From 3703fb5a82a8cde1181fa67a550ec65c3ebaf7d5 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 22 Jul 2019 12:50:54 +0100
Subject: [PATCH] DOC: Formatting, tweaks
---
fsl/transform/flirt.py | 1 -
fsl/transform/nonlinear.py | 5 +++--
fsl/transform/x5.py | 4 ++--
fsl/utils/idle.py | 2 +-
fsl/wrappers/wrapperutils.py | 2 +-
5 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/fsl/transform/flirt.py b/fsl/transform/flirt.py
index 9a17a27ef..e1c84b761 100644
--- a/fsl/transform/flirt.py
+++ b/fsl/transform/flirt.py
@@ -79,7 +79,6 @@ def fromFlirt(xform, src, ref, from_='voxel', to='world'):
:returns: ``numpy`` array of shape ``(4, 4)`` containing a matrix
encoding a transformation from the source ``from_`` to
the reference ``to`` coordinate systems.
-
"""
premat = src.getAffine(from_, 'fsl')
postmat = ref.getAffine('fsl', to)
diff --git a/fsl/transform/nonlinear.py b/fsl/transform/nonlinear.py
index ab1a9641f..ec2cef142 100644
--- a/fsl/transform/nonlinear.py
+++ b/fsl/transform/nonlinear.py
@@ -174,7 +174,8 @@ class DeformationField(NonLinearTransform):
It is assumed that the a ``DeformationField`` is aligned with the
reference image in their world coordinate systems (i.e. their ``sform``
- affines project both images into alignment).
+ affines project the reference image and the deformation field into
+ alignment).
"""
@@ -686,7 +687,7 @@ def applyDeformation(image, field, ref=None, order=1, mode=None, cval=None):
If an alternate reference image is provided via the ``ref`` argument,
the deformation field is resampled into its space, and then applied to
- the input image. It is therefore assumed that an alternate ``ref``is
+ the input image. It is therefore assumed that an alternate ``ref`` is
aligned in world coordinates with the field's actual reference image.
:arg image: :class:`.Image` to be transformed
diff --git a/fsl/transform/x5.py b/fsl/transform/x5.py
index f14a165a0..3c784a8b6 100644
--- a/fsl/transform/x5.py
+++ b/fsl/transform/x5.py
@@ -555,9 +555,9 @@ def _readDeformation(group):
:arg group: A ``h5py.Group`` object
:returns: A tuple containing
- - A ``numpy.arrayThe`` containing the deformation field
+ - A ``numpy.array`` containing the deformation field
- - A ``numpy.array`` of shape ``(4, 4) `` containing the
+ - A ``numpy.array`` of shape ``(4, 4)`` containing the
voxel to world affine for the deformation field
- The deformation type - either ``'absolute'`` or
diff --git a/fsl/utils/idle.py b/fsl/utils/idle.py
index 1425ba191..c1513708e 100644
--- a/fsl/utils/idle.py
+++ b/fsl/utils/idle.py
@@ -278,7 +278,7 @@ class IdleTask(object):
def _wxIdleLoop(ev):
"""Function which is called on ``wx.EVT_IDLE`` events, and occasionally
- on ``wx.EVT_TIMER` events via the :attr:`_idleTimer`. If there
+ on ``wx.EVT_TIMER`` events via the :attr:`_idleTimer`. If there
is a function on the :attr:`_idleQueue`, it is popped and called.
.. note:: The ``wx.EVT_IDLE`` event is only triggered on user interaction
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 373bcf08b..541c383a5 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -446,7 +446,7 @@ class _FileOrThing(object):
Functions decorated with a ``_FileOrThing`` decorator will always return a
``dict``-like object, where the function's actual return value is
- accessible via an attribute called `output`. All output arguments with a
+ accessible via an attribute called ``output``. All output arguments with a
value of ``LOAD`` will be present as dictionary entries, with the keyword
argument names used as keys. Any ``LOAD``ed output arguments which were not
generated by the function will not be present in the dictionary.
--
GitLab