from hwTest import Alimentation, Current, Voltage, Multiplexer
# -*- coding: utf-8 -*-
"""
created on January 6, 2020.
Updates dec 2022.
Hardware: Licensed under CERN-OHL-S v2 or any later version
Software: Licensed under the GNU General Public License v3.0
Ohmpi.py is a program to control a low-cost and open hardware resistivity meter OhmPi that has been developed by
Rémi CLEMENT (INRAE), Vivien DUBOIS (INRAE), Hélène GUYARD (IGE), Nicolas FORQUET (INRAE), Yannick FARGIER (IFSTTAR)
Olivier KAUFMANN (UMONS), Arnaud WATLET (UMONS) and Guillaume BLANCHY (FNRS/ULiege).
"""
import os
from utils import get_platform
import json
import warnings
from copy import deepcopy
import numpy as np
import csv
import time
import shutil
from datetime import datetime
from termcolor import colored
import threading
from logging_setup import setup_loggers
from config import MQTT_CONTROL_CONFIG, OHMPI_CONFIG, EXEC_LOGGING_CONFIG
from logging import DEBUG
# finish import (done only when class is instantiated as some libs are only available on arm64 platform)
try:
from gpiozero import CPUTemperature # noqa
arm64_imports = True
except ImportError as error:
if EXEC_LOGGING_CONFIG['logging_level'] == DEBUG:
print(colored(f'Import error: {error}', 'yellow'))
arm64_imports = False
except Exception as error:
print(colored(f'Unexpected error: {error}', 'red'))
arm64_imports = None
class OhmPi(object):
""" OhmPi class.
"""
def __init__(self, settings=None, sequence=None, use_mux=False, mqtt=True, onpi=None, idps=False):
"""Constructs the ohmpi object
Parameters
----------
settings:
sequence:
use_mux:
if True use the multiplexor to select active electrodes
mqtt: bool, defaut: True
if True publish on mqtt topics while logging, otherwise use other loggers only
onpi: bool,None default: None
if None, the platform on which the class is instantiated is determined to set on_pi to either True or False.
if False the behaviour of an ohmpi will be partially emulated and return random data.
idps:
if true uses the DPS
"""
if onpi is None:
_, onpi = get_platform()
self._sequence = sequence
self.nb_samples = 0
self.use_mux = use_mux
self.on_pi = onpi # True if run from the RaspberryPi with the hardware, otherwise False for random data
self.status = 'idle' # either running or idle
self.thread = None # contains the handle for the thread taking the measurement
# set loggers
config_exec_logger, _, config_data_logger, _, _, msg = setup_loggers(mqtt=mqtt) # TODO: add SOH
self.data_logger = config_data_logger
self.exec_logger = config_exec_logger
self.soh_logger = None # TODO: Implement the SOH logger
print(msg)
# read in hardware parameters (config.py)
self._read_hardware_config() # TODO should go to hw.py
# default acquisition settings
self.settings = {
'injection_duration': 0.2,
'nb_meas': 1,
'sequence_delay': 1,
'nb_stack': 1,
'export_path': 'data/measurement.csv'
}
# read in acquisition settings
if settings is not None:
self.update_settings(settings)
self.exec_logger.debug('Initialized with settings:' + str(self.settings))
# read quadrupole sequence
if sequence is not None:
self.load_sequence(sequence)
self.idps = idps # flag to use dps for injection or not
# connect to components on the OhmPi board
if self.on_pi:
# initialize hardware
self.alim = Alimentation()
self.voltage = Voltage()
self.current = Current()
self.mux = Multiplexer()
# set controller
self.mqtt = mqtt
self.cmd_id = None
if self.mqtt:
import paho.mqtt.client as mqtt_client
self.exec_logger.debug(f"Connecting to control topic {MQTT_CONTROL_CONFIG['ctrl_topic']}"
f" on {MQTT_CONTROL_CONFIG['hostname']} broker")
def connect_mqtt() -> mqtt_client:
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']}")
else:
self.exec_logger.warning(f'Failed to connect to control broker. Return code : {rc}')
client = mqtt_client.Client(f"ohmpi_{OHMPI_CONFIG['id']}_listener", clean_session=False)
client.username_pw_set(MQTT_CONTROL_CONFIG['auth'].get('username'),
MQTT_CONTROL_CONFIG['auth']['password'])
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()
except Exception as e:
self.exec_logger.debug(f'Unable to connect control broker: {e}')
self.controller = None
if self.controller is not None:
self.exec_logger.debug(f"Subscribing to control topic {MQTT_CONTROL_CONFIG['ctrl_topic']}")
try:
self.controller.subscribe(MQTT_CONTROL_CONFIG['ctrl_topic'], MQTT_CONTROL_CONFIG['qos'])
msg = f"Subscribed to control topic {MQTT_CONTROL_CONFIG['ctrl_topic']}" \
f" on {MQTT_CONTROL_CONFIG['hostname']} broker"
self.exec_logger.debug(msg)
print(colored(f'\u2611 {msg}', 'blue'))
except Exception as e:
self.exec_logger.warning(f'Unable to subscribe to control topic : {e}')
self.controller = None
publisher_config = MQTT_CONTROL_CONFIG.copy()
publisher_config['topic'] = MQTT_CONTROL_CONFIG['ctrl_topic']
publisher_config.pop('ctrl_topic')
def on_message(client, userdata, message):
command = message.payload.decode('utf-8')
self.exec_logger.debug(f'Received command {command}')
self._process_commands(command)
self.controller.on_message = on_message
else:
self.controller = None
self.exec_logger.warning('No connection to control broker.'
' Use python/ipython to interact with OhmPi object...')
@staticmethod
def append_and_save(filename: str, last_measurement: dict, cmd_id=None):
"""Appends and saves the last measurement dict.
Parameters
----------
filename : str
filename to save the last measurement dataframe
last_measurement : dict
Last measurement taken in the form of a python dictionary
cmd_id : str, optional
Unique command identifier
"""
last_measurement = deepcopy(last_measurement)
if 'fulldata' in last_measurement:
d = last_measurement['fulldata']
n = d.shape[0]
if n > 1:
idic = dict(zip(['i' + str(i) for i in range(n)], d[:, 0]))
udic = dict(zip(['u' + str(i) for i in range(n)], d[:, 1]))
tdic = dict(zip(['t' + str(i) for i in range(n)], d[:, 2]))
last_measurement.update(idic)
last_measurement.update(udic)
last_measurement.update(tdic)
last_measurement.pop('fulldata')
if os.path.isfile(filename):
# Load data file and append data to it
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(filename, 'a') as f:
w = csv.DictWriter(f, last_measurement.keys())
w.writeheader()
w.writerow(last_measurement)
def _compute_tx_volt(self, best_tx_injtime=0.1, strategy='vmax', tx_volt=5):
"""Estimates best Tx voltage based on different strategies.
At first a half-cycle is made for a short duration with a fixed
known voltage. This gives us Iab and Rab. We also measure Vmn.
A constant c = vmn/iab is computed (only depends on geometric
factor and ground resistivity, that doesn't change during a
quadrupole). Then depending on the strategy, we compute which
vab to inject to reach the minimum/maximum Iab current or
min/max Vmn.
Parameters
----------
best_tx_injtime : float, optional
Time in milliseconds for the half-cycle used to compute Rab.
strategy : str, optional
Either:
- vmin : compute Vab to reach a minimum Iab and Vmn
- vmax : compute Vab to reach a maximum Iab and Vmn
- constant : apply given Vab
tx_volt : float, optional
Voltage apply to try to guess the best voltage. 5 V applied
by default. If strategy "constant" is chosen, constant voltage
to applied is "tx_volt".
Returns
-------
vab : float
Proposed Vab according to the given strategy.
"""
# hardware limits
voltage_min = self.voltage.vmin # V
voltage_max = self.voltage.vmax
current_min = self.current.imin # A
current_max = self.current.imax
tx_max = 40. # volt
# check of V
volt = tx_volt
if volt > tx_max:
self.exec_logger.warning('Sorry, cannot inject more than 40 V, set it back to 5 V')
volt = 5.
# make sure we are not injecting
self.alim.stop_injection()
# select a polarity to start with
self.alim.set_polarity(True)
# set voltage for test
self.alim.turn_on()
self.alim.set_tx_voltage(volt)
time.sleep(best_tx_injtime) # inject for given tx time
self.alim.start_injection()
# autogain: set best gain
self.current.set_best_gain()
self.voltage.set_best_gain()
# we measure the voltage on both A0 and A2 to guess the polarity
values = self.read_values(duration=0.1)
self.alim.stop_injection()
iab = values[-1, 1]
vmn = values[-1, 2]
# compute constant
c = vmn / iab
Rab = (volt * 1000.) / iab # noqa
self.exec_logger.debug(f'Rab = {Rab:.2f} Ohms')
# implement different strategies
if strategy == 'vmax':
vmn_max = c * current_max
if voltage_max > vmn_max > voltage_min:
vab = current_max * Rab
self.exec_logger.debug('target max current')
else:
iab = voltage_max / c
vab = iab * Rab
self.exec_logger.debug('target max voltage')
if vab > 25.:
vab = 25.
vab = vab * 0.9
elif strategy == 'vmin':
vmn_min = c * current_min
if voltage_min < vmn_min < voltage_max:
vab = current_min * Rab
self.exec_logger.debug('target min current')
else:
iab = voltage_min / c
vab = iab * Rab
self.exec_logger.debug('target min voltage')
if vab < 1.:
vab = 1.
vab = vab * 1.1
elif strategy == 'constant':
vab = volt
else:
vab = 5
return vab
def get_data(self, survey_names=None, cmd_id=None):
"""Get available data.
Parameters
----------
survey_names : list of str, optional
List of filenames already available from the html interface. So
their content won't be returned again. Only files not in the list
will be read.
cmd_id : str, optional
Unique command identifier
"""
# get all .csv file in data folder
if survey_names is None:
survey_names = []
fnames = [fname for fname in os.listdir('data/') if fname[-4:] == '.csv']
ddic = {}
if cmd_id is None:
cmd_id = 'unknown'
for fname in fnames:
if ((fname != 'readme.txt')
and ('_rs' not in fname)
and (fname.replace('.csv', '') not in survey_names)):
try:
data = np.loadtxt('data/' + fname, delimiter=',',
skiprows=1, usecols=(1, 2, 3, 4, 8))
data = data[None, :] if len(data.shape) == 1 else data
ddic[fname.replace('.csv', '')] = {
'a': data[:, 0].astype(int).tolist(),
'b': data[:, 1].astype(int).tolist(),
'm': data[:, 2].astype(int).tolist(),
'n': data[:, 3].astype(int).tolist(),
'rho': data[:, 4].tolist(),
}
except Exception as e:
print(fname, ':', e)
rdic = {'cmd_id': cmd_id, 'data': ddic}
self.data_logger.info(json.dumps(rdic))
return ddic
def interrupt(self, cmd_id=None):
"""Interrupts the acquisition when launched in async mode.
Parameters
----------
cmd_id : str, optional
Unique command identifier
"""
self.status = 'stopping'
if self.thread is not None:
self.thread.join()
self.exec_logger.debug('Interrupted sequence acquisition...')
else:
self.exec_logger.debug('No sequence measurement thread to interrupt.')
self.exec_logger.debug(f'Status: {self.status}')
def load_sequence(self, filename: str, cmd_id=None):
"""Reads quadrupole sequence from file.
Parameters
----------
filename : str
Path of the .csv or .txt file with A, B, M and N electrodes.
Electrode index start at 1.
cmd_id : str, optional
Unique command identifier
Returns
-------
sequence : numpy.array
Array of shape (number quadrupoles * 4).
"""
self.exec_logger.debug(f'Loading sequence {filename}')
try:
sequence = np.loadtxt(filename, delimiter=" ", dtype=np.uint32) # load quadrupole file
self.exec_logger.debug(f'Sequence of {sequence.shape[0]:d} quadrupoles read.')
self.set_sequence(sequence)
except Exception as e:
self.exec_logger.debug('ERROR in load_sequence(): ' + str(e))
if sequence is not None:
self.exec_logger.info(f'Sequence {filename} of {sequence.shape[0]:d} quadrupoles loaded.')
else:
self.exec_logger.warning(f'Unable to load sequence {filename}')
def set_sequence(self, sequence):
"""Set a sequence of quadrupoles.
Parameters
----------
sequence : list of list or np.array
2D array with 1 row per quadrupole.
"""
# locate lines where the electrode index exceeds the maximum number of electrodes
test_index_elec = np.array(np.where(sequence > self.max_elec))
# reshape in case we have a 1D array (=1 quadrupole)
if len(sequence.shape) == 1:
sequence = sequence[None, :]
# test for elec A == B
test_same_elec = np.where(sequence[:, 0] == sequence[:, 1])[0]
ok = True
# 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, :])):
ok = False
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)
sequence = None
if len(test_same_elec) != 0:
for i in range(len(test_same_elec)):
ok = False
self.exec_logger.error(f'An electrode index A == B detected at line {str(test_same_elec[i] + 1)}')
# sys.exit(1)
sequence = None
# set sequence attribute
if ok:
self.sequence = sequence
else:
self.exec_logger.error('Unable to set sequence. Fix sequence first.')
def _process_commands(self, message: str):
"""Processes commands received from the controller(s)
Parameters
----------
message : str
message containing a command and arguments or keywords and arguments
"""
status = False
cmd_id = '?'
try:
decoded_message = json.loads(message)
self.exec_logger.debug(f'Decoded message {decoded_message}')
cmd_id = decoded_message.pop('cmd_id', None)
cmd = decoded_message.pop('cmd', None)
kwargs = decoded_message.pop('kwargs', None)
self.exec_logger.debug(f"Calling method {cmd}({str(kwargs) if kwargs is not None else ''})")
if cmd_id is None:
self.exec_logger.warning('You should use a unique identifier for cmd_id')
if cmd is not None:
try:
if kwargs is None:
output = getattr(self, cmd)()
else:
output = getattr(self, cmd)(**kwargs)
status = True
except Exception as e:
self.exec_logger.error(
f"Unable to execute {cmd}({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}')
status = False
finally:
reply = {'cmd_id': cmd_id, 'status': status}
reply = json.dumps(reply)
self.exec_logger.debug(f'Execution report: {reply}')
def quit(self, cmd_id=None):
"""Quits OhmPi
Parameters
----------
cmd_id : str, optional
Unique command identifier
"""
self.exec_logger.debug(f'Quitting ohmpi.py following command {cmd_id}')
exit()
def _read_hardware_config(self):
"""Reads hardware configuration from config.py
"""
self.exec_logger.debug('Getting hardware config')
self.id = OHMPI_CONFIG['id'] # ID of the OhmPi
self.Imax = OHMPI_CONFIG['Imax'] # maximum current
self.exec_logger.debug(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.nb_samples = OHMPI_CONFIG['nb_samples'] # 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_version = OHMPI_CONFIG['board_version']
self.exec_logger.debug(f'OHMPI_CONFIG = {str(OHMPI_CONFIG)}')
def remove_data(self, cmd_id=None):
"""Remove all data in the data folder
Parameters
----------
cmd_id : str, optional
Unique command identifier
"""
self.exec_logger.debug(f'Removing all data following command {cmd_id}')
shutil.rmtree('data')
os.mkdir('data')
def restart(self, cmd_id=None):
"""Restarts the Raspberry Pi
Parameters
----------
cmd_id : str, optional
Unique command identifier
"""
if self.on_pi:
self.exec_logger.info(f'Restarting pi following command {cmd_id}...')
os.system('reboot')
else:
self.exec_logger.warning('Not on Raspberry Pi, skipping reboot...')
def set_best_gain(self):
"""Set best gain."""
self.current.set_best_gain()
gain0 = self.voltage.get_best_gain(channel=0)
gain2 = self.voltage.get_best_gain(channel=2)
self.voltage.set_gain(np.min([gain0, gain2]))
def read_values(self, duration=0.2, sampling=0.01):
"""Read voltage during a given time for current and voltage ADS.
Parameters
----------
duration : int, optional
Time in seconds to monitor the voltage.
sampling : int, optional
Time between two samples in seconds.
Returns
-------
meas : numpy.array
Array with first column time in ms from start,
second column, current in mA, then voltage in mV
from the different channels.
"""
# compute maximum number of samples possible
# we probably harvest less samples but like this
# we can already allocated the array and that makes
# the collection faster
nsamples = int((int(duration * 1000) // sampling) + 1)
# measurement of current i and voltage u during injection
nchannel = len(self.voltage.read_all())
meas = np.zeros((nsamples, 2 + nchannel)) * np.nan
start_time = time.time() # stating measurement time
elapsed = 0
for i in range(0, nsamples):
# reading current value on ADS channels
elapsed = time.time() - start_time # real injection time (s)
if elapsed >= (duration):
break
meas[i, 0] = elapsed
meas[i, 1] = self.current.read()
meas[i, 2:] = self.voltage.read_all()
time.sleep(sampling)
return meas[:i-1, :]
def run_measurement(self, quad=[0, 0, 0, 0], nb_stack=None, injection_duration=None,
autogain=True, strategy='constant', tx_volt=5, best_tx_injtime=0.1,
duty=1, cmd_id=None):
"""Measures on a quadrupole and returns transfer resistance.
Parameters
----------
quad : iterable (list of int)
Quadrupole to measure, just for labelling. Only switch_mux_on/off
really creates the route to the electrodes.
nb_stack : int, optional
Number of stacks. A stacl is considered two half-cycles (one
positive, one negative).
injection_duration : int, optional
Injection time in seconds.
autogain : bool, optional
If True, will adapt the gain of the ADS1115 to maximize the
resolution of the reading.
strategy : str, optional
(V3.0 only) If we search for best voltage (tx_volt == 0), we can choose
different strategy:
- vmin: find the lowest voltage that gives us a signal
- vmax: find the highest voltage that stays in the range
For a constant value, just set the tx_volt.
tx_volt : float, optional
(V3.0 only) If specified, voltage will be imposed. If 0, we will look
for the best voltage. If the best Tx cannot be found, no
measurement will be taken and values will be NaN.
best_tx_injtime : float, optional
(V3.0 only) Injection time in seconds used for finding the best voltage.
duty : float, optional
Proportion of time spent on injection vs no injection time.
cmd_id : str, optional
Command ID.
"""
self.exec_logger.debug('Starting measurement')
if nb_stack is None:
nb_stack = self.settings['nb_stack']
if injection_duration is None:
injection_duration = self.settings['injection_duration']
tx_volt = float(tx_volt)
# let's define the pin again as if we run through measure()
# as it's run in another thread, it doesn't consider these
# and this can lead to short circuit!
self.alim = Alimentation() # TODO carefully test that
self.alim.stop_injection()
# get best voltage to inject AND polarity
if self.idps:
tx_volt, polarity = self._compute_tx_volt(
best_tx_injtime=best_tx_injtime, strategy=strategy, tx_volt=tx_volt)
self.exec_logger.debug(f'Best vab found is {tx_volt:.3f}V')
# first reset the gain to 2/3 before trying to find best gain (mode 0 is continuous)
self.current.set_gain(2/3)
self.voltage.set_gain(2/3)
# turn on the power supply
if self.alim.on == False:
self.alim.turn_on()
self.alim.set_tx_voltage(tx_volt)
time.sleep(0.05) # let it time to reach tx_volt
if tx_volt > 0: # we found a Vab in the range so we measure
# find best gain during injection
if autogain:
self.alim.start_injection()
time.sleep(injection_duration)
self.set_best_gain()
self.alim.stop_injection()
# make sure we are not injecting
self.alim.stop_injection()
# full data for waveform
fulldata = []
# we sample every 10 ms (as using AnalogIn for both current
# and voltage takes about 7 ms). When we go over the injection
# duration, we break the loop and truncate the meas arrays
# only the last values in meas will be taken into account
start_delay = time.time()
injtimes = np.zeros(nb_stack * 2)
for n in range(0, nb_stack * 2): # for each half-cycles
# current injection polarity
if (n % 2) == 0:
self.alim.set_polarity(True)
else:
self.alim.set_polarity(False)
self.alim.start_injection()
# reading voltages and currents
elapsed = time.time() - start_delay
values = self.read_values(duration=injection_duration)
injtimes[n] = values[-1, 0]
values[:, 0] += elapsed
fulldata.append(values)
# stop current injection
self.alim.stop_injection()
# waiting time (no injection) before next half-cycle
if duty < 1:
duration = injection_duration * (1 - duty)
elapsed = time.time() - start_delay
values = self.read_values(duration=duration)
values[:, 0] += elapsed
fulldata.append(values)
else:
fulldata.append(np.array([[], [], [], []]).T)
# TODO get battery voltage and warn if battery is running low
# TODO send a message on SOH stating the battery level
# let's do some calculation (out of the stacking loop)
stacks = np.zeros((len(fulldata) // 2, fulldata[0].shape[1]-1))
# define number of sample to average for the injection half-cycle
n2avg = int(fulldata[0].shape[0] // 3)
# compute average for the injection half-cycle
for n, meas in enumerate(fulldata[::2]):
stacks[n, :] = np.mean(meas[-n2avg:, 1:], axis=0)
# identify which of U0 or U2 is on top
a = 1
b = 0
if stacks[0, 1] > stacks[0, 2]:
a = 0
b = 1
# compute average vmn and i
iab = np.mean(stacks[:, 1])
vmn = np.mean(stacks[a::2, 1] + stacks[b::2, 2])
# self-potential estimated during on-time
spon = np.mean(stacks[a::2, 1] - stacks[b::2, 2])
# remove the average sp computed on injection half-cycle
vmn = vmn - spon
# compute average self potential between injection half-cycle
if duty < 1:
spoff = 0
n2avg = int(fulldata[0].shape[0] // 3)
for n, meas in enumerate(fulldata[1::2]):
spoff += np.mean(meas[-n2avg:, 2])
spoff = spoff / len(fulldata) * 2
else:
iab = np.nan
vmn = np.nan
spon = np.nan
fulldata = None
# set a low voltage for safety
self.alim.set_tx_voltage(12)
# reshape full data to an array of good size
# we need an array of regular size to save in the csv
if tx_volt > 0: # TODO what if have different array size?
for a in fulldata:
print(a.shape)
fulldata = np.vstack(fulldata)
# we create a big enough array given nb_samples, number of
# half-cycles (1 stack = 2 half-cycles), and twice as we
# measure decay as well
nsamples = int((int(injection_duration * 1000) / duty) // 0.01 + 1)
a = np.zeros((nb_stack * nsamples * 2, fulldata.shape[1])) * np.nan
a[:fulldata.shape[0], :] = fulldata
fulldata = a
# create a dictionary and compute averaged values from all stacks
d = {
"time": datetime.now().isoformat(),
"A": quad[0],
"B": quad[1],
"M": quad[2],
"N": quad[3],
"injtime [ms]": np.mean(injtimes),
"Vmn [mV]": vmn,
"I [mA]": iab,
"R [ohm]": vmn/iab,
"Ps [mV]": spon,
"nbStack": nb_stack,
"tmp [degC]": CPUTemperature().temperature if arm64_imports else -10,
"Nb samples [-]": n2avg,
"stacks": stacks,
"fulldata": fulldata,
}
# to the data logger
dd = d.copy()
dd.pop('fulldata') # too much for logger
dd.update({'A': str(dd['A'])})
dd.update({'B': str(dd['B'])})
dd.update({'M': str(dd['M'])})
dd.update({'N': str(dd['N'])})
# round float to 2 decimal
for key in dd.keys():
if isinstance(dd[key], float):
dd[key] = np.round(dd[key], 3)
dd['cmd_id'] = str(cmd_id)
self.data_logger.info(dd)
return d
def run_sequence(self, cmd_id=None, **kwargs):
"""Runs sequence synchronously (=blocking on main thread).
Additional arguments are passed to run_measurement().
Parameters
----------
cmd_id : str, optional
Unique command identifier.
kwargs : optional
Optional keyword arguments passed to run_measurement().
See help(OhmPi.run_measurement).
"""
self.status = 'running'
self.exec_logger.debug(f'Status: {self.status}')
self.exec_logger.debug(f'Measuring sequence: {self.sequence}')
# 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.mux.reset()
# measure all quadrupole of the sequence
if self.sequence is None:
seq = np.array([[0, 0, 0, 0]])
else:
seq = self.sequence.copy()
for i in range(0, seq.shape[0]):
quad = seq[i, :]
if self.status == 'stopping':
break
# call the switch_mux function to switch to the right electrodes
self.switch_mux_on(quad)
# run a measurement
acquired_data = self.run_measurement(quad, **kwargs)
self.data_logger.info(acquired_data)
# 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}/{seq.shape[0]: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 : str, optional
Unique command identifier
"""
def func():
self.run_sequence(**kwargs)
self.thread = threading.Thread(target=func)
self.thread.start()
self.status = 'idle'
def run_multiple_sequences(self, sequence_delay=None, nb_meas=None, cmd_id=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 : str, optional
Unique command identifier
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()
def _quad2qdic(self, quad):
"""Convert a quadrupole to a more flexible qdic
of format {'A': [1], 'B': [2], 'M': [3], 'N': [4]}.
This format enable to inject at several electrodes and
is more flexible for multichannelling (we can add M1, N1, ...).
Parameters
----------
quad : list of int,
List of quadrupoles. Electrodes equal to 0 are ignored.
Returns
-------
Dictionnary in the form: {role: [list of electrodes]}.
"""
return dict(zip(['A', 'B', 'M', 'N'], [[a] for a in quad if a > 0]))
def switch_mux_on(self, quad):
""""Switch quadrupoles on.
Parameters
----------
quad : list of int,
List of quadrupoles. Electrodes equal to 0 are ignored.
"""
qdic = self._quad2qdic(quad)
self.mux.switch(qdic, 'on')
def switch_mux_off(self, quad):
"""Switch quadrupoles off.
Parameters
----------
quad : list of int,
List of quadrupoles. Electrodes equal to 0 are ignored.
"""
qdic = self._quad2qdic(quad)
self.mux.switch(qdic, 'off')
def reset_mux(self):
"""Reset the mux, make sure all relays are off.
"""
self.mux.reset()
def rs_check(self, tx_volt=12., cmd_id=None):
"""Checks contact resistances.
Parameters
----------
tx_volt : float, optional
Voltage of the injection.
cmd_id : str, optional
Unique command identifier.
"""
# create custom sequence where MN == AB
# we only check the electrodes which are in the sequence (not all might be connected)
if self.sequence is None:
quads = np.array([[1, 2, 0, 0]], dtype=np.uint32)
else:
elec = np.sort(np.unique(self.sequence.flatten())) # assumed order
quads = np.vstack([
elec[:-1],
elec[1:],
np.zeros(len(elec)-1),
np.zeros(len(elec)-1)
]).T
# create filename to store RS
export_path_rs = self.settings['export_path'].replace('.csv', '') \
+ '_' + datetime.now().strftime('%Y%m%dT%H%M%S') + '_rs.csv'
# perform RS check
self.status = 'running'
# make sure all mux are off to start with
self.mux.reset()
# turn on alim
self.alim.turn_on()
self.alim.set_tx_voltage(tx_volt)
# measure all quad of the RS sequence
for i in range(0, quads.shape[0]):
quad = quads[i, :] # quadrupole
self.switch_mux_on(quad) # put before raising the pins (otherwise conflict i2c)
d = self.run_measurement(
quad=quad, nb_stack=1, injection_duration=0.2,
tx_volt=tx_volt, autogain=False)
self.switch_mux_off(quad)
voltage = d['Tx [V]']
current = d['I [mA]'] / 1000.
# compute resistance measured (= contact resistance)
resist = abs(voltage / current) / 1000.
# 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'
self.exec_logger.debug(msg)
# if contact resistance = 0 -> we have a short circuit!!
if resist < 1e-5:
msg = f'!!!SHORT CIRCUIT!!! {str(quad):s}: {resist:.3f} kOhm'
self.exec_logger.warning(msg)
# save data in a text file
self.append_and_save(export_path_rs, {
'A': quad[0],
'B': quad[1],
'RS [kOhm]': resist,
})
self.alim.turn_off()
self.status = 'idle'
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)
- 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
----------
settings : str, dict
Path to the .json settings file or dictionary of settings.
cmd_id : str, optional
Unique command identifier
"""
status = False
if settings is not None:
try:
if isinstance(settings, dict):
self.settings.update(settings)
else:
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: # noqa
self.exec_logger.warning('Unable to update settings.')
status = False
else:
self.exec_logger.warning('Settings are missing...')
return status
def stop(self, **kwargs):
warnings.warn('This function is deprecated. Use interrupt instead.', DeprecationWarning)
self.interrupt(**kwargs)
def _update_acquisition_settings(self, config):
warnings.warn('This function is deprecated, use update_settings() instead.', DeprecationWarning)
self.update_settings(settings=config)
# Properties
@property
def sequence(self):
"""Gets sequence"""
if self._sequence is not None:
assert isinstance(self._sequence, np.ndarray)
return self._sequence
# TODO not sure if the below is still needed now we have a
# method set_sequence()
@sequence.setter
def sequence(self, sequence):
"""Sets sequence"""
if sequence is not None:
assert isinstance(sequence, np.ndarray)
self.use_mux = True
else:
self.use_mux = False
self._sequence = sequence
VERSION = '3.0.0'
print(colored(r' ________________________________' + '\n' +
r'| _ | | | || \/ || ___ \_ _|' + '\n' +
r'| | | | |_| || . . || |_/ / | |' + '\n' +
r'| | | | _ || |\/| || __/ | |' + '\n' +
r'\ \_/ / | | || | | || | _| |_' + '\n' +
r' \___/\_| |_/\_| |_/\_| \___/ ', 'red'))
print('Version:', VERSION)
platform, on_pi = get_platform()
if on_pi:
print(colored(f'\u2611 Running on {platform} platform', 'green'))
# 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'))
else:
print(colored(f'\u26A0 Not running on the Raspberry Pi platform.\nFor simulation purposes only...', 'yellow'))
current_time = datetime.now()
print(f'local date and time : {current_time.strftime("%Y-%m-%d %H:%M:%S")}')
# for testing
if __name__ == "__main__":
ohmpi = OhmPi(settings=OHMPI_CONFIG['settings'])
if ohmpi.controller is not None:
ohmpi.controller.loop_forever()