def test_hnccorr_single_segment(mocker, dummy, neurofinder_data,
matlab_segmentation):
seeder = LocalCorrelationSeeder(3, 0.4, 4, 5)
postprocessor = SizePostprocessor(40, 200, 80)
segmentor = HncParametricWrapper(0, 100000)
positive_seed_selector = PositiveSeedSelector(0)
# negative seed selector is mocked due to a bug in the matlab code.
# Matlab passes the argument to sin(x)/cos(x) in degrees instead of radians.
# This results in slightly wrong negative seeds.
negative_seed_selector = mocker.patch("hnccorr.seeds.NegativeSeedSelector",
autospec=True)(dummy, dummy)
negative_seed_selector.select.return_value = {
(283, 447),
(273, 435),
(285, 427),
(292, 440),
(278, 445),
(274, 431),
(289, 429),
(289, 444),
(274, 442),
(278, 427),
}
edge_selector = SparseComputationEmbeddingWrapper(3,
1 / 35.0,
dimension_reducer=PCA(3))
graph_constructor = GraphConstructor(
edge_selector, lambda a, b: exponential_distance_decay(a, b, 1.0))
patch_size = 31
H = HNCcorr(
seeder,
postprocessor,
segmentor,
positive_seed_selector,
negative_seed_selector,
graph_constructor,
Candidate,
Patch,
CorrelationEmbedding,
patch_size,
)
H.movie = Movie("Neurofinder02.00", neurofinder_data)
center_seed = (282, 436)
c = Candidate(center_seed, H)
best_segmentation = c.segment()
assert best_segmentation.selection == matlab_segmentation.selection
assert best_segmentation.weight == pytest.approx(
matlab_segmentation.weight)
def test_candidate_clean_segmentations(self, dummy, mock_segmentor,
mock_segmentation_class, hnccorr):
mock_segmentor.solve.return_value = [
mock_segmentation_class(dummy, dummy),
mock_segmentation_class(dummy, dummy),
]
mock_segmentation_class.return_value.clean.return_value = "clean"
c = Candidate(1, hnccorr)
assert c.clean_segmentations is None
c.segment()
assert c.clean_segmentations == ["clean", "clean"]
def test_candidate_segment(
self,
hnccorr,
dummy,
mock_movie,
mock_postprocessor,
mock_segmentor,
mock_pos_seed_selector,
mock_neg_seed_selector,
mock_graph_constructor,
mock_patch_class,
mock_embedding_class,
mock_segmentation_class,
):
mock_pos_seed_selector.select.return_value = "positive_seed"
mock_neg_seed_selector.select.return_value = "negative_seed"
mock_embedding_class.return_value = "embedding_class"
mock_postprocessor.select.return_value = "best segmentation"
mock_graph_constructor.construct.return_value = "graph"
mock_patch_class.return_value = "patch"
mock_segmentation_class.return_value.clean.return_value = "clean"
center_seed = 1
mock_segmentor.solve.return_value = [
mock_segmentation_class(dummy, dummy),
mock_segmentation_class(dummy, dummy),
]
candidate = Candidate(center_seed, hnccorr)
assert candidate.segment() == mock_postprocessor.select.return_value
mock_pos_seed_selector.select.assert_called_once_with(
center_seed, mock_movie)
mock_neg_seed_selector.select.assert_called_once_with(
center_seed, mock_movie)
mock_patch_class.assert_called_once_with(mock_movie, center_seed,
"patch_size")
mock_embedding_class.assert_called_once_with(
mock_patch_class.return_value)
mock_graph_constructor.construct.assert_called_once_with(
mock_patch_class.return_value, mock_embedding_class.return_value)
mock_segmentor.solve.assert_called_once_with(
mock_graph_constructor.construct.return_value,
mock_pos_seed_selector.select.return_value,
mock_neg_seed_selector.select.return_value,
)
mock_postprocessor.select.assert_called_once_with(["clean", "clean"])
def candidate(H):
return Candidate(H.seeder.return_val, H)
def test_candidate_best_segmentations(self, hnccorr, mock_postprocessor):
c = Candidate(1, hnccorr)
assert c.best_segmentation is None
c.segment()
assert c.best_segmentation == mock_postprocessor.select.return_value
def test_candidate_center_seed(self):
assert Candidate(1, "a").center_seed == 1
def test_candidate_segmentations(self, hnccorr, mock_segmentor):
c = Candidate(1, hnccorr)
assert c.segmentations is None
c.segment()
assert c.segmentations == mock_segmentor.solve.return_value
def test_candidate_equality_wrong_class(self):
class FakeCandidate:
pass
assert Candidate(1, "a") != FakeCandidate()
def test_candidate_equality(self):
assert Candidate(1, "a") == Candidate(1, "a")
assert Candidate(1, "a") != Candidate(2, "a")
assert Candidate(1, "a") != Candidate(1, "b")