def export_comparison_to_file(nda_original, nda_projected, path_to_file, resize, extension="png"): dir_tmp = os.path.join(DIR_TMP, "ImageMagick") ph.clear_directory(dir_tmp, verbose=False) for k in range(nda_original.shape[0]): ctr = k + 1 # Export as individual image side-by-side _export_image_side_by_side( nda_left=nda_original[k, :, :], nda_right=nda_projected[k, :, :], label_left="original", label_right="projected", path_to_file=os.path.join(dir_tmp, "%03d.%s" % (ctr, extension)), ctr=ctr, resize=resize, extension=extension, ) # Combine all side-by-side images to single pdf _export_pdf_from_side_by_side_images(dir_tmp, path_to_file, extension=extension) ph.print_info("Side-by-side comparison exported to '%s'" % path_to_file) # Delete tmp directory ph.delete_directory(dir_tmp, verbose=False)
def _export_image_side_by_side( nda_left, nda_right, label_left, label_right, path_to_file, ctr, resize, extension, border=10, background="black", fill_ctr="orange", fill_label="white", font="Arial", pointsize=12, ): dir_output = os.path.join(DIR_TMP, "ImageMagick", "side-by-side") ph.clear_directory(dir_output, verbose=False) path_to_left = os.path.join(dir_output, "left.%s" % extension) path_to_right = os.path.join(dir_output, "right.%s" % extension) ph.write_image(nda_left, path_to_left, verbose=False) ph.write_image(nda_right, path_to_right, verbose=False) _resize_image(path_to_left, resize=resize) _resize_image(path_to_right, resize=resize) cmd_args = [] cmd_args.append("-geometry +%d+%d" % (border, border)) cmd_args.append("-background %s" % background) cmd_args.append("-font %s" % font) cmd_args.append("-pointsize %s" % pointsize) cmd_args.append("-fill %s" % fill_ctr) cmd_args.append("-gravity SouthWest -draw \"text 0,0 '%d'\"" % ctr) cmd_args.append("-fill %s" % fill_label) cmd_args.append("-label '%s' %s" % (label_left, path_to_left)) cmd_args.append("-label '%s' %s" % (label_right, path_to_right)) cmd_args.append("%s" % path_to_file) cmd = "montage %s" % (" ").join(cmd_args) ph.execute_command(cmd, verbose=False)
def _run(self, id=""): # Clean output directory first ph.clear_directory(self._dir_tmp, verbose=0) self._run_registration_[self._registration_type](id)
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
def main(): parser = argparse.ArgumentParser(description="Create video from volume") parser.add_argument( '--image', required=True, type=str, help="Path to 3D image (*.nii.gz or *.nii)", ) parser.add_argument( '--fps', required=False, type=float, help="Frames per second", default=1, ) parser.add_argument( '--axis', required=False, type=int, help="Axis to sweep through the volume", default=2, ) parser.add_argument( '--begin', required=False, type=int, help="Starting slice for video", default=None, ) parser.add_argument( '--end', required=False, type=int, help="End slice for video", default=None, ) parser.add_argument( '--output', required=True, type=str, help="Path to output video (*.mp4)", ) args = parser.parse_args() image_sitk = sitk.ReadImage(args.image) image_nda = sitk.GetArrayFromImage(image_sitk) scale = np.max(image_nda) filename = os.path.basename(args.output).split(".")[0] dir_output = os.path.dirname(args.output) dir_output_slices = os.path.join(dir_output, "slices") ph.create_directory(dir_output_slices) ph.clear_directory(dir_output_slices) splitter = vol_split.VolumeSplitter(image_nda, axis=args.axis) splitter.rescale_array(scale=scale) splitter.export_slices( dir_output=dir_output_slices, filename=filename, begin=args.begin, end=args.end, ) splitter.create_video( dir_input_slices=dir_output_slices, path_to_video=args.output, fps=args.fps, ) return 0
def main(): time_start = ph.start_timing() flag_individual_cases_only = 1 flag_batch_script = 0 batch_ctr = [32] flag_correct_bias_field = 0 # flag_correct_intensities = 0 flag_collect_segmentations = 0 flag_select_images_segmentations = 0 flag_reconstruct_volume_subject_space = 0 flag_reconstruct_volume_subject_space_irtk = 0 flag_reconstruct_volume_subject_space_show_comparison = 0 flag_register_to_template = 0 flag_register_to_template_irtk = 0 flag_show_srr_template_space = 0 flag_reconstruct_volume_template_space = 0 flag_collect_volumetric_reconstruction_results = 0 flag_show_volumetric_reconstruction_results = 0 flag_rsync_stuff = 0 # Analysis flag_remove_failed_cases_for_analysis = 1 flag_postop = 2 # 0... preop, 1...postop, 2... pre+postop flag_evaluate_image_similarities = 0 flag_analyse_image_similarities = 1 flag_evaluate_slice_residual_similarities = 0 flag_analyse_slice_residual_similarities = 0 flag_analyse_stacks = 0 flag_analyse_qualitative_assessment = 0 flag_collect_data_blinded_analysis = 0 flag_anonymize_data_blinded_analysis = 0 provide_comparison = 0 intensity_correction = 1 isotropic_resolution = 0.75 alpha = 0.02 outlier_rejection = 1 threshold = 0.7 threshold_first = 0.6 # metric = "ANTSNeighborhoodCorrelation" # metric_radius = 5 # multiresolution = 0 prefix_srr = "srr_" prefix_srr_qa = "masked_" # ----------------------------------Set Up--------------------------------- if flag_correct_bias_field: dir_batch = os.path.join(utils.DIR_BATCH_ROOT, "BiasFieldCorrection") elif flag_reconstruct_volume_subject_space: dir_batch = os.path.join(utils.DIR_BATCH_ROOT, "VolumetricReconstructionSubjectSpace") elif flag_register_to_template: dir_batch = os.path.join(utils.DIR_BATCH_ROOT, "VolumetricReconstructionRegisterToTemplate") elif flag_reconstruct_volume_template_space: dir_batch = os.path.join(utils.DIR_BATCH_ROOT, "VolumetricReconstructionTemplateSpace") else: dir_batch = os.path.join(utils.DIR_BATCH_ROOT, "foo") file_prefix_batch = os.path.join(dir_batch, "command") if flag_batch_script: verbose = 0 else: verbose = 1 data_reader = dr.ExcelSheetDataReader(utils.EXCEL_FILE) data_reader.read_data() cases = data_reader.get_data() if flag_analyse_qualitative_assessment: data_reader = dr.ExcelSheetQualitativeAssessmentReader(utils.QA_FILE) data_reader.read_data() qualitative_assessment = data_reader.get_data() statistical_evaluation = se.StatisticalEvaluation( qualitative_assessment) statistical_evaluation.run_tests(ref="seg_manual") ph.exit() cases_similarities = [] cases_stacks = [] if flag_individual_cases_only: N_cases = len(INDIVIDUAL_CASE_IDS) else: N_cases = len(cases.keys()) i_case = 0 for case_id in sorted(cases.keys()): if flag_individual_cases_only and case_id not in INDIVIDUAL_CASE_IDS: continue if not flag_analyse_image_similarities and \ not flag_analyse_slice_residual_similarities: i_case += 1 ph.print_title("%d/%d: %s" % (i_case, N_cases, case_id)) if flag_rsync_stuff: dir_output = utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode="") dir_input = re.sub("Volumes/spina/", "Volumes/medic-volumetric_res/SpinaBifida/", dir_output) cmd = "rsync -avuhn --exclude 'motion_correction' %sseg_manual %s" % ( dir_input, dir_output) ph.print_execution(cmd) # ph.execute_command(cmd) # -------------------------Correct Bias Field-------------------------- if flag_correct_bias_field: filenames = utils.get_filenames_preprocessing_bias_field(case_id) paths_to_filenames = [ os.path.join(utils.get_directory_case_original(case_id), f) for f in filenames ] dir_output = utils.get_directory_case_preprocessing( case_id, stage="01_N4ITK") # no image found matching the pattern if len(paths_to_filenames) == 0: continue cmd_args = [] cmd_args.append("--filenames %s" % " ".join(paths_to_filenames)) cmd_args.append("--dir-output %s" % dir_output) cmd_args.append("--prefix-output ''") cmd = "niftymic_correct_bias_field %s" % (" ").join(cmd_args) ph.execute_command(cmd, flag_print_to_file=flag_batch_script, path_to_file="%s%d.txt" % (file_prefix_batch, ph.add_one(batch_ctr))) # # Skip case in case segmentations have not been provided yet # if not ph.directory_exists(utils.get_directory_case_segmentation( # case_id, utils.SEGMENTATION_INIT, SEG_MODES[0])): # continue # ------------------------Collect Segmentations------------------------ if flag_collect_segmentations: # Skip case in case segmentations have been collected already if ph.directory_exists( utils.get_directory_case_segmentation( case_id, utils.SEGMENTATION_SELECTED, SEG_MODES[0])): ph.print_info("skipped") continue filenames = utils.get_segmented_image_filenames( case_id, subfolder=utils.SEGMENTATION_INIT) for i_seg_mode, seg_mode in enumerate(SEG_MODES): directory_selected = utils.get_directory_case_segmentation( case_id, utils.SEGMENTATION_SELECTED, seg_mode) ph.create_directory(directory_selected) paths_to_filenames_init = [ os.path.join( utils.get_directory_case_segmentation( case_id, utils.SEGMENTATION_INIT, seg_mode), f) for f in filenames ] paths_to_filenames_selected = [ os.path.join(directory_selected, f) for f in filenames ] for i in range(len(filenames)): cmd = "cp -p %s %s" % (paths_to_filenames_init[i], paths_to_filenames_selected[i]) # ph.print_execution(cmd) ph.execute_command(cmd) if flag_select_images_segmentations: filenames = utils.get_segmented_image_filenames( case_id, subfolder=utils.SEGMENTATION_SELECTED) paths_to_filenames = [ os.path.join( utils.get_directory_case_preprocessing(case_id, stage="01_N4ITK"), f) for f in filenames ] paths_to_filenames_masks = [ os.path.join( utils.get_directory_case_segmentation( case_id, utils.SEGMENTATION_SELECTED, "seg_manual"), f) for f in filenames ] for i in range(len(filenames)): ph.show_niftis( [paths_to_filenames[i]], segmentation=paths_to_filenames_masks[i], # viewer="fsleyes", ) ph.pause() ph.killall_itksnap() # # -------------------------Correct Intensities----------------------- # if flag_correct_intensities: # filenames = utils.get_segmented_image_filenames(case_id) # paths_to_filenames_bias = [os.path.join( # utils.get_directory_case_preprocessing( # case_id, stage="01_N4ITK"), f) for f in filenames] # print paths_to_filenames_bias # -----------------Reconstruct Volume in Subject Space----------------- if flag_reconstruct_volume_subject_space: filenames = utils.get_segmented_image_filenames( case_id, subfolder=utils.SEGMENTATION_SELECTED) # filenames = filenames[0:2] paths_to_filenames = [ os.path.join( utils.get_directory_case_preprocessing(case_id, stage="01_N4ITK"), f) for f in filenames ] # Estimate target stack target_stack_index = utils.get_target_stack_index( case_id, utils.SEGMENTATION_SELECTED, "seg_auto", filenames) for i, seg_mode in enumerate(SEG_MODES): # Get mask filenames paths_to_filenames_masks = [ os.path.join( utils.get_directory_case_segmentation( case_id, utils.SEGMENTATION_SELECTED, seg_mode), f) for f in filenames ] if flag_reconstruct_volume_subject_space_irtk: if seg_mode != "seg_manual": continue utils.export_irtk_call_to_workstation( case_id=case_id, filenames=filenames, seg_mode=seg_mode, isotropic_resolution=isotropic_resolution, target_stack_index=target_stack_index, kernel_mask_dilation=(15, 15, 4)) else: dir_output = utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="subject_space", seg_mode=seg_mode) # dir_output = "/tmp/foo" cmd_args = [] cmd_args.append("--filenames %s" % " ".join(paths_to_filenames)) cmd_args.append("--filenames-masks %s" % " ".join(paths_to_filenames_masks)) cmd_args.append("--dir-output %s" % dir_output) cmd_args.append("--use-masks-srr 0") cmd_args.append("--isotropic-resolution %f" % isotropic_resolution) cmd_args.append("--target-stack-index %d" % target_stack_index) cmd_args.append("--intensity-correction %d" % intensity_correction) cmd_args.append("--outlier-rejection %d" % outlier_rejection) cmd_args.append("--threshold-first %f" % threshold_first) cmd_args.append("--threshold %f" % threshold) # cmd_args.append("--metric %s" % metric) # cmd_args.append("--multiresolution %d" % multiresolution) # cmd_args.append("--metric-radius %s" % metric_radius) # if i > 0: # cmd_args.append("--reconstruction-space %s" % ( # utils.get_path_to_recon( # utils.get_directory_case_recon_seg_mode( # case_id, "seg_manual")))) # cmd_args.append("--two-step-cycles 0") cmd_args.append("--verbose %d" % verbose) cmd_args.append("--provide-comparison %d" % provide_comparison) # cmd_args.append("--iter-max 1") cmd = "niftymic_reconstruct_volume %s" % ( " ").join(cmd_args) ph.execute_command( cmd, flag_print_to_file=flag_batch_script, path_to_file="%s%d.txt" % (file_prefix_batch, ph.add_one(batch_ctr))) if flag_reconstruct_volume_subject_space_show_comparison: recon_paths = [] for seg_mode in SEG_MODES: path_to_recon = utils.get_path_to_recon( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="subject_space", seg_mode=seg_mode)) recon_paths.append(path_to_recon) recon_path_irtk = os.path.join( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="subject_space", seg_mode="IRTK"), "IRTK_SRR.nii.gz") show_modes = list(SEG_MODES) if ph.file_exists(recon_path_irtk): recon_paths.append(recon_path_irtk) show_modes.append("irtk") ph.show_niftis(recon_paths) ph.print_info("Sequence: %s" % (" -- ").join(show_modes)) ph.pause() ph.killall_itksnap() # -------------------------Register to template------------------------ if flag_register_to_template: for seg_mode in SEG_MODES: cmd_args = [] # register seg_auto-recon to template space if seg_mode == "seg_auto": path_to_recon = utils.get_path_to_recon( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="subject_space", seg_mode=seg_mode)) template_stack_estimator = \ tse.TemplateStackEstimator.from_mask( ph.append_to_filename(path_to_recon, "_mask")) path_to_reference = \ template_stack_estimator.get_path_to_template() dir_input_motion_correction = os.path.join( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="subject_space", seg_mode=seg_mode), "motion_correction") dir_output = utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode=seg_mode) # dir_output = "/home/mebner/tmp" # # ------- DELETE ----- # dir_output = re.sub("data", "foo+1", dir_output) # dir_output = re.sub( # "volumetric_reconstruction/20180126/template_space/seg_auto", # "", dir_output) # # ------- # cmd_args.append("--use-fixed-mask 1") cmd_args.append("--use-moving-mask 1") # HACK path_to_initial_transform = os.path.join( utils.DIR_INPUT_ROOT_DATA, case_id, "volumetric_reconstruction", "20180126", "template_space", "seg_manual", "registration_transform_sitk.txt") cmd_args.append("--initial-transform %s" % path_to_initial_transform) cmd_args.append("--use-flirt 0") cmd_args.append("--use-regaladin 1") cmd_args.append("--test-ap-flip 0") # register remaining recons to registered seg_auto-recon else: path_to_reference = utils.get_path_to_recon( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode="seg_auto"), suffix="ResamplingToTemplateSpace", ) path_to_initial_transform = os.path.join( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode="seg_auto"), "registration_transform_sitk.txt") path_to_recon = utils.get_path_to_recon( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="subject_space", seg_mode=seg_mode)) dir_input_motion_correction = os.path.join( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="subject_space", seg_mode=seg_mode), "motion_correction") dir_output = utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode=seg_mode) cmd_args.append("--use-fixed-mask 0") cmd_args.append("--use-moving-mask 0") cmd_args.append("--initial-transform %s" % path_to_initial_transform) cmd_args.append("--use-flirt 0") cmd_args.append("--use-regaladin 1") cmd_args.append("--test-ap-flip 0") cmd_args.append("--moving %s" % path_to_recon) cmd_args.append("--fixed %s" % path_to_reference) cmd_args.append("--dir-input %s" % dir_input_motion_correction) cmd_args.append("--dir-output %s" % dir_output) cmd_args.append("--write-transform 1") cmd_args.append("--verbose %d" % verbose) cmd = "niftymic_register_image %s" % (" ").join(cmd_args) ph.execute_command(cmd, flag_print_to_file=flag_batch_script, path_to_file="%s%d.txt" % (file_prefix_batch, ph.add_one(batch_ctr))) if flag_register_to_template_irtk: dir_input = utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="subject_space", seg_mode="IRTK") dir_output = utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode="IRTK") path_to_recon = os.path.join(dir_input, "IRTK_SRR.nii.gz") path_to_reference = utils.get_path_to_recon( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode="seg_manual"), suffix="ResamplingToTemplateSpace", ) path_to_initial_transform = os.path.join( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode="seg_manual"), "registration_transform_sitk.txt") cmd_args = [] cmd_args.append("--fixed %s" % path_to_reference) cmd_args.append("--moving %s" % path_to_recon) cmd_args.append("--initial-transform %s" % path_to_initial_transform) cmd_args.append("--use-fixed-mask 0") cmd_args.append("--use-moving-mask 0") cmd_args.append("--use-flirt 0") cmd_args.append("--use-regaladin 1") cmd_args.append("--test-ap-flip 0") cmd_args.append("--dir-output %s" % dir_output) cmd_args.append("--verbose %d" % verbose) cmd = "niftymic_register_image %s" % (" ").join(cmd_args) ph.execute_command(cmd) if flag_show_srr_template_space: recon_paths = [] show_modes = list(SEG_MODES) # show_modes.append("IRTK") for seg_mode in show_modes: dir_input = utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode=seg_mode) # # ------- DELETE ----- # dir_input = re.sub("data", "foo+1", dir_input) # dir_input = re.sub( # "volumetric_reconstruction/20180126/template_space/seg_auto", # "", dir_input) # # ------- path_to_recon_space = utils.get_path_to_recon( dir_input, suffix="ResamplingToTemplateSpace", ) recon_paths.append(path_to_recon_space) ph.show_niftis(recon_paths) ph.print_info("Sequence: %s" % (" -- ").join(show_modes)) ph.pause() ph.killall_itksnap() # -----------------Reconstruct Volume in Template Space---------------- if flag_reconstruct_volume_template_space: for seg_mode in SEG_MODES: path_to_recon_space = utils.get_path_to_recon( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode=seg_mode), suffix="ResamplingToTemplateSpace", ) dir_input = os.path.join( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode=seg_mode), "motion_correction") dir_output = utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode=seg_mode) # dir_output = os.path.join("/tmp/spina/template_space/%s-%s" % ( # case_id, seg_mode)) cmd_args = [] cmd_args.append("--dir-input %s" % dir_input) cmd_args.append("--dir-output %s" % dir_output) cmd_args.append("--reconstruction-space %s" % path_to_recon_space) cmd_args.append("--alpha %s" % alpha) cmd_args.append("--verbose %s" % verbose) cmd_args.append("--use-masks-srr 0") # cmd_args.append("--minimizer L-BFGS-B") # cmd_args.append("--alpha 0.006") # cmd_args.append("--reconstruction-type HuberL2") # cmd_args.append("--data-loss arctan") # cmd_args.append("--iterations 5") # cmd_args.append("--data-loss-scale 0.7") cmd = "niftymic_reconstruct_volume_from_slices %s" % \ (" ").join(cmd_args) ph.execute_command(cmd, flag_print_to_file=flag_batch_script, path_to_file="%s%d.txt" % (file_prefix_batch, ph.add_one(batch_ctr))) # ----------------Collect SRR results in Template Space---------------- if flag_collect_volumetric_reconstruction_results: directory = utils.get_directory_case_recon_summary(case_id) ph.create_directory(directory) # clear potentially existing files cmd = "rm -f %s/*.nii.gz" % (directory) ph.execute_command(cmd) # Collect SRRs for seg_mode in SEG_MODES: path_to_recon_src = utils.get_path_to_recon( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode=seg_mode), ) path_to_recon = os.path.join( directory, "%s%s.nii.gz" % (prefix_srr, seg_mode)) cmd = "cp -p %s %s" % (path_to_recon_src, path_to_recon) ph.execute_command(cmd) # Collect IRTK recon path_to_recon_src = os.path.join( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode="IRTK"), "IRTK_SRR_LinearResamplingToTemplateSpace.nii.gz") path_to_recon = os.path.join(directory, "%s%s.nii.gz" % (prefix_srr, "irtk")) cmd = "cp -p %s %s" % (path_to_recon_src, path_to_recon) ph.execute_command(cmd) # Collect evaluation mask path_to_recon = utils.get_path_to_recon( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="subject_space", seg_mode="seg_auto")) template_stack_estimator = \ tse.TemplateStackEstimator.from_mask( ph.append_to_filename(path_to_recon, "_mask")) path_to_template = \ template_stack_estimator.get_path_to_template() path_to_template_mask_src = ph.append_to_filename( path_to_template, "_mask_dil") path_to_template_mask = "%s/" % directory cmd = "cp -p %s %s" % (path_to_template_mask_src, path_to_template_mask) ph.execute_command(cmd) if flag_show_volumetric_reconstruction_results: dir_output = utils.get_directory_case_recon_summary(case_id) paths_to_recons = [] for seg_mode in RECON_MODES: path_to_recon = os.path.join( dir_output, "%s%s.nii.gz" % (prefix_srr, seg_mode)) paths_to_recons.append(path_to_recon) path_to_mask = "%s/STA*.nii.gz" % dir_output cmd = ph.show_niftis(paths_to_recons, segmentation=path_to_mask) sitkh.write_executable_file([cmd], dir_output=dir_output) ph.pause() ph.killall_itksnap() # ---------------------Evaluate Image Similarities--------------------- if flag_evaluate_image_similarities: dir_input = utils.get_directory_case_recon_summary(case_id) dir_output = utils.get_directory_case_recon_similarities(case_id) paths_to_recons = [] for seg_mode in ["seg_auto", "detect", "irtk"]: path_to_recon = os.path.join( dir_input, "%s%s.nii.gz" % (prefix_srr, seg_mode)) paths_to_recons.append(path_to_recon) path_to_reference = os.path.join( dir_input, "%s%s.nii.gz" % (prefix_srr, "seg_manual")) path_to_reference_mask = utils.get_path_to_mask(dir_input) cmd_args = [] cmd_args.append("--filenames %s" % " ".join(paths_to_recons)) cmd_args.append("--reference %s" % path_to_reference) cmd_args.append("--reference-mask %s" % path_to_reference_mask) # cmd_args.append("--verbose 1") cmd_args.append("--dir-output %s" % dir_output) exe = re.sub("pyc", "py", os.path.abspath(evaluate_image_similarity.__file__)) cmd_args.insert(0, exe) # clear potentially existing files cmd = "rm -f %s/*.txt" % (dir_output) ph.execute_command(cmd) cmd = "python %s" % " ".join(cmd_args) ph.execute_command(cmd) # -----------------Evaluate Slice Residual Similarities---------------- if flag_evaluate_slice_residual_similarities: path_to_reference_mask = utils.get_path_to_mask( utils.get_directory_case_recon_summary(case_id)) dir_output_root = \ utils.get_directory_case_slice_residual_similarities(case_id) # clear potentially existing files # cmd = "rm -f %s/*.txt" % (dir_output_root) # ph.execute_command(cmd) for seg_mode in SEG_MODES: dir_input = os.path.join( utils.get_directory_case_recon_seg_mode( case_id=case_id, recon_space="template_space", seg_mode=seg_mode, ), "motion_correction") path_to_reference = os.path.join( utils.get_directory_case_recon_summary(case_id), "%s%s.nii.gz" % (prefix_srr, seg_mode)) dir_output = os.path.join(dir_output_root, seg_mode) cmd_args = [] cmd_args.append("--dir-input %s" % dir_input) cmd_args.append("--reference %s" % path_to_reference) cmd_args.append("--reference-mask %s" % path_to_reference_mask) cmd_args.append("--use-reference-mask 1") cmd_args.append("--use-slice-masks 0") # cmd_args.append("--verbose 1") cmd_args.append("--dir-output %s" % dir_output) exe = re.sub("pyc", "py", os.path.abspath(esrs.__file__)) cmd_args.insert(0, exe) cmd = "python %s" % " ".join(cmd_args) ph.execute_command(cmd) # Collect data for blinded analysis if flag_collect_data_blinded_analysis: if flag_remove_failed_cases_for_analysis and case_id in RECON_FAILED_CASE_IDS: continue dir_input = utils.get_directory_case_recon_summary(case_id) # pattern = "STA([0-9]+)[_]mask.nii.gz" pattern = "STA([0-9]+)[_]mask_dil.nii.gz" p = re.compile(pattern) gw = [ p.match(f).group(1) for f in os.listdir(dir_input) if p.match(f) ][0] dir_output = os.path.join( utils.get_directory_blinded_analysis(case_id, "open"), case_id) exe = re.sub("pyc", "py", os.path.abspath(mswm.__file__)) recons = [] for seg_mode in RECON_MODES: path_to_recon = os.path.join( dir_input, "%s%s.nii.gz" % (prefix_srr, seg_mode)) cmd_args = [] cmd_args.append("--filename %s" % path_to_recon) cmd_args.append("--gestational-age %s" % gw) cmd_args.append("--dir-output %s" % dir_output) cmd_args.append("--prefix-output %s" % prefix_srr_qa) cmd_args.append("--verbose 0") cmd_args.insert(0, exe) cmd = "python %s" % " ".join(cmd_args) # ph.execute_command(cmd) recon = "%s%s" % (prefix_srr_qa, os.path.basename(path_to_recon)) recons.append(recon) ph.write_show_niftis_exe(recons, dir_output) if flag_anonymize_data_blinded_analysis: dir_input = os.path.join( utils.get_directory_blinded_analysis(case_id, "open"), case_id) dir_output_dictionaries = utils.get_directory_anonymized_dictionares( case_id) dir_output_anonymized_images = os.path.join( utils.get_directory_blinded_analysis(case_id, "anonymized"), case_id) if not ph.directory_exists(dir_input): continue ph.create_directory(dir_output_dictionaries) ph.create_directory(dir_output_anonymized_images) data_anonymizer = da.DataAnonymizer() # Create random dictionary (only required once) # data_anonymizer.set_prefix_identifiers("%s_" % case_id) # data_anonymizer.read_nifti_filenames_from_directory(dir_input) # data_anonymizer.generate_identifiers() # data_anonymizer.generate_randomized_dictionary() # data_anonymizer.write_dictionary( # dir_output_dictionaries, "dictionary_%s" % case_id) # Read dictionary data_anonymizer.read_dictionary(dir_output_dictionaries, "dictionary_%s" % case_id) # Anonymize files if 0: ph.clear_directory(dir_output_anonymized_images) data_anonymizer.anonymize_files(dir_input, dir_output_anonymized_images) # Write executable script filenames = [ "%s.nii.gz" % f for f in sorted(data_anonymizer.get_identifiers()) ] ph.write_show_niftis_exe(filenames, dir_output_anonymized_images) # Reveal anonymized files if 1: filenames = data_anonymizer.reveal_anonymized_files( dir_output_anonymized_images) filenames = sorted(["%s" % f for f in filenames]) ph.write_show_niftis_exe(filenames, dir_output_anonymized_images) # Reveal additional, original files # data_anonymizer.reveal_original_files(dir_output) # relative_directory = re.sub( # utils.get_directory_blinded_analysis(case_id, "anonymized"), # ".", # dir_output_anonymized_images) # paths_to_filenames = [os.path.join( # relative_directory, f) for f in filenames] # ---------------------Analyse Image Similarities--------------------- if flag_analyse_image_similarities or \ flag_analyse_slice_residual_similarities or \ flag_analyse_stacks: if flag_remove_failed_cases_for_analysis: if case_id in RECON_FAILED_CASE_IDS: continue if cases[case_id]['postrep'] == flag_postop or flag_postop == 2: cases_similarities.append(case_id) cases_stacks.append( utils.get_segmented_image_filenames( case_id, # subfolder=utils.SEGMENTATION_INIT, subfolder=utils.SEGMENTATION_SELECTED, )) dir_output_analysis = os.path.join( # "/Users/mebner/UCL/UCL/Publications", "/home/mebner/Dropbox/UCL/Publications", "2018_MICCAI/brain_reconstruction_paper") if flag_analyse_image_similarities: dir_inputs = [] filename = "image_similarities_postop%d.txt" % flag_postop for case_id in cases_similarities: dir_inputs.append( utils.get_directory_case_recon_similarities(case_id)) cmd_args = [] cmd_args.append("--dir-inputs %s" % " ".join(dir_inputs)) cmd_args.append("--dir-output %s" % dir_output_analysis) cmd_args.append("--filename %s" % filename) exe = re.sub("pyc", "py", os.path.abspath(src.analyse_image_similarities.__file__)) cmd_args.insert(0, exe) cmd = "python %s" % " ".join(cmd_args) ph.execute_command(cmd) if flag_analyse_slice_residual_similarities: dir_inputs = [] filename = "slice_residuals_postop%d.txt" % flag_postop for case_id in cases_similarities: dir_inputs.append( utils.get_directory_case_slice_residual_similarities(case_id)) cmd_args = [] cmd_args.append("--dir-inputs %s" % " ".join(dir_inputs)) cmd_args.append("--subfolder %s" % " ".join(SEG_MODES)) cmd_args.append("--dir-output %s" % dir_output_analysis) cmd_args.append("--filename %s" % filename) exe = re.sub( "pyc", "py", os.path.abspath(src.analyse_slice_residual_similarities.__file__)) cmd_args.insert(0, exe) cmd = "python %s" % " ".join(cmd_args) # print len(cases_similarities) # print cases_similarities ph.execute_command(cmd) if flag_analyse_stacks: cases_stacks_N = [len(s) for s in cases_stacks] ph.print_subtitle("%d cases -- Number of stacks" % len(cases_stacks)) ph.print_info("min: %g" % np.min(cases_stacks_N)) ph.print_info("mean: %g" % np.mean(cases_stacks_N)) ph.print_info("median: %g" % np.median(cases_stacks_N)) ph.print_info("max: %g" % np.max(cases_stacks_N)) elapsed_time = ph.stop_timing(time_start) ph.print_title("Summary") print("Computational Time for Pipeline: %s" % (elapsed_time)) return 0