From 0258fda1bc6738f874412b3035b2dad8d9528436 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 4 Mar 2018 12:02:22 +0000
Subject: [PATCH] fsl.utils.run.dryrun() calls will now return the command
line. Useful for testing. Tweaks to various wrapper functions. fslmaths
returns results dict, rather than file name (for testing).
---
fsl/utils/run.py | 4 +++-
fsl/wrappers/fslmaths.py | 2 +-
fsl/wrappers/fugue.py | 13 ++++++++++--
fsl/wrappers/melodic.py | 4 ++--
fsl/wrappers/misc.py | 44 +++++++++++++---------------------------
5 files changed, 31 insertions(+), 36 deletions(-)
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index b4b46f24d..f3a07b38f 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -45,6 +45,8 @@ class FSLNotPresent(Exception):
def dryrun(*args):
"""Context manager which causes all calls to :func:`run` to be logged but
not executed. See the :data:`DRY_RUN` flag.
+
+ The returned standard output will be equal to ``' '.join(args)``.
"""
global DRY_RUN
@@ -106,7 +108,7 @@ def run(*args, **kwargs):
log.debug('run: {}'.format(' '.join(args)))
if DRY_RUN:
- stdout = '<dryrun>'
+ stdout = ' '.join(args)
stderr = ''
else:
proc = sp.Popen(args, stdout=sp.PIPE, stderr=sp.PIPE)
diff --git a/fsl/wrappers/fslmaths.py b/fsl/wrappers/fslmaths.py
index db5858f04..5fa790ab4 100644
--- a/fsl/wrappers/fslmaths.py
+++ b/fsl/wrappers/fslmaths.py
@@ -151,7 +151,7 @@ class fslmaths(object):
# will only be one entry in
# the result dict.
if output is None: return list(result.values())[0]
- else: return output
+ else: return result
@wutils.fileOrImage()
@wutils.fslwrapper
diff --git a/fsl/wrappers/fugue.py b/fsl/wrappers/fugue.py
index 19fdcf94b..ced52f226 100644
--- a/fsl/wrappers/fugue.py
+++ b/fsl/wrappers/fugue.py
@@ -17,9 +17,13 @@ from . import wrapperutils as wutils
@wutils.fileOrImage('in', 'unwarp', 'warp', 'phasemap', 'savefmap',
'loadfmap', 'saveshift', 'loadshift', 'mask')
@wutils.fslwrapper
-def fugue(**kwargs):
+def fugue(input=None, **kwargs):
"""Wrapper for the ``fugue`` command."""
+ argmap = {
+ 'input' : 'in'
+ }
+
valmap = {
'dwelltoasym' : wutils.SHOW_IF_TRUE,
'median' : wutils.SHOW_IF_TRUE,
@@ -37,7 +41,12 @@ def fugue(**kwargs):
'verbose' : wutils.SHOW_IF_TRUE,
}
- cmd = ['fugue'] + wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
+ kwargs.update({'input' : input})
+
+ cmd = ['fugue'] + wutils.applyArgStyle('--=',
+ argmap=argmap,
+ valmap=valmap,
+ **kwargs)
return cmd
diff --git a/fsl/wrappers/melodic.py b/fsl/wrappers/melodic.py
index d95b33fa5..e5ceb738b 100644
--- a/fsl/wrappers/melodic.py
+++ b/fsl/wrappers/melodic.py
@@ -52,7 +52,7 @@ def melodic(input, **kwargs):
asrt.assertIsNifti(input)
- cmd = ['melodic', '--in', input]
+ cmd = ['melodic', '--in={}'.format(input)]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
@@ -77,6 +77,6 @@ def fsl_regfilt(input, out, design, **kwargs):
'--in={}'.format(input),
'--out={}'.format(out),
'--design={}'.format(design)]
- cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
+ cmd += wutils.applyArgStyle('--=', valsep=',', valmap=valmap, **kwargs)
return cmd
diff --git a/fsl/wrappers/misc.py b/fsl/wrappers/misc.py
index 3b7a0615e..9c2188828 100644
--- a/fsl/wrappers/misc.py
+++ b/fsl/wrappers/misc.py
@@ -31,49 +31,33 @@ def fslreorient2std(input, output=None):
@wutils.fileOrImage('input', 'output')
@wutils.fslwrapper
-def fslroi(input, output, xmin=None, xsize=None, ymin=None, ysize=None,
- zmin=None, zsize=None, tmin=None, tsize=None):
+def fslroi(input, output, *args):
"""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)), \
- "either time min/size or x/y/z min/size must be provided"
- cmd = ['fslroi', input, output]
+ asrt.assertIsNifti(input)
- if xmin is not None:
- cmd += [str(v) for v in [xmin, xsize, ymin, ysize, zmin, zsize]]
- if tmin is not None:
- cmd += [str(tmin), str(tsize)]
+ cmd = ['fslroi', input, output] + [str(a) for a in args]
return cmd
@wutils.fileOrImage('input', 'input2')
@wutils.fslwrapper
-def slicer(input, input2=None, label=None, lut=None, intensity=None,
- edgethreshold=None, x=None, y=None, z=None):
+def slicer(input, input2=None, **kwargs):
"""Wrapper for the ``slicer`` command. """
- cmd = "slicer {0}".format(input)
+ cmd = ['slicer', input]
if input2 is not None:
- cmd += " {0}".format(input2)
- if label is not None:
- cmd += " -L {0}".format(label)
- if lut is not None:
- cmd += " -l {0}".format(lut)
- if intensity is not None:
- cmd += " -i {0} {1}".format(intensity[0], intensity[1])
- if edgethreshold is not None:
- cmd += " -e {0}".format(edgethreshold)
- if x is not None:
- cmd += " -x {0} {1}".format(x[0], x[1])
- if y is not None:
- cmd += " -y {0} {1}".format(y[0], y[1])
- if z is not None:
- cmd += " -z {0} {1}".format(z[0], z[1])
+ cmd.append(input2)
+
+ # slicer output options must be
+ # applied after other options
+ outopts = ['x', 'y', 'z', 'a', 'A', 'S']
+ outargs = { k : kwargs.pop(k) for k in outopts if k in kwargs}
+
+ cmd = cmd + wutils.applyArgStyle('-', **kwargs) + \
+ wutils.applyArgStyle('-', **outargs)
return cmd
--
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