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Merge pull request camicroscope#459 from camicroscope/develop
For 3.8.3
2 parents 9cc49a9 + bb33221 commit b61df7f

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‎HISTORY.md

Lines changed: 8 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,9 +23,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
2323
* **Version 1**
2424
* [1.0.x](#camicroscope-10)
2525

26-
### caMicroscope [Unreleased](https://github.com/camicroscope/camicroscope/compare/v3.8.2...camicroscope:develop)
26+
### caMicroscope [Unreleased](https://github.com/camicroscope/camicroscope/compare/v3.8.3...camicroscope:develop)
2727
###### TBD
28-
* TBD
28+
*
29+
30+
### caMicroscope [Unreleased](https://github.com/camicroscope/camicroscope/compare/v3.8.2...camicroscope:v3.8.3)
31+
###### 2020-12-03
32+
* Bugfix: Model Failed to read coordinates [#454](https://github.com/camicroscope/caMicroscope/pull/454)[#455](https://github.com/camicroscope/caMicroscope/pull/455)
33+
* multislide explorer [#456](https://github.com/camicroscope/caMicroscope/pull/456)
34+
* Model Class List Edit Field Defaults [#457](https://github.com/camicroscope/caMicroscope/pull/457)
2935

3036
### caMicroscope [3.8.2](https://github.com/camicroscope/camicroscope/compare/v3.8.1...camicroscope:v3.8.2)
3137
###### 2020-11-10

‎apps/model/model.js

Lines changed: 8 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -188,7 +188,7 @@ async function initUIcomponents() {
188188
provideContent: true,
189189
content: `
190190
<div class = "message" >
191-
191+
192192
<h3> Please select a model</h3></div><br>
193193
<table id = 'roitable'>
194194
<thead>
@@ -503,7 +503,7 @@ function camicStopDraw(e) {
503503
const viewer = $CAMIC.viewer;
504504
const canvasDraw = viewer.canvasDrawInstance;
505505
const imgColl = canvasDraw.getImageFeatureCollection();
506-
if (imgColl.features.length > 0) {
506+
if (imgColl.features.length > 0 && imgColl.features[0].bound.coordinates[0].length >= 5) {
507507
// Check size first
508508
const box = checkSize(imgColl, viewer.imagingHelper);
509509

@@ -539,8 +539,8 @@ function checkSize(imgColl, imagingHelper) {
539539
// slide images svsslide images svs
540540
// get position on viewer
541541

542-
const topLeft = imgColl.features[0].bound[0];
543-
const bottomRight = imgColl.features[0].bound[2];
542+
const topLeft = imgColl.features[0].bound.coordinates[0][0];
543+
const bottomRight = imgColl.features[0].bound.coordinates[0][2];
544544
const min = imagingHelper._viewer.viewport.imageToViewportCoordinates(topLeft[0], topLeft[1]);
545545
const max = imagingHelper._viewer.viewport.imageToViewportCoordinates(bottomRight[0], bottomRight[1]);
546546
const rect = new OpenSeadragon.Rect(min.x, min.y, max.x-min.x, max.y-min.y);
@@ -956,7 +956,7 @@ async function showInfo() {
956956
deleteModel(name);
957957
});
958958
document.getElementById('chngClassListBtn' + modelCount).addEventListener('click', () => {
959-
showNewClassInput(name);
959+
showNewClassInput(name, classes);
960960
});
961961
modelCount += 1;
962962
};
@@ -968,12 +968,13 @@ async function showInfo() {
968968
}
969969

970970

971-
function showNewClassInput(name) {
971+
function showNewClassInput(name, classes) {
972972
const self = $UI.chngClassLst;
973973
self.body.innerHTML = `
974974
<input id ="new_classList" type="text"/>
975975
<button class="btn btn-primary btn-xs my-xs-btn btn-final-change" id='chngbtn' type="button">Change Class List</button>
976976
`;
977+
document.getElementById('new_classList').defaultValue = classes;
977978
$UI.chngClassLst.open(); // Open the box to take input from user
978979
document.getElementById('chngbtn').addEventListener('click', () => {
979980
// $UI.chngClassLst.close();
@@ -1061,7 +1062,7 @@ function dataURItoBlob(dataURI) {
10611062
* Convert image coordinates
10621063
*/
10631064
function convertCoordinates(imagingHelper, bound) {
1064-
const newArray = bound.map(function(arr) {
1065+
const newArray = bound.coordinates[0].map(function(arr) {
10651066
return arr.slice(); // copy
10661067
});
10671068

‎apps/multi/multi.html

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
<!DOCTYPE html>
2+
<html>
3+
<head>
4+
<script type="text/javascript" src="../../core/openseadragon/openseadragon.js"></script>
5+
<script src="../../core/Store.js"></script>
6+
<script src="../../common/PathdbMods.js"></script>
7+
<link rel="stylesheet" href="./style.css">
8+
<title>Select an Image</title>
9+
</head>
10+
<body>
11+
<h1> Images </h1>
12+
<div id="pages"></div>
13+
<div id="workspace" class="flex-grid"></div>
14+
</body>
15+
<script src="./multi.js"></script>
16+
</html>

‎apps/multi/multi.js

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,90 @@
1+
// initalize dependencies and params
2+
let store = new Store('../../data/');
3+
const urlParams = new URLSearchParams(window.location.search);
4+
const page = parseInt(urlParams.get('p'), 10) || 0;
5+
const mode = urlParams.get('mode');
6+
const MAX_TILES = parseInt(urlParams.get('mt'), 10) || 16;
7+
const prefixUrl = 'https://cdn.jsdelivr.net/npm/[email protected]/build/openseadragon/images/';
8+
let query = JSON.parse(urlParams.get('q') || '{}');
9+
let list = JSON.parse(urlParams.get('l') || '[]');
10+
11+
let viewers = [];
12+
13+
// run the pathdb mods as needed
14+
if (mode == 'pathdb') {
15+
PathDbMods();
16+
}
17+
18+
const workspace = document.getElementById('workspace');
19+
20+
function addTile(url, i, name, dest) {
21+
let d = document.createElement('div');
22+
d.id = 'osd' + i;
23+
d.className = 'osd col';
24+
// tile size, and hidden to start
25+
d.style = 'min-width: 400px; width:22%; height:400px';
26+
// add link to slide
27+
let b = document.createElement('a');
28+
b.id = 'link' + i;
29+
b.innerText = name;
30+
b.href=dest;
31+
d.appendChild(b);
32+
d.appendChild(document.createElement('br'));
33+
workspace.appendChild(d);
34+
viewers[i] = OpenSeadragon({
35+
id: d.id,
36+
prefixUrl: prefixUrl,
37+
tileSources: url,
38+
});
39+
}
40+
41+
function onInit() {
42+
let promises = [];
43+
if (list.length) {
44+
for (j of list) {
45+
promises.push(store.getSlide(j));
46+
}
47+
} else {
48+
promises.push(store.findSlide(null, null, null, null, query));
49+
}
50+
Promise.all(promises).then((xx)=>{
51+
let x = xx.flat();
52+
// pagination
53+
// previous?
54+
if (page > 0) {
55+
let p = document.createElement('a');
56+
let prevParam = new URLSearchParams(window.location.search);
57+
p.id = 'prevPage';
58+
prevParam.set('p', page-1);
59+
p.innerText = 'Prev';
60+
p.href = './multi.html?' + prevParam.toString();
61+
document.getElementById('pages').append(p);
62+
}
63+
// next?
64+
if (page < Math.floor(x.length/MAX_TILES)-1) {
65+
let p = document.createElement('a');
66+
let nextParam = new URLSearchParams(window.location.search);
67+
p.id = 'nextPage';
68+
nextParam.set('p', page+1);
69+
p.innerText = 'Next';
70+
p.href = './multi.html?' + nextParam.toString();
71+
document.getElementById('pages').append(p);
72+
}
73+
// tiles
74+
let start = MAX_TILES * page;
75+
let stop = Math.min(x.length, start+MAX_TILES);
76+
for (let n = start; n < stop; n++) {
77+
let item = x[n];
78+
let loc = '../../img/IIP/raw/?DeepZoom=' + item.location + '.dzi';
79+
let dest = '../viewer/viewer.html?slideId=' + item._id['$oid'];
80+
if (mode == 'pathdb') {
81+
dest += '&mode=pathdb';
82+
}
83+
addTile(loc, n, item.name, dest);
84+
}
85+
});
86+
}
87+
88+
// TODO pagination
89+
90+
window.onload = onInit;

‎apps/multi/style.css

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
body{
2+
margin: 25px;
3+
}
4+
.flex-grid {
5+
display: flex;
6+
flex-wrap: wrap;
7+
}
8+
.col {
9+
flex: 1;
10+
}
11+
12+
.osd{
13+
margin: 10px;
14+
padding: 10px;
15+
background-color: HoneyDew;
16+
}

‎apps/segment/segment.js

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -574,8 +574,8 @@ function checkSize(imgColl, imagingHelper) {
574574

575575
// get position on viewer
576576

577-
const topLeft = imgColl.features[0].bound[0];
578-
const bottomRight = imgColl.features[0].bound[2];
577+
const topLeft = imgColl.features[0].bound.coordinates[0][0];
578+
const bottomRight = imgColl.features[0].bound.coordinates[0][2];
579579
const min = imagingHelper._viewer.viewport.imageToViewportCoordinates(topLeft[0], topLeft[1]);
580580
const max = imagingHelper._viewer.viewport.imageToViewportCoordinates(bottomRight[0], bottomRight[1]);
581581
const rect = new OpenSeadragon.Rect(min.x, min.y, max.x-min.x, max.y-min.y);
@@ -1377,7 +1377,7 @@ function dataURItoBlob(dataURI) {
13771377
* Convert image coordinates
13781378
*/
13791379
function convertCoordinates(imagingHelper, bound) {
1380-
const newArray = bound.map(function(arr) {
1380+
const newArray = bound.coordinates[0].map(function(arr) {
13811381
return arr.slice(); // copy
13821382
});
13831383

‎common/PathdbMods.js

Lines changed: 10 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -124,14 +124,16 @@ function PathDbMods() {
124124
})
125125
}
126126

127-
StatesHelper.prototype.default_getCurrentStatesURL = StatesHelper.prototype.getCurrentStatesURL;
128-
getCurrentStatesURL = function(isImageCoordinate=false){
129-
let states = StatesHelper.getCurrentStates(isImageCoordinate);
130-
if(!states)return;
131-
console.log(states);
132-
states = StatesHelper.encodeStates(states);
133-
return `${location.origin}${location.pathname}?slideId=${$D.params.slideId}&states=${$D.params.states}&mode=${$D.params.mode}`
134-
};
127+
if (!(typeof StatesHelper === 'undefined')){
128+
StatesHelper.prototype.default_getCurrentStatesURL = StatesHelper.prototype.getCurrentStatesURL;
129+
getCurrentStatesURL = function(isImageCoordinate=false){
130+
let states = StatesHelper.getCurrentStates(isImageCoordinate);
131+
if(!states)return;
132+
console.log(states);
133+
states = StatesHelper.encodeStates(states);
134+
return `${location.origin}${location.pathname}?slideId=${$D.params.slideId}&states=${$D.params.states}&mode=${$D.params.mode}`
135+
};
136+
}
135137

136138
console.warn("This Setup Is Intended For Pathdb")
137139
}

‎core/Store.js

Lines changed: 22 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -547,27 +547,33 @@ class Store {
547547

548548
/**
549549
* find overlays matching name and/or type
550-
* @param {string} [name] - the slide name
551-
* @param {string} [location] - the slide location, supporting regex match
550+
* @param {string} [name] - the slide's name
551+
* @param {string} [specimen] - the slide's noted specimen
552+
* @param {string} [study] - the slide's noted study
553+
* @param {string} [location] - the slide's file location
554+
* @param {string} [q] - override query - ignores all other params if set
552555
* @return {promise} - promise which resolves with data
553556
**/
554-
findSlide(slide, specimen, study, location) {
557+
findSlide(slide, specimen, study, location, q) {
558+
let query;
555559
const suffix = 'Slide/find';
556560
const url = this.base + suffix;
557-
const query = {};
558-
if (slide) {
559-
query.slide = slide;
560-
}
561-
if (study) {
562-
query.study = study;
563-
}
564-
if (specimen) {
565-
query.specimen = specimen;
566-
}
567-
if (location) {
568-
query.location = location;
561+
if (q) {
562+
query = q;
563+
} else {
564+
if (slide) {
565+
query.slide = slide;
566+
}
567+
if (study) {
568+
query.study = study;
569+
}
570+
if (specimen) {
571+
query.specimen = specimen;
572+
}
573+
if (location) {
574+
query.location = location;
575+
}
569576
}
570-
571577
return fetch(url + '?' + objToParamStr(query), {
572578
credentials: 'include',
573579
mode: 'cors',

‎package.json

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@
44
"description": "",
55
"scripts": {
66
"test": "mocha test --recursive",
7-
"lint": "eslint ./core/*.js ./components/**/*.js ./apps/*.js ./apps/port/*.js ./apps/heatmap/*.js ./apps/labeling/*.js ./apps/loader/*.js ./apps/model/*.js ./apps/segment/*.js ./apps/model/**/*.js ./apps/segment/**/*.js ./apps/viewer/*.js --quiet",
8-
"lint-fix": "eslint ./core/*.js ./components/**/*.js ./apps/*.js ./apps/port/*.js ./apps/heatmap/*.js ./apps/labeling/*.js ./apps/loader/*.js ./apps/model/*.js ./apps/segment/*.js ./apps/model/**/*.js ./apps/segment/**/*.js ./apps/viewer/*.js --quiet --fix"
7+
"lint": "eslint ./core/*.js ./components/**/*.js ./apps/*.js ./apps/port/*.js ./apps/heatmap/*.js ./apps/multi/*.js ./apps/labeling/*.js ./apps/loader/*.js ./apps/model/*.js ./apps/segment/*.js ./apps/model/**/*.js ./apps/segment/**/*.js ./apps/viewer/*.js --quiet",
8+
"lint-fix": "eslint ./core/*.js ./components/**/*.js ./apps/*.js ./apps/port/*.js ./apps/heatmap/*.js ./apps/multi/*.js ./apps/labeling/*.js ./apps/loader/*.js ./apps/model/*.js ./apps/segment/*.js ./apps/model/**/*.js ./apps/segment/**/*.js ./apps/viewer/*.js --quiet --fix"
99
},
1010
"author": "",
1111
"license": "NONE",

‎test/ui/operationpanel-test-cases.js

Lines changed: 2 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -42,18 +42,7 @@ describe('Operation Panel Component',function(){
4242

4343
//
4444
describe('constructor:options', function () {
45-
// let singleElt;
46-
// let multipleElt;
47-
// before(function(){
48-
// singleElt = dom.window.document.getElementById('single');
49-
// multipleElt = dom.window.document.getElementById('multiple');
50-
// });
51-
// Options Error: No Schema Error
52-
// it('Options Error: No Schema Error', function () {
53-
// let error = dom.window.document.getElementById('error1');
54-
// assert.equal(error.textContent,'OperationPanel:No Form Schema ...');
55-
// });
56-
45+
5746
// Options Error: No Action Error
5847
it('Options Error: No Action Error', function () {
5948
let error = dom.window.document.getElementById('error2');
@@ -65,10 +54,8 @@ describe('Operation Panel Component',function(){
6554
const btn1 = singleElt.querySelector('.action');
6655
const btn2 = multipleElt.querySelector('.action');
6756
assert.equal(btn1.textContent,'Save');
68-
//assert.equal(btn1.disabled,true);
6957
assert.equal(btn2.textContent,'Submit');
70-
//assert.equal(btn2.disabled,true);
71-
});
58+
});
7259

7360
// check callback
7461
it('Options:check callback',function(){

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