def add_new_brush_label_element(label_id: LabelID, slice_index: int,
width: int, height: int, image: bytes,
label_tag: LabelTag) -> LabelElementID:
"""Add new Brush Element for given Label.
:param label_id: Label's ID
:param width: width of the Label's image
:param height: height of the Label's image
:param image: bytes with image representation of a binary mask
:param label_tag: Label Tag object
:return: ID of a Element
""" # pylint: disable=too-many-arguments
with db_session() as session:
brush_label_element = BrushLabelElement(slice_index, width, height,
label_tag)
brush_label_element.label_id = label_id
session.add(brush_label_element)
BrushLabelElementStorage.create(id=brush_label_element.id, image=image)
return brush_label_element.id
def test_add_brush_label(prepare_environment: Any,
synchronous_celery: Any) -> None:
"""Test for adding a Label made with Brush tool."""
api_client = get_api_client()
user_token = get_token_for_logged_in_user('admin')
# Step 1. Add Scan to the system
payload = {'category': 'KIDNEYS', 'number_of_slices': 3}
response = api_client.post('/api/v1/scans/',
data=json.dumps(payload),
headers=get_headers(token=user_token,
json=True))
assert response.status_code == 201
json_response = json.loads(response.data)
scan_id = json_response['scan_id']
# Step 2. Label it with Brush
create_tag_and_assign_to_category('EXAMPLE_TAG', 'Example tag', 'KIDNEYS')
payload = {
'elements': [{
'slice_index': 0,
'width': 128,
'height': 128,
'image_key': 'SLICE_1',
'tag': 'EXAMPLE_TAG',
'tool': 'BRUSH',
}],
'labeling_time':
12.34,
}
with open('tests/assets/example_labels/binary_mask.png', 'rb') as image:
data = {
'label': json.dumps(payload),
'SLICE_1': (image, 'slice_1'),
}
response = api_client.post('/api/v1/scans/{}/label'.format(scan_id),
data=data,
headers=get_headers(token=user_token,
multipart=True))
assert response.status_code == 201
json_response = json.loads(response.data)
assert isinstance(json_response, dict)
label_id = json_response['label_id']
assert isinstance(label_id, str)
assert len(label_id) >= 1
# Step 3. Fetch details about above Label and check image storage
response = api_client.get('/api/v1/labels/' + label_id,
headers=get_headers(token=user_token))
assert response.status_code == 200
json_response = json.loads(response.data)
assert isinstance(json_response, dict)
label_element_id = json_response['elements'][0]['label_element_id']
brush_label_element = BrushLabelElement.get(id=label_element_id)
assert brush_label_element.image
def get_predefined_brush_label_elements(scan_id: ScanID, task_id: int,
begin: int, count: int) -> Iterable[Tuple[BrushLabelElement, bytes]]:
"""Fetch Predefined Brush Label Elements for given Scan and Task.
:param scan_id: ID of a given Scan
:param task_id: ID of a given Task
:param begin: first Slice index
:param count: number of Slices for which Label Elements will be returned
:return: generator for Brush Label Elements and its images
"""
label_elements = LabelsRepository.get_predefined_brush_label_elements(scan_id, task_id, begin, count)
for label_element in label_elements:
storage_brush_label_element = StorageBrushLabelElement.get(id=label_element.id)
yield label_element, storage_brush_label_element.image
def test_add_brush_label(prepare_environment: Any,
synchronous_celery: Any) -> None:
"""Test for adding a Label made with Brush tool."""
api_client = get_api_client()
user_token = get_token_for_logged_in_user('admin')
# Step 1. Prepare a structure for the test
DatasetsRepository.add_new_dataset('KIDNEYS', 'Kidneys')
task = TasksRepository.add_task('MARK_KIDNEYS', 'Mark Kidneys',
'path/to/image', ['KIDNEYS'], [])
LabelTagsRepository.add_new_tag('EXAMPLE_TAG', 'Example Tag',
[LabelTool.BRUSH], task.id)
# Step 2. Add Scan to the system
payload = {'dataset': 'KIDNEYS', 'number_of_slices': 3}
response = api_client.post('/api/v1/scans',
data=json.dumps(payload),
headers=get_headers(token=user_token,
json=True))
assert response.status_code == 201
json_response = json.loads(response.data)
scan_id = json_response['scan_id']
# Step 3. Label it with Brush
payload = {
'elements': [{
'slice_index': 0,
'width': 128,
'height': 128,
'image_key': 'SLICE_1',
'tag': 'EXAMPLE_TAG',
'tool': LabelTool.BRUSH.value,
}],
'labeling_time':
12.34,
'task_id':
TasksRepository.get_task_by_key('MARK_KIDNEYS').id,
}
with open('tests/assets/example_labels/binary_mask.png', 'rb') as image:
data = {
'label': json.dumps(payload),
'SLICE_1': (image, 'slice_1'),
}
response = api_client.post(
'/api/v1/scans/{}/MARK_KIDNEYS/label'.format(scan_id),
data=data,
headers=get_headers(token=user_token, multipart=True))
assert response.status_code == 201
json_response = json.loads(response.data)
assert isinstance(json_response, dict)
label_id = json_response['label_id']
assert isinstance(label_id, str)
assert len(label_id) >= 1
# Step 4. Fetch details about above Label and check image storage
response = api_client.get('/api/v1/labels/' + label_id,
headers=get_headers(token=user_token))
assert response.status_code == 200
json_response = json.loads(response.data)
assert isinstance(json_response, dict)
label_element_id = json_response['elements'][0]['label_element_id']
brush_label_element = BrushLabelElement.get(id=label_element_id)
assert brush_label_element.image
def delete_brush_element_from_storage(mapper: Mapper, connection: Connection, target: Slice) -> None:
"""Delete BrushLabelElement from storage."""
brush_label_element = StorageBrushLabelElement.get(id=target.id)
brush_label_element.delete()
def test_delete_scan_with_labels(prepare_environment: Any,
synchronous_celery: Any) -> None:
"""Test deleting scan with at least 1 slice and with labels made with all tools."""
api_client = get_api_client()
web_socket_client = get_web_socket_client(namespace='/slices')
user_token = get_token_for_logged_in_user('admin')
# Step 1. Prepare a structure for the test
DatasetsRepository.add_new_dataset('KIDNEYS', 'Kidneys')
task = TasksRepository.add_task('MARK_KIDNEYS', 'Mark Kidneys',
'path/to/image', ['KIDNEYS'], [])
LabelTagsRepository.add_new_tag('EXAMPLE_TAG', 'Example Tag', [
LabelTool.RECTANGLE, LabelTool.CHAIN, LabelTool.POINT, LabelTool.BRUSH
], task.id)
# Step 2. Add Scan to the system
payload = {'dataset': 'KIDNEYS', 'number_of_slices': 1}
response = api_client.post('/api/v1/scans',
data=json.dumps(payload),
headers=get_headers(token=user_token,
json=True))
assert response.status_code == 201
json_response = json.loads(response.data)
assert isinstance(json_response, dict)
scan_id: ScanID = json_response['scan_id']
assert isinstance(scan_id, str)
assert len(scan_id) >= 1
# Step 3. Send slices
with open('tests/assets/example_scan/slice_1.dcm', 'rb') as image:
response = api_client.post('/api/v1/scans/{}/slices'.format(scan_id),
data={
'image': (image, 'slice_1.dcm'),
},
content_type='multipart/form-data',
headers=get_headers(token=user_token))
assert response.status_code == 201
json_response = json.loads(response.data)
assert isinstance(json_response, dict)
slice_id: SliceID = json_response['slice_id']
assert isinstance(slice_id, str)
assert len(slice_id) >= 1
# Step 4. Get scan
response = api_client.get('/api/v1/scans/{}'.format(scan_id),
headers=get_headers(token=user_token))
assert response.status_code == 200
json_response = json.loads(response.data)
assert isinstance(json_response, dict)
assert json_response['scan_id'] == scan_id
assert json_response['number_of_slices'] == 1
assert json_response['width'] == 512
assert json_response['height'] == 512
# Step 5. Get slices from the server
payload = {
'scan_id': scan_id,
'task_key': 'MARK_KIDNEYS',
'begin': 0,
'count': 1
}
web_socket_client.emit('request_slices', payload, namespace='/slices')
responses = web_socket_client.get_received(namespace='/slices')
assert len(responses) == 1
response = responses[0]
assert response['name'] == 'slice'
assert response['args'][0]['scan_id'] == scan_id
assert response['args'][0]['index'] == 0
assert isinstance(response['args'][0]['image'], bytes)
# Step 6. Label it with all available tools
payload = {
'elements': [{
'x': 0.5,
'y': 0.5,
'slice_index': 0,
'width': 0.1,
'height': 0.1,
'tag': 'EXAMPLE_TAG',
'tool': LabelTool.RECTANGLE.value,
}, {
'slice_index': 0,
'width': 128,
'height': 128,
'image_key': 'SLICE_1',
'tag': 'EXAMPLE_TAG',
'tool': LabelTool.BRUSH.value,
}, {
'slice_index': 0,
'x': 0.25,
'y': 0.5,
'tag': 'EXAMPLE_TAG',
'tool': LabelTool.POINT.value,
}, {
'slice_index':
0,
'points': [
{
'x': 0.2,
'y': 0.3,
},
{
'x': 0.5,
'y': 0.8,
},
],
'tag':
'EXAMPLE_TAG',
'tool':
LabelTool.CHAIN.value,
'loop':
False,
}],
'labeling_time':
12.34,
}
with open('tests/assets/example_labels/binary_mask.png', 'rb') as image:
data = {
'label': json.dumps(payload),
'SLICE_1': (image, 'slice_1'),
}
response = api_client.post(
'/api/v1/scans/{}/MARK_KIDNEYS/label'.format(scan_id),
data=data,
headers=get_headers(token=user_token, multipart=True))
assert response.status_code == 201
json_response = json.loads(response.data)
assert isinstance(json_response, dict)
label_id = json_response['label_id']
assert isinstance(label_id, str)
assert len(label_id) >= 1
# Step 7. Fetch details about above Label and check image storage
response = api_client.get('/api/v1/labels/' + label_id,
headers=get_headers(token=user_token))
assert response.status_code == 200
json_response = json.loads(response.data)
assert isinstance(json_response, dict)
label_element_id = json_response['elements'][1]['label_element_id']
brush_label_element = BrushLabelElement.get(id=label_element_id)
assert brush_label_element.image
# Step 7. Delete scan from the system
ScansRepository.delete_scan_by_id(scan_id)
# Step 8. Check that scan has been deleted
response = api_client.get('/api/v1/scans/{}'.format(scan_id),
headers=get_headers(token=user_token))
assert response.status_code == 404
# Step 9. Check that slices has been deleted
with pytest.raises(NoResultFound):
SliceRepository.get_slice_by_id(slice_id)
# Step 10. Check that slices original image has been deleted from storage
with pytest.raises(DoesNotExist):
OriginalSlice.get(id=slice_id)
# Step 11. Check that slices processed image has been deleted from storage
with pytest.raises(DoesNotExist):
ProcessedSlice.get(id=slice_id)
# Step 12. Check that labels has been deleted
response = api_client.get('/api/v1/labels/{}'.format(label_id),
headers=get_headers(token=user_token))
assert response.status_code == 404
# Step 13. Check that Brush Label was deleted from storage
with pytest.raises(DoesNotExist):
BrushLabelElement.get(id=label_element_id)