Updated lesionTable to store measurement ID. Worked on refactoring functions in lesionTable.js to allow loading of series from a click on a row

LesionTracker/client/components/init.js

@@ -8,4 +8,6 @@ Meteor.startup(function() {
         mouse: cornerstoneTools.nonTarget,
         touch: cornerstoneTools.nonTargetTouch
     });
+
+    toolManager.setAlwaysEnabledTools(['lesion', 'nonTarget']);
 });

Packages/lesiontracker/compatibility/lesionTool.js

@@ -9,7 +9,7 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
 
     var configuration = {
         getLesionLocationCallback: getLesionLocationCallback,
-        changeLesionLocationCallback: changeLesionLocationCallback,
+        changeLesionLocationCallback: changeLesionLocationCallback
     };
 
     // Define a callback to get your text annotation
@@ -179,19 +179,19 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
         return cornerstoneMath.point.insideRect(coords, handle.boundingBox);
     }
 
-    function suscribeLesionToolSelectedEvent(element) {
+    function subscribeLesionToolSelectedEvent(element) {
         var elementEvents = $._data(element, "events");
         var index = Object.keys(elementEvents).indexOf("LesionToolSelected");
         if (index < 0) {
-            // Subscribe LesionToolSelected and calls measurementModified function when lesion measurement is changed or updated.
+            // Subscribe LesionToolSelected and calls loadImage when lesion measurement is changed or updated.
-            $(element).on("LesionToolSelected", measurementModified);
+            $(element).on("LesionToolSelected", loadImage);
         }
 
     }
     ///////// BEGIN IMAGE RENDERING ///////
     function onImageRendered(e, eventData) {
 
-        suscribeLesionToolSelectedEvent(e.currentTarget);
+        subscribeLesionToolSelectedEvent(e.currentTarget);
 
         // if we have no toolData for this element, return immediately as there is nothing to do
         var toolData = cornerstoneTools.getToolState(e.currentTarget, toolType);
@@ -228,14 +228,13 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
         var color;
         var element = eventData.element;
         var lineWidth = cornerstoneTools.toolStyle.getToolWidth();
-        var font = cornerstoneTools.textStyle.getFont();
         var config = cornerstoneTools.lesion.getConfiguration();
 
         // configurable shadow from CornerstoneTools
         if (config && config.shadow) {
             context.shadowColor = '#000000';
-            context.shadowOffsetX = +1;
+            context.shadowOffsetX = 1;
-            context.shadowOffsetY = +1;
+            context.shadowOffsetY = 1;
         }
 
         if (data.active) {
@@ -364,21 +363,23 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
     }
 
 
+    // TODO=Refactor because this function is repeated in nonTargetTool!
     function loadImage(e, eventData) {
         // If type is active, load image and activate lesion
         // If type is inactive, update lesions of enabledElement as inactive
-
+        log.info('lesionTool loadImage');
+        var element = eventData.enabledElement.element;
+        var imageId = eventData.lesionData.imageId;
         if (eventData.type === "active") {
-            var stackToolDataSource = cornerstoneTools.getToolState(e.currentTarget, 'stack');
+            var stackToolDataSource = cornerstoneTools.getToolState(element, 'stack');
             var stackData = stackToolDataSource.data[0];
-            var imageIds = stackData.imageIds;
+            var imageIdIndex = stackData.imageIds.indexOf(imageId);
-            var imageIdIndex = imageIds.indexOf(eventData.lesionData.imageId);
             if (imageIdIndex < 0) {
                 return;
             }
 
             cornerstone.loadAndCacheImage(imageIds[imageIdIndex]).then(function(image) {
-                cornerstone.displayImage(eventData.enabledElement.element, image);
+                cornerstone.displayImage(element, image);
                 updateLesion(e, eventData);
             });
         } else if (eventData.type === "inactive") {
@@ -386,11 +387,6 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
         }
     }
 
-    //This function is called from cornerstone-viewport.html and updates lesion measurement and makes the lesion active
-    function measurementModified(e, eventData) {
-        loadImage(e, eventData);
-    }
-
     // module exports
     cornerstoneTools.lesion = cornerstoneTools.mouseButtonTool({
         createNewMeasurement: createNewMeasurement,

Packages/lesiontracker/compatibility/nonTargetTool.js

@@ -186,19 +186,18 @@
         context.fill();
     }
 
-    function suscribeNonTargetToolModifiedEvent(element) {
+    function subscribeNonTargetToolModifiedEvent(element) {
         var elementEvents = $._data(element, "events");
         var index = Object.keys(elementEvents).indexOf("NonTargetToolSelected");
         if (index < 0) {
-            // Subscribe LesionToolModified and calls measurementModified function when lesion measurement is changed or updated.
+            // Subscribe LesionToolModified and calls loadImage function when lesion measurement is changed or updated.
-            $(element).on("NonTargetToolSelected", measurementModified);
+            $(element).on("NonTargetToolSelected", loadImage);
         }
 
     }
     ///////// BEGIN IMAGE RENDERING ///////
     function onImageRendered(e, eventData) {
-
+        subscribeNonTargetToolModifiedEvent(e.currentTarget);
-        suscribeNonTargetToolModifiedEvent(e.currentTarget);
 
         // if we have no toolData for this element, return immediately as there is nothing to do
         var toolData = cornerstoneTools.getToolState(e.currentTarget, toolType);
@@ -268,7 +267,7 @@
         context.beginPath();
         context.strokeStyle = color;
         context.lineWidth = 1 / eventData.viewport.scale;
-        var mid = {
+         mid = {
             x: mid.x,
             y: mid.y
         };
@@ -390,7 +389,7 @@
 
         // if we have no toolData for this element, return immediately as there is nothing to do
         var toolData = cornerstoneTools.getToolState(e.currentTarget, toolType);
-        if (toolData === undefined) {
+        if (!toolData) {
             return;
         }
 
@@ -463,31 +462,27 @@
         onImageRendered(e, eventData);
     }
 
-    function loadImage(e, eventObject) {
+    function loadImage(e, eventData) {
         // If type is active, load image and activate lesion
         // If type is inactive, update lesions of enabledElement as inactive
-
+        log.info('nonTargetTool loadImage');
-        if (eventObject.type === "active") {
+        var element = eventData.enabledElement.element;
-            var stackToolDataSource = cornerstoneTools.getToolState(e.currentTarget, 'stack');
+        var imageId = eventData.lesionData.imageId;
+        if (eventData.type === "active") {
+            var stackToolDataSource = cornerstoneTools.getToolState(element, 'stack');
             var stackData = stackToolDataSource.data[0];
-            var imageIdsArr = stackData.imageIds;
+            var imageIdIndex = stackData.imageIds.indexOf(imageId);
-            var indexOfImage = imageIdsArr.indexOf(eventObject.lesionData.imageId);
+            if (imageIdIndex < 0) {
-            if (indexOfImage > -1) {
+                return;
-                cornerstone.loadAndCacheImage(stackData.imageIds[indexOfImage]).then(function(image) {
+            }
-                    cornerstone.displayImage(eventObject.enabledElement.element, image);
+
-                    updateLesion(e, eventObject);
+            cornerstone.loadAndCacheImage(stackData.imageIds[imageIdIndex]).then(function(image) {
+                cornerstone.displayImage(element, image);
+                updateLesion(e, eventData);
             });
+        } else if (eventData.type === "inactive") {
+            updateLesion(e, eventData);
         }
-        } else if (eventObject.type === "inactive") {
-            updateLesion(e, eventObject);
-        }
-
-
-    }
-
-    //This function is called from cornerstone-viewport.html and updates lesion measurement and makes the lesion active
-    function measurementModified(e, eventObject) {
-        loadImage(e, eventObject);
     }
 
     cornerstoneTools.nonTarget = cornerstoneTools.mouseButtonTool({

Packages/lesiontracker/components/lesionTable/lesionTable.js

@@ -1,50 +1,46 @@
-// Get enabled elements in viewport
+/**
-// Returns enabled elements with associated elements as object array
+ * Returns timepoint object based on timepoint id of the enabled element
-function getEnabledElementsInViewport() {
+ *
-    var enabledElementsInViewport = [];
+ * @param timepoints
+ * @param enabledElement
+ * @returns {*|{}} Timepoint object based on timepoint id of the enabled element (or an empty Object)
+ */
+function getTimepointObject(imageId) {
+    var study = cornerstoneTools.metaData.get('study', imageId);
 
-    $(".imageViewerViewport").each(function(index, element) {
+    var timepoint = Timepoints.findOne({timepointName: study.studyDate});
-        var enabledElement = cornerstone.getEnabledElement(element);
+    return timepoint;
-        if (!enabledElement) {
-            return;
-        }
-
-        enabledElementsInViewport.push({element: element, enabledElement: enabledElement});
-    });
-
-    return enabledElementsInViewport;
 }
 
-// Switch to the image of the correct image index
+/**
-// Activate the selected measurement on the switched image (color to be green)
+ * Switch to the image of the correct image index
-// Deactivate all other measurements on the switched image (color to be white)
+ * Activate the selected measurement on the switched image (color to be green)
-function activateMeasurementsInRelatedImages(timepoints, lesionNumber, isTarget) {
+ * Deactivate all other measurements on the switched image (color to be white)
+ */
+function activateMeasurements(element, measurementId) {
+    // TODO=Switch this to use the new CornerstoneToolMeasurementModified event,
+    // Once it has 'modified on activation' set up
 
-    //TODO: This is a bad hack! We need to listen an event of the element and handle it when rendering of the element is completed
+    var enabledElement = cornerstone.getEnabledElement(element);
-    //TODO:  we can switch to the related image and activate the selected measurement on the switched image.
+    var imageId = enabledElement.image.imageId;
-    var intervalListener = setInterval(function() {
+    var timepointData = getTimepointObject(imageId);
-        window.clearInterval(intervalListener);
+    var measurementData = Measurements.findOne(measurementId);
 
-        var enabledElementsInViewport = getEnabledElementsInViewport();
+    var measurementAtTimepoint = measurementData.timepoints[timepointData.timepointID];
-
+    if (!measurementAtTimepoint) {
-        for(var i = 0; i < enabledElementsInViewport.length; i++) {
+        return;
-            var element = enabledElementsInViewport[i].element;
-            var enabledElement = enabledElementsInViewport[i].enabledElement;
-            var timepointObject = getTimepointObject(timepoints, enabledElement);
-
-            if (timepointObject === undefined) {
-                continue;
     }
 
     // Defines event data
     var eventData = {
         enabledElement: enabledElement,
         lesionData: {
-                    isTarget: isTarget,
+            id: measurementId,
-                    lesionNumber: lesionNumber,
+            isTarget: measurementData.isTarget,
-                    imageId: timepointObject.imageId,
+            lesionNumber: measurementData.lesionNumber,
-                    seriesInstanceUid: timepointObject.seriesInstanceUid,
+            imageId: imageId,
-                    studyInstanceUid: timepointObject.studyInstanceUid
+            seriesInstanceUid: measurementAtTimepoint.seriesInstanceUid,
+            studyInstanceUid: measurementAtTimepoint.studyInstanceUid
         },
         type: "active"
     };
@@ -67,87 +63,75 @@ function activateMeasurementsInRelatedImages(timepoints, lesionNumber, isTarget)
         // Deactivate nonTarget tool measurements
         eventData.type = "inactive";
 
-                // Triggger event for nonTarget measurements
+        // Trigger event for nonTarget measurements
         // Inactivate all nonTarget measurements if any measurement is active
         $(element).trigger("NonTargetToolSelected", eventData);
     }
-        }
-    }, 100);
 }
 
-// Returns timepoint object based on timepoint id of the enabled element
+/**
-function getTimepointObject(timepoints, enabledElement) {
+ * Activates a set of lesions when lesion table row is clicked
-    var imageId = enabledElement.image.imageId;
+ *
-    var study = cornerstoneTools.metaData.get('study', imageId);
+ * @param measurementId The unique key for a specific Measurement
-    var series = cornerstoneTools.metaData.get('series', imageId);
+ */
-
+function activateLesion(measurementId) {
-    // Get the timepointID related to the image viewer viewport
+    // Find Measurement data for this lesion
-    // from the DOM itself. This will be changed later when a
+    var measurementData = Measurements.findOne(measurementId);
-    // real association between viewports and timepoints is created.
-    var timepoint = Timepoints.findOne({timepointName: study.studyDate});
-    if (!timepoint) {
-        return;
-    }
-    var timepointID = timepoint.timepointID;
-
-    var timepointObject = timepoints[timepointID];
-
-    if (timepointObject === undefined) {
-        return;
-    }
-
-    if (!timepointObject ) {
-        timepointObject = {}
-    }
-
-    return timepointObject;
-}
-
-// Activate selected lesions when lesion table row is clicked
-function updateLesions(e) {
-    // lesionNumber of measurement = id of row
-    var lesionNumber = parseInt($(e.currentTarget).attr("id"), 10);
-
-    // TODO= Clarify this
-    // Get Target column value
-    // Search and update data according to target type
-    var isTarget = $(e.currentTarget).find('td').eq(2).html().trim() === 'N'?false:true;
-
-    // Find data for specific lesion
-    var measurementData = Measurements.findOne({
-        lesionNumber: lesionNumber,
-        isTarget: isTarget
-    });
 
+    // If there is no measurement with this ID, stop here
     if (!measurementData) {
+        log.warn('No Measurements entry associated to an ID in a lesion table row');
         return;
     }
 
+    // Get the timepoint data from this Measurement
     var timepoints = measurementData.timepoints;
-    var enabledElementsInViewport = getEnabledElementsInViewport();
 
-    //  Render related series
+    // Loop through the viewports and display each timepoint
-    for(var i = 0; i < enabledElementsInViewport.length; i++) {
+    $(".imageViewerViewport").each(function(viewportIndex, element) {
-        var element = enabledElementsInViewport[i].element;
+        // Stop if we run out of timepoints before viewports
-        var enabledElement = enabledElementsInViewport[i].enabledElement;
+        if (viewportIndex >= Object.keys(timepoints).length) {
-
+            return false;
-        var timepointObject = getTimepointObject(timepoints, enabledElement);
-
-        if (timepointObject === undefined || timepointObject.seriesInstanceUid === "") {
-            continue;
         }
 
-        var newSeriesData = {
+        // Find the image that is currently in this viewport
-            seriesInstanceUid: timepointObject.seriesInstanceUid,
+        var enabledElement = cornerstone.getEnabledElement(element);
-            studyInstanceUid: timepointObject.studyInstanceUid
+        if (!enabledElement || !enabledElement.image) {
+            return;
+        }
+
+        // Find measurements related to the Nth timepoint
+        // TODO=Re-evaluate this approach to populating viewports with timepoints
+        // What is the desired behaviour here?
+        var key = Object.keys(measurementData.timepoints)[viewportIndex];
+        var measurementAtTimepoint = measurementData.timepoints[key];
+
+        // If there is no measurement data to display, stop here
+        if (!measurementAtTimepoint) {
+            return;
+        }
+
+        // Check which study and series are required to display the measurement at this timepoint
+        var requiredSeriesData = {
+            seriesInstanceUid: measurementAtTimepoint.seriesInstanceUid,
+            studyInstanceUid: measurementAtTimepoint.studyInstanceUid
         };
 
-        // Rerender the viewport using data for new series
+        // Check if the study / series we need is already the one in the viewport
-        rerenderViewportWithNewSeries(element, newSeriesData);
+        var currentSeriesData = OHIF.viewer.loadedSeriesData[viewportIndex];
+        if (currentSeriesData.seriesInstanceUid === measurementAtTimepoint.seriesInstanceUid &&
+            currentSeriesData.studyInstanceUid === measurementAtTimepoint.studyInstanceUid) {
+            // If it is, activate the measurements in this viewport and stop here
+            activateMeasurements(element, measurementId);
+            return;
         }
 
-    // Activate selected measurements on the rendered series
+        // Otherwise, re-render the viewport with the required study/series, then
-    activateMeasurementsInRelatedImages(timepoints, lesionNumber, isTarget);
+        // add an onRendered callback to activate the measurements
+        rerenderViewportWithNewSeries(element, requiredSeriesData, function(element) {
+            activateMeasurements(element, measurementId);
+        });
+    });
 }
 
 Template.lesionTable.helpers({
@@ -155,12 +139,14 @@ Template.lesionTable.helpers({
         return Measurements.find({}, {sort: {number: 1}});
     },
     'timepoints': function() {
-        return Timepoints.find();
+        return Timepoints.find({}, {sort: {timepointName: 1}});
     }
 });
 
 Template.lesionTable.events({
     'click table#tblLesion tbody tr': function(e) {
-        updateLesions(e);
+        // Retrieve the lesion id from the DOM data for this row
+        var measurementId = $(e.currentTarget).data('measurementid');
+        activateLesion(measurementId);
     }
 });

Packages/lesiontracker/components/lesionTableRow/lesionTableRow.html

@@ -1,5 +1,5 @@
 <template name="lesionTableRow">
-    <tr id="{{lesionNumber}}" class="lesionTableRow">
+    <tr id="{{lesionNumber}}" class="lesionTableRow" data-measurementid="{{_id}}">
         <td class='lesionNumber'>{{number}}</td>
         <td class='location'>{{location}}</td>
         <td class='target'>{{#if isTarget}} Y {{else}} N {{/if}}</td>

Packages/lesiontracker/components/lesionTableRow/lesionTableRow.js

@@ -1,5 +1,5 @@
 Template.lesionTableRow.helpers({
     'timepoints': function() {
-        return Timepoints.find();
+        return Timepoints.find({}, {sort: {timepointName: 1}});
     }
 });

Packages/viewerbase/components/studyBrowser/thumbnailEntry/thumbnailEntry.js

@@ -199,9 +199,10 @@ Template.thumbnailEntry.onRendered(function() {
 Template.thumbnailEntry.events({
     // Touch drag/drop events
     'touchstart .thumbnailEntry, mousedown .thumbnailEntry': function(e) {
-        var data = Template.parentData(2);
+        var data = {
-        data.studyInstanceUid = this.stack.studyInstanceUid;
+            studyInstanceUid: this.stack.studyInstanceUid,
-        data.seriesInstanceUid = this.stack.seriesInstanceUid;
+            seriesInstanceUid: this.stack.seriesInstanceUid
+        };
         thumbnailDragStartHandler(e, data);
     },
     'touchmove .thumbnailEntry': function(e) {

Packages/viewerbase/components/viewer/imageViewerViewport/imageViewerViewport.js

@@ -146,16 +146,6 @@ function loadSeriesIntoViewport(data) {
 
     // Start loading the image.
     cornerstone.loadAndCacheImage(imageId).then(function(image) {
-        // Fire an event to give notice that a new series was loaded in the viewport
-        var eventType = "ViewerBaseSeriesLoaded";
-        var eventData = {
-            element: element,
-            stack: stack,
-            study: data.study,
-            series: data.series
-        };
-        $(document).trigger(eventType, eventData);
-        
         // If there is a saved object containing Cornerstone viewport data
         // (e.g. scale, invert, window settings) in the input data, apply it now.
         //
@@ -311,6 +301,11 @@ function loadSeriesIntoViewport(data) {
         if (viewportIndex === Session.get('activeViewport')) {
             enablePrefetchOnElement(element);
         }
+
+        // Run any renderedCallback that exists in the data context
+        if (data.renderedCallback && typeof data.renderedCallback === "function") {
+            data.renderedCallback(element);
+        }
     }, function(error) {
         // If something goes wrong while loading the image, fire the error handler.
         errorLoadingHandler(element, imageId, error);
@@ -392,7 +387,7 @@ Template.imageViewerViewport.onRendered(function() {
 
     // If no seriesInstanceUid or studyInstanceUid were supplied, display the drag/drop
     // instructions and then stop here since we don't know what to display in the viewport.
-    if (this.data.seriesInstanceUid === undefined || this.data.studyInstanceUid === undefined) {
+    if (!this.data.seriesInstanceUid || !this.data.studyInstanceUid) {
         element.classList.add('empty');
         $(element).siblings('.imageViewerLoadingIndicator').css('display', 'none');
         $(element).siblings('.viewportInstructions').show();

Packages/viewerbase/lib/rerenderViewportWithNewSeries.js

@@ -5,8 +5,9 @@
  *
  * @param element
  * @param data An object containing a seriesIndex and studyIndex for a study to load into this viewport
+ * @function renderedCallback An optional callback to be executed after the new template is rendered
  */
-rerenderViewportWithNewSeries = function(element, data) {
+rerenderViewportWithNewSeries = function(element, data, renderedCallback) {
     // Get the container and index of the current viewport.
     // The parent container is identified because it is later removed from the DOM
     var container = $(element).parents('.viewportContainer').get(0);
@@ -37,6 +38,11 @@ rerenderViewportWithNewSeries = function(element, data) {
 
     container.appendChild(newViewportContainer);
 
+    // Pass the renderedCallback to the imageViewerViewport template
+    if (renderedCallback && typeof renderedCallback === "function") {
+        data.renderedCallback = renderedCallback;
+    }
+
     // Render and insert the template
     UI.renderWithData(Template.imageViewerViewport, data, newViewportContainer);
 };

Packages/viewerbase/lib/toolManager.js

@@ -1,5 +1,7 @@
 var activeTool;
 
+var alwaysEnabledTools;
+
 var tools = {};
 
 var initialized = false;
@@ -72,6 +74,9 @@ toolManager = {
     addTool: function(name, base) {
         tools[name] = base;
     },
+    setAlwaysEnabledTools: function(tools) {
+        alwaysEnabledTools = tools;
+    },
     setActiveTool: function(tool) {
         if (!initialized) {
             toolManager.init();
@@ -83,7 +88,10 @@ toolManager = {
 
         $('.imageViewerViewport').each(function(index, element) {
             var canvases = $(element).find('canvas');
-            if (!element.classList.contains('empty') && canvases.length > 0) {
+            if (element.classList.contains('empty') || !canvases.length) {
+                return;
+            }
+
             // First, deactivate the current active tool
             tools[activeTool].mouse.deactivate(element, 1);
 
@@ -91,7 +99,12 @@ toolManager = {
                 tools[activeTool].touch.deactivate(element);
             }
 
-                // First, get the stack toolData
+            // Enable any tools set as 'Always enabled'
+            alwaysEnabledTools.forEach(function(toolType) {
+                cornerstoneTools[toolType].enable(element);
+            });
+
+            // Get the stack toolData
             var toolData = cornerstoneTools.getToolState(element, 'stack');
             if (!toolData || !toolData.data || !toolData.data.length) {
                 return;
@@ -137,7 +150,6 @@ toolManager = {
 
             cornerstoneTools.zoomTouchPinch.activate(element);
             cornerstoneTools.panMultiTouch.activate(element);
-            }
         });
         activeTool = tool;
     },

Packages/viewerbase/lib/windowManager.js

@@ -86,7 +86,7 @@ function getMammoHangingProtocol() {
                 SelectorCSValue: 'R CC',
                 FilterByCategory: 'SERIES_DESCRIPTION',
                 FilterByOperator: 'MEMBER_OF'
-            }],
+            }]
         }, {
             // Right side image (L MLO Current)
             ImageSetNumber: 1,
@@ -102,7 +102,9 @@ function getMammoHangingProtocol() {
                 FilterByCategory: 'SERIES_DESCRIPTION',
                 FilterByOperator: 'MEMBER_OF'
             }]
-        }, {
+        },
+            // Stage 3
+            {
             // Left side image (R MLO Current)
             ImageSetNumber: 1,
             DisplaySetNumber: 1,