From 36ef308c7349eacd188c04d8f414940d34f52aef Mon Sep 17 00:00:00 2001
From: jkl <sagitta1618@gmail.com>
Date: Thu, 19 Oct 2023 12:47:59 +0200
Subject: [PATCH] Fix interrupt in OhmPi for UI
---
index.html | 789 +++++++++++++++++++++++++++++++++++++++++++++++++
index_old.html | 704 +++++++++++++++++++++++++++++++++++++++++++
ohmpi/ohmpi.py | 35 ++-
3 files changed, 1510 insertions(+), 18 deletions(-)
create mode 100755 index.html
create mode 100644 index_old.html
diff --git a/index.html b/index.html
new file mode 100755
index 00000000..65ed3d53
--- /dev/null
+++ b/index.html
@@ -0,0 +1,789 @@
+<!DOCTYPE html>
+<!--
+ To access the interface,
+ 1. connect to the 'raspi-webgui' wifi with the given password
+ Open a browserdebugging instruction to see the messages passing on the RPi
+mosquitto_sub -h raspberrypi.local -t ohmpi_0001/ctrl
+-->
+<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-2.26.0.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>
+ <meta name="viewport" content="width=device-width, initial-scale=1">
+</head>
+<body>
+ <div class='container-fluid'>
+ <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=""/>
+ <input id="cmax" type="number" value=""/>
+ <button id="capplyBtn" type="button" class="btn btn-info">Apply</button>
+ <div id="gd"></div>
+
+ <!-- trace figure -->
+ <div class="mb3 row">
+ <label for="quadSelect">Quadrupole:</label>
+ <div class="col-sm-10">
+ <select id='quadSelect' class='custom-select'></select>
+ </div>
+ </div>
+ <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>
+
+ <!-- Inversion plot -->
+ <select id="surveySelectInv" class='custom-select'>
+ </select>
+ <button id="invertBtn" type="button" class="btn btn-info">Run inversion</button>
+ <input id="cminInv" type="number" value=""/>
+ <input id="cmaxInv" type="number" value=""/>
+ <button id="capplyBtnInv" type="button" class="btn btn-info">Apply</button>
+ <div id="inv"></div>
+
+ <!-- Additional buttons -->
+ <button id="downloadBtn" type="button" class="btn btn-primary">Download data</button>
+ <a id="download"></a>
+
+ <button id="restartBtn" type="button" class="btn btn-danger">Restart</button>
+ <button id="shutdownBtn" type="button" class="btn btn-danger">Shutdown</button>
+
+ <!-- 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="nb_electrodes" class="col-sm-2 col-form-label">Nb electrodes</label>
+ <div class="col-sm-10">
+ <input type="number" class="form-control-number" id="nb_electrodes" value="64">
+ </div>
+ </div>
+ <div class="form-group row">
+ <label for="injection_duration" class="col-sm-2 col-form-label">Injection duration [s]</label>
+ <div class="col-sm-10">
+ <input type="number" class="form-control-number" id="injection_duration" value="0.2">
+ </div>
+ </div>
+ <div class="form-group row">
+ <label for="nb_meas" class="col-sm-2 col-form-label">Nb Measurements</label>
+ <div class="col-sm-10">
+ <input type="number" class="form-control-number" id="nb_meas" value="1">
+ </div>
+ </div>
+ <div class="form-group row">
+ <label for="sequence_delay" class="col-sm-2 col-form-label">Sequence delay [s]</label>
+ <div class="col-sm-10">
+ <input type="number" class="form-control-number" id="sequence_delay" value="100">
+ </div>
+ </div>
+ <div class="form-group row">
+ <label for="nb_stack" class="col-sm-2 col-form-label">Nb stack</label>
+ <div class="col-sm-10">
+ <input type="number" class="form-control-number" id="nb_stack" value="1">
+ </div>
+ </div>
+ <div class="form-group row">
+ <label for="duty_cycle" class="col-sm-2 col-form-label">Duty cycle [0 -> 1]</label>
+ <div class="col-sm-10">
+ <input type="number" class="form-control-number" id="duty_cycle" value="0.5">
+ </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>
+ <footer>v0.3.0</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)
+ let invertedData = [{
+ rho: [[10, 10.625, 12.5, 15.625, 20],
+ [5.625, 6.25, 8.125, 11.25, 15.625],
+ [2.5, 3.125, 5., 8.125, 12.5],
+ [0.625, 1.25, 3.125, 6.25, 10.625],
+ [0, 0.625, 2.5, 5.625, 10]],
+ x: [-9, -6, -5 , -3, -1],
+ y: [0, 1, 4, 5, 7],
+ }] // store inverted data
+
+ // 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 = ''
+ let userName = 'jkl' // can be ask to the user
+ let password = 'jkl'
+
+ // create client
+ client = new Paho.MQTT.Client(hostname, port, clientId)
+ client.onConnectionLost = onConnectionLost
+ client.onMessageArrived = onMessageArrived
+ client.connect({onSuccess: onConnect})
+// client.connect({userName: username, password: password, 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) {
+ try {
+ let payload = message.payloadString
+ if (message.topic == topic_data) {
+ // process data
+ msg = payload // for accessing the variable from the console
+ console.log('DATA LOG:', payload)
+ let ddic = JSON.parse(payload.split('INFO:')[1])
+
+ // check cmd_id is any
+ processMessage(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 = {
+ 'nb_electrodes': parseInt(document.getElementById('nb_electrodes').value),
+ 'injection_duration': parseFloat(document.getElementById('injection_duration').value),
+ 'nb_meas': parseInt(document.getElementById('nb_meas').value),
+ 'sequence_delay': parseFloat(document.getElementById('sequence_delay').value),
+ 'nb_stack': parseInt(document.getElementById('nb_stack').value),
+ 'duty_cycle': parseFloat(document.getElementById('duty_cycle').value),
+ }
+ console.log(formVals)
+
+ // 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', () => {
+ // parse the file and make it a list of list of int
+ var a = reader.result.split(/\r?\n|\r|\n/g)
+ var seq = new Array()
+ var eof = false
+ for (var i = 0; i < a.length; i++) {
+ b = a[i].split(' ')
+ var arr = new Array(4)
+ for (var j = 0; j < b.length; j++) {
+ val = parseInt(b[j])
+ if (isNaN(val) == true) {
+ eof = true
+ break
+ }
+ arr[j] = val
+ }
+ if (eof == true) {
+ break
+ }
+ seq.push(arr)
+ }
+ formVals['sequence'] = seq
+ configCallback()
+ }, false)
+ } else {
+ console.log('no sequence uploaded')
+ formVals['sequence'] = ''
+ configCallback()
+ }
+
+ // define callback to send settings to Pi
+ function configCallback() {
+ sendCommand(JSON.stringify({
+ 'cmd': 'update_settings',
+ 'kwargs': {
+ 'settings': formVals
+ }
+ }), function(x) {
+ console.log('update_settings', x)
+ })
+ }
+
+ }
+ 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, {responsive: true})
+
+ // 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, {responsive: true})
+
+ // 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, {responsive: true})
+ 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, {responsive: true})
+ }
+ 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 emin = Math.min(...[a[i], b[i], m[i], n[i]])
+ let emax = Math.max(...[a[i], b[i], m[i], n[i]])
+ let dist = Math.abs(emax - emin)
+ xpos.push(emin + dist/2)
+ ypos.push(Math.sqrt(2)/2 * dist)
+ // let ab = (a[i] + b[i])/2
+ // let mn = (m[i] + n[i])/2
+ // 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)
+ }
+ // 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, {responsive: true})
+
+ // run RS check
+ function rsBtnFunc() {
+ sendCommand('{"cmd": "rs_check"}', 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, {responsive: true})
+ }
+ 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)')
+ )
+ }
+
+ // processMessage
+ function processMessage(ddic) {
+ //if (('status' in ddic) | ('data' in ddic)) {
+ if (ddic.constructor == Object) { // it's a dictionnary
+ // acquisition related
+ processData(ddic)
+ } else {
+ // inversion related
+ invertedData = ddic
+ showInvFunc()
+ }
+ }
+
+ // 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 survey for inversion
+ surveySelectInv.removeEventListener('change', showInvFunc)
+ surveySelectInv.innerHTML = '' // clearing all child nodes
+ for (let surveyName of surveyNames) {
+ let option = document.createElement('option')
+ option.innerText = surveyName
+ option.value = surveyName
+ surveySelectInv.appendChild(option)
+ }
+ surveySelectInv.addEventListener('change', showInvFunc)
+ surveySelectInv.value = surveyNames[surveyNames.length - 1]
+
+
+ // 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})
+ })
+
+ // plot inverted data
+ function showInvFunc() {
+ let cmin = document.getElementById('cminInv').value
+ let cmax = document.getElementById('cmaxInv').value
+
+ var invData = [{
+ z: invertedData[0]['rho'],
+ x: invertedData[0]['x'],
+ y: invertedData[0]['z'],
+ type: 'contour',
+ colorscale: 'Viridis',
+ autocontour: true, // set to false if cmin is given
+ contours: {
+ start: cmin,
+ end: cmax,
+ size: 10
+ },
+ }]
+
+ var invLayout = {
+ title: 'Inverted section',
+ yaxis: {
+ title: 'Z [m]',
+ },
+ xaxis: {
+ title: 'X [m]'
+ }
+ }
+
+ Plotly.newPlot('inv', invData, invLayout, {responsive: true})
+ var btn = document.getElementById('invertBtn')
+ btn.innerText = 'Run inversion'
+ btn.className = 'btn btn-info'
+
+ }
+ showInvFunc()
+
+ // invert data
+ function invertBtnFunc() {
+ let survey_name = document.getElementById('surveySelectInv').value
+ var btn = document.getElementById('invertBtn')
+ btn.innerText = 'Inverting...'
+ btn.className = 'btn btn-warning'
+ sendCommand(JSON.stringify({
+ 'cmd': 'run_inversion',
+ 'kwargs': {
+ 'survey_names': [survey_name + '.csv']
+ }
+ }), function(x) {
+ console.log('inversion results', x)
+ })
+ }
+ let invertBtn = document.getElementById('invertBtn')
+ invertBtn.addEventListener('click', invertBtnFunc)
+
+ // apply new colorscale for inversion
+ let capplyBtnInv = document.getElementById('capplyBtnInv')
+ capplyBtnInv.addEventListener('click', function() {
+ showInvFunc()
+ })
+
+ // 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": "remove_data"}',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)
+
+ // 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_old.html b/index_old.html
new file mode 100644
index 00000000..b334d18b
--- /dev/null
+++ b/index_old.html
@@ -0,0 +1,704 @@
+<!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/ohmpi.py b/ohmpi/ohmpi.py
index 8672af17..d75f0766 100644
--- a/ohmpi/ohmpi.py
+++ b/ohmpi/ohmpi.py
@@ -273,10 +273,6 @@ class OhmPi(object):
if header == 'R [ohm]':
headers[i] = 'R [Ohm]'
icols = list(np.where(np.in1d(headers, ['A', 'B', 'M', 'N', 'R [Ohm]']))[0])
- print(headers)
- print('+++++', icols)
- print(np.array(headers)[np.array(icols)])
- print(np.loadtxt(os.path.join(ddir, fname), delimiter=',', skiprows=1, usecols=icols).shape)
data = np.loadtxt(os.path.join(ddir, fname), delimiter=',',
skiprows=1, usecols=icols)
data = data[None, :] if len(data.shape) == 1 else data
@@ -307,6 +303,7 @@ class OhmPi(object):
self.exec_logger.debug('Interrupted sequence acquisition...')
else:
self.exec_logger.debug('No sequence measurement thread to interrupt.')
+ self.status = 'idle'
self.exec_logger.debug(f'Status: {self.status}')
def load_sequence(self, filename: str, cmd_id=None):
@@ -353,7 +350,7 @@ class OhmPi(object):
message : str
message containing a command and arguments or keywords and arguments
"""
- status = False
+ self.status = 'idle'
cmd_id = '?'
try:
decoded_message = json.loads(message)
@@ -374,12 +371,10 @@ 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}")
- status = False
except Exception as e:
self.exec_logger.warning(f'Unable to decode command {message}: {e}')
- status = False
finally:
- reply = {'cmd_id': cmd_id, 'status': status}
+ reply = {'cmd_id': cmd_id, 'status': self.status}
reply = json.dumps(reply)
self.exec_logger.debug(f'Execution report: {reply}')
@@ -596,6 +591,12 @@ class OhmPi(object):
self.exec_logger.debug(f'Status: {self.status}')
self.exec_logger.debug(f'Measuring sequence: {self.sequence}')
+ # # kill previous running thread
+ # if self.thread is not None:
+ # self.exec_logger.info('Removing previous thread')
+ # self.thread.stop()
+ # self.thread.join()
+
def func():
for g in range(0, nb_meas): # for time-lapse monitoring
if self.status == 'stopping':
@@ -603,12 +604,13 @@ class OhmPi(object):
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:
+ if self.status == 'stopping':
+ break
time.sleep(dt) # waiting for next measurement (time-lapse)
self.status = 'idle'
@@ -706,9 +708,11 @@ class OhmPi(object):
# 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._hw.pwr_state = 'off'
- self.status = 'idle'
+
+ # reset to idle if we didn't interrupt the sequence
+ if self.status != 'stopping':
+ 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()'.
@@ -828,10 +832,8 @@ class OhmPi(object):
try:
self.sequence = np.array(sequence).astype(int)
# 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 switch_mux_on(self, quadrupole, bypass_check=False, cmd_id=None):
"""Switches on multiplexer relays for given quadrupole.
@@ -920,7 +922,6 @@ class OhmPi(object):
cmd_id : str, optional
Unique command identifier
"""
- status = False
if settings is not None:
try:
if isinstance(settings, dict):
@@ -932,10 +933,10 @@ class OhmPi(object):
dic = json.load(json_file)
self.settings.update(dic)
self.exec_logger.debug('Acquisition parameters updated: ' + str(self.settings))
- status = True
+ self.status = 'idle (acquisition updated)'
except Exception as e: # noqa
self.exec_logger.warning('Unable to update settings.')
- status = False
+ self.status = 'idle (unable to update settings)'
else:
self.exec_logger.warning('Settings are missing...')
@@ -945,8 +946,6 @@ class OhmPi(object):
self.settings['export_dir'] = os.path.split(self.settings['export_path'])[0]
self.settings['export_name'] = os.path.split(self.settings['export_path'])[1]
- return status
-
def run_inversion(self, survey_names=[], elec_spacing=1, **kwargs):
"""Run a simple 2D inversion using ResIPy.
--
GitLab