liom_toolkit.segmentation package

Subpackages

• liom_toolkit.segmentation.vseg package
  • Submodules
    • liom_toolkit.segmentation.vseg.cldice module
      • cl_dice()
      • cl_score()
    • liom_toolkit.segmentation.vseg.data module
      • PatchDataset
    • liom_toolkit.segmentation.vseg.loss module
      • DiceBCELoss
      • DiceLoss
    • liom_toolkit.segmentation.vseg.make_dataset module
      • make_train_val()
    • liom_toolkit.segmentation.vseg.model module
      • ConvBlock
      • DecoderBlock
      • EncoderBlock
      • VsegModel
    • liom_toolkit.segmentation.vseg.predict_one module
      • predict_one()
    • liom_toolkit.segmentation.vseg.training module
      • create_images()
      • evaluate()
      • mask_image()
      • train()
      • train_model()
    • liom_toolkit.segmentation.vseg.utils module
      • add_patch_to_empty_array()
      • calculate_metrics()
      • create_dir()
      • create_patches()
      • crop_image()
      • epoch_time()
      • matplotlib_imshow()
      • numeric_filesort()
      • patch()
      • process_image()
      • seeding()
    • liom_toolkit.segmentation.vseg.validation module
      • show_diff()
      • validate_model()
  • Module contents

Submodules

• liom_toolkit.segmentation.plane_segmentation module
  • erode_mask()
  • estimate_tissue_mask()
  • frangi_filter()
  • li_threshold_image()
  • remove_small_structures()
  • sauvola_threshold_image()
  • segment_2d_image()
  • subtract_background()
• liom_toolkit.segmentation.stats module
  • calculate_density()
  • calculate_regional_density()
  • compute_average_diameter()
  • compute_mask_area()
  • compute_slice_metrics()
  • create_filter_image()
  • create_heatmap()
  • draw_branch_point_circles()
  • filter_image_to_region()
  • generate_itk_id_list_of_region()
  • get_branching_point_count()
  • get_branching_points()
  • get_vessel_region()
• liom_toolkit.segmentation.volume_segmentation module
  • fill_holes_2d_3d()
  • segment_3d_brain()

Module contents