Commit 0690befb authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

Documentation bugfixes

parent 6926d57f
...@@ -18,10 +18,10 @@ wrappers around functionality provided by Chris Rorden's ``dcm2niix`` program: ...@@ -18,10 +18,10 @@ wrappers around functionality provided by Chris Rorden's ``dcm2niix`` program:
scanDir scanDir
loadSeries loadSeries
See: https://github.com/rordenlab/dcm2niix/
.. note:: These functions will not work if an executable called ``dcm2niix`` .. note:: These functions will not work if an executable called ``dcm2niix``
cannot be found. cannot be found.
.. see:: https://github.com/rordenlab/dcm2niix/
""" """
......
...@@ -129,7 +129,7 @@ class Mesh(notifier.Notifier, meta.Meta): ...@@ -129,7 +129,7 @@ class Mesh(notifier.Notifier, meta.Meta):
selected vertex set. selected vertex set.
**Metadata* **Metadata**
The ``Mesh`` class also inherits from the :class:`Meta` class, so The ``Mesh`` class also inherits from the :class:`Meta` class, so
...@@ -625,13 +625,14 @@ class Mesh(notifier.Notifier, meta.Meta): ...@@ -625,13 +625,14 @@ class Mesh(notifier.Notifier, meta.Meta):
triangle vertices. triangle vertices.
:returns: A tuple containing :returns: A tuple containing
- A ``(m, 2, 3)`` array containing ``m`` vertices: - A ``(m, 2, 3)`` array containing ``m`` vertices:
of a set of lines, defining the plane intersection of a set of lines, defining the plane intersection
- A ``(m,)`` array containing the indices of the - A ``(m,)`` array containing the indices of the
``m`` triangles that were intersected. ``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 containing the barycentric coordinates of each
line vertex with respect to its intersected line vertex with respect to its intersected
triangle. triangle.
......
...@@ -32,9 +32,9 @@ class MGHImage(fslimage.Image): ...@@ -32,9 +32,9 @@ class MGHImage(fslimage.Image):
"""The ``MGHImage`` class is a NIFTI :class:`Image` which has been converted """The ``MGHImage`` class is a NIFTI :class:`Image` which has been converted
from a Freesurfer ``.mgh`` file. from a Freesurfer ``.mgh`` file.
.. see:: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat See:
- https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
.. see:: http://nipy.org/nibabel/reference/nibabel.freesurfer.html - http://nipy.org/nibabel/reference/nibabel.freesurfer.html
""" """
def __init__(self, image, *args, **kwargs): def __init__(self, image, *args, **kwargs):
......
...@@ -12,7 +12,7 @@ A handful of convenience functions are also in this module: ...@@ -12,7 +12,7 @@ A handful of convenience functions are also in this module:
.. autosummary:: .. autosummary::
:nosignatures: :nosignatures:
loadVTKPolyDataFile loadVTKPolydataFile
getFIRSTPrefix getFIRSTPrefix
findReferenceImage findReferenceImage
......
...@@ -8,7 +8,7 @@ ...@@ -8,7 +8,7 @@
directories. It currently only contains one function: directories. It currently only contains one function:
.. autosummary:: .. autosummary::
:nosignature: :nosignatures:
tempdir tempdir
""" """
......
...@@ -5,8 +5,8 @@ ...@@ -5,8 +5,8 @@
# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk> # Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com> # Author: Paul McCarthy <pauldmccarthy@gmail.com>
# #
"""This module provides wrapper functions for the FSL `MELODIC """This module provides wrapper functions for the FSL
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC>`_ tool, and other `MELODIC <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC>`_ tool, and other
related utilities. related utilities.
.. autosummary:: .. autosummary::
...@@ -25,7 +25,7 @@ from . import wrapperutils as wutils ...@@ -25,7 +25,7 @@ from . import wrapperutils as wutils
@wutils.fileOrImage('input', 'mask', 'ICs', 'bgimage') @wutils.fileOrImage('input', 'mask', 'ICs', 'bgimage')
@wutils.fslwrapper @wutils.fslwrapper
def melodic(input, **kwargs): def melodic(input, **kwargs):
"""Multivariate Exploratory Linear Optimised ICA.""" """Wrapper for the ``melodic`` command."""
valmap = { valmap = {
'Oall' : wutils.SHOW_IF_TRUE, 'Oall' : wutils.SHOW_IF_TRUE,
...@@ -62,7 +62,7 @@ def melodic(input, **kwargs): ...@@ -62,7 +62,7 @@ def melodic(input, **kwargs):
@wutils.fileOrArray('design', 'out_mix') @wutils.fileOrArray('design', 'out_mix')
@wutils.fslwrapper @wutils.fslwrapper
def fsl_regfilt(input, out, design, **kwargs): def fsl_regfilt(input, out, design, **kwargs):
"""Wrapper for the ``fsl_regfilt``command. """ """Wrapper for the ``fsl_regfilt`` command. """
asrt.assertIsNifti(input, out) asrt.assertIsNifti(input, out)
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment