def testSSLWorkflowBuilder(self):
segmenter = DumbSegmenter()
builder = SSLWorkflowBuilder()
builder.set_n_jobs(5)
builder.set_tile_size(512, 768)
builder.set_overlap(3)
builder.set_distance_tolerance(7)
builder.set_background_class(5)
builder.set_logger(StandardOutputLogger(Logger.DEBUG))
with self.assertRaises(MissingComponentException):
builder.get()
builder.set_segmenter(segmenter)
builder.set_default_tile_builder()
workflow = builder.get()
self.assertIsInstance(workflow, SSLWorkflow)
self.assertEqual(workflow._n_jobs, 5)
self.assertEqual(workflow._tile_overlap, 3)
self.assertEqual(workflow._tile_max_height, 512)
self.assertEqual(workflow._tile_max_width, 768)
self.assertIsInstance(workflow._tile_builder, DefaultTileBuilder)
self.assertIsInstance(workflow.logger, StandardOutputLogger)
self.assertEqual(workflow._locator._background, 5)
def main(argv):
with CytomineJob.from_cli(argv) as job:
model_path = os.path.join(str(Path.home()), "models", "thyroid-unet")
model_filepath = pick_model(model_path, job.parameters.tile_size,
job.parameters.cytomine_zoom_level)
device = torch.device(job.parameters.device)
unet = Unet(job.parameters.init_fmaps, n_classes=1)
unet.load_state_dict(torch.load(model_filepath, map_location=device))
unet.to(device)
unet.eval()
segmenter = UNetSegmenter(device=job.parameters.device,
unet=unet,
classes=[0, 1],
threshold=job.parameters.threshold)
working_path = os.path.join(str(Path.home()), "tmp")
tile_builder = CytomineTileBuilder(working_path)
builder = SSLWorkflowBuilder()
builder.set_n_jobs(1)
builder.set_overlap(job.parameters.tile_overlap)
builder.set_tile_size(job.parameters.tile_size,
job.parameters.tile_size)
builder.set_tile_builder(tile_builder)
builder.set_border_tiles(Workflow.BORDER_TILES_EXTEND)
builder.set_background_class(0)
builder.set_distance_tolerance(1)
builder.set_seg_batch_size(job.parameters.batch_size)
builder.set_segmenter(segmenter)
workflow = builder.get()
slide = CytomineSlide(img_instance=ImageInstance().fetch(
job.parameters.cytomine_id_image),
zoom_level=job.parameters.cytomine_zoom_level)
results = workflow.process(slide)
print("-------------------------")
print(len(results))
print("-------------------------")
collection = AnnotationCollection()
for obj in results:
wkt = shift_poly(obj.polygon,
slide,
zoom_level=job.parameters.cytomine_zoom_level).wkt
collection.append(
Annotation(location=wkt,
id_image=job.parameters.cytomine_id_image,
id_terms=[154005477],
id_project=job.project.id))
collection.save(n_workers=job.parameters.n_jobs)
return {}
def main(argv):
with CytomineJob.from_cli(argv) as cj:
# use only images from the current project
cj.job.update(progress=1, statusComment="Preparing execution")
# extract images to process
if cj.parameters.cytomine_zoom_level > 0 and (
cj.parameters.cytomine_tile_size != 256
or cj.parameters.cytomine_tile_overlap != 0):
raise ValueError(
"when using zoom_level > 0, tile size should be 256 "
"(given {}) and overlap should be 0 (given {})".format(
cj.parameters.cytomine_tile_size,
cj.parameters.cytomine_tile_overlap))
cj.job.update(
progress=1,
statusComment="Preparing execution (creating folders,...).")
# working path
root_path = str(Path.home())
working_path = os.path.join(root_path, "images")
os.makedirs(working_path, exist_ok=True)
# load training information
cj.job.update(progress=5,
statusComment="Extract properties from training job.")
train_job = Job().fetch(cj.parameters.cytomine_id_job)
properties = PropertyCollection(train_job).fetch().as_dict()
binary = str2bool(properties["binary"].value)
classes = parse_domain_list(properties["classes"].value)
cj.job.update(progress=10, statusComment="Download the model file.")
attached_files = AttachedFileCollection(train_job).fetch()
model_file = attached_files.find_by_attribute("filename",
"model.joblib")
model_filepath = os.path.join(root_path, "model.joblib")
model_file.download(model_filepath, override=True)
pyxit = joblib.load(model_filepath)
# set n_jobs
pyxit.base_estimator.n_jobs = cj.parameters.n_jobs
pyxit.n_jobs = cj.parameters.n_jobs
cj.job.update(progress=45, statusComment="Build workflow.")
builder = SSLWorkflowBuilder()
builder.set_tile_size(cj.parameters.cytomine_tile_size,
cj.parameters.cytomine_tile_size)
builder.set_overlap(cj.parameters.cytomine_tile_overlap)
builder.set_tile_builder(
CytomineTileBuilder(working_path, n_jobs=cj.parameters.n_jobs))
builder.set_logger(StandardOutputLogger(level=Logger.INFO))
builder.set_n_jobs(1)
builder.set_background_class(0)
# value 0 will prevent merging but still requires to run the merging check
# procedure (inefficient)
builder.set_distance_tolerance(2 if cj.parameters.union_enabled else 0)
builder.set_segmenter(
ExtraTreesSegmenter(
pyxit=pyxit,
classes=classes,
prediction_step=cj.parameters.pyxit_prediction_step,
background=0,
min_std=cj.parameters.tile_filter_min_stddev,
max_mean=cj.parameters.tile_filter_max_mean))
workflow = builder.get()
area_checker = AnnotationAreaChecker(
min_area=cj.parameters.min_annotation_area,
max_area=cj.parameters.max_annotation_area)
def get_term(label):
if binary:
if "cytomine_id_predict_term" not in cj.parameters:
return []
else:
return [int(cj.parameters.cytomine_id_predict_term)]
# multi-class
return [label]
zones = extract_images_or_rois(cj.parameters)
for zone in cj.monitor(zones,
start=50,
end=90,
period=0.05,
prefix="Segmenting images/ROIs"):
results = workflow.process(zone)
annotations = AnnotationCollection()
for obj in results:
if not area_checker.check(obj.polygon):
continue
polygon = obj.polygon
if isinstance(zone, ImageWindow):
polygon = affine_transform(
polygon,
[1, 0, 0, 1, zone.abs_offset_x, zone.abs_offset_y])
polygon = change_referential(polygon, zone.base_image.height)
if cj.parameters.cytomine_zoom_level > 0:
zoom_mult = (2**cj.parameters.cytomine_zoom_level)
polygon = affine_transform(
polygon, [zoom_mult, 0, 0, zoom_mult, 0, 0])
annotations.append(
Annotation(location=polygon.wkt,
id_terms=get_term(obj.label),
id_project=cj.project.id,
id_image=zone.base_image.image_instance.id))
annotations.save()
cj.job.update(status=Job.TERMINATED,
status_comment="Finish",
progress=100)