# @author: msharrock

# version: 0.0.1

'''

Extraction methods for DeepBleed 

'''

import os

import nibabel as nib

from fsl.wrappers import fslmaths, bet

def brain(image):

        '''

        Brain Extraction with FSL 

        Params:

        - image: nifti object, scan to brain extract

        Output: 

        - brain_image: nifti object, extracted brain

        '''

        affine = image.affine

        header = image.header

        tmpfile = 'tmpfile.nii.gz'

        image.to_filename(tmpfile)

        # FSL calls

        mask = fslmaths(image).thr('0.000000').uthr('100.000000').bin().fillh().run()

        fslmaths(image).mas(mask).run(tmpfile)

        bet(tmpfile, tmpfile, fracintensity = 0.01)

        mask = fslmaths(tmpfile).bin().fillh().run()

        image = fslmaths(image).mas(mask).run()

        image = nib.Nifti1Image(image.get_data(), affine, header)

        os.remove(tmpfile)

        return image