def test_median_otsu_flow():
with TemporaryDirectory() as out_dir:
data_path, _, _ = get_data('small_25')
volume = nib.load(data_path).get_data()
save_masked = True
median_radius = 3
numpass = 3
autocrop = False
vol_idx = [0]
dilate = 0
mo_flow = MedianOtsuFlow()
mo_flow.run(data_path, out_dir=out_dir, save_masked=save_masked,
median_radius=median_radius, numpass=numpass,
autocrop=autocrop, vol_idx=vol_idx, dilate=dilate)
mask_name = mo_flow.last_generated_outputs['out_mask']
masked_name = mo_flow.last_generated_outputs['out_masked']
masked, mask = median_otsu(volume, median_radius,
numpass, autocrop,
vol_idx, dilate)
result_mask_data = nib.load(join(out_dir, mask_name)).get_data()
npt.assert_array_equal(result_mask_data, mask)
result_masked_data = nib.load(join(out_dir, masked_name)).get_data()
npt.assert_array_equal(result_masked_data, masked)
def test_median_otsu_flow():
with TemporaryDirectory() as out_dir:
data_path, _, _ = get_data('small_25')
volume = nib.load(data_path).get_data()
save_masked = True
median_radius = 3
numpass = 3
autocrop = False
vol_idx = [0]
dilate = 0
mo_flow = MedianOtsuFlow()
mo_flow.run(data_path, out_dir=out_dir, save_masked=save_masked,
median_radius=median_radius, numpass=numpass,
autocrop=autocrop, vol_idx=vol_idx, dilate=dilate)
mask_name = mo_flow.last_generated_outputs['out_mask']
masked_name = mo_flow.last_generated_outputs['out_masked']
masked, mask = median_otsu(volume, median_radius,
numpass, autocrop,
vol_idx, dilate)
result_mask_data = nib.load(join(out_dir, mask_name)).get_data()
npt.assert_array_equal(result_mask_data, mask)
result_masked_data = nib.load(join(out_dir, masked_name)).get_data()
npt.assert_array_equal(result_masked_data, masked)
def test_force_overwrite():
with TemporaryDirectory() as out_dir:
data_path, _, _ = get_data('small_25')
mo_flow = MedianOtsuFlow(output_strategy='absolute')
# Generate the first results
mo_flow.run(data_path, out_dir=out_dir)
mask_file = mo_flow.last_generated_outputs['out_mask']
first_time = os.path.getmtime(mask_file)
# re-run with no force overwrite, modified time should not change
mo_flow.run(data_path, out_dir=out_dir)
mask_file = mo_flow.last_generated_outputs['out_mask']
second_time = os.path.getmtime(mask_file)
assert first_time == second_time
# re-run with force overwrite, modified time should change
mo_flow = MedianOtsuFlow(output_strategy='absolute', force=True)
# Make sure that at least one second elapsed, so that time-stamp is
# different (sometimes measured in whole seconds)
time.sleep(1)
mo_flow.run(data_path, out_dir=out_dir)
mask_file = mo_flow.last_generated_outputs['out_mask']
third_time = os.path.getmtime(mask_file)
assert third_time != second_time
def test_force_overwrite():
with TemporaryDirectory() as out_dir:
data_path, _, _ = get_data('small_25')
mo_flow = MedianOtsuFlow(output_strategy='absolute')
# Generate the first results
mo_flow.run(data_path, out_dir=out_dir)
mask_file = mo_flow.last_generated_outputs['out_mask']
first_time = os.path.getmtime(mask_file)
# re-run with no force overwrite, modified time should not change
mo_flow.run(data_path, out_dir=out_dir)
mask_file = mo_flow.last_generated_outputs['out_mask']
second_time = os.path.getmtime(mask_file)
assert first_time == second_time
# re-run with force overwrite, modified time should change
mo_flow = MedianOtsuFlow(output_strategy='absolute', force=True)
# Make sure that at least one second elapsed, so that time-stamp is
# different (sometimes measured in whole seconds)
time.sleep(1)
mo_flow.run(data_path, out_dir=out_dir)
mask_file = mo_flow.last_generated_outputs['out_mask']
third_time = os.path.getmtime(mask_file)
assert third_time != second_time
def test_median_otsu_flow():
with TemporaryDirectory() as out_dir:
data_path, _, _ = get_fnames('small_25')
volume = load_nifti_data(data_path)
save_masked = True
median_radius = 3
numpass = 3
autocrop = False
vol_idx = [0]
dilate = 0
mo_flow = MedianOtsuFlow()
mo_flow.run(data_path,
out_dir=out_dir,
save_masked=save_masked,
median_radius=median_radius,
numpass=numpass,
autocrop=autocrop,
vol_idx=vol_idx,
dilate=dilate)
mask_name = mo_flow.last_generated_outputs['out_mask']
masked_name = mo_flow.last_generated_outputs['out_masked']
masked, mask = median_otsu(volume,
vol_idx=vol_idx,
median_radius=median_radius,
numpass=numpass,
autocrop=autocrop,
dilate=dilate)
result_mask_data = load_nifti_data(join(out_dir, mask_name))
npt.assert_array_equal(result_mask_data.astype(np.uint8), mask)
result_masked = nib.load(join(out_dir, masked_name))
result_masked_data = np.asanyarray(result_masked.dataobj)
npt.assert_array_equal(np.round(result_masked_data), masked)
