From cbc856c9d94c11f92d44caa4e703da7679392235 Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Fri, 18 Nov 2022 13:41:09 -0500 Subject: [PATCH 01/24] add 3.10.1 and missing history elements. --- HISTORY.md | 24 +++++++++++++++++++----- 1 file changed, 19 insertions(+), 5 deletions(-) diff --git a/HISTORY.md b/HISTORY.md index c6d501d0..1cc43a45 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## Index * **Version 3** + * [3.10.x](#camicroscope-3100) * [3.9.x](#camicroscope-390) * [3.8.x](#camicroscope-380) * [3.7.x](#camicroscope-377) @@ -24,17 +25,30 @@ 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/v3.9.10...camicroscope:develop) +### caMicroscope [Unreleased](https://github.com/camicroscope/camicroscope/compare/v3.10.1...camicroscope:develop) ###### TBD -### caMicroscope [3.9.9](https://github.com/camicroscope/camicroscope/compare/v3.9.8...camicroscope:v3.9.9) -###### 2021-11-08 -* Fix and enhance Human Readable URL support +### caMicroscope [3.10.1](https://github.com/camicroscope/camicroscope/compare/v3.10.0...camicroscope:v3.10.1) +###### 2022-11-18 +* Bugfix for Magnifying glass with slide token auth + +### caMicroscope [3.10.0](https://github.com/camicroscope/camicroscope/compare/v3.9.11...camicroscope:v3.10.0) +###### 2022-10-25 +* Result Export Page [caMicroscope/566](https://github.com/camicroscope/caMicroscope/pull/566) +* Slide Token injection [caMicroscope/567](https://github.com/camicroscope/caMicroscope/pull/567) + +### caMicroscope [3.9.11](https://github.com/camicroscope/camicroscope/compare/v3.9.10...camicroscope:v3.9.11) +###### 2021-08-15 +* Add Redir App/Page -### caMicroscope [3.9.10](https://github.com/camicroscope/camicroscope/compare/v3.9.8...camicroscope:v3.9.10) +### caMicroscope [3.9.10](https://github.com/camicroscope/camicroscope/compare/v3.9.9...camicroscope:v3.9.10) ###### 2021-01-20 * Human Readable Urls for pathdb +### caMicroscope [3.9.9](https://github.com/camicroscope/camicroscope/compare/v3.9.8...camicroscope:v3.9.9) +###### 2021-11-08 +* Fix and enhance Human Readable URL support + ### caMicroscope [3.9.8](https://github.com/camicroscope/camicroscope/compare/v3.9.6...camicroscope:v3.9.8) ###### 2021-10-21 * Add Segmentation -> Annotation Functionality [#542](https://github.com/camicroscope/caMicroscope/pull/542) From 6cf53e2e96d2eca0b74048bbb72b4ba6970cb9ed Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 30 Dec 2022 22:38:56 +0000 Subject: [PATCH 02/24] Bump flat and mocha Bumps [flat](https://github.com/hughsk/flat) to 5.0.2 and updates ancestor dependency [mocha](https://github.com/mochajs/mocha). These dependencies need to be updated together. Updates `flat` from 4.1.1 to 5.0.2 - [Release notes](https://github.com/hughsk/flat/releases) - [Commits](https://github.com/hughsk/flat/compare/4.1.1...5.0.2) Updates `mocha` from 7.2.0 to 10.2.0 - [Release notes](https://github.com/mochajs/mocha/releases) - [Changelog](https://github.com/mochajs/mocha/blob/master/CHANGELOG.md) - [Commits](https://github.com/mochajs/mocha/compare/v7.2.0...v10.2.0) --- updated-dependencies: - dependency-name: flat dependency-type: indirect - dependency-name: mocha dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- package-lock.json | 774 ++++++++++++++++++++-------------------------- package.json | 2 +- 2 files changed, 329 insertions(+), 447 deletions(-) diff --git a/package-lock.json b/package-lock.json index e1e1a7d1..0e3176b7 100644 --- a/package-lock.json +++ b/package-lock.json @@ -89,9 +89,9 @@ } }, "ansi-colors": { - "version": "3.2.3", - "resolved": "https://registry.npmjs.org/ansi-colors/-/ansi-colors-3.2.3.tgz", - "integrity": "sha512-LEHHyuhlPY3TmuUYMh2oz89lTShfvgbmzaBcxve9t/9Wuy7Dwf4yoAKcND7KFT1HAQfqZ12qtc+DUrBMeKF9nw==" + "version": "4.1.1", + "resolved": "https://registry.npmjs.org/ansi-colors/-/ansi-colors-4.1.1.tgz", + "integrity": "sha512-JoX0apGbHaUJBNl6yF+p6JAFYZ666/hhCGKN5t9QFjbJQKUU/g8MNbFDbvfrgKXvI1QpZplPOnwIo99lX/AAmA==" }, "ansi-escapes": { "version": "4.3.1", @@ -122,9 +122,9 @@ } }, "anymatch": { - "version": "3.1.1", - "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-3.1.1.tgz", - "integrity": "sha512-mM8522psRCqzV+6LhomX5wgp25YVibjh8Wj23I5RPkPppSVSjyKD2A2mBJmWGa+KN7f2D6LNh9jkBCeyLktzjg==", + "version": "3.1.3", + "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-3.1.3.tgz", + "integrity": "sha512-KMReFUr0B4t+D+OBkjR3KYqvocp2XaSzO55UcB6mgQMd3KbcE+mWTyvVV7D/zsdEbNnV6acZUutkiHQXvTr1Rw==", "requires": { "normalize-path": "^3.0.0", "picomatch": "^2.0.4" @@ -248,24 +248,15 @@ "resolved": "https://registry.npmjs.org/bytes/-/bytes-3.1.0.tgz", "integrity": "sha512-zauLjrfCG+xvoyaqLoV8bLVXXNGC4JqlxFCutSDWA6fJrTo2ZuvLYTqZ7aHBLZSMOopbzwv8f+wZcVzfVTI2Dg==" }, - 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"lodash": "^4.17.15", - "yargs": "^13.3.0" + "camelcase": "^6.0.0", + "decamelize": "^4.0.0", + "flat": "^5.0.2", + "is-plain-obj": "^2.1.0" } + }, + "yocto-queue": { + "version": "0.1.0", + "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", + "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==" } } } diff --git a/package.json b/package.json index 8a457be4..df8b25ae 100644 --- a/package.json +++ b/package.json @@ -16,7 +16,7 @@ "express": "^4.16.2", "jsdom": "^16.5.0", "lodash": "^4.17.21", - "mocha": "^7.2.0", + "mocha": "^10.2.0", "node-fetch": "^2.6.7", "tippy": "0.0.0" } From 2f59d76e1672c151c666acef643d82d2af4bfc54 Mon Sep 17 00:00:00 2001 From: Nan Li Date: Wed, 11 Jan 2023 16:01:32 -0600 Subject: [PATCH 03/24] 1. point to point 2. selection download --- apps/segment/segment.js | 1 - apps/viewer/init.js | 36 +++ apps/viewer/uicallbacks.js | 183 ++++++++++++++- apps/viewer/viewer.html | 1 + .../simplecontextmenu/simplecontextmenu.css | 2 +- .../simplecontextmenu/simplecontextmenu.js | 13 +- core/Store.js | 29 ++- .../openseadragon-canvas-draw-overlay.js | 216 +++++++++++++++++- css/style.css | 4 + 9 files changed, 472 insertions(+), 13 deletions(-) diff --git a/apps/segment/segment.js b/apps/segment/segment.js index ba91a628..e164cbb0 100644 --- a/apps/segment/segment.js +++ b/apps/segment/segment.js @@ -488,7 +488,6 @@ function setFilter(filter) { * @param e */ function drawRectangle(e) { - console.log(e); const canvas = $CAMIC.viewer.drawer.canvas; // Original Canvas canvas.style.cursor = e.checked ? 'crosshair' : 'default'; diff --git a/apps/viewer/init.js b/apps/viewer/init.js index 4bb0e76c..e9a0f8cc 100644 --- a/apps/viewer/init.js +++ b/apps/viewer/init.js @@ -310,6 +310,33 @@ function initCore() { // initialize all UI components async function initUIcomponents() { /* create UI components */ + $UI.downloadSelectionModal = new ModalBox({ + id: 'downloadSelectionModal', + hasHeader: true, + headerText: 'Download Selection', + hasFooter: true, + }); + const header = $UI.downloadSelectionModal.elt.querySelector('.modalbox-header') + header.querySelector('span.close').style.display = 'None'; + const footer = $UI.downloadSelectionModal.elt.querySelector('.modalbox-footer') + const cancelBtn = document.createElement('button'); + cancelBtn.classList.add('btn'); + cancelBtn.classList.add('btn-sm'); + cancelBtn.classList.add('btn-secondary'); + cancelBtn.textContent = 'Cancel'; + const downloadBtn = document.createElement('button'); + downloadBtn.classList.add('btn'); + downloadBtn.classList.add('btn-sm'); + downloadBtn.classList.add('btn-info'); + downloadBtn.textContent = 'Download'; + footer.innerHTML = ''; + footer.classList.add('footer'); + footer.appendChild(cancelBtn); + footer.appendChild(downloadBtn); + + cancelBtn.addEventListener('click', hideDownloadSelection); + downloadBtn.addEventListener('click', downloadSelection); + $UI.modalbox = new ModalBox({ id: 'modalbox', @@ -396,6 +423,15 @@ async function initUIcomponents() { callback: toggleMeasurement, }); } + // donwload selection + subToolsOpt.push({ + name: 'download_selection', + icon: 'get_app', // material icons' name + title: 'Download Selection', + type: 'check', + value: 'download', + callback: toggleDownloadSelection, + }); // enhance subToolsOpt.push({ name: 'Enhance', diff --git a/apps/viewer/uicallbacks.js b/apps/viewer/uicallbacks.js index dc62328f..fd533497 100644 --- a/apps/viewer/uicallbacks.js +++ b/apps/viewer/uicallbacks.js @@ -312,10 +312,12 @@ function toolsOff() { case 'normal': annotationOff(); break; - case 'label': presetLabelOff(); break; + case 'download_selection': + downloadSelectionOff(); + break; } } @@ -458,6 +460,33 @@ function toggleMeasurement(data) { } } +/** + * switches download Selection tool on, called from toggleMeasurement + */ + function downloadSelectionOn() { + if (!$CAMIC.viewer.canvasDrawInstance) return; + $CAMIC.viewer.canvasDrawInstance.drawOn(); + getDrawOption() + $CAMIC.viewer.canvasDrawInstance.drawMode = 'rect'; + $CAMIC.viewer.canvasDrawInstance.style.color = '#000'; + const li = $UI.toolbar.getSubTool('download_selection'); + li.querySelector('input[type=checkbox]').checked = true; + $CAMIC.status = 'download_selection'; +} + +/** + * switches downloadSelection tool off, called from toggleMeasurement + */ +function downloadSelectionOff() { + if (!$CAMIC.viewer.canvasDrawInstance) return; + $CAMIC.viewer.canvasDrawInstance.drawOff(); + $CAMIC.viewer.canvasDrawInstance.clear(); + setDrawOption() + const li = $UI.toolbar.getSubTool('download_selection'); + li.querySelector('input[type=checkbox]').checked = false; + $CAMIC.status = null; +} + /** * switches measuring tool on, called from toggleMeasurement */ @@ -975,6 +1004,54 @@ function algoCallback(data) { * @param {Object} data */ const heatmapDefaultColor = '#1034a6'; + +const drawOptionRecord = {} +function getDrawOption() { + drawOptionRecord.drawMode = $CAMIC.viewer.canvasDrawInstance.drawMode; + drawOptionRecord.color = $CAMIC.viewer.canvasDrawInstance.style.color; +} +function setDrawOption() { + $CAMIC.viewer.canvasDrawInstance.drawMode = drawOptionRecord.drawMode || 'free'; + $CAMIC.viewer.canvasDrawInstance.style.color = drawOptionRecord.color || '#7cfc00'; +} + +function toggleDownloadSelection(data){ + // const canvasDraw = $CAMIC.viewer.canvasDrawInstance; + + // if(e.checked) { + // downloadSelectionOn(); + // } else { + // downloadSelectionOff(); + // } + if (!$CAMIC.viewer.canvasDrawInstance) { + console.warn('No Draw Tool'); + return; + } + if (data.checked) { + // trun off the main menu + $UI.layersSideMenu.close(); + if ($CAMIC.status == 'download_selection') { + downloadSelectionOn(); + return; + } + // turn off download SelectionOn + toolsOff(); + var checkAllToolsOff = setInterval(function() { + if ($CAMIC && $CAMIC.status == null) { + // all tool has turn off + clearInterval(checkAllToolsOff); + downloadSelectionOn(); + } + }, 100); + // turn off magnifier + // magnifierOff(); + } else { + downloadSelectionOff(); + } + +} + + async function callback(data) { const viewerName = this.toString(); let camic = null; @@ -988,7 +1065,6 @@ async function callback(data) { default: break; } - // console.log(data) // return; data.forEach(function(d) { @@ -1531,6 +1607,16 @@ function saveAnalytics() { console.log('saveAnalytics'); } function startDrawing(e) { + // + if ( + $UI.toolbar.getSubTool('download_selection') && + $UI.toolbar.getSubTool('download_selection').querySelector('input[type=checkbox]') + .checked + ) { + console.log('start download_selection'); + return; + } + if ( $UI.toolbar.getSubTool('preset_label') && $UI.toolbar.getSubTool('preset_label').querySelector('input[type=checkbox]') @@ -1551,7 +1637,98 @@ function startDrawing(e) { // : !$UI.annotOptPanel._form_.isValid(); return; } +function downloadSelection() { + const chks = $UI.downloadSelectionModal.body.querySelectorAll('input[type=checkbox][name=downloadSelection]:checked'); + if(!chks.length) { + alert('Please Check Annotation to Download.'); + return; + } + // + const execIds = []; + chks.forEach(chk=>execIds.push(chk.dataset.id)) + // get annotation by + const bbox = $CAMIC.viewer.canvasDrawInstance._draws_data_[0].bound.coordinates[0] + const height = $CAMIC.viewer.imagingHelper.imgHeight; + const width = $CAMIC.viewer.imagingHelper.imgWidth; + const x0 = bbox[0][0]/width; + const y0 = bbox[0][1]/height; + const x1 = bbox[2][0]/width; + const y1 = bbox[2][1]/height; + // + $CAMIC.store.getMarkByIds(execIds, $D.params.slideId, null, 'computer', null, x0, x1, y0, y1).then((data)=>{ + const element = document.createElement('a'); + const blob = new Blob([JSON.stringify(data)], {type: "application/json"}); + const uri = URL.createObjectURL(blob); + element.setAttribute('href', uri); + element.setAttribute('download', `${$D.params.data.name}_${new Date().toISOString()}.json`); + element.style.display = 'none'; + document.body.appendChild(element); + element.click(); + document.body.removeChild(element); + hideDownloadSelection(); + }) + + +} + +function showDownloadSelection() { + // get selection area + const height = $CAMIC.viewer.imagingHelper.imgHeight; + const width = $CAMIC.viewer.imagingHelper.imgWidth; + // get annotation by + const bbox = $CAMIC.viewer.canvasDrawInstance._draws_data_[0].bound.coordinates[0] + const x0 = bbox[0][0]/width; + const y0 = bbox[0][1]/height; + const x1 = bbox[2][0]/width; + const y1 = bbox[2][1]/height; + // show up loading + $UI.downloadSelectionModal.body.innerHTML = 'Loading ...'; + $CAMIC.store.markSegmentationCount($D.params.slideId, x0, x1, y0, y1).then((data)=>{ + if(data&&Array.isArray(data)&&data.length) { + createSegmentTable(data); + } else { + $UI.downloadSelectionModal.body.innerHTML = 'No Data loaded ...'; + } + + }) + $UI.downloadSelectionModal.open(); +} +function createSegmentTable(data) { + $UI.downloadSelectionModal.body.innerHTML = ''; + $UI.downloadSelectionModal.body.innerHTML = ` + + + + + + + + + ${data.sort((a,b)=> b._id - a._id).map((d)=>` + + + + `).join('')} + +
NameCountDownload
Segmentation / ${d._id}${d.count}
` +} +function hideDownloadSelection() { + downloadSelectionOff(); + $UI.downloadSelectionModal.close(); +} + function stopDrawing(e) { + + if ( + $UI.toolbar.getSubTool('download_selection') && + $UI.toolbar.getSubTool('download_selection').querySelector('input[type=checkbox]') + .checked + ) { + // + showDownloadSelection(); + return; + } + // preset label annotation if ( $UI.toolbar.getSubTool('preset_label') && @@ -2036,7 +2213,6 @@ function deleteRulerHandler(execId) { $CAMIC.store .deleteMarkByExecId(execId, $D.params.data.slide) .then((datas) => { - console.log(datas); // server error if (datas.error) { const errorMessage = `${datas.text}: ${datas.url}`; @@ -2240,7 +2416,6 @@ function onAddRuler(ruler) { } async function rootCallback({root, parent, parentName, items}) { - console.log({root, parent, items}); // start a message openLoadStatus(`${root==parent?root:`${root} - ${parentName}`}`); // diff --git a/apps/viewer/viewer.html b/apps/viewer/viewer.html index 9046410d..6cbb8217 100644 --- a/apps/viewer/viewer.html +++ b/apps/viewer/viewer.html @@ -358,6 +358,7 @@
+
diff --git a/components/simplecontextmenu/simplecontextmenu.css b/components/simplecontextmenu/simplecontextmenu.css index 0604d295..7406dc4b 100644 --- a/components/simplecontextmenu/simplecontextmenu.css +++ b/components/simplecontextmenu/simplecontextmenu.css @@ -154,7 +154,7 @@ height:102px; } .style:hover { - width: 66px; + width: 86px; height: 24px; } diff --git a/components/simplecontextmenu/simplecontextmenu.js b/components/simplecontextmenu/simplecontextmenu.js index 66f8a1e9..625664aa 100644 --- a/components/simplecontextmenu/simplecontextmenu.js +++ b/components/simplecontextmenu/simplecontextmenu.js @@ -225,7 +225,6 @@ */ $.SimpleContextMenu.prototype.raiseEvent = function( eventName, eventArgs ) { // uncomment if you want to get a log of all events - // $.console.log( eventName ); const handler = this.getHandler( eventName ); if ( handler ) { @@ -311,6 +310,7 @@ style.classList.add('item'); style.title = 'Style'; const free = document.createElement('li'); + free.title = 'Free'; free.classList.add('active'); free.dataset.model = 'free'; const styleFree = document.createElement('a'); @@ -321,6 +321,7 @@ const rect = document.createElement('li'); rect.dataset.model = 'rect'; + free.title = 'Rectangle'; // free.classList.add('active'); const styleRect = document.createElement('a'); styleRect.classList.add('material-icons'); @@ -329,16 +330,26 @@ const point = document.createElement('li'); point.dataset.model = 'point'; + point.title = 'Point'; // free.classList.add('active'); const stylePoint = document.createElement('a'); stylePoint.classList.add('material-icons'); stylePoint.textContent = 'fiber_manual_record'; point.appendChild(stylePoint); + const pointToPoint = document.createElement('li'); + pointToPoint.title = 'Point To Point'; + pointToPoint.dataset.model = 'pointToPoint'; + // free.classList.add('active'); + const stylePointToPoint = document.createElement('a'); + stylePointToPoint.classList.add('material-icons'); + stylePointToPoint.textContent = 'timeline'; + pointToPoint.appendChild(stylePointToPoint); style.appendChild(free); style.appendChild(rect); style.appendChild(point); + style.appendChild(pointToPoint); elt.appendChild(style); return elt; diff --git a/core/Store.js b/core/Store.js index 85cee4a8..416551fe 100644 --- a/core/Store.js +++ b/core/Store.js @@ -195,7 +195,31 @@ class Store { mode: 'cors', }).then(this.errorHandler).then((x) => this.filterBroken(x, 'mark')); } - + markSegmentationCount(slide, x0, x1, y0, y1) { + const suffix = 'Mark/segmentationCount'; + const url = this.base + suffix; + const query = {}; + if (slide) { + query['provenance.image.slide'] = slide; + } + query['provenance.analysis.source'] = 'computer'; + if (x0) { + query.x0 = x0; + } + if (x1) { + query.x1 = x1; + } + if (y0) { + query.y0 = y0; + } + if (y1) { + query.y1 = y1; + } + return fetch(url + '?' + objToParamStr(query), { + credentials: 'include', + mode: 'cors', + }).then(this.errorHandler) + } getMarkByIds(ids, slide, notes, source, footprint, x0, x1, y0, y1) { if (!slide) { return { @@ -237,7 +261,6 @@ class Store { if (y1) { query.y1 = y1; } - return fetch(url, { method: 'POST', credentials: 'include', @@ -882,7 +905,6 @@ class Store { updateSlideName(id, newName) { const suffix = 'Slide/update'; const url = this.base + suffix; - console.log(id + ' ' + newName); const query = { '_id': id, }; @@ -1108,7 +1130,6 @@ class Store { updateSlideReview(id, newStatus) { const suffix = 'Slide/update'; const url = this.base + suffix; - console.log(id + ' ' + newStatus); const query = { '_id': id, }; diff --git a/core/extension/openseadragon-canvas-draw-overlay.js b/core/extension/openseadragon-canvas-draw-overlay.js index 3c43c005..cb745fe0 100644 --- a/core/extension/openseadragon-canvas-draw-overlay.js +++ b/core/extension/openseadragon-canvas-draw-overlay.js @@ -110,6 +110,8 @@ start: this.startDrawing.bind(this), stop: this.stopDrawing.bind(this), drawing: this.drawing.bind(this), + pointMove: this.pointMove.bind(this), + pointClick: this.pointClick.bind(this), updateView: this.updateView.bind(this), }; @@ -184,7 +186,7 @@ this.isMoving = false; // creat supplies free, square, rectangle, line - this.drawMode = options.drawMode || 'rect'; // 'free', 'square', 'rect', 'line', 'grid' + this.drawMode = options.drawMode || 'rect'; // 'free', 'square', 'rect', 'line', 'grid', clickable this.size = options.size || null; // ctx styles opt this.style = { @@ -368,9 +370,14 @@ // add Event listeners this._div.addEventListener('mousemove', this._event.drawing); + this._div.addEventListener('mouseout', this._event.stop); this._div.addEventListener('mouseup', this._event.stop); this._div.addEventListener('mousedown', this._event.start); + + // point to point + this._div.addEventListener('mousemove', this._event.pointMove); + this._div.addEventListener('click', this._event.pointClick); this._viewer.addHandler('update-viewport', this._event.updateView); this._viewer.addHandler('open', this._event.updateView); @@ -415,6 +422,9 @@ * as the mouse steps in */ startDrawing: function(e) { + if(this.drawMode == 'pointToPoint') { + return; + } // prevent to open context menu when click on drawing mode let isRight; @@ -509,13 +519,203 @@ this.__newFeature(this._last.slice()); } }, + pointMove: function(e) { + if(this.isOn && this.drawMode == 'pointToPoint') { + let point = new OpenSeadragon.Point(e.clientX, e.clientY); + let img_point = this._viewer.viewport.windowToImageCoordinates(point); + if ( + 0 > img_point.x || + this.imgWidth < img_point.x || + 0 > img_point.y || + this.imgHeight < img_point.y + ) { + return; + } + img_point.x = Math.round(img_point.x); + img_point.y = Math.round(img_point.y); + + // drawing anchor and lines + var line = $.isEmptyObject(this._current_path_)? + []: + [].concat(this._current_path_.geometry.coordinates[0]); + line = line.concat([[img_point.x,img_point.y]]); + if(line.length == 1) return; + this.drawOnCanvas( + this._draw_ctx_, + function() { + // case 1: only one point + // if(line.length > 1) { + // // end point + // this._draw_ctx_.strokeStyle = 'red'; + // DrawHelper.drawCircle( + // this._draw_ctx_, + // img_point.x, + // img_point.y, + // this.style.lineWidth * 3, + // ); + // } else { + // draw line + DrawHelper.setStyle(this._draw_ctx_, this.style); + DrawHelper.drawMultiline( + this._draw_ctx_, + line, + ) + + // draw circle + // get start point (x, y) + const sx = line[0][0]; + const sy = line[0][1]; + // get end point (x, y) + const ex = line[line.length - 1][0]; + const ey = line[line.length - 1][1]; + if(line.length == 2) { // case 2: has two points + this._draw_ctx_.strokeStyle = 'red'; + } else { // case 3: more than 2 points + // calculate distance between start and end points + const distance = getDistance( + this._viewer, + new OpenSeadragon.Point(sx, sy), + new OpenSeadragon.Point(ex, ey) + ) + + this._draw_ctx_.strokeStyle = distance > 14 ? 'red' : 'blue'; + } + // start point + DrawHelper.drawCircle( + this._draw_ctx_, + sx, + sy, + this.style.lineWidth * 3, + ); + // end point + DrawHelper.drawCircle( + this._draw_ctx_, + img_point.x, + img_point.y, + this.style.lineWidth * 3, + ); + // } + + }.bind(this)) + } + + }, + pointClick: function(e) { + + this.raiseEvent('start-drawing', {originalEvent: e}); + if (this.stop) { + this.stop = false; + return; + } + + if(this.isOn && this.drawMode == 'pointToPoint') { + let point = new OpenSeadragon.Point(e.clientX, e.clientY); + let img_point = this._viewer.viewport.windowToImageCoordinates(point); + if ( + 0 > img_point.x || + this.imgWidth < img_point.x || + 0 > img_point.y || + this.imgHeight < img_point.y + ) { + return; + } + img_point.x = Math.round(img_point.x); + img_point.y = Math.round(img_point.y); + this._last = [img_point.x, img_point.y]; + if($.isEmptyObject(this._current_path_)) { + this.__newFeature(this._last.slice()); + } else { + this._current_path_.geometry.coordinates[0].push(this._last.slice()); + } + // get current lines + var line = this._current_path_.geometry.coordinates[0]; + // save point to point if the + if(line.length > 2 && getDistance( + this._viewer, + new OpenSeadragon.Point(line[0][0], line[0][1]), + new OpenSeadragon.Point(line[line.length - 1][0], line[line.length - 1][1]) + ) <= 14) { // save annotations + this.__endNewFeature(); + try { + // custom event on stop + this.raiseEvent('stop-drawing', {originalEvent: e}); + } catch (e) { + // statements + console.error('draw-overlay:stop-drawing error:'); + console.error(e); + } + return; + } + + // drawing anchor and lines + if(line.length == 1) return; + this.drawOnCanvas( + this._draw_ctx_, + function() { + // case 1: only one point + // if(line.length == 1) { + // // end point + // this._draw_ctx_.strokeStyle = 'red'; + // DrawHelper.drawCircle( + // this._draw_ctx_, + // img_point.x, + // img_point.y, + // this.style.lineWidth * 3, + // ); + // } else { + // draw line + DrawHelper.setStyle(this._draw_ctx_, this.style); + DrawHelper.drawMultiline( + this._draw_ctx_, + line, + ) + // draw circle + // get start point (x, y) + const sx = line[0][0]; + const sy = line[0][1]; + // get end point (x, y) + const ex = line[line.length - 1][0]; + const ey = line[line.length - 1][1]; + if(line.length == 2) { // case 2: has two points + this._draw_ctx_.strokeStyle = 'red'; + } else { // case 3: more than 2 points + // calculate distance between start and end points + const distance = getDistance( + this._viewer, + new OpenSeadragon.Point(sx, sy), + new OpenSeadragon.Point(ex, ey) + ) + this._draw_ctx_.strokeStyle = distance > 14 ? 'red' : 'blue'; + } + // start point + DrawHelper.drawCircle( + this._draw_ctx_, + sx, + sy, + this.style.lineWidth * 3, + ); + // end point + DrawHelper.drawCircle( + this._draw_ctx_, + img_point.x, + img_point.y, + this.style.lineWidth * 3, + ); + //} + }.bind(this)) + } + }, /** * @private * each drawing and collects the path data as point, as the mouse moves * @param {Event} e the event */ drawing: function(e) { + // stop if the draw mode is pointToPoint + if(this.drawMode == 'pointToPoint') { + return; + } // anything happening? if (!(this.isDrawing) && !(this.isMoving)) return; @@ -719,6 +919,10 @@ * stop drawing on the drawing canvas, when the mouse is up */ stopDrawing: function(e) { + // stop if the draw mode is pointToPoint + if(this.drawMode == 'pointToPoint') { + return; + } // if any movement or drawing if ((this.isDrawing) || (this.isMoving)) { // add style and data to data collection @@ -1193,7 +1397,15 @@ $.extend($.CanvasDraw.prototype, $.EventSource.prototype); - + function getDistance(viewer, start, end) { + start = viewer.viewport.imageToWindowCoordinates(start); + end = viewer.viewport.imageToWindowCoordinates(end); + + const dx = Math.round(Math.abs(start.x - end.x)); + const dy = Math.round(Math.abs(start.y - end.y)); + + return Math.sqrt(dx * dx + dy * dy); + } function getBounds(points) { let max; let min; points.forEach((point) => { diff --git a/css/style.css b/css/style.css index 17729581..ab6f82fb 100644 --- a/css/style.css +++ b/css/style.css @@ -52,6 +52,10 @@ body { height: 100%; } +.modalbox .modalbox-footer.footer { + display: flex; + justify-content: space-between; +} /*#minor_viewer.display { height: 100%; width: 100%; From adcdfeb1ca00744ea9eedd905d9f3e8a7889fcc3 Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Sun, 26 Feb 2023 20:55:53 -0500 Subject: [PATCH 04/24] lint fix --- apps/viewer/init.js | 8 ++-- apps/viewer/uicallbacks.js | 43 ++++++++----------- .../simplecontextmenu/simplecontextmenu.js | 2 +- core/Store.js | 2 +- 4 files changed, 25 insertions(+), 30 deletions(-) diff --git a/apps/viewer/init.js b/apps/viewer/init.js index e9a0f8cc..da010fe3 100644 --- a/apps/viewer/init.js +++ b/apps/viewer/init.js @@ -316,9 +316,9 @@ async function initUIcomponents() { headerText: 'Download Selection', hasFooter: true, }); - const header = $UI.downloadSelectionModal.elt.querySelector('.modalbox-header') + const header = $UI.downloadSelectionModal.elt.querySelector('.modalbox-header'); header.querySelector('span.close').style.display = 'None'; - const footer = $UI.downloadSelectionModal.elt.querySelector('.modalbox-footer') + const footer = $UI.downloadSelectionModal.elt.querySelector('.modalbox-footer'); const cancelBtn = document.createElement('button'); cancelBtn.classList.add('btn'); cancelBtn.classList.add('btn-sm'); @@ -327,7 +327,7 @@ async function initUIcomponents() { const downloadBtn = document.createElement('button'); downloadBtn.classList.add('btn'); downloadBtn.classList.add('btn-sm'); - downloadBtn.classList.add('btn-info'); + downloadBtn.classList.add('btn-info'); downloadBtn.textContent = 'Download'; footer.innerHTML = ''; footer.classList.add('footer'); @@ -431,7 +431,7 @@ async function initUIcomponents() { type: 'check', value: 'download', callback: toggleDownloadSelection, - }); + }); // enhance subToolsOpt.push({ name: 'Enhance', diff --git a/apps/viewer/uicallbacks.js b/apps/viewer/uicallbacks.js index fd533497..f2e55ed4 100644 --- a/apps/viewer/uicallbacks.js +++ b/apps/viewer/uicallbacks.js @@ -463,10 +463,10 @@ function toggleMeasurement(data) { /** * switches download Selection tool on, called from toggleMeasurement */ - function downloadSelectionOn() { +function downloadSelectionOn() { if (!$CAMIC.viewer.canvasDrawInstance) return; $CAMIC.viewer.canvasDrawInstance.drawOn(); - getDrawOption() + getDrawOption(); $CAMIC.viewer.canvasDrawInstance.drawMode = 'rect'; $CAMIC.viewer.canvasDrawInstance.style.color = '#000'; const li = $UI.toolbar.getSubTool('download_selection'); @@ -481,7 +481,7 @@ function downloadSelectionOff() { if (!$CAMIC.viewer.canvasDrawInstance) return; $CAMIC.viewer.canvasDrawInstance.drawOff(); $CAMIC.viewer.canvasDrawInstance.clear(); - setDrawOption() + setDrawOption(); const li = $UI.toolbar.getSubTool('download_selection'); li.querySelector('input[type=checkbox]').checked = false; $CAMIC.status = null; @@ -1005,7 +1005,7 @@ function algoCallback(data) { */ const heatmapDefaultColor = '#1034a6'; -const drawOptionRecord = {} +const drawOptionRecord = {}; function getDrawOption() { drawOptionRecord.drawMode = $CAMIC.viewer.canvasDrawInstance.drawMode; drawOptionRecord.color = $CAMIC.viewer.canvasDrawInstance.style.color; @@ -1015,9 +1015,9 @@ function setDrawOption() { $CAMIC.viewer.canvasDrawInstance.style.color = drawOptionRecord.color || '#7cfc00'; } -function toggleDownloadSelection(data){ +function toggleDownloadSelection(data) { // const canvasDraw = $CAMIC.viewer.canvasDrawInstance; - + // if(e.checked) { // downloadSelectionOn(); // } else { @@ -1048,7 +1048,6 @@ function toggleDownloadSelection(data){ } else { downloadSelectionOff(); } - } @@ -1607,7 +1606,7 @@ function saveAnalytics() { console.log('saveAnalytics'); } function startDrawing(e) { - // + // if ( $UI.toolbar.getSubTool('download_selection') && $UI.toolbar.getSubTool('download_selection').querySelector('input[type=checkbox]') @@ -1616,7 +1615,7 @@ function startDrawing(e) { console.log('start download_selection'); return; } - + if ( $UI.toolbar.getSubTool('preset_label') && $UI.toolbar.getSubTool('preset_label').querySelector('input[type=checkbox]') @@ -1639,17 +1638,17 @@ function startDrawing(e) { } function downloadSelection() { const chks = $UI.downloadSelectionModal.body.querySelectorAll('input[type=checkbox][name=downloadSelection]:checked'); - if(!chks.length) { + if (!chks.length) { alert('Please Check Annotation to Download.'); return; } // const execIds = []; - chks.forEach(chk=>execIds.push(chk.dataset.id)) + chks.forEach((chk)=>execIds.push(chk.dataset.id)); // get annotation by - const bbox = $CAMIC.viewer.canvasDrawInstance._draws_data_[0].bound.coordinates[0] + const bbox = $CAMIC.viewer.canvasDrawInstance._draws_data_[0].bound.coordinates[0]; const height = $CAMIC.viewer.imagingHelper.imgHeight; - const width = $CAMIC.viewer.imagingHelper.imgWidth; + const width = $CAMIC.viewer.imagingHelper.imgWidth; const x0 = bbox[0][0]/width; const y0 = bbox[0][1]/height; const x1 = bbox[2][0]/width; @@ -1657,7 +1656,7 @@ function downloadSelection() { // $CAMIC.store.getMarkByIds(execIds, $D.params.slideId, null, 'computer', null, x0, x1, y0, y1).then((data)=>{ const element = document.createElement('a'); - const blob = new Blob([JSON.stringify(data)], {type: "application/json"}); + const blob = new Blob([JSON.stringify(data)], {type: 'application/json'}); const uri = URL.createObjectURL(blob); element.setAttribute('href', uri); element.setAttribute('download', `${$D.params.data.name}_${new Date().toISOString()}.json`); @@ -1666,9 +1665,7 @@ function downloadSelection() { element.click(); document.body.removeChild(element); hideDownloadSelection(); - }) - - + }); } function showDownloadSelection() { @@ -1676,7 +1673,7 @@ function showDownloadSelection() { const height = $CAMIC.viewer.imagingHelper.imgHeight; const width = $CAMIC.viewer.imagingHelper.imgWidth; // get annotation by - const bbox = $CAMIC.viewer.canvasDrawInstance._draws_data_[0].bound.coordinates[0] + const bbox = $CAMIC.viewer.canvasDrawInstance._draws_data_[0].bound.coordinates[0]; const x0 = bbox[0][0]/width; const y0 = bbox[0][1]/height; const x1 = bbox[2][0]/width; @@ -1684,13 +1681,12 @@ function showDownloadSelection() { // show up loading $UI.downloadSelectionModal.body.innerHTML = 'Loading ...'; $CAMIC.store.markSegmentationCount($D.params.slideId, x0, x1, y0, y1).then((data)=>{ - if(data&&Array.isArray(data)&&data.length) { + if (data&&Array.isArray(data)&&data.length) { createSegmentTable(data); } else { $UI.downloadSelectionModal.body.innerHTML = 'No Data loaded ...'; } - - }) + }); $UI.downloadSelectionModal.open(); } function createSegmentTable(data) { @@ -1704,13 +1700,13 @@ function createSegmentTable(data) { - ${data.sort((a,b)=> b._id - a._id).map((d)=>` + ${data.sort((a, b)=> b._id - a._id).map((d)=>` Segmentation / ${d._id} ${d.count} `).join('')} -` +`; } function hideDownloadSelection() { downloadSelectionOff(); @@ -1718,7 +1714,6 @@ function hideDownloadSelection() { } function stopDrawing(e) { - if ( $UI.toolbar.getSubTool('download_selection') && $UI.toolbar.getSubTool('download_selection').querySelector('input[type=checkbox]') diff --git a/components/simplecontextmenu/simplecontextmenu.js b/components/simplecontextmenu/simplecontextmenu.js index 625664aa..07250364 100644 --- a/components/simplecontextmenu/simplecontextmenu.js +++ b/components/simplecontextmenu/simplecontextmenu.js @@ -344,7 +344,7 @@ const stylePointToPoint = document.createElement('a'); stylePointToPoint.classList.add('material-icons'); stylePointToPoint.textContent = 'timeline'; - pointToPoint.appendChild(stylePointToPoint); + pointToPoint.appendChild(stylePointToPoint); style.appendChild(free); style.appendChild(rect); diff --git a/core/Store.js b/core/Store.js index 416551fe..07c326a5 100644 --- a/core/Store.js +++ b/core/Store.js @@ -218,7 +218,7 @@ class Store { return fetch(url + '?' + objToParamStr(query), { credentials: 'include', mode: 'cors', - }).then(this.errorHandler) + }).then(this.errorHandler); } getMarkByIds(ids, slide, notes, source, footprint, x0, x1, y0, y1) { if (!slide) { From e142ef0f6d0bd9b33b5aec5b20727b6738cd08d0 Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Sun, 26 Feb 2023 22:15:44 -0500 Subject: [PATCH 05/24] package audit --- package-lock.json | 805 +++++++++++++++++++++------------------------- package.json | 4 +- 2 files changed, 369 insertions(+), 440 deletions(-) diff --git a/package-lock.json b/package-lock.json index 0e3176b7..82f5854d 100644 --- a/package-lock.json +++ b/package-lock.json @@ -27,6 +27,11 @@ "js-tokens": "^4.0.0" } }, + "@tootallnate/once": { + "version": "1.1.2", + "resolved": "https://registry.npmjs.org/@tootallnate/once/-/once-1.1.2.tgz", + "integrity": "sha512-RbzJvlNzmRq5c3O09UipeuXno4tA1FE6ikOjxZK0tuxVv3412l64l5t1W5pj4+rJq9vpkm/kwiR07aZXnsKPxw==" + }, "@types/color-name": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/@types/color-name/-/color-name-1.1.1.tgz", @@ -38,18 +43,33 @@ "integrity": "sha512-j2afSsaIENvHZN2B8GOpF566vZ5WVk5opAiMTvWgaQT8DkbOqsTfvNAvHoRGU2zzP8cPoqys+xHTRDWW8L+/BA==" }, "accepts": { - 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"chai": "^4.3.0", + "chai": "^4.3.7", "eslint": "^6.8.0", "eslint-config-google": "^0.14.0", - "express": "^4.16.2", + "express": "^4.18.2", "jsdom": "^16.5.0", "lodash": "^4.17.21", "mocha": "^10.2.0", From 9940275be3450dc8007fde50569a65cd57970e11 Mon Sep 17 00:00:00 2001 From: gokul Date: Wed, 1 Mar 2023 07:16:20 +0530 Subject: [PATCH 06/24] On the slide page, The reload button is not responsive. The button's right edges are cut into small devices. It also makes less Ui. So, I fixxed the issue --- apps/table.html | 2 +- package-lock.json | 3535 ++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 3512 insertions(+), 25 deletions(-) diff --git a/apps/table.html b/apps/table.html index 7590fff4..db7706c1 100644 --- a/apps/table.html +++ b/apps/table.html @@ -135,7 +135,7 @@

caMicroscope

-
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"integrity": "sha512-xbbCH5dCYU5T8LcEhhuh7HJ88HXuW3qsI3Y0zOZFKfZEHcpWiHU/Jxzk629Brsab/mMiHQti9wMP+845RPe3Vg==" - }, "lodash": { "version": "4.17.21", "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.21.tgz", @@ -2579,7 +6065,8 @@ "ws": { "version": "7.5.8", "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.8.tgz", - "integrity": "sha512-ri1Id1WinAX5Jqn9HejiGb8crfRio0Qgu8+MtL36rlTA6RLsMdWt1Az/19A2Qij6uSHUMphEFaTKa4WG+UNHNw==" + "integrity": "sha512-ri1Id1WinAX5Jqn9HejiGb8crfRio0Qgu8+MtL36rlTA6RLsMdWt1Az/19A2Qij6uSHUMphEFaTKa4WG+UNHNw==", + "requires": {} }, "xml-name-validator": { "version": "3.0.0", From 321f2ef2d47fcfc98384abcd7aab285e51c363da Mon Sep 17 00:00:00 2001 From: Shivam Kaushik <105926192+ShivamKaushik316@users.noreply.github.com> Date: Thu, 2 Mar 2023 20:12:49 +0530 Subject: [PATCH 07/24] fixed Workbench Navbar Overlapping --- apps/dev-workbench/workbench.html | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/apps/dev-workbench/workbench.html b/apps/dev-workbench/workbench.html index a0516f64..19e19f65 100644 --- a/apps/dev-workbench/workbench.html +++ b/apps/dev-workbench/workbench.html @@ -70,9 +70,16 @@
-       - - Workbench + + + +
+ Workbench + +
+
+ +
  •   Help/User Guide +
+
From ea9e9c93d0bc3eac500d6c5d0eb6a46baf3e0b10 Mon Sep 17 00:00:00 2001 From: Shivam Kaushik <105926192+ShivamKaushik316@users.noreply.github.com> Date: Thu, 2 Mar 2023 20:13:51 +0530 Subject: [PATCH 08/24] Fixed Wokbench Navbar Issue --- apps/dev-workbench/workbench.css | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/apps/dev-workbench/workbench.css b/apps/dev-workbench/workbench.css index 8a57720f..03318640 100644 --- a/apps/dev-workbench/workbench.css +++ b/apps/dev-workbench/workbench.css @@ -35,3 +35,23 @@ #toastPlaceholder { display: none; } + + +#goBack{ + display: flex; + padding :20px; +} +@media only screen and (max-width: 551px) { + nav { + flex-direction: column; + } + + nav ul { + flex-direction: column; + } + + nav ul li { + margin: 10px 0; + } +} + From 1fe12b5325a647f4e44d04a5e4cf824919bc7a49 Mon Sep 17 00:00:00 2001 From: JayashTripathy Date: Sun, 12 Mar 2023 01:07:10 +0530 Subject: [PATCH 09/24] style: :art: Fixed fat hamburger icon & alignment issues of dropdown navbar fixed the big fat hamburger only on home section(other places it is working fine) & done some style changes in ul section of navbar and made it perfectly aligned --- README.md | 2 +- apps/Info.html | 2 +- apps/landing/landing.html | 2 +- apps/landing/main.css | 5 +- apps/signup/signup.css | 5 +- apps/signup/signup.html | 2 +- apps/table.css | 4 +- apps/table.html | 2 +- package-lock.json | 3535 ++++++++++++++++++++++++++++++++++++- 9 files changed, 3520 insertions(+), 39 deletions(-) diff --git a/README.md b/README.md index a8bc6790..aaa695f2 100644 --- a/README.md +++ b/README.md @@ -84,7 +84,7 @@ Source code organization ie the file structure of caMicroscope can be found in [ ## Fast Local Changes When using the hosted setup, you can have the distribution host the changes from your local. Follow these steps : - Clone this repository, the [Caracal repository](https://github.com/camicroscope/Caracal/) and [the distribution](https://github.com/camicroscope/Distro/) in the same parent directory -- Set the build to build your local changes instead of the hosted git versions by editing the ca-back container section of your develop.yml. Replace the build context section with the path to your caracal checkout ("../Caracal"), and add `- ../caMicroscope:/src/camicroscope` to the volumes. +- Set the build to build your local changes inste ad of the hosted git versions by editing the ca-back container section of your develop.yml. Replace the build context section with the path to your caracal checkout ("../Caracal"), and add `- ../caMicroscope:/src/camicroscope` to the volumes. - Remove this line from 'Dockerfile' in Caracal repository : ``` RUN git clone https://github.com/${fork:-camicroscope}/camicroscope.git --branch=${viewer:-master} diff --git a/apps/Info.html b/apps/Info.html index dbca95c1..1605832a 100644 --- a/apps/Info.html +++ b/apps/Info.html @@ -59,7 +59,7 @@