---
title: "Dataset"
date: 2019-09-27 16:41
draft: false
---
<link rel="stylesheet" type="text/css" href="/css/modal.css" />
<link rel="stylesheet" type="text/css" href="/css/form.css" />
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<script src="/js/tableToCSV.js"></script>
<script src="/js/texparser.js"></script>
<script src="/js/unicodetable.js"></script>
<script src="/js/MoleculeFormater.js"></script>
<script>
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          const source = submol.find((d) => {
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          if (source !== undefined) {
            for (const dat of submol.filter((d) => d !== source)) {
              dat.CopyExcitationsTypeFrom(source)
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          }
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    window.defaultDats = window.defaultDats.sort((datfA, datfB) => {
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    processingIndicator.isActive = false
    await reloadGeoms()
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  async function reloadGeoms(){
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    window.geoms = await GeometriesLoader.loadForAsync(uniq(window.defaultDats.map(d=>{
    return {
      set:d.set.name,
      molecule:d.molecule
    }
    })))
    processingIndicator.isActive = false
    reloadSizeSelector()
  }
  function reloadSizeSelector() {
    if (window.geoms && window.dats) {
      const nHnums=window.geoms.map((g)=>{
        return g.molecule.atoms.count((a)=>a.label!=="H")
      })
      const nHmin = ss.min(nHnums)
      const nMin=$("#nHmin")
      nMin.attr("min",nHmin)
      const nHmax = ss.max(nHnums)
      const nMax=$("#nHmax")
      nMax.attr("max",nHmax)
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      init = nMax.attr("data-init")
      if (typeof init !== undefined && init !== false) {
        nMin.removeAttr("data-init")
        nMax.val(nHmax)
        updateNumberRange(nMax[0])
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        nHUnknowDiv.show()
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        nHUnknowDiv.hide()
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  }
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    window.customDats = []
    window.dats = window.defaultDats
    const kinds = new Map([["file_abs", VertExcitationKinds.Absorbtion], ["file_fluo", VertExcitationKinds.Fluorescence]])
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      if (kinds.has(el.name)) {
        const kind=kinds.get(el.name)
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          const dat = await VertDataFile.loadAsync(f, kind)
          window.customDats.push(dat)
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      }
    }
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      if (defdat.method.isTBE) {
        for (const custdat of window.customDats) {
          if (custdat.molecule===defdat.molecule) {
            custdat.CopyExcitationsTypeFrom(defdat)  
          }
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      }
    }
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    processingIndicator.isActive = false
    reloadSizeSelector()
    reloadSelect("sets")
    refreshExportGeoms()
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  async function reloadSelect(name) {
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    var selects = getAllSelectBefore(name, true)
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      AllValsCache.set(this.name,getAllVals(this))
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    var AAllValsCache = Array.from(AllValsCache)
    var vals = uniq(window.dats.filter(d => {
      return AAllValsCache.every(([k,v]) => {
        return v.indexOf(getSelectValue(d, k)) !== -1
      })
    }).map((d) => getSelectValue(d, name)))
    if (name!="sets") {
      vals = vals.sort((a,b)=>{
        a = textSelctor(a)
        b = textSelctor(b)
        if (a === b) {
          return 0
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        else {
          switch (name) {
            case "method":
              if (a.startsWith("TBE") && b.startsWith("TBE")) {
                return (a === "TBE" ? -1 : 1)
              }
              else if(a.startsWith("TBE")) {
                return -1
              }
              else if (b.startsWith("TBE")) {
                return 1
              }
              else {
                return a.localeCompare(b)
              }
              break;
              case "basis":
                if (a === "aug-cc-pVTZ") {
                  return -1
                }
                else if (b === "aug-cc-pVTZ") {
                  return 1
                }
                else {
                  return a.localeCompare(b)
                }
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        }).text(textSelctor(val)).appendTo(currentselect)
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  function getSelectValue(data, name) {
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      case "method":
        return data.method.name
        break;
      case "basis":
        return data.method.basis
        break;
      case "sets":
        return data.set.name
        break;
      default:
        return data[name]
        break;
    }
  }
  async function reloadStat() {
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    var stb = $("#stat_table > tbody")
    $("#graph_div").empty()
    $(stb).empty()
    var refstr = $("#sel_ref option:selected").val()
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      const SetName = d.set.name
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        sdatdic.set(key, new Map())
      }
      const myT1s = T1ref.get(d.molecule)
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        const T1Key = JSON.stringify((exc.initial, exc.final))
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            allowT1 = true
          }
        }
        const key2 = JSON.stringify([d.molecule, exc.initial, exc.final, exc.VertExcitationKind])
        const keydic = sdatdic.get(key)
        if ((!exc.isUnsafe || window.filterParams.unsafe) && ((exc.type & window.filterParams.exType) !== 0) && ((exc.VertExcitationKind & window.filterParams.exVertKind) !== 0) && allowT1) {
          if (!(keydic.has(key2))) {
            keydic.set(key2, exc.value)
          }
        }
      }
    }

    var sdic = new Map()
    for (const [key, sdat] of sdatdic) {
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        if (!(sdic.has(key))) {
          sdic.set(key, [])
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    var graphdat = []
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      row = $("<tr/>")
      key = JSON.parse(keystr)
      Reflect.setPrototypeOf(key, method.prototype)
      th = $("<th/>", { scope: "column" })
      const meth = key
      const span = $("<span/>",{"data-csvtext":meth.toString()}).text(meth.toString("\n").split('-').join('\u2011'))
      th.clone().append(span).appendTo(row)
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        $("<td/>").text(noNanFixed(val, 2)).appendTo(row)
      }
      $(stb).append(row)
      var box = {
        x: noNanVals,
        amean: ss.mean(avals).toFixed(3),
        name: `${key.toString()} MAE : ${ss.mean(avals).toPrecision(4)} eV` ,
        type: 'box',
        boxmean: 'sd'
      };
      graphdat.push(box)
    }
    var layout = {
      paper_bgcolor: 'rgba(0,0,0,0)',
      plot_bgcolor: 'rgba(0,0,0,0)',
      gap: 0,
      legend: {
        traceorder: 'reversed',
      },
      xaxis: {
        title: {
          text: 'Error (eV)',
        }
      },
      bgcolor: '#E2E2E2',
      bordercolor: '#FFFFFF',
      borderwidth: 2,
      // autosize: false,
      width: 1275,
      height: 750,
      margin: {
        l: 0,
        r: 10,
        // b: 15,
        t: 20,
        pad: 0,
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      exType: Array.from(Array.from($("#cb_exTypeList>li>input[type=checkbox]:checked")).map(el => parseInt(el.value))).reduce((pv, cv) => pv + cv, 0),
      exVertKind: Array.from(Array.from($("#cb_exVertKindList>li>input[type=checkbox]:checked")).map(el => parseInt(el.value))).reduce((pv, cv) => pv + cv, 0),
      T1: {
        min: parseFloat($("#T1min").val()),
        max: parseFloat($("#T1max").val())
      },
      nHnum: {
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        max: parseInt($("#nHmax").val(),10),
        allowUnknow:$("#cb_nHUnknow").is(':checked')
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    window.filtData = window.dats
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        delete (val)
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      const geom=window.geoms.find((g)=>{
        const met=g.parseMetadata()
        return met.molecule === d.molecule && JSON.stringify(met.method) === JSON.stringify(d.geometry)
      })
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        return (allowednHSize.min <= size && size <= allowednHSize.max)
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      else {
        return allowednHSize.allowUnknow
      }
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    var exSets = new uniq(window.filtData.map((d) => d.set))
    var mols = new Set(window.filtData.map((d) => d.molecule))
    for (const exSet of exSets) {
      const DOI= await exSet.getDOIAsync()
      if (DOI!=null) {
        publiCache.set(DOI,await PubliData.loadAsync(DOI))
      }      
      const setName = exSet.name
      for (const mol of mols) {
        window.T1ref.set(mol, new Map())
        var TBESortdat = window.dats.filter((d)=> d.molecule === mol).sort((d1, d2) => {
          if (d1.method.isTBE && !d2.method.isTBE) {
            return -1
          } else if (!d1.method.isTBE && d2.method.isTBE) {
            return 1
          } else if (d1.method.isTBE && d2.method.isTBE) {
            if (d1.method.name === "TBE" && d2.method.name === "TBE(Full)") {
              return -1
            } else if (d1.method.name === "TBE(Full)" && d2.method.name === "TBE") {
              return 1
            }
            else {
              return 0
            }
          }
        })
        if (TBESortdat.length > 0 && TBESortdat[0].method.isTBE) {
          for (const exc of TBESortdat[0].excitations) {
            window.T1ref.get(mol).set(JSON.stringify((exc.initial, exc.final)), exc.T1)
          }
        }
      }
    }
    $(sel_ref).empty()
    for (const me of uniq(window.filtData.map(d => d.method))) {
      op = $("<option/>", {
        value: JSON.stringify(me)
      }).text(me)
      if (me.name.includes("TBE")) {
        $(sel_ref).prepend(op)
      }
      else {
        $(sel_ref).append(op)
      }
    }
    $(sel_ref).prop("selectedIndex", 0);
    var data = $("#data")
    $(data).empty();
    if (window.filtData.length > 0) {
      var PreviousSetName = undefined
      var CurrentsetName = undefined
      for (const exSet of exSets) {
        paperdata = window.filtData.filter((d) => {
          return d.set.name === exSet.name && d.set.index === exSet.index
        })
        var methods = uniq(paperdata.map(d => d.method))
        const sortedMethods = methods.sort((a, b) => {
          if (a.isTBE && !b.isTBE) {
            return -1
          }
          else if (a.isTBE && b.isTBE) {
            if (a.basis !== "CBS" && b.basis === "CBS") {
              return -1
            }
            else {
              return 1
            }
          }
          else if (!a.isTBE && b.isTBE) {
            return 1
          }
          else {
            return 0
          }
        })
        var div = $('<div/>').appendTo(data)
        CurrentsetName = exSet.name
        if (PreviousSetName !== CurrentsetName) {
          $("<h1/>").text(CurrentsetName).appendTo(div)
        }
        var doi= await exSet.getDOIAsync()
        if (publiCache.has(doi)) {
          const publiDat = publiCache.get(doi)
          $("<h2/>").append($("<a>",{href:publiDat.URL,target:"_blank"}).text(publiDat.title)).appendTo(div)
        }
        var table = $("<table/>").addClass("datatable").appendTo(div)
        $(table).before($("#stat_table").prevAll("button:first").clone())
        var head = $("<tr/>")
        $("<thead/>").addClass("sticky").append(head).appendTo(table)
        var tbody = $("<tbody/>").appendTo(table)
        var th = $("<th/>", { scope: "column" })
        head.append(["Molecule", "Transition"].map(x => th.clone().text(x)))
        head.append(sortedMethods.map(x => {
          const span = $("<span/>",{"data-csvtext":x.toString()}).text(x.toString("\n").split('-').join('\u2011'))
          return th.clone().append(span)
        }))
        adjustSticky();
        datadic = new Map()
        for (const dat of paperdata) {
          const setName = dat.set.name
          const key1 = dat.molecule;
          const myT1s = T1ref.get(dat.molecule)
          if (!datadic.has(key1)) {
            datadic.set(key1, new Map())
          }
          const key3 = JSON.stringify(dat.method)
          for (const ex of dat.excitations) {
            Reflect.setPrototypeOf(ex.type, excitationType.prototype)
            var allowT1 = false
            const T1Key = JSON.stringify((ex.initial, ex.final))
            const T1range = filterParams.T1
            if (T1range.min === 0 && T1range.max === 100) {
              allowT1 = true
            } else if (myT1s.has(T1Key)) {
              const T1Val = myT1s.get(T1Key)
              if (T1range.min <= T1Val && T1Val <= T1range.max) {
                allowT1 = true
              }
            }
            if (((window.filterParams.exType & ex.type) !== 0) && ((window.filterParams.exVertKind & ex.VertExcitationKind) !== 0) && allowT1) {
              const key2 = JSON.stringify([ex.initial, ex.final, ex.type, ex.VertExcitationKind])
              if (!datadic.get(key1).has(key2)) {
                datadic.get(key1).set(key2, new Map())
              }
              datadic.get(key1).get(key2).set(key3, [ex.value, ex.isUnsafe])
            }
          }
        }
        for (const [molecule, moldat] of datadic.entries()) {
          var printmol = true;
          for (const [jsonex, exdat] of moldat.entries()) {
            const ex = JSON.parse(jsonex)
            Reflect.setPrototypeOf(ex[0], state.prototype)
            Reflect.setPrototypeOf(ex[1], state.prototype)
            Reflect.setPrototypeOf(ex[2], excitationType.prototype)
            Reflect.setPrototypeOf(ex[3], VertExcitationKind.prototype)
            var tr = $("<tr/>")
            if (printmol) {
              $("<th/>", { scope: "row", rowspan: moldat.size }).text(moleculeFormater.toWebLatex(molecule)).appendTo(tr)
              printmol = false
            }
            var Vertkindtext = ""
            if (ex[3].Value == VertExcitationKinds.Fluorescence.Value) {
              Vertkindtext = String.raw`[\mathrm{F}]`
            }
            desctex = ""
            if (ex[2].description.string) {
              desctex = "(" + ex[2].description.string + ")"
            }
            $("<th/>", { scope: "rowgroup" }).text(MathJaxUtils.getMathJaxString(String.raw`${ex[0].toLaTeX()} \rightarrow ${ex[1].toLaTeX()} ${Vertkindtext} ${desctex}`)).appendTo(tr)
            var entries = Array.from(exdat.entries())
            for (const method of sortedMethods) {
              td = $("<td/>").addClass("NumberCell")
              kv = entries.find(x => {
                return JSON.stringify(method) == x[0]
              })
              if (kv !== undefined) {
                const [val, unsafe] = kv[1]
                if (unsafe) {
                  td.append($("<span/>", { title: "unsafe value", role: "img", "aria-label": "Warning", "data-csvtext":"(Unsafe)"}).addClass("emoji").text('⚠'))
                }
                if (unsafe && !filterParams.unsafe) {
                  td.append($("<s/>").append(val.toString()))
                }
                else {
                  td.append(val.toString())
                }
              }
              tr.append(td)
            }
            tbody.append(tr)
          }
        }
        PreviousSetName = CurrentsetName
      }
      await MathJax.typesetPromise()
    }
    await reloadRef()
  }
  async function reloadRef() {
    $(sel_ref).empty()
    for (const el of uniq(window.filtData.map(d => d.method))) {
      op = $("<option/>", {
        value: JSON.stringify(el)
      }).text(el)
      if (el.name.includes("TBE")) {
        $(sel_ref).prepend(op)
      }
      else {
        $(sel_ref).append(op)
      }
    }
    $(sel_ref).prop("selectedIndex", 0);
    $(sel_ref).trigger("change")
  }
  async function submitdat() {
    if (!DebugMode.Enabled) {
      window.onbeforeunload = () => { return ''; }
    }
    await reloadContent();
  }

  function exportTableToCSV(table,title = null,allowTitleOverride = false) {
    const tableCaption = $(table).find('caption').text()
    if (tableCaption !== "" && (title === null || allowTitleOverride)) {
      title = tableCaption
    }
    const csv = tableToCSV(table)
    const blob = new Blob([csv],{type:"text/csv"})
    saveAs(blob,`${title}.csv`)
  }
  function OnExportTable(event) {
    const table=$(event.target).nextAll('table:first')
    exportTableToCSV(table,"table")
  }

  function refreshExportGeoms() {
    const vals=$("#mol_select").val()
    const disable = vals === null || vals.length===0
    $("#btn_export_geoms").prop("disabled",disable)
  }
  
  async function moleculeSelectionChanged(event) {
    refreshExportGeoms()
    await reloadNextSelect(event)
  }

  async function exportGeoms() {
    const folderName = "molecules"
    var mols = new Set($("#mol_select").val())
    if (mols.size!==0) {
      const zip = JSZip();
      const root=zip.folder(folderName)
      const geomDic=new Map()
      for (const geom of window.geoms) {
        const molecule =geom.parseMetadata().molecule
        if (mols.has(molecule)) {
          if (!geomDic.has(molecule)) {
            geomDic.set(molecule,new Set())
          }
          geomDic.get(molecule).add(geom.toXYZ())
        }
      }
      for (const [molecule,geometries] of geomDic) {
        const xyz=Array.from(geometries).join("\n\n")
        var blob=new Blob([xyz],{type: 'chemical/x-xyz'})
        root.file(`${mhchemCE.extract(molecule).toLowerCase().replace(" ","_")}.xyz`,blob)
      }
      const zipFile = await zip.generateAsync({type: 'blob'})
      saveAs(zipFile, `${folderName}.zip`)
    }
  }
</script>
{{< getDataFilesName >}}
<noscript>
  <p style="background-color: red; color: white; font-size: 20; font-weight: bold;">
    <span role="img" aria-label="Warning" class="emoji">⚠</span>
    <span>This website work only if JavaScript is enable. You must enable
      JavaScript.
      <a href="https://www.enable-javascript.com/" target="_blank">How to enable JavaScript ?</a></span>
  </p>
</noscript>
<p>
  This page allows you to compare multiple dataset and perform statistical analyses to evaluate the accuracy of a given method.
  All fields marked with an asterisk (<span style="color: red;">*</span>) are mandatory).
</p>
<form id="form_dat" action="javascript:submitdat()">
  <fieldset class="main">
    <fieldset>
      <legend>Import custom files</legend>
      <p>
        Import a custom file to compare its data to the reference dataset.
      </p>
      <div>
        <label for="absFiles_input">Import custom absorption data files</label>
        <input type="file" multiple onchange="reloadCustomFiles()" id="absFiles_input" name="file_abs"></input>
      </div>
      <div>
        <label for="fluoFiles_input">Import custom fluorescence data files</label>
        <input type="file" multiple onchange="reloadCustomFiles()" id="fluoFiles_input" name="file_fluo"></input>
      </div>
    </fieldset>
    <br>
    <fieldset class="table">
      <legend>Data selection</legend>
      <p>Select parameters. You can use <button
          disabled>Select all</button> to select all items <span hidden
          data-needbrowser='{"Engine":["WebKit","Blink"],"Platform":["desktop"]}'> or the shortcut key <kbd
            data-needbrowser='{"OS":["MacOS"]}'>⌘</kbd><kbd
            data-neednotbrowser='{"OS":["MacOS"]}'>Ctrl</kbd>+<kbd>A</kbd></span>
      </p>
      <div style="display: inline-block;">
        <label for="DOI_select" class="required">Set</label>
        <button class="selectButton" type="button" onclick="selectSelectAll_click(event)">Select all</button>
        <select multiple id="DOI_select" required name="sets" onchange="reloadNextSelect(event)"></select>
      </div>
      <div style="display:inline-block">
        <label for="mol_select" class="required">Molecule</label>
        <button class="selectButton" type="button" onclick="selectSelectAll_click(event)">Select all</button>
        <select multiple id="mol_select" required name="molecule" onchange="moleculeSelectionChanged(event)"></select>
        <button id="btn_export_geoms" class="selectButton" type="button" disabled onclick="exportGeoms()" title="Export the above geometries as a ZIP archive">Export geometries</button>
      </div>
      <br />
      <div style="display: inline-block;">
        <label for="method_select" class="required">Method</label>
        <button class="selectButton" type="button" onclick="selectSelectAll_click(event)">Select all</button>
        <select multiple id="method_select" required name="method" onchange="reloadNextSelect(event)"></select>
      </div>
      <div style="display: inline-block;">
        <label for="basis_select" class="required">Basis set</label>
        <button class="selectButton" type="button" onclick="selectSelectAll_click(event)">Select all</button>
        <select multiple id="basis_select" required name="basis" onchange="reloadNextSelect(event)"></select>
      </div>
    </fieldset>
    <br>
    <fieldset>
      <legend class="required">Nature of vertical excitations</legend>
      <p>Select the kind of vertical excitations you want to consider</p>
      <ul class="nestedCbList" style="padding-left: 0em;">
        <li>
          <input type="checkbox" data-onerequired="true" checked onchange="nestedCheckbox_change(event)"
            id="cb_fileType_All"></input>
          <label for="cb_fileType_All"> All</label>
        </li>
        <ul class="nestedCbList" id="cb_exVertKindList">
          <li>
            <input type="checkbox" onchange="nestedCheckbox_change(event)" id="cb_abs" value="1" name="datatype">
            <label for="cb_abs">Absorption</label>
          </li>
          <li>
            <input type="checkbox" onchange="nestedCheckbox_change(event)" id="cb_fluo" value="2" name="datatype">
            <label for="fluo">Fluorescence</label>
          </li>
        </ul>
      </ul>
    </fieldset>
    <br>
    <fieldset id="excitationFilter">
      <legend class="required">Filters</legend>
      <p>Select nature of the excited states and/or transitions</p>
      <ul class="nestedCbList" style="padding-left: 0em;">
        <li>
          <input type="checkbox" data-onerequired="true" onchange="nestedCheckbox_change(event)"
            id="cb_exType_All"></input>
          <label for="cb_exType_All"> All</label>
        </li>
        <ul id="cb_exTypeList" class="nestedCbList">
        </ul>
        <p>Select if you want to include unsafe reference values in the statistics</p>
        <li id="li_cb_unsafe">
          <input type="checkbox" id="cb_unsafe" name="unsafe">
          <label for="cb_unsafe">Unsafe</label>
        </li>
    </fieldset>
    <br>
    <fieldset>
      <legend>Molecule Size</legend>
      <p>Select the molecule size (by the number of non H atoms)</p>
      <input class="range min" airia-label="Minimum value" data-init type="number" id="nHmin" onchange="numberRangeChange(event)">
      <span>\(\leq \text{non-H atoms} \leq\)</span>
      <input class="range max" airia-label="Maximum value" data-init type="number" id="nHmax" onchange="numberRangeChange(event)">
      <div hidden=true>
        <input type="checkbox" id="cb_nHUnknow" name="nHUnknoww">
        <label for="cb_nHUnknow">Unknow size</label>
      </div>
    </fieldset>
    <br>
    <fieldset>
      <legend>\(\mathrm{\%T_1}\)</legend>
      <p>Select the range of single-excitation percentage \(\mathrm{\%T_1}\) of the transitions </p>
      <input class="range min" airia-label="Minimum value" type="number" id="T1min" onchange="numberRangeChange(event)"
        min="0" value="0">
      <span>\(\leq \mathrm{\%T_1} \leq\)</span>
      <input class="range max" airia-label="Maximum value" type="number" id="T1max" onchange="numberRangeChange(event)"
        max="100" value="100">
    </fieldset>
    <br>
  </fieldset>
  <input type="submit" value="Load"></input>
</form>
<form id="form_ref">
  <fieldset class="main">
    <fieldset>
      <legend>Reference data for statistical analyses</legend>
      <p>Select a reference from <strong>already selected data</strong> (by default <abbr
          title="Theoretical best estimate">TBE</abbr> if selected)</p>
      <label for="sel_ref">Reference</label>
      <select id="sel_ref" onchange="reloadStat()"></select>
    </fieldset>
    <br>
  </fieldset>
</form>
<p>List of selected data and their corresponding statistical analysis</p>
<section id="data">
</section>
<section>
  <button onclick="OnExportTable(event)" title="Export the table below as a CSV file">Export table</button>
  <table id="stat_table" class="datatable">
    <thead class="sticky">
      <th scope="col">Method</th>
      <th scope="col">Count</th>
      <th scope="col">Min</th>
      <th scope="col">Max</th>
      <th scope="col"><abbr title="Mean signed error">MSE</abbr></th>
      <th scope="col"><abbr title="Mean absolute error">MAE</abbr></th>
      <th scope="col">Median</th>
      <th scope="col">Absolute Median</th>
      <th scope="col"><abbr title="Root-mean square error ">RMSE</abbr></th>
      <th scope="col">Variance</th>
      <th scope="col"><abbr title="Standard deviation of the errors">SDE</abbr></th>
    </thead>
    <tbody>
    </tbody>
  </table>
  <div id="graph_div"></div>
</section>
{{< waitModal >}}