#!/usr/bin/env python
#
# imcp.py - Copy image files.
#
# Author: Paul McCarthy <paulmc@fmrib.ox.ac.uk>
#
"""This module defines the ``imcp`` application, for copying NIFTI image
files.
The :func:`main` function is essentially a wrapper around the
:func:`fsl.utils.imcp.imcp` function - see its documentation for more details.
"""
import os.path as op
import sys
import logging
import fsl.utils.path as fslpath
import fsl.utils.imcp as imcp
import fsl.data.image as fslimage
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(fslimage.ALLOWED_EXTENSIONS))
[docs]
def main(argv=None):
"""Parses CLI arguments (see the usage string), and calls the
:func:`fsl.utils.imcp.imcp` function on each input.
"""
if argv is None:
argv = sys.argv[1:]
if len(argv) < 2:
print(usage)
return 1
srcs = argv[:-1]
dest = argv[ -1]
if len(srcs) > 1 and not op.isdir(dest):
print(usage)
return 1
# When converting to NIFTI2, nibabel
# emits an annoying message via log.warning:
# sizeof_hdr should be 540; set sizeof_hdr to 540
logging.getLogger('nibabel').setLevel(logging.ERROR)
try:
srcs = [fslimage.fixExt(s) for s in srcs]
srcs = fslpath.removeDuplicates(
srcs,
allowedExts=fslimage.ALLOWED_EXTENSIONS,
fileGroups=fslimage.FILE_GROUPS)
for src in srcs:
imcp.imcp(src, dest, useDefaultExt=True, overwrite=True)
except Exception as e:
print(str(e))
return 1
return 0
if __name__ == '__main__':
sys.exit(main())