def test_imaging_dataset_3d():
global tmp_dir
path = example_hdf5()
seq = Sequence.create('HDF5', path, 'yxt')
filepath = os.path.join(tmp_dir, "test_imaging_dataset_3d.sima")
ds = ImagingDataset([seq, seq], filepath)
assert_equal((ds.num_sequences,) + (ds.num_frames,) + ds.frame_shape,
(2, 40, 1, 128, 256, 1))
def test_imaging_dataset_3d():
global tmp_dir
path = example_hdf5()
seq = Sequence.create('HDF5', path, 'yxt')
filepath = os.path.join(tmp_dir, "test_imaging_dataset_3d.sima")
ds = ImagingDataset([seq, seq], filepath)
assert_equal((ds.num_sequences, ) + (ds.num_frames, ) + ds.frame_shape,
(2, 40, 1, 128, 256, 1))
def setup(self):
for frame in Sequence.create('HDF5', example_hdf5(), 'yxt'):
break
frame_shifts = [np.array([[[0, 0]], [[-5, -10]]])]
self.frame_shifts = [np.array([[[5, 10]], [[0, 0]]])]
self.correlations = [np.array([[1], [0.9301478]])]
shifted = frame.copy()
shifted = np.roll(shifted, -frame_shifts[0][1, 0, 1], axis=2)
shifted = np.roll(shifted, -frame_shifts[0][1, 0, 0], axis=1)
frames = np.array([frame, shifted])
self.hm2d = hmm.HiddenMarkov2D(n_processes=1, verbose=False)
self.dataset = sima.ImagingDataset(
[Sequence.create('ndarray', frames)], None)
def setup(self):
for frame in Sequence.create('HDF5', example_hdf5(), 'yxt'):
break
frame_shifts = [np.array([[[0, 0]], [[-5, -10]]])]
self.frame_shifts = [np.array([[[5, 10]], [[0, 0]]])]
self.correlations = [np.array([[1], [0.9301478]])]
shifted = frame.copy()
shifted = np.roll(shifted, -frame_shifts[0][1, 0, 1], axis=2)
shifted = np.roll(shifted, -frame_shifts[0][1, 0, 0], axis=1)
frames = np.array([frame, shifted])
self.hm2d = hmm.HiddenMarkov2D(n_processes=1, verbose=False)
self.dataset = sima.ImagingDataset(
[Sequence.create('ndarray', frames)], None)
def setup(self):
global tmp_dir
path = example_hdf5()
seq = Sequence.create('HDF5', path, 'yxt')
self.filepath = os.path.join(tmp_dir, "test_imaging_dataset.sima")
self.ds = ImagingDataset([seq, seq], self.filepath)
self.filepath_tiffs = os.path.join(tmp_dir, "test_dataset_tiffs.sima")
seq = Sequence.create(
'TIFFs', [[example_tiffs(), example_tiffs()],
[example_tiffs(), example_tiffs()],
[example_tiffs(), example_tiffs()],
[example_tiffs(), example_tiffs()]])
self.ds_tiffs = ImagingDataset([seq, seq], self.filepath_tiffs)
