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April 24, 2020 17:22
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| """Conforming input data.""" | |
| from pathlib import Path | |
| from tempfile import mkdtemp | |
| import numpy as np | |
| import nibabel as nb | |
| from scipy.ndimage import map_coordinates | |
| def conform_data(in_file, out_file=None, out_size=(256, 256, 256), out_zooms=(1.0, 1.0, 1.0), order=3): | |
| """Conform the input dataset to the canonical orientation.""" | |
| if isinstance(in_file, (str, Path)): | |
| in_file = nb.load(in_file) | |
| # Drop axes with just 1 sample (typically, a 3D file stored as 4D) | |
| in_file = nb.squeeze_image(in_file) | |
| dtype = in_file.header.get_data_dtype() | |
| # Reorient to closest canonical | |
| in_file = nb.as_closest_canonical(in_file) | |
| data = np.asanyarray(in_file.dataobj) | |
| # Calculate the factors to normalize voxel size to out_zooms | |
| normed = np.array(out_zooms) / np.array(in_file.header.get_zooms()[:3]) | |
| # Calculate the new indexes, sampling at 1mm^3 with out_size sizes. | |
| # center_ijk = 0.5 * (np.array(in_file.shape) - 1) | |
| new_ijk = normed[:, np.newaxis] * np.array(np.meshgrid( | |
| np.arange(out_size[0]), | |
| np.arange(out_size[1]), | |
| np.arange(out_size[2]), | |
| indexing="ij") | |
| ).reshape((3, -1)) | |
| offset = 0.5 * (np.max(new_ijk, axis=1) - np.array(in_file.shape)) | |
| # Align the centers of the two sampling extents | |
| new_ijk -= offset[:, np.newaxis] | |
| # Resample data in the new grid | |
| resampled = map_coordinates( | |
| data, | |
| new_ijk, | |
| output=dtype, | |
| order=order, | |
| mode="constant", | |
| cval=0, | |
| prefilter=True, | |
| ).reshape(out_size) | |
| resampled[resampled < 0] = 0 | |
| # Create a new x-form affine, aligned with cardinal axes, 1mm3 and centered. | |
| newaffine = np.eye(4) | |
| newaffine[:3, 3] = -0.5 * (np.array(out_size) - 1) | |
| nii = nb.Nifti1Image(resampled, newaffine, None) | |
| if out_file is None: | |
| out_file = Path(mkdtemp()) / "conformed.nii.gz" | |
| out_file = Path(out_file).absolute() | |
| nii.to_filename(out_file) | |
| return out_file |
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