Annotation Extraction
WSI.annotation module
Title: ValidPath Toolbox - Annotation Extraction Module
Description: This is the Annotation Extraction module for the ValidPath toolbox. It is includes AnnotationExtractor class and several methods.
Classes: AnnotationExtractor
Methods: AnnotationExtractor.extract_ann (Save_dir: str,XMLs: array , WSIs: array)
- class WSI.annotation.AnnotationExtractor[source]
Bases:
object- extract_ann(save_dir, XMLs, WSIs, vis=False, save_mask=False)[source]
This method extracts different types for annotations from Whole Slide Images. It can save the extracted annottions to the output directory as defined in inputs. This code also handles several annotations per slide. The output directory will be generated based on the strucutr of the input directories.
- Parameters:
- save_dirstring
The path to the directory in order to save the annotations
- WSIslist
List of whole slide image files
- XMLslist
List of annotation files in XML format
- Returns:
Image (array) – annotation files