Source code for dipy.workflows.nn

import logging

import numpy as np

from dipy.io.image import load_nifti, save_nifti
from dipy.nn.evac import EVACPlus
from dipy.workflows.workflow import Workflow




class EVACPlusFlow(Workflow):


    @classmethod
    def get_short_name(cls):
        return "evacplus"




    def run(
        self,
        input_files,
        save_masked=False,
        out_dir="",
        out_mask="brain_mask.nii.gz",
        out_masked="dwi_masked.nii.gz",
    ):
        """Extract brain using EVAC+.

        See :footcite:p:`Park2024` for further details about EVAC+.

        Parameters
        ----------
        input_files : string
            Path to the input volumes. This path may contain wildcards to
            process multiple inputs at once.
        save_masked : bool, optional
            Save mask.
        out_dir : string, optional
            Output directory. (default current directory)
        out_mask : string, optional
            Name of the mask volume to be saved.
        out_masked : string, optional
            Name of the masked volume to be saved.

        References
        ----------
        .. footbibliography::
        """
        io_it = self.get_io_iterator()
        empty_flag = True

        for fpath, mask_out_path, masked_out_path in io_it:
            logging.info(f"Applying evac+ brain extraction on {fpath}")

            data, affine, img, voxsize = load_nifti(
                fpath, return_img=True, return_voxsize=True
            )
            evac = EVACPlus()
            mask_volume = evac.predict(data, affine, voxsize=voxsize)
            masked_volume = mask_volume * data

            save_nifti(mask_out_path, mask_volume.astype(np.float64), affine)

            logging.info(f"Mask saved as {mask_out_path}")

            if save_masked:
                save_nifti(masked_out_path, masked_volume, affine, hdr=img.header)

                logging.info(f"Masked volume saved as {masked_out_path}")
            empty_flag = False
        if empty_flag:
            raise ValueError(
                "All output paths exists."
                " If you want to overwrite "
                "please use the --force option."
            )

        return io_it