Python script as a plugin

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1

Hi,

I wanted to add python script as a plugin:

 import logging
from typing import List, Tuple

from labthings import fields, find_component
from labthings.views import ActionView

from openflexure_microscope.utilities import axes_to_array

import board
import busio
import adafruit_ads1x15.ads1115 as ADS
from adafruit_ads1x15.analog_in import AnalogIn
import time
import collections
from multiprocessing import Process, Pipe


def adcMonitor(conn):
    i2c = busio.I2C(board.SCL, board.SDA)
    ads = ADS.ADS1115(i2c)
    ads.gain = 16
    ads.mode = ADS.Mode.CONTINUOUS
    ads.data_rate = 860
    chan = AnalogIn(ads, ADS.P0)

    while True:
        if (conn.recv() == "start"):
            running = True
            buffer = []
            lastValue = 0
            while (running == True):

                # Should we stop?
                if (conn.poll()):
                    if (conn.recv() == "stop"):
                        running = False

                # Get value and make sure it's unique
                nextValue = chan.value
                if (nextValue != lastValue):
                    buffer.append(chan.value)
            
            # Send back the ADC readings
            conn.send(buffer)


parent_conn, child_conn = Pipe()
p = Process(target=adcMonitor, args=(child_conn,))
p.start()

class MeasureZAPI(ActionView):
    args = {
        "absolute": fields.Boolean(
            missing=False, example=False, description="Move to an absolute position"
        ),
        "x": fields.Int(missing=0, example=100),
        "y": fields.Int(missing=0, example=100),
        "z": fields.Int(missing=0, example=20),
        "z2": fields.Int(missing=0, example=100),
    }

    def post(self, args):
        """
        Move the microscope stage in x, y, z
        """
        microscope = find_component("org.openflexure.microscope")
        # Handle absolute positioning (calculate a relative move from current position and target)
        if (args.get("absolute")) and (microscope.stage):  # Only if stage exists
            target_position: List[int] = axes_to_array(args, ["x", "y", "z"])
            logging.debug("TARGET: %s", (target_position))
            position: Tuple[int, int, int] = (
                target_position[i] - microscope.stage.position[i] for i in range(3)
            )

            logging.debug("DELTA: %s", (position))

        else:
            # Get coordinates from payload
            position = axes_to_array(args, ["x", "y", "z"], [0, 0, 0])

        # Get second coordinate position
        if (args.get("absolute")) and (microscope.stage):  # Only if stage exists
            target_position: List[int] = axes_to_array(args, ["x", "y", "z2"])
            logging.debug("TARGET: %s", (target_position))
            position2: Tuple[int, int, int] = (
                target_position[i] - microscope.stage.position[i] for i in range(3)
            )

            logging.debug("DELTA: %s", (position2))

        else:
            # Get coordinates from payload
            position2 = axes_to_array(args, ["x", "y", "z2"], [0, 0, 0])

        logging.debug(position)
        logging.debug(position2)

        # Move if stage exists
        if microscope.stage:
            # Explicitally acquire lock with 1s timeout
            with microscope.stage.lock(timeout=1):
                microscope.stage.move_rel(position)

            # start the measurement
            parent_conn.send("start")
            with microscope.stage.lock(timeout=1):
                microscope.stage.move_rel(position2)
            parent_conn.send("stop")

        else:
            logging.warning("Unable to move. No stage found.")

        return parent_conn.recv()



i2c = busio.I2C(board.SCL, board.SDA)
ads = ADS.ADS1115(i2c)
ads.gain = 16
ads.mode = ADS.Mode.SINGLE

chan = AnalogIn(ads, ADS.P0)

class MoveMeasureAPI(ActionView):
    args = {
        "absolute": fields.Boolean(
            missing=False, example=False, description="Move to an absolute position"
        ),
        "x": fields.Int(missing=0, example=100),
        "y": fields.Int(missing=0, example=100),
        "z": fields.Int(missing=0, example=20),
        "measurements": fields.Int(missing=0, example=100),
    }

    def post(self, args):
        """
        Move the microscope stage in x, y, z
        """
        microscope = find_component("org.openflexure.microscope")
        # Handle absolute positioning (calculate a relative move from current position and target)
        if (args.get("absolute")) and (microscope.stage):  # Only if stage exists
            target_position: List[int] = axes_to_array(args, ["x", "y", "z"])
            logging.debug("TARGET: %s", (target_position))
            position: Tuple[int, int, int] = (
                target_position[i] - microscope.stage.position[i] for i in range(3)
            )

            logging.debug("DELTA: %s", (position))

        else:
            # Get coordinates from payload
            position = axes_to_array(args, ["x", "y", "z"], [0, 0, 0])

        logging.debug(position)

        v = []
        for i in range(0, args['measurements']):
            v.push(chan.value)
           
        return v

class MoveStageAPI(ActionView):
    args = {
        "absolute": fields.Boolean(
            missing=False, example=False, description="Move to an absolute position"
        ),
        "x": fields.Int(missing=0, example=100),
        "y": fields.Int(missing=0, example=100),
        "z": fields.Int(missing=0, example=20),
    }

    def post(self, args):
        """
        Move the microscope stage in x, y, z
        """
        microscope = find_component("org.openflexure.microscope")

        # Handle absolute positioning (calculate a relative move from current position and target)
        if (args.get("absolute")) and (microscope.stage):  # Only if stage exists
            target_position: List[int] = axes_to_array(args, ["x", "y", "z"])
            logging.debug("TARGET: %s", (target_position))
            position: Tuple[int, int, int] = (
                target_position[i] - microscope.stage.position[i] for i in range(3)
            )
            logging.debug("DELTA: %s", (position))

        else:
            # Get coordinates from payload
            position = axes_to_array(args, ["x", "y", "z"], [0, 0, 0])

        logging.debug(position)

        # Move if stage exists
        if microscope.stage:
            # Explicitally acquire lock with 1s timeout
            with microscope.stage.lock(timeout=1):
                microscope.stage.move_rel(position)
        else:
            logging.warning("Unable to move. No stage found.")

        return microscope.state["stage"]["position"]

class ZeroStageAPI(ActionView):
    def post(self):
        """
        Zero the stage coordinates.
        Does not move the stage, but rather makes the current position read as [0, 0, 0]
        """
        microscope = find_component("org.openflexure.microscope")

        with microscope.stage.lock(timeout=1):
            microscope.stage.zero_position()

        return microscope.state["stage"]

but I get an error with openflexure_microscope module.
How to fix this?

2

Hi @pawel1010, I guess the first question is how you’re running the script - is it being correctly picked up as a plugin, or are you running it directly with python from the command line? If the latter, you’d need to be in the right virtual environment for it to load properly - on the Raspberry Pi you can do this by running ofm activate in the terminal. However, running the Python file won’t allow you to use the HTTP interface to the plugin. In order to do that, the simplest way to do it is to put your script in \var\openflexure\extensions\microscope_extensions\ (NB I’ve not checked this path - the folder should exist, but it might be called microscope_plugins or something). After doing that, run ofm restart, and it should load your script as a plugin. If it fails, there should be errors in the log explaining why. If you run ofm serve those errors should also be printed to the console.

I’m working on an improved plugin architecture for v3, it won’t change the plugins very much but it should make it much clearer how to enable/disable them,

3

Thank you for explanation.
I probably successfully installed the plugin, because I get an error with establishing new connection on my PC, details are on my GitHub in section issues.