From fe8f32274c1bff498a5daaf4838b30b75c3e7c23 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 7 Nov 2017 18:39:22 +0000
Subject: [PATCH] imglob made into a standalone function
---
fsl/scripts/imglob.py | 67 ++++++++++++++++++++++++++++++++-----------
1 file changed, 50 insertions(+), 17 deletions(-)
diff --git a/fsl/scripts/imglob.py b/fsl/scripts/imglob.py
index 815b38ef8..ba26af1fc 100644
--- a/fsl/scripts/imglob.py
+++ b/fsl/scripts/imglob.py
@@ -26,24 +26,33 @@ exts = fslimage.ALLOWED_EXTENSIONS
groups = fslimage.FILE_GROUPS
-def main(argv=None):
- """The ``imglob`` utility. Given a list of file names, identifies and prints
- the unique NIFTI/ANALYZE image files.
+def imglob(paths, output=None):
+ """Given a list of file names, identifies and returns the unique
+ NIFTI/ANALYZE image files that exist.
+
+ :arg paths: Sequence of paths/prefixes to glob.
+
+ :arg output: One of ``'prefix'`` (the default), ``'all'``, or
+ ``'primary'``:
+
+ - ``'prefix'``: Returns the files without extensions.
+ - ``'all'``: Returns all files that match (e.g. both
+ ``.img`` and ``.hdr`` files will be
+ returned).
+ - ``'primary'``: Returns only the primary file of each
+ matching file group, e.g. only the
+ ``.hdr`` file would be returned from
+ an ``.img``/``.hdr`` pair.
+
+ :returns: A sequence of resolved path names, in the form specified
+ by the ``output`` parameter.
"""
- if argv is None:
- argv = sys.argv[1:]
-
- if len(argv) < 1:
- print(usage)
- return 1
-
- if argv[0] == '-extension': output = 'primary'
- elif argv[0] == '-extensions': output = 'all'
- else: output = 'prefix'
+ if output is None:
+ output = 'prefix'
- if output == 'prefix': paths = argv
- else: paths = argv[1:]
+ if output not in ('prefix', 'all', 'primary'):
+ raise ValueError('Unsupported output format: {}'.format(output))
imgfiles = []
@@ -51,6 +60,7 @@ def main(argv=None):
# hdr and img and otherwise) that match
for path in paths:
try:
+ path = fslimage.removeExt(path)
imgfiles.extend(fslimage.addExt(path, unambiguous=False))
except fslpath.PathError:
continue
@@ -66,9 +76,32 @@ def main(argv=None):
allowedExts=exts,
fileGroups=groups)
- imgfiles = sorted(set(imgfiles))
+ return list(sorted(set(imgfiles)))
+
+
+def main(argv=None):
+ """The ``imglob`` application. 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:
+ print(usage)
+ return 1
+
+ if argv[0] == '-extension': output = 'primary'
+ elif argv[0] == '-extensions': output = 'all'
+ else: output = 'prefix'
+
+ if output == 'prefix': paths = argv
+ else: paths = argv[1:]
+
+ imgfiles = imglob(paths, output)
- print(' '.join(imgfiles))
+ if len(imgfiles) > 0:
+ print(' '.join(imgfiles))
return 0
--
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