[wip] Integrating pH / DO probes (software only)

Assume there is available DO or pH measurements over i2c. Users would like to do the following:

1. Display the measurements in the UI
2. Act on the measurements (dosing, air valve, etc)
3. Export the historical measurements

pH and DO can be two different plugins. Below, I'll use pH, but DO should like very similar.

Database table

Open up pio db and paste the following:

CREATE TABLE IF NOT EXISTS pH_readings (
    experiment               TEXT NOT NULL,
    pioreactor_unit          TEXT NOT NULL,
    timestamp                TEXT NOT NULL,
    pH_reading               REAL NOT NULL
);

CREATE INDEX IF NOT EXISTS pH_measurements_ix
ON pH_readings (experiment);

.q to quit.

Chart yaml for UI

1. Add the following to ~/.pioreactor/plugins/ui/contrib/charts/ph.yaml
2. Add ph_readings=1 under [ui.overview.charts] in your configuration.

---
data_source: pH_readings # SQL table
data_source_column: ph_reading
title: pH 
mqtt_topic: pH_reading/pH
chart_key: ph_readings
source: pH_readings_plugin
y_axis_label: pH
interpolation: stepAfter
y_axis_domain: [6, 8]
lookback: 100000
fixed_decimals: 2

pH measurement reading job

Add the following to ~/.pioreactor/plugins/ph_reading.py

# -*- coding: utf-8 -*-
import json
import click
import busio
from time import sleep
from pioreactor.whoami import get_unit_name, get_assigned_experiment_name
from pioreactor.config import config
from pioreactor.background_jobs.base import BackgroundJobContrib
from pioreactor.utils import clamp
from pioreactor.utils.timing import RepeatedTimer
from pioreactor import hardware
from pioreactor.background_jobs.leader.mqtt_to_db_streaming import produce_metadata
from pioreactor.background_jobs.leader.mqtt_to_db_streaming import register_source_to_sink
from pioreactor.background_jobs.leader.mqtt_to_db_streaming import TopicToParserToTable
from pioreactor import types as pt


def __dir__():
    return ['click_pH_reading']


def parser(topic, payload) -> dict:
    metadata = produce_metadata(topic)
    return {
        "experiment": metadata.experiment,
        "pioreactor_unit": metadata.pioreactor_unit,
        "timestamp": timing.current_utc_timestamp(),
        "pH_reading": float(payload),
    }


register_source_to_sink(
    TopicToParserToTable(
        ["pioreactor/+/+/pH_reading/pH"],
        parser,
        "pH_readings",
    )
)



class PHReader(BackgroundJobContrib):

    job_name="ph_reading"
    published_settings = {
        "pH": {"datatype": "float", "settable": False},
    }

    def __init__(self, unit, experiment, **kwargs) -> None:
        super().__init__(unit=unit, experiment=experiment, plugin_name="ph_reading", **kwargs)

        time_between_readings = config.getfloat("ph_reading.config", "time_between_readings")
        assert time_between_readings >= 2.0

        self.i2c_channel = int(config.get("ph_reading.config", "i2c_channel_hex"), base=16)
        self.i2c = busio.I2C(3,2)
        self.timer_thread = RepeatedTimer(time_between_readings, self.read_pH, job_name=self.job_name, run_immediately=True).start()

    def read_pH(self):
        samples = 2
        running_sum = 0.0
        for _ in range(samples):
            running_sum += self.query("R")
            sleep(0.05)

        self.pH = running_sum/samples
        return pH

    def on_ready_to_sleeping(self) -> None:
        self.timer_thread.pause()

    def on_sleeping_to_ready(self) -> None:
        self.timer_thread.unpause()

    def on_disconnect(self) -> None:
        self.timer_thread.cancel()

    def write(self, cmd):
        cmd_bytes = bytes(cmd + "\x00", "latin-1")  # Null-terminated command
        self.i2c.writeto(self.i2c_channel, cmd_bytes)

    @staticmethod
    def handle_raspi_glitch(response):
        return [chr(x & ~0x80) for x in response]

    def read(self, num_of_bytes=31):
        result = bytearray(num_of_bytes)
        self.i2c.readfrom_into(self.i2c_channel, result)
        response = self.get_response(result)
        char_list = self.handle_raspi_glitch(response[1:])
        return float(''.join(char_list))

    def query(self, command):
        self.write(command)
        current_timeout = 1.5
        sleep(current_timeout)
        return self.read()

    @staticmethod
    def get_response(raw_data):
        return [i for i in raw_data if i != 0]


@click.command(name="pH_reading")
def click_pH_reading():
    """
    Start pH reading
    """
    unit = get_unit_name()
    job = PHReader(
        unit=unit,
        experiment=get_assigned_experiment_name(unit),
    )
    job.block_until_disconnected()

Dosing automation to target a pH

Open questions

1. What is the frequency of measurements?

Start by reviewing the proposed schema via pio db, the chart definition at ~/.pioreactor/plugins/ui/contrib/charts/ph.yaml, and the plugin entry point ~/.pioreactor/plugins/ph_reading.py. Clarify measurement frequency and the scope of dosing automation before implementing. Done should cover displaying, acting on, and exporting pH or DO measurements.