def test_processing_disabled(self, input_path):
pre = DataPreProcessing3D([input_path], state=False)
post = DataPostProcessing3D([input_path], state=False)
# assert that output paths are equal to input paths
assert pre() == [input_path]
assert post() == [input_path]
def test_postprocessing_tiff(self, input_path):
post = DataPostProcessing3D([input_path], save_directory="PostProcessing", out_ext=".tiff")
# run postprocessing
output_paths = post()
# assert output path correctness
basepath, basename = os.path.split(input_path)
assert output_paths[0] == os.path.join(basepath, "PostProcessing", os.path.splitext(basename)[0] + '.tiff')
def _create_postprocessing_step(input_paths, input_type, config):
output_type = config.get('output_type', input_type)
save_directory = config.get('save_directory', 'PostProcessing')
factor = config.get('factor', [1, 1, 1])
out_ext = ".tiff" if config["tiff"] else ".h5"
state = config.get('state', True)
return DataPostProcessing3D(input_paths,
input_type=input_type,
output_type=output_type,
save_directory=save_directory,
factor=factor,
out_ext=out_ext,
state=state)
def test_postprocessing_factor(self, input_path):
factor = [1, 2, 2]
post = DataPostProcessing3D([input_path], save_directory="PostProcessing", factor=factor)
# run postprocessing
output_paths = post()
# assert output path correctness
basepath, basename = os.path.split(input_path)
assert output_paths[0] == os.path.join(basepath, "PostProcessing", basename)
# assert output shape
with h5py.File(input_path, 'r') as f:
original = f['segmentation'][...]
with h5py.File(output_paths[0], 'r') as f:
rescaled = f['segmentation'][...]
assert np.array_equal(np.array(rescaled.shape), np.array(original.shape) * factor)
def test_tiff_voxel_size(self, input_path):
"""
Take input h5, convert to tiff, convert to h5, check if the voxel size matches the original
"""
# convert to h5 to tiff
post = DataPostProcessing3D([input_path], input_type="labels", output_type="labels", out_ext='.tiff')
output_paths = post()
# convert tiff to h5
pre = DataPreProcessing3D(output_paths, input_type="labels", output_type="labels")
output_paths = pre()
# check output voxel_size
with h5py.File(input_path, 'r') as f:
expected_voxel_size = f['raw'].attrs['element_size_um']
with h5py.File(output_paths[0], 'r') as f:
voxel_size = f['raw'].attrs['element_size_um']
assert np.array_equal(expected_voxel_size, voxel_size)