From f879120a1bcfaedbb6f5f28882bf37a24a8ed82b Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 20 Jul 2020 11:32:05 +0100
Subject: [PATCH] ENH: New imrm script. fsl.scripts package is pkgutils, so can
be used by other projects
---
fsl/scripts/__init__.py | 9 +++++-
fsl/scripts/imrm.py | 62 +++++++++++++++++++++++++++++++++++++++++
2 files changed, 70 insertions(+), 1 deletion(-)
create mode 100644 fsl/scripts/imrm.py
diff --git a/fsl/scripts/__init__.py b/fsl/scripts/__init__.py
index 4ef1e04be..499b22176 100644
--- a/fsl/scripts/__init__.py
+++ b/fsl/scripts/__init__.py
@@ -5,5 +5,12 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""The ``fsl.scripts`` package contains all of the executable scripts provided
-by ``fslpy``.
+by ``fslpy``, and other python-based FSL packages.
+
+.. note:: The ``fsl.scripts`` namespace is a ``pkgutil``-style *namespace
+ package* - it can be used across different projects - see
+ https://packaging.python.org/guides/packaging-namespace-packages/ for
+ details.
"""
+
+__path__ = __import__('pkgutil').extend_path(__path__, __name__) # noqa
diff --git a/fsl/scripts/imrm.py b/fsl/scripts/imrm.py
new file mode 100644
index 000000000..b9c6315f8
--- /dev/null
+++ b/fsl/scripts/imrm.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python
+#
+# imrm.py - Remove image files.
+#
+# Author: Paul McCarthy <paulmc@fmrib.ox.ac.uk>
+#
+"""This module defines the ``imrm`` application, for removing NIFTI image
+files.
+"""
+
+
+from __future__ import print_function
+
+import itertools as it
+import os.path as op
+import os
+import sys
+import warnings
+import contextlib
+
+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
+
+
+usage = """Usage: {} <list of image names to remove>
+NB: filenames can be basenames or not
+""".strip()
+
+
+ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
+"""List of file extensions that are removed by ``imrm``. """
+
+
+def main(argv=None):
+ """Removes all images which are specified on the command line. """
+
+ if argv is None:
+ argv = sys.argv
+
+ if len(argv) < 2:
+ exe = op.abspath(argv[0])
+ print(usage.format(exe))
+ return 1
+
+ prefixes = [fslpath.removeExt(p, ALLOWED_EXTENSIONS) for p in argv[1:]]
+
+ for prefix, ext in it.product(prefixes, ALLOWED_EXTENSIONS):
+
+ path = f'{prefix}{ext}'
+
+ if op.exists(path):
+ os.remove(path)
+
+ return 0
+
+
+if __name__ == '__main__':
+ sys.exit(main())
--
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