Merge pull request #450 from camicroscope/develop

For 3.8.1
camicroscope · Oct 5, 2020 · 629cb3d · 629cb3d
2 parents e7b6fa5 + 8c11858
commit 629cb3d
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Showing 11 changed files with 88 additions and 21 deletions.
diff --git a/HISTORY.md b/HISTORY.md
@@ -23,10 +23,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * **Version 1**
     * [1.0.x](#camicroscope-10)
 
-### caMicroscope [Unreleased](https://github.com/camicroscope/camicroscope/compare/v3.8.0...camicroscope:develop)
+### caMicroscope [Unreleased](https://github.com/camicroscope/camicroscope/compare/v3.8.1...camicroscope:develop)
 ###### TBD
 * TBD
 
+### caMicroscope [3.8.1](https://github.com/camicroscope/camicroscope/compare/v3.8.0...camicroscope:v3.8.1)
+###### 2020-10-05
+* Added baked-in default annotation schema
+* Loader Bugfix
+
 ### caMicroscope [3.8.0](https://github.com/camicroscope/camicroscope/compare/v3.7.7...camicroscope:v3.8.0)
 ###### 2020-09-04
 * Incorperation of the Machine Learning Development Workbench (GSOC 2020 @akhil-rana) [#438](https://github.com/camicroscope/caMicroscope/pull/438)

diff --git a/apps/loader/loader.js b/apps/loader/loader.js
@@ -10,7 +10,6 @@ function changeStatus(step, text, reset=true) {
   // Reset the status bar
   console.log('Previous: ', document.getElementById('load_status').innerHTML);
   document.getElementById('load_status').innerHTML='';
-
   // Display JSON as table:
   if (typeof text === 'object') { // If the text arg is a JSON
     var col = []; // List of column headers
@@ -51,7 +50,7 @@ function changeStatus(step, text, reset=true) {
       tr = table.insertRow(-1);
       for (var j = 0; j < col.length; j++) {
         var tabCell = tr.insertCell(-1);
-        if (text[col[j]].length>65&&step == 'CHECK') {
+        if (text[col[j]] && text[col[j]].length>65&&step == 'CHECK') {
           tabCell.innerHTML= `${text[col[j]].substr(0, 65)}<span class="collapse" id="more-${j}">
              ${text[col[j]].substr(65)}    </span>
     <span><a href="#more-${j}" data-toggle="collapse">... <i class="fa fa-caret-down"></i></span>`;
@@ -127,7 +126,7 @@ function handleDownload(id) {
           throw new Error('Slide not found');
         }
       }).then((location) => {
-        fileName= location.substring(location.lastIndexOf('/')+1, location.length);
+        fileName = location.substring(location.lastIndexOf('/')+1, location.length);
         console.log(fileName);
         return fileName;
       }).then((fileName) =>{

diff --git a/apps/convert/index.html → apps/port/index.html b/apps/convert/index.html → apps/port/index.html
@@ -1,24 +1,30 @@
 <!DOCTYPE html>
 <html>
 <head>
+  <script src="../../core/Store.js"></script>
+  <script src="./port.js"></script>
   <script src="./xml2geo.js"></script>
   <link rel="stylesheet" href="./style.css">
+  <title>Import and Export [caMicroscope]</title>
 </head>
 <body>
-  <h1>Convert Annotations from XML</h1>
+  <h1>Import Annotations</h1>
   <h3>Info</h3>
   <div class="form">
   <label for="slide_id">Slide Id:</label>
   <input type="text" id="slide_id" name="slide_id"><br>
   <label for="annot_name">Annotation Name:</label>
   <input type="text" id="annot_name" name="annot_name"><br>
   <h3>File Contents</h3>
-  <label for="annot_name">XML Contents:</label>
-  <textarea id="xml_in" name="input" rows="10" cols="30"></textarea><br>
-  <button id="convert_btn" onclick="xml2geo()" type="button">Convert</button>
+  <label for="annot_name">Input:</label>
+  <textarea id="input" name="input" rows="10" cols="30"></textarea><br>
+  <button id="convert_btn" onclick="xml2geo()" type="button">Convert from XML</button>
+  <button id="prepare_btn" onclick="prepareAnnot()" type="button">Prepare JSON</button>
   </div>
   <br><br>
   <h3>Output</h3>
   <textarea id="output" rows="10" cols="30"></textarea>
+  <br>
+  <button id="post_btn" onclick="saveAnnot()" type="button">Post</button>
 </body>
 </html>
diff --git a/apps/port/port.js b/apps/port/port.js
@@ -0,0 +1,22 @@
+const store = new Store('../../data');
+
+function prepareAnnot() {
+  try {
+    let output = JSON.parse(document.getElementById('input'));
+    output['provenance']['image']['slide'] = document.getElementById('slide_id').value;
+    output['provenance']['analysis']['execution'] = document.getElementById('annot_name').value;
+    output['properties']['annotations']['name'] = document.getElementById('annot_name').value;
+  } catch (e) {
+    alert(e);
+  }
+  document.getElementById('output').innerHTML = JSON.stringify(output);
+}
+
+function saveAnnot() {
+  try {
+    let doc = JSON.parse(document.getElementById('output'));
+  } catch (e) {
+    alert(e);
+  }
+  store.addMark(doc).then((x)=>alert('done!')).catch((e)=>alert(e));
+}
diff --git a/apps/convert/style.css → apps/port/style.css b/apps/convert/style.css → apps/port/style.css
diff --git a/apps/convert/xml2geo.js → apps/port/xml2geo.js b/apps/convert/xml2geo.js → apps/port/xml2geo.js
@@ -9,6 +9,7 @@ var template = {
       'source': 'human',
       'execution_id': 'TEMPLATE',
       'name': 'TEMPLATE',
+      'coordinate': 'image',
     },
   },
   'properties': {

diff --git a/components/operationpanel/operationpanel.js b/components/operationpanel/operationpanel.js
@@ -104,8 +104,35 @@ function OperationPanel(options) {
   // check form schema
   if (!this.setting.formSchemas || this.setting.formSchemas.length == 0) {
     // console.error(`${this.name}:No Form Schema ...`);
-    this.elt.textContent = `${this.name}:No Form Schema ...`;
-    return;
+    // this.elt.textContent = `${this.name}:No Form Schema ...`;
+    this.setting.formSchemas = [{
+      '_id': '0',
+      'type': 'object',
+      'id': 'annotation-form',
+      'name': 'AnnotSchema',
+      'description': '',
+      'links': [
+
+      ],
+      'additionalProperties': false,
+      'properties': {
+        'name': {
+          'id': 'a0',
+          'title': 'Identity Name',
+          'type': 'string',
+          'required': true,
+          'description': 'note name',
+        },
+        'notes': {
+          'id': 'a1',
+          'title': 'Notes: ',
+          'type': 'string',
+          'format': 'textarea',
+          'maxLength': 128,
+        },
+      },
+    }];
+  // return;
   }
   if (!this.setting.action || !this.setting.action.callback) {
     // console.error(`${this.name}:No Action ...`);

diff --git a/core/extension/openseadragon-canvas-draw-overlay.js b/core/extension/openseadragon-canvas-draw-overlay.js
@@ -693,7 +693,10 @@
             type: "Point",
             coordinates: [...point]
           },
-          bound: [...point]
+          bound: {
+            type: "Point",
+            coordinates: [...point]
+          }
         };
         return;
       }
@@ -710,6 +713,13 @@
               : "Polygon",
           coordinates: [[point]],
           path: null
+        },
+        bound: {
+          type:
+            this.drawMode === "line" || this.drawMode === "grid"
+              ? "LineString"
+              : "Polygon",
+          coordinates: [[point]]
         }
       };
 
@@ -841,7 +851,7 @@
         }
       }
       // create bounds
-      this._current_path_.bound = getBounds(
+      this._current_path_.bound.coordinates[0] = getBounds(
         this._current_path_.geometry.coordinates[0]
       );
 

diff --git a/core/extension/osd-heatmap-overlay.js b/core/extension/osd-heatmap-overlay.js
@@ -696,9 +696,6 @@
         finalData = this.__thresholdingData();
         // set patch color
         this._display_ctx_.fillStyle = this._color;
-        // get the patch's size on the screen
-        //const w = logicalToPhysicalDistanceX(this._size[0],this._viewer.imagingHelper);
-        //const h = logicalToPhysicalDistanceY(this._size[1],this._viewer.imagingHelper);
 
         // start to draw each patch
         this._display_ctx_.beginPath();

diff --git a/package.json b/package.json
@@ -4,8 +4,8 @@
   "description": "",
   "scripts": {
     "test": "mocha test --recursive",
-    "lint": "eslint ./core/*.js  ./components/**/*.js  ./apps/*.js ./apps/convert/*.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",
-    "lint-fix": "eslint ./core/*.js  ./components/**/*.js ./apps/*.js  ./apps/convert/*.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"
+    "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",
+    "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"
   },
   "author": "",
   "license": "NONE",

diff --git a/test/ui/operationpanel-test-cases.js b/test/ui/operationpanel-test-cases.js
@@ -49,10 +49,10 @@ describe('Operation Panel Component',function(){
         //  multipleElt = dom.window.document.getElementById('multiple');
         // });
         // Options Error: No Schema Error
-        it('Options Error: No Schema Error', function () {
-            let error = dom.window.document.getElementById('error1');
-            assert.equal(error.textContent,'OperationPanel:No Form Schema ...');
-        });
+        // it('Options Error: No Schema Error', function () {
+        //     let error = dom.window.document.getElementById('error1');
+        //     assert.equal(error.textContent,'OperationPanel:No Form Schema ...');
+        // });
 
         // Options Error: No Action Error
         it('Options Error: No Action Error', function () {