DOC: Formatting, tweaks

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)

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

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

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

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.