Source code for dipy.workflows.mask

#!/usr/bin/env python3

import logging

import numpy as np

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




class MaskFlow(Workflow):


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




    def run(self, input_files, lb, ub=np.inf, out_dir="", out_mask="mask.nii.gz"):
        """Workflow for creating a binary mask

        Parameters
        ----------
        input_files : string
           Path to image to be masked.
        lb : float
            Lower bound value.
        ub : float, optional
            Upper bound value.
        out_dir : string, optional
           Output directory. (default current directory)
        out_mask : string, optional
           Name of the masked file.
        """
        if lb >= ub:
            logging.error(
                "The upper bound(less than) should be greater"
                " than the lower bound (greater_than)."
            )
            return

        io_it = self.get_io_iterator()

        for input_path, out_mask_path in io_it:
            logging.info(f"Creating mask of {input_path}")
            data, affine = load_nifti(input_path)
            mask = np.bitwise_and(data > lb, data < ub)
            save_nifti(out_mask_path, mask.astype(np.ubyte), affine)
            logging.info(f"Mask saved at {out_mask_path}")