From d99bff5f4d7bbacad82d0547849c8a2081714b3d Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 20 Oct 2020 14:15:28 +0100
Subject: [PATCH] RF: Make tbss available at fsl.wrappers package level, minor
clean ups
---
fsl/wrappers/__init__.py | 1 +
fsl/wrappers/tbss.py | 52 +++++++++++++++++++++-------------------
2 files changed, 29 insertions(+), 24 deletions(-)
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index 25f5ff9f1..60b715a0f 100644
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -109,3 +109,4 @@ from .misc import (fslreorient2std, # noqa
slicer,
cluster,
gps)
+from . import tbss # noqa
diff --git a/fsl/wrappers/tbss.py b/fsl/wrappers/tbss.py
index e40f4dcd4..b84cd75a8 100755
--- a/fsl/wrappers/tbss.py
+++ b/fsl/wrappers/tbss.py
@@ -1,28 +1,30 @@
#!/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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