ModelOpts.coordSpace now defaults to pixdim-flip, as this is what

FIRST outputs. Changed glmodel draw routine - I think, if the
vertex transformation has a positive determinant, the face order
needs to be inverted.

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' : [

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]]
             

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)

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',