Contents

pyluna-pathology.luna.pathology.cli.dsa package

pyluna-pathology.luna.pathology.cli.dsa package

Submodules

pyluna-pathology.luna.pathology.cli.dsa.dsa_api_handler module

luna.pathology.cli.dsa.dsa_api_handler.get_collection_metadata(collection_name: str, gc) → Optional[Tuple[str, Dict[str, any]]][source]

A function used to get the stylehseet associated with a DSA collection. The stylesheet can store the labels used in the annotation process

Parameters

  • collection_name (str) – name of DSA collection used to store the slides

  • gc – girder client

Returns

a tuple consisting of the collection uuid

and thei stylesheet in JSON format or None if no stylesheet is associated with the provided collection

Return type

Optional[Tuple[str, Dict[str, any]]]

luna.pathology.cli.dsa.dsa_api_handler.get_collection_uuid(gc, collection_name: str) → Optional[str][source]

Returns the DSA collection uuid from the provided collection_name

Parameters

  • gc – girder client

  • collection_name (string) – name of the collection in DSA

Returns

DSA collection uuid. None if nothing matches the collection name or an

error in the get request

Return type

string

luna.pathology.cli.dsa.dsa_api_handler.get_item_uuid(image_name: str, collection_name: str, gc) → Optional[str][source]

Returns the DSA item uuid from the provided image_name

Parameters

  • image_name (string) – name of the image in DSA e.g. 123.svs

  • collection_name (str) – name of DSA collection

  • gc – girder client

Returns

DSA item uuid. None if nothing matches the collection/image name.

Return type

string

luna.pathology.cli.dsa.dsa_api_handler.get_slide_annotation(slide_id: str, annotation_name: str, collection_name: str, gc) → Optional[Tuple[str, Dict[str, any], Dict[str, any]]][source]

A helper function that pulls json annotations along with metadata for a particular slide from DSA. Used for both point and regional annotation types.

Parameters

  • slide_id (str) – id of WSI on DSA (filename without extension).

  • annotation_name (str) – name of annotation, or label, created on DSA

  • collection_name (str) – name of DSA collection the WSI belongs to

  • gc – girder client

Returns

Optional[Tuple[str, dict[str, any], dict[str, any]. A tuple consisting of the slide id,

a json formatted annotation from slideviweer and slide metadata or None if the annotation can’t be found (ie if image_id, annotation_name or collection_name are mis-specified)

luna.pathology.cli.dsa.dsa_api_handler.get_slides_from_collection(collection_uuid: str, gc) → Optional[List[str]][source]

A helper function that retrieves all slide names from a provided collection via accessing DSA resource tree

Parameters

  • collection_uuid (str) – DSA collection uuid

  • gc – girder client

Returns

a list of all slide file names belonging to the collection

Return type

List[str]

luna.pathology.cli.dsa.dsa_api_handler.push_annotation_to_dsa_image(item_uuid: str, dsa_annotation_json: Dict[str, any], uri: str, gc)[source]

Pushes annotation to DSA, adding given item_uuid (slide-specific id)

Parameters

  • item_uuid (str) – DSA item uuid to be tied to the annotation

  • dsa_annotation_json (Dict[str, any]) – annotation JSON in DSA compatable format

  • uri (str) – DSA host:port e.g. localhost:8080

  • gc – girder client

Returns

0 for successful upload, 1 otherwise

Return type

int

luna.pathology.cli.dsa.dsa_api_handler.system_check(gc)[source]

Check DSA connection with the girder client

Parameters

gc – girder client

Returns

0 for successful connection, 1 otherwise

Return type

int

pyluna-pathology.luna.pathology.cli.dsa.dsa_upload module

pyluna-pathology.luna.pathology.cli.dsa.dsa_viz module

luna.pathology.cli.dsa.dsa_viz.bitmask_polygon(data_config)[source]

Build DSA annotation json from bitmask PNGs

Vectorizes and simplifies contours from the bitmask.

Parameters

  • data_config (string) – path to your data config file that includes input/output parameters.

  • input (map) – map of {label:path_to_bitmask_png}

  • output_folder (string) – directory where the DSA compatible annotation json file will be saved

  • image_filename (string) – name of the image file in DSA e.g. 123.svs

  • annotation_name (string) – name of the annotation to be displayed in DSA

  • line_colors (map, optional) – line color map with {feature name:rgb values}

  • fill_colors (map, optional) – fill color map with {feature name:rgba values}

Returns

annotation file path. None if error in writing the file.

Return type

string

luna.pathology.cli.dsa.dsa_viz.check_filepaths_valid(filepaths)[source]

Checks if all paths exist.

Parameters

filepaths (list) – file paths

Returns

True if all file paths exist, False otherwise

Return type

bool

luna.pathology.cli.dsa.dsa_viz.heatmap(data_config)[source]

Generate heatmap based on the tile scores

Creates a heatmap for the given column, using the color palette viridis to set a fill value - the color ranges from purple to yellow, for scores from 0 to 1.

Parameters

  • data_config (string) – path to your data config file that includes input/output parameters.

  • input (string) – path to CSV with tile scores

  • output_folder (string) – directory where the DSA compatible annotation json file will be saved

  • image_filename (string) – name of the image file in DSA e.g. 123.svs

  • annotation_name (string) – name of the annotation to be displayed in DSA

  • column (string) – column to visualize e.g. tile_score

  • tile_size (int) – size of tiles

  • scale_factor (int, optional) – scale to match the image on DSA. By default, 1.

Returns

annotation file path. None if error in writing the file.

Return type

string

luna.pathology.cli.dsa.dsa_viz.qupath_polygon(data_config)[source]

Build DSA annotation json from Qupath polygon geojson

Parameters

  • data_config (string) – path to your data config file that includes input/output parameters.

  • input (string) – path to Qupath polygon geojson

  • output_folder (string) – directory where the DSA compatible annotation json file will be saved

  • image_filename (string) – name of the image file in DSA e.g. 123.svs

  • annotation_name (string) – name of the annotation to be displayed in DSA

  • classes_to_include (list) – list of classification labels to visualize e.g. [“Tumor”, “Stroma”, …]

  • line_colors (map, optional) – line color map with {feature name:rgb values}

  • fill_colors (map, optional) – fill color map with {feature name:rgba values}

Returns

annotation file path. None if error in writing the file.

Return type

string

luna.pathology.cli.dsa.dsa_viz.regional_polygon(data_config)[source]

Build DSA annotation json from regional annotation geojson

Parameters

  • data_config (string) – path to your data config file that includes input/output parameters.

  • input (string) – path to regional annotation geojson

  • output_folder (string) – directory where the DSA compatible annotation json file will be saved

  • image_filename (string) – name of the image file in DSA e.g. 123.svs

  • annotation_name (string) – name of the annotation to be displayed in DSA

  • line_colors (map, optional) – line color map with {feature name:rgb values}

  • fill_colors (map, optional) – fill color map with {feature name:rgba values}

Returns

annotation file path. None if error in writing the file.

Return type

string

luna.pathology.cli.dsa.dsa_viz.save_dsa_annotation(base_annotation, elements, annotation_name, output_folder, image_filename)[source]

Helper function to save annotation elements to a json file.

Parameters

  • base_annotation (dict) – base annotation structure for DSA

  • elements (list) – list of annotation elements

  • annotation_name (string) – annotation name for HistomicsUI

  • output_folder (string) – path to a directory to save the annotation file

  • image_filename (string) – name of the image in DSA e.g. 123.svs

Returns

annotation file path. None if error in writing the file.

Return type

string

luna.pathology.cli.dsa.dsa_viz.stardist_cell(data_config)[source]

Build DSA annotation json from TSV classification data generated by stardist

Processes a cell classification data generated by Qupath/stardist and adds the center coordinates of the cells as annotation elements.

Parameters

  • data_config (string) – path to your data config file that includes input/output parameters.

  • input (string) – path to TSV classification data generated by stardist

  • output_folder (string) – directory where the DSA compatible annotation json file will be saved

  • image_filename (string) – name of the image file in DSA e.g. 123.svs

  • annotation_name (string) – name of the annotation to be displayed in DSA

  • line_colors (map, optional) – line color map with {feature name:rgb values}

  • fill_colors (map, optional) – fill color map with {feature name:rgba values}

Returns

annotation file path. None if error in writing the file.

Return type

string

luna.pathology.cli.dsa.dsa_viz.stardist_polygon(data_config)[source]

Build DSA annotation json from stardist geojson classification results

Parameters

  • data_config (string) – path to your data config file that includes input/output parameters.

  • input (string) – path to stardist geojson classification results

  • output_folder (string) – directory where the DSA compatible annotation json file will be saved

  • image_filename (string) – name of the image file in DSA e.g. 123.svs

  • annotation_name (string) – name of the annotation to be displayed in DSA

  • line_colors (map, optional) – user-provided line color map with {feature name:rgb values}

  • fill_colors (map, optional) – user-provided fill color map with {feature name:rgba values}

Returns

annotation file path. None if error in writing the file.

Return type

string

pyluna-pathology.luna.pathology.cli.dsa.utils module

luna.pathology.cli.dsa.utils.get_color(name, line_colors={}, fill_colors={}, alpha=100)[source]

Get colors for cells/regions based on discrete categories.

Parameters

  • name (string) – feature name e.g. Stroma, Tumor

  • line_colors (dict, optional) – line color map with {feature name:rgb values}

  • fill_colors (dict, optional) – fill color map with {feature name:rgba values}

  • alpha (int, optional) – alpha value for the fill color. 100 by default

Returns

RGBA values for line and fill colors

Return type

string

luna.pathology.cli.dsa.utils.get_continuous_color(value, outline_color='same_as_fill', alpha=100)[source]

Get RGBA line and fill colors for value.

Use color palette viridis to set a fill value - the color ranges from purple to yellow,

for the values from 0 to 1. This function is used in generating a heatmap.

Parameters

  • value (float) – continuous value in [0,1]

  • outline_color (string, optional) – manages the color used to outline the border of the annotation. by default, uses the same color as fill_color.

  • alpha (int, optional) – alpha value for the fill color. 100 by default

Returns

RGBA line and fill colors

Return type

string

luna.pathology.cli.dsa.utils.vectorize_np_array_bitmask_by_pixel_value(bitmask_np, label_num=255, polygon_tolerance=1, contour_level=0.5)[source]

Get simplified contours from the bitmask

Parameters

  • bitmask_np (np.array) – a numpy bitmask

  • label_num (int, optional) – numeric value to filter the numpy array

  • polygon_tolerance (float, optional) – Maximum distance from original points of polygon to approximated polygonal chain. If tolerance is 0, the original coordinate array is returned.

  • contour_level (float, optional) – Value along which to find contours in the array. 0.5 by default

Returns

simplified approximated contours

Return type

list

pyluna-pathology.luna.pathology.cli.dsa.dsa_regional_annotations module

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