anatomical.py 文件源码

def _run_interface(self, runtime):

        in_file = nb.load(self.inputs.in_file)
        wm_mask = nb.load(self.inputs.wm_mask).get_data()
        wm_mask[wm_mask < 0.9] = 0
        wm_mask[wm_mask > 0] = 1
        wm_mask = wm_mask.astype(np.uint8)

        if self.inputs.erodemsk:
            # Create a structural element to be used in an opening operation.
            struc = nd.generate_binary_structure(3, 2)
            # Perform an opening operation on the background data.
            wm_mask = nd.binary_erosion(wm_mask, structure=struc).astype(np.uint8)

        data = in_file.get_data()
        data *= 1000.0 / np.median(data[wm_mask > 0])

        out_file = fname_presuffix(self.inputs.in_file,
                                   suffix='_harmonized', newpath='.')
        in_file.__class__(data, in_file.affine, in_file.header).to_filename(
            out_file)

        self._results['out_file'] = out_file

        return runtime