# Copyright 2020 MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import numpy as np
import nibabel as nib
[docs]def write_nifti(data, affine, file_name, target_affine=None, dtype="float32"):
"""Write numpy data into nifti files to disk.
Args:
data (numpy.ndarray): input data to write to file.
affine (numpy.ndarray): affine information for the data.
file_name (string): expected file name that saved on disk.
target_affine (numpy.ndarray, optional):
before saving the (data, affine), transform the data into the orientation defined by `target_affine`.
dtype (np.dtype, optional): convert the image to save to this data type.
"""
assert isinstance(data, np.ndarray), 'input data must be numpy array.'
if affine is None:
affine = np.eye(4)
if target_affine is None:
results_img = nib.Nifti1Image(data.astype(dtype), affine)
else:
start_ornt = nib.orientations.io_orientation(affine)
target_ornt = nib.orientations.io_orientation(target_affine)
ornt_transform = nib.orientations.ornt_transform(start_ornt, target_ornt)
reverted_results = nib.orientations.apply_orientation(data, ornt_transform)
results_img = nib.Nifti1Image(reverted_results.astype(dtype), target_affine)
nib.save(results_img, file_name)