magmap.atlas package

Submodules

• magmap.atlas.atlas_refiner module
  • aggr_smoothing_metrics()
  • check_mirrorred()
  • crop_to_orig()
  • extend_edge()
  • find_labels_lost()
  • find_symmetric_axis()
  • import_atlas()
  • label_smoothing_metric()
  • make_labels_fg()
  • match_atlas_labels()
  • measure_atlas_refinement()
  • measure_overlap()
  • measure_overlap_combined_labels()
  • measure_overlap_labels()
  • mirror_planes()
  • smooth_labels()
  • transpose_img()
  • truncate_labels()
• magmap.atlas.edge_seg module
  • edge_aware_segmentation()
  • edge_distances()
  • erode_labels()
  • make_edge_images()
  • make_sub_segmented_labels()
  • merge_atlas_segmentations()
• magmap.atlas.labels_meta module
  • LabelsMeta
    • LabelsMeta.PATH_LABELS_META
    • LabelsMeta.load()
    • LabelsMeta.save()
    • LabelsMeta.save_path
• magmap.atlas.ontology module
  • LabelColumns
    • LabelColumns.FROM_LABEL
    • LabelColumns.TO_LABEL
  • LabelsRef
    • LabelsRef.create_aba_reverse_lookup()
    • LabelsRef.create_lookup_pd()
    • LabelsRef.create_ref_lookup()
    • LabelsRef.create_reverse_lookup()
    • LabelsRef.get_node()
    • LabelsRef.get_ref_lookup_as_df()
    • LabelsRef.load()
    • LabelsRef.load_labels_ref()
  • convert_itksnap_to_df()
  • get_children_from_id()
  • get_children_from_id_df()
  • get_label()
  • get_label_at_level()
  • get_label_ids_from_position()
  • get_label_item()
  • get_label_name()
  • get_label_side()
  • get_region_middle()
  • labels_to_parent()
  • make_labels_level()
  • rel_to_abs_ages()
  • replace_labels()
  • scale_coords()
• magmap.atlas.reg_tasks module
  • build_labels_diff_images()
• magmap.atlas.register module
  • RegImgs
    • RegImgs.atlas
    • RegImgs.atlas_mask
    • RegImgs.borders
    • RegImgs.exp
    • RegImgs.exp_mask
    • RegImgs.exp_orig
    • RegImgs.get_order()
    • RegImgs.labels
    • RegImgs.labels_markers
    • RegImgs.update_fields()
  • curate_img()
  • get_scaled_regionprops()
  • main()
  • make_label_ids_set()
  • overlay_registered_imgs()
  • register()
  • register_duo()
  • register_group()
  • register_repeat()
  • register_rev()
  • volumes_by_id()
  • volumes_by_id_compare()
• magmap.atlas.transformer module
  • Downsampler
    • Downsampler.img
    • Downsampler.rescale_sub_roi()
    • Downsampler.set_data()
  • get_transposed_image_path()
  • make_modifier_plane()
  • make_modifier_resized()
  • make_modifier_scale()
  • preprocess_img()
  • rotate_img()
  • transpose_img()