ENH: new imln script

fsl/scripts/imln.py

+#!/usr/bin/env python
+#
+# imln.py - Create symbolic links to image files.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module defines the ``imln`` application, for creating sym-links
+to NIFTI image files.
+
+.. note:: When creating links to relative paths, ln requires that the path is
+          relative to the link location, rather than the invocation
+          location. This is *not* currently supported by imln, and possibly
+          never will be.
+"""
+
+
+import os.path        as op
+import                   os
+import                   sys
+import                   warnings
+
+import fsl.utils.path as fslpath
+
+
+# See atlasq.py for explanation
+with warnings.catch_warnings():
+    warnings.filterwarnings("ignore", category=FutureWarning)
+    import fsl.data.image as fslimage
+
+
+ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
+"""List of file extensions that are supported by ``imln``. """
+
+
+usage = """
+Usage: imln <file1> <file2>
+  Makes a link (called file2) to file1
+  NB: filenames can be basenames or include an extension
+""".strip()
+
+
+def main(argv=None):
+    """``imln`` - create sym-links to images. """
+
+    if argv is None:
+        argv = sys.argv[1:]
+
+    if len(argv) != 2:
+        print(usage)
+        return 1
+
+    target, linkbase = argv
+    target           = fslpath.removeExt(target,   ALLOWED_EXTENSIONS)
+    linkbase         = fslpath.removeExt(linkbase, ALLOWED_EXTENSIONS)
+
+    # Target must exist, so we can
+    # infer the correct extension(s).
+    # Error on incomplete file groups
+    # (e.g. a.img without a.hdr).
+    try:
+        targets = fslpath.getFileGroup(target,
+                                       allowedExts=ALLOWED_EXTENSIONS,
+                                       fileGroups=fslimage.FILE_GROUPS,
+                                       unambiguous=True)
+    except Exception as e:
+        print(f'Error: {e}')
+        return 1
+
+    for target in targets:
+        if not op.exists(target):
+            continue
+
+        ext  = fslpath.getExt(target, ALLOWED_EXTENSIONS)
+        link = f'{linkbase}{ext}'
+
+        try:
+
+            # emulate old imln behaviour - if
+            # link already exists, it is removed
+            if op.exists(link):
+                os.remove(link)
+
+            os.symlink(target, link)
+
+        except Exception as e:
+            print(f'Error: {e}')
+            return 1
+
+    return 0
+
+
+if __name__ == '__main__':
+    sys.exit(main())