@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/brainImaging-NIPQWFWO.js

@@ -1,423 +0,0 @@
-import {
-  controlsInit,
-  renderTable,
-  svgLegend,
-  term0_term2_defaultQ
-} from "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import {
-  dofetch3
-} from "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import {
-  linear
-} from "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/brainImaging.js
-var BrainImaging = class _BrainImaging {
-  static type = "brainImaging";
-  constructor(opts) {
-    this.opts = opts;
-    this.type = _BrainImaging.type;
-    setInteractivity(this);
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    const holder = this.opts.holder;
-    if (this.opts.header)
-      this.opts.header.style("padding-left", "7px").style("color", "rgb(85, 85, 85)").html(`Brain Imaging: ${state.config.queryKey}/${state.config.selectedSampleFileNames.join(" ")}`);
-    const controlsHolder = holder.append("div").style("display", "inline-block").style("vertical-align", "top");
-    const rightDiv = holder.append("div").style("display", "inline-block").style("vertical-align", "top");
-    const headerHolder = rightDiv.append("div").style("display", "inline-block").style("vertical-align", "top").style("padding", "10px");
-    const contentHolder = rightDiv.append("div").style("vertical-align", "top");
-    const table = contentHolder.append("table").style("border-collapse", "collapse");
-    const headerTr = table.append("tr");
-    const contentTr = table.append("tr").style("background-color", "black");
-    const tdL = contentTr.append("td");
-    const tdF = contentTr.append("td");
-    const tdT = contentTr.append("td");
-    const legendHolder = contentHolder.append("svg").style("width", "100%").on("mouseup", this.legendLabelMouseup);
-    const legendMenu = new Menu({ padding: "0px" });
-    this.dom = {
-      headerHolder,
-      contentHolder,
-      headerTr,
-      tdL,
-      tdF,
-      tdT,
-      legendHolder,
-      legendMenu
-    };
-    this.addSliders(state.config.settings.brainImaging);
-    const configInputsOptions = this.getConfigInputsOptions(state);
-    this.components = {
-      controls: await controlsInit({
-        app: this.app,
-        id: this.id,
-        holder: controlsHolder,
-        inputs: configInputsOptions
-      })
-    };
-    this.components.controls.on("downloadClick.brainImaging", () => {
-      const urls = [];
-      for (const key in this.imagesData)
-        for (const category in this.imagesData[key].dataUrls) {
-          const dataUrl = this.imagesData[key].dataUrls[category].url;
-          urls.push(dataUrl);
-        }
-      this.downloadImage(urls);
-    });
-    this.legendRenderer = svgLegend({ holder: this.dom.legendHolder });
-  }
-  addSliders(settings) {
-    const tr = this.dom.headerTr;
-    let td = tr.append("td");
-    td.append("label").attr("for", "saggital").text("Sagittal:");
-    this.dom.saggitalSlider = td.append("input").attr("id", "saggital").attr("type", "range").attr("min", 0).attr("max", 192).attr("value", settings.brainImageL).on("change", (e) => {
-      this.editBrainImage("brainImageL", e.target.value);
-    });
-    this.dom.saggitalInput = td.append("input").attr("type", "number").attr("min", 0).attr("max", 192).attr("value", settings.brainImageL).on("change", (e) => {
-      this.editBrainImage("brainImageL", e.target.value);
-    }).style("vertical-align", "top");
-    td = tr.append("td");
-    td.append("label").attr("for", "coronal").text("Coronal:");
-    this.dom.coronalSlider = td.append("input").attr("type", "range").attr("min", 0).attr("max", 228).attr("value", settings.brainImageF).on("change", (e) => {
-      this.editBrainImage("brainImageF", e.target.value);
-    });
-    this.dom.coronalInput = td.append("input").attr("type", "number").attr("min", 0).attr("max", 192).attr("value", settings.brainImageF).on("change", (e) => {
-      this.editBrainImage("brainImageF", e.target.value);
-    }).style("vertical-align", "top");
-    td = tr.append("td");
-    td.append("label").attr("for", "axial").text("Axial:");
-    this.dom.axialSlider = td.append("input").attr("id", "axial").attr("type", "range").attr("min", 0).attr("max", 192).attr("value", settings.brainImageT).on("change", (e) => {
-      this.editBrainImage("brainImageT", e.target.value);
-    });
-    this.dom.axialInput = td.append("input").attr("type", "number").attr("min", 0).attr("max", 192).attr("value", settings.brainImageT).on("change", (e) => {
-      this.editBrainImage("brainImageT", e.target.value);
-    });
-  }
-  editBrainImage(key, value) {
-    if (!value) return;
-    const settings = { [key]: Number(value) };
-    this.app.dispatch({ type: "plot_edit", id: this.id, config: { settings: { brainImaging: settings } } });
-  }
-  downloadImage(dataUrls) {
-    for (const dataUrl of dataUrls) {
-      const downloadImgName = "brainImaging";
-      const a = document.createElement("a");
-      document.body.appendChild(a);
-      a.addEventListener(
-        "click",
-        () => {
-          a.download = downloadImgName + ".png";
-          a.href = dataUrl;
-          document.body.removeChild(a);
-        },
-        false
-      );
-      a.click();
-    }
-  }
-  getConfigInputsOptions(state) {
-    if (state.config.selectedSampleFileNames.length == 1) return [];
-    const mandatoryConfigInputOptions = [
-      {
-        label: "Divide by",
-        type: "term",
-        chartType: "brainImaging",
-        configKey: "divideByTW",
-        title: "Categories to divide by",
-        usecase: { target: "brainImaging", detail: "term0" },
-        vocabApi: this.app.vocabApi,
-        numericEditMenuVersion: ["discrete"],
-        defaultQ4fillTW: term0_term2_defaultQ
-      },
-      {
-        label: "Color by",
-        type: "term",
-        chartType: "brainImaging",
-        configKey: "overlayTW",
-        title: "Categories to color the samples",
-        usecase: { target: "brainImaging", detail: "term2" },
-        vocabApi: this.app.vocabApi,
-        numericEditMenuVersion: ["discrete"],
-        defaultQ4fillTW: term0_term2_defaultQ
-      }
-    ];
-    return mandatoryConfigInputOptions;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    return {
-      config,
-      dslabel: appState.vocab.dslabel,
-      genome: appState.vocab.genome,
-      RefNIdata: appState.termdbConfig.queries.NIdata[config.queryKey]
-    };
-  }
-  async main() {
-    this.config = structuredClone(this.state.config);
-    this.settings = this.state.config.settings.brainImaging;
-    this.dom.saggitalSlider.property("value", this.settings.brainImageL);
-    this.dom.saggitalInput.property("value", this.settings.brainImageL);
-    this.dom.coronalSlider.property("value", this.settings.brainImageF);
-    this.dom.coronalInput.property("value", this.settings.brainImageF);
-    this.dom.axialSlider.property("value", this.settings.brainImageT);
-    this.dom.axialInput.property("value", this.settings.brainImageT);
-    const data = await Promise.all([
-      this.requestImage("l", this.settings.brainImageL),
-      this.requestImage("f", this.settings.brainImageF),
-      this.requestImage("t", this.settings.brainImageT)
-    ]);
-    this.imagesData = {
-      brainImageL: { dataUrls: {}, td: this.dom.tdL, data: data[0] },
-      brainImageF: { dataUrls: {}, td: this.dom.tdF, data: data[1] },
-      brainImageT: { dataUrls: {}, td: this.dom.tdT, data: data[2] }
-    };
-    for (const img of Object.values(this.imagesData)) this.renderImages(img);
-    this.renderLegend();
-  }
-  async requestImage(key, value) {
-    const body = {
-      genome: this.state.genome,
-      dslabel: this.state.dslabel,
-      refKey: this.state.config.queryKey,
-      [key]: value,
-      selectedSampleFileNames: this.state.config.selectedSampleFileNames,
-      divideByTW: this.state.config.divideByTW,
-      overlayTW: this.state.config.overlayTW,
-      legendFilter: this.state.config.legendFilter
-    };
-    return await dofetch3("brainImaging", { body });
-  }
-  renderImages({ data, td, dataUrls }) {
-    this.legendValues = data.legend;
-    if (data.error) throw data.error;
-    for (const [termV, result] of Object.entries(data.brainImage)) {
-      dataUrls[termV] = result;
-    }
-    td.selectAll("*").remove();
-    for (const [termV, result] of Object.entries(dataUrls)) {
-      if (this.state.config.divideByTW)
-        td.append("div").attr("class", "pp-chart-title").style("text-align", "center").text(`${termV} (n=${result.catNum})`).style("font-weight", "600").style("color", "white").style("font-size", "24px").style("margin-bottom", "5px").style("margin-top", "5px").style("display", "block");
-      td.append("div").append("img").attr("src", result.url);
-    }
-  }
-  renderLegend() {
-    const legendItems = [];
-    for (const [label, v] of Object.entries(this.legendValues)) {
-      const scale = linear(["white", v.color], [0, v.maxLength]).clamp(true);
-      legendItems.push({
-        text: label == "default" ? "Combined Intensity" : label,
-        width: 100,
-        scale,
-        colors: ["white", v.color],
-        domain: [0, v.maxLength],
-        key: label,
-        crossedOut: v.crossedOut
-      });
-    }
-    this.legendItems = legendItems;
-    const legendRendererData = [
-      {
-        items: legendItems
-      }
-    ];
-    this.legendRenderer(legendRendererData, {
-      settings: {
-        fontsize: 16,
-        iconh: 14,
-        iconw: 14,
-        dimensions: {
-          xOffset: 0
-        }
-      }
-    });
-  }
-};
-function makeChartBtnMenu(holder, chartsInstance) {
-  chartsInstance.dom.tip.clear();
-  const menuDiv = holder.append("div");
-  if (chartsInstance.state.termdbConfig.queries.NIdata) {
-    for (const [refKey, ref] of Object.entries(chartsInstance.state.termdbConfig.queries.NIdata)) {
-      const refDiv = menuDiv.append("div");
-      const refOption = refDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text(refKey).on("click", async () => {
-        refOption.attr("class", "sja_menuoption_not_interactive");
-        refOption.on("click", null);
-        const body = {
-          genome: chartsInstance.opts.vocab.genome,
-          dslabel: chartsInstance.opts.vocab.dslabel,
-          refKey,
-          samplesOnly: true
-        };
-        const result = await dofetch3("brainImagingSamples", { body });
-        const samples = result.samples;
-        const [rows, columns] = await getTableData(chartsInstance, samples, chartsInstance.state, refKey);
-        const applybt = {
-          text: "APPLY",
-          class: "sjpp_apply_btn sja_filter_tag_btn",
-          callback: (indexes) => {
-            chartsInstance.dom.tip.hide();
-            const selectedSampleFileNames = indexes.map((i) => samples[i].sample + ".nii");
-            const config = {
-              chartType: "brainImaging",
-              queryKey: refKey,
-              settings: {
-                brainImaging: {
-                  brainImageL: ref.parameters.l,
-                  brainImageF: ref.parameters.f,
-                  brainImageT: ref.parameters.t
-                }
-              },
-              selectedSampleFileNames
-            };
-            chartsInstance.app.dispatch({
-              type: "plot_create",
-              config
-            });
-          }
-        };
-        renderTable({
-          rows,
-          columns,
-          resize: true,
-          singleMode: false,
-          div: refDiv.append("div"),
-          maxHeight: "40vh",
-          buttons: [applybt]
-        });
-      });
-    }
-  }
-}
-var brainImaging = getCompInit(BrainImaging);
-var componentInit = brainImaging;
-async function getPlotConfig(opts) {
-  const settings = {
-    brainImaging: { brainImageL: 76, brainImageF: 116, brainImageT: 80 }
-  };
-  const config = { chartType: "brainImaging", settings, hidePlotFilter: true };
-  return copyMerge(config, opts);
-}
-async function getTableData(self, samples, state, refKey) {
-  const rows = [];
-  for (const sample of samples) {
-    const row = [{ value: sample.sample }];
-    for (const c of state.termdbConfig.queries.NIdata[refKey].sampleColumns || []) {
-      row.push({ value: sample[c.termid] });
-    }
-    rows.push(row);
-  }
-  const columns = [{ label: "Sample" }];
-  for (const c of state.termdbConfig.queries.NIdata[refKey].sampleColumns || []) {
-    columns.push({
-      label: (await self.app.vocabApi.getterm(c.termid)).name
-    });
-  }
-  return [rows, columns];
-}
-function setInteractivity(self) {
-  self.legendLabelMouseup = (event) => {
-    const targetData = event.target.__data__;
-    if (!targetData || targetData.key == "default") return;
-    const legendMenu = self.dom.legendMenu.clear();
-    const legendMenuDiv = legendMenu.d.append("div");
-    const legendFilter = self.state.config.legendFilter ? [...self.state.config.legendFilter] : [];
-    const legendFilterIndex = legendFilter.indexOf(targetData.key);
-    if (legendFilterIndex !== -1 || legendFilter.length + 1 !== self.legendItems.length) {
-      legendMenuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text(legendFilterIndex == -1 ? "Hide" : "Show").on("click", () => {
-        legendMenu.hide();
-        if (legendFilterIndex == -1) legendFilter.push(targetData.key);
-        else legendFilter.splice(legendFilterIndex, 1);
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.id,
-          config: { legendFilter }
-        });
-      });
-    }
-    legendMenuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Show only").on("click", () => {
-      legendMenu.hide();
-      const legendFilter2 = [];
-      for (const legendCat of self.legendItems) {
-        if (legendCat.key !== targetData.key) legendFilter2.push(legendCat.key);
-      }
-      self.app.dispatch({
-        type: "plot_edit",
-        id: self.id,
-        config: { legendFilter: legendFilter2 }
-      });
-    });
-    legendMenuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Show all").on("click", () => {
-      legendMenu.hide();
-      self.app.dispatch({
-        type: "plot_edit",
-        id: self.id,
-        config: { legendFilter: [] }
-      });
-    });
-    if (self.state.config.overlayTW.term.type != "geneVariant") {
-      let color = self.state.config.overlayTW?.term?.values?.[targetData.key]?.color || "red";
-      color = rgb(color).formatHex();
-      legendMenuDiv.append("div").attr("class", "sja_sharp_border").style("padding", "0px 10px").text("Color:").append("input").attr("type", "color").attr("value", color).on("change", (e) => {
-        self.changeColor(targetData.key, e.target.value);
-      });
-    }
-    legendMenu.showunder(event.target);
-  };
-  self.changeColor = async function(key, color) {
-    const tw = self.config.overlayTW;
-    if (!(tw.term.type == "geneVariant" && tw.q.type == "values") && tw.term.values[key])
-      tw.term.values[key].color = color;
-    else {
-      if (!tw.term.values) tw.term.values = {};
-      if (!tw.term.values[key]) tw.term.values[key] = {};
-      tw.term.values[key].color = color;
-    }
-    await self.app.dispatch({
-      type: "plot_edit",
-      id: self.id,
-      config: { overlayTW: tw }
-    });
-  };
-}
-export {
-  brainImaging,
-  componentInit,
-  getPlotConfig,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=brainImaging-NIPQWFWO.js.map

package/dist/brainImaging-NIPQWFWO.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/brainImaging.js"],
-  "sourcesContent": ["import { getCompInit, copyMerge } from '#rx'\nimport { controlsInit, term0_term2_defaultQ } from './controls'\nimport { dofetch3 } from '#common/dofetch'\nimport { renderTable } from '../dom/table.ts'\nimport svgLegend from '#dom/svg.legend'\nimport { scaleLinear } from 'd3-scale'\nimport { Menu } from '#dom/menu'\nimport { rgb } from 'd3-color'\n\nclass BrainImaging {\n\tstatic type = 'brainImaging'\n\n\tconstructor(opts) {\n\t\tthis.opts = opts\n\t\tthis.type = BrainImaging.type\n\t\tsetInteractivity(this)\n\t}\n\n\tasync init(appState) {\n\t\tconst state = this.getState(appState)\n\t\tconst holder = this.opts.holder\n\t\tif (this.opts.header)\n\t\t\tthis.opts.header\n\t\t\t\t.style('padding-left', '7px')\n\t\t\t\t.style('color', 'rgb(85, 85, 85)')\n\t\t\t\t.html(`Brain Imaging: ${state.config.queryKey}/${state.config.selectedSampleFileNames.join(' ')}`)\n\t\tconst controlsHolder = holder.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\t\tconst rightDiv = holder.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\t\tconst headerHolder = rightDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('padding', '10px')\n\t\tconst contentHolder = rightDiv.append('div').style('vertical-align', 'top')\n\t\tconst table = contentHolder.append('table').style('border-collapse', 'collapse')\n\t\tconst headerTr = table.append('tr')\n\t\tconst contentTr = table.append('tr').style('background-color', 'black')\n\t\tconst tdL = contentTr.append('td')\n\t\tconst tdF = contentTr.append('td')\n\t\tconst tdT = contentTr.append('td')\n\t\tconst legendHolder = contentHolder.append('svg').style('width', '100%').on('mouseup', this.legendLabelMouseup)\n\t\tconst legendMenu = new Menu({ padding: '0px' })\n\n\t\tthis.dom = {\n\t\t\theaderHolder,\n\t\t\tcontentHolder,\n\t\t\theaderTr,\n\t\t\ttdL,\n\t\t\ttdF,\n\t\t\ttdT,\n\t\t\tlegendHolder,\n\t\t\tlegendMenu\n\t\t}\n\t\tthis.addSliders(state.config.settings.brainImaging)\n\n\t\tconst configInputsOptions = this.getConfigInputsOptions(state)\n\n\t\tthis.components = {\n\t\t\tcontrols: await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: controlsHolder,\n\t\t\t\tinputs: configInputsOptions\n\t\t\t})\n\t\t}\n\t\tthis.components.controls.on('downloadClick.brainImaging', () => {\n\t\t\tconst urls = []\n\t\t\tfor (const key in this.imagesData)\n\t\t\t\tfor (const category in this.imagesData[key].dataUrls) {\n\t\t\t\t\tconst dataUrl = this.imagesData[key].dataUrls[category].url\n\t\t\t\t\turls.push(dataUrl)\n\t\t\t\t}\n\t\t\tthis.downloadImage(urls)\n\t\t})\n\t\tthis.legendRenderer = svgLegend({ holder: this.dom.legendHolder })\n\t}\n\n\taddSliders(settings) {\n\t\tconst tr = this.dom.headerTr\n\t\tlet td = tr.append('td')\n\t\ttd.append('label').attr('for', 'saggital').text('Sagittal:')\n\t\tthis.dom.saggitalSlider = td\n\t\t\t.append('input')\n\t\t\t.attr('id', 'saggital')\n\t\t\t.attr('type', 'range')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', 192)\n\t\t\t.attr('value', settings.brainImageL)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageL', e.target.value)\n\t\t\t})\n\t\tthis.dom.saggitalInput = td\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', 192)\n\t\t\t.attr('value', settings.brainImageL)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageL', e.target.value)\n\t\t\t})\n\t\t\t.style('vertical-align', 'top')\n\n\t\ttd = tr.append('td')\n\n\t\ttd.append('label').attr('for', 'coronal').text('Coronal:')\n\t\tthis.dom.coronalSlider = td\n\t\t\t.append('input')\n\t\t\t.attr('type', 'range')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', 228)\n\t\t\t.attr('value', settings.brainImageF)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageF', e.target.value)\n\t\t\t})\n\t\tthis.dom.coronalInput = td\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', 192)\n\t\t\t.attr('value', settings.brainImageF)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageF', e.target.value)\n\t\t\t})\n\t\t\t.style('vertical-align', 'top')\n\n\t\ttd = tr.append('td')\n\n\t\ttd.append('label').attr('for', 'axial').text('Axial:')\n\t\tthis.dom.axialSlider = td\n\t\t\t.append('input')\n\t\t\t.attr('id', 'axial')\n\t\t\t.attr('type', 'range')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', 192)\n\t\t\t.attr('value', settings.brainImageT)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageT', e.target.value)\n\t\t\t})\n\t\tthis.dom.axialInput = td\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', 192)\n\t\t\t.attr('value', settings.brainImageT)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageT', e.target.value)\n\t\t\t})\n\t}\n\n\teditBrainImage(key, value) {\n\t\tif (!value) return\n\t\tconst settings = { [key]: Number(value) }\n\n\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: { settings: { brainImaging: settings } } })\n\t}\n\n\tdownloadImage(dataUrls) {\n\t\tfor (const dataUrl of dataUrls) {\n\t\t\tconst downloadImgName = 'brainImaging'\n\t\t\tconst a = document.createElement('a')\n\t\t\tdocument.body.appendChild(a)\n\n\t\t\ta.addEventListener(\n\t\t\t\t'click',\n\t\t\t\t() => {\n\t\t\t\t\t// Download the image\n\t\t\t\t\ta.download = downloadImgName + '.png'\n\t\t\t\t\ta.href = dataUrl\n\t\t\t\t\tdocument.body.removeChild(a)\n\t\t\t\t},\n\t\t\t\tfalse\n\t\t\t)\n\t\t\ta.click()\n\t\t}\n\t}\n\n\tgetConfigInputsOptions(state) {\n\t\tif (state.config.selectedSampleFileNames.length == 1) return []\n\t\tconst mandatoryConfigInputOptions = [\n\t\t\t{\n\t\t\t\tlabel: 'Divide by',\n\t\t\t\ttype: 'term',\n\t\t\t\tchartType: 'brainImaging',\n\t\t\t\tconfigKey: 'divideByTW',\n\t\t\t\ttitle: 'Categories to divide by',\n\t\t\t\tusecase: { target: 'brainImaging', detail: 'term0' },\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Color by',\n\t\t\t\ttype: 'term',\n\t\t\t\tchartType: 'brainImaging',\n\t\t\t\tconfigKey: 'overlayTW',\n\t\t\t\ttitle: 'Categories to color the samples',\n\t\t\t\tusecase: { target: 'brainImaging', detail: 'term2' },\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ\n\t\t\t}\n\t\t]\n\t\treturn mandatoryConfigInputOptions\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\n\t\treturn {\n\t\t\tconfig,\n\t\t\tdslabel: appState.vocab.dslabel,\n\t\t\tgenome: appState.vocab.genome,\n\t\t\tRefNIdata: appState.termdbConfig.queries.NIdata[config.queryKey]\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.config = structuredClone(this.state.config) //to modify config on plot_edit\n\t\tthis.settings = this.state.config.settings.brainImaging\n\n\t\t//settings may be edited by the slider or the input, so we update the sliders and inputs to reflect the current settings\n\t\tthis.dom.saggitalSlider.property('value', this.settings.brainImageL)\n\t\tthis.dom.saggitalInput.property('value', this.settings.brainImageL)\n\t\tthis.dom.coronalSlider.property('value', this.settings.brainImageF)\n\t\tthis.dom.coronalInput.property('value', this.settings.brainImageF)\n\t\tthis.dom.axialSlider.property('value', this.settings.brainImageT)\n\t\tthis.dom.axialInput.property('value', this.settings.brainImageT)\n\n\t\tconst data = await Promise.all([\n\t\t\tthis.requestImage('l', this.settings.brainImageL),\n\t\t\tthis.requestImage('f', this.settings.brainImageF),\n\t\t\tthis.requestImage('t', this.settings.brainImageT)\n\t\t])\n\n\t\tthis.imagesData = {\n\t\t\tbrainImageL: { dataUrls: {}, td: this.dom.tdL, data: data[0] },\n\t\t\tbrainImageF: { dataUrls: {}, td: this.dom.tdF, data: data[1] },\n\t\t\tbrainImageT: { dataUrls: {}, td: this.dom.tdT, data: data[2] }\n\t\t}\n\n\t\tfor (const img of Object.values(this.imagesData)) this.renderImages(img)\n\n\t\tthis.renderLegend()\n\t}\n\n\tasync requestImage(key, value) {\n\t\tconst body = {\n\t\t\tgenome: this.state.genome,\n\t\t\tdslabel: this.state.dslabel,\n\t\t\trefKey: this.state.config.queryKey,\n\t\t\t[key]: value,\n\t\t\tselectedSampleFileNames: this.state.config.selectedSampleFileNames,\n\t\t\tdivideByTW: this.state.config.divideByTW,\n\t\t\toverlayTW: this.state.config.overlayTW,\n\t\t\tlegendFilter: this.state.config.legendFilter\n\t\t}\n\t\treturn await dofetch3('brainImaging', { body })\n\t}\n\n\trenderImages({ data, td, dataUrls }) {\n\t\tthis.legendValues = data.legend\n\t\tif (data.error) throw data.error\n\t\tfor (const [termV, result] of Object.entries(data.brainImage)) {\n\t\t\tdataUrls[termV] = result\n\t\t}\n\n\t\ttd.selectAll('*').remove()\n\t\tfor (const [termV, result] of Object.entries(dataUrls)) {\n\t\t\tif (this.state.config.divideByTW)\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.attr('class', 'pp-chart-title')\n\t\t\t\t\t.style('text-align', 'center')\n\t\t\t\t\t.text(`${termV} (n=${result.catNum})`)\n\t\t\t\t\t.style('font-weight', '600')\n\t\t\t\t\t.style('color', 'white')\n\t\t\t\t\t.style('font-size', '24px')\n\t\t\t\t\t.style('margin-bottom', '5px')\n\t\t\t\t\t.style('margin-top', '5px')\n\t\t\t\t\t.style('display', 'block')\n\t\t\ttd.append('div').append('img').attr('src', result.url)\n\t\t}\n\t}\n\n\trenderLegend() {\n\t\tconst legendItems = []\n\t\tfor (const [label, v] of Object.entries(this.legendValues)) {\n\t\t\tconst scale = scaleLinear(['white', v.color], [0, v.maxLength]).clamp(true)\n\t\t\tlegendItems.push({\n\t\t\t\ttext: label == 'default' ? 'Combined Intensity' : label,\n\t\t\t\twidth: 100,\n\t\t\t\tscale,\n\t\t\t\tcolors: ['white', v.color],\n\t\t\t\tdomain: [0, v.maxLength],\n\t\t\t\tkey: label,\n\t\t\t\tcrossedOut: v.crossedOut\n\t\t\t})\n\t\t}\n\t\tthis.legendItems = legendItems\n\t\tconst legendRendererData = [\n\t\t\t{\n\t\t\t\titems: legendItems\n\t\t\t}\n\t\t]\n\n\t\tthis.legendRenderer(legendRendererData, {\n\t\t\tsettings: {\n\t\t\t\tfontsize: 16,\n\t\t\t\ticonh: 14,\n\t\t\t\ticonw: 14,\n\t\t\t\tdimensions: {\n\t\t\t\t\txOffset: 0\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n}\n\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\tchartsInstance.dom.tip.clear()\n\tconst menuDiv = holder.append('div')\n\tif (chartsInstance.state.termdbConfig.queries.NIdata) {\n\t\tfor (const [refKey, ref] of Object.entries(chartsInstance.state.termdbConfig.queries.NIdata)) {\n\t\t\tconst refDiv = menuDiv.append('div')\n\n\t\t\tconst refOption = refDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text(refKey)\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\trefOption.attr('class', 'sja_menuoption_not_interactive')\n\t\t\t\t\trefOption.on('click', null)\n\t\t\t\t\tconst body = {\n\t\t\t\t\t\tgenome: chartsInstance.opts.vocab.genome,\n\t\t\t\t\t\tdslabel: chartsInstance.opts.vocab.dslabel,\n\t\t\t\t\t\trefKey,\n\t\t\t\t\t\tsamplesOnly: true\n\t\t\t\t\t}\n\t\t\t\t\tconst result = await dofetch3('brainImagingSamples', { body })\n\t\t\t\t\tconst samples = result.samples\n\n\t\t\t\t\tconst [rows, columns] = await getTableData(chartsInstance, samples, chartsInstance.state, refKey)\n\n\t\t\t\t\tconst applybt = {\n\t\t\t\t\t\ttext: 'APPLY',\n\t\t\t\t\t\tclass: 'sjpp_apply_btn sja_filter_tag_btn',\n\t\t\t\t\t\tcallback: indexes => {\n\t\t\t\t\t\t\tchartsInstance.dom.tip.hide()\n\t\t\t\t\t\t\tconst selectedSampleFileNames = indexes.map(i => samples[i].sample + '.nii')\n\t\t\t\t\t\t\tconst config = {\n\t\t\t\t\t\t\t\tchartType: 'brainImaging',\n\t\t\t\t\t\t\t\tqueryKey: refKey,\n\t\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\t\tbrainImaging: {\n\t\t\t\t\t\t\t\t\t\tbrainImageL: ref.parameters.l,\n\t\t\t\t\t\t\t\t\t\tbrainImageF: ref.parameters.f,\n\t\t\t\t\t\t\t\t\t\tbrainImageT: ref.parameters.t\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\tselectedSampleFileNames\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tchartsInstance.app.dispatch({\n\t\t\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\t\t\tconfig\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\n\t\t\t\t\trenderTable({\n\t\t\t\t\t\trows,\n\t\t\t\t\t\tcolumns,\n\t\t\t\t\t\tresize: true,\n\t\t\t\t\t\tsingleMode: false,\n\t\t\t\t\t\tdiv: refDiv.append('div'),\n\t\t\t\t\t\tmaxHeight: '40vh',\n\t\t\t\t\t\tbuttons: [applybt]\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t}\n\t}\n}\n\nexport const brainImaging = getCompInit(BrainImaging)\nexport const componentInit = brainImaging\n\nexport async function getPlotConfig(opts) {\n\tconst settings = {\n\t\tbrainImaging: { brainImageL: 76, brainImageF: 116, brainImageT: 80 }\n\t}\n\tconst config = { chartType: 'brainImaging', settings, hidePlotFilter: true }\n\treturn copyMerge(config, opts)\n}\n\nasync function getTableData(self, samples, state, refKey) {\n\tconst rows = []\n\tfor (const sample of samples) {\n\t\t// first cell is sample name\n\t\tconst row = [{ value: sample.sample }]\n\n\t\t// optional sample columns\n\t\tfor (const c of state.termdbConfig.queries.NIdata[refKey].sampleColumns || []) {\n\t\t\trow.push({ value: sample[c.termid] })\n\t\t}\n\t\trows.push(row)\n\t}\n\n\t// first column is sample and is hardcoded\n\tconst columns = [{ label: 'Sample' }]\n\n\t// add in optional sample columns\n\tfor (const c of state.termdbConfig.queries.NIdata[refKey].sampleColumns || []) {\n\t\tcolumns.push({\n\t\t\tlabel: (await self.app.vocabApi.getterm(c.termid)).name\n\t\t})\n\t}\n\n\treturn [rows, columns]\n}\n\nfunction setInteractivity(self) {\n\tself.legendLabelMouseup = event => {\n\t\tconst targetData = event.target.__data__\n\t\tif (!targetData || targetData.key == 'default') return\n\t\tconst legendMenu = self.dom.legendMenu.clear()\n\t\tconst legendMenuDiv = legendMenu.d.append('div')\n\t\tconst legendFilter = self.state.config.legendFilter ? [...self.state.config.legendFilter] : []\n\n\t\tconst legendFilterIndex = legendFilter.indexOf(targetData.key)\n\n\t\tif (legendFilterIndex !== -1 || legendFilter.length + 1 !== self.legendItems.length) {\n\t\t\t// only show the Hide option when the cat is not the last shown cat\n\t\t\tlegendMenuDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text(legendFilterIndex == -1 ? 'Hide' : 'Show')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tlegendMenu.hide()\n\t\t\t\t\tif (legendFilterIndex == -1) legendFilter.push(targetData.key)\n\t\t\t\t\telse legendFilter.splice(legendFilterIndex, 1)\n\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\tconfig: { legendFilter }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t}\n\n\t\tlegendMenuDiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text('Show only')\n\t\t\t.on('click', () => {\n\t\t\t\tlegendMenu.hide()\n\t\t\t\tconst legendFilter = []\n\t\t\t\tfor (const legendCat of self.legendItems) {\n\t\t\t\t\tif (legendCat.key !== targetData.key) legendFilter.push(legendCat.key)\n\t\t\t\t}\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: { legendFilter }\n\t\t\t\t})\n\t\t\t})\n\n\t\tlegendMenuDiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text('Show all')\n\t\t\t.on('click', () => {\n\t\t\t\tlegendMenu.hide()\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: { legendFilter: [] }\n\t\t\t\t})\n\t\t\t})\n\n\t\t//TODO: support changing color for grouped geneVariant term\n\t\tif (self.state.config.overlayTW.term.type != 'geneVariant') {\n\t\t\tlet color = self.state.config.overlayTW?.term?.values?.[targetData.key]?.color || 'red'\n\t\t\tcolor = rgb(color).formatHex() //so that the color is in the correct format to be shown in the input\n\t\t\tlegendMenuDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('padding', '0px 10px')\n\t\t\t\t.text('Color:')\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'color')\n\t\t\t\t.attr('value', color)\n\t\t\t\t.on('change', e => {\n\t\t\t\t\tself.changeColor(targetData.key, e.target.value)\n\t\t\t\t})\n\t\t}\n\t\tlegendMenu.showunder(event.target)\n\t}\n\n\tself.changeColor = async function (key, color) {\n\t\tconst tw = self.config.overlayTW\n\n\t\tif (!(tw.term.type == 'geneVariant' && tw.q.type == 'values') && tw.term.values[key])\n\t\t\ttw.term.values[key].color = color\n\t\telse {\n\t\t\tif (!tw.term.values) tw.term.values = {}\n\t\t\tif (!tw.term.values[key]) tw.term.values[key] = {}\n\t\t\ttw.term.values[key].color = color\n\t\t}\n\n\t\tawait self.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: { overlayTW: tw }\n\t\t})\n\t}\n}\n"],
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