Python interface

environment.yml

@@ -9,3 +9,4 @@ dependencies:
     - python-dotenv
     - -e ./packages/agave-renderer
     - -e ./packages/remote-image
+    - itkwasm-image-io

model/README.md

@@ -0,0 +1,8 @@
+# itk-viewer model
+
+A [LinkML] model of itk-viewer's architecture.
+
+The viewer is built on the [Actor Model]. This model defines the Actors and their relationships. It also defines the Events, which are the messages sent to Actors. It defines all the Events an Actor can receive. The data model of the Events is also used to generate the corresponding TypeScript interfaces and Python pydantic dataclasses.
+
+.. LinkML: https://linkml.io/
+.. Actor Model: https://en.wikipedia.org/wiki/Actor_model

model/gen-docs.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+# Generate documentation for the model
+
+script_dir="`cd $(dirname $0); pwd`"
+cd $script_dir
+
+gen-markdown -d ../docs/model ./itk-viewer.yml

model/gen-python.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+# Generate python code for the model
+
+script_dir="`cd $(dirname $0); pwd`"
+cd $script_dir
+
+gen-pydantic ./itk-viewer.yml --pydantic-version 2 > ../packages/viewer/python/itkviewer/model.py

model/itk-viewer.yml

@@ -0,0 +1,258 @@
+id: https://w3id.org/itk/viewer
+name: itk-viewer
+version: 0.0.1
+description: >-
+  The itk-viewer model defines the classes and relationships for a viewer that allows users to view and interact with multi-dimensional images, geometry, and point sets.
+license: https://creativecommons.org/publicdomain/zero/1.0/
+prefixes:
+  itk: https://w3id.org/itk/
+  wasm: https://w3id.org/itk/wasm
+  viewer: https://w3id.org/itk/viewer
+  linkml: https://w3id.org/linkml/
+imports:
+  - linkml:types
+default_range: string
+default_prefix: viewer
+
+classes:
+  Actor:
+    abstract: true
+    description: >-
+      In the Actor Model mathematical of computation, an actor is a computational entity that,
+      in response to a message it receives, can concurrently:
+
+      - send a finite number of messages to other actors;
+      - create a finite number of new actors;
+      - designate the behavior to be used for the next message it receives.
+
+      Supported messages are defined in the Event classes. The valid Events' for an Actor are defined
+      defined by the `receives` relationship. To send an Event to an Actor, use the `send` method.
+
+      Actors are typically implement as finite state machines.
+    class_uri: viewer:Actor
+    slots:
+      - unknownEventAction
+
+  Viewer:
+    abstract: true
+    is_a: Actor
+    tree_root: true
+    description: >-
+      A viewer is an interface that allows users to view and interact with
+      multi-dimensional images, geometry, and point sets.
+    class_uri: viewer:Viewer
+    attributes:
+      title:
+        description: >-
+          The title of the viewer.
+        range: string
+        ifabsent: string("ITK Viewer")
+      dataManager:
+        description: >-
+          The data manager for the viewer.
+        range: DataManager
+
+  Viewport:
+    abstract: true
+    is_a: Actor
+    description: >-
+      A viewport is a rectangular region of a viewer that displays a rendering of the scene.
+    class_uri: viewer:Viewport
+    attributes:
+      width:
+        description: >-
+          The width of the viewport in pixels.
+        range: integer
+        required: true
+        ifabsent: int(640)
+      height:
+        description: >-
+          The height of the viewport in pixels.
+        range: integer
+        required: true
+        ifabsent: int(480)
+
+  Image:
+    description: >-
+      An itk-wasm Image to be displayed in the viewer.
+    class_uri: wasm:Image
+
+  StoreModel:
+    abstract: true
+    description: >-
+      Parameters of a Zarr store following the data model implied by Zarr-Python.
+    attributes:
+      type:
+        description: >-
+          The type of the Zarr store model.
+        designates_type: true
+        range: string
+        required: true
+
+  DirectoryStore:
+    is_a: StoreModel
+    description: >-
+      A Zarr store that is backed by a directory on the file system.
+    attributes:
+      path:
+        description: >-
+          The path to the directory on the file system that contains the Zarr store.
+        range: string
+        required: true
+
+  FSStore:
+    is_a: StoreModel
+    description: >-
+      A Zarr store that can be wrapped an fsspec.FSMap in Python to give access to arbitrary filesystems
+    attributes:
+      url:
+        description: >-
+          Protocol and path, like “s3://bucket/root.zarr” or "https://example.com/image.ome.zarr".
+        range: string
+        required: true
+
+  ImageData:
+    description: >-
+      Image data displayed in the viewer.
+    class_uri: viewer:ImageData
+    attributes:
+      imageJson:
+        description: >-
+          The image data in JSON format. An ITK-Wasm Image with the pixel data zstd compressed and base64-encoded.
+        range: string
+      store:
+        description: >-
+          The OME-Zarr store model for the image data.
+        range: StoreModel
+
+  MultiscaleImage:
+    abstract: true
+    is_a: Actor
+    description: >-
+      A multiscale image is a multi-dimensional image, based on the OME-Zarr data model, often preprocessed,
+      that supports efficient rendering at multiple resolutions.
+    class_uri: viewer:MultiscaleImage
+
+  DataManager:
+    abstract: true
+    is_a: Actor
+    description: >-
+      A data manager is an actor that manages the loading and caching of data for rendering.
+    class_uri: viewer:DataManager
+    slots:
+      - images
+
+  Renderer:
+    abstract: true
+    is_a: Actor
+    description: >-
+      A renderer is an actor that renders a scene to an in-memory RGB image for display in a viewport.
+    class_uri: viewer:Renderer
+    attributes:
+      width:
+        description: >-
+          The width of the canvas in pixels.
+        range: integer
+        required: true
+        ifabsent: int(640)
+      height:
+        description: >-
+          The height of the canvas in pixels.
+        range: integer
+        required: true
+        ifabsent: int(480)
+    slots:
+      - viewport
+
+
+  Event:
+    abstract: true
+    description: >-
+      An event is a message that can be sent to an actor. The actor can respond to the event
+      by changing its state, sending messages to other actors, or creating new actors.
+    class_uri: viewer:Event
+    attributes:
+      type:
+        designates_type: true
+        description: >-
+          The type of the event.
+        range: string
+        required: true
+
+  ViewerEvent:
+    abstract: true
+    is_a: Event
+    description: >-
+      A ViewerEvent is an Event that can be sent to a Viewer.
+    class_uri: viewer:ViewerEvent
+
+  SetImageEvent:
+    is_a: ViewerEvent
+    description: >-
+      A SetImageEvent is an Event that sets an image to be displayed in a viewer.
+    class_uri: viewer:SetImageEvent
+    slots:
+      - image
+    attributes:
+      name:
+        description: >-
+          The name of the image to be displayed in the viewer.
+        range: string
+
+  RendererEvent:
+    abstract: true
+    is_a: Event
+    description: >-
+      A RendererEvent is an Event supported by a Renderer.
+    class_uri: viewer:RendererEvent
+
+  RenderEvent:
+    is_a: RendererEvent
+    description: >-
+      A render event is a message that instructs a renderer to render a scene to an in-memory RGB image.
+    class_uri: viewer:RenderEvent
+
+slots:
+  viewport:
+    description: >-
+      The viewport that displays the rendered RGB image.
+    domain: Renderer
+    range: Viewport
+    required: true
+
+  unknownEventAction:
+    description: >-
+      The action to take when an unknown event is received.
+    domain: Actor
+    range: UnknownEventAction
+
+  image:
+    description: >-
+      The image to be displayed in the viewer.
+    domain: SetImageEvent
+    range: Image
+    required: true
+
+  images:
+    description: >-
+      The images displayed by the viewer.
+    domain: DataManager
+    range: ImageData
+    multivalued: true
+    required: true
+
+enums:
+  UnknownEventAction:
+    description: >-
+      The types of actions that can be taken when an unknown event is received.
+    enum_uri: viewer:UnknownEventAction
+    permissible_values:
+      Ignore:
+        description: >-
+          Ignore the event.
+      Warn:
+        description: >-
+          Log a warning and ignore the event.
+      Error:
+        description: >-
+          Throw an error.

model/requirements.txt

@@ -0,0 +1 @@
+linkml

packages/agave-renderer/itk_viewer_agave_renderer/__init__.py

@@ -2,4 +2,4 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
-from .renderer import Renderer
+from .renderer import AgaveRenderer

packages/agave-renderer/itk_viewer_agave_renderer/renderer.py

@@ -16,6 +16,7 @@
 import fractions
 from av import VideoFrame
 from aiortc import MediaStreamTrack
+from itkviewer import Viewport, Renderer, UnknownEventAction
 
 # Should match constant in connected clients.
 # The WebRTC service id is different from this
@@ -40,7 +41,7 @@ async def recv(self):
 
         frame = VideoFrame.from_image(img)
 
-        frame.pts = self.count 
+        frame.pts = self.count
         self.count+=1
         frame.time_base = fractions.Fraction(1, 1000)
         return frame
@@ -64,22 +65,16 @@ def memory_redraw(self):
         return img
 
 
-# how to handle unknown events
-class UnknownEventAction(Enum):
-    ERROR = auto()
-    WARNING = auto()
-    IGNORE = auto()
-
-
-class Renderer:
+class AgaveRenderer(Renderer):
     def __init__(
-        self, width=500, height=400, unknown_event_action=UnknownEventAction.WARNING
+        self, viewport: Viewport, width: int=500, height: int=400, unknown_event_action: UnknownEventAction=UnknownEventAction.Warning
     ):
         self.width = width
         self.height = height
         self.unknown_event_action = unknown_event_action
         self.render_time = .1
         self.agave = None
+        super().__init__(viewport, width, height, unknown_event_action)
 
     async def setup(self):
         # Note: the agave websocket server needs to be running
@@ -167,11 +162,11 @@ async def update_renderer(self, events):
 
     def handle_unknown_event(self, event_type):
         match self.unknown_event_action:
-            case UnknownEventAction.ERROR:
-                raise Exception(f"Unknown event type: {event_type}")
-            case UnknownEventAction.WARNING:
+            case UnknownEventAction.Error:
+                raise ValueError(f"Unknown event type: {event_type}")
+            case UnknownEventAction.Warning:
                 print(f"Unknown event type: {event_type}", flush=True)
-            case UnknownEventAction.IGNORE:
+            case UnknownEventAction.Ignore:
                 pass