diff --git a/config.py b/config.py
index 30cba4822299c5e28a9ba2e75b14e18eb5fbdc5a..90f74494c0c70744633c63180351c8f01e4ddadc 100644
--- a/config.py
+++ b/config.py
@@ -17,7 +17,7 @@ OHMPI_CONFIG = {
# Execution logging configuration
EXEC_LOGGING_CONFIG = {
- 'debug_mode': False,
+ 'debug_mode': True,
'logging_to_console': False,
'file_name': 'ohmpi_log',
'max_bytes': 262144,
@@ -29,6 +29,7 @@ EXEC_LOGGING_CONFIG = {
# Data logging configuration
DATA_LOGGING_CONFIG = {
'file_name': 'data_log',
+ 'logging_to_console': False,
'max_bytes': 16777216,
'backup_count': 1024,
'when': 'd',
@@ -38,6 +39,7 @@ DATA_LOGGING_CONFIG = {
# State of Health logging configuration
SOH_LOGGING_CONFIG = {
'file_name': 'soh_log',
+ 'logging_to_console': True,
'max_bytes': 16777216,
'backup_count': 1024,
'when': 'd',
@@ -53,7 +55,7 @@ MQTT_LOGGING_CONFIG = {
'keepalive': 60,
'will': None,
'auth': None,
- 'tls':None,
+ 'tls': None,
'protocol': MQTTv31,
'transport': 'tcp',
'client_id': f'ohmpi_sn_{OHMPI_CONFIG["id"]}',
diff --git a/index.html b/index.html
index 8db1d579bbde5831aa10ff194b5b2713a6287324..540edc3b1c27b2689305081a369a69fbd701504b 100644
--- a/index.html
+++ b/index.html
@@ -108,8 +108,8 @@
let output = document.getElementById('output')
let data = {} // hold data of all surveys
let interv = null // hold interval for automatic data retrieval
- let quads = [] // available quadrupoles for time-serie figure
- let squads = [] // selected quadrupoles for time-serie figure
+ let quads = [] // available quadrupoles for time-series figure
+ let squads = [] // selected quadrupoles for time-series figure
// useful functions
function sendCommand(query, callback=null) {
@@ -201,10 +201,10 @@
}
Plotly.newPlot('gd', [trace], layout)
- // make time-serie plot
+ // make time-series plot
let tdata = []
let layout2 = {
- title: 'Time-serie',
+ title: 'Time-series',
yaxis: {
title: 'App. res. [Ohm.m]'
},
@@ -214,7 +214,7 @@
}
Plotly.newPlot('ts', tdata, layout2)
- // add trace to time-serie plot
+ // add trace to time-series plot
function addTraceBtnFunc() {
let val = document.getElementById('quadSelect').value
squads.push(val.split(', '))
@@ -230,7 +230,7 @@
let addTraceBtn = document.getElementById('addTraceBtn')
addTraceBtn.addEventListener('click', addTraceBtnFunc)
- // remove all traces from time-serie plot
+ // remove all traces from time-series plot
function removeTracesBtnFunc() {
squads = []
tdata = []
@@ -250,7 +250,7 @@
output.innerHTML = 'Status: ' + ddic['status']
// update data dic with new data
- data = { // destructuring assignement (magic! :o)
+ data = { // destructuring assignment (magic! :o)
...data,
...ddic['data'] // value from second dic are preferred
}
@@ -307,7 +307,7 @@
surveySelect.value = surveyNames[surveyNames.length - 1]
// call the function directly
- // (as progammatically chaging the value does not trigger the event)
+ // (as programmatically changing the value does not trigger the event)
surveySelectFunc({'target': surveySelect})
// update list of quadrupoles if any
@@ -327,7 +327,7 @@
console.log('quads=', quads)
}
- // update time-serie figure
+ // update time-series figure
if (squads.length > 0) {
// transform all surveyNames to datetime
@@ -362,7 +362,7 @@
}
}
- // update trace dictionnary
+ // update trace dictionary
tdata[k]['x'] = x
tdata[k]['y'] = y
}
diff --git a/logging_setup.py b/logging_setup.py
index 232e66635c47ef462893f390313e2db3c5753bf8..1e2e1f88d22d8fbbc8122040e8961999c2adb194 100644
--- a/logging_setup.py
+++ b/logging_setup.py
@@ -36,10 +36,11 @@ def setup_loggers(mqtt=True):
# Set message logging format and level
log_format = '%(asctime)-15s | %(process)d | %(levelname)s: %(message)s'
logging_to_console = EXEC_LOGGING_CONFIG['logging_to_console']
- exec_handler = CompressedSizedTimedRotatingFileHandler(exec_log_filename, max_bytes=EXEC_LOGGING_CONFIG['max_bytes'],
- backup_count=EXEC_LOGGING_CONFIG['backup_count'],
- when=EXEC_LOGGING_CONFIG['when'],
- interval=EXEC_LOGGING_CONFIG['interval'])
+ exec_handler = CompressedSizedTimedRotatingFileHandler(exec_log_filename,
+ max_bytes=EXEC_LOGGING_CONFIG['max_bytes'],
+ backup_count=EXEC_LOGGING_CONFIG['backup_count'],
+ when=EXEC_LOGGING_CONFIG['when'],
+ interval=EXEC_LOGGING_CONFIG['interval'])
exec_formatter = logging.Formatter(log_format)
exec_formatter.converter = gmtime
exec_formatter.datefmt = '%Y/%m/%d %H:%M:%S UTC'
@@ -55,21 +56,39 @@ def setup_loggers(mqtt=True):
mqtt_msg_handler.setFormatter(exec_formatter)
exec_logger.addHandler(mqtt_msg_handler)
- # Set data logging level and handler
- data_logger.setLevel(logging.INFO)
- data_handler = CompressedSizedTimedRotatingFileHandler(data_log_filename,
+ # Set data logging format and level
+ log_format = '%(asctime)-15s | %(process)d | %(levelname)s: %(message)s'
+ logging_to_console = DATA_LOGGING_CONFIG['logging_to_console']
+
+ data_handler = CompressedSizedTimedRotatingFileHandler(exec_log_filename,
max_bytes=DATA_LOGGING_CONFIG['max_bytes'],
backup_count=DATA_LOGGING_CONFIG['backup_count'],
when=DATA_LOGGING_CONFIG['when'],
interval=DATA_LOGGING_CONFIG['interval'])
+ data_formatter = logging.Formatter(log_format)
+ data_formatter.converter = gmtime
+ data_formatter.datefmt = '%Y/%m/%d %H:%M:%S UTC'
+ data_handler.setFormatter(exec_formatter)
data_logger.addHandler(data_handler)
+ data_logger.setLevel(logging_level)
+
+ if logging_to_console:
+ data_logger.addHandler(logging.StreamHandler())
+ if mqtt:
+ mqtt_data_handler = MQTTHandler(MQTT_LOGGING_CONFIG['hostname'], MQTT_LOGGING_CONFIG['data_topic'])
+ mqtt_data_handler.setLevel(logging_level)
+ mqtt_data_handler.setFormatter(data_formatter)
+ data_logger.addHandler(mqtt_data_handler)
- if not init_logging(exec_logger, logging_level, log_path, data_log_filename):
- print('ERROR: Could not initialize logging!')
- return exec_logger, exec_log_filename, data_logger, data_log_filename, logging_level
+ try:
+ init_logging(exec_logger, data_logger, logging_level, log_path, data_log_filename)
+ except Exception as err:
+ print(f'ERROR: Could not initialize logging!\n{err}')
+ finally:
+ return exec_logger, exec_log_filename, data_logger, data_log_filename, logging_level
-def init_logging(exec_logger, logging_level, log_path, data_log_filename):
+def init_logging(exec_logger, data_logger, logging_level, log_path, data_log_filename):
""" This is the init sequence for the logging system """
init_logging_status = True
@@ -95,4 +114,5 @@ def init_logging(exec_logger, logging_level, log_path, data_log_filename):
exec_logger.info(f'{k}:\n{v}')
exec_logger.info('')
exec_logger.info(f'init_logging_status: {init_logging_status}')
+ data_logger.info('Starting_session')
return init_logging_status
diff --git a/mqtt_setup.py b/mqtt_setup.py
deleted file mode 100644
index 66296df93ef71b8e3637c85a57b37ae90940a7b6..0000000000000000000000000000000000000000
--- a/mqtt_setup.py
+++ /dev/null
@@ -1,18 +0,0 @@
-from settings import MQTT_LOGGING_CONFIG
-import paho.mqtt.client as mqtt
-
-
-def on_message(client, userdata, message):
- m = str(message.payload.decode("utf-8"))
- print(f'message received {m}')
- print(f'topic: {message.topic}')
- print(f'qos: {message.qos}')
- print(f'retain flag: {message.retain}')
- client.publish(MQTT_LOGGING_CONFIG['measurements_topic'], f'{m} 45 ohm.m')
-
-
-def mqtt_client_setup():
- client = mqtt.Client(MQTT_LOGGING_CONFIG['client_id'], protocol=5) # create new client instance
- client.connect(MQTT_LOGGING_CONFIG['mqtt_broker'])
- client.on_message = on_message
- return client, MQTT_LOGGING_CONFIG['measurements_topic']
\ No newline at end of file
diff --git a/ohmpi.py b/ohmpi.py
index 649857cbc308d939af526245d07dde8a7c748c9c..61b47fa3a737413421e38ff4fdc33b4b289bd120 100644
--- a/ohmpi.py
+++ b/ohmpi.py
@@ -19,19 +19,19 @@ import threading
from logging_setup import setup_loggers
# from mqtt_setup import mqtt_client_setup
-# finish import (done only when class is instantiated as some libs are
-# only available on arm64 platform)
+# finish import (done only when class is instantiated as some libs are only available on arm64 platform)
+arm_64_imports = False
try:
- import board
- import busio
- import adafruit_tca9548a
- import adafruit_ads1x15.ads1115 as ads
- from adafruit_ads1x15.analog_in import AnalogIn
- from adafruit_mcp230xx.mcp23008 import MCP23008
- from adafruit_mcp230xx.mcp23017 import MCP23017
- import digitalio
- from digitalio import Direction
- from gpiozero import CPUTemperature
+ import board # noqa
+ import busio # noqa
+ import adafruit_tca9548a # noqa
+ import adafruit_ads1x15.ads1115 as ads # noqa
+ from adafruit_ads1x15.analog_in import AnalogIn # noqa
+ from adafruit_mcp230xx.mcp23008 import MCP23008 # noqa
+ from adafruit_mcp230xx.mcp23017 import MCP23017 # noqa
+ import digitalio # noqa
+ from digitalio import Direction # noqa
+ from gpiozero import CPUTemperature # noqa
arm64_imports = True
except ImportError as error:
print(colored(f'Import error: {error}', 'yellow'))
@@ -51,24 +51,27 @@ class OhmPi(object):
sequence : str, optional
Path to the .txt where the sequence is read. By default, a 1 quadrupole
sequence: 1, 2, 3, 4 is used.
- output : str, optional
- Either 'print' for a console output or 'mqtt' for publication onto
- MQTT broker.
"""
- def __init__(self, config=None, sequence=None, output='print', data_logger=None, exec_logger=None, soh_logger=None,
- on_pi=None):
+ def __init__(self, config=None, sequence=None, mqtt=True, on_pi=None):
# flags and attributes
if on_pi is None:
_, on_pi = OhmPi.get_platform()
+ self.sequence = sequence
self.on_pi = on_pi # True if run from the RaspberryPi with the hardware, otherwise False for random data
- self.output = output # type of output print
self.status = 'idle' # either running or idle
self.run = False # flag is True when measuring
self.thread = None # contains the handle for the thread taking the measurement
self.path = 'data/' # where to save the .csv
- self.data_logger = data_logger
- self.exec_logger = exec_logger
- self.soh_logger = soh_logger
+
+ # set loggers
+ config_exec_logger, _, config_data_logger, _, _ = setup_loggers(mqtt=mqtt) # TODO: add SOH
+ self.data_logger = config_data_logger
+ self.exec_logger = config_exec_logger
+ self.soh_logger = None
+ print('Loggers:')
+ print(colored(f'Exec logger {self.exec_logger.handlers if self.exec_logger is not None else "None"}', 'blue'))
+ print(colored(f'Data logger {self.data_logger.handlers if self.data_logger is not None else "None"}', 'blue'))
+ print(colored(f'SOH logger {self.soh_logger.handlers if self.soh_logger is not None else "None"}', 'blue'))
# read in hardware parameters (settings.py)
self._read_hardware_parameters()
@@ -86,7 +89,7 @@ class OhmPi(object):
if config is not None:
self._read_acquisition_parameters(config)
- self.log_exec('Initialized with configuration:' + str(self.pardict), level='debug')
+ self.exec_logger.debug('Initialized with configuration:' + str(self.pardict))
# read quadrupole sequence
if sequence is None:
@@ -97,7 +100,7 @@ class OhmPi(object):
# connect to components on the OhmPi board
if self.on_pi:
# activation of I2C protocol
- self.i2c = busio.I2C(board.SCL, board.SDA)
+ self.i2c = busio.I2C(board.SCL, board.SDA) # noqa
# I2C connexion to MCP23008, for current injection
self.mcp = MCP23008(self.i2c, address=0x20)
@@ -108,32 +111,6 @@ class OhmPi(object):
# ADS1115 for voltage measurement (MN)
self.ads_voltage = ads.ADS1115(self.i2c, gain=2/3, data_rate=860, address=0x49)
- def log_exec(self, msg, level='debug'):
- """Function for output management.
-
- Parameters
- ----------
- msg : str
- Body of the message.
- level : str, optional
- Level of the message, either: 'error', 'warn', 'debug'
- """
- # TODO all message to be logged using python logging library and rotating log
-
- if self.exec_logger is not None:
- self.exec_logger.info(msg)
- # if self.output == 'print':
- # if level == 'error':
- # print(colored(level.upper() + ' : ' + msg, 'red'))
- # elif level == 'warn':
- # print(colored(level.upper() + ' : ' + msg, 'yellow'))
- # else:
- # print(level.upper() + ' : ' + msg)
- # elif self.output == 'mqtt':
- # if level == 'debug':
- # # TODO mqtt transmission here
- # pass
-
def _read_acquisition_parameters(self, config):
"""Read acquisition parameters.
Parameters can be:
@@ -155,7 +132,7 @@ class OhmPi(object):
with open(config) as json_file:
dic = json.load(json_file)
self.pardict.update(dic)
- self.log_exec('Acquisition parameters updated: ' + str(self.pardict), level='debug')
+ self.exec_logger.debug('Acquisition parameters updated: ' + str(self.pardict))
def _read_hardware_parameters(self):
"""Read hardware parameters from settings.py.
@@ -164,16 +141,16 @@ class OhmPi(object):
self.id = OHMPI_CONFIG['id'] # ID of the OhmPi
self.r_shunt = OHMPI_CONFIG['R_shunt'] # reference resistance value in ohm
self.Imax = OHMPI_CONFIG['Imax'] # maximum current
- self.log_exec(f'The maximum current cannot be higher than {self.Imax} mA', level='warn')
+ self.exec_logger.warning(f'The maximum current cannot be higher than {self.Imax} mA')
self.coef_p2 = OHMPI_CONFIG['coef_p2'] # slope for current conversion for ads.P2, measurement in V/V
self.coef_p3 = OHMPI_CONFIG['coef_p3'] # slope for current conversion for ads.P3, measurement in V/V
- self.offset_p2 = OHMPI_CONFIG['offset_p2']
- self.offset_p3 = OHMPI_CONFIG['offset_p3']
+ # self.offset_p2 = OHMPI_CONFIG['offset_p2'] parameter removed
+ # self.offset_p3 = OHMPI_CONFIG['offset_p3'] parameter removed
self.nb_samples = OHMPI_CONFIG['integer'] # number of samples measured for each stack
self.version = OHMPI_CONFIG['version'] # hardware version
self.max_elec = OHMPI_CONFIG['max_elec'] # maximum number of electrodes
self.board_address = OHMPI_CONFIG['board_address']
- self.log_exec('OHMPI_CONFIG = ' + str(OHMPI_CONFIG), level='debug')
+ self.exec_logger.debug(f'OHMPI_CONFIG = {str(OHMPI_CONFIG)}')
@staticmethod
def find_identical_in_line(quads):
@@ -254,19 +231,18 @@ class OhmPi(object):
# if statement with exit cases (TODO rajouter un else if pour le deuxième cas du ticket #2)
if test_index_elec.size != 0:
for i in range(len(test_index_elec[0, :])):
- self.log_exec('Error: An electrode index at line ' + str(test_index_elec[0, i] + 1) +
- ' exceeds the maximum number of electrodes', level='error')
+ self.exec_logger.error(f'An electrode index at line {str(test_index_elec[0, i] + 1)} '
+ f'exceeds the maximum number of electrodes')
# sys.exit(1)
output = None
elif len(test_same_elec) != 0:
for i in range(len(test_same_elec)):
- self.log_exec('Error: An electrode index A == B detected at line ' + str(test_same_elec[i] + 1),
- level="error")
+ self.exec_logger.error(f'An electrode index A == B detected at line {str(test_same_elec[i] + 1)}')
# sys.exit(1)
output = None
if output is not None:
- self.log_exec('Sequence of {:d} quadrupoles read.'.format(output.shape[0]), level='debug')
+ self.exec_logger.debug('Sequence of {:d} quadrupoles read.'.format(output.shape[0]))
self.sequence = output
@@ -319,12 +295,12 @@ class OhmPi(object):
else:
mcp2.get_pin(relay_nr-1).value = False
- self.log_exec(f'Switching relay {relay_nr} {state} for electrode {electrode_nr}', level='debug')
+ self.exec_logger.debug(f'Switching relay {relay_nr} {state} for electrode {electrode_nr}')
else:
- self.log_exec(f'Unable to address electrode nr {electrode_nr}', level='warn')
+ self.exec_logger.warning(f'Unable to address electrode nr {electrode_nr}')
def switch_mux_on(self, quadrupole):
- """Switch on multiplexer relays for given quadrupole.
+ """ Switch on multiplexer relays for given quadrupole.
Parameters
----------
@@ -337,10 +313,10 @@ class OhmPi(object):
for i in range(0, 4):
self.switch_mux(quadrupole[i], 'on', roles[i])
else:
- self.log_exec('A == B -> short circuit detected!', level='error')
+ self.exec_logger.error('A == B -> short circuit risk detected!')
def switch_mux_off(self, quadrupole):
- """Switch off multiplexer relays for given quadrupole.
+ """ Switch off multiplexer relays for given quadrupole.
Parameters
----------
@@ -357,7 +333,7 @@ class OhmPi(object):
for i in range(0, 4):
for j in range(1, self.max_elec + 1):
self.switch_mux(j, 'off', roles[i])
- self.log_exec('All MUX switched off.', level='debug')
+ self.exec_logger.debug('All MUX switched off.')
def run_measurement(self, quad, nb_stack=None, injection_duration=None): # NOTE: quad not used?!
""" Do a 4 electrode measurement and measure transfer resistance obtained.
@@ -392,7 +368,9 @@ class OhmPi(object):
pin1.direction = Direction.OUTPUT
pin0.value = False
pin1.value = False
-
+
+ self.exec_logger.debug('Starting measurement')
+ self.data_logger.info('Waiting for data')
# TODO I don't get why 3 + 2*nb_stack - 1? why not just rnage(nb_stack)?
# or do we consider 1 stack = one full polarity? do we discard the first 3 readings?
for n in range(0, 3+2*nb_stack-1):
@@ -443,7 +421,7 @@ class OhmPi(object):
# create a dictionary and compute averaged values from all stacks
d = {
- "time": [datetime.now()],
+ "time": [datetime.now().isoformat()],
"A": [1],
"B": [2],
"M": [3],
@@ -469,13 +447,13 @@ class OhmPi(object):
val = d[k]
output += f'{val}\t'
output = output[:-1]
- self.log_exec(output, level='debug')
+ self.exec_logger.debug(output)
time.sleep(1) # NOTE: why this?
return d
def rs_check(self):
- """Check contact resistance.
+ """ Check contact resistance.
"""
# create custom sequence where MN == AB
nelec = self.sequence.max() # number of elec used in the sequence
@@ -495,7 +473,7 @@ class OhmPi(object):
self.sequence = quads
# run the RS check
- self.log_exec('RS check (check contact resistance)', level='debug')
+ self.exec_logger.debug('RS check (check contact resistance)')
self.measure()
# restore
@@ -503,29 +481,29 @@ class OhmPi(object):
self.sequence = sequence
# TODO if interrupted, we would need to restore the values
- # TODO or we offer the possiblity in 'run_measurement' to have rs_check each time?
+ # TODO or we offer the possibility in 'run_measurement' to have rs_check each time?
@staticmethod
- def append_and_save(fname, last_measurement):
+ def append_and_save(filename, last_measurement):
"""Append and save last measurement dataframe.
Parameters
----------
- fname : str
+ filename : str
filename to save the last measurement dataframe
last_measurement : dict
Last measurement taken in the form of a python dictionary
"""
- if os.path.isfile(fname):
+ if os.path.isfile(filename):
# Load data file and append data to it
- with open(fname, 'a') as f:
+ with open(filename, 'a') as f:
w = csv.DictWriter(f, last_measurement.keys())
w.writerow(last_measurement)
# last_measurement.to_csv(f, header=False)
else:
# create data file and add headers
- with open(fname, 'a') as f:
+ with open(filename, 'a') as f:
w = csv.DictWriter(f, last_measurement.keys())
w.writeheader()
w.writerow(last_measurement)
@@ -536,19 +514,19 @@ class OhmPi(object):
"""
self.run = True
self.status = 'running'
- self.log_exec('status = ' + self.status, level='debug')
+ self.exec_logger.debug(f'Status: {self.status}')
def func():
for g in range(0, self.pardict["nbr_meas"]): # for time-lapse monitoring
if self.run is False:
- self.log_exec('INTERRUPTED', level='debug')
+ self.exec_logger.warning('Data acquisition interrupted')
break
t0 = time.time()
# create filename with timestamp
- fname = self.pardict["export_path"].replace('.csv', '_' + datetime.now().strftime('%Y%m%dT%H%M%S')
- + '.csv')
- self.log_exec('saving to ' + fname, level='debug')
+ filename = self.pardict["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()
@@ -575,9 +553,11 @@ class OhmPi(object):
# switch mux off
self.switch_mux_off(quad)
+ # log data to the data logger
+ self.data_logger.info(f'{current_measurement}')
# save data and print in a text file
- self.append_and_save(fname, current_measurement)
- self.log_exec('{:d}/{:d}'.format(i + 1, self.sequence.shape[0]), level='debug')
+ self.append_and_save(filename, current_measurement)
+ self.exec_logger.debug('{:d}/{:d}'.format(i + 1, self.sequence.shape[0]))
# compute time needed to take measurement and subtract it from interval
# between two sequence run (= sequence_delay)
@@ -587,8 +567,8 @@ class OhmPi(object):
if sleep_time < 0:
# it means that the measuring time took longer than the sequence delay
sleep_time = 0
- self.log_exec('The measuring time is longer than the sequence delay. Increase the sequence delay',
- level='warn')
+ self.exec_logger.warning('The measuring time is longer than the sequence delay. '
+ 'Increase the sequence delay')
# sleeping time between sequence
if self.pardict["nbr_meas"] > 1:
@@ -603,13 +583,15 @@ class OhmPi(object):
self.run = False
if self.thread is not None:
self.thread.join()
- self.log_exec('status = ' + self.status)
+ self.exec_logger.debug(f'Status: {self.status}')
+
+
+# exec_logger, exec_log_filename, data_logger, data_log_filename, logging_level = setup_loggers() # TODO: add SOH
-exec_logger, exec_log_filename, data_logger, data_log_filename, logging_level = setup_loggers() # TODO: add SOH
# mqtt_client, measurement_topic = mqtt_client_setup()
-VERSION = '2.0.1'
+VERSION = '2.0.2'
print(colored(r' ________________________________' + '\n' +
r'| _ | | | || \/ || ___ \_ _|' + '\n' +
@@ -622,7 +604,8 @@ print('Version:', VERSION)
platform, on_pi = OhmPi.get_platform()
if on_pi:
print(colored(f'Running on {platform} platform', 'green'))
- # TODO: check model for compatible platforms (e.g. Raspberry Pi 3B is not supported...) and emit a warning otherwise
+ # TODO: check model for compatible platforms (exclude Raspberry Pi versions that are not supported...)
+ # and emit a warning otherwise
if not arm64_imports:
print(colored(f'Warning: Required packages are missing.\n'
f'Please run . env.sh at command prompt to update your virtual environment\n', 'yellow'))