pyluna-pathology.luna.pathology.common package#

Submodules#

pyluna-pathology.luna.pathology.common.EnsureByteContext module#

Created on November 04, 2020

@author: aukermaa@mskcc.org

class luna.pathology.common.EnsureByteContext.EnsureByteContext[source]#

Bases: object

pyluna-pathology.luna.pathology.common.annotation_utils module#

pyluna-pathology.luna.pathology.common.build_geojson module#

luna.pathology.common.build_geojson.add_contours_for_label(annotation_geojson: Dict[str, any], annotation: numpy.ndarray, label_num: int, mappings: dict, contour_level: float) → Dict[str, any][source]#

creates geoJSON feature dictionary for labels

Finds the contours for a label mask, builds a polygon and then converts the polygon to geoJSON feature dictionary

Parameters

  • annotation_geojson (dict[str, any]) – geoJSON result to populate

  • annotation (np.ndarray) – npy array of bitmap

  • label_num (int) – the integer cooresponding to the annotated label

  • mappings (dict) – label map for specified label set

  • contour_level (float) – value along which to find contours in the array

Returns

geoJSON with label countours

Return type

dict[str, any]

luna.pathology.common.build_geojson.build_all_geojsons_from_default(default_annotation_geojson: Dict[str, any], all_labelsets: List[dict], contour_level: float) → dict[source]#

builds geoJSON objects from a set of labels

wraps build_labelset_specific_geojson with logic to generate annotations from multiple labelsets

Parameters

  • default_annotation_geojson (dict[str, any]) – input geoJSON

  • all_labelsets (list[dict]) – a list of dictionaries containing label sets

  • contour_level (float) – value along which to find contours

Returns

a dictionary with labelset name and cooresponding geoJSON as key, value pairs

Return type

dict

luna.pathology.common.build_geojson.build_default_geojson_from_annotation(annotation_npy_filepath: str, all_labelsets: dict, contour_level: float)[source]#

builds geoJSONS from numpy annotation with default label set

Parameters

  • annotation_npy_filepath (str) – string to numpy annotation

  • all_labelsets (dict) – a dictionary of label sets

  • contour_level (float) – value along which to find contours

Returns

the default geoJSON annotation

Return type

dict[str, any]

luna.pathology.common.build_geojson.build_geojson_from_annotation(df: pandas.core.frame.DataFrame) → pandas.core.frame.DataFrame[source]#

Builds geoJSON for all annotation labels in the specified labelset.

Parameters

df (pandas.DataFrame) – input regional annotation table

Returns

dataframe with geoJSON field poopulated

Return type

pandasDataFrame

luna.pathology.common.build_geojson.build_geojson_from_pointclick_json(labelsets: dict, labelset: str, sv_json: List[dict]) → list[source]#

Build geoJSON m slideviewer JSON

This method extracts point annotations from a slideviwer json object and converts them to a standardized geoJSON format

Parameters

  • labelsets (dict) – dictionary of label set as string (e.g. {labelset: {label_number: label_name}})

  • labelset (str) – the name of the labelset e.g. default_labels

  • sv_json (list[dict]) – annotatations from slideviwer in the form of a list of dictionaries

Returns

a list of geoJSON annotation objects

Return type

list

luna.pathology.common.build_geojson.build_labelset_specific_geojson(default_annotation_geojson: Dict[str, any], labelset: dict) → Dict[str, any][source]#

builds geoJSON for labelset

Instead of working with a large geJSON object, you can extact polygons that coorspond to specific labels into a smaller object.

Parameters

  • default_annotation_geojson (dict[str, any]) – geoJSON annotation file

  • labelset (dict) – label set dictionary

Returns

geoJSON with only polygons from provided labelset

Return type

dict[str, any]

luna.pathology.common.build_geojson.concatenate_regional_geojsons(geojson_list: List[Dict[str, any]]) → Dict[str, any][source]#

concatenate regional annotations

Concatenates geojsons if there are more than one annotations for the labelset.

Parameters

geojson_list (list[dict[str, any]]) – list of geoJSON strings

Returns

a single concatenated geoJSON

Return type

dict[str, any]

luna.pathology.common.build_geojson.find_parents(polygons: list) → list[source]#

determines of parent child relationships of polygons

Returns a list of size n (where n is the number of input polygons in the input list polygons) where the value at index n cooresponds to the nth polygon’s parent. In the case of no parent, -1 is used. for example, parent_nums[0] = 2 means that polygon 0’s parent is polygon 2

Parameters

polygons (list) – a list of shapely polygon objects

Returns

a list of parent-child relationships for the polygon objects

Return type

list

luna.pathology.common.build_geojson.handler(signum: str, frame: str) → None[source]#

signal handler for geojson

Parameters

  • signum (str) – signal number

  • fname (str) – filename for which exception occurred

Returns

None

pyluna-pathology.luna.pathology.common.ml module#

pyluna-pathology.luna.pathology.common.preprocess module#

pyluna-pathology.luna.pathology.common.slideviewer_client module#

Created on January 31, 2021

@author: pashaa@mskcc.org

Functions for downloading annotations from SlideViewer

luna.pathology.common.slideviewer_client.download_sv_point_annotation(url: str) → Dict[str, any][source]#

download slideviwer point annotation

Calls slideviewer API with the given url

Parameters

url (str) – slide viewer api to call

Returns

json response

Return type

dict[str, any]

luna.pathology.common.slideviewer_client.download_zip(url: str, dest_path: str, chunk_size: int = 128) → bool[source]#

Download zip file

Downloads zip from the specified URL and saves it to the specified file path. see https://stackoverflow.com/questions/9419162/download-returned-zip-file-from-url

Parameters

  • url (str) – slideviewer url to download zip from

  • dest_path (str) – file path where zipfile should be saved

  • chunk_size (int) – size in bytes of chunks to batch out during download

Returns

True if zipfile downloaded and saved successfully, else false

Return type

bool

luna.pathology.common.slideviewer_client.fetch_slide_ids(url: str, project_id: int, dest_dir: str, csv_file: Optional[str] = None) → list[source]#

get slide ids

Fetch the list of slide ids from the slideviewer server for the project with the specified project id. Alternately, a slideviewer csv file may be provided to override download from server.

Parameters

  • url (str or None) – slideviewer url. url may be None if csv_file is specified.

  • project_id (int) – slideviewer project id from which to fetch slide ids

  • dest_dir (str) – directory where csv file should be downloaded

  • csv_file (str) – slideviewer csv file may be provided to override the need

  • file (to download the) –

Returns

list of (slideviewer_path, slide_id, sv_project_id)

Return type

list

luna.pathology.common.slideviewer_client.get_slide_id(full_filename: str) → str[source]#

get slide id

Get slide id from the slideviewer full file name. The full_filename in the slideview csv is of the format: year;HOBS_ID;slide_id.svs for example: 2013;HobS13-283072057510;1435197.svs

Parameters

full_filename (str) – full filename of slide

Returns

numeric slide id

Return type

str

luna.pathology.common.slideviewer_client.unzip(zipfile_path: str) → any[source]#

unzip zip file

Parameters

zipfile_path (str) – path of zipfile to unzip

Returns

readfile pointer to unzippped file if successfully unzippped, else None

pyluna-pathology.luna.pathology.common.utils module#

Module contents#