From 4fb33a008c95c1de56eec2f0184d0e9f94c2467c Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 19 Jan 2018 13:56:29 +0000
Subject: [PATCH] Melodic analysis is detected if either melodic_IC or
melodic_oIC are present
---
fsl/data/melodicanalysis.py | 32 +++++++++++++++++++++++---------
fsl/data/melodicimage.py | 2 +-
2 files changed, 24 insertions(+), 10 deletions(-)
diff --git a/fsl/data/melodicanalysis.py b/fsl/data/melodicanalysis.py
index e13dd1e99..f3779d5cc 100644
--- a/fsl/data/melodicanalysis.py
+++ b/fsl/data/melodicanalysis.py
@@ -48,14 +48,18 @@ def isMelodicImage(path):
try:
- path = fslimage.addExt(path, mustExist=True)
+ path = fslimage.addExt(path)
except fslimage.PathError:
return False
dirname = op.dirname( path)
filename = op.basename(path)
+ filename = fslimage.removeExt(filename)
- return filename.startswith('melodic_IC') and isMelodicDir(dirname)
+ prefixes = ['melodic_IC',
+ 'melodic_oIC']
+
+ return any([filename == p for p in prefixes]) and isMelodicDir(dirname)
def isMelodicDir(path):
@@ -63,7 +67,8 @@ def isMelodicDir(path):
a MELODIC directory, ``False`` otherwise. A melodic directory:
- Must be named ``*.ica``.
- - Must contain a file called ``melodic_IC.nii.gz``.
+ - Must contain a file called ``melodic_IC.nii.gz`` or
+ ``melodic_oIC.nii.gz``.
- Must contain a file called ``melodic_mix``.
- Must contain a file called ``melodic_FTmix``.
"""
@@ -78,10 +83,16 @@ def isMelodicDir(path):
if not any([dirname.endswith(suf) for suf in sufs]):
return False
- # Must contain an image file called melodic_IC
- try:
- fslimage.addExt(op.join(dirname, 'melodic_IC'), mustExist=True)
- except fslimage.PathError:
+ # Must contain an image file called
+ # melodic_IC or melodic_oIC
+ prefixes = ['melodic_IC', 'melodic_oIC']
+ for p in prefixes:
+ try:
+ fslimage.addExt(op.join(dirname, p))
+ break
+ except fslimage.PathError:
+ pass
+ else:
return False
# Must contain files called
@@ -128,7 +139,7 @@ def getDataFile(meldir):
dataFile = op.join(topDir, 'filtered_func_data')
- try: return fslimage.addExt(dataFile, mustExist=True)
+ try: return fslimage.addExt(dataFile)
except fslimage.PathError: return None
@@ -139,7 +150,10 @@ def getMeanFile(meldir):
def getICFile(meldir):
"""Returns the path to the melodic IC image. """
- return fslimage.addExt(op.join(meldir, 'melodic_IC'))
+ try:
+ return fslimage.addExt(op.join(meldir, 'melodic_IC'))
+ except fslimage.PathError:
+ return fslimage.addExt(op.join(meldir, 'melodic_oIC'))
def getMixFile(meldir):
diff --git a/fsl/data/melodicimage.py b/fsl/data/melodicimage.py
index 074b2a1f5..4d7f05809 100644
--- a/fsl/data/melodicimage.py
+++ b/fsl/data/melodicimage.py
@@ -55,7 +55,7 @@ class MelodicImage(fslimage.Image):
"""
if op.isdir(path):
- path = op.join(path, 'melodic_IC')
+ path = melanalysis.getICFile(path)
if not melanalysis.isMelodicImage(path):
raise ValueError('{} does not appear to be a '
--
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