pyluna-pathology.luna.pathology.common package¶
Submodules¶
pyluna-pathology.luna.pathology.common.EnsureByteContext module¶
Created on November 04, 2020
@author: aukermaa@mskcc.org
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
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