From 4dcba47bf422c751fe6a863b464ee78a729101e5 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 17 Nov 2016 13:31:06 +0000
Subject: [PATCH] New function defaultExt, which checks FSLOUTPUTTYPE, and
returns an appropriate extension
---
fsl/data/image.py | 29 +++++++++++++++++++++++------
1 file changed, 23 insertions(+), 6 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index cff154493..5e2a49195 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -27,12 +27,14 @@ and file names:
looksLikeImage
removeExt
addExt
+ defaultExt
loadIndexedImageFile
"""
-import logging
+import os
import os.path as op
+import logging
import six
import numpy as np
@@ -758,10 +760,6 @@ ambiguities - see :func:`fsl.utils.path.addExt`.
"""
-DEFAULT_EXTENSION = '.nii.gz'
-"""The default file extension (TODO read this from ``$FSLOUTPUTTYPE``)."""
-
-
PathError = fslpath.PathError
"""Error raised by :mod:`fsl.utils.path` functions when an error occurs.
Made available in this module for convenience.
@@ -809,10 +807,29 @@ def addExt(prefix, mustExist=True):
return fslpath.addExt(prefix,
ALLOWED_EXTENSIONS,
mustExist,
- DEFAULT_EXTENSION,
+ defaultExt(),
fileGroups=FILE_GROUPS)
+def defaultExt():
+ """Returns the default NIFTI file extension that should be used.
+
+ If the ``$FSLOUTPUTTYPE`` variable is set, its value is used.
+ Otherwise, ``.nii.gz`` is returned.
+ """
+
+ # TODO: Add analyze support.
+ options = {
+ 'NIFTI' : '.nii',
+ 'NIFTI_PAIR' : '.img',
+ 'NIFTI_GZ' : '.nii.gz',
+ }
+
+ outputType = os.environ.get('FSLOUTPUTTYPE', 'NIFTI_GZ')
+
+ return options.get(outputType, '.nii.gz')
+
+
def loadIndexedImageFile(filename):
"""Loads the given image file using ``nibabel`` and ``indexed_gzip``.
--
GitLab