Merge pull request #825 from mo-gaafar/mep_visualization

Neuronavigation: TMS Motor Mapping Visualization

invesalius/constants.py

@@ -801,9 +801,10 @@
 TARGET_COLUMN = 4
 Z_OFFSET_COLUMN = 5
 POINT_OF_INTEREST_TARGET_COLUMN = 6
-X_COLUMN = 7
-Y_COLUMN = 8
-Z_COLUMN = 9
+MEP_COLUMN = 7
+X_COLUMN = 8
+Y_COLUMN = 9
+Z_COLUMN = 10
 
 # ------------ Navigation defaults -------------------
 
@@ -1004,10 +1005,89 @@
 }
 
 MARKER_FILE_MAGICK_STRING = "##INVESALIUS3_MARKER_FILE_"
-CURRENT_MARKER_FILE_VERSION = 3
-SUPPORTED_MARKER_FILE_VERSIONS = [0, 1, 2, 3]
+CURRENT_MARKER_FILE_VERSION = 4
+SUPPORTED_MARKER_FILE_VERSIONS = [0, 1, 2, 3, 4]
 WILDCARD_MARKER_FILES = _("Marker scanner coord files (*.mkss)|*.mkss")
 
+# Motor mapping visualization
+
+DEFAULT_MEP_CONFIG_PARAMS = {
+    "mep_enabled": False,
+    "enabled_once": False,
+    "threshold_down": 0,
+    "range_up": 1,
+    "brain_surface_index": None,
+    "mep_colormap": "Viridis",
+    "gaussian_sharpness": 0.4,
+    "gaussian_radius": 20,
+    "bounds": None,
+    "colormap_range_uv": {"min": 50, "low": 200, "mid": 600, "max": 1000},
+}
+
+
+MEP_COLORMAP_DEFINITIONS = {
+    "BlueCyanYellowRed": {  # Blue, Cyan, Yellow, Red
+        "min": (0.0, 0.0, 1.0),
+        "low": (0.0, 1.0, 1.0),
+        "mid": (1.0, 1.0, 0.0),
+        "max": (1.0, 0.0, 0.0),
+    },
+    "GreenYellowOrangeRed": {  # Green, Yellow, Orange, Red
+        "min": (0.0, 1.0, 0.0),
+        "low": (1.0, 1.0, 0.0),
+        "mid": (1.0, 0.647, 0.0),
+        "max": (1.0, 0.0, 0.0),
+    },
+    "PurpleBlueGreenYellow": {  # Purple, Blue, Green, Yellow
+        "min": (0.5, 0.0, 0.5),
+        "low": (0.0, 0.0, 1.0),
+        "mid": (0.0, 1.0, 0.0),
+        "max": (1.0, 1.0, 0.0),
+    },
+    "BlackGrayWhiteRed": {  # Black, Gray, White, Red (grayscale with highlight)
+        "min": (0.0, 0.0, 0.0),
+        "low": (0.5, 0.5, 0.5),
+        "mid": (1.0, 1.0, 1.0),
+        "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),
+    },
+    "Grayscale": {  # Grayscale (often used for CT/MRI)
+        "min": (0.0, 0.0, 0.0),  # Black
+        "low": (0.25, 0.25, 0.25),  # Dark Gray
+        "mid": (0.75, 0.75, 0.75),  # Light Gray
+        "max": (1.0, 1.0, 1.0),  # White
+    },
+    "HotMetal": {  # Hot Metal (useful for highlighting hot spots)
+        "min": (0.0, 0.0, 0.0),  # Black
+        "low": (0.5, 0.0, 0.0),  # Dark Red
+        "mid": (1.0, 0.5, 0.0),  # Orange
+        "max": (1.0, 1.0, 1.0),  # White
+    },
+    "Rainbow": {  # Rainbow (although not perceptually uniform, still common)
+        "min": (0.0, 0.0, 1.0),  # Blue
+        "low": (0.0, 1.0, 0.0),  # Green
+        "mid": (1.0, 1.0, 0.0),  # Yellow
+        "max": (1.0, 0.0, 0.0),  # Red
+    },
+    "Bone": {  # Bone (specifically designed for CT bone visualization)
+        "min": (0.0, 0.0, 0.0),  # Black
+        "low": (0.388, 0.224, 0.0),  # Brown
+        "mid": (0.902, 0.827, 0.631),  # Beige
+        "max": (1.0, 1.0, 1.0),  # White
+    },
+    "InvertedGrayscale": {  # Inverted Grayscale (sometimes used for PET)
+        "min": (1.0, 1.0, 1.0),  # White
+        "low": (0.75, 0.75, 0.75),  # Light Gray
+        "mid": (0.25, 0.25, 0.25),  # Dark Gray
+        "max": (0.0, 0.0, 0.0),  # Black
+    },
+}
+
 # Keycodes for moving markers using the keyboard
 MOVE_MARKER_LEFT_KEYCODE = 65  # A
 MOVE_MARKER_RIGHT_KEYCODE = 68  # D

invesalius/data/markers/marker.py

@@ -75,6 +75,9 @@ class Marker:
     z_offset: float = 0.0
     visualization: dict = dataclasses.field(default_factory=dict)
     marker_uuid: str = ""
+    # #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)
 
     # x, y, z can be jointly accessed as position
     @property
@@ -160,7 +163,11 @@ def to_csv_header(cls):
         res = [
             field.name
             for field in dataclasses.fields(cls)
-            if (field.name != "version" and field.name != "marker_uuid")
+            if (
+                field.name != "version"
+                and field.name != "marker_uuid"
+                and field.name != "visualization"
+            )
         ]
         res.extend(["x_world", "y_world", "z_world", "alpha_world", "beta_world", "gamma_world"])
         return "\t".join(map(lambda x: f'"{x}"', res))
@@ -217,6 +224,7 @@ def to_dict(self):
             "cortex_position_orientation": self.cortex_position_orientation,
             "z_rotation": self.z_rotation,
             "z_offset": self.z_offset,
+            "mep_value": self.mep_value,
         }
 
     def from_dict(self, d):
@@ -245,33 +253,23 @@ def from_dict(self, d):
             else:
                 marker_type = MarkerType.COIL_TARGET.value
 
-        if all(
-            [
-                k in d
-                for k in [
-                    "x_cortex",
-                    "y_cortex",
-                    "z_cortex",
-                    "alpha_cortex",
-                    "beta_cortex",
-                    "gamma_cortex",
-                ]
-            ]
-        ):
-            cortex_position_orientation = [
+        cortex_position_orientation = (
+            d["cortex_position_orientation"]
+            if "cortex_position_orientation" in d
+            else [
                 d["x_cortex"],
                 d["y_cortex"],
                 d["z_cortex"],
                 d["alpha_cortex"],
                 d["beta_cortex"],
                 d["gamma_cortex"],
             ]
-        else:
-            cortex_position_orientation = [None, None, None, None, None, None]
+        )
 
         z_offset = d.get("z_offset", 0.0)
         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)
 
         self.size = d["size"]
         self.label = d["label"]
@@ -287,6 +285,7 @@ def from_dict(self, d):
         self.cortex_position_orientation = cortex_position_orientation
         self.z_offset = z_offset
         self.z_rotation = z_rotation
+        self.mep_value = mep_value
 
         return self
 

invesalius/data/surface.py

@@ -216,6 +216,7 @@ def __bind_events(self):
         Publisher.subscribe(self.OnSplitSurface, "Split surface")
         Publisher.subscribe(self.OnLargestSurface, "Create surface from largest region")
         Publisher.subscribe(self.OnSeedSurface, "Create surface from seeds")
+        Publisher.subscribe(self.GetVisibleSurfaceActor, "Get visible surface actor")
 
         Publisher.subscribe(self.OnDuplicate, "Duplicate surfaces")
         Publisher.subscribe(self.OnRemove, "Remove surfaces")
@@ -1129,6 +1130,20 @@ def OnChangeSurfaceName(self, index, name):
     def OnShowSurface(self, index, visibility):
         self.ShowActor(index, visibility)
 
+    def GetVisibleSurfaceActor(self):
+        """
+        Gets the first visible surface actor.
+        """
+        index = 0
+        for key in self.actors_dict:
+            if self.actors_dict[key].GetVisibility():
+                index = key
+                break
+
+        Publisher.sendMessage(
+            "Load visible surface actor", actor=self.actors_dict[index], index=index
+        )
+
     def ShowActor(self, index, value):
         """
         Show or hide actor, according to given actor index and value.