Commit 7d5e6305 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

RF: Handle case where fslmaths wrapper is passed output=LOAD. Fix/clarify

usage docs.
parent 8460b25c
......@@ -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
......@@ -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::
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
import nibabel as nib
input = nib.load('input.nii')
output = fslmaths(input).thr(0.25).mul(-1).run()
def __init__(self, input):
......@@ -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
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