PySeq 2501 Web Interface

This repo is now merged into the main PySeq2501 repo.

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This is the web interface and the communication system for PySeq 2501. Click on the badge above to see an example site!

Usage

Installation

For development

• Install npm.
• Install poetry.
  • If you have a conda environment, you can create a new environment with python=3.10 poetry as dependencies.

  conda create -n {NAME REPLACE THIS} python=3.10 poetry

Then,

git clone https://github.com/chaichontat/pyseq2501-web
cd pyseq2501-web
poetry install
npm i
npm run build

A tox environment is available to make sure everything works.

Run

pyseq2server --fake

Usage: pyseq2server [OPTIONS]

Options:
  -p, --port INTEGER  Port to run the server on (default: 8000).
  -h, --host TEXT     Hostname to bind to (default: localhost). Set 0.0.0.0
                      for network access.
  -o, --open          Open a web browser
  --fake              Use fake machine interface.
  --donothost         Only host the websocket, not the interface. Useful when
                      developing Svelte.
  --help              Show this message and exit.

The interface should be waiting for you at http://localhost:8000/!

Dependencies

graph LR
  subgraph pyseq2_
    pyseq2
    .config
    .experiment
    .imager
    .utils
    .utils.coords
  end

  pyseq2 --> ps2s.api.types
  pyseq2 --> ps2s.routers.mancommand
  pyseq2 --> ps2s.routers.status
  pyseq2 --> ps2s.server
  pyseq2 --> ps2s.utils.log
  .config --> pyseq2
  .config --> ps2s.routers.status
  .experiment --> ps2s.api.types
  .experiment --> ps2s.routers.mancommand
  .imager --> pyseq2
  .imager --> ps2s.routers.status
  .utils --> pyseq2
  .utils --> .imager
  .utils --> ps2s.api.types
  .utils --> ps2s.server
  .utils.coords --> ps2s.api.types
  .utils.coords --> ps2s.server

  subgraph pyseq2server
    ps2s.api.types --> ps2s.routers.mancommand
    ps2s.api.types --> ps2s.routers.user
    ps2s.api.types --> ps2s.server
    ps2s.imaging --> ps2s.routers.mancommand
    ps2s.imaging --> ps2s.server
    ps2s.routers --> ps2s.server
    ps2s.routers.mancommand --> ps2s.server
    ps2s.routers.status --> ps2s.routers.mancommand
    ps2s.routers.status --> ps2s.server
    ps2s.routers.user --> ps2s.server
    ps2s.server --> ps2s.__main__
    ps2s.utils --> ps2s.__main__
    ps2s.utils --> ps2s.routers.mancommand
    ps2s.utils.log --> ps2s.__main__
    ps2s.utils.utils --> ps2s.routers.mancommand
  end

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Sequence

sequenceDiagram
    participant FastAPI
    participant Experiment
        loop Every 5 seconds or when log is available
            Imager-->FastAPI: State
            FastAPI-->Camera: Log
        end

    FastAPI->>Experiment: run
    Note right of FastAPI: with userSettings as TakeImage

    Experiment->>Imager: run
    Note right of Experiment: Divide x and z into <br> multiple take commands
    Imager->>Camera: Start acquisition
    activate Camera

    loop every 2 bundles
        Camera->>FastAPI: "N bundles captured"
    end

    Camera->>Imager: All bundles captured
    deactivate Camera
    Imager->>FastAPI: Image
    Note right of FastAPI: "imgReady" via cmdStore<br> with image through GET

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