From 75bf69d4bb3324c46fdbb230031ffedb50cffbe1 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 3 May 2019 14:33:09 +0100
Subject: [PATCH] ENH: New resample_image script
---
fsl/scripts/resample_image.py | 159 ++++++++++++++++++++++++++++++++++
1 file changed, 159 insertions(+)
create mode 100644 fsl/scripts/resample_image.py
diff --git a/fsl/scripts/resample_image.py b/fsl/scripts/resample_image.py
new file mode 100644
index 000000000..57a22143a
--- /dev/null
+++ b/fsl/scripts/resample_image.py
@@ -0,0 +1,159 @@
+#!/usr/bin/env python
+#
+# resample_image.py - Script to resample an image
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module defines the ``resample_image`` script, for resampling
+a NIfTI image.
+"""
+
+
+import textwrap as tw
+import sys
+import argparse
+
+import numpy as np
+
+import fsl.utils.parse_data as parse_data
+import fsl.utils.image.resample as resample
+import fsl.data.image as fslimage
+
+
+ARGS = {
+ 'input' : ('input',),
+ 'output' : ('output',),
+ 'shape' : ('-s', '--shape'),
+ 'dim' : ('-d', '--dim'),
+ 'reference' : ('-r', '--reference'),
+ 'interp' : ('-i', '--interp'),
+ 'origin' : ('-o', '--origin'),
+ 'dtype' : ('-dt', '--dtype'),
+ 'smooth' : ('-n', '--nosmooth')}
+
+
+OPTS = {
+ 'input' : dict(type=parse_data.Image),
+ 'output' : dict(type=parse_data.ImageOut),
+ 'reference' : dict(type=parse_data.Image, metavar='IMAGE'),
+ 'shape' : dict(type=int, nargs=3, metavar=('X', 'Y', 'Z')),
+ 'dim' : dict(type=float, nargs=3, metavar=('X', 'Y', 'Z')),
+ 'interp' : dict(choices=('nearest', 'linear', 'cubic'),
+ default='linear'),
+ 'origin' : dict(choices=('centre', 'corner'), default='centre'),
+ 'dtype' : dict(choices=('char', 'short', 'int', 'float', 'double')),
+ 'smooth' : dict(dest='smooth', action='store_false')}
+
+
+HELPS = {
+ 'input' : 'Input image',
+ 'output' : 'Output image',
+ 'shape' : 'Output shape',
+ 'dim' : 'Output voxel dimensions',
+ 'reference' : 'Resample input to the space of this reference image'
+ '(overrides --origin)',
+ 'interp' : 'Interpolation (default: linear)',
+ 'origin' : 'Resampling origin (default: centre)',
+ 'dtype' : 'Data type (default: data type of input image)',
+ 'smooth' : 'Do not smooth image when downsampling'}
+
+
+DESC = tw.dedent("""
+Resample an image to different dimensions.
+""").strip()
+
+
+DEST_DESC = tw.dedent("""
+Specify the resampling destination space using one of the following
+options. Note that the --reference option will cause the field-of-view
+of the input image to be changed to that of the reference image.
+""").strip()
+
+
+USAGE = 'resample_image (--shape|--dim|--reference) [options] input output'
+
+
+INTERPS = {'nearest' : 0,
+ 'linear' : 1,
+ 'cubic' : 3}
+DTYPES = {'char' : np.uint8,
+ 'short' : np.int16,
+ 'int' : np.int32,
+ 'float' : np.float32,
+ 'double' : np.float64}
+
+
+def parseArgs(argv):
+ """Parses command-line arguments.
+
+ :arg argv: Sequence of command-line arguments
+ :returns: An ``argparse.Namespace`` object containing parsed arguments.
+ """
+
+ parser = argparse.ArgumentParser(prog='resample_image',
+ usage=USAGE,
+ description=DESC)
+ dest = parser.add_argument_group('Resampling destination', DEST_DESC)
+ dest = dest.add_mutually_exclusive_group(required=True)
+
+ for a in ('input', 'output', 'interp', 'origin',
+ 'dtype', 'smooth'):
+ parser.add_argument(*ARGS[a], help=HELPS[a], **OPTS[a])
+
+ for a in ('shape', 'dim', 'reference'):
+ dest.add_argument(*ARGS[a], help=HELPS[a], **OPTS[a])
+
+ args = parser.parse_args(argv)
+ args.interp = INTERPS[ args.interp]
+ args.dtype = DTYPES.get(args.dtype, args.input.dtype)
+
+ return args
+
+
+def main(argv=None):
+ """Entry point for ``resample_image``. Parses arguments, resamples the
+ input image, and saves it to the specified output file.
+
+ :arg argv: Sequence of command-line arguments. If not provided, taken
+ from ``sys.argv``.
+ """
+
+ if argv is None:
+ argv = sys.argv[1:]
+
+ args = parseArgs(argv)
+ reskwargs = {
+ 'dtype' : args.dtype,
+ 'order' : args.interp,
+ 'smooth' : args.smooth,
+ 'origin' : args.origin}
+
+ # One of these is guaranteed to be set
+ if args.shape is not None:
+ func = resample.resample
+ resargs = (args.input, args.shape)
+
+ elif args.dim is not None:
+ func = resample.resampleToPixdims
+ resargs = (args.input, args.dim)
+
+ elif args.reference is not None:
+ func = resample.resampleToReference
+ resargs = (args.input, args.reference)
+
+ resampled, xform = func(*resargs, **reskwargs)
+
+ if args.reference is None:
+ hdr = args.input.header
+ else:
+ hdr = args.reference.header
+ xform = None
+
+ resampled = fslimage.Image(resampled, xform=xform, header=hdr)
+ resampled.save(args.output)
+
+ return 0
+
+
+if __name__ == '__main__':
+ sys.exit(main())
--
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