def test_get_predefined_label_for_scan_in_task__predefined_label(
prepare_environment: Any) -> None:
"""Test for fetching Predefined Label that exists."""
# Step 1. Prepare a structure for the test
dataset = 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], task.id)
scan = ScansRepository.add_new_scan(dataset, 0)
user_id = UsersRepository.add_new_user(
User('user@medtagger', 'HASH', 'Admin', 'Admin'))
user = UsersRepository.get_user_by_id(user_id)
# Step 2. Add Label which is predefined
label = LabelsRepository.add_new_label(scan.id,
task.key,
user,
LabelingTime(0),
is_predefined=True)
# Step 3. Check if there is is Predefined Label
predefined_label = LabelsRepository.get_predefined_label_for_scan_in_task(
scan, task)
assert predefined_label
assert predefined_label.id == label.id
def test_get_predefined_brush_label_elements(prepare_environment: Any) -> None:
"""Test for fetching Predefined Brush Label Elements."""
# Step 1. Prepare a structure for the test
dataset = DatasetsRepository.add_new_dataset('KIDNEYS', 'Kidneys')
task = TasksRepository.add_task('MARK_KIDNEYS', 'Mark Kidneys',
'path/to/image', ['KIDNEYS'], [])
label_tag = LabelTagsRepository.add_new_tag('EXAMPLE_TAG', 'Example Tag',
[LabelTool.RECTANGLE], task.id)
scan = ScansRepository.add_new_scan(dataset, 3)
user_id = UsersRepository.add_new_user(
User('user@medtagger', 'HASH', 'Admin', 'Admin'))
user = UsersRepository.get_user_by_id(user_id)
# Step 2. Add Label with Brush Elements
label = LabelsRepository.add_new_label(scan.id,
task.key,
user,
LabelingTime(0),
is_predefined=True)
LabelsRepository.add_new_brush_label_element(label.id, 0, 0, 0, b'',
label_tag)
LabelsRepository.add_new_brush_label_element(label.id, 1, 0, 0, b'',
label_tag)
LabelsRepository.add_new_brush_label_element(label.id, 2, 0, 0, b'',
label_tag)
# Step 3. Check if there is is Predefined Label
brush_label_elements = LabelsRepository.get_predefined_brush_label_elements(
scan.id, task.id, 0, 3)
assert len(brush_label_elements) == 3
brush_label_elements = LabelsRepository.get_predefined_brush_label_elements(
scan.id, task.id, 0, 1)
assert len(brush_label_elements) == 1
def test_parsing_chain_label_elements(prepare_environment: Any) -> None:
"""Test parsing Chain Label Element to numpy array."""
user_id = UsersRepository.add_new_user(
models.User('user@medtagger', 'HASH', 'Admin', 'Admin'))
user = UsersRepository.get_user_by_id(user_id)
scan, label_tag = helpers.prepare_scan_and_tag_for_labeling()
label = helpers.prepare_empty_label(scan, user)
for slice_index in range(3):
points = [
Point(x=0, y=0),
Point(x=1, y=0),
Point(x=1, y=1),
Point(x=0, y=1),
]
LabelsRepository.add_new_chain_label_element(label.id,
slice_index,
label_tag,
points,
loop=True)
query = models.ChainLabelElement.query.join(models.Label)
query = query.filter(models.Label.scan_id == scan.id)
label_elements = query.all()
parser = chain.ChainLabelElementParser()
data = parser.convert_to_numpy(label_elements)
assert data.shape == (3, SLICE_WIDTH * SLICE_HEIGHT)
assert data.sum(
) == 3 * SLICE_WIDTH * SLICE_HEIGHT # Squares fill whole Slice
def test_data_set_generator(prepare_environment: Any) -> None: # pylint: disable=too-many-locals
"""Test Data Set Generator against rectangular Label Elements from real database."""
user_id = UsersRepository.add_new_user(
models.User('user@medtagger', 'HASH', 'Admin', 'Admin'))
user = UsersRepository.get_user_by_id(user_id)
scan, label_tag = helpers.prepare_scan_and_tag_for_labeling()
label_a = helpers.prepare_empty_label(scan, user)
for slice_index in range(3):
LabelsRepository.add_new_rectangular_label_element(
label_a.id, LabelPosition(x=1, y=1, slice_index=slice_index),
LabelShape(width=0, height=0), label_tag)
label_b = helpers.prepare_empty_label(scan, user)
for slice_index in range(3):
LabelsRepository.add_new_rectangular_label_element(
label_b.id, LabelPosition(x=0, y=0, slice_index=slice_index),
LabelShape(width=1, height=1), label_tag)
label_c = helpers.prepare_empty_label(scan, user)
for slice_index in range(3):
LabelsRepository.add_new_rectangular_label_element(
label_c.id, LabelPosition(x=1, y=1, slice_index=slice_index),
LabelShape(width=0, height=0), label_tag)
algorithm = majority_voting.MajorityVotingAlgorithm()
data_set_generator = generator.DataSetGenerator(algorithm)
query = models.RectangularLabelElement.query.join(models.Label)
query = query.filter(models.Label.scan_id == scan.id)
label_elements = query.all()
ground_truth_for_slice_id = data_set_generator.generate(label_elements)
assert sorted(list(ground_truth_for_slice_id.keys())) == sorted(
[_slice.id for _slice in scan.slices])
example_slice_id = scan.slices[0].id
expected_ground_truth = np.array([1, 1, 1, 1])
assert ground_truth_for_slice_id[
example_slice_id].shape == expected_ground_truth.shape
ground_truth = ground_truth_for_slice_id[example_slice_id]
for i in range(expected_ground_truth.shape[0]):
assert math.isclose(ground_truth[i],
expected_ground_truth[i],
abs_tol=1e-5)
def test_get_predefined_label_for_scan_in_task__predefined_label_for_given_task(
prepare_environment: Any) -> None:
"""Test for fetching Predefined Label only for specific Task."""
# Step 1. Prepare a structure for the test
dataset = DatasetsRepository.add_new_dataset('KIDNEYS', 'Kidneys')
task_left = TasksRepository.add_task('MARK_LEFT', 'Mark Left',
'path/to/image', ['KIDNEYS'], '', [],
[])
task_right = TasksRepository.add_task('MARK_RIGHT', 'Mark Right',
'path/to/image', ['KIDNEYS'], '', [],
[])
LabelTagsRepository.add_new_tag('EXAMPLE_TAG', 'Example Tag',
[LabelTool.RECTANGLE], task_left.id)
scan = ScansRepository.add_new_scan(dataset, 0)
user_id = UsersRepository.add_new_user(
User('user@medtagger', 'HASH', 'Admin', 'Admin'))
user = UsersRepository.get_user_by_id(user_id)
# Step 2. Add Labels for each Task
label_left = LabelsRepository.add_new_label(scan.id,
task_left.key,
user,
LabelingTime(0),
is_predefined=True)
label_right = LabelsRepository.add_new_label(scan.id,
task_right.key,
user,
LabelingTime(0),
is_predefined=True)
# Step 3. Check if there are these Predefined Labels
predefined_label = LabelsRepository.get_predefined_label_for_scan_in_task(
scan, task_left)
assert predefined_label
assert predefined_label.id == label_left.id
predefined_label = LabelsRepository.get_predefined_label_for_scan_in_task(
scan, task_right)
assert predefined_label
assert predefined_label.id == label_right.id
def test_parsing_rectangle_label_elements(prepare_environment: Any) -> None:
"""Test parsing Rectangle Label Element to numpy array."""
user_id = UsersRepository.add_new_user(
models.User('user@medtagger', 'HASH', 'Admin', 'Admin'))
user = UsersRepository.get_user_by_id(user_id)
scan, label_tag = helpers.prepare_scan_and_tag_for_labeling()
label = helpers.prepare_empty_label(scan, user)
for slice_index in range(3):
LabelsRepository.add_new_rectangular_label_element(
label.id, LabelPosition(x=1, y=1, slice_index=slice_index),
LabelShape(width=0, height=0), label_tag)
query = models.RectangularLabelElement.query.join(models.Label)
query = query.filter(models.Label.scan_id == scan.id)
label_elements = query.all()
parser = rectangle.RectangleLabelElementParser()
data = parser.convert_to_numpy(label_elements)
assert data.shape == (3, 4)
expected_data = (1, 1, 1, 1)
for i in range(4):
assert math.isclose(data[0][i], expected_data[i], abs_tol=1e-5)
def create_user(email: str, password: str, first_name: str,
last_name: str) -> Tuple[int, str]:
"""Create user with the given user information. Password is being hashed.
:param email: user email in string format
:param password: user password in string format
:param first_name: user first name in string format
:param last_name: user last name in string format
:return: tuple with user id and authentication token
"""
user = UsersRepository.get_user_by_email(email)
if user:
raise InvalidArgumentsException('User with this email already exists')
password_hash = hash_password(password)
new_user = User(email, password_hash, first_name, last_name)
role = RolesRepository.get_role_with_name('volunteer')
if not role:
raise InvalidArgumentsException('Role does not exist.')
new_user.roles.append(role)
user_id = UsersRepository.add_new_user(new_user)
user_token = generate_auth_token(new_user)
return user_id, user_token
