From fe5c855ad2903773964e5e48b749ee68d5d78cd3 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Fri, 17 Feb 2017 16:04:02 +0000
Subject: [PATCH] N-d gifti vertex data arrays can be loaded.
---
fsl/data/gifti.py | 133 ++++++++++++++++++++++++++++++----------------
fsl/data/mesh.py | 3 ++
2 files changed, 90 insertions(+), 46 deletions(-)
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index 97227b4f6..7f1cd7f12 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -25,9 +25,11 @@ are available:
import glob
import os.path as op
+import numpy as np
import nibabel as nib
import fsl.utils.path as fslpath
+from . import constants
from . import mesh
@@ -52,10 +54,12 @@ class GiftiSurface(mesh.TriangleMesh):
data using the :func:`extractGiftiSurface` function.
:arg infile: A GIFTI surface file (``*.surf.gii``).
+
+ .. todo:: Allow loading from a ``.topo.gii`` and ``.coord.gii`` file?
+ Maybe.
"""
- surfimg = nib.load(infile)
- vertices, indices = loadGiftiSurface(surfimg)
+ surfimg, vertices, indices = loadGiftiSurface(infile)
mesh.TriangleMesh.__init__(self, vertices, indices)
@@ -71,27 +75,15 @@ class GiftiSurface(mesh.TriangleMesh):
"""Overrides the :meth:`.TriangleMesh.loadVertexData` method.
Attempts to load data associated with each vertex of this
- ``GiftiSurface`` from the given ``dataSource``.
-
- Currently, only the first ``DataArray`` contained in the
- file is returned.
-
- - ``*.func.gii``
- - ``*.shape.gii``
- - ``*.label.gii``
- - ``*.time.gii``
+ ``GiftiSurface`` from the given ``dataSource``, which may be
+ a GIFTI file or a plain text file which contains vertex data.
"""
if dataSource.endswith('.gii'):
-
- # TODO support 4D
- # TODO make this more robust
- vdata = nib.load(dataSource)
- vdata = vdata.darrays[0].data
-
+ vdata = loadGiftiVertexData(dataSource)[1]
else:
vdata = None
-
+
return mesh.TriangleMesh.loadVertexData(self, dataSource, vdata)
@@ -106,7 +98,7 @@ EXTENSION_DESCRIPTIONS = ['GIFTI surface file', 'GIFTI surface file']
"""
-def loadGiftiSurface(surfimg):
+def loadGiftiSurface(filename):
"""Extracts surface data from the given ``nibabel.gifti.GiftiImage``.
The image is expected to contain the following``<DataArray>`` elements:
@@ -117,10 +109,12 @@ def loadGiftiSurface(surfimg):
A ``ValueError`` will be raised if this is not the case.
- :arg surfimg: A ``GiftiImage`` containing surface data.
+ :arg filename: Name of a GIFTI file containing surface data.
:returns: A tuple containing these values:
+ - The loaded ``nibabel.gifti.GiftiImage`` instance
+
- A :math:`N\\times 3` ``numpy`` array containing :math:`N`
vertices.
@@ -128,37 +122,84 @@ def loadGiftiSurface(surfimg):
vertex indices for :math:`M` triangles.
"""
- from nibabel import gifti
+ gimg = nib.load(filename)
- codes = gifti.gifti.intent_codes.code
+ pointsetCode = constants.NIFTI_INTENT_POINTSET
+ triangleCode = constants.NIFTI_INTENT_TRIANGLE
+
+ pointsets = [d for d in gimg.darrays if d.intent == pointsetCode]
+ triangles = [d for d in gimg.darrays if d.intent == triangleCode]
+
+ if len(gimg.darrays) != 2:
+ raise ValueError('GIFTI surface files must contain exactly '
+ 'one pointset array and one triangle array')
- indices = None
- vertices = None
+ if len(pointsets) != 1:
+ raise ValueError('GIFTI surface files must contain '
+ 'exactly one pointset array')
- for darray in surfimg.darrays:
-
- if darray.intent == codes['pointset']:
-
- if vertices is not None:
- raise ValueError('multiple arrays with intent "{}"'.format(
- darray.intent))
-
- vertices = darray.data
-
- elif darray.intent == codes['triangle']:
- if indices is not None:
- raise ValueError('multiple arrays with intent "{}"'.format(
- darray.intent))
-
- indices = darray.data
-
- if vertices is None:
- raise ValueError('no array with intent "pointset" found')
+ if len(triangles) != 1:
+ raise ValueError('GIFTI surface files must contain '
+ 'exactly one triangle array')
+
+ vertices = pointsets[0].data
+ indices = triangles[0].data
+
+ return gimg, vertices, indices
+
+
+def loadGiftiVertexData(filename):
+ """Loads vertex data from the given GIFTI file.
+
+ It is assumed that the given file does not contain any
+ ``NIFTI_INTENT_POINTSET`` or ``NIFTI_INTENT_TRIANGLE`` data arrays, and
+ which contains either:
+
+ - One ``(M, N)`` data array containing ``N`` data points for ``M``
+ vertices
+
+ - One or more ``(M, 1)`` data arrays each containing a single data point
+ for ``M`` vertices, and all with the same intent code
+
+ Returns a tuple containing:
- if indices is None:
- raise ValueError('no array witbh intent "triangle"found')
+ - The loaded ``nibabel.gifti.GiftiImage`` object
+
+ - A ``(M, N)`` numpy array containing ``N`` data points for ``M``
+ vertices
+ """
+
+ gimg = nib.load(filename)
+
+ intents = set([d.intent for d in gimg.darrays])
+
+ if len(intents) != 1:
+ raise ValueError('{} contains multiple (or no) intents'
+ ': {}'.format(filename, intents))
+
+ intent = intents.pop()
+
+ if intent in (constants.NIFTI_INTENT_POINTSET,
+ constants.NIFTI_INTENT_TRIANGLE):
+
+ raise ValueError('{} contains surface data'.format(filename))
+
+ # Just a single array - return it as-is.
+ # n.b. Storing (M, N) data in a single
+ # DataArray goes against the GIFTI spec,
+ # but hey, it happens.
+ if len(gimg.darrays) == 1:
+ return gimg.darrays[0].data
+
+ # Otherwise extract and concatenate
+ # multiple 1-dimensional arrays
+ vdata = [d.data for d in gimg.darrays]
+
+ if any([len(d.shape) != 1 for d in vdata]):
+ raise ValueError('{} contains one or more non-vector '
+ 'darrays'.format(filename))
- return vertices, indices
+ return gimg, np.vstack(vdata).T
def relatedFiles(fname):
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index ee3e0dea5..20c728c49 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -139,6 +139,9 @@ class TriangleMesh(object):
:arg dataSource: Path to the vertex data to load
:arg vertexData: The vertex data itself, if it has already been
loaded.
+
+ :returns: A ``(M, N)``) array, which contains ``N`` data points
+ for ``M`` vertices.
"""
nvertices = self.vertices.shape[0]
--
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