Agave test

.gitignore

@@ -34,7 +34,8 @@ types/
 
 .npmrc
 .pnpm-store
+.env
 
 # temp transpiled TS files that don't always get cleaned up
 vite.config.ts.timestamp-*.mjs
-vite.config.ts.timestamp-*.mts
+vite.config.ts.timestamp-*.mts

package.json

@@ -11,7 +11,7 @@
     "lint": "pnpm prettier --check . && pnpm eslint .",
     "lint:fix": "pnpm prettier --write . && pnpm eslint --fix .",
     "setup-micromamba": "setup-micromamba --micromamba-binary-path ./micromamba/micromamba --micromamba-root-path ./micromamba --init-shell none --create-environment true --environment-file environment.yml --log-level info --run-command \"clean -fya\"",
-    "start-hypha": "pnpm setup-micromamba && ./micromamba/micromamba run -r micromamba -n itk-viewer hypha --host=127.0.0.1 --port=37580",
+    "start-hypha": "pnpm setup-micromamba && ./micromamba/micromamba run -r micromamba -n itk-viewer hypha --host=127.0.0.1 --port=9000 --startup-functions ./test/agave-startup.py:hypha_startup ./test/ome-zarr-startup.py:hypha_startup",
     "test": "pnpm test:downloadData && concurrently -n \"hypha,cypress\" --success first -k \"pnpm start-hypha\" \"pnpm cy:component\"",
     "test:downloadData": "node test/downloadData.mjs",
     "cy:watch": "cypress open --component -b chrome",

packages/agave-renderer/itk_viewer_agave_renderer/renderer.py

@@ -40,7 +40,7 @@ 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
@@ -118,7 +118,7 @@ async def draw_frame(self):
         img = r.memory_redraw()
         self.render_time = time.time() - start_time
         return img
-    
+
     def get_render_time(self):
         return self.render_time
 
@@ -187,21 +187,14 @@ async def on_ended():
 
     async def connect(
         self,
-        hypha_server_url,
+        server,
         load_image_into_agave_fn,
         visibility="public",
-        identifier="agave-renderer-rtc",
+        identifier=f"{RENDERER_SERVICE_ID}-rtc",
     ):
         self.load_image = functools.partial(load_image_into_agave_fn, self)
 
         service_id = identifier
-        client_id = service_id + "-client"
-        server = await connect_to_server(
-            {
-                "client_id": client_id,
-                "server_url": hypha_server_url,
-            }
-        )
 
         await server.register_service(
             {

packages/agave-renderer/pyproject.toml

@@ -16,11 +16,11 @@ authors = [
 classifiers = [
   "Development Status :: 4 - Beta",
   "Programming Language :: Python",
-  "Programming Language :: Python :: 3.7",
   "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: Implementation :: CPython",
   "Programming Language :: Python :: Implementation :: PyPy",
 ]
@@ -59,7 +59,7 @@ cov = [
 ]
 
 [[tool.hatch.envs.all.matrix]]
-python = ["3.7", "3.8", "3.9", "3.10", "3.11"]
+python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
 [tool.hatch.envs.lint]
 detached = true

packages/element/.env.example

@@ -1,4 +1,4 @@
 VITE_HYPHA_URL=http://127.0.0.1:9000
 VITE_HYPHA_RENDER_SERVICE_ID=agave-renderer-rtc
 VITE_HYPHA_REMOTE_ZARR_SERVICE_ID=remote-zarr
-VITE_IMAGE=data/aneurism.ome.tif
+VITE_IMAGE=input/ome-ngff-prototypes/single_image/v0.4/zyx.ome.zarr

packages/remote-image/itk_viewer_remote_image/remote_zarr.py

@@ -4,7 +4,6 @@
 
 from pathlib import Path
 
-from imjoy_rpc.hypha import connect_to_server
 import zarr
 from ngff_zarr import (
     detect_cli_io_backend,
@@ -47,37 +46,34 @@ def __init__(self):
         pass
 
     async def get_store(self, image_path):
-        print(f"get_store: {image_path}", flush=True)
+        print(f"image_path: {image_path}", flush=True)
 
         mapped_path = self.map_path(image_path)
+        print(f"mapped_path: {mapped_path}", flush=True)
 
         if mapped_path.find("://") == -1 and not Path(mapped_path).exists():
             print(f"File not found: {mapped_path}\n", flush=True)
             raise Exception(f"File not found: {mapped_path}\n")
 
         backend = detect_cli_io_backend([mapped_path])
         if backend is ConversionBackend.NGFF_ZARR:
-            return zarr.storage.DirectoryStore(mapped_path)
+            return zarr.storage.DirectoryStore(mapped_path, dimension_separator="/")
 
         # TODO: code below does not work yet
         image = cli_input_to_ngff_image(backend, [mapped_path])
-        multiscales = to_multiscales(image, method=Methods.DASK_IMAGE_GAUSSIAN)
+        multiscales = to_multiscales(image, method=Methods.ITKWASM_GAUSSIAN)
         store, chunk_store = _make_multiscale_store()
         to_ngff_zarr(store, multiscales, chunk_store=chunk_store)
 
         return store
 
     async def connect(
         self,
-        hypha_server_url,
+        server,
         map_path=lambda p: p,
         visibility="public",
         identifier="remote-zarr",
     ):
-        server = await connect_to_server(
-            {"name": "remote-zarr", "server_url": hypha_server_url}
-        )
-
         self.map_path = map_path
 
         await server.register_service(

packages/remote-image/pyproject.toml

@@ -7,7 +7,7 @@ name = "itk-viewer-remote-image"
 dynamic = ["version"]
 description = ''
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 license = "Apache-2.0"
 keywords = []
 authors = [
@@ -17,16 +17,16 @@ authors = [
 classifiers = [
   "Development Status :: 4 - Beta",
   "Programming Language :: Python",
-  "Programming Language :: Python :: 3.7",
   "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: Implementation :: CPython",
   "Programming Language :: Python :: Implementation :: PyPy",
 ]
 dependencies = [
-  "ngff-zarr[dask-image]",
+  "ngff-zarr",
   "zarr",
   "hypha",
   "numpy",
@@ -59,7 +59,7 @@ cov = [
 ]
 
 [[tool.hatch.envs.all.matrix]]
-python = ["3.7", "3.8", "3.9", "3.10", "3.11"]
+python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
 [tool.hatch.envs.lint]
 detached = true

packages/remote-image/tests/get_store.py

@@ -1,11 +1,12 @@
+import os
 import asyncio
 from imjoy_rpc.hypha import connect_to_server
 
-HYPHA_SERVER_URL = "https://hypha.website"
-
+from dotenv import load_dotenv
 
 async def main():
-    server = await connect_to_server({"server_url": HYPHA_SERVER_URL})
+    hypha_server_url = os.environ.get("HYPHA_SERVER_URL", "https://hypha.website")
+    server = await connect_to_server({"server_url": hypha_server_url})
 
     svc = await server.get_service("remote-zarr")
 

packages/remote-image/tests/service.py

@@ -1,17 +1,29 @@
+import os
 import asyncio
+from pathlib import Path
 
-from itk_viewer_remote_image import RemoteZarr
-
-HYPHA_SERVER_URL = "https://hypha.website"
+from imjoy_rpc.hypha import connect_to_server
 
-remoteZarr = RemoteZarr()
+from dotenv import load_dotenv
 
+from itk_viewer_remote_image import RemoteZarr
 
 def map_path(image_path) -> str:
-    return f"../../../test/data/input/{image_path}"
+    script_dir = os.path.dirname(os.path.realpath(__file__))
+    image_path_mapped = Path(script_dir) / '..' / '..' / '..' / 'test' / 'data' / 'input' / image_path
+    return str(image_path_mapped)
+
+async def hypha_startup():
+    hypha_server_url = os.environ.get("HYPHA_SERVER_URL", "https://hypha.website")
+    server = await connect_to_server(
+        {"name": "remote-zarr-client", "server_url": hypha_server_url}
+    )
+
+    remote_zarr = RemoteZarr()
+    await remote_zarr.connect(server, map_path)
 
 
 if __name__ == "__main__":
     loop = asyncio.new_event_loop()
-    task = loop.create_task(remoteZarr.connect(HYPHA_SERVER_URL, map_path))
+    task = loop.create_task(hypha_startup())
     loop.run_forever()

test/agave-startup.py

@@ -0,0 +1,37 @@
+import os
+import websockets
+
+from dotenv import load_dotenv
+
+from itk_viewer_agave_renderer import Renderer
+
+load_dotenv()
+
+async def check_websocket_server():
+    try:
+        async with websockets.connect('ws://localhost:1235') as ws:
+            return True
+    except Exception as e:
+        print(f"Failed to connect: {e}")
+        return False
+
+async def load_image(renderer, image_path="", multiresolution_level=0, channels=[], region=[]):
+    agave_renderer = renderer.agave
+
+    script_dir = os.path.dirname(os.path.realpath(__file__))
+    image_path_mapped = os.path.join(script_dir, f"data/{image_path}")
+
+    agave_renderer.load_data(
+        image_path_mapped, 0, multiresolution_level, 0, channels, region
+    )
+
+async def hypha_startup(server):
+    renderer = Renderer()
+
+    server_is_listening = await check_websocket_server()
+    if not server_is_listening:
+        print("Server is not listening, start with `agave --server`")
+        print("Skipping tests...")
+        return
+
+    await renderer.connect(server, load_image)

test/ome-zarr-startup.py

@@ -0,0 +1,18 @@
+import os
+from pathlib import PosixPath
+
+from dotenv import load_dotenv
+
+from itk_viewer_remote_image import RemoteZarr
+
+load_dotenv()
+
+def map_path(image_path) -> str:
+    script_dir = os.path.dirname(os.path.realpath(__file__))
+    image_path_mapped = PosixPath(script_dir) / "data" / image_path
+    return str(image_path_mapped.resolve())
+
+async def hypha_startup(server):
+    remote_zarr = RemoteZarr()
+
+    await remote_zarr.connect(server, map_path)