diff --git a/architecture.pdf b/architecture.pdf
index a1025d0dccfa2174568c747a27517452214cd4bf..9c53a687468d97f5f0494d70b9e4fbf0cb3b9887 100644
Binary files a/architecture.pdf and b/architecture.pdf differ
diff --git a/examples/basic_ohmpi_flows_node-red.json b/examples/basic_ohmpi_flows_node-red.json
new file mode 100644
index 0000000000000000000000000000000000000000..2cdf5c89c42d46bb1d079a260d169214b5072505
--- /dev/null
+++ b/examples/basic_ohmpi_flows_node-red.json
@@ -0,0 +1 @@
+[{"id":"61c1655c50bd371c","type":"tab","label":"Flow 1","disabled":false,"info":""},{"id":"2d6881abe9336fbf","type":"mqtt in","z":"61c1655c50bd371c","name":"","topic":"ohmpi_0001/exec","qos":"2","datatype":"auto-detect","broker":"6ae7e77e.04c64","nl":false,"rap":false,"inputs":0,"x":390,"y":40,"wires":[["02e94bb48ce2cded"]]},{"id":"e2590e574c551cb9","type":"mqtt in","z":"61c1655c50bd371c","name":"","topic":"ohmpi_0001/data","qos":"2","datatype":"auto","broker":"6ae7e77e.04c64","nl":false,"rap":false,"inputs":0,"x":380,"y":140,"wires":[["b9a9d56fd4fb0b8c"]]},{"id":"e2c109f78f9e714c","type":"mqtt out","z":"61c1655c50bd371c","name":"MQTT ctrl","topic":"ohmpi_0001/ctrl","qos":"2","retain":"false","respTopic":"","contentType":"","userProps":"","correl":"","expiry":"","broker":"6ae7e77e.04c64","x":820,"y":340,"wires":[]},{"id":"e1d067d8532ff36b","type":"mqtt in","z":"61c1655c50bd371c","name":"","topic":"ohmpi_0001/soh","qos":"2","datatype":"auto","broker":"6ae7e77e.04c64","nl":false,"rap":false,"inputs":0,"x":380,"y":240,"wires":[["f5c9dacaafac51d0"]]},{"id":"a7a6f6068e01c7eb","type":"ui_button","z":"61c1655c50bd371c","name":"Run sequence","group":"142ad6ae.d55e29","order":1,"width":"1","height":"1","passthru":false,"label":"⏺","tooltip":"run sequence","color":"red","bgcolor":"lightgrey","className":"","icon":"","payload":"{\"cmd_id\" :\"0\", \"cmd\":\"run_sequence_async\"}","payloadType":"str","topic":"topic","topicType":"msg","x":380,"y":340,"wires":[["e2c109f78f9e714c"]]},{"id":"d82912d9c5b122fe","type":"ui_button","z":"61c1655c50bd371c","name":"Interrupt","group":"142ad6ae.d55e29","order":2,"width":"1","height":"1","passthru":false,"label":" ◾","tooltip":"interrupt sequence","color":"black","bgcolor":"lightgrey","className":"","icon":"","payload":"{\"cmd_id\" :\"0\", \"cmd\":\"interrupt\"}","payloadType":"str","topic":"topic","topicType":"msg","x":360,"y":400,"wires":[["e2c109f78f9e714c"]]},{"id":"02e94bb48ce2cded","type":"ui_text","z":"61c1655c50bd371c","group":"64a75353.37700c","order":2,"width":"16","height":"3","name":"MQTT exec","label":"Execution","format":"{{msg.payload}}","layout":"row-spread","className":"","x":830,"y":40,"wires":[]},{"id":"b9a9d56fd4fb0b8c","type":"ui_text","z":"61c1655c50bd371c","group":"64a75353.37700c","order":3,"width":"16","height":"3","name":"MQTT Data","label":"Data","format":"{{msg.payload}}","layout":"row-spread","className":"","x":830,"y":140,"wires":[]},{"id":"f5c9dacaafac51d0","type":"ui_text","z":"61c1655c50bd371c","group":"64a75353.37700c","order":4,"width":0,"height":0,"name":"MQTT SOH","label":"SOH","format":"{{msg.payload}}","layout":"row-spread","className":"","x":830,"y":240,"wires":[]},{"id":"329591d611aa2704","type":"ui_button","z":"61c1655c50bd371c","name":"","group":"64a75353.37700c","order":1,"width":0,"height":0,"passthru":false,"label":"clear messages","tooltip":"","color":"","bgcolor":"","className":"","icon":"","payload":" ","payloadType":"str","topic":"topic","topicType":"msg","x":580,"y":160,"wires":[["f5c9dacaafac51d0","b9a9d56fd4fb0b8c","02e94bb48ce2cded"]]},{"id":"25d69085f401beae","type":"ui_dropdown","z":"61c1655c50bd371c","name":"","label":"command","tooltip":"","place":"Select option","group":"142ad6ae.d55e29","order":5,"width":0,"height":0,"passthru":true,"multiple":false,"options":[{"label":"","value":"load_sequence","type":"str"},{"label":"","value":"reset_mux","type":"str"},{"label":"","value":"set_sequence","type":"str"},{"label":"","value":"update_settings","type":"str"}],"payload":"","topic":"command","topicType":"str","className":"","x":140,"y":480,"wires":[["182249692ee7502c"]]},{"id":"edbd2d507fbf085a","type":"ui_text_input","z":"61c1655c50bd371c","name":"","label":"kwargs","tooltip":"","group":"142ad6ae.d55e29","order":5,"width":0,"height":0,"passthru":false,"mode":"text","delay":"0","topic":"kwargs","sendOnBlur":true,"className":"","topicType":"str","x":140,"y":600,"wires":[["679471976db01c0e"]]},{"id":"679471976db01c0e","type":"json","z":"61c1655c50bd371c","name":"","property":"payload","action":"","pretty":false,"x":290,"y":600,"wires":[["b11654144c63d1b2"]]},{"id":"435a126aec0c424c","type":"debug","z":"61c1655c50bd371c","name":"debug 5","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"false","statusVal":"","statusType":"auto","x":640,"y":480,"wires":[]},{"id":"45c95568bb348470","type":"join","z":"61c1655c50bd371c","name":"","mode":"custom","build":"merged","property":"payload","propertyType":"msg","key":"topic","joiner":"\\n","joinerType":"str","accumulate":true,"timeout":"","count":"3","reduceRight":false,"reduceExp":"","reduceInit":"","reduceInitType":"","reduceFixup":"","x":650,"y":540,"wires":[["41122cfe96dd471a","e2c109f78f9e714c"]]},{"id":"41122cfe96dd471a","type":"ui_text","z":"61c1655c50bd371c","group":"142ad6ae.d55e29","order":6,"width":"2","height":"3","name":"","label":"Command to send","format":"{{msg.payload}}","layout":"row-spread","className":"","x":870,"y":600,"wires":[]},{"id":"182249692ee7502c","type":"function","z":"61c1655c50bd371c","name":"set cmd","func":"var newMsg = { payload: {\"cmd\": msg.payload }};\nreturn newMsg;","outputs":1,"noerr":0,"initialize":"","finalize":"","libs":[],"x":300,"y":480,"wires":[["435a126aec0c424c","45c95568bb348470"]]},{"id":"1549f01b20537e60","type":"ui_button","z":"61c1655c50bd371c","name":"","group":"142ad6ae.d55e29","order":7,"width":0,"height":0,"passthru":false,"label":"Send command","tooltip":"","color":"","bgcolor":"","className":"","icon":"","payload":"","payloadType":"str","topic":"topic","topicType":"msg","x":160,"y":700,"wires":[["c81857e22b65ef26","ae78c7b9e5aaeede"]]},{"id":"d4f6486f114c987d","type":"change","z":"61c1655c50bd371c","name":"","rules":[{"t":"set","p":"complete","pt":"msg","to":"true","tot":"bool"}],"action":"","property":"","from":"","to":"","reg":false,"x":590,"y":700,"wires":[["45c95568bb348470"]]},{"id":"b11654144c63d1b2","type":"function","z":"61c1655c50bd371c","name":"set kwargs","func":"var newMsg = { payload: {\"kwargs\": msg.payload }};\nreturn newMsg;","outputs":1,"noerr":0,"initialize":"","finalize":"","libs":[],"x":450,"y":600,"wires":[["45c95568bb348470"]]},{"id":"c81857e22b65ef26","type":"uuid","z":"61c1655c50bd371c","uuidVersion":"v1","namespaceType":"","namespace":"","namespaceCustom":"","name":"","field":"payload","fieldType":"msg","x":310,"y":660,"wires":[["1f97edbce5f88461"]]},{"id":"ae78c7b9e5aaeede","type":"delay","z":"61c1655c50bd371c","name":"","pauseType":"delay","timeout":"250","timeoutUnits":"milliseconds","rate":"1","nbRateUnits":"1","rateUnits":"second","randomFirst":"1","randomLast":"5","randomUnits":"seconds","drop":false,"allowrate":false,"outputs":1,"x":390,"y":700,"wires":[["d4f6486f114c987d"]]},{"id":"1f97edbce5f88461","type":"function","z":"61c1655c50bd371c","name":"set cmd_id","func":"var newMsg = { payload: {\"cmd_id\": msg.payload }};\nreturn newMsg;","outputs":1,"noerr":0,"initialize":"","finalize":"","libs":[],"x":490,"y":660,"wires":[["45c95568bb348470"]]},{"id":"6ae7e77e.04c64","type":"mqtt-broker","name":"ohmpi_mqtt_broker","broker":"mg3d-dev.umons.ac.be","port":"1883","clientid":"","autoConnect":true,"usetls":false,"compatmode":false,"protocolVersion":"4","keepalive":"60","cleansession":true,"birthTopic":"","birthQos":"0","birthPayload":"","birthMsg":{},"closeTopic":"","closeQos":"0","closePayload":"","closeMsg":{},"willTopic":"","willQos":"0","willPayload":"","willMsg":{},"userProps":"","sessionExpiry":""},{"id":"142ad6ae.d55e29","type":"ui_group","name":"Commands","tab":"5d888f29.07334","order":1,"disp":true,"width":"6","collapse":false,"className":""},{"id":"64a75353.37700c","type":"ui_group","name":"Messages","tab":"5d888f29.07334","order":2,"disp":true,"width":"16","collapse":true},{"id":"5d888f29.07334","type":"ui_tab","name":"Simple OhmPi controller","icon":"dashboard","disabled":false,"hidden":false}]
\ No newline at end of file
diff --git a/mqtt_controller.py b/examples/mqtt_controller.py
similarity index 92%
rename from mqtt_controller.py
rename to examples/mqtt_controller.py
index dd2e6a5c21636c82faa5294c961aa331d8137a65..a9d42e117e4ea2b1c877297bbc3086aeab882287 100644
--- a/mqtt_controller.py
+++ b/examples/mqtt_controller.py
@@ -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)
diff --git a/mqtt_interface.py b/mqtt_interface.py
deleted file mode 100644
index f90a6ae0df2f3bb583e47541c03127f5c74aae81..0000000000000000000000000000000000000000
--- a/mqtt_interface.py
+++ /dev/null
@@ -1,53 +0,0 @@
-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)
diff --git a/ohmpi.py b/ohmpi.py
index a4eb24da1bbf4452258504e4775cbc355b316525..5f6630a1651b54c3d16b327c1e1bdcda9a8f7ce2 100644
--- a/ohmpi.py
+++ b/ohmpi.py
@@ -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: