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): 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)