Random observations with first axon integration

[beniroquai]

@MarcoFrankeAxon the backend is now communicating with your frontend <3

Very brief points

• Neighborpoint list should contain center point, too / or rather have them all in the right order @beniroquai
• I thikn every major/single point should treat sub points as neighbourpoints
• Also the tabs for state/epxeriment are not equal on both sides
• Current state:
  
• Axon Tab should have a meaningful name @beniroquai
• How do we store the data wisely? @beniroquai
• Check Experiment state (based on backend)
  available states:

    def get_status(self):
        if not hasattr(self, "current_context") or self.current_context is None:
            return {"status": "idle"}
        if self.current_context.should_stop:
            return {"status": "stopping"}
        if self.current_context.should_pause:
            return {"status": "paused"}
        return {"status": "running"}

• there is an issue with the position callback (Fixed)
• the virtualstage is still hardcoded (still @MarcoFrankeAxon const url = https://imswitch.openuc2.com/PositionerController/movePositioner?positionerName=ESP32Stage&speed=20000&axis=`;`/Users/bene/Downloads/microscope-app/src/axon/PositionControllerComponent.js`
• I have pushed eveything into my mainbranch and made some minor modifications
• Found something hardcoded: const url = https://imswitch.openuc2.com/PositionerController/movePositioner?positionerName=VirtualStage&axis=`;`
• The go-to-position only transmits information in the X-direction - right? INFO: 127.0.0.1:50218 - "GET /PositionerController/homeAxis?positionerName=ESP32Stage&axis=X&isBlocking=false HTTP/1.1" 200 OK (fixed)
• Speed should be transmitted, too (@MarcoFrankeAxon set speed in gui please
• we need a force-stop button to stop the stage entirely (@MarcoFrankeAxon in move camera, https://localhost:8001/PositionerController/stopAxis?axis=X)
• A z+/- button would be great too (@MarcoFrankeAxon next to jogdial)
• Not sure if we can copy this button http://wiki.fluidnc.com/en/features/webui

- scan pattern should be snake to save time (@beniroquai ) - Start/stop Experiment should be under / over list (@beniroquai ) - We need a calibration routine tab (e.g. go to center, have special sample inside with hole in the very center and position incrementally in x/y in the liveview to hit the crosshair

Next steps:

• Adapt to real-world microscope (done)
• use proper pixelsize: @MarcoFrankeAxon

Name: sigObjectiveChanged

Args: {"p0":0.2,"p1":0.5,"p2":10,"p3":"10x"}

https://localhost:8001/ObjectiveController/getstatus

  "x1": 3600.036,
  "x2": 13860,
  "pos": 9091,
  "isHomed": 0,
  "state": 1,
  "isRunning": 1,
"fovx_um":100, 
"fovx_um":100,
"pixelsize_camera_x": 1,
"pixelsize_camera_y": 1
}

• how to integrate the objective switcher? integration of objective switcher #27 ((@beniroquai ))

@MarcoFrankeAxon Please modify the ObjectiveController to integrate the API for MovePositioner and replace the socket with the redux states. Sänk ju

CC: @Mikrodoktor @OrganaLeia @KillerInk @ranranking

[beniroquai]

update in real live

[KillerInk]

i know that xyz control from printrun/pronterface and esp3dwebui
so i dont see a problem to use it^^

[beniroquai]

I went through their code but couldn'T get the webui working - so I couldn't find the Controls joystick in Webui ^^
Somewhere here:
https://github.com/luc-github/ESP3D-WEBUI/blob/773e3edc8f27efa2debfd6e14d164c5ad26db4b6/www/sub/controlspanel.html#L6

[KillerInk]

and

https://github.com/luc-github/ESP3D-WEBUI/blob/773e3edc8f27efa2debfd6e14d164c5ad26db4b6/www/js/controls.js#L9-L28

https://raw.githubusercontent.com/luc-github/ESP3D-WEBUI/773e3edc8f27efa2debfd6e14d164c5ad26db4b6/www/images/jogdial1.svg

and then handel the onclick stuff and send the commands

[beniroquai]

Wait, you can have interactive SVGs? How come i missed that one :D

Is there dark version of this 😎

[beniroquai]

@christiankuttke as a calibration sample - maybe it's wise to use a stenzil or a pcb with vias? This can generate a pattern for calibration - we should observe vias under a microscope. Maybe a perfect pinhole already?

[beniroquai]

not too bad :D

[KillerInk]

Wait, you can have interactive SVGs? How come i missed that one :D

Is there dark version of this 😎

hm dark version would be a darker background, seems to be translucent

[beniroquai]

@MarcoFrankeAxon objective response:
https://localhost:8001/ObjectiveController/getstatus

{
  "x1": 0,
  "x2": 0,
  "pos": 0,
  "isHomed": 0,
  "state": 0,
  "isRunning": 0,
  "FOV": [
    100,
    100
  ],
  "pixelsize": 0.2
}

same via socket

Name: sigObjectiveChanged

Args: {"p0":0.2,"p1":0.5,"p2":10,"p3":"10x","p4":100,"p5":100}

    sigObjectiveChanged = Signal(float, float, float, str, float, float) # pixelsize, NA, magnification, objectiveName, FOVx, FOVy

[MarcoFrankeAxon]

@beniroquai can you provide the new ObjectiveController/getstatus interface at https://imswitch.openuc2.com?

[beniroquai]

Unfortunately, the objectivecontroller only works with the ESP32 configuration as of now (the online-version has the virtual-stage, etc. - if you need this functionality, this would take me some time to construct). I can provide you with the openapi.json, then you can use this for further investigation?

The backend code lives here:
https://github.com/openUC2/ImSwitch/blob/ded06eb7a7c5458e43315d9355f933547b8b74db/imswitch/imcontrol/controller/controllers/ObjectiveController.py#L123

[MarcoFrankeAxon]

Args: {"p0":0.2,"p1":0.5,"p2":10,"p3":"10x","p4":100,"p5":100}

   sigObjectiveChanged = Signal(float, float, float, str, float, float) # pixelsize, NA, magnification, objectiveName, FOVx, FOVy

@beniroquai you should prefer to give the fields p0-p5 specific names. for example, use the meaning “fovx” for “p5”. To do this, you have to remap the structure in the backend. The advantage is that it is more clear. Preferably the same names as in the get status response.
Nevertheless, I'll implement it as it is for now.

[MarcoFrankeAxon]

@beniroquai I have modified the ObjectiveController so that it uses api, fetch and states. Unfortunately, a few things are unclear to me, which is why I couldn't finish converting them.
Ssome state data has been moved to the ObjectiveSlice. Also the requesting and setting of data via the state handling (fetch) was integrated.
I would suggest you take a look at it and we can discuss it together.

For example, I'm not sure whether the detector gets its own slice.
I also don't quite understand why some data are collected via the sigUpdateImage.

[beniroquai]

@beniroquai you should prefer to give the fields p0-p5 specific names. for example, use the meaning “fovx” for “p5”. To do this, you have to remap the structure in the backend. The advantage is that it is more clear. Preferably the same names as in the get status response.
Nevertheless, I'll implement it as it is for now.

It would be possible to change the signature of the signal I suppose, but instead I can also provide a dictionary with key/value pairs - works?

We could have this basetype for both the socket and server:

class ObjectiveStatusModel(BaseModel):
    x1: float
    x2: float
    z1: float
    z2: float
    pos: float
    isHomed: bool
    state: int
    isRunning: bool
    FOV: Tuple[float, float]
    pixelsize: float

where z values are the coresponding z refocussing values to have both plane in focus