def test_STICA():
ds = ImagingDataset.load(example_data())
method = segment.STICA(components=5)
method.append(segment.SparseROIsFromMasks(min_size=50))
method.append(segment.SmoothROIBoundaries(radius=3))
method.append(segment.MergeOverlapping(0.5))
ds.segment(method)
def test_STICA():
ds = ImagingDataset.load(example_data())
method = segment.STICA(components=5)
method.append(segment.SparseROIsFromMasks(min_size=50))
method.append(segment.SmoothROIBoundaries(tolerance=1, min_verts=8))
method.append(segment.MergeOverlapping(0.5))
ds.segment(method)
def test_hmm_tmp(self): # TODO: remove when displacements.pkl is updated
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
corrected = self.hm2d.correct(
[frames], os.path.join(tmp_dir, 'test_hmm_2.sima'))
with open(misc.example_data() + '/displacements.pkl', 'rb') as fh:
displacements = [d.reshape((20, 1, 128, 2))
for d in pickle.load(fh)]
displacements_ = [seq.displacements for seq in corrected]
assert_(abs(displacements_[0] - displacements[0]).max() <= 1)
def test_hmm(self):
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
corrected = self.hm2d.correct(
[frames], os.path.join(tmp_dir, 'test_hmm.sima'))
with open(misc.example_data() + '/displacements.pkl', 'rb') as fh:
displacements = [d.reshape((20, 1, 128, 2))
for d in pickle.load(fh)]
displacements_ = [seq.displacements for seq in corrected]
assert_almost_equal(displacements_, displacements)
def test_hmm_tmp(self): # TODO: remove when displacements.pkl is updated
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
corrected = self.hm2d.correct(
[frames], os.path.join(tmp_dir, 'test_hmm_2.sima'))
with open(misc.example_data() + '/displacements.pkl', 'rb') as fh:
displacements = [d.reshape((20, 1, 128, 2))
for d in pickle.load(fh)]
displacements_ = [seq.displacements for seq in corrected]
diffs = displacements_[0] - displacements[0]
assert_(
((diffs - diffs.mean(axis=2).mean(axis=1).mean(axis=0)) > 1).mean()
<= 0.001)
def test_hmm(self):
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
corrected = self.hm2d.correct(
[frames], os.path.join(tmp_dir, 'test_hmm.sima'))
with open(misc.example_data() + '/displacements.pkl', 'rb') as fh:
displacements = [d.reshape((20, 1, 128, 2))
for d in pickle.load(fh)]
displacements_ = [seq.displacements for seq in corrected]
assert_almost_equal(displacements_, displacements)
def test_PlaneCA1PC():
ds = ImagingDataset.load(example_data())[:, :, :, :50, :50]
method = segment.PlaneCA1PC(num_pcs=5)
ds.segment(method)
def test_PlaneNormalizedCuts():
ds = ImagingDataset.load(example_data())[:, :, :, :50, :50]
affinty_method = segment.BasicAffinityMatrix(num_pcs=5)
method = segment.PlaneWiseSegmentation(
segment.PlaneNormalizedCuts(affinty_method))
ds.segment(method)
def test_PlaneCA1PC():
ds = ImagingDataset.load(example_data())[:, :, :, :50, :50]
method = segment.PlaneCA1PC(num_pcs=5)
ds.segment(method)
def test_PlaneNormalizedCuts():
ds = ImagingDataset.load(example_data())[:, :, :, :50, :50]
affinty_method = segment.BasicAffinityMatrix(num_pcs=5)
method = segment.PlaneWiseSegmentation(
segment.PlaneNormalizedCuts(affinty_method))
ds.segment(method)
def test_STICA():
ds = ImagingDataset.load(example_data())
method = segment.STICA(components=5)
ds.segment(method)
def test_PlaneSTICA():
ds = ImagingDataset.load(example_data())
method = segment.PlaneSTICA(components=5)
ds.segment(method)