feat: changes to how atlas and primitive mesh handle individual objec…

…t data

models/csharp/urchin/AtlasModel.cs

@@ -5,12 +5,6 @@ public struct AtlasModel
 {
     public string Name;
     public Vector3 ReferenceCoord;
-    public string[] Acronyms;
-    public bool[] Visible;
-    public Color[] Colors;
-    public int[] Sides;
+    public StructureModel[] Areas;
     public string Colormap;
-    public float[] Intensities;
-    public float[] Alphas;
-    public string[] Materials;
 }

models/csharp/urchin/PrimitiveMeshModel.cs

@@ -0,0 +1,7 @@
+
+
+
+public struct PrimitiveMeshModel
+{
+    public MeshModel[] Data;
+}

models/csharp/urchin/StructureModel.cs

@@ -0,0 +1,14 @@
+
+using UnityEngine;
+
+public struct StructureModel
+{
+    public string Name;
+    public string Acronym;
+    public int AtlasId;
+    public bool Visible;
+    public Color Color;
+    public float ColorIntensity;
+    public int Side;
+    public string Material;
+}

models/schemas/urchin/AtlasModel.json

@@ -1 +1 @@
-{"$defs": {"Color": {"properties": {"r": {"maximum": 1.0, "minimum": 0.0, "title": "R", "type": "number"}, "g": {"maximum": 1.0, "minimum": 0.0, "title": "G", "type": "number"}, "b": {"maximum": 1.0, "minimum": 0.0, "title": "B", "type": "number"}, "a": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "A", "type": "number"}}, "required": ["r", "g", "b"], "title": "Color", "type": "object"}, "Vector3": {"properties": {"x": {"default": 0.0, "title": "X", "type": "number"}, "y": {"default": 0.0, "title": "Y", "type": "number"}, "z": {"default": 0.0, "title": "Z", "type": "number"}}, "title": "Vector3", "type": "object"}}, "properties": {"Name": {"title": "Name", "type": "string"}, "ReferenceCoord": {"$ref": "#/$defs/Vector3"}, "Acronyms": {"items": {"type": "string"}, "title": "Acronyms", "type": "array"}, "Visible": {"items": {"type": "boolean"}, "title": "Visible", "type": "array"}, "Colors": {"items": {"$ref": "#/$defs/Color"}, "title": "Colors", "type": "array"}, "Sides": {"items": {"type": "integer"}, "title": "Sides", "type": "array"}, "Colormap": {"default": "", "title": "Colormap", "type": "string"}, "Intensities": {"default": [], "items": {"type": "number"}, "title": "Intensities", "type": "array"}, "Alphas": {"items": {"type": "number"}, "title": "Alphas", "type": "array"}, "Materials": {"items": {"type": "string"}, "title": "Materials", "type": "array"}}, "required": ["Name", "ReferenceCoord", "Acronyms", "Visible", "Colors", "Sides", "Alphas", "Materials"], "title": "AtlasModel", "type": "object"}
+{"$defs": {"Color": {"properties": {"r": {"maximum": 1.0, "minimum": 0.0, "title": "R", "type": "number"}, "g": {"maximum": 1.0, "minimum": 0.0, "title": "G", "type": "number"}, "b": {"maximum": 1.0, "minimum": 0.0, "title": "B", "type": "number"}, "a": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "A", "type": "number"}}, "required": ["r", "g", "b"], "title": "Color", "type": "object"}, "StructureModel": {"properties": {"Name": {"title": "Name", "type": "string"}, "Acronym": {"title": "Acronym", "type": "string"}, "AtlasId": {"title": "Atlasid", "type": "integer"}, "Visible": {"default": false, "title": "Visible", "type": "boolean"}, "Color": {"allOf": [{"$ref": "#/$defs/Color"}], "default": {"r": 1.0, "g": 0.0, "b": 0.0, "a": 1.0}}, "ColorIntensity": {"default": 0, "title": "Colorintensity", "type": "number"}, "Side": {"default": 0, "title": "Side", "type": "integer"}, "Material": {"default": "default", "title": "Material", "type": "string"}}, "required": ["Name", "Acronym", "AtlasId"], "title": "StructureModel", "type": "object"}, "Vector3": {"properties": {"x": {"default": 0.0, "title": "X", "type": "number"}, "y": {"default": 0.0, "title": "Y", "type": "number"}, "z": {"default": 0.0, "title": "Z", "type": "number"}}, "title": "Vector3", "type": "object"}}, "properties": {"Name": {"title": "Name", "type": "string"}, "ReferenceCoord": {"allOf": [{"$ref": "#/$defs/Vector3"}], "default": null}, "Areas": {"items": {"$ref": "#/$defs/StructureModel"}, "title": "Areas", "type": "array"}, "Colormap": {"default": "", "title": "Colormap", "type": "string"}}, "required": ["Name", "Areas"], "title": "AtlasModel", "type": "object"}

models/schemas/urchin/PrimitiveMeshModel.json

@@ -0,0 +1 @@
+{"$defs": {"Color": {"properties": {"r": {"maximum": 1.0, "minimum": 0.0, "title": "R", "type": "number"}, "g": {"maximum": 1.0, "minimum": 0.0, "title": "G", "type": "number"}, "b": {"maximum": 1.0, "minimum": 0.0, "title": "B", "type": "number"}, "a": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "A", "type": "number"}}, "required": ["r", "g", "b"], "title": "Color", "type": "object"}, "MeshModel": {"properties": {"ID": {"title": "Id", "type": "string"}, "Shape": {"title": "Shape", "type": "string"}, "Position": {"$ref": "#/$defs/Vector3"}, "Color": {"$ref": "#/$defs/Color"}, "Scale": {"$ref": "#/$defs/Vector3"}, "Material": {"title": "Material", "type": "string"}, "Interactive": {"title": "Interactive", "type": "boolean"}}, "required": ["ID", "Shape", "Position", "Color", "Scale", "Material", "Interactive"], "title": "MeshModel", "type": "object"}, "Vector3": {"properties": {"x": {"default": 0.0, "title": "X", "type": "number"}, "y": {"default": 0.0, "title": "Y", "type": "number"}, "z": {"default": 0.0, "title": "Z", "type": "number"}}, "title": "Vector3", "type": "object"}}, "properties": {"Data": {"items": {"$ref": "#/$defs/MeshModel"}, "title": "Data", "type": "array"}}, "required": ["Data"], "title": "PrimitiveMeshModel", "type": "object"}

models/schemas/urchin/StructureModel.json

@@ -0,0 +1 @@
+{"$defs": {"Color": {"properties": {"r": {"maximum": 1.0, "minimum": 0.0, "title": "R", "type": "number"}, "g": {"maximum": 1.0, "minimum": 0.0, "title": "G", "type": "number"}, "b": {"maximum": 1.0, "minimum": 0.0, "title": "B", "type": "number"}, "a": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "A", "type": "number"}}, "required": ["r", "g", "b"], "title": "Color", "type": "object"}}, "properties": {"Name": {"title": "Name", "type": "string"}, "Acronym": {"title": "Acronym", "type": "string"}, "AtlasId": {"title": "Atlasid", "type": "integer"}, "Visible": {"default": false, "title": "Visible", "type": "boolean"}, "Color": {"allOf": [{"$ref": "#/$defs/Color"}], "default": {"r": 1.0, "g": 0.0, "b": 0.0, "a": 1.0}}, "ColorIntensity": {"default": 0, "title": "Colorintensity", "type": "number"}, "Side": {"default": 0, "title": "Side", "type": "integer"}, "Material": {"default": "default", "title": "Material", "type": "string"}}, "required": ["Name", "Acronym", "AtlasId"], "title": "StructureModel", "type": "object"}

src/vbl_aquarium/models/urchin.py

@@ -41,16 +41,20 @@ class CustomMeshModel(VBLBaseModel):
 
 class AtlasModel(VBLBaseModel):
     name: str
-    reference_coord: Vector3
-    acronyms: List[str]
-    visible: List[bool]
-    colors: List[Color]
-    sides: List[int]
+    reference_coord: Vector3 = None
+    areas: List[StructureModel]
     colormap: str = ''
-    intensities: List[float] = []
-    alphas: List[float]
-    materials: List[str]
 
+class StructureModel(VBLBaseModel):
+    name: str
+    acronym: str
+    atlas_id: int
+    color: Color
+    # values that come with defaults:
+    visible: bool = False
+    color_intensity: float = -1
+    side: int = 0
+    material: str = 'default'
 
 # Camera
 
@@ -74,6 +78,8 @@ class CameraMode(str, Enum):
 
 # Individual mesh neuron
 
+class PrimitiveMeshModel(VBLBaseModel):
+    data: List[MeshModel]
 
 class MeshModel(VBLBaseModel):
     id: str = Field(alias="ID")