Merge branch 'rf/scaledvoxel' into 'master'

BF: Use 'pixdim' affine for scaled voxel display space, not 'pixdim-flip', as the latter will potentially L/R flip some images

See merge request fsl/fsleyes/fsleyes!289

CHANGELOG.rst

@@ -9,6 +9,18 @@ This document contains the ``fsleyes`` release history in reverse
 chronological order.
 
 
+1.2.1 (Under development)
+-------------------------
+
+
+Fixed
+^^^^^
+
+* The **Display space** |right_arrow| *Scaled voxel coordinates* setting no
+  longer applies a L/R flip for images with neurological data storage order
+  (!289).
+
+
 1.2.0 (Monday 13th September 2021)
 ----------------------------------
 

fsleyes/displaycontext/displaycontext.py

@@ -185,7 +185,7 @@ class DisplayContext(props.SyncableHasProperties):
        system, with origin set to the centre of voxel ``(0, 0, 0)``, and
        voxels scaled by image pixdims. This is accomplished by setting the
        :attr:`.NiftiOpts.transform` property for every ``Nifti`` overlay to
-       ``pixdim-flip``.
+       ``pixdim``.
 
     3. **Reference image** space
 
@@ -533,7 +533,10 @@ class DisplayContext(props.SyncableHasProperties):
         # (reference image), we decide based on the ref
         # image.
         elif space == 'scaledVoxel':
-            space = self.getSelectedOverlay()
+            space    = self.getSelectedOverlay()
+            srcSpace = 'pixdim'
+        else:
+            srcSpace = 'pixdim-flip'
 
         # Use the FSL / FLIRT convention - if the affine
         # determinant is negative, assume neurological
@@ -542,7 +545,7 @@ class DisplayContext(props.SyncableHasProperties):
             ref = self.getOpts(space).referenceImage
             if ref is not None:
                 opts  = self.getOpts(space)
-                xform = opts.getTransform('pixdim-flip', 'display')
+                xform = opts.getTransform(srcSpace, 'display')
                 return npla.det(xform) > 0
 
         # no nifti overlays loaded
@@ -901,7 +904,7 @@ class DisplayContext(props.SyncableHasProperties):
         # listener on the bounds property.
         with props.skip(opts, 'bounds', self.__name, ignoreInvalid=True):
             if   space == 'world':       opts.transform = 'affine'
-            elif space == 'scaledVoxel': opts.transform = 'pixdim-flip'
+            elif space == 'scaledVoxel': opts.transform = 'pixdim'
             elif image is space:         opts.transform = 'pixdim-flip'
             else:                        opts.transform = 'reference'
 
@@ -1168,7 +1171,7 @@ class DisplayContext(props.SyncableHasProperties):
 
         if self.displaySpace == 'scaledVoxel':
             ref      = self.getSelectedOverlay()
-            srcSpace = 'pixdim-flip'
+            srcSpace = 'pixdim'
         else:
             ref      = self.displaySpace
             srcSpace = 'display'

fsleyes/displaycontext/niftiopts.py

@@ -36,7 +36,8 @@ in one of several ways:
                                 image appears to be stored in neurological
                                 order, the X (left-right) axis is
                                 inverted. The origin is fixed at the centre of
-                                voxel ``(0, 0, 0)``.
+                                voxel ``(0, 0, 0)`` (or ``(X-1, 0, 0)`` for
+                                 inverted images).
 
  **world**                      (a.k.a. ``affine``) The image data voxel
                                 coordinates are transformed by the
@@ -445,7 +446,7 @@ class NiftiOpts(fsldisplay.DisplayOpts):
         if ds == 'world':
             voxToRefMat = voxToWorldMat
         elif ds == 'scaledVoxel':
-            voxToRefMat = voxToPixFlipMat
+            voxToRefMat = voxToPixdimMat
         elif ds is self.overlay:
             voxToRefMat = voxToPixFlipMat
         else:

fsleyes/tests/__init__.py

@@ -672,6 +672,40 @@ def fliporient(filename):
     return outfile
 
 
+def swapdim(filename, d0, d1, d2):
+
+    indices = { 'x' : 0, '-x' : 0,
+                'y' : 1, '-y' : 1,
+                'z' : 2, '-z' : 2}
+    base    = fslimage.removeExt(filename)
+    outfile = '{}_swapdim_{}_{}_{}'.format(base, d0, d1, d2)
+    img     = fslimage.Image(filename)
+
+    s0, s1, s2 = [-1 if d.startswith('-') else 1 for d in (d0, d1, d2)]
+    d0, d1, d2 = [indices[d]                     for d in (d0, d1, d2)]
+
+    if len(img.shape) == 3:
+        order = (d0, d1, d2)
+    else:
+        order =  (d0, d1, d2) + tuple(range(3, len(img.shape)))
+
+    data = img.data
+    if s0 < 0: data = np.flip(data, d0)
+    if s1 < 0: data = np.flip(data, d1)
+    if s2 < 0: data = np.flip(data, d2)
+    data = data.transpose(order)
+
+    aff        = np.zeros((4, 4))
+    aff[0, d0] = s0
+    aff[1, d1] = s1
+    aff[2, d2] = s2
+    aff[3, 3]  = 1
+    aff        = affine.concat(aff, img.voxToWorldMat)
+
+    img = fslimage.Image(data, xform=aff)
+    img.save(outfile)
+    return outfile
+
 
 def roi(fname, roi):
 

fsleyes/tests/test_displayspace.py

@@ -7,7 +7,7 @@
 
 import pytest
 
-from fsleyes.tests import run_cli_tests, resampled, roi, rotate
+from fsleyes.tests import run_cli_tests, resampled, roi, rotate, swapdim
 
 
 pytestmark = pytest.mark.clitest
@@ -24,6 +24,16 @@ tests = """
 -ds 3d_rotated_20_20_20 3d {{rotate('3d', 20, 20, 20)}} -cm red-yellow -a 50
 -ds world               3d {{rotate('3d', 20, 20, 20)}} -cm red-yellow -a 50
 -ds scaledVoxel         3d {{rotate('3d', 20, 20, 20)}} -cm red-yellow -a 50
+
+-ds 3d                  3d {{swapdim('3d', '-x', 'y', 'z')}}                 -cm red-yellow -a 50
+-ds 3d_swapdim_-x_y_z   3d {{swapdim('3d', '-x', 'y', 'z')}}                 -cm red-yellow -a 50
+-ds scaledVoxel         3d {{swapdim('3d', '-x', 'y', 'z')}}                 -cm red-yellow -a 50
+-ds world               3d {{swapdim('3d', '-x', 'y', 'z')}}                 -cm red-yellow -a 50
+
+-ds 3d                              3d {{resampled(swapdim('3d', '-x', 'y', 'z'), 0.5)}} -cm red-yellow -a 50
+-ds 3d_swapdim_-x_y_z_resampled_0.5 3d {{resampled(swapdim('3d', '-x', 'y', 'z'), 0.5)}} -cm red-yellow -a 50
+-ds scaledVoxel                     3d {{resampled(swapdim('3d', '-x', 'y', 'z'), 0.5)}} -cm red-yellow -a 50
+-ds world                           3d {{resampled(swapdim('3d', '-x', 'y', 'z'), 0.5)}} -cm red-yellow -a 50
 """
 
 
@@ -31,6 +41,7 @@ def test_displayspace():
     extras = {
         'roi'       : roi,
         'resampled' : resampled,
-        'rotate'    : rotate
+        'rotate'    : rotate,
+        'swapdim'   : swapdim
     }
     run_cli_tests('test_displayspace', tests, extras=extras)