Commit 0aa6585f authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

Make imglob work.

parent 67538f10
......@@ -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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