def extract_images_or_rois(parameters):
# work at image level or ROIs by term
images = ImageInstanceCollection()
if parameters.cytomine_id_images is not None:
id_images = parse_domain_list(parameters.cytomine_id_images)
images.extend([ImageInstance().fetch(_id) for _id in id_images])
else:
images = images.fetch_with_filter("project",
parameters.cytomine_id_project)
slides = [
CytomineSlide(img, parameters.cytomine_zoom_level) for img in images
]
if parameters.cytomine_id_roi_term is None:
return slides
# fetch ROI annotations, all users
collection = AnnotationCollection(
terms=[parameters.cytomine_id_roi_term],
reviewed=parameters.cytomine_reviewed_roi,
project=parameters.cytomine_id_project,
showWKT=True,
includeAlgo=True).fetch()
slides_map = {slide.image_instance.id: slide for slide in slides}
regions = list()
for annotation in collection:
if annotation.image not in slides_map:
continue
slide = slides_map[annotation.image]
regions.append(
get_iip_window_from_annotation(slide, annotation,
parameters.cytomine_zoom_level))
return regions
def extract_images_or_rois(parameters):
id_annotations = parse_domain_list(parameters.cytomine_roi_annotations)
# if ROI annotations are provided
if len(id_annotations) > 0:
image_cache = dict() # maps ImageInstance id with CytomineSlide object
zones = list()
for id_annot in id_annotations:
annotation = Annotation().fetch(id_annot)
if annotation.image not in image_cache:
image_cache[annotation.image] = CytomineSlide(
annotation.image, parameters.cytomine_zoom_level)
window = get_iip_window_from_annotation(
image_cache[annotation.image], annotation,
parameters.cytomine_zoom_level)
zones.append(window)
return zones
# work at image level or ROIs by term
images = ImageInstanceCollection()
if parameters.cytomine_id_images is not None:
id_images = parse_domain_list(parameters.cytomine_id_images)
images.extend([ImageInstance().fetch(_id) for _id in id_images])
else:
images = images.fetch_with_filter("project",
parameters.cytomine_id_project)
slides = [
CytomineSlide(img, parameters.cytomine_zoom_level) for img in images
]
if parameters.cytomine_id_roi_term is None:
return slides
# fetch ROI annotations
collection = AnnotationCollection(
terms=[parameters.cytomine_id_roi_term],
reviewed=parameters.cytomine_reviewed_roi,
showWKT=True)
collection.fetch_with_filter(project=parameters.cytomine_id_project)
slides_map = {slide.image_instance.id: slide for slide in slides}
regions = list()
for annotation in collection:
if annotation.image not in slides_map:
continue
slide = slides_map[annotation.image]
regions.append(
get_iip_window_from_annotation(slide, annotation,
parameters.cytomine_zoom_level))
return regions