diff --git a/http_interface.py b/http_interface.py
index 4a42e878f005ae49f1a332001b3859f800bc0b36..6b8e85d6243c1d27144c5b1c81fb4686a130d524 100644
--- a/http_interface.py
+++ b/http_interface.py
@@ -92,19 +92,25 @@ class MyServer(SimpleHTTPRequestHandler):
dic = json.loads(self.rfile.read(int(self.headers['Content-Length'])))
rdic = {} # response dictionary
if dic['cmd'] == 'run_sequence':
- payload = json.dumps({'cmd_id': cmd_id, 'cmd': 'run_sequence'})
+ payload = json.dumps({'cmd_id': cmd_id, 'cmd': 'run_multiple_sequences'})
publish.single(payload=payload, **publisher_config)
elif dic['cmd'] == 'interrupt':
payload = json.dumps({'cmd_id': cmd_id, 'cmd': 'interrupt'})
publish.single(payload=payload, **publisher_config)
elif dic['cmd'] == 'getData':
+ print(dic)
# get all .csv file in data folder
- fnames = [fname for fname in os.listdir('data/') if fname[-4:] == '.csv']
+ fnames = sorted([fname for fname in os.listdir('data/') if fname[-4:] == '.csv'])
ddic = {}
+ fdownloaded = True
+ if dic['lastSurvey'] == '0':
+ fdownloaded = False
for fname in fnames:
- if (fname.replace('.csv', '') not in dic['surveyNames']
- and fname != 'readme.txt'
- and '_rs' not in fname):
+ if (((fname != 'readme.txt')
+ and ('_rs' not in fname))
+ and ((fname.replace('.csv', '') == dic['lastSurvey'])
+ or (fdownloaded == False))):
+ fdownloaded = False
df = pd.read_csv('data/' + fname)
ddic[fname.replace('.csv', '')] = {
'a': df['A'].tolist(),
diff --git a/index.html b/index.html
index db104d009f47532bc3ed3fcbdd304433b72c4496..f16bc60e9bc9e468517682e7c3ab20167ff7af0d 100644
--- a/index.html
+++ b/index.html
@@ -34,8 +34,8 @@
<!-- Pseudo section -->
<select id='surveySelect' class='custom-select'>
</select>
- <input id="cmin" type="number" value="0"/>
- <input id="cmax" type="number" value="150"/>
+ <input id="cmin" type="number" value=""/>
+ <input id="cmax" type="number" value=""/>
<button id="capplyBtn" type="button" class="btn btn-info">Apply</button>
<div id="gd"></div>
<div class="mb3 row">
@@ -163,9 +163,9 @@
// run button
function runBtnFunc() {
- sendCommand('{"cmd": "run_sequence"}', function(x) {
- console.log(x['status'])
- if (x['status'] == 'running') {
+ sendCommand('{"cmd": "run_multiple_sequences"}', function(x) {
+ console.log(x['ohmpi_status'])
+ if (x['ohmpi_status'] == 'running') {
output.innerHTML = 'Status: measuring...'
}
})
@@ -176,7 +176,7 @@
// interrupt button
function stopBtnFunc() {
sendCommand('{"cmd": "interrupt"}', function(x) {
- output.innerHTML = 'Status: ' + x['status']
+ output.innerHTML = 'Status: ' + x['ohmpi_status']
clearInterval(interv)
getData()
})
@@ -375,13 +375,17 @@
// getData
function getData() {
+ let lastSurvey = '0'
+ if (Object.keys(data).length > 1) {
+ lastSurvey = Object.keys(data).slice(-2, -1)
+ }
sendCommand(JSON.stringify({
'cmd': 'getData',
- 'surveyNames': Object.keys(data).slice(0, -1)
+ 'lastSurvey': lastSurvey
// last survey is often partial so we download it again
}), function(ddic) {
// update status
- output.innerHTML = 'Status: ' + ddic['status']
+ //output.innerHTML = 'Status: ' + ddic['status']
// update data dic with new data
data = { // destructuring assignement (magic! :o)
@@ -499,7 +503,7 @@
function removeDataBtnFunc() {
sendCommand('{"cmd": "removeData"}',function(x) {
data = {}
- output.innerHTML = 'Status: ' + x['status'] + ' (all data cleared)'
+ output.innerHTML = 'Status: ' + x['ohmpi_status'] + ' (all data cleared)'
console.log('all data removed')
})
}
diff --git a/ohmpi.py b/ohmpi.py
index a3577a507da4465590d3285a47c9b92864d4083b..7b2a6a5d0a0017f51fffd141ac7b4cd1937f4e76 100644
--- a/ohmpi.py
+++ b/ohmpi.py
@@ -380,7 +380,7 @@ class OhmPi(object):
else:
mcp2.get_pin(relay_nr - 1).value = False
- self.exec_logger.debug(f'Switching relay {relay_nr} {state} for electrode {electrode_nr}')
+ self.exec_logger.debug(f'Switching relay {relay_nr} ({str(hex(self.board_addresses[role]))}) {state} for electrode {electrode_nr}')
else:
self.exec_logger.warning(f'Unable to address electrode nr {electrode_nr}')
@@ -428,11 +428,13 @@ class OhmPi(object):
Parameters
----------
- channel:
+ channel : object
+ Instance of ADS where voltage is measured.
Returns
-------
- float
+ gain : float
+ Gain to be applied on ADS1115.
"""
gain = 2 / 3
if (abs(channel.voltage) < 2.040) and (abs(channel.voltage) >= 1.023):
@@ -443,7 +445,7 @@ class OhmPi(object):
gain = 8
elif abs(channel.voltage) < 0.256:
gain = 16
- self.exec_logger.debug(f'Setting gain to {gain}')
+ #self.exec_logger.debug(f'Setting gain to {gain}')
return gain
def _compute_tx_volt(self, best_tx_injtime=0.1, strategy='vmax', tx_volt=5):
@@ -587,7 +589,8 @@ class OhmPi(object):
def run_measurement(self, quad=None, nb_stack=None, injection_duration=None,
- autogain=True, strategy='constant', tx_volt=5, best_tx_injtime=0.1):
+ autogain=True, strategy='constant', tx_volt=5, best_tx_injtime=0.1,
+ cmd_id=None):
"""Do a 4 electrode measurement and measure transfer resistance obtained.
Parameters
@@ -711,7 +714,7 @@ class OhmPi(object):
else:
self.pin0.value = False
self.pin1.value = True # current injection nr2
- self.exec_logger.debug(str(n) + ' ' + str(self.pin0.value) + ' ' + str(self.pin1.value))
+ self.exec_logger.debug('Stack ' + str(n) + ' ' + str(self.pin0.value) + ' ' + str(self.pin1.value))
# measurement of current i and voltage u during injection
meas = np.zeros((self.nb_samples, 3)) * np.nan
@@ -842,17 +845,6 @@ class OhmPi(object):
d = {'time': datetime.now().isoformat(), 'A': quad[0], 'B': quad[1], 'M': quad[2], 'N': quad[3],
'R [ohm]': np.abs(np.random.randn(1)).tolist()}
- # round number to two decimal for nicer string output
- output = [f'{k}\t' for k in d.keys()]
- output = str(output)[:-1] + '\n'
- for k in d.keys():
- if isinstance(d[k], float):
- val = np.round(d[k], 2)
- else:
- val = d[k]
- output += f'{val}\t'
- output = output[:-1]
-
# to the data logger
dd = d.copy()
dd.pop('fulldata') # too much for logger
@@ -860,7 +852,14 @@ class OhmPi(object):
dd.update({'B': str(dd['B'])})
dd.update({'M': str(dd['M'])})
dd.update({'N': str(dd['N'])})
- self.data_logger.info(json.dumps(dd))
+
+ # 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
@@ -891,49 +890,47 @@ class OhmPi(object):
# self.run = True
self.status = 'running'
- if self.on_pi:
- # make sure all mux are off to start with
- self.reset_mux()
+ # make sure all mux are off to start with
+ self.reset_mux()
- # 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=1, tx_volt=tx_volt, autogain=False)
+ # 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=0.25, tx_volt=tx_volt, autogain=False)
- if self.idps:
- voltage = tx_volt * 1000. # imposed voltage on dps5005
- else:
- voltage = d['Vmn [mV]']
- current = d['I [mA]']
-
- # 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 = '!!!SHORT CIRCUIT!!! {:s}: {:.3f} kOhm'.format(
- str(quad), resist)
- self.exec_logger.warning(msg)
- print(msg)
-
- # save data and print in a text file
- self.append_and_save(export_path_rs, {
- 'A': quad[0],
- 'B': quad[1],
- 'RS [kOhm]': resist,
- })
-
- # close mux path and put pin back to GND
- self.switch_mux_off(quad)
- self.reset_mux()
+ if self.idps:
+ voltage = tx_volt * 1000. # imposed voltage on dps5005
+ else:
+ voltage = d['Vmn [mV]']
+ current = d['I [mA]']
+
+ # 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 = '!!!SHORT CIRCUIT!!! {:s}: {:.3f} kOhm'.format(
+ str(quad), resist)
+ self.exec_logger.warning(msg)
+ print(msg)
+
+ # save data and print in a text file
+ self.append_and_save(export_path_rs, {
+ 'A': quad[0],
+ 'B': quad[1],
+ 'RS [kOhm]': resist,
+ })
+
+ # close mux path and put pin back to GND
+ self.switch_mux_off(quad)
else:
pass
self.status = 'idle'
@@ -1016,6 +1013,11 @@ class OhmPi(object):
while not self.status == 'idle':
time.sleep(0.1)
status = True
+ elif cmd == 'run_multiple_sequences':
+ self.run_multiple_sequences(cmd_id)
+ while not self.status == 'idle':
+ time.sleep(0.1)
+ status = True
elif cmd == 'interrupt':
self.interrupt()
status = True
@@ -1039,10 +1041,9 @@ class OhmPi(object):
self.exec_logger.warning(f'Unable to decode command {command}: {e}')
status = False
finally:
- reply = {'cmd_id': cmd_id, 'status': status}
+ reply = {'cmd_id': cmd_id, 'status':status, 'ohmpi_status': self.status}
reply = json.dumps(reply)
self.exec_logger.debug(f'Execution report: {reply}')
-
def set_sequence(self, args):
try:
@@ -1052,15 +1053,13 @@ class OhmPi(object):
self.exec_logger.warning(f'Unable to set sequence: {e}')
status = False
- def run_sequence(self, cmd_id=None, **kwargs):
+ def run_sequence(self, **kwargs):
"""Run 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',
@@ -1087,173 +1086,62 @@ class OhmPi(object):
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))
- }
-
+ acquired_data = self.run_measurement(quad, **kwargs)
+
# 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}')
- print(f'{acquired_data}')
# save data and print in a text file
self.append_and_save(filename, acquired_data)
self.exec_logger.debug(f'{i+1:d}/{n:d}')
self.status = 'idle'
- def run_sequence_async(self, cmd_id=None, **kwargs):
+ def run_sequence_async(self, **kwargs):
""" Run the sequence in a separate thread. Can be stopped by 'OhmPi.interrupt()'.
Additional arguments are passed to run_measurement().
"""
- # self.run = True
- self.status = 'running'
- self.exec_logger.debug(f'Status: {self.status}')
- self.exec_logger.debug(f'Measuring sequence: {self.sequence}')
-
def func():
- # if self.status != 'running':
- # self.exec_logger.warning('Data acquisition interrupted')
- # break
- 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}')
- print(f'{acquired_data}')
- # save data and print in a text file
- self.append_and_save(filename, acquired_data)
- self.exec_logger.debug(f'{i+1:d}/{n:d}')
-
- self.status = 'idle'
-
+ self.run_sequence(**kwargs)
+
self.thread = threading.Thread(target=func)
self.thread.start()
+ self.status = 'idle'
def measure(self, *args, **kwargs):
warnings.warn('This function is deprecated. Use run_multiple_sequences() instead.', DeprecationWarning)
- self.run_sequence(self, *args, **kwargs)
+ self.run_multiple_sequences(self, *args, **kwargs)
- def run_multiple_sequences(self, cmd_id=None, **kwargs):
+ def run_multiple_sequences(self, sequence_delay=None, **kwargs):
""" Run multiple sequences in a separate thread for monitoring mode.
Can be stopped by 'OhmPi.interrupt()'.
Additional arguments are passed to run_measurement().
+
+ Parameters
+ ----------
+ sequence_delay : int, optional
+ Number of seconds at which the sequence must be started from each others.
+ kwargs : dict, optional
+ See help(k.run_measurement) for more info.
"""
# self.run = True
+ if sequence_delay == None:
+ sequence_delay = self.settings['sequence_delay']
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, self.settings["nb_meas"]): # for time-lapse monitoring
if self.status != 'running':
self.exec_logger.warning('Data acquisition interrupted')
break
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}')
- print(f'{acquired_data}')
- # save data and print in a text file
- self.append_and_save(filename, acquired_data)
- self.exec_logger.debug(f'{i+1:d}/{n:d}')
-
- # compute time needed to take measurement and subtract it from interval
- # between two sequence run (= sequence_delay)
- measuring_time = time.time() - t0
- sleep_time = self.settings["sequence_delay"] - measuring_time
-
- if sleep_time < 0:
- # it means that the measuring time took longer than the sequence delay
- sleep_time = 0
- self.exec_logger.warning('The measuring time is longer than the sequence delay. '
- 'Increase the sequence delay')
+ self.run_sequence(**kwargs)
# sleeping time between sequence
+ dt = sequence_delay - (time.time() - t0)
+ if dt < 0:
+ dt = 0
if self.settings["nb_meas"] > 1:
- time.sleep(sleep_time) # waiting for next measurement (time-lapse)
+ time.sleep(dt) # waiting for next measurement (time-lapse)
self.status = 'idle'
self.thread = threading.Thread(target=func)
diff --git a/test_ohmpi_mux.py b/test_ohmpi_mux.py
index cf09c17eac674d056349699993058cb89a472f44..ed3222f6b4cd2e79c282d71f9e025f1f57455181 100644
--- a/test_ohmpi_mux.py
+++ b/test_ohmpi_mux.py
@@ -4,6 +4,7 @@ import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import os
+import time
# configure testing
idps = False
@@ -102,12 +103,13 @@ if use_mux:
# run sequence asynchronously and save data to file
k.run_sequence_async(nb_stack=1, injection_duration=0.25)
- time.sleep(2)
+ time.sleep(2) # if too short, it will still be resetting the mux (= no effect)
k.interrupt() # will kill the asynchronous sequence running
# run a series of asynchronous sequences
+ k.settings['nb_meas'] = 2 # run the sequence twice
k.run_multiple_sequences(nb_stack=1, injection_duration=0.25)
- time.sleep(2)
+ time.sleep(5)
k.interrupt()