From 5ba5b95023161669f68f5b6ce867dced5d2923c4 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Sun, 21 May 2017 03:24:50 +0100 Subject: [PATCH 001/371] download data prototype --- .../interface/dicomViewer/DicomViewer.js | 10 +++++----- .../webapp/js/components/widgets/AWidget.js | 19 +++++++++++++++---- 2 files changed, 20 insertions(+), 9 deletions(-) diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js index 6acabc150..ed434570e 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js @@ -28,6 +28,7 @@ define(function (require) { this.changeMode = this.changeMode.bind(this); this.changeOrientation = this.changeOrientation.bind(this); + this.download = this.download.bind(this); } loadSingleView() { @@ -75,16 +76,11 @@ define(function (require) { $("#" + this.props.id).on("dialogresizestop", function (event, ui) { camera.canvas = { - // width: ui.size.width - 260 - 30, - // height: ui.size.height - 30, width: container.offsetWidth, height: container.offsetHeight, }; camera.fitBox(2); - - // renderer.setSize(ui.size.width - 260 - 30, ui.size.height - 30); renderer.setSize(container.offsetWidth, container.offsetHeight); - }); /** @@ -920,6 +916,10 @@ define(function (require) { this.stackHelper.index = Math.floor(this.stackHelper.orientationMaxIndex/2); } + download(){ + window.location = this.props.files; + } + render() { var dicomViewerContent; if (this.state.mode == "single_view") { diff --git a/src/main/webapp/js/components/widgets/AWidget.js b/src/main/webapp/js/components/widgets/AWidget.js index ce835618e..3437194df 100644 --- a/src/main/webapp/js/components/widgets/AWidget.js +++ b/src/main/webapp/js/components/widgets/AWidget.js @@ -434,6 +434,13 @@ define(function (require) { })); } + addDownloadButton(downloadFunction){ + var that = this; + this.addButtonToTitleBar($("
").click(function () { + that.download(); + })); + } + /** * Makes the widget draggable or not * @@ -577,6 +584,9 @@ define(function (require) { this.container = this.$el.children().get(0); var dialogParent = this.$el.parent(); + this.modal = $("
"); + this.modal.appendTo(this.$el); + this.spinner = GEPPETTO.ComponentFactory.renderComponent(React.createFactory(spinner)(), this.modal.get(0)); //add history this.showHistoryIcon(true); @@ -592,6 +602,11 @@ define(function (require) { //add help button this.addHelpButton(); + //add download button + if (super.download) { + this.addDownloadButton(super.download); + } + // initialize content this.size = this.state.defaultSize; this.position = this.state.defaultPosition; @@ -642,10 +657,6 @@ define(function (require) { }); } - // setController(controller) { - // this.controller = controller; - // } - showHistoryIcon(show) { var that = this; if (show && this.$el.parent().find(".history-icon").length == 0) { From b046bbfe59c4074151db00f59cc2b0c661a8fd49 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Sun, 21 May 2017 03:31:44 +0100 Subject: [PATCH 002/371] revert spinner tests --- src/main/webapp/js/components/widgets/AWidget.js | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/main/webapp/js/components/widgets/AWidget.js b/src/main/webapp/js/components/widgets/AWidget.js index 3437194df..10f932f4c 100644 --- a/src/main/webapp/js/components/widgets/AWidget.js +++ b/src/main/webapp/js/components/widgets/AWidget.js @@ -584,10 +584,6 @@ define(function (require) { this.container = this.$el.children().get(0); var dialogParent = this.$el.parent(); - this.modal = $("
"); - this.modal.appendTo(this.$el); - this.spinner = GEPPETTO.ComponentFactory.renderComponent(React.createFactory(spinner)(), this.modal.get(0)); - //add history this.showHistoryIcon(true); From 66ba153aeedb7ae818dd0c35c05084bae8ec3317 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Sun, 21 May 2017 05:09:57 +0100 Subject: [PATCH 003/371] refactor,adding api, etc --- .../interface/dicomViewer/DicomViewer.js | 888 +----------------- .../dicomViewer/DicomViewerEngine.js | 859 +++++++++++++++++ 2 files changed, 882 insertions(+), 865 deletions(-) create mode 100644 src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js index ed434570e..a55ed16d2 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js @@ -2,18 +2,9 @@ define(function (require) { var React = require('react'); window.THREE = require('three'); - var AMI = require('./ami.min.js'); - - var LoadersVolume = AMI.default.Loaders.Volume; - var CamerasOrthographic = AMI.default.Cameras.Orthographic; - var ControlsOrthographic = AMI.default.Controls.TrackballOrtho; - var HelpersStack = AMI.default.Helpers.Stack; - var ControlsTrackball = AMI.default.Controls.Trackball; - var HelpersBoundingBox = AMI.default.Helpers.BoundingBox; - var ModelsStack = AMI.default.Models.Stack; - var HelpersLocalizer = AMI.default.Helpers.Localizer; require('./DicomViewer.less'); + var DicomViewerEngine = require('./DicomViewerEngine'); var AbstractComponent = require('../../AComponent'); @@ -22,7 +13,12 @@ define(function (require) { constructor(props) { super(props); + if (this.props.mode === undefined){ + this.props.mode = "quad_view"; + } + this.state = { + files: this.props.files, mode: this.props.mode }; @@ -31,864 +27,26 @@ define(function (require) { this.download = this.download.bind(this); } - loadSingleView() { - // Setup renderer - var container = document.getElementById(this.props.id).getElementsByClassName('dicomViewer')[0]; - var renderer = new THREE.WebGLRenderer({ - antialias: true, - }); - renderer.setSize(container.offsetWidth, container.offsetHeight); - renderer.setClearColor(0x353535, 1); - renderer.setPixelRatio(window.devicePixelRatio); - container.appendChild(renderer.domElement); - - // Setup scene - var scene = new THREE.Scene(); - - // Setup camera - var camera = new CamerasOrthographic( - container.clientWidth / -2, container.clientWidth / 2, - container.clientHeight / 2, container.clientHeight / -2, - 0.1, 10000); - - this.camera = camera; - - // Setup controls - var controls = new ControlsOrthographic(camera, container); - controls.staticMoving = true; - controls.noRotate = true; - camera.controls = controls; - - /** - * Handle window resize - */ - var _this = this; - function onWindowResize() { - camera.canvas = { - width: container.offsetWidth, - height: container.offsetHeight, - }; - camera.fitBox(2); - - renderer.setSize(container.offsetWidth, container.offsetHeight); - } - window.addEventListener('resize', onWindowResize, false); - - $("#" + this.props.id).on("dialogresizestop", function (event, ui) { - camera.canvas = { - width: container.offsetWidth, - height: container.offsetHeight, - }; - camera.fitBox(2); - renderer.setSize(container.offsetWidth, container.offsetHeight); - }); - - /** - * Start animation loop - */ - function animate() { - controls.update(); - renderer.render(scene, camera); - - // request new frame - requestAnimationFrame(function () { - if (_this.state.mode == "single_view") { - animate(); - } - }); - } - animate(); - - // Setup loader - var _this = this; - var loader = new LoadersVolume(container); - loader.load(this.props.files) - .then(function () { - // merge files into clean series/stack/frame structure - var series = loader.data[0].mergeSeries(loader.data); - var stack = series[0].stack[0]; - loader.free(); - loader = null; - // be carefull that series and target stack exist! - var stackHelper = new HelpersStack(stack); - _this.stackHelper = stackHelper; - // stackHelper.orientation = 2; - stackHelper.index = Math.floor(stack._dimensionsIJK.z/2); - - // tune bounding box - stackHelper.bbox.visible = false; - - // tune slice border - stackHelper.border.color = 0xFF9800; - // stackHelper.border.visible = false; - - scene.add(stackHelper); - - // hook up callbacks - controls.addEventListener('OnScroll', function (e) { - if (e.delta > 0) { - if (stackHelper.index >= stackHelper.orientationMaxIndex - 1) { - return false; - } - stackHelper.index += 1; - } else { - if (stackHelper.index <= 0) { - return false; - } - stackHelper.index -= 1; - } - - }); - - // center camera and interactor to center of bouding box - // for nicer experience - // set camera - var worldbb = stack.worldBoundingBox(); - var lpsDims = new THREE.Vector3( - worldbb[1] - worldbb[0], - worldbb[3] - worldbb[2], - worldbb[5] - worldbb[4] - ); - - // box: {halfDimensions, center} - var box = { - center: stack.worldCenter().clone(), - halfDimensions: - new THREE.Vector3(lpsDims.x + 10, lpsDims.y + 10, lpsDims.z + 10), - }; - - // init and zoom - var canvas = { - width: container.clientWidth, - height: container.clientHeight, - }; - - camera.directions = [stack.xCosine, stack.yCosine, stack.zCosine]; - camera.box = box; - camera.canvas = canvas; - camera.update(); - - // Not working properly. See issue: https://github.com/FNNDSC/ami/issues/120 - //camera.fitBox(2, 2); - camera.fitBox(2); - }) - .catch(function (error) { - window.console.log('oops... something went wrong...'); - window.console.log(error); - }); + setData(files) { + this.setState({ files: files }); } - loadQuadView() { - let ready = false; - // 3d renderer - let r0 = { - domId: 'r0', - domElement: null, - renderer: null, - color: 0x212121, - targetID: 0, - camera: null, - controls: null, - scene: null, - light: null, - }; - - // 2d axial renderer - let r1 = { - domId: 'r1', - domElement: null, - renderer: null, - color: 0x121212, - sliceOrientation: 'axial', - sliceColor: 0xFF1744, - targetID: 1, - camera: null, - controls: null, - scene: null, - light: null, - stackHelper: null, - localizerHelper: null, - localizerScene: null, - }; - - // 2d sagittal renderer - let r2 = { - domId: 'r2', - domElement: null, - renderer: null, - color: 0x121212, - sliceOrientation: 'sagittal', - sliceColor: 0xFFEA00, - targetID: 2, - camera: null, - controls: null, - scene: null, - light: null, - stackHelper: null, - localizerHelper: null, - localizerScene: null, - }; - - - // 2d coronal renderer - let r3 = { - domId: 'r3', - domElement: null, - renderer: null, - color: 0x121212, - sliceOrientation: 'coronal', - sliceColor: 0x76FF03, - targetID: 3, - camera: null, - controls: null, - scene: null, - light: null, - stackHelper: null, - localizerHelper: null, - localizerScene: null, - }; - - // data to be loaded - // let dataInfo = [ - // ['adi1', { - // location: - // 'https://cdn.rawgit.com/FNNDSC/data/master/dicom/adi_brain/mesh.stl', - // label: 'Left', - // loaded: false, - // material: null, - // materialFront: null, - // materialBack: null, - // mesh: null, - // meshFront: null, - // meshBack: null, - // color: 0xe91e63, - // opacity: 0.7, - // }], - // ['adi2', { - // location: - // 'https://cdn.rawgit.com/FNNDSC/data/master/dicom/adi_brain/mesh2.stl', - // label: 'Right', - // loaded: false, - // material: null, - // materialFront: null, - // materialBack: null, - // mesh: null, - // meshFront: null, - // meshBack: null, - // color: 0x03a9f4, - // opacity: 1, - // }], - // ]; - // let data = new Map(dataInfo); - - // extra variables to show mesh plane intersections in 2D renderers - let sceneClip = new THREE.Scene(); - let clipPlane1 = new THREE.Plane(new THREE.Vector3(0, 0, 0), 0); - let clipPlane2 = new THREE.Plane(new THREE.Vector3(0, 0, 0), 0); - let clipPlane3 = new THREE.Plane(new THREE.Vector3(0, 0, 0), 0); - - function initRenderer3D(renderObj) { - // renderer - renderObj.domElement = document.getElementById(renderObj.domId); - renderObj.renderer = new THREE.WebGLRenderer({ - antialias: true, - }); - renderObj.renderer.setSize( - renderObj.domElement.clientWidth, renderObj.domElement.clientHeight); - renderObj.renderer.setClearColor(renderObj.color, 1); - renderObj.renderer.domElement.id = renderObj.targetID; - renderObj.domElement.appendChild(renderObj.renderer.domElement); - - // camera - renderObj.camera = new THREE.PerspectiveCamera( - 45, renderObj.domElement.clientWidth / renderObj.domElement.clientHeight, - 0.1, 100000); - renderObj.camera.position.x = 250; - renderObj.camera.position.y = 250; - renderObj.camera.position.z = 250; - - // controls - renderObj.controls = new ControlsTrackball( - renderObj.camera, renderObj.domElement); - renderObj.controls.rotateSpeed = 5.5; - renderObj.controls.zoomSpeed = 1.2; - renderObj.controls.panSpeed = 0.8; - renderObj.controls.staticMoving = true; - renderObj.controls.dynamicDampingFactor = 0.3; - - // scene - renderObj.scene = new THREE.Scene(); - - // light - renderObj.light = new THREE.DirectionalLight(0xffffff, 1); - renderObj.light.position.copy(renderObj.camera.position); - renderObj.scene.add(renderObj.light); - - } - - function initRenderer2D(rendererObj) { - // renderer - rendererObj.domElement = document.getElementById(rendererObj.domId); - rendererObj.renderer = new THREE.WebGLRenderer({ - antialias: true, - }); - rendererObj.renderer.autoClear = false; - rendererObj.renderer.localClippingEnabled = true; - rendererObj.renderer.setSize( - rendererObj.domElement.clientWidth, rendererObj.domElement.clientHeight); - rendererObj.renderer.setClearColor(0x121212, 1); - rendererObj.renderer.domElement.id = rendererObj.targetID; - rendererObj.domElement.appendChild(rendererObj.renderer.domElement); - - // camera - rendererObj.camera = new CamerasOrthographic( - rendererObj.domElement.clientWidth / -2, - rendererObj.domElement.clientWidth / 2, - rendererObj.domElement.clientHeight / 2, - rendererObj.domElement.clientHeight / -2, - 1, 1000); - - // controls - rendererObj.controls = new ControlsOrthographic( - rendererObj.camera, rendererObj.domElement); - rendererObj.controls.staticMoving = true; - rendererObj.controls.noRotate = true; - rendererObj.camera.controls = rendererObj.controls; - - // scene - rendererObj.scene = new THREE.Scene(); - } - - function initHelpersStack(rendererObj, stack) { - rendererObj.stackHelper = new HelpersStack(stack); - rendererObj.stackHelper.bbox.visible = false; - rendererObj.stackHelper.borderColor = rendererObj.sliceColor; - rendererObj.stackHelper.slice.canvasWidth = - rendererObj.domElement.clientWidth; - rendererObj.stackHelper.slice.canvasHeight = - rendererObj.domElement.clientHeight; - - // set camera - let worldbb = stack.worldBoundingBox(); - let lpsDims = new THREE.Vector3( - (worldbb[1] - worldbb[0]) / 2, - (worldbb[3] - worldbb[2]) / 2, - (worldbb[5] - worldbb[4]) / 2 - ); - - // box: {halfDimensions, center} - let box = { - center: stack.worldCenter().clone(), - halfDimensions: - new THREE.Vector3(lpsDims.x + 10, lpsDims.y + 10, lpsDims.z + 10), - }; - - // init and zoom - let canvas = { - width: rendererObj.domElement.clientWidth, - height: rendererObj.domElement.clientHeight, - }; - - rendererObj.camera.directions = - [stack.xCosine, stack.yCosine, stack.zCosine]; - rendererObj.camera.box = box; - rendererObj.camera.canvas = canvas; - rendererObj.camera.orientation = rendererObj.sliceOrientation; - rendererObj.camera.update(); - rendererObj.camera.fitBox(2, 1); - - rendererObj.stackHelper.orientation = rendererObj.camera.stackOrientation; - rendererObj.stackHelper.index = - Math.floor(rendererObj.stackHelper.orientationMaxIndex / 2); - rendererObj.scene.add(rendererObj.stackHelper); - } - - function initHelpersLocalizer(rendererObj, stack, referencePlane, localizers) { - rendererObj.localizerHelper = new HelpersLocalizer( - stack, rendererObj.stackHelper.slice.geometry, referencePlane); - - for (let i = 0; i < localizers.length; i++) { - rendererObj.localizerHelper['plane' + (i + 1)] = localizers[i].plane; - rendererObj.localizerHelper['color' + (i + 1)] = localizers[i].color; - } - - rendererObj.localizerHelper.canvasWidth = - rendererObj.domElement.clientWidth; - rendererObj.localizerHelper.canvasHeight = - rendererObj.domElement.clientHeight; - - rendererObj.localizerScene = new THREE.Scene(); - rendererObj.localizerScene.add(rendererObj.localizerHelper); + loadView() { + if (this.state.mode == "single_view") { + DicomViewerEngine.loadSingleView(this); } - - var _this = this; - /** - * Init the quadview - */ - function init() { - /** - * Called on each animation frame - */ - function animate() { - // we are ready when both meshes have been loaded - if (ready) { - // render - r0.controls.update(); - r1.controls.update(); - r2.controls.update(); - r3.controls.update(); - - r0.light.position.copy(r0.camera.position); - r0.renderer.render(r0.scene, r0.camera); - - // r1 - r1.renderer.clear(); - r1.renderer.render(r1.scene, r1.camera); - // mesh - //r1.renderer.clearDepth(); - // data.forEach(function (object, key) { - // object.materialFront.clippingPlanes = [clipPlane1]; - // object.materialBack.clippingPlanes = [clipPlane1]; - // }); - //r1.renderer.render(sceneClip, r1.camera); - // localizer - r1.renderer.clearDepth(); - r1.renderer.render(r1.localizerScene, r1.camera); - - // r2 - r2.renderer.clear(); - r2.renderer.render(r2.scene, r2.camera); - // mesh - //r2.renderer.clearDepth(); - // data.forEach(function (object, key) { - // object.materialFront.clippingPlanes = [clipPlane2]; - // object.materialBack.clippingPlanes = [clipPlane2]; - // }); - //r2.renderer.render(sceneClip, r2.camera); - // localizer - r2.renderer.clearDepth(); - r2.renderer.render(r2.localizerScene, r2.camera); - - // r3 - r3.renderer.clear(); - r3.renderer.render(r3.scene, r3.camera); - // mesh - //r3.renderer.clearDepth(); - // data.forEach(function (object, key) { - // object.materialFront.clippingPlanes = [clipPlane3]; - // object.materialBack.clippingPlanes = [clipPlane3]; - // }); - //r3.renderer.render(sceneClip, r3.camera); - // localizer - r3.renderer.clearDepth(); - r3.renderer.render(r3.localizerScene, r3.camera); - } - - // request new frame - requestAnimationFrame(function () { - if (_this.state.mode == "quad_view") { - animate(); - } - }); - } - - // renderers - initRenderer3D(r0); - initRenderer2D(r1); - initRenderer2D(r2); - initRenderer2D(r3); - - // start rendering loop - animate(); + else if (this.state.mode == "quad_view") { + DicomViewerEngine.loadQuadView(this); } - - // init threeJS - init(); - - - // load sequence for each file - // instantiate the loader - // it loads and parses the dicom image - var _this = this; - let loader = new LoadersVolume(); - loader.load(this.props.files) - .then(function () { - let series = loader.data[0].mergeSeries(loader.data)[0]; - loader.free(); - loader = null; - // get first stack from series - let stack = series.stack[0]; - stack.prepare(); - - // center 3d camera/control on the stack - let centerLPS = stack.worldCenter(); - r0.camera.lookAt(centerLPS.x, centerLPS.y, centerLPS.z); - r0.camera.updateProjectionMatrix(); - r0.controls.target.set(centerLPS.x, centerLPS.y, centerLPS.z); - - // bouding box - let boxHelper = new HelpersBoundingBox(stack); - r0.scene.add(boxHelper); - - // red slice - initHelpersStack(r1, stack); - r0.scene.add(r1.scene); - - // yellow slice - initHelpersStack(r2, stack); - r0.scene.add(r2.scene); - - // green slice - initHelpersStack(r3, stack); - r0.scene.add(r3.scene); - - // create new mesh with Localizer shaders - let plane1 = r1.stackHelper.slice.cartesianEquation(); - let plane2 = r2.stackHelper.slice.cartesianEquation(); - let plane3 = r3.stackHelper.slice.cartesianEquation(); - - // localizer red slice - initHelpersLocalizer(r1, stack, plane1, [ - { - plane: plane2, - color: new THREE.Color(r2.stackHelper.borderColor), - }, - { - plane: plane3, - color: new THREE.Color(r3.stackHelper.borderColor), - }, - ]); - - // localizer yellow slice - initHelpersLocalizer(r2, stack, plane2, [ - { - plane: plane1, - color: new THREE.Color(r1.stackHelper.borderColor), - }, - { - plane: plane3, - color: new THREE.Color(r3.stackHelper.borderColor), - }, - ]); - - // localizer green slice - initHelpersLocalizer(r3, stack, plane3, [ - { - plane: plane1, - color: new THREE.Color(r1.stackHelper.borderColor), - }, - { - plane: plane2, - color: new THREE.Color(r2.stackHelper.borderColor), - }, - ]); - - - - /** - * Update Layer Mix - */ - function updateLocalizer(refObj, targetLocalizersHelpers) { - let refHelper = refObj.stackHelper; - let localizerHelper = refObj.localizerHelper; - let plane = refHelper.slice.cartesianEquation(); - localizerHelper.referencePlane = plane; - - // bit of a hack... works fine for this application - for (let i = 0; i < targetLocalizersHelpers.length; i++) { - for (let j = 0; j < 4; j++) { - let targetPlane = targetLocalizersHelpers[i]['plane' + (j + 1)]; - if (targetPlane && - plane.x === targetPlane.x && - plane.y === targetPlane.y && - plane.z === targetPlane.z) { - targetLocalizersHelpers[i]['plane' + (j + 1)] = plane; - } - } - } - - // update the geometry will create a new mesh - localizerHelper.geometry = refHelper.slice.geometry; - } - - function updateClipPlane(refObj, clipPlane) { - const stackHelper = refObj.stackHelper; - const camera = refObj.camera; - let vertices = stackHelper.slice.geometry.vertices; - let p1 = new THREE.Vector3(vertices[0].x, vertices[0].y, vertices[0].z) - .applyMatrix4(stackHelper._stack.ijk2LPS); - let p2 = new THREE.Vector3(vertices[1].x, vertices[1].y, vertices[1].z) - .applyMatrix4(stackHelper._stack.ijk2LPS); - let p3 = new THREE.Vector3(vertices[2].x, vertices[2].y, vertices[2].z) - .applyMatrix4(stackHelper._stack.ijk2LPS); - - clipPlane.setFromCoplanarPoints(p1, p2, p3); - - let cameraDirection = new THREE.Vector3(1, 1, 1); - cameraDirection.applyQuaternion(camera.quaternion); - - if (cameraDirection.dot(clipPlane.normal) > 0) { - clipPlane.negate(); - } - } - - function onYellowChanged() { - updateLocalizer(r2, [r1.localizerHelper, r3.localizerHelper]); - updateClipPlane(r2, clipPlane2); - } - - function onRedChanged() { - updateLocalizer(r1, [r2.localizerHelper, r3.localizerHelper]); - updateClipPlane(r1, clipPlane1); - } - - function onGreenChanged() { - updateLocalizer(r3, [r1.localizerHelper, r2.localizerHelper]); - updateClipPlane(r3, clipPlane3); - } - - function onDoubleClick(event) { - const canvas = event.srcElement.parentElement; - const id = event.target.id; - const mouse = { - x: ((event.clientX - canvas.offsetLeft) / canvas.clientWidth) * 2 - 1, - y: - ((event.clientY - canvas.offsetTop) / canvas.clientHeight) * 2 + 1, - }; - // - let camera = null; - let stackHelper = null; - let scene = null; - switch (id) { - case '0': - camera = r0.camera; - stackHelper = r1.stackHelper; - scene = r0.scene; - break; - case '1': - camera = r1.camera; - stackHelper = r1.stackHelper; - scene = r1.scene; - break; - case '2': - camera = r2.camera; - stackHelper = r2.stackHelper; - scene = r2.scene; - break; - case '3': - camera = r3.camera; - stackHelper = r3.stackHelper; - scene = r3.scene; - break; - } - - const raycaster = new THREE.Raycaster(); - raycaster.setFromCamera(mouse, camera); - - const intersects = raycaster.intersectObjects(scene.children, true); - if (intersects.length > 0) { - let ijk = - ModelsStack.worldToData(stackHelper.stack, intersects[0].point); - r1.stackHelper.index = - ijk.getComponent((r1.stackHelper.orientation + 2) % 3); - r2.stackHelper.index = - ijk.getComponent((r2.stackHelper.orientation + 2) % 3); - r3.stackHelper.index = - ijk.getComponent((r3.stackHelper.orientation + 2) % 3); - - onGreenChanged(); - onRedChanged(); - onYellowChanged(); - } - } - - // event listeners - r0.domElement.addEventListener('dblclick', onDoubleClick); - r1.domElement.addEventListener('dblclick', onDoubleClick); - r2.domElement.addEventListener('dblclick', onDoubleClick); - r3.domElement.addEventListener('dblclick', onDoubleClick); - - function onScroll(event) { - const id = event.target.domElement.id; - let stackHelper = null; - switch (id) { - case 'r1': - stackHelper = r1.stackHelper; - break; - case 'r2': - stackHelper = r2.stackHelper; - break; - case 'r3': - stackHelper = r3.stackHelper; - break; - } - - if (event.delta > 0) { - if (stackHelper.index >= stackHelper.orientationMaxIndex - 1) { - return false; - } - stackHelper.index += 1; - } else { - if (stackHelper.index <= 0) { - return false; - } - stackHelper.index -= 1; - } - - onGreenChanged(); - onRedChanged(); - onYellowChanged(); - } - - // event listeners - r1.controls.addEventListener('OnScroll', onScroll); - r2.controls.addEventListener('OnScroll', onScroll); - r3.controls.addEventListener('OnScroll', onScroll); - - function windowResize2D(rendererObj) { - rendererObj.camera.canvas = { - width: rendererObj.domElement.clientWidth, - height: rendererObj.domElement.clientHeight, - }; - rendererObj.camera.fitBox(2, 1); - rendererObj.renderer.setSize( - rendererObj.domElement.clientWidth, - rendererObj.domElement.clientHeight); - - // update info to draw borders properly - rendererObj.stackHelper.slice.canvasWidth = - rendererObj.domElement.clientWidth; - rendererObj.stackHelper.slice.canvasHeight = - rendererObj.domElement.clientHeight; - rendererObj.localizerHelper.canvasWidth = - rendererObj.domElement.clientWidth; - rendererObj.localizerHelper.canvasHeight = - rendererObj.domElement.clientHeight; - } - - function onWindowResize() { - // update 3D - r0.camera.aspect = r0.domElement.clientWidth / r0.domElement.clientHeight; - r0.camera.updateProjectionMatrix(); - r0.renderer.setSize( - r0.domElement.clientWidth, r0.domElement.clientHeight); - - // update 2d - windowResize2D(r1); - windowResize2D(r2); - windowResize2D(r3); - } - - window.addEventListener('resize', onWindowResize, false); - - $("#" + _this.props.id).on("dialogresizestop", function (event, ui) { - // update 3D - r0.camera.aspect = r0.domElement.clientWidth / r0.domElement.clientHeight; - r0.camera.updateProjectionMatrix(); - r0.renderer.setSize( - r0.domElement.clientWidth, r0.domElement.clientHeight); - - // update 2d - windowResize2D(r1); - windowResize2D(r2); - windowResize2D(r3); - - }); - - - ready = true; - - // load meshes on the stack is all set - // let meshesLoaded = 0; - // function loadSTLObject(object) { - // const stlLoader = new THREE.STLLoader(); - // stlLoader.load(object.location, function (geometry) { - // // 3D mesh - // object.material = new THREE.MeshLambertMaterial({ - // opacity: object.opacity, - // color: object.color, - // clippingPlanes: [], - // side: THREE.DoubleSide, - // transparent: true, - // }); - // object.mesh = new THREE.Mesh(geometry, object.material); - // const RASToLPS = new THREE.Matrix4(); - // RASToLPS.set(-1, 0, 0, 0, - // 0, -1, 0, 0, - // 0, 0, 1, 0, - // 0, 0, 0, 1); - // object.mesh.applyMatrix(RASToLPS); - // r0.scene.add(object.mesh); - - // // front - // object.materialFront = new THREE.MeshBasicMaterial({ - // color: object.color, - // side: THREE.FrontSide, - // depthWrite: true, - // opacity: 0, - // transparent: true, - // clippingPlanes: [], - // }); - - // object.meshFront = new THREE.Mesh(geometry, object.materialFront); - // object.meshFront.applyMatrix(RASToLPS); - // sceneClip.add(object.meshFront); - - // // back - // object.materialBack = new THREE.MeshBasicMaterial({ - // color: object.color, - // side: THREE.BackSide, - // depthWrite: true, - // opacity: object.opacity, - // transparent: true, - // clippingPlanes: [], - // }); - - // object.meshBack = new THREE.Mesh(geometry, object.materialBack); - // object.meshBack.applyMatrix(RASToLPS); - // sceneClip.add(object.meshBack); - - // meshesLoaded++; - - // onGreenChanged(); - // onRedChanged(); - // onYellowChanged(); - - // // good to go - // if (meshesLoaded === data.size) { - // ready = true; - // } - // }); - // } - - // data.forEach(function (object, key) { - // loadSTLObject(object); - // }); - }) - .catch(function (error) { - window.console.log('oops... something went wrong...'); - window.console.log(error); - }); } componentDidMount() { - - if (this.state.mode == "single_view") { - this.loadSingleView(); - } - else if (this.state.mode == "quad_view") { - this.loadQuadView(); - } + this.loadView(); } componentDidUpdate() { - - if (this.state.mode == "single_view") { - this.loadSingleView(); - } - else if (this.state.mode == "quad_view") { - this.loadQuadView(); - } + this.loadView(); } changeMode() { @@ -917,7 +75,7 @@ define(function (require) { } download(){ - window.location = this.props.files; + window.location = this.state.files; } render() { @@ -931,10 +89,10 @@ define(function (require) { else if (this.state.mode == "quad_view") { dicomViewerContent = (
-
-
-
-
+
+
+
+
) } @@ -942,7 +100,7 @@ define(function (require) {
) From d3d9df3a44142aa943d84a72875fd7d8ed16c287 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 22 May 2017 21:11:17 +0100 Subject: [PATCH 010/371] add set data for instances --- .../interface/dicomViewer/DicomViewer.js | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js index 615ff449b..c4bbd6174 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js @@ -27,11 +27,20 @@ define(function (require) { this.download = this.download.bind(this); } - setData(files) { - this.setState({ files: files }); + setData(data) { + if (data.getMetaType == undefined){ + this.setState({ files: files }); + } + else if (data.getMetaType() == "Instance"){ + if (data.getVariable().getInitialValues()[0].value.format == "NIFTI"){ + this.setState({ files: [data.getVariable().getInitialValues()[0].value.data] }); + } + else if (data.getVariable().getInitialValues()[0].value.format == "DCM"){ + // WHAT do we do here? + } + } } - loadView() { if (this.state.mode == "single_view") { DicomViewerEngine.loadSingleView(this); From 9a90c85e22293900dc3085b0e58b739378cde9f5 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Tue, 23 May 2017 22:33:22 +0100 Subject: [PATCH 011/371] removing buttons images for highresviewer --- .../images/fullpage_grouphover.png | Bin 4907 -> 0 bytes .../bigImageViewer/images/fullpage_hover.png | Bin 5214 -> 0 bytes .../bigImageViewer/images/fullpage_pressed.png | Bin 5213 -> 0 bytes .../bigImageViewer/images/fullpage_rest.png | Bin 5155 -> 0 bytes .../bigImageViewer/images/home_grouphover.png | Bin 4808 -> 0 bytes .../bigImageViewer/images/home_hover.png | Bin 5107 -> 0 bytes .../bigImageViewer/images/home_pressed.png | Bin 5138 -> 0 bytes .../bigImageViewer/images/home_rest.png | Bin 5061 -> 0 bytes .../bigImageViewer/images/next_grouphover.png | Bin 3004 -> 0 bytes .../bigImageViewer/images/next_hover.png | Bin 3433 -> 0 bytes .../bigImageViewer/images/next_pressed.png | Bin 3503 -> 0 bytes .../bigImageViewer/images/next_rest.png | Bin 3061 -> 0 bytes .../images/previous_grouphover.png | Bin 2987 -> 0 bytes .../bigImageViewer/images/previous_hover.png | Bin 3461 -> 0 bytes .../bigImageViewer/images/previous_pressed.png | Bin 3499 -> 0 bytes .../bigImageViewer/images/previous_rest.png | Bin 3064 -> 0 bytes .../images/rotateleft_grouphover.png | Bin 1902 -> 0 bytes .../bigImageViewer/images/rotateleft_hover.png | Bin 2289 -> 0 bytes .../bigImageViewer/images/rotateleft_pressed.png | Bin 2242 -> 0 bytes .../bigImageViewer/images/rotateleft_rest.png | Bin 1943 -> 0 bytes .../images/rotateright_grouphover.png | Bin 1970 -> 0 bytes .../bigImageViewer/images/rotateright_hover.png | Bin 2338 -> 0 bytes .../images/rotateright_pressed.png | Bin 2228 -> 0 bytes .../bigImageViewer/images/rotateright_rest.png | Bin 1961 -> 0 bytes .../bigImageViewer/images/zoomin_grouphover.png | Bin 4794 -> 0 bytes .../bigImageViewer/images/zoomin_hover.png | Bin 5126 -> 0 bytes .../bigImageViewer/images/zoomin_pressed.png | Bin 5172 -> 0 bytes .../bigImageViewer/images/zoomin_rest.png | Bin 5041 -> 0 bytes .../bigImageViewer/images/zoomout_grouphover.png | Bin 4596 -> 0 bytes .../bigImageViewer/images/zoomout_hover.png | Bin 4931 -> 0 bytes .../bigImageViewer/images/zoomout_pressed.png | Bin 5007 -> 0 bytes .../bigImageViewer/images/zoomout_rest.png | Bin 4811 -> 0 bytes 32 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/fullpage_grouphover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/fullpage_hover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/fullpage_pressed.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/fullpage_rest.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/home_grouphover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/home_hover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/home_pressed.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/home_rest.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/next_grouphover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/next_hover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/next_pressed.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/next_rest.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/previous_grouphover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/previous_hover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/previous_pressed.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/previous_rest.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/rotateleft_grouphover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/rotateleft_hover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/rotateleft_pressed.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/rotateleft_rest.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/rotateright_grouphover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/rotateright_hover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/rotateright_pressed.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/rotateright_rest.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/zoomin_grouphover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/zoomin_hover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/zoomin_pressed.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/zoomin_rest.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/zoomout_grouphover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/zoomout_hover.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/zoomout_pressed.png delete mode 100644 src/main/webapp/js/components/interface/bigImageViewer/images/zoomout_rest.png diff --git 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zozVR0>FGZf3WZ^%R96V$FtaCw@QimHA%r7@kk-TOWS74!6OqJe zG)*HSa)Th)&= zeh7k~;5d%+Bp4#1BuV0SyWL)1UT$~0U9Gi-5W-tnSP&~KD{U(c^qR0iF!aqg-`w7@ zV@EbSJ6qIRH_|kvG)>b^r=x1MTHA3P*;ixMb(mUfQc972w6T;@20>7~di83yw6s(+ zeU7$^Z9fbFP+xuZ)l#)ueXwuezD=Iz)uSki%ztF6?JwR&M@I|G%gf_)b93!xvstrR ziM+pA17l~O6SxpsBT{Ukc(lj@-C$N$E*=I}jdi^$l zwgJjp(zPwbi!Z)tdnN@C-@SYH>-XP(KlVItYpGNkAtITkDSoaIkt~%;Bh0+@?Afz% zv)Q}{pkZKQt1i)++GN ycj~=+2!x-_6g@Upja0oOT>%d!O}=~gE@`dXM6^OgKNx_P z@kGm-o}>?CEzH)fTYG}){{8#?3c)i#q48911tCNUK!KUH8BAF^scTs@NUB)s;xWwR z%l9@qm0hbQQx@$yR4`ys^Y@H~N<9Lv~&A~iNY4&Sv z)hBPYtt1D5tbr*M3Tr@Y>-*v$2Z(>!S5l}?{QoG#IvB@sdIJ2%z6JcqCy{m4zfW!c l^oJnp?SJbge(MANKLGgW6Oj(y!CC+S002ovPDHLkV1hX!DhdDq From 30ce9e7828d3abe9a0d6460fe5e05a0e7434cd25 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Tue, 23 May 2017 22:34:02 +0100 Subject: [PATCH 012/371] integrate with model --- .../bigImageViewer/BigImageViewer.js | 23 ++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js b/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js index 7016f3de8..9210bbd5d 100644 --- a/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js +++ b/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js @@ -21,7 +21,7 @@ define(function (require) { this.state = { settings: $.extend(settings, this.props.settings), - file: this.props.file + file: this.extractFilePath(this.props.file) }; this.download = this.download.bind(this); @@ -29,13 +29,30 @@ define(function (require) { loadViewer() { this.state.settings.tileSources = this.state.file; - this.state.settings.showNavigator = this.state.showNavigator; - this.viewer = OpenSeadragon(this.state.settings); } download() { //What do we do here? + console.log("Downloading data..."); + } + + extractFilePath(data) { + if (data === undefined){ + return undefined; + } + else if (data.getMetaType == undefined) { + return data; + } + else if (data.getMetaType() == "Instance") { + if (data.getVariable().getInitialValues()[0].value.format == "DZI") { + return data.getVariable().getInitialValues()[0].value.data; + } + } + } + + setData(data) { + this.setState({ file: this.extractFilePath(data) }); } componentDidUpdate() { From cd8ef84af36a789bc00d0ba663c41d0987589721 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Tue, 23 May 2017 22:34:23 +0100 Subject: [PATCH 013/371] convert to less --- .../googleViewer/{GoogleViewer.css => GoogleViewer.less} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/main/webapp/js/components/interface/googleViewer/{GoogleViewer.css => GoogleViewer.less} (100%) diff --git a/src/main/webapp/js/components/interface/googleViewer/GoogleViewer.css b/src/main/webapp/js/components/interface/googleViewer/GoogleViewer.less similarity index 100% rename from src/main/webapp/js/components/interface/googleViewer/GoogleViewer.css rename to src/main/webapp/js/components/interface/googleViewer/GoogleViewer.less From bf2d888cec4015fb1e58ad4db7d868f75ccb7e0d Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Tue, 23 May 2017 22:34:44 +0100 Subject: [PATCH 014/371] add download and require less --- .../interface/googleViewer/GoogleViewer.js | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/main/webapp/js/components/interface/googleViewer/GoogleViewer.js b/src/main/webapp/js/components/interface/googleViewer/GoogleViewer.js index bdeb17b8b..7ec98c099 100644 --- a/src/main/webapp/js/components/interface/googleViewer/GoogleViewer.js +++ b/src/main/webapp/js/components/interface/googleViewer/GoogleViewer.js @@ -1,11 +1,6 @@ define(function (require) { - var link = document.createElement("link"); - link.type = "text/css"; - link.rel = "stylesheet"; - link.href = "geppetto/js/components/interface/googleViewer/GoogleViewer.css"; - document.getElementsByTagName("head")[0].appendChild(link); - + require('./GoogleViewer.less'); var React = require('react'); var GoogleMapsLoader = require('google-maps'); var AbstractComponent = require('../../AComponent'); @@ -98,6 +93,11 @@ define(function (require) { }); } + download() { + //What do we do here? + console.log("Downloading data..."); + } + render () { return (

From 0057b692e4ac736bebf70e6b5f9434c2940745b6 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Tue, 23 May 2017 22:35:16 +0100 Subject: [PATCH 015/371] integrate with model and bug fixing --- .../interface/dicomViewer/DicomViewer.js | 33 +++++++++++-------- 1 file changed, 20 insertions(+), 13 deletions(-) diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js index c4bbd6174..a898281c1 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js @@ -13,12 +13,12 @@ define(function (require) { constructor(props) { super(props); - if (this.props.mode === undefined){ + if (this.props.mode === undefined) { this.props.mode = "quad_view"; } this.state = { - files: this.props.files, + files: this.extractFilesPath(this.props.files), mode: this.props.mode }; @@ -28,14 +28,21 @@ define(function (require) { } setData(data) { - if (data.getMetaType == undefined){ - this.setState({ files: files }); + this.setState({ files: this.extractFilesPath(data) }); + } + + extractFilesPath(data) { + if (data === undefined){ + return undefined; } - else if (data.getMetaType() == "Instance"){ - if (data.getVariable().getInitialValues()[0].value.format == "NIFTI"){ - this.setState({ files: [data.getVariable().getInitialValues()[0].value.data] }); + else if (data.getMetaType == undefined) { + return data; + } + else if (data.getMetaType() == "Instance") { + if (data.getVariable().getInitialValues()[0].value.format == "NIFTI") { + return data.getVariable().getInitialValues()[0].value.data; } - else if (data.getVariable().getInitialValues()[0].value.format == "DCM"){ + else if (data.getVariable().getInitialValues()[0].value.format == "DCM") { // WHAT do we do here? } } @@ -68,25 +75,25 @@ define(function (require) { } changeOrientation() { - if (this.camera.orientation == "coronal"){ + if (this.camera.orientation == "coronal") { this.camera.orientation = "sagittal"; } - else if (this.camera.orientation == "sagittal"){ + else if (this.camera.orientation == "sagittal") { this.camera.orientation = "axial"; } - else if (this.camera.orientation == "axial"){ + else if (this.camera.orientation == "axial") { this.camera.orientation = "coronal"; } this.camera.update() this.camera.fitBox(2) this.stackHelper.orientation = this.camera.stackOrientation; - this.stackHelper.index = Math.floor(this.stackHelper.orientationMaxIndex/2); + this.stackHelper.index = Math.floor(this.stackHelper.orientationMaxIndex / 2); } download() { GEPPETTO.Utility.createZipFromRemoteFiles(this.state.files, "data.zip"); } - + render() { var dicomViewerContent; if (this.state.mode == "single_view") { From dc973b3503d57e0cf94ad60dcebb77552359ee2d Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Wed, 24 May 2017 20:58:28 +0100 Subject: [PATCH 016/371] rename data property --- .../interface/dicomViewer/DicomViewer.js | 25 ++++++++++--------- 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js index a898281c1..467f6fdb6 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js @@ -18,7 +18,7 @@ define(function (require) { } this.state = { - files: this.extractFilesPath(this.props.files), + files: this.extractFilesPath(this.props.data), mode: this.props.mode }; @@ -32,20 +32,21 @@ define(function (require) { } extractFilesPath(data) { - if (data === undefined){ - return undefined; - } - else if (data.getMetaType == undefined) { - return data; - } - else if (data.getMetaType() == "Instance") { - if (data.getVariable().getInitialValues()[0].value.format == "NIFTI") { - return data.getVariable().getInitialValues()[0].value.data; + var files; + if (data != undefined){ + if (data.getMetaType == undefined) { + files = data; } - else if (data.getVariable().getInitialValues()[0].value.format == "DCM") { - // WHAT do we do here? + else if (data.getMetaType() == "Instance") { + if (data.getVariable().getInitialValues()[0].value.format == "NIFTI") { + files = data.getVariable().getInitialValues()[0].value.data; + } + else if (data.getVariable().getInitialValues()[0].value.format == "DCM") { + // WHAT do we do here? + } } } + return files; } loadView() { From 67e928dfde55c83a3eda49188291a461f7b60f80 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Wed, 24 May 2017 21:50:37 +0100 Subject: [PATCH 017/371] refactors and polish api --- .../bigImageViewer/BigImageViewer.js | 19 ++++++------ .../interface/googleViewer/GoogleViewer.js | 29 +++++++++++++++---- 2 files changed, 33 insertions(+), 15 deletions(-) diff --git a/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js b/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js index 9210bbd5d..c6fbbd57b 100644 --- a/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js +++ b/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js @@ -21,7 +21,7 @@ define(function (require) { this.state = { settings: $.extend(settings, this.props.settings), - file: this.extractFilePath(this.props.file) + file: this.extractFilePath(this.props.data) }; this.download = this.download.bind(this); @@ -38,17 +38,16 @@ define(function (require) { } extractFilePath(data) { - if (data === undefined){ - return undefined; - } - else if (data.getMetaType == undefined) { - return data; - } - else if (data.getMetaType() == "Instance") { - if (data.getVariable().getInitialValues()[0].value.format == "DZI") { - return data.getVariable().getInitialValues()[0].value.data; + var file; + if (data != undefined){ + if (data.getMetaType == undefined) { + file = data; + } + else if (data.getMetaType() == "Instance" && data.getVariable().getInitialValues()[0].value.format == "DZI") { + file = data.getVariable().getInitialValues()[0].value.data; } } + return file; } setData(data) { diff --git a/src/main/webapp/js/components/interface/googleViewer/GoogleViewer.js b/src/main/webapp/js/components/interface/googleViewer/GoogleViewer.js index 7ec98c099..d6ec0129a 100644 --- a/src/main/webapp/js/components/interface/googleViewer/GoogleViewer.js +++ b/src/main/webapp/js/components/interface/googleViewer/GoogleViewer.js @@ -18,6 +18,7 @@ define(function (require) { mapTypeControl: false } + var path = this.extractFilesPath(this.props.data); var imageMapTypeSettings = { getTileUrl: function (coord, zoom) { var normalizedCoord = _this.getNormalizedCoord(coord, zoom); @@ -32,20 +33,38 @@ define(function (require) { isPng: false, maxZoom: 11, minZoom: 0, - radius: 1738000 + radius: 1738000, + path: path } + + this.state = { mapSettings: $.extend(mapSettings, this.props.mapSettings), imageMapTypeSettings: $.extend(imageMapTypeSettings, this.props.imageMapTypeSettings), tileWidth: (this.props.tileWidth != undefined)?this.props.tileWidth:256 , tileHeight: (this.props.tileHeight != undefined)?this.props.tileHeight:256, - path: this.props.path + path: path }; } - shouldComponentUpdate() { - return false; + extractFilesPath(data) { + var path; + if (data != undefined){ + if (data.getMetaType == undefined) { + path = data; + } + else if (data.getMetaType() == "Instance") { + if (data.getVariable().getInitialValues()[0].value.format == "GOOGLE_MAP") { + path = data.getVariable().getInitialValues()[0].value.data; + } + } + } + return path; + } + + setData(data) { + this.setState({ path: this.extractFilesPath(data) }); } // Normalizes the coords that tiles repeat across the x axis (horizontally) @@ -73,7 +92,7 @@ define(function (require) { componentDidMount () { var _this = this; - GoogleMapsLoader.KEY = this.props.googleKey; + GoogleMapsLoader.KEY = 'AIzaSyAtAf8S4uU54ZogtLqbzc8pvQI6phGDL1Q'; GoogleMapsLoader.load(function (google) { var container = document.getElementById(_this.props.id + "_component"); From c88957f155fef15f677da372a8b44099b6c53d1d Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Wed, 24 May 2017 22:13:15 +0100 Subject: [PATCH 018/371] improve casper readme --- .../webapp/js/pages/tests/casperjs/README.md | 26 +++++++++++-------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/src/main/webapp/js/pages/tests/casperjs/README.md b/src/main/webapp/js/pages/tests/casperjs/README.md index 364a48d63..c382bf56b 100644 --- a/src/main/webapp/js/pages/tests/casperjs/README.md +++ b/src/main/webapp/js/pages/tests/casperjs/README.md @@ -1,23 +1,27 @@ -##Run with +## Prereqs -`casperjs test LiveTests.js --engine=slimerjs` +* node.js +* npm -to test that Casper is properly installed. +## Install with: -Run `casperjs test UITests.js --engine=slimerjs` to run Geppetto UI Tests. +`npm install -g phantomjs casperjs slimerjs` -Run `casperjs test --includes=CoreTestsUtility.js CoreTests.js --engine=slimerjs` to run Core projects Tests +## Run with -##Prereqs +To test that Casper is properly installed: -* node.js -* npm +`casperjs test LiveTests.js --engine=slimerjs` + +To run Geppetto UI Tests: + +`casperjs test UITests.js --engine=slimerjs` -##Install with: +To run Core projects Tests: -`npm install -g phantomjs npm install -g casperjs npm install -g slimerjs` +`casperjs test --includes=CoreTestsUtility.js CoreTests.js --engine=slimerjs` -##documentation +## documentation * [CasperJS Test API documentation](http://docs.casperjs.org/en/latest/modules/tester.html) - assert API * [CasperJS Core API documentation](http://docs.casperjs.org/en/latest/modules/casper.html) - actions like clicks. From 7a8256a17937309133f14d8d40996de0d8fa0720 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Thu, 25 May 2017 22:31:06 +0100 Subject: [PATCH 019/371] validating if there are files --- .../interface/dicomViewer/DicomViewer.js | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js index 467f6fdb6..3087db245 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js @@ -95,6 +95,29 @@ define(function (require) { GEPPETTO.Utility.createZipFromRemoteFiles(this.state.files, "data.zip"); } + /** + * + * @returns {{widgetType, isWidget}|{size: {height: *, width: *}, position: {left: *, top: *}}} + */ + getView() { + // add data-type and data field + any other custom fields in the component-specific attribute + var baseView = super.getView(); + baseView.data = this.props.data; + return baseView; + } + + /** + * + * @param view + */ + setView(view) { + // set base properties + super.setView(view) + if (view.data != undefined){ + this.setData(view.data); + } + } + render() { var dicomViewerContent; if (this.state.mode == "single_view") { From d962af2a1e32ffaad10b49ba0f41ad3583596731 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Thu, 25 May 2017 22:37:34 +0100 Subject: [PATCH 020/371] initial work adding new patienthm sample project and testing new widgets --- .../js/pages/tests/casperjs/CoreTests.js | 23 ++++++++++++++++++- .../pages/tests/casperjs/CoreTestsUtility.js | 12 +++++++++- 2 files changed, 33 insertions(+), 2 deletions(-) diff --git a/src/main/webapp/js/pages/tests/casperjs/CoreTests.js b/src/main/webapp/js/pages/tests/casperjs/CoreTests.js index 2da477ad6..71c23e6b6 100644 --- a/src/main/webapp/js/pages/tests/casperjs/CoreTests.js +++ b/src/main/webapp/js/pages/tests/casperjs/CoreTests.js @@ -30,6 +30,7 @@ casper.test.begin('Geppetto basic tests', 52, function suite(test) { test.assertExists('div[project-id="16"]', "Project width id 16 from core bundle are present"); test.assertExists('div[project-id="18"]', "Project width id 18 from core bundle are present"); test.assertExists('div[project-id="58"]', "Project width id 58 from core bundle are present"); + test.assertExists('div[project-id="82"]', "Project width id 10 from core bundle are present"); }, null, 3000); }); @@ -88,6 +89,12 @@ casper.test.begin('Geppetto basic tests', 52, function suite(test) { casper.thenOpen(urlBase+baseFollowUp+cElegansPVDR,function() { casper.then(function(){launchTest(test,"cElegansPVDR",180000);}); }); + + /**Tests patientHM project**/ + casper.thenOpen(urlBase+baseFollowUp+patientHM,function() { + casper.then(function(){launchTest(test,"patientHM",180000);}); + casper.then(function(){patientHMTest(test);}); + }); casper.run(function() { test.done(); @@ -461,10 +468,24 @@ function c302Connectome(test){ }, null, 30000); } - function c302PVDR(test){ casper.echo("------------STARTING C302 Muscle Model TEST--------------"); casper.waitForSelector('div[id="Popup1"]', function() { this.echo("I've waited for Popup1 to load."); }, null, 30000); +} + +function patientHMTest(test){ + casper.echo("------------STARTING Patient HM TEST--------------"); + + // casper.waitForSelector('div[id="DicomViewer1"]', function() { + // this.echo("I've waited for DicomViewer1 to load."); + // testDicomWidget(test, "DicomViewer1"); + // }, null, 5000); + + // casper.waitForSelector('div[id="DicomViewer1"]', function() { + // this.echo("I've waited for DicomViewer1 to load."); + // testDicomWidget(test, "DicomViewer1"); + // }, null, 5000); + } \ No newline at end of file diff --git a/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js b/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js index b1d9e5faf..3b7b0c5b6 100644 --- a/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js +++ b/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js @@ -11,6 +11,7 @@ var cElegansPVDR = "load_project_from_id=8"; var eyeWire = "load_project_from_id=9"; var nwbSample = "load_project_from_id=18"; var Pharyngeal = "load_project_from_id=58"; +var patientHM = "load_project_from_id=82"; var defaultColor = [0.00392156862745098,0.6,0.9098039215686274]; var zoomClicks = 50, panClicks=10, rotateClicks=20; @@ -379,4 +380,13 @@ function testingConnectionLines(test, expectedLines){ test.assertEquals(expectedLines, connectionLines, "The control panel opened with right amount of rows"); }); -} \ No newline at end of file +} + +function testBaseWidget(test, id){ + test.assertExists('div[id="'+id+'"]', id + " exists"); +} + +function testDicomWidget(test, id){ + testBaseWidget(test, id); + +} \ No newline at end of file From 2da334e837b9e137019fe3ea319ab103ca8e2b21 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Thu, 25 May 2017 23:36:48 +0100 Subject: [PATCH 021/371] fix scroll on quad view --- .../js/components/interface/dicomViewer/DicomViewer.js | 8 ++++---- .../components/interface/dicomViewer/DicomViewerEngine.js | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js index 3087db245..32f59498f 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js @@ -129,10 +129,10 @@ define(function (require) { else if (this.state.mode == "quad_view") { dicomViewerContent = (
-
-
-
-
+
+
+
+
) } diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js index 599b4f4fd..614de77b7 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js @@ -692,7 +692,7 @@ module.exports = { r3.domElement.addEventListener('dblclick', onDoubleClick); function onScroll(event) { - const id = event.target.domElement.id; + const id = $(event.target.domElement).data("id"); let stackHelper = null; switch (id) { case 'r1': From 5d292520aba37afda143d8ba3e784bd4370c29bc Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Fri, 26 May 2017 00:48:36 +0100 Subject: [PATCH 022/371] fixing double click event --- .../components/interface/dicomViewer/DicomViewerEngine.js | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js index 614de77b7..f2fa10b2d 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js @@ -635,10 +635,11 @@ module.exports = { const canvas = event.srcElement.parentElement; const id = event.target.id; const mouse = { - x: ((event.clientX - canvas.offsetLeft) / canvas.clientWidth) * 2 - 1, - y: - ((event.clientY - canvas.offsetTop) / canvas.clientHeight) * 2 + 1, + x: ((event.clientX - $(canvas).offset().left) / canvas.clientWidth) * 2 - 1, + y: - ((event.clientY - $(canvas).offset().top) / canvas.clientHeight) * 2 + 1, }; - // + + let camera = null; let stackHelper = null; let scene = null; From 383382883b564ec88a27152c49d19d0979259073 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 29 May 2017 20:34:24 +0100 Subject: [PATCH 023/371] complete refactor: implemented onclick, ctrl + click, scroll, load improvements, clean up code --- .../interface/dicomViewer/DicomViewer.js | 502 ++++++++-- .../dicomViewer/DicomViewerEngine.js | 857 ------------------ .../interface/dicomViewer/DicomViewerUtils.js | 193 ++++ 3 files changed, 628 insertions(+), 924 deletions(-) delete mode 100644 src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js create mode 100644 src/main/webapp/js/components/interface/dicomViewer/DicomViewerUtils.js diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js index 32f59498f..cd9545c47 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js @@ -4,22 +4,93 @@ define(function (require) { window.THREE = require('three'); require('./DicomViewer.less'); - var DicomViewerEngine = require('./DicomViewerEngine'); + var DicomViewerUtils = require('./DicomViewerUtils'); var AbstractComponent = require('../../AComponent'); + var AMI = require('./ami.min.js'); + var LoadersVolume = AMI.default.Loaders.Volume; + var HelpersStack = AMI.default.Helpers.Stack; + var HelpersBoundingBox = AMI.default.Helpers.BoundingBox; + var ModelsStack = AMI.default.Models.Stack; + var HelpersLocalizer = AMI.default.Helpers.Localizer; + return class DicomViewer extends AbstractComponent { constructor(props) { super(props); - if (this.props.mode === undefined) { - this.props.mode = "quad_view"; - } - this.state = { files: this.extractFilesPath(this.props.data), - mode: this.props.mode + mode: (this.props.mode === undefined) ? "quad_view" : this.props.mode, + orientation: (this.props.orientation === undefined) ? "coronal" : this.props.orientation + }; + + // 3d renderer + this.r0 = { + domClass: 'r0', + domElement: null, + renderer: null, + color: 0x212121, + targetID: 0, + camera: null, + controls: null, + scene: null, + light: null, + }; + + // 2d axial renderer + this.r1 = { + domClass: 'r1', + domElement: null, + renderer: null, + color: 0x121212, + sliceOrientation: 'axial', + sliceColor: 0xFF1744, + targetID: 1, + camera: null, + controls: null, + scene: null, + light: null, + stackHelper: null, + localizerHelper: null, + localizerScene: null, + }; + + // 2d sagittal renderer + this.r2 = { + domClass: 'r2', + domElement: null, + renderer: null, + color: 0x121212, + sliceOrientation: 'sagittal', + sliceColor: 0xFFEA00, + targetID: 2, + camera: null, + controls: null, + scene: null, + light: null, + stackHelper: null, + localizerHelper: null, + localizerScene: null, + }; + + // 2d coronal renderer + this.r3 = { + domClass: 'r3', + domElement: null, + renderer: null, + color: 0x121212, + sliceOrientation: 'coronal', + sliceColor: 0x76FF03, + targetID: 3, + camera: null, + controls: null, + scene: null, + light: null, + stackHelper: null, + localizerHelper: null, + localizerScene: null, }; this.changeMode = this.changeMode.bind(this); @@ -33,7 +104,7 @@ define(function (require) { extractFilesPath(data) { var files; - if (data != undefined){ + if (data != undefined) { if (data.getMetaType == undefined) { files = data; } @@ -49,21 +120,352 @@ define(function (require) { return files; } - loadView() { - if (this.state.mode == "single_view") { - DicomViewerEngine.loadSingleView(this); + componentDidMount() { + this.ready = false; + var _this = this; + + /** + * Init the quadview + */ + function init() { + /** + * Called on each animation frame + */ + function animate() { + // we are ready when both meshes have been loaded + if (_this.ready) { + // render + _this.r0.controls.update(); + _this.r1.controls.update(); + _this.r2.controls.update(); + _this.r3.controls.update(); + + _this.r0.light.position.copy(_this.r0.camera.position); + _this.r0.renderer.render(_this.r0.scene, _this.r0.camera); + + // r1 + _this.r1.renderer.clear(); + _this.r1.renderer.render(_this.r1.scene, _this.r1.camera); + // localizer + _this.r1.renderer.clearDepth(); + _this.r1.renderer.render(_this.r1.localizerScene, _this.r1.camera); + + // r2 + _this.r2.renderer.clear(); + _this.r2.renderer.render(_this.r2.scene, _this.r2.camera); + // localizer + _this.r2.renderer.clearDepth(); + _this.r2.renderer.render(_this.r2.localizerScene, _this.r2.camera); + + // r3 + _this.r3.renderer.clear(); + _this.r3.renderer.render(_this.r3.scene, _this.r3.camera); + // localizer + _this.r3.renderer.clearDepth(); + _this.r3.renderer.render(_this.r3.localizerScene, _this.r3.camera); + } + + // request new frame + requestAnimationFrame(function () { + animate(); + }); + } + + // renderers + DicomViewerUtils.initRenderer3D(_this.r0, _this.getContainer()); + DicomViewerUtils.initRenderer2D(_this.r1, _this.getContainer()); + DicomViewerUtils.initRenderer2D(_this.r2, _this.getContainer()); + DicomViewerUtils.initRenderer2D(_this.r3, _this.getContainer()); + + // start rendering loop + animate(); } - else if (this.state.mode == "quad_view") { - DicomViewerEngine.loadQuadView(this); + + // init threeJS + init(); + + // load sequence for each file + // instantiate the loader + // it loads and parses the dicom image + let loader = new LoadersVolume(); + loader.load(this.state.files) + .then(function () { + let series = loader.data[0].mergeSeries(loader.data)[0]; + loader.free(); + loader = null; + // get first stack from series + let stack = series.stack[0]; + stack.prepare(); + + // center 3d camera/control on the stack + let centerLPS = stack.worldCenter(); + _this.r0.camera.lookAt(centerLPS.x, centerLPS.y, centerLPS.z); + _this.r0.camera.updateProjectionMatrix(); + _this.r0.controls.target.set(centerLPS.x, centerLPS.y, centerLPS.z); + + // bouding box + let boxHelper = new HelpersBoundingBox(stack); + _this.r0.scene.add(boxHelper); + + // red slice + DicomViewerUtils.initHelpersStack(_this.r1, stack); + _this.r0.scene.add(_this.r1.scene); + + // yellow slice + DicomViewerUtils.initHelpersStack(_this.r2, stack); + _this.r0.scene.add(_this.r2.scene); + + // green slice + DicomViewerUtils.initHelpersStack(_this.r3, stack); + _this.r0.scene.add(_this.r3.scene); + + // create new mesh with Localizer shaders + let plane1 = _this.r1.stackHelper.slice.cartesianEquation(); + let plane2 = _this.r2.stackHelper.slice.cartesianEquation(); + let plane3 = _this.r3.stackHelper.slice.cartesianEquation(); + + // localizer red slice + DicomViewerUtils.initHelpersLocalizer(_this.r1, stack, plane1, [ + { + plane: plane2, + color: new THREE.Color(_this.r2.stackHelper.borderColor), + }, + { + plane: plane3, + color: new THREE.Color(_this.r3.stackHelper.borderColor), + }, + ]); + + // localizer yellow slice + DicomViewerUtils.initHelpersLocalizer(_this.r2, stack, plane2, [ + { + plane: plane1, + color: new THREE.Color(_this.r1.stackHelper.borderColor), + }, + { + plane: plane3, + color: new THREE.Color(_this.r3.stackHelper.borderColor), + }, + ]); + + // localizer green slice + DicomViewerUtils.initHelpersLocalizer(_this.r3, stack, plane3, [ + { + plane: plane1, + color: new THREE.Color(_this.r1.stackHelper.borderColor), + }, + { + plane: plane2, + color: new THREE.Color(_this.r2.stackHelper.borderColor), + }, + ]); + + _this.configureEvents(); + _this.ready = true; + + }) + .catch(function (error) { + window.console.log('oops... something went wrong...'); + window.console.log(error); + }); + + + } + + configureEvents() { + + var _this = this; + function goToPoint(event) { + const canvas = event.srcElement.parentElement; + const id = event.target.id; + const mouse = { + x: ((event.clientX - $(canvas).offset().left) / canvas.clientWidth) * 2 - 1, + y: - ((event.clientY - $(canvas).offset().top) / canvas.clientHeight) * 2 + 1, + }; + + + let camera = null; + let stackHelper = null; + let scene = null; + switch (id) { + case '0': + camera = _this.r0.camera; + stackHelper = _this.r1.stackHelper; + scene = _this.r0.scene; + break; + case '1': + camera = _this.r1.camera; + stackHelper = _this.r1.stackHelper; + scene = _this.r1.scene; + break; + case '2': + camera = _this.r2.camera; + stackHelper = _this.r2.stackHelper; + scene = _this.r2.scene; + break; + case '3': + camera = _this.r3.camera; + stackHelper = _this.r3.stackHelper; + scene = _this.r3.scene; + break; + } + + const raycaster = new THREE.Raycaster(); + raycaster.setFromCamera(mouse, camera); + + const intersects = raycaster.intersectObjects(scene.children, true); + if (intersects.length > 0) { + let ijk = + ModelsStack.worldToData(stackHelper.stack, intersects[0].point); + _this.r1.stackHelper.index = + ijk.getComponent((_this.r1.stackHelper.orientation + 2) % 3); + _this.r2.stackHelper.index = + ijk.getComponent((_this.r2.stackHelper.orientation + 2) % 3); + _this.r3.stackHelper.index = + ijk.getComponent((_this.r3.stackHelper.orientation + 2) % 3); + + DicomViewerUtils.updateLocalizer(_this.r2, [_this.r1.localizerHelper, _this.r3.localizerHelper]); + DicomViewerUtils.updateLocalizer(_this.r1, [_this.r2.localizerHelper, _this.r3.localizerHelper]); + DicomViewerUtils.updateLocalizer(_this.r3, [_this.r1.localizerHelper, _this.r2.localizerHelper]); + } } + + function goToSingleView(event){ + const id = event.target.id; + let orientation = null; + switch (id) { + case '1': + orientation = "sagittal"; + break; + case '2': + orientation = "axial"; + break; + case '3': + orientation = "coronal"; + break; + } + _this.setState({ mode: "single_view", orientation: orientation }); + } + + function onClick(event) { + + if (event.ctrlKey){ + goToSingleView(event); + } + else{ + goToPoint(event); + } + } + + function onScroll(event) { + const id = $(event.target.domElement).data("id"); + let stackHelper = null; + switch (id) { + case 'r1': + stackHelper = _this.r1.stackHelper; + break; + case 'r2': + stackHelper = _this.r2.stackHelper; + break; + case 'r3': + stackHelper = _this.r3.stackHelper; + break; + } + + if (event.delta > 0) { + if (stackHelper.index >= stackHelper.orientationMaxIndex - 1) { + return false; + } + stackHelper.index += 1; + } else { + if (stackHelper.index <= 0) { + return false; + } + stackHelper.index -= 1; + } + + DicomViewerUtils.updateLocalizer(_this.r2, [_this.r1.localizerHelper, _this.r3.localizerHelper]); + DicomViewerUtils.updateLocalizer(_this.r1, [_this.r2.localizerHelper, _this.r3.localizerHelper]); + DicomViewerUtils.updateLocalizer(_this.r3, [_this.r1.localizerHelper, _this.r2.localizerHelper]); + } + + // event listeners + // _this.r0.domElement.addEventListener('dblclick', onDoubleClick); + // _this.r1.domElement.addEventListener('dblclick', onDoubleClick); + // _this.r2.domElement.addEventListener('dblclick', onDoubleClick); + // _this.r3.domElement.addEventListener('dblclick', onDoubleClick); + + // event listeners + this.r0.domElement.addEventListener('click', onClick); + this.r1.domElement.addEventListener('click', onClick); + this.r2.domElement.addEventListener('click', onClick); + this.r3.domElement.addEventListener('click', onClick); + + // event listeners + this.r1.controls.addEventListener('OnScroll', onScroll); + this.r2.controls.addEventListener('OnScroll', onScroll); + this.r3.controls.addEventListener('OnScroll', onScroll); + + + window.addEventListener('resize', this.setLayout, false); + + $(this.getContainer()).parent().on("dialogresizestop", function (event, ui) { + this.setLayout() + }); } - componentDidMount() { - this.loadView(); + setQuadLayout() { + // update 3D + this.r0.camera.aspect = this.r0.domElement.clientWidth / this.r0.domElement.clientHeight; + this.r0.camera.updateProjectionMatrix(); + this.r0.renderer.setSize( + this.r0.domElement.clientWidth, this.r0.domElement.clientHeight); + + // update 2d + DicomViewerUtils.windowResize2D(this.r1); + DicomViewerUtils.windowResize2D(this.r2); + DicomViewerUtils.windowResize2D(this.r3); } - componentDidUpdate() { - this.loadView(); + setSingleLayout() { + var rendererObj; + switch (this.state.orientation) { + case 'sagittal': + rendererObj = this.r1; + break; + case 'axial': + rendererObj = this.r2; + break; + case 'coronal': + rendererObj = this.r3; + break; + } + + + var container = this.getContainer(); + rendererObj.camera.canvas = { + width: container.offsetWidth, + height: container.offsetHeight, + }; + rendererObj.stackHelper.slice.canvasWidth = + container.offsetWidth; + rendererObj.stackHelper.slice.canvasHeight = + container.offsetHeight + 20; + rendererObj.camera.fitBox(2); + rendererObj.renderer.setSize(container.offsetWidth, container.offsetHeight); + } + + setLayout() { + if (this.state.mode == 'single_view') { + this.setSingleLayout(); + } + else { + this.setQuadLayout(); + } + } + + componentDidUpdate(prevProps, prevState) { + this.setLayout(); } changeMode() { @@ -76,66 +478,26 @@ define(function (require) { } changeOrientation() { - if (this.camera.orientation == "coronal") { - this.camera.orientation = "sagittal"; + var newOrientation; + if (this.state.orientation == "coronal") { + newOrientation = "sagittal"; } - else if (this.camera.orientation == "sagittal") { - this.camera.orientation = "axial"; + else if (this.state.orientation == "sagittal") { + newOrientation = "axial"; } - else if (this.camera.orientation == "axial") { - this.camera.orientation = "coronal"; + else if (this.state.orientation == "axial") { + newOrientation = "coronal"; } - this.camera.update() - this.camera.fitBox(2) - this.stackHelper.orientation = this.camera.stackOrientation; - this.stackHelper.index = Math.floor(this.stackHelper.orientationMaxIndex / 2); + + this.setState({ orientation: newOrientation }); } download() { GEPPETTO.Utility.createZipFromRemoteFiles(this.state.files, "data.zip"); } - /** - * - * @returns {{widgetType, isWidget}|{size: {height: *, width: *}, position: {left: *, top: *}}} - */ - getView() { - // add data-type and data field + any other custom fields in the component-specific attribute - var baseView = super.getView(); - baseView.data = this.props.data; - return baseView; - } - - /** - * - * @param view - */ - setView(view) { - // set base properties - super.setView(view) - if (view.data != undefined){ - this.setData(view.data); - } - } - render() { - var dicomViewerContent; - if (this.state.mode == "single_view") { - dicomViewerContent = ( -
-
- ) - } - else if (this.state.mode == "quad_view") { - dicomViewerContent = ( -
-
-
-
-
-
- ) - } + return (
) } diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js deleted file mode 100644 index f2fa10b2d..000000000 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewerEngine.js +++ /dev/null @@ -1,857 +0,0 @@ -var AMI = require('./ami.min.js'); -var LoadersVolume = AMI.default.Loaders.Volume; -var CamerasOrthographic = AMI.default.Cameras.Orthographic; -var ControlsOrthographic = AMI.default.Controls.TrackballOrtho; -var HelpersStack = AMI.default.Helpers.Stack; -var ControlsTrackball = AMI.default.Controls.Trackball; -var HelpersBoundingBox = AMI.default.Helpers.BoundingBox; -var ModelsStack = AMI.default.Models.Stack; -var HelpersLocalizer = AMI.default.Helpers.Localizer; - -module.exports = { - loadSingleView: function (component) { - - // Setup renderer - var container = component.getContainer().getElementsByClassName('dicomViewer')[0]; - container.innerHTML = ''; - var renderer = new THREE.WebGLRenderer({ - antialias: true, - }); - renderer.setSize(container.offsetWidth, container.offsetHeight); - renderer.setClearColor(0x353535, 1); - renderer.setPixelRatio(window.devicePixelRatio); - container.appendChild(renderer.domElement); - - // Setup scene - var scene = new THREE.Scene(); - - // Setup camera - var camera = new CamerasOrthographic( - container.clientWidth / -2, container.clientWidth / 2, - container.clientHeight / 2, container.clientHeight / -2, - 0.1, 10000); - - component.camera = camera; - - // Setup controls - var controls = new ControlsOrthographic(camera, container); - controls.staticMoving = true; - controls.noRotate = true; - camera.controls = controls; - - /** - * Handle window resize - */ - function onWindowResize() { - camera.canvas = { - width: container.offsetWidth, - height: container.offsetHeight, - }; - camera.fitBox(2); - - renderer.setSize(container.offsetWidth, container.offsetHeight); - } - window.addEventListener('resize', onWindowResize, false); - - $("#" + component.props.id).on("dialogresizestop", function (event, ui) { - camera.canvas = { - width: container.offsetWidth, - height: container.offsetHeight, - }; - camera.fitBox(2); - renderer.setSize(container.offsetWidth, container.offsetHeight); - }); - - /** - * Start animation loop - */ - function animate() { - controls.update(); - renderer.render(scene, camera); - - // request new frame - requestAnimationFrame(function () { - if (component.state.mode == "single_view") { - animate(); - } - }); - } - animate(); - - // Setup loader - var loader = new LoadersVolume(container); - loader.load(component.state.files) - .then(function () { - // merge files into clean series/stack/frame structure - var series = loader.data[0].mergeSeries(loader.data); - var stack = series[0].stack[0]; - loader.free(); - loader = null; - // be carefull that series and target stack exist! - var stackHelper = new HelpersStack(stack); - component.stackHelper = stackHelper; - // stackHelper.orientation = 2; - stackHelper.index = Math.floor(stack._dimensionsIJK.z / 2); - - // tune bounding box - stackHelper.bbox.visible = false; - - // tune slice border - stackHelper.border.color = 0xFF9800; - // stackHelper.border.visible = false; - - scene.add(stackHelper); - - // hook up callbacks - controls.addEventListener('OnScroll', function (e) { - if (e.delta > 0) { - if (stackHelper.index >= stackHelper.orientationMaxIndex - 1) { - return false; - } - stackHelper.index += 1; - } else { - if (stackHelper.index <= 0) { - return false; - } - stackHelper.index -= 1; - } - - }); - - // center camera and interactor to center of bouding box - // for nicer experience - // set camera - var worldbb = stack.worldBoundingBox(); - var lpsDims = new THREE.Vector3( - worldbb[1] - worldbb[0], - worldbb[3] - worldbb[2], - worldbb[5] - worldbb[4] - ); - - // box: {halfDimensions, center} - var box = { - center: stack.worldCenter().clone(), - halfDimensions: - new THREE.Vector3(lpsDims.x + 10, lpsDims.y + 10, lpsDims.z + 10), - }; - - // init and zoom - var canvas = { - width: container.clientWidth, - height: container.clientHeight, - }; - - camera.directions = [stack.xCosine, stack.yCosine, stack.zCosine]; - camera.box = box; - camera.canvas = canvas; - camera.update(); - - // Not working properly. See issue: https://github.com/FNNDSC/ami/issues/120 - //camera.fitBox(2, 2); - camera.fitBox(2); - }) - .catch(function (error) { - window.console.log('oops... something went wrong...'); - window.console.log(error); - }); - - - - }, - - loadQuadView: function (component) { - - let ready = false; - - // 3d renderer - let r0 = { - domClass: 'r0', - domElement: null, - renderer: null, - color: 0x212121, - targetID: 0, - camera: null, - controls: null, - scene: null, - light: null, - }; - - // 2d axial renderer - let r1 = { - domClass: 'r1', - domElement: null, - renderer: null, - color: 0x121212, - sliceOrientation: 'axial', - sliceColor: 0xFF1744, - targetID: 1, - camera: null, - controls: null, - scene: null, - light: null, - stackHelper: null, - localizerHelper: null, - localizerScene: null, - }; - - // 2d sagittal renderer - let r2 = { - domClass: 'r2', - domElement: null, - renderer: null, - color: 0x121212, - sliceOrientation: 'sagittal', - sliceColor: 0xFFEA00, - targetID: 2, - camera: null, - controls: null, - scene: null, - light: null, - stackHelper: null, - localizerHelper: null, - localizerScene: null, - }; - - - // 2d coronal renderer - let r3 = { - domClass: 'r3', - domElement: null, - renderer: null, - color: 0x121212, - sliceOrientation: 'coronal', - sliceColor: 0x76FF03, - targetID: 3, - camera: null, - controls: null, - scene: null, - light: null, - stackHelper: null, - localizerHelper: null, - localizerScene: null, - }; - - // data to be loaded - // let dataInfo = [ - // ['adi1', { - // location: - // 'https://cdn.rawgit.com/FNNDSC/data/master/dicom/adi_brain/mesh.stl', - // label: 'Left', - // loaded: false, - // material: null, - // materialFront: null, - // materialBack: null, - // mesh: null, - // meshFront: null, - // meshBack: null, - // color: 0xe91e63, - // opacity: 0.7, - // }], - // ['adi2', { - // location: - // 'https://cdn.rawgit.com/FNNDSC/data/master/dicom/adi_brain/mesh2.stl', - // label: 'Right', - // loaded: false, - // material: null, - // materialFront: null, - // materialBack: null, - // mesh: null, - // meshFront: null, - // meshBack: null, - // color: 0x03a9f4, - // opacity: 1, - // }], - // ]; - // let data = new Map(dataInfo); - - // extra variables to show mesh plane intersections in 2D renderers - let sceneClip = new THREE.Scene(); - let clipPlane1 = new THREE.Plane(new THREE.Vector3(0, 0, 0), 0); - let clipPlane2 = new THREE.Plane(new THREE.Vector3(0, 0, 0), 0); - let clipPlane3 = new THREE.Plane(new THREE.Vector3(0, 0, 0), 0); - - function initRenderer3D(renderObj) { - // renderer - renderObj.domElement = component.getContainer().getElementsByClassName(renderObj.domClass)[0]; - renderObj.domElement.innerHTML = ''; - - renderObj.renderer = new THREE.WebGLRenderer({ - antialias: true, - }); - renderObj.renderer.setSize( - renderObj.domElement.clientWidth, renderObj.domElement.clientHeight); - renderObj.renderer.setClearColor(renderObj.color, 1); - renderObj.renderer.domElement.id = renderObj.targetID; - renderObj.domElement.appendChild(renderObj.renderer.domElement); - - // camera - renderObj.camera = new THREE.PerspectiveCamera( - 45, renderObj.domElement.clientWidth / renderObj.domElement.clientHeight, - 0.1, 100000); - renderObj.camera.position.x = 250; - renderObj.camera.position.y = 250; - renderObj.camera.position.z = 250; - - // controls - renderObj.controls = new ControlsTrackball( - renderObj.camera, renderObj.domElement); - renderObj.controls.rotateSpeed = 5.5; - renderObj.controls.zoomSpeed = 1.2; - renderObj.controls.panSpeed = 0.8; - renderObj.controls.staticMoving = true; - renderObj.controls.dynamicDampingFactor = 0.3; - - // scene - renderObj.scene = new THREE.Scene(); - - // light - renderObj.light = new THREE.DirectionalLight(0xffffff, 1); - renderObj.light.position.copy(renderObj.camera.position); - renderObj.scene.add(renderObj.light); - - } - - function initRenderer2D(rendererObj) { - // renderer - rendererObj.domElement = component.getContainer().getElementsByClassName(rendererObj.domClass)[0]; - rendererObj.domElement.innerHTML = ''; - rendererObj.renderer = new THREE.WebGLRenderer({ - antialias: true, - }); - rendererObj.renderer.autoClear = false; - rendererObj.renderer.localClippingEnabled = true; - rendererObj.renderer.setSize( - rendererObj.domElement.clientWidth, rendererObj.domElement.clientHeight); - rendererObj.renderer.setClearColor(0x121212, 1); - rendererObj.renderer.domElement.id = rendererObj.targetID; - rendererObj.domElement.appendChild(rendererObj.renderer.domElement); - - // camera - rendererObj.camera = new CamerasOrthographic( - rendererObj.domElement.clientWidth / -2, - rendererObj.domElement.clientWidth / 2, - rendererObj.domElement.clientHeight / 2, - rendererObj.domElement.clientHeight / -2, - 1, 1000); - - // controls - rendererObj.controls = new ControlsOrthographic( - rendererObj.camera, rendererObj.domElement); - rendererObj.controls.staticMoving = true; - rendererObj.controls.noRotate = true; - rendererObj.camera.controls = rendererObj.controls; - - // scene - rendererObj.scene = new THREE.Scene(); - } - - function initHelpersStack(rendererObj, stack) { - rendererObj.stackHelper = new HelpersStack(stack); - rendererObj.stackHelper.bbox.visible = false; - rendererObj.stackHelper.borderColor = rendererObj.sliceColor; - rendererObj.stackHelper.slice.canvasWidth = - rendererObj.domElement.clientWidth; - rendererObj.stackHelper.slice.canvasHeight = - rendererObj.domElement.clientHeight; - - // set camera - let worldbb = stack.worldBoundingBox(); - let lpsDims = new THREE.Vector3( - (worldbb[1] - worldbb[0]) / 2, - (worldbb[3] - worldbb[2]) / 2, - (worldbb[5] - worldbb[4]) / 2 - ); - - // box: {halfDimensions, center} - let box = { - center: stack.worldCenter().clone(), - halfDimensions: - new THREE.Vector3(lpsDims.x + 10, lpsDims.y + 10, lpsDims.z + 10), - }; - - // init and zoom - let canvas = { - width: rendererObj.domElement.clientWidth, - height: rendererObj.domElement.clientHeight, - }; - - rendererObj.camera.directions = - [stack.xCosine, stack.yCosine, stack.zCosine]; - rendererObj.camera.box = box; - rendererObj.camera.canvas = canvas; - rendererObj.camera.orientation = rendererObj.sliceOrientation; - rendererObj.camera.update(); - rendererObj.camera.fitBox(2, 1); - - rendererObj.stackHelper.orientation = rendererObj.camera.stackOrientation; - rendererObj.stackHelper.index = - Math.floor(rendererObj.stackHelper.orientationMaxIndex / 2); - rendererObj.scene.add(rendererObj.stackHelper); - } - - function initHelpersLocalizer(rendererObj, stack, referencePlane, localizers) { - rendererObj.localizerHelper = new HelpersLocalizer( - stack, rendererObj.stackHelper.slice.geometry, referencePlane); - - for (let i = 0; i < localizers.length; i++) { - rendererObj.localizerHelper['plane' + (i + 1)] = localizers[i].plane; - rendererObj.localizerHelper['color' + (i + 1)] = localizers[i].color; - } - - rendererObj.localizerHelper.canvasWidth = - rendererObj.domElement.clientWidth; - rendererObj.localizerHelper.canvasHeight = - rendererObj.domElement.clientHeight; - - rendererObj.localizerScene = new THREE.Scene(); - rendererObj.localizerScene.add(rendererObj.localizerHelper); - } - - /** - * Init the quadview - */ - function init() { - /** - * Called on each animation frame - */ - function animate() { - // we are ready when both meshes have been loaded - if (ready) { - // render - r0.controls.update(); - r1.controls.update(); - r2.controls.update(); - r3.controls.update(); - - r0.light.position.copy(r0.camera.position); - r0.renderer.render(r0.scene, r0.camera); - - // r1 - r1.renderer.clear(); - r1.renderer.render(r1.scene, r1.camera); - // mesh - //r1.renderer.clearDepth(); - // data.forEach(function (object, key) { - // object.materialFront.clippingPlanes = [clipPlane1]; - // object.materialBack.clippingPlanes = [clipPlane1]; - // }); - //r1.renderer.render(sceneClip, r1.camera); - // localizer - r1.renderer.clearDepth(); - r1.renderer.render(r1.localizerScene, r1.camera); - - // r2 - r2.renderer.clear(); - r2.renderer.render(r2.scene, r2.camera); - // mesh - //r2.renderer.clearDepth(); - // data.forEach(function (object, key) { - // object.materialFront.clippingPlanes = [clipPlane2]; - // object.materialBack.clippingPlanes = [clipPlane2]; - // }); - //r2.renderer.render(sceneClip, r2.camera); - // localizer - r2.renderer.clearDepth(); - r2.renderer.render(r2.localizerScene, r2.camera); - - // r3 - r3.renderer.clear(); - r3.renderer.render(r3.scene, r3.camera); - // mesh - //r3.renderer.clearDepth(); - // data.forEach(function (object, key) { - // object.materialFront.clippingPlanes = [clipPlane3]; - // object.materialBack.clippingPlanes = [clipPlane3]; - // }); - //r3.renderer.render(sceneClip, r3.camera); - // localizer - r3.renderer.clearDepth(); - r3.renderer.render(r3.localizerScene, r3.camera); - } - - // request new frame - requestAnimationFrame(function () { - if (component.state.mode == "quad_view") { - animate(); - } - }); - } - - // renderers - initRenderer3D(r0); - initRenderer2D(r1); - initRenderer2D(r2); - initRenderer2D(r3); - - // start rendering loop - animate(); - } - - // init threeJS - init(); - - - // load sequence for each file - // instantiate the loader - // it loads and parses the dicom image - let loader = new LoadersVolume(); - loader.load(component.state.files) - .then(function () { - let series = loader.data[0].mergeSeries(loader.data)[0]; - loader.free(); - loader = null; - // get first stack from series - let stack = series.stack[0]; - stack.prepare(); - - // center 3d camera/control on the stack - let centerLPS = stack.worldCenter(); - r0.camera.lookAt(centerLPS.x, centerLPS.y, centerLPS.z); - r0.camera.updateProjectionMatrix(); - r0.controls.target.set(centerLPS.x, centerLPS.y, centerLPS.z); - - // bouding box - let boxHelper = new HelpersBoundingBox(stack); - r0.scene.add(boxHelper); - - // red slice - initHelpersStack(r1, stack); - r0.scene.add(r1.scene); - - // yellow slice - initHelpersStack(r2, stack); - r0.scene.add(r2.scene); - - // green slice - initHelpersStack(r3, stack); - r0.scene.add(r3.scene); - - // create new mesh with Localizer shaders - let plane1 = r1.stackHelper.slice.cartesianEquation(); - let plane2 = r2.stackHelper.slice.cartesianEquation(); - let plane3 = r3.stackHelper.slice.cartesianEquation(); - - // localizer red slice - initHelpersLocalizer(r1, stack, plane1, [ - { - plane: plane2, - color: new THREE.Color(r2.stackHelper.borderColor), - }, - { - plane: plane3, - color: new THREE.Color(r3.stackHelper.borderColor), - }, - ]); - - // localizer yellow slice - initHelpersLocalizer(r2, stack, plane2, [ - { - plane: plane1, - color: new THREE.Color(r1.stackHelper.borderColor), - }, - { - plane: plane3, - color: new THREE.Color(r3.stackHelper.borderColor), - }, - ]); - - // localizer green slice - initHelpersLocalizer(r3, stack, plane3, [ - { - plane: plane1, - color: new THREE.Color(r1.stackHelper.borderColor), - }, - { - plane: plane2, - color: new THREE.Color(r2.stackHelper.borderColor), - }, - ]); - - - - /** - * Update Layer Mix - */ - function updateLocalizer(refObj, targetLocalizersHelpers) { - let refHelper = refObj.stackHelper; - let localizerHelper = refObj.localizerHelper; - let plane = refHelper.slice.cartesianEquation(); - localizerHelper.referencePlane = plane; - - // bit of a hack... works fine for this application - for (let i = 0; i < targetLocalizersHelpers.length; i++) { - for (let j = 0; j < 4; j++) { - let targetPlane = targetLocalizersHelpers[i]['plane' + (j + 1)]; - if (targetPlane && - plane.x === targetPlane.x && - plane.y === targetPlane.y && - plane.z === targetPlane.z) { - targetLocalizersHelpers[i]['plane' + (j + 1)] = plane; - } - } - } - - // update the geometry will create a new mesh - localizerHelper.geometry = refHelper.slice.geometry; - } - - function updateClipPlane(refObj, clipPlane) { - const stackHelper = refObj.stackHelper; - const camera = refObj.camera; - let vertices = stackHelper.slice.geometry.vertices; - let p1 = new THREE.Vector3(vertices[0].x, vertices[0].y, vertices[0].z) - .applyMatrix4(stackHelper._stack.ijk2LPS); - let p2 = new THREE.Vector3(vertices[1].x, vertices[1].y, vertices[1].z) - .applyMatrix4(stackHelper._stack.ijk2LPS); - let p3 = new THREE.Vector3(vertices[2].x, vertices[2].y, vertices[2].z) - .applyMatrix4(stackHelper._stack.ijk2LPS); - - clipPlane.setFromCoplanarPoints(p1, p2, p3); - - let cameraDirection = new THREE.Vector3(1, 1, 1); - cameraDirection.applyQuaternion(camera.quaternion); - - if (cameraDirection.dot(clipPlane.normal) > 0) { - clipPlane.negate(); - } - } - - function onYellowChanged() { - updateLocalizer(r2, [r1.localizerHelper, r3.localizerHelper]); - updateClipPlane(r2, clipPlane2); - } - - function onRedChanged() { - updateLocalizer(r1, [r2.localizerHelper, r3.localizerHelper]); - updateClipPlane(r1, clipPlane1); - } - - function onGreenChanged() { - updateLocalizer(r3, [r1.localizerHelper, r2.localizerHelper]); - updateClipPlane(r3, clipPlane3); - } - - function onDoubleClick(event) { - const canvas = event.srcElement.parentElement; - const id = event.target.id; - const mouse = { - x: ((event.clientX - $(canvas).offset().left) / canvas.clientWidth) * 2 - 1, - y: - ((event.clientY - $(canvas).offset().top) / canvas.clientHeight) * 2 + 1, - }; - - - let camera = null; - let stackHelper = null; - let scene = null; - switch (id) { - case '0': - camera = r0.camera; - stackHelper = r1.stackHelper; - scene = r0.scene; - break; - case '1': - camera = r1.camera; - stackHelper = r1.stackHelper; - scene = r1.scene; - break; - case '2': - camera = r2.camera; - stackHelper = r2.stackHelper; - scene = r2.scene; - break; - case '3': - camera = r3.camera; - stackHelper = r3.stackHelper; - scene = r3.scene; - break; - } - - const raycaster = new THREE.Raycaster(); - raycaster.setFromCamera(mouse, camera); - - const intersects = raycaster.intersectObjects(scene.children, true); - if (intersects.length > 0) { - let ijk = - ModelsStack.worldToData(stackHelper.stack, intersects[0].point); - r1.stackHelper.index = - ijk.getComponent((r1.stackHelper.orientation + 2) % 3); - r2.stackHelper.index = - ijk.getComponent((r2.stackHelper.orientation + 2) % 3); - r3.stackHelper.index = - ijk.getComponent((r3.stackHelper.orientation + 2) % 3); - - onGreenChanged(); - onRedChanged(); - onYellowChanged(); - } - } - - // event listeners - r0.domElement.addEventListener('dblclick', onDoubleClick); - r1.domElement.addEventListener('dblclick', onDoubleClick); - r2.domElement.addEventListener('dblclick', onDoubleClick); - r3.domElement.addEventListener('dblclick', onDoubleClick); - - function onScroll(event) { - const id = $(event.target.domElement).data("id"); - let stackHelper = null; - switch (id) { - case 'r1': - stackHelper = r1.stackHelper; - break; - case 'r2': - stackHelper = r2.stackHelper; - break; - case 'r3': - stackHelper = r3.stackHelper; - break; - } - - if (event.delta > 0) { - if (stackHelper.index >= stackHelper.orientationMaxIndex - 1) { - return false; - } - stackHelper.index += 1; - } else { - if (stackHelper.index <= 0) { - return false; - } - stackHelper.index -= 1; - } - - onGreenChanged(); - onRedChanged(); - onYellowChanged(); - } - - // event listeners - r1.controls.addEventListener('OnScroll', onScroll); - r2.controls.addEventListener('OnScroll', onScroll); - r3.controls.addEventListener('OnScroll', onScroll); - - function windowResize2D(rendererObj) { - rendererObj.camera.canvas = { - width: rendererObj.domElement.clientWidth, - height: rendererObj.domElement.clientHeight, - }; - rendererObj.camera.fitBox(2, 1); - rendererObj.renderer.setSize( - rendererObj.domElement.clientWidth, - rendererObj.domElement.clientHeight); - - // update info to draw borders properly - rendererObj.stackHelper.slice.canvasWidth = - rendererObj.domElement.clientWidth; - rendererObj.stackHelper.slice.canvasHeight = - rendererObj.domElement.clientHeight; - rendererObj.localizerHelper.canvasWidth = - rendererObj.domElement.clientWidth; - rendererObj.localizerHelper.canvasHeight = - rendererObj.domElement.clientHeight; - } - - function onWindowResize() { - // update 3D - r0.camera.aspect = r0.domElement.clientWidth / r0.domElement.clientHeight; - r0.camera.updateProjectionMatrix(); - r0.renderer.setSize( - r0.domElement.clientWidth, r0.domElement.clientHeight); - - // update 2d - windowResize2D(r1); - windowResize2D(r2); - windowResize2D(r3); - } - - window.addEventListener('resize', onWindowResize, false); - - $("#" + component.props.id).on("dialogresizestop", function (event, ui) { - // update 3D - r0.camera.aspect = r0.domElement.clientWidth / r0.domElement.clientHeight; - r0.camera.updateProjectionMatrix(); - r0.renderer.setSize( - r0.domElement.clientWidth, r0.domElement.clientHeight); - - // update 2d - windowResize2D(r1); - windowResize2D(r2); - windowResize2D(r3); - - }); - - - ready = true; - - // load meshes on the stack is all set - // let meshesLoaded = 0; - // function loadSTLObject(object) { - // const stlLoader = new THREE.STLLoader(); - // stlLoader.load(object.location, function (geometry) { - // // 3D mesh - // object.material = new THREE.MeshLambertMaterial({ - // opacity: object.opacity, - // color: object.color, - // clippingPlanes: [], - // side: THREE.DoubleSide, - // transparent: true, - // }); - // object.mesh = new THREE.Mesh(geometry, object.material); - // const RASToLPS = new THREE.Matrix4(); - // RASToLPS.set(-1, 0, 0, 0, - // 0, -1, 0, 0, - // 0, 0, 1, 0, - // 0, 0, 0, 1); - // object.mesh.applyMatrix(RASToLPS); - // r0.scene.add(object.mesh); - - // // front - // object.materialFront = new THREE.MeshBasicMaterial({ - // color: object.color, - // side: THREE.FrontSide, - // depthWrite: true, - // opacity: 0, - // transparent: true, - // clippingPlanes: [], - // }); - - // object.meshFront = new THREE.Mesh(geometry, object.materialFront); - // object.meshFront.applyMatrix(RASToLPS); - // sceneClip.add(object.meshFront); - - // // back - // object.materialBack = new THREE.MeshBasicMaterial({ - // color: object.color, - // side: THREE.BackSide, - // depthWrite: true, - // opacity: object.opacity, - // transparent: true, - // clippingPlanes: [], - // }); - - // object.meshBack = new THREE.Mesh(geometry, object.materialBack); - // object.meshBack.applyMatrix(RASToLPS); - // sceneClip.add(object.meshBack); - - // meshesLoaded++; - - // onGreenChanged(); - // onRedChanged(); - // onYellowChanged(); - - // // good to go - // if (meshesLoaded === data.size) { - // ready = true; - // } - // }); - // } - - // data.forEach(function (object, key) { - // loadSTLObject(object); - // }); - }) - .catch(function (error) { - window.console.log('oops... something went wrong...'); - window.console.log(error); - }); - } -}; diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewerUtils.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewerUtils.js new file mode 100644 index 000000000..6500350e4 --- /dev/null +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewerUtils.js @@ -0,0 +1,193 @@ +var AMI = require('./ami.min.js'); +// var LoadersVolume = AMI.default.Loaders.Volume; +var CamerasOrthographic = AMI.default.Cameras.Orthographic; +var ControlsOrthographic = AMI.default.Controls.TrackballOrtho; +var HelpersStack = AMI.default.Helpers.Stack; +var ControlsTrackball = AMI.default.Controls.Trackball; +// var HelpersBoundingBox = AMI.default.Helpers.BoundingBox; +// var ModelsStack = AMI.default.Models.Stack; +var HelpersLocalizer = AMI.default.Helpers.Localizer; + +module.exports = { + windowResize2D: function (rendererObj) { + rendererObj.camera.canvas = { + width: rendererObj.domElement.clientWidth, + height: rendererObj.domElement.clientHeight, + }; + rendererObj.camera.fitBox(2, 1); + rendererObj.renderer.setSize( + rendererObj.domElement.clientWidth, + rendererObj.domElement.clientHeight); + + // update info to draw borders properly + rendererObj.stackHelper.slice.canvasWidth = + rendererObj.domElement.clientWidth; + rendererObj.stackHelper.slice.canvasHeight = + rendererObj.domElement.clientHeight; + rendererObj.localizerHelper.canvasWidth = + rendererObj.domElement.clientWidth; + rendererObj.localizerHelper.canvasHeight = + rendererObj.domElement.clientHeight; + }, + + initHelpersStack: function (rendererObj, stack) { + rendererObj.stackHelper = new HelpersStack(stack); + rendererObj.stackHelper.bbox.visible = false; + rendererObj.stackHelper.borderColor = rendererObj.sliceColor; + rendererObj.stackHelper.slice.canvasWidth = + rendererObj.domElement.clientWidth; + rendererObj.stackHelper.slice.canvasHeight = + rendererObj.domElement.clientHeight; + + // set camera + let worldbb = stack.worldBoundingBox(); + let lpsDims = new THREE.Vector3( + (worldbb[1] - worldbb[0]) / 2, + (worldbb[3] - worldbb[2]) / 2, + (worldbb[5] - worldbb[4]) / 2 + ); + + // box: {halfDimensions, center} + let box = { + center: stack.worldCenter().clone(), + halfDimensions: + new THREE.Vector3(lpsDims.x + 10, lpsDims.y + 10, lpsDims.z + 10), + }; + + // init and zoom + let canvas = { + width: rendererObj.domElement.clientWidth, + height: rendererObj.domElement.clientHeight, + }; + + rendererObj.camera.directions = + [stack.xCosine, stack.yCosine, stack.zCosine]; + rendererObj.camera.box = box; + rendererObj.camera.canvas = canvas; + rendererObj.camera.orientation = rendererObj.sliceOrientation; + rendererObj.camera.update(); + rendererObj.camera.fitBox(2, 1); + + rendererObj.stackHelper.orientation = rendererObj.camera.stackOrientation; + rendererObj.stackHelper.index = + Math.floor(rendererObj.stackHelper.orientationMaxIndex / 2); + rendererObj.scene.add(rendererObj.stackHelper); + }, + + initHelpersLocalizer: function (rendererObj, stack, referencePlane, localizers) { + rendererObj.localizerHelper = new HelpersLocalizer( + stack, rendererObj.stackHelper.slice.geometry, referencePlane); + + for (let i = 0; i < localizers.length; i++) { + rendererObj.localizerHelper['plane' + (i + 1)] = localizers[i].plane; + rendererObj.localizerHelper['color' + (i + 1)] = localizers[i].color; + } + + rendererObj.localizerHelper.canvasWidth = + rendererObj.domElement.clientWidth; + rendererObj.localizerHelper.canvasHeight = + rendererObj.domElement.clientHeight; + + rendererObj.localizerScene = new THREE.Scene(); + rendererObj.localizerScene.add(rendererObj.localizerHelper); + }, + + updateLocalizer: function (refObj, targetLocalizersHelpers) { + let refHelper = refObj.stackHelper; + let localizerHelper = refObj.localizerHelper; + let plane = refHelper.slice.cartesianEquation(); + localizerHelper.referencePlane = plane; + + // bit of a hack... works fine for this application + for (let i = 0; i < targetLocalizersHelpers.length; i++) { + for (let j = 0; j < 4; j++) { + let targetPlane = targetLocalizersHelpers[i]['plane' + (j + 1)]; + if (targetPlane && + plane.x === targetPlane.x && + plane.y === targetPlane.y && + plane.z === targetPlane.z) { + targetLocalizersHelpers[i]['plane' + (j + 1)] = plane; + } + } + } + + // update the geometry will create a new mesh + localizerHelper.geometry = refHelper.slice.geometry; + }, + + initRenderer2D: function (rendererObj, parentContainer) { + // renderer + rendererObj.domElement = parentContainer.getElementsByClassName(rendererObj.domClass)[0]; + rendererObj.domElement.innerHTML = ''; + rendererObj.renderer = new THREE.WebGLRenderer({ + antialias: true, + }); + rendererObj.renderer.autoClear = false; + rendererObj.renderer.localClippingEnabled = true; + rendererObj.renderer.setSize( + rendererObj.domElement.clientWidth, rendererObj.domElement.clientHeight); + rendererObj.renderer.setClearColor(0x121212, 1); + rendererObj.renderer.setPixelRatio(window.devicePixelRatio); + rendererObj.renderer.domElement.id = rendererObj.targetID; + rendererObj.domElement.appendChild(rendererObj.renderer.domElement); + + // camera + rendererObj.camera = new CamerasOrthographic( + rendererObj.domElement.clientWidth / -2, + rendererObj.domElement.clientWidth / 2, + rendererObj.domElement.clientHeight / 2, + rendererObj.domElement.clientHeight / -2, + 1, 1000); + + // controls + rendererObj.controls = new ControlsOrthographic( + rendererObj.camera, rendererObj.domElement); + rendererObj.controls.staticMoving = true; + rendererObj.controls.noRotate = true; + rendererObj.camera.controls = rendererObj.controls; + + // scene + rendererObj.scene = new THREE.Scene(); + }, + + initRenderer3D: function (renderObj, parentContainer) { + // renderer + renderObj.domElement = parentContainer.getElementsByClassName(renderObj.domClass)[0]; + renderObj.domElement.innerHTML = ''; + + renderObj.renderer = new THREE.WebGLRenderer({ + antialias: true, + }); + renderObj.renderer.setSize( + renderObj.domElement.clientWidth, renderObj.domElement.clientHeight); + renderObj.renderer.setClearColor(renderObj.color, 1); + renderObj.renderer.domElement.id = renderObj.targetID; + renderObj.domElement.appendChild(renderObj.renderer.domElement); + + // camera + renderObj.camera = new THREE.PerspectiveCamera( + 45, renderObj.domElement.clientWidth / renderObj.domElement.clientHeight, + 0.1, 100000); + renderObj.camera.position.x = 250; + renderObj.camera.position.y = 250; + renderObj.camera.position.z = 250; + + // controls + renderObj.controls = new ControlsTrackball( + renderObj.camera, renderObj.domElement); + renderObj.controls.rotateSpeed = 5.5; + renderObj.controls.zoomSpeed = 1.2; + renderObj.controls.panSpeed = 0.8; + renderObj.controls.staticMoving = true; + renderObj.controls.dynamicDampingFactor = 0.3; + + // scene + renderObj.scene = new THREE.Scene(); + + // light + renderObj.light = new THREE.DirectionalLight(0xffffff, 1); + renderObj.light.position.copy(renderObj.camera.position); + renderObj.scene.add(renderObj.light); + + } +}; From f258266c693b5cf3340635b333cd82722c22c1f9 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 29 May 2017 20:41:11 +0100 Subject: [PATCH 024/371] exclude ami.js --- src/main/webapp/webpack.config.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/webapp/webpack.config.js b/src/main/webapp/webpack.config.js index d7a4cde42..efcef2f41 100644 --- a/src/main/webapp/webpack.config.js +++ b/src/main/webapp/webpack.config.js @@ -148,7 +148,8 @@ module.exports = { noParse: [/node_modules\/plotly.js\/dist\/plotly.js/, /js\/components\/interface\/dicomViewer\/ami.min.js/], loaders: [ { - test: /\.(js)$/, exclude: [/node_modules/, /build/, /\.bundle/], loader: ['babel-loader'], + test: /\.(js)$/, exclude: [/node_modules/, /build/, /\.bundle/, /ami.min.js/], loader: ['babel-loader'], + query: { presets: ['react', 'es2015'] } From 38460ee2a803d69269f48a5980c1257f1154112d Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 29 May 2017 21:26:57 +0100 Subject: [PATCH 025/371] change download button --- src/main/webapp/js/components/widgets/AWidget.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/js/components/widgets/AWidget.js b/src/main/webapp/js/components/widgets/AWidget.js index 10f932f4c..6d8ba3630 100644 --- a/src/main/webapp/js/components/widgets/AWidget.js +++ b/src/main/webapp/js/components/widgets/AWidget.js @@ -436,7 +436,7 @@ define(function (require) { addDownloadButton(downloadFunction){ var that = this; - this.addButtonToTitleBar($("
").click(function () { + this.addButtonToTitleBar($("
").click(function () { that.download(); })); } From 9b174debeb10d9b4744a8547a2831426384273f9 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 29 May 2017 23:03:04 +0100 Subject: [PATCH 026/371] add widget button bar component --- .../widgetButtonBar/WidgetButtonBar.js | 27 +++++++++++++++++++ .../widgetButtonBar/WidgetButtonBar.less | 14 ++++++++++ 2 files changed, 41 insertions(+) create mode 100644 src/main/webapp/js/components/controls/widgetButtonBar/WidgetButtonBar.js create mode 100644 src/main/webapp/js/components/controls/widgetButtonBar/WidgetButtonBar.less diff --git a/src/main/webapp/js/components/controls/widgetButtonBar/WidgetButtonBar.js b/src/main/webapp/js/components/controls/widgetButtonBar/WidgetButtonBar.js new file mode 100644 index 000000000..5bc450402 --- /dev/null +++ b/src/main/webapp/js/components/controls/widgetButtonBar/WidgetButtonBar.js @@ -0,0 +1,27 @@ +define(function (require) { + + var React = require('react'); + require("./WidgetButtonBar.less"); + + var WidgetButtonBar = React.createClass({ + getInitialState: function () { + return { + + }; + }, + + componentDidMount: function () { + + }, + + render: function () { + return ( +
+ {this.props.children} +
+ ); + } + }); + + return WidgetButtonBar; +}); \ No newline at end of file diff --git a/src/main/webapp/js/components/controls/widgetButtonBar/WidgetButtonBar.less b/src/main/webapp/js/components/controls/widgetButtonBar/WidgetButtonBar.less new file mode 100644 index 000000000..0e6f29825 --- /dev/null +++ b/src/main/webapp/js/components/controls/widgetButtonBar/WidgetButtonBar.less @@ -0,0 +1,14 @@ +.displayArea{ + position: absolute; + top: 0; + left: 0; + width: 20px; + margin: 6px; +} + +.displayArea > button{ + padding: 0; + z-index: 999; + border: 0; + background: transparent !important; +} From 35329541bb48e7c6cfe411de574056add2fc8906 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 29 May 2017 23:03:25 +0100 Subject: [PATCH 027/371] use widget button bar component --- .../bigImageViewer/BigImageViewer.js | 33 ++++--------------- 1 file changed, 7 insertions(+), 26 deletions(-) diff --git a/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js b/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js index c6fbbd57b..5f2583dc1 100644 --- a/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js +++ b/src/main/webapp/js/components/interface/bigImageViewer/BigImageViewer.js @@ -4,6 +4,7 @@ define(function (require) { var React = require('react'); var OpenSeaDragon = require('openseadragon'); + var WidgetButtonBar = require('../../controls/widgetButtonBar/WidgetButtonBar'); var AbstractComponent = require('../../AComponent'); return class BigImageViewer extends AbstractComponent { @@ -65,32 +66,12 @@ define(function (require) { render() { return (
-
-
+ +
) } From 60de98cd8070211af98bb33b7031ef622821b0d7 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 29 May 2017 23:04:14 +0100 Subject: [PATCH 028/371] use widget button bar component, clean up, fix resize event, bug fixing --- .../interface/dicomViewer/DicomViewer.js | 53 +++++++------------ .../interface/dicomViewer/DicomViewerUtils.js | 3 -- 2 files changed, 20 insertions(+), 36 deletions(-) diff --git a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js index cd9545c47..adc4afbac 100644 --- a/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js +++ b/src/main/webapp/js/components/interface/dicomViewer/DicomViewer.js @@ -2,12 +2,6 @@ define(function (require) { var React = require('react'); window.THREE = require('three'); - - require('./DicomViewer.less'); - var DicomViewerUtils = require('./DicomViewerUtils'); - - var AbstractComponent = require('../../AComponent'); - var AMI = require('./ami.min.js'); var LoadersVolume = AMI.default.Loaders.Volume; var HelpersStack = AMI.default.Helpers.Stack; @@ -15,6 +9,11 @@ define(function (require) { var ModelsStack = AMI.default.Models.Stack; var HelpersLocalizer = AMI.default.Helpers.Localizer; + require('./DicomViewer.less'); + var DicomViewerUtils = require('./DicomViewerUtils'); + var WidgetButtonBar = require('../../controls/widgetButtonBar/WidgetButtonBar'); + var AbstractComponent = require('../../AComponent'); + return class DicomViewer extends AbstractComponent { constructor(props) { @@ -330,7 +329,7 @@ define(function (require) { } } - function goToSingleView(event){ + function goToSingleView(event) { const id = event.target.id; let orientation = null; switch (id) { @@ -344,15 +343,18 @@ define(function (require) { orientation = "coronal"; break; } - _this.setState({ mode: "single_view", orientation: orientation }); + + if (orientation != null) { + _this.setState({ mode: "single_view", orientation: orientation }); + } } function onClick(event) { - - if (event.ctrlKey){ + + if (event.ctrlKey) { goToSingleView(event); } - else{ + else { goToPoint(event); } } @@ -407,10 +409,10 @@ define(function (require) { this.r3.controls.addEventListener('OnScroll', onScroll); - window.addEventListener('resize', this.setLayout, false); + window.addEventListener('resize', function(){_this.setLayout();}, false); - $(this.getContainer()).parent().on("dialogresizestop", function (event, ui) { - this.setLayout() + $(this.getContainer()).parent().on("resizeEnd", function (event, ui) { + _this.setLayout() }); } @@ -500,25 +502,10 @@ define(function (require) { return (
-
) From bc4cf72817ffd068ca3add64ad50b7c47b531a39 Mon Sep 17 00:00:00 2001 From: jrmartin Date: Mon, 12 Jun 2017 12:05:09 -0700 Subject: [PATCH 055/371] shows tooltip for experiment's table icon status only if it's in view --- .../interface/experimentsTable/ExperimentsTable.js | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/main/webapp/js/components/interface/experimentsTable/ExperimentsTable.js b/src/main/webapp/js/components/interface/experimentsTable/ExperimentsTable.js index 082dbc95d..47dff9fa6 100644 --- a/src/main/webapp/js/components/interface/experimentsTable/ExperimentsTable.js +++ b/src/main/webapp/js/components/interface/experimentsTable/ExperimentsTable.js @@ -678,8 +678,9 @@ define(function (require) { } }, + //Determines if an element inside the experiments table is in view isInView : function(elem){ - var docViewTop = $('#experimentsTable').scrollTop(); + var docViewTop = $('#experimentsTable').offset().top; var docViewBottom = docViewTop + $('#experimentsTable').height(); var elemTop = $(elem).offset().top; var elemBottom = elemTop + $(elem).height(); @@ -707,7 +708,7 @@ define(function (require) { tdStatus.attr("data-status", experiment.getStatus()); tdStatus.attr("data-custom-title", GEPPETTO.Resources.ExperimentStatus.Descriptions[experiment.getStatus()]); - if(self.isInView($(this))) { + if(self.isInView(tdStatus)) { // make the tooltip pop-out for a bit to attract attention tdStatus.mouseover().delay(2000).queue(function () { $(this).mouseout().dequeue(); From 1730e3b20c84ae8097f424d464b1a73cf855f372 Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Tue, 13 Jun 2017 14:53:10 +0100 Subject: [PATCH 056/371] keep colors when switching geometry types --- .../webapp/js/components/interface/3dCanvas/ThreeDEngine.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js b/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js index a2aec801d..f9632789c 100644 --- a/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js +++ b/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js @@ -1155,7 +1155,7 @@ define(['jquery'], function () { color = GEPPETTO.Resources.COLORS.DEFAULT; } var material = new THREE.LineBasicMaterial(options); - material.color.setHex(color); + this.setThreeColor(material.color, color); material.defaultColor = color; material.defaultOpacity = GEPPETTO.Resources.OPACITY.DEFAULT; return material; @@ -1177,7 +1177,7 @@ define(['jquery'], function () { shading: THREE.SmoothShading }); - material.color.setHex(color); + this.setThreeColor(material.color, color); material.defaultColor = color; material.defaultOpacity = GEPPETTO.Resources.OPACITY.DEFAULT; return material; From 8c8f3b9115502ac673da58c67064bd54b7b7ec50 Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Tue, 13 Jun 2017 16:51:48 +0100 Subject: [PATCH 057/371] making connectivity widget colors match populations --- .../widgets/connectivity/Connectivity.js | 18 +++++++++++++++++- .../components/widgets/connectivity/chords.js | 6 ++---- 2 files changed, 19 insertions(+), 5 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js index a9e9a6b43..55b57464c 100644 --- a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js +++ b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js @@ -28,6 +28,7 @@ define(function (require) { dataset: {}, connectivityOptions: {}, + nodeColormap: {}, defaultConnectivityOptions: { width: 660, height: 500, @@ -47,10 +48,25 @@ define(function (require) { } }, - + initialize: function (options) { this.options = options; + this.nodeColormap = function(){ + var pops = GEPPETTO.ModelFactory.getAllInstancesOf( + GEPPETTO.ModelFactory.getAllTypesOfType(GEPPETTO.ModelFactory.geppettoModel.neuroml.network)[0])[0].getChildren(); + var domain = []; + var range = []; + for (var i=0; i Date: Wed, 14 Jun 2017 00:47:34 +0100 Subject: [PATCH 058/371] add default parameters --- src/main/webapp/webpack.config.js | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/src/main/webapp/webpack.config.js b/src/main/webapp/webpack.config.js index d7a4cde42..8d6c6fd93 100644 --- a/src/main/webapp/webpack.config.js +++ b/src/main/webapp/webpack.config.js @@ -7,16 +7,24 @@ var ExtractTextPlugin = require("extract-text-webpack-plugin"); console.log("\nThe arguments passed to webpack are:\n"); console.log(process.argv); +var defaultValues = { + '--contextPath': 'org.geppetto.frontend', + '--useSsl': false, + '--embedded': false, + '--embedderURL': '/' + }; + var getCLIParameter=function(param){ - for(var i=0;i Date: Wed, 14 Jun 2017 00:48:17 +0100 Subject: [PATCH 059/371] add onchange profile --- src/main/webapp/package.json | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/main/webapp/package.json b/src/main/webapp/package.json index c13755d2a..656186cdf 100644 --- a/src/main/webapp/package.json +++ b/src/main/webapp/package.json @@ -8,7 +8,8 @@ "build": "webpack -p --progress", "build-dev": "webpack --devtool eval", "build-dev-noTest": "webpack --devtool eval --noTest", - "start": "node --max_old_space_size=2048 node_modules/webpack-dev-server/bin/webpack-dev-server.js --progress --config webpack.config.dev.js --contextPath=org.geppetto.frontend --useSsl=false --embedded=false --embedderURL=/" + "build-dev-noTest:watch": "onchange 'js/**/*.*' 'extensions/**/*.*' 'style/**/*.*' -- npm run build-dev-noTest", + "start": "node --max_old_space_size=2048 node_modules/webpack-dev-server/bin/webpack-dev-server.js --progress --config webpack.config.dev.js" }, "devDependencies": { "anchorme": "^0.7.1", @@ -54,6 +55,7 @@ "less": "^2.7.2", "less-loader": "^2.2.3", "mathjs": "^3.5.3", + "onchange": "^3.2.1", "openseadragon": "^2.2.1", "pako": "^1.0.3", "pixi.js": "4.2.3", @@ -63,7 +65,7 @@ "react": "15.4.1", "react-dom": "15.4.1", "react-jsonschema-form": "^0.48.0", - "react-player" : "^0.18.0", + "react-player": "^0.18.0", "react-router": "^4.1.1", "react-router-dom": "^4.1.1", "react-simpletabs": "^0.7.0", From cdaee5e34cbdf02ee0961354dfab3196b3067214 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Wed, 14 Jun 2017 00:51:41 +0100 Subject: [PATCH 060/371] exclude ami.js --- src/main/webapp/webpack.config.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/webpack.config.js b/src/main/webapp/webpack.config.js index 8d6c6fd93..3edff8408 100644 --- a/src/main/webapp/webpack.config.js +++ b/src/main/webapp/webpack.config.js @@ -156,7 +156,7 @@ module.exports = { noParse: [/node_modules\/plotly.js\/dist\/plotly.js/, /js\/components\/interface\/dicomViewer\/ami.min.js/], loaders: [ { - test: /\.(js)$/, exclude: [/node_modules/, /build/, /\.bundle/], loader: ['babel-loader'], + test: /\.(js)$/, exclude: [/node_modules/, /build/, /\.bundle/, /ami.min.js/], loader: ['babel-loader'], query: { presets: ['react', 'es2015'] } From 93cfe82e5a61061d0fbf9b19c54ef1c42e2fa35a Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Wed, 14 Jun 2017 12:34:42 +0100 Subject: [PATCH 061/371] Progress, not working yet --- .../geppettoJupyter/GeppettoJupyterGUISync.js | 4 ++- .../webapp/js/components/ComponentFactory.js | 35 ++++++++++++------- 2 files changed, 25 insertions(+), 14 deletions(-) diff --git a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js index b1cfd62af..0981790b8 100644 --- a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js +++ b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js @@ -103,7 +103,9 @@ define(function (require, exports, module) { }, display: function () { - this.set('component', GEPPETTO.ComponentFactory.renderComponent(this.getComponent())); + var comp = this.getComponent(); + this.set('component', GEPPETTO.ComponentFactory._addComponent(comp, "PANEL", { items: this.getChildren(), parentStyle: this.get('parentStyle') }, + document.getElementById('widgetContainer'), undefined, true)); // On close send a message to python to remove objects var that = this; diff --git a/src/main/webapp/js/components/ComponentFactory.js b/src/main/webapp/js/components/ComponentFactory.js index e3a90ab72..f4eb04d19 100644 --- a/src/main/webapp/js/components/ComponentFactory.js +++ b/src/main/webapp/js/components/ComponentFactory.js @@ -104,16 +104,14 @@ define(function (require) { return this.camelize(id); }, - _createComponent: function(componentType, properties, container, callback, isWidget){ - var that=this; - require(["./" + GEPPETTO.ComponentFactory.components[componentType]], function(loadedModule){ + _addComponent: function(componentToAdd, componentType, properties, container, callback, isWidget){ // Prepare properties if (properties === undefined){ properties = {}; } properties.componentType = componentType; if (!("id" in properties)){ - properties["id"] = that.getAvailableComponentId(componentType); + properties["id"] = this.getAvailableComponentId(componentType); } if (!("isStateless" in properties)){ properties["isStateless"] = false; @@ -121,18 +119,12 @@ define(function (require) { properties["parentContainer"] = container; // Create component/widget - var type = loadedModule; + var type = componentToAdd; if (isWidget){ - type = addWidget(loadedModule); + type = addWidget(componentToAdd); } var component = React.createFactory(type)(properties); - var renderedComponent = window[properties.id] = that.renderComponent(component, container, callback); - - // Register in component map - if (!(componentType in that.componentsMap)){ - that.componentsMap[componentType] = [] - } - that.componentsMap[componentType].push(renderedComponent); + var renderedComponent = window[properties.id] = this.renderComponent(component, container, callback); // Register widget/controller for events, etc if (isWidget){ @@ -144,6 +136,23 @@ define(function (require) { renderedComponent.container = container; } + return renderedComponent; + + }, + + _createComponent: function(componentType, properties, container, callback, isWidget){ + var that=this; + + require(["./" + GEPPETTO.ComponentFactory.components[componentType]], function(loadedModule){ + + var renderedComponent = that._addComponent(loadedModule, componentType, properties, container, callback, isWidget); + + // Register in component map + if (!(componentType in that.componentsMap)){ + that.componentsMap[componentType] = [] + } + that.componentsMap[componentType].push(renderedComponent); + return renderedComponent; }); }, From df1af37093afa72ea1c2c2be77698d0814aab273 Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Wed, 14 Jun 2017 12:41:30 +0100 Subject: [PATCH 062/371] Progress --- .../geppettoJupyter/GeppettoJupyterGUISync.js | 17 ++++---- .../webapp/js/components/ComponentFactory.js | 40 +++++++++++++------ 2 files changed, 37 insertions(+), 20 deletions(-) diff --git a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js index b1cfd62af..fd1039b36 100644 --- a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js +++ b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js @@ -13,7 +13,7 @@ define(function (require, exports, module) { var jupyter_widgets = require('jupyter-js-widgets'); var GEPPETTO = require('geppetto'); - var $ = require('jquery'); + var $ = require('jquery'); var _ = require('underscore'); var ComponentSync = jupyter_widgets.WidgetModel.extend({ @@ -41,15 +41,16 @@ define(function (require, exports, module) { model.send({ event: 'blur', data: value }); }, - getComponent: function (componentItem, parameters) { + getComponent: function (componentItem, parameters, container, isWidget) { parameters['id'] = this.get('widget_id'); parameters['name'] = this.get('widget_name'); parameters['sync_value'] = this.get('sync_value'); parameters['handleChange'] = this.handleChange.bind(null, this); parameters['handleBlur'] = this.handleBlur.bind(null, this); - var component = React.createFactory(componentItem)(parameters); - this.set('component', component); + this.set('component', GEPPETTO.ComponentFactory._addComponent(componentItem, this.componentType, parameters, + container, undefined, isWidget)); + return component; } }); @@ -61,6 +62,7 @@ define(function (require, exports, module) { position_y: null, width: null, height: null, + componentType: "PANEL", properties: {}, triggerClose: true }), @@ -80,7 +82,7 @@ define(function (require, exports, module) { getComponent: function () { var parameters = { items: this.getChildren(), parentStyle: this.get('parentStyle') }; - return PanelSync.__super__.getComponent.apply(this, [PanelComp, parameters]); + return PanelSync.__super__.getComponent.apply(this, [PanelComp, parameters, null, true]); }, forceRender: function () { @@ -213,14 +215,15 @@ define(function (require, exports, module) { var ButtonSync = ComponentSync.extend({ defaults: _.extend({}, ComponentSync.prototype.defaults, { - + componentType: "RAISEDBUTTON" }), + initialize: function (options) { ButtonSync.__super__.initialize.apply(this, arguments); }, getComponent: function () { var parameters = { handleClick: this.handleClick.bind(null, this) }; - return ButtonSync.__super__.getComponent.apply(this, [RaisedButtonComp, parameters]); + return ButtonSync.__super__.getComponent.apply(this, [RaisedButtonComp, parameters, null, false]); }, handleClick: function (model) { diff --git a/src/main/webapp/js/components/ComponentFactory.js b/src/main/webapp/js/components/ComponentFactory.js index e3a90ab72..252748267 100644 --- a/src/main/webapp/js/components/ComponentFactory.js +++ b/src/main/webapp/js/components/ComponentFactory.js @@ -104,35 +104,32 @@ define(function (require) { return this.camelize(id); }, - _createComponent: function(componentType, properties, container, callback, isWidget){ - var that=this; - require(["./" + GEPPETTO.ComponentFactory.components[componentType]], function(loadedModule){ + _addComponent: function(componentToAdd, componentType, properties, container, callback, isWidget){ // Prepare properties if (properties === undefined){ properties = {}; } properties.componentType = componentType; if (!("id" in properties)){ - properties["id"] = that.getAvailableComponentId(componentType); + properties["id"] = this.getAvailableComponentId(componentType); } if (!("isStateless" in properties)){ properties["isStateless"] = false; } + + if(container==null && isWidget){ + //FIXME Redundant, see addWidget + container=document.getElementById('widgetContainer'); + } properties["parentContainer"] = container; // Create component/widget - var type = loadedModule; + var type = componentToAdd; if (isWidget){ - type = addWidget(loadedModule); + type = addWidget(componentToAdd); } var component = React.createFactory(type)(properties); - var renderedComponent = window[properties.id] = that.renderComponent(component, container, callback); - - // Register in component map - if (!(componentType in that.componentsMap)){ - that.componentsMap[componentType] = [] - } - that.componentsMap[componentType].push(renderedComponent); + var renderedComponent = window[properties.id] = this.renderComponent(component, container, callback); // Register widget/controller for events, etc if (isWidget){ @@ -144,6 +141,23 @@ define(function (require) { renderedComponent.container = container; } + return renderedComponent; + + }, + + _createComponent: function(componentType, properties, container, callback, isWidget){ + var that=this; + + require(["./" + GEPPETTO.ComponentFactory.components[componentType]], function(loadedModule){ + + var renderedComponent = that._addComponent(loadedModule, componentType, properties, container, callback, isWidget); + + // Register in component map + if (!(componentType in that.componentsMap)){ + that.componentsMap[componentType] = [] + } + that.componentsMap[componentType].push(renderedComponent); + return renderedComponent; }); }, From 46662e45273e3b82f60a9048a635d05409b7728d Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Wed, 14 Jun 2017 12:43:50 +0100 Subject: [PATCH 063/371] Progress --- .../webapp/js/components/ComponentFactory.js | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/src/main/webapp/js/components/ComponentFactory.js b/src/main/webapp/js/components/ComponentFactory.js index 252748267..9d7fec846 100644 --- a/src/main/webapp/js/components/ComponentFactory.js +++ b/src/main/webapp/js/components/ComponentFactory.js @@ -129,6 +129,18 @@ define(function (require) { type = addWidget(componentToAdd); } var component = React.createFactory(type)(properties); + + return component; + + }, + + _createComponent: function(componentType, properties, container, callback, isWidget){ + var that=this; + + require(["./" + GEPPETTO.ComponentFactory.components[componentType]], function(loadedModule){ + + var component = that._addComponent(loadedModule, componentType, properties, container, callback, isWidget); + var renderedComponent = window[properties.id] = this.renderComponent(component, container, callback); // Register widget/controller for events, etc @@ -140,18 +152,6 @@ define(function (require) { GEPPETTO.Console.updateTags(componentType, renderedComponent); renderedComponent.container = container; } - - return renderedComponent; - - }, - - _createComponent: function(componentType, properties, container, callback, isWidget){ - var that=this; - - require(["./" + GEPPETTO.ComponentFactory.components[componentType]], function(loadedModule){ - - var renderedComponent = that._addComponent(loadedModule, componentType, properties, container, callback, isWidget); - // Register in component map if (!(componentType in that.componentsMap)){ that.componentsMap[componentType] = [] From 42bd2138a175726392ccc7e0528f2199534cc11a Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Wed, 14 Jun 2017 12:44:14 +0100 Subject: [PATCH 064/371] Progress --- src/main/webapp/js/components/ComponentFactory.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/js/components/ComponentFactory.js b/src/main/webapp/js/components/ComponentFactory.js index 9d7fec846..02a28668e 100644 --- a/src/main/webapp/js/components/ComponentFactory.js +++ b/src/main/webapp/js/components/ComponentFactory.js @@ -141,7 +141,7 @@ define(function (require) { var component = that._addComponent(loadedModule, componentType, properties, container, callback, isWidget); - var renderedComponent = window[properties.id] = this.renderComponent(component, container, callback); + var renderedComponent = window[properties.id] = that.renderComponent(component, container, callback); // Register widget/controller for events, etc if (isWidget){ From aa9998606b3338a468a0b84ece53d892b8cbb097 Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Wed, 14 Jun 2017 12:57:14 +0100 Subject: [PATCH 065/371] extend to hives, fix legend for forces --- .../widgets/connectivity/Connectivity.js | 37 ++++++++++--------- .../components/widgets/connectivity/forces.js | 3 +- .../components/widgets/connectivity/hives.js | 2 +- 3 files changed, 22 insertions(+), 20 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js index 55b57464c..07722a72a 100644 --- a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js +++ b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js @@ -27,8 +27,8 @@ define(function (require) { return Widget.View.extend({ dataset: {}, - connectivityOptions: {}, nodeColormap: {}, + connectivityOptions: {}, defaultConnectivityOptions: { width: 660, height: 500, @@ -47,25 +47,11 @@ define(function (require) { return 1; } }, - initialize: function (options) { this.options = options; - this.nodeColormap = function(){ - var pops = GEPPETTO.ModelFactory.getAllInstancesOf( - GEPPETTO.ModelFactory.getAllTypesOfType(GEPPETTO.ModelFactory.geppettoModel.neuroml.network)[0])[0].getChildren(); - var domain = []; - var range = []; - for (var i=0; i Date: Wed, 14 Jun 2017 14:03:44 +0100 Subject: [PATCH 066/371] modifying jupyter gui and component factory to work with latest geppetto --- .../geppettoJupyter/GeppettoJupyterGUISync.js | 21 +- .../webapp/js/components/ComponentFactory.js | 180 +++++++++--------- .../js/components/controls/panel/Panel.js | 115 +++++------ 3 files changed, 166 insertions(+), 150 deletions(-) diff --git a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js index c441efd16..e4555db64 100644 --- a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js +++ b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js @@ -41,15 +41,20 @@ define(function (require, exports, module) { model.send({ event: 'blur', data: value }); }, - getComponent: function (componentItem, parameters, container, isWidget) { + getParameters: function(parameters){ parameters['id'] = this.get('widget_id'); parameters['name'] = this.get('widget_name'); parameters['sync_value'] = this.get('sync_value'); parameters['handleChange'] = this.handleChange.bind(null, this); parameters['handleBlur'] = this.handleBlur.bind(null, this); + return parameters; + }, - this.set('component', GEPPETTO.ComponentFactory._addComponent(componentItem, this.componentType, parameters, - container, undefined, isWidget)); + getComponent: function (componentItem, parameters, container) { + + var component = GEPPETTO.ComponentFactory._addComponent(componentItem, this.componentType, this.getParameters(parameters), + container, undefined, (this.get("embedded") == false)); + this.set('component', component); return component; } @@ -82,7 +87,7 @@ define(function (require, exports, module) { getComponent: function () { var parameters = { items: this.getChildren(), parentStyle: this.get('parentStyle') }; - return PanelSync.__super__.getComponent.apply(this, [PanelComp, parameters, null, true]); + return PanelSync.__super__.getComponent.apply(this, [PanelComp, parameters, null]); }, forceRender: function () { @@ -106,8 +111,10 @@ define(function (require, exports, module) { display: function () { var comp = this.getComponent(); - this.set('component', GEPPETTO.ComponentFactory._addComponent(comp, "PANEL", { items: this.getChildren(), parentStyle: this.get('parentStyle') }, - document.getElementById('widgetContainer'), undefined, true)); + //this.set('component', GEPPETTO.ComponentFactory._addComponent(comp, "PANEL", { items: this.getChildren(), parentStyle: this.get('parentStyle') }, + // document.getElementById('widgetContainer'), undefined, true)); + GEPPETTO.ComponentFactory._renderComponent(comp, "PANEL", this.getParameters({ items: this.getChildren(), parentStyle: this.get('parentStyle') }), + document.getElementById('widgetContainer'), undefined, true); // On close send a message to python to remove objects var that = this; @@ -225,7 +232,7 @@ define(function (require, exports, module) { }, getComponent: function () { var parameters = { handleClick: this.handleClick.bind(null, this) }; - return ButtonSync.__super__.getComponent.apply(this, [RaisedButtonComp, parameters, null, false]); + return ButtonSync.__super__.getComponent.apply(this, [RaisedButtonComp, parameters, null]); }, handleClick: function (model) { diff --git a/src/main/webapp/js/components/ComponentFactory.js b/src/main/webapp/js/components/ComponentFactory.js index 02a28668e..e8c12d798 100644 --- a/src/main/webapp/js/components/ComponentFactory.js +++ b/src/main/webapp/js/components/ComponentFactory.js @@ -5,38 +5,38 @@ define(function (require) { var React = require('react'); var ReactDOM = require('react-dom'); - var spinner=require('./interface/loadingSpinner/LoadingSpinner.js'); + var spinner = require('./interface/loadingSpinner/LoadingSpinner.js'); var addWidget = require('./widgets/AWidget.js'); - + GEPPETTO.ComponentFactory = { //All the components potentially instantiable go here - components : { - 'FORM':'interface/form/Form', - 'PANEL':'controls/panel/Panel', - 'LOGO':'interface/logo/Logo', - 'LOADINGSPINNER':'interface/loadingSpinner/LoadingSpinner', - 'SAVECONTROL':'interface/save/SaveControl', - 'TOGGLEBUTTON' : 'controls/toggleButton/ToggleButton', - 'CONTROLPANEL':'interface/controlPanel/controlpanel', - 'SPOTLIGHT':'interface/spotlight/spotlight', - 'MENUBUTTON':'controls/menuButton/MenuButton', - 'FOREGROUND':'interface/foregroundControls/ForegroundControls', - 'EXPERIMENTSTABLE':'interface/experimentsTable/ExperimentsTable', - 'HOME':'interface/home/HomeControl', - 'SIMULATIONCONTROLS':'interface/simulationControls/ExperimentControls', + components: { + 'FORM': 'interface/form/Form', + 'PANEL': 'controls/panel/Panel', + 'LOGO': 'interface/logo/Logo', + 'LOADINGSPINNER': 'interface/loadingSpinner/LoadingSpinner', + 'SAVECONTROL': 'interface/save/SaveControl', + 'TOGGLEBUTTON': 'controls/toggleButton/ToggleButton', + 'CONTROLPANEL': 'interface/controlPanel/controlpanel', + 'SPOTLIGHT': 'interface/spotlight/spotlight', + 'MENUBUTTON': 'controls/menuButton/MenuButton', + 'FOREGROUND': 'interface/foregroundControls/ForegroundControls', + 'EXPERIMENTSTABLE': 'interface/experimentsTable/ExperimentsTable', + 'HOME': 'interface/home/HomeControl', + 'SIMULATIONCONTROLS': 'interface/simulationControls/ExperimentControls', 'CAMERACONTROLS': 'interface/cameraControls/CameraControls', - 'SHARE':'interface/share/Share', - 'INFOMODAL':'controls/modals/InfoModal', - 'MDMODAL':'controls/modals/MarkDownModal', - 'QUERY':'interface/query/query', - 'TUTORIAL':'interface/tutorial/Tutorial', + 'SHARE': 'interface/share/Share', + 'INFOMODAL': 'controls/modals/InfoModal', + 'MDMODAL': 'controls/modals/MarkDownModal', + 'QUERY': 'interface/query/query', + 'TUTORIAL': 'interface/tutorial/Tutorial', 'PYTHONCONSOLE': 'interface/pythonConsole/PythonConsole', 'CHECKBOX': 'controls/Checkbox', 'TEXTFIELD': 'controls/TextField', 'RAISEDBUTTON': 'controls/RaisedButton', - 'BUTTON':'controls/button/Button', + 'BUTTON': 'controls/button/Button', 'DICOMVIEWER': 'interface/dicomViewer/DicomViewer', 'GOOGLEVIEWER': 'interface/googleViewer/GoogleViewer', 'BIGIMAGEVIEWER': 'interface/bigImageViewer/BigImageViewer', @@ -50,20 +50,20 @@ define(function (require) { // componentsShortcut : { // "1": "POPUP" // }, - - loadSpinner:function(){ + + loadSpinner: function () { //We require this synchronously to properly show spinner when loading projects - this.renderComponent(React.createFactory(spinner)(),document.getElementById("load-spinner")); + this.renderComponent(React.createFactory(spinner)(), document.getElementById("load-spinner")); }, componentsMap: {}, - getComponents: function(){ + getComponents: function () { return this.componentsMap; }, camelize(str) { - return str.replace(/(?:^\w|[A-Z]|\b\w|\s+)/g, function(match, index) { + return str.replace(/(?:^\w|[A-Z]|\b\w|\s+)/g, function (match, index) { if (+match === 0) return ""; // or if (/\s+/.test(match)) for white spaces return index == 0 ? match.toUpperCase() : match.toLowerCase(); }); @@ -77,13 +77,13 @@ define(function (require) { * @param {Array} widgetsList * @returns {String} id - Available id for a widget */ - getAvailableComponentId (componentType) { + getAvailableComponentId(componentType) { var index = 0; var id = ""; var available; var components = []; - if (componentType in this.componentsMap){ + if (componentType in this.componentsMap) { components = this.componentsMap[componentType]; } @@ -91,7 +91,7 @@ define(function (require) { index++; id = componentType + index; available = true; - + for (var componentsIndex in components) { if (components[componentsIndex].props.id.toUpperCase() == id.toUpperCase()) { available = false; @@ -104,93 +104,99 @@ define(function (require) { return this.camelize(id); }, - _addComponent: function(componentToAdd, componentType, properties, container, callback, isWidget){ - // Prepare properties - if (properties === undefined){ - properties = {}; - } - properties.componentType = componentType; - if (!("id" in properties)){ - properties["id"] = this.getAvailableComponentId(componentType); - } - if (!("isStateless" in properties)){ - properties["isStateless"] = false; - } + _addComponent: function (componentToAdd, componentType, properties, container, callback, isWidget) { + // Prepare properties + if (properties === undefined) { + properties = {}; + } + properties.componentType = componentType; + if (!("id" in properties)) { + properties["id"] = this.getAvailableComponentId(componentType); + } + if (!("isStateless" in properties)) { + properties["isStateless"] = false; + } - if(container==null && isWidget){ - //FIXME Redundant, see addWidget - container=document.getElementById('widgetContainer'); - } - properties["parentContainer"] = container; - - // Create component/widget - var type = componentToAdd; - if (isWidget){ - type = addWidget(componentToAdd); - } - var component = React.createFactory(type)(properties); - - return component; + if (container == null && isWidget) { + //FIXME Redundant, see addWidget + container = document.getElementById('widgetContainer'); + } + properties["parentContainer"] = container; + + // Create component/widget + var type = componentToAdd; + if (isWidget) { + type = addWidget(componentToAdd); + } + var component = React.createFactory(type)(properties); + + return component; }, - _createComponent: function(componentType, properties, container, callback, isWidget){ - var that=this; + _createComponent: function (componentType, properties, container, callback, isWidget) { + var that = this; - require(["./" + GEPPETTO.ComponentFactory.components[componentType]], function(loadedModule){ + require(["./" + GEPPETTO.ComponentFactory.components[componentType]], function (loadedModule) { var component = that._addComponent(loadedModule, componentType, properties, container, callback, isWidget); - var renderedComponent = window[properties.id] = that.renderComponent(component, container, callback); + var renderedComponent = that._renderComponent(component, componentType, properties, container, callback, isWidget) + - // Register widget/controller for events, etc - if (isWidget){ - var widgetController = GEPPETTO.NewWidgetFactory.getController(componentType); - widgetController.registerWidget(renderedComponent) - } - else{ - GEPPETTO.Console.updateTags(componentType, renderedComponent); - renderedComponent.container = container; - } - // Register in component map - if (!(componentType in that.componentsMap)){ - that.componentsMap[componentType] = [] - } - that.componentsMap[componentType].push(renderedComponent); - return renderedComponent; }); }, - - addComponent: function(componentType, properties, container, callback){ + + _renderComponent: function (component, componentType, properties, container, callback, isWidget) { + var renderedComponent = window[properties.id] = this.renderComponent(component, container, callback); + + // Register widget/controller for events, etc + if (isWidget) { + var widgetController = GEPPETTO.NewWidgetFactory.getController(componentType); + widgetController.registerWidget(renderedComponent) + } + else { + GEPPETTO.Console.updateTags(componentType, renderedComponent); + renderedComponent.container = container; + } + // Register in component map + if (!(componentType in this.componentsMap)) { + this.componentsMap[componentType] = [] + } + this.componentsMap[componentType].push(renderedComponent); + return renderedComponent; + }, + + addComponent: function (componentType, properties, container, callback) { this._createComponent(componentType, properties, container, callback, false); }, - - addWidget: function(componentType, properties, callback){ - - if (componentType in this.components){ + + addWidget: function (componentType, properties, callback) { + + if (componentType in this.components) { this._createComponent(componentType, properties, document.getElementById('widgetContainer'), callback, true); } - else{ + else { var isStateless = false; - if (properties !== undefined && "isStateless" in properties){ + if (properties !== undefined && "isStateless" in properties) { isStateless = properties["isStateless"]; } var widget = GEPPETTO.WidgetFactory.addWidget(componentType, isStateless); // Register in component map - if (!(componentType in this.componentsMap)){ + if (!(componentType in this.componentsMap)) { this.componentsMap[componentType] = [] } this.componentsMap[componentType].push(widget); return widget; } - + }, - renderComponent: function(component, container, callback){ + renderComponent: function (component, container, callback) { return ReactDOM.render(component, container, callback); } - }; + }; }; }); diff --git a/src/main/webapp/js/components/controls/panel/Panel.js b/src/main/webapp/js/components/controls/panel/Panel.js index 09c2ffd4b..92463ee1d 100644 --- a/src/main/webapp/js/components/controls/panel/Panel.js +++ b/src/main/webapp/js/components/controls/panel/Panel.js @@ -2,60 +2,63 @@ define(function (require) { var React = require('react'); require("./Panel.less") - var defaultChildStyle = {'alignSelf': 'auto', 'flexGrow': 0, 'order': 0}; - - var panelComponent = React.createClass({ - - getInitialState: function() { - var defaultParentStyle = {'flexDirection':'column','justifyContent':'flex-start','alignItems':'flex-start','flexWrap':'nowrap','alignContent':'flex-start','display':'flex'}; - - return { - parentStyle: $.extend(defaultParentStyle, this.props.parentStyle), - items: this.props.items - }; - }, - - addChildren: function(items){ - this.setState({ items: this.state.items.concat(items) }); - }, - - setChildren: function(items){ - this.setState({ items: items }); - }, - - componentWillReceiveProps: function(nextProps) { - this.setState({ - items: nextProps.items - }); - }, - - setDirection: function(direction){ - var currentStyle = this.state.parentStyle; - currentStyle['flexDirection'] = direction; - this.setState({ parentStyle: currentStyle}); - }, - - componentDidMount : function(){ - var comp = $('#' + this.props.id); - if (comp.parent().hasClass('dialog')){ - comp.parent().height(comp.height() + 10); - comp.parent().parent().width(comp.width() + 70); - } - }, - - render: function(){ - var itemComponents = this.state.items.map(function (item) { - return (
{item}
); - }); - - return ( -
- {itemComponents} -
- ); - } - }); - - return panelComponent; - + var defaultChildStyle = { 'alignSelf': 'auto', 'flexGrow': 0, 'order': 0 }; + + var AbstractComponent = require('../../AComponent'); + + return class Panel extends AbstractComponent { + + constructor(props) { + super(props); + + var defaultParentStyle = { 'flexDirection': 'column', 'justifyContent': 'flex-start', 'alignItems': 'flex-start', 'flexWrap': 'nowrap', 'alignContent': 'flex-start', 'display': 'flex' }; + + this.state = { + parentStyle: $.extend(defaultParentStyle, this.props.parentStyle), + items: this.props.items + }; + + + } + + addChildren(items) { + this.setState({ items: this.state.items.concat(items) }); + } + + setChildren(items) { + this.setState({ items: items }); + } + + componentWillReceiveProps(nextProps) { + this.setState({ + items: nextProps.items + }); + } + + setDirection(direction) { + var currentStyle = this.state.parentStyle; + currentStyle['flexDirection'] = direction; + this.setState({ parentStyle: currentStyle }); + } + + componentDidMount() { + var comp = $('#' + this.props.id); + if (comp.parent().hasClass('dialog')) { + comp.parent().height(comp.height() + 10); + comp.parent().parent().width(comp.width() + 70); + } + } + + render() { + var itemComponents = this.state.items.map(function (item) { + return (
{item}
); + }); + + return ( +
+ {itemComponents} +
+ ); + } + }; }); \ No newline at end of file From 70d8af55126030a6755d7e2243744b7ae883a3ab Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Wed, 14 Jun 2017 14:17:54 +0100 Subject: [PATCH 067/371] more fixes --- .../communication/geppettoJupyter/GeppettoJupyterGUISync.js | 4 ++-- .../communication/geppettoJupyter/GeppettoJupyterModelSync.js | 3 ++- src/main/webapp/js/components/controls/panel/Panel.js | 3 --- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js index e4555db64..b3e09f7a0 100644 --- a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js +++ b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js @@ -113,8 +113,8 @@ define(function (require, exports, module) { var comp = this.getComponent(); //this.set('component', GEPPETTO.ComponentFactory._addComponent(comp, "PANEL", { items: this.getChildren(), parentStyle: this.get('parentStyle') }, // document.getElementById('widgetContainer'), undefined, true)); - GEPPETTO.ComponentFactory._renderComponent(comp, "PANEL", this.getParameters({ items: this.getChildren(), parentStyle: this.get('parentStyle') }), - document.getElementById('widgetContainer'), undefined, true); + this.set('component', GEPPETTO.ComponentFactory._renderComponent(comp, "PANEL", this.getParameters({ items: this.getChildren(), parentStyle: this.get('parentStyle') }), + document.getElementById('widgetContainer'), undefined, true)); // On close send a message to python to remove objects var that = this; diff --git a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js index 2c3f1cc90..fc8b528ee 100644 --- a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js +++ b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js @@ -227,7 +227,8 @@ define(function (require, exports, module) { for (var i = 0; i < this.get('geometries').length; i++) { elements[this.get('geometries')[i].id] = ""; } - GEPPETTO.SceneController.splitGroups(window.Instances[0], elements); + //GEPPETTO.SceneController.splitGroups(window.Instances[0], elements); + Canvas1.engine.splitGroups(window.Instances[0], elements); } }, diff --git a/src/main/webapp/js/components/controls/panel/Panel.js b/src/main/webapp/js/components/controls/panel/Panel.js index 92463ee1d..fb3e5f897 100644 --- a/src/main/webapp/js/components/controls/panel/Panel.js +++ b/src/main/webapp/js/components/controls/panel/Panel.js @@ -12,13 +12,10 @@ define(function (require) { super(props); var defaultParentStyle = { 'flexDirection': 'column', 'justifyContent': 'flex-start', 'alignItems': 'flex-start', 'flexWrap': 'nowrap', 'alignContent': 'flex-start', 'display': 'flex' }; - this.state = { parentStyle: $.extend(defaultParentStyle, this.props.parentStyle), items: this.props.items }; - - } addChildren(items) { From 6168bc1198d10baafc3c321377fd6b2d2531da6a Mon Sep 17 00:00:00 2001 From: jrmartin Date: Wed, 14 Jun 2017 20:37:38 -0700 Subject: [PATCH 068/371] mmore caspers tests --- .../widgets/connectivity/Connectivity.js | 4 +- .../js/pages/tests/casperjs/CoreTests.js | 103 +++++++++++++++++- .../pages/tests/casperjs/CoreTestsUtility.js | 2 +- .../webapp/js/pages/tests/casperjs/UITests.js | 75 ++++++++++++- 4 files changed, 175 insertions(+), 9 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js index a9e9a6b43..1725ba109 100644 --- a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js +++ b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js @@ -429,7 +429,9 @@ define(function (require) { // add data baseView.dataType = 'object'; - baseView.data = this.dataset["root"].getPath(); + if(this.dataset["root"]!=undefined){ + baseView.data = this.dataset["root"].getPath(); + } return baseView; }, diff --git a/src/main/webapp/js/pages/tests/casperjs/CoreTests.js b/src/main/webapp/js/pages/tests/casperjs/CoreTests.js index 9ef313071..f64e7e833 100644 --- a/src/main/webapp/js/pages/tests/casperjs/CoreTests.js +++ b/src/main/webapp/js/pages/tests/casperjs/CoreTests.js @@ -165,14 +165,25 @@ function hhcellTest(test,name){ GEPPETTO.SceneController.addColorFunction(GEPPETTO.ModelFactory.instances.getInstance(GEPPETTO.ModelFactory.getAllPotentialInstancesEndingWith('.v'),false), window.voltage_color); Project.getActiveExperiment().play({step:1}); Plot1.setPosition(0,300); + G.addWidget(1).setMessage("Hhcell popup"); + G.addWidget(1).setData(hhcell); + var customHandler = function(node, path, widget) {}; + Popup2.addCustomNodeHandler(customHandler,'click'); }); + casper.mouseEvent('click', 'button#tutorialBtn', "attempting to open tutorial"); + var mesh = casper.evaluate(function(){ var mesh = Canvas2.engine.getRealMeshesForInstancePath("hhcell.hhpop[0]").length; return mesh; }); test.assertEquals(mesh, 1, "Canvas widget has hhcell"); + casper.evaluate(function(){ + $(".nextBtn").click(); + $(".nextBtn").click(); + }); + casper.echo("-------Testing Camera Controls--------"); testCameraControlsWithCanvasWidget(test, [0,0,30.90193733102435]); casper.wait(1000, function(){ @@ -182,7 +193,48 @@ function hhcellTest(test,name){ test3DMeshColorNotEquals(test,defaultColor,"hhcell.hhpop[0]"); casper.echo("Done Playing, now exiting"); }) - }) + }); + + casper.then(function(){launchTest(test,"Hhcell",30000);}); + + casper.then(function(){ + test.assertVisible('div#Canvas2', "Canvas2 is correctly open on reload."); + test.assertVisible('div#Plot1', "Plot1 is correctly open on reload"); + test.assertVisible('div#Popup1', "Popup1 is correctly open on reload"); + test.assertVisible('div#Popup2', "Popup2 is correctly open on reload"); + test.assertVisible('div#Tutorial1', "Tutorial1 is correctly open on reload"); + + var tutorialStep = casper.evaluate(function() { + return Tutorial1.state.currentStep; + }); + + test.assertEquals(tutorialStep, 2, "Tutorial1 step restored correctly"); + + var popUpMessage = casper.evaluate(function() { + return $("#Popup1").html(); + }); + + test.assertEquals(popUpMessage, "Hhcell popup", "Popup1 message restored correctly"); + + var popUpCustomHandler = casper.evaluate(function() { + return Popup2.customHandlers; + }); + + test.assertEquals(popUpCustomHandler.length, 1, "Popup2 custom handlers restored correctly"); + test.assertEquals(popUpCustomHandler[0]["event"], "click", "Popup2 custom handlers event restored correctly"); + + var meshInCanvas2Exists = casper.evaluate(function() { + var mesh = Canvas1.engine.meshes["hhcell.hhpop[0]"]; + + if(mesh!=null && mesh!=undefined){ + return true; + } + + return false; + }); + + test.assertEquals(meshInCanvas2Exists, true, "Canvas2 hhcell set correctly"); + }); }; /** @@ -191,7 +243,7 @@ function hhcellTest(test,name){ function acnetTest(test){ casper.echo("------------STARTING ACNET TEST--------------"); casper.then(function(){ - removeAllDialogs(); + removeAllPlots(); }); casper.then(function(){ casper.echo("-------Testing Camera Controls--------"); @@ -287,6 +339,51 @@ function acnetTest(test){ test3DMeshOpacity(test,1, "acnet2.baskets_12[4]"); test3DMeshOpacity(test,1, "acnet2.baskets_12[1]"); + casper.evaluate(function(){ + acnet2.pyramidals_48[0].setGeometryType("cylinders") + }); + + //test mesh set geometry + var meshType = casper.evaluate(function(){ + return Canvas1.engine.getRealMeshesForInstancePath("acnet2.pyramidals_48[0]")[0].type; + }); + test.assertEquals(meshType, "Mesh", "Correctly set mesh to cylinders"); + + var meshTotal = casper.evaluate(function(){ + return Object.keys(Canvas1.engine.meshes).length; + }); + test.assertEquals(meshTotal, 60, "Correctly amount of meshes after applying cylinders"); + + casper.evaluate(function(){ + acnet2.pyramidals_48[0].setGeometryType("lines") + }); + + //test mesh set geometry + meshType = casper.evaluate(function(){ + return Canvas1.engine.getRealMeshesForInstancePath("acnet2.pyramidals_48[0]")[0].type; + }); + test.assertEquals(meshType, "LineSegments", "Correctly set mesh to lines"); + + var meshTotal = casper.evaluate(function(){ + return Object.keys(Canvas1.engine.meshes).length; + }); + test.assertEquals(meshTotal, 60, "Correctly amount of meshes after applying cylinders"); + + casper.evaluate(function(){ + acnet2.pyramidals_48[0].setGeometryType("cylinders") + }); + + //test mesh set geometry + var meshType = casper.evaluate(function(){ + return Canvas1.engine.getRealMeshesForInstancePath("acnet2.pyramidals_48[0]")[0].type; + }); + test.assertEquals(meshType, "Mesh", "Correctly set mesh to cylinders"); + + var meshTotal = casper.evaluate(function(){ + return Object.keys(Canvas1.engine.meshes).length; + }); + test.assertEquals(meshTotal, 60, "Correctly amount of meshes after applying cylinders"); + //test color function casper.wait(2000, function(){ test3DMeshColorNotEquals(test,defaultColor,"acnet2.baskets_12[2].soma_0"); @@ -312,7 +409,7 @@ function c302Test(test){ }); casper.then(function(){ - removeAllDialogs(); + removeAllPlots(); }); casper.then(function(){ diff --git a/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js b/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js index 61abd3888..0f73382a1 100644 --- a/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js +++ b/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js @@ -60,7 +60,7 @@ function removeAllPlots(){ function removeAllDialogs(){ casper.then(function(){ casper.evaluate(function() { - $("div.ui-widget").remove(); + $("div.dialog").remove(); }); }); } diff --git a/src/main/webapp/js/pages/tests/casperjs/UITests.js b/src/main/webapp/js/pages/tests/casperjs/UITests.js index 893906118..bdbe4cc60 100644 --- a/src/main/webapp/js/pages/tests/casperjs/UITests.js +++ b/src/main/webapp/js/pages/tests/casperjs/UITests.js @@ -5,7 +5,7 @@ var PROJECT_URL_SUFFIX_2 = "?load_project_from_url=https://raw.githubusercontent var PROJECT_URL_SUFFIX_3 = "?load_project_from_url=https://raw.githubusercontent.com/openworm/org.geppetto.samples/development/UsedInUnitTests/balanced/project.json"; var projectID; -casper.test.begin('Geppetto basic tests', 109, function suite(test) { +casper.test.begin('Geppetto basic tests', 127, function suite(test) { casper.options.viewportSize = { width: 1340, height: 768 @@ -64,6 +64,10 @@ casper.test.begin('Geppetto basic tests', 109, function suite(test) { this.echo("Project id to delete : "+projectID); }); + casper.then(function () { + reloadProjectTest(test, TARGET_URL + port+"/org.geppetto.frontend/geppetto?load_project_from_id="+projectID); + }); + casper.then(function () { deleteProject(test, TARGET_URL + port+"/org.geppetto.frontend",projectID); }); @@ -80,6 +84,10 @@ casper.test.begin('Geppetto basic tests', 109, function suite(test) { this.echo("Project id to delete : "+projectID); }); + casper.then(function () { + reloadProjectTest(test, TARGET_URL + port+"/org.geppetto.frontend/geppetto?load_project_from_id="+projectID,2); + }); + casper.then(function () { deleteProject(test, TARGET_URL + port+"/org.geppetto.frontend",projectID); }); @@ -96,6 +104,10 @@ casper.test.begin('Geppetto basic tests', 109, function suite(test) { this.echo("Project id to delete : "+projectID); }); + casper.then(function () { + reloadProjectTest(test, TARGET_URL + port+"/org.geppetto.frontend/geppetto?load_project_from_id="+projectID,1); + }); + casper.then(function () { deleteProject(test, TARGET_URL + port+"/org.geppetto.frontend",projectID); }); @@ -103,6 +115,19 @@ casper.test.begin('Geppetto basic tests', 109, function suite(test) { //TODO: log back in as other users. Check more things //TODO: exercise the run loop, check the changing experiment status, try to make experiment fail + casper.thenOpen(TARGET_URL + port+"/org.geppetto.frontend/logout", function () { + }); + + casper.thenOpen(TARGET_URL + port+"/org.geppetto.frontend/login?username=admin&password=admin", function () { + }); + + casper.thenOpen(TARGET_URL+ port+"/org.geppetto.frontend/admin", function () { + this.waitForSelector('div[class="griddle"]', function () { + this.echo("I've waited for the admin panel to load."); + }, null, 30000); + }); + + casper.run(function () { test.done(); }); @@ -110,7 +135,7 @@ casper.test.begin('Geppetto basic tests', 109, function suite(test) { function deleteProject(test, url,id){ casper.thenOpen(url, function () { - this.echo("Loading an external model that is not persisted at " + url); + this.echo("Loading an external model that is persisted at " + url); casper.then(function () { @@ -145,6 +170,38 @@ function deleteProject(test, url,id){ }); } + +function reloadProjectTest(test, url, customHandlers,widgetCanvasObject){ + casper.thenOpen(url, function () { + this.echo("Reloading persisted project at " + url); + + casper.waitWhileVisible('div[id="loading-spinner"]', function () { + this.echo("I've waited for "+url+" project to load."); + + casper.then(function () { + casper.wait(2000, function () {}); + test.assertVisible('div#Canvas2', "Canvas2 is correctly open on reload."); + test.assertVisible('div#Popup1', "Popup1 is correctly open on reload"); + test.assertVisible('div#Tutorial1', "Tutorial1 is correctly open on reload"); + test.assertVisible('div#Connectivity1', "Connectivity1 is correctly open on reload"); + + var tutorialStep = casper.evaluate(function() { + return Tutorial1.state.currentStep; + }); + + test.assertEquals(tutorialStep, 2, "Tutorial1 step restored correctly"); + + var popUpCustomHandler = casper.evaluate(function() { + return Popup1.customHandlers; + }); + + test.assertEquals(popUpCustomHandler.length, customHandlers, "Popup1 custom handlers restored correctly"); + test.assertEquals(popUpCustomHandler[0]["event"], "click", "Popup2 custom handlers event restored correctly"); + }); + },null,300000); + }); +} + function testProject(test, url, expect_error, persisted, spotlight_record_variable, spotlight_set_parameter, testConsole) { casper.thenOpen(url, function () { @@ -171,7 +228,7 @@ function testProject(test, url, expect_error, persisted, spotlight_record_variab //do checks on the state of the project if it is not persisted if (persisted == false) { - casper.then(function () { + casper.then(function () { // make sure experiment panel is open this.evaluate(function() { $('a[href=experiments]').click(); @@ -182,6 +239,16 @@ function testProject(test, url, expect_error, persisted, spotlight_record_variab }); casper.then(function () { + casper.mouseEvent('click', 'button#tutorialBtn', "attempting to open tutorial"); + casper.evaluate(function(widgetCanvasObject) { + G.addWidget(6); + GEPPETTO.ComponentFactory.addWidget('CANVAS', {name: '3D Canvas',}, function () {this.setName('Widget Canvas');this.setPosition();}); + G.addWidget(1).setMessage("Hhcell popup"); + var customHandler = function(node, path, widget) {}; + Popup1.addCustomNodeHandler(customHandler,'click'); + $(".nextBtn").click(); + $(".nextBtn").click(); + }); this.echo("Checking content of experiment row"); // test or wait for control panel stuff to be there if(this.exists('a[href="#experiments"]')){ @@ -206,7 +273,7 @@ function testProject(test, url, expect_error, persisted, spotlight_record_variab }); casper.then(function () { - + this.waitForSelector('button.btn.SaveButton', function () { test.assertVisible('button.btn.SaveButton', "Persist button is present"); }); From 291b9ed0a98a772ee38becfafeb9dfe95c662c62 Mon Sep 17 00:00:00 2001 From: jrmartin Date: Wed, 14 Jun 2017 21:08:00 -0700 Subject: [PATCH 069/371] checks content of canvas --- .../webapp/js/pages/tests/casperjs/UITests.js | 32 ++++++++++++++----- 1 file changed, 24 insertions(+), 8 deletions(-) diff --git a/src/main/webapp/js/pages/tests/casperjs/UITests.js b/src/main/webapp/js/pages/tests/casperjs/UITests.js index bdbe4cc60..9075b820d 100644 --- a/src/main/webapp/js/pages/tests/casperjs/UITests.js +++ b/src/main/webapp/js/pages/tests/casperjs/UITests.js @@ -5,7 +5,7 @@ var PROJECT_URL_SUFFIX_2 = "?load_project_from_url=https://raw.githubusercontent var PROJECT_URL_SUFFIX_3 = "?load_project_from_url=https://raw.githubusercontent.com/openworm/org.geppetto.samples/development/UsedInUnitTests/balanced/project.json"; var projectID; -casper.test.begin('Geppetto basic tests', 127, function suite(test) { +casper.test.begin('Geppetto basic tests', 133, function suite(test) { casper.options.viewportSize = { width: 1340, height: 768 @@ -54,7 +54,7 @@ casper.test.begin('Geppetto basic tests', 127, function suite(test) { casper.then(function () { testProject(test, TARGET_URL + port+"/org.geppetto.frontend/geppetto" + PROJECT_URL_SUFFIX, true, - false, 'hhcell.hhpop[0].v', 'Model.neuroml.pulseGen1.delay', true); + false, 'hhcell.hhpop[0].v', 'Model.neuroml.pulseGen1.delay', true,"hhcell"); }); casper.then(function () { @@ -65,7 +65,7 @@ casper.test.begin('Geppetto basic tests', 127, function suite(test) { }); casper.then(function () { - reloadProjectTest(test, TARGET_URL + port+"/org.geppetto.frontend/geppetto?load_project_from_id="+projectID); + reloadProjectTest(test, TARGET_URL + port+"/org.geppetto.frontend/geppetto?load_project_from_id="+projectID,1); }); casper.then(function () { @@ -74,7 +74,7 @@ casper.test.begin('Geppetto basic tests', 127, function suite(test) { casper.then(function () { testProject(test, TARGET_URL + port+"/org.geppetto.frontend/geppetto" + PROJECT_URL_SUFFIX_2, false, - false, 'c302_A_Pharyngeal.M1[0].v', 'Model.neuroml.generic_neuron_iaf_cell.C', false); + false, 'c302_A_Pharyngeal.M1[0].v', 'Model.neuroml.generic_neuron_iaf_cell.C', false,"c302_A_Pharyngeal"); }); casper.then(function () { @@ -94,7 +94,7 @@ casper.test.begin('Geppetto basic tests', 127, function suite(test) { casper.then(function () { testProject(test, TARGET_URL +port+"/org.geppetto.frontend/geppetto" + PROJECT_URL_SUFFIX_3, false, - false, '', '', false); + false, '', '', false,"Balanced_240cells_36926conns"); }); casper.then(function () { @@ -197,12 +197,20 @@ function reloadProjectTest(test, url, customHandlers,widgetCanvasObject){ test.assertEquals(popUpCustomHandler.length, customHandlers, "Popup1 custom handlers restored correctly"); test.assertEquals(popUpCustomHandler[0]["event"], "click", "Popup2 custom handlers event restored correctly"); + + var meshInCanvas2Exists = casper.evaluate(function() { + var mesh = $.isEmptyObject(Canvas1.engine.meshes); + + return mesh; + }); + + test.assertEquals(meshInCanvas2Exists, false, "Canvas2 has mesh set correctly"); }); },null,300000); }); } -function testProject(test, url, expect_error, persisted, spotlight_record_variable, spotlight_set_parameter, testConsole) { +function testProject(test, url, expect_error, persisted, spotlight_record_variable, spotlight_set_parameter, testConsole,widgetCanvasObject) { casper.thenOpen(url, function () { this.echo("Loading an external model that is not persisted at " + url); @@ -241,14 +249,22 @@ function testProject(test, url, expect_error, persisted, spotlight_record_variab casper.then(function () { casper.mouseEvent('click', 'button#tutorialBtn', "attempting to open tutorial"); casper.evaluate(function(widgetCanvasObject) { + var canvasObject = null; + if(widgetCanvasObject=="hhcell"){ + canvasObject = hhcell; + }else if(widgetCanvasObject=="c302_A_Pharyngeal"){ + canvasObject = c302_A_Pharyngeal; + }else if(widgetCanvasObject=="Balanced_240cells_36926conns"){ + canvasObject = Balanced_240cells_36926conns; + } G.addWidget(6); - GEPPETTO.ComponentFactory.addWidget('CANVAS', {name: '3D Canvas',}, function () {this.setName('Widget Canvas');this.setPosition();}); + GEPPETTO.ComponentFactory.addWidget('CANVAS', {name: '3D Canvas',}, function () {this.setName('Widget Canvas');this.setPosition();this.display([canvasObject])}); G.addWidget(1).setMessage("Hhcell popup"); var customHandler = function(node, path, widget) {}; Popup1.addCustomNodeHandler(customHandler,'click'); $(".nextBtn").click(); $(".nextBtn").click(); - }); + },widgetCanvasObject); this.echo("Checking content of experiment row"); // test or wait for control panel stuff to be there if(this.exists('a[href="#experiments"]')){ From 7c5fffe2202dd6f2dd7d0b03281c9683dd9ae0f2 Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Thu, 15 Jun 2017 12:09:26 +0100 Subject: [PATCH 070/371] start removing neuroml specific code --- .../widgets/connectivity/Connectivity.js | 28 ++++++------------- 1 file changed, 8 insertions(+), 20 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js index 07722a72a..095604b58 100644 --- a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js +++ b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js @@ -51,8 +51,6 @@ define(function (require) { initialize: function (options) { this.options = options; - this.nodeColormap = this.getNodeColormap(); - Widget.View.prototype.initialize.call(this, options); this.setOptions(this.defaultConnectivityOptions); @@ -80,23 +78,6 @@ define(function (require) { }); }, - getNodeColormap: function () { - var cells = GEPPETTO.ModelFactory.getAllInstancesOf( - GEPPETTO.ModelFactory.getAllTypesOfType(GEPPETTO.ModelFactory.geppettoModel.neuroml.network)[0])[0].getChildren(); - var domain = []; - var range = []; - for (var i=0; i Date: Thu, 15 Jun 2017 13:42:48 +0100 Subject: [PATCH 071/371] add nodecolormap to state --- .../webapp/js/components/widgets/connectivity/Connectivity.js | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js index 095604b58..7aa5be7af 100644 --- a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js +++ b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js @@ -437,6 +437,8 @@ define(function (require) { // add data baseView.dataType = 'object'; baseView.data = this.dataset["root"].getPath(); + baseView.nodeColormap = {domain: this.nodeColormap.domain(), + range: this.nodeColormap.range()}; return baseView; }, @@ -459,7 +461,7 @@ define(function (require) { var that = this; // resolve connections and pass the line below as a callback Model.neuroml.resolveAllImportTypes(function(){ - that.setData(obj, deserializedOptions); + that.setData(obj, deserializedOptions, view.nodeColormap); }); } From b28f469b980e5cd283cbb3be17786e474909a6d9 Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Thu, 15 Jun 2017 14:30:10 +0100 Subject: [PATCH 072/371] uniform handling of default color formats --- .../webapp/js/common/GEPPETTO.Resources.js | 42 +++++++++---------- .../interface/3dCanvas/ThreeDEngine.js | 10 ++--- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/src/main/webapp/js/common/GEPPETTO.Resources.js b/src/main/webapp/js/common/GEPPETTO.Resources.js index 9b9d2adee..515f83c07 100644 --- a/src/main/webapp/js/common/GEPPETTO.Resources.js +++ b/src/main/webapp/js/common/GEPPETTO.Resources.js @@ -38,27 +38,27 @@ define(function (require) { }, COLORS: { - DEFAULT: "0X199e8", - SELECTED: "0Xffcc00", - INPUT_TO_SELECTED: "0Xffdfc6", - OUTPUT_TO_SELECTED: "0Xff5a02", - HIGHLIGHTED: "0Xff1a02", - INPUT_AND_OUTPUT: "0X649615", - SPLIT: "0XCFCFA6", - ENTITY_NODE: "0xcc0000", - ASPECT_NODE: "0xcc6600", - ASPECT_SUBTREE_NODE: "0xcccc00", - COMPOSITE_NODE: "0x66cc00", - CONNECTION_NODE: "0x00cc00", - DYNAMICS_SPECIFICATION_NODE: "0x00cc66", - FUNCTION_NODE: "0x00cccc", - PARAMETER_NODE: "0x0066cc", - PARAMETER_SPECIFICATION_NODE: "0x0000cc", - TEXT_METADATA_NODE: "0x6600cc", - URL_METADATA_NODE: "0xcc00cc", - VARIABLE_NODE: "0xcc0066", - VISUAL_OBJECT_REFERENCE_NODE: "0x606060", - VISUAL_GROUP_ELEMENT_NODE: "0xffffff", + DEFAULT: "#0199e8", + SELECTED: "#ffcc00", + INPUT_TO_SELECTED: "#ffdfc6", + OUTPUT_TO_SELECTED: "#ff5a02", + HIGHLIGHTED: "#ff1a02", + INPUT_AND_OUTPUT: "#649615", + SPLIT: "#CFCFA6", + ENTITY_NODE: "#cc0000", + ASPECT_NODE: "#cc6600", + ASPECT_SUBTREE_NODE: "#cccc00", + COMPOSITE_NODE: "#66cc00", + CONNECTION_NODE: "#00cc00", + DYNAMICS_SPECIFICATION_NODE: "#00cc66", + FUNCTION_NODE: "#00cccc", + PARAMETER_NODE: "#0066cc", + PARAMETER_SPECIFICATION_NODE: "#0000cc", + TEXT_METADATA_NODE: "#6600cc", + URL_METADATA_NODE: "#cc00cc", + VARIABLE_NODE: "#cc0066", + VISUAL_OBJECT_REFERENCE_NODE: "#606060", + VISUAL_GROUP_ELEMENT_NODE: "#ffffff", }, /** diff --git a/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js b/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js index a2aec801d..574446801 100644 --- a/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js +++ b/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js @@ -899,7 +899,7 @@ define(['jquery'], function () { scene.traverse(function (child) { if (child instanceof THREE.Mesh) { - child.material.color.setHex(GEPPETTO.Resources.COLORS.DEFAULT); + this.setThreeColor(child.material.color, GEPPETTO.Resources.COLORS.DEFAULT); child.material.wireframe = this.wireframe; child.material.defaultColor = GEPPETTO.Resources.COLORS.DEFAULT; child.material.defaultOpacity = GEPPETTO.Resources.OPACITY.DEFAULT; @@ -1155,7 +1155,7 @@ define(['jquery'], function () { color = GEPPETTO.Resources.COLORS.DEFAULT; } var material = new THREE.LineBasicMaterial(options); - material.color.setHex(color); + this.setThreeColor(material.color, color) material.defaultColor = color; material.defaultOpacity = GEPPETTO.Resources.OPACITY.DEFAULT; return material; @@ -1177,7 +1177,7 @@ define(['jquery'], function () { shading: THREE.SmoothShading }); - material.color.setHex(color); + this.setThreeColor(material.color, color); material.defaultColor = color; material.defaultOpacity = GEPPETTO.Resources.OPACITY.DEFAULT; return material; @@ -1197,7 +1197,7 @@ define(['jquery'], function () { depthTest: false, transparent: true }); - pMaterial.color.setHex(GEPPETTO.Resources.COLORS.DEFAULT); + this.setThreeColor(pMaterial.color, GEPPETTO.Resources.COLORS.DEFAULT); pMaterial.defaultColor = GEPPETTO.Resources.COLORS.DEFAULT; pMaterial.opacity = GEPPETTO.Resources.OPACITY.DEFAULT; pMaterial.defaultOpacity = GEPPETTO.Resources.OPACITY.DEFAULT; @@ -2263,7 +2263,7 @@ define(['jquery'], function () { } var material = new THREE.LineDashedMaterial({dashSize: 3, gapSize: 1}); - material.color.setHex(colour); + this.setThreeColor(material.color, colour); var line = new THREE.LineSegments(geometry, material); line.updateMatrixWorld(true); From 9e46baf4b2882379b3dca75b9e1291bb7a3d27c3 Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Thu, 15 Jun 2017 15:58:41 +0100 Subject: [PATCH 073/371] factor out more neuroml explicit references --- .../components/widgets/connectivity/Connectivity.js | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js index 7aa5be7af..e18312cc9 100644 --- a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js +++ b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js @@ -117,10 +117,9 @@ define(function (require) { }, createDataFromConnections: function () { - //TODO: remove Hardcoded NeuroML stuff - if(Model.neuroml.connection){ + if(this.options.library.connection){ - var connectionVariables = Model.neuroml.connection.getVariableReferences(); + var connectionVariables = this.options.library.connection.getVariableReferences(); if(connectionVariables.length>0) { if (this.dataset["root"].getMetaType() == GEPPETTO.Resources.INSTANCE_NODE) { @@ -385,12 +384,11 @@ define(function (require) { var modalContent=$('') .append(this.createLayoutSelector()[0].outerHTML).modal(); function handleFirstClick(event) { - //TODO: remove Hardcoded NeuroML stuff - var netTypes = GEPPETTO.ModelFactory.getAllTypesOfType(GEPPETTO.ModelFactory.geppettoModel.neuroml.network); - var netInstances = _.flatten(_.map(netTypes, function(x){return GEPPETTO.ModelFactory.getAllInstancesOf(x)})); + var netTypes = GEPPETTO.ModelFactory.getAllTypesOfType(that.options.library.network); + var netInstances = _.flatten(_.map(netTypes, function(x){return GEPPETTO.ModelFactory.getAllInstancesOf(x)})) function synapseFromConnection(conn) { - var synapses=GEPPETTO.ModelFactory.getAllVariablesOfType(conn.getParent(),GEPPETTO.ModelFactory.geppettoModel.neuroml.synapse); + var synapses=GEPPETTO.ModelFactory.getAllVariablesOfType(conn.getParent(), that.options.library.synapse); if(synapses.length>0){ return synapses[0].getId(); } From c322ebdd48604c4afa9e76afbecf6f81d4b64d95 Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Thu, 15 Jun 2017 15:59:48 +0100 Subject: [PATCH 074/371] no overflow for dashboard (prevent global scrollbar, cf. issue #618) --- src/main/webapp/js/pages/dashboard/css/application.css | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/webapp/js/pages/dashboard/css/application.css b/src/main/webapp/js/pages/dashboard/css/application.css index d4863d0fb..b8d43ca6b 100644 --- a/src/main/webapp/js/pages/dashboard/css/application.css +++ b/src/main/webapp/js/pages/dashboard/css/application.css @@ -8,6 +8,7 @@ body { font-weight: 200; -webkit-font-smoothing: antialiased; background-color: #f5f5f5; + overflow: hidden; } .dashboardAlert{ From 276c332de8f7cd965e57900aa64237ddf088f14d Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Thu, 15 Jun 2017 16:49:55 +0100 Subject: [PATCH 075/371] use d3 colorscheme if no custom population colors --- .../components/widgets/connectivity/Connectivity.js | 11 ++++++++--- .../js/components/widgets/connectivity/chords.js | 5 +++-- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js index e18312cc9..f3358766c 100644 --- a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js +++ b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js @@ -92,9 +92,14 @@ define(function (require) { }, setNodeColormap: function(nodeColormap) { - if (typeof nodeColormap != 'undefined') - this.nodeColormap = d3.scaleOrdinal(nodeColormap.range) - .domain(nodeColormap.domain); + if (typeof nodeColormap != 'undefined') { + if (typeof nodeColormap.range == 'undefined') + this.nodeColormap = d3.scaleOrdinal(d3.schemeCategory20) + .domain(nodeColormap.domain); + else + this.nodeColormap = d3.scaleOrdinal(nodeColormap.range) + .domain(nodeColormap.domain); + } }, setData: function (root, options, nodeColormap) { diff --git a/src/main/webapp/js/components/widgets/connectivity/chords.js b/src/main/webapp/js/components/widgets/connectivity/chords.js index dceb14de3..926586dca 100644 --- a/src/main/webapp/js/components/widgets/connectivity/chords.js +++ b/src/main/webapp/js/components/widgets/connectivity/chords.js @@ -15,8 +15,9 @@ define(function (require) { var innerRadius = Math.min(context.options.innerWidth, context.options.innerHeight) * .41, outerRadius = innerRadius * 1.05; - var fill = context.nodeColormap - .domain(context.dataset.nodeTypes); + // if no custom colors set then use d3 provided color scheme + var fill = context.nodeColormap.range ? context.nodeColormap : d3.scaleOrdinal(d3.schemeCategory20); + fill.domain(context.dataset.nodeTypes); var svg = context.svg.append("g") .attr("transform", "translate(" + context.options.innerWidth / 2 + "," + context.options.innerHeight / 2 + ")"); From 42ed7f0d49da0cc8165c4c533082476d3d3a8d64 Mon Sep 17 00:00:00 2001 From: jrmartin Date: Thu, 15 Jun 2017 19:57:01 -0700 Subject: [PATCH 076/371] tests for setgeometrytype and more checks for default extension --- .../extensions/extensionsConfiguration.json | 4 +- .../js/pages/tests/casperjs/CoreTests.js | 54 +++++++++++++------ .../pages/tests/casperjs/CoreTestsUtility.js | 12 +++++ .../webapp/js/pages/tests/casperjs/UITests.js | 21 +++++--- 4 files changed, 67 insertions(+), 24 deletions(-) diff --git a/src/main/webapp/extensions/extensionsConfiguration.json b/src/main/webapp/extensions/extensionsConfiguration.json index 1cc5f3dd8..5bac2b9a4 100644 --- a/src/main/webapp/extensions/extensionsConfiguration.json +++ b/src/main/webapp/extensions/extensionsConfiguration.json @@ -1,6 +1,6 @@ { - "geppetto-default/ComponentsInitialization": true, - "geppetto-osb/ComponentsInitialization": false, + "geppetto-default/ComponentsInitialization": false, + "geppetto-osb/ComponentsInitialization": true, "geppetto-vfb/ComponentsInitialization": false, "geppetto-neuron/ComponentsInitialization": false, "geppetto-hm/ComponentsInitialization": false diff --git a/src/main/webapp/js/pages/tests/casperjs/CoreTests.js b/src/main/webapp/js/pages/tests/casperjs/CoreTests.js index f64e7e833..e9b2fa9cc 100644 --- a/src/main/webapp/js/pages/tests/casperjs/CoreTests.js +++ b/src/main/webapp/js/pages/tests/casperjs/CoreTests.js @@ -159,6 +159,7 @@ function hhcellTest(test,name){ casper.then(function(){ closeSpotlight(); casper.echo("-------Testing Canvas Widget and Color Function--------"); + //adding few widgets to the project to test View state later casper.evaluate(function(){ hhcell.deselect(); GEPPETTO.ComponentFactory.addWidget('CANVAS', {name: '3D Canvas',}, function () {this.setName('Widget Canvas');this.setPosition();this.display([hhcell])}); @@ -171,14 +172,19 @@ function hhcellTest(test,name){ Popup2.addCustomNodeHandler(customHandler,'click'); }); - casper.mouseEvent('click', 'button#tutorialBtn', "attempting to open tutorial"); - + //toggle tutorial if tutorial button exists + if(casper.exists('#tutorialBtn')){ + casper.mouseEvent('click', 'button#tutorialBtn', "attempting to open tutorial"); + } + + //tests widget canvas has mesh var mesh = casper.evaluate(function(){ var mesh = Canvas2.engine.getRealMeshesForInstancePath("hhcell.hhpop[0]").length; return mesh; }); test.assertEquals(mesh, 1, "Canvas widget has hhcell"); + //click on next step for Tutorial casper.evaluate(function(){ $(".nextBtn").click(); $(".nextBtn").click(); @@ -195,44 +201,45 @@ function hhcellTest(test,name){ }) }); + //reload test, needed for testing view comes up casper.then(function(){launchTest(test,"Hhcell",30000);}); + //testing widgets stored in View state come up casper.then(function(){ test.assertVisible('div#Canvas2', "Canvas2 is correctly open on reload."); test.assertVisible('div#Plot1', "Plot1 is correctly open on reload"); test.assertVisible('div#Popup1', "Popup1 is correctly open on reload"); test.assertVisible('div#Popup2', "Popup2 is correctly open on reload"); - test.assertVisible('div#Tutorial1', "Tutorial1 is correctly open on reload"); - - var tutorialStep = casper.evaluate(function() { - return Tutorial1.state.currentStep; - }); - - test.assertEquals(tutorialStep, 2, "Tutorial1 step restored correctly"); + //if tutorial button exists, tests existence of Tutorial + if(casper.exists('#tutorialBtn')){ + test.assertVisible('div#Tutorial1', "Tutorial1 is correctly open on reload"); + var tutorialStep = casper.evaluate(function() { + return Tutorial1.state.currentStep; + }); + test.assertEquals(tutorialStep, 2, "Tutorial1 step restored correctly"); + } + //Tests content of Popup1 var popUpMessage = casper.evaluate(function() { return $("#Popup1").html(); }); - test.assertEquals(popUpMessage, "Hhcell popup", "Popup1 message restored correctly"); + //Tests popup has custom handlers var popUpCustomHandler = casper.evaluate(function() { return Popup2.customHandlers; }); - test.assertEquals(popUpCustomHandler.length, 1, "Popup2 custom handlers restored correctly"); test.assertEquals(popUpCustomHandler[0]["event"], "click", "Popup2 custom handlers event restored correctly"); + //Test canvas widget has mesh var meshInCanvas2Exists = casper.evaluate(function() { var mesh = Canvas1.engine.meshes["hhcell.hhpop[0]"]; - if(mesh!=null && mesh!=undefined){ return true; } - return false; }); - test.assertEquals(meshInCanvas2Exists, true, "Canvas2 hhcell set correctly"); }); }; @@ -320,6 +327,8 @@ function acnetTest(test){ casper.then(function(){ closeSpotlight(); //close spotlight before continuing casper.echo("-------Testing Canvas Widget and Color Function--------"); + + //adding few widgets to the project to test View state later casper.evaluate(function(){ acnet2.pyramidals_48[0].deselect(); GEPPETTO.ComponentFactory.addWidget('CANVAS', {name: '3D Canvas',}, function () {this.setName('Widget Canvas');this.setPosition();this.display([acnet2])}); @@ -329,8 +338,10 @@ function acnetTest(test){ acnet2.baskets_12[4].getVisualGroups()[0].show(true); }); + //tests camera controls are working by checking camera has moved testCameraControlsWithCanvasWidget(test,[231.95608349343888,508.36555704435455,1849.8390363191731]); + //applies visual group to instance and tests colors testVisualGroup(test,"acnet2.baskets_12[0]",2,[[],[0,0.4,1],[0.6,0.8,0]]); testVisualGroup(test,"acnet2.baskets_12[5]",2,[[],[0,0.4,1],[0.6,0.8,0]]); @@ -339,6 +350,8 @@ function acnetTest(test){ test3DMeshOpacity(test,1, "acnet2.baskets_12[4]"); test3DMeshOpacity(test,1, "acnet2.baskets_12[1]"); + casper.echo("Testing setGeometry"); + casper.evaluate(function(){ acnet2.pyramidals_48[0].setGeometryType("cylinders") }); @@ -354,31 +367,42 @@ function acnetTest(test){ }); test.assertEquals(meshTotal, 60, "Correctly amount of meshes after applying cylinders"); + //retrieve original color pre setGeomtry + var color = getMeshColor(test,"acnet2.pyramidals_48[0]"); casper.evaluate(function(){ acnet2.pyramidals_48[0].setGeometryType("lines") }); + casper.echo("Testing color post setGeometryType"); + test3DMeshColor(test,color,"acnet2.pyramidals_48[0]"); + //test mesh set geometry meshType = casper.evaluate(function(){ return Canvas1.engine.getRealMeshesForInstancePath("acnet2.pyramidals_48[0]")[0].type; }); test.assertEquals(meshType, "LineSegments", "Correctly set mesh to lines"); + //testsing same amount of meshes exists after changing a mesh to lines var meshTotal = casper.evaluate(function(){ return Object.keys(Canvas1.engine.meshes).length; }); test.assertEquals(meshTotal, 60, "Correctly amount of meshes after applying cylinders"); + //Set geometry type to cylinders casper.evaluate(function(){ acnet2.pyramidals_48[0].setGeometryType("cylinders") }); - //test mesh set geometry + //test set geometry type in a mesh var meshType = casper.evaluate(function(){ return Canvas1.engine.getRealMeshesForInstancePath("acnet2.pyramidals_48[0]")[0].type; }); test.assertEquals(meshType, "Mesh", "Correctly set mesh to cylinders"); + casper.echo("Testing color post setGeometryType to cylinders"); + test3DMeshColor(test,color,"acnet2.pyramidals_48[0]"); + + //testing same amount of meshes exists after changing a mesh to cylinders var meshTotal = casper.evaluate(function(){ return Object.keys(Canvas1.engine.meshes).length; }); diff --git a/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js b/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js index 0f73382a1..3b737de8e 100644 --- a/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js +++ b/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js @@ -153,6 +153,18 @@ function test3DMeshColor(test,testColor,variableName,index){ test.assertEquals(color[2],testColor[2],"Black default color is correct for " +variableName); } +function getMeshColor(test,variableName,index){ + if(index==undefined){ + index=0; + } + var color = casper.evaluate(function(variableName,index) { + var color = Canvas1.engine.getRealMeshesForInstancePath(variableName)[index].material.color; + return [color.r, color.g, color.b]; + },variableName,index); + + return color; +} + function test3DMeshOpacity(test,opactityExpected,variableName,index){ if(index==undefined){ index=0; diff --git a/src/main/webapp/js/pages/tests/casperjs/UITests.js b/src/main/webapp/js/pages/tests/casperjs/UITests.js index 9075b820d..f85b91ca2 100644 --- a/src/main/webapp/js/pages/tests/casperjs/UITests.js +++ b/src/main/webapp/js/pages/tests/casperjs/UITests.js @@ -182,14 +182,17 @@ function reloadProjectTest(test, url, customHandlers,widgetCanvasObject){ casper.wait(2000, function () {}); test.assertVisible('div#Canvas2', "Canvas2 is correctly open on reload."); test.assertVisible('div#Popup1', "Popup1 is correctly open on reload"); - test.assertVisible('div#Tutorial1', "Tutorial1 is correctly open on reload"); test.assertVisible('div#Connectivity1', "Connectivity1 is correctly open on reload"); - var tutorialStep = casper.evaluate(function() { - return Tutorial1.state.currentStep; - }); - - test.assertEquals(tutorialStep, 2, "Tutorial1 step restored correctly"); + if(casper.exists('#tutorialBtn')){ + test.assertVisible('div#Tutorial1', "Tutorial1 is correctly open on reload"); + + var tutorialStep = casper.evaluate(function() { + return Tutorial1.state.currentStep; + }); + + test.assertEquals(tutorialStep, 2, "Tutorial1 step restored correctly"); + } var popUpCustomHandler = casper.evaluate(function() { return Popup1.customHandlers; @@ -247,7 +250,9 @@ function testProject(test, url, expect_error, persisted, spotlight_record_variab }); casper.then(function () { - casper.mouseEvent('click', 'button#tutorialBtn', "attempting to open tutorial"); + if(casper.exists('#tutorialBtn')){ + casper.mouseEvent('click', 'button#tutorialBtn', "attempting to open tutorial"); + } casper.evaluate(function(widgetCanvasObject) { var canvasObject = null; if(widgetCanvasObject=="hhcell"){ @@ -265,6 +270,8 @@ function testProject(test, url, expect_error, persisted, spotlight_record_variab $(".nextBtn").click(); $(".nextBtn").click(); },widgetCanvasObject); + + casper.wait(2000, function () {}); this.echo("Checking content of experiment row"); // test or wait for control panel stuff to be there if(this.exists('a[href="#experiments"]')){ From c410a684270902422a7a84d9c9fdab7775a37d7c Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Fri, 16 Jun 2017 12:08:16 +0100 Subject: [PATCH 077/371] better handling of state (library as path) --- .../js/components/widgets/connectivity/Connectivity.js | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js index f3358766c..26292a087 100644 --- a/src/main/webapp/js/components/widgets/connectivity/Connectivity.js +++ b/src/main/webapp/js/components/widgets/connectivity/Connectivity.js @@ -401,7 +401,7 @@ define(function (require) { return "Gap junction"; } } - that.setData(netInstances[0], {layout: event.currentTarget.id, linkType: synapseFromConnection}); //TODO: add option to select what to plot if #netInstance>1? + that.setData(netInstances[0], {layout: event.currentTarget.id, linkType: synapseFromConnection, library: that.connectivityOptions.library}); //TODO: add option to select what to plot if #netInstance>1? firstClick=true; } @@ -429,6 +429,9 @@ define(function (require) { if (typeof this.connectivityOptions[item] === "function") { serializedItem.value = this.connectivityOptions[item].toString(); serializedItem.type = 'function'; + } else if (item === "library") { + serializedItem.value = this.connectivityOptions[item].getPath(); + serializedItem.type = 'library'; } else { serializedItem.value = this.connectivityOptions[item]; serializedItem.type = 'primitive'; @@ -454,7 +457,7 @@ define(function (require) { var obj = eval(view.data); var deserializedOptions = {}; for(var item in view.options){ - if(view.options[item].type == "function"){ + if(view.options[item].type == "function" || view.options[item].type == "library"){ deserializedOptions[item] = eval('(' + view.options[item].value + ')'); } else { deserializedOptions[item] = view.options[item].value; From 85ca8dea72b29ff5fa83f0e483e564bc2619c469 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 19 Jun 2017 14:27:50 +0100 Subject: [PATCH 078/371] fix for split volumens --- .../webapp/js/components/interface/3dCanvas/ThreeDEngine.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js b/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js index f9632789c..f8771b0fb 100644 --- a/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js +++ b/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js @@ -1465,7 +1465,7 @@ define(['jquery'], function () { var instance = eval(instancePath); // Behaviour: help exploration of networks by ghosting and not highlighting non connected or selected - if (instance.getConnections().length > 0) { + if (instance !== undefined && instance.getConnections().length > 0) { // allOtherMeshes will contain a list of all the non connected entities in the scene var allOtherMeshes = $.extend({}, this.meshes); // look on the simulation selection options and perform necessary operations From 4f48c51adc2c440dee789fa97192359134e317d2 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 19 Jun 2017 15:40:27 +0100 Subject: [PATCH 079/371] fix plit space and split groups --- .../geppettoJupyter/GeppettoJupyterModelSync.js | 3 +-- .../js/components/interface/3dCanvas/Canvas.js | 14 ++++++++++++-- .../interface/3dCanvas/SceneController.js | 16 ++++++++++++++-- .../interface/3dCanvas/ThreeDEngine.js | 9 ++++----- .../js/geppettoModel/model/VisualGroupElement.js | 2 +- 5 files changed, 32 insertions(+), 12 deletions(-) diff --git a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js index fc8b528ee..2c3f1cc90 100644 --- a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js +++ b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js @@ -227,8 +227,7 @@ define(function (require, exports, module) { for (var i = 0; i < this.get('geometries').length; i++) { elements[this.get('geometries')[i].id] = ""; } - //GEPPETTO.SceneController.splitGroups(window.Instances[0], elements); - Canvas1.engine.splitGroups(window.Instances[0], elements); + GEPPETTO.SceneController.splitGroups(window.Instances[0], elements); } }, diff --git a/src/main/webapp/js/components/interface/3dCanvas/Canvas.js b/src/main/webapp/js/components/interface/3dCanvas/Canvas.js index 83055875f..ee2e3c7a9 100644 --- a/src/main/webapp/js/components/interface/3dCanvas/Canvas.js +++ b/src/main/webapp/js/components/interface/3dCanvas/Canvas.js @@ -345,6 +345,16 @@ define(function (require) { return this; } + /** + * Split merged mesh into individual meshes + * @param instances + * @param groupElements + */ + splitGroups(instance, groupElements){ + this.engine.splitGroups(instance, groupElements); + return this; + } + /** * Associate a color function to a group of instances * @@ -382,8 +392,8 @@ define(function (require) { * @param instance * @returns {Canvas} */ - showVisualGroupsForInstance(instance) { - this.engine.showVisualGroupsForInstance(instance); + showVisualGroupsForInstance(instance, visualGroupElement) { + this.engine.showVisualGroupsForInstance(instance, visualGroupElement); return this; } diff --git a/src/main/webapp/js/components/interface/3dCanvas/SceneController.js b/src/main/webapp/js/components/interface/3dCanvas/SceneController.js index d9b03814d..c48adce94 100644 --- a/src/main/webapp/js/components/interface/3dCanvas/SceneController.js +++ b/src/main/webapp/js/components/interface/3dCanvas/SceneController.js @@ -313,9 +313,9 @@ define(['jquery'], function () { * * @param instance */ - showVisualGroupsForInstance: function (instance) { + showVisualGroupsForInstance: function (instance, visualGroupElement) { for (var i = 0; i < this.canvasComponents.length; i++) { - this.canvasComponents[i].showVisualGroupsForInstance(instance); + this.canvasComponents[i].showVisualGroupsForInstance(instance, visualGroupElement); } }, @@ -331,6 +331,18 @@ define(['jquery'], function () { } }, + + /** + * Split merged mesh into individual meshes + * @param instances + * @param groupElements + */ + splitGroups: function (instance, groupElements) { + for (var i = 0; i < this.canvasComponents.length; i++) { + this.canvasComponents[i].splitGroups(instance, groupElements); + } + }, + /** * Associate a color function to a group of instances for all the existing canvas. * The visual instance that will be colored is the one associated with the composite type diff --git a/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js b/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js index f8771b0fb..ad342292e 100644 --- a/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js +++ b/src/main/webapp/js/components/interface/3dCanvas/ThreeDEngine.js @@ -2391,8 +2391,7 @@ define(['jquery'], function () { this.setThreeColor(groupMesh.material.color, splitHighlightedGroups[groupName].color.getHex()); } } - } - , + }, /** * Split merged mesh into individual meshes @@ -2614,7 +2613,7 @@ define(['jquery'], function () { * @param instance * @param meshesContainer */ - showVisualGroupsForInstance: function (instance) { + showVisualGroupsForInstance: function (instance, visualGroupElement) { if (!this.hasInstance(instance)) { return; } @@ -2634,8 +2633,8 @@ define(['jquery'], function () { var groupElementsReference = object.getInitialValue().value.groupElements; for (var i = 0; i < groupElementsReference.length; i++) { var objectGroup = GEPPETTO.ModelFactory.resolve(groupElementsReference[i].$ref).getId(); - if (objectGroup == this.getId()) { - elements[object.getId()] = {'color': this.getColor()} + if (objectGroup == visualGroupElement.getId()) { + elements[object.getId()] = {'color': visualGroupElement.getColor()} } } } diff --git a/src/main/webapp/js/geppettoModel/model/VisualGroupElement.js b/src/main/webapp/js/geppettoModel/model/VisualGroupElement.js index 7735ff760..d801b59bf 100644 --- a/src/main/webapp/js/geppettoModel/model/VisualGroupElement.js +++ b/src/main/webapp/js/geppettoModel/model/VisualGroupElement.js @@ -76,7 +76,7 @@ define(function (require) { } for (var i = 0; i < instances.length; i++) { - GEPPETTO.SceneController.showVisualGroup(instances[i]); + GEPPETTO.SceneController.showVisualGroupsForInstance(instances[i], this); } }; From 75cea75647180ca78a31b36abd55f98e2466dcc7 Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Mon, 19 Jun 2017 16:03:56 +0100 Subject: [PATCH 080/371] initial working connectivity matrix pre/post pop indicators --- .../widgets/connectivity/matrices.js | 42 +++++++++++++++++-- 1 file changed, 39 insertions(+), 3 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/matrices.js b/src/main/webapp/js/components/widgets/connectivity/matrices.js index 574e9e505..4feaaf5db 100644 --- a/src/main/webapp/js/components/widgets/connectivity/matrices.js +++ b/src/main/webapp/js/components/widgets/connectivity/matrices.js @@ -7,7 +7,7 @@ define(function (require) { createMatrixLayout: function (context) { var d3 = require("d3"); - var margin = { top: 30, right: 10, bottom: 10, left: 0 }; + var margin = { top: 45, right: 10, bottom: 10, left: 15 }; var legendWidth = 120; var matrixDim = (context.options.innerHeight < (context.options.innerWidth - legendWidth)) ? (context.options.innerHeight) : (context.options.innerWidth - legendWidth); @@ -18,7 +18,7 @@ define(function (require) { // Colors c = d3.scaleOrdinal(d3.schemeCategory10); - var labelTop = margin.top - 10; + var labelTop = margin.top - 25; var tooltip = context.svg .append("g") .attr("transform", "translate(" + margin.left + "," + labelTop + ")") @@ -80,9 +80,45 @@ define(function (require) { var rect = container .append("rect") .attr("class", "background") - .attr("width", matrixDim - margin.left) + .attr("width", matrixDim - margin.left - 30) .attr("height", matrixDim - margin.top); + var types = nodes.map(function(x) { return x.id; }); + + var popIndicator = function(pos) { + return function(d,i) { + d3.select(this).selectAll(".cell") + .data(d) + .enter().append("circle") + .attr("class", "cell") + .attr(pos, function (d, i) { + return x(i); + }) + .attr("r", x.bandwidth()/2) + .attr("title", function (d) { + return d.id; + }) + .style("fill", function (d) { + return eval(GEPPETTO.ModelFactory.getAllPotentialInstancesEndingWith(d)[0]).getColor(); + }) + }; + }; + + var prePop = container.selectAll(".prePop") + .data([types]) + .enter() + .append("g") + .attr("class", "prePop") + .attr("transform", "translate(4,-10)") + .each(popIndicator("cx")); + var postPop = container.selectAll(".postPop") + .data([types]) + .enter() + .append("g") + .attr("class", "postPop") + .attr("transform", "translate(-10,4)") + .each(popIndicator("cy")); + var row = container.selectAll(".row") .data(matrix) .enter().append("g") From f2f5390f307b594757c6a37cd368ca23fd1f4b24 Mon Sep 17 00:00:00 2001 From: johnidol Date: Mon, 19 Jun 2017 16:18:20 +0100 Subject: [PATCH 081/371] more generic implementation - the other version wasn't working on chrome macosx --- .../experimentsTable/ExperimentsTable.js | 20 +++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/src/main/webapp/js/components/interface/experimentsTable/ExperimentsTable.js b/src/main/webapp/js/components/interface/experimentsTable/ExperimentsTable.js index 47dff9fa6..4e0c63f33 100644 --- a/src/main/webapp/js/components/interface/experimentsTable/ExperimentsTable.js +++ b/src/main/webapp/js/components/interface/experimentsTable/ExperimentsTable.js @@ -679,12 +679,20 @@ define(function (require) { }, //Determines if an element inside the experiments table is in view - isInView : function(elem){ - var docViewTop = $('#experimentsTable').offset().top; - var docViewBottom = docViewTop + $('#experimentsTable').height(); - var elemTop = $(elem).offset().top; - var elemBottom = elemTop + $(elem).height(); - return ((elemBottom <= docViewBottom) && (elemTop >= docViewTop)); + isInView : function(el){ + // grab vanilla dom element from jquery element + el = el[0]; + var rect = el.getBoundingClientRect(), top = rect.top, height = rect.height, + el = el.parentNode; + do { + rect = el.getBoundingClientRect(); + if (top <= rect.bottom === false) return false; + // Check if the element is out of view due to a container scrolling + if ((top + height) <= rect.top) return false; + el = el.parentNode; + } while (el != document.body); + // Check its within the document viewport + return top <= document.documentElement.clientHeight; }, /** From ecd425c119c6f6c7c937d3427a3f43d9376a37d0 Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 19 Jun 2017 16:36:31 +0100 Subject: [PATCH 082/371] remove wrong condition --- src/main/webapp/js/geppettoProject/ExperimentsController.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/js/geppettoProject/ExperimentsController.js b/src/main/webapp/js/geppettoProject/ExperimentsController.js index 02b4ce3f6..e248ff3ce 100644 --- a/src/main/webapp/js/geppettoProject/ExperimentsController.js +++ b/src/main/webapp/js/geppettoProject/ExperimentsController.js @@ -262,7 +262,7 @@ define(function (require) { if (experiment.status == GEPPETTO.Resources.ExperimentStatus.COMPLETED) { // playExperimentReady true even if some variables // do not have value, so if playAll then we get state here - if (!this.playExperimentReady || this.playOptions.playAll) { + if (!this.playExperimentReady) { this.getExperimentState(experiment.getParent().getId(), experiment.id, null); return "Play Experiment"; } else { From d1d542c17d366356204d3fa085f97bf910927639 Mon Sep 17 00:00:00 2001 From: johnidol Date: Mon, 19 Jun 2017 16:37:05 +0100 Subject: [PATCH 083/371] Semi-colon-fest 2017 --- .../js/pages/tests/casperjs/CoreTests.js | 22 +++++++++---------- .../pages/tests/casperjs/CoreTestsUtility.js | 6 ++--- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/main/webapp/js/pages/tests/casperjs/CoreTests.js b/src/main/webapp/js/pages/tests/casperjs/CoreTests.js index e9b2fa9cc..781145d47 100644 --- a/src/main/webapp/js/pages/tests/casperjs/CoreTests.js +++ b/src/main/webapp/js/pages/tests/casperjs/CoreTests.js @@ -114,11 +114,11 @@ function hhcellTest(test,name){ casper.then(function(){ casper.echo("-------Testing Control Panel--------"); testInitialControlPanelValues(test,3); - }) + }); casper.then(function(){ casper.echo("-------Testing Mesh Visibility--------"); testVisibility(test,"hhcell.hhpop[0]","#hhcell_hhpop_0__visibility_ctrlPanel_btn"); - }) + }); casper.then(function () { casper.echo("-------Testing Plotting from Control Panel--------"); buttonClick("#stateVariablesFilterBtn"); @@ -242,7 +242,7 @@ function hhcellTest(test,name){ }); test.assertEquals(meshInCanvas2Exists, true, "Canvas2 hhcell set correctly"); }); -}; +} /** * Main method for testing ACNet @@ -270,7 +270,7 @@ function acnetTest(test){ casper.then(function(){ casper.echo("-------Testing Mesh Visibility--------"); testVisibility(test,"acnet2.pyramidals_48[0]","#acnet2_pyramidals_48_0__visibility_ctrlPanel_btn"); - }) + }); casper.then(function () { casper.echo("-------Testing Plotting from Control Panel--------"); buttonClick("#stateVariablesFilterBtn"); @@ -458,7 +458,7 @@ function c302Test(test){ this.waitUntilVisible('button[id="c302_ADAL_0__v_plot_ctrlPanel_btn"]', function () { buttonClick("#c302_ADAL_0__v_plot_ctrlPanel_btn"); }); - }) + }); casper.then(function(){ this.waitUntilVisible('div[id="Plot1"]', function () { @@ -477,12 +477,12 @@ function c302Test(test){ testSpotlight(test, "c302.ADAL[0].v",'div[id="Plot2"]',true,false); }); }); - }) + }); casper.then(function(){ casper.echo("-------Testing Spotlight--------"); testSpotlight(test, "c302.ADAL[0].v",'div[id="Plot2"]',true,false); - }) + }); casper.then(function(){ closeSpotlight(); //close spotlight before continuing @@ -504,8 +504,8 @@ function c302Test(test){ //test color function test3DMeshColorNotEquals(test,defaultColor,"c302.PVDR[0]"); casper.echo("Done Playing, now exiting"); - }) - }) + }); + }); } function ca1Test(test){ @@ -528,7 +528,7 @@ function ca1Test(test){ this.evaluate(function(){ $("#anyProjectFilterBtn").click(); }); - }) + }); casper.then(function(){ casper.evaluate(function() { @@ -552,7 +552,7 @@ function pharyngealTest(test){ casper.then(function(){ testInitialControlPanelValues(test,10); }); -}; +} function nwbSampleTest(test){ casper.waitForSelector('div[id="Popup1"]', function() { diff --git a/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js b/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js index 3b737de8e..cbacb48a9 100644 --- a/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js +++ b/src/main/webapp/js/pages/tests/casperjs/CoreTestsUtility.js @@ -33,7 +33,7 @@ function resetCameraTestWithCanvasWidget(test,expectedCameraPosition){ buttonClick("#panHomeBtn"); casper.evaluate(function(){ $("#Canvas2_component").find(".position-toolbar").find(".pan-home").click(); - }) + }); testCameraPosition(test,expectedCameraPosition); } @@ -297,7 +297,7 @@ function testSpotlight(test, variableName,plotName,expectButton,testSelect, sele */ function testCameraControls(test, expectedCameraPosition){ casper.then(function(){ - casper.echo("------Zoom-------") + casper.echo("------Zoom-------"); casper.repeat(zoomClicks, function() { this.thenClick("button#zoomInBtn", function() {}); }); @@ -334,7 +334,7 @@ function testCameraControls(test, expectedCameraPosition){ function testCameraControlsWithCanvasWidget(test, expectedCameraPosition){ casper.echo("-------Testing Camera Controls while playing experiment--------"); casper.then(function(){ - casper.echo("------Zoom-------") + casper.echo("------Zoom-------"); casper.repeat(zoomClicks*2, function() { this.thenClick("button#zoomInBtn", function() {}); this.thenClick("#Canvas2 button#zoomInBtn", function() {}); From fa7ed15b0a7a330a70d860ce9571b818273cb16e Mon Sep 17 00:00:00 2001 From: Adrian Quintana Date: Mon, 19 Jun 2017 17:10:35 +0100 Subject: [PATCH 084/371] implementing a quick solution for now to the add3dsphere and modify3dsphere --- .../communication/geppettoJupyter/GeppettoJupyterModelSync.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js index 2c3f1cc90..5cadb5525 100644 --- a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js +++ b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterModelSync.js @@ -381,11 +381,11 @@ define(function (require, exports, module) { else if (msg.type === 'draw_sphere') { var content = msg.content; if (this.point_process_sphere) { - this.point_process_sphere = GEPPETTO.SceneFactory.modify3DSphere(this.point_process_sphere, content.x, content.y, content.z, content.radius); + this.point_process_sphere = Canvas1.engine.modify3DSphere(this.point_process_sphere, content.x, content.y, content.z, content.radius); this.point_process_sphere.visible = true; } else { - this.point_process_sphere = GEPPETTO.SceneFactory.add3DSphere(content.x, content.y, content.z, content.radius); + this.point_process_sphere = Canvas1.engine.add3DSphere(content.x, content.y, content.z, content.radius); } } else if (msg.type === 'remove_sphere') { From 76914aa5f9a52e8166a19b17238442caea5570b3 Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Mon, 19 Jun 2017 17:22:11 +0100 Subject: [PATCH 085/371] use d3 palette when no custom colors set --- .../js/components/widgets/connectivity/matrices.js | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/matrices.js b/src/main/webapp/js/components/widgets/connectivity/matrices.js index 4feaaf5db..817c7b8b0 100644 --- a/src/main/webapp/js/components/widgets/connectivity/matrices.js +++ b/src/main/webapp/js/components/widgets/connectivity/matrices.js @@ -85,9 +85,9 @@ define(function (require) { var types = nodes.map(function(x) { return x.id; }); - var popIndicator = function(pos) { + var popIndicator = function(pos, colormap) { return function(d,i) { - d3.select(this).selectAll(".cell") + d3.select(this).selectAll(".cell") .data(d) .enter().append("circle") .attr("class", "cell") @@ -99,7 +99,9 @@ define(function (require) { return d.id; }) .style("fill", function (d) { - return eval(GEPPETTO.ModelFactory.getAllPotentialInstancesEndingWith(d)[0]).getColor(); + return colormap( + eval(GEPPETTO.ModelFactory.getAllPotentialInstancesEndingWith(d)[0]) + .getType().getId()); }) }; }; @@ -109,15 +111,15 @@ define(function (require) { .enter() .append("g") .attr("class", "prePop") - .attr("transform", "translate(4,-10)") - .each(popIndicator("cx")); + .attr("transform", "translate(3,-10)") + .each(popIndicator("cx", context.nodeColormap)); var postPop = container.selectAll(".postPop") .data([types]) .enter() .append("g") .attr("class", "postPop") .attr("transform", "translate(-10,4)") - .each(popIndicator("cy")); + .each(popIndicator("cy", context.nodeColormap)); var row = container.selectAll(".row") .data(matrix) From 123b81bb9083f55a5931b3585128a41fa9a10d8d Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Mon, 19 Jun 2017 17:57:07 +0100 Subject: [PATCH 086/371] Use API instead of directly tinkering with the DOM --- .../geppettoJupyter/GeppettoJupyterGUISync.js | 26 +- .../webapp/js/components/widgets/AWidget.js | 18 +- .../webapp/js/components/widgets/Widget.js | 413 +++++++++--------- 3 files changed, 237 insertions(+), 220 deletions(-) diff --git a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js index b3e09f7a0..a99db7320 100644 --- a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js +++ b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js @@ -47,6 +47,7 @@ define(function (require, exports, module) { parameters['sync_value'] = this.get('sync_value'); parameters['handleChange'] = this.handleChange.bind(null, this); parameters['handleBlur'] = this.handleBlur.bind(null, this); + parameters['isStateless'] = true; return parameters; }, @@ -77,9 +78,10 @@ define(function (require, exports, module) { this.on("msg:custom", this.handle_custom_messages, this); this.on("comm:close", this.close_panel, this); this.on("change:widget_name", function (model, value, options) { - $("#" + this.get('widget_id') + "_dialog").dialog('option', 'title', this.get("widget_name")); + this.get("component").setName(this.get("widget_name")); }); }, + close_panel: function (msg) { this.set('triggerClose', false); $("." + this.get('widget_id') + "_dialog").find(".ui-dialog-titlebar-close").click(); @@ -124,6 +126,7 @@ define(function (require, exports, module) { } }); + // Do not allow resizable for parent panel var selector = $("." + this.get('widget_id') + "_dialog"); selector.resizable('destroy'); @@ -131,23 +134,14 @@ define(function (require, exports, module) { // Do not allow close depending on property for (var propertyName in this.get("properties")){ if (propertyName == "closable" && this.get("properties")["closable"] == false){ - selector.find(".ui-dialog-titlebar-close").hide(); + this.get("component").showCloseButton(false); } } - // Resize widget dim and pos - if (this.get('position_x') > 0) { - selector.css({ left: this.get('position_x') }); - } - if (this.get('position_y') > 0) { - selector.css({ top: this.get('position_y') }); - } - if (this.get('width') > 0) { - selector.css({ width: this.get('width') }); - } - if (this.get('height') > 0) { - selector.css({ height: this.get('height') }); - } + this.get("component").setPosition(this.get('position_x'), this.get('position_y')); + this.get("component").setSize(this.get('height'), this.get('width')); + this.get("component").showHistoryIcon(false); + }, handle_custom_messages: function (msg) { @@ -155,7 +149,7 @@ define(function (require, exports, module) { this.display(); } else if (msg.type === 'shake') { - $('#' + this.get('widget_id') + "_dialog").parent().effect('shake', {distance:5, times: 3}, 500); + this.get("component").shake(); } } }, { diff --git a/src/main/webapp/js/components/widgets/AWidget.js b/src/main/webapp/js/components/widgets/AWidget.js index ce835618e..b3c26d91c 100644 --- a/src/main/webapp/js/components/widgets/AWidget.js +++ b/src/main/webapp/js/components/widgets/AWidget.js @@ -119,15 +119,21 @@ define(function (require) { return this; } + + /** * @command setPosition(left,top) * @param {Integer} left -Left position of the widget * @param {Integer} top - Top position of the widget */ setPosition(left, top) { - this.position.left = left; - this.position.top = top; + if (left != null && left != undefined) { + this.position.left = left; + } + if (top != null && top != undefined) { + this.position.top = top; + } this.$el.dialog( 'option', 'position', { my: "left+" + this.position.left + " top+" + this.position.top, @@ -148,7 +154,13 @@ define(function (require) { * @param {Integer} w - Width of the widget */ setSize(h, w) { - this.size = {height: h, width:w}; + if (h != null && h != undefined && h!=-1) { + this.size.height = h; + } + if (w != null && w != undefined && w!=-1) { + this.size.width = w; + } + this.$el.dialog({ height: this.size.height, width: this.size.width }).dialogExtend(); this.$el.trigger('resizeEnd'); diff --git a/src/main/webapp/js/components/widgets/Widget.js b/src/main/webapp/js/components/widgets/Widget.js index 3be4eb6d7..130d1fef7 100644 --- a/src/main/webapp/js/components/widgets/Widget.js +++ b/src/main/webapp/js/components/widgets/Widget.js @@ -10,7 +10,7 @@ define(function (require) { var Backbone = require('backbone'); var $ = require('jquery'); require("./jquery.dialogextend.min"); - + return { /** @@ -30,20 +30,20 @@ define(function (require) { size: {}, position: {}, registeredEvents: null, - executedAction : 0, - title : null, - previousMaxTransparency : false, - previousMaxSize : {}, - maximize : false, - collapsed : false, + executedAction: 0, + title: null, + previousMaxTransparency: false, + previousMaxSize: {}, + maximize: false, + collapsed: false, widgetType: null, stateless: false, showTitleBar: true, transparentBackground: false, dirtyView: false, - defaultSize : function(){return {height: 300, width: 350}}, - defaultPosition : function(){return {left: "50%", top: "50%"}}, + defaultSize: function () { return { height: 300, width: 350 } }, + defaultPosition: function () { return { left: "50%", top: "50%" } }, /** * Initializes the widget * @@ -63,24 +63,24 @@ define(function (require) { this.stateless = (options.stateless != undefined) ? options.stateless : false; this.registeredEvents = []; this.dirtyView = false; - + var self = this; $(self.historyMenu.el).on('click', function (event) { - var itemId = $(event.target).attr('id'); - var registeredItem = self.historyMenu.getClickedItem(itemId); - if(registeredItem != null || registeredItem!=undefined){ - var label = registeredItem["label"]; - self.title = label; - $("#"+self.id).parent().find(".ui-dialog-title").html(self.title); - } + var itemId = $(event.target).attr('id'); + var registeredItem = self.historyMenu.getClickedItem(itemId); + if (registeredItem != null || registeredItem != undefined) { + var label = registeredItem["label"]; + self.title = label; + $("#" + self.id).parent().find(".ui-dialog-title").html(self.title); + } }); - window.addEventListener('resize', function(event){ - if(self.maximize){ - self.maximize = false; - self.setSize(window.innerHeight,window.innerWidth); - self.$el.trigger('resizeEnd', ["maximize"]); - self.maximize = true; - } + window.addEventListener('resize', function (event) { + if (self.maximize) { + self.maximize = false; + self.setSize(window.innerHeight, window.innerWidth); + self.$el.trigger('resizeEnd', ["maximize"]); + self.maximize = true; + } }); }, @@ -131,7 +131,7 @@ define(function (require) { * * @returns {int} */ - getComponentType: function(){ + getComponentType: function () { return this.widgetType; }, @@ -168,20 +168,24 @@ define(function (require) { * @param {Integer} top - Top position of the widget */ setPosition: function (left, top) { - this.position.left = left; - this.position.top = top; + if (left != null && left != undefined) { + this.position.left = left; + } + if (top != null && top != undefined) { + this.position.top = top; + } - this.$el.dialog( - 'option', 'position', { - my: "left+" + this.position.left + " top+" + this.position.top, - at: "left top", - of: $(window) - }).dialogExtend(); + this.$el.dialog( + 'option', 'position', { + my: "left+" + this.position.left + " top+" + this.position.top, + at: "left top", + of: $(window) + }).dialogExtend(); // set flag to indicate something changed this.dirtyView = true; - return this; + return this; }, /** @@ -191,15 +195,21 @@ define(function (require) { * @param {Integer} w - Width of the widget */ setSize: function (h, w) { - this.size.height = h; - this.size.width = w; - this.$el.dialog({height: this.size.height, width: this.size.width}).dialogExtend(); - this.$el.trigger('resizeEnd'); + if (h != null && h != undefined && h!=-1) { + this.size.height = h; + } + if (w != null && w != undefined && w!=-1) { + this.size.width = w; + } + this.$el.dialog({ height: this.size.height, width: this.size.width }).dialogExtend(); + + this.$el.trigger('resizeEnd'); + // set flag to indicate something changed this.dirtyView = true; - return this; + return this; }, /** @@ -236,7 +246,7 @@ define(function (require) { * @param {Boolean} true|false - enables / disables resizability */ setResizable: function (resize) { - this.$el.dialog('option', 'resizable', resize).dialogExtend(); + this.$el.dialog('option', 'resizable', resize).dialogExtend(); return this; }, @@ -244,7 +254,7 @@ define(function (require) { * @command setAutoWidth() */ setAutoWidth: function () { - this.$el.dialog('option', 'width', 'auto').dialogExtend(); + this.$el.dialog('option', 'width', 'auto').dialogExtend(); return this; }, @@ -252,7 +262,7 @@ define(function (require) { * @command setAutoHeigth() */ setAutoHeight: function () { - this.$el.dialog('option', 'height', 'auto').dialogExtend(); + this.$el.dialog('option', 'height', 'auto').dialogExtend(); return this; }, @@ -357,7 +367,7 @@ define(function (require) { getItems: function (history, name) { var data = []; for (var i = 0; i < history.length; i++) { - var action = this.getId() + "[" + this.getId() + "."+name+"[" + i + "].method].apply(" + this.getId() + ", " + this.getId() + "."+name+"[" + i + "].arguments)"; + var action = this.getId() + "[" + this.getId() + "." + name + "[" + i + "].method].apply(" + this.getId() + ", " + this.getId() + "." + name + "[" + i + "].arguments)"; data.push({ "label": history[i].label, "action": [action], @@ -418,9 +428,9 @@ define(function (require) { this.showTitleBar = show; if (show) { - this.$el.parent().find(".ui-dialog-titlebar").show(); + this.$el.parent().find(".ui-dialog-titlebar").show(); } else { - this.$el.parent().find(".ui-dialog-titlebar").hide(); + this.$el.parent().find(".ui-dialog-titlebar").hide(); } // set flag to indicate something changed @@ -428,59 +438,59 @@ define(function (require) { return this; }, - - updateNavigationHistoryBar : function(){ - var disabled = "arrow-disabled"; - if(this.getItems(this.controller.history, "controller.history").length<=1){ - if(!$("#"+this.id + "-left-nav").hasClass(disabled)){ - $("#"+this.id + "-left-nav").addClass(disabled); - $("#"+this.id + "-right-nav").addClass(disabled); - } - }else{ - if($("#"+this.id + "-left-nav").hasClass(disabled)){ - $("#"+this.id + "-left-nav").removeClass(disabled); - $("#"+this.id + "-right-nav").removeClass(disabled); - } - } - }, - - showHistoryNavigationBar : function(show){ - var leftNav = $("#"+this.id + "-left-nav"); - var rightNav = $("#"+this.id + "-right-nav"); - - if (show) { - if((leftNav.length ==0) && (rightNav.length == 0)){ - - var disabled = ""; - if(this.getItems(this.controller.history, "controller.history").length<=1){ - disabled = "arrow-disabled "; - } - - var that = this; - var button = $("
"+ - "
").click(function (event) { - var historyItems = that.getItems(that.controller.history, "controller.history"); - var item; - if(event.target.id == (that.id + "-left-nav") || (that.id + "-right-nav")){ - that.executedAction = historyItems.length-1; - } - item = historyItems[that.executedAction].action[0]; - GEPPETTO.Console.executeImplicitCommand(item); - $("#"+that.id).parent().find(".ui-dialog-title").html(historyItems[that.executedAction].label); - event.stopPropagation(); - }); - - var dialogParent = this.$el.parent(); - button.insertBefore(dialogParent.find("span.ui-dialog-title")); - $(button).addClass("widget-title-bar-button"); - } - } else { - if(leftNav.is(":visible") && rightNav.is(":visible")){ - leftNav.remove(); - rightNav.remove(); - this.executedAction =0; - } - } + + updateNavigationHistoryBar: function () { + var disabled = "arrow-disabled"; + if (this.getItems(this.controller.history, "controller.history").length <= 1) { + if (!$("#" + this.id + "-left-nav").hasClass(disabled)) { + $("#" + this.id + "-left-nav").addClass(disabled); + $("#" + this.id + "-right-nav").addClass(disabled); + } + } else { + if ($("#" + this.id + "-left-nav").hasClass(disabled)) { + $("#" + this.id + "-left-nav").removeClass(disabled); + $("#" + this.id + "-right-nav").removeClass(disabled); + } + } + }, + + showHistoryNavigationBar: function (show) { + var leftNav = $("#" + this.id + "-left-nav"); + var rightNav = $("#" + this.id + "-right-nav"); + + if (show) { + if ((leftNav.length == 0) && (rightNav.length == 0)) { + + var disabled = ""; + if (this.getItems(this.controller.history, "controller.history").length <= 1) { + disabled = "arrow-disabled "; + } + + var that = this; + var button = $("
" + + "
").click(function (event) { + var historyItems = that.getItems(that.controller.history, "controller.history"); + var item; + if (event.target.id == (that.id + "-left-nav") || (that.id + "-right-nav")) { + that.executedAction = historyItems.length - 1; + } + item = historyItems[that.executedAction].action[0]; + GEPPETTO.Console.executeImplicitCommand(item); + $("#" + that.id).parent().find(".ui-dialog-title").html(historyItems[that.executedAction].label); + event.stopPropagation(); + }); + + var dialogParent = this.$el.parent(); + button.insertBefore(dialogParent.find("span.ui-dialog-title")); + $(button).addClass("widget-title-bar-button"); + } + } else { + if (leftNav.is(":visible") && rightNav.is(":visible")) { + leftNav.remove(); + rightNav.remove(); + this.executedAction = 0; + } + } }, /** @@ -488,23 +498,23 @@ define(function (require) { */ showCloseButton: function (show) { if (show) { - this.$el.parent().find(".ui-dialog-titlebar-close").show(); + this.$el.parent().find(".ui-dialog-titlebar-close").show(); } else { - this.$el.parent().find(".ui-dialog-titlebar-close").hide(); + this.$el.parent().find(".ui-dialog-titlebar-close").hide(); } }, - addButtonToTitleBar: function(button){ - var dialogParent = this.$el.parent(); - dialogParent.find("div.ui-dialog-titlebar").prepend(button); - $(button).addClass("widget-title-bar-button"); + addButtonToTitleBar: function (button) { + var dialogParent = this.$el.parent(); + dialogParent.find("div.ui-dialog-titlebar").prepend(button); + $(button).addClass("widget-title-bar-button"); }, - + addHelpButton: function () { - var that=this; + var that = this; this.addButtonToTitleBar($("
").click(function () { GEPPETTO.ComponentFactory.addComponent('MDMODAL', { - title: that.id.slice(0,-1) + ' help', + title: that.id.slice(0, -1) + ' help', content: that.getHelp(), show: true }, document.getElementById("modal-region")); @@ -518,11 +528,11 @@ define(function (require) { */ setDraggable: function (draggable) { if (draggable) { - this.$el.parent().draggable({disabled: false}); + this.$el.parent().draggable({ disabled: false }); // NOTE: this will wipe any class applied to the widget... this.setClass(''); } else { - this.$el.parent().draggable({disabled: true}); + this.$el.parent().draggable({ disabled: true }); this.setClass('noStyleDisableDrag'); } }, @@ -532,14 +542,14 @@ define(function (require) { * * @param isTransparent */ - setTrasparentBackground: function(isTransparent) { + setTrasparentBackground: function (isTransparent) { this.transparentBackground = isTransparent; - if(isTransparent){ - this.$el.parent().addClass('transparent-back'); - this.previousMaxTransparency = true; + if (isTransparent) { + this.$el.parent().addClass('transparent-back'); + this.previousMaxTransparency = true; } else { - this.$el.parent().removeClass('transparent-back'); + this.$el.parent().removeClass('transparent-back'); } return this; }, @@ -548,27 +558,27 @@ define(function (require) { * Inject CSS for custom behaviour */ setClass: function (className) { - this.$el.dialog({dialogClass: className}).dialogExtend(); + this.$el.dialog({ dialogClass: className }).dialogExtend(); }, /** * Perform a jquery ui effect to the widget */ - perfomEffect: function (effect, options, speed){ + perfomEffect: function (effect, options, speed) { this.$el.parent().effect(effect, options, speed); }, /** * Perform a shake effect to the widget */ - shake: function (options, speed){ - if (options === undefined){ - options = {distance:5, times: 3} + shake: function (options, speed) { + if (options === undefined) { + options = { distance: 5, times: 3 } } - if (speed === undefined){ + if (speed === undefined) { speed = 500 } - + this.$el.parent().effect('shake', options, speed) }, @@ -576,8 +586,8 @@ define(function (require) { * Renders the widget dialog window */ render: function () { - - var that = this; + + var that = this; //create the dialog window for the widget this.dialog = $("
").dialog( @@ -593,64 +603,65 @@ define(function (require) { that.destroy(); } } - }).dialogExtend({"closable" : true, - "maximizable" : true, - "minimizable" : true, - "collapsable" : true, - "restore" : true, + }).dialogExtend({ + "closable": true, + "maximizable": true, + "minimizable": true, + "collapsable": true, + "restore": true, "minimizeLocation": "right", - "icons" : { - "maximize" : "fa fa-window-maximize", - "minimize" : "fa fa-window-minimize", - "collapse" : "fa fa-chevron-circle-up", - "restore" : "fa fa-window-restore", - }, - "load" : function(evt, dlg){ - var icons = $("#"+that.id).parent().find(".ui-icon"); - for(var i =0 ; ionline documentation instead.'; + 'Try the online documentation instead.'; }, - - setController : function(controller){ - this.controller = controller; + + setController: function (controller) { + this.controller = controller; }, - - showHistoryIcon: function(show){ - var that=this; - if(show && this.$el.parent().find(".history-icon").length==0){ + + showHistoryIcon: function (show) { + var that = this; + if (show && this.$el.parent().find(".history-icon").length == 0) { this.addButtonToTitleBar($("
").click(function (event) { that.showHistoryMenu(event); event.stopPropagation(); })); - } - else{ - this.$el.parent().find(".history-icon").remove(); - } + } + else { + this.$el.parent().find(".history-icon").remove(); + } }, /** @@ -714,11 +725,11 @@ define(function (require) { * * @returns {{size: {height: *, width: *}, position: {left: *, top: *}}} */ - getView: function(){ + getView: function () { // get default stuff such as id, position and size return { widgetType: this.widgetType, - isWidget: this.isWidget(), + isWidget: this.isWidget(), showTitleBar: this.showTitleBar, transparentBackground: this.transparentBackground, name: this.name, @@ -738,9 +749,9 @@ define(function (require) { * * @param view */ - setView: function(view){ + setView: function (view) { // set default stuff such as position and size - if(view.size != undefined && view.size.height != 0 && view.size.width != 0){ + if (view.size != undefined && view.size.height != 0 && view.size.width != 0) { this.setSize(view.size.height, view.size.width); } else { // trigger auto size if we have no size info @@ -748,19 +759,19 @@ define(function (require) { this.setAutoHeight(); } - if(view.position != undefined){ + if (view.position != undefined) { this.setPosition(view.position.left, view.position.top); } - if(view.name != undefined){ + if (view.name != undefined) { this.setName(view.name); } - if(view.showTitleBar != undefined){ + if (view.showTitleBar != undefined) { this.showTitleBar(view.showTitleBar); } - if(view.transparentBackground != undefined){ + if (view.transparentBackground != undefined) { this.setTrasparentBackground(view.transparentBackground); } @@ -768,11 +779,11 @@ define(function (require) { this.dirtyView = false; }, - isStateLess(){ + isStateLess() { return this.stateless; }, - isWidget (){ + isWidget() { return true; } }) From 59deb7a8766a74942801d7ecd5b9f00f93780dc4 Mon Sep 17 00:00:00 2001 From: johnidol Date: Mon, 19 Jun 2017 18:05:12 +0100 Subject: [PATCH 087/371] optimize selector --- src/main/webapp/js/pages/tests/casperjs/CoreTests.js | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/main/webapp/js/pages/tests/casperjs/CoreTests.js b/src/main/webapp/js/pages/tests/casperjs/CoreTests.js index 781145d47..13e9b94ee 100644 --- a/src/main/webapp/js/pages/tests/casperjs/CoreTests.js +++ b/src/main/webapp/js/pages/tests/casperjs/CoreTests.js @@ -185,9 +185,10 @@ function hhcellTest(test,name){ test.assertEquals(mesh, 1, "Canvas widget has hhcell"); //click on next step for Tutorial - casper.evaluate(function(){ - $(".nextBtn").click(); - $(".nextBtn").click(); + casper.evaluate(function () { + var nextBtnSelector = $(".nextBtn"); + nextBtnSelector.click(); + nextBtnSelector.click(); }); casper.echo("-------Testing Camera Controls--------"); From 1712989e0182bb907d00f038dba75034549784c5 Mon Sep 17 00:00:00 2001 From: jrmartin Date: Mon, 19 Jun 2017 13:10:56 -0700 Subject: [PATCH 088/371] Fix failing tests --- src/main/webapp/js/pages/tests/casperjs/UITests.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/webapp/js/pages/tests/casperjs/UITests.js b/src/main/webapp/js/pages/tests/casperjs/UITests.js index f85b91ca2..a3981fa9b 100644 --- a/src/main/webapp/js/pages/tests/casperjs/UITests.js +++ b/src/main/webapp/js/pages/tests/casperjs/UITests.js @@ -85,7 +85,7 @@ casper.test.begin('Geppetto basic tests', 133, function suite(test) { }); casper.then(function () { - reloadProjectTest(test, TARGET_URL + port+"/org.geppetto.frontend/geppetto?load_project_from_id="+projectID,2); + reloadProjectTest(test, TARGET_URL + port+"/org.geppetto.frontend/geppetto?load_project_from_id="+projectID,1); }); casper.then(function () { @@ -179,7 +179,7 @@ function reloadProjectTest(test, url, customHandlers,widgetCanvasObject){ this.echo("I've waited for "+url+" project to load."); casper.then(function () { - casper.wait(2000, function () {}); + casper.wait(5000, function () {}); test.assertVisible('div#Canvas2', "Canvas2 is correctly open on reload."); test.assertVisible('div#Popup1', "Popup1 is correctly open on reload"); test.assertVisible('div#Connectivity1', "Connectivity1 is correctly open on reload"); @@ -271,7 +271,7 @@ function testProject(test, url, expect_error, persisted, spotlight_record_variab $(".nextBtn").click(); },widgetCanvasObject); - casper.wait(2000, function () {}); + casper.wait(5000, function () {}); this.echo("Checking content of experiment row"); // test or wait for control panel stuff to be there if(this.exists('a[href="#experiments"]')){ From 79ca6bf8583fcb9e04a2c4d9aafe6c94d1d8ff25 Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Tue, 20 Jun 2017 11:05:47 +0100 Subject: [PATCH 089/371] Fix for panel name --- .../js/communication/geppettoJupyter/GeppettoJupyterGUISync.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js index a99db7320..fefde4762 100644 --- a/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js +++ b/src/main/webapp/js/communication/geppettoJupyter/GeppettoJupyterGUISync.js @@ -141,7 +141,7 @@ define(function (require, exports, module) { this.get("component").setPosition(this.get('position_x'), this.get('position_y')); this.get("component").setSize(this.get('height'), this.get('width')); this.get("component").showHistoryIcon(false); - + this.get("component").setName(this.get("widget_name")); }, handle_custom_messages: function (msg) { From 305ceb4ab5f2f507ce891b6441ee22616041c780 Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Tue, 20 Jun 2017 12:07:14 +0100 Subject: [PATCH 090/371] minor refactoring --- .../widgets/connectivity/matrices.js | 85 +++++++++++-------- 1 file changed, 51 insertions(+), 34 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/matrices.js b/src/main/webapp/js/components/widgets/connectivity/matrices.js index 817c7b8b0..5bc92693f 100644 --- a/src/main/webapp/js/components/widgets/connectivity/matrices.js +++ b/src/main/webapp/js/components/widgets/connectivity/matrices.js @@ -83,41 +83,67 @@ define(function (require) { .attr("width", matrixDim - margin.left - 30) .attr("height", matrixDim - margin.top); - var types = nodes.map(function(x) { return x.id; }); + // we store the 'conn' key in case we want to + // eg. conditionally colour the indicator if there + // are actually connections in that row/column + var pre = nodes.map(function(x,i) { return {id: x.id, conn: (matrix[i].filter((d)=>d.z).length > 0) ? true : false }}); + var matrixT = matrix[0].map(function(col, i) { + return matrix.map(function(row) { + return row[i]; + }) + }); + var post = nodes.map(function(x,i) { return {id: x.id, conn: (matrixT[i].filter((d)=>d.z).length > 0) ? true : false }}); + + var typeIdFromId = function(id) { + return eval(GEPPETTO.ModelFactory.getAllPotentialInstancesEndingWith(id)[0]).getType().getId(); + }; + + var showTooltip = function(msg) { + d3.select(this.parentNode.appendChild(this)).transition().duration(100). + style('stroke-opacity', 1).style('stroke', 'white').style('stroke-width', 2); + d3.select("body").style('cursor', 'pointer'); + return tooltip.transition().duration(100).text(msg); + } + + var hideTooltip = function() { + d3.select(this).transition().duration(100).style('stroke-opacity', 0).style('stroke', 'white'); + d3.select("body").style('cursor', 'default'); + return tooltip.text(""); + }; var popIndicator = function(pos, colormap) { return function(d,i) { d3.select(this).selectAll(".cell") - .data(d) - .enter().append("circle") - .attr("class", "cell") - .attr(pos, function (d, i) { - return x(i); - }) - .attr("r", x.bandwidth()/2) - .attr("title", function (d) { - return d.id; - }) - .style("fill", function (d) { - return colormap( - eval(GEPPETTO.ModelFactory.getAllPotentialInstancesEndingWith(d)[0]) - .getType().getId()); - }) + .data(d) + .enter().append("circle") + .attr("class", "cell") + .attr(pos, function (d, i) { + return x(i); + }) + .attr("r", x.bandwidth()/2) + .attr("title", function (d) { + return d.id; + }) + .style("fill", function (d) { + return colormap(typeIdFromId(d.id)); + }) + .on("mouseover", function(d){ $.proxy(showTooltip, this)(typeIdFromId(d.id)) }) + .on("mouseout", $.proxy(hideTooltip)) }; }; - var prePop = container.selectAll(".prePop") - .data([types]) + var postPop = container.selectAll(".postPop") + .data([post]) .enter() .append("g") - .attr("class", "prePop") + .attr("class", "postPop") .attr("transform", "translate(3,-10)") .each(popIndicator("cx", context.nodeColormap)); - var postPop = container.selectAll(".postPop") - .data([types]) + var prePop = container.selectAll(".prePop") + .data([pre]) .enter() .append("g") - .attr("class", "postPop") + .attr("class", "prePop") .attr("transform", "translate(-10,4)") .each(popIndicator("cy", context.nodeColormap)); @@ -221,19 +247,10 @@ define(function (require) { eval(root.getId() + "." + nodes[d.y].id).select(); eval(root.getId() + "." + nodes[d.y].id).showConnectionLines(false); }) - .on("mouseover", function (d) { - d3.select(this.parentNode.appendChild(this)).transition().duration(100). - style('stroke-opacity', 1).style('stroke', 'white').style('stroke-width', 2); - d3.select("body").style('cursor', 'pointer'); - return tooltip.transition().duration(100).text(nodes[d.y].id + " is connected to " + nodes[d.x].id); - }) - .on("mouseout", function () { - d3.select(this).transition().duration(100).style('stroke-opacity', 0).style('stroke', 'white'); - d3.select("body").style('cursor', 'default'); - return tooltip.text(""); - }); + .on("mouseover", function (d) { $.proxy(showTooltip, this)(nodes[d.y].id + " is connected to " + nodes[d.x].id); }) + .on("mouseout", $.proxy(hideTooltip)); } } } -}); \ No newline at end of file +}); From 70f8dffa952e0e8a89bfe3d727a10f9f82b7514b Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Tue, 20 Jun 2017 14:29:55 +0100 Subject: [PATCH 091/371] transitions --- .../widgets/connectivity/matrices.js | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/matrices.js b/src/main/webapp/js/components/widgets/connectivity/matrices.js index 5bc92693f..a5499b9fe 100644 --- a/src/main/webapp/js/components/widgets/connectivity/matrices.js +++ b/src/main/webapp/js/components/widgets/connectivity/matrices.js @@ -205,10 +205,26 @@ define(function (require) { .delay(function (d) { return x(d.x) * 4; }) - .attr("x", function (d) { + .attr("x", function (d) { return x(d.x); }); + t.selectAll(".postPop .cell") + .delay(function (d, i) { + return x(i) * 4; + }) + .attr("cx", function (d, i) { + return x(i); + }); + + t.selectAll(".prePop .cell") + .delay(function (d, i) { + return x(i) * 4; + }) + .attr("cy", function (d, i) { + return x(i); + }); + t.selectAll(".column") .delay(function (d, i) { return x(i) * 4; From 33ca53437d201ced09afa1174b344bed5712c55a Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Tue, 20 Jun 2017 14:53:46 +0100 Subject: [PATCH 092/371] minor refactoring and show populations in legend (not instances) --- .../widgets/connectivity/matrices.js | 21 ++++++++++--------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/matrices.js b/src/main/webapp/js/components/widgets/connectivity/matrices.js index a5499b9fe..5f5193a7f 100644 --- a/src/main/webapp/js/components/widgets/connectivity/matrices.js +++ b/src/main/webapp/js/components/widgets/connectivity/matrices.js @@ -18,13 +18,14 @@ define(function (require) { // Colors c = d3.scaleOrdinal(d3.schemeCategory10); - var labelTop = margin.top - 25; + var labelTop = margin.top - 25; + var defaultTooltipText = "Hover the squares to see the connections."; var tooltip = context.svg .append("g") .attr("transform", "translate(" + margin.left + "," + labelTop + ")") .append("text") .attr('class', 'connectionlabel') - .text("Hover the squares to see the connections."); + .text(defaultTooltipText); var container = context.svg .append("g") @@ -98,17 +99,17 @@ define(function (require) { return eval(GEPPETTO.ModelFactory.getAllPotentialInstancesEndingWith(id)[0]).getType().getId(); }; - var showTooltip = function(msg) { + var mouseoverCell = function(msg) { d3.select(this.parentNode.appendChild(this)).transition().duration(100). style('stroke-opacity', 1).style('stroke', 'white').style('stroke-width', 2); d3.select("body").style('cursor', 'pointer'); return tooltip.transition().duration(100).text(msg); } - var hideTooltip = function() { + var mouseoutCell = function() { d3.select(this).transition().duration(100).style('stroke-opacity', 0).style('stroke', 'white'); d3.select("body").style('cursor', 'default'); - return tooltip.text(""); + return tooltip.text(defaultTooltipText); }; var popIndicator = function(pos, colormap) { @@ -127,8 +128,8 @@ define(function (require) { .style("fill", function (d) { return colormap(typeIdFromId(d.id)); }) - .on("mouseover", function(d){ $.proxy(showTooltip, this)(typeIdFromId(d.id)) }) - .on("mouseout", $.proxy(hideTooltip)) + .on("mouseover", function(d){ $.proxy(mouseoverCell, this)(typeIdFromId(d.id)) }) + .on("mouseout", $.proxy(mouseoutCell)) }; }; @@ -170,7 +171,7 @@ define(function (require) { column.append("line") .attr("x1", -context.options.innerWidth); - context.createLegend('legend', c, { x: matrixDim, y: 0 }); + context.createLegend('legend', context.nodeColormap, { x: matrixDim, y: 0 }); //Sorting matrix entries by criteria specified via combobox var orderContainer = $('
', { @@ -263,8 +264,8 @@ define(function (require) { eval(root.getId() + "." + nodes[d.y].id).select(); eval(root.getId() + "." + nodes[d.y].id).showConnectionLines(false); }) - .on("mouseover", function (d) { $.proxy(showTooltip, this)(nodes[d.y].id + " is connected to " + nodes[d.x].id); }) - .on("mouseout", $.proxy(hideTooltip)); + .on("mouseover", function (d) { $.proxy(mouseoverCell, this)(nodes[d.y].id + " is connected to " + nodes[d.x].id); }) + .on("mouseout", $.proxy(mouseoutCell)); } } } From 34fc90684585fe76c77fd40ba441d29fc096901c Mon Sep 17 00:00:00 2001 From: Matt Earnshaw Date: Tue, 20 Jun 2017 14:54:35 +0100 Subject: [PATCH 093/371] formatting --- .../widgets/connectivity/matrices.js | 518 +++++++++--------- 1 file changed, 259 insertions(+), 259 deletions(-) diff --git a/src/main/webapp/js/components/widgets/connectivity/matrices.js b/src/main/webapp/js/components/widgets/connectivity/matrices.js index 5f5193a7f..0faa17dc7 100644 --- a/src/main/webapp/js/components/widgets/connectivity/matrices.js +++ b/src/main/webapp/js/components/widgets/connectivity/matrices.js @@ -3,271 +3,271 @@ */ define(function (require) { - return { - createMatrixLayout: function (context) { - var d3 = require("d3"); - - var margin = { top: 45, right: 10, bottom: 10, left: 15 }; - var legendWidth = 120; - - var matrixDim = (context.options.innerHeight < (context.options.innerWidth - legendWidth)) ? (context.options.innerHeight) : (context.options.innerWidth - legendWidth); - - var x = d3.scaleBand().range([0, matrixDim - margin.top]), - // Opacity - z = d3.scaleLinear().domain([0, 4]).clamp(true), - // Colors - c = d3.scaleOrdinal(d3.schemeCategory10); - - var labelTop = margin.top - 25; - var defaultTooltipText = "Hover the squares to see the connections."; - var tooltip = context.svg - .append("g") - .attr("transform", "translate(" + margin.left + "," + labelTop + ")") - .append("text") - .attr('class', 'connectionlabel') - .text(defaultTooltipText); - - var container = context.svg - .append("g") - .attr("transform", "translate(" + margin.left + "," + margin.top + ")"); - - - var matrix = []; - var nodes = context.dataset.nodes; - var root = context.dataset.root; - var n = nodes.length; - - // Compute index per node. - nodes.forEach(function (node, i) { - node.pre_count = 0; - node.post_count = 0; - matrix[i] = d3.range(n).map(function (j) { - return { x: j, y: i, z: 0 }; - }); + return { + createMatrixLayout: function (context) { + var d3 = require("d3"); + + var margin = { top: 45, right: 10, bottom: 10, left: 15 }; + var legendWidth = 120; + + var matrixDim = (context.options.innerHeight < (context.options.innerWidth - legendWidth)) ? (context.options.innerHeight) : (context.options.innerWidth - legendWidth); + + var x = d3.scaleBand().range([0, matrixDim - margin.top]), + // Opacity + z = d3.scaleLinear().domain([0, 4]).clamp(true), + // Colors + c = d3.scaleOrdinal(d3.schemeCategory10); + + var labelTop = margin.top - 25; + var defaultTooltipText = "Hover the squares to see the connections."; + var tooltip = context.svg + .append("g") + .attr("transform", "translate(" + margin.left + "," + labelTop + ")") + .append("text") + .attr('class', 'connectionlabel') + .text(defaultTooltipText); + + var container = context.svg + .append("g") + .attr("transform", "translate(" + margin.left + "," + margin.top + ")"); + + + var matrix = []; + var nodes = context.dataset.nodes; + var root = context.dataset.root; + var n = nodes.length; + + // Compute index per node. + nodes.forEach(function (node, i) { + node.pre_count = 0; + node.post_count = 0; + matrix[i] = d3.range(n).map(function (j) { + return { x: j, y: i, z: 0 }; + }); + }); + + // Convert links to matrix; count pre / post conns. + context.dataset.links.forEach(function (link) { + //TODO: think about zero weight lines + //matrix[link.source][link.target].z = link.weight ? link.type : 0; + matrix[link.source][link.target].z = link.type; + nodes[link.source].pre_count += 1; + nodes[link.target].post_count += 1; + }); + + //Sorting matrix entries. + //TODO: runtime specified sorting criteria + var sortOptions = { + 'id': 'By entity name', + 'pre_count': 'By # pre', + 'post_count': 'By # post' + }; + // Precompute the orders. + var orders = { + id: d3.range(n).sort(function (a, b) { + return d3.ascending(nodes[a].id, nodes[b].id); + }), + pre_count: d3.range(n).sort(function (a, b) { + return nodes[b].pre_count - nodes[a].pre_count; + }), + post_count: d3.range(n).sort(function (a, b) { + return nodes[b].post_count - nodes[a].post_count; + }), + //community: d3.range(n).sort(function(a, b) { return nodes[b].community - nodes[a].community; }), + }; + // Default sort order. + x.domain(orders.id); + + var rect = container + .append("rect") + .attr("class", "background") + .attr("width", matrixDim - margin.left - 30) + .attr("height", matrixDim - margin.top); + + // we store the 'conn' key in case we want to + // eg. conditionally colour the indicator if there + // are actually connections in that row/column + var pre = nodes.map(function(x,i) { return {id: x.id, conn: (matrix[i].filter((d)=>d.z).length > 0) ? true : false }}); + var matrixT = matrix[0].map(function(col, i) { + return matrix.map(function(row) { + return row[i]; + }) + }); + var post = nodes.map(function(x,i) { return {id: x.id, conn: (matrixT[i].filter((d)=>d.z).length > 0) ? true : false }}); + + var typeIdFromId = function(id) { + return eval(GEPPETTO.ModelFactory.getAllPotentialInstancesEndingWith(id)[0]).getType().getId(); + }; + + var mouseoverCell = function(msg) { + d3.select(this.parentNode.appendChild(this)).transition().duration(100). + style('stroke-opacity', 1).style('stroke', 'white').style('stroke-width', 2); + d3.select("body").style('cursor', 'pointer'); + return tooltip.transition().duration(100).text(msg); + } + + var mouseoutCell = function() { + d3.select(this).transition().duration(100).style('stroke-opacity', 0).style('stroke', 'white'); + d3.select("body").style('cursor', 'default'); + return tooltip.text(defaultTooltipText); + }; + + var popIndicator = function(pos, colormap) { + return function(d,i) { + d3.select(this).selectAll(".cell") + .data(d) + .enter().append("circle") + .attr("class", "cell") + .attr(pos, function (d, i) { + return x(i); + }) + .attr("r", x.bandwidth()/2) + .attr("title", function (d) { + return d.id; + }) + .style("fill", function (d) { + return colormap(typeIdFromId(d.id)); + }) + .on("mouseover", function(d){ $.proxy(mouseoverCell, this)(typeIdFromId(d.id)) }) + .on("mouseout", $.proxy(mouseoutCell)) + }; + }; + + var postPop = container.selectAll(".postPop") + .data([post]) + .enter() + .append("g") + .attr("class", "postPop") + .attr("transform", "translate(3,-10)") + .each(popIndicator("cx", context.nodeColormap)); + var prePop = container.selectAll(".prePop") + .data([pre]) + .enter() + .append("g") + .attr("class", "prePop") + .attr("transform", "translate(-10,4)") + .each(popIndicator("cy", context.nodeColormap)); + + var row = container.selectAll(".row") + .data(matrix) + .enter().append("g") + .attr("class", "row") + .attr("transform", function (d, i) { + return "translate(0," + x(i) + ")"; + }) + .each(row); + + row.append("line") + .attr("x2", context.options.innerWidth); + + var column = container.selectAll(".column") + .data(matrix) + .enter().append("g") + .attr("class", "column") + .attr("transform", function (d, i) { + return "translate(" + x(i) + ")rotate(-90)"; + }); + + column.append("line") + .attr("x1", -context.options.innerWidth); + + context.createLegend('legend', context.nodeColormap, { x: matrixDim, y: 0 }); + + //Sorting matrix entries by criteria specified via combobox + var orderContainer = $('
', { + id: context.id + '-ordering', + style: 'width:' + legendWidth + 'px;left:' + (matrixDim + context.widgetMargin) + 'px;top:' + (matrixDim - 32) + 'px;', + class: 'connectivity-ordering' + }).appendTo(context.connectivityContainer); + + var orderCombo = $(''); - $.each(sortOptions, function (k, v) { - $('