Commit d99bff5f authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

RF: Make tbss available at fsl.wrappers package level, minor clean ups

parent 27fb3a8b
......@@ -109,3 +109,4 @@ from .misc import (fslreorient2std, # noqa
slicer,
cluster,
gps)
from . import tbss # noqa
#!/usr/bin/env python3
#
# tbss.py - Wrappers for FSL command-line tools for tract based spatial statistics (TBSS).
# tbss.py - Wrappers for FSL command-line tools for tract based spatial
# statistics (TBSS).
#
# Author: Evan Edmond <eedmond@gmail.com>
#
"""This module contains wrapper functions for various `FSL
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`_ command-line tools.
"""This module contains wrapper functions for various `TBSS
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/>`_ command-line tools.
"""
import os
import fsl.utils.assertions as asrt
from . import wrapperutils as wutils
@wutils.fslwrapper
def preproc(*images, **kwargs):
def preproc(*images):
"""Wrapper for the ``tbss_1_preproc`` command.
Usage: tbss_1_preproc(<image1>, <image2>, ...)
Usage: ``tbss_1_preproc(<image1>, <image2>, ...)``
"""
for img in images:
asrt.assertIsNifti(img)
return ["tbss_1_preproc"] + images
return ["tbss_1_preproc"] + list(images)
@wutils.fslwrapper
def reg(**kwargs):
......@@ -32,7 +34,6 @@ def reg(**kwargs):
valmap = {
'T' : wutils.SHOW_IF_TRUE,
't' : wutils.SHOW_IF_TRUE,
'n' : wutils.SHOW_IF_TRUE,
}
......@@ -40,13 +41,14 @@ def reg(**kwargs):
cmd += wutils.applyArgStyle("-", valmap=valmap, valsep=" ", **kwargs)
return cmd
@wutils.fslwrapper
def postreg(**kwargs):
"""Wrapper for the ``tbss_3_postreg`` command.
Refer to the ``tbss_3_postreg`` command-line help for details on all arguments.
Refer to the ``tbss_3_postreg`` command-line help for details on all
arguments.
"""
valmap = {
'T' : wutils.SHOW_IF_TRUE,
'S' : wutils.SHOW_IF_TRUE,
......@@ -56,23 +58,26 @@ def postreg(**kwargs):
cmd += wutils.applyArgStyle("-", valmap=valmap, **kwargs)
return cmd
@wutils.fslwrapper
def prestats(threshold, **kwargs):
def prestats(threshold):
"""Wrapper for the ``tbss_4_prestats`` command.
The normal recommendation for <threshold> is 0.2
"""
return ["tbss_4_prestats", threshold]
return ["tbss_4_prestats", f'{threshold}']
@wutils.fslwrapper
def non_FA(alt_img_root, **kwargs):
def non_FA(alt_img_root):
"""Wrapper for the ``tbss_non_FA`` command.
e.g.: tbss_non_FA("L2")
e.g.: ``tbss_non_FA("L2")``
"""
return ["tbss_non_FA", alt_img_root]
@wutils.fileOrImage("stats_image", "mean_FA", "output")
@wutils.fslwrapper
def fill(stats_image, threshold, mean_FA, output, **kwargs):
......@@ -82,9 +87,8 @@ def fill(stats_image, threshold, mean_FA, output, **kwargs):
valmap = {
'n' : wutils.SHOW_IF_TRUE,
}
cmd = ["tbss_fill", stats_image, threshold, mean_FA, output]
cmd = ["tbss_fill", stats_image, f'{threshold}', mean_FA, output]
cmd += wutils.applyArgStyle("-", valmap=valmap, **kwargs)
return cmd
return cmd
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