Source code for sdcflows.interfaces.brainmask

# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""Brain extraction interfaces."""
from nipype.interfaces.base import (
    traits,
    BaseInterfaceInputSpec,
    TraitedSpec,
    File,
    SimpleInterface,
)
from ..utils.tools import brain_masker


class _BrainExtractionInputSpec(BaseInterfaceInputSpec):
    in_file = File(exists=True, mandatory=True, desc="file to mask")


class _BrainExtractionOutputSpec(TraitedSpec):
    out_file = File(exists=True, desc="the input file, after masking")
    out_mask = File(exists=True, desc="the binary brain mask")
    out_probseg = File(exists=True, desc="the probabilistic brain mask")


[docs] class BrainExtraction(SimpleInterface): """Brain extraction for EPI and GRE data.""" input_spec = _BrainExtractionInputSpec output_spec = _BrainExtractionOutputSpec def _run_interface(self, runtime): from nipype.utils.filemanip import fname_presuffix ( self._results["out_file"], self._results["out_probseg"], self._results["out_mask"], ) = brain_masker( self.inputs.in_file, fname_presuffix(self.inputs.in_file, suffix="_mask", newpath=runtime.cwd), ) return runtime
class _BinaryDilationInputSpec(BaseInterfaceInputSpec): in_file = File(exists=True, mandatory=True, desc="binary file to dilate") radius = traits.Float(3, usedefault=True, desc="structure element (ball) radius") class _BinaryDilationOutputSpec(TraitedSpec): out_file = File(exists=True, desc="the input file, after binary dilation")
[docs] class BinaryDilation(SimpleInterface): """Brain extraction for EPI and GRE data.""" input_spec = _BinaryDilationInputSpec output_spec = _BinaryDilationOutputSpec def _run_interface(self, runtime): self._results["out_file"] = _dilate( self.inputs.in_file, self.inputs.radius, newpath=runtime.cwd, ) return runtime
class _UnionInputSpec(BaseInterfaceInputSpec): in1 = File(exists=True, mandatory=True, desc="binary file") in2 = File(exists=True, mandatory=True, desc="binary file") class _UnionOutputSpec(TraitedSpec): out_file = File(exists=True, desc="the input file, after binary dilation")
[docs] class Union(SimpleInterface): """Brain extraction for EPI and GRE data.""" input_spec = _UnionInputSpec output_spec = _UnionOutputSpec def _run_interface(self, runtime): self._results["out_file"] = _union( self.inputs.in1, self.inputs.in2, newpath=runtime.cwd, ) return runtime
def _dilate(in_file, radius=3, newpath=None): """Dilate (binary) input mask.""" from pathlib import Path import numpy as np import nibabel as nb from scipy import ndimage from skimage.morphology import ball from nipype.utils.filemanip import fname_presuffix mask = nb.load(in_file) newdata = ndimage.binary_dilation( np.asanyarray(mask.dataobj) > 0, ball(radius) ) hdr = mask.header.copy() hdr.set_data_dtype("uint8") out_file = fname_presuffix(in_file, suffix="_dil", newpath=newpath or Path.cwd()) mask.__class__(newdata.astype("uint8"), mask.affine, hdr).to_filename( out_file ) return out_file def _union(in1, in2, newpath=None): """Dilate (binary) input mask.""" from pathlib import Path import numpy as np import nibabel as nb from nipype.utils.filemanip import fname_presuffix mask = nb.load(in1) data = ( np.asanyarray(mask.dataobj) + np.asanyarray(nb.load(in2).dataobj) ) > 0 hdr = mask.header.copy() hdr.set_data_dtype("uint8") out_file = fname_presuffix(in1, suffix="_union", newpath=newpath or Path.cwd()) mask.__class__(data.astype("uint8"), mask.affine, hdr).to_filename( out_file ) return out_file