From df1135e488e9d21dcc0e3ce7e2459760f04f11c7 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Tue, 29 Nov 2016 10:37:34 +0000
Subject: [PATCH] fsl.data.model module has a couple of convenience functions
for trying to find identifying reference image associated with a FIRST vtk
file.
---
fsl/data/model.py | 37 +++++++++++++++++++++++++++++++++++++
fsl/utils/async.py | 2 +-
2 files changed, 38 insertions(+), 1 deletion(-)
diff --git a/fsl/data/model.py b/fsl/data/model.py
index ededc41a5..13b3510e6 100644
--- a/fsl/data/model.py
+++ b/fsl/data/model.py
@@ -23,6 +23,8 @@ import numpy as np
import six
+from . import image as fslimage
+
log = logging.getLogger(__name__)
@@ -149,3 +151,38 @@ def loadVTKPolydataFile(infile):
indexOffset += polygonLengths[i]
return vertices, polygonLengths, indices
+
+
+def getFIRSTPrefix(modelfile):
+ """If the given ``vtk`` file was generated by `FIRST
+ <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST>`_, this function
+ will return the file prefix. Otherwise an ``Exception`` will be
+ raised.
+ """
+
+ if not modelfile.endswith('first.vtk'):
+ raise ValueError('Not a first vtk file: {}'.format(modelfile))
+
+ modelfile = op.basename(modelfile)
+ prefix = modelfile.split('-')
+ prefix = '-'.join(prefix[:-1])
+
+ return prefix
+
+
+def findReferenceImage(modelfile):
+ """Given a ``vtk`` file, attempts to find a corresponding ``NIFTI``
+ image file. Return the path to the image, or ``None`` if no image was
+ found.
+
+ Currently this function will only return an image for ``vtk`` files
+ generated by `FIRST <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST>`_.
+ """
+
+ try:
+
+ prefix = getFIRSTPrefix(modelfile)
+ return fslimage.addExt(prefix, mustExist=True)
+
+ except:
+ return None
diff --git a/fsl/utils/async.py b/fsl/utils/async.py
index 4b835e28e..4b403d794 100644
--- a/fsl/utils/async.py
+++ b/fsl/utils/async.py
@@ -372,7 +372,7 @@ def idle(task, *args, **kwargs):
.. note:: You will run into difficulties if you schedule a function that
expects/accepts its own keyword arguments called ``name``,
- ``skipIfQueued``, ``after``, or ``timeout``.
+ ``skipIfQueued``, ``after``, ``timeout``, or ``alwaysQueue``.
"""
global _idleRegistered
--
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