From 7d5e6305aaf2fb2908f59ccfd273561e709c93c8 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 2 Dec 2019 20:49:35 +0000
Subject: [PATCH] RF: Handle case where fslmaths wrapper is passed output=LOAD.
Fix/clarify usage docs.
---
fsl/wrappers/__init__.py | 4 ++--
fsl/wrappers/fslmaths.py | 37 +++++++++++++++++++++++++++++++------
2 files changed, 33 insertions(+), 8 deletions(-)
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index b37413ed3..453313f2c 100644
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -63,11 +63,11 @@ if we want to FLIRT two images and get the result, we can do this::
Similarly, we can run a ``fslmaths`` command on in-memory images::
import nibabel as nib
- from fsl.wrappers import fslmaths, LOAD
+ from fsl.wrappers import fslmaths
image = nib.load('image.nii')
mask = nib.load('mask.nii')
- output = fslmaths(image).mas(mask).bin().run(LOAD)
+ output = fslmaths(image).mas(mask).bin().run()
If you are *writing* wrapper functions, take a look at the
diff --git a/fsl/wrappers/fslmaths.py b/fsl/wrappers/fslmaths.py
index 5fa790ab4..bc1318c52 100644
--- a/fsl/wrappers/fslmaths.py
+++ b/fsl/wrappers/fslmaths.py
@@ -13,7 +13,28 @@ from . import wrapperutils as wutils
class fslmaths(object):
- """Perform mathematical manipulation of images."""
+ """Perform mathematical manipulation of images.
+
+ ``fslmaths`` is unlike the other FSL wrapper tools in that it provdes
+ an object-oriented interface which is hopefully easier to use than
+ constructing a ``fslmaths`` command-line call. For example, the
+ following call to the ``fslmaths`` wrapper function::
+
+ fslmaths('input.nii').thr(0.25).mul(-1).run('output.nii')
+
+ will be translated into the following command-line call::
+
+ fslmaths input.nii -thr 0.25 -mul -1 output.nii
+
+ The ``fslmaths`` wrapper function can also be used with in-memory
+ images. If no output file name is passed to the :meth:`run` method, the
+ result is loaded into memory and returned as a ``nibabel`` image. For
+ example::
+
+ import nibabel as nib
+ input = nib.load('input.nii')
+ output = fslmaths(input).thr(0.25).mul(-1).run()
+ """
def __init__(self, input):
"""Constructor."""
@@ -138,20 +159,24 @@ class fslmaths(object):
return self
def run(self, output=None):
- """Save output of operations to image."""
+ """Save output of operations to image. Set ``output`` to a filename to have
+ the result saved to file, or omit ``output`` entirely to have the
+ result returned as a ``nibabel`` image.
+ """
cmd = ['fslmaths', self.__input] + self.__args
- if output is None: cmd += [wutils.LOAD]
- else: cmd += [output]
+ if output is None:
+ output = wutils.LOAD
+ cmd += [output]
result = self.__run(*cmd)
# if output is LOADed, there
# will only be one entry in
# the result dict.
- if output is None: return list(result.values())[0]
- else: return result
+ if output == wutils.LOAD: return list(result.values())[0]
+ else: return result
@wutils.fileOrImage()
@wutils.fslwrapper
--
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