diff --git a/monai/data/writers/niftiwriter.py b/monai/data/writers/niftiwriter.py new file mode 100644 index 0000000000..9ba9e52c01 --- /dev/null +++ b/monai/data/writers/niftiwriter.py @@ -0,0 +1,38 @@ +# 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 + + +def write_nifti(data, affine, file_name, revert_canonical, 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. + revert_canonical (bool): whether to revert canonical. + dtype (np.dtype, optional): convert the loaded image to this data type. + + """ + assert isinstance(data, np.ndarray), 'input data must be numpy array.' + if affine is None: + affine = np.eye(4) + + if revert_canonical: + codes = nib.orientations.axcodes2ornt(nib.orientations.aff2axcodes(np.linalg.inv(affine))) + reverted_results = nib.orientations.apply_orientation(np.squeeze(data), codes) + results_img = nib.Nifti1Image(reverted_results.astype(dtype), affine) + else: + results_img = nib.Nifti1Image(np.squeeze(data).astype(dtype), np.squeeze(affine)) + + nib.save(results_img, file_name)