From 2aaf5fa92d327b8a953f7dc9fbeaa86eb8af41c2 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 11 Jan 2019 15:20:49 +0000
Subject: [PATCH] RF: Fixes to support loading of multiple vertex sets and data
from one gifti file
---
fsl/data/gifti.py | 28 ++++++++++++++++++----------
1 file changed, 18 insertions(+), 10 deletions(-)
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index 1b3f26eaa..c4d8ce9c7 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -35,13 +35,13 @@ import fsl.data.constants as constants
import fsl.data.mesh as fslmesh
-ALLOWED_EXTENSIONS = ['.gii']
+ALLOWED_EXTENSIONS = ['.surf.gii', '.gii']
"""List of file extensions that a file containing Gifti surface data
is expected to have.
"""
-EXTENSION_DESCRIPTIONS = ['GIFTI file']
+EXTENSION_DESCRIPTIONS = ['GIFTII surface file', 'GIFTI file']
"""A description for each of the :data:`ALLOWED_EXTENSIONS`. """
@@ -83,8 +83,10 @@ class GiftiMesh(fslmesh.Mesh):
name=name,
dataSource=infile)
- for v in vertices:
- self.addVertices(v, infile, fixWinding=fixWinding)
+ for i, v in enumerate(vertices):
+ if i == 0: key = infile
+ else: key = '{} [{}]'.format(infile, i)
+ self.addVertices(v, key, select=(i == 0), fixWinding=fixWinding)
self.setMeta(infile, surfimg)
if vdata is not None:
@@ -95,18 +97,21 @@ class GiftiMesh(fslmesh.Mesh):
# as the specfiied one.
if loadAll:
- nvertices = vertices.shape[0]
+ nvertices = vertices[0].shape[0]
surfFiles = relatedFiles(infile, ALLOWED_EXTENSIONS)
for sfile in surfFiles:
- surfimg, vertices, _ = loadGiftiMesh(sfile)
+ try:
+ surfimg, _, vertices, _ = loadGiftiMesh(sfile)
+ except Exception:
+ continue
- if vertices.shape[0] != nvertices:
+ if vertices[0].shape[0] != nvertices:
continue
- self.addVertices(vertices, sfile, select=False)
- self.setMeta( sfile, surfimg)
+ self.addVertices(vertices[0], sfile, select=False)
+ self.setMeta(sfile, surfimg)
def loadVertices(self, infile, key=None, *args, **kwargs):
@@ -126,7 +131,7 @@ class GiftiMesh(fslmesh.Mesh):
if key is None:
key = infile
- surfimg, vertices, _ = loadGiftiMesh(infile)
+ surfimg, _, vertices, _ = loadGiftiMesh(infile)
vertices = self.addVertices(vertices, key, *args, **kwargs)
@@ -229,6 +234,9 @@ def loadGiftiVertexData(filename):
def prepareGiftiVertexData(darrays, filename=None):
"""Prepares vertex data from the given list of GIFTI data arrays.
+ All of the data arrays are concatenated into one ``(M, N)`` array,
+ containing ``N`` data points for ``M`` vertices.
+
It is assumed that the given file does not contain any
``NIFTI_INTENT_POINTSET`` or ``NIFTI_INTENT_TRIANGLE`` data arrays, and
which contains either:
--
GitLab