def log_config(self,
file,
prefix="config"):
# parser returns options with underscores, e.g. 'dir_output'
dic_with_underscores = vars(self._parser.parse_args())
# get output directory to write log/config file
try:
dir_output = dic_with_underscores["dir_output"]
except KeyError:
dir_output = os.path.dirname(dic_with_underscores["output"])
# build output file name
name = os.path.basename(file).split(".")[0]
time_stamp = "%s-%s" % (ph.get_current_date(), ph.get_current_time())
path_to_config_file = os.path.join(
dir_output,
"%s_%s_%s.json" % (prefix, name, time_stamp))
# exclude config file (as setting in parameters reflected anyway)
dic_with_underscores.pop(re.sub("--", "", self._config_arg))
# replace underscore by dashes for correct commandline parsing,
# e.g. "dir-output" instead of "dir_output"
dic = {
re.sub("_", "-", k): v
for k, v in six.iteritems(dic_with_underscores)}
dic["version"] = niftymic.__version__
# write config file to output
ph.write_dictionary_to_json(dic, path_to_config_file, verbose=True)
def log_config(self, file, prefix="config"):
# parser returns options with underscores, e.g. 'dir_output'
dic_with_underscores = vars(self._parser.parse_args())
# get output directory to write log/config file
try:
dir_output = dic_with_underscores["dir_output"]
except KeyError:
dir_output = os.path.dirname(dic_with_underscores["output"])
# build output file name
name = os.path.basename(file).split(".")[0]
now = datetime.datetime.now()
time_stamp = now.strftime("%Y%m%d-%H%M%S")
path_to_config_file = os.path.join(
dir_output, "%s_%s_%s.json" % (prefix, name, time_stamp))
# exclude config file (as setting in parameters reflected anyway)
dic_with_underscores.pop(re.sub("--", "", self._config_arg))
# replace underscore by dashes for correct commandline parsing,
# e.g. "dir-output" instead of "dir_output"
dic = {
re.sub("_", "-", k): v
for k, v in six.iteritems(dic_with_underscores)
}
# add user info to config file
try:
login = os.getlogin()
except OSError as e:
login = "******"
node = platform.node()
info_args = []
info_args.append("Python %s" % platform.python_version())
info_args.append(platform.system())
info_args.append(platform.release())
info_args.append(platform.version())
info_args.append(platform.machine())
info_args.append(platform.processor())
user = "******" % (login, node, ", ".join(info_args))
dic["user"] = user
# add date of execution to config file
dic["date"] = now.strftime("%Y-%m-%d %H:%M:%S")
# add version number to config file
dic["version"] = niftymic.__version__
# write config file to output
ph.write_dictionary_to_json(dic, path_to_config_file, verbose=True)
def main():
time_start = ph.start_timing()
# Set print options for numpy
np.set_printoptions(precision=3)
input_parser = InputArgparser(
description="Volumetric MRI reconstruction framework to reconstruct "
"an isotropic, high-resolution 3D volume from multiple stacks of 2D "
"slices with motion correction. The resolution of the computed "
"Super-Resolution Reconstruction (SRR) is given by the in-plane "
"spacing of the selected target stack. A region of interest can be "
"specified by providing a mask for the selected target stack. Only "
"this region will then be reconstructed by the SRR algorithm which "
"can substantially reduce the computational time.",
)
input_parser.add_filenames(required=True)
input_parser.add_filenames_masks()
input_parser.add_output(required=True)
input_parser.add_suffix_mask(default="_mask")
input_parser.add_target_stack(default=None)
input_parser.add_search_angle(default=45)
input_parser.add_multiresolution(default=0)
input_parser.add_shrink_factors(default=[3, 2, 1])
input_parser.add_smoothing_sigmas(default=[1.5, 1, 0])
input_parser.add_sigma(default=1)
input_parser.add_reconstruction_type(default="TK1L2")
input_parser.add_iterations(default=15)
input_parser.add_alpha(default=0.015)
input_parser.add_alpha_first(default=0.2)
input_parser.add_iter_max(default=10)
input_parser.add_iter_max_first(default=5)
input_parser.add_dilation_radius(default=3)
input_parser.add_extra_frame_target(default=10)
input_parser.add_bias_field_correction(default=0)
input_parser.add_intensity_correction(default=1)
input_parser.add_isotropic_resolution(default=1)
input_parser.add_log_config(default=1)
input_parser.add_subfolder_motion_correction()
input_parser.add_write_motion_correction(default=1)
input_parser.add_verbose(default=0)
input_parser.add_two_step_cycles(default=3)
input_parser.add_use_masks_srr(default=0)
input_parser.add_boundary_stacks(default=[10, 10, 0])
input_parser.add_metric(default="Correlation")
input_parser.add_metric_radius(default=10)
input_parser.add_reference()
input_parser.add_reference_mask()
input_parser.add_outlier_rejection(default=1)
input_parser.add_threshold_first(default=0.5)
input_parser.add_threshold(default=0.8)
input_parser.add_interleave(default=3)
input_parser.add_slice_thicknesses(default=None)
input_parser.add_viewer(default="itksnap")
input_parser.add_v2v_method(default="RegAladin")
input_parser.add_argument(
"--v2v-robust", "-v2v-robust",
action='store_true',
help="If given, a more robust volume-to-volume registration step is "
"performed, i.e. four rigid registrations are performed using four "
"rigid transform initializations based on "
"principal component alignment of associated masks."
)
input_parser.add_argument(
"--s2v-hierarchical", "-s2v-hierarchical",
action='store_true',
help="If given, a hierarchical approach for the first slice-to-volume "
"registration cycle is used, i.e. sub-packages defined by the "
"specified interleave (--interleave) are registered until each "
"slice is registered independently."
)
input_parser.add_argument(
"--sda", "-sda",
action='store_true',
help="If given, the volumetric reconstructions are performed using "
"Scattered Data Approximation (Vercauteren et al., 2006). "
"'alpha' is considered the final 'sigma' for the "
"iterative adjustment. "
"Recommended value is, e.g., --alpha 0.8"
)
input_parser.add_option(
option_string="--transforms-history",
type=int,
help="Write entire history of applied slice motion correction "
"transformations to motion correction output directory",
default=0,
)
args = input_parser.parse_args()
input_parser.print_arguments(args)
rejection_measure = "NCC"
threshold_v2v = -2 # 0.3
debug = False
if args.v2v_method not in V2V_METHOD_OPTIONS:
raise ValueError("v2v-method must be in {%s}" % (
", ".join(V2V_METHOD_OPTIONS)))
if np.alltrue([not args.output.endswith(t) for t in ALLOWED_EXTENSIONS]):
raise ValueError(
"output filename invalid; allowed extensions are: %s" %
", ".join(ALLOWED_EXTENSIONS))
if args.alpha_first < args.alpha and not args.sda:
raise ValueError("It must hold alpha-first >= alpha")
if args.threshold_first > args.threshold:
raise ValueError("It must hold threshold-first <= threshold")
dir_output = os.path.dirname(args.output)
ph.create_directory(dir_output)
if args.log_config:
input_parser.log_config(os.path.abspath(__file__))
# --------------------------------Read Data--------------------------------
ph.print_title("Read Data")
data_reader = dr.MultipleImagesReader(
file_paths=args.filenames,
file_paths_masks=args.filenames_masks,
suffix_mask=args.suffix_mask,
stacks_slice_thicknesses=args.slice_thicknesses,
)
if len(args.boundary_stacks) is not 3:
raise IOError(
"Provide exactly three values for '--boundary-stacks' to define "
"cropping in i-, j-, and k-dimension of the input stacks")
data_reader.read_data()
stacks = data_reader.get_data()
ph.print_info("%d input stacks read for further processing" % len(stacks))
if all(s.is_unity_mask() is True for s in stacks):
ph.print_warning("No mask is provided! "
"Generated reconstruction space may be very big!")
ph.print_warning("Consider using a mask to speed up computations")
# args.extra_frame_target = 0
# ph.wrint_warning("Overwritten: extra-frame-target set to 0")
# Specify target stack for intensity correction and reconstruction space
if args.target_stack is None:
target_stack_index = 0
else:
try:
target_stack_index = args.filenames.index(args.target_stack)
except ValueError as e:
raise ValueError(
"--target-stack must correspond to an image as provided by "
"--filenames")
# ---------------------------Data Preprocessing---------------------------
ph.print_title("Data Preprocessing")
segmentation_propagator = segprop.SegmentationPropagation(
# registration_method=regflirt.FLIRT(use_verbose=args.verbose),
# registration_method=niftyreg.RegAladin(use_verbose=False),
dilation_radius=args.dilation_radius,
dilation_kernel="Ball",
)
data_preprocessing = dp.DataPreprocessing(
stacks=stacks,
segmentation_propagator=segmentation_propagator,
use_cropping_to_mask=True,
use_N4BiasFieldCorrector=args.bias_field_correction,
target_stack_index=target_stack_index,
boundary_i=args.boundary_stacks[0],
boundary_j=args.boundary_stacks[1],
boundary_k=args.boundary_stacks[2],
unit="mm",
)
data_preprocessing.run()
time_data_preprocessing = data_preprocessing.get_computational_time()
# Get preprocessed stacks
stacks = data_preprocessing.get_preprocessed_stacks()
# Define reference/target stack for registration and reconstruction
if args.reference is not None:
reference = st.Stack.from_filename(
file_path=args.reference,
file_path_mask=args.reference_mask,
extract_slices=False)
else:
reference = st.Stack.from_stack(stacks[target_stack_index])
# ------------------------Volume-to-Volume Registration--------------------
if len(stacks) > 1:
if args.v2v_method == "FLIRT":
# Define search angle ranges for FLIRT in all three dimensions
search_angles = ["-searchr%s -%d %d" %
(x, args.search_angle, args.search_angle)
for x in ["x", "y", "z"]]
options = (" ").join(search_angles)
# options += " -noresample"
vol_registration = regflirt.FLIRT(
registration_type="Rigid",
use_fixed_mask=True,
use_moving_mask=True,
options=options,
use_verbose=False,
)
else:
vol_registration = niftyreg.RegAladin(
registration_type="Rigid",
use_fixed_mask=True,
use_moving_mask=True,
# options="-ln 2 -voff",
use_verbose=False,
)
v2vreg = pipeline.VolumeToVolumeRegistration(
stacks=stacks,
reference=reference,
registration_method=vol_registration,
verbose=debug,
robust=args.v2v_robust,
)
v2vreg.run()
stacks = v2vreg.get_stacks()
time_registration = v2vreg.get_computational_time()
else:
time_registration = ph.get_zero_time()
# ---------------------------Intensity Correction--------------------------
if args.intensity_correction:
ph.print_title("Intensity Correction")
intensity_corrector = ic.IntensityCorrection()
intensity_corrector.use_individual_slice_correction(False)
intensity_corrector.use_reference_mask(True)
intensity_corrector.use_stack_mask(True)
intensity_corrector.use_verbose(False)
for i, stack in enumerate(stacks):
if i == target_stack_index:
ph.print_info("Stack %d (%s): Reference image. Skipped." % (
i + 1, stack.get_filename()))
continue
else:
ph.print_info("Stack %d (%s): Intensity Correction ... " % (
i + 1, stack.get_filename()), newline=False)
intensity_corrector.set_stack(stack)
intensity_corrector.set_reference(
stacks[target_stack_index].get_resampled_stack(
resampling_grid=stack.sitk,
interpolator="NearestNeighbor",
))
intensity_corrector.run_linear_intensity_correction()
stacks[i] = intensity_corrector.get_intensity_corrected_stack()
print("done (c1 = %g) " %
intensity_corrector.get_intensity_correction_coefficients())
# ---------------------------Create first volume---------------------------
time_tmp = ph.start_timing()
# Isotropic resampling to define HR target space
ph.print_title("Reconstruction Space Generation")
HR_volume = reference.get_isotropically_resampled_stack(
resolution=args.isotropic_resolution)
ph.print_info(
"Isotropic reconstruction space with %g mm resolution is created" %
HR_volume.sitk.GetSpacing()[0])
if args.reference is None:
# Create joint image mask in target space
joint_image_mask_builder = imb.JointImageMaskBuilder(
stacks=stacks,
target=HR_volume,
dilation_radius=1,
)
joint_image_mask_builder.run()
HR_volume = joint_image_mask_builder.get_stack()
ph.print_info(
"Isotropic reconstruction space is centered around "
"joint stack masks. ")
# Crop to space defined by mask (plus extra margin)
HR_volume = HR_volume.get_cropped_stack_based_on_mask(
boundary_i=args.extra_frame_target,
boundary_j=args.extra_frame_target,
boundary_k=args.extra_frame_target,
unit="mm",
)
# Create first volume
# If outlier rejection is activated, eliminate obvious outliers early
# from stack and re-run SDA to get initial volume without them
ph.print_title("First Estimate of HR Volume")
if args.outlier_rejection and threshold_v2v > -1:
ph.print_subtitle("SDA Approximation")
SDA = sda.ScatteredDataApproximation(
stacks, HR_volume, sigma=args.sigma)
SDA.run()
HR_volume = SDA.get_reconstruction()
# Identify and reject outliers
ph.print_subtitle("Eliminate slice outliers (%s < %g)" % (
rejection_measure, threshold_v2v))
outlier_rejector = outre.OutlierRejector(
stacks=stacks,
reference=HR_volume,
threshold=threshold_v2v,
measure=rejection_measure,
verbose=True,
)
outlier_rejector.run()
stacks = outlier_rejector.get_stacks()
ph.print_subtitle("SDA Approximation Image")
SDA = sda.ScatteredDataApproximation(
stacks, HR_volume, sigma=args.sigma)
SDA.run()
HR_volume = SDA.get_reconstruction()
ph.print_subtitle("SDA Approximation Image Mask")
SDA = sda.ScatteredDataApproximation(
stacks, HR_volume, sigma=args.sigma, sda_mask=True)
SDA.run()
# HR volume contains updated mask based on SDA
HR_volume = SDA.get_reconstruction()
HR_volume.set_filename(SDA.get_setting_specific_filename())
time_reconstruction = ph.stop_timing(time_tmp)
if args.verbose:
tmp = list(stacks)
tmp.insert(0, HR_volume)
sitkh.show_stacks(tmp, segmentation=HR_volume, viewer=args.viewer)
# -----------Two-step Slice-to-Volume Registration-Reconstruction----------
if args.two_step_cycles > 0:
# Slice-to-volume registration set-up
if args.metric == "ANTSNeighborhoodCorrelation":
metric_params = {"radius": args.metric_radius}
else:
metric_params = None
registration = regsitk.SimpleItkRegistration(
moving=HR_volume,
use_fixed_mask=True,
use_moving_mask=True,
interpolator="Linear",
metric=args.metric,
metric_params=metric_params,
use_multiresolution_framework=args.multiresolution,
shrink_factors=args.shrink_factors,
smoothing_sigmas=args.smoothing_sigmas,
initializer_type="SelfGEOMETRY",
optimizer="ConjugateGradientLineSearch",
optimizer_params={
"learningRate": 1,
"numberOfIterations": 100,
"lineSearchUpperLimit": 2,
},
scales_estimator="Jacobian",
use_verbose=debug,
)
# Volumetric reconstruction set-up
if args.sda:
recon_method = sda.ScatteredDataApproximation(
stacks,
HR_volume,
sigma=args.sigma,
use_masks=args.use_masks_srr,
)
alpha_range = [args.sigma, args.alpha]
else:
recon_method = tk.TikhonovSolver(
stacks=stacks,
reconstruction=HR_volume,
reg_type="TK1",
minimizer="lsmr",
alpha=args.alpha_first,
iter_max=np.min([args.iter_max_first, args.iter_max]),
verbose=True,
use_masks=args.use_masks_srr,
)
alpha_range = [args.alpha_first, args.alpha]
# Define the regularization parameters for the individual
# reconstruction steps in the two-step cycles
alphas = np.linspace(
alpha_range[0], alpha_range[1], args.two_step_cycles)
# Define outlier rejection threshold after each S2V-reg step
thresholds = np.linspace(
args.threshold_first, args.threshold, args.two_step_cycles)
two_step_s2v_reg_recon = \
pipeline.TwoStepSliceToVolumeRegistrationReconstruction(
stacks=stacks,
reference=HR_volume,
registration_method=registration,
reconstruction_method=recon_method,
cycles=args.two_step_cycles,
alphas=alphas[0:args.two_step_cycles - 1],
outlier_rejection=args.outlier_rejection,
threshold_measure=rejection_measure,
thresholds=thresholds,
interleave=args.interleave,
viewer=args.viewer,
verbose=args.verbose,
use_hierarchical_registration=args.s2v_hierarchical,
)
two_step_s2v_reg_recon.run()
HR_volume_iterations = \
two_step_s2v_reg_recon.get_iterative_reconstructions()
time_registration += \
two_step_s2v_reg_recon.get_computational_time_registration()
time_reconstruction += \
two_step_s2v_reg_recon.get_computational_time_reconstruction()
stacks = two_step_s2v_reg_recon.get_stacks()
# no two-step s2v-registration/reconstruction iterations
else:
HR_volume_iterations = []
# Write motion-correction results
ph.print_title("Write Motion Correction Results")
if args.write_motion_correction:
dir_output_mc = os.path.join(
dir_output, args.subfolder_motion_correction)
ph.clear_directory(dir_output_mc)
for stack in stacks:
stack.write(
dir_output_mc,
write_stack=False,
write_mask=False,
write_slices=False,
write_transforms=True,
write_transforms_history=args.transforms_history,
)
if args.outlier_rejection:
deleted_slices_dic = {}
for i, stack in enumerate(stacks):
deleted_slices = stack.get_deleted_slice_numbers()
deleted_slices_dic[stack.get_filename()] = deleted_slices
# check whether any stack was removed entirely
stacks0 = data_preprocessing.get_preprocessed_stacks()
if len(stacks) != len(stacks0):
stacks_remain = [s.get_filename() for s in stacks]
for stack in stacks0:
if stack.get_filename() in stacks_remain:
continue
# add info that all slices of this stack were rejected
deleted_slices = [
slice.get_slice_number()
for slice in stack.get_slices()
]
deleted_slices_dic[stack.get_filename()] = deleted_slices
ph.print_info(
"All slices of stack '%s' were rejected entirely. "
"Information added." % stack.get_filename())
ph.write_dictionary_to_json(
deleted_slices_dic,
os.path.join(
dir_output,
args.subfolder_motion_correction,
"rejected_slices.json"
)
)
# ---------------------Final Volumetric Reconstruction---------------------
ph.print_title("Final Volumetric Reconstruction")
if args.sda:
recon_method = sda.ScatteredDataApproximation(
stacks,
HR_volume,
sigma=args.alpha,
use_masks=args.use_masks_srr,
)
else:
if args.reconstruction_type in ["TVL2", "HuberL2"]:
recon_method = pd.PrimalDualSolver(
stacks=stacks,
reconstruction=HR_volume,
reg_type="TV" if args.reconstruction_type == "TVL2" else "huber",
iterations=args.iterations,
use_masks=args.use_masks_srr,
)
else:
recon_method = tk.TikhonovSolver(
stacks=stacks,
reconstruction=HR_volume,
reg_type="TK1" if args.reconstruction_type == "TK1L2" else "TK0",
use_masks=args.use_masks_srr,
)
recon_method.set_alpha(args.alpha)
recon_method.set_iter_max(args.iter_max)
recon_method.set_verbose(True)
recon_method.run()
time_reconstruction += recon_method.get_computational_time()
HR_volume_final = recon_method.get_reconstruction()
ph.print_subtitle("Final SDA Approximation Image Mask")
SDA = sda.ScatteredDataApproximation(
stacks, HR_volume_final, sigma=args.sigma, sda_mask=True)
SDA.run()
# HR volume contains updated mask based on SDA
HR_volume_final = SDA.get_reconstruction()
time_reconstruction += SDA.get_computational_time()
elapsed_time_total = ph.stop_timing(time_start)
# Write SRR result
filename = recon_method.get_setting_specific_filename()
HR_volume_final.set_filename(filename)
dw.DataWriter.write_image(
HR_volume_final.sitk,
args.output,
description=filename)
dw.DataWriter.write_mask(
HR_volume_final.sitk_mask,
ph.append_to_filename(args.output, "_mask"),
description=SDA.get_setting_specific_filename())
HR_volume_iterations.insert(0, HR_volume_final)
for stack in stacks:
HR_volume_iterations.append(stack)
if args.verbose:
sitkh.show_stacks(
HR_volume_iterations,
segmentation=HR_volume_final,
viewer=args.viewer,
)
# Summary
ph.print_title("Summary")
exe_file_info = os.path.basename(os.path.abspath(__file__)).split(".")[0]
print("%s | Computational Time for Data Preprocessing: %s" %
(exe_file_info, time_data_preprocessing))
print("%s | Computational Time for Registrations: %s" %
(exe_file_info, time_registration))
print("%s | Computational Time for Reconstructions: %s" %
(exe_file_info, time_reconstruction))
print("%s | Computational Time for Entire Reconstruction Pipeline: %s" %
(exe_file_info, elapsed_time_total))
ph.print_line_separator()
return 0