Merge pull request #869 from rmatsuda/sub-list-ctrl-for-brain-targets

Create a sub list ctrl for brain targets for mTMS

invesalius/constants.py

@@ -802,9 +802,23 @@
 Z_OFFSET_COLUMN = 5
 POINT_OF_INTEREST_TARGET_COLUMN = 6
 MEP_COLUMN = 7
-X_COLUMN = 8
-Y_COLUMN = 9
-Z_COLUMN = 10
+UUID = 8
+X_COLUMN = 9
+Y_COLUMN = 10
+Z_COLUMN = 11
+
+# The column order in the brain marker panel
+#
+BRAIN_ID_COLUMN = 0
+BRAIN_SESSION_COLUMN = 1
+BRAIN_MARKER_TYPE_COLUMN = 2
+BRAIN_LABEL_COLUMN = 3
+BRAIN_MEP_COLUMN = 4
+BRAIN_X_MTMS = 5
+BRAIN_Y_MTMS = 6
+BRAIN_R_MTMS = 7
+BRAIN_INTENSITY_MTMS = 8
+BRAIN_UUID = 9
 
 # ------------ Navigation defaults -------------------
 
@@ -1049,10 +1063,10 @@
         "max": (1.0, 0.0, 0.0),
     },
     "Viridis": {  # Viridis (perceptually uniform)
-        "min": (0.267004, 0.004874, 0.329415),
-        "low": (0.226337, 0.31071, 0.577055),
-        "mid": (0.993248, 0.906157, 0.143936),
-        "max": (0.968627, 0.813008, 0.0),
+        "min": (0.267, 0.004, 0.329),
+        "low": (0.192, 0.408, 0.556),
+        "mid": (0.137, 0.718, 0.475),
+        "max": (0.993, 0.906, 0.144),
     },
     "Grayscale": {  # Grayscale (often used for CT/MRI)
         "min": (0.0, 0.0, 0.0),  # Black

invesalius/data/markers/marker.py

@@ -64,9 +64,9 @@ class Marker:
     is_target: bool = False
     is_point_of_interest: bool = False
     session_id: int = 1
-    x_cortex: float = 0
-    y_cortex: float = 0
-    z_cortex: float = 0
+    x_cortex: float = dataclasses.field(default=None)
+    y_cortex: float = dataclasses.field(default=None)
+    z_cortex: float = dataclasses.field(default=None)
     alpha_cortex: float = dataclasses.field(default=None)
     beta_cortex: float = dataclasses.field(default=None)
     gamma_cortex: float = dataclasses.field(default=None)
@@ -78,6 +78,7 @@ class Marker:
     # #TODO: add a reference to original coil marker to relate it to MEP
     # in micro Volts (but scale in milli Volts for display)
     mep_value: float = dataclasses.field(default=None)
+    brain_target_list: list = dataclasses.field(default_factory=list)
 
     # x, y, z can be jointly accessed as position
     @property
@@ -209,6 +210,24 @@ def to_csv_row(self):
         )
         return res
 
+    def to_brain_targets_dict(self):
+        return {
+            "position": self.position,
+            "orientation": self.orientation,
+            "colour": self.colour,
+            "size": self.size,
+            "label": self.label,
+            "is_target": self.is_target,
+            "marker_type": self.marker_type.value,
+            "session_id": self.session_id,
+            "mep_value": self.mep_value,
+            "marker_uuid": self.marker_uuid,
+            "x_mtms": self.x_mtms,
+            "y_mtms": self.y_mtms,
+            "r_mtms": self.r_mtms,
+            "intensity_mtms": self.intensity_mtms,
+        }
+
     def to_dict(self):
         return {
             "position": self.position,
@@ -225,6 +244,8 @@ def to_dict(self):
             "z_rotation": self.z_rotation,
             "z_offset": self.z_offset,
             "mep_value": self.mep_value,
+            "brain_target_list": self.brain_target_list,
+            "marker_uuid": self.marker_uuid,
         }
 
     def from_dict(self, d):
@@ -270,6 +291,8 @@ def from_dict(self, d):
         z_rotation = d.get("z_rotation", 0.0)
         is_point_of_interest = d.get("is_point_of_interest", False)
         mep_value = d.get("mep_value", None)
+        brain_target_list = d.get("brain_target_list", [])
+        marker_uuid = d.get("marker_uuid", "")
 
         self.size = d["size"]
         self.label = d["label"]
@@ -286,6 +309,8 @@ def from_dict(self, d):
         self.z_offset = z_offset
         self.z_rotation = z_rotation
         self.mep_value = mep_value
+        self.brain_target_list = brain_target_list
+        self.marker_uuid = marker_uuid
 
         return self
 

invesalius/data/visualization/coil_visualizer.py

@@ -139,7 +139,7 @@ def ShowCoil(self, state, coil_name=None):
 
         if self.target_coil_actor is not None:
             self.target_coil_actor.SetVisibility(state)
-        # self.vector_field_assembly.SetVisibility(state) # LUKATODO: Keep this hidden for now
+        self.vector_field_assembly.SetVisibility(state)  # LUKATODO: Keep this hidden for now
 
         if not self.is_navigating:
             Publisher.sendMessage("Render volume viewer")
@@ -262,7 +262,7 @@ def AddCoil(self, coil_name, coil_path):
         self.coils[coil_name]["path"] = coil_path
 
         # LUKATODO: Vector field assembly follows a different pattern for addition, should unify.
-        # self.vector_field_assembly.SetVisibility(1)
+        self.vector_field_assembly.SetVisibility(1)
 
     def RemoveCoil(self, coil_name=None):
         if coil_name is not None:
@@ -301,4 +301,5 @@ def UpdateCoilPoses(self, m_imgs, coords):
             self.coils[name]["center_actor"].SetUserMatrix(m_img_vtk)
 
             # LUKATODO
-            # self.vector_field_assembly.SetUserMatrix(m_img_vtk)
+
+            self.vector_field_assembly.SetUserMatrix(m_img_vtk)

invesalius/data/visualization/marker_visualizer.py

@@ -75,23 +75,33 @@ def __bind_events(self):
         Publisher.subscribe(self.UnsetTarget, "Unset target")
         Publisher.subscribe(self.SetTargetTransparency, "Set target transparency")
         Publisher.subscribe(self.SetCoilAtTarget, "Coil at target")
-        Publisher.subscribe(self.UpdateVectorField, "Update vector field")
+        Publisher.subscribe(self.UpdateBrainTargets, "Update brain targets")
         Publisher.subscribe(self.UpdateNavigationStatus, "Navigation status")
         Publisher.subscribe(self.UpdateTargetMode, "Set target mode")
+        Publisher.subscribe(
+            self.UpdateVectorFieldAssemblyVisibility, "Set vector field assembly visibility"
+        )
 
     def UpdateNavigationStatus(self, nav_status, vis_status):
         self.is_navigating = nav_status
 
     def UpdateTargetMode(self, enabled=False):
         self.is_target_mode = enabled
 
-    def UpdateVectorField(self):
+    def UpdateVectorFieldAssemblyVisibility(self, enabled=False):
+        self.vector_field_assembly.SetVisibility(enabled)
+        # If not navigating, render the scene.
+        if not self.is_navigating:
+            self.interactor.Render()
+
+    def UpdateBrainTargets(self, brain_targets):
         """
         Update the vector field assembly to reflect the current vector field.
         """
         # Create a new vector field assembly.
-        new_vector_field_assembly = self.vector_field_visualizer.CreateVectorFieldAssembly()
-
+        new_vector_field_assembly = self.vector_field_visualizer.CreateVectorFieldAssembly(
+            brain_targets
+        )
         # Replace the old vector field assembly with the new one.
         self.actor_factory.ReplaceActor(
             self.renderer, self.vector_field_assembly, new_vector_field_assembly
@@ -446,13 +456,13 @@ def HighlightMarker(self, marker, render=True):
 
         # If the marker is a coil target, show the vector field assembly and update its position and orientation,
         # otherwise, hide the vector field assembly.
-        if marker_type == MarkerType.COIL_TARGET:
-            self.vector_field_assembly.SetVisibility(1)
-
-            self.vector_field_assembly.SetPosition(position_flipped)
-            self.vector_field_assembly.SetOrientation(orientation)
-        else:
-            self.vector_field_assembly.SetVisibility(0)
+        # if marker_type == MarkerType.COIL_TARGET:
+        #     self.vector_field_assembly.SetVisibility(1)
+        #
+        #     self.vector_field_assembly.SetPosition(position_flipped)
+        #     self.vector_field_assembly.SetOrientation(orientation)
+        # else:
+        #     self.vector_field_assembly.SetVisibility(0)
 
         # Return early if the marker is a target and the coil is at the target.
         #

invesalius/data/visualization/mep_visualizer.py

@@ -84,6 +84,9 @@ def __bind_events(self):
         # Publisher.subscribe(self.UpdateMEPPoints, "Update marker list")
         # Publisher.subscribe(self.SetBrainSurface, "Set MEP brain surface")
         Publisher.subscribe(self.UpdateMEPPoints, "Redraw MEP mapping")
+        Publisher.subscribe(
+            self.UpdateMEPPointsFromBrainTargets, "Redraw MEP mapping from brain targets"
+        )
         Publisher.subscribe(self.UpdateNavigationStatus, "Navigation status")
         Publisher.subscribe(self.SetBrainSurface, "Load brain surface actor")
         Publisher.subscribe(self.OnCloseProject, "Close project data")
@@ -131,6 +134,7 @@ def DisplayMotorMap(self, show: bool):
             self.UpdateVisualization()
             progress_dialog.Update(value=50, msg="Preparing brain surface...")
             self.UpdateMEPPoints()
+            self.UpdateMEPPointsFromBrainTargets()
             progress_dialog.Close()
         else:
             self._config_params["mep_enabled"] = False
@@ -353,6 +357,50 @@ def UpdateMEPPoints(self):
         if self._config_params["mep_enabled"]:
             self.UpdateVisualization()
 
+    def UpdateMEPPointsFromBrainTargets(self):
+        """
+        Updates or creates the point data with MEP values from a list of markers.
+
+        Args:
+            markers (List[Marker]): The list of marker objects to add/update points for.
+            clear_old (bool, default=False): If True, clears all existing points before updating.
+        """
+        if not self._config_params["mep_enabled"]:
+            return
+        if not self.surface:
+            return
+        brain_markers = []
+        for marker in MarkersControl().list:
+            if marker.brain_target_list:
+                for m in marker.brain_target_list:
+                    brain_markers.append(m)
+
+        if not brain_markers:
+            self.points = vtkPolyData()
+            self.UpdateVisualization()
+            return
+
+        points = vtkPoints()
+
+        point_data = self.points.GetPointData()
+        mep_array = vtkDoubleArray()
+        mep_array.SetName("MEP")
+        point_data.AddArray(mep_array)
+
+        for marker in brain_markers:
+            points.InsertNextPoint(
+                marker["position"][0], -marker["position"][1], marker["position"][2]
+            )
+            mep_value = marker["mep_value"] or 0
+            mep_array.InsertNextValue(mep_value)
+        MarkersControl().SaveState()
+
+        self.points.SetPoints(points)
+        self.points.GetPointData().SetActiveScalars("MEP")
+        self.points.Modified()
+        if self._config_params["mep_enabled"]:
+            self.UpdateVisualization()
+
     def UpdateVisualization(self):
         if not self._config_params["mep_enabled"] or not self.surface:
             return

invesalius/data/visualization/vector_field_visualizer.py

@@ -27,10 +27,12 @@ def SetVectorField(self, vector_field):
         self.vector_field = vector_field
         Publisher.sendMessage("Update vector field")
 
-    def CreateVectorFieldAssembly(self):
+    def CreateVectorFieldAssembly(self, vector_field=None):
         """
         Create an assembly for the current vector field.
         """
+        if not vector_field:
+            vector_field = self.vector_field
         assembly = vtk.vtkAssembly()
 
         actors = [
@@ -40,7 +42,7 @@ def CreateVectorFieldAssembly(self):
                 colour=vector["color"],
                 length_multiplier=vector["length"],
             )
-            for vector in self.vector_field
+            for vector in vector_field
         ]
 
         for actor in actors:

invesalius/gui/dialogs.py

@@ -1207,9 +1207,9 @@ def ShowEnterMarkerID(default: str) -> str:
 def ShowEnterMEPValue(default):
     msg = _("Enter the MEP value (uV)")
     if sys.platform == "darwin":
-        dlg = wx.TextEntryDialog(None, "", msg, defaultValue=default)
+        dlg = wx.TextEntryDialog(None, "", msg, defaultValue=str(default))
     else:
-        dlg = wx.TextEntryDialog(None, msg, "InVesalius 3", value=default)
+        dlg = wx.TextEntryDialog(None, msg, "InVesalius 3", value=str(default))
     dlg.ShowModal()
     result = dlg.GetValue()
     # check if the value is a number