fix: Rotation applied in surface_image_stencil() based on image orien…

…tation

src/deepali/utils/vtk/image.py

@@ -8,7 +8,6 @@
     vtkImageData,
     vtkImageStencilData,
     vtkImageStencilToImage,
-    vtkMatrixToLinearTransform,
     vtkPolyData,
     vtkPolyDataToImageStencil,
     vtkTransformPolyDataFilter,
@@ -41,30 +40,33 @@ def surface_mesh_grid(*mesh: vtkPolyData, resolution: Optional[float] = None) ->
     )
 
 
-def surface_image_stencil(mesh: vtkPolyData, grid: Grid) -> vtkImageStencilData:
-    r"""Convert vtkPolyData surface mesh to image stencil."""
-    max_index = [n - 1 for n in grid.size().tolist()]
-
-    rot = np.eye(4, dtype=np.float)
-    rot[:3, :3] = np.array(grid.direction).reshape(3, 3)
-    rot = numpy_to_vtk_matrix4x4(rot)
-
-    transform = vtkMatrixToLinearTransform()
-    transform.SetInput(rot)
+def surface_image_stencil(mesh: vtkPolyData, grid: GridAttrs) -> vtkImageStencilData:
+    r"""Convert vtkPolyData surface mesh to image stencil."""    
+    # Create the transform
+    transform = vtkTransform()
+    transform.Translate(grid.center)
+    transform.Concatenate(numpy_to_vtk_matrix4x4(grid.dcm.T))  # type: ignore
+    transform.Translate(tuple(-x for x in grid.center))
 
+    # Apply the transform to the polydata
     transformer = vtkTransformPolyDataFilter()
     transformer.SetInputData(mesh)
     transformer.SetTransform(transform)
-
-    converter = vtkPolyDataToImageStencil()
-    converter.SetInputConnection(transformer.GetOutputPort())
-    converter.SetOutputOrigin(grid.origin().tolist())
-    converter.SetOutputSpacing(grid.spacing().tolist())
-    converter.SetOutputWholeExtent([0, max_index[0], 0, max_index[1], 0, max_index[2]])
-    converter.Update()
-
+    transformer.Update()
+
+    # Convert the transformed polydata to an image stencil
+    grid_extent = [0, grid.size[0] - 1, 0, grid.size[1] - 1, 0, grid.size[2] - 1]
+    grid_no_direction = GridAttrs(size=grid.size, spacing=grid.spacing, center=grid.center)
+    polydata_to_stencil = vtkPolyDataToImageStencil()
+    polydata_to_stencil.SetInputConnection(transformer.GetOutputPort())
+    polydata_to_stencil.SetOutputOrigin(grid_no_direction.origin)
+    polydata_to_stencil.SetOutputSpacing(grid.spacing)
+    polydata_to_stencil.SetOutputWholeExtent(grid_extent)
+    polydata_to_stencil.Update()
+
+    # Get the output stencil
     stencil = vtkImageStencilData()
-    stencil.DeepCopy(converter.GetOutput())
+    stencil.DeepCopy(polydata_to_stencil.GetOutput())
     return stencil