enh: cli to apply transforms

Author: mgxd

nitransforms/cli.py

@@ -0,0 +1,79 @@
+from argparse import ArgumentParser, RawDescriptionHelpFormatter
+from textwrap import dedent
+
+import nibabel as nb
+
+from .linear import load as linload
+from .nonlinear import load as nlinload
+
+def cli_apply(**kwargs):
+    """
+    Apply a transformation to an image, resampling on the reference
+
+    Usage:
+
+        $ nt apply moving.nii.gz xform.fsl --reference reference.nii.gz
+    """
+    try:
+        xfm = linload(xform)
+    except:
+        xfm = nlinload(xform)
+
+    xfm.apply(moving, **kwargs)
+
+
+def get_parser():
+    desc = dedent(
+        """
+        NiTransforms command-line utility.
+
+        Commands:
+
+            apply       Apply a transformation to an image
+
+        For command specific information, use 'nt <command> -h'.
+        """
+    )
+
+    parser = ArgumentParser(
+        description=desc, formatter_class=RawDescriptionHelpFormatter
+    )
+    subparsers = parser.add_subparsers(dest='command')
+    def _add_subparser(name, description):
+        subp = subparsers.add_parser(
+            name,
+            description=dedent(description),
+            formatter_class=RawDescriptionHelpFormatter,
+        )
+        return subp
+
+    applyp = _add_subparser('apply', cli_apply.__doc__)
+    applyp.add_argument('transform', help='The transform file')
+    applyp.add_argument(
+        'moving', help='The image containing the data to be resampled'
+    )
+    applyp.add_argument('reference', help='The reference space to resample onto')
+    applyp.add_argument('--order', help='The order of the spline transformation')
+    applyp.add_argument(
+        '--mode', 
+        help='Determines how the input image is extended when the resampling overflows a border'
+    )
+    applyp.add_argument('--cval', help='Constant used when using "constant" mode')
+    applyp.add_argument(
+        '--prefilter', 
+        action='store_true', 
+        help="Determines if the image's data array is prefiltered with a spline filter before "
+             "interpolation"
+    )
+    return parser
+
+
+def main(pargs=None):
+    parser = get_parser()
+    pargs = parser.parse_args(pargs)
+    if pargs.command is None:
+        parser.print_help()
+        return
+
+    if pargs.command == 'apply':
+        cli_apply(**vars(pargs))

setup.cfg

@@ -28,6 +28,10 @@ tests =
 all =
     %(test)s
 
+[options.entry_points]
+console_scripts =
+    nt = nitransforms.cli:main
+
 [flake8]
 max-line-length = 100
 ignore = D100,D101,D102,D103,D104,D105,D200,D201,D202,D204,D205,D208,D209,D210,D300,D301,D400,D401,D403,E24,E121,E123,E126,E226,E266,E402,E704,E731,F821,I100,I101,I201,N802,N803,N804,N806,W503,W504,W605