diff --git a/fsl/fsleyes/controls/overlaydisplaypanel.py b/fsl/fsleyes/controls/overlaydisplaypanel.py
index 96d394199908b4b17ff3ea6bff965a621960c74a..21e968d9d211d197e3117a5680f8d58601f9ff84 100644
--- a/fsl/fsleyes/controls/overlaydisplaypanel.py
+++ b/fsl/fsleyes/controls/overlaydisplaypanel.py
@@ -392,7 +392,7 @@ _DISPLAY_PROPS = td.TypeDict({
# props.Widget('showName'),
props.Widget('coordSpace',
enabledWhen=lambda o, ri: ri != 'none',
- labels=strings.choices['Nifti1Opts.transform'],
+ labels=strings.choices['ModelOpts.coordSpace'],
dependencies=['refImage'])],
'TensorOpts' : [
diff --git a/fsl/fsleyes/displaycontext/modelopts.py b/fsl/fsleyes/displaycontext/modelopts.py
index 8ff9ff0a0faa8a887f7e739c13f29ea100c6f482..626adf98b05e6db9c0a35c11bd22a21cf1156850 100644
--- a/fsl/fsleyes/displaycontext/modelopts.py
+++ b/fsl/fsleyes/displaycontext/modelopts.py
@@ -9,8 +9,6 @@ for displaying :class:`.Model` overlays.
"""
-import copy
-
import numpy as np
import props
@@ -21,8 +19,6 @@ import fsl.fsleyes.colourmaps as colourmaps
import fsl.data.image as fslimage
import fsl.utils.transform as transform
-import volumeopts
-
class ModelOpts(fsldisplay.DisplayOpts):
"""The ``ModelOpts`` class defines settings for displaying :class:`.Model`
@@ -65,10 +61,37 @@ class ModelOpts(fsldisplay.DisplayOpts):
"""
- coordSpace = copy.copy(volumeopts.Nifti1Opts.transform)
+ # This property is implicitly tightly-coupled to
+ # the Nifti1Opts.getTransform method - the choices
+ # defined in this property are assumed to be valid
+ # inputs to that method.
+ coordSpace = props.Choice(('affine', 'pixdim', 'pixdim-flip', 'id'),
+ default='pixdim-flip')
"""If :attr:`refImage` is not ``None``, this property defines the
reference image coordinate space in which the model coordinates are
defined (i.e. voxels, scaled voxels, or world coordinates).
+
+ =============== =========================================================
+ ``affine`` The model coordinates are defined in the reference image
+ world coordinate system.
+
+ ``id`` The model coordinates are defined in the reference image
+ voxel coordinate system.
+
+ ``pixdim`` The model coordinates are defined in the reference image
+ voxel coordinate system, scaled by the voxel pixdims.
+
+ ``pixdim-flip`` The model coordinates are defined in the reference image
+ voxel coordinate system, scaled by the voxel pixdims. If
+ the reference image transformation matrix has a positive
+ determinant, the X axis is flipped.
+ =============== =========================================================
+
+ The default value is ``pixdim-flip``, as this is the coordinate system
+ used in the VTK sub-cortical segmentation model files output by FIRST.
+ See also the :ref:`note on coordinate systems
+ <volumeopts-coordinate-systems>`, and the :meth:`.Nifti1Opts.getTransform`
+ method.
"""
@@ -77,12 +100,6 @@ class ModelOpts(fsldisplay.DisplayOpts):
to the :class:`.DisplayOpts` constructor.
"""
- # The Nifti1Opts.transform property has a
- # 'custom' option which is not applicable
- # to our coordSpace property.
- coordSpace = self.getProp('coordSpace')
- coordSpace.removeChoice('custom', self)
-
# Create a random, highly
# saturated colour
colour = colourmaps.randomBrightColour()
@@ -162,11 +179,12 @@ class ModelOpts(fsldisplay.DisplayOpts):
the :class:`.Model` vertex coordinates into the display coordinate
system.
- If no :attr:`refImage` is selected, this method returns ``None``.
+ If no :attr:`refImage` is selected, this method returns an identity
+ transformation.
"""
if self.refImage is None:
- return None
+ return np.eye(4)
opts = self.displayCtx.getOpts(self.refImage)
@@ -346,11 +364,9 @@ class ModelOpts(fsldisplay.DisplayOpts):
lo, hi = self.overlay.getBounds()
xform = self.getCoordSpaceTransform()
- if xform is not None:
-
- lohi = transform.transform([lo, hi], xform)
- lohi.sort(axis=0)
- lo, hi = lohi[0, :], lohi[1, :]
+ lohi = transform.transform([lo, hi], xform)
+ lohi.sort(axis=0)
+ lo, hi = lohi[0, :], lohi[1, :]
self.bounds = [lo[0], hi[0], lo[1], hi[1], lo[2], hi[2]]
diff --git a/fsl/fsleyes/gl/glmodel.py b/fsl/fsleyes/gl/glmodel.py
index 0e348889ee4716e777f7d36b571e24ed68c7e74b..d11bbc8e621ffca7ed8ff1d3009882caf3c4cad0 100644
--- a/fsl/fsleyes/gl/glmodel.py
+++ b/fsl/fsleyes/gl/glmodel.py
@@ -9,8 +9,9 @@ to render :class:`.Model` overlays.
"""
-import numpy as np
-import OpenGL.GL as gl
+import numpy as np
+import numpy.linalg as npla
+import OpenGL.GL as gl
import globject
import fsl.utils.transform as transform
@@ -173,10 +174,9 @@ class GLModel(globject.GLObject):
vertices = self.overlay.vertices
indices = self.overlay.indices
+ xform = self.opts.getCoordSpaceTransform()
- xform = self.opts.getCoordSpaceTransform()
-
- if xform is not None:
+ if not np.all(xform == np.eye(4)):
vertices = transform.transform(vertices, xform)
self.vertices = np.array(vertices, dtype=np.float32)
@@ -330,16 +330,19 @@ class GLModel(globject.GLObject):
# plane.
gl.glStencilFunc(gl.GL_ALWAYS, 0, 0)
- # I don't understand why, but if any of the
- # display system axes are inverted, we need
- # to render the back faces first, otherwise
- # the cross-section mask will not be created
- # correctly.
+ # If the model coordinate transformation
+ # has a positive determinant, we need to
+ # render the back faces first, otherwise
+ # the cross-section mask will not be
+ # created correctly. Something to do with
+ # the vertex unwinding order, I guess.
direction = [gl.GL_INCR, gl.GL_DECR]
-
- if np.any(np.array(hi) < 0.0): faceOrder = [gl.GL_FRONT, gl.GL_BACK]
- else: faceOrder = [gl.GL_BACK, gl.GL_FRONT]
+ if npla.det(opts.getCoordSpaceTransform()) > 0:
+ faceOrder = [gl.GL_BACK, gl.GL_FRONT]
+ else:
+ faceOrder = [gl.GL_FRONT, gl.GL_BACK]
+
for face, direction in zip(faceOrder, direction):
gl.glStencilOp(gl.GL_KEEP, gl.GL_KEEP, direction)
diff --git a/fsl/fsleyes/strings.py b/fsl/fsleyes/strings.py
index 31030ec4b52f9f705ce0b620dba9f762388c465b..14bacad2a4e144f1b48ad88f921d17766dc8e959 100644
--- a/fsl/fsleyes/strings.py
+++ b/fsl/fsleyes/strings.py
@@ -416,16 +416,22 @@ labels = TypeDict({
'OverlayInfoPanel.MelodicImage' : 'NIFTI1 image '
'(MELODIC analysis)',
'OverlayInfoPanel.MelodicImage.melodicInfo' : 'MELODIC information',
- 'OverlayInfoPanel.Model' : 'VTK model',
- 'OverlayInfoPanel.Model.numVertices' : 'Number of vertices',
- 'OverlayInfoPanel.Model.numIndices' : 'Number of indices',
- 'OverlayInfoPanel.Model.displaySpace' : 'Display space',
- 'OverlayInfoPanel.Model.refImage' : 'Reference image',
- 'OverlayInfoPanel.Model.coordSpace' : 'Vertices defined in',
- 'OverlayInfoPanel.Model.coordSpace.id' : 'Voxels ({})',
- 'OverlayInfoPanel.Model.coordSpace.pixdim' : 'Scaled voxels ({})',
- 'OverlayInfoPanel.Model.coordSpace.affine' : 'World coordinates ({})',
- 'OverlayInfoPanel.Model.coordSpace.display' : 'Display coordinate system',
+
+ 'OverlayInfoPanel.Model' : 'VTK model',
+ 'OverlayInfoPanel.Model.numVertices' : 'Number of vertices',
+ 'OverlayInfoPanel.Model.numIndices' : 'Number of indices',
+ 'OverlayInfoPanel.Model.displaySpace' : 'Display space',
+ 'OverlayInfoPanel.Model.refImage' : 'Reference image',
+ 'OverlayInfoPanel.Model.coordSpace' : 'Vertices defined in',
+ 'OverlayInfoPanel.Model.coordSpace.id' : 'Voxels ({})',
+ 'OverlayInfoPanel.Model.coordSpace.pixdim' : 'Scaled voxels ({})',
+ 'OverlayInfoPanel.Model.coordSpace.pixdim-flip' : 'Scaled voxels forced '
+ 'to radiological '
+ 'orientation ({})',
+ 'OverlayInfoPanel.Model.coordSpace.affine' : 'World coordinates ({})',
+ 'OverlayInfoPanel.Model.coordSpace.display' : 'Display coordinate '
+ 'system',
+
'OverlayInfoPanel.dataSource' : 'Data source',
'OverlayInfoPanel.TensorImage' : 'NIFTI1 diffusion '
@@ -651,6 +657,12 @@ choices = TypeDict({
'ModelOpts.refImage.none' : 'No reference image',
+ 'ModelOpts.coordSpace' : {'affine' : 'World coordinates',
+ 'pixdim' : 'Scaled voxels',
+ 'pixdim-flip' : 'Scaled voxels forced to '
+ 'radiological orientation',
+ 'id' : 'Voxels'},
+
'TensorOpts.tensorResolution.min' : 'Low',
'TensorOpts.tensorResolution.max' : 'High',