Web UI

[nilsmechtel]

Register data providing service in pyodide environment to:

• serve image files from the mounted folder (/mnt/)
• save annotation masks to the annotations folder (/mnt/annotations/)

Challenge:

• Run loop.run_forever() but return the annotator_url from pyodide to the main thread

Notes:

• Multiple options are listed in docs/services.py
• The value of annotationURL is currently being displayed in the Sidebar for testing purposes
• With the initial commit the annotator_url can be found in the logs, but the link doesn't work.

---

General question, does an imjoy plugin work with hypha-rpc?
Plugin: https://github.com/bioimage-io/bioimageio-colab/blob/web-ui/plugins/bioimageio-colab-annotator.imjoy.html
Generation of annotator URL:

bioimageio-colab/docs/services.py

Lines 93 to 98 in 4d3bd61

	annotation_sid = svc["id"]
	config_str = f'{{"server_url": "{SERVER_URL}", "annotation_service_id": "{annotation_sid}", "token": "{token}"}}'
	encoded_config = urllib.parse.quote(
	config_str, safe="/", encoding=None, errors=None
	)
	annotator_url = f"https://imjoy.io/lite?plugin={PLUGIN_URL}&config={encoded_config}"

[nilsmechtel]

@oeway do you have an idea how to communicate the annotation URL to the main thread?

[oeway]

Hi @nilsmechtel Found a solution for you, you can basically break the code into 3 blocks and run it in 3 times (calling runCode): 1) run the code to get the register_service function 2) register the service (here you can then get the url from its return) 3) you can do run_forever;

I will make a commit soon.

[oeway]

Hi @nilsmechtel I made some comments to help you understand my changes.

[oeway]

@nilsmechtel This is for saving file handle into indexeddb, so we don't need to select the folder every time when the page reload

[oeway]

I used a promise here, so we can defer the loading process, only wait for it when the user click deploy annotation. You can see how Promise works.

[oeway]

here the token is saved so we can pass it to the pyodide worker later.

[oeway]

This is when we actually wait for the worker ready (it start loading when the page loaded, and keep loading in the background).

[oeway]

The worker has a mechanism to detect service, so we use the type 'service' to capture directly the registered service instead of parsing the stdout (this is a prefered approach), once you get the service url, you can then create an annotation url in js.

[oeway]

Note that the annotation plugin need to updated to use hypha rpc instead of imjoy rpc. Also I would create this annotation url in js instead of python.