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Commit 65deb7ef authored by Olivier Kaufmann's avatar Olivier Kaufmann
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Adds basic_ohmpi_flows_node-red. Updates architecture.pdf. Moves... 

Adds basic_ohmpi_flows_node-red. Updates architecture.pdf. Moves mqtt_controller.py in examples and updates it.
parent fcc9d5f6
master EGU23 MUX_board_v2024 battery_charger board_v4 code_refactor dev2 mqtt revert-559ef012 v2023.0.0
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architecture.pdf
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examples/basic_ohmpi_flows_node-red.json 0 → 100644
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\ No newline at end of file
mqtt_controller.py → examples/mqtt_controller.py
+ 3
− 3
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......@@ -22,13 +22,13 @@ settings = {
}
cmd_id = uuid.uuid4().hex
payload = json.dumps({'cmd_id': cmd_id, 'cmd': 'update_settings', 'args': settings})
payload = json.dumps({'cmd_id': cmd_id, 'cmd': 'update_settings', 'kwargs': {'settings' : settings}})
print(f'Update settings setup message: {payload} to {publisher_config["topic"]} with config {publisher_config}')
publish.single(payload=payload, **publisher_config)
sequence = [[1, 2, 3, 4]]
cmd_id = uuid.uuid4().hex
payload = json.dumps({'cmd_id': cmd_id, 'cmd': 'set_sequence', 'args': sequence})
payload = json.dumps({'cmd_id': cmd_id, 'cmd': 'set_sequence', 'kwargs': {'sequence': sequence}})
print(f'Set sequence message: {payload} to {publisher_config["topic"]} with config {publisher_config}')
publish.single(payload=payload, **publisher_config)
cmd_id = uuid.uuid4().hex
......@@ -38,7 +38,7 @@ publish.single(payload=payload, **publisher_config)
for i in range(4):
cmd_id = uuid.uuid4().hex
payload = json.dumps({'cmd_id': cmd_id, 'cmd': 'start'})
payload = json.dumps({'cmd_id': cmd_id, 'cmd': 'run_sequence_async'})
print(f'Publishing message {i}: {payload} to {publisher_config["topic"]} with config {publisher_config}')
publish.single(payload=payload, **publisher_config)
time.sleep(1)
......
mqtt_interface.py deleted 100644 → 0
+ 0
− 53
View file @ fcc9d5f6
import paho.mqtt.client as mqtt
from config import MQTT_CONTROL_CONFIG, CONTROL_CONFIG, OHMPI_CONFIG
import time
from queue import Queue
import zmq
ctrl_queue = Queue()
def on_message(client, userdata, message):
global socket
# Send the command
print(f'Sending command {message.payload.decode("utf-8")}')
socket.send(message.payload)
# Get the reply
reply = socket.recv()
print(f'Received reply {message.payload.decode("utf-8")}: {reply}')
mqtt_client = mqtt.Client(f'ohmpi_{OHMPI_CONFIG["id"]}_listener', clean_session=False) # create new instance
print('connecting command listener to broker')
trials = 0
trials_max = 10
broker_connected = False
while trials < trials_max:
try:
mqtt_client.username_pw_set(MQTT_CONTROL_CONFIG['auth'].get('username'),
MQTT_CONTROL_CONFIG['auth']['password'])
mqtt_client.connect(MQTT_CONTROL_CONFIG['hostname'])
trials = trials_max
broker_connected = True
except:
print('trying again...')
time.sleep(2)
trials += 1
if broker_connected:
print('Subscribing to topic', MQTT_CONTROL_CONFIG['ctrl_topic'])
mqtt_client.subscribe(MQTT_CONTROL_CONFIG['ctrl_topic'], MQTT_CONTROL_CONFIG['qos'])
mqtt_client.on_message = on_message
mqtt_client.loop_start()
context = zmq.Context()
# Socket to talk to server
print("Connecting to ohmpi control server")
socket = context.socket(zmq.REQ)
socket.connect(f'tcp://localhost:{CONTROL_CONFIG["tcp_port"]}')
while True:
time.sleep(.1)
else:
print("Unable to connect to control broker")
exit(1)
ohmpi.py
+ 42
− 295
View file @ 65deb7ef
......@@ -15,7 +15,6 @@ from copy import deepcopy
import numpy as np
import csv
import time
from io import StringIO
from datetime import datetime
from termcolor import colored
import threading
......@@ -35,7 +34,8 @@ try:
import digitalio # noqa
from digitalio import Direction # noqa
from gpiozero import CPUTemperature # noqa
import minimalmodbus # noqa
import minimalmodbus # noqa
arm64_imports = True
except ImportError as error:
if EXEC_LOGGING_CONFIG['logging_level'] == DEBUG:
......@@ -130,13 +130,13 @@ class OhmPi(object):
# current injection module
if self.idps:
self.DPS = minimalmodbus.Instrument(port='/dev/ttyUSB0', slaveaddress=1) # port name, address (decimal)
self.DPS.serial.baudrate = 9600 # Baud rate 9600 as listed in doc
self.DPS.serial.bytesize = 8 #
self.DPS.serial.timeout = 1 # greater than 0.5 for it to work
self.DPS.debug = False #
self.DPS.serial.parity = 'N' # No parity
self.DPS.mode = minimalmodbus.MODE_RTU # RTU mode
self.DPS.write_register(0x0001, 40, 0) # max current allowed (36 mA for relays)
self.DPS.serial.baudrate = 9600 # Baud rate 9600 as listed in doc
self.DPS.serial.bytesize = 8 #
self.DPS.serial.timeout = 1 # greater than 0.5 for it to work
self.DPS.debug = False #
self.DPS.serial.parity = 'N' # No parity
self.DPS.mode = minimalmodbus.MODE_RTU # RTU mode
self.DPS.write_register(0x0001, 40, 0) # max current allowed (36 mA for relays)
# (last number) 0 is for mA, 3 is for A
# injection courant and measure (TODO check if it works, otherwise back in run_measurement())
......@@ -157,7 +157,7 @@ class OhmPi(object):
f" on {MQTT_CONTROL_CONFIG['hostname']} broker")
def connect_mqtt() -> mqtt_client:
def on_connect(client, userdata, flags, rc):
def on_connect(mqttclient, userdata, flags, rc):
if rc == 0:
self.exec_logger.debug(f"Successfully connected to control broker:"
f" {MQTT_CONTROL_CONFIG['hostname']}")
......@@ -170,6 +170,7 @@ class OhmPi(object):
client.on_connect = on_connect
client.connect(MQTT_CONTROL_CONFIG['hostname'], MQTT_CONTROL_CONFIG['port'])
return client
try:
self.exec_logger.debug(f"Connecting to control broker: {MQTT_CONTROL_CONFIG['hostname']}")
self.controller = connect_mqtt()
......@@ -209,6 +210,7 @@ class OhmPi(object):
Parameters
----------
cmd_id
filename : str
filename to save the last measurement dataframe
last_measurement : dict
......@@ -305,8 +307,8 @@ class OhmPi(object):
time.sleep(best_tx_injtime) # inject for given tx time
# autogain
self.ads_current = ads.ADS1115(self.i2c, gain=2/3, data_rate=860, address=self.ads_current_address)
self.ads_voltage = ads.ADS1115(self.i2c, gain=2/3, data_rate=860, address=self.ads_voltage_address)
self.ads_current = ads.ADS1115(self.i2c, gain=2 / 3, data_rate=860, address=self.ads_current_address)
self.ads_voltage = ads.ADS1115(self.i2c, gain=2 / 3, data_rate=860, address=self.ads_voltage_address)
# print('current P0', AnalogIn(self.ads_current, ads.P0).voltage)
# print('voltage P0', AnalogIn(self.ads_voltage, ads.P0).voltage)
# print('voltage P2', AnalogIn(self.ads_voltage, ads.P2).voltage)
......@@ -320,8 +322,8 @@ class OhmPi(object):
# we measure the voltage on both A0 and A2 to guess the polarity
I = AnalogIn(self.ads_current, ads.P0).voltage * 1000. / 50 / self.r_shunt # noqa measure current
U0 = AnalogIn(self.ads_voltage, ads.P0).voltage * 1000. # measure voltage
U2 = AnalogIn(self.ads_voltage, ads.P2).voltage * 1000.
U0 = AnalogIn(self.ads_voltage, ads.P0).voltage * 1000. # noqa measure voltage
U2 = AnalogIn(self.ads_voltage, ads.P2).voltage * 1000. # noqa
# print('I (mV)', I*50*self.r_shunt)
# print('I (mA)', I)
# print('U0 (mV)', U0)
......@@ -337,7 +339,7 @@ class OhmPi(object):
# compute constant
c = vmn / I
Rab = (volt * 1000.) / I
Rab = (volt * 1000.) / I # noqa
self.exec_logger.debug(f'Rab = {Rab:.2f} Ohms')
......@@ -444,6 +446,7 @@ class OhmPi(object):
Parameters
----------
cmd_id
filename : str
Path of the .csv or .txt file with A, B, M and N electrodes.
Electrode index start at 1.
......@@ -546,8 +549,6 @@ class OhmPi(object):
except Exception as e:
self.exec_logger.error(
f"Unable to execute {cmd}({str(kwargs) if kwargs is not None else ''}): {e}")
# f"Unable to execute {cmd}({str(args) + ', ' if args is not None else ''}"
# f"{str(kwargs) if kwargs is not None else ''}): {e}")
status = False
except Exception as e:
self.exec_logger.warning(f'Unable to decode command {message}: {e}')
......@@ -699,7 +700,7 @@ class OhmPi(object):
self.pin1.value = False
# one stack = 2 half-cycles (one positive, one negative)
pinMN = 0 if polarity > 0 else 2
pinMN = 0 if polarity > 0 else 2 # noqa
# sampling for each stack at the end of the injection
sampling_interval = 10 # ms
......@@ -752,7 +753,7 @@ class OhmPi(object):
end_delay = time.time()
# truncate the meas array if we didn't fill the last samples
meas = meas[:k+1]
meas = meas[:k + 1]
# measurement of current i and voltage u during off time
measpp = np.zeros((meas.shape[0], 3)) * np.nan
......@@ -779,13 +780,13 @@ class OhmPi(object):
end_delay = time.time()
# truncate the meas array if we didn't fill the last samples
measpp = measpp[:k+1]
measpp = measpp[:k + 1]
# we alternate on which ADS1115 pin we measure because of sign of voltage
if pinMN == 0:
pinMN = 2
pinMN = 2 # noqa
else:
pinMN = 0
pinMN = 0 # noqa
# store data for full wave form
fulldata.append(meas)
......@@ -799,8 +800,8 @@ class OhmPi(object):
# take average from the samples per stack, then sum them all
# average for the last third of the stacked values
# is done outside the loop
sum_i = sum_i + (np.mean(meas[-int(meas.shape[0]//3):, 0]))
vmn1 = np.mean(meas[-int(meas.shape[0]//3), 1])
sum_i = sum_i + (np.mean(meas[-int(meas.shape[0] // 3):, 0]))
vmn1 = np.mean(meas[-int(meas.shape[0] // 3), 1])
if (n % 2) == 0:
sum_vmn = sum_vmn - vmn1
sum_ps = sum_ps + vmn1
......@@ -913,121 +914,7 @@ class OhmPi(object):
if nb_meas > 1:
time.sleep(dt) # waiting for next measurement (time-lapse)
self.status = 'idle'
self.thread = threading.Thread(target=func)
self.thread.start()
def run_sequence(self, cmd_id=None, **kwargs):
"""Runs sequence synchronously (=blocking on main thread).
Additional arguments are passed to run_measurement().
"""
self.status = 'running'
self.exec_logger.debug(f'Status: {self.status}')
self.exec_logger.debug(f'Measuring sequence: {self.sequence}')
t0 = time.time()
# create filename with timestamp
filename = self.settings["export_path"].replace('.csv',
f'_{datetime.now().strftime("%Y%m%dT%H%M%S")}.csv')
self.exec_logger.debug(f'Saving to {filename}')
# make sure all multiplexer are off
self.reset_mux()
# measure all quadrupole of the sequence
if self.sequence is None:
n = 1
else:
n = self.sequence.shape[0]
for i in range(0, n):
if self.sequence is None:
quad = np.array([0, 0, 0, 0])
else:
quad = self.sequence[i, :] # quadrupole
if self.status == 'stopping':
break
# call the switch_mux function to switch to the right electrodes
self.switch_mux_on(quad)
# run a measurement
if self.on_pi:
acquired_data = self.run_measurement(quad, **kwargs)
else: # for testing, generate random data
acquired_data = {
'A': [quad[0]], 'B': [quad[1]], 'M': [quad[2]], 'N': [quad[3]],
'R [ohm]': np.abs(np.random.randn(1))
}
# switch mux off
self.switch_mux_off(quad)
# add command_id in dataset
acquired_data.update({'cmd_id': cmd_id})
# log data to the data logger
# self.data_logger.info(f'{acquired_data}')
# save data and print in a text file
self.append_and_save(filename, acquired_data)
self.exec_logger.debug(f'quadrupole {i + 1:d}/{n:d}')
self.status = 'idle'
def run_sequence_async(self, cmd_id=None, **kwargs):
"""Runs the sequence in a separate thread. Can be stopped by 'OhmPi.interrupt()'.
Additional arguments are passed to run_measurement().
Parameters
----------
cmd_id:
"""
def func():
self.run_sequence(**kwargs)
self.thread = threading.Thread(target=func)
self.thread.start()
self.status = 'idle'
def run_multiple_sequences(self, cmd_id=None, sequence_delay=None, nb_meas=None, **kwargs):
"""Runs multiple sequences in a separate thread for monitoring mode.
Can be stopped by 'OhmPi.interrupt()'.
Additional arguments are passed to run_measurement().
Parameters
----------
cmd_id :
sequence_delay : int, optional
Number of seconds at which the sequence must be started from each others.
nb_meas : int, optional
Number of time the sequence must be repeated.
kwargs : dict, optional
See help(k.run_measurement) for more info.
"""
# self.run = True
if sequence_delay is None:
sequence_delay = self.settings['sequence_delay']
sequence_delay = int(sequence_delay)
if nb_meas is None:
nb_meas = self.settings['nb_meas']
self.status = 'running'
self.exec_logger.debug(f'Status: {self.status}')
self.exec_logger.debug(f'Measuring sequence: {self.sequence}')
def func():
for g in range(0, nb_meas): # for time-lapse monitoring
if self.status == 'stopping':
self.exec_logger.warning('Data acquisition interrupted')
break
t0 = time.time()
self.run_sequence(**kwargs)
# sleeping time between sequence
dt = sequence_delay - (time.time() - t0)
if dt < 0:
dt = 0
if nb_meas > 1:
time.sleep(dt) # waiting for next measurement (time-lapse)
self.status = 'idle'
self.thread = threading.Thread(target=func)
self.thread.start()
......@@ -1079,7 +966,7 @@ class OhmPi(object):
# add command_id in dataset
acquired_data.update({'cmd_id': cmd_id})
# log data to the data logger
# self.data_logger.info(f'{acquired_data}') # already in run_measurement()
# self.data_logger.info(f'{acquired_data}')
# save data and print in a text file
self.append_and_save(filename, acquired_data)
self.exec_logger.debug(f'quadrupole {i + 1:d}/{n:d}')
......@@ -1149,8 +1036,8 @@ class OhmPi(object):
# print(str(quad) + '> I: {:>10.3f} mA, V: {:>10.3f} mV, R: {:>10.3f} kOhm'.format(
# current, voltage, resist))
msg = f'Contact resistance {str(quad):s}: I: {current * 1000.:>10.3f} mA, ' \
f'V: {voltage :>10.3f} mV, ' \
f'R: {resist :>10.3f} kOhm'
f'V: {voltage :>10.3f} mV, ' \
f'R: {resist :>10.3f} kOhm'
self.exec_logger.debug(msg)
......@@ -1171,95 +1058,11 @@ class OhmPi(object):
else:
pass
self.status = 'idle'
#
# # TODO if interrupted, we would need to restore the values
# # TODO or we offer the possibility in 'run_measurement' to have rs_check each time?
def set_sequence(self, sequence=None):
try:
self.sequence = np.loadtxt(StringIO(sequence)).astype('uint32')
status = True
except Exception as e:
self.exec_logger.warning(f'Unable to set sequence: {e}')
status = False
def stop(self):
warnings.warn('This function is deprecated. Use interrupt instead.', DeprecationWarning)
self.interrupt()
def _switch_mux(self, electrode_nr, state, role):
"""Selects the right channel for the multiplexer cascade for a given electrode.
Parameters
----------
electrode_nr : int
Electrode index to be switched on or off.
state : str
Either 'on' or 'off'.
role : str
Either 'A', 'B', 'M' or 'N', so we can assign it to a MUX board.
"""
if not self.use_mux or not self.on_pi:
if not self.on_pi:
self.exec_logger.warning('Cannot reset mux while in simulation mode...')
else:
self.exec_logger.warning('You cannot use the multiplexer because use_mux is set to False.'
' Set use_mux to True to use the multiplexer...')
elif self.sequence is None:
self.exec_logger.warning('Unable to switch MUX without a sequence')
else:
# choose with MUX board
tca = adafruit_tca9548a.TCA9548A(self.i2c, self.board_addresses[role])
# find I2C address of the electrode and corresponding relay
# considering that one MCP23017 can cover 16 electrodes
i2c_address = 7 - (electrode_nr - 1) // 16 # quotient without rest of the division
relay_nr = electrode_nr - (electrode_nr // 16) * 16 + 1
if i2c_address is not None:
# select the MCP23017 of the selected MUX board
mcp2 = MCP23017(tca[i2c_address])
mcp2.get_pin(relay_nr - 1).direction = digitalio.Direction.OUTPUT
if state == 'on':
mcp2.get_pin(relay_nr - 1).value = True
else:
mcp2.get_pin(relay_nr - 1).value = False
self.exec_logger.debug(f'Switching relay {relay_nr} '
f'({str(hex(self.board_addresses[role]))}) {state} for electrode {electrode_nr}')
else:
self.exec_logger.warning(f'Unable to address electrode nr {electrode_nr}')
def switch_mux_on(self, quadrupole):
"""Switches on multiplexer relays for given quadrupole.
Parameters
----------
quadrupole : list of 4 int
List of 4 integers representing the electrode numbers.
"""
roles = ['A', 'B', 'M', 'N']
# another check to be sure A != B
if quadrupole[0] != quadrupole[1]:
for i in range(0, 4):
if quadrupole[i] > 0:
self._switch_mux(quadrupole[i], 'on', roles[i])
else:
self.exec_logger.error('Not switching MUX : A == B -> short circuit risk detected!')
def switch_mux_off(self, quadrupole):
"""Switches off multiplexer relays for given quadrupole.
Parameters
----------
quadrupole : list of 4 int
List of 4 integers representing the electrode numbers.
"""
roles = ['A', 'B', 'M', 'N']
for i in range(0, 4):
if quadrupole[i] > 0:
self._switch_mux(quadrupole[i], 'off', roles[i])
def set_sequence(self, sequence=None, cmd_id=None):
try:
self.sequence = np.array(sequence).astype(int)
......@@ -1269,9 +1072,9 @@ class OhmPi(object):
self.exec_logger.warning(f'Unable to set sequence: {e}')
status = False
def stop(self, cmd_id=None):
def stop(self, **kwargs):
warnings.warn('This function is deprecated. Use interrupt instead.', DeprecationWarning)
self.interrupt()
self.interrupt(**kwargs)
def _switch_mux(self, electrode_nr, state, role):
"""Selects the right channel for the multiplexer cascade for a given electrode.
......@@ -1322,6 +1125,7 @@ class OhmPi(object):
Parameters
----------
cmd_id
quadrupole : list of 4 int
List of 4 integers representing the electrode numbers.
"""
......@@ -1339,6 +1143,7 @@ class OhmPi(object):
Parameters
----------
cmd_id
quadrupole : list of 4 int
List of 4 integers representing the electrode numbers.
"""
......@@ -1347,65 +1152,6 @@ class OhmPi(object):
if quadrupole[i] > 0:
self._switch_mux(quadrupole[i], 'off', roles[i])
def reset_mux(self):
"""Switches off all multiplexer relays."""
if self.on_pi and self.use_mux:
roles = ['A', 'B', 'M', 'N']
for i in range(0, 4):
for j in range(1, self.max_elec + 1):
self._switch_mux(j, 'off', roles[i])
self.exec_logger.debug('All MUX switched off.')
elif not self.on_pi:
self.exec_logger.warning('Cannot reset mux while in simulation mode...')
else:
self.exec_logger.warning('You cannot use the multiplexer because use_mux is set to False.'
' Set use_mux to True to use the multiplexer...')
def _update_acquisition_settings(self, config):
warnings.warn('This function is deprecated, use update_settings() instead.', DeprecationWarning)
self.update_settings(config)
def update_settings(self, config):
"""Updates acquisition settings from a json file or dictionary.
Parameters can be:
- nb_electrodes (number of electrode used, if 4, no MUX needed)
- injection_duration (in seconds)
- nb_meas (total number of times the sequence will be run)
- sequence_delay (delay in second between each sequence run)
- nb_stack (number of stack for each quadrupole measurement)
- export_path (path where to export the data, timestamp will be added to filename)
Parameters
----------
config : str, dict
Path to the .json settings file or dictionary of settings.
"""
status = False
if config is not None:
try:
if isinstance(config, dict):
self.settings.update(config)
else:
with open(config) as json_file:
dic = json.load(json_file)
self.settings.update(dic)
self.exec_logger.debug('Acquisition parameters updated: ' + str(self.settings))
status = True
except Exception as e:
self.exec_logger.warning('Unable to update settings.')
status = False
else:
self.exec_logger.warning('Settings are missing...')
return status
# Properties
@property
def sequence(self):
"""Gets sequence"""
if self._sequence is not None:
assert isinstance(self._sequence, np.ndarray)
return self._sequence
def reset_mux(self, cmd_id=None):
"""Switches off all multiplexer relays."""
if self.on_pi and self.use_mux:
......@@ -1422,9 +1168,9 @@ class OhmPi(object):
def _update_acquisition_settings(self, config):
warnings.warn('This function is deprecated, use update_settings() instead.', DeprecationWarning)
self.update_settings(config)
self.update_settings(settings=config)
def update_settings(self, config:str, cmd_id=None):
def update_settings(self, settings: str, cmd_id=None):
"""Updates acquisition settings from a json file or dictionary.
Parameters can be:
- nb_electrodes (number of electrode used, if 4, no MUX needed)
......@@ -1436,21 +1182,22 @@ class OhmPi(object):
Parameters
----------
config : str, dict
cmd_id
settings : str, dict
Path to the .json settings file or dictionary of settings.
"""
status = False
if config is not None:
if settings is not None:
try:
if isinstance(config, dict):
self.settings.update(config)
if isinstance(settings, dict):
self.settings.update(settings)
else:
with open(config) as json_file:
with open(settings) as json_file:
dic = json.load(json_file)
self.settings.update(dic)
self.exec_logger.debug('Acquisition parameters updated: ' + str(self.settings))
status = True
except Exception as e:
except Exception as e: # noqa
self.exec_logger.warning('Unable to update settings.')
status = False
else:
......
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