def testSLDCWorkflowWithRuleDispatcher(self):
# pre build components
segmenter = DumbSegmenter()
tile_builder = DefaultTileBuilder()
dispatcher = DumbDispatcher()
classifier1 = DumbClassifier()
classifier2 = DumbClassifier()
rule1 = DumbRule()
rule2 = DumbRule()
builder = SLDCWorkflowBuilder()
builder.set_segmenter(segmenter)
builder.set_tile_builder(tile_builder)
builder.add_classifier(rule1, classifier1)
builder.add_classifier(rule2, classifier2)
with self.assertRaises(InvalidBuildingException):
builder.set_one_shot_dispatcher(dispatcher, {"default": classifier1})
workflow = builder.get()
self.assertIsInstance(workflow, SLDCWorkflow)
self.assertEqual(len(workflow._dispatch_classifier._classifiers), 2)
self.assertEqual(workflow._dispatch_classifier._classifiers[0], classifier1)
self.assertEqual(workflow._dispatch_classifier._classifiers[1], classifier2)
self.assertIsInstance(workflow._dispatch_classifier._dispatcher, RuleBasedDispatcher)
self.assertEqual(len(workflow._dispatch_classifier._dispatcher._rules), 2)
self.assertEqual(workflow._dispatch_classifier._dispatcher._rules[0], rule1)
self.assertEqual(workflow._dispatch_classifier._dispatcher._rules[1], rule2)
def main(argv):
with CytomineJob.from_cli(argv) as job:
if not os.path.exists(job.parameters.working_path):
os.makedirs(job.parameters.working_path)
# create workflow component
logger = StandardOutputLogger(Logger.INFO)
random_state = check_random_state(int(job.parameters.rseed))
tile_builder = CytomineTileBuilder(
working_path=job.parameters.working_path)
segmenter = DemoSegmenter(job.parameters.threshold)
area_rule = ValidAreaRule(job.parameters.min_area)
classifier = PyxitClassifierAdapter.build_from_pickle(
job.parameters.pyxit_model_path,
tile_builder,
logger,
random_state=random_state,
n_jobs=job.parameters.n_jobs,
working_path=job.parameters.working_path)
builder = SLDCWorkflowBuilder()
builder.set_n_jobs(job.parameters.n_jobs)
builder.set_logger(logger)
builder.set_overlap(job.parameters.sldc_tile_overlap)
builder.set_tile_size(job.parameters.sldc_tile_width,
job.parameters.sldc_tile_height)
builder.set_tile_builder(tile_builder)
builder.set_segmenter(segmenter)
builder.add_classifier(area_rule,
classifier,
dispatching_label="valid")
workflow = builder.get()
slide = CytomineSlide(job.parameters.cytomine_image_id)
results = workflow.process(slide)
# Upload results
for polygon, label, proba, dispatch in results:
if label is not None:
# if image is a window, the polygon must be translated
if isinstance(slide, ImageWindow):
polygon = translate(polygon, slide.abs_offset_x,
slide.abs_offset_y)
# upload the annotation
polygon = affine_transform(
polygon, [1, 0, 0, -1, 0, slide.image_instance.height])
annotation = Annotation(
location=polygon.wkt,
id_image=slide.image_instance.id).save()
AlgoAnnotationTerm(id_annotation=annotation.id,
id_term=label,
rate=float(proba)).save()
def testSLDCWorkflowWithOneShotDispatcher(self):
# pre build components
segmenter = DumbSegmenter()
dispatcher = DumbDispatcher()
classifier = DumbClassifier()
rule = DumbRule()
logger = StandardOutputLogger(Logger.DEBUG)
builder = SLDCWorkflowBuilder()
builder.set_tile_size(512, 768)
builder.set_overlap(3)
builder.set_distance_tolerance(5)
builder.set_n_jobs(5)
builder.set_logger(logger)
builder.set_parallel_dc(True)
builder.set_tile_builder(None)
with self.assertRaises(MissingComponentException):
builder.get()
builder.set_segmenter(segmenter)
with self.assertRaises(MissingComponentException):
builder.get()
builder.set_default_tile_builder()
with self.assertRaises(MissingComponentException):
builder.get()
builder.set_one_shot_dispatcher(dispatcher, {"default": classifier})
with self.assertRaises(InvalidBuildingException):
builder.add_classifier(rule, classifier, dispatching_label="default")
with self.assertRaises(InvalidBuildingException):
builder.add_catchall_classifier(classifier, dispatching_label="default")
workflow = builder.get()
self.assertIsInstance(workflow, SLDCWorkflow)
self.assertEqual(workflow._segmenter, segmenter)
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.assertEqual(workflow.logger, logger)
self.assertIsInstance(workflow._tile_builder, DefaultTileBuilder)
self.assertEqual(workflow._dispatch_classifier._dispatcher, dispatcher)
self.assertEqual(len(workflow._dispatch_classifier._classifiers), 1)
self.assertEqual(workflow._dispatch_classifier._classifiers[0], classifier)
def testSLDCWorkflowWithCatchAllClassifier(self):
# pre build components
segmenter = DumbSegmenter()
tile_builder = DefaultTileBuilder()
dispatcher = DumbDispatcher()
classifier = DumbClassifier()
builder = SLDCWorkflowBuilder()
builder.set_segmenter(segmenter)
builder.set_tile_builder(tile_builder)
builder.add_catchall_classifier(classifier)
with self.assertRaises(InvalidBuildingException):
builder.set_one_shot_dispatcher(dispatcher, {"default": classifier})
workflow = builder.get()
self.assertIsInstance(workflow, SLDCWorkflow)
self.assertIsInstance(workflow._dispatch_classifier._dispatcher, RuleBasedDispatcher)
self.assertEqual(len(workflow._dispatch_classifier._classifiers), 1)
self.assertEqual(workflow._dispatch_classifier._classifiers[0], classifier)
self.assertIsInstance(workflow._dispatch_classifier._dispatcher, RuleBasedDispatcher)
self.assertEqual(len(workflow._dispatch_classifier._dispatcher._rules), 1)
self.assertIsInstance(workflow._dispatch_classifier._dispatcher._rules[0], CatchAllRule)