From 17e022325c9f1f19f2eaf40617ec02847e5ec888 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 27 Mar 2020 14:48:03 +0000
Subject: [PATCH] RF: fslstats returns a numpy array instead of lists
---
fsl/wrappers/fslstats.py | 78 ++++++++++++++++++----------------------
1 file changed, 35 insertions(+), 43 deletions(-)
diff --git a/fsl/wrappers/fslstats.py b/fsl/wrappers/fslstats.py
index 77479a2ab..b1ccc691b 100644
--- a/fsl/wrappers/fslstats.py
+++ b/fsl/wrappers/fslstats.py
@@ -12,8 +12,9 @@ for the ``fslstats`` command-line tool.
"""
-import six
+import io
import functools as ft
+import numpy as np
import fsl.data.image as fslimage
from . import wrapperutils as wutils
@@ -122,23 +123,18 @@ class fslstats(object):
fslstats('image_4d.nii.gz', K='mask.nii.gz')
- then the value returned by :meth:`run` will contain a list-of-lists,
- with each child list containing the results:
-
- - for each 3D volume contained within the input image (if ``t``
- is set), or
- - for each sub-mask contained within the mask image (if ``K``
- is set)
-
+ then :meth:`run` will return a 2D ``numpy`` array of shape ``(nvols,
+ nvals)`` if ``t`` is set, or ``(nlabels, nvals)`` if ``K`` is set.
If both of the ``t`` and ``K`` pre-options are set, e.g.::
fslstats('image_4d.nii.gz', t=True, K='mask.nii.gz')
- then the result will be a list-of-lists-of-lists, where each child
- list corresponds to each 3D volume (``t``), and each grand-child list
- corresponds to each sub-mask (``K``).
+ then the result will be a 3D numpy array of shape ``(nvols, nlabels,
+ nvals)``.
+ If neither ``t`` or ``K`` are set, then the result will be a scalar,
+ or a 1D ``numpy`` array.
:arg input: Input image - either a file name, or an
:class:`.Image` object, or a ``nibabel.Nifti1Image``
@@ -166,7 +162,8 @@ class fslstats(object):
def __getattr__(self, name):
- """Intercepts attribute accesses,...
+ """Intercepts attribute accesses and stages ``fslstats`` command-line
+ flags accordingly.
"""
# options which take no args
@@ -198,53 +195,48 @@ class fslstats(object):
def run(self):
- """Run the ``fslstats`` command-line tool. The results are returned as
- floating point numbers.
- """
+ """Run the ``fslstats`` command-line tool. See :meth:`__init__` for a
+ description of the return value.
- result = self.__run('fslstats', *self.__options, log=None)
- result = result.stdout[0].strip()
- result = [line.split() for line in result.split('\n')]
+ :returns: Result of ``fslstats`` as a scalar or ``numpy`` array.
+ """
+ # The parsing logic below will not work
+ # with versions of fslstats prior to fsl
+ # 6.0.2, due to a quirk in the output
+ # formatting of older versions.
+
+ # The default behaviour of run/runfsl
+ # 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 = np.genfromtxt(io.StringIO(result.stdout[0].strip()))
sepvols = '-t' in self.__options
lblmask = '-K' in self.__options
- # This parsing logic will not work with
- # versions of fslstats prior to fsl 6.0.2,
- # due to a quirk in the output formatting
- # of older versions.
-
# One line of output for each volume and
# for each label (with volume the slowest
- # changing).
+ # changing). Reshape to 3D.
if sepvols and lblmask:
- # One line of output for
- # each volume and label
- result = [[float(v) for v in line] for line in result]
-
# We need know the number of volumes
# (or the number of labels) in order
- # to know how to nest the results.
+ # to know how to shape the results.
img = fslimage.Image(self.__input, loadData=False)
if img.ndim >= 4: nvols = img.shape[3]
else: nvols = 1
- # split the result up into
- # nlbls lines for each volume
- nlbls = len(result) / nvols
- offsets = range(0, nvols * nlbls, nlbls)
- result = [result[off:off + nlbls] for off in offsets]
+ # reshape the result into
+ # (nvals, nvols, nlbls)
+ nlbls = int(len(result) / nvols)
+ result = result.reshape((nvols, nlbls, -1))
- # One line of output
- # for each volume/label
- elif sepvols or lblmask:
- result = [[float(v) for v in line] for line in result]
-
- # One line of output
- else:
- result = [float(v) for v in result[0]]
+ # Scalar - use numpy indexing weirdness
+ # to get our single value out.
+ elif result.size == 1:
+ result = result[()]
return result
--
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