From 195cb21f7d68b73737a9fd2d39023cc79b6a4fc3 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 27 Mar 2020 16:20:56 +0000
Subject: [PATCH] RF: Hook to get the raw output, for testing
---
fsl/wrappers/fslstats.py | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/fsl/wrappers/fslstats.py b/fsl/wrappers/fslstats.py
index b1ccc691b..f77a36723 100644
--- a/fsl/wrappers/fslstats.py
+++ b/fsl/wrappers/fslstats.py
@@ -194,10 +194,13 @@ class fslstats(object):
return self
- def run(self):
+ def run(self, raw=False):
"""Run the ``fslstats`` command-line tool. See :meth:`__init__` for a
description of the return value.
+ :arg raw: Defaults to ``False``. If ``True``, the raw standard output
+ and error is returned, instead of a scalar/numpy array.
+
:returns: Result of ``fslstats`` as a scalar or ``numpy`` array.
"""
@@ -210,7 +213,11 @@ class fslstats(object):
# is to tee the command output streams
# to the calling process streams. We
# can disable this via log=None.
- result = self.__run('fslstats', *self.__options, log=None)
+ result = self.__run('fslstats', *self.__options, log=None)
+
+ if raw:
+ return result.stdout
+
result = np.genfromtxt(io.StringIO(result.stdout[0].strip()))
sepvols = '-t' in self.__options
lblmask = '-K' in self.__options
--
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