def test_thumbnail_endpoint_authenticated_no_perm(self, client,
django_user_model):
image = ImageFactoryWithImageFile()
url = reverse("retina:image-thumbnail", args=[image.id])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_403_FORBIDDEN
def test_access(self, client, user, expected_status):
image = ImageFactoryWithImageFile()
image.permit_viewing_by_retina_users()
url = reverse("retina:api:image-element-spacing-view", args=[image.pk])
client, _ = client_login(client, user=user)
response = client.get(url)
assert response.status_code == expected_status
def test_access(self, client, user, expected_status):
image = ImageFactoryWithImageFile()
image.permit_viewing_by_retina_users()
url = reverse("retina:api:image-element-spacing-view", args=[image.pk])
client, _ = client_login(client, user=user)
response = client.get(url)
assert response.status_code == expected_status
def test_archive_view_returns_correct_error_on_empty_cache(
self, client, monkeypatch
):
# Clear cache manually
cache.clear()
# Mock celery task
is_called = False
def call_task():
nonlocal is_called
is_called = True
monkeypatch.setattr(cache_archive_data, "delay", call_task)
# login client
client, _ = client_login(client, user="******")
url = reverse("retina:api:archives-api-view")
response = client.get(url, HTTP_ACCEPT="application/json")
response_data = json.loads(response.content)
# check if correct error is sent
assert response_data == {
"error": [
1,
"Archive data task triggered. Try again in 2 minutes.",
]
}
assert is_called
def test_thumbnail_endpoint_authenticated_no_perm(
self, client, django_user_model
):
image = ImageFactoryWithImageFile()
url = reverse("retina:image-thumbnail", args=[image.id])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_403_FORBIDDEN
def test_returns_correct_spacing(self, client):
image = ImageFactoryWithImageFile()
image.permit_viewing_by_retina_users()
url = reverse("retina:api:image-element-spacing-view", args=[image.pk])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_200_OK
r = response.json()
assert list(image.get_sitk_image().GetSpacing()) == r
def test_numpy_endpoint_authenticated_status(self, client,
django_user_model):
image = ImageFactoryWithImageFile()
image.permit_viewing_by_retina_users()
url = reverse("retina:image-numpy", args=[image.id])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_200_OK
assert response["Content-type"] == "application/octet-stream"
def test_thumbnail_endpoint_authenticated_non_existant(
self, client, django_user_model):
image = ImageFactoryWithImageFile()
url = reverse("retina:image-thumbnail", args=[image.id])
# login client
client, _ = client_login(client, user="******")
image.delete() # remove model so response must return 404
response = client.get(url)
assert response.status_code == status.HTTP_404_NOT_FOUND
def test_returns_correct_spacing(self, client):
image = ImageFactoryWithImageFile()
image.permit_viewing_by_retina_users()
url = reverse("retina:api:image-element-spacing-view", args=[image.pk])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_200_OK
r = response.json()
assert list(image.get_sitk_image().GetSpacing()) == r
def test_archive_view_retina_auth(self, client):
# Create data
create_datastructures_data()
# login client
client, _ = client_login(client, user="******")
url = reverse("retina:api:archives-api-view")
response = client.get(url, HTTP_ACCEPT="application/json")
assert response.status_code == status.HTTP_200_OK
def test_archive_view_retina_auth(self, client):
# Create data
create_datastructures_data()
# login client
client, _ = client_login(client, user="******")
url = reverse("retina:api:archives-api-view")
response = client.get(url, HTTP_ACCEPT="application/json")
assert response.status_code == status.HTTP_200_OK
def test_thumbnail_endpoint_authenticated_non_existant(
self, client, django_user_model
):
image = ImageFactoryWithImageFile()
url = reverse("retina:image-thumbnail", args=[image.id])
# login client
client, _ = client_login(client, user="******")
image.delete() # remove model so response must return 404
response = client.get(url)
assert response.status_code == status.HTTP_404_NOT_FOUND
def test_numpy_endpoint_authenticated_status(
self, client, django_user_model
):
image = ImageFactoryWithImageFile()
image.permit_viewing_by_retina_users()
url = reverse("retina:image-numpy", args=[image.id])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_200_OK
assert response["Content-type"] == "application/octet-stream"
def test_numpy_endpoint_authenticated_images_correspond(
self, client, django_user_model):
image = ImageFactoryWithImageFile(
modality__modality=settings.MODALITY_CF)
image.permit_viewing_by_retina_users()
url = reverse("retina:image-numpy", args=[image.id])
client, _ = client_login(client, user="******")
response = client.get(url)
response_np = np.load(io.BytesIO(response.content))
sitk_image = image.get_sitk_image()
nda_image = sitk.GetArrayFromImage(sitk_image)
request_image_arr = nda_image.astype(np.int8)
assert np.array_equal(response_np, request_image_arr)
def test_caching(self, client):
# Clear cache manually
cache.clear()
# Perform normal request
datastructures, _, _, _ = create_datastructures_data()
client, _ = client_login(client, user="******")
url = reverse("retina:api:archives-api-view")
response = client.get(url, HTTP_ACCEPT="application/json")
response_data = json.loads(response.content)
# Remove archive and perform request again
datastructures["archive"].delete()
response = client.get(url, HTTP_ACCEPT="application/json")
# Check that response is cached so it is not changed
assert json.loads(response.content) == response_data
def test_numpy_endpoint_authenticated_images_correspond(
self, client, django_user_model
):
image = ImageFactoryWithImageFile(
modality__modality=settings.MODALITY_CF
)
image.permit_viewing_by_retina_users()
url = reverse("retina:image-numpy", args=[image.id])
client, _ = client_login(client, user="******")
response = client.get(url)
response_np = np.load(io.BytesIO(response.content))
sitk_image = image.get_sitk_image()
nda_image = sitk.GetArrayFromImage(sitk_image)
request_image_arr = nda_image.astype(np.int8)
assert np.array_equal(response_np, request_image_arr)
def test_archive_view_returns_correct_data_from_cache(self, client):
# Clear cache manually
cache.clear()
# Set cached data
test_data = {"test": "data", "object": 1}
ArchiveDataModel.objects.update_or_create(
pk=1, defaults={"value": test_data},
)
# login client
client, _ = client_login(client, user="******")
url = reverse("retina:api:archives-api-view")
response = client.get(url, HTTP_ACCEPT="application/json")
response_data = json.loads(response.content)
# check if correct data is sent
assert response_data == test_data
def test_returns_correct_spacing_changed(self, client):
image = ImageFactoryWithImageFile()
image.permit_viewing_by_retina_users()
element_spacing = (1.5, 0.5)
response = create_element_spacing_request(
client, image_name=image.name, es=element_spacing
)
assert response.status_code == status.HTTP_200_OK
r = response.json()
assert r["success"]
assert element_spacing == image.get_sitk_image().GetSpacing()
url = reverse("retina:api:image-element-spacing-view", args=[image.pk])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_200_OK
r = response.json()
assert list(image.get_sitk_image().GetSpacing()) == r
def test_thumbnail_endpoint_authenticated(self, client, django_user_model):
image = ImageFactoryWithImageFile()
image.permit_viewing_by_retina_users()
url = reverse("retina:image-thumbnail", args=[image.id])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_200_OK
assert response["Content-type"] == "image/png"
response_np = np.array(PILImage.open(io.BytesIO(response.content)),
np.uint8)
sitk_image = image.get_sitk_image()
depth = sitk_image.GetDepth()
nda_image = sitk.GetArrayFromImage(sitk_image)
if depth > 0:
nda_image = nda_image[depth // 2]
expected_np = nda_image.astype(np.uint8)
assert np.array_equal(response_np, expected_np)
def test_thumbnail_endpoint_authenticated(self, client, django_user_model):
image = ImageFactoryWithImageFile()
image.permit_viewing_by_retina_users()
url = reverse("retina:image-thumbnail", args=[image.id])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_200_OK
assert response["Content-type"] == "image/png"
response_np = np.array(
PILImage.open(io.BytesIO(response.content)), np.uint8
)
sitk_image = image.get_sitk_image()
depth = sitk_image.GetDepth()
nda_image = sitk.GetArrayFromImage(sitk_image)
if depth > 0:
nda_image = nda_image[depth // 2]
expected_np = nda_image.astype(np.uint8)
assert np.array_equal(response_np, expected_np)
def test_numpy_endpoint_normal_non_authenticated(self, client):
image = ImageFactoryWithImageFile()
url = reverse("retina:image-numpy", args=[image.id])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_403_FORBIDDEN
def test_archive_view_returns_correct_data(self, client):
# Clear cache manually (this is not done by pytest-django for some reason...)
cache.clear()
# Create data
datastructures, datastructures_aus, oct_obs_registration, oct_obs_registration_aus = (
create_datastructures_data())
# login client
client, _ = client_login(client, user="******")
url = reverse("retina:api:archives-api-view")
response = client.get(url, HTTP_ACCEPT="application/json")
response_data = json.loads(response.content)
# check if correct data is sent
expected_response_data = {
"subfolders": {
datastructures["archive"].name: {
"subfolders": {
datastructures["patient"].name: {
"subfolders": {
datastructures["study_oct"].name: {
"info": "level 5",
"images": {
datastructures["image_oct"].name: {
"images": {
"trc_000":
"no info",
"obs_000":
str(datastructures["image_obs"]
.id),
"mot_comp":
"no info",
"trc_001":
"no info",
"oct":
str(datastructures["image_oct"]
.id),
},
"info": {
"voxel_size": {
"axial": 0,
"lateral": 0,
"transversal": 0,
},
"date":
datastructures["study_oct"].
datetime.strftime(
"%Y/%m/%d %H:%M:%S"),
"registration": {
"obs":
"Checked separately",
"trc": [0, 0, 0, 0],
},
},
}
},
"name": datastructures["study_oct"].name,
"id": str(datastructures["study_oct"].id),
"subfolders": {},
},
datastructures["study"].name: {
"info": "level 5",
"images": {
datastructures["image_cf"].name:
str(datastructures["image_cf"].id)
},
"name": datastructures["study"].name,
"id": str(datastructures["study"].id),
"subfolders": {},
},
},
"info": "level 4",
"name": datastructures["patient"].name,
"id": str(datastructures["patient"].id),
"images": {},
}
},
"info": "level 3",
"name": datastructures["archive"].name,
"id": str(datastructures["archive"].id),
"images": {},
},
datastructures_aus["archive"].name: {
"subfolders": {
datastructures_aus["patient"].name: {
"subfolders": {},
"info": "level 4",
"name": datastructures_aus["patient"].name,
"id": str(datastructures_aus["patient"].id),
"images": {
datastructures_aus["image_oct"].name: {
"images": {
"trc_000":
"no info",
"obs_000":
str(datastructures_aus["image_obs"].id
),
"mot_comp":
"no info",
"trc_001":
"no info",
"oct":
str(datastructures_aus["image_oct"].id
),
},
"info": {
"voxel_size": {
"axial": 0,
"lateral": 0,
"transversal": 0,
},
"date":
datastructures_aus["study_oct"].
datetime.strftime("%Y/%m/%d %H:%M:%S"),
"registration": {
"obs": "Checked separately",
"trc": [0, 0, 0, 0],
},
},
},
datastructures_aus["image_cf"].name:
str(datastructures_aus["image_cf"].id),
},
}
},
"info": "level 3",
"name": datastructures_aus["archive"].name,
"id": str(datastructures_aus["archive"].id),
"images": {},
},
},
"info": "level 2",
"name": "Archives",
"id": "none",
"images": {},
}
# Compare floats separately because of intricacies of floating-point arithmetic in python
try:
# Get info objects of both archives in response data
response_archive_info = (response_data.get("subfolders").get(
datastructures["archive"].name).get("subfolders").get(
datastructures["patient"].name).get("subfolders").get(
datastructures["study_oct"].name).get("images").get(
datastructures["image_oct"].name).get("info"))
response_archive_australia_info = (
response_data.get("subfolders").get(
datastructures_aus["archive"].name).get("subfolders").get(
datastructures_aus["patient"].name).get("images").get(
datastructures_aus["image_oct"].name).get("info"))
floats_to_compare = (
[]) # list of (response_float, expected_float, name) tuples
for archive, response_info, ds, oor in (
(
"Rotterdam",
response_archive_info,
datastructures,
oct_obs_registration,
),
(
"Australia",
response_archive_australia_info,
datastructures_aus,
oct_obs_registration_aus,
),
):
# oct obs registration
response_obs = response_info.get("registration").get("obs")
rv = oor.registration_values
floats_to_compare.append((
response_obs[0],
rv[0][0],
archive + " obs oct registration top left x",
))
floats_to_compare.append((
response_obs[1],
rv[0][1],
archive + " obs oct registration top left y",
))
floats_to_compare.append((
response_obs[2],
rv[1][0],
archive + " obs oct registration bottom right x",
))
floats_to_compare.append((
response_obs[3],
rv[1][1],
archive + " obs oct registration bottom right y",
))
# Compare floats
for result, expected, name in floats_to_compare:
if result != pytest.approx(expected):
pytest.fail(name + " does not equal expected value")
# Clear voxel and obs registration objects before response object to expected object comparison
response_data["subfolders"][datastructures["archive"].name][
"subfolders"][datastructures["patient"].name]["subfolders"][
datastructures["study_oct"].name]["images"][
datastructures["image_oct"].name]["info"][
"registration"]["obs"] = "Checked separately"
response_data["subfolders"][datastructures_aus["archive"].name][
"subfolders"][datastructures_aus["patient"].name]["images"][
datastructures_aus["image_oct"].
name]["info"]["registration"]["obs"] = "Checked separately"
except (AttributeError, KeyError, TypeError):
pytest.fail("Response object structure is not correct")
assert response_data == expected_response_data
def test_no_access(self, client, user):
image = ImageFactoryWithImageFile()
url = reverse("retina:api:image-element-spacing-view", args=[image.pk])
client, _ = client_login(client, user=user)
response = client.get(url)
assert response.status_code == status.HTTP_403_FORBIDDEN
def test_no_access(self, client, user):
image = ImageFactoryWithImageFile()
url = reverse("retina:api:image-element-spacing-view", args=[image.pk])
client, _ = client_login(client, user=user)
response = client.get(url)
assert response.status_code == status.HTTP_403_FORBIDDEN
def test_numpy_endpoint_normal_non_authenticated(self, client):
image = ImageFactoryWithImageFile()
url = reverse("retina:image-numpy", args=[image.id])
client, _ = client_login(client, user="******")
response = client.get(url)
assert response.status_code == status.HTTP_403_FORBIDDEN
def test_archive_view_returns_correct_data(self, client):
# Clear cache manually (this is not done by pytest-django for some reason...)
cache.clear()
# Create data
datastructures, datastructures_aus, oct_obs_registration, oct_obs_registration_aus = (
create_datastructures_data()
)
# login client
client, _ = client_login(client, user="******")
url = reverse("retina:api:archives-api-view")
response = client.get(url, HTTP_ACCEPT="application/json")
response_data = json.loads(response.content)
# check if correct data is sent
expected_response_data = {
"subfolders": {
datastructures["archive"].name: {
"subfolders": {
datastructures["patient"].name: {
"subfolders": {
datastructures["study_oct"].name: {
"info": "level 5",
"images": {
datastructures["image_oct"].name: {
"images": {
"trc_000": "no info",
"obs_000": str(
datastructures[
"image_obs"
].id
),
"mot_comp": "no info",
"trc_001": "no info",
"oct": str(
datastructures[
"image_oct"
].id
),
},
"info": {
"voxel_size": {
"axial": 0,
"lateral": 0,
"transversal": 0,
},
"date": datastructures[
"study_oct"
].datetime.strftime(
"%Y/%m/%d %H:%M:%S"
),
"registration": {
"obs": "Checked separately",
"trc": [0, 0, 0, 0],
},
},
}
},
"name": datastructures["study_oct"].name,
"id": str(datastructures["study_oct"].id),
"subfolders": {},
},
datastructures["study"].name: {
"info": "level 5",
"images": {
datastructures["image_cf"].name: str(
datastructures["image_cf"].id
)
},
"name": datastructures["study"].name,
"id": str(datastructures["study"].id),
"subfolders": {},
},
},
"info": "level 4",
"name": datastructures["patient"].name,
"id": str(datastructures["patient"].id),
"images": {},
}
},
"info": "level 3",
"name": datastructures["archive"].name,
"id": str(datastructures["archive"].id),
"images": {},
},
datastructures_aus["archive"].name: {
"subfolders": {
datastructures_aus["patient"].name: {
"subfolders": {},
"info": "level 4",
"name": datastructures_aus["patient"].name,
"id": str(datastructures_aus["patient"].id),
"images": {
datastructures_aus["image_oct"].name: {
"images": {
"trc_000": "no info",
"obs_000": str(
datastructures_aus["image_obs"].id
),
"mot_comp": "no info",
"trc_001": "no info",
"oct": str(
datastructures_aus["image_oct"].id
),
},
"info": {
"voxel_size": {
"axial": 0,
"lateral": 0,
"transversal": 0,
},
"date": datastructures_aus[
"study_oct"
].datetime.strftime(
"%Y/%m/%d %H:%M:%S"
),
"registration": {
"obs": "Checked separately",
"trc": [0, 0, 0, 0],
},
},
},
datastructures_aus["image_cf"].name: str(
datastructures_aus["image_cf"].id
),
},
}
},
"info": "level 3",
"name": datastructures_aus["archive"].name,
"id": str(datastructures_aus["archive"].id),
"images": {},
},
},
"info": "level 2",
"name": "Archives",
"id": "none",
"images": {},
}
# Compare floats separately because of intricacies of floating-point arithmetic in python
try:
# Get info objects of both archives in response data
response_archive_info = (
response_data.get("subfolders")
.get(datastructures["archive"].name)
.get("subfolders")
.get(datastructures["patient"].name)
.get("subfolders")
.get(datastructures["study_oct"].name)
.get("images")
.get(datastructures["image_oct"].name)
.get("info")
)
response_archive_australia_info = (
response_data.get("subfolders")
.get(datastructures_aus["archive"].name)
.get("subfolders")
.get(datastructures_aus["patient"].name)
.get("images")
.get(datastructures_aus["image_oct"].name)
.get("info")
)
floats_to_compare = (
[]
) # list of (response_float, expected_float, name) tuples
for archive, response_info, ds, oor in (
(
"Rotterdam",
response_archive_info,
datastructures,
oct_obs_registration,
),
(
"Australia",
response_archive_australia_info,
datastructures_aus,
oct_obs_registration_aus,
),
):
# oct obs registration
response_obs = response_info.get("registration").get("obs")
rv = oor.registration_values
floats_to_compare.append(
(
response_obs[0],
rv[0][0],
archive + " obs oct registration top left x",
)
)
floats_to_compare.append(
(
response_obs[1],
rv[0][1],
archive + " obs oct registration top left y",
)
)
floats_to_compare.append(
(
response_obs[2],
rv[1][0],
archive + " obs oct registration bottom right x",
)
)
floats_to_compare.append(
(
response_obs[3],
rv[1][1],
archive + " obs oct registration bottom right y",
)
)
# Compare floats
for result, expected, name in floats_to_compare:
if result != pytest.approx(expected):
pytest.fail(name + " does not equal expected value")
# Clear voxel and obs registration objects before response object to expected object comparison
response_data["subfolders"][datastructures["archive"].name][
"subfolders"
][datastructures["patient"].name]["subfolders"][
datastructures["study_oct"].name
][
"images"
][
datastructures["image_oct"].name
][
"info"
][
"registration"
][
"obs"
] = "Checked separately"
response_data["subfolders"][datastructures_aus["archive"].name][
"subfolders"
][datastructures_aus["patient"].name]["images"][
datastructures_aus["image_oct"].name
][
"info"
][
"registration"
][
"obs"
] = "Checked separately"
except (AttributeError, KeyError, TypeError):
pytest.fail("Response object structure is not correct")
assert response_data == expected_response_data
