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index.html
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<!DOCTYPE html>
<html>
<head>
<title>TissUUmaps</title>
<meta
name="viewport"
content="width=device-width, initial-scale=1, shrink-to-fit=no"
/>
<meta charset="utf-8" />
<script src="vendor/d3/d3.v4.min.js"></script>
<script src="vendor/d3-plugins/d3-scale-chromaticV3.js"></script>
<script src="vendor/jquery-3.5.1/jquery-3.5.1.min.js"></script>
<script src="vendor/chosen/chosen.jquery.min.js"></script>
<script src="vendor/jquery-3.5.1/jquery.autocomplete.min.js"></script>
<link rel="stylesheet" href="vendor/chosen/chosen.min.css" />
<link
rel="stylesheet"
href="vendor/bootstrap-5.1.1/dist/css/bootstrap.min.css"
/>
<link
rel="stylesheet"
href="vendor/bootstrap-icons-1.5.0/bootstrap-icons.css"
/>
<link rel="stylesheet" href="css/style.css" />
</head>
<body>
<div
id="main-ui"
class="container-fluid px-0 d-flex flex-column vh-100 overflow-hidden"
>
<nav
id="main-navbar"
class="navbar navbar-expand-lg navbar-dark border-bottom border-dark flex-shrink-0"
>
<div class="container-fluid">
<a class="navbar-brand" href="https://tissuumaps.research.it.uu.se/">
<img
src="misc/uulogowhitetuum.png"
width="166"
height="40"
alt="Uppsala University Logotype"
/>
</a>
<button
class="navbar-toggler"
type="button"
data-bs-toggle="collapse"
data-bs-target="#navbar-menu"
aria-controls="navbar-menu"
aria-expanded="false"
aria-label="Toggle navigation"
>
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbar-menu">
<ul class="navbar-nav">
<li class="nav-item dropdown">
<a
class="nav-link dropdown-toggle active"
id="a_menubar_File"
href="#"
id="navbarDropdownMenuLink"
role="button"
data-bs-toggle="dropdown"
aria-expanded="false"
>
File
</a>
<ul
class="dropdown-menu"
id="menubar_File"
aria-labelledby="navbarDropdownMenuLink"
>
<li id="menubar_File_Import">
<a class="dropdown-item" href="#" id="load_project_menu">
<span>Import TMAP project</span>
</a>
</li>
<li id="menubar_File_Export">
<a class="dropdown-item" href="#" id="save_project_menu">
<span>Export TMAP project</span>
</a>
</li>
<li>
<a class="dropdown-item" href="#" id="capture_viewport">
<span>Capture viewport</span>
</a>
</li>
</ul>
</li>
<li class="nav-item" id="nav-item-title">
<a
class="nav-link active"
aria-current="page"
id="project_title"
href="#"
>
Default title</a
>
</li>
</ul>
</div>
</div>
</nav>
<div class="row mx-0 flex-grow-1 overflow-hidden">
<!-- Row for viewer -->
<div class="col px-0 position-relative" id="ISS_viewer_container">
<a
id="floating-navbar-toggler"
class="hook in floating-menu-btn shadow navbar-dark p-2 d-none"
data-bs-toggle="collapse"
data-bs-target="#main-navbar"
role="button"
aria-expanded="false"
aria-controls="main-navbar"
href="#"
>
<span class="navbar-toggler-icon"></span>
</a>
<!-- The id is what OSD will look for to draw the viewer, the class is our own css to stylize
The ID will give the prefix for all the objects related to the viewer in this case ISS-->
<div id="ISS_viewer" class="ISS_viewer h-100"></div>
<!-- Global marker size slider -->
<div id="ISS_globalmarkersize" class="d-none px-1 mx-1 viewer-layer">
<label class="form-label"
>Marker size:
<em class="form-label" id="ISS_globalmarkersize_label"
>100</em
></label
><br />
<input
class="form-range"
type="range"
id="ISS_globalmarkersize_text"
value="100"
min="0"
max="500"
step="10"
oninput="document.getElementById('ISS_globalmarkersize_label').innerHTML = this.value;"
/>
</div>
</div>
<div
id="ISS_menu"
class="ISS_menu col-xl-4 col-lg-5 col-md-6 col-sm-8 col-xs-12 mh-100 overflow-auto"
>
<div class="row pb-2">
<!-- Level 0 tabs -->
<ul id="main-tabs-menu" class="nav nav-tabs pt-1 sticky-top">
<li class="nav-item">
<button
data-bs-target="#markers-iss-gui"
data-bs-toggle="tab"
aria-expanded="true"
class="nav-link active"
id="title-tab-markers"
>
Markers
</button>
</li>
<li>
<button
data-bs-target="#markers-regions-gui"
data-bs-toggle="tab"
aria-expanded="false"
class="nav-link"
id="title-tab-regions"
>
Regions
</button>
</li>
<li>
<button
data-bs-target="#image-gui"
data-bs-toggle="tab"
aria-expanded="false"
class="nav-link"
id="title-tab-image"
>
Image layers
</button>
</li>
<li>
<button
data-bs-target="#plugins-gui"
data-bs-toggle="tab"
aria-expanded="false"
class="nav-link d-none"
id="title-tab-plugins"
>
Plugins
</button>
</li>
</ul>
<div id="TM-tabs" class="tab-content">
<!-- TAB 1.1 ISS data -------------------------------------------------------------------------------- -->
<div class="tab-pane active" id="markers-iss-gui">
<div class="panel panel-default">
<div class="panel-body">
<div class="row" id="divMarkersDownloadButtons"></div>
<!-- 1.1 Row nav tabs -->
<ul
class="nav nav-tabs mt-2"
id="level-1-tabs"
role="tablist"
>
<li class="nav-item" id="plus-1" role="presentation">
<button
class="nav-link"
id="plus-1-button"
data-bs-toggle="tab"
data-bs-target="#"
type="button"
role="tab"
aria-controls="plus"
aria-selected="false"
>
<strong>+</strong>
</button>
</li>
</ul>
<div class="tab-content" id="level-1-tabsContent"></div>
</div>
</div>
</div>
<!-- TAB 1.3 Region data ----------------------------------------------------------------------------- -->
<div class="tab-pane" id="markers-regions-gui">
<div class="panel panel-default">
<div class="panel-body">
<div class="row">
<!-- Tabs 1.3.0 region subtabs -->
<ul class="nav nav-tabs mt-2">
<li class="nav-item">
<button
class="nav-link active"
data-bs-target="#markers-regions-project-gui"
data-bs-toggle="tab"
aria-expanded="true"
>
Regions
</button>
</li>
<li class="nav-item">
<button
class="nav-link"
data-bs-target="#markers-regions-import-gui"
data-bs-toggle="tab"
aria-expanded="false"
>
Import
</button>
</li>
<li class="nav-item">
<button
class="nav-link"
data-bs-target="#markers-regions-export-gui"
data-bs-toggle="tab"
aria-expanded="false"
>
Export
</button>
</li>
</ul>
<div id="markers-region-subtabs" class="tab-content">
<!-- Tabs 1.3.1 -->
<div
class="tab-pane show active"
id="markers-regions-project-gui"
>
<div class="panel panel-default">
<div class="panel-body">
<div id="divRegionsDownloadButtons"></div>
<div class="row my-1">
<button
id="ISS_drawregions_btn"
class="btn btn-primary col mx-1"
type="button"
>
<i
id="ISS_drawregions_icon"
class="bi bi-circle"
></i>
Draw regions
</button>
<button
id="ISS_fillregions_btn"
class="btn btn-primary col mx-1"
type="button"
>
Fill all regions
</button>
</div>
<div id="regionAccordions"></div>
<div id="markers-regions-div">
<div
class="my-1"
id="markers-regions-panel"
></div>
</div>
</div>
</div>
</div>
<!-- Tabs 1.3.2 -->
<div class="tab-pane" id="markers-regions-import-gui">
<div class="panel panel-default">
<div class="panel-body">
<div class="row">
<div class="col-9">
<input
class="form-control-file form-control"
type="file"
id="ISS_region_files_import"
name="files[]"
/>
</div>
<div class="col-3">
<button
id="ISS_import_regions"
class="btn btn-primary"
type="button"
>
Import
</button>
</div>
</div>
</div>
</div>
</div>
<!-- Tabs 1.3.3 -->
<div class="tab-pane" id="markers-regions-export-gui">
<div class="panel panel-default">
<div class="panel-body">
<label for="ISS_region_file_name"
>Download regions for later use</label
>
<div class="row">
<div class="col-9">
<input
class="form-control"
type="text"
id="ISS_region_file_name"
placeholder="regions.json"
value="regions.json"
/>
</div>
<div class="col-3">
<button
id="ISS_export_regions"
class="btn btn-primary"
type="button"
>
Export
</button>
</div>
</div>
<label for="ISS_region_csv_name"
>Download expression in regions</label
>
<div class="row">
<div class="col-9">
<input
class="form-control"
type="text"
id="ISS_region_csv_name"
placeholder="regions.csv"
value="regions.csv"
/>
</div>
<div class="col-3">
<button
id="ISS_export_regions_csv"
class="btn btn-primary"
type="button"
>
Export
</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- TAB 1.4 Overlay data ----------------------------------------------------------------------------- -->
<div class="tab-pane" id="image-gui">
<div class="panel panel-default">
<div class="panel-body">
<div
class="row overflow-auto mb-2"
id="image-overlay-panel"
></div>
<div id="filterSettingsAccordions">
<div class="accordion-item">
<h2 class="accordion-header" id="filterSettingsHeaders">
<button
type="button"
class="accordion-button collapsed"
data-bs-toggle="collapse"
data-bs-target="#filterSettings"
aria-expanded="false"
aria-controls="filterSettings"
>
<i class="bi bi-gear-fill"></i> Filter settings
</button>
</h2>
<div
class="accordion-collapse p-2 collapse"
id="filterSettings"
aria-labelledby="filterSettingsHeaders"
data-bs-parent="#filterSettingsAccordions"
>
<div class="col-12 px-1" id="filterSettings"></div>
</div>
</div>
</div>
</div>
</div>
<!-- end of a main panel -->
</div>
<!-- end of image-gui-->
<!-- TAB 1.4 Plugin data ----------------------------------------------------------------------------- -->
<div class="tab-pane" id="plugins-gui">
<div class="panel panel-default">
<div class="panel-body">
<h6 class="my-2">List of plugins:</h6>
<div id="pluginsAccordions"></div>
</div>
</div>
<!-- end of a main panel -->
</div>
<!-- end of Plugin-gui-->
</div>
<!-- end of TM-tabs-->
</div>
<!-- end of Level 0 tabs -->
</div>
<!-- end of lateral panel -->
<div
id="ISS_collapser"
class="d-flex align-self-center justify-content-end px-0 position-absolute"
>
<div class="btn btn-primary" id="ISS_collapse_btn">
<i class="bi bi-caret-right-fill"></i>
</div>
</div>
</div>
<!-- end of single row -->
</div>
<!-- end of container-fuild-->
<div
id="powered_by_tissuumaps"
class="d-none"
style="left: 10px; bottom: 10px; z-index: 100"
>
<div class="px-1 me-3 viewer-layer">
<small
><img src="misc/logo.svg" height="22px" /> Powered by
<a href="https://tissuumaps.github.io/" target="_blank"
>TissUUmaps</a
></small
>
</div>
</div>
</body>
<script src="vendor/bootstrap-5.1.1/dist/js/bootstrap.bundle.min.js"></script>
<script src="vendor/openseadragon-bin-3.0.0/openseadragon.min.js"></script>
<script src="vendor/openseadragon-plugins/openseadragon-filtering.js"></script>
<script src="vendor/openseadragon-plugins/openseadragon-svg-overlay.js"></script>
<script src="vendor/openseadragon-plugins/openseadragon-scalebar.js"></script>
<script src="vendor/CamanJS-4.1.2/dist/caman.min.js"></script>
<script src="vendor/PapaParse-5.0.2/papaparse.min.js"></script>
<script src="vendor/sorttable/sorttable.js"></script>
<script src="js/utils/interfaceUtils.js"></script>
<script src="js/utils/dataUtils.js"></script>
<script src="js/utils/h5Utils.js"></script>
<script src="js/utils/markerUtils.js"></script>
<script src="js/utils/OSDViewerUtils.js"></script>
<script src="js/utils/HTMLElementUtils.js"></script>
<script src="js/utils/regionUtils.js"></script>
<script src="js/utils/overlayUtils.js"></script>
<script src="js/utils/filterUtils.js"></script>
<script src="js/utils/glUtils.js"></script>
<script src="js/utils/pluginUtils.js"></script>
<script src="js/utils/projectUtils.js"></script>
<script src="js/tmapp.js"></script>
<script>
document.getElementById("project_title").innerText = "Project title";
if (window != window.top) {
/* I'm in a frame! */
document.getElementById("main-navbar").classList.add("collapse");
document
.getElementById("floating-navbar-toggler")
.classList.remove("d-none");
//document.html.style.zoom=0.6
document.getElementById("ISS_menu").style.zoom = 0.7;
document.getElementById("ISS_menu").classList.remove("col-xl-4");
document.getElementById("ISS_menu").classList.remove("col-lg-5");
document.getElementById("ISS_menu").classList.remove("col-md-6");
document.getElementById("ISS_menu").classList.remove("col-sm-8");
document.getElementById("ISS_menu").classList.add("col-xl-2");
document.getElementById("ISS_menu").classList.add("col-lg-3");
document.getElementById("ISS_menu").classList.add("col-md-4");
document.getElementById("ISS_menu").classList.add("col-sm-6");
}
// ----------
$(document).ready(function () {
const queryString = window.location.search;
const urlParams = new URLSearchParams(queryString);
const tmapFile = urlParams.get('tmap');
if (tmapFile != null) {
projectUtils.loadProjectFileFromServer(tmapFile);
}
else {
/*tmapp.layers =[
{name:"Fluo",tileSource:"data/breastcancer/fluo.dzi"},
{name:"HE",tileSource:"data/breastcancer/HE.dzi"}
];*/
}
tmapp.registerActions();
tmapp.init();
if (window != window.top) {
elt = document.getElementById("powered_by_tissuumaps");
tmapp["ISS_viewer"].addControl(elt, {
anchor: OpenSeadragon.ControlAnchor.BOTTOM_LEFT,
});
elt.classList.remove("d-none");
}
});
</script>
</html>