From ad0019838e9afeb17250ba585fb3e12fbfa13082 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sat, 3 Mar 2018 12:49:09 +0000
Subject: [PATCH] cleaned up misc module
---
fsl/wrappers/misc.py | 66 +++++++++++++++++++++++++++++---------------
1 file changed, 43 insertions(+), 23 deletions(-)
diff --git a/fsl/wrappers/misc.py b/fsl/wrappers/misc.py
index 94df91ac7..4d912dee2 100644
--- a/fsl/wrappers/misc.py
+++ b/fsl/wrappers/misc.py
@@ -1,47 +1,58 @@
#!/usr/bin/env python
#
-# misc.py -
+# misc.py - Wrappers for miscellaneous FSL command-line tools.
#
+# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+"""This module contains wrapper functions for various `FSL
+<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`_ command-line tools.
+"""
import fsl.utils.run as run
import fsl.utils.assertions as asrt
+from . import wrapperutils as wutils
-def fslreorient2std(input, output):
- """reorient to match the approx. orientation of the standard (MNI152)."""
+@wutils.fileOrImage('input', 'output')
+def fslreorient2std(input, output=None):
+ """Wrapper for the ``fsreorient2std`` tool."""
- asrt.assertIsNifti(input, output)
- asrt.assertFileExists(input)
+ asrt.assertIsNifti(input)
+
+ cmd = ['fslreorient2std', input]
+
+ if output is not None:
+ cmd.append(output)
- cmd = 'fslreorient2std {0} {1}'.format(input, output)
return run.runfsl(cmd)
+@wutils.fileOrImage('input', 'output')
def fslroi(input, output, xmin=None, xsize=None, ymin=None, ysize=None,
zmin=None, zsize=None, tmin=None, tsize=None):
- """Extract region of interest (ROI) from an image."""
+ """Wrapper for the ``fslroi`` tool."""
assert ((tmin is not None and tsize is not None) or
(xmin is not None and xsize is not None and
- ymin is not None and ysize is not None and
- zmin is not None and zsize is not None)), \
+ ymin is not None and ysize is not None and
+ zmin is not None and zsize is not None)), \
"either time min/size or x/y/z min/size must be provided"
- cmd = "fslroi {0} {1}".format(input, output)
+ cmd = ['fslroi', input, output]
if xmin is not None:
- cmd += " {0} {1} {2} {3} {4} {5}".format(xmin, xsize, ymin, ysize,
- zmin, zsize)
+ cmd += [str(v) for v in [xmin, xsize, ymin, ysize, zmin, zsize]]
if tmin is not None:
- cmd += " {0} {1}".format(tmin, tsize)
+ cmd += [str(tmin), str(tsize)]
return run.runfsl(cmd)
+@wutils.fileOrImage('input', 'input2')
def slicer(input, input2=None, label=None, lut=None, intensity=None,
edgethreshold=None, x=None, y=None, z=None):
+ """Wrapper for the ``slicer`` command. """
cmd = "slicer {0}".format(input)
@@ -65,17 +76,26 @@ def slicer(input, input2=None, label=None, lut=None, intensity=None,
return run.runfsl(cmd)
-def cluster(infile, thresh, oindex=None, no_table=False):
- """
- Form clusters, report information about clusters and/or perform
- cluster-based inference.
- """
- cmd = "cluster --in={0} --thresh={1}".format(infile, thresh)
- if oindex is not None:
- cmd += " -o {0}".format(oindex)
+@wutils.fileOrImage('input', 'cope', 'oindex', 'othresh', 'olmaxim', 'osize',
+ 'omax', 'omean', 'opvals', 'stdvol', 'warpvol',
+ 'empiricalNull')
+@wutils.fileOrArray('xfm')
+def cluster(input, thresh, **kwargs):
+ """Wrapper for the ``cluster`` command. """
+
+ valmap = {
+ 'fractional' : wutils.SHOW_IF_TRUE,
+ 'mm' : wutils.SHOW_IF_TRUE,
+ 'min' : wutils.SHOW_IF_TRUE,
+ 'no_table' : wutils.SHOW_IF_TRUE,
+ 'minclustersize' : wutils.SHOW_IF_TRUE,
+ 'verbose' : wutils.SHOW_IF_TRUE,
+ 'voxthresh' : wutils.SHOW_IF_TRUE,
+ 'voxuncthresh' : wutils.SHOW_IF_TRUE,
+ }
- if no_table:
- cmd += " --no_table"
+ cmd = ['cluster', '--in={}'.format(input), '--thresh={}'.format(thresh)]
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return run.runfsl(cmd)
--
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