Commit 6d912c17 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

DOC: Fixes and tweaks

parent c0156439
......@@ -456,7 +456,7 @@ class CoefficientField(NonLinearTransform):
:arg premat: If ``True``, the inverse :meth:`srcToRefMat` is applied
to the coordinates after the displacements have been
addd.
added.
:returns: ``coords``, transformed into the source image space
"""
......@@ -465,7 +465,7 @@ class CoefficientField(NonLinearTransform):
def displacements(self, coords):
"""Calculate the relative displacemenets for the given coordinates.
"""Calculate the relative displacements for the given coordinates.
:arg coords: ``(N, 3)`` array of reference image voxel coordinates.
:return: A ``(N, 3)`` array of relative displacements to the
......
......@@ -88,18 +88,18 @@ shape, dimensions, and voxel-to-world affine transformation.
Groups of type *space* have the following fields:
+-------------+-----------+---------------------------------------------------+
| **Name** | **Type** | **Value/Description** |
+-------------+-----------+---------------------------------------------------+
| ``Type`` | attribute | ``'image'`` |
+-------------+-----------+---------------------------------------------------+
| ``Size`` | attribute | ``uint64`` ``(X, Y, Z)`` voxel dimensions |
+-------------+-----------+---------------------------------------------------+
| ``Scales`` | attribute | ``float64`` ``(X, Y, Z)`` voxel pixdims |
+-------------+-----------+---------------------------------------------------+
| ``Mapping`` | affine | The image voxel-to-world transformation (its |
| | | ``sform``) |
+-------------+-----------+---------------------------------------------------+
+--------------+-----------+--------------------------------------------------+
| **Name** | **Type** | **Value/Description** |
+--------------+-----------+--------------------------------------------------+
| ``Type`` | attribute | ``'image'`` |
+--------------+-----------+--------------------------------------------------+
| ``Size`` | attribute | ``uint64`` ``(X, Y, Z)`` voxel dimensions |
+--------------+-----------+--------------------------------------------------+
| ``Scales`` | attribute | ``float64`` ``(X, Y, Z)`` voxel pixdims |
+--------------+-----------+--------------------------------------------------+
| ``Mapping/`` | affine | The image voxel-to-world transformation (its |
| | | ``sform``) |
+--------------+-----------+--------------------------------------------------+
*deformation*
......@@ -131,19 +131,19 @@ coordinate system.
Groups of type *deformation* have the following fields:
+-------------+-----------+---------------------------------------------------+
| **Name** | **Type** | **Value/Description** |
+-------------+-----------+---------------------------------------------------+
| ``Type`` | attribute | ``'deformation'`` |
+-------------+-----------+---------------------------------------------------+
| ``SubType`` | attribute | ``'absolute'`` or ``'relative'``. |
+-------------+-----------+---------------------------------------------------+
| ``Matrix`` | dataset | The deformation field - a ``float64`` array of |
| | | shape ``(X, Y, Z, 3)`` |
+-------------+-----------+---------------------------------------------------+
| ``Mapping`` | affine | The field voxel-to-world transformation (its |
| | | ``sform``) |
+-------------+-----------+---------------------------------------------------+
+--------------+-----------+--------------------------------------------------+
| **Name** | **Type** | **Value/Description** |
+--------------+-----------+--------------------------------------------------+
| ``Type`` | attribute | ``'deformation'`` |
+--------------+-----------+--------------------------------------------------+
| ``SubType`` | attribute | ``'absolute'`` or ``'relative'``. |
+--------------+-----------+--------------------------------------------------+
| ``Matrix`` | dataset | The deformation field - a ``float64`` array of |
| | | shape ``(X, Y, Z, 3)`` |
+--------------+-----------+--------------------------------------------------+
| ``Mapping/`` | affine | The field voxel-to-world transformation (its |
| | | ``sform``) |
+--------------+-----------+--------------------------------------------------+
Linear X5 files
......@@ -204,7 +204,7 @@ between FLIRT-style matrices and X5 style matrices.
.. [*] For a given image, FSL coordinates are voxel coordinates scaled by the
``pixdim`` values in the NIFTI header, and an inversion along the X
``pixdim`` values in the NIFTI header, with an inversion along the X
axis if the voxel-to-world affine (the ``sform``) has a positive
determinant.
......@@ -269,9 +269,9 @@ Storage of FSL FNIRT warp fields in non-linear X5 files
-------------------------------------------------------
FLIRT outputs the result of a non-linear registration from a source image to a
reference image as either a warp field, or a coefficient field which can be
used to generate a warp field. A warp field is defined in terms of the
FLIRT outputs the result of a non-linear registration between a source image
and a reference image as either a warp field, or a coefficient field which can
be used to generate a warp field. A warp field is defined in terms of the
reference image - the warp field has the same shape and FOV as the reference
image, and contains either:
......@@ -316,6 +316,7 @@ to source image world coordinates.
The :mod:`fsl.transform.fnirt` module contains functions which can be used to
perform all of the conversions and adjustments required to store FNIRT
transformations as X5 files.
"""
......@@ -341,11 +342,11 @@ class X5Error(Exception):
def inferType(fname):
"""Return the type of the given X5 file - either ``'linear'``or
"""Return the type of the given X5 file - either ``'linear'`` or
``'nonlinear'``.
:arg fname: Name of a X5 file
:returns: ``'linear'``or ``'nonlinear'``
:returns: ``'linear'`` or ``'nonlinear'``
"""
with h5py.File(fname, 'r') as f:
......@@ -405,7 +406,7 @@ def readNonLinearX5(fname):
"""Read a nonlinear X5 transformation file from ``fname``.
:arg fname: File name to read from
:returns: A :class:`.DisplacementField` or :class:`.CoefficientField`
:returns: A :class:`.DeformationField`
"""
with h5py.File(fname, 'r') as f:
......@@ -432,7 +433,7 @@ def writeNonLinearX5(fname, field):
"""Write a nonlinear X5 transformation to ``fname``.
:arg fname: File name to write to
:arg field: A :class:`.DisplacementField` or :class:`.CoefficientField`
:arg field: A :class:`.DeformationField`
"""
with h5py.File(fname, 'w') as f:
......
......@@ -448,7 +448,7 @@ class _FileOrThing(object):
``dict``-like object, where the function's actual return value is
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
argument names used as keys. Any ``LOAD`` output arguments which were not
generated by the function will not be present in the dictionary.
......
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