From 09762d6cea5c80dbe77a655aa4f3becde1d98817 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Sat, 2 Apr 2016 13:54:05 +0100
Subject: [PATCH] Nifti1Opts stores pixdim-flip transformations (scaled voxels,
forced to radiological orientation). This is to be used by ModelOpts soon.
---
fsl/fsleyes/displaycontext/volumeopts.py | 165 +++++++++++++++--------
1 file changed, 110 insertions(+), 55 deletions(-)
diff --git a/fsl/fsleyes/displaycontext/volumeopts.py b/fsl/fsleyes/displaycontext/volumeopts.py
index b9e00c026..489cea05a 100644
--- a/fsl/fsleyes/displaycontext/volumeopts.py
+++ b/fsl/fsleyes/displaycontext/volumeopts.py
@@ -9,6 +9,7 @@
.. _volumeopts-coordinate-systems:
+
---------------------------------------
An important note on coordinate systems
---------------------------------------
@@ -72,7 +73,8 @@ to the centre of a voxel.
import logging
-import numpy as np
+import numpy as np
+import numpy.linalg as npla
import props
@@ -238,50 +240,79 @@ class Nifti1Opts(fsldisplay.DisplayOpts):
image = self.overlay
- voxToIdMat = np.eye(4)
- voxToPixdimMat = np.diag(list(image.pixdim[:3]) + [1.0])
- voxToAffineMat = image.voxToWorldMat.T
- voxToCustomMat = self.customXform
-
- idToVoxMat = transform.invert(voxToIdMat)
- idToPixdimMat = transform.concat(idToVoxMat, voxToPixdimMat)
- idToAffineMat = transform.concat(idToVoxMat, voxToAffineMat)
- idToCustomMat = transform.concat(idToVoxMat, voxToCustomMat)
-
- pixdimToVoxMat = transform.invert(voxToPixdimMat)
- pixdimToIdMat = transform.concat(pixdimToVoxMat, voxToIdMat)
- pixdimToAffineMat = transform.concat(pixdimToVoxMat, voxToAffineMat)
- pixdimToCustomMat = transform.concat(pixdimToVoxMat, voxToCustomMat)
-
- affineToVoxMat = image.worldToVoxMat.T
- affineToIdMat = transform.concat(affineToVoxMat, voxToIdMat)
- affineToPixdimMat = transform.concat(affineToVoxMat, voxToPixdimMat)
- affineToCustomMat = transform.concat(affineToVoxMat, voxToCustomMat)
-
- customToVoxMat = transform.invert(voxToCustomMat)
- customToIdMat = transform.concat(customToVoxMat, voxToIdMat)
- customToPixdimMat = transform.concat(customToVoxMat, voxToPixdimMat)
- customToAffineMat = transform.concat(customToVoxMat, voxToAffineMat)
-
- self.__xforms['id', 'id'] = np.eye(4)
- self.__xforms['id', 'pixdim'] = idToPixdimMat
- self.__xforms['id', 'affine'] = idToAffineMat
- self.__xforms['id', 'custom'] = idToCustomMat
-
- self.__xforms['pixdim', 'pixdim'] = np.eye(4)
- self.__xforms['pixdim', 'id'] = pixdimToIdMat
- self.__xforms['pixdim', 'affine'] = pixdimToAffineMat
- self.__xforms['pixdim', 'custom'] = pixdimToCustomMat
+ voxToIdMat = np.eye(4)
+ voxToPixdimMat = np.diag(list(image.pixdim[:3]) + [1.0])
+ voxToPixFlipMat = np.array(voxToPixdimMat)
+ voxToAffineMat = image.voxToWorldMat.T
+ voxToCustomMat = self.customXform
+
+ # pixdim-flip space differs from
+ # pixdim space only if the affine
+ # matrix has a positive determinant
+ if npla.det(voxToAffineMat) > 0:
+ x = image.shape[0]
+ flip = transform.scaleOffsetXform([-1, 1, 1], [x, 0, 0])
+ voxToPixFlipMat = transform.concat(voxToPixFlipMat, flip)
+
+ idToVoxMat = transform.invert(voxToIdMat)
+ idToPixdimMat = transform.concat(idToVoxMat, voxToPixdimMat)
+ idToPixFlipMat = transform.concat(idToVoxMat, voxToPixFlipMat)
+ idToAffineMat = transform.concat(idToVoxMat, voxToAffineMat)
+ idToCustomMat = transform.concat(idToVoxMat, voxToCustomMat)
+
+ pixdimToVoxMat = transform.invert(voxToPixdimMat)
+ pixdimToIdMat = transform.concat(pixdimToVoxMat, voxToIdMat)
+ pixdimToPixFlipMat = transform.concat(pixdimToVoxMat, voxToPixFlipMat)
+ pixdimToAffineMat = transform.concat(pixdimToVoxMat, voxToAffineMat)
+ pixdimToCustomMat = transform.concat(pixdimToVoxMat, voxToCustomMat)
+
+ pixFlipToVoxMat = transform.invert(voxToPixFlipMat)
+ pixFlipToIdMat = transform.concat(pixFlipToVoxMat, voxToIdMat)
+ pixFlipToPixdimMat = transform.concat(pixFlipToVoxMat, voxToPixdimMat)
+ pixFlipToAffineMat = transform.concat(pixFlipToVoxMat, voxToAffineMat)
+ pixFlipToCustomMat = transform.concat(pixFlipToVoxMat, voxToCustomMat)
+
+ affineToVoxMat = image.worldToVoxMat.T
+ affineToIdMat = transform.concat(affineToVoxMat, voxToIdMat)
+ affineToPixdimMat = transform.concat(affineToVoxMat, voxToPixdimMat)
+ affineToPixFlipMat = transform.concat(affineToVoxMat, voxToPixFlipMat)
+ affineToCustomMat = transform.concat(affineToVoxMat, voxToCustomMat)
+
+ customToVoxMat = transform.invert(voxToCustomMat)
+ customToIdMat = transform.concat(customToVoxMat, voxToIdMat)
+ customToPixdimMat = transform.concat(customToVoxMat, voxToPixdimMat)
+ customToPixFlipMat = transform.concat(customToVoxMat, voxToPixFlipMat)
+ customToAffineMat = transform.concat(customToVoxMat, voxToAffineMat)
+
+ self.__xforms['id', 'id'] = np.eye(4)
+ self.__xforms['id', 'pixdim'] = idToPixdimMat
+ self.__xforms['id', 'pixdim-flip'] = idToPixFlipMat
+ self.__xforms['id', 'affine'] = idToAffineMat
+ self.__xforms['id', 'custom'] = idToCustomMat
+
+ self.__xforms['pixdim', 'pixdim'] = np.eye(4)
+ self.__xforms['pixdim', 'id'] = pixdimToIdMat
+ self.__xforms['pixdim', 'pixdim-flip'] = pixdimToPixFlipMat
+ self.__xforms['pixdim', 'affine'] = pixdimToAffineMat
+ self.__xforms['pixdim', 'custom'] = pixdimToCustomMat
+
+ self.__xforms['pixdim-flip', 'pixdim-flip'] = np.eye(4)
+ self.__xforms['pixdim-flip', 'id'] = pixFlipToIdMat
+ self.__xforms['pixdim-flip', 'pixdim'] = pixFlipToPixdimMat
+ self.__xforms['pixdim-flip', 'affine'] = pixFlipToAffineMat
+ self.__xforms['pixdim-flip', 'custom'] = pixFlipToCustomMat
- self.__xforms['affine', 'affine'] = np.eye(4)
- self.__xforms['affine', 'id'] = affineToIdMat
- self.__xforms['affine', 'pixdim'] = affineToPixdimMat
- self.__xforms['affine', 'custom'] = affineToCustomMat
+ self.__xforms['affine', 'affine'] = np.eye(4)
+ self.__xforms['affine', 'id'] = affineToIdMat
+ self.__xforms['affine', 'pixdim'] = affineToPixdimMat
+ self.__xforms['affine', 'pixdim-flip'] = affineToPixFlipMat
+ self.__xforms['affine', 'custom'] = affineToCustomMat
- self.__xforms['custom', 'custom'] = np.eye(4)
- self.__xforms['custom', 'id'] = customToIdMat
- self.__xforms['custom', 'pixdim'] = customToPixdimMat
- self.__xforms['custom', 'affine'] = customToAffineMat
+ self.__xforms['custom', 'custom'] = np.eye(4)
+ self.__xforms['custom', 'id'] = customToIdMat
+ self.__xforms['custom', 'pixdim'] = customToPixdimMat
+ self.__xforms['custom', 'pixdim-flip'] = customToPixFlipMat
+ self.__xforms['custom', 'affine'] = customToAffineMat
def getTransform(self, from_, to, xform=None):
@@ -290,29 +321,51 @@ class Nifti1Opts(fsldisplay.DisplayOpts):
are:
- =========== ======================================================
- ``id`` Voxel coordinates
+ =============== ======================================================
+ ``id`` Voxel coordinates
- ``voxel`` Equivalent to ``id``.
+ ``voxel`` Equivalent to ``id``.
- ``pixdim`` Voxel coordinates, scaled by voxel dimensions
+ ``pixdim`` Voxel coordinates, scaled by voxel dimensions
+
+ ``pixdim-flip`` Voxel coordinates, scaled by voxel dimensions, and
+ with the X axis flipped if the affine matrix has
+ a positivie determinant. If the affine matrix does
+ not have a positive determinant, this is equivalent to
+ ``pixdim``.
+
+ ``pixflip`` Equivalent to ``pixdim-flip``.
- ``affine`` World coordinates, as defined by the NIFTI1
- ``qform``/``sform``. See :attr:`.Image.voxToWorldMat`.
+ ``affine`` World coordinates, as defined by the NIFTI1
+ ``qform``/``sform``. See :attr:`.Image.voxToWorldMat`.
- ``world`` Equivalent to ``affine``.
+ ``world`` Equivalent to ``affine``.
- ``custom`` Coordinates in the space defined by the custom
- transformation matrix, as specified via the
- :attr:`customXform` property.
+ ``custom`` Coordinates in the space defined by the custom
+ transformation matrix, as specified via the
+ :attr:`customXform` property.
- ``display`` Equivalent to the current value of :attr:`transform`.
- =========== ======================================================
+ ``display`` Equivalent to the current value of :attr:`transform`.
+ =============== ======================================================
If the ``xform`` parameter is provided, and one of ``from_`` or ``to``
is ``display``, the value of ``xform`` is used instead of the current
value of :attr:`transform`.
+
+
+ .. note:: While the ``pixdim-flip`` space is not a display option for
+ ``Nifti1``, the transformations for this space are made
+ available theough this method as it is the coordinate system
+ used internally by many of the FSL tools. Most importantly,
+ this is the coordinate system used in the VTK sub-cortical
+ segmentation model files output by FIRST, and is hence used
+ by the :class:`.ModelOpts` class to transform VTK model
+ coordinates.
+
+ http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ#What_is_the_\
+ format_of_the_matrix_used_by_FLIRT.2C_and_how_does_it_\
+ relate_to_the_transformation_parameters.3F
"""
if xform is None:
@@ -321,10 +374,12 @@ class Nifti1Opts(fsldisplay.DisplayOpts):
if from_ == 'display': from_ = xform
elif from_ == 'world': from_ = 'affine'
elif from_ == 'voxel': from_ = 'id'
+ elif from_ == 'pixflip': from_ = 'pixdim-flip'
if to == 'display': to = xform
elif to == 'world': to = 'affine'
elif to == 'voxel': to = 'id'
+ elif to == 'pixflip': to = 'pixdim-flip'
return self.__xforms[from_, to]
--
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