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_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_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_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_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_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_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
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(self, app):
# single 2 x 2 frame with one feature; cell 1 in top row, cell 2 in bottom row
labels = np.reshape([1, 1, 2, 2], (1, 2, 2, 1))
project = models.Project.create(DummyLoader(labels=labels))
edit = label.Edit(project)
cell1 = 1
cell2 = 2
feature = 0
expected_swap = np.array([[2, 2], [1, 1]])
with app.app_context():
edit.action_swap_single_frame(cell1, cell2)
np.testing.assert_array_equal(edit.frame[..., feature],
expected_swap)
assert edit.y_changed
assert edit.labels_changed
def test_def_cell_info_one_frame(self):
labels = np.ones((2, 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
feature = 0
cell = 1
frame = 1
# Remove from second frame only
edit.del_cell_info(cell, frame)
assert cell in cell_ids[feature]
assert cell in cell_info[feature]
assert frame not in cell_info[feature][frame]['frames']
assert edit.y_changed
assert edit.labels_changed
def test_action_new_track_first_frame_of_track(self, app):
"""A new track on the first frame a label appears does nothing."""
# two 1x1 frames with one feature; cell starts on second frame
labels = np.reshape([0, 1], (2, 1, 1, 1))
project = models.Project.create(
DummyLoader(labels=labels, path='test.trk'))
cell = 1
frame = 1
feature = 0
project.frame = frame
project.feature = feature
edit = label.Edit(project)
tracks = edit.tracks
prev_track = tracks[cell].copy()
with app.app_context():
edit.action_new_track(cell)
assert cell in edit.frame[..., feature]
assert prev_track == tracks[cell]
def test_del_cell_info_last_frame(self):
labels = np.ones((1, 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
feature = 0
cell = 1
frame = 0
# Remove the label completely (only remaining frame)
edit.del_cell_info(cell, frame)
assert cell not in cell_ids[feature]
assert cell not in cell_info[feature]
assert edit.y_changed
assert edit.labels_changed
np.testing.assert_array_equal(cell_ids[feature], np.array([]))
assert edit.labels.cell_info[feature] == {}
def test_remove_daughter_only_daughter(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
with app.app_context():
edit.action_remove_daughter(daughter)
tracks = edit.tracks
parent_track = tracks[parent]
daughter_track = tracks[daughter]
assert not parent_track['capped']
assert parent_track['daughters'] == []
assert parent_track['frame_div'] is None
assert daughter_track['parent'] is None
def test_add_daughter_new_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))
project = models.Project.create(
DummyLoader(labels=labels, path='test.trk'))
project.frame = 1
edit = label.Edit(project)
parent = 1
daughter = 2
with app.app_context():
edit.action_add_daughter(parent, daughter)
tracks = edit.tracks
parent_track = tracks[parent]
daughter_track = tracks[daughter]
assert parent_track['capped']
assert daughter in parent_track['daughters']
assert parent_track['frame_div'] == 1
assert daughter_track['parent'] == parent
def test_action_new_track(self, app):
"""Create a new track on the second frame of a label."""
# two 1x1 frames with one feature; cell appears in both frames
labels = np.reshape([1, 1], (2, 1, 1, 1))
project = models.Project.create(
DummyLoader(labels=labels, path='test.trk'))
cell = 1
frame = 1
feature = 0
expected_new_cell = 2
project.frame = frame
edit = label.Edit(project)
tracks = edit.tracks
prev_track = tracks[cell].copy()
with app.app_context():
edit.action_new_track(cell)
assert cell not in edit.frame[..., feature]
assert expected_new_cell in edit.frame[..., feature]
assert expected_new_cell in edit.labels.cell_ids[feature]
assert prev_track['frames'] == (
tracks[cell]['frames'] + tracks[expected_new_cell]['frames'])
def test_add_self_as_daughter(self, app):
"""
Add parent as a daughter of itself, creating a new label
"""
labels = np.reshape([1, 1], (2, 1, 1, 1))
cell_info = {
0: {
1: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': None,
'frames': [0, 1],
}
}
}
expected_labels = np.reshape([1, 2], (2, 1, 1, 1))
loader = DummyLoader(labels=labels,
cell_info=cell_info,
path='test.trk')
project = models.Project.create(loader)
project.frame = 1
edit = label.Edit(project)
parent = 1
daughter = 1
with app.app_context():
edit.action_add_daughter(parent, daughter)
tracks = edit.tracks
np.testing.assert_equal(project.label_array, expected_labels)
assert tracks[1]['capped']
assert tracks[1]['daughters'] == [2]
assert tracks[1]['frame_div'] == 1
assert tracks[1]['parent'] is None
assert not tracks[2]['capped']
assert tracks[2]['frame_div'] is None
assert tracks[2]['daughters'] == []
assert tracks[2]['parent'] == 1
def test_zstack_add_cell_info(self):
labels = np.zeros((1, 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
frame = 0
feature = 0
# Add new label to first frame
edit.add_cell_info(cell, frame)
assert cell in cell_ids[feature]
assert cell_info[feature][cell] == {
'label': 1,
'frames': [frame],
'parent': None,
'frame_div': None,
'daughters': [],
'capped': False,
}
assert edit.y_changed
assert edit.labels_changed
def test_replace_with_parent_daughter_divides_in_future(self, app):
"""
Replaces daughter with parent when the daughter divides after the parent.
"""
labels = np.reshape([1, 0, 0, 2, 3, 0, 4, 5, 3], (3, 3, 1, 1))
cell_info = {
0: {
1: {
'capped': True,
'frame_div': 1,
'daughters': [2, 3],
'parent': None,
'frames': [0],
},
2: {
'capped': True,
'frame_div': 2,
'daughters': [4, 5],
'parent': 1,
'frames': [1],
},
3: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 1,
'frames': [1],
},
4: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 2,
'frames': [2],
},
5: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 2,
'frames': [2],
},
}
}
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, 0, 0, 1, 3, 0, 4, 5, 3], (3, 3, 1, 1))
expected_cell_info = {
0: {
1: {
'capped': True,
'frame_div': 2,
'daughters': [4, 5],
'parent': None,
'frames': [0, 1],
},
3: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': None,
'frames': [1],
},
4: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 1,
'frames': [2],
},
5: {
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 1,
'frames': [2],
},
}
}
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_add_self_as_daughter_to_existing_division(self, app):
"""
Add parent as a daughter of itself when parent has a division in the future.
"""
labels = np.reshape([0, 1, 2, 1], (2, 2, 1, 1))
cell_info = {
0: {
1: {
'label': 1,
'capped': True,
'frame_div': 1,
'daughters': [2],
'parent': None,
'frames': [0, 1],
},
2: {
'label': 2,
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 1,
'frames': [1],
},
}
}
expected_labels = np.reshape([0, 1, 2, 3], (2, 2, 1, 1))
expected_lineage = {
1: {
'label': 1,
'capped': True,
'frame_div': 1,
'daughters': [2, 3],
'parent': None,
'frames': [0],
},
2: {
'label': 2,
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 1,
'frames': [1],
},
3: {
'label': 3,
'capped': False,
'frame_div': None,
'daughters': [],
'parent': 1,
'frames': [1],
},
}
loader = DummyLoader(labels=labels,
cell_info=cell_info,
path='test.trk')
project = models.Project.create(loader)
project.frame = 1
edit = label.Edit(project)
parent = 1
daughter = 1
with app.app_context():
edit.action_add_daughter(parent, daughter)
tracks = edit.tracks
np.testing.assert_equal(project.label_array, expected_labels)
assert tracks == expected_lineage
