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import streamlit as st
import paho.mqtt.client as mqtt
import json
import time
import os
import asyncio
import pandas as pd
from datetime import datetime
import pytz
# The web app that will connect to the PioReactor MQTT broker and control the reactor
# Author: Enrui (Edison) Lin
experiment = None
running = []
temp_graph = None
od_graph = None
norm_od_graph = None
growth_rate_graph = None
all_graph = False
temp_mqtt_auto = None
rpm_mqtt = None
led_mqtt = None
experiments = []
# if st.session_state.get("channels", None) is not None:
# st.session_state["channel_a"] = int(st.session_state["channels"].get("A", 0))
# st.session_state["channel_b"] = int(st.session_state["channels"].get("B", 0))
# st.session_state["channel_c"] = int(st.session_state["channels"].get("C", 0))
# st.session_state["channel_d"] = int(st.session_state["channels"].get("D", 0))
REQUEST_INTERVAL = 120
if "experiment" not in st.session_state:
st.session_state["experiment"] = None
st.session_state["jobs"] = {
"temperature_automation": False,
"growth_rate_calculating": False,
"stirring": False,
"od_reading": False,
"led_automation": False,
"dosing_automation": False
}
st.session_state["client"] = None
# Create a form to get the MQTT broker details
st.title("PioReactor MQTT Client")
# Create a button to choose whether or not to use custom credentials
use_custom_credentials = st.checkbox("Use Custom Credentials")
if use_custom_credentials:
with st.form("mqtt_form"):
# hivemq_host = st.text_input("HiveMQ Host", type="password")
# hivemq_username = st.text_input("HiveMQ Username", type="password")
# hivemq_password = st.text_input("HiveMQ Password", type="password")
# hivemq_port = st.number_input("HiveMQ Port", min_value=1, max_value=65535, step=1, value=8883)
# reactor = st.text_input("PioReactor")
hivemq_host = st.text_input("HiveMQ Host", type="password")
hivemq_username = st.text_input("HiveMQ Username", type="password")
hivemq_password = st.text_input("HiveMQ Password", type="password")
hivemq_port = st.number_input("HiveMQ Port", min_value=1, max_value=65535, step=1, value=8883)
reactor = st.text_input("PioReactor")
submit_button = st.form_submit_button("Connect")
else:
hivemq_host = os.getenv("host")
hivemq_username = os.getenv("username")
hivemq_password = os.getenv("password")
hivemq_port = int(os.getenv("port"))
reactor = os.getenv("reactor")
# button to submit the form
if st.session_state["experiment"] is None:
submit_button = st.button("Connect")
else:
submit_button = st.button("Reconnect")
# Create the MQTT client
# @st.cache_resource
def create_mqtt_client(hivemq_host, hivemq_port, hivemq_username, hivemq_password):
client = mqtt.Client()
# Set authentication and TLS settings
client.username_pw_set(hivemq_username, hivemq_password)
client.tls_set(tls_version=mqtt.ssl.PROTOCOL_TLS_CLIENT)
# Define callback functions
def on_connect(client, userdata, flags, rc):
if rc == 0:
st.success("Connected to HiveMQ successfully!")
else:
st.error(f"Failed to connect, return code {rc}")
client.on_connect = on_connect
return client
def on_message_worker(client, userdata, message):
payload = message.payload.decode("utf-8")
data = json.loads(payload)
global experiment
global running
global temp_mqtt_auto
global rpm_mqtt
global led_mqtt
global experiments
experiment = data.get("experiment", None)
running = data.get("running", [])
temp_mqtt_auto = data.get("temperature_automation", None)
rpm_mqtt = data.get("stirring", None)
led_mqtt = data.get("leds", None)
experiments = data.get("experiments", [])
def on_message(client, userdata, message):
payload = message.payload.decode("utf-8")
data = json.loads(payload)
global temp_graph
global od_graph
global norm_od_graph
global growth_rate_graph
temp_graph = data.get("temperature", None)
od_graph = data.get("od", None)
norm_od_graph = data.get("normalized_od", None)
growth_rate_graph = data.get("growth_rate", None)
async def publish_temperature_request(client, experiment, filter_mod_N, lookback, reactor):
"""Publish a temperature request to the request topic."""
payload = {
"command": "get_temperature_readings",
"experiment": experiment,
"filter_mod": filter_mod_N,
"lookback": lookback,
"reactor": reactor
}
payload_str = json.dumps(payload)
client.publish("pioreactor/control", payload_str)
async def periodic_temp_reading(client, reactor, experiment, placeholder):
try:
while True:
await publish_temperature_request(client, experiment, 1, 100000, reactor)
global temp_graph
placeholder.write(temp_graph)
await asyncio.sleep(REQUEST_INTERVAL)
except asyncio.CancelledError:
pass
async def run_mqtt_client(client, placeholder):
client.subscribe(f"pioreactor/{reactor}/temp_reading")
client.subscribe(f"pioreactor/{reactor}/od_reading")
client.subscribe(f"pioreactor/{reactor}/growth_rate")
client.on_message = on_message
client.loop_start()
await periodic_temp_reading(client, reactor, st.session_state["experiment"], placeholder)
def get_running_jobs(client, reactor):
payload = {
"command": "get_worker",
"reactor": reactor
}
payload_str = json.dumps(payload)
client.publish("pioreactor/control", payload_str)
global experiment
experiment = None
running = []
client.subscribe(f"pioreactor/{reactor}/worker")
client.message_callback_add(f"pioreactor/{reactor}/worker", on_message_worker)
timeout = 10
start_time = time.time()
while experiment is None and (time.time() - start_time) < timeout:
time.sleep(1)
if experiment is None:
st.error("Failed to get info")
st.session_state["experiment"] = None
time.sleep(3)
st.rerun()
if experiment != st.session_state["experiment"]:
st.session_state["experiment"] = experiment
if st.session_state["jobs"]["temperature_automation"]:
if temp_mqtt_auto == "thermostat":
st.session_state["temp_auto"] = "Heat To Temp"
elif temp_mqtt_auto == "only_record_temperature":
st.session_state["temp_auto"] = "Record Temp Only"
st.session_state["temp"] = None
if st.session_state["jobs"]["stirring"]:
print(rpm_mqtt)
st.session_state["stirring_speed"] = rpm_mqtt
# st.session_state["channels"] = led_mqtt
if led_mqtt is not None:
st.session_state["channel_a"] = int(led_mqtt.get("A", 0))
st.session_state["channel_b"] = int(led_mqtt.get("B", 0))
st.session_state["channel_c"] = int(led_mqtt.get("C", 0))
st.session_state["channel_d"] = int(led_mqtt.get("D", 0))
st.session_state["experiments"] = experiments
for run in running:
st.session_state["jobs"][run] = True
async def get_graph(placeholder):
try:
st.session_state["client"].loop_start()
st.session_state["client"].subscribe(f"pioreactor/{reactor}/temperature")
st.session_state["client"].message_callback_add(f"pioreactor/{reactor}/temperature", on_message)
while True:
await publish_temperature_request(st.session_state["client"], st.session_state["experiment"], 1, 100000, reactor)
await asyncio.sleep(REQUEST_INTERVAL)
global temp_graph
placeholder.write(temp_graph)
except asyncio.CancelledError:
pass
if submit_button:
client = create_mqtt_client(hivemq_host, hivemq_port, hivemq_username, hivemq_password)
# Publish a message to the MQTT broker
if client:
client.connect(hivemq_host, hivemq_port)
client.loop_start()
# Subscribe to the worker topic
client.subscribe(f"pioreactor/{reactor}/worker")
client.message_callback_add(f"pioreactor/{reactor}/worker", on_message_worker)
payload = {
"command": "get_worker",
"reactor": reactor
}
payload_str = json.dumps(payload)
client.publish("pioreactor/control", payload_str)
timeout = 10
start_time = time.time()
while experiment is None and (time.time() - start_time) < timeout:
time.sleep(1)
st.session_state["experiment"] = experiment
# Unsubscribe from the worker topic
# client.unsubscribe(f"pioreactor/{reactor}/worker")
# client.message_callback_remove(f"pioreactor/{reactor}/worker")
client.loop_stop()
if st.session_state["experiment"] is None:
st.error("No experiment assigned to the reactor.")
for run in running:
st.session_state["jobs"][run] = True
if st.session_state["jobs"]["temperature_automation"]:
if temp_mqtt_auto == "thermostat":
st.session_state["temp_auto"] = "Heat To Temp"
elif temp_mqtt_auto == "only_record_temperature":
st.session_state["temp_auto"] = "Record Temp Only"
st.session_state["temp"] = None
if st.session_state["jobs"]["stirring"]:
print(rpm_mqtt)
st.session_state["stirring_speed"] = rpm_mqtt
if led_mqtt is not None:
st.session_state["channel_a"] = int(led_mqtt.get("A", 0))
st.session_state["channel_b"] = int(led_mqtt.get("B", 0))
st.session_state["channel_c"] = int(led_mqtt.get("C", 0))
st.session_state["channel_d"] = int(led_mqtt.get("D", 0))
st.session_state["experiments"] = experiments
# Save the client to the session state
st.session_state["client"] = client
# Display the experiment and running jobs if available
if st.session_state["experiment"] is not None:
st.title(f"Experiment: {st.session_state['experiment']}")
st.header("Running Jobs")
cols = st.columns(6)
with cols[0]:
st.write("Temperature")
st.write(st.session_state["jobs"]["temperature_automation"])
with cols[1]:
st.write("Growth Rate")
st.write(st.session_state["jobs"]["growth_rate_calculating"])
with cols[2]:
st.write("Stirring")
st.write(st.session_state["jobs"]["stirring"])
with cols[3]:
st.write("OD Reading")
st.write(st.session_state["jobs"]["od_reading"])
with cols[4]:
st.write("LED")
st.write(st.session_state["jobs"]["led_automation"])
with cols[5]:
st.write("Dosing")
st.write(st.session_state["jobs"]["dosing_automation"])
st.divider()
with st.form("experiment_form"):
new_name = st.text_input("New Experiment Name")
submit_new_experiment = st.form_submit_button("Create New Experiment")
change_experiment_submit = False
delete_experiment = False
with st.form("experiment_edit"):
if len(st.session_state["experiments"]) > 0:
experiment_change = st.selectbox("Select Experiment", st.session_state["experiments"])
cols = st.columns(2)
with cols[0]:
change_experiment_submit = st.form_submit_button("Change Experiment")
with cols[1]:
delete_experiment = st.form_submit_button("Delete Experiment")
else:
st.write("No experiments available.")
st.form_submit_button("Nothing Button")
if submit_new_experiment:
payload = {
"command": "new_experiment",
"experiment": new_name,
"reactor": reactor
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
get_running_jobs(st.session_state["client"], reactor)
if new_name in st.session_state["experiments"]:
st.success("Experiment created successfully!")
else:
st.error("Failed to create experiment.")
st.session_state["client"].loop_stop()
time.sleep(3)
st.rerun()
if change_experiment_submit:
payload = {
"command": "change_experiment",
"experiment": st.session_state["experiment"],
"experiment_new": experiment_change,
"reactor": reactor
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(3)
get_running_jobs(st.session_state["client"], reactor)
if experiment_change == st.session_state["experiment"]:
st.success("Experiment changed successfully!")
else:
st.error("Failed to change experiment.")
st.info(f"Experiment name changed to {experiment_change} from {st.session_state['experiment']}")
st.session_state["client"].loop_stop()
time.sleep(3)
st.rerun()
if delete_experiment:
payload = {
"command": "delete_experiment",
"experiment": experiment_change,
"reactor": reactor
}
payload_str = json.dumps(payload)
time.sleep(1)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
get_running_jobs(st.session_state["client"], reactor)
if experiment_change not in st.session_state["experiments"]:
st.success("Experiment deleted successfully!")
else:
st.error("Failed to delete experiment.")
st.session_state["client"].loop_stop()
time.sleep(3)
st.rerun()
st.divider()
# Display the job details
st.header("Stirring")
if st.session_state["jobs"]["stirring"]:
with st.form("stirring_form"):
if st.session_state.get("stirring_speed", None) is None:
st.write("Current Stirring Speed Unknown")
else:
st.write(f"Current Stirring Speed: {st.session_state['stirring_speed']} RPM")
stirring_speed = st.slider("Stirring Speed", min_value=100, max_value=3000, step=50, value=st.session_state.get("stirring_speed", 500))
cols = st.columns(2)
with cols[0]:
stirring = st.form_submit_button("Update Stirring Speed")
with cols[1]:
stop_stirring = st.form_submit_button("Stop Stirring")
else:
with st.form("stirring_form"):
stirring_speed = st.slider("Stirring Speed", min_value=100, max_value=3000, step=50, value=500)
stirring = st.form_submit_button("Start Stirring")
stop_stirring = False
if stirring:
if st.session_state["jobs"]["stirring"]:
payload = {
"command": "update_stirring_rpm",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"rpm": stirring_speed
}
else:
payload = {
"command": "start_stirring",
"experiment": st.session_state["experiment"],
"reactor": reactor,
"rpm": stirring_speed
}
payload_str = json.dumps(payload)
# Start looping
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
# Check if the stirring job is running
payload = {
"command": "get_worker",
"reactor": reactor
}
experiment = None
running = []
st.session_state["client"].subscribe(f"pioreactor/{reactor}/worker")
st.session_state["client"].message_callback_add(f"pioreactor/{reactor}/worker", on_message_worker)
payload_str = json.dumps(payload)
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
timeout = 10
start_time = time.time()
while experiment is None and (time.time() - start_time) < timeout:
time.sleep(1)
st.session_state["client"].loop_stop()
if "stirring" in running and st.session_state["jobs"]["stirring"]:
st.success("Stirring speed updated successfully!")
st.session_state["stirring_speed"] = stirring_speed
elif "stirring" in running:
st.success("Stirring started successfully!")
st.session_state["jobs"]["stirring"] = True
st.session_state["stirring_speed"] = stirring_speed
else:
st.error("Failed to update stirring speed.")
st.session_state["experiment"] = None
st.session_state["jobs"]["stirring_speed"] = None
time.sleep(3)
st.rerun()
if stop_stirring:
payload = {
"command": "stop_stirring",
"reactor": reactor,
"experiment": st.session_state["experiment"]
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
st.session_state["client"].loop_stop()
# Check if the stirring job is running
payload = {
"command": "get_worker",
"reactor": reactor
}
st.session_state["client"].subscribe(f"pioreactor/{reactor}/worker")
st.session_state["client"].message_callback_add(f"pioreactor/{reactor}/worker", on_message_worker)
experiment = None
running = []
payload_str = json.dumps(payload)
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
timeout = 10
start_time = time.time()
while experiment is None and (time.time() - start_time) < timeout:
time.sleep(1)
if "stirring" not in running:
st.success("Stirring stopped successfully!")
st.session_state["stirring_speed"] = None
st.session_state["jobs"]["stirring"] = False
else:
st.error("Failed to stop stirring.")
time.sleep(3)
st.rerun()
st.divider()
st.header("Temperature Automation")
if st.session_state["jobs"]["temperature_automation"]:
temp = None
if st.session_state.get("temp_auto", None) is None:
st.write("Current Temperature Automation Unknown, changes will result in restart of the automation to new settings.")
temp_auto = st.selectbox("Temperature Automation", ["Record Temp Only", "Heat To Temp"], placeholder="UNKNOWN")
with st.form("temperature_form"):
if temp_auto == "Heat To Temp":
temp = st.slider("Temperature", min_value=0, max_value=60, step=1, value=30)
cols = st.columns(2)
with cols[0]:
temp_submit = st.form_submit_button("Restart Temperature Automation")
with cols[1]:
temp_stop = st.form_submit_button("Stop Temperature Automation")
elif temp_auto == "Record Temp Only":
cols = st.columns(2)
with cols[0]:
temp_submit = st.form_submit_button("Restart Temperature Automation")
with cols[1]:
temp_stop = st.form_submit_button("Stop Temperature Automation")
else:
if st.session_state["temp_auto"] == "Heat To Temp":
index = 1
elif st.session_state["temp_auto"] == "Record Temp Only":
index = 0
temp_auto = st.selectbox("Temperature Automation", ["Record Temp Only", "Heat To Temp"], index=index)
with st.form("temperature_form"):
st.write(f"Current Temperature Automation: {st.session_state['temp_auto']}")
if temp_auto == "Heat To Temp":
if st.session_state.get("temp", None) is not None:
st.write(f"Current Temperature: {st.session_state['temp']} °C")
temp = st.slider("Temperature", min_value=0, max_value=60, step=1, value=st.session_state["temp"] if st.session_state["temp"] is not None else 30)
cols = st.columns(2)
with cols[0]:
temp_submit = st.form_submit_button("Update Temperature Automation")
with cols[1]:
temp_stop = st.form_submit_button("Stop Temperature Automation")
elif temp_auto == "Record Temp Only":
cols = st.columns(2)
with cols[0]:
temp_submit = st.form_submit_button("Update Temperature Automation", disabled=(st.session_state["temp_auto"] == "Record Temp Only"))
with cols[1]:
temp_stop = st.form_submit_button("Stop Temperature Automation")
else:
temp = None
temp_auto = st.selectbox("Temperature Automation", ["Record Temp Only", "Heat To Temp"], placeholder="Select an option")
with st.form("temperature_form"):
if temp_auto == "Heat To Temp":
temp = st.slider("Temperature", min_value=0, max_value=60, step=1, value=30)
temp_submit = st.form_submit_button("Start Temperature Automation")
temp_stop = False
elif temp_auto == "Record Temp Only":
temp_submit = st.form_submit_button("Start Temperature Automation")
temp_stop = False
if temp_submit:
# Convert the temperature automation to the payload
if temp_auto == "Heat To Temp":
payload_auto = "thermostat"
elif temp_auto == "Record Temp Only":
payload_auto = "only_record_temperature"
# Update the temperature automation
if st.session_state["jobs"]["temperature_automation"]:
#Check if the temperature automation is the same as the current one
if temp_auto == st.session_state.get("temp_auto", None):
# Same automation, update the temperature
# Update the temperature automation
payload = {
"command": "temp_update",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"settings": {
"target_temperature": temp
}
}
else:
# Different automation, restart the automation
payload = {
"command": "temp_restart",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"automation": payload_auto,
"temp": temp
}
else:
# Start the temperature automation
payload = {
"command": "set_temperature_automation",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"automation": payload_auto,
"temp": temp
}
payload_str = json.dumps(payload)
# Start looping
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
# Check if the stirring job is running
payload = {
"command": "get_worker",
"reactor": reactor
}
experiment = None
running = []
st.session_state["client"].subscribe(f"pioreactor/{reactor}/worker")
st.session_state["client"].message_callback_add(f"pioreactor/{reactor}/worker", on_message_worker)
payload_str = json.dumps(payload)
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
timeout = 10
start_time = time.time()
while experiment is None and (time.time() - start_time) < timeout:
time.sleep(1)
st.session_state["client"].loop_stop()
if "temperature_automation" in running and st.session_state["jobs"]["temperature_automation"]:
st.success("Temperature automation updated!")
st.session_state["temp_auto"] = temp_auto
st.session_state["temp"] = temp
elif "temperature_automation" in running:
st.success("Temperature automation started successfully!")
st.session_state["jobs"]["temperature_automation"] = True
st.session_state["temp_auto"] = temp_auto
st.session_state["temp"] = temp
else:
st.error("Failed to update temperature automation speed.")
st.session_state["experiment"] = None
st.session_state["jobs"]["temperature_automation"] = None
time.sleep(3)
st.rerun()
if temp_stop:
payload = {
"command": "temp_update",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"settings": {
"$state": "disconnected"
}
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
# Check if the temperature automation job has stopped
payload = {
"command": "get_worker",
"reactor": reactor
}
experiment = None
running = []
st.session_state["client"].subscribe(f"pioreactor/{reactor}/worker")
st.session_state["client"].message_callback_add(f"pioreactor/{reactor}/worker", on_message_worker)
payload_str = json.dumps(payload)
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
timeout = 10
start_time = time.time()
while experiment is None and (time.time() - start_time) < timeout:
time.sleep(1)
if "temperature_automation" not in running:
st.success("Temperature automation stopped successfully!")
st.session_state["temp_auto"] = None
st.session_state["temp"] = None
else:
st.error("Failed to stop temperature automation.")
st.session_state["experiment"] = None
time.sleep(3)
st.rerun()
st.divider()
cols = st.columns(2)
start_od = False
stop_od = False
start_growth = False
stop_growth = False
with cols[0]:
st.header("OD Reading")
if st.session_state["jobs"]["od_reading"]:
stop_od = st.button("Stop OD Reading")
else:
start_od = st.button("Start OD Reading")
with cols[1]:
st.header("Growth Rate")
if st.session_state["jobs"]["growth_rate_calculating"]:
stop_growth = st.button("Stop Growth Rate Calculation")
else:
start_growth = st.button("Start Growth Rate Calculation")
if start_od:
payload = {
"command": "start_od_reading",
"reactor": reactor,
"experiment": st.session_state["experiment"]
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(2)
# Check if the OD reading job is running
get_running_jobs(st.session_state["client"], reactor)
st.session_state["client"].loop_stop()
if "od_reading" in running:
st.success("OD Reading started successfully!")
st.session_state["jobs"]["od_reading"] = True
else:
st.error("Failed to start OD Reading.")
st.session_state["experiment"] = None
for run in running:
st.session_state["jobs"][run] = True
st.session_state["experiment"] = experiment
time.sleep(3)
st.rerun()
if stop_od:
payload = {
"command": "stop_od_reading",
"reactor": reactor,
"experiment": st.session_state["experiment"]
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
# Check if the OD reading job has stopped
get_running_jobs(st.session_state["client"], reactor)
st.session_state["client"].loop_stop()
if "od_reading" not in running:
st.success("OD Reading stopped successfully!")
st.session_state["jobs"]["od_reading"] = False
else:
st.error("Failed to stop OD Reading.")
st.session_state["experiment"] = None
for run in running:
st.session_state["jobs"][run] = True
st.session_state["experiment"] = experiment
time.sleep(3)
st.rerun()
if start_growth:
payload = {
"command": "start_growth_rate",
"reactor": reactor,
"experiment": st.session_state["experiment"]
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
# Check if the growth rate job is running
get_running_jobs(st.session_state["client"], reactor)
st.session_state["client"].loop_stop()
if "growth_rate_calculating" in running:
st.success("Growth Rate Calculation started successfully!")
st.session_state["jobs"]["growth_rate_calculating"] = True
else:
st.error("Failed to start Growth Rate Calculation.")
st.session_state["experiment"] = None
for run in running:
st.session_state["jobs"][run] = True
st.session_state["experiment"] = experiment
time.sleep(3)
st.rerun()
if stop_growth:
payload = {
"command": "stop_growth_rate",
"reactor": reactor,
"experiment": st.session_state["experiment"]
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
# Check if the growth rate job has stopped
get_running_jobs(st.session_state["client"], reactor)
st.session_state["client"].loop_stop()
if "growth_rate_calculating" not in running:
st.success("Growth Rate Calculation stopped successfully!")
st.session_state["jobs"]["growth_rate_calculating"] = False
else:
st.error("Failed to stop Growth Rate Calculation.")
st.session_state["experiment"] = None
for run in running:
st.session_state["jobs"][run] = True
st.session_state["experiment"] = experiment
time.sleep(3)
st.rerun()
st.divider()
# Display the temperature graph
# Using asyncio to run the loop in the background and periodically update the graph
# st.header("LED Automation")
# with st.form("led_form"):
# channel_a = st.slider("Channel A", min_value=0, max_value=100, step=1, value=0)
# channel_a_submit = st.form_submit_button("Update Channel A")
# if channel_a_submit:
# payload = {
# "command": "set_led_intensity",
# "reactor": reactor,
# "experiment": st.session_state["experiment"],
# "brightness": channel_a,
# "led": "A"
# }
# payload_str = json.dumps(payload)
# st.session_state["client"].loop_start()
# st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
# time.sleep(1)
# # Check if the LED automation job is running
# get_running_jobs(st.session_state["client"], reactor)
# st.session_state["client"].loop_stop()
# if "led_automation" in running:
# st.success("LED Automation updated!")
# else:
# st.error("Failed to update LED Automation.")
# st.session_state["experiment"] = None
# for run in running:
# st.session_state["jobs"][run] = True
# st.session_state["experiment"] = experiment
# time.sleep(3)
# st.rerun()
# with st.form("led_form_b"):
# channel_b = st.slider("Channel B", min_value=0, max_value=100, step=1, value=0)
# channel_b_submit = st.form_submit_button("Update Channel B")
# if channel_b_submit:
# payload = {
# "command": "set_led_intensity",
# "reactor": reactor,
# "experiment": st.session_state["experiment"],
# "brightness": channel_b,
# "led": "B"
# }
# payload_str = json.dumps(payload)
# st.session_state["client"].loop_start()
# st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
# time.sleep(1)
# # Check if the LED automation job is running
# get_running_jobs(st.session_state["client"], reactor)
# st.session_state["client"].loop_stop()
# if "led_automation" in running:
# st.success("LED Automation updated!")
# else:
# st.error("Failed to update LED Automation.")
# st.session_state["experiment"] = None
# for run in running:
# st.session_state["jobs"][run] = True
# st.session_state["experiment"] = experiment
# time.sleep(3)
# st.rerun()
# with st.form("led_form_c"):
# channel_c = st.slider("Channel C", min_value=0, max_value=100, step=1, value=0)
# channel_c_submit = st.form_submit_button("Update Channel C")
# if channel_c_submit:
# payload = {
# "command": "set_led_intensity",
# "reactor": reactor,
# "experiment": st.session_state["experiment"],
# "brightness": channel_c,
# "led": "C"
# }
# payload_str = json.dumps(payload)
# st.session_state["client"].loop_start()
# st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
# time.sleep(1)
# # Check if the LED automation job is running
# get_running_jobs(st.session_state["client"], reactor)
# st.session_state["client"].loop_stop()
# if "led_automation" in running:
# st.success("LED Automation updated!")
# else:
# st.error("Failed to update LED Automation.")
# st.session_state["experiment"] = None
# for run in running:
# st.session_state["jobs"][run] = True
# st.session_state["experiment"] = experiment
# time.sleep(3)
# st.rerun()
# with st.form("led_form_d"):
# channel_d = st.slider("Channel D", min_value=0, max_value=100, step=1, value=0)
# channel_d_submit = st.form_submit_button("Update Channel D")
# if channel_d_submit:
# payload = {
# "command": "set_led_intensity",
# "reactor": reactor,
# "experiment": st.session_state["experiment"],
# "brightness": channel_d,
# "led": "D"
# }
# payload_str = json.dumps(payload)
# st.session_state["client"].loop_start()
# st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
# time.sleep(1)
# # Check if the LED automation job is running
# get_running_jobs(st.session_state["client"], reactor)
# st.session_state["client"].loop_stop()
# if "led_automation" in running:
# st.success("LED Automation updated!")
# else:
# st.error("Failed to update LED Automation.")
# st.session_state["experiment"] = None
# for run in running:
# st.session_state["jobs"][run] = True
# st.session_state["experiment"] = experiment
# time.sleep(3)
# st.rerun()
# st.divider()
st.header("LEDS")
cols = st.columns(4)
with cols[0]:
st.write("Channel A")
with st.form("led_form_a"):
channel_a_placeholder = st.empty()
channel_a_submit = st.form_submit_button("Update Channel A")
with cols[1]:
st.write("Channel B")
with st.form("led_form_b"):
channel_b_placeholder = st.empty()
channel_b_submit = st.form_submit_button("Update Channel B")
with cols[2]:
st.write("Channel C")
with st.form("led_form_c"):
channel_c_placeholder = st.empty()
channel_c_submit = st.form_submit_button("Update Channel C")
with cols[3]:
st.write("Channel D")
with st.form("led_form_d"):
channel_d_placeholder = st.empty()
channel_d_submit = st.form_submit_button("Update Channel D")
channel_a = channel_a_placeholder.number_input("Channel A", min_value=0, max_value=100, step=1, value=st.session_state.get("channel_a", 0))
channel_b = channel_b_placeholder.number_input("Channel B", min_value=0, max_value=100, step=1, value=st.session_state.get("channel_b", 0))
channel_c = channel_c_placeholder.number_input("Channel C", min_value=0, max_value=100, step=1, value=st.session_state.get("channel_c", 0))
channel_d = channel_d_placeholder.number_input("Channel D", min_value=0, max_value=100, step=1, value=st.session_state.get("channel_d", 0))
if channel_a_submit:
pass
if channel_b_submit:
payload = {
"command": "set_led_intensity",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"brightness": channel_b,
"led": "B"
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
channel_a_placeholder.empty()
channel_b_placeholder.empty()
channel_c_placeholder.empty()
channel_d_placeholder.empty()
# Check if the LED automation job is running
get_running_jobs(st.session_state["client"], reactor)
st.session_state["client"].loop_stop()
if channel_b == int(led_mqtt.get("B", 0)):
st.success("LED Intensity updated!")
else:
st.error("Failed to update LED Intensity.")
st.session_state["experiment"] = None
for run in running:
st.session_state["jobs"][run] = True
st.session_state["experiment"] = experiment
time.sleep(3)
st.rerun()
if channel_c_submit:
payload = {
"command": "set_led_intensity",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"brightness": channel_c,
"led": "C"
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
channel_a_placeholder.empty()
channel_b_placeholder.empty()
channel_c_placeholder.empty()
channel_d_placeholder.empty()
# Check if the LED automation job is running
get_running_jobs(st.session_state["client"], reactor)
st.session_state["client"].loop_stop()
if channel_c == int(led_mqtt.get("C", 0)):
st.success("LED Intensity updated!")
else:
st.error("Failed to update LED Intensity.")
st.session_state["experiment"] = None
for run in running:
st.session_state["jobs"][run] = True
st.session_state["experiment"] = experiment
time.sleep(3)
st.rerun()
if channel_d_submit:
payload = {
"command": "set_led_intensity",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"brightness": channel_d,
"led": "D"
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
channel_a_placeholder.empty()
channel_b_placeholder.empty()
channel_c_placeholder.empty()
channel_d_placeholder.empty()
# Check if the LED automation job is running
get_running_jobs(st.session_state["client"], reactor)
st.session_state["client"].loop_stop()
if channel_d == int(led_mqtt.get("D", 0)):
st.success("LED Intensity updated!")
else:
st.error("Failed to update LED Intensity.")
st.session_state["experiment"] = None
for run in running:
st.session_state["jobs"][run] = True
st.session_state["experiment"] = experiment
time.sleep(3)
st.rerun()
st.divider()
st.header("Dosing")
cols = st.columns(3)
with cols[0]:
st.subheader("Add Media")
with st.form("media_form"):
media_ml = st.number_input("Media (mL)", min_value=0, step=1, value=0)
media_submit = st.form_submit_button("Add Media")
with cols[1]:
st.subheader("Remove Waste")
with st.form("waste_form"):
waste_ml = st.number_input("Waste (mL)", min_value=0, step=1, value=0)
waste_submit = st.form_submit_button("Remove Waste")
with cols[2]:
st.subheader("Cycle Media")
with st.form("cycle_form"):
cycle_s = st.number_input("Cycle (s)", min_value=0, step=1, value=0)
cycle_submit = st.form_submit_button("Cycle Media")
if media_submit:
payload = {
"command": "pump_add_media",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"volume": media_ml
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
# Check if the dosing job is running
# get_running_jobs(st.session_state["client"], reactor)
# st.session_state["client"].loop_stop()
# if "dosing" in running:
# st.success("Media added successfully!")
# else:
# st.error("Failed to add media.")
# st.session_state["experiment"] = None
# for run in running:
# st.session_state["jobs"][run] = True
# st.session_state["experiment"] = experiment
st.success("Media added successfully!")
time.sleep(3)
st.rerun()
if waste_submit:
payload = {
"command": "pump_remove_media",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"volume": waste_ml
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
# Check if the dosing job is running
# get_running_jobs(st.session_state["client"], reactor)
# st.session_state["client"].loop_stop()
# if "dosing" in running:
# st.success("Waste removed successfully!")
# else:
# st.error("Failed to remove waste.")
# st.session_state["experiment"] = None
# for run in running:
# st.session_state["jobs"][run] = True
# st.session_state["experiment"] = experiment
st.success("Waste removed successfully!")
time.sleep(3)
st.rerun()
if cycle_submit:
payload = {
"command": "circulate_media",
"reactor": reactor,
"experiment": st.session_state["experiment"],
"duration": cycle_s
}
payload_str = json.dumps(payload)
st.session_state["client"].loop_start()
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
time.sleep(1)
# Check if the dosing job is running
# get_running_jobs(st.session_state["client"], reactor)
# st.session_state["client"].loop_stop()
# if "dosing" in running:
# st.success("Media cycled successfully!")
# else:
# st.error("Failed to cycle media.")
# st.session_state["experiment"] = None
# for run in running:
# st.session_state["jobs"][run] = True
# st.session_state["experiment"] = experiment
st.success("Media cycled successfully!")
time.sleep(3)
st.rerun()
st.divider()
st.header("Graphs")
st.session_state["client"].loop_start()
st.session_state["client"].subscribe(f"pioreactor/{reactor}/readings")
st.session_state["client"].message_callback_add(f"pioreactor/{reactor}/readings", on_message)
temp_graph_actual = []
st.subheader("Temperature Graph")
amount_of_data = st.radio("Amount of data", ["1 hour", "24 hours", "All data"], index=1, key="temperature")
placeholder = st.empty()
st.subheader("OD Reading Graph")
amount_of_data2 = st.radio("Amount of data", ["1 hour", "24 hours", "All data"], index=1, key="od")
placeholder2 = st.empty()
st.subheader("Normalized OD Reading Graph")
amount_of_data3 = st.radio("Amount of data", ["1 hour", "24 hours", "All data"], index=1, key="norm_od")
placeholder3 = st.empty()
st.subheader("Growth Rate Graph")
amount_of_data4 = st.radio("Amount of data", ["1 hour", "24 hours", "All data"], index=1, key="growth_rate")
placeholder4 = st.empty()
# get_graph(placeholder)
while True:
if st.session_state.get("df", None) is not None and st.session_state.get("temp_radio", None) == amount_of_data:
placeholder.line_chart(st.session_state["df"], x_label="Time", y_label="Temperature (°C)")
if st.session_state.get("df2", None) is not None and st.session_state.get("od_radio", None) == amount_of_data2:
placeholder2.line_chart(st.session_state["df2"], x_label="Time", y_label="OD Reading")
if st.session_state.get("df3", None) is not None and st.session_state.get("norm_od_radio", None) == amount_of_data3:
placeholder3.line_chart(st.session_state["df3"], x_label="Time", y_label="Normalized OD Reading")
if st.session_state.get("df4", None) is not None and st.session_state.get("growth_rate_radio", None) == amount_of_data4:
placeholder4.line_chart(st.session_state["df4"], x_label="Time", y_label="Growth Rate")
st.session_state["temp_radio"] = amount_of_data
st.session_state["od_radio"] = amount_of_data2
st.session_state["norm_od_radio"] = amount_of_data3
st.session_state["growth_rate_radio"] = amount_of_data4
temp_graph = None
od_graph = None
norm_od_graph = None
growth_rate_graph = None
payload = {
"command": "get_readings",
"experiment": st.session_state["experiment"],
"reactor": reactor,
"filter_mod": 1,
"lookback": 10000000,
"filter_mod2": 1,
"lookback2": 10000000,
"filter_mod3": 1,
"lookback3": 10000000,
"filter_mod4": 1,
"lookback4": 10000000,
"amount": amount_of_data,
"amount2": amount_of_data2,
"amount3": amount_of_data3,
"amount4": amount_of_data4
}
payload_str = json.dumps(payload)
st.session_state["client"].publish("pioreactor/control", payload_str, qos=1)
timeout = 10
start_time = time.time()
while (temp_graph is None or od_graph is None or norm_od_graph is None or growth_rate_graph is None) and (time.time() - start_time) < timeout:
time.sleep(1)
# Check if all is None
# if temp_graph is None and od_graph is None and norm_od_graph is None and growth_rate_graph is None:
# st.error("Failed to retrieve data.")
# st.stop()
if len(temp_graph) != 0:
for temp in temp_graph:
utc_time = datetime.strptime(temp["x"], "%Y-%m-%dT%H:%M:%S.%fZ")
local_tz = pytz.timezone("America/New_York")
utc_time = utc_time.replace(tzinfo=pytz.utc)
local_time = utc_time.astimezone(local_tz)
temp["x"] = local_time.strftime("%Y-%m-%d %H:%M:%S")
df = pd.DataFrame(temp_graph)
df = df.set_index("x")
placeholder.line_chart(df, x_label="Time", y_label="Temperature (°C)")
st.session_state["df"] = df
if len(od_graph) != 0:
for od in od_graph:
utc_time = datetime.strptime(od["x"], "%Y-%m-%dT%H:%M:%S.%fZ")
local_tz = pytz.timezone("America/New_York")
utc_time = utc_time.replace(tzinfo=pytz.utc)
local_time = utc_time.astimezone(local_tz)
od["x"] = local_time.strftime("%Y-%m-%d %H:%M:%S")
df2 = pd.DataFrame(od_graph)
df2 = df2.set_index("x")
placeholder2.line_chart(df2, x_label="Time", y_label="OD Reading")
st.session_state["df2"] = df2
if len(norm_od_graph) != 0:
for norm_od in norm_od_graph:
utc_time = datetime.strptime(norm_od["x"], "%Y-%m-%dT%H:%M:%S.%fZ")
local_tz = pytz.timezone("America/New_York")
utc_time = utc_time.replace(tzinfo=pytz.utc)
local_time = utc_time.astimezone(local_tz)
norm_od["x"] = local_time.strftime("%Y-%m-%d %H:%M:%S")
df3 = pd.DataFrame(norm_od_graph)
df3 = df3.set_index("x")
placeholder3.line_chart(df3, x_label="Time", y_label="Normalized OD Reading")
st.session_state["df3"] = df3
if len(growth_rate_graph) != 0:
for growth_rate in growth_rate_graph:
utc_time = datetime.strptime(growth_rate["x"], "%Y-%m-%dT%H:%M:%S.%fZ")
local_tz = pytz.timezone("America/New_York")
utc_time = utc_time.replace(tzinfo=pytz.utc)
local_time = utc_time.astimezone(local_tz)
growth_rate["x"] = local_time.strftime("%Y-%m-%d %H:%M:%S")
df4 = pd.DataFrame(growth_rate_graph)
df4 = df4.set_index("x")
placeholder4.line_chart(df4, x_label="Time", y_label="Growth Rate")
st.session_state["df4"] = df4
# Filter the data based on the amount of data requested
# Data is in 4 minute intervals
time.sleep(REQUEST_INTERVAL)
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