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init.js
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init.js
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// CAMIC is an instance of camicroscope core
// $CAMIC in there
let $CAMIC = null;
let tracker;
const $minorCAMIC = {};
// for all instances of UI components
const $UI = new Map();
// preset pens
// const PEN_CONFIG = [
// {
// title: "Lymph",
// value: "Lymph",
// children: [
// {
// title: "Positive",
// value: "Positive",
// children: [
// {
// title: 100,
// value: 100,
// color: "#ff6296",
// checked: true,
// data: {
// color: "#ff6296",
// mode: "grid",
// type: "Lymph-Positive",
// size: 100
// }
// },
// {
// title: "Point",
// value: "Point",
// color: "#ff6296",
// data: { color: "#ff6296", mode: "point", type: "Lymph-Positive" }
// }
// ]
// },
// {
// title: "Negative",
// value: "Negative",
// children: [
// {
// title: 100,
// value: 100,
// color: "#62ffcb",
// data: {
// color: "#62ffcb",
// mode: "grid",
// type: "Lymph-Negative",
// size: 100
// }
// },
// {
// title: "Point",
// value: "Point",
// color: "#62ffcb",
// data: {
// color: "#62ffcb",
// mode: "point",
// type: "Lymph-Negative"
// }
// }
// ]
// }
// ]
// },
// {
// title: "Neutrophil",
// value: "Neutrophil",
// children: [
// {
// title: "Positive",
// value: "Positive",
// color: "#ffcb62",
// data: {
// color: "#ffcb62",
// mode: "grid",
// type: "Neutrophil-Positive",
// size: 50
// }
// },
// {
// title: "Negative",
// value: "Negative",
// color: "#6296ff",
// data: {
// color: "#6296ff",
// mode: "grid",
// type: "Neutrophil-Negative",
// size: 50
// }
// }
// ]
// },
// {
// title: "Necrosis",
// value: "Necrosis",
// children: [
// {
// title: "Positive",
// value: "Positive",
// children: [
// {
// title: 100,
// value: 100,
// color: "#ff00d9",
// data: {
// color: "#ff00d9",
// mode: "grid",
// type: "Necrosis-Positive",
// size: 100
// }
// },
// {
// title: 500,
// value: 500,
// color: "#ff00d9",
// data: {
// color: "#ff00d9",
// mode: "grid",
// type: "Necrosis-Positive",
// size: 500
// }
// }
// ]
// },
// {
// title: "Negative",
// value: "Negative",
// children: [
// {
// title: 100,
// value: 100,
// color: "#00ff26",
// data: {
// color: "#00ff26",
// mode: "grid",
// type: "Necrosis-Negative",
// size: 100
// }
// },
// {
// title: 500,
// value: 500,
// color: "#00ff26",
// data: {
// color: "#00ff26",
// mode: "grid",
// type: "Necrosis-Negative",
// size: 500
// }
// }
// ]
// }
// ]
// },
// {
// title: "Tumor",
// value: "Tumor",
// children: [
// {
// title: "Positive",
// value: "Positive",
// children: [
// {
// title: 100,
// value: 100,
// color: "#790cff",
// data: {
// color: "#790cff",
// mode: "grid",
// type: "Tumor-Positive",
// size: 100
// }
// },
// {
// title: 300,
// value: 300,
// color: "#790cff",
// data: {
// color: "#790cff",
// mode: "grid",
// type: "Tumor-Positive",
// size: 300
// }
// },
// {
// title: 1000,
// value: 1000,
// color: "#790cff",
// data: {
// color: "#790cff",
// mode: "grid",
// type: "Tumor-Positive",
// size: 1000
// }
// },
// {
// title: 2000,
// value: 2000,
// color: "#790cff",
// data: {
// color: "#790cff",
// mode: "grid",
// type: "Tumor-Positive",
// size: 2000
// }
// }
// ]
// },
// {
// title: "Negative",
// value: "Negative",
// children: [
// {
// title: 100,
// value: 100,
// color: "#92ff0c",
// data: {
// color: "#92ff0c",
// mode: "grid",
// type: "Tumor-Negative",
// size: 100
// }
// },
// {
// title: 300,
// value: 300,
// color: "#92ff0c",
// data: {
// color: "#92ff0c",
// mode: "grid",
// type: "Tumor-Negative",
// size: 300
// }
// },
// {
// title: 1000,
// value: 1000,
// color: "#92ff0c",
// data: {
// color: "#92ff0c",
// mode: "grid",
// type: "Tumor-Negative",
// size: 1000
// }
// },
// {
// title: 2000,
// value: 2000,
// color: "#92ff0c",
// data: {
// color: "#92ff0c",
// mode: "grid",
// type: "Tumor-Negative",
// size: 2000
// }
// }
// ]
// }
// ]
// },
// {
// title: "Prostate",
// value: "Prostate",
// children: [
// {
// title: "Benign",
// value: "Benign",
// color: "#8dd3c7",
// checked: true,
// data: { color: "#8dd3c7", mode: "free", type: "Prostate-Benign" }
// },
// {
// title: "Gleason 3",
// value: "Gleason 3",
// color: "#ffffb3",
// data: { color: "#ffffb3", mode: "free", type: "Prostate-Gleason 3" }
// },
// {
// title: "Gleason 4",
// value: "Gleason 4",
// color: "#bebada",
// data: { color: "#bebada", mode: "free", type: "Prostate-Gleason 4" }
// },
// {
// title: "Gleason 5",
// value: "Gleason 5",
// color: "#fb8072",
// data: { color: "#fb8072", mode: "free", type: "Prostate-Gleason 5" }
// },
// {
// title: "Cancer NOS",
// value: "Cancer NOS",
// color: "#80b1d3",
// data: { color: "#80b1d3", mode: "free", type: "Prostate-Cancer NOS" }
// }
// ]
// },
// {
// title: "NSCLC",
// value: "NSCLC",
// children: [
// {
// title: "Benign",
// value: "Benign",
// color: "#fdb462",
// data: { color: "#fdb462", mode: "free", type: "NSCLC-Benign" }
// },
// {
// title: "Squamous CA",
// value: "Squamous CA",
// color: "#b3de69",
// data: { color: "#b3de69", mode: "free", type: "NSCLC-Squamous CA" }
// },
// {
// title: "Adeno CA (all)",
// value: "Adeno CA (all)",
// color: "#fccde5",
// data: { color: "#fccde5", mode: "free", type: "NSCLC-Adeno CA (all)" }
// },
// {
// title: "Acinar",
// value: "Acinar",
// color: "#d9d9d9",
// data: { color: "#d9d9d9", mode: "free", type: "NSCLC-Acinar" }
// },
// {
// title: "Lapidic",
// value: "Lapidic",
// color: "#bc80bd",
// data: { color: "#bc80bd", mode: "free", type: "NSCLC-Lapidic" }
// },
// {
// title: "Solid",
// value: "Solid",
// color: "#ccebc5",
// data: { color: "#ccebc5", mode: "free", type: "NSCLC-Solid" }
// },
// {
// title: "Papillary",
// value: "Papillary",
// color: "#ffed6f",
// data: { color: "#ffed6f", mode: "free", type: "NSCLC-Papillary" }
// },
// {
// title: "Micropapillary",
// value: "Micropapillary",
// color: "#6a3d9a",
// data: { color: "#6a3d9a", mode: "free", type: "NSCLC-Micropapillary" }
// }
// ]
// }
// ];
const $D = {
pages: {
home: '../table.html',
table: '../table.html',
},
params: null, // parameter from url - slide Id and status in it (object).
overlayers: null, // array for each layers
templates: null, // json schema for prue-form
segments: [],
};
window.addEventListener('keydown', (e) => {
if (!$CAMIC || !$CAMIC.viewer) return;
const keyCode = e.keyCode;
// escape key to close all operations
if (keyCode == 27) {
magnifierOff();
measurementOff();
annotationOff();
}
// open annotation (ctrl + a)
if (e.ctrlKey && keyCode == 65 && $CAMIC.viewer.canvasDrawInstance) {
const li = $UI.toolbar.getSubTool('annotation');
eventFire(li, 'click');
return;
}
// open magnifier (ctrl + m)
if (e.ctrlKey && keyCode == 77 && $UI.spyglass) {
const li = $UI.toolbar.getSubTool('magnifier');
const chk = li.querySelector('input[type=checkbox]');
chk.checked = !chk.checked;
eventFire(chk, 'change');
return;
}
// open measurement (ctrl + r)
if (e.ctrlKey && keyCode == 82 && $CAMIC.viewer.measureInstance) {
e.preventDefault();
const li = $UI.toolbar.getSubTool('measurement');
const chk = li.querySelector('input[type=checkbox]');
chk.checked = !chk.checked;
eventFire(chk, 'click');
return;
}
// open side-by-side (ctrl + s)
if (e.ctrlKey && keyCode == 83) {
e.preventDefault();
const li = $UI.toolbar.getSubTool('sbsviewer');
const chk = li.querySelector('input[type=checkbox]');
chk.checked = !chk.checked;
eventFire(chk, 'click');
return;
}
});
// initialize viewer page
function initialize() {
var checkPackageIsReady = setInterval(function() {
if (IsPackageLoading) {
clearInterval(checkPackageIsReady);
// create a viewer and set up
initCore();
// loading the form template data
FormTempaltesLoader();
// loading the overlayers data
OverlayersLoader();
// loading the heatmap overlayers data
HeatmaplayersLoader();
}
}, 100);
}
// setting core functionalities
function initCore() {
// start initial
// create the message queue
$UI.message = new MessageQueue();
// zoom info and mmp
const opt = {
draw: {
// extend context menu btn group
btns: [
{
// annotation
type: 'btn',
title: 'Annotation',
class: 'material-icons',
text: 'description',
callback: saveAnnotation,
},
{
// analytics
type: 'btn',
title: 'Analytics',
class: 'material-icons',
text: 'settings_backup_restore',
callback: saveAnalytics,
},
],
},
};
// set states if exist
if ($D.params.states) {
opt.states = $D.params.states;
}
// pathdb home directly
if ($D.params.mode == 'pathdb') {
$D.pages.home = '../../../';
$D.pages.table = '../../../';
}
try {
const slideQuery = {};
slideQuery.id = $D.params.slideId;
slideQuery.name = $D.params.slide;
slideQuery.location = $D.params.location;
$CAMIC = new CaMic('main_viewer', slideQuery, opt);
} catch (error) {
Loading.close();
$UI.message.addError('Core Initialization Failed');
console.error(error);
return;
}
$CAMIC.loadImg(function(e) {
// image loaded
if (e.hasError) {
$UI.message.addError(e.message);
// can't reach Slide and return to home page
if (e.isServiceError) redirect($D.pages.table, e.message, 0);
} else {
$D.params.data = e;
// popup panel
$CAMIC.viewer.addHandler('canvas-lay-click', function(e) {
if (!e.data) {
$UI.annotPopup.close();
return;
}
// for support QUIP 2.0
const data = Array.isArray(e.data) ? e.data[e.data.selected] : e.data;
const type = data.provenance.analysis.source;
let body;
let attributes;
let warning = null;
switch (type) {
case 'human':
let area;
let circumference;
if (data.geometries) {
if (
(data.selected != null || data.selected != undefined) &&
data.geometries.features[data.selected] &&
data.geometries.features[data.selected].properties.area
) {
area = `${Math.round(
data.geometries.features[data.selected].properties.area,
)}μm^2`;
}
if (
(data.selected != null || data.selected != undefined) &&
data.geometries.features[data.selected] &&
data.geometries.features[data.selected].properties.circumference
) {
circumference = `${Math.round(
data.geometries.features[data.selected].properties
.circumference,
)}μm`;
}
} // othereise, don't try to calculate area and circumference
// human
attributes = data.properties.annotations;
if (area) attributes.area = area;
if (circumference) attributes.circumference = circumference;
body = convertHumanAnnotationToPopupBody(attributes);
if (
data.geometries &&
data.geometries.features[data.selected].properties.isIntersect
) {
warning = `<div style='color:red;text-align: center;font-size:12px;'>Inaccurate Area and Circumference</div>`;
}
if (
data.geometries &&
data.geometries.features[data.selected].properties.nommp
) {
warning = `<div style='color:red;text-align: center;font-size:12px;'>This slide has no mpp</div>`;
}
$UI.annotPopup.showFooter();
break;
case 'computer':
// handle data.provenance.analysis.computation = `segmentation`
attributes = data.properties.scalar_features[0].nv;
body = {type: 'map', data: attributes};
$UI.annotPopup.hideFooter();
break;
default:
return;
// statements_def
break;
}
$UI.annotPopup.data = {
id: data.provenance.analysis.execution_id,
oid: data._id.$oid,
annotation: attributes,
selected: e.data.selected,
};
$UI.annotPopup.setTitle(`id:${data.provenance.analysis.execution_id}`);
$UI.annotPopup.setBody(body);
if (warning) $UI.annotPopup.body.innerHTML += warning;
$UI.annotPopup.open(e.position);
});
// create the message bar TODO for reading slide Info TODO
$UI.slideInfos = new CaMessage({
/* opts that need to think of*/
id: 'cames',
defaultText: `Slide: ${$D.params.data.name}`,
});
// spyglass
$UI.spyglass = new Spyglass({
targetViewer: $CAMIC.viewer,
imgsrc: $D.params.data.url,
});
}
});
$CAMIC.viewer.addHandler('open', function() {
$CAMIC.viewer.canvasDrawInstance.addHandler('start-drawing', startDrawing);
$CAMIC.viewer.canvasDrawInstance.addHandler('stop-drawing', stopDrawing);
// init UI -- some of them need to wait data loader to load data
// because UI components need data to initialize
initUIcomponents();
// action tracker start
tracker = new Tracker($CAMIC, $D.params.data._id.$oid, getUserId());
tracker.start();
});
}
// initialize all UI components
async function initUIcomponents() {
/* create UI components */
$UI.modalbox = new ModalBox({
id: 'modalbox',
hasHeader: true,
headerText: 'HeatMap List',
hasFooter: false,
});
const subToolsOpt = [];
// home
if (ImgloaderMode == 'iip') {
subToolsOpt.push({
name: 'home',
icon: 'home', // material icons' name
title: 'Home',
type: 'btn', // btn/check/dropdown
value: 'home',
callback: goHome,
});
}
// pen
subToolsOpt.push({
name: 'annotation',
icon: 'create', // material icons' name
title: 'Draw',
type: 'multistates',
callback: draw,
});
// example for dropdownlist has icon in each item
// subToolsOpt.push({
// name: "test",
// icon: "vpn_key", // material icons' name
// title: "test",
// type: "dropdown",
// value: "test",
// callback: function(e) {
// console.log(e);
// },
// dropdownList: [
// {
// name: "add",
// icon: "add",
// value:"add",
// title: "add"
// },
// {
// name: "add_box",
// icon: "add_box",
// value:"add_box",
// title: "add_box"
// }, {
// name: "add_circle",
// icon: "add_circle",
// value:"add_circle",
// title: "add_circle"
// }, {
// name: "block",
// icon: "block",
// value:"block",
// title: "block"
// }
// ]
// });
// brush
// subToolsOpt.push({
// name: "brush",
// icon: "brush", // material icons' name
// title: "Brush Labels",
// type: "multi-dropdown",
// value: "brush",
// callback: toggleBrush,
// dropdownList: BRUSH_CONFIG
// });
$D.preset_list = null;
$D.preset_list = await $CAMIC.store.getConfigByName('preset_label').then((list)=>list.length==0?null:list[0]);
if ($D.preset_list) {
subToolsOpt.push({
name: 'preset_label',
icon: 'colorize', // material icons' name
title: 'Preset Labels',
type: 'multi-dropdown',
value: 'prelabels',
callback: drawLabel,
dropdownList: $D.preset_list.configuration,
});
}
// magnifier
subToolsOpt.push({
name: 'magnifier',
icon: 'search',
title: 'Magnifier',
type: 'dropdown',
value: 'magn',
dropdownList: [
{
value: 0.5,
title: '0.5',
checked: true,
},
{
value: 1,
title: '1.0',
},
{
value: 2,
title: '2.0',
},
],
callback: toggleMagnifier,
});
// measurement tool
if ($CAMIC.viewer.measureInstance) {
subToolsOpt.push({
name: 'measurement',
icon: 'space_bar',
title: 'Measurement',
type: 'check',
value: 'measure',
callback: toggleMeasurement,
});
}
// share
if (ImgloaderMode == 'iip') {
subToolsOpt.push({
name: 'share',
icon: 'share',
title: 'Share View',
type: 'btn',
value: 'share',
callback: shareURL,
});
}
// side-by-side
subToolsOpt.push({
name: 'sbsviewer',
icon: 'view_carousel',
title: 'Side By Side Viewer',
value: 'dbviewers',
type: 'check',
callback: toggleViewerMode,
});
// heatmap
subToolsOpt.push({
name: 'heatmap',
icon: 'satellite',
title: 'Heat Map',
value: 'heatmap',
type: 'btn',
callback: openHeatmap,
});
subToolsOpt.push({
name: 'labeling',
icon: 'label',
title: 'Labeling',
value: 'labeling',
type: 'btn',
callback: function() {
window.location.href = `../labeling/labeling.html${window.location.search}`;
},
});
subToolsOpt.push({
name: 'segment',
icon: 'timeline',
type: 'btn',
value: 'rect',
title: 'Segment',
callback: function() {
if (window.location.search.length > 0) {
window.location.href =
'../segment/segment.html' + window.location.search;
} else {
window.location.href = '../segment/segment.html';
}
},
});
subToolsOpt.push({
name: 'model',
icon: 'aspect_ratio',
type: 'btn',
value: 'rect',
title: 'Predict',
callback: function() {
if (window.location.search.length > 0) {
window.location.href = '../model/model.html' + window.location.search;
} else {
window.location.href = '../model/model.html';
}
},
});
// -- For Nano borb Start -- //
if (ImgloaderMode == 'imgbox') {
// download
subToolsOpt.push({
name: 'downloadmarks',
icon: 'cloud_download',
title: 'Download Marks',
type: 'btn',
value: 'download',
callback: Store.prototype.DownloadMarksToFile,
});
subToolsOpt.push({
name: 'uploadmarks',
icon: 'cloud_upload',
title: 'Load Marks',
type: 'btn',
value: 'upload',
callback: Store.prototype.LoadMarksFromFile,
});
}
// -- For Nano borb End -- //
// bug report
subToolsOpt.push({
name: 'bugs',
icon: 'bug_report',
title: 'Bug Report',
value: 'bugs',
type: 'btn',
callback: () => {
window.open('https://goo.gl/forms/mgyhx4ADH0UuEQJ53', '_blank').focus();
},
});
// create the tool bar
$UI.toolbar = new CaToolbar({
/* opts that need to think of*/
id: 'ca_tools',
zIndex: 601,
mainToolsCallback: mainMenuChange,
subTools: subToolsOpt,
});
// create two side menus for tools
$UI.appsSideMenu = new SideMenu({
id: 'side_apps',
width: 300,
// , isOpen:true
callback: toggleSideMenu,
});
$UI.layersSideMenu = new SideMenu({
id: 'side_layers',
width: 300,
contentPadding: 5,
// , isOpen:true
callback: toggleSideMenu,
});
const loading = `<div class="cover" style="z-index: 500;"><div class="block"><span>loading layers...</span><div class="bar"></div></div></div>`;
$UI.layersSideMenu.addContent(loading);
/* annotation popup */
$UI.annotPopup = new PopupPanel({
footer: [
// { // edit
// title:'Edit',
// class:'material-icons',
// text:'notes',
// callback:anno_edit
// },
{
// delete
title: 'Delete',
class: 'material-icons',
text: 'delete_forever',
callback: anno_delete,
},
],
});
var checkOverlaysDataReady = setInterval(function() {
if (
$D.params.data &&
_l &&
_h &&
$D.overlayers &&
$CAMIC &&
$CAMIC.viewer &&
$CAMIC.viewer.omanager
) {
clearInterval(checkOverlaysDataReady);
// for segmentation
$CAMIC.viewer.createSegment({
store: $CAMIC.store,
slide: $D.params.data.slide,
data: [],
});
// create control
// create main layer viewer items with states
const mainViewerData = $D.overlayers.map((d) => {
const isShow =
$D.params.states &&
$D.params.states.l &&
$D.params.states.l.includes(d.id) ?
true :
false;
return {item: d, isShow: isShow};
});
// create monir layer viewer items
const minorViewerData = $D.overlayers.map((d) => {
return {item: d, isShow: false};
});
// create UI and set data
$UI.layersViewer = createLayerViewer(
'overlayers',
mainViewerData,
callback.bind('main'),
);
// create UI and set data - minor
$UI.layersViewerMinor = createLayerViewer(
'overlayersMinor',
minorViewerData,
callback.bind('minor'),
);
//
if ($D.params.states && $D.params.states.l) {
$D.params.states.l.forEach((id) =>
loadAnnotationById($CAMIC, $UI.layersViewer.getDataItemById(id), null),
);
}
$UI.layersList = new CollapsibleList({
id: 'layerslist',
list: [
{
id: 'left',
title: 'Left Viewer',
// icon:'border_color',
content: 'No Template Loaded', // $UI.annotOptPanel.elt
// isExpand:true
},
{
id: 'right',
// icon:'find_replace',
title: 'Right Viewer',
content: 'No Template Loaded', // $UI.algOptPanel.elt,
},
],
changeCallBack: function(e) {
// console.log(e);
},
});
$UI.layersSideMenu.clearContent();
// add to layers side menu
const title = document.createElement('div');
title.classList.add('item_head');
title.textContent = 'Layers Manager';
$UI.layersSideMenu.addContent(title);
// zoom locker control
$UI.lockerPanel = document.createElement('div');
$UI.lockerPanel.classList.add('lock_panel');
$UI.lockerPanel.style.display = 'none';
$UI.lockerPanel.innerHTML = `<label>Zoom Lock<input type="checkbox" checked></label>`;
$UI.lockerPanel
.querySelector('input[type=checkbox]')
.addEventListener('change', (e) => {
isLock = !isLock;
if (isLock) {
$minorCAMIC.viewer.viewport.zoomTo(
$CAMIC.viewer.viewport.getZoom(true),
$CAMIC.viewer.viewport.getCenter(true),
true,
);
$CAMIC.viewer.controls.bottomright.style.display = 'none';
} else {
$CAMIC.viewer.controls.bottomright.style.display = '';
}
});
$UI.layersSideMenu.addContent($UI.lockerPanel);
$UI.layersList.clearContent('left');
$UI.layersList.addContent('left', $UI.layersViewer.elt);
$UI.layersList.clearContent('right');
$UI.layersList.addContent('right', $UI.layersViewerMinor.elt);
$UI.layersList.elt.parentNode.removeChild($UI.layersList.elt);
closeMinorControlPanel();
$UI.layersSideMenu.addContent($UI.layersList.elt);
}
}, 300);
var checkTemplateSchemasDataReady = setInterval(function() {
if ($D.templates) {
clearInterval(checkTemplateSchemasDataReady);