From 0690befb32ed3e764fcbdc2b77b7aa402d55bcae Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 4 Mar 2018 13:11:30 +0000
Subject: [PATCH] Documentation bugfixes
---
fsl/data/dicom.py | 4 ++--
fsl/data/mesh.py | 5 +++--
fsl/data/mghimage.py | 6 +++---
fsl/data/vtk.py | 2 +-
fsl/utils/tempdir.py | 2 +-
fsl/wrappers/melodic.py | 8 ++++----
6 files changed, 14 insertions(+), 13 deletions(-)
diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py
index 756e1ccb1..57e0a227d 100644
--- a/fsl/data/dicom.py
+++ b/fsl/data/dicom.py
@@ -18,10 +18,10 @@ wrappers around functionality provided by Chris Rorden's ``dcm2niix`` program:
scanDir
loadSeries
+See: https://github.com/rordenlab/dcm2niix/
+
.. note:: These functions will not work if an executable called ``dcm2niix``
cannot be found.
-
-.. see:: https://github.com/rordenlab/dcm2niix/
"""
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index 829a911e3..59fc266c7 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -129,7 +129,7 @@ class Mesh(notifier.Notifier, meta.Meta):
selected vertex set.
- **Metadata*
+ **Metadata**
The ``Mesh`` class also inherits from the :class:`Meta` class, so
@@ -625,13 +625,14 @@ class Mesh(notifier.Notifier, meta.Meta):
triangle vertices.
:returns: A tuple containing
+
- A ``(m, 2, 3)`` array containing ``m`` vertices:
of a set of lines, defining the plane intersection
- A ``(m,)`` array containing the indices of the
``m`` triangles that were intersected.
- - (if ``distances is True``) A ``(m, 2, 3)`` arra
+ - (if ``distances is True``) A ``(m, 2, 3)`` array
containing the barycentric coordinates of each
line vertex with respect to its intersected
triangle.
diff --git a/fsl/data/mghimage.py b/fsl/data/mghimage.py
index 485b687e3..6c36340d9 100644
--- a/fsl/data/mghimage.py
+++ b/fsl/data/mghimage.py
@@ -32,9 +32,9 @@ class MGHImage(fslimage.Image):
"""The ``MGHImage`` class is a NIFTI :class:`Image` which has been converted
from a Freesurfer ``.mgh`` file.
- .. see:: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
-
- .. see:: http://nipy.org/nibabel/reference/nibabel.freesurfer.html
+ See:
+ - https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
+ - http://nipy.org/nibabel/reference/nibabel.freesurfer.html
"""
def __init__(self, image, *args, **kwargs):
diff --git a/fsl/data/vtk.py b/fsl/data/vtk.py
index f39a868ef..62ee14111 100644
--- a/fsl/data/vtk.py
+++ b/fsl/data/vtk.py
@@ -12,7 +12,7 @@ A handful of convenience functions are also in this module:
.. autosummary::
:nosignatures:
- loadVTKPolyDataFile
+ loadVTKPolydataFile
getFIRSTPrefix
findReferenceImage
diff --git a/fsl/utils/tempdir.py b/fsl/utils/tempdir.py
index 9896c9158..b819058f8 100644
--- a/fsl/utils/tempdir.py
+++ b/fsl/utils/tempdir.py
@@ -8,7 +8,7 @@
directories. It currently only contains one function:
.. autosummary::
- :nosignature:
+ :nosignatures:
tempdir
"""
diff --git a/fsl/wrappers/melodic.py b/fsl/wrappers/melodic.py
index e5ceb738b..b95aeabfa 100644
--- a/fsl/wrappers/melodic.py
+++ b/fsl/wrappers/melodic.py
@@ -5,8 +5,8 @@
# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""This module provides wrapper functions for the FSL `MELODIC
-<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC>`_ tool, and other
+"""This module provides wrapper functions for the FSL
+`MELODIC <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC>`_ tool, and other
related utilities.
.. autosummary::
@@ -25,7 +25,7 @@ from . import wrapperutils as wutils
@wutils.fileOrImage('input', 'mask', 'ICs', 'bgimage')
@wutils.fslwrapper
def melodic(input, **kwargs):
- """Multivariate Exploratory Linear Optimised ICA."""
+ """Wrapper for the ``melodic`` command."""
valmap = {
'Oall' : wutils.SHOW_IF_TRUE,
@@ -62,7 +62,7 @@ def melodic(input, **kwargs):
@wutils.fileOrArray('design', 'out_mix')
@wutils.fslwrapper
def fsl_regfilt(input, out, design, **kwargs):
- """Wrapper for the ``fsl_regfilt``command. """
+ """Wrapper for the ``fsl_regfilt`` command. """
asrt.assertIsNifti(input, out)
--
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