From 309da9517e0cb534aa88f44e0e658e68c84c1e42 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 21 Jul 2019 16:31:20 +0100
Subject: [PATCH] ENH: New fsl_apply_x5 script, to apply a X5 transformation to
an image
---
fsl/scripts/fsl_apply_x5.py | 135 ++++++++++++++++++++++++++++++++++++
1 file changed, 135 insertions(+)
create mode 100644 fsl/scripts/fsl_apply_x5.py
diff --git a/fsl/scripts/fsl_apply_x5.py b/fsl/scripts/fsl_apply_x5.py
new file mode 100644
index 000000000..8128ec348
--- /dev/null
+++ b/fsl/scripts/fsl_apply_x5.py
@@ -0,0 +1,135 @@
+#!/usr/bin/env python
+#
+# fsl_apply_x5.py - Apply an X5 transformation to an image.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""The ``fsl_apply_x5`` script can be used to apply an X5 transformation file
+to resample an image.
+"""
+
+
+import functools as ft
+import sys
+import argparse
+
+import fsl.transform.x5 as x5
+import fsl.transform.nonlinear as nonlinear
+import fsl.utils.parse_data as parse_data
+import fsl.utils.image.resample as resample
+import fsl.data.image as fslimage
+
+
+def parseArgs(args=None):
+ """Parses command-line arguments.
+
+ :arg args: Sequence of command-line arguments. If ``None``, ``sys.argv``
+ is used
+ :returns: An ``argparse.Namespace`` object containing parsed arguments
+ """
+
+ parser = argparse.ArgumentParser('fsl_apply_x5')
+ flags = {
+ 'input' : ('input',),
+ 'xform' : ('xform',),
+ 'output' : ('output',),
+ 'interp' : ('-i', '--interp'),
+ 'ref' : ('-r', '--ref'),
+ }
+
+ helps = {
+ 'input' : 'Input image',
+ 'xform' : 'X5 transformation file',
+ 'output' : 'Output image',
+ 'interp' : 'Interpolation (default: linear)',
+ 'ref' : 'Alternate reference image (default: '
+ 'reference specified in X5 file)',
+ }
+ opts = {
+ 'input' : dict(helps['input'],
+ type=parse_data.Image),
+ 'xform' : dict(helps['xform']),
+ 'output' : dict(helps['output'],
+ type=parse_data.ImageOut),
+ 'interp' : dict(helps['interp'],
+ choices=('nearest', 'linear', 'cubic'),
+ default='linear'),
+ 'ref' : dict(helps['ref'],
+ type=ft.partial(parse_data.Image, loadData=False)),
+ }
+
+ parser.add_argument(*flags['input'], **opts['input'])
+ parser.add_argument(*flags['xform'], **opts['xform'])
+ parser.add_argument(*flags['output'], **opts['output'])
+ parser.add_argument(*flags['interp'], **opts['interp'])
+ parser.add_argument(*flags['ref'], **opts['ref'])
+
+ args = parser.parse_args(args)
+
+ if args.interp == 'nearest': args.interp = 0
+ elif args.interp == 'linear': args.interp = 1
+ elif args.interp == 'cubic': args.interp = 3
+
+ return args
+
+
+def applyLinear(args):
+ """Applies a linear X5 transformation file to the input.
+
+ :arg args: ``argparse.Namespace`` object
+ :returns: The transformed input as an :class:`.Image` object
+ """
+
+ input = args.input
+ xform, src, ref = x5.readLinearX5(args.xform)
+
+ if args.ref is not None:
+ ref = args.ref
+
+ res, xform = resample.resampleToReference(input,
+ ref,
+ matrix=xform,
+ order=args.interp)
+
+ return fslimage.Image(res, xform=xform, header=ref.header)
+
+
+def applyNonlinear(args):
+ """Applies a non-linear X5 transformation file to the input.
+
+ :arg args: ``argparse.Namespace`` object
+ :returns: The transformed input as an :class:`.Image` object
+ """
+
+ field = x5.readNonLinearX5(args.xform)
+
+ if args.ref is None: ref = field.ref
+ else: ref = args.ref
+
+ result = nonlinear.applyDeformation(args.input,
+ field,
+ ref=ref,
+ order=args.interp,
+ mode='constant')
+
+ return fslimage.Image(result, header=ref.header)
+
+
+def main(args=None):
+ """Entry point. Parse command-line arguments, then calls
+ :func:`applyLinear` or :func:`applyNonlinear` depending on the x5 file
+ type.
+ """
+
+ args = parseArgs(args)
+
+ if x5.inferType(args.xform) == 'linear':
+ result = applyLinear(args)
+ else:
+ result = applyNonlinear(args)
+
+ result.save(args.output)
+
+
+if __name__ == '__main__':
+ sys.exit(main())
--
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