From e1afbc10417560b4559ac455f51216c9e28b08cd Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Fri, 18 Mar 2016 13:05:20 +0000
Subject: [PATCH] Made tensor data prefix function a bit more robust.
---
fsl/data/image.py | 12 ++++++----
fsl/data/tensorimage.py | 52 ++++++++++++++++++++++++++++-------------
2 files changed, 44 insertions(+), 20 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index fe179c4e7..449878b4e 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -23,7 +23,7 @@ file names:
.. autosummary::
:nosignatures:
- isSupported
+ looksLikeImage
removeExt
addExt
loadImage
@@ -556,8 +556,8 @@ DEFAULT_EXTENSION = '.nii.gz'
"""The default file extension (TODO read this from ``$FSLOUTPUTTYPE``)."""
-def isSupported(filename, allowedExts=None):
- """Returns ``True`` if the given file has a supported extension, ``False``
+def looksLikeImage(filename, allowedExts=None):
+ """Returns ``True`` if the given file looks like an image, ``False``
otherwise.
:arg filename: The file name to test.
@@ -568,6 +568,9 @@ def isSupported(filename, allowedExts=None):
if allowedExts is None: allowedExts = ALLOWED_EXTENSIONS
+ # TODO A much more robust approach would be
+ # to try loading the file using nibabel.
+
return any(map(lambda ext: filename.endswith(ext), allowedExts))
@@ -787,7 +790,8 @@ def saveImage(image, fromDir=None):
path = dlg.GetPath()
nibImage = image.nibImage
- if not isSupported(path):
+ # Add a file extension if not specified
+ if not looksLikeImage(path):
path = addExt(path, False)
# this is an image which has been
diff --git a/fsl/data/tensorimage.py b/fsl/data/tensorimage.py
index 838910c8a..0bc0627ac 100644
--- a/fsl/data/tensorimage.py
+++ b/fsl/data/tensorimage.py
@@ -34,26 +34,46 @@ def getTensorDataPrefix(path):
fas = glob.glob(op.join(path, '*_FA.*'))
mds = glob.glob(op.join(path, '*_MD.*'))
files = [v1s, v2s, v3s, l1s, l2s, l3s, fas, mds]
-
- # Make sure there is exactly one
- # of each of the above files
- def lenone(l):
- return len(l) == 1
-
- if not all(map(lenone, files)):
- return None
- files = [f[0] for f in files]
-
- # Make sure that all of the above
- # files have the same prefix
+ # Gather all of the existing file
+ # prefixes into a dictionary of
+ # prefix : [file list] mappings.
pattern = '^(.*)_(?:V1|V2|V3|L1|L2|L3|FA|MD).*$'
- prefixes = [re.findall(pattern, f)[0] for f in files]
-
- if any([p != prefixes[0] for p in prefixes]):
+ prefixes = {}
+
+ for f in [f for flist in files for f in flist]:
+ prefix = re.findall(pattern, f)[0]
+
+ if prefix not in prefixes: prefixes[prefix] = [f]
+ else: prefixes[prefix].append(f)
+
+ # Discard any prefixes which are
+ # not present for every file type.
+ for prefix, files in list(prefixes.items()):
+ if len(files) != 8:
+ prefixes.pop(prefix)
+
+ # Discard any prefixes which
+ # match any files that do
+ # not look like image files
+ for prefix, files in list(prefixes.items()):
+ if not all([fslimage.looksLikeImage(f) for f in files]):
+ prefixes.pop(prefix)
+
+ prefixes = list(prefixes.keys())
+
+ # No more prefixes remaining -
+ # this is probably not a dtifit
+ # directory
+ if len(prefixes) == 0:
return None
- # And there's our prefix
+ # If there's more than one remaining
+ # prefix, I don't know what to do -
+ # just return the first one.
+ if len(prefixes) > 1:
+ log.warning('Multiple dtifit prefixes detected: {}'.format(prefixes))
+
return op.basename(prefixes[0])
--
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