Work with tracker coordinate system where stylus points in x-axis as …

…opposed to y-axis

invesalius/data/coregistration.py

@@ -190,8 +190,11 @@ def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id, icp=[None, N
     m_img = m_change @ m_probe_ref
     m_img = apply_icp(m_img, icp)
 
+    # Rotate from trk system where stylus points in x-axis to vtk-system where stylus points in y-axis
+    R = tr.euler_matrix(*np.radians([0, 0, -90]), axes="rxyz")[:3, :3]
+
     # rotate m_probe_ref from tracker to image space
-    r_img = r_stylus @ m_probe_ref[:3, :3]
+    r_img = r_stylus @ R @ m_probe_ref[:3, :3] @ np.linalg.inv(R)
     m_img[:3, :3] = r_img[:3, :3]
 
     # compute rotation angles

invesalius/navigation/navigation.py

@@ -441,9 +441,12 @@ def SetStylusOrientation(self, coord_raw):
             # up_vtk: orientation 'stylus pointing up along head' in vtk space
             up_vtk = tr.euler_matrix(*np.radians([90.0, 0.0, 0.0]), axes="rxyz")[:3, :3]
 
-            # Rotation from tracker to VTK coordinate system
-            self.r_stylus = up_vtk @ np.linalg.inv(up_trk)
+            # Rotate 90 degrees around z-axis from trk system where stylus points in x-axis
+            # to vtk-system where stylus points in y-axis
+            R = tr.euler_matrix(*np.radians([0, 0, -90]), axes="rxyz")[:3, :3]
 
+            # Rotation from tracker to VTK coordinate system
+            self.r_stylus = up_vtk @ np.linalg.inv(R @ up_trk @ np.linalg.inv(R))
             # Save r_stylus to config file
             session = ses.Session()
             if (nav_config := session.GetConfig("navigation")) is not None: