def test_fp_division_evaluation_at_beginning_of_gt(self):
cells, edges, roi = self.getTrack1()
gt_cells = cells.copy()
gt_edges = edges.copy()
gt_track_graph = self.create_graph(gt_cells, gt_edges, roi)
# add split at beginning of reconstruction
for cell in cells:
cell[1]['y'] += 1
cells.append((5, {'t': 1, 'z': 2, 'y': 1, 'x': 0}))
edges.append((5, 1))
rec_track_graph = self.create_graph(cells, edges, roi)
scores = e.evaluate(gt_track_graph,
rec_track_graph,
matching_threshold=2,
sparse=True)
self.assertEqual(scores.matched_edges, 3)
self.assertEqual(scores.fp_edges, 0)
self.assertEqual(scores.fn_edges, 0)
self.assertEqual(scores.gt_tracks, 1)
self.assertEqual(scores.gt_matched_tracks, 1)
self.assertEqual(scores.rec_matched_tracks, 1)
self.assertEqual(scores.rec_tracks, 1)
self.assertAlmostEqual(scores.aeftl, 3)
self.assertAlmostEqual(scores.erl, 3)
self.assertEqual(scores.identity_switches, 0)
self.assertEqual(scores.gt_divisions, 0)
self.assertEqual(scores.fn_divisions, 0)
self.assertEqual(scores.fp_divisions, 1)
self.assertAlmostEqual(scores.precision, 1.0)
self.assertAlmostEqual(scores.recall, 1.0)
self.delete_db()
def test_fn_division_evaluation2(self):
cells, edges, roi = self.getDivisionTrack()
# introduce a false positive edge
gt_cells = cells.copy()
gt_edges = edges.copy()
del gt_cells[0]
del gt_edges[0]
gt_track_graph = self.create_graph(gt_cells, gt_edges, roi)
for cell in cells:
cell[1]['y'] += 1
# introduce a split error
edges.remove((5, 2))
rec_track_graph = self.create_graph(cells, edges, roi)
scores = e.evaluate(gt_track_graph,
rec_track_graph,
matching_threshold=2,
sparse=True)
self.assertEqual(scores.matched_edges, 4)
self.assertEqual(scores.fp_edges, 0)
self.assertEqual(scores.fn_edges, 1)
self.assertEqual(scores.gt_tracks, 1)
self.assertEqual(scores.gt_matched_tracks, 1)
self.assertEqual(scores.rec_matched_tracks, 2)
self.assertEqual(scores.rec_tracks, 2)
self.assertAlmostEqual(scores.aeftl, 2.)
self.assertAlmostEqual(scores.erl, 8. / 5)
self.assertEqual(scores.identity_switches, 0)
self.assertEqual(scores.gt_divisions, 1)
self.assertEqual(scores.fn_divisions, 1)
self.assertEqual(scores.fp_divisions, 0)
self.assertAlmostEqual(scores.precision, 1.0)
self.assertAlmostEqual(scores.recall, 4. / 5)
self.delete_db()
def test_fp_division_evaluation(self):
cells, edges, roi = self.getDivisionTrack()
gt_cells = cells.copy()
gt_edges = edges.copy()
# remove division from gt
gt_edges.remove((5, 2))
gt_track_graph = self.create_graph(gt_cells, gt_edges, roi)
for cell in cells:
cell[1]['y'] += 1
rec_track_graph = self.create_graph(cells, edges, roi)
scores = e.evaluate(gt_track_graph,
rec_track_graph,
matching_threshold=2,
sparse=True)
self.assertEqual(scores.matched_edges, 5)
self.assertEqual(scores.fp_edges, 0)
self.assertEqual(scores.fn_edges, 0)
self.assertEqual(scores.gt_tracks, 2)
self.assertEqual(scores.gt_matched_tracks, 2)
self.assertEqual(scores.rec_matched_tracks, 1)
self.assertEqual(scores.rec_tracks, 1)
self.assertAlmostEqual(scores.aeftl, 5. / 3)
self.assertAlmostEqual(scores.erl, 9. / 5)
self.assertEqual(scores.identity_switches, 0)
self.assertEqual(scores.gt_divisions, 0)
self.assertEqual(scores.fn_divisions, 0)
self.assertEqual(scores.fp_divisions, 1)
self.assertAlmostEqual(scores.precision, 1.0)
self.assertAlmostEqual(scores.recall, 1.0)
self.delete_db()
def test_imperfect_evaluation(self):
cells, edges, roi = self.getTrack1()
gt_track_graph = self.create_graph(cells, edges, roi)
for cell in cells:
cell[1]['y'] += 1
# introduce a split error
del edges[1]
rec_track_graph = self.create_graph(cells, edges, roi)
scores = e.evaluate(gt_track_graph,
rec_track_graph,
matching_threshold=2,
sparse=True)
self.assertEqual(scores.matched_edges, 2)
self.assertEqual(scores.fp_edges, 0)
self.assertEqual(scores.fn_edges, 1)
self.assertEqual(scores.gt_tracks, 1)
self.assertEqual(scores.gt_matched_tracks, 1)
self.assertEqual(scores.rec_matched_tracks, 2)
self.assertEqual(scores.rec_tracks, 2)
self.assertEqual(scores.aeftl, 1)
self.assertAlmostEqual(scores.erl, 2. / 3)
self.assertEqual(scores.identity_switches, 0)
self.assertEqual(scores.gt_divisions, 0)
self.assertEqual(scores.fn_divisions, 0)
self.assertEqual(scores.fp_divisions, 0)
self.assertAlmostEqual(scores.precision, 1.0)
self.assertAlmostEqual(scores.recall, 2. / 3)
self.assertAlmostEqual(scores.f_score, 4. / 5)
self.delete_db()
def test_one_off_fp_division_evaluation2(self):
roi = daisy.Roi((0, 0, 0, 0), (10, 5, 5, 5))
gt_cells = [
(251, {
't': 0,
'z': 0,
'y': 0,
'x': 0
}),
(261, {
't': 1,
'z': 0,
'y': 0,
'x': 0
}),
(271, {
't': 2,
'z': 0,
'y': 0,
'x': 0
}),
(281, {
't': 3,
'z': 0,
'y': 0,
'x': 0
}),
(282, {
't': 3,
'z': 3,
'y': 0,
'x': 0
}),
(291, {
't': 4,
'z': 0,
'y': 0,
'x': 0
}),
(292, {
't': 4,
'z': 3,
'y': 0,
'x': 0
}),
(301, {
't': 5,
'z': 0,
'y': 0,
'x': 0
}),
(302, {
't': 5,
'z': -3,
'y': 0,
'x': 0
}),
]
gt_edges = [
(261, 251),
(271, 261),
(281, 271),
(282, 271),
(291, 281),
(292, 282),
(301, 291),
(302, 291),
]
gt_track_graph = self.create_graph(gt_cells, gt_edges, roi)
cells = [
(2297, {
't': 0,
'z': 0,
'y': 0,
'x': 0
}),
(2788, {
't': 1,
'z': 0,
'y': 0,
'x': 0
}),
(2944, {
't': 2,
'z': 0,
'y': 0,
'x': 0
}),
(2453, {
't': 3,
'z': 0,
'y': 0,
'x': 0
}),
(3108, {
't': 2,
'z': 1,
'y': 0,
'x': 0
}),
(2990, {
't': 3,
'z': 3,
'y': 0,
'x': 0
}),
(2497, {
't': 4,
'z': 0,
'y': 0,
'x': 0
}),
(2498, {
't': 5,
'z': 0,
'y': 0,
'x': 0
}),
(2499, {
't': 5,
'z': -3,
'y': 0,
'x': 0
}),
(2991, {
't': 3,
'z': 4,
'y': 0,
'x': 0
}),
(2992, {
't': 4,
'z': 3,
'y': 0,
'x': 0
}),
]
edges = [
(2788, 2297),
(2944, 2788),
(3108, 2788),
(2990, 3108),
(2453, 2944),
(2497, 2453),
(2498, 2497),
(2499, 2497),
(2992, 2991),
]
for cell in cells:
cell[1]['y'] += 1
rec_track_graph = self.create_graph(cells, edges, roi)
scores = e.evaluate(gt_track_graph,
rec_track_graph,
matching_threshold=2,
sparse=True)
self.assertEqual(scores.identity_switches, 1)
self.assertEqual(scores.gt_divisions, 2)
self.assertEqual(scores.fn_divs_unconnected_child, 1)
self.assertEqual(scores.fn_divs_unconnected_parent, 0)
self.assertEqual(scores.fn_divs_no_connections, 0)
self.assertEqual(scores.fn_divisions, 1)
self.assertEqual(scores.fp_divisions, 1)
self.assertEqual(scores.fn_edges, 0)
self.delete_db()