From 15ecde79fb1d74ee2f2a2b2e21fbda66767a3fda Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 15 Feb 2017 15:13:24 +0000
Subject: [PATCH] TriangleMesh/GiftiSurface classes have method to load vertex
data. I/O will be kept in these classes, instead of in FSLeyes.
---
fsl/data/gifti.py | 13 ++++++++++++-
fsl/data/mesh.py | 17 +++++++++++++++++
2 files changed, 29 insertions(+), 1 deletion(-)
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index ea14b4e2c..41d38e3ba 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -23,6 +23,8 @@ are available:
import os.path as op
+import nibabel as nib
+
import fsl.utils.path as fslpath
from . import mesh
@@ -50,7 +52,6 @@ class GiftiSurface(mesh.TriangleMesh):
:arg infile: A GIFTI surface file
"""
- import nibabel as nib
surfimg = nib.load(infile)
vertices, indices = extractGiftiSurface(surfimg)
@@ -65,6 +66,16 @@ class GiftiSurface(mesh.TriangleMesh):
self.surfImg = surfimg
+ def loadVertexData(self, dataSource):
+ """Attempts to load scalar data associated with each vertex of this
+ ``GiftiSurface`` from the given ``dataSource``.
+ """
+
+ # TODO make this more robust
+ norms = nib.load(dataSource)
+ return norms.darrays[0].data
+
+
ALLOWED_EXTENSIONS = ['.surf.gii', '.gii']
"""List of file extensions that a file containing Gifti surface data
is expected to have.
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index 978fbbdd9..d9afd3cf2 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -55,6 +55,14 @@ class TriangleMesh(object):
the vertex indices for :math:`M` triangles
============== ====================================================
+
+ And the following methods:
+
+ .. autosummary::
+ :nosignatures:
+
+ getBounds
+ loadVertexData
"""
@@ -117,6 +125,15 @@ class TriangleMesh(object):
return (self.__loBounds, self.__hiBounds)
+ def loadVertexData(self, dataSource):
+ """Attempts to load scalar data associated with each vertex of this
+ ``TriangleMesh`` from the given ``dataSource``.
+
+ This method may be overridden by sub-classes.
+ """
+ raise NotImplementedError('Not implemented yet')
+
+
ALLOWED_EXTENSIONS = ['.vtk']
"""A list of file extensions which could contain :class:`TriangleMesh` data.
"""
--
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