From 5d644d61140a245d044213346ecdaac9dde8271f Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Mon, 14 Nov 2016 18:27:08 +0000
Subject: [PATCH] Wrapper scripts around immv/imcp functions.
---
bin/imcp | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
bin/immv | 73 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
setup.py | 5 ++++
3 files changed, 150 insertions(+)
create mode 100755 bin/imcp
create mode 100755 bin/immv
diff --git a/bin/imcp b/bin/imcp
new file mode 100755
index 000000000..bef56cc74
--- /dev/null
+++ b/bin/imcp
@@ -0,0 +1,72 @@
+#!/usr/bin/env python
+#
+# immv.py - Copy image files.
+#
+# Author: Paul McCarthy <paulmc@fmrib.ox.ac.uk>
+#
+
+
+from __future__ import print_function
+
+import os.path as op
+import sys
+import fsl.utils.path as fslpath
+
+
+SUPPORTED_EXTENSIONS = [
+ '.nii', '.nii.gz',
+ '.hdr', '.hdr.gz',
+ '.img', '.img.gz',
+ '.mnc', '.mnc.gz'
+]
+
+
+FILE_GROUPS = [
+ ('.img', '.hdr'),
+ ('.img.gz', '.hdr.gz')
+]
+
+
+usage = """Usage:
+ imcp <file1> <file2>
+ imcp <file1> <directory>
+ imcp <file1> <file2> ... <fileN> <directory>
+
+Copy images from <file1> to <file2>, or copy all <file>s to <directory>
+
+NB: filenames can be basenames or include an extension.
+
+Recognised file extensions: {}
+""".format(', '.join(SUPPORTED_EXTENSIONS))
+
+
+def main():
+ """Parses CLI arguments (see the usage string), and calls the
+ fsl.utils.path.imcp function on each input.
+ """
+
+ if len(sys.argv) < 2:
+ print(usage)
+ sys.exit(1)
+
+ srcs = sys.argv[1:-1]
+ dest = sys.argv[ -1]
+
+ if len(srcs) > 1 and not op.isdir(dest):
+ print(usage)
+ sys.exit(1)
+
+ for src in srcs:
+ try:
+ fslpath.imcp(src,
+ dest,
+ allowedExts=SUPPORTED_EXTENSIONS,
+ fileGroups=FILE_GROUPS)
+
+ except Exception as e:
+ print(e)
+ break
+
+
+if __name__ == '__main__':
+ main()
diff --git a/bin/immv b/bin/immv
new file mode 100755
index 000000000..6054693e4
--- /dev/null
+++ b/bin/immv
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+#
+# immv.py - Move image files.
+#
+# Author: Paul McCarthy <paulmc@fmrib.ox.ac.uk>
+#
+
+
+from __future__ import print_function
+
+import os.path as op
+import sys
+import fsl.utils.path as fslpath
+
+
+SUPPORTED_EXTENSIONS = [
+ '.nii', '.nii.gz',
+ '.hdr', '.hdr.gz',
+ '.img', '.img.gz',
+ '.mnc', '.mnc.gz'
+]
+
+
+
+FILE_GROUPS = [
+ ('.img', '.hdr'),
+ ('.img.gz', '.hdr.gz')
+]
+
+
+usage = """Usage:
+ immv <file1> <file2>
+ immv <file1> <directory>
+ immv <file1> <file2> ... <fileN> <directory>
+
+Moves images from <file1> to <file2>, or move all <file>s to <directory>
+
+NB: filenames can be basenames or include an extension.
+
+Recognised file extensions: {}
+""".format(', '.join(SUPPORTED_EXTENSIONS))
+
+
+def main():
+ """Parses CLI arguments (see the usage string), and calls the
+ fsl.utils.path.immv function on each input.
+ """
+
+ if len(sys.argv) < 2:
+ print(usage)
+ sys.exit(1)
+
+ srcs = sys.argv[1:-1]
+ dest = sys.argv[ -1]
+
+ if len(srcs) > 1 and not op.isdir(dest):
+ print(usage)
+ sys.exit(1)
+
+ for src in srcs:
+ try:
+ fslpath.immv(src,
+ dest,
+ allowedExts=SUPPORTED_EXTENSIONS,
+ fileGroups=FILE_GROUPS)
+
+ except Exception as e:
+ print(e)
+ break
+
+
+if __name__ == '__main__':
+ main()
diff --git a/setup.py b/setup.py
index 932946572..0b8573d8c 100644
--- a/setup.py
+++ b/setup.py
@@ -59,4 +59,9 @@ setup(
setup_requires=['pytest-runner'],
tests_require=['pytest', 'pytest-runner'],
test_suite='tests',
+
+ scripts=[
+ op.join('bin', 'imcp'),
+ op.join('bin', 'immv'),
+ ]
)
--
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