Show coil center/target even when coil is hidden. Handle exceptions w…

…hen loading state file. Update environment.yml. Minor refactors ie. naming changes.

environment.yml

@@ -30,7 +30,7 @@ dependencies:
     - pyclaron
     - polhemusFT
     - polhemus
-    - pypolaris==0.0.7
+    - pypolaris==0.0.8
     - scikit-image==0.24.0
     - scikit-learn==1.5.0
     - Trekker==0.9

invesalius/data/viewer_volume.py

@@ -309,12 +309,11 @@ def __init__(self, parent):
         # An object to manage visualizing coils in the 3D viewer.
         self.coil_visualizer = CoilVisualizer(
             renderer=self.ren,
-            interactor=self.interactor,
             actor_factory=self.actor_factory,
             vector_field_visualizer=self.vector_field_visualizer,
         )
 
-        self.probe_visualizer = ProbeVisualizer(self.ren, self.interactor)
+        self.probe_visualizer = ProbeVisualizer(self.ren)
 
         self.seed_offset = const.SEED_OFFSET
         self.radius_list = vtkIdList()

invesalius/data/visualization/coil_visualizer.py

@@ -22,9 +22,8 @@ class CoilVisualizer:
     # Color for the marker for target when the coil at the target.
     COIL_AT_TARGET_COLOR = vtk.vtkNamedColors().GetColor3d("Green")
 
-    def __init__(self, renderer, interactor, actor_factory, vector_field_visualizer):
+    def __init__(self, renderer, actor_factory, vector_field_visualizer):
         self.renderer = renderer
-        self.interactor = interactor
         self.tracker = Tracker()
 
         # Keeps track of whether tracker fiducials have been set.
@@ -96,7 +95,7 @@ def UpdateVectorField(self):
 
         # If not navigating, render the scene.
         if not self.is_navigating:
-            self.interactor.Render()
+            Publisher.sendMessage("Render volume viewer")
 
     def SetCoilAtTarget(self, state):
         self.coil_at_target = state
@@ -119,14 +118,14 @@ def ShowCoil(self, state, coil_name=None):
         if coil_name is None:  # Show/hide all coils
             for coil in self.coils.values():
                 coil["actor"].SetVisibility(state)
-                coil["center_actor"].SetVisibility(state)
+                coil["center_actor"].SetVisibility(True)  # Always show the center donut actor
             if self.target_coil_actor is not None:  # LUKATODO: target mode...
-                self.target_coil_actor.SetVisibility(state)
+                self.target_coil_actor.SetVisibility(True)  # Keep target visible for now
         elif (coil := self.coils.get(coil_name, None)) is not None:
             # Just toggle the visibility when dealing with specific coils
             new_state = not coil["actor"].GetVisibility()
             coil["actor"].SetVisibility(new_state)
-            coil["center_actor"].SetVisibility(new_state)
+            coil["center_actor"].SetVisibility(True)  # Always show the center donut actor
 
             # If all coils are hidden/shown, update the color of Show-coil button
             coils_visible = [coil["actor"].GetVisibility() for coil in self.coils.values()]
@@ -138,7 +137,7 @@ def ShowCoil(self, state, coil_name=None):
         # self.vector_field_assembly.SetVisibility(state) # LUKATODO: Keep this hidden for now
 
         if not self.is_navigating:
-            self.interactor.Render()
+            Publisher.sendMessage("Render volume viewer")
 
     def AddTargetCoil(self, m_target):
         self.RemoveTargetCoil()
@@ -191,7 +190,7 @@ def AddTargetCoil(self, m_target):
         self.renderer.AddActor(self.target_coil_actor)
 
         if not self.is_navigating:
-            self.interactor.Render()
+            Publisher.sendMessage("Render volume viewer")
 
     def RemoveTargetCoil(self):
         if self.target_coil_actor is None:
@@ -274,7 +273,7 @@ def RemoveCoil(self, coil_name=None):
 
         # self.vector_field_assembly.SetVisibility(0)
         if not self.is_navigating:
-            self.interactor.Render()
+            Publisher.sendMessage("Render volume viewer")
 
     def ResetCoilVisualizer(self, n_coils):
         self.RemoveCoil()  # Remove all coils

invesalius/data/visualization/probe_visualizer.py

@@ -12,9 +12,8 @@ class ProbeVisualizer:
     A class for visualizing probe in the volume viewer.
     """
 
-    def __init__(self, renderer, interactor):
+    def __init__(self, renderer):
         self.renderer = renderer
-        self.interactor = interactor
 
         self.probe_actor = None
         self.probe_path = os.path.join(inv_paths.OBJ_DIR, "stylus.stl")
@@ -38,7 +37,7 @@ def ShowProbe(self, state):
         if self.probe_actor:
             self.probe_actor.SetVisibility(self.show_probe)
             if not self.is_navigating:
-                self.interactor.Render()
+                Publisher.sendMessage("Render volume viewer")
 
     def AddProbeActor(self, probe_path):
         vtk_colors = vtk.vtkNamedColors()

invesalius/gui/preferences.py

@@ -851,7 +851,7 @@ def DeleteCoil(event, name):
             (lambda event, name=name: self.OnSaveCoilToOBR(event, coil_name=name)),
             save_coil,
         )
-        self.PopupMenu(menu, event.GetPosition())
+        self.PopupMenu(menu)
         menu.Destroy()
 
     def OnCreateNewCoil(self, event=None):

invesalius/gui/task_navigator.py

@@ -1080,7 +1080,7 @@ def onRecord(self, evt):
         )
 
         if marker_visibilities[0] and marker_visibilities[1]:  # if probe and head are visible
-            if self.navigation.SetStylusOrientation(coord_raw) and not self.done:
+            if self.navigation.OnRecordStylusOrientation(coord_raw) and not self.done:
                 # if successfully created r_stylus in navigation for the first time: make the illustration green to show success
                 self.done = True
                 self.help.Destroy()  # show a colored (green) bitmap as opposed to grayscale
@@ -2060,7 +2060,10 @@ def __init__(self, parent, nav_hub):
         )
 
         # In the future, it would be better if the panel could initialize itself based on markers in MarkersControl
-        self.markers.LoadState()
+        try:
+            self.markers.LoadState()
+        except:
+            self.session.DeleteStateFile()  # Delete state file if it is erroneous
 
         # Add all lines into main sizer
         group_sizer = wx.BoxSizer(wx.VERTICAL)

invesalius/navigation/image.py

@@ -128,9 +128,14 @@ def UpdateFiducialMarkers(self):
     def OnStateProject(self, state):
         if state:
             if self.load_from_state:
-                self.LoadState()
                 self.load_from_state = False
+                try:
+                    self.LoadState()
+                except:
+                    ses.Session.DeleteStateFile()
+                    self.LoadProject()  # Load project if failed to load from state
             else:
                 self.LoadProject()
+
         self.SaveState()
         self.UpdateFiducialMarkers()

invesalius/navigation/iterativeclosestpoint.py

@@ -32,7 +32,10 @@ def __init__(self):
         self.m_icp = None
         self.icp_fre = None
 
-        self.LoadState()
+        try:
+            self.LoadState()
+        except:
+            ses.Session().DeleteStateFile()
 
     def SaveState(self):
         m_icp = self.m_icp.tolist() if self.m_icp is not None else None

invesalius/navigation/navigation.py

@@ -473,7 +473,7 @@ def EstimateTrackerToInVTransformationMatrix(self, tracker, image):
             self.all_fiducials[3:, :].T, self.all_fiducials[:3, :].T, shear=False, scale=False
         )
 
-    def SetStylusOrientation(self, coord_raw):
+    def OnRecordStylusOrientation(self, coord_raw):
         if self.m_change is not None:
             m_probe = dcr.compute_marker_transformation(coord_raw, 0)
 

invesalius/navigation/tracker.py

@@ -51,7 +51,10 @@ def __init__(self):
 
         self.TrackerCoordinates = dco.TrackerCoordinates()
 
-        self.LoadState()
+        try:
+            self.LoadState()
+        except:
+            ses.Session().DeleteStateFile()
 
     def SaveState(self):
         tracker_id = self.tracker_id