def nifti_rw(self, test_data, reader, writer, dtype, resample=True):
test_data = test_data.astype(dtype)
ndim = len(test_data.shape) - 1
for p in TEST_NDARRAYS:
output_ext = ".nii.gz"
filepath = f"testfile_{ndim}d"
saver = SaveImage(output_dir=self.test_dir,
output_ext=output_ext,
resample=resample,
separate_folder=False,
writer=writer)
saver(
p(test_data),
{
"filename_or_obj":
f"{filepath}.png",
"affine":
np.eye(4),
"original_affine":
np.array([[0, 1, 0, 0], [1, 0, 0, 0], [0, 0, 1, 0],
[0, 0, 0, 1]]),
},
)
saved_path = os.path.join(self.test_dir,
filepath + "_trans" + output_ext)
self.assertTrue(os.path.exists(saved_path))
loader = LoadImage(reader=reader, squeeze_non_spatial_dims=True)
data, meta = loader(saved_path)
if meta["original_channel_dim"] == -1:
_test_data = moveaxis(test_data, 0, -1)
else:
_test_data = test_data[0]
if resample:
_test_data = moveaxis(_test_data, 0, 1)
assert_allclose(data, _test_data)
def png_rw(self, test_data, reader, writer, dtype, resample=True):
test_data = test_data.astype(dtype)
ndim = len(test_data.shape) - 1
for p in TEST_NDARRAYS:
output_ext = ".png"
filepath = f"testfile_{ndim}d"
saver = SaveImage(output_dir=self.test_dir,
output_ext=output_ext,
resample=resample,
separate_folder=False,
writer=writer)
saver(p(test_data), {
"filename_or_obj": f"{filepath}.png",
"spatial_shape": (6, 8)
})
saved_path = os.path.join(self.test_dir,
filepath + "_trans" + output_ext)
self.assertTrue(os.path.exists(saved_path))
loader = LoadImage(reader=reader)
data, meta = loader(saved_path)
if meta["original_channel_dim"] == -1:
_test_data = moveaxis(test_data, 0, -1)
else:
_test_data = test_data[0]
assert_allclose(data, _test_data)