def test_add_cell_info_multiple_frames(self):
num_frames = 5
labels = np.zeros((num_frames, 1, 1, 1))
project = models.Project.create(DummyLoader(labels=labels))
edit = label.Edit(project)
cell_ids = edit.labels.cell_ids
cell_info = edit.labels.cell_info
cell = 1
feature = 0
# Add new label to all frames
for frame in range(num_frames):
edit.add_cell_info(cell, frame)
assert cell in cell_ids[feature]
assert cell_info[feature][cell] == {
'label': 1,
'frames': list(range(frame + 1)),
'parent': None,
'frame_div': None,
'daughters': [],
'capped': False,
}
assert edit.y_changed
assert edit.labels_changed
def test_redo_frame_not_changed_in_next_action():
"""
Tests redoing when a frame may not be stored in the next action.
"""
# Create project with two frames
project = models.Project.create(DummyLoader(raw=np.zeros((2, 1, 1, 1))))
# Mock action on both frame
for frame in project.label_frames:
frame.frame[:] = 1
project.create_memento('both_frames')
project.update()
# Mock action on first frame
project.label_frames[0].frame[:] = 2
project.create_memento('first_frame_only')
project.update()
# Undo both action
project.undo()
project.undo()
# Redo first action
project.redo()
assert 0 not in project.label_array
assert 2 not in project.label_array
assert 1 in project.label_frames[0].frame
assert 1 in project.label_frames[1].frame
def test_raw_frame_init():
"""Test constructing the raw frames for a project."""
project = models.Project.create(DummyLoader())
raw_frames = project.raw_frames
for frame in raw_frames:
assert len(frame.frame.shape) == 3 # Height, width, channels
assert frame.frame_id is not None
def test_export_npz(self, app, db_session):
with app.app_context():
db_session.autoflush = False
project = models.Project.create(DummyLoader())
exporter = exporters.Exporter(project, 'npz')
file_ = exporter.export()
assert isinstance(file_, io.BytesIO)
def test_label_frame_init():
"""Test constructing the label frames for a project."""
project = models.Project.create(DummyLoader())
label_frames = project.label_frames
for frame in label_frames:
assert frame.frame.ndim == 3 # Height, width, features
assert frame.frame_id is not None
def test_get_max_label_two_frames():
labels = np.array([[[[1]]], [[[2]]]])
project = models.Project.create(DummyLoader(labels=labels))
feature = 0
project.feature = feature
project.update()
max_label = project.get_max_label(feature)
assert max_label == 2
def test_get_max_label_all_ones():
labels = np.ones((1, 1, 1, 1))
project = models.Project.create(DummyLoader(labels=labels))
feature = 0
project.feature = feature
project.update()
max_label = project.get_max_label(feature)
assert max_label == 1
def test_export(self, mocker, app, db_session):
with app.app_context():
mocked = mocker.patch('boto3.s3.inject.upload_fileobj')
db_session.autoflush = False
project = models.Project.create(DummyLoader())
exporter = exporters.S3Exporter(project, 'npz')
exporter.export('test')
mocked.assert_called()
def test_labels_init():
"""Test constructing the Labels row for a Project."""
project = models.Project.create(DummyLoader())
labels = project.labels
assert len(labels.cell_ids) == project.num_features
assert len(labels.cell_info) == project.num_features
for feature in range(project.num_features):
assert len(labels.cell_ids[feature]) == len(labels.cell_info[feature])
def test_redo_no_next_action():
"""Test redoing at the end of the action history."""
project = models.Project.create(DummyLoader())
action = project.action
num_actions = project.num_actions
project.redo()
assert project.action is action
assert project.num_actions == num_actions
def test_undo_no_previous_action():
"""Test undoing at the start of the action history."""
project = models.Project.create(DummyLoader())
action = project.action
num_actions = project.num_actions
project.undo()
assert project.action is action
assert project.num_actions == num_actions
def test_get_project():
"""
Test getting a project from the Projects table.
creates a project, then gets it again.
"""
project = models.Project.create(DummyLoader())
valid_id = project.token
found_project = models.Project.get(valid_id)
assert found_project == project
def test_frames_init():
"""Test that raw, and label frames within a project are all compatible."""
project = models.Project.create(DummyLoader())
raw_frames = project.raw_frames
label_frames = project.label_frames
assert len(raw_frames) == len(label_frames)
for raw_frame, label_frame in zip(raw_frames, label_frames):
assert raw_frame.frame.shape[:-1] == label_frame.frame.shape[:-1]
assert raw_frame.frame_id == label_frame.frame_id
assert raw_frame.project_id == label_frame.project_id
def test_replace_with_parent_with_overlap(self, app):
"""
Replaces daughter with parent when the daughter exists before the div.
"""
labels = np.reshape([1, 2, 1, 2], (2, 2, 1, 1))
cell_info = {
0: {
1: {
'capped': True,
'frame_div': 1,
'daughters': [2],
'parent': None,
'frames': [0, 1],
},
2: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 1,
'frames': [0, 1],
},
}
}
loader = DummyLoader(labels=labels,
cell_info=cell_info,
path='test.trk')
project = models.Project.create(loader)
edit = label.Edit(project)
daughter = 2
expected_labels = np.reshape([1, 2, 1, 1], (2, 2, 1, 1))
expected_cell_info = {
0: {
1: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': None,
'frames': [0, 1],
},
2: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': None,
'frames': [0],
},
}
}
with app.app_context():
edit.action_replace_with_parent(daughter)
np.testing.assert_equal(project.label_array, expected_labels)
assert edit.tracks == expected_cell_info[0]
def test_undo(client):
# Project not found
response = client.post('/api/undo/0')
assert response.status_code == 404
# Create a project
project = models.Project.create(DummyLoader())
# Undo with no action to undo silently does nothing
response = client.post('/api/undo/{}'.format(project.token))
assert response.status_code == 200
def test_redo(client):
# Project not found
response = client.post('/api/redo/0')
assert response.status_code == 404
# Create a project
project = models.Project.create(DummyLoader())
# Redo with no action to redo silently does nothing
response = client.post(f'/api/redo/{project.token}')
assert response.status_code == 200
def test_action_replace_single(self, app):
# single 2 x 2 frame with two labels: 1s in top row, 2s in bottom
labels = np.reshape([1, 1, 2, 2], (1, 2, 2, 1))
project = models.Project.create(DummyLoader(labels=labels))
edit = label.Edit(project)
expected_labels = np.array([[[1], [1]], [[1], [1]]])
cell1 = 1
cell2 = 2
with app.app_context():
edit.action_replace_single(cell1, cell2)
np.testing.assert_array_equal(edit.frame, expected_labels)
assert 2 not in edit.tracks
def test_action_dilate_other_labels_unchanged(self, app):
"""Tests that other labels not affected by dilating a label."""
labels = np.reshape([1, 1, 2, 2], (1, 2, 2, 1))
project = models.Project.create(DummyLoader(labels=labels))
edit = label.Edit(project)
cell = 1
other_cell = 2
with app.app_context():
edit.action_dilate(cell)
np.testing.assert_array_equal(labels[project.frame] == other_cell,
edit.frame == other_cell)
def test_project_init():
"""
Test constructor for Project table.
"""
project = models.Project(DummyLoader())
# Check columns filled in by constructor
assert project.path is not None
assert project.source is not None
assert project.num_frames is not None
assert project.height is not None
assert project.width is not None
assert project.num_channels is not None
assert project.num_features is not None
def test_action_erode_delete_label(self, app):
"""Tests that a label is correctly removed when eroding deletes all of its pixels."""
labels = np.zeros((1, 3, 3, 1))
labels[0, 1, 1, 0] = 1
project = models.Project.create(DummyLoader(labels=labels))
edit = label.Edit(project)
cell = 1
with app.app_context():
edit.action_erode(cell)
assert cell not in edit.frame
assert cell not in project.labels.cell_ids[project.feature]
assert cell not in project.labels.cell_info[project.feature]
def test_track_replace_daughter_that_divides_with_parent(self, app):
labels = np.reshape([1, 2, 3], (3, 1, 1, 1))
cell_info = {
0: {
1: {
'capped': True,
'frame_div': 1,
'daughters': [2],
'parent': None,
'frames': [0],
},
2: {
'capped': True,
'frame_div': 2,
'daughters': [3],
'parent': 1,
'frames': [1],
},
3: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 2,
'frames': [2],
},
}
}
project = models.Project.create(
DummyLoader(labels=labels, cell_info=cell_info, path='test.trk'))
edit = label.Edit(project)
expected_labels = np.reshape([1, 1, 3], (3, 1, 1, 1))
parent = 1
daughter = 2
granddaughter = 3
with app.app_context():
edit.action_replace_with_parent(daughter)
tracks = edit.tracks
parent_track = tracks[parent]
granddaughter_track = tracks[granddaughter]
assert daughter not in tracks
assert parent_track['capped']
assert parent_track['daughters'] == [3]
assert parent_track['frame_div'] == 2
assert parent_track['frames'] == [0, 1]
assert granddaughter_track['parent'] == 1
np.testing.assert_array_equal(edit.project.label_array,
expected_labels)
def test_action_active_contour_label_too_large(self, app):
"""Tests that a label that is larger than the raw objects is made
smaller by active contouring."""
raw = np.zeros((1, 10, 10, 1))
labels = np.ones((1, 10, 10, 1))
raw[0, 3:6, 3:6, 0] = 1
project = models.Project.create(DummyLoader(raw=raw, labels=labels))
edit = label.Edit(project)
cell = 1
with app.app_context():
edit.action_active_contour(cell)
assert int(
(edit.frame == 1).sum()) < (labels[project.frame] == 1).sum()
def test_finish_project():
"""
Test finishing a project.
Checks that the project's relationship are also finished.
"""
# create project
project = models.Project.create(DummyLoader())
project.finish()
assert project.finished is not None
assert project.labels.cell_ids is None
assert project.labels.cell_info is None
for raw, label in zip(project.raw_frames, project.label_frames):
assert raw.frame is None
assert label.frame is None
def test_get_labeled_array():
"""
Test outlined label arrays to send to the front-end.
"""
project = models.Project.create(DummyLoader())
frame = 0
feature = 0
expected_frame = project.label_frames[frame].frame[..., feature]
label_arr = project.get_labeled_array(frame, feature)
assert label_arr.shape == (project.height, project.width)
np.testing.assert_array_equal(label_arr[label_arr >= 0],
expected_frame[label_arr >= 0])
np.testing.assert_array_equal(label_arr[label_arr < 0],
-expected_frame[label_arr < 0])
def test_add_channel(client):
project = models.Project.create(DummyLoader(raw=np.zeros((1, 1, 1, 1))))
npz = io.BytesIO()
np.savez(npz, new_channel=np.ones((1, 1, 1, 1)))
npz.seek(0)
data = {'file': (npz, 'test.npz')}
response = client.post(f'/api/raw/{project.token}',
data=data,
content_type='multipart/form-data')
assert response.status_code == 200
assert response.json.get('numChannels') == 2
assert project.raw_array.shape == (1, 1, 1, 2)
assert 0 in project.raw_array
assert 1 in project.raw_array
def test_action_handle_draw_add_label(self, app):
"""Adding a label with by drawing it in."""
labels = np.reshape([0], (1, 1, 1, 1))
project = models.Project.create(DummyLoader(labels=labels))
edit = label.Edit(project)
trace, foreground, background, brush_size = [(0, 0)], 1, 0, 1
feature = 0
expected_draw = np.reshape([1], (1, 1))
with app.app_context():
edit.action_handle_draw(trace, foreground, background, brush_size)
np.testing.assert_array_equal(edit.frame[..., feature],
expected_draw)
assert foreground in edit.labels.cell_info[feature]
assert foreground in edit.labels.cell_ids[feature]
def test_action_active_contour_other_labels_unchanged(self, app):
"""
Tests that other labels not affected by active contouring a label
"""
labels = np.ones((1, 10, 10, 1))
labels[:, 5:, :, :] = 2
project = models.Project.create(DummyLoader(labels=labels))
edit = label.Edit(project)
cell = 1
other_cell = 2
with app.app_context():
edit.action_active_contour(cell)
np.testing.assert_array_equal(labels[project.frame] == other_cell,
edit.frame == other_cell)
def test_add_daughter_existing_division(self, app):
# two 2 x 1 frames
# one label in the first frame and two in the second frame
labels = np.reshape([0, 1, 2, 3], (2, 2, 1, 1))
cell_info = {
0: {
1: {
'capped': True,
'frame_div': 1,
'daughters': [2],
'parent': None
},
2: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 1
},
3: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': None,
},
}
}
project = models.Project.create(
DummyLoader(labels=labels, cell_info=cell_info, path='test.trk'))
edit = label.Edit(project)
parent = 1
daughter = 2
other_daughter = 3
frame_div = 1
with app.app_context():
edit.action_add_daughter(parent, other_daughter)
tracks = edit.tracks
parent_track = tracks[parent]
daughter_track = tracks[daughter]
other_daughter_track = tracks[other_daughter]
assert parent_track['capped']
assert daughter in parent_track['daughters']
assert other_daughter in parent_track['daughters']
assert parent_track['frame_div'] == frame_div
assert daughter_track['parent'] == parent
assert other_daughter_track['parent'] == parent
def test_action_flood_background(self, app):
"""Flooding background does NOT spread to diagonal areas."""
# 3 x 3 frame with label in diamond shape
labels = np.reshape([0, 1, 0, 1, 0, 1, 0, 1, 0], (1, 3, 3, 1))
project = models.Project.create(DummyLoader(labels=labels))
edit = label.Edit(project)
flood_label, x_loc, y_loc = 2, 1, 1
feature = 0
expected_flood = np.reshape([0, 1, 0, 1, 2, 1, 0, 1, 0], (3, 3))
with app.app_context():
edit.action_flood(flood_label, x_loc, y_loc)
np.testing.assert_array_equal(edit.frame[..., feature],
expected_flood)
assert edit.y_changed
assert edit.labels_changed
def test_action_swap_single_frame_with_label_not_in_frame(self, app):
"""Tests that swapping with a cell not in frame updates the cell info."""
labels = np.reshape([1], (1, 1, 1, 1))
project = models.Project.create(DummyLoader(labels=labels))
edit = label.Edit(project)
cell1 = 1
cell2 = 2
expected_labels = np.reshape([2], (1, 1, 1, 1))
with app.app_context():
edit.action_swap_single_frame(cell1, cell2)
np.testing.assert_array_equal(project.label_array, expected_labels)
assert edit.y_changed
assert edit.labels_changed
assert cell2 in edit.tracks
assert cell1 not in edit.tracks