feat: allow seg gen to control the segments shown, have random colour…

…s, and the mesh render scale

also keep the names for "mesh" generation to distinguish from "seg" generation so that the interface can stay the same, but use aliases where there is no difference in the function

cryoet_data_portal_neuroglancer/models/json_generator.py

@@ -186,17 +186,19 @@ def _get_shader(self):
 class SegmentationJSONGenerator(RenderingJSONGenerator):
     """Generates JSON Neuroglancer config for segmentation mask."""
 
-    color: str
+    color: str | None = None
     is_visible: bool = True
     display_mesh: bool = True
     display_bounding_box: bool = False
     highlight_on_hover: bool = False
+    mesh_render_scale: float = 1.0
+    visible_segments: tuple[int, ...] = (1,)
 
     def __post_init__(self):
         self._type = RenderingTypes.SEGMENTATION
 
     def generate_json(self) -> dict:
-        return {
+        state = {
             "type": self.layer_type,
             "name": f"{self.name}",
             "source": {
@@ -210,48 +212,19 @@ def generate_json(self) -> dict:
             "tab": "rendering",
             "selectedAlpha": 1,
             "hoverHighlight": self.highlight_on_hover,
-            "segments": [
-                1,
-            ],
-            "segmentDefaultColor": self.color,
+            "segments": sorted((self.visible_segments)),
             "visible": self.is_visible,
+            "meshRenderScale": self.mesh_render_scale,
         }
+        # self.color === None means that the color will be random
+        # This is useful for multiple segmentations
+        if self.color is not None:
+            state["segmentDefaultColor"] = self.color
+        return state
 
 
-@dataclass
-class MeshJSONGenerator(RenderingJSONGenerator):
-    """Generates JSON Neuroglancer config for mesh that are alone (without any segmentation)."""
-
-    color: str
-    is_visible: bool = True
-    display_mesh: bool = True
-    display_bounding_box: bool = False
-    highlight_on_hover: bool = False
-
-    def __post_init__(self):
-        self._type = RenderingTypes.SEGMENTATION
-
-    def generate_json(self) -> dict:
-        return {
-            "type": self.layer_type,
-            "name": f"{self.name}",
-            "source": {
-                **create_source(f"precomputed://{self.source}", self.scale, self.scale),
-                "subsources": {
-                    "default": True,
-                    "mesh": self.display_mesh,
-                },
-                "enableDefaultSubsources": self.display_bounding_box,
-            },
-            "tab": "rendering",
-            "selectedAlpha": 1,
-            "hoverHighlight": self.highlight_on_hover,
-            "segments": [
-                1,
-            ],
-            "segmentDefaultColor": self.color,
-            "visible": self.is_visible,
-        }
+# Alias for SegmentationJSONGenerator - for future compatibility
+MeshJSONGenerator = SegmentationJSONGenerator
 
 
 @dataclass

cryoet_data_portal_neuroglancer/state_generator.py

@@ -87,12 +87,14 @@ def generate_segmentation_mask_layer(
     source: str,
     name: str | None = None,
     url: str | None = None,
-    color: str = "#FFFFFF",
+    color: str | None = "#FFFFFF",
     scale: float | tuple[float, float, float] = (1.0, 1.0, 1.0),
     is_visible: bool = True,
     display_bounding_box: bool = False,
     display_mesh: bool = True,
     highlight_on_hover: bool = False,
+    mesh_render_scale: float = 2.0,
+    visible_segments: tuple[int, ...] = (1,),
 ) -> dict[str, Any]:
     source, name, url, _, scale = _setup_creation(source, name, url, scale=scale)
     _validate_color(color)
@@ -105,6 +107,8 @@ def generate_segmentation_mask_layer(
         display_bounding_box=display_bounding_box,
         display_mesh=display_mesh,
         highlight_on_hover=highlight_on_hover,
+        mesh_render_scale=mesh_render_scale,
+        visible_segments=visible_segments,
     ).to_json()
 
 
@@ -118,6 +122,8 @@ def generate_mesh_layer(
     display_bounding_box: bool = False,
     display_mesh: bool = True,
     highlight_on_hover: bool = False,
+    mesh_render_scale: float = 2.0,
+    visible_segments: tuple[int, ...] = (1,),
 ) -> dict[str, Any]:
     source, name, url, _, scale = _setup_creation(source, name, url, scale=scale)
     _validate_color(color)
@@ -130,6 +136,8 @@ def generate_mesh_layer(
         display_bounding_box=display_bounding_box,
         display_mesh=display_mesh,
         highlight_on_hover=highlight_on_hover,
+        mesh_render_scale=mesh_render_scale,
+        visible_segments=visible_segments,
     ).to_json()
 
 
@@ -143,19 +151,22 @@ def generate_oriented_point_mesh_layer(
     display_bounding_box: bool = False,
     display_mesh: bool = True,
     highlight_on_hover: bool = False,
+    mesh_render_scale: float = 4.0,
+    visible_segments: tuple[int, ...] = (1,),
 ) -> dict[str, Any]:
-    source, name, url, _, scale = _setup_creation(source, name, url, scale=scale)
-    _validate_color(color)
-    return MeshJSONGenerator(
+    return generate_mesh_layer(
         source=source,
         name=name,
+        url=url,
         color=color,
         scale=scale,
         is_visible=is_visible,
         display_bounding_box=display_bounding_box,
         display_mesh=display_mesh,
         highlight_on_hover=highlight_on_hover,
-    ).to_json()
+        mesh_render_scale=mesh_render_scale,
+        visible_segments=visible_segments,
+    )
 
 
 def generate_image_layer(