ENH: Wrappers for tbss scripts

fsl/wrappers/tbss.py

+#!/usr/bin/env python3
+#
+# 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.
+"""
+
+import os
+import fsl.utils.assertions as asrt
+from . import wrapperutils  as wutils
+
+
+@wutils.fslwrapper
+def preproc(*images, **kwargs):
+    """Wrapper for the ``tbss_1_preproc`` command.
+    Usage: tbss_1_preproc(<image1>, <image2>, ...)
+    """
+    for img in images:
+        asrt.assertIsNifti(img)
+    
+    return ["tbss_1_preproc"] + images
+     
+
+@wutils.fslwrapper
+def reg(**kwargs):
+    """Wrapper for the ``tbss_2_reg`` command.
+    Refer to the ``tbss_2_reg`` command-line help for details on all arguments.
+    """
+
+    valmap = {
+        'T' : wutils.SHOW_IF_TRUE,
+        't' : wutils.SHOW_IF_TRUE,
+        'n' : wutils.SHOW_IF_TRUE,
+    }
+
+    cmd = ["tbss_2_reg"]
+    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.
+    """
+    
+    valmap = {
+        'T' : wutils.SHOW_IF_TRUE,
+        'S' : wutils.SHOW_IF_TRUE,
+    }
+
+    cmd = ["tbss_3_postreg"]
+    cmd += wutils.applyArgStyle("-", valmap=valmap, **kwargs)
+
+    return cmd
+    
+@wutils.fslwrapper
+def prestats(threshold, **kwargs):
+    """Wrapper for the ``tbss_4_prestats`` command.
+    The normal recommendation for <threshold> is 0.2
+    """
+    
+    return ["tbss_4_prestats", threshold]
+
+@wutils.fslwrapper
+def non_FA(alt_img_root, **kwargs):
+    """Wrapper for the ``tbss_non_FA`` command.
+    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):
+    """Wrapper for the ``tbss_fill`` command.
+    Refer to the ``tbss_fill`` command-line help for details on all arguments.
+    """
+    valmap = {
+        'n' : wutils.SHOW_IF_TRUE,
+    }
+    
+    cmd = ["tbss_fill", stats_image, threshold, mean_FA, output]
+    cmd += wutils.applyArgStyle("-", valmap=valmap, **kwargs)
+    
+    return cmd
+