ENH: Add simple nib-convert tool

Author: effigies

nibabel/cmdline/convert.py

@@ -0,0 +1,66 @@
+#!python
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+"""
+Convert neuroimaging file to new parameters
+"""
+
+import argparse
+from pathlib import Path
+import warnings
+
+import nibabel as nib
+
+
+def _get_parser():
+    """Return command-line argument parser."""
+    p = argparse.ArgumentParser(description=__doc__)
+    p.add_argument("infile",
+                   help="Neuroimaging volume to convert")
+    p.add_argument("outfile",
+                   help="Name of output file")
+    p.add_argument("--out-dtype", action="store",
+                   help="On-disk data type; valid argument to numpy.dtype()")
+    p.add_argument("--image-type", action="store",
+                   help="Name of NiBabel image class to create, e.g. Nifti1Image. "
+                        "If specified, will be used prior to setting dtype. If unspecified, "
+                        "a new image like `infile` will be created and converted to a type "
+                        "matching the extension of `outfile`.")
+    p.add_argument("-f", "--force", action="store_true",
+                   help="Ignore warnings if possible")
+    p.add_argument("-V", "--version", action="version", version=f"{p.prog} {nib.__version__}")
+
+    return p
+
+
+def main(args=None):
+    """Main program function."""
+    parser = _get_parser()
+    opts = parser.parse_args(args)
+    orig = nib.load(opts.infile)
+
+    if not opts.force and Path(opts.outfile).exists():
+        raise FileExistsError(f"Output file exists: {opts.outfile}")
+
+    if opts.image_type:
+        klass = getattr(nib, opts.image_type)
+    else:
+        klass = orig.__class__
+
+    out_img = klass.from_image(orig)
+    if opts.out_dtype:
+        try:
+            out_img.set_data_dtype(opts.out_dtype)
+        except Exception as e:
+            if opts.force:
+                warnings.warn(f"Ignoring error: {e!r}")
+            else:
+                raise
+
+    nib.save(out_img, opts.outfile)

setup.cfg

@@ -76,6 +76,7 @@ all =
 [options.entry_points]
 console_scripts =
     nib-conform=nibabel.cmdline.conform:main
+    nib-convert=nibabel.cmdline.convert:main
     nib-ls=nibabel.cmdline.ls:main
     nib-dicomfs=nibabel.cmdline.dicomfs:main
     nib-diff=nibabel.cmdline.diff:main