From 0aa6585f7265e786fb93d8c9b69065fbc9b7d608 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 2 Nov 2017 17:36:47 +0000
Subject: [PATCH] Make imglob work.
---
fsl/scripts/imglob.py | 49 ++++++++++++++++++++++++-------------------
1 file changed, 27 insertions(+), 22 deletions(-)
diff --git a/fsl/scripts/imglob.py b/fsl/scripts/imglob.py
index 543a8ecbf..49afc65b9 100644
--- a/fsl/scripts/imglob.py
+++ b/fsl/scripts/imglob.py
@@ -4,16 +4,15 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""This module defines the ``imglob`` application, for expanding glob patterns
-involving NIFTI/ANALYZE image file name.
+"""This module defines the ``imglob`` application, which identifies unique
+NIFTI/ANALYZE image files.
"""
from __future__ import print_function
-import os.path as op
import sys
-import glob
+import itertools as it
import fsl.utils.path as fslpath
import fsl.data.image as fslimage
@@ -29,44 +28,50 @@ groups = fslimage.FILE_GROUPS
def main(argv=None):
- """The ``imglob`` utility. Prints image files which match one or more
- shell-style wildcard patterns.
+ """The ``imglob`` utility. Given a list of file names, identifies and prints
+ the unique NIFTI/ANALYZE image files.
"""
if argv is None:
argv = sys.argv[1:]
if len(argv) < 1:
- raise RuntimeError(usage)
+ print(usage)
+ return 1
if argv[0] == '-extension': output = 'primary'
elif argv[0] == '-extensions': output = 'all'
else: output = 'prefix'
- if output == 'prefix': patterns = argv
- else: patterns = argv[1:]
+ if output == 'prefix': paths = argv
+ else: paths = argv[1:]
- paths = []
+ imgfiles = []
- for pattern in patterns:
+ # Build a list of all image files (both
+ # hdr and img and otherwise) that match
+ for path in paths:
+ try:
+ imgfiles.extend(fslimage.addExt(path, unambiguous=False))
+ except fslpath.PathError:
+ continue
- hits = glob.glob(pattern)
- hits = [fslimage.looksLikeImage(h) for h in hits]
-
- if output == 'prefix':
-
- hits = fslpath.removeDuplicates(hits,
+ if output == 'prefix':
+ imgfiles = fslpath.removeDuplicates(imgfiles,
allowedExts=exts,
fileGroups=groups)
- hits = [fslpath.removeExt(h, exts) for h in hits]
- elif output == 'primary':
- hits = fslpath.removeDuplicates(hits,
+ imgfiles = [fslpath.removeExt(f, exts) for f in imgfiles]
+
+ elif output == 'primary':
+ imgfiles = fslpath.removeDuplicates(imgfiles,
allowedExts=exts,
fileGroups=groups)
- paths.extend(hits)
+ imgfiles = sorted(set(imgfiles))
+
+ print(' '.join(imgfiles))
- print(' '.join(paths))
+ return 0
if __name__ == '__main__':
--
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