add nib-conform

Author: kaczmarj

bin/nib-conform

@@ -0,0 +1,17 @@
+#!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.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+"""
+Conform a volume to a new shape and/or voxel size.
+"""
+
+from nibabel.cmdline.conform import main
+
+if __name__ == '__main__':
+    main()

nibabel/cmdline/conform.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.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+"""
+Conform neuroimaging volume to arbitrary shape and voxel size.
+"""
+
+import argparse
+from pathlib import Path
+import sys
+
+import numpy as np
+
+from nibabel import __version__
+from nibabel.loadsave import load
+from nibabel.processing import conform
+
+
+def _get_parser():
+    """Return command-line argument parser."""
+    p = argparse.ArgumentParser(description=__doc__)
+    p.add_argument("infile",
+                   help="Neuroimaging volume to conform.")
+    p.add_argument("outfile",
+                   help="Name of output file.")
+    p.add_argument("--out-shape", nargs=3, default=(256, 256, 256),
+                   help="Shape of the conformed output.")
+    p.add_argument("--voxel-size", nargs=3, default=(1, 1, 1),
+                   help="Voxel size in millimeters of the conformed output.")
+    p.add_argument("--orientation", default="RAS",
+                   help="Orientation of the conformed output.")
+    p.add_argument("-f", "--force", action="store_true",
+                   help="Overwrite existing output files.")
+    p.add_argument("-V", "--version", action="version", version="{} {}".format(p.prog, __version__))
+
+    return p
+
+
+def main(args=None):
+    """Main program function."""
+    parser = _get_parser()
+    if args is None:
+        namespace = parser.parse_args(sys.argv[1:])
+    else:
+        namespace = parser.parse_args(args)
+
+    kwargs = vars(namespace)
+    from_img = load(kwargs["infile"])
+
+    if not kwargs["force"] and Path(kwargs["outfile"]).exists():
+        raise FileExistsError("Output file exists: {}".format(kwargs["outfile"]))
+
+    out_img = conform(from_img=from_img,
+        out_shape=kwargs["out_shape"],
+        voxel_size=kwargs["voxel_size"],
+        order=3,
+        cval=0.0,
+        orientation=kwargs["orientation"])
+
+    out_img.to_filename(kwargs["outfile"])