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startpage.php
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startpage.php
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<?php
ob_start();
$token_params = http_build_query(array(
"grant_type" => "authorization_code",
"code" => filter_input(INPUT_GET, "code"),
"redirect_uri" => getenv("ebrains_redirect_wa"),
"client_id" => getenv("ebrains_id_wa"),
"client_secret" => getenv("ebrains_secret_wa")
));
$token_ch = curl_init(getenv("ebrains_token"));
curl_setopt_array($token_ch, array(
CURLOPT_RETURNTRANSFER => true,
CURLOPT_POST => true,
CURLOPT_POSTFIELDS => $token_params
));
$token_res = curl_exec($token_ch);
curl_close($token_ch);
$token_obj = json_decode($token_res, true);
$token = $token_obj["access_token"];
$json= json_decode(urldecode(filter_input(INPUT_GET, "state")), true);
$json["token"]=$token;
?>
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<title></title>
<script src="dppick.js"></script>
<script src="https://cdn.jsdelivr.net/gh/Tevemadar/NetUnzip/inflater.min.js"></script>
<script src="https://cdn.jsdelivr.net/gh/Tevemadar/NetUnzip/netunzip.min.js"></script>
<style>
.error{
color: red;
font-weight: bold;
}
</style>
<script>
const state=<?php echo json_encode($json);?>;
async function dpjson(params) {
const response = await fetch(
`https://data-proxy.ebrains.eu/api/v1/buckets/${params}`,{
headers:{
accept:"application/json",
authorization:`Bearer ${state.token}`
}
});
return response.json();
}
async function startup(){
if(state.hasOwnProperty("filename")){
state.embedded=true;
location.href="webalign.html?"+encodeURIComponent(JSON.stringify(state));
return;
}
const choice=await dppick({
bucket:state["clb-collab-id"],
token:state.token,
title:"Select WebAlign descriptor",
extensions:[".waln","wwrp"],
create:".waln",
createplaceholder:"Create new WebAlign series",
createnowarn:true,
nocancel:true
});
if(choice.pick){
state.filename=choice.pick;
location.href="webalign.html?"+encodeURIComponent(JSON.stringify(state));
}else{
state.filename=choice.create;
newseries();
}
}
function newseries(){
document.getElementById("newseries").hidden=false;
document.getElementById("filename").innerText="New series "+state.filename;
document.getElementById("collab").value=state["clb-collab-id"];
document.getElementById("atlas").selectedIndex=-1;
trycollect();
}
function cancel(){
document.getElementById("newseries").hidden=true;
startup();
}
let collection;
let ctime;
function tryshow(){
// document.getElementById("filebody").innerHTML=
// collection.map(item=>`<tr><td>${item.filename.split("/").slice(-1)[0]}</td><td>${item.format}</td>
// <td>${item.width}</td><td>${item.height}</td><td>${item.tilesize}</td><td>${item.overlap}</td></tr>`).join("");
const copy=collection;
collection=[];
let error=false;
document.getElementById("filebody").innerHTML=
copy.map(item=>{
const filename=item.filename.split("/").slice(-1)[0];
const fail=!filename.match(/_s\d+/);
if(fail)
error=true;
else
collection.push(item);
return `<tr><td ${fail?"class='error'":""}>${filename}</td><td>${item.format}</td>`+
`<td>${item.width}</td><td>${item.height}</td><td>${item.tilesize}</td><td>${item.overlap}</td></tr>`;
}).join("");
if(error)
document.getElementById("log").innerText="Sections marked in red do not follow the expected numbering convention and will not be part of the series.";
else if(collection.length)
document.getElementById("log").innerText="Ready.";
document.getElementById("filetable").hidden=copy.length===0;
document.getElementById("create").disabled=collection.length===0 || document.getElementById("atlas").selectedIndex===-1;
}
function clear(){
collection=[];
oldisv=false;
tryshow();
}
function dzisection(dzi,filename){
return {
filename,
width:parseInt(dzi.match(/Width="(\d+)"/m)[1]),
height:parseInt(dzi.match(/Height="(\d+)"/m)[1]),
tilesize:parseInt(dzi.match(/TileSize="(\d+)"/m)[1]),
overlap:parseInt(dzi.match(/Overlap="(\d+)"/m)[1]),
format:dzi.match(/Format="([^"]+)"/m)[1]
};
}
let dzipbundles;
let bucket;
const wfprefix=".nesysWorkflowFiles/zippedPyramids/";
async function trycollect(){
clear();
const current=ctime=Date.now();
const button=document.getElementById("create");
button.disabled=true;
const prg=document.getElementById("log");
document.getElementById("filetable").hidden=true;
const btns=document.getElementById("dzipbuttons");
btns.hidden=true;
dzipbundles=new Map();
try{
bucket=document.getElementById("collab").value.replaceAll(/[^-\w().!]/g, "");
const dzips = await dpjson(`${bucket}?prefix=${wfprefix}&limit=10000`);
if(dzips.objects.length<2){
const result = await dpjson(`${bucket}?delimiter=/&limit=10000`);
if(result.hasOwnProperty("objects")){
const images=result.objects.filter(item=>item.hasOwnProperty("subdir")&&item.subdir.includes("."));
for(const image of images){
prg.innerText="Fetching DZI "+(collection.length+1)+"/"+images.length;
const subdir=image.subdir;
const pos=subdir.lastIndexOf(".");
const name=subdir.substring(0,pos);
const urljson=await dpjson(`${bucket}/${subdir+name}.dzi?redirect=false`);
const dzi=await fetch(urljson.url).then(response=>response.text());
if(current!==ctime)
return;
collection.push(dzisection(dzi,subdir.substring(0,subdir.length-1)));
}
}
} else {
for(const item of dzips.objects) {
const parts=item.name.substring(wfprefix.length).split("/");
if(parts.length===2 && parts[1].endsWith(".dzip")) {
if(!dzipbundles.has(parts[0]))
dzipbundles.set(parts[0],[]);
dzipbundles.get(parts[0]).push(parts[1]);
}
}
dzipbundles.forEach((v,k)=>btns.innerHTML+=`<button onclick="dzicollect('${k}')">${k} (${v.length})</button> `);
btns.hidden=dzipbundles.size===0;
}
}catch(ex){console.log(ex);}
tryshow();
}
async function dzicollect(dzipbundle){
clear();
const current=ctime=Date.now();
const prg=document.getElementById("log");
const dzips=dzipbundles.get(dzipbundle);
for(let i=0;i<dzips.length;i++) {
if(current!==ctime)return;
prg.innerText="Fetching DZI "+(collection.length+1)+"/"+dzips.length;
const dzip=dzips[i];
const zipdir=await netunzip(
()=>dpjson(`${bucket}/${wfprefix}${dzipbundle}/${dzip}?redirect=false`).then(json=>json.url));
for(const [_,entry] of zipdir.entries) {
if(entry.name.endsWith(".dzi")) {
const data=await zipdir.get(entry);
if(current!==ctime)return;
const dzi=new TextDecoder().decode(data);
collection.push(dzisection(dzi,dzipbundle+"/"+dzip));
break;
}
}
}
tryshow();
}
// https://object.cscs.ch/v1/AUTH_08c08f9f119744cbbf77e216988da3eb/imgsvc-be74b890-2c14-4404-b187-678ab8cacc9e/ext-d000018_mouse3_calb_s193.tif/ext-d000018_mouse3_calb_s193.dzi
// https://localizoom.apps.hbp.eu/filmstripzoom.html?atlas=ABA_Mouse_CCFv3_2017_25um&series=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000018_CalbindinDistr-NormalMouse_pub/Mouse3/mouse3_nonlinear_lz.json&pyramids=imgsvc-be74b890-2c14-4404-b187-678ab8cacc9e&tools&nl
let oldisv;
async function import_link(event) {
clear();
const link=event.target.value;
if(!link.startsWith("https://localizoom.apps.hbp.eu/filmstripzoom.html?"))
return;
const params=link.split("?")[1].split("&").reduce((acc,item)=>{
const pair=item.split("=");
acc.set(pair[0],pair.length===1?true:pair[1]);
return acc;
},new Map());
if(params.get("pyramids").startsWith("buckets/")){
bucket=document.getElementById("collab").value=params.get("pyramids").substring("buckets/".length);
}else{
bucket=false;
document.getElementById("collab").value="---";
oldisv=params.get("pyramids");
}
const select=document.getElementById("atlas");
atlas.selectedIndex=-1;
for(let i=0;i<atlas.options.length;i++)
if(atlas.options[i].value===params.get("atlas"))
atlas.selectedIndex=i;
// bucket=document.getElementById("collab").value=params.get("pyramids").substring("buckets/".length);
const series=await fetch(params.get("series")).then(response=>response.json());
collection=await Promise.all(series.slices.map(async slice=>{
const filename=slice.filename;
const name=filename.substring(0,filename.lastIndexOf("."))
let dzi,section;
try {
dzi=await fetch((bucket?"https://data-proxy.ebrains.eu/api/v1/buckets/":"https://object.cscs.ch/v1/AUTH_08c08f9f119744cbbf77e216988da3eb/")+
`${bucket?bucket:oldisv}/${filename}/${name}.dzi`)
.then(response=>response.text());
section=dzisection(dzi,filename);
} catch(ex) {
dzi=await fetch((bucket?"https://data-proxy.ebrains.eu/api/v1/buckets/":"https://object.cscs.ch/v1/AUTH_08c08f9f119744cbbf77e216988da3eb/")+
`${bucket?bucket:oldisv}/${name}.tif/${name}.dzi`)
.then(response=>response.text());
section=dzisection(dzi,name+".tif");
}
if(slice.hasOwnProperty("anchoring"))
section.ouv=slice.anchoring;
if(slice.hasOwnProperty("markers"))
section.markers=slice.markers.map(marker=>({
x:marker[0]*section.width/slice.width,
y:marker[1]*section.height/slice.height,
nx:marker[2]*section.width/slice.width,
ny:marker[3]*section.height/slice.height
}));
return section;
}));
tryshow();
}
async function create(){
document.getElementById("create").disabled=true;
const series={
atlas:document.getElementById("atlas").value,
sections:collection
};
if(bucket)series.bucket=bucket;
if(oldisv)series.oldisv=oldisv;
const upload=await fetch(
`https://data-proxy.ebrains.eu/api/v1/buckets/${state["clb-collab-id"]}/${state.filename}`,{
method: "PUT",
headers:{
accept:"application/json",
authorization:`Bearer ${state.token}`
}
}
).then(response=>response.json());
if (!upload.hasOwnProperty("url")) {
document.getElementById("log").innerHTML=("Possible error happened:<br>" + JSON.stringify(upload));
return;
}
await fetch(upload.url, {
method: "PUT",
headers: {
'Content-Type': 'application/x.webalign'
},
body: JSON.stringify(series)
});
location.href="webalign.html?"+encodeURIComponent(JSON.stringify(state));
}
</script>
</head>
<body onload="startup()">
<div id="newseries" hidden>
<div id="filename"></div>
<input oninput="import_link(event)" placeholder="Import LocaliZoom link"><br><br>
Enter name of image-chunk collab: <input id="collab" oninput="trycollect()"><br>
Target atlas:
<select id="atlas" onchange="tryshow()">
<option value="WHS_SD_Rat_v4_39um">WHS SD Rat v4 39um</option>
<option value="WHS_SD_Rat_v3_39um">WHS SD Rat v3 39um</option>
<option value="ABA_Mouse_CCFv3_2017_25um">ABA Mouse CCFv3 2017 25um</option>
</select><br>
<button id="create" onclick="create()" disabled>Create</button><button onclick="cancel()">Cancel</button>
<pre id="log"></pre>
<div id="dzipbuttons"></div>
<table id="filetable">
<thead>
<th>name</th><th>format</th><th>width</th><th>height</th><th>tilesize</th><th>overlap</th>
</thead>
<tbody id="filebody"></tbody>
</table>
</div>
</body>
</html>