diff --git a/README.md b/README.md
index 25aeda550050520c27e9e0c7312d34fe0b2b9538..243403d4ef388883a3e09fbc844d2e7e3958e256 100644
--- a/README.md
+++ b/README.md
@@ -23,6 +23,8 @@ We strongly recommend users to create a virtual environment to run the code and
* you should run you code within the virtual environment
* to leave the virtual environment simply type: `deactivate`
+To enable to Python module, we need to add the 'ohmpi' folder to the python path. This can be done by `source .env` or manually by adding `export PYTHONPATH=$PYTHONPATH:/home/<username>/OhmPi` to /home/<username>/.bashrc.
+
## First run with four electrodes
In the examples folder, you will find the code "simple_measurement.py".
diff --git a/configs/config_mb_2023.py b/configs/config_mb_2023.py
index 3b6b704a195a7930eab97492e552242aa08e4ad6..8bd970d8096ec3515ced1a1c9d11ea5e2aeabbc7 100644
--- a/configs/config_mb_2023.py
+++ b/configs/config_mb_2023.py
@@ -19,7 +19,7 @@ OHMPI_CONFIG = {
HARDWARE_CONFIG = {
'ctl': {'model': 'raspberry_pi'},
- 'pwr': {'model': 'pwr_batt', 'voltage': 12.},
+ 'pwr': {'model': 'pwr_batt', 'voltage': 12., 'interface_name': 'none'},
'tx': {'model': 'mb_2023_0_X',
'voltage_max': 12., # Maximum voltage supported by the TX board [V]
'adc_voltage_max': 4800., # Maximum voltage read by the current ADC on the TX board [mA]
diff --git a/configs/config_mb_2024_0_2.py b/configs/config_mb_2024_0_2.py
index e90350deab5262485d623a7013ae297d49ddfca5..f99c214d235e821f4b55fca27db02d6b5bff2760 100644
--- a/configs/config_mb_2024_0_2.py
+++ b/configs/config_mb_2024_0_2.py
@@ -18,7 +18,7 @@ OHMPI_CONFIG = {
HARDWARE_CONFIG = {
'ctl': {'model': 'raspberry_pi'},
- 'pwr': {'model': 'pwr_batt', 'voltage': 12.},
+ 'pwr': {'model': 'pwr_batt', 'voltage': 12., 'interface_name': 'none'},
'tx': {'model': 'mb_2024_0_2',
'voltage_max': 50., # Maximum voltage supported by the TX board [V]
'current_max': 4800, # Maximum voltage read by the current ADC on the TX board [mA]
diff --git a/configs/config_mb_2024_0_2__1_mux_2024.py b/configs/config_mb_2024_0_2__1_mux_2024.py
index e83edf46062718979a6f96fdb8c95dcd1585d9a7..a9a91e4d052bb426c4f5c9e3765578b0a7f73a19 100644
--- a/configs/config_mb_2024_0_2__1_mux_2024.py
+++ b/configs/config_mb_2024_0_2__1_mux_2024.py
@@ -18,7 +18,7 @@ OHMPI_CONFIG = {
HARDWARE_CONFIG = {
'ctl': {'model': 'raspberry_pi'},
- 'pwr': {'model': 'pwr_batt', 'voltage': 12.},
+ 'pwr': {'model': 'pwr_batt', 'voltage': 12., 'interface_name': 'none'},
'tx': {'model': 'mb_2024_0_2',
'voltage_max': 50., # Maximum voltage supported by the TX board [V]
'current_max': 4800, # Maximum voltage read by the current ADC on the TX board [mA]
diff --git a/configure_second_I2C_bus.sh b/configure_second_I2C_bus.sh
new file mode 100644
index 0000000000000000000000000000000000000000..43e8b4509f750f3fb975bdec257e47c00b62bd92
--- /dev/null
+++ b/configure_second_I2C_bus.sh
@@ -0,0 +1,2 @@
+sudo apt-get install -y i2c-tools
+echo -e "[all]\ndtoverlay=i2c-gpio,bus=4,i2c_gpio_delay_us=1,i2c_gpio_sda=22,i2c_gpio_scl=23" | sudo tee -a /boot/config.txt
diff --git a/dev/test_mb_2023_0_mux.py b/dev/test_mb_2023_0_mux.py
new file mode 100644
index 0000000000000000000000000000000000000000..4dfafdf74eeb36d7368fdfd1c67018929b840e5f
--- /dev/null
+++ b/dev/test_mb_2023_0_mux.py
@@ -0,0 +1,117 @@
+import matplotlib
+matplotlib.use('TkAgg')
+from ohmpi.utils import change_config
+change_config('../configs/config_mb_2023.py', verbose=False)
+import importlib
+import time
+import logging
+from ohmpi.config import HARDWARE_CONFIG
+
+stand_alone = False
+part_of_hardware_system = False
+within_ohmpi = True
+
+# Stand alone
+if stand_alone:
+
+ ctl_module = importlib.import_module(f'ohmpi.hardware_components.{HARDWARE_CONFIG["ctl"].pop("model")}')
+ pwr_module = importlib.import_module(f'ohmpi.hardware_components.{HARDWARE_CONFIG["pwr"].pop("model")}')
+ tx_module = importlib.import_module(f'ohmpi.hardware_components.{HARDWARE_CONFIG["tx"].pop("model")}')
+ rx_module = importlib.import_module(f'ohmpi.hardware_components.{HARDWARE_CONFIG["rx"].pop("model")}')
+
+ ctl = ctl_module.Ctl()
+ HARDWARE_CONFIG['tx'].update({'ctl': ctl, 'exec_logger': ctl.exec_logger, 'soh_logger': ctl.soh_logger})
+ HARDWARE_CONFIG['rx'].update({'ctl': ctl, 'exec_logger': ctl.exec_logger, 'soh_logger': ctl.soh_logger})
+ HARDWARE_CONFIG['tx'].update({'connection': HARDWARE_CONFIG['tx'].pop('connection',
+ ctl.interfaces[
+ HARDWARE_CONFIG['tx'].pop(
+ 'interface_name', 'i2c')])})
+ HARDWARE_CONFIG['rx'].update({'connection': HARDWARE_CONFIG['rx'].pop('connection',
+ ctl.interfaces[
+ HARDWARE_CONFIG['rx'].pop(
+ 'interface_name', 'i2c')])})
+
+ HARDWARE_CONFIG['pwr'].update({'connection': HARDWARE_CONFIG['pwr'].pop('connection',
+ ctl.interfaces[
+ HARDWARE_CONFIG['pwr'].pop(
+ 'interface_name', None)])})
+
+
+ rx = rx_module.Rx(**HARDWARE_CONFIG['rx'])
+ tx = tx_module.Tx(**HARDWARE_CONFIG['tx'])
+ pwr = pwr_module.Pwr(**HARDWARE_CONFIG['pwr'])
+
+ # mux_ids = ['mux_02', 'mux_05']
+ # for m,mux_id in enumerate(mux_ids):
+ # mux_module = importlib.import_module(
+ # f'ohmpi.hardware_components.{HARDWARE_CONFIG["mux"]["boards"][mux_id].pop("model")}')
+
+ # MUX_CONFIG = HARDWARE_CONFIG['mux']['boards'][mux_id]
+
+ # MUX_CONFIG.update({'ctl': ctl, 'connection': MUX_CONFIG.pop('connection', ctl.interfaces[
+ # MUX_CONFIG.pop('interface_name', 'i2c_ext')]), 'exec_logger': ctl.exec_logger,
+ # 'soh_logger': ctl.soh_logger})
+ # MUX_CONFIG.update({'id': mux_id})
+ # mux = mux_module.Mux(**MUX_CONFIG)
+
+ # # tx.polarity = 1
+ # # time.sleep(1)
+ # # tx.polarity = 0
+ # # mux.switch(elec_dict={'A': [1], 'B': [4], 'M': [2], 'N': [3]}, state='on')
+ # # time.sleep(1)
+ # # voltage = rx.voltage
+ # # current = tx.current
+ # # mux.switch(elec_dict={'A': [1], 'B': [4], 'M': [2], 'N': [3]}, state='off')
+ # # print(f'Resistance: {voltage / current :.2f} ohm, voltage: {voltage:.2f} mV, current: {current:.2f} mA')
+ # mux.reset()
+ # mux.test({'A': [i+8*m for i in range(1, 9)], 'B': [i+8*m for i in range(1, 9)],
+ # 'M': [i+8*m for i in range(1, 9)], 'N': [i+8*m for i in range(1, 9)]}, activation_time=.1)
+ # mux.reset()
+
+# mux as part of a OhmPiHardware system
+if part_of_hardware_system:
+ from ohmpi.hardware_system import OhmPiHardware
+ print('Starting test of as part of an OhmPiHardware system.')
+ # mux_id = 'mux_03'
+ k = OhmPiHardware()
+ k.exec_logger.setLevel(logging.DEBUG)
+ # Test mux switching
+ k.reset_mux()
+ # k.switch_mux(electrodes=[1, 4, 2, 3], roles=['A', 'B', 'M', 'N'], state='on')
+ # time.sleep(1.)
+ # k.switch_mux(electrodes=[1, 4, 2, 3], roles=['A', 'B', 'M', 'N'], state='off')
+ # k.mux_boards[mux_id].test(activation_time=.4)
+ k.test_mux()
+ k.reset_mux()
+
+if within_ohmpi:
+ from ohmpi.ohmpi import OhmPi
+ # from ohmpi.plots import plot_exec_log
+
+ print('Starting test with OhmPi.')
+ k = OhmPi()
+ # A, B, M, N = (32, 29, 31, 30)
+ k.reset_mux()
+ # k.test_mux(mux_id='mux_03')
+ # k._hw.switch_mux([A, B, M, N], state='on')
+ # k._hw.vab_square_wave(12.,1., cycles=2)
+ # k._hw.switch_mux([A, B, M, N], state='off')
+ # k._hw.calibrate_rx_bias() # electrodes 1 4 2 3 should be connected to a reference circuit
+ # k._hw.rx._bias = -1.38
+ # print(f'Resistance: {k._hw.last_rho :.2f} ohm, dev. {k._hw.last_dev:.2f} %, rx bias: {k._hw.rx._bias:.2f} mV')
+ # k._hw._plot_readings()
+ A, B, M, N = (0, 0, 0, 0)
+ # k._hw.switch_mux([A, B, M, N], state='on')
+ # k._hw.vab_square_wave(12., cycle_duration=10., cycles=3)
+ # k._hw.switch_mux([A, B, M, N], state='off')
+ # print(f'OhmPiHardware Resistance: {k._hw.last_rho :.2f} ohm, dev. {k._hw.last_dev:.2f} %, rx bias: {k._hw.rx._bias:.2f} mV')
+ # k._hw._plot_readings()
+ print('using OhmPi')
+ d = k.run_measurement([A, B, M, N], injection_duration=1., nb_stack=2, duty_cycle=0.5)
+ print(d)
+ # k._hw._plot_readings()
+ print(f'OhmPiHardware: Resistance: {k._hw.last_resistance() :.2f} ohm, dev. {k._hw.last_dev():.2f} %, sp: {k._hw.sp:.2f} mV, rx bias: {k._hw.rx._bias:.2f} mV')
+ print(f'OhmPi: Resistance: {d["R [ohm]"] :.2f} ohm, dev. {d["R_std [%]"]:.2f} %, rx bias: {k._hw.rx._bias:.2f} mV')
+ k._hw._plot_readings(save_fig=False)
+ # plot_exec_log('ohmpi/logs/exec.log')
+change_config('../configs/config_default.py', verbose=False)
diff --git a/index-mqtt.html b/index-mqtt.html
deleted file mode 100755
index 070d4fe13ea81700590c04d23493fbab8dcb512a..0000000000000000000000000000000000000000
--- a/index-mqtt.html
+++ /dev/null
@@ -1,654 +0,0 @@
-<!DOCTYPE html>
-<html>
-<head>
- <meta charset="utf8"/>
- <title>OhmPi Acquisition Board</title>
- <link rel="shortcut icon" type="image/jpg" href="logo_ohmpi.jpg"/>
-
- <!-- dependencies (need to be local as no internet in AP mode)-->
- <script src="js/plotly-basic-2.8.3.min.js"></script>
- <script src="js/jquery-3.4.1.min.js"></script>
- <link type="text/css" href="css/bootstrap.min.css" rel="stylesheet">
- <!-- <script src="https://code.jquery.com/jquery-3.4.1.min.js"></script> -->
- <!-- <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-eOJMYsd53ii+scO/bJGFsiCZc+5NDVN2yr8+0RDqr0Ql0h+rP48ckxlpbzKgwra6" crossorigin="anonymous"> -->
- <!-- <script src="js/danfojs/bundle.min.js"></script> -->
- <!-- <script src="js/mqtt.min.js"></script> -->
- <script src="js/paho/paho-mqtt.js"></script>
-</head>
-<body>
- <div class='container'>
- <h1>OhmPi Acquisition Board</h1>
- <!-- nb stacks, on-time -->
- <button id="update_settingsBtn" type="button" class="btn btn-secondary" data-toggle="modal" data-target="#exampleModal">Settings</button>
- <button id='runBtn' type="button" class="btn btn-primary">▶</button>
- <button id='stopBtn' type="button" class="btn btn-warning">◼</button>
- <!-- upload button for csv which display the table ABMN -->
- <button id="removeDataBtn" type="button" class="btn btn-danger">Clear data</button>
- <button id="getDataBtn" type="button" class="btn btn-info">Get data</button>
- <div class="form-check">
- <input id="dataRetrievalCheck" class="form-check-input" type="checkbox" value="">
- <label class="form-check-label" for="dataRetrievalCheck">
- Automaticaly get data every 1 secondStart
- </label>
- </div>
- <div id='output'>Status: idle</div>
-
- <!-- Pseudo section -->
- <select id='surveySelect' class='custom-select'>
- </select>
- <input id="cmin" type="number" value="0"/>
- <input id="cmax" type="number" value="150"/>
- <button id="capplyBtn" type="button" class="btn btn-info">Apply</button>
- <div id="gd"></div>
- <div class="mb3 row">
- <label for="quadSelect">Quadrupole:</label>
- <div class="col-sm-10">
- <select id='quadSelect' class='custom-select'></select>
- </div>
- </div>
-
- <!-- trace figure -->
- <button id="addTraceBtn" type="button" class="btn btn-info">Add trace</button>
- <button id="removeTracesBtn" type="button" class="btn btn-info">Remove all traces</button>
- <div id="ts"></div>
-
- <!-- RS check -->
- <button id="rsBtn" type="button" class="btn btn-info">Check contact resistance</button>
- <button id="rsClearBtn" type="button" class="btn btn-info">Clear plot</button>
- <div id="rs"></div>
-
- <!-- Additional buttons -->
- <button id="downloadBtn" type="button" class="btn btn-primary">Download data</button>
- <!-- <button id="invertBtn" type="button" class="btn btn-primary">Invert</button> -->
- <a id="download"></a>
-
- <!-- Modal for configuration -->
- <div class="modal fade" id="exampleModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
- <div class="modal-dialog" role="document">
- <div class="modal-content">
- <div class="modal-header">
- <h5 class="modal-title" id="exampleModalLabel">OhmPi configuration</h5>
- <button type="button" class="close" data-dismiss="modal" aria-label="Close">
- <span aria-hidden="true">×</span>
- </button>
- </div>
- <div class="modal-body">
- <form>
- <div class="form-group row">
- <label for="nbElectrodes" class="col-sm-2 col-form-label">Nb electrodes</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="nbElectrodes" value="64">
- </div>
- </div>
- <div class="form-group row">
- <label for="injectionDuration" class="col-sm-2 col-form-label">Injection duration [s]</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="injectionDuration" value="0.2">
- </div>
- </div>
- <div class="form-group row">
- <label for="nbMeasurements" class="col-sm-2 col-form-label">Nb Measurements</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="nbMeasurements" value="1">
- </div>
- </div>
- <div class="form-group row">
- <label for="sequenceDelay" class="col-sm-2 col-form-label">Sequence delay [s]</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="sequenceDelay" value="100">
- </div>
- </div>
- <div class="form-group row">
- <label for="nbStack" class="col-sm-2 col-form-label">Nb stack</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="nbStack" value="1">
- </div>
- </div>
- <div class="form-group row">
- <label for="sequence" class="col-sm-2 col-form-label">Sequence</label>
- <div class="col-sm-10">
- <input type="file" class="form-control" id="sequence">
- </div>
- </div>
- <div class="form-group row">
- <label for="elecSpacing" class="col-sm-2 col-form-label">Electrode spacing [m]</label>
- <div class="col-sm-10">
- <input type="number" class="form-control" id="elecSpacing", value="1">
- </div>
- </div>
- </form>
- </div>
- <div class="modal-footer">
- <button type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button>
- <button id="saveConfigBtn" type="button" data-dismiss="modal" class="btn btn-primary">Save</button>
- </div>
- </div>
- </div>
- </div>
- <button id="restartBtn" type="button" class="btn btn-danger">Restart</button>
- <button id="shutdownBtn" type="button" class="btn btn-danger">Shutdown</button>
- <footer>v0.2.0</footer>
- </div>
-
- <script type="text/javascript">
- //let serverUrl = 'http://10.3.141.1:8080'
- //let serverUrl = 'http://0.0.0.0:8080'
- //let serverUrl = 'http://localhost:8080'
- let serverUrl = 'http://' + window.location.host
- console.log('serverUrl =', serverUrl)
- 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 commands = {} // store commands and their id
- let callbacks = {} // store callback (might not be needed)
-
- // function with MQTT
- let topic = 'ohmpi_0001' // we could change this through a drop-down to connect to a different ohmpi
- let topic_ctrl = topic + '/ctrl'
- let topic_exec = topic + '/exec'
- let topic_data = topic + '/data'
- let hostname = location.hostname
- let port = 9001
- let clientId = 'ohmpi_0001_html'
- let message = null
- let msg = ''
-
- // create client
- client = new Paho.MQTT.Client(hostname, port, clientId);
- client.onConnectionLost = onConnectionLost;
- client.onMessageArrived = onMessageArrived;
- client.connect({onSuccess:onConnect});
-
- function onConnect() {
- console.log("onConnect")
- client.subscribe(topic_data)
- client.subscribe(topic_exec)
-
- // send welcome message
- message = new Paho.MQTT.Message("Hello from index.html")
- message.destinationName = topic_ctrl
- client.send(message)
- }
-
- function onConnectionLost(responseObject) {
- if (responseObject.errorCode !== 0)
- console.log("onConnectionLost:" + responseObject.errorMessage)
- }
-
- function onMessageArrived(message) {
- console.log("onMessageArrived:" + message.payloadString)
- try {
- let payload = message.payloadString
- if (message.topic == topic_data) {
- // process data
- msg = payload // for accessing the variable from the console
- console.log('DATA', payload)
- let ddic = JSON.parse(payload.split('INFO:')[1])
-
- // check cmd_id is any
- processData(ddic)
-
- // usually these don't have a cmd_id so we are not sure when
-
- } else if (message.topic == topic_exec) {
- // display it in the log
- console.log('EXEC LOG:', payload)
- }
-
- // let response = JSON.parse(message.payloadString)
- // console.log('response=', response)
- // // check ID of message against our dictionnary of callback
- // let cmd_id = response['cmd_id']
- // if (callbacks.hasOwnProperty(cmd_id)) {
- // console.log('++ execute callback')
- // callbacks[cmd_id](response['content']) // execute callback
- // }
- } catch (e) {
- console.log(e)
- }
- // client.disconnect()
- }
-
- // useful functions
- function generateUniqSerial() {
- return 'xxxx-xxxx-xxx-xxxx'.replace(/[x]/g, (c) => {
- const r = Math.floor(Math.random() * 16);
- return r.toString(16);
- });
- }
-
- // sending commands to the OhmPi
- function sendCommand(query, callback=null) {
- // dic in the form: {'cmd': X, ...} as JSON
- if (callback == null) {
- function callback(x) {
- console.log('default callback:', x)
- }
- }
-
- /*
- let xhr = new XMLHttpRequest();
- xhr.onreadystatechange = function() {
- if (this.readyState == 4) {
- if (xhr.status == 200) {
- callback(JSON.parse(xhr.response))
- }
- }
- }
- xhr.open('POST', serverUrl)
- xhr.setRequestHeader('Content-Type', 'application/json')
- xhr.send(query)
- */
-
- // generate a unique command id to be associated with the commands
- let uuid = generateUniqSerial()
- commands[uuid] = query
- callbacks[uuid] = callback // store the callback to be processed later when message arrives
- let payload = '{"cmd_id": "' + uuid + '",' + query.slice(1)
- console.log('sendCommand()', payload)
- message = new Paho.MQTT.Message(payload)
- message.destinationName = topic_ctrl
- client.send(message)
- }
-
- // run button
- function runBtnFunc() {
- sendCommand('{"cmd": "run_multiple_sequences"}', function(x) {
- console.log(x['status'])
- if (x['status'] == 'running') {
- output.innerHTML = 'Status: measuring...'
- }
- })
- }
- let runBtn = document.getElementById('runBtn')
- runBtn.addEventListener('click', runBtnFunc)
-
- // interrupt button
- function stopBtnFunc() {
- sendCommand('{"cmd": "interrupt"}', function(x) {
- output.innerHTML = 'Status: ' + x['status']
- clearInterval(interv)
- getData()
- })
- }
- let stopBtn = document.getElementById('stopBtn')
- stopBtn.addEventListener('click', stopBtnFunc)
-
- // set configuration
- function saveConfigBtnFunc() {
- // collect values from modal
- let formVals = {}
- for (let field of ['nbElectrodes', 'injectionDuration',
- 'nbMeasurements', 'sequenceDelay', 'nbStack']) {
- formVals[field] = document.getElementById(field).value
- }
- console.log(formVals)
-
- // define callback to send settings to Pi
- function configCallback() {
- sendCommand(JSON.stringify({
- 'cmd': 'update_settings',
- 'kwargs': {
- 'config': formVals
- }
- }), function(x) {
- console.log('update_settings', x)
- })
- }
-
- // deal with the potential file containing the sequence
- // https://stackoverflow.com/questions/19038919/is-it-possible-to-upload-a-text-file-to-input-in-html-js
- if (!window.FileReader) {
- alert('Your browser is not supported');
- return false;
- }
- let input = document.getElementById('sequence')
- if (input.files.length) {
- const reader = new FileReader()
- reader.readAsText(input.files[0])
- reader.addEventListener('load', () => {
- formVals['sequence'] = reader.result
- console.log('file==', reader.result)
- configCallback()
- }, false)
- } else {
- console.log('no sequence uploaded')
- formVals['sequence'] = ''
- configCallback()
- }
-
-
- }
- let saveConfigBtn = document.getElementById('saveConfigBtn')
- saveConfigBtn.addEventListener('click', saveConfigBtnFunc)
-
- // make pseudo plot
- var trace = {
- x: [],
- y: [],
- mode: 'markers',
- marker: {
- size: 40,
- color: [],
- colorbar: {
- title: 'App. res. [Ohm.m]',
- cmin: 0,
- cmax: 100,
- }
- }
- }
- let layout = {
- title: 'Pseudo-section',
- yaxis: {
- title: 'Pseudo-depth',
- autorange: 'reversed'
- },
- xaxis: {
- title: 'X'
- }
-
- }
- Plotly.newPlot('gd', [trace], layout)
-
- // make time-serie plot
- let tdata = []
- let layout2 = {
- title: 'Time-serie',
- yaxis: {
- title: 'App. res. [Ohm.m]'
- },
- xaxis: {
- title: 'Sampling time'
- }
- }
- Plotly.newPlot('ts', tdata, layout2)
-
- // add trace to time-serie plot
- function addTraceBtnFunc() {
- let val = document.getElementById('quadSelect').value
- squads.push(val.split(', '))
- tdata.push({
- x: [],
- y: [],
- name: val,
- type: 'scatter'
- })
- Plotly.newPlot('ts', tdata, layout2)
- getData()
- }
- let addTraceBtn = document.getElementById('addTraceBtn')
- addTraceBtn.addEventListener('click', addTraceBtnFunc)
-
- // remove all traces from time-serie plot
- function removeTracesBtnFunc() {
- squads = []
- tdata = []
- Plotly.newPlot('ts', tdata, layout2)
- }
- let removeTracesBtn = document.getElementById('removeTracesBtn')
- removeTracesBtn.addEventListener('click', removeTracesBtnFunc)
-
- // callback function to draw the plot
- function surveySelectFunc(el) {
- let surveyName = el['target'].value
- let df = data[surveyName]
- if (df != undefined) {
- let a = df['a']
- let b = df['b']
- let m = df['m']
- let n = df['n']
- // let's assume electrodes are 1 m distance
- // compute pseudo-depth (assume no topo)
- // compute app res (assumping flat, line survey)
- let xpos = []
- let ypos = []
- let app = []
- for (let i = 0; i < a.length; i++) {
- let ab = (a[i] + b[i])/2
- let mn = (m[i] + n[i])/2
- let dist = Math.abs(ab - mn)
- xpos.push(Math.min(ab, mn) + dist/2)
- ypos.push(Math.sqrt(2)/2*dist)
- let am = Math.abs(a[i] - m[i])
- let bm = Math.abs(b[i] - m[i])
- let an = Math.abs(a[i] - n[i])
- let bn = Math.abs(a[i] - n[i])
- let K = (2*Math.PI)/((1/am)-(1/an)-(1/an)+(1/bn))
- app.push(df['rho'][i]*-K)
- }
- console.log(app)
- // update the trace and redraw the figure
- trace['x'] = xpos
- trace['y'] = ypos
- trace['marker']['color'] = app
- trace['marker']['cmax'] = document.getElementById('cmax').value
- trace['marker']['cmin'] = document.getElementById('cmin').value
- Plotly.redraw('gd')
- }
- }
- let surveySelect = document.getElementById('surveySelect')
-
- // bar chart for contact resistance
- let rsdata = []
- let rslayout = {
- title: 'Contact resistances',
- yaxis: {
- title: 'Resistance [kOhm]'
- },
- xaxis: {
- title: 'Consecutive electrodes'
- }
- }
- Plotly.newPlot('rs', rsdata, rslayout)
-
- // run RS check
- function rsBtnFunc() {
- sendCommand('{"cmd": "rsCheck"}', function (res) {
- // update the bar plot
- rsdata.push({
- x: res['data']['AB'],
- y: res['data']['res'],
- name: 'RS',
- type: 'bar'
- })
- Plotly.redraw('rs')
- })
- }
- let rsBtn = document.getElementById('rsBtn')
- rsBtn.addEventListener('click', rsBtnFunc)
-
- // clear RS graph
- function rsClearBtnFunc() {
- rsdata = []
- Plotly.newPlot('rs', rsdata, rslayout)
- }
- let rsClearBtn = document.getElementById('rsClearBtn')
- rsClearBtn.addEventListener('click', rsClearBtnFunc)
-
- // getData
- function getData() {
- sendCommand(JSON.stringify({
- 'cmd': 'get_data',
- 'survey_names': Object.keys(data).slice(0, -1)
- // last survey is often partial so we download it again
- }), console.log('processData(ddic)')
- )
- }
-
- // processData
- function processData(ddic) {
- // update status
- output.innerHTML = 'Status: ' + ddic['status']
-
- // update data dic with new data
- data = { // destructuring assignement (magic! :o)
- ...data,
- ...ddic['data'] // value from second dic are preferred
- }
-
- // dropdown with number of surveys and +++
- let surveyNames = Object.keys(data).sort()
-
- // remove listener as we will replace the choices
- surveySelect.removeEventListener('change', surveySelectFunc)
- surveySelect.innerHTML = '' // clearing all child nodes
-
- // add choices again
- for (let surveyName of surveyNames) {
- let option = document.createElement('option')
- option.innerText = surveyName
- option.value = surveyName
- surveySelect.appendChild(option)
- }
-
- // listener again
- surveySelect.addEventListener('change', surveySelectFunc)
-
- // plot last one by default
- surveySelect.value = surveyNames[surveyNames.length - 1]
-
- // call the function directly
- // (as progammatically chaging the value does not trigger the event)
- surveySelectFunc({'target': surveySelect})
-
- // update list of quadrupoles if any
- if (quads.length == 0) {
- console.log('updating list of quadrupoles')
- let df = data[surveyNames[0]]
- let quadSelect = document.getElementById('quadSelect')
- quadSelect.innerHTML = ''
- for (let i = 0; i < df['a'].length; i++) {
- quad = [df['a'][i], df['b'][i], df['m'][i], df['n'][i]]
- quads.push(quad)
- let option = document.createElement('option')
- option.value = quad.join(', ')
- option.innerText = quad.join(', ')
- quadSelect.appendChild(option)
- }
- console.log('quads=', quads)
- }
-
- // update time-serie figure
- if (squads.length > 0) {
-
- // transform all surveyNames to datetime
- let xt = []
- for (surveyName of surveyNames) {
- let a = surveyName.split('_').slice(-1)[0]
- xt.push(a.slice(0, 4) + '-'
- + a.slice(4, 6) + '-'
- + a.slice(6, 8) + ' '
- + a.slice(9, 11) + ':'
- + a.slice(11, 13) + ':'
- + a.slice(13, 15))
- }
- //console.log(xt)
-
- // create one new trace per selected quadrupole
- for (let k = 0; k < squads.length; k++) {
- squad = squads[k]
- let x = []
- let y = []
- for (let i = 0; i < surveyNames.length; i++) {
- df = data[surveyNames[i]]
- for (let j = 0; j < df['a'].length; j++) {
- if (df['a'][j] == squad[0]
- && df['b'][j] == squad[1]
- && df['m'][j] == squad[2]
- && df['n'][j] == squad[3]) {
- y.push(df['rho'][j])
- x.push(xt[i])
- break
- }
- }
- }
-
- // update trace dictionnary
- tdata[k]['x'] = x
- tdata[k]['y'] = y
- }
- //console.log(tdata)
- Plotly.redraw('ts')
- }
- }
-
- let getDataBtn = document.getElementById('getDataBtn')
- getDataBtn.addEventListener('click', getData)
-
- // apply new colorscale
- let capplyBtn = document.getElementById('capplyBtn')
- capplyBtn.addEventListener('click', function() {
- surveySelectFunc({'target': surveySelect})
- })
-
- // checkbox interaction for data download
- function dataRetrievalCheckFunc(x) {
- if (x['target'].checked == true) {
- interv = setInterval(getData, 1000) // every 5s
- } else {
- clearInterval(interv)
- }
- }
- let dataRetrievalCheck = document.getElementById('dataRetrievalCheck')
- dataRetrievalCheck.addEventListener('change', dataRetrievalCheckFunc)
-
- // remove data
- function removeDataBtnFunc() {
- sendCommand('{"cmd": "removeData"}',function(x) {
- data = {}
- output.innerHTML = 'Status: ' + x['status'] + ' (all data cleared)'
- console.log('all data removed')
- })
- }
- let removeDataBtn = document.getElementById('removeDataBtn')
- removeDataBtn.addEventListener('click', removeDataBtnFunc)
-
- // shutdown Pi
- function shutdownBtnFunc() {
- sendCommand('{"cmd": "shutdown"}', function(x) {
- console.log('shuting down...')
- })
- }
- let shutdownBtn = document.getElementById('shutdownBtn')
- shutdownBtn.addEventListener('click', shutdownBtnFunc)
-
- // restart Pi
- function restartBtnFunc() {
- sendCommand('{"cmd": "restart"}', function(x) {
- console.log('rebooting...')
- })
- }
- let restartBtn = document.getElementById('restartBtn')
- restartBtn.addEventListener('click', restartBtnFunc)
-
- // invert data
- // function invertBtnFunc() {
- // sendCommand('{"cmd": "invert"}', function(x) {
- // console.log('inversion results', x)
- // })
- // }
- // let invertBtn = document.getElementById('invertBtn')
- // invertBtn.addEventListener('click', invertBtnFunc)
-
- // download data
- function downloadBtnFunc() {
- sendCommand('{"cmd": "download"}', function(x) {
- let dwl = document.getElementById('download')
- dwl.setAttribute('href', serverUrl + '/data.zip')
- dwl.setAttribute('download', 'data.zip')
- dwl.click()
- })
- }
- let downloadBtn = document.getElementById('downloadBtn')
- downloadBtn.addEventListener('click', downloadBtnFunc)
-
-
- </script>
-
- <!-- Boostrap scripts (at the end of the page for faster loading time)-->
- <script src="js/bootstrap.bundle.min.js"></script>
- <!-- <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/js/bootstrap.bundle.min.js" integrity="sha384-JEW9xMcG8R+pH31jmWH6WWP0WintQrMb4s7ZOdauHnUtxwoG2vI5DkLtS3qm9Ekf" crossorigin="anonymous"></script> -->
-</body>
-</html>
diff --git a/index.html b/index.html
deleted file mode 100644
index b334d18b47d1f8ab64e32028a15fac4c0b513d7e..0000000000000000000000000000000000000000
--- a/index.html
+++ /dev/null
@@ -1,704 +0,0 @@
-<!DOCTYPE html>
-<html>
-<head>
- <meta charset="utf8"/>
- <title>OhmPi Acquisition Board</title>
- <link rel="shortcut icon" type="image/jpg" href="logo_ohmpi.jpg"/>
-
- <!-- dependencies (need to be local as no internet in AP mode)-->
- <script src="js/plotly-basic-2.8.3.min.js"></script>
- <script src="js/jquery-3.4.1.min.js"></script>
- <link type="text/css" href="css/bootstrap.min.css" rel="stylesheet">
- <!-- <script src="https://code.jquery.com/jquery-3.4.1.min.js"></script> -->
- <!-- <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-eOJMYsd53ii+scO/bJGFsiCZc+5NDVN2yr8+0RDqr0Ql0h+rP48ckxlpbzKgwra6" crossorigin="anonymous"> -->
- <!-- <script src="js/danfojs/bundle.min.js"></script> -->
-</head>
-<body>
- <div class='container'>
- <h1>OhmPi Acquisition Board</h1>
- <!-- nb stacks, on-time -->
- <button id="update_settingsBtn" type="button" class="btn btn-secondary" data-toggle="modal" data-target="#exampleModal">Settings</button>
- <button id='runBtn' type="button" class="btn btn-primary">▶</button>
- <button id='stopBtn' type="button" class="btn btn-warning">◼</button>
- <!-- upload button for csv which display the table ABMN -->
- <button id="removeDataBtn" type="button" class="btn btn-danger">Clear data</button>
- <button id="getDataBtn" type="button" class="btn btn-info">Get data</button>
- <div class="form-check">
- <input id="dataRetrievalCheck" class="form-check-input" type="checkbox" value="">
- <label class="form-check-label" for="dataRetrievalCheck">
- Automaticaly get data every 1 second
- </label>
- </div>
- <div id='output'>Status: idle</div>
-
- <!-- Pseudo section -->
- <select id='surveySelect' class='custom-select'>
- </select>
- <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 id="hoverinfo" style="margin-left:80px;"></div>
- <div class="mb3 row">
- <label for="quadSelect">Quadrupole:</label>
- <div class="col-sm-10">
- <select id='quadSelect' class='custom-select'></select>
- </div>
- </div>
-
- <!-- trace figure -->
- <button id="addTraceBtn" type="button" class="btn btn-info">Add trace</button>
- <button id="removeTracesBtn" type="button" class="btn btn-info">Remove all traces</button>
- <div id="ts"></div>
-
- <!-- RS check -->
- <button id="rsBtn" type="button" class="btn btn-info">Check contact resistance</button>
- <button id="getRsBtn" type="button" class="btn btn-info">Get contact resistance</button>
- <button id="rsClearBtn" type="button" class="btn btn-info">Clear plot</button>
- <div id="rs"></div>
-
- <!-- Additional buttons -->
- <button id="downloadBtn" type="button" class="btn btn-primary">Download data</button>
- <!-- <button id="invertBtn" type="button" class="btn btn-primary">Invert</button> -->
- <a id="download"></a>
-
- <!-- Modal for settings -->
- <div class="modal fade" id="exampleModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
- <div class="modal-dialog" role="document">
- <div class="modal-content">
- <div class="modal-header">
- <h5 class="modal-title" id="exampleModalLabel">OhmPi settings</h5>
- <button type="button" class="close" data-dismiss="modal" aria-label="Close">
- <span aria-hidden="true">×</span>
- </button>
- </div>
- <div class="modal-body">
- <form>
- <div class="form-group row">
- <label for="nbElectrodes" class="col-sm-2 col-form-label">Nb electrodes</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="nbElectrodes" value=64>
- </div>
- </div>
- <div class="form-group row">
- <label for="injectionDuration" class="col-sm-2 col-form-label">Injection duration [s]</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="injectionDuration" value=0.2>
- </div>
- </div>
- <div class="form-group row">
- <label for="nbMeasurements" class="col-sm-2 col-form-label">Nb Measurements</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="nbMeasurements" value="1">
- </div>
- </div>
- <div class="form-group row">
- <label for="sequenceDelay" class="col-sm-2 col-form-label">Sequence delay [s]</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="sequenceDelay" value="100">
- </div>
- </div>
- <div class="form-group row">
- <label for="nbStack" class="col-sm-2 col-form-label">Nb stack</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="nbStack" value="1">
- </div>
- </div>
- <div class="form-group row">
- <label for="sequence" class="col-sm-2 col-form-label">Sequence</label>
- <div class="col-sm-10">
- <input type="file" class="form-control" id="sequence">
- </div>
- </div>
- <div class="form-group row">
- <label for="elecSpacing" class="col-sm-2 col-form-label">Electrode spacing [m]</label>
- <div class="col-sm-10">
- <input type="number" class="form-control" id="elecSpacing", value="1">
- </div>
- </div>
- </form>
- </div>
- <div class="modal-footer">
- <button type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button>
- <button id="saveConfigBtn" type="button" data-dismiss="modal" class="btn btn-primary">Save</button>
- </div>
- </div>
- </div>
- </div>
- <button id="restartBtn" type="button" class="btn btn-danger">Restart</button>
- <button id="shutdownBtn" type="button" class="btn btn-danger">Shutdown</button>
- <footer>v0.2.0</footer>
- </div>
-
- <script type="text/javascript">
- //let serverUrl = 'http://10.3.141.1:8080'
- //let serverUrl = 'http://0.0.0.0:8080'
- //let serverUrl = 'http://localhost:8080'
- let serverUrl = 'http://' + window.location.host
- console.log('serverUrl =', serverUrl)
- 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 elecSpacing = 1 // 1 m
-
- // useful functions
- function sendCommand(query, callback=null) {
- // dic in the form: {'cmd': X, ...} as JSON
- if (callback == null) {
- function callback(x) {
- console.log('default callback:', x)
- }
- }
- let xhr = new XMLHttpRequest();
- xhr.onreadystatechange = function() {
- if (this.readyState == 4) {
- if (xhr.status == 200) {
- callback(JSON.parse(xhr.response))
- }
- }
- }
- xhr.open('POST', serverUrl)
- xhr.setRequestHeader('Content-Type', 'application/json')
- xhr.send(query)
- }
-
- // run button
- function runBtnFunc() {
- sendCommand('{"cmd": "run_multiple_sequences"}', function(x) {
- console.log(x['ohmpi_status'])
- if (x['ohmpi_status'] == 'running') {
- output.innerHTML = 'Status: measuring...'
- }
- })
- }
- let runBtn = document.getElementById('runBtn')
- runBtn.addEventListener('click', runBtnFunc)
-
- // interrupt button
- function stopBtnFunc() {
- sendCommand('{"cmd": "interrupt"}', function(x) {
- output.innerHTML = 'Status: ' + x['ohmpi_status']
- clearInterval(interv)
- getData()
- })
- }
- let stopBtn = document.getElementById('stopBtn')
- stopBtn.addEventListener('click', stopBtnFunc)
-
- // set configuration
- function saveSettingsBtnFunc() {
- // collect values from modal
- let formVals = {}
- formVals['nb_electrodes'] = parseInt(document.getElementById('nbElectrodes').value)
- formVals['injection_duration'] = parseFloat(document.getElementById('injectionDuration').value)
- formVals['nb_meas'] = parseInt(document.getElementById('nbMeasurements').value)
- formVals['sequence_delay'] = parseInt(document.getElementById('sequenceDelay').value)
- formVals['nb_stack'] = parseInt(document.getElementById('nbStack').value)
- formVals['elec_spacing'] = parseFloat(document.getElementById('elecSpacing').value)
- console.log(formVals)
- elecSpacing = formVals['elec_spacing']
-
- // define callback to send settigs to Pi
- function settingsCallback() {
- sendCommand(JSON.stringify({
- 'cmd': 'update_settings',
- 'config': formVals
- }), function(x) {
- console.log('update_settings', x)
- })
- }
-
- // deal with the potential file containing the sequence
- // https://stackoverflow.com/questions/19038919/is-it-possible-to-upload-a-text-file-to-input-in-html-js
- if (!window.FileReader) {
- alert('Your browser is not supported');
- return false;
- }
- let input = document.getElementById('sequence')
- if (input.files.length) {
- const reader = new FileReader()
- reader.readAsText(input.files[0])
- reader.addEventListener('load', () => {
- formVals['sequence'] = reader.result
- console.log('file==', reader.result)
- settingsCallback()
- }, false)
- } else {
- console.log('no sequence uploaded')
- formVals['sequence'] = ''
- settingsCallback()
- }
-
-
- }
- let saveConfigBtn = document.getElementById('saveConfigBtn')
- saveConfigBtn.addEventListener('click', saveSettingsBtnFunc)
-
- // make pseudo plot
- var trace = {}
- let layout = {}
- let tdata = []
- let layout2 = {}
- let rsdata = []
- let rslayout = {}
-
- // initialize all plots
- function initPlots() {
- trace = {
- x: [],
- y: [],
- mode: 'markers',
- marker: {
- size: 40,
- color: [],
- colorbar: {
- title: 'App. res. [Ohm.m]',
- cmin: 0,
- cmax: 100,
- }
- }
- }
- layout = {
- title: 'Pseudo-section',
- yaxis: {
- title: 'Pseudo-depth',
- autorange: 'reversed'
- },
- xaxis: {
- title: 'X'
- }
-
- }
- Plotly.newPlot('gd', [trace], layout)
-
- // make time-serie plot
- tdata = []
- layout2 = {
- title: 'Time-serie',
- yaxis: {
- title: 'App. res. [Ohm.m]'
- },
- xaxis: {
- title: 'Sampling time'
- }
- }
- Plotly.newPlot('ts', tdata, layout2)
-
- // bar chart for contact resistance
- rsdata = []
- rslayout = {
- title: 'Contact resistances',
- yaxis: {
- title: 'Resistance [kOhm]'
- },
- xaxis: {
- title: 'Consecutive electrodes'
- }
- }
- Plotly.newPlot('rs', rsdata, rslayout)
- }
- initPlots()
-
- // hover function
- var hoverInfo = document.getElementById('hoverinfo')
- document.getElementById('gd').on('plotly_hover', function(data){
- var infotext = data.points.map(function(d){
- return (Math.round(d.data.marker.color[d.pointIndex], 2) + ' Ohm.m');
- });
- hoverInfo.innerHTML = infotext.join('<br/>');
- })
- .on('plotly_unhover', function(data){
- hoverInfo.innerHTML = '';
- });
-
- // add trace to time-serie plot
- function addTraceBtnFunc() {
- let val = document.getElementById('quadSelect').value
- squads.push(val.split(', '))
- tdata.push({
- x: [],
- y: [],
- name: val,
- type: 'scatter'
- })
- Plotly.newPlot('ts', tdata, layout2)
- getData()
- }
- let addTraceBtn = document.getElementById('addTraceBtn')
- addTraceBtn.addEventListener('click', addTraceBtnFunc)
-
- // remove all traces from time-serie plot
- function removeTracesBtnFunc() {
- squads = []
- tdata = []
- Plotly.newPlot('ts', tdata, layout2)
- }
- let removeTracesBtn = document.getElementById('removeTracesBtn')
- removeTracesBtn.addEventListener('click', removeTracesBtnFunc)
-
- // callback function to draw the plot
- function surveySelectFunc(el) {
- let surveyName = el['target'].value
- let df = data[surveyName]
- if (df != undefined) {
- // let's assume electrodes are 1 m distance
- // compute pseudo-depth (assume no topo)
- // compute app res (assumping flat, line survey)
- let xpos = []
- let ypos = []
- let app = []
- for (let i = 0; i < df['a'].length; i++) {
- let a = df['a'][i]
- let b = df['b'][i]
- let m = df['m'][i]
- let n = df['n'][i]
-
- // compute geometric factor assuming flat 2D surface
- let am = Math.abs(a - m)*elecSpacing
- let bm = Math.abs(b - m)*elecSpacing
- let an = Math.abs(a - n)*elecSpacing
- let bn = Math.abs(b - n)*elecSpacing
- let K = 2*Math.PI/((1/am)-(1/bm)-(1/an)+(1/bn))
- app.push(df['rho'][i]*K)
- //console.log(K) // same as resipy for the wenner case
-
- // computing pseudo-depth assuming 2D flat array
- // let's sort the electrodes AB are the two left, MN, the two right
- let abmn = [a, b, m, n]
- abmn = abmn.sort((a, b) => a - b)
- let ab = (abmn[0] + abmn[1])/2
- let mn = (abmn[2] + abmn[3])/2
- let dist = Math.abs(ab - mn)
- xpos.push((Math.min(ab, mn) + dist/2)*elecSpacing)
- ypos.push((Math.sqrt(2)/2*dist)*elecSpacing)
-
- /*
- lookupDict = dict(zip(self.elec['label'], np.arange(self.elec.shape[0])))
- array = self.df[['a','b','m','n']].replace(lookupDict).values.astype(int)
- elecm = self.elec[['x','y','z']].values.astype(float).copy() # electrode matrix - should be array of floats so np.inf work properly
-
- ### first determine if measurements are nested ###
- #find mid points of AB
- AB = (elecm[array[:,0]] + elecm[array[:,1]]) / 2 # mid points of AB
- MN = (elecm[array[:,2]] + elecm[array[:,3]]) / 2 # mid points of MN
- ABrad = np.sqrt(np.sum((elecm[array[:,0]] - AB)**2,axis=1)) # radius of AB circle
- MNrad = np.sqrt(np.sum((elecm[array[:,2]] - MN)**2,axis=1)) # radius of MN circle
-
- Amn = np.sqrt(np.sum((elecm[array[:,0]] - MN)**2,axis=1)) # distance of A to mid point of MN
- Bmn = np.sqrt(np.sum((elecm[array[:,1]] - MN)**2,axis=1)) # distance of B to mid point of MN
- Nab = np.sqrt(np.sum((elecm[array[:,2]] - AB)**2,axis=1)) # distance of N to mid point of AB
- Mab = np.sqrt(np.sum((elecm[array[:,3]] - AB)**2,axis=1)) # distance of M to mid point of AB
-
- iABinMN = (Amn < MNrad) & (Bmn < MNrad)
- iMNinAB = (Nab < ABrad) & (Mab < ABrad)
- inested = iABinMN | iMNinAB #if AB encompasses MN or MN encompasses AB
-
- # so it will never be taken as minimium
- elecm[self.elec['remote'].values,:] = np.inf
-
- # compute midpoint position of AB and MN dipoles
- elecx = elecm[:,0]
- elecy = elecm[:,1]
-
- #CURRENT ELECTRODE MIDPOINTS
- caddx = np.abs(elecx[array[:,0]]-elecx[array[:,1]])/2
- caddy = np.abs(elecy[array[:,0]]-elecy[array[:,1]])/2
- caddx[np.isinf(caddx)] = 0
- caddy[np.isinf(caddy)] = 0
- cmiddlex = np.min([elecx[array[:,0]], elecx[array[:,1]]], axis=0) + caddx
- cmiddley = np.min([elecy[array[:,0]], elecy[array[:,1]]], axis=0) + caddy
-
- #POTENTIAL ELECTRODE MIDPOINTS
- paddx = np.abs(elecx[array[:,2]]-elecx[array[:,3]])/2
- paddy = np.abs(elecy[array[:,2]]-elecy[array[:,3]])/2
- paddx[np.isinf(paddx)] = 0
- paddy[np.isinf(paddy)] = 0
- pmiddlex = np.min([elecx[array[:,2]], elecx[array[:,3]]], axis=0) + paddx
- pmiddley = np.min([elecy[array[:,2]], elecy[array[:,3]]], axis=0) + paddy
-
-
- # for non-nested measurements
- xposNonNested = np.min([cmiddlex, pmiddlex], axis=0) + np.abs(cmiddlex-pmiddlex)/2
- yposNonNested = np.min([cmiddley, pmiddley], axis=0) + np.abs(cmiddley-pmiddley)/2
- pcdist = np.sqrt((cmiddlex-pmiddlex)**2 + (cmiddley-pmiddley)**2)
-
- # zposNonNested = np.sqrt(2)/2*pcdist
- zposNonNested = pcdist/4
-
- if np.all(cmiddley-pmiddley == 0):
- zposNonNested = 0.25*pcdist
- else: # for 3D arrays where there are mid-line measurements, this works closer to inversion results
- zposNonNested = np.sqrt(2)/2*pcdist
-
- # for nested measurements use formula of Dalhin 2006
- xposNested = np.zeros(len(pmiddlex))
- yposNested = np.zeros(len(pmiddlex))
- outerElec1 = np.zeros((len(pmiddlex), 2)) # position of one electrode of outer dipole
- outerElec2 = np.zeros((len(pmiddlex), 2)) # position of one electrode of outer dipole
- # innerMid = np.zeros((len(pmiddlex), 2)) # middle of inner dipole
- if np.sum(iMNinAB) > 0:
- xposNested[iMNinAB] = pmiddlex[iMNinAB]
- yposNested[iMNinAB] = pmiddley[iMNinAB]
- outerElec1[iMNinAB] = np.c_[elecx[array[iMNinAB,0]], elecy[array[iMNinAB,0]]]
- outerElec2[iMNinAB] = np.c_[elecx[array[iMNinAB,1]], elecy[array[iMNinAB,1]]]
-
- if np.sum(iABinMN) > 0:
- xposNested[iABinMN] = cmiddlex[iABinMN]
- yposNested[iABinMN] = cmiddley[iABinMN]
- outerElec1[iABinMN] = np.c_[elecx[array[iABinMN,2]], elecy[array[iABinMN,2]]]
- outerElec2[iABinMN] = np.c_[elecx[array[iABinMN,3]], elecy[array[iABinMN,3]]]
-
- innerMid = np.c_[pmiddlex, pmiddley] # always use potential dipole
-
- apdist = np.sqrt(np.sum((outerElec1-innerMid)**2, axis=1))
- bpdist = np.sqrt(np.sum((outerElec2-innerMid)**2, axis=1))
- zposNested = np.min([apdist, bpdist], axis=0)/3
-
- xpos = np.zeros_like(pmiddlex)
- ypos = np.zeros_like(pmiddlex)
- zpos = np.zeros_like(pmiddlex)
-
- xpos[~inested] = xposNonNested[~inested]
- xpos[inested] = xposNested[inested]
-
- ypos[~inested] = yposNonNested[~inested]
- ypos[inested] = yposNested[inested]
-
- zpos[~inested] = zposNonNested[~inested]
- zpos[inested] = zposNested[inested]
-
- */
- }
- //console.log(app)
- // update the trace and redraw the figure
- trace['x'] = xpos
- trace['y'] = ypos
- trace['marker']['color'] = app
- trace['marker']['cmax'] = document.getElementById('cmax').value
- trace['marker']['cmin'] = document.getElementById('cmin').value
- Plotly.redraw('gd')
- }
- }
- let surveySelect = document.getElementById('surveySelect')
-
- // run RS check
- function rsBtnFunc() {
- sendCommand('{"cmd": "rsCheck"}', function (a) {})
- }
- let rsBtn = document.getElementById('rsBtn')
- rsBtn.addEventListener('click', rsBtnFunc)
-
- // get RS check data
- function getRsBtnFunc() {
- sendCommand('{"cmd": "getRsCheck"}', function(res) {
- // update the bar plot
- rsdata.push({
- x: res['data']['AB'],
- y: res['data']['res'],
- name: 'RS',
- type: 'bar'
- })
- Plotly.redraw('rs')
- })
- }
- let getRsBtn = document.getElementById('getRsBtn')
- getRsBtn.addEventListener('click', getRsBtnFunc)
-
- // clear RS graph
- function rsClearBtnFunc() {
- rsdata = []
- Plotly.newPlot('rs', rsdata, rslayout)
- }
- let rsClearBtn = document.getElementById('rsClearBtn')
- rsClearBtn.addEventListener('click', rsClearBtnFunc)
-
- // getData
- function getData() {
- let surveyNames = []
- sendCommand(JSON.stringify({
- 'cmd': 'getData',
- 'surveyNames': surveyNames
- // last survey is often partial so we download it again
- }), function(ddic) {
- // update status
- //output.innerHTML = 'Status: ' + ddic['status']
-
- // update data dic with new data
- data = { // destructuring assignement (magic! :o)
- ...data,
- ...ddic['data'] // value from second dic are preferred
- }
-
- // dropdown with number of surveys
- surveyNames = Object.keys(data).sort()
-
- // remove listener as we will replace the choices
- surveySelect.removeEventListener('change', surveySelectFunc)
- surveySelect.innerHTML = '' // clearing all child nodes
-
- // add choices again
- for (let surveyName of surveyNames) {
- let option = document.createElement('option')
- option.innerText = surveyName
- option.value = surveyName
- surveySelect.appendChild(option)
- }
-
- // listener again
- surveySelect.addEventListener('change', surveySelectFunc)
-
- // plot last one by default
- surveySelect.value = surveyNames[surveyNames.length - 1]
-
- // call the function directly
- // (as progammatically chaging the value does not trigger the event)
- surveySelectFunc({'target': surveySelect})
-
- // update list of quadrupoles if any
- let idiff = false
- if (data[surveyNames[0]] != undefined) {
- idiff = quads.length != data[surveyNames[0]]['a'].length
- }
- //console.log('idiff=', idiff, quads.length, data[surveyNames[0]]['a'].length)
- if (((quads.length == 0) | idiff) & (data[surveyNames[0]] != undefined)){
- console.log('updating list of quadrupoles')
- quads = []
- let df = data[surveyNames[0]]
- let quadSelect = document.getElementById('quadSelect')
- quadSelect.innerHTML = ''
- for (let i = 0; i < df['a'].length; i++) {
- quad = [df['a'][i], df['b'][i], df['m'][i], df['n'][i]]
- quads.push(quad)
- let option = document.createElement('option')
- option.value = quad.join(', ')
- option.innerText = quad.join(', ')
- quadSelect.appendChild(option)
- }
- console.log('quads=', quads)
- }
-
- // update time-serie figure
- if (squads.length > 0) {
-
- // transform all surveyNames to datetime
- let xt = []
- for (surveyName of surveyNames) {
- let a = surveyName.split('_').slice(-1)[0]
- xt.push(a.slice(0, 4) + '-'
- + a.slice(4, 6) + '-'
- + a.slice(6, 8) + ' '
- + a.slice(9, 11) + ':'
- + a.slice(11, 13) + ':'
- + a.slice(13, 15))
- }
- //console.log(xt)
-
- // create one new trace per selected quadrupole
- for (let k = 0; k < squads.length; k++) {
- squad = squads[k]
- let x = []
- let y = []
- for (let i = 0; i < surveyNames.length; i++) {
- df = data[surveyNames[i]]
- for (let j = 0; j < df['a'].length; j++) {
- if (df['a'][j] == squad[0]
- && df['b'][j] == squad[1]
- && df['m'][j] == squad[2]
- && df['n'][j] == squad[3]) {
- y.push(df['rho'][j])
- x.push(xt[i])
- break
- }
- }
- }
-
- // update trace dictionnary
- tdata[k]['x'] = x
- tdata[k]['y'] = y
- }
- //console.log(tdata)
- Plotly.redraw('ts')
- }
- })
- }
- let getDataBtn = document.getElementById('getDataBtn')
- getDataBtn.addEventListener('click', getData)
-
- // apply new colorscale
- let capplyBtn = document.getElementById('capplyBtn')
- capplyBtn.addEventListener('click', function() {
- surveySelectFunc({'target': surveySelect})
- })
-
- // checkbox interaction for data download
- function dataRetrievalCheckFunc(x) {
- if (x['target'].checked == true) {
- interv = setInterval(getData, 1000) // every 5s
- } else {
- clearInterval(interv)
- }
- }
- let dataRetrievalCheck = document.getElementById('dataRetrievalCheck')
- dataRetrievalCheck.addEventListener('change', dataRetrievalCheckFunc)
-
- // remove data
- function removeDataBtnFunc() {
- sendCommand('{"cmd": "removeData"}',function(x) {
- data = {}
- output.innerHTML = 'Status: ' + x['ohmpi_status'] + ' (all data cleared)'
- console.log('all data removed')
- initPlots() // reset all plots
- })
- }
- let removeDataBtn = document.getElementById('removeDataBtn')
- removeDataBtn.addEventListener('click', removeDataBtnFunc)
-
- // shutdown Pi
- function shutdownBtnFunc() {
- sendCommand('{"cmd": "shutdown"}', function(x) {
- console.log('shuting down...')
- })
- }
- let shutdownBtn = document.getElementById('shutdownBtn')
- shutdownBtn.addEventListener('click', shutdownBtnFunc)
-
- // restart Pi
- function restartBtnFunc() {
- sendCommand('{"cmd": "restart"}', function(x) {
- console.log('rebooting...')
- })
- }
- let restartBtn = document.getElementById('restartBtn')
- restartBtn.addEventListener('click', restartBtnFunc)
-
- // invert data
- // function invertBtnFunc() {
- // sendCommand('{"cmd": "invert"}', function(x) {
- // console.log('inversion results', x)
- // })
- // }
- // let invertBtn = document.getElementById('invertBtn')
- // invertBtn.addEventListener('click', invertBtnFunc)
-
- // download data
- function downloadBtnFunc() {
- sendCommand('{"cmd": "download"}', function(x) {
- let dwl = document.getElementById('download')
- dwl.setAttribute('href', serverUrl + '/data.zip')
- dwl.setAttribute('download', 'data.zip')
- dwl.click()
- })
- }
- let downloadBtn = document.getElementById('downloadBtn')
- downloadBtn.addEventListener('click', downloadBtnFunc)
-
-
- </script>
-
- <!-- Boostrap scripts (at the end of the page for faster loading time)-->
- <script src="js/bootstrap.bundle.min.js"></script>
- <!-- <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/js/bootstrap.bundle.min.js" integrity="sha384-JEW9xMcG8R+pH31jmWH6WWP0WintQrMb4s7ZOdauHnUtxwoG2vI5DkLtS3qm9Ekf" crossorigin="anonymous"></script> -->
-</body>
-</html>
diff --git a/ohmpi/__init__.py b/ohmpi/__init__.py
index 09c495ea868bac310c7f76790aca8a1b691d6de6..d1c1cf1ce4567059e2106febb97432bcdad4cfa1 100644
--- a/ohmpi/__init__.py
+++ b/ohmpi/__init__.py
@@ -1 +1,2 @@
# from .ohmpi import OhmPi
+#from ohmpi.ohmpi import OhmPi
diff --git a/ohmpi/hardware_components/pwr_batt.py b/ohmpi/hardware_components/pwr_batt.py
index 650b5dcde3e86f10d7866aa53049032051ce0ee7..dc67c8b88a742df803691446e0474d5f9c557e83 100644
--- a/ohmpi/hardware_components/pwr_batt.py
+++ b/ohmpi/hardware_components/pwr_batt.py
@@ -8,7 +8,8 @@ from ohmpi.utils import enforce_specs
SPECS = {'model': {'default': os.path.basename(__file__).rstrip('.py')},
'voltage': {'default': 12., 'max': 12., 'min': 12.},
'current_adjustable': {'default': False},
- 'voltage_adjustable': {'default': False}
+ 'voltage_adjustable': {'default': False},
+ 'interface': {'default': 'none'},
}
diff --git a/ohmpi/hardware_components/raspberry_pi.py b/ohmpi/hardware_components/raspberry_pi.py
index f2a59642824a9869d1cb4e7b23f437e278e2a86a..d45ad095c3cf7f7ef977d8a67677378f9d38521b 100644
--- a/ohmpi/hardware_components/raspberry_pi.py
+++ b/ohmpi/hardware_components/raspberry_pi.py
@@ -34,6 +34,9 @@ class Ctl(CtlAbstract):
super().__init__(**kwargs)
self.interfaces = dict()
+ # None interface for battery
+ self.interfaces['none'] = None
+
# warnings.filterwarnings("error") # to filter out adafruit warning about setting I2C frequency
# I2C
try:
diff --git a/ohmpi/hardware_system.py b/ohmpi/hardware_system.py
index aa2161f9c2d6356d4433b20edee3213982185e0a..d1efa5779a8200d4623489d7ad504e2f67052771 100644
--- a/ohmpi/hardware_system.py
+++ b/ohmpi/hardware_system.py
@@ -104,11 +104,11 @@ class OhmPiHardware:
if isinstance(ctl_mod, str):
ctl_mod = importlib.import_module(f'ohmpi.hardware_components.{ctl_mod}')
HARDWARE_CONFIG['pwr']['ctl'] = ctl_mod.Ctl(**HARDWARE_CONFIG['pwr']['ctl'])
- HARDWARE_CONFIG['pwr'].update({'connection':
- HARDWARE_CONFIG['pwr'].pop('connection',
- HARDWARE_CONFIG['pwr']['ctl'].interfaces[
- HARDWARE_CONFIG['pwr'].pop(
- 'interface_name', None)])})
+ #if 'interface_name' in HARDWARE_CONFIG['pwr']:
+ HARDWARE_CONFIG['pwr'].update({
+ 'connection': HARDWARE_CONFIG['pwr'].pop(
+ 'connection', HARDWARE_CONFIG['pwr']['ctl'].interfaces[
+ HARDWARE_CONFIG['pwr'].pop('interface_name', None)])})
HARDWARE_CONFIG['pwr'].update({'exec_logger': self.exec_logger, 'data_logger': self.data_logger,
'soh_logger': self.soh_logger})
@@ -167,6 +167,22 @@ class OhmPiHardware:
self._start_time = None # time of the beginning of a readings acquisition
self._pulse = 0 # pulse number
self.exec_logger.event(f'OhmPiHardware\tinit\tend\t{datetime.datetime.utcnow()}')
+ self._pwr_state = 'off'
+
+ @property
+ def pwr_state(self):
+ return self._pwr_state
+
+ @pwr_state.setter
+ def pwr_state(self, state):
+ if state == 'on':
+ self.tx.pwr_state = 'on'
+ self._pwr_state = 'on'
+ self.exec_logger.debug(f'{self.model} cannot be switched on')
+ elif state == 'off':
+ self.tx.pwr_state = 'off'
+ self._pwr_state = 'off'
+ self.exec_logger.debug(f'{self.model} cannot be switched off')
def _clear_values(self):
self.readings = np.array([])
@@ -420,8 +436,8 @@ class OhmPiHardware:
append=False):
self.exec_logger.event(f'OhmPiHardware\tvab_square_wave\tbegin\t{datetime.datetime.utcnow()}')
switch_pwr_off, switch_tx_pwr_off = False, False
- if self.tx.pwr_state == 'off':
- self.tx.pwr_state = 'on'
+ if self.pwr_state == 'off':
+ self.pwr_state = 'on'
switch_tx_pwr_off = True
# if self.tx.pwr.pwr_state == 'off':
# self.tx.pwr.pwr_state = 'on'
@@ -442,7 +458,7 @@ class OhmPiHardware:
if switch_pwr_off:
self.tx.pwr.pwr_state = 'off'
if switch_tx_pwr_off:
- self.tx.pwr_state = 'off'
+ self.pwr_state = 'off'
def _vab_pulse(self, vab=None, duration=1., sampling_rate=None, polarity=1, append=False):
""" Gets VMN and IAB from a single voltage pulse
@@ -466,8 +482,8 @@ class OhmPiHardware:
def _vab_pulses(self, vab, durations, sampling_rate, polarities=None, append=False):
switch_pwr_off, switch_tx_pwr_off = False, False
- if self.tx.pwr_state == 'off':
- self.tx.pwr_state = 'on'
+ if self.pwr_state == 'off':
+ self.pwr_state = 'on'
switch_pwr_off = True
n_pulses = len(durations)
self.exec_logger.debug(f'n_pulses: {n_pulses}')
@@ -492,7 +508,8 @@ class OhmPiHardware:
if switch_pwr_off:
self.tx.pwr.pwr_state = 'off'
if switch_tx_pwr_off:
- self.tx.pwr_state = 'off'
+ self.pwr_state = 'off'
+
def switch_mux(self, electrodes, roles=None, state='off', **kwargs):
"""Switches on multiplexer relays for given quadrupole.
diff --git a/ohmpi/ohmpi.py b/ohmpi/ohmpi.py
index cc260ae63f23341ae43831edcb5152ff5c6a4b45..2b49830e20d7af8611fa47c5810fa21f7ecf8891 100644
--- a/ohmpi/ohmpi.py
+++ b/ohmpi/ohmpi.py
@@ -451,6 +451,12 @@ class OhmPi(object):
cmd_id : str, optional
Unique command identifier
"""
+ # check pwr is on, if not, let's turn it on
+ switch_power_off = False
+ if self._hw.pwr_state == 'off':
+ self._hw.pwr_state = 'on'
+ switch_power_off = True
+
self.exec_logger.debug('Starting measurement')
self.exec_logger.debug('Waiting for data')
@@ -532,6 +538,11 @@ class OhmPi(object):
else:
self.exec_logger.info(f'Skipping {quad}')
self.switch_mux_off(quad, cmd_id)
+
+ # if power was off before measurement, let's turn if off
+ if switch_power_off:
+ self._hw.pwr_state = 'off'
+
return d
def run_multiple_sequences(self, cmd_id=None, sequence_delay=None, nb_meas=None, **kwargs): # NOTE : could be renamed repeat_sequence
@@ -588,6 +599,8 @@ class OhmPi(object):
cmd_id : str, optional
Unique command identifier
"""
+ # switch power on
+ self._hw.pwr_state = 'on'
self.status = 'running'
self.exec_logger.debug(f'Status: {self.status}')
self.exec_logger.debug(f'Measuring sequence: {self.sequence}')
@@ -669,7 +682,7 @@ class OhmPi(object):
self.append_and_save(filename, acquired_data)
self.exec_logger.debug(f'quadrupole {i + 1:d}/{n:d}')
- # self.switch_dps('off')
+ self._hw.pwr_state = 'off'
self.status = 'idle'
def run_sequence_async(self, cmd_id=None, **kwargs):
@@ -810,7 +823,7 @@ class OhmPi(object):
self.exec_logger.debug(f'tx pwr voltage: {self._hw.tx.pwr.voltage}, rx max voltage: {self._hw.rx._voltage_max}')
return False
else:
- if np.array(quadrupole).all() == np.array([0, 0, 0, 0]).all(): # NOTE: No mux
+ if quadrupole == [0, 0, 0, 0]: # NOTE: No mux
return True
else:
return self._hw.switch_mux(electrodes=quadrupole, state='on', bypass_check=bypass_check)