#!/usr/bin/env python
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Handling surfaces
-----------------
"""
import os
import re
import numpy as np
import nibabel as nb
from niworkflows.nipype.interfaces.base import (
BaseInterfaceInputSpec, TraitedSpec, File, traits, isdefined,
SimpleInterface
)
class NormalizeSurfInputSpec(BaseInterfaceInputSpec):
in_file = File(mandatory=True, exists=True, desc='Freesurfer-generated GIFTI file')
transform_file = File(exists=True, desc='FSL or LTA affine transform file')
class NormalizeSurfOutputSpec(TraitedSpec):
out_file = File(desc='output file with re-centered GIFTI coordinates')
[docs]class NormalizeSurf(SimpleInterface):
""" Normalizes a FreeSurfer-generated GIFTI image
FreeSurfer includes an offset to the center of the brain volume that is not
respected by all software packages.
Normalization involves adding this offset to the coordinates of all
vertices, and zeroing out that offset, to ensure consistent behavior
across software packages.
In particular, this normalization is consistent with the Human Connectome
Project pipeline (see `AlgorithmSurfaceApplyAffine`_ and
`FreeSurfer2CaretConvertAndRegisterNonlinear`_), although the the HCP
may not zero out the offset.
GIFTI files with ``midthickness``/``graymid`` in the name are also updated
to include the following metadata entries::
{
AnatomicalStructureSecondary: MidThickness,
GeometricType: Anatomical
}
This interface is intended to be applied uniformly to GIFTI surface files
generated from the ``?h.white``/``?h.smoothwm`` and ``?h.pial`` surfaces,
as well as externally-generated ``?h.midthickness``/``?h.graymid`` files.
In principle, this should apply safely to any other surface, although it is
less relevant to surfaces that don't describe an anatomical structure.
.. _AlgorithmSurfaceApplyAffine: https://github.com/Washington-University/workbench/blob/1b79e56/src/Algorithms/AlgorithmSurfaceApplyAffine.cxx#L73-L91
.. _FreeSurfer2CaretConvertAndRegisterNonlinear: https://github.com/Washington-University/Pipelines/blob/ae69b9a/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh#L147-154
"""
input_spec = NormalizeSurfInputSpec
output_spec = NormalizeSurfOutputSpec
def _run_interface(self, runtime):
transform_file = self.inputs.transform_file
if not isdefined(transform_file):
transform_file = None
self._results['out_file'] = normalize_surfs(self.inputs.in_file, transform_file)
return runtime
class GiftiNameSourceInputSpec(BaseInterfaceInputSpec):
in_file = File(mandatory=True, exists=True, desc='input GIFTI file')
pattern = traits.Str(mandatory=True,
desc='input file name pattern (must capture named group "LR")')
template = traits.Str(mandatory=True, desc='output file name template')
class GiftiNameSourceOutputSpec(TraitedSpec):
out_name = traits.Str(desc='(partial) filename formatted according to template')
class GiftiNameSource(SimpleInterface):
"""Construct a new filename based on an input filename, a matching pattern,
and a related template.
This interface is intended for use with GIFTI files, to generate names
conforming to Section 9.0 of the `GIFTI Standard`_.
Patterns are expected to have named groups, including one named "LR" that
matches "l" or "r".
These groups must correspond to named format elements in the template.
.. testsetup::
>>> open('lh.pial.gii', 'w').close()
>>> open('rh.fsaverage.gii', 'w').close()
.. doctest::
>>> from fmriprep.interfaces import GiftiNameSource
>>> surf_namer = GiftiNameSource()
>>> surf_namer.inputs.pattern = r'(?P<LR>[lr])h.(?P<surf>\w+).gii'
>>> surf_namer.inputs.template = r'{surf}.{LR}.surf'
>>> surf_namer.inputs.in_file = 'lh.pial.gii'
>>> res = surf_namer.run()
>>> res.outputs.out_name
'pial.L.surf'
>>> func_namer = GiftiNameSource()
>>> func_namer.inputs.pattern = r'(?P<LR>[lr])h.(?P<space>\w+).gii'
>>> func_namer.inputs.template = r'space-{space}.{LR}.func'
>>> func_namer.inputs.in_file = 'rh.fsaverage.gii'
>>> res = func_namer.run()
>>> res.outputs.out_name
'space-fsaverage.R.func'
.. testcleanup::
>>> import os
>>> os.unlink('lh.pial.gii')
>>> os.unlink('rh.fsaverage.gii')
.. _GIFTI Standard: https://www.nitrc.org/frs/download.php/2871/GIFTI_Surface_Format.pdf
"""
input_spec = GiftiNameSourceInputSpec
output_spec = GiftiNameSourceOutputSpec
def _run_interface(self, runtime):
in_format = re.compile(self.inputs.pattern)
in_file = os.path.basename(self.inputs.in_file)
info = in_format.match(in_file).groupdict()
info['LR'] = info['LR'].upper()
filefmt = self.inputs.template
self._results['out_name'] = filefmt.format(**info)
return runtime
class GiftiSetAnatomicalStructureInputSpec(BaseInterfaceInputSpec):
in_file = File(mandatory=True, exists=True,
desc='GIFTI file beginning with "lh." or "rh."')
class GiftiSetAnatomicalStructureOutputSpec(TraitedSpec):
out_file = File(desc='output file with updated AnatomicalStructurePrimary entry')
class GiftiSetAnatomicalStructure(SimpleInterface):
"""Set AnatomicalStructurePrimary attribute of GIFTI image based on
filename.
For files that begin with ``lh.`` or ``rh.``, update the metadata to
include::
{
AnatomicalStructurePrimary: (CortexLeft | CortexRight),
}
If ``AnatomicalStructurePrimary`` is already set, this function has no
effect.
"""
input_spec = GiftiSetAnatomicalStructureInputSpec
output_spec = GiftiSetAnatomicalStructureOutputSpec
def _run_interface(self, runtime):
img = nb.load(self.inputs.in_file)
if any(nvpair.name == 'AnatomicalStruturePrimary' for nvpair in img.meta.data):
out_file = self.inputs.in_file
else:
fname = os.path.basename(self.inputs.in_file)
if fname[:3] in ('lh.', 'rh.'):
asp = 'CortexLeft' if fname[0] == 'l' else 'CortexRight'
else:
raise ValueError(
"AnatomicalStructurePrimary cannot be derived from filename")
img.meta.data.insert(0, nb.gifti.GiftiNVPairs('AnatomicalStructurePrimary', asp))
out_file = os.path.abspath(fname)
img.to_filename(out_file)
self._results['out_file'] = out_file
return runtime
def normalize_surfs(in_file, transform_file):
""" Re-center GIFTI coordinates to fit align to native T1 space
For midthickness surfaces, add MidThickness metadata
Coordinate update based on:
https://github.com/Washington-University/workbench/blob/1b79e56/src/Algorithms/AlgorithmSurfaceApplyAffine.cxx#L73-L91
and
https://github.com/Washington-University/Pipelines/blob/ae69b9a/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh#L147
"""
img = nb.load(in_file)
transform = load_transform(transform_file)
pointset = img.get_arrays_from_intent('NIFTI_INTENT_POINTSET')[0]
coords = pointset.data.T
c_ras_keys = ('VolGeomC_R', 'VolGeomC_A', 'VolGeomC_S')
ras = np.array([[float(pointset.metadata[key])]
for key in c_ras_keys])
ones = np.ones((1, coords.shape[1]), dtype=coords.dtype)
# Apply C_RAS translation to coordinates, then transform
pointset.data = transform.dot(np.vstack((coords + ras, ones)))[:3].T.astype(coords.dtype)
secondary = nb.gifti.GiftiNVPairs('AnatomicalStructureSecondary', 'MidThickness')
geom_type = nb.gifti.GiftiNVPairs('GeometricType', 'Anatomical')
has_ass = has_geo = False
for nvpair in pointset.meta.data:
# Remove C_RAS translation from metadata to avoid double-dipping in FreeSurfer
if nvpair.name in c_ras_keys:
nvpair.value = '0.000000'
# Check for missing metadata
elif nvpair.name == secondary.name:
has_ass = True
elif nvpair.name == geom_type.name:
has_geo = True
fname = os.path.basename(in_file)
# Update metadata for MidThickness/graymid surfaces
if 'midthickness' in fname.lower() or 'graymid' in fname.lower():
if not has_ass:
pointset.meta.data.insert(1, secondary)
if not has_geo:
pointset.meta.data.insert(2, geom_type)
img.to_filename(fname)
return os.path.abspath(fname)
def load_transform(fname):
"""Load affine transform from file
Parameters
----------
fname : str or None
Filename of an LTA or FSL-style MAT transform file.
If ``None``, return an identity transform
Returns
-------
affine : (4, 4) numpy.ndarray
"""
if fname is None:
return np.eye(4)
if fname.endswith('.mat'):
return np.loadtxt(fname)
elif fname.endswith('.lta'):
with open(fname, 'rb') as fobj:
for line in fobj:
if line.startswith(b'1 4 4'):
break
lines = fobj.readlines()[:4]
return np.genfromtxt(lines)
raise ValueError("Unknown transform type; pass FSL (.mat) or LTA (.lta)")