fusion_tools package

• fusion_tools.components package
  • fusion_tools.components.maps module
  • fusion_tools.components.tools module
• fusion_tools.utils package
  • fusion_tools.utils.shapes module
    • align_object_props()
    • aperio_to_geojson()
    • detect_geojson()
    • detect_histomics()
    • detect_image_overlay()
    • export_annotations()
    • extract_geojson_properties()
    • extract_listed_prop()
    • extract_nested_prop()
    • find_intersecting()
    • find_nested_levels()
    • geojson_to_histomics()
    • histomics_to_geojson()
    • indices_to_path()
    • load_annotations()
    • load_aperio()
    • load_geojson()
    • load_histomics()
    • load_label_mask()
    • load_parquet()
    • load_polygon_csv()
    • load_visium()
    • load_visiumhd()
    • merge_dict()
    • path_to_indices()
    • path_to_mask()
    • process_filters_queries()
    • spatially_aggregate()
    • structures_within_poly()
• fusion_tools.visualization package
  • fusion_tools.visualization.components module
  • fusion_tools.visualization.vis_utils module

fusion_tools.handler module

fusion_tools.tileserver module

Base classes for tools

fusion_tools.asyncio_db_loop(method)

Decorator for checking that an event loop is present for handling asynchronous callse

Parameters:

method (None) – Function which has asynchronous process

fusion_tools.dataset module

Dataset sub-module for fusion-tools

class fusion_tools.dataset.ClassificationDataset(slides: list = [], annotations: list | dict | None = None, label_property: list | str | None = None, transforms: None | Callable = None, label_transforms: None | Callable = None, patch_size: list = [256, 256], patch_mode: str = 'bbox', patch_region: str | list | dict = 'all', spatial_filters: list | None = None, property_filters: list | None = None, use_structures: str | list = 'all', use_cache: bool = True, shuffle: bool = True, seed_val: int = 1701, verbose: bool = False, use_parallel: bool = True, n_jobs: int = 1)

Bases: object

export_configs(save_path: str)

gen_slide_patches()

get_next_image(idx: int)

make_image_and_label(bbox: list, slide_idx: int, features: list)

make_patch(bbox: list, slide_idx: int, annotations: GeoDataFrame)

plant_seed(seed_val)

process_annotations()

class fusion_tools.dataset.FUSIONDataset(slides: list = [], annotations: list | dict | None = None, image_transforms: Callable | None = None, target_transforms: Callable | None = None, patch_size: list = [256, 256], patch_mode: str = 'bbox', patch_region: str | list | dict = 'all', overlap: float | None = None, spatial_filters: list | None = None, property_filters: list | None = None, use_cache: bool = False, shuffle: bool = True, seed_val: int = 1701, verbose: bool = False, use_parallel: bool = True, n_jobs: int = 1)

Bases: object

find_tissue()

gen_slide_patches()

plant_seed(seed_val)

process_annotations()

class fusion_tools.dataset.SegmentationDataset(slides: list = [], annotations: list | dict | None = None, transforms: None | Callable = None, target_transforms: None | Callable = None, mask_key: dict | None = None, patch_size: list = [256, 256], patch_mode: str = 'bbox', patch_region: str | list | dict = 'all', spatial_filters: list | None = None, property_filters: list | None = None, use_structures: str | list = 'all', use_cache: bool = True, shuffle: bool = True, seed_val: int = 1701, verbose: bool = False, use_parallel: bool = True, n_jobs: int = 1)

Bases: object

export_configs(save_path: str)

find_tissue(slide_tile_source, slide_metadata)

gen_slide_patches()

get_next_image(idx: int)

make_image_and_mask(bbox: list, slide_idx: int, features: list)

make_patch(bbox: list, slide_idx: int, annotations: GeoDataFrame)

plant_seed(seed_val)

process_annotations()

fusion_tools.feature_extraction module