Index

A

add_background_fluctuation() (in module algotom.util.simulation) add_noise() (in module algotom.util.simulation) add_stripe_artifact() (in module algotom.util.simulation) algotom module algotom.io.converter module algotom.io.loadersaver module algotom.post.postprocessing module algotom.prep.calculation module algotom.prep.conversion module algotom.prep.correction module algotom.prep.filtering module algotom.prep.phase module algotom.prep.removal module

algotom.rec.reconstruction module algotom.rec.vertrec module algotom.util.calibration module algotom.util.correlation module algotom.util.simulation module algotom.util.utility module align_image_stacks() (in module algotom.prep.phase) apply_1d_regularizer() (in module algotom.util.utility) apply_circular_ramp_filter() (in module algotom.rec.reconstruction) apply_filter_to_wavelet_component() (in module algotom.util.utility) apply_gaussian_filter() (in module algotom.util.utility) apply_method_to_multiple_sinograms() (in module algotom.util.utility) apply_ramp_filter() (in module algotom.rec.reconstruction) apply_regularization_filter() (in module algotom.util.utility) apply_wavelet_decomposition() (in module algotom.util.utility) apply_wavelet_reconstruction() (in module algotom.util.utility) astra_reconstruction() (in module algotom.rec.reconstruction)

B

back_projection_cpu() (in module algotom.rec.reconstruction) back_projection_gpu() (in module algotom.rec.reconstruction) back_projection_gpu_chunk() (in module algotom.rec.reconstruction)

beam_hardening_correction() (in module algotom.prep.correction) binarize_image() (in module algotom.util.calibration) bpf_reconstruction() (in module algotom.rec.reconstruction)

C

calculate_center_metric() (in module algotom.prep.calculation) calculate_curvature() (in module algotom.prep.calculation) calculate_distance() (in module algotom.util.calibration) calculate_maximum_index() (in module algotom.prep.calculation) calculate_reconstructable_height() (in module algotom.prep.calculation) calculate_regularization_coefficient() (in module algotom.util.utility) calculate_threshold() (in module algotom.util.calibration) check_dot_size() (in module algotom.util.calibration)

check_level() (in module algotom.util.utility) check_zinger_size() (in module algotom.prep.removal) coarse_search_cor() (in module algotom.prep.calculation) complex_gradient() (in module algotom.prep.calculation) convert_sinogram_180_to_360() (in module algotom.prep.conversion) convert_sinogram_360_to_180() (in module algotom.prep.conversion) convert_tif_to_hdf() (in module algotom.io.converter) convert_to_Xray_image() (in module algotom.util.simulation) correlation_metric() (in module algotom.prep.calculation)

D

detect_sample() (in module algotom.util.utility) detect_stripe() (in module algotom.util.utility) dfi_reconstruction() (in module algotom.rec.reconstruction) double_wedge_filter() (in module algotom.prep.filtering)

downsample() (in module algotom.post.postprocessing) downsample_cor() (in module algotom.prep.calculation) downsample_dataset() (in module algotom.post.postprocessing) dtype (algotom.io.converter.HdfEmulatorFromTif property)

E

extend_sinogram() (in module algotom.prep.conversion)

extract_tif_from_hdf() (in module algotom.io.converter)

F

fbp_reconstruction() (in module algotom.rec.reconstruction) find_center_360() (in module algotom.prep.calculation) find_center_based_phase_correlation() (in module algotom.prep.calculation) find_center_based_slice_metric() (in module algotom.rec.reconstruction) find_center_projection() (in module algotom.prep.calculation) find_center_vertical_slice() (in module algotom.rec.vertrec) find_center_visual_sinograms() (in module algotom.util.utility) find_center_visual_slices() (in module algotom.rec.reconstruction) (in module algotom.util.utility) find_center_visual_vertical_slices() (in module algotom.rec.vertrec) find_center_vo() (in module algotom.prep.calculation) find_file() (in module algotom.io.loadersaver) find_global_shift_based_local_shifts() (in module algotom.util.correlation) find_hdf_key() (in module algotom.io.loadersaver) find_local_shifts() (in module algotom.util.correlation)

find_local_shifts_umpa() (in module algotom.util.correlation) find_overlap() (in module algotom.prep.calculation) find_overlap_multiple() (in module algotom.prep.calculation) find_shift_based_correlation_map() (in module algotom.util.correlation) find_shift_based_phase_correlation() (in module algotom.prep.calculation) find_shift_between_image_stacks() (in module algotom.prep.phase) find_shift_between_sample_images() (in module algotom.prep.phase) find_tilt_roll() (in module algotom.util.calibration) find_tilt_roll_based_ellipse_fit() (in module algotom.util.calibration) find_tilt_roll_based_linear_fit() (in module algotom.util.calibration) fine_search_cor() (in module algotom.prep.calculation) fit_points_to_ellipse() (in module algotom.util.calibration) fix_non_sample_areas() (in module algotom.util.utility) flat_field_correction() (in module algotom.prep.correction) fresnel_filter() (in module algotom.prep.filtering)

G

generate_blob_mask() (in module algotom.prep.removal) generate_correlation_map() (in module algotom.util.correlation) generate_fitted_image() (in module algotom.util.utility) generate_full_sinogram_helical_scan() (in module algotom.prep.conversion) generate_mapping_coordinate() (in module algotom.rec.reconstruction) generate_sinogram_helical_scan() (in module algotom.prep.conversion) generate_spiral_positions() (in module algotom.util.utility) generate_tilted_profile_chunk() (in module algotom.prep.correction) generate_tilted_profile_line() (in module algotom.prep.correction) generate_tilted_sinogram() (in module algotom.prep.correction) generate_tilted_sinogram_chunk() (in module algotom.prep.correction) get_dot_size() (in module algotom.util.calibration)

get_hdf_information() (in module algotom.io.loadersaver) get_hdf_tree() (in module algotom.io.loadersaver) get_image_stack() (in module algotom.io.loadersaver) get_quality_map() (in module algotom.prep.phase) get_reference_sample_stacks() (in module algotom.io.loadersaver) get_reference_sample_stacks_dls() (in module algotom.io.loadersaver) get_statistical_information() (in module algotom.post.postprocessing) get_statistical_information_dataset() (in module algotom.post.postprocessing) get_tif_stack() (in module algotom.io.loadersaver) get_transmission_dark_field_signal() (in module algotom.prep.phase) get_weight_mask() (in module algotom.prep.phase) gridrec_reconstruction() (in module algotom.rec.reconstruction)

H

HdfEmulatorFromTif (class in algotom.io.converter)

I

interpolate_inside_stripe() (in module algotom.util.utility)

invert_dot_contrast() (in module algotom.util.calibration)

J

join_image() (in module algotom.prep.conversion)

join_image_multiple() (in module algotom.prep.conversion)

L

load_distortion_coefficient() (in module algotom.io.loadersaver) load_hdf() (in module algotom.io.loadersaver) load_image() (in module algotom.io.loadersaver)

load_image_multiple() (in module algotom.io.loadersaver) locate_peak() (in module algotom.util.correlation) locate_slice() (in module algotom.util.utility) locate_slice_chunk() (in module algotom.util.utility)

M

make_2d_butterworth_window() (in module algotom.util.utility) make_2d_damping_window() (in module algotom.util.utility) make_2d_gaussian_window() (in module algotom.util.utility) make_2d_ramp_window() (in module algotom.rec.reconstruction) make_circle_mask() (in module algotom.util.utility) make_circular_ramp_window() (in module algotom.rec.reconstruction) make_double_wedge_mask() (in module algotom.prep.filtering) make_elliptic_mask() (in module algotom.util.simulation) make_face_phantom() (in module algotom.util.simulation) make_file_name() (in module algotom.io.loadersaver) make_folder() (in module algotom.io.loadersaver) make_folder_name() (in module algotom.io.loadersaver) make_fresnel_window() (in module algotom.prep.filtering) make_inverse_double_wedge_mask() (in module algotom.prep.calculation) make_line_target() (in module algotom.util.simulation) make_rectangular_mask() (in module algotom.util.simulation) make_sinogram() (in module algotom.util.simulation) make_smoothing_window() (in module algotom.rec.reconstruction) make_triangular_mask() (in module algotom.util.simulation)

make_weight_matrix() (in module algotom.prep.conversion) mapping() (in module algotom.util.utility) module algotom algotom.io.converter algotom.io.loadersaver algotom.post.postprocessing algotom.prep.calculation algotom.prep.conversion algotom.prep.correction algotom.prep.filtering algotom.prep.phase algotom.prep.removal algotom.rec.reconstruction algotom.rec.vertrec algotom.util.calibration algotom.util.correlation algotom.util.simulation algotom.util.utility mtf_deconvolution() (in module algotom.prep.correction)

N

non_linear_function() (in module algotom.prep.correction) normalize_background() (in module algotom.util.calibration)

normalize_background_based_fft() (in module algotom.util.calibration) normalize_image() (in module algotom.util.correlation)

O

open_hdf_stream() (in module algotom.io.loadersaver)

P

parallel_process_slices() (in module algotom.util.utility)

polar_from_rectangular() (in module algotom.util.utility)

R

reconstruct_surface_from_gradient_FC_method() (in module algotom.prep.phase) reconstruct_surface_from_gradient_SCS_method() (in module algotom.prep.phase) rectangular_from_polar() (in module algotom.util.utility) remove_all_stripe() (in module algotom.prep.removal) remove_blob() (in module algotom.prep.removal) remove_blob_1d() (in module algotom.prep.removal) remove_dead_stripe() (in module algotom.prep.removal) remove_large_stripe() (in module algotom.prep.removal) remove_ring_based_fft() (in module algotom.post.postprocessing) remove_ring_based_wavelet_fft() (in module algotom.post.postprocessing) remove_stripe_based_2d_filtering_sorting() (in module algotom.prep.removal) remove_stripe_based_fft() (in module algotom.prep.removal)

remove_stripe_based_filtering() (in module algotom.prep.removal) remove_stripe_based_fitting() (in module algotom.prep.removal) remove_stripe_based_interpolation() (in module algotom.prep.removal) remove_stripe_based_normalization() (in module algotom.prep.removal) remove_stripe_based_regularization() (in module algotom.prep.removal) remove_stripe_based_sorting() (in module algotom.prep.removal) remove_stripe_based_wavelet_fft() (in module algotom.prep.removal) remove_zinger() (in module algotom.prep.removal) rescale() (in module algotom.post.postprocessing) rescale_dataset() (in module algotom.post.postprocessing) reslice_dataset() (in module algotom.post.postprocessing) retrieve_phase_based_speckle_tracking() (in module algotom.prep.phase)

S

save_distortion_coefficient() (in module algotom.io.loadersaver) save_image() (in module algotom.io.loadersaver) save_image_multiple() (in module algotom.io.loadersaver) search_overlap() (in module algotom.prep.calculation) select_dot_based_size() (in module algotom.util.calibration) select_zinger() (in module algotom.prep.removal)

separate_frequency_component() (in module algotom.util.utility) shape (algotom.io.converter.HdfEmulatorFromTif property) sort_backward() (in module algotom.util.utility) sort_forward() (in module algotom.util.utility) stitch_image() (in module algotom.prep.conversion) stitch_image_multiple() (in module algotom.prep.conversion)

T

transform_1d_window_to_2d() (in module algotom.util.utility)

transform_slice_backward() (in module algotom.util.utility) transform_slice_forward() (in module algotom.util.utility)

U

unwarp_projection() (in module algotom.prep.correction) unwarp_sinogram() (in module algotom.prep.correction) unwarp_sinogram_chunk() (in module algotom.prep.correction)

unwrap_phase_based_cosine_transform() (in module algotom.prep.phase) unwrap_phase_based_fft() (in module algotom.prep.phase) unwrap_phase_iterative_fft() (in module algotom.prep.phase) upsample_sinogram() (in module algotom.prep.correction)

V

vertical_back_projection_cpu() (in module algotom.rec.vertrec) vertical_back_projection_cpu_chunk() (in module algotom.rec.vertrec) vertical_back_projection_gpu() (in module algotom.rec.vertrec)

vertical_back_projection_gpu_chunk() (in module algotom.rec.vertrec) vertical_reconstruction() (in module algotom.rec.vertrec) vertical_reconstruction_different_angles() (in module algotom.rec.vertrec) vertical_reconstruction_multiple() (in module algotom.rec.vertrec)