Index

A

abdo (ai_ct_scans.data_loading.PatientLoader attribute) abs_dist_cost_matrix() (in module ai_ct_scans.point_matching) ai_ct_scans module ai_ct_scans.data_loading module ai_ct_scans.data_writing module ai_ct_scans.GUI module ai_ct_scans.GUI.image_viewer module ai_ct_scans.GUI.scan_viewer module ai_ct_scans.GUI.ui_stack_window module ai_ct_scans.GUI.viewer_widget module ai_ct_scans.image_processing_utils module ai_ct_scans.keypoint_alignment module

ai_ct_scans.model_trainers module ai_ct_scans.models module ai_ct_scans.non_rigid_alignment module ai_ct_scans.phase_correlation module ai_ct_scans.phase_correlation_image_processing module ai_ct_scans.point_matching module ai_ct_scans.scan_tool module ai_ct_scans.sectioning module align_2D_using_CPD() (in module ai_ct_scans.non_rigid_alignment) align_3D_using_CPD() (in module ai_ct_scans.non_rigid_alignment) align_image() (in module ai_ct_scans.keypoint_alignment) align_via_phase_correlation_2d() (in module ai_ct_scans.phase_correlation) AXIAL (ai_ct_scans.GUI.viewer_widget.SliceDirection attribute)

B

blank_frames (ai_ct_scans.GUI.viewer_widget.ViewerWidget attribute) blur() (in module ai_ct_scans.model_trainers) BodyPartLoader (class in ai_ct_scans.data_loading) border_mask_builder() (ai_ct_scans.model_trainers.InfillTrainer method)

build_batch() (ai_ct_scans.model_trainers.InfillTrainer method) build_decoder_convs() (ai_ct_scans.models.Infiller method) build_encoder_convs() (ai_ct_scans.models.Infiller method) build_latent_space_bridge() (ai_ct_scans.models.Infiller method) build_sample_texton_set() (ai_ct_scans.sectioning.TextonSectioner method)

C

calculate_non_rigid_alignment() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) change_orientation() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) choose_data_dir() (ai_ct_scans.GUI.ui_stack_window.UiStackWindow method) circle() (in module ai_ct_scans.phase_correlation_image_processing) clear_scan() (ai_ct_scans.data_loading.ScanLoader method)

convert_for_viewer() (ai_ct_scans.GUI.scan_viewer.ScanViewer static method) convolve() (in module ai_ct_scans.phase_correlation_image_processing) CORONAL (ai_ct_scans.GUI.viewer_widget.SliceDirection attribute) cpd_aligned_scan (ai_ct_scans.GUI.viewer_widget.ViewerWidget attribute) create_dicom_file() (in module ai_ct_scans.data_writing) CTEllipsoidFitter (class in ai_ct_scans.sectioning)

D

data (ai_ct_scans.GUI.viewer_widget.ViewerWidget attribute) data_path (ai_ct_scans.GUI.ui_stack_window.UiStackWindow attribute) data_root_directory() (in module ai_ct_scans.data_loading) debug_plot() (in module ai_ct_scans.model_trainers) delete_memmap() (ai_ct_scans.data_loading.ScanLoader method) det() (in module ai_ct_scans.model_trainers) detect_ellipses() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) dicom_paths (ai_ct_scans.data_loading.ScanLoader attribute)

DinoSectioner (class in ai_ct_scans.sectioning) dir_dicom_paths() (in module ai_ct_scans.data_loading) display_data() (ai_ct_scans.GUI.scan_viewer.ScanViewer method) display_results() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) display_sectioned_slice() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) display_slice() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) draw_ellipses_2d() (ai_ct_scans.sectioning.CTEllipsoidFitter method) draw_ellipsoid_walls() (ai_ct_scans.sectioning.CTEllipsoidFitter method)

E

EllipseFitter (class in ai_ct_scans.sectioning) estimate_3D_alignment_transform() (in module ai_ct_scans.non_rigid_alignment)

extract_centre_coordinates_from_string() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) extract_ellipse_overlay_info() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method)

F

find_ellipsoids() (ai_ct_scans.sectioning.CTEllipsoidFitter method) find_homography() (in module ai_ct_scans.keypoint_alignment) find_shift_via_phase_correlation_2d() (in module ai_ct_scans.phase_correlation) fit() (ai_ct_scans.sectioning.HierarchicalMeanShift method) (ai_ct_scans.sectioning.MeanShiftWithProbs method)

fit_ellipses() (ai_ct_scans.sectioning.EllipseFitter method) forward() (ai_ct_scans.models.Infiller method) (ai_ct_scans.models.SingleDecoderLayer method) (ai_ct_scans.models.SingleEncoderLayer method) full_scan (ai_ct_scans.data_loading.ScanLoader attribute) full_scan_to_memmap() (ai_ct_scans.data_loading.ScanLoader method)

G

generate_overlay_2d() (in module ai_ct_scans.phase_correlation_image_processing)

get_keypoints_and_descriptors() (in module ai_ct_scans.keypoint_alignment) get_warp_overlay() (in module ai_ct_scans.non_rigid_alignment)

H

handle_item_selection() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method)

HierarchicalMeanShift (class in ai_ct_scans.sectioning)

I

ImageViewer (class in ai_ct_scans.GUI.image_viewer)

Infiller (class in ai_ct_scans.models) InfillTrainer (class in ai_ct_scans.model_trainers)

L

label_im() (ai_ct_scans.sectioning.TextonSectioner method) lmr() (in module ai_ct_scans.phase_correlation_image_processing) load() (ai_ct_scans.sectioning.DinoSectioner method) (ai_ct_scans.sectioning.TextonSectioner method) load_2d_array() (ai_ct_scans.data_loading.ScanLoader method) load_data() (ai_ct_scans.GUI.ui_stack_window.UiStackWindow method) load_dino_model() (ai_ct_scans.sectioning.DinoSectioner method) load_full_memmap() (ai_ct_scans.data_loading.ScanLoader method)

load_memmap() (in module ai_ct_scans.data_loading) load_memmap_and_clear_scan() (ai_ct_scans.data_loading.ScanLoader method) load_model() (ai_ct_scans.model_trainers.InfillTrainer method) load_patient_metadata() (ai_ct_scans.data_loading.ScanLoader method) load_scan() (ai_ct_scans.data_loading.ScanLoader method) load_validation_set() (in module ai_ct_scans.data_loading) local_region (ai_ct_scans.GUI.viewer_widget.ViewerWidget attribute) loss() (ai_ct_scans.model_trainers.InfillTrainer method)

M

main() (in module ai_ct_scans.non_rigid_alignment) (in module ai_ct_scans.scan_tool) MainWindow (class in ai_ct_scans.scan_tool) MainWindow.Ui (class in ai_ct_scans.scan_tool) match_descriptors() (in module ai_ct_scans.keypoint_alignment) match_indices() (in module ai_ct_scans.point_matching) max_shape_from_image_list() (in module ai_ct_scans.phase_correlation_image_processing) mean_axial_thickness() (ai_ct_scans.data_loading.ScanLoader method) MeanShiftWithProbs (class in ai_ct_scans.sectioning) module ai_ct_scans ai_ct_scans.data_loading ai_ct_scans.data_writing ai_ct_scans.GUI ai_ct_scans.GUI.image_viewer ai_ct_scans.GUI.scan_viewer ai_ct_scans.GUI.ui_stack_window ai_ct_scans.GUI.viewer_widget ai_ct_scans.image_processing_utils ai_ct_scans.keypoint_alignment ai_ct_scans.model_trainers ai_ct_scans.models ai_ct_scans.non_rigid_alignment ai_ct_scans.phase_correlation ai_ct_scans.phase_correlation_image_processing ai_ct_scans.point_matching ai_ct_scans.scan_tool ai_ct_scans.sectioning

MultiPatientAxialStreamer (class in ai_ct_scans.data_loading) MultiPatientLoader (class in ai_ct_scans.data_loading)

N

ndarray_to_memmap() (in module ai_ct_scans.data_writing)

normalise() (in module ai_ct_scans.image_processing_utils)

O

orientation (ai_ct_scans.GUI.viewer_widget.ViewerWidget attribute)

overlay_warp_on_slice() (in module ai_ct_scans.image_processing_utils)

P

pad_nd() (in module ai_ct_scans.phase_correlation_image_processing) painter_element() (ai_ct_scans.GUI.image_viewer.ImageViewer method) paintEvent() (ai_ct_scans.GUI.image_viewer.ImageViewer method) patient_paths (ai_ct_scans.data_loading.MultiPatientLoader attribute) PatientLoader (class in ai_ct_scans.data_loading) patients (ai_ct_scans.data_loading.MultiPatientLoader attribute) phase_correlation_shift (ai_ct_scans.GUI.viewer_widget.ViewerWidget attribute) pixmap (ai_ct_scans.GUI.image_viewer.ImageViewer attribute) plane_mask_builder() (ai_ct_scans.model_trainers.InfillTrainer method)

pre_process_data() (ai_ct_scans.GUI.scan_viewer.ScanViewer static method) predict() (ai_ct_scans.sectioning.HierarchicalMeanShift method) predict_full() (ai_ct_scans.sectioning.HierarchicalMeanShift method) predict_proba() (ai_ct_scans.sectioning.HierarchicalMeanShift method) (ai_ct_scans.sectioning.MeanShiftWithProbs method) predict_proba_secondary() (ai_ct_scans.sectioning.HierarchicalMeanShift method) predict_secondary() (ai_ct_scans.sectioning.HierarchicalMeanShift method) probabilities_im() (ai_ct_scans.sectioning.TextonSectioner method) process_full_scan() (ai_ct_scans.model_trainers.InfillTrainer method)

R

random_axial_slicer() (ai_ct_scans.model_trainers.InfillTrainer method) random_coronal_slicer() (ai_ct_scans.model_trainers.InfillTrainer method) random_sagittal_slicer() (ai_ct_scans.model_trainers.InfillTrainer method) raw_transverse_pixel_spacing_and_shape() (ai_ct_scans.data_loading.ScanLoader method)

read_transform() (in module ai_ct_scans.non_rigid_alignment) rescale_depth() (ai_ct_scans.data_loading.ScanLoader method) reset_indices() (ai_ct_scans.data_loading.MultiPatientAxialStreamer method) root_dir (ai_ct_scans.data_loading.MultiPatientLoader attribute)

S

SAGITTAL (ai_ct_scans.GUI.viewer_widget.SliceDirection attribute) save() (ai_ct_scans.sectioning.DinoSectioner method) (ai_ct_scans.sectioning.TextonSectioner method) save_model() (ai_ct_scans.model_trainers.InfillTrainer method) scale_factor() (ai_ct_scans.GUI.image_viewer.ImageViewer method) scan_1 (ai_ct_scans.data_loading.BodyPartLoader attribute) scan_2 (ai_ct_scans.data_loading.BodyPartLoader attribute) ScanLoader (class in ai_ct_scans.data_loading) ScanViewer (class in ai_ct_scans.GUI.scan_viewer) ScanViewer.Ui (class in ai_ct_scans.GUI.scan_viewer) set_data() (ai_ct_scans.GUI.scan_viewer.ScanViewer method) (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) set_image() (ai_ct_scans.GUI.image_viewer.ImageViewer method) setup_orientation() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) shift_image_2d() (in module ai_ct_scans.phase_correlation) shift_nd() (in module ai_ct_scans.phase_correlation)

shift_via_phase_correlation_nd() (in module ai_ct_scans.phase_correlation) shifts_via_local_region() (in module ai_ct_scans.phase_correlation) show_phase_correlation() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) sieve_matches_lowe() (in module ai_ct_scans.keypoint_alignment) single_image_texton_descriptors() (ai_ct_scans.sectioning.DinoSectioner method) (ai_ct_scans.sectioning.TextonSectioner method) SingleDecoderLayer (class in ai_ct_scans.models) SingleEncoderLayer (class in ai_ct_scans.models) SliceDirection (class in ai_ct_scans.GUI.viewer_widget) sphere() (in module ai_ct_scans.phase_correlation_image_processing) staticMetaObject (ai_ct_scans.GUI.image_viewer.ImageViewer attribute) (ai_ct_scans.GUI.scan_viewer.ScanViewer attribute) (ai_ct_scans.GUI.ui_stack_window.UiStackWindow attribute) (ai_ct_scans.GUI.viewer_widget.ViewerWidget attribute) (ai_ct_scans.scan_tool.MainWindow attribute) stream_next() (ai_ct_scans.data_loading.MultiPatientAxialStreamer method)

T

TextonSectioner (class in ai_ct_scans.sectioning) toggle_ellipse_table() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) toggle_ellipse_table_button() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) toggle_non_rigid_2d_controls() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) toggle_phase_correlation_controls() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) toggle_tissue_sectioning() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) toggle_warp_display() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method)

train_clusterers() (ai_ct_scans.sectioning.TextonSectioner method) train_for_iterations() (ai_ct_scans.model_trainers.InfillTrainer method) train_step() (ai_ct_scans.model_trainers.InfillTrainer method) training (ai_ct_scans.models.Infiller attribute) (ai_ct_scans.models.SingleDecoderLayer attribute) (ai_ct_scans.models.SingleEncoderLayer attribute) transform_3d_volume() (in module ai_ct_scans.non_rigid_alignment) transform_3d_volume_in_chunks() (in module ai_ct_scans.non_rigid_alignment)

U

ui (ai_ct_scans.GUI.ui_stack_window.UiStackWindow attribute) (ai_ct_scans.GUI.viewer_widget.ViewerWidget attribute) (ai_ct_scans.scan_tool.MainWindow attribute) UiStackWindow (class in ai_ct_scans.GUI.ui_stack_window)

UiStackWindow.Ui (class in ai_ct_scans.GUI.ui_stack_window) update_ellipse_table() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) update_local_region() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) update_scan() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method) update_scan_toggle() (ai_ct_scans.GUI.viewer_widget.ViewerWidget method)

V

viewer_data (ai_ct_scans.GUI.scan_viewer.ScanViewer attribute) ViewerWidget (class in ai_ct_scans.GUI.viewer_widget)

ViewerWidget.Ui (class in ai_ct_scans.GUI.viewer_widget) volume_plot (ai_ct_scans.GUI.scan_viewer.ScanViewer attribute)

W

write_transform() (in module ai_ct_scans.non_rigid_alignment)

Z

zero_crossings() (in module ai_ct_scans.phase_correlation_image_processing)