diff --git a/fsl/data/image.py b/fsl/data/image.py
index ec8b9fd39c6852785c091c83be789b72049ec0a7..08543981bd3c4f81687c8a65ee0a6e2f8edd83a8 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -87,6 +87,55 @@ class Nifti(notifier.Notifier):
================= ====================================================
+ The ``header`` field may either be a ``nifti1``, ``nifti2``, or
+ ``analyze`` header object. Make sure to take this into account if you are
+ writing code that should work with all three. Use the :meth:`niftiVersion`
+ property if you need to know what type of image you are dealing with.
+
+
+ The ``shape`` attribute may not precisely match the image shape as
+ reported in the NIFTI header, because trailing dimensions of size 1 are
+ squeezed out. See the :meth:`__determineShape` and :meth:`mapIndices`
+ methods.
+
+
+ **The affine transformation**
+
+
+ The :meth:`voxToWorldMat` and :meth:`worldToVoxMat` attributes contain
+ transformation matrices for transforming between voxel and world
+ coordinates. The ``Nifti`` class follows the same process as ``nibabel``
+ in selecting the affine (see
+ http://nipy.org/nibabel/nifti_images.html#the-nifti-affines):
+
+
+ 1. If ``sform_code != 0`` ("unknown") use the sform affine; else
+ 2. If ``qform_code != 0`` ("unknown") use the qform affine; else
+ 3. Use the fall-back affine.
+
+
+ However, the *fall-back* affine used by the ``Nifti`` class differs to
+ that used by ``nibabel``. In ``nibabel``, the origin (world coordinates
+ (0, 0, 0)) is set to the centre of the image. Here in the ``Nifti``
+ class, we set the world coordinate orign to be the corner of the image,
+ i.e. the corner of voxel (0, 0, 0).
+
+
+ You may change the ``voxToWorldMat`` of a ``Nifti`` instance (unless it
+ is an Analyze image). When you do so:
+
+ - Only the ``sform`` of the underlying ``Nifti1Header`` object is changed
+
+ - The ``qform`` is not modified.
+
+ - If the ``sform_code`` was previously set to ``NIFTI_XFORM_UNKNOWN``,
+ it is changed to ``NIFTI_XFORM_ALIGNED_ANAT``. Otherwise, the
+ ``sform_code`` is not modified.
+
+
+ **ANALYZE support**
+
+
A ``Nifti`` instance expects to be passed either a
``nibabel.nifti1.Nifti1Header`` or a ``nibabel.nifti2.Nifti2Header``, but
can als encapsulate a ``nibabel.analyze.AnalyzeHeader``. In this case:
@@ -104,6 +153,9 @@ class Nifti(notifier.Notifier):
:attr:`.constants.NIFTI_XFORM_ANALYZE`.
+ **Notification**
+
+
The ``Nifti`` class implements the :class:`.Notifier` interface -
listeners may register to be notified on the following topics:
@@ -111,19 +163,6 @@ class Nifti(notifier.Notifier):
``'transform'`` The affine transformation matrix has changed. This topic
will occur when the ``voxToWorldMat`` is changed.
=============== ========================================================
-
-
- .. warning:: The ``header`` field may either be a ``nifti1``, ``nifti2``,
- or ``analyze`` header object. Make sure to take this into
- account if you are writing code that should work with all
- three. Use the :meth:`niftiVersion` property if you need to
- know what type of image you are dealing with.
-
-
- .. note:: The ``shape`` attribute may not precisely match the image shape
- as reported in the NIFTI header, because trailing dimensions of
- size 1 are squeezed out. See the :meth:`__determineShape` and
- :meth:`mapIndices` methods.
"""
@@ -294,19 +333,27 @@ class Nifti(notifier.Notifier):
@voxToWorldMat.setter
def voxToWorldMat(self, xform):
- """Update the ``voxToWorldMat``. The ``worldToVoxMat`` and ``pixdim``
- values are also updated. This will result in notification on the
- ``'transform'`` topic.
+ """Update the ``voxToWorldMat``. The ``worldToVoxMat`` value is also
+ updated. This will result in notification on the ``'transform'``
+ topic.
"""
- header = self.header
+ # Can't do much with
+ # an analyze image
+ if self.niftiVersion == 0:
+ raise Exception('voxToWorldMat cannot be '
+ 'changed for an ANALYZE image')
+
+ header = self.header
+ sformCode = header['sform_code']
- header.set_qform(xform)
- header.set_sform(xform)
+ if sformCode == constants.NIFTI_XFORM_UNKNOWN:
+ sformCode = constants.NIFTI_XFORM_ALIGNED_ANAT
+
+ header.set_sform(xform, code=sformCode)
self.__voxToWorldMat = self.__determineTransform(header)
self.__worldToVoxMat = transform.invert(self.__voxToWorldMat)
- self.__pixdim = header.get_zooms()
log.debug('Affine changed:\npixdims: '
'{}\nsform: {}\nqform: {}'.format(
@@ -366,12 +413,11 @@ class Nifti(notifier.Notifier):
if code is not None:
code = self.header[code]
- # If a specific code is not
- # specified, we check both.
- # If the sform is present,
- # we return it. Otherwise,
- # if the qform is present,
- # we return that.
+ # If the caller did not specify
+ # a code, we check both. If the
+ # sform is present, we return it.
+ # Otherwise, if the qform is
+ # present, we return that.
else:
sform_code = self.header['sform_code']
@@ -574,7 +620,7 @@ class Image(Nifti):
:arg name: A name for the image.
- :arg header: If not ``None``, assumed to be a
+ :arg header: If not ``None``, assumed to be a
:class:`nibabel.nifti1.Nifti1Header` or
:class:`nibabel.nifti2.Nifti2Header` to be used as the
image header. Not applied to images loaded from file,
@@ -582,8 +628,10 @@ class Image(Nifti):
:arg xform: A :math:`4\\times 4` affine transformation matrix
which transforms voxel coordinates into real world
- coordinates. Only used if ``image`` is a ``numpy``
- array, and ``header`` is ``None``.
+ coordinates. If not provided, and a ``header`` is
+ provided, the transformation in the header is used.
+ If neither a ``xform`` nor a ``header`` are provided,
+ an identity matrix is used.
:arg loadData: If ``True`` (the default) the image data is loaded
in to memory. Otherwise, only the image header
@@ -681,6 +729,10 @@ class Image(Nifti):
Nifti.__init__(self, nibImage.get_header())
+ print name
+ print self.voxToWorldMat
+
+
self.name = name
self.__lName = '{}_{}'.format(id(self), self.name)
self.__dataSource = dataSource
@@ -801,9 +853,9 @@ class Image(Nifti):
Nifti.voxToWorldMat.fset(self, xform)
xform = self.voxToWorldMat
+ code = self.header['sform_code']
- self.__nibImage.set_sform(xform)
- self.__nibImage.set_qform(xform)
+ self.__nibImage.set_sform(xform, code)
def __transformChanged(self, *args, **kwargs):