move models to their own folder, and update omero model

latest/models/image.py

@@ -0,0 +1,83 @@
+from __future__ import annotations
+from typing import Literal, Optional
+from pydantic import BaseModel, ConfigDict, conlist
+from typing import Annotated, Hashable, List, TypeVar
+from pydantic_core import PydanticCustomError
+from pydantic import AfterValidator, Field, ValidationError
+import json
+
+T = TypeVar('T', bound=Hashable)
+
+def _validate_unique_list(v: list[T]) -> list[T]:
+    if len(v) != len(set(v)):
+        raise PydanticCustomError('unique_list', 'List must be unique')
+    return v
+
+UniqueList = Annotated[List[T], AfterValidator(_validate_unique_list), Field(json_schema_extra={'uniqueItems': True})]
+
+class Axis(BaseModel, frozen=True):
+    name: str
+    type: Optional[str] = None
+    unit: Optional[str] = None
+
+class ScaleTransform(BaseModel, frozen=True):
+    type: Literal["scale"]
+    scale: conlist(float, min_length=1)
+
+class TranslationTransform(BaseModel, frozen=True):
+    type: Literal["translation"]
+    translation: conlist(float, min_length=1)
+
+class Dataset(BaseModel, frozen=True):
+    path: str
+    coordinateTransformations: tuple[ScaleTransform] | tuple[ScaleTransform, TranslationTransform]
+
+class Multiscale(BaseModel, frozen=True):
+    """
+    The multiscale datasets for this image
+    """
+    name: Optional[str] = None
+    datasets: conlist(Dataset, min_length=1)
+    axes: UniqueList[Axis]
+    coordinateTransformations: Optional[tuple[ScaleTransform] | tuple[ScaleTransform, TranslationTransform]] = None
+    version: Literal['0.5-dev']
+
+class Window(BaseModel, frozen=True):
+    start: float
+    end: float
+    min: float
+    max: float
+
+class OmeroRenderingSettings(BaseModel, frozen=True):
+    window: Window
+    label: str
+    family: str
+    color: str
+    active: bool
+
+class OmeroRdef(BaseModel, frozen=True):
+    defaultT: int
+    defaultZ: int
+    model: str
+
+class Omero(BaseModel, frozen=True):
+    channels: list[OmeroRenderingSettings]
+    rdefs: OmeroRdef
+
+class GroupMetadata(BaseModel, frozen=True):
+    """
+    JSON from OME-NGFF .zattrs
+    """
+    model_config = ConfigDict(title="NGFF Image")
+    multiscales: conlist(Multiscale, min_length=1)
+    omero: Optional[Omero] = None
+
+def make_schema():
+    schema = GroupMetadata.model_json_schema()
+    schema["$schema"] = "https://json-schema.org/draft/2020-12/schema"
+    schema["$id"] = "https://ngff.openmicroscopy.org/latest/schemas/image.schema"
+
+    print(json.dumps(schema, indent=2))
+
+if __name__ == '__main__':
+    make_schema()

latest/schemas/image.schema

@@ -163,19 +163,46 @@
       "properties": {
         "channels": {
           "items": {
-            "$ref": "#/$defs/RenderingSettings"
+            "$ref": "#/$defs/OmeroRenderingSettings"
           },
           "title": "Channels",
           "type": "array"
+        },
+        "rdefs": {
+          "$ref": "#/$defs/OmeroRdef"
         }
       },
       "required": [
-        "channels"
+        "channels",
+        "rdefs"
       ],
       "title": "Omero",
       "type": "object"
     },
-    "RenderingSettings": {
+    "OmeroRdef": {
+      "properties": {
+        "defaultT": {
+          "title": "Defaultt",
+          "type": "integer"
+        },
+        "defaultZ": {
+          "title": "Defaultz",
+          "type": "integer"
+        },
+        "model": {
+          "title": "Model",
+          "type": "string"
+        }
+      },
+      "required": [
+        "defaultT",
+        "defaultZ",
+        "model"
+      ],
+      "title": "OmeroRdef",
+      "type": "object"
+    },
+    "OmeroRenderingSettings": {
       "properties": {
         "window": {
           "$ref": "#/$defs/Window"
@@ -204,7 +231,7 @@
         "color",
         "active"
       ],
-      "title": "RenderingSettings",
+      "title": "OmeroRenderingSettings",
       "type": "object"
     },
     "ScaleTransform": {