def test_multiple_polygonsets_for_one_grader_distinct(self):
grader = UserFactory()
grader.groups.add(
Group.objects.get(name=settings.RETINA_GRADERS_GROUP_NAME)
)
polygon_sets = [
self.annotation_set.polygonset1,
PolygonAnnotationSetFactory(
grader=grader, image=self.annotation_set.polygonset1.image
),
PolygonAnnotationSetFactory(
grader=grader, image=self.annotation_set.polygonset1.image
),
]
force_authenticate(self.request, user=self.retina_admin)
response = self.view(self.request, **self.kwargs)
graders = (
get_user_model()
.objects.filter(
polygonannotationset__in=polygon_sets,
groups__name=settings.RETINA_GRADERS_GROUP_NAME,
)
.distinct()
)
expected_response = UserSerializer(graders, many=True).data
expected_response.sort(key=lambda k: k["id"])
assert response.status_code == status.HTTP_200_OK
response.data.sort(key=lambda k: k["id"])
assert response.data == expected_response
def test_testsetretinapathologies_old(self):
PolygonAnnotationSetFactory(name="No match")
PolygonAnnotationSetFactory(name="retina::too_small")
result = set_retina_pathologies(PolygonAnnotationSet.objects.all())
assert result["pathology_set"] == 0
assert result["old_annotation"] == 2
assert len(result["non_matching_pathology"]) == 0
def generate_two_polygon_annotation_sets(retina_grader=False):
graders = (UserFactory(), UserFactory())
if retina_grader:
add_to_graders_group(graders)
polygonsets = (
PolygonAnnotationSetFactory(grader=graders[0]),
PolygonAnnotationSetFactory(grader=graders[1]),
)
# Create child models for polygon annotation set
singlepolygonbatches = (
SinglePolygonAnnotationFactory.create_batch(
10, annotation_set=polygonsets[0]
),
SinglePolygonAnnotationFactory.create_batch(
10, annotation_set=polygonsets[1]
),
)
return TwoPolygonAnnotationSets(
grader1=graders[0],
grader2=graders[1],
polygonset1=polygonsets[0],
polygonset2=polygonsets[1],
)
def test_testmigratelesionnames_already_migrated(self):
image = ImageFactory(modality=ImagingModalityFactory(modality="OCT"))
PolygonAnnotationSetFactory(name="retina::oct::macular::Drusen",
image=image)
PolygonAnnotationSetFactory(
name="retina::enface::rf_present::Hard drusen")
result = migrate_annotations(PolygonAnnotationSet.objects.all())
assert result["translated"] == 0
assert result["already_translated"] == 2
def test_testmigratelesionnames_no_match_enface(self):
annotation = PolygonAnnotationSetFactory(
name=
"amd_present::Drusen and drusen like structures::Conical drusen")
result = migrate_annotations(PolygonAnnotationSet.objects.all())
assert result["translated"] == 0
assert result["enface_no_match"] == [annotation.id]
def generate_annotation_set(retina_grader=False):
grader = UserFactory()
if retina_grader:
add_to_graders_group([grader])
measurement = MeasurementAnnotationFactory(grader=grader)
boolean = BooleanClassificationAnnotationFactory(grader=grader)
integer = IntegerClassificationAnnotationFactory(grader=grader)
polygon = PolygonAnnotationSetFactory(grader=grader)
coordinatelist = CoordinateListAnnotationFactory(grader=grader)
landmark = LandmarkAnnotationSetFactory(grader=grader)
etdrs = ETDRSGridAnnotationFactory(grader=grader)
# Create child models for polygon annotation set
SinglePolygonAnnotationFactory.create_batch(10, annotation_set=polygon)
# Create child models for landmark annotation set (3 per image)
for i in range(5):
image = ImageFactory()
SingleLandmarkAnnotationFactory(annotation_set=landmark, image=image)
return AnnotationSet(
grader=grader,
measurement=measurement,
boolean=boolean,
polygon=polygon,
coordinatelist=coordinatelist,
landmark=landmark,
etdrs=etdrs,
integer=integer,
)
def test_multiple_graders_some_retina_grader(self):
graders = (
UserFactory(),
UserFactory(),
UserFactory(),
UserFactory(),
UserFactory(),
)
polygon_sets = [self.annotation_set.polygonset1]
for index, grader in enumerate(graders):
if index % 2 == 0:
grader.groups.add(
Group.objects.get(name=settings.RETINA_GRADERS_GROUP_NAME)
)
polygon_sets.append(
PolygonAnnotationSetFactory(
grader=grader, image=self.annotation_set.polygonset1.image
)
)
force_authenticate(self.request, user=self.retina_admin)
response = self.view(self.request, **self.kwargs)
graders = get_user_model().objects.filter(
polygonannotationset__in=polygon_sets,
groups__name=settings.RETINA_GRADERS_GROUP_NAME,
)
expected_response = UserSerializer(graders, many=True).data
expected_response.sort(key=lambda k: k["id"])
assert response.status_code == status.HTTP_200_OK
response.data.sort(key=lambda k: k["id"])
assert response.data == expected_response
def test_create_view_wrong_user_id(
self, TwoRetinaPolygonAnnotationSets, rf, user_type
):
model_build = PolygonAnnotationSetFactory.build()
model_serialized = PolygonAnnotationSetSerializer(model_build).data
image = ImageFactory()
model_serialized["image"] = str(image.id)
other_user = UserFactory()
model_serialized["grader"] = other_user.id
model_json = json.dumps(model_serialized)
response = view_test(
"create",
user_type,
self.namespace,
self.basename,
TwoRetinaPolygonAnnotationSets.grader1,
TwoRetinaPolygonAnnotationSets.polygonset1,
rf,
PolygonAnnotationSetViewSet,
model_json,
check_response_status_code=False,
)
if user_type == "retina_admin":
model_serialized["id"] = response.data["id"]
response.data["image"] = str(response.data["image"])
assert response.data == model_serialized
elif user_type == "retina_grader":
assert response.status_code == status.HTTP_400_BAD_REQUEST
assert (
str(response.data["grader"][0])
== "User is not allowed to create annotation for other grader"
)
else:
assert response.status_code == status.HTTP_403_FORBIDDEN
def test_update_view(self, TwoRetinaPolygonAnnotationSets, rf, user_type):
model_serialized = SinglePolygonAnnotationSerializer(
TwoRetinaPolygonAnnotationSets.polygonset1.singlepolygonannotation_set.first()
).data
annotation_set = PolygonAnnotationSetFactory(
grader=TwoRetinaPolygonAnnotationSets.grader1
)
model_serialized["annotation_set"] = str(annotation_set.id)
model_json = json.dumps(model_serialized)
response = view_test(
"update",
user_type,
self.namespace,
self.basename,
TwoRetinaPolygonAnnotationSets.grader1,
TwoRetinaPolygonAnnotationSets.polygonset1.singlepolygonannotation_set.first(),
rf,
SinglePolygonViewSet,
model_json,
)
if user_type in ("retina_grader", "retina_admin"):
response.data["annotation_set"] = str(
response.data["annotation_set"]
)
assert response.data == model_serialized
def test_create_view(self, TwoRetinaPolygonAnnotationSets, rf, user_type):
model_build = SinglePolygonAnnotationFactory.build()
model_serialized = SinglePolygonAnnotationSerializer(model_build).data
annotation_set = PolygonAnnotationSetFactory(
grader=TwoRetinaPolygonAnnotationSets.grader1
)
model_serialized["annotation_set"] = str(annotation_set.id)
model_json = json.dumps(model_serialized)
response = view_test(
"create",
user_type,
self.namespace,
self.basename,
TwoRetinaPolygonAnnotationSets.grader1,
None,
rf,
SinglePolygonViewSet,
model_json,
)
if user_type in ("retina_grader", "retina_admin"):
model_serialized["id"] = response.data["id"]
response.data["annotation_set"] = str(
response.data["annotation_set"]
)
assert response.data == model_serialized
def test_create_view_wrong_user_id(
self, TwoRetinaPolygonAnnotationSets, rf, user_type
):
model_build = PolygonAnnotationSetFactory.build()
model_serialized = PolygonAnnotationSetSerializer(model_build).data
image = ImageFactory()
model_serialized["image"] = str(image.id)
other_user = UserFactory()
model_serialized["grader"] = other_user.id
model_json = json.dumps(model_serialized)
response = view_test(
"create",
user_type,
self.namespace,
self.basename,
TwoRetinaPolygonAnnotationSets.grader1,
TwoRetinaPolygonAnnotationSets.polygonset1,
rf,
PolygonAnnotationSetViewSet,
model_json,
check_response_status_code=False,
)
if user_type == "retina_admin":
model_serialized["id"] = response.data["id"]
response.data["image"] = str(response.data["image"])
assert response.data == model_serialized
elif user_type == "retina_grader":
assert response.status_code == status.HTTP_400_BAD_REQUEST
assert (
str(response.data["grader"][0])
== "User is not allowed to create annotation for other grader"
)
else:
assert response.status_code == status.HTTP_403_FORBIDDEN
def test_testmigratelesionnames_no_match_oct_boolean(self):
image = ImageFactory(modality=ImagingModalityFactory(modality="OCT"))
annotation = PolygonAnnotationSetFactory(
name="other_present::Vascular::Branch retinal artery occlusion",
image=image,
)
result = migrate_annotations(PolygonAnnotationSet.objects.all())
assert result["translated"] == 0
assert result["boolean_oct_no_match"] == [annotation.id]
def create_load_data(data_type, ds, grader):
if data_type == "Registration":
model = LandmarkAnnotationSetFactory(grader=grader)
SingleLandmarkAnnotationFactory(
annotation_set=model, image=ds["image_cf"]
),
if ds["archive"].name == "Australia":
# Australia does not allow obs images so create a new cf image for Australia test
img = ImageFactory(study=ds["study"])
SingleLandmarkAnnotationFactory(annotation_set=model, image=img)
else:
SingleLandmarkAnnotationFactory(
annotation_set=model, image=ds["image_obs"]
),
elif data_type == "ETDRS":
model = ETDRSGridAnnotationFactory(grader=grader, image=ds["image_cf"])
elif data_type == "GA" or data_type == "kappa":
model_macualar = PolygonAnnotationSetFactory(
grader=grader, image=ds["image_cf"], name="macular"
)
SinglePolygonAnnotationFactory(annotation_set=model_macualar)
SinglePolygonAnnotationFactory(annotation_set=model_macualar)
SinglePolygonAnnotationFactory(annotation_set=model_macualar)
model_peripapillary = PolygonAnnotationSetFactory(
grader=grader, image=ds["image_cf"], name="peripapillary"
)
SinglePolygonAnnotationFactory(annotation_set=model_peripapillary)
SinglePolygonAnnotationFactory(annotation_set=model_peripapillary)
SinglePolygonAnnotationFactory(annotation_set=model_peripapillary)
model = [model_macualar, model_peripapillary]
elif data_type == "Measure":
model = [
MeasurementAnnotationFactory(grader=grader, image=ds["image_cf"]),
MeasurementAnnotationFactory(grader=grader, image=ds["image_cf"]),
MeasurementAnnotationFactory(grader=grader, image=ds["image_cf"]),
]
elif data_type == "Fovea":
model = BooleanClassificationAnnotationFactory(
grader=grader, image=ds["image_cf"], name="fovea_affected"
)
return model
def test_testmigratelesionnames_no_match_oct(self):
image = ImageFactory(modality=ImagingModalityFactory(modality="OCT"))
annotation = PolygonAnnotationSetFactory(
name=
"amd_present::Pigment changes & RPE degeneration::Increased pigmentation",
image=image,
)
result = migrate_annotations(PolygonAnnotationSet.objects.all())
assert result["translated"] == 0
assert result["oct_no_match"] == [annotation.id]
def test_testmigratelesionnames_unique_violation_appends(self):
annotation = PolygonAnnotationSetFactory(
name="drusen and drusen like structures::hard drusen")
SinglePolygonAnnotationFactory(annotation_set=annotation),
SinglePolygonAnnotationFactory(annotation_set=annotation),
annotation_dup = PolygonAnnotationSetFactory(
name="retina::enface::rf_present::Hard drusen",
grader=annotation.grader,
image=annotation.image,
created=annotation.created,
)
SinglePolygonAnnotationFactory(annotation_set=annotation_dup),
SinglePolygonAnnotationFactory(annotation_set=annotation_dup),
assert annotation_dup.singlepolygonannotation_set.count() == 2
result = migrate_annotations(PolygonAnnotationSet.objects.all())
assert result["translated"] == 1
assert result["already_translated"] == 1
assert PolygonAnnotationSet.objects.count() == 1
annotation_dup.refresh_from_db()
assert annotation_dup.singlepolygonannotation_set.count() == 4
def test_testsetretinapathologies_no_match(self):
annotation = PolygonAnnotationSetFactory(
name="retina::enface::non_matching_pathology::bla")
result = set_retina_pathologies(PolygonAnnotationSet.objects.all())
assert result["pathology_set"] == 0
assert result["old_annotation"] == 0
assert len(result["non_matching_pathology"]) == 1
assert result["non_matching_pathology"] == [{
"id": annotation.id,
"name": annotation.name
}]
def generate_annotation_set(retina_grader=False, image=False):
grader = UserFactory()
if retina_grader:
add_to_graders_group([grader])
create_options = {"grader": grader}
if image:
create_options_with_image = {"image": image, **create_options}
else:
create_options_with_image = create_options
measurement = MeasurementAnnotationFactory(**create_options_with_image)
boolean = BooleanClassificationAnnotationFactory(
**create_options_with_image
)
integer = IntegerClassificationAnnotationFactory(
**create_options_with_image
)
polygon = PolygonAnnotationSetFactory(**create_options_with_image)
coordinatelist = CoordinateListAnnotationFactory(
**create_options_with_image
)
etdrs = ETDRSGridAnnotationFactory(**create_options_with_image)
landmark = LandmarkAnnotationSetFactory(**create_options)
# Create child models for polygon annotation set
SinglePolygonAnnotationFactory.create_batch(10, annotation_set=polygon)
# Create child models for landmark annotation set (3 per image)
single_landmarks = []
for i in range(5):
if i > 0 or not image:
image = ImageFactory()
single_landmarks.append(
SingleLandmarkAnnotationFactory(
annotation_set=landmark, image=image
)
)
return AnnotationSet(
grader=grader,
measurement=measurement,
boolean=boolean,
polygon=polygon,
coordinatelist=coordinatelist,
landmark=landmark,
singlelandmarks=single_landmarks,
etdrs=etdrs,
integer=integer,
)
def test_testmigratelesionnames_correctly_migrated(self):
image = ImageFactory(modality=ImagingModalityFactory(modality="OCT"))
annotation_oct = PolygonAnnotationSetFactory(
name="amd_present::Drusen and drusen like structures::Hard Drusen",
image=image,
)
annotation_enface = PolygonAnnotationSetFactory(
name="drusen and drusen like structures::hard drusen")
result = migrate_annotations(PolygonAnnotationSet.objects.all())
assert result["translated"] == 2
annotation_enface.refresh_from_db()
assert (annotation_enface.name ==
"retina::enface::rf_present::Hard drusen")
annotation_oct.refresh_from_db()
assert annotation_oct.name == "retina::oct::macular::Drusen"
def test_testmigratelesionnames_correctly_migrated_case_insensitive(self):
image = ImageFactory(modality=ImagingModalityFactory(modality="OCT"))
annotation_oct = PolygonAnnotationSetFactory(
name="amd_present::DrUsEn AnD DrUsEn lIkE sTruCtUrEs::HARD dRuSeN",
image=image,
)
annotation_enface = PolygonAnnotationSetFactory(
name="DrUsEn AnD DrUsEn lIkE sTruCtUrEs::HARD dRuSeN")
result = migrate_annotations(PolygonAnnotationSet.objects.all())
assert result["translated"] == 2
annotation_enface.refresh_from_db()
assert (annotation_enface.name ==
"retina::enface::rf_present::Hard drusen")
annotation_oct.refresh_from_db()
assert annotation_oct.name == "retina::oct::macular::Drusen"
def test_testsetretinapathologies_created(self):
annotation = PolygonAnnotationSetFactory(
name=f"retina::enface::{pathology_options_enface[0]}::bla")
assert RetinaImagePathologyAnnotation.objects.all().count() == 0
result = set_retina_pathologies(PolygonAnnotationSet.objects.all())
assert result["pathology_set"] == 1
assert result["old_annotation"] == 0
assert len(result["non_matching_pathology"]) == 0
assert RetinaImagePathologyAnnotation.objects.all().count() == 1
pathology_annotation = RetinaImagePathologyAnnotation.objects.first()
assert pathology_annotation.image == annotation.image
assert pathology_annotation.grader == annotation.grader
for v in pathology_options_enface:
assert getattr(pathology_annotation,
v) == (v == pathology_options_enface[0])
def test_testmigratelesionnames_correctly_migrated_boolean(self):
annotation_enface = PolygonAnnotationSetFactory(
name="other_present::Vascular::Branch retinal artery occlusion")
assert BooleanClassificationAnnotation.objects.count() == 0
result = migrate_annotations(PolygonAnnotationSet.objects.all())
assert result["translated"] == 1
assert PolygonAnnotationSet.objects.count() == 0
assert BooleanClassificationAnnotation.objects.count() == 1
annotation = BooleanClassificationAnnotation.objects.first()
assert (annotation.name ==
"retina::enface::Branch retinal artery occlusion")
assert annotation.value
assert annotation.grader == annotation_enface.grader
assert annotation.image == annotation_enface.image
assert annotation.created == annotation_enface.created
def test_testsetretinapathologies_oct(self):
annotation = PolygonAnnotationSetFactory(
name=f"retina::oct::{pathology_options_oct[0]}::bla")
assert OctRetinaImagePathologyAnnotation.objects.all().count() == 0
result = set_retina_pathologies(PolygonAnnotationSet.objects.all())
assert result["pathology_set"] == 1
assert result["old_annotation"] == 0
assert len(result["non_matching_pathology"]) == 0
assert RetinaImagePathologyAnnotation.objects.all().count() == 0
assert OctRetinaImagePathologyAnnotation.objects.all().count() == 1
oct_pathology_annotation = (
OctRetinaImagePathologyAnnotation.objects.first())
assert oct_pathology_annotation.image == annotation.image
assert oct_pathology_annotation.grader == annotation.grader
assert (getattr(oct_pathology_annotation, pathology_options_oct[0]) is
True)
def test_testsetretinapathologies_updated(self):
annotation = PolygonAnnotationSetFactory(
name=f"retina::enface::{pathology_options_enface[0]}::bla")
pathology_annotation = RetinaImagePathologyAnnotationFactory(
**{
"image": annotation.image,
"grader": annotation.grader,
pathology_options_enface[0]: False,
})
assert RetinaImagePathologyAnnotation.objects.all().count() == 1
result = set_retina_pathologies(PolygonAnnotationSet.objects.all())
assert result["pathology_set"] == 1
assert result["old_annotation"] == 0
assert len(result["non_matching_pathology"]) == 0
assert RetinaImagePathologyAnnotation.objects.all().count() == 1
pathology_annotation.refresh_from_db()
assert pathology_annotation.image == annotation.image
assert pathology_annotation.grader == annotation.grader
assert (getattr(pathology_annotation, pathology_options_enface[0]) is
True)
def test_create_view(self, TwoRetinaPolygonAnnotationSets, rf, user_type):
model_build = PolygonAnnotationSetFactory.build()
model_serialized = PolygonAnnotationSetSerializer(model_build).data
image = ImageFactory()
model_serialized["image"] = str(image.id)
model_serialized["grader"] = TwoRetinaPolygonAnnotationSets.grader1.id
model_json = json.dumps(model_serialized)
response = view_test(
"create",
user_type,
self.namespace,
self.basename,
TwoRetinaPolygonAnnotationSets.grader1,
TwoRetinaPolygonAnnotationSets.polygonset1,
rf,
PolygonAnnotationSetViewSet,
model_json,
)
if user_type in ("retina_grader", "retina_admin"):
model_serialized["id"] = response.data["id"]
response.data["image"] = str(response.data["image"])
assert response.data == model_serialized
def test_create_view(self, TwoRetinaPolygonAnnotationSets, rf, user_type):
model_build = PolygonAnnotationSetFactory.build()
model_serialized = PolygonAnnotationSetSerializer(model_build).data
image = ImageFactory()
model_serialized["image"] = str(image.id)
model_serialized["grader"] = TwoRetinaPolygonAnnotationSets.grader1.id
model_json = json.dumps(model_serialized)
response = view_test(
"create",
user_type,
self.namespace,
self.basename,
TwoRetinaPolygonAnnotationSets.grader1,
TwoRetinaPolygonAnnotationSets.polygonset1,
rf,
PolygonAnnotationSetViewSet,
model_json,
)
if user_type in ("retina_grader", "retina_admin"):
model_serialized["id"] = response.data["id"]
response.data["image"] = str(response.data["image"])
assert response.data == model_serialized
def test_update_view_wrong_user_id(
self, TwoRetinaPolygonAnnotationSets, rf, user_type
):
model_serialized = SinglePolygonAnnotationSerializer(
TwoRetinaPolygonAnnotationSets.polygonset1.singlepolygonannotation_set.first()
).data
annotation_set = PolygonAnnotationSetFactory()
model_serialized["annotation_set"] = str(annotation_set.id)
model_json = json.dumps(model_serialized)
response = view_test(
"update",
user_type,
self.namespace,
self.basename,
TwoRetinaPolygonAnnotationSets.grader1,
TwoRetinaPolygonAnnotationSets.polygonset1.singlepolygonannotation_set.first(),
rf,
SinglePolygonViewSet,
model_json,
check_response_status_code=False,
)
if user_type == "retina_admin":
model_serialized["id"] = response.data["id"]
response.data["annotation_set"] = str(
response.data["annotation_set"]
)
assert response.data == model_serialized
elif user_type == "retina_grader":
assert response.status_code == status.HTTP_400_BAD_REQUEST
assert (
str(response.data["non_field_errors"][0])
== "User is not allowed to create annotation for other grader"
)
else:
assert response.status_code == status.HTTP_403_FORBIDDEN
def test_testmigratelesionnames_combined(self):
image = ImageFactory(modality=ImagingModalityFactory(modality="OCT"))
annotation_oct = PolygonAnnotationSetFactory(
name="amd_present::Drusen and drusen like structures::Hard Drusen",
image=image,
)
annotation_enface = PolygonAnnotationSetFactory(
name="drusen and drusen like structures::hard drusen")
PolygonAnnotationSetFactory(name="retina::oct::macular::Drusen",
image=image)
PolygonAnnotationSetFactory(
name="retina::enface::rf_present::Hard drusen")
PolygonAnnotationSetFactory(
name="other_present::Vascular::Branch retinal artery occlusion", )
annotation_oct_no_match_boolean = PolygonAnnotationSetFactory(
name="other_present::Vascular::Branch retinal artery occlusion",
image=image,
)
annotation_oct_no_match = PolygonAnnotationSetFactory(
name=
"amd_present::Pigment changes & RPE degeneration::Increased pigmentation",
image=image,
)
annotation_enface_no_match = PolygonAnnotationSetFactory(
name=
"amd_present::Drusen and drusen like structures::Conical drusen")
annotation_no_match = PolygonAnnotationSetFactory(name="No match")
assert BooleanClassificationAnnotation.objects.count() == 0
result = migrate_annotations(PolygonAnnotationSet.objects.all())
assert result["translated"] == 3
assert BooleanClassificationAnnotation.objects.count() == 1
assert result["already_translated"] == 2
assert result["boolean_oct_no_match"] == [
annotation_oct_no_match_boolean.id
]
assert result["oct_no_match"] == [annotation_oct_no_match.id]
assert result["enface_no_match"] == [annotation_enface_no_match.id]
assert result["no_match"] == [annotation_no_match.id]
annotation_enface.refresh_from_db()
assert (annotation_enface.name ==
"retina::enface::rf_present::Hard drusen")
annotation_oct.refresh_from_db()
assert annotation_oct.name == "retina::oct::macular::Drusen"
def test_testmigratelesionnames_no_match(self):
annotation = PolygonAnnotationSetFactory(name="No match")
result = migrate_annotations(PolygonAnnotationSet.objects.all())
assert result["translated"] == 0
assert result["no_match"] == [annotation.id]
