def create_from_tilesummaries(self,
tilesummaries:List[tile_extraction.tiles.TileSummary],
patient_id_getter:Callable,
case_id_getter:Callable,
slide_id_getter:Callable,
labels_getter:Callable):
"""
Inits self.patients from tilesummaries.
On how to create tilesummaries:
https://github.com/FAU-DLM/wsi_processing_pipeline/blob/master/tile_extraction/example.ipynb
Arguments:
tilesummaries:
patient_id_getter: method that maps from the tilesummary's whole-slide image path to a patient id
case_id_getter: method that maps from the tilesummary's whole-slide image path to a case id
slide_id_getter: method that maps from the tilesummary's whole-slide image path to a slide id
labels_getter: method that maps from the tilesummary's whole-slide image path and a RegionOfInterest
to a list ob labels
"""
# empty the lists, in case this function is called multiple times
self.__patients = []
__rois = []
#key: patient_id; value: Patient object
patient_id_to_patient = {}
for tilesummary in tqdm(tilesummaries):
# skip tilesummaries with 0 tiles
if(len(tilesummary.top_tiles()) == 0):
continue
###
# patient
###
current_patient = None
patient_id = patient_id_getter(tilesummary.wsi_path)
if(patient_id not in patient_id_to_patient.keys()):
current_patient = Patient(patient_id=patient_id, patient_manager=self)
patient_id_to_patient[patient_id] = current_patient
self.add_patient(current_patient)
else:
current_patient = patient_id_to_patient[patient_id]
###
# case
###
case_id = case_id_getter(tilesummary.wsi_path)
current_case = None
for case in current_patient.get_cases():
if(case.case_id == case_id):
current_case = case
break;
if(current_case == None):
current_case = Case(case_id=case_id, patient=current_patient)
current_patient.add_case(current_case)
###
# whole-slide
###
slide_id = slide_id_getter(tilesummary.wsi_path)
current_slide = WholeSlideImage(slide_id=slide_id, case=current_case, path=tilesummary.wsi_path)
current_case.add_whole_slide_image(current_slide)
###
# regions of interest
###
rois = tilesummary.rois
assert (rois != None and len(rois) > 0)
for roi in rois:
__rois.append(roi)
roi.reset_tiles() #reset tiles in case this function is called multiple times
current_slide.add_region_of_interest(roi)
roi.whole_slide_image = current_slide
roi.labels = labels_getter(tilesummary.wsi_path, roi)
for tile in tilesummary.top_tiles():
if(tile.roi.roi_id == roi.roi_id):
tile.set_removed_flag(value=False) # this flag might still be True from a previous call
roi.add_tile(tile)
tile.labels = roi.labels
#__rois = self.get_rois(dataset_type=shared.enums.DatasetType.all)
roi_ids = [r.roi_id for r in __rois]
if(len(roi_ids) != len(set(roi_ids))):
raise ValueError('The rois do not have unique ids.')
def create_from_preextracted_tiles(self,
tile_paths:List[pathlib.Path],
patient_id_getter:Callable,
case_id_getter:Callable,
slide_id_getter:Callable,
labels_getter:Callable):
"""
Inits self.patients from paths to already extracted tiles.
Arguments:
paths: paths to the tiles
patient_id_getter: method that maps from the tile image path to a patient id
case_id_getter: method that maps from the tile image path to a case id
slide_id_getter: method that maps from the tile image path to a slide id
labels_getter: function that maps from a tile_path to the tile's labels
"""
# empty the list, in case this function is called multiple times
self.patients = []
#key: patient_id; value: Patient object
patient_id_to_patient = {}
for tile_path in tqdm(tile_paths):
###
# patient
###
current_patient = None
patient_id = patient_id_getter(tile_path)
if(patient_id not in patient_id_to_patient.keys()):
current_patient = Patient(patient_id=patient_id, patient_manager=self)
patient_id_to_patient[patient_id] = current_patient
self.add_patient(current_patient)
else:
current_patient = patient_id_to_patient[patient_id]
###
# case
###
case_id = case_id_getter(tile_path)
current_case = None
for case in current_patient.get_cases():
if(case.case_id == case_id):
current_case = case
break;
if(current_case == None):
current_case = Case(case_id=case_id, patient=current_patient)
current_patient.add_case(current_case)
###
# whole-slide
###
slide_id = slide_id_getter(tile_path)
current_slide = None
for slide in current_case.get_whole_slide_images():
if(slide.slide_id == slide_id):
current_slide = slide
break;
if(current_slide == None):
current_slide = WholeSlideImage(slide_id=slide_id, case=current_case)
current_case.add_whole_slide_image(current_slide)
###
# region of interest; just one dummy roi per wsi
###
current_roi = None
if(len(current_slide.get_regions_of_interest()) == 0):
current_roi = roi.RegionOfInterestDummy(slide_id, current_slide)
current_slide.add_region_of_interest(current_roi)
else:
current_roi = current_slide.get_regions_of_interest()[0]
tile = Tile(roi=current_roi, tile_path=tile_path, labels=labels_getter(tile_path))
current_roi.add_tile(tile)
