histomicstk.workflows.workflow_runner

Created on Mon Sep 30 22:09:40 2019.

@author: mtageld

class histomicstk.workflows.workflow_runner.Annotation_iterator(gc, slide_id, callback=None, callback_kwargs=None, **kwargs)

Bases: Base_HTK_Class

Iterate through annotations in a girder item (slide).

apply_callback_to_all_annotations()

Apply callback to all annotations and return output list.

yield_callback_output_for_annotation()

Yield callback output for one annotation at a time.

class histomicstk.workflows.workflow_runner.Slide_iterator(gc, source_folder_id, **kwargs)

Bases: Base_HTK_Class

Iterate through large_image items in a girder folder.

run()

Yield information on one slide at a time.

set_slide_ids()

Get dict of slide idx, indexed by name.

class histomicstk.workflows.workflow_runner.Workflow_runner(slide_iterator, workflow, workflow_kwargs, recursive=False, catch_exceptions=True, **kwargs)

Bases: Base_HTK_Class

Run workflow for all slides in a girder folder.

run()

Run workflow for all slides.