] if "/exchange/data_dark" in f_in: im_dark = _medianize(f_in['/exchange/data_dark']) else: skipdark = True else: skipflat = True # Nothing to do in this case # Prepare plan for dynamic flat fielding with 16 repetitions: if not skipflat: EFF, filtEFF = dff_prepare_plan(flat_dset, 16, im_dark) # Read input image: im = tdf.read_sino(dset,idx).astype(float32) f_in.close() # Perform pre-processing (flat fielding, extended FOV, ring removal): if not skipflat: if dynamic_ff: # Dynamic flat fielding with downsampling = 2: im = dynamic_flat_fielding(im, idx, EFF, filtEFF, 2, im_dark, norm_sx, norm_dx) else: im = flat_fielding(im, idx, corrplan, flat_end, half_half, half_half_line, norm_sx, norm_dx) if ext_fov: im = extfov_correction(im, ext_fov_rot_right, ext_fov_overlap, ext_fov_normalize, ext_fov_average) if not skipflat and not dynamic_ff: im = ring_correction (im, ringrem, flat_end, corrplan['skip_flat_after'], half_half, half_half_line, ext_fov) else: im = ring_correction (im, ringrem, False, False, half_half, half_half_line, ext_fov) # Write down reconstructed preview file (file name modified with metadata): im = im.astype(float32) outfile = outfile + '_' + str(im.shape[1]) + 'x' + str(im.shape[0]) + '_' + str( nanmin(im)) + '$' + str( nanmax(im) ) im.tofile(outfile)
def process_gridrec(lock, int_from, int_to, num_sinos, infile, outpath, preprocessing_required, corr_plan, norm_sx, norm_dx, flat_end, half_half, half_half_line, ext_fov, ext_fov_rot_right, ext_fov_overlap, ringrem, angles, offset, logtransform, param1, circle, scale, pad, zerone_mode, dset_min, dset_max, decim_factor, downsc_factor, corr_offset, postprocess_required, convert_opt, crop_opt, outprefix, logfilename): """To do... """ # Process the required subset of images: for i in range(int_from, int_to + 1, 2): # Read two sinograms: t0 = time() f_in = getHDF5(infile, 'r') if "/tomo" in f_in: dset = f_in['tomo'] else: dset = f_in['exchange/data'] im1 = tdf.read_sino(dset,i).astype(float32) if ( (i + 1) <= (int_to + 1) ): im2 = tdf.read_sino(dset,i + 1).astype(float32) else: im2 = im1 f_in.close() t1 = time() # Perform the preprocessing of the sinograms (if required): if (preprocessing_required): im1 = flat_fielding (im1, i, corr_plan, flat_end, half_half, half_half_line, norm_sx, norm_dx).astype(float32) im1 = extfov_correction (im1, ext_fov, ext_fov_rot_right, ext_fov_overlap) im1 = ring_correction (im1, ringrem, flat_end, corr_plan['skip_flat_after'], half_half, half_half_line, ext_fov) im2 = flat_fielding (im2, i + 1, corr_plan, flat_end, half_half, half_half_line, norm_sx, norm_dx).astype(float32) im2 = extfov_correction (im2, ext_fov, ext_fov_rot_right, ext_fov_overlap) im2 = ring_correction (im2, ringrem, flat_end, corr_plan['skip_flat_after'], half_half, half_half_line, ext_fov) # Actual reconstruction: [im1, im2] = reconstruct_gridrec(im1, im2, angles, offset, logtransform, param1, circle, scale, pad, zerone_mode, dset_min, dset_max, decim_factor, downsc_factor, corr_offset) # Appy post-processing (if required): if postprocess_required: im1 = postprocess(im1, convert_opt, crop_opt, circle) im2 = postprocess(im2, convert_opt, crop_opt, circle) else: # Create the circle mask for fancy output: if (circle == True): siz = im1.shape[1] if siz % 2: rang = arange(-siz / 2 + 1, siz / 2 + 1) else: rang = arange(-siz / 2,siz / 2) x,y = meshgrid(rang,rang) z = x ** 2 + y ** 2 a = (z < (siz / 2 - int(round(abs(offset)/downsc_factor)) ) ** 2) im1 = im1 * a im2 = im2 * a # Write down reconstructed slices: t2 = time() fname1 = outpath + outprefix + '_' + str(i).zfill(4) + '.tif' imsave(fname1, im1) fname2 = outpath + outprefix + '_' + str(i + 1).zfill(4) + '.tif' imsave(fname2, im2) t3 = time() # Write log (atomic procedure - lock used): write_log_gridrec(lock, fname1, fname2, logfilename, t2 - t1, (t3 - t2) + (t1 - t0) )
def process_gridrec(lock, int_from, int_to, num_sinos, infile, outpath,
preprocessing_required, skipflat, corr_plan, norm_sx,
norm_dx, flat_end, half_half, half_half_line, ext_fov,
ext_fov_rot_right, ext_fov_overlap, ext_fov_normalize,
ext_fov_average, ringrem, angles, angles_projfrom,
angles_projto, offset, logtransform, param1, circle, scale,
pad, rolling, roll_shift, zerone_mode, dset_min, dset_max,
decim_factor, downsc_factor, corr_offset,
postprocess_required, polarfilt_opt, convert_opt, crop_opt,
dynamic_ff, EFF, filtEFF, im_dark, outprefix, logfilename):
"""To do...
"""
# Process the required subset of images:
for i in range(int_from, int_to + 1, 2):
# Read two sinograms:
t0 = time()
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
im1 = tdf.read_sino(dset, i * downsc_factor).astype(float32)
if ((i + downsc_factor) <= (int_to + 1)):
im2 = tdf.read_sino(dset, i * downsc_factor +
downsc_factor).astype(float32)
else:
im2 = im1
f_in.close()
t1 = time()
# Apply projection removal (if required):
im1 = im1[angles_projfrom:angles_projto, :]
im2 = im2[angles_projfrom:angles_projto, :]
# Apply decimation and downscaling (if required):
im1 = im1[::decim_factor, ::downsc_factor]
im2 = im2[::decim_factor, ::downsc_factor]
#i = i / downsc_factor
# Perform the preprocessing of the sinograms (if required):
if (preprocessing_required):
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im1 = dynamic_flat_fielding(im1, i, EFF, filtEFF, 2,
im_dark, norm_sx, norm_dx)
else:
im1 = flat_fielding(im1, i, corr_plan, flat_end, half_half,
half_half_line / decim_factor, norm_sx,
norm_dx).astype(float32)
if ext_fov:
im1 = extfov_correction(im1, ext_fov_rot_right,
ext_fov_overlap / downsc_factor,
ext_fov_normalize, ext_fov_average)
if not skipflat:
im1 = ring_correction(im1, ringrem, flat_end,
corr_plan['skip_flat_after'], half_half,
half_half_line / decim_factor, ext_fov)
else:
im1 = ring_correction(im1, ringrem, False, False, half_half,
half_half_line / decim_factor, ext_fov)
if not skipflat:
if dynamic_ff:
# Dynamic flat fielding with downsampling = 2:
im2 = dynamic_flat_fielding(im2, i + 1, EFF, filtEFF, 2,
im_dark, norm_sx, norm_dx)
else:
im2 = flat_fielding(im2, i + 1, corr_plan, flat_end,
half_half,
half_half_line / decim_factor, norm_sx,
norm_dx).astype(float32)
if ext_fov:
im2 = extfov_correction(im2, ext_fov_rot_right,
ext_fov_overlap / downsc_factor,
ext_fov_normalize, ext_fov_average)
if not skipflat and not dynamic_ff:
im2 = ring_correction(im2, ringrem, flat_end,
corr_plan['skip_flat_after'], half_half,
half_half_line / decim_factor, ext_fov)
else:
im2 = ring_correction(im2, ringrem, False, False, half_half,
half_half_line, ext_fov)
# Actual reconstruction:
[im1,
im2] = reconstruct_gridrec(im1, im2, angles, offset / downsc_factor,
logtransform, param1, circle, scale, pad,
rolling, roll_shift, zerone_mode, dset_min,
dset_max, decim_factor, downsc_factor,
corr_offset)
# Appy post-processing (if required):
if postprocess_required:
# Filter (if required):
im1 = polarfilter(im1, polarfilt_opt)
im2 = polarfilter(im2, polarfilt_opt)
im1 = croprescale(im1, convert_opt, crop_opt, circle)
im2 = croprescale(im2, convert_opt, crop_opt, circle)
else:
# Create the circle mask for fancy output:
if (circle == True):
siz = im1.shape[1]
if siz % 2:
rang = arange(-siz / 2 + 1, siz / 2 + 1)
else:
rang = arange(-siz / 2, siz / 2)
x, y = meshgrid(rang, rang)
z = x**2 + y**2
a = (z <
(siz / 2 - int(round(abs(offset) / downsc_factor)))**2)
im1 = im1 * a
im2 = im2 * a
# Write down reconstructed slices:
t2 = time()
fname1 = outpath + outprefix + '_' + str(i).zfill(4) + '.tif'
imsave(fname1, im1)
fname2 = outpath + outprefix + '_' + str(i + 1).zfill(4) + '.tif'
imsave(fname2, im2)
t3 = time()
# Write log (atomic procedure - lock used):
write_log_gridrec(lock, fname1, fname2, logfilename, t2 - t1,
(t3 - t2) + (t1 - t0))
def process(sino_idx, num_sinos, infile, outpath, preprocessing_required,
corr_plan, norm_sx, norm_dx, flat_end, half_half, half_half_line,
ext_fov, ext_fov_rot_right, ext_fov_overlap, ext_fov_normalize,
ext_fov_average, ringrem, phaseretrieval_required, phrtmethod,
phrt_param1, phrt_param2, energy, distance, pixsize, phrtpad,
approx_win, angles, angles_projfrom, angles_projto, offset,
logtransform, param1, circle, scale, pad, method, zerone_mode,
dset_min, dset_max, decim_factor, downsc_factor, corr_offset,
postprocess_required, convert_opt, crop_opt, nr_threads, off_from,
off_to, logfilename, lock, slice_prefix):
"""To do...
"""
slice_nr = sino_idx
# Perform reconstruction (on-the-fly preprocessing and phase retrieval, if required):
if (phaseretrieval_required):
# In this case a bunch of sinograms is loaded into memory:
#
# Load the temporary data structure reading the input TDF file.
# To know the right dimension the first sinogram is pre-processed.
#
# Open the TDF file and get the dataset:
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
# Downscaling and decimation factors considered when determining the approximation window:
zrange = arange(sino_idx - approx_win * downsc_factor / 2,
sino_idx + approx_win * downsc_factor / 2,
downsc_factor)
zrange = zrange[(zrange >= 0)]
zrange = zrange[(zrange < num_sinos)]
approx_win = zrange.shape[0]
# Approximation window cannot be odd:
if (approx_win % 2 == 1):
approx_win = approx_win - 1
zrange = zrange[0:approx_win]
# Read one sinogram to get the proper dimensions:
test_im = tdf.read_sino(dset,
zrange[0] * downsc_factor).astype(float32)
# Apply projection removal (if required):
test_im = test_im[angles_projfrom:angles_projto, :]
# Apply decimation and downscaling (if required):
test_im = test_im[::decim_factor, ::downsc_factor]
# Perform the pre-processing of the first sinogram to get the right dimension:
if (preprocessing_required):
test_im = flat_fielding(test_im, zrange[0], corr_plan, flat_end,
half_half, half_half_line / decim_factor,
norm_sx, norm_dx).astype(float32)
if ext_fov:
test_im = extfov_correction(test_im, ext_fov_rot_right,
ext_fov_overlap / downsc_factor,
ext_fov_normalize,
ext_fov_average).astype(float32)
test_im = ring_correction(test_im, ringrem, flat_end,
corr_plan['skip_flat_after'], half_half,
half_half_line / decim_factor,
ext_fov).astype(float32)
# Now we can allocate memory for the bunch of slices:
tmp_im = empty((approx_win, test_im.shape[0], test_im.shape[1]),
dtype=float32)
tmp_im[0, :, :] = test_im
# Reading all the the sinos from TDF file and close:
for ct in range(1, approx_win):
test_im = tdf.read_sino(dset,
zrange[ct] * downsc_factor).astype(float32)
# Apply projection removal (if required):
test_im = test_im[angles_projfrom:angles_projto, :]
# Apply decimation and downscaling (if required):
test_im = test_im[::decim_factor, ::downsc_factor]
# Perform the pre-processing for each sinogram of the bunch:
if (preprocessing_required):
test_im = flat_fielding(test_im, zrange[ct], corr_plan,
flat_end, half_half,
half_half_line / decim_factor, norm_sx,
norm_dx).astype(float32)
if ext_fov:
test_im = extfov_correction(
test_im, ext_fov_rot_right,
ext_fov_overlap / downsc_factor, ext_fov_normalize,
ext_fov_average).astype(float32)
test_im = ring_correction(test_im, ringrem, flat_end,
corr_plan['skip_flat_after'],
half_half,
half_half_line / decim_factor,
ext_fov).astype(float32)
tmp_im[ct, :, :] = test_im
f_in.close()
# Now everything has to refer to a downscaled dataset:
sino_idx = ((zrange == sino_idx).nonzero())
#
# Perform phase retrieval:
#
# Prepare the plan:
if (phrtmethod == 0):
# Paganin's:
phrtplan = tiehom_plan(tmp_im[:, 0, :],
phrt_param1,
phrt_param2,
energy,
distance,
pixsize * downsc_factor,
padding=phrtpad)
else:
phrtplan = phrt_plan(tmp_im[:, 0, :],
energy,
distance,
pixsize * downsc_factor,
phrt_param2,
phrt_param1,
phrtmethod,
padding=phrtpad)
# Process each projection (whose height depends on the size of the bunch):
for ct in range(0, tmp_im.shape[1]):
if (phrtmethod == 0):
tmp_im[:, ct, :] = tiehom(tmp_im[:, ct, :],
phrtplan).astype(float32)
else:
tmp_im[:, ct, :] = phrt(tmp_im[:, ct, :], phrtplan,
phrtmethod).astype(float32)
# Extract the requested sinogram:
im = tmp_im[sino_idx[0], :, :].squeeze()
else:
# Read only one sinogram:
f_in = getHDF5(infile, 'r')
if "/tomo" in f_in:
dset = f_in['tomo']
else:
dset = f_in['exchange/data']
im = tdf.read_sino(dset, sino_idx * downsc_factor).astype(float32)
f_in.close()
# Apply projection removal (if required):
im = im[angles_projfrom:angles_projto, :]
# Downscale and decimate the sinogram:
im = im[::decim_factor, ::downsc_factor]
#sino_idx = sino_idx/downsc_factor
# Perform the preprocessing of the sinogram (if required):
if (preprocessing_required):
im = flat_fielding(im, sino_idx, corr_plan, flat_end, half_half,
half_half_line / decim_factor, norm_sx,
norm_dx).astype(float32)
if ext_fov:
im = extfov_correction(im, ext_fov_rot_right,
ext_fov_overlap / downsc_factor,
ext_fov_normalize, ext_fov_average)
im = ring_correction(im, ringrem, flat_end,
corr_plan['skip_flat_after'], half_half,
half_half_line / decim_factor, ext_fov)
# Log infos:
log = open(logfilename, "a")
log.write(
linesep +
"\tPerforming reconstruction with multiple centers of rotation...")
log.write(linesep + "\t--------------")
log.close()
# Split the computation into multiple processes:
for num in range(nr_threads):
start = ((off_to - off_from + 1) / nr_threads) * num + off_from
if (num == nr_threads - 1):
end = off_to
else:
end = ((off_to - off_from + 1) / nr_threads) * (num +
1) + off_from - 1
Process(target=reconstruct,
args=(im, angles, angles_projfrom, angles_projto,
offset / downsc_factor, logtransform, param1, circle,
scale, pad, method, zerone_mode, dset_min, dset_max,
corr_offset, postprocess_required, convert_opt, crop_opt,
start, end, outpath, slice_nr, downsc_factor,
logfilename, lock, slice_prefix)).start()
def main(argv): """To do... Usage ----- Parameters --------- Example -------------------------- The following line processes the first ten TIFF files of input path "/home/in" and saves the processed files to "/home/out" with the application of the Boin and Haibel filter with smoothing via a Butterworth filter of order 4 and cutoff frequency 0.01: destripe /home/in /home/out 1 10 1 0.01 4 """ lock = Lock() skip_ringrem = False skip_flat = False skip_flat_after = True first_done = False # Get the number of sino to pre-process: idx = int(argv[0]) # Get paths: infile = argv[1] outfile = argv[2] # Normalization parameters: norm_sx = int(argv[3]) norm_dx = int(argv[4]) # Params for flat fielding with post flats/darks: flat_end = True if argv[5] == "True" else False half_half = True if argv[6] == "True" else False half_half_line = int(argv[7]) # Params for extended FOV: ext_fov = True if argv[8] == "True" else False ext_fov_rot_right = argv[9] if ext_fov_rot_right == "True": ext_fov_rot_right = True if (ext_fov): norm_sx = 0 else: ext_fov_rot_right = False if (ext_fov): norm_dx = 0 ext_fov_overlap = int(argv[10]) # Method and parameters coded into a string: ringrem = argv[11] # Tmp path and log file: tmppath = argv[12] if not tmppath.endswith(sep): tmppath += sep logfilename = argv[13] # Open the HDF5 file: f_in = getHDF5(infile, 'r') if "/tomo" in f_in: dset = f_in['tomo'] else: dset = f_in['exchange/data'] prov_dset = f_in['provenance/detector_output'] num_proj = tdf.get_nr_projs(dset) num_sinos = tdf.get_nr_sinos(dset) # Check if the HDF5 makes sense: if (num_sinos == 0): log = open(logfilename,"a") log.write(linesep + "\tNo projections found. Process will end.") log.close() exit() # Get flat and darks from cache or from file: try: corrplan = cache2plan(infile, tmppath) except Exception as e: #print "Error(s) when reading from cache" corrplan = extract_flatdark(f_in, flat_end, logfilename) plan2cache(corrplan, infile, tmppath) # Read input image: im = tdf.read_sino(dset,idx).astype(float32) f_in.close() # Perform pre-processing (flat fielding, extended FOV, ring removal): im = flat_fielding(im, idx, corrplan, flat_end, half_half, half_half_line, norm_sx, norm_dx) im = extfov_correction(im, ext_fov, ext_fov_rot_right, ext_fov_overlap) im = ring_correction (im, ringrem, flat_end, corrplan['skip_flat_after'], half_half, half_half_line, ext_fov) # Write down reconstructed preview file (file name modified with metadata): im = im.astype(float32) outfile = outfile + '_' + str(im.shape[1]) + 'x' + str(im.shape[0]) + '_' + str( nanmin(im)) + '$' + str( nanmax(im) ) im.tofile(outfile)