Fixed bug LT-85 (Location Response Selections). Work on LT-9 and LT-12

LesionTracker/client/components/init.js

@@ -14,9 +14,16 @@ Meteor.startup(function() {
         touch: cornerstoneTools.biDirectionalTouch
     });
 
+    toolManager.addTool('deleteLesionKeyboardTool', {
+        mouse: cornerstoneTools.deleteLesionKeyboardTool,
+        touch: cornerstoneTools.deleteLesionKeyboardTool
+    });
+
     var states = toolManager.getToolDefaultStates();
     states.deactivate.push('lesion');
     states.deactivate.push('nonTarget');
-
+    states.deactivate.push('biDirectional');
+    
+    states.activate.push('deleteLesionKeyboardTool');
     toolManager.setToolDefaultStates(states);
 });

LesionTracker/client/components/viewer.html

@@ -1,7 +1,9 @@
 <template name="viewer">
     <div id="viewer">
+        {{>confirmDeleteDialog}}
         {{>lesionLocationDialog}}
         {{>nonTargetLesionDialog}}
+        {{>nonTargetResponseDialog}}
         {{>timepointTextDialog}}
 
         {{>hidingPanel}}

LesionTracker/client/components/viewer.js

@@ -52,9 +52,6 @@ Template.viewer.onCreated(function() {
     OHIF.viewer.defaultHotkeys.lesion = "T"; // Target
     OHIF.viewer.defaultHotkeys.nonTarget = "N"; // Non-target
 
-    // Enable hotkeys
-    enableHotkeys();
-
     if (isTouchDevice()) {
         OHIF.viewer.tooltipConfig = {
             trigger: 'manual'
@@ -101,66 +98,111 @@ Template.viewer.onCreated(function() {
         self.subscribe('timepoints', patientId);
         self.subscribe('measurements', patientId);
 
-        if (!self.subscriptionsReady()) {
-            return;
+        if (self.subscriptionsReady()) {
+            ViewerStudies.find().observe({
+                added: function(study) {
+                    // TODO = Replace this whole section when we have a
+                    // timepoint-to-study association modal
+
+                    // First, check if we have a timepoint related to this
+                    // study date already
+                    var timepoint = Timepoints.findOne({
+                        timepointName: study.studyDate
+                    });
+
+                    // If we do, stop here
+                    if (timepoint) {
+                        log.warn("A timepoint with that study date already exists!");
+                        return;
+                    }
+
+                    // Next, check the first timepoint in the collection
+                    var testTimepoint = Timepoints.findOne({});
+
+                    // If it relates to another subject, we need to stop here as well
+                    // because the tab may be changing.
+                    if (testTimepoint && testTimepoint.patientId !== study.patientId) {
+                        log.warn("Timepoints collection related to the wrong subject");
+                        return;
+                    }
+
+                    // Otherwise, we need to add a timepoint related to this study date
+                    log.info('Inserting a new timepoint');
+                    Timepoints.insert({
+                        patientId: study.patientId,
+                        timepointName: study.studyDate,
+                        timepointID: uuid.v4()
+                    });
+                }
+            });
+
+            // This is used to re-add tools from the database into the
+            // Cornerstone ToolData structure
+            Measurements.find().observe({
+                added: function(data) {
+                    if (data.toolDataInsertedManually === true) {
+                        return;
+                    }
+
+                    // Activate first measurements in image box as default if exists
+                    if (!firstMeasurementsActivated) {
+                        var templateData = {
+                            contentId: Session.get("activeContentId")
+                        };
+
+                        // Activate measurement
+                        activateLesion(data._id, templateData);
+                        firstMeasurementsActivated = true;
+                    }
+
+                    log.info('Measurement added');
+
+                    addMeasurementAsToolData(data);
+
+                    updateRelatedElements(data.imageId);
+                },
+                removed: function(data) {
+                    // Check that this Measurement actually contains timepoint data
+                    if (!data.timepoints) {
+                        return;
+                    }
+
+                    // Get the Measurement ID and relevant tool so we can remove
+                    // tool data for this Measurement
+                    var measurementId = data._id;
+                    var toolType = data.isTarget ? 'lesion' : 'nonTarget';
+
+                    // Find the list of imageIds that needs to be updated
+                    var imageIds = [];
+                    Object.keys(data.timepoints).forEach(function(timepointID) {
+                        // Clear the toolData for this timepoint
+                        var imageId = data.timepoints[timepointID].imageId;
+                        removeToolDataWithMeasurementId(imageId, toolType, measurementId);
+
+                        // Add this imageId to the list to be updated
+                        // (if they are currently displayed)
+                        imageIds.push(imageId);
+                    });
+
+                    // Find the enabled Cornerstone elements currently displaying these image IDs
+                    var enabledElements = [];
+                    imageIds.forEach(function(imageId) {
+                        var elems = cornerstone.getEnabledElementsByImageId(imageId);
+                        enabledElements = enabledElements.concat(elems);
+                    });
+
+                    // Update each related viewport
+                    enabledElements.forEach(function(enabledElement) {
+                        // Skip thumbnails or other elements that are not primary viewports
+                        var element = enabledElement.element;
+                        if (!element.classList.contains('imageViewerViewport')) {
+                            return;
+                        }
+                        cornerstone.updateImage(element);
+                    });
+                }
+            });
         }
-
-        ViewerStudies.find().observe({
-            added: function(study) {
-                var timepoint = Timepoints.findOne({timepointName: study.studyDate});
-                if (timepoint) {
-                    log.warn("A timepoint with that study date already exists!");
-                    return;
-                }
-
-                var timepointID = uuid.v4();
-
-                var testTimepoint = Timepoints.findOne({});
-                if (testTimepoint && testTimepoint.patientId !== study.patientId) {
-                    log.warn("Timepoints collection related to the wrong subject");
-                    return;
-                }
-
-                log.info('Inserting a new timepoint');
-                Timepoints.insert({
-                    patientId: study.patientId,
-                    timepointID: timepointID,
-                    timepointName: study.studyDate
-                });
-            }
-        });
-
-        // This is used to re-add tools from the database into the
-        // Cornerstone ToolData structure
-        Measurements.find().observe({
-            added: function (data) {
-                if (data.toolDataInsertedManually === true) {
-                    return;
-                }
-
-                // Activate first measurements in image box as default if exists
-                if (!firstMeasurementsActivated) {
-                    var templateData = {contentId: Session.get("activeContentId")};
-                    // Activate measurement
-                    activateLesion(data._id, templateData);
-                    firstMeasurementsActivated = true;
-                }
-
-                log.info('Measurement added');
-
-                addMeasurementAsToolData(data);
-
-                updateRelatedElements(data.imageId);
-            },
-            changed: function(data) {
-                log.info('Measurement changed');
-                updateRelatedElements(data.imageId);
-            },
-            removed: function(data) {
-                log.info('Measurement removed');
-                updateRelatedElements(data.imageId);
-            }
-        });
     });
 
     OHIF.viewer.updateImageSynchronizer = new cornerstoneTools.Synchronizer("CornerstoneNewImage", cornerstoneTools.updateImageSynchronizer);
@@ -252,6 +294,11 @@ function addMeasurementAsToolData(data) {
     });
 }
 
+Template.viewer.onRendered(function() {
+    // Enable hotkeys
+    enableHotkeys();
+});
+
 Template.viewer.onDestroyed(function() {
     log.info("onDestroyed");
 
@@ -277,7 +324,7 @@ function handleMeasurementModified(e, eventData) {
     switch (eventData.toolType) {
         case 'nonTarget':
         case 'lesion':
-            measurementManagerDAL.updateTimepointData(measurementData);
+            LesionManager.updateLesionData(measurementData);
             break;
     }
 }
@@ -285,18 +332,19 @@ function handleMeasurementModified(e, eventData) {
 function handleMeasurementRemoved(e, eventData) {
     log.info('CornerstoneToolsMeasurementRemoved');
     var measurementData = eventData.measurementData;
-    var databaseEntry;
 
     switch (eventData.toolType) {
         case 'nonTarget':
         case 'lesion':
-            databaseEntry = Measurements.findOne(measurementData.id, {reactive: false});
-            if (!databaseEntry) {
+            var measurement = Measurements.findOne(measurementData.id, {
+                reactive: false
+            });
+
+            if (!measurement) {
                 return;
             }
 
-            // TODO= Fix this when we have Findings that relate to more than one viewport
-            Measurements.remove(databaseEntry._id);
+            clearMeasurementTimepointData(measurement._id, measurementData.timepointID);
             break;
     }
 }

Packages/cornerstone/client/cornerstoneTools.js

@@ -1,4 +1,4 @@
-/*! cornerstoneTools - v0.7.7 - 2015-11-26 | (c) 2014 Chris Hafey | https://github.com/chafey/cornerstoneTools */
+/*! cornerstoneTools - v0.7.7 - 2015-12-18 | (c) 2014 Chris Hafey | https://github.com/chafey/cornerstoneTools */
 // Begin Source: src/header.js
 if (typeof cornerstone === 'undefined') {
     cornerstone = {};
@@ -56,6 +56,9 @@ if (typeof cornerstoneTools === 'undefined') {
     var mouseWheelEvents = 'mousewheel DOMMouseScroll';
 
     function enable(element) {
+        // Prevent handlers from being attached multiple times
+        disable(element);
+        
         $(element).on(mouseWheelEvents, mouseWheel);
     }
 
@@ -897,6 +900,13 @@ if (typeof cornerstoneTools === 'undefined') {
                 handleMover = cornerstoneTools.moveNewHandle;
             }
 
+            var preventHandleOutsideImage;
+            if (mouseToolInterface.options.preventHandleOutsideImage !== undefined) {
+                preventHandleOutsideImage = mouseToolInterface.options.preventHandleOutsideImage;
+            } else {
+                preventHandleOutsideImage = false;
+            }
+
             handleMover(mouseEventData, mouseToolInterface.toolType, measurementData, measurementData.handles.end, function() {
                 measurementData.active = false;
                 measurementData.invalidated = true;
@@ -914,7 +924,7 @@ if (typeof cornerstoneTools === 'undefined') {
                 }
 
                 cornerstone.updateImage(element);
-            });
+            }, preventHandleOutsideImage);
         }
 
         function mouseDownActivateCallback(e, eventData) {
@@ -994,6 +1004,14 @@ if (typeof cornerstoneTools === 'undefined') {
 
                 // now check to see if there is a handle we can move
                 if (toolData) {
+
+                    var preventHandleOutsideImage;
+                    if (mouseToolInterface.options && mouseToolInterface.options.preventHandleOutsideImage !== undefined) {
+                        preventHandleOutsideImage = mouseToolInterface.options.preventHandleOutsideImage;
+                    } else {
+                        preventHandleOutsideImage = false;
+                    }
+
                     for (i = 0; i < toolData.data.length; i++) {
                         data = toolData.data[i];
                         var distanceSq = 25;
@@ -1001,7 +1019,7 @@ if (typeof cornerstoneTools === 'undefined') {
                         if (handle) {
                             $(element).off('CornerstoneToolsMouseMove', mouseToolInterface.mouseMoveCallback || mouseMoveCallback);
                             data.active = true;
-                            cornerstoneTools.moveHandle(eventData, mouseToolInterface.toolType, data, handle, handleDoneMove);
+                            cornerstoneTools.moveHandle(eventData, mouseToolInterface.toolType, data, handle, handleDoneMove, preventHandleOutsideImage);
                             e.stopImmediatePropagation();
                             return false;
                         }
@@ -1011,7 +1029,7 @@ if (typeof cornerstoneTools === 'undefined') {
                 // Now check to see if there is a line we can move
                 // now check to see if we have a tool that we can move
                 if (toolData && mouseToolInterface.pointNearTool) {
-                    var options = {
+                    var options = mouseToolInterface.options || {
                         deleteIfHandleOutsideImage: true,
                         preventHandleOutsideImage: false
                     };
@@ -2452,7 +2470,14 @@ if (typeof cornerstoneTools === 'undefined') {
                     startLoadingHandler(targetElement);
                 }
 
-                cornerstone.loadAndCacheImage(stackData.imageIds[newImageIdIndex]).then(function(image) {
+                var loader;
+                if (stackData.preventCache === true) {
+                    loader = cornerstone.loadImage(stackData.imageIds[newImageIdIndex]);
+                } else {
+                    loader = cornerstone.loadAndCacheImage(stackData.imageIds[newImageIdIndex]);
+                }
+
+                loader.then(function(image) {
                     var viewport = cornerstone.getViewport(targetElement);
                     stackData.currentImageIdIndex = newImageIdIndex;
                     cornerstone.displayImage(targetElement, image, viewport);
@@ -3214,8 +3239,13 @@ if (typeof cornerstoneTools === 'undefined') {
         var data = toolData.data[config.currentTool];
 
         // Set the mouseLocation handle
-        config.mouseLocation.handles.start.x = eventData.currentPoints.image.x;
-        config.mouseLocation.handles.start.y = eventData.currentPoints.image.y;
+        var x = Math.max(eventData.currentPoints.image.x, 0);
+        x = Math.min(x, eventData.image.width);
+        config.mouseLocation.handles.start.x = x;
+
+        var y = Math.max(eventData.currentPoints.image.y, 0);
+        y = Math.min(y, eventData.image.height);
+        config.mouseLocation.handles.start.y = y;
 
         var currentHandle = config.currentHandle;
 
@@ -5943,29 +5973,33 @@ if (typeof cornerstoneTools === 'undefined') {
 
     function keyPress(e) {
         var element = e.currentTarget;
-        var startingCoords = cornerstone.pageToPixel(element, mouseX, mouseY);
-
-        e = window.event || e; // old IE support
 
         var keyPressData = {
+            event: window.event || e, // old IE support
             element: element,
             viewport: cornerstone.getViewport(element),
             image: cornerstone.getEnabledElement(element).image,
-            pageX: mouseX,
-            pageY: mouseY,
-            imageX: startingCoords.x,
-            imageY: startingCoords.y,
+            currentPoints: {
+                page: {
+                    x: mouseX,
+                    y: mouseY
+                },
+                image: cornerstone.pageToPixel(element, mouseX, mouseY),
+            },
             keyCode: e.keyCode,
             which: e.which
         };
 
-        if (e.type === 'keydown') {
-            $(element).trigger('CornerstoneToolsKeyDown', keyPressData);
-        } else if (e.type === 'keypress') {
-            $(element).trigger('CornerstoneToolsKeyPress', keyPressData);
-        } else if (e.type === 'keyup') {
-            $(element).trigger('CornerstoneToolsKeyUp', keyPressData);
-        }
+        keyPressData.currentPoints.canvas = cornerstone.pixelToCanvas(element, keyPressData.currentPoints.image);
+
+        var keyPressEvents = {
+            keydown: 'CornerstoneToolsKeyDown',
+            keypress: 'CornerstoneToolsKeyPress',
+            keyup: 'CornerstoneToolsKeyUp',
+
+        };
+
+        $(element).trigger(keyPressEvents[e.type], keyPressData);
     }
 
     function mouseMove(e) {
@@ -5976,12 +6010,16 @@ if (typeof cornerstoneTools === 'undefined') {
     var keyboardEvent = 'keydown keypress keyup';
 
     function enable(element) {
-        $(element).bind(keyboardEvent, keyPress);
+        // Prevent handlers from being attached multiple times
+        disable(element);
+
+        $(element).on(keyboardEvent, keyPress);
         $(element).on('mousemove', mouseMove);
     }
 
     function disable(element) {
-        $(element).unbind(keyboardEvent, keyPress);
+        $(element).off(keyboardEvent, keyPress);
+        $(element).off('mousemove', mouseMove);
     }
 
     // module exports
@@ -7097,7 +7135,7 @@ if (typeof cornerstoneTools === 'undefined') {
 
     function requestPoolManager() {
 
-        function addRequest(element, imageId, type, doneCallback, failCallback) {
+        function addRequest(element, imageId, type, preventCache, doneCallback, failCallback) {
             if (!requestPool.hasOwnProperty(type)) {
                 throw 'Request type must be one of interaction, thumbnail, or prefetch';
             }
@@ -7110,6 +7148,7 @@ if (typeof cornerstoneTools === 'undefined') {
             var requestDetails = {
                 type: type,
                 imageId: imageId,
+                preventCache: preventCache,
                 doneCallback: doneCallback,
                 failCallback: failCallback
             };
@@ -7154,7 +7193,6 @@ if (typeof cornerstoneTools === 'undefined') {
             setTimeout(function() {
                 var requestDetails = getNextRequest();
                 if (!requestDetails) {
-                    awake = false;
                     return;
                 }
 
@@ -7191,8 +7229,15 @@ if (typeof cornerstoneTools === 'undefined') {
                 return;
             }
 
+            var loader;
+            if (requestDetails.preventCache === true) {
+                loader = cornerstone.loadImage(imageId);
+            } else {
+                loader = cornerstone.loadAndCacheImage(imageId);
+            }
+
             // Load and cache the image
-            cornerstone.loadAndCacheImage(imageId).then(function(image) {
+            loader.then(function(image) {
                 numRequests[type]--;
                 // console.log(numRequests);
                 doneCallback(image);
@@ -7366,7 +7411,15 @@ if (typeof cornerstoneTools === 'undefined') {
                 }
 
                 var viewport = cornerstone.getViewport(element);
-                cornerstone.loadAndCacheImage(stackData.imageIds[newImageIdIndex]).then(function(image) {
+
+                var loader;
+                if (stackData.preventCache === true) {
+                    loader = cornerstone.loadImage(stackData.imageIds[newImageIdIndex]);
+                } else {
+                    loader = cornerstone.loadAndCacheImage(stackData.imageIds[newImageIdIndex]);
+                }
+
+                loader.then(function(image) {
                     stackData.currentImageIdIndex = newImageIdIndex;
                     cornerstone.displayImage(element, image, viewport);
                     if (endLoadingHandler) {
@@ -7611,7 +7664,8 @@ Display scroll progress bar across bottom of image.
         var nearest = nearestIndex(stackPrefetch.indicesToRequest, stack.currentImageIdIndex);
 
         var imageId,
-            nextImageIdIndex;
+            nextImageIdIndex,
+            preventCache = false;
 
         // Prefetch images around the current image (before and after)
         var lowerIndex = nearest.low;
@@ -7620,13 +7674,13 @@ Display scroll progress bar across bottom of image.
             if (lowerIndex >= 0 ) {
                 nextImageIdIndex = stackPrefetch.indicesToRequest[lowerIndex--];
                 imageId = stack.imageIds[nextImageIdIndex];
-                requestPoolManager.addRequest(element, imageId, requestType, doneCallback, failCallback);
+                requestPoolManager.addRequest(element, imageId, requestType, preventCache, doneCallback, failCallback);
             }
 
             if (higherIndex < stackPrefetch.indicesToRequest.length) {
                 nextImageIdIndex = stackPrefetch.indicesToRequest[higherIndex++];
                 imageId = stack.imageIds[nextImageIdIndex];
-                requestPoolManager.addRequest(element, imageId, requestType, doneCallback, failCallback);
+                requestPoolManager.addRequest(element, imageId, requestType, preventCache, doneCallback, failCallback);
             }
         }
 
@@ -7702,6 +7756,12 @@ Display scroll progress bar across bottom of image.
 
         var stack = stackData.data[0];
 
+        // Check if we are allowed to cache images in this stack
+        if (stack.preventCache === true) {
+            console.warn('A stack that should not be cached was given the stackPrefetch');
+            return;
+        }
+
         // Use the currentImageIdIndex from the stack as the initalImageIdIndex
         var stackPrefetchData = {
             indicesToRequest: range(0, stack.imageIds.length - 1),
@@ -8765,7 +8825,14 @@ Display scroll progress bar across bottom of image.
             startLoadingHandler(targetElement);
         }
 
-        cornerstone.loadAndCacheImage(targetStackData.imageIds[newImageIdIndex]).then(function(image) {
+        var loader;
+        if (targetStackData.preventCache === true) {
+            loader = cornerstone.loadImage(targetStackData.imageIds[newImageIdIndex]);
+        } else {
+            loader = cornerstone.loadAndCacheImage(targetStackData.imageIds[newImageIdIndex]);
+        }
+
+        loader.then(function(image) {
             var viewport = cornerstone.getViewport(targetElement);
             targetStackData.currentImageIdIndex = newImageIdIndex;
             synchronizer.displayImage(targetElement, image, viewport);
@@ -8843,7 +8910,14 @@ Display scroll progress bar across bottom of image.
             startLoadingHandler(targetElement);
         }
 
-        cornerstone.loadAndCacheImage(stackData.imageIds[newImageIdIndex]).then(function(image) {
+        var loader;
+        if (stackData.preventCache === true) {
+            loader = cornerstone.loadImage(stackData.imageIds[newImageIdIndex]);
+        } else {
+            loader = cornerstone.loadAndCacheImage(stackData.imageIds[newImageIdIndex]);
+        }
+
+        loader.then(function(image) {
             var viewport = cornerstone.getViewport(targetElement);
             stackData.currentImageIdIndex = newImageIdIndex;
             synchronizer.displayImage(targetElement, image, viewport);
@@ -8913,7 +8987,14 @@ Display scroll progress bar across bottom of image.
         }
 
         if (newImageIdIndex !== -1) {
-            cornerstone.loadAndCacheImage(stackData.imageIds[newImageIdIndex]).then(function(image) {
+            var loader;
+            if (stackData.preventCache === true) {
+                loader = cornerstone.loadImage(stackData.imageIds[newImageIdIndex]);
+            } else {
+                loader = cornerstone.loadAndCacheImage(stackData.imageIds[newImageIdIndex]);
+            }
+
+            loader.then(function(image) {
                 var viewport = cornerstone.getViewport(targetElement);
                 stackData.currentImageIdIndex = newImageIdIndex;
                 synchronizer.displayImage(targetElement, image, viewport);
@@ -8977,7 +9058,14 @@ Display scroll progress bar across bottom of image.
             startLoadingHandler(targetElement);
         }
 
-        cornerstone.loadAndCacheImage(stackData.imageIds[newImageIdIndex]).then(function(image) {
+        var loader;
+        if (stackData.preventCache === true) {
+            loader = cornerstone.loadImage(stackData.imageIds[newImageIdIndex]);
+        } else {
+            loader = cornerstone.loadAndCacheImage(stackData.imageIds[newImageIdIndex]);
+        }
+
+        loader.then(function(image) {
             var viewport = cornerstone.getViewport(targetElement);
             stackData.currentImageIdIndex = newImageIdIndex;
             synchronizer.displayImage(targetElement, image, viewport);
@@ -9348,7 +9436,14 @@ Display scroll progress bar across bottom of image.
         var samples = [];
 
         measurementData.timeSeries.stacks.forEach(function(stack) {
-            cornerstone.loadAndCacheImage(stack.imageIds[measurementData.imageIdIndex]).then(function(image) {
+            var loader;
+            if (stack.preventCache === true) {
+                loader = cornerstone.loadImage(stack.imageIds[measurementData.imageIdIndex]);
+            } else {
+                loader = cornerstone.loadAndCacheImage(stack.imageIds[measurementData.imageIdIndex]);
+            }
+
+            loader.then(function(image) {
                 var offset = Math.round(measurementData.handles.end.x) + Math.round(measurementData.handles.end.y) * image.width;
                 var sample = image.getPixelData()[offset];
                 samples.push(sample);
@@ -9484,7 +9579,14 @@ Display scroll progress bar across bottom of image.
                 startLoadingHandler(element);
             }
 
-            cornerstone.loadAndCacheImage(newStack.imageIds[currentImageIdIndex]).then(function(image) {
+            var loader;
+            if (newStack.preventCache === true) {
+                loader = cornerstone.loadImage(newStack.imageIds[currentImageIdIndex]);
+            } else {
+                loader = cornerstone.loadAndCacheImage(newStack.imageIds[currentImageIdIndex]);
+            }
+
+            loader.then(function(image) {
                 if (timeSeriesData.currentImageIdIndex !== currentImageIdIndex) {
                     newStack.currentImageIdIndex = currentImageIdIndex;
                     timeSeriesData.currentStackIndex = newStackIndex;
@@ -10373,7 +10475,10 @@ Display scroll progress bar across bottom of image.
 
         cornerstoneTools.requestPoolManager.clearRequestStack(type);
 
-        requestPoolManager.addRequest(element, newImageId, type, doneCallback, failCallback);
+        // Convert the preventCache value in stack data to a boolean
+        var preventCache = !!stackData.preventCache;
+
+        requestPoolManager.addRequest(element, newImageId, type, preventCache, doneCallback, failCallback);
         requestPoolManager.startGrabbing();
 
         $(element).trigger('CornerstoneStackScroll', eventData);

Packages/lesiontracker/client/collections/LocationResponses.js

@@ -12,12 +12,6 @@ LocationResponses.insert({
     description: ""
 });
 
-LocationResponses.insert({
-    text: "Complete response",
-    code: "CR",
-    description: ""
-});
-
 LocationResponses.insert({
     text: "Stable disease",
     code: "SD",
@@ -25,14 +19,8 @@ LocationResponses.insert({
 });
 
 LocationResponses.insert({
-    text: "Non-measurable",
-    code: "NM",
-    description: ""
-});
-
-LocationResponses.insert({
-    text: "Unknown",
-    code: "UN",
+    text: "Present",
+    code: false,
     description: ""
 });
 

Packages/lesiontracker/client/compatibility/LesionManager.js

@@ -0,0 +1,174 @@
+var LesionManager = (function() {
+    PatientLocations = new Meteor.Collection(null);
+
+    /**
+     * Retrieve a location name (e.g. Liver Right) from the
+     * PatientLocations Collection by id, if it exists. Otherwise,
+     * return an empty string.
+     *
+     * @param id
+     * @returns {*|string}
+     */
+    function getLocationName(id) {
+        var locationObject = PatientLocations.findOne(id);
+        if (!locationObject || !locationObject.location) {
+            return '';
+        }
+        
+        return locationObject.location;
+    }
+
+    /**
+     * Update the Timepoint object for a specific Measurement.
+     * If no measurement exists yet, one will be created.
+     *
+     * Input is toolData from the lesion or nonTarget tool
+     *
+     * @param lesionData
+     */
+    function updateLesionData(lesionData) {
+        // Find the related Timepoint from the Timepoints Collection
+        var timepointID = lesionData.timepointID;
+        var timepoint = Timepoints.findOne({timepointID: timepointID});
+        if (!timepoint) {
+            log.warn('Timepoint in an image is not present in the Timepoints Collection?');
+            return;
+        }
+
+        // Find the specific lesion to be updated
+        var existingMeasurement;
+        if (lesionData.id) {
+            existingMeasurement = Measurements.findOne(lesionData.id);
+        } else {
+            existingMeasurement = Measurements.findOne({
+                lesionNumber: lesionData.lesionNumber,
+                isTarget: lesionData.isTarget
+            });
+        }
+
+        // Create a structure for the timepointData based
+        // on this Lesion's toolData
+        var timepointData = {
+            seriesInstanceUid: lesionData.seriesInstanceUid,
+            studyInstanceUid: lesionData.studyInstanceUid,
+            handles: lesionData.handles,
+            imageId: lesionData.imageId
+        };
+
+        if (lesionData.isTarget === true) {
+            // TODO = Add short axis
+            timepointData.longestDiameter = lesionData.measurementText;
+        } else {
+            timepointData.response = lesionData.response;
+        }
+
+        // If no such lesion exists, we need to add one
+        if (!existingMeasurement) {
+            // Create a data structure for the Measurement
+            // based on the current tool data
+            var measurement = {
+                lesionNumber: lesionData.lesionNumber,
+                isTarget: lesionData.isTarget,
+                patientId: lesionData.patientId,
+                id: lesionData.id
+            };
+
+            // Retrieve the location name given the locationUID
+            if (lesionData.locationUID !== undefined) {
+                measurement.location = getLocationName(lesionData.locationUID);
+            }
+
+            // Add toolData parameters to the Measurement at this Timepoint
+            measurement.timepoints = {};
+            measurement.timepoints[timepointID] = timepointData;
+
+            // Set a flag to prevent duplication of toolData
+            measurement.toolDataInsertedManually = true;
+
+            // Increment and store the Lesion Number for this Measurement
+            measurement.lesionNumber = Measurements.find().count() + 1;
+
+            // Insert this into the Measurements Collection
+            // Save the ID into the toolData (not sure if this works?)
+            measurement.id = Measurements.insert(measurement);
+        } else {
+            lesionData.id = existingMeasurement._id;
+
+            // Update timepoints from lesion data
+            existingMeasurement.timepoints[timepointID] = timepointData;
+
+            Measurements.update(existingMeasurement._id, {
+                $set: {
+                    timepoints: existingMeasurement.timepoints
+                }
+            });
+        }
+    }
+
+    /**
+     * Returns new lesion number according to timepointID
+     * @param timepointID
+     * @param isTarget
+     * @returns {*}
+     */
+    function getNewLesionNumber(timepointID, isTarget) {
+        // Get all current lesion measurements
+        var measurements = Measurements.find({
+            isTarget: isTarget
+        }, {
+            sort: {lesionNumber: 1}
+        }).fetch();
+
+        // If no measurements exist yet, start at 1
+        if (!measurements.length) {
+            return 1;
+        }
+
+        // If measurements exist, find the last lesion number
+        // from the given timepoint
+        var lesionNumberCounter = 1;
+        var numMeasurements = measurements.length;
+
+        // Search through Measurements to see which ones
+        // already have data for this Timepoint
+        for (var i = 0; i < numMeasurements; i++) {
+            var measurement = measurements[i];
+
+            // If this measurement has no data for this Timepoint,
+            // use this as the current Measurement
+            if (!measurement.timepoints[timepointID]) {
+                return measurement.lesionNumber;
+            }
+
+            lesionNumberCounter++;
+        }
+
+        return lesionNumberCounter;
+    }
+
+    /**
+     * If the current Lesion Number already exists
+     * for any other timepoint, returns lesion locationUID
+     * @param lesionData
+     * @returns {*}
+     */
+    function lesionNumberExists(lesionData) {
+        var measurement = Measurements.findOne({
+            lesionNumber: lesionData.lesionNumber,
+            isTarget: lesionData.isTarget
+        });
+
+        if (!measurement) {
+            return;
+        }
+
+        return measurement.locationUID;
+    }
+
+    return {
+        updateLesionData: updateLesionData,
+        getNewLesionNumber: getNewLesionNumber,
+        lesionNumberExists: lesionNumberExists,
+        getLocationName: getLocationName
+    };
+})();

Packages/lesiontracker/client/compatibility/biDirectionalTool.js

@@ -856,7 +856,7 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
 
         if (lesionData.timepointID && lesionData.timepointID !== "") {
             // Update Measurements Collection
-            measurementManagerDAL.updateTimepointData(lesionData);
+            LesionManager.updateLesionData(lesionData);
         }
     }
 

Packages/lesiontracker/client/compatibility/deleteLesionKeyboardTool.js

@@ -0,0 +1,91 @@
+(function(cornerstoneTools) {
+
+    'use strict';
+
+    // Delete a lesion if Ctrl+D or DELETE is pressed while a lesion is selected
+    var keys = {
+        D: 68,
+        DELETE: 46
+    };
+
+    function removeMeasurementTimepoint(data, index, toolType) {
+        var imageId = data.imageId;
+        var enabledElements = cornerstone.getEnabledElementsByImageId(imageId);
+        enabledElements.forEach(function(enabledElement) {
+            var element = enabledElement.element;
+
+            // The HandleMeasurementRemoved handler should do the rest
+            cornerstoneTools.removeToolState(element, toolType, data);
+
+            //Update element
+            cornerstone.updateImage(element);
+        });
+    }
+
+    function getNearbyToolData(element, coords, toolTypes) {
+        var allTools = toolManager.getTools();
+        var pointNearTool = false;
+        var touchDevice = isTouchDevice();
+        var nearbyTool,
+            nearbyToolIndex,
+            nearbyToolType;
+
+        toolTypes.forEach(function(toolType){
+            var toolData = cornerstoneTools.getToolState(element, toolType);
+            if (!toolData) {
+                return;
+            }
+
+            for (var i = 0; i < toolData.data.length; i++) {
+                var data = toolData.data[i];
+
+                var toolInterface;
+                if (touchDevice) {
+                    toolInterface = allTools[toolType].touch;
+                } else {
+                    toolInterface = allTools[toolType].mouse;
+                }
+
+                if (toolInterface.pointNearTool(element, data, coords)) {
+                    pointNearTool = true;
+                    nearbyTool = data;
+                    nearbyToolIndex = i;
+                    nearbyToolType = toolType;
+                    break;
+                }
+            }
+
+            if (pointNearTool === true) {
+                return false;
+            }
+        });
+
+        if (pointNearTool === true) {
+            return {
+                nearbyTool: nearbyTool,
+                nearbyToolIndex: nearbyToolIndex,
+                nearbyToolType: nearbyToolType
+            };
+        }
+    }
+
+    function keyDownCallback(e, eventData) {
+        var keyCode = eventData.keyCode;
+        if (keyCode === keys.DELETE ||
+            (keyCode === keys.D && eventData.event.ctrlKey === true)) {
+
+            var toolTypes = ["lesion", "nonTarget"];
+            var nearbyToolData = getNearbyToolData(eventData.element, eventData.currentPoints.canvas, toolTypes);
+
+            if (nearbyToolData) {
+                removeMeasurementTimepoint(nearbyToolData.nearbyTool,
+                                           nearbyToolData.nearbyToolIndex,
+                                           nearbyToolData.nearbyToolType);
+            }
+        }
+    }
+
+    // module/private exports
+    cornerstoneTools.deleteLesionKeyboardTool = cornerstoneTools.keyboardTool(keyDownCallback);
+
+})(cornerstoneTools);

Packages/lesiontracker/client/compatibility/lesionTool.js

@@ -78,8 +78,6 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
             $(element).on('CornerstoneToolsMouseDown', eventData, cornerstoneTools.lesion.mouseDownCallback);
             $(element).on('CornerstoneToolsMouseDownActivate', eventData, cornerstoneTools.lesion.mouseDownActivateCallback);
             cornerstone.updateImage(element);
-
-            updateLesionCollection(measurementData);
         });
     }
 
@@ -287,18 +285,6 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
         }
     }
 
-    function updateLesionCollection(lesionData) {
-        // TODO = Remove this in favour of measurement events
-        if (!lesionData.active) {
-            return;
-        }
-
-        if (lesionData.timepointID && lesionData.timepointID !== "") {
-            // Update Measurements Collection
-            measurementManagerDAL.updateTimepointData(lesionData);
-        }
-    }
-
     function doubleClickCallback(e, eventData) {
         // Prevent other double click handlers from firing after this one
         //e.stopImmediatePropagation();
@@ -310,16 +296,7 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
             if (deleteTool === true) {
                 cornerstoneTools.removeToolState(element, toolType, data);
                 cornerstone.updateImage(element);
-                //return;
             }
-
-            /*// TODO= Find a better way to do this! This is very messy
-            config.setLesionNumberCallback(data, eventData, function(lesionNumber) {
-                data.lesionName = "Target " + lesionNumber;
-                data.lesionNumber = lesionNumber;
-                data.active = false;
-                cornerstone.updateImage(element);
-            });*/
         }
 
         if (e.data && e.data.mouseButtonMask && !cornerstoneTools.isMouseButtonEnabled(eventData.which, e.data.mouseButtonMask)) {

Packages/lesiontracker/client/compatibility/measurementManagerDAL.js

@@ -1,167 +0,0 @@
-var measurementManagerDAL = (function() {
-    PatientLocations = new Meteor.Collection(null);
-
-    function getLocationName(id) {
-        var locationObject = PatientLocations.findOne(id);
-        return locationObject.location || "";
-    }
-
-    // Add timepoint data to Measurements collection
-    function addTimepointData(lesionData) {
-        var timepoints = Timepoints.find().fetch();
-
-        var timepointsObject = {};
-
-        for (var i = 0; i < timepoints.length; i++) {
-            var timepointId = timepoints[i].timepointID;
-            var lesionTimepointId = lesionData.timepointID;
-
-            var timepointObject;
-            if (timepointId === lesionTimepointId) {
-                // Add real measurement
-                timepointObject = {
-                    longestDiameter: lesionData.measurementText,
-                    imageId: lesionData.imageId,
-                    seriesInstanceUid: lesionData.seriesInstanceUid,
-                    studyInstanceUid: lesionData.studyInstanceUid,
-                    handles: lesionData.handles
-                };
-            } else {
-                // Add null measurement
-                timepointObject = {
-                    longestDiameter: "",
-                    imageId: "",
-                    seriesInstanceUid: "",
-                    studyInstanceUid: "",
-                    handles: undefined
-                };
-            }
-            timepointsObject[timepointId] = timepointObject;
-        }
-
-        var lesionDataObject = lesionData;
-
-        lesionDataObject.patientId = timepoints[0].patientId;
-        lesionDataObject.location = getLocationName(lesionData.locationUID);
-        lesionDataObject.timepoints = timepointsObject;
-
-        // Is there a use for this?
-        lesionDataObject.number = Measurements.find().count() + 1;
-
-        lesionDataObject.id = Measurements.insert(lesionDataObject);
-    }
-
-    // Update timepoint data in Measurements collection
-    function updateTimepointData(lesionData) {
-        // Find the specific lesion to be updated
-        var measurement = Measurements.findOne({
-            lesionNumber: lesionData.lesionNumber,
-            isTarget: lesionData.isTarget
-        });
-
-        // If no such lesion exists, stop here
-        if (!measurement) {
-            return;
-        }
-
-        // Update this specific lesion at the given timepoint
-        var timepointID = lesionData.timepointID;
-
-        // Update timepoints from lesion data
-        var timepoints = measurement.timepoints;
-        if (timepoints[timepointID] === undefined) {
-           timepoints[timepointID] = {};
-        }
-
-        timepoints[timepointID].longestDiameter = lesionData.measurementText;
-        timepoints[timepointID].imageId = lesionData.imageId;
-        timepoints[timepointID].seriesInstanceUid = lesionData.seriesInstanceUid;
-        timepoints[timepointID].studyInstanceUid = lesionData.studyInstanceUid;
-        timepoints[timepointID].handles = lesionData.handles;
-
-        lesionData.id = measurement._id;
-
-        Measurements.update(measurement._id, {
-            $set: {
-                timepoints: timepoints
-            }
-        });
-    }
-
-    // Check timepointData is found in Measurements collection
-    function hasTimepointData(lesionData) {
-        var timepointData = Measurements.findOne({
-            lesionNumber: lesionData.lesionNumber,
-            isTarget: lesionData.isTarget
-        });
-
-        if (timepointData) {
-            return true;
-        }
-        return false;
-    }
-
-    // Adds new timepoint item to timepoints array
-    function addLesionData(lesionData) {
-        if (hasTimepointData(lesionData)) {
-            // Update data
-            updateTimepointData(lesionData);
-        } else {
-            // Insert data
-            addTimepointData(lesionData);
-        }
-    }
-
-    // Returns new lesion number according to timepointID
-    function getNewLesionNumber(timepointID, isTarget) {
-        // Get all current lesion measurements
-        var measurements = Measurements.find({isTarget: isTarget},{sort: {lesionNumber: 1}}).fetch();
-
-        // If no measurements exist yet, start at 1
-        if (!measurements.length) {
-            return 1;
-        }
-
-        // If measurements exist, find the last lesion number
-        // from the given timepoint
-        var lesionNumberCounter = 0;
-        for (var i = 0; i < measurements.length; i++) {
-            var measurement = measurements[i];
-            var timepoints = measurement.timepoints;
-
-            if (!timepoints[timepointID]) {
-                // Find lesion number for this timepointID
-                return measurement.lesionNumber;
-            }
-
-            if (timepoints[timepointID].longestDiameter === '') {
-                return measurement.lesionNumber;
-            } else {
-                lesionNumberCounter = lesionNumberCounter + 1;
-            }
-        }
-        return lesionNumberCounter + 1;
-    }
-
-    // If lesion number is added for any timepoint, returns lesion locationUID
-    function lesionNumberExists(lesionData) {
-        if (!hasTimepointData(lesionData)) {
-            return;
-        }
-
-        var measurement = Measurements.findOne({
-            lesionNumber: lesionData.lesionNumber,
-            isTarget: lesionData.isTarget
-        });
-
-        return measurement.locationUID;
-    }
-
-    return {
-        addLesionData: addLesionData,
-        getNewLesionNumber: getNewLesionNumber,
-        lesionNumberExists: lesionNumberExists,
-        updateTimepointData: updateTimepointData,
-        getLocationName: getLocationName
-    };
-})();

Packages/lesiontracker/client/compatibility/nonTargetTool.js

@@ -32,7 +32,6 @@
     /// --- Mouse Tool --- ///
     ///////// BEGIN ACTIVE TOOL ///////
     function addNewMeasurement(mouseEventData) {
-
         var element = mouseEventData.element;
 
         function doneCallback(lesionNumber) {
@@ -53,9 +52,9 @@
 
         // since we are dragging to another place to drop the end point, we can just activate
         // the end point and let the moveHandle move it for us.
-        $(mouseEventData.element).off('CornerstoneToolsMouseMove', cornerstoneTools.nonTarget.mouseMoveCallback);
-        $(mouseEventData.element).off('CornerstoneToolsMouseDown', cornerstoneTools.nonTarget.mouseDownCallback);
-        $(mouseEventData.element).off('CornerstoneToolsMouseDownActivate', cornerstoneTools.nonTarget.mouseDownActivateCallback);
+        $(element).off('CornerstoneToolsMouseMove', cornerstoneTools.nonTarget.mouseMoveCallback);
+        $(element).off('CornerstoneToolsMouseDown', cornerstoneTools.nonTarget.mouseDownCallback);
+        $(element).off('CornerstoneToolsMouseDownActivate', cornerstoneTools.nonTarget.mouseDownActivateCallback);
 
         var config = cornerstoneTools.nonTarget.getConfiguration();
 
@@ -75,9 +74,9 @@
 
             }
 
-            $(mouseEventData.element).on('CornerstoneToolsMouseMove', eventData, cornerstoneTools.nonTarget.mouseMoveCallback);
-            $(mouseEventData.element).on('CornerstoneToolsMouseDown', eventData, cornerstoneTools.nonTarget.mouseDownCallback);
-            $(mouseEventData.element).on('CornerstoneToolsMouseDownActivate', eventData, cornerstoneTools.nonTarget.mouseDownActivateCallback);
+            $(element).on('CornerstoneToolsMouseMove', eventData, cornerstoneTools.nonTarget.mouseMoveCallback);
+            $(element).on('CornerstoneToolsMouseDown', eventData, cornerstoneTools.nonTarget.mouseDownCallback);
+            $(element).on('CornerstoneToolsMouseDownActivate', eventData, cornerstoneTools.nonTarget.mouseDownActivateCallback);
 
             cornerstone.updateImage(mouseEventData.element);
         });
@@ -127,8 +126,7 @@
             studyInstanceUid: studyInstanceUid,
             patientId: patientId,
             measurementText: '',
-            isTarget: false,
-            uid: uuid.v4()
+            isTarget: false
         };
 
         return measurementData;
@@ -184,8 +182,8 @@
             // configurable shadow from CornerstoneTools
             if (config && config.shadow) {
                 context.shadowColor = '#000000';
-                context.shadowOffsetX = +1;
-                context.shadowOffsetY = +1;
+                context.shadowOffsetX = 1;
+                context.shadowOffsetY = 1;
             }
 
             if (data.active) {
@@ -286,6 +284,7 @@
             if (deleteTool === true) {
                 cornerstoneTools.removeToolState(element, toolType, data);
                 cornerstone.updateImage(element);
+                return;
             }
 
             data.active = false;

Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.html

@@ -0,0 +1,8 @@
+<template name="confirmDeleteDialog">
+    <div id="confirmDeleteDialog">
+        <h5>Remove Measurement?</h5>
+        <p>Are you sure you would like to remove this measurement?</p>
+        <button id="cancel" class="btn btn-link">Cancel</button>
+        <button id="confirm" class="btn btn-primary">OK</button>
+    </div>
+</template>

Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.js

@@ -0,0 +1,51 @@
+function closeHandler() {
+    // Hide the lesion dialog
+    $("#confirmDeleteDialog").css('display', 'none');
+
+    // Remove the backdrop
+    $(".removableBackdrop").remove();
+
+    // Remove the callback from the template data
+    delete Template.confirmDeleteDialog.doneCallback;
+}
+
+showConfirmDialog = function(doneCallback) {
+    // Show the backdrop
+    UI.render(Template.removableBackdrop, document.body);
+
+    // Make sure the context menu is closed when the user clicks away
+    $(".removableBackdrop").one('mousedown touchstart', function() {
+        closeHandler();
+    });
+
+    $("#confirmDeleteDialog").css('display', 'block');
+
+    if (doneCallback && typeof doneCallback === 'function') {
+        Template.confirmDeleteDialog.doneCallback = doneCallback;
+    }
+};
+
+Template.confirmDeleteDialog.events({
+    'click #cancel, click #close': function() {
+        closeHandler();
+    },
+    'click #confirm': function() {
+        var doneCallback = Template.confirmDeleteDialog.doneCallback;
+
+        if (doneCallback && typeof doneCallback === 'function') {
+            doneCallback();
+        }
+
+        closeHandler();
+    },
+    'keypress #confirmDeleteDialog': function(e) {
+        if (this.keyPressAllowed === false) {
+            return;
+        }
+
+        // If Enter is pressed, close the dialog
+        if (e.which === 13) {
+            closeHandler();
+        }
+    }
+});

Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.styl

@@ -0,0 +1,24 @@
+#confirmDeleteDialog
+  display: none
+  position: absolute
+  top: 0
+  bottom: 0
+  left: 0
+  right: 0
+  z-index: 100
+  width: 300px
+  height: fit-content
+  margin: auto
+  border-radius: 5px
+  padding: 10px 20px 10px 20px
+  background-color: rgba(255,255,255,1)
+
+  .btn
+    outline: none
+    text-decoration: none
+
+  #cancel
+    float: left
+
+  #confirm
+    float: right

Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.js

@@ -23,7 +23,7 @@ function setLesionNumberCallback(measurementData, eventData, doneCallback) {
 
     // Get a lesion number for this lesion, depending on whether or not the same lesion previously
     // exists at a different timepoint
-    var lesionNumber = measurementManagerDAL.getNewLesionNumber(measurementData.timepointID, isTarget=true);
+    var lesionNumber = LesionManager.getNewLesionNumber(measurementData.timepointID, isTarget=true);
     measurementData.lesionNumber = lesionNumber;
 
     // Set lesion number
@@ -57,13 +57,13 @@ function getLesionLocationCallback(measurementData, eventData) {
 
     // Find out if this lesion number is already added in the lesion manager for another timepoint
     // If it is, stop here because we don't need the dialog.
-    var locationUID = measurementManagerDAL.lesionNumberExists(measurementData);
+    var locationUID = LesionManager.lesionNumberExists(measurementData);
     if (locationUID) {
         // Add an ID value to the tool data to link it to the Measurements collection
         measurementData.id = 'notready';
 
         measurementData.locationUID = locationUID;
-        measurementManagerDAL.updateTimepointData(measurementData);
+        LesionManager.updateLesionData(measurementData);
         closeHandler();
         return;
     }
@@ -90,7 +90,7 @@ function getLesionLocationCallback(measurementData, eventData) {
     dialog.css(dialogProperty);
 }
 
-function changeLesionLocationCallback(measurementData, eventData, doneCallback) {
+changeLesionLocationCallback = function(measurementData, eventData, doneCallback) {
     Template.lesionLocationDialog.measurementData = measurementData;
     Template.lesionLocationDialog.doneCallback = doneCallback;
 
@@ -107,21 +107,22 @@ function changeLesionLocationCallback(measurementData, eventData, doneCallback)
     });
 
     // Show the lesion location dialog above
-    var dialogProperty =  {
-        top: eventData.currentPoints.page.y - dialog.outerHeight() - 40,
-        left: eventData.currentPoints.page.x - dialog.outerWidth() / 2,
+    var dialogProperty = {
         display: 'block'
     };
 
     // Device is touch device or not
     // If device is touch device, set position center of screen vertically and horizontally
-    if (isTouchDevice()) {
+    if (!eventData || isTouchDevice()) {
         // add dialogMobile class to provide a black,transparent background
         dialog.addClass("dialogMobile");
         dialogProperty.top = 0;
         dialogProperty.left = 0;
         dialogProperty.right = 0;
         dialogProperty.bottom = 0;
+    } else {
+        dialogProperty.top = eventData.currentPoints.page.y - dialog.outerHeight() - 40;
+        dialogProperty.left = eventData.currentPoints.page.x - dialog.outerWidth() / 2;
     }
 
     dialog.css(dialogProperty);
@@ -131,20 +132,24 @@ function changeLesionLocationCallback(measurementData, eventData, doneCallback)
         return;
     }
 
+    LesionLocations.update({},
+        {$set: {selected: false}},
+        { multi: true });
+
     var currentLocation = LesionLocations.findOne({
         id: measurement.locationId
     });
 
-    LesionLocations.update({},
-        {$set: {selected: false}},
-        { multi: true });
+    if (!currentLocation) {
+        return;
+    }
 
     LesionLocations.update(currentLocation._id, {
         $set: {
             selected: true
         }
     });
-}
+};
 
 var config = {
     setLesionNumberCallback: setLesionNumberCallback,
@@ -189,6 +194,7 @@ Template.lesionLocationDialog.events({
             measurementData.id = 'notready';
 
             // Link locationUID with active lesion measurementData
+            measurementData.location = locationObj.location;
             measurementData.locationId = locationObj.id;
             measurementData.locationUID = id;
 
@@ -196,7 +202,7 @@ Template.lesionLocationDialog.events({
             measurementData.isTarget = true;
 
             // Adds lesion data to timepoints array
-            measurementManagerDAL.addLesionData(measurementData);
+            LesionManager.updateLesionData(measurementData);
         } else {
             Measurements.update(measurementData.id, {
                 $set: {
@@ -219,10 +225,12 @@ Template.lesionLocationDialog.events({
         var doneCallback = Template.lesionLocationDialog.doneCallback;
         var dialog = Template.lesionLocationDialog.dialog;
 
-        if (doneCallback && typeof doneCallback === 'function') {
-            var deleteTool = true;
-            doneCallback(measurementData, deleteTool);
-        }
+        showConfirmDialog(function() {
+            if (doneCallback && typeof doneCallback === 'function') {
+                var deleteTool = true;
+                doneCallback(measurementData, deleteTool);
+            }
+        });
 
         closeHandler(dialog);
     },

Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.styl

@@ -7,6 +7,7 @@
   right: 0
   z-index: 100
   width: 300px
+  margin: auto
   border-radius: 5px
   padding: 10px 20px 10px 20px
   background-color: rgba(255,255,255,1)

Packages/lesiontracker/client/components/lesionTable/lesionTable.js

@@ -1,221 +1,17 @@
-/**
- * Activates a set of lesions when lesion table row is clicked
- *
- * @param measurementId The unique key for a specific Measurement
- */
-activateLesion =  function(measurementId, templateData) {
-
-    // Set background color of selected row
-    $("tr[data-measurementid="+measurementId+"]").addClass("selectedRow").siblings().removeClass("selectedRow");
-
-    var measurementData = Measurements.findOne(measurementId);
-
-    // 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;
-
-    // Get all non-dummy timepoint entries in the Measurement
-    // TODO=Re-evaluate this approach to populating viewports with timepoints
-    // What is the desired behaviour here?
-    var timepointsWithEntries = [];
-    Object.keys(timepoints).forEach(function(key) {
-        var timepoint = timepoints[key];
-
-        if (timepoint.imageId === "" ||
-           timepoint.studyInstanceUid === "" ||
-           timepoint.seriesInstanceUid === "") {
-           return;
-        }
-
-        timepointsWithEntries.push(timepoint);
-    });
-
-    // If there are no non-dummy timepoint entries, stop here
-    if (!timepointsWithEntries.length) {
-        return;
-    }
-
-    // Loop through the viewports and display each timepoint
-    $(".imageViewerViewport").each(function(viewportIndex, element) {
-        // Stop if we run out of timepoints before viewports
-        if (viewportIndex >= timepointsWithEntries.length) {
-            // Update the element anyway, to remove any other highlights that are present
-            deactivateAllToolData(element, 'lesion');
-            deactivateAllToolData(element, 'nonTarget');
-            cornerstone.updateImage(element);
-
-            return false;
-        }
-
-        // Find measurements related to the Nth timepoint
-        // TODO=Re-evaluate this approach to populating viewports with timepoints
-        // What is the desired behaviour here?
-        var measurementAtTimepoint = timepointsWithEntries[viewportIndex];
-
-        // Find the image that is currently in this viewport
-        var enabledElement = cornerstone.getEnabledElement(element);
-        if (!enabledElement || !enabledElement.image) {
-            return;
-        }
-
-        // If there is no measurement data to display, stop here
-        if (!measurementAtTimepoint) {
-            // Update the element anyway, to remove any other highlights that are present
-            deactivateAllToolData(element, 'lesion');
-            deactivateAllToolData(element, 'nonTarget');
-            cornerstone.updateImage(element);
-            return;
-        }
-
-        // Check which study and series are required to display the measurement at this timepoint
-        var requiredSeriesData = {
-            seriesInstanceUid: measurementAtTimepoint.seriesInstanceUid,
-            studyInstanceUid: measurementAtTimepoint.studyInstanceUid
-        };
-
-        // Check if the study / series we need is already the one in the viewport
-        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, templateData, viewportIndex);
-            return;
-        }
-
-        // Otherwise, re-render the viewport with the required study/series, then
-        // add an onRendered callback to activate the measurements
-        rerenderViewportWithNewSeries(element, requiredSeriesData, function(element) {
-            activateMeasurements(element, measurementId, templateData, viewportIndex);
-        });
-    });
-}
-
-/**
- * Returns timepoint object based on timepoint id of the enabled element
- *
- * @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);
-    return Timepoints.findOne({timepointName: study.studyDate});
-}
-
-/**
- * Switch to the image of the correct image index
- * Activate the selected measurement on the switched image (color to be green)
- * Deactivate all other measurements on the switched image (color to be white)
- */
-function activateMeasurements(element, measurementId, templateData, viewportIndex) {
-    // TODO=Switch this to use the new CornerstoneToolMeasurementModified event,
-    // Once it has 'modified on activation' set up
-
-    var enabledElement = cornerstone.getEnabledElement(element);
-    var imageId = enabledElement.image.imageId;
-    var timepointData = getTimepointObject(imageId);
-    var measurementData = Measurements.findOne(measurementId);
-
-    var measurementAtTimepoint = measurementData.timepoints[timepointData.timepointID];
-    if (!measurementAtTimepoint) {
-        return;
-    }
-
-    // If type is active, load image and activate lesion
-    // If type is inactive, update lesions of enabledElement as inactive
-    //TODO: !stackData.currentImageIdIndex returns incorrect value
-    // Get loadedSeriesData currentImageIdIndex from ViewerData
-    var contentId = templateData.contentId;
-    var viewerData = ViewerData[contentId];
-    var elementCurrentImageIdIndex = viewerData.loadedSeriesData[viewportIndex].currentImageIdIndex;
-
-    var stackToolDataSource = cornerstoneTools.getToolState(element, 'stack');
-    var stackData = stackToolDataSource.data[0];
-    var imageIds = stackData.imageIds;
-    var imageIdIndex = imageIds.indexOf(measurementAtTimepoint.imageId);
-
-    if (imageIdIndex < 0) {
-        return;
-    }
-
-    if (imageIdIndex === elementCurrentImageIdIndex){
-        activateTool(element, measurementData, timepointData.timepointID);
-    } else {
-        cornerstone.loadAndCacheImage(imageIds[imageIdIndex]).then(function(image) {
-            cornerstone.displayImage(element, image);
-            activateTool(element, measurementData, timepointData.timepointID);
-        });
-    }
-}
-
-/**
- * Activates a specific tool data instance and deactivates all other
- * target and non-target measurement data
- *
- * @param element
- * @param measurementData
- * @param timepointID
- */
-function activateTool(element, measurementData, timepointID) {
-    deactivateAllToolData(element, 'lesion');
-    deactivateAllToolData(element, 'nonTarget');
-
-    var toolType = measurementData.isTarget ? 'lesion' : 'nonTarget';
-    var toolData = cornerstoneTools.getToolState(element, toolType);
-    if (!toolData) {
-        return;
-    }
-
-    var measurementAtTimepoint = measurementData.timepoints[timepointID];
-
-    for (var i = 0; i < toolData.data.length; i++) {
-        data = toolData.data[i];
-
-        // When click a row of table measurements, measurement will be active and color will be green
-        // TODO= Remove this with the measurementId once it is in the tool data
-        if (data.seriesInstanceUid === measurementAtTimepoint.seriesInstanceUid &&
-            data.studyInstanceUid === measurementAtTimepoint.studyInstanceUid &&
-            data.lesionNumber === measurementData.lesionNumber &&
-            data.isTarget == measurementData.isTarget) {
-
-            data.active = true;
-            break;
-        }
-    }
-
-    cornerstone.updateImage(element);
-}
-
-/**
- * Sets all tool data entries value for 'active' to false
- * This is used to remove the active color on entire sets of tools
- *
- * @param element The Cornerstone element that is being used
- * @param toolType The tooltype of the tools that will be deactivated
- */
-function deactivateAllToolData(element, toolType) {
-    var toolData = cornerstoneTools.getToolState(element, toolType);
-    if (!toolData) {
-        return;
-    }
-
-    for (var i = 0; i < toolData.data.length; i++) {
-        var data = toolData.data[i];
-        data.active = false;
-    }
-}
-
 Template.lesionTable.helpers({
     'measurement': function() {
-        return Measurements.find({}, {sort: {number: 1}});
+        return Measurements.find({}, {
+            sort: {
+                lesionNumber: 1
+            }
+        });
     },
     'timepoints': function() {
-        return Timepoints.find({}, {sort: {timepointName: 1}});
+        return Timepoints.find({}, {
+            sort: {
+                timepointName: 1
+            }
+        });
     }
 });
 
@@ -224,9 +20,8 @@ Template.lesionTable.events({
         // Retrieve the lesion id from the DOM data for this row
         var measurementId = $(e.currentTarget).data('measurementid');
 
-        activateLesion(measurementId,template.data);
+        activateLesion(measurementId, template.data);
     },
-
     'mousedown div#dragbar': function(e, template) {
         var pY = e.pageY;
         var draggableParent = $(e.currentTarget).parent();
@@ -235,7 +30,6 @@ Template.lesionTable.events({
 
         $(document).on('mouseup', function(e) {
             template.dragging.set(false);
-            console.log(e.pageY);
             $(document).off('mouseup').off('mousemove');
         });
 
@@ -244,7 +38,7 @@ Template.lesionTable.events({
             var newHeight = startHeight - topPosition;
 
             // Min lesion table height = 5px
-            if(newHeight < 5) {
+            if (newHeight < 5) {
                 return;
             }
 
@@ -256,76 +50,67 @@ Template.lesionTable.events({
             var viewportAndLesionTableHeight = $("#viewportAndLesionTable").height();
             var newPercentageHeightofLesionTable = (startHeight - topPosition) / viewportAndLesionTableHeight * 100;
             var newPercentageHeightofViewermain = 100 - newPercentageHeightofLesionTable;
-            $(".viewerMain").height(newPercentageHeightofViewermain+"%");
+            $(".viewerMain").height(newPercentageHeightofViewermain + "%");
 
             // Resize viewport
             resizeViewportElements();
-
         });
     }
 });
 
-Template.lesionTable.onCreated(function(){
-     this.dragging = new ReactiveVar(false);
-    // Bind document mouse events
-    // $(document).on('mousemove', dragbarMove);
+Template.lesionTable.onCreated(function() {
+    this.dragging = new ReactiveVar(false);
 });
 
-Template.lesionTable.onDestroyed(function(){
+Template.lesionTable.onRendered(function() {
+    var self = this;
 
-});
+    // Track ViewerData to get active timepoints
+    // Put a visual indicator (<) in timepoint header in lesion table for active timepoints
+    // timepointLoaded property is used to put indicator for loaded timepoints in viewport
+    self.autorun(function() {
+        // Get study dates of imageViewerViewport elements
+        var loadedStudyDates = {
+            patientId: "",
+            dates: []
+        };
 
-// Track ViewerData to get active timepoints
-// Put a visual indicator(<) in timepoint header in lesion table for active timepoints
-// timepointLoaded property is used to put indicator for loaded timepoints in viewport
-Tracker.autorun(function () {
-    var allViewerData = Session.get('ViewerData');
-    var contentId = Session.get('activeContentId');
-    if(allViewerData && contentId) {
-        var viewerData = allViewerData[contentId];
-        if (viewerData) {
-            // Get study dates of imageViewerViewport elements
-            var loadedStudyDates = {
-                patientId: "",
-                dates: []
-            };
-
-            $(".imageViewerViewport").each(function(viewportIndex, element) {
-                var enabledElement = cornerstone.getEnabledElement(element);
-                if(enabledElement && enabledElement.image){
-                    var imageId = enabledElement.image.imageId;
-                    var study = cornerstoneTools.metaData.get('study', imageId);
-                    var studyDate = study.studyDate;
-                    loadedStudyDates.patientId = study.patientId;
-                    // Check studyDate is added before
-                    if (loadedStudyDates.dates.indexOf(studyDate) < 0) {
-                        loadedStudyDates.dates.push(studyDate);
-                    }
-
-
-                }
-            });
-
-            // If study date is loaded into viewport, set timepointLoaded property in Timepoints collection as true
-            // Else set timepointLoaded property as false
-            if(loadedStudyDates.dates.length) {
-                var timepoints = Timepoints.find({patientId: loadedStudyDates.patientId}).fetch();
-                timepoints.forEach(function(timepoint){
-                    var timepointLoaded = false;
-                    if(loadedStudyDates.dates.indexOf(timepoint.timepointName) > -1) {
-                        timepointLoaded = true;
-                    }
-
-                    Timepoints.update(timepoint._id,{
-                        $set: {
-                            timepointLoaded: timepointLoaded
-                        }
-                    });
-                });
+        $(".imageViewerViewport").each(function(viewportIndex, element) {
+            var enabledElement = cornerstone.getEnabledElement(element);
+            if (!enabledElement || !enabledElement.image) {
+                return;
             }
+
+            var imageId = enabledElement.image.imageId;
+            var study = cornerstoneTools.metaData.get('study', imageId);
+            var studyDate = study.studyDate;
+            loadedStudyDates.patientId = study.patientId;
+
+            // Check whether or not studyDate has been added before
+            if (loadedStudyDates.dates.indexOf(studyDate) < 0) {
+                loadedStudyDates.dates.push(studyDate);
+            }
+        });
+
+        // If study date is loaded into viewport, set timepointLoaded property in Timepoints collection as true
+        // Else set timepointLoaded property as false
+        if (loadedStudyDates.dates.length) {
+            var timepoints = Timepoints.find({
+                patientId: loadedStudyDates.patientId
+            }).fetch();
+
+            timepoints.forEach(function(timepoint) {
+                var timepointLoaded = false;
+                if (loadedStudyDates.dates.indexOf(timepoint.timepointName) > -1) {
+                    timepointLoaded = true;
+                }
+
+                Timepoints.update(timepoint._id, {
+                    $set: {
+                        timepointLoaded: timepointLoaded
+                    }
+                });
+            });
         }
-    }
-
-});
-
-
+    });
+});

Packages/lesiontracker/client/components/lesionTableRow/lesionTableRow.html

@@ -1,7 +1,7 @@
 <template name="lesionTableRow">
     <tr id="{{lesionNumber}}" class="lesionTableRow" data-measurementid="{{_id}}">
-        <td class='lesionNumber'>{{number}}</td>
-        <td class='location'>{{location}}</td>
+        <td class='lesionNumber'>{{lesionNumber}}</td>
+        <td class='location' tabindex="0">{{location}}</td>
         <td class='target'>{{#if isTarget}} Y {{else}} N {{/if}}</td>
         <!--Each time point as a column-->
         {{# each timepoints }}

Packages/lesiontracker/client/components/lesionTableRow/lesionTableRow.js

@@ -3,3 +3,40 @@ Template.lesionTableRow.helpers({
         return Timepoints.find({}, {sort: {timepointName: 1}});
     }
 });
+
+function doneCallback(measurementData, deleteTool) {
+    // If a Lesion or Non-Target is removed via a dialog
+    // opened by the Lesion Table, we should clear the data for
+    // the specified Timepoint Cell
+    if (deleteTool === true) {
+        Meteor.call("removeMeasurement", measurementData.id, function(error, response) {
+            console.log('Removed!');
+        });
+    }
+}
+
+Template.lesionTableRow.events({
+    'dblclick .location': function() {
+        log.info('Double clicked on Lesion Location cell');
+
+        var measurementData = this;
+
+        // TODO = Fix this weird issue? Need to set toolData's ID properly..
+        measurementData.id = this._id;
+
+        changeLesionLocationCallback(measurementData, null, doneCallback);
+    },
+    'keypress .location': function(e) {
+        var keyCode = e.keyCode;
+        if (keyCode === keys.DELETE ||
+            (keyCode === keys.D && e.ctrlKey === true)) {
+            var currentMeasurement = Template.parentData(1);
+            var currentTimepointID = this.timepointID;
+
+            showConfirmDialog(function() {
+                log.info('Removing Lesion: ' + currentMeasurement._id);
+                clearMeasurementTimepointData(currentMeasurement._id, currentTimepointID);
+            });
+        }
+    }
+});

Packages/lesiontracker/client/components/lesionTableRow/lesionTableRow.styl

@@ -0,0 +1,3 @@
+.lesionTableRow .location
+  &:hover
+    font-weight: bold

Packages/lesiontracker/client/components/lesionTableTimepointCell/lesionTableTimepointCell.html

@@ -1,3 +1,11 @@
 <template name="lesionTableTimepointCell">
-    <td class="lesionTableTimepointCell">{{longestDiameter}}</td>
+    {{ #if hasDataAtThisTimepoint }}
+        {{ #if isTarget }}
+            <td class="lesionTableTimepointCell target" tabindex="1">{{displayData}}</td>
+        {{ else }}
+            <td class="lesionTableTimepointCell nonTarget" tabindex="2">{{displayData}}</td>
+        {{ /if }}
+    {{ else }}
+    <td class="lesionTableTimepointCell empty"></td>
+    {{ /if }}
 </template>

Packages/lesiontracker/client/components/lesionTableTimepointCell/lesionTableTimepointCell.js

@@ -1,5 +1,13 @@
 Template.lesionTableTimepointCell.helpers({
-    'longestDiameter': function() {
+    'hasDataAtThisTimepoint': function() {
+        // This simple function just checks whether or not timepoint data
+        // exists for this Measurement at this Timepoint
+        var lesionData = Template.parentData(1);
+        return (lesionData &&
+            lesionData.timepoints &&
+            lesionData.timepoints[this.timepointID]);
+    },
+    'displayData': function() {
         // Search Measurements by lesion and timepoint
         var lesionData = Template.parentData(1);
         if (!lesionData ||
@@ -8,6 +16,75 @@ Template.lesionTableTimepointCell.helpers({
             return;
         }
 
-        return lesionData.timepoints[this.timepointID].longestDiameter;
+        var data = lesionData.timepoints[this.timepointID];
+
+        if (lesionData.isTarget === true) {
+            // TODO = Add short axis data here
+            //return 'LD: ' + data.longestDiameter;
+            return data.longestDiameter;
+        } else {
+            return data.response;
+        }
+    },
+    'isTarget': function() {
+        var lesionData = Template.parentData(1);
+        return lesionData.isTarget;
+    }
+});
+
+function doneCallback(measurementData, deleteTool) {
+    // If a Lesion or Non-Target is removed via a dialog
+    // opened by the Lesion Table, we should clear the data for
+    // the specified Timepoint Cell
+    if (deleteTool === true) {
+        log.info('Confirm clicked!');
+        clearMeasurementTimepointData(measurementData.id, measurementData.timepointID);
+    }
+}
+
+// Delete a lesion if Ctrl+D or DELETE is pressed while a lesion is selected
+var keys = {
+    D: 68,
+    DELETE: 46
+};
+
+Template.lesionTableTimepointCell.events({
+    'dblclick .lesionTableTimepointCell': function() {
+        log.info('Double clicked on a timepoint cell');
+        // Search Measurements by lesion and timepoint
+        var currentMeasurement = Template.parentData(1);
+
+        // Create some fake measurement data
+        var currentTimepointID = this.timepointID;
+
+        var timepointData = currentMeasurement.timepoints[currentTimepointID];
+        var measurementData = {
+            id: currentMeasurement._id,
+            timepointID: currentTimepointID,
+            response: timepointData.response,
+            imageId: timepointData.imageId,
+            handles: timepointData.handles,
+            seriesInstanceUid: timepointData.seriesInstanceUid,
+            studyInstanceUid: timepointData.studyInstanceUid
+        };
+
+        if (currentMeasurement.isTarget) {
+            showConfirmDialog(function() {
+                log.info('Confirm clicked!');
+                clearMeasurementTimepointData(currentMeasurement._id, currentTimepointID);
+            });
+        } else {
+            changeNonTargetResponse(measurementData, null, doneCallback);
+        }
+    },
+    'keypress .lesionTableTimepointCell': function(e) {
+        var keyCode = e.keyCode;
+        if (keyCode === keys.DELETE ||
+            (keyCode === keys.D && e.ctrlKey === true)) {
+            var currentMeasurement = Template.parentData(1);
+            log.info('Removing Lesion: ' + currentMeasurement._id);
+            // TODO = Add confirm dialog first!
+            clearMeasurementTimepointData(currentMeasurement._id, this.timepointID);
+        }
     }
 });

Packages/lesiontracker/client/components/lesionTableTimepointCell/lesionTableTimepointCell.styl

@@ -0,0 +1,8 @@
+.lesionTableTimepointCell
+  &:hover
+    font-weight: bold
+  .nonTarget
+    &:hover
+      color: red
+
+

Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.html

@@ -18,7 +18,11 @@
                 <select id="selectNonTargetLesionLocationResponse">
                     <option value="-1"></option>
                     {{ #each locationResponses}}
-                    <option value='{{code}}'>{{code}} - {{text}}</option>
+                    {{ #if code }}
+                        <option value='{{code}}'>{{code}} - {{text}}</option>
+                    {{ else }}
+                        <option value={{text}}}>{{text}}</option>
+                    {{ /if }}
                     {{ /each}}
                 </select>
             </div>
@@ -38,7 +42,7 @@
                 <select id="selectNonTargetLesionLocation">
                     <option value="-1"></option>
                     {{ #each lesionLocations}}
-                    <option value='{{_id}}'>{{location}}</option>
+                    <option value='{{_id}}' selected={{selected}}>{{location}}</option>
                     {{ /each}}
                 </select>
             </div>
@@ -47,13 +51,16 @@
                 <select id="selectNonTargetLesionLocationResponse">
                     <option value="-1"></option>
                     {{ #each locationResponses}}
-                    <option value='{{code}}'>{{code}} - {{text}}</option>
+                    {{ #if code }}
+                    <option value={{code}} selected={{selected}}>{{code}} - {{text}}</option>
+                    {{ else }}
+                    <option value={{text}}} selected={{selected}}>{{text}}</option>
+                    {{ /if }}
                     {{ /each}}
                 </select>
             </div>
             <div class="locationOK">
                 <button class="btn btn-link" id="removeLesion">Remove</button>
-
                 <button class="btn btn-primary" id="nonTargetLesionOK">OK</button>
             </div>
         </div>

Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.js

@@ -26,7 +26,7 @@ function setLesionNumberCallback(measurementData, eventData, doneCallback) {
 
     // Get a lesion number for this lesion, depending on whether or not the same lesion previously
     // exists at a different timepoint
-    var lesionNumber = measurementManagerDAL.getNewLesionNumber(measurementData.timepointID, isTarget=false);
+    var lesionNumber = LesionManager.getNewLesionNumber(measurementData.timepointID, isTarget=false);
     measurementData.lesionNumber = lesionNumber;
 
     // Set lesion number
@@ -63,19 +63,20 @@ function getLesionLocationCallback(measurementData, eventData) {
 
     // Find out if this lesion number is already added in the lesion manager for another timepoint
     // If it is, disable selector location
-    var locationUID = measurementManagerDAL.lesionNumberExists(measurementData);
+    var locationUID = LesionManager.lesionNumberExists(measurementData);
     if (locationUID) {
         // Add an ID value to the tool data to link it to the Measurements collection
         measurementData.id = 'notready';
 
         measurementData.locationUID = locationUID;
+
         // Disable the selection of a new location
         disableLocationSelection(measurementData.locationUID);
     }
 
     // Disable selector location to prevent selecting a new location
     function disableLocationSelection(locationUID) {
-        var locationName = measurementManagerDAL.getLocationName(locationUID);
+        var locationName = LesionManager.getLocationName(locationUID);
         selectorLocation.find('option').each(function() {
             if ($(this).text() === locationName) {
                 // Select location in locations dropdown list
@@ -88,8 +89,8 @@ function getLesionLocationCallback(measurementData, eventData) {
 
     // Show the nonTargetLesion dialog above
     var dialogProperty =  {
-        top: eventData.currentPoints.page.y,
-        left: eventData.currentPoints.page.x,
+        top: eventData.currentPoints.page.y - dialog.outerHeight() - 40,
+        left: eventData.currentPoints.page.x - dialog.outerWidth() / 2,
         display: 'block'
     };
 
@@ -107,7 +108,7 @@ function getLesionLocationCallback(measurementData, eventData) {
     dialog.css(dialogProperty);
 }
 
-function changeLesionLocationCallback(measurementData, eventData, doneCallback) {
+changeNonTargetLocationCallback = function(measurementData, eventData, doneCallback) {
     Template.nonTargetLesionDialog.measurementData = measurementData;
     Template.nonTargetLesionDialog.doneCallback = doneCallback;
 
@@ -132,7 +133,6 @@ function changeLesionLocationCallback(measurementData, eventData, doneCallback)
     var selectorLocation = dialog.find("select#selectNonTargetLesionLocation");
     var selectorResponse = dialog.find("select#selectNonTargetLesionLocationResponse");
 
-    log.info(measurementData);
     selectorLocation.find("option:first").prop("selected", "selected");
     selectorResponse.find("option:first").prop("selected", "selected");
 
@@ -141,29 +141,75 @@ function changeLesionLocationCallback(measurementData, eventData, doneCallback)
 
     // Show the nonTargetLesion dialog above
     var dialogProperty =  {
-        top: eventData.currentPoints.page.y,
-        left: eventData.currentPoints.page.x,
         display: 'block'
     };
 
     // Device is touch device or not
     // If device is touch device, set position center of screen vertically and horizontally
-    if (isTouchDevice()) {
+    if (!eventData || isTouchDevice()) {
         // add dialogMobile class to provide a black,transparent background
         dialog.addClass("dialogMobile");
         dialogProperty.top = 0;
         dialogProperty.left = 0;
         dialogProperty.right = 0;
         dialogProperty.bottom = 0;
+    } else {
+        dialogProperty.top = eventData.currentPoints.page.y - dialog.outerHeight() - 40;
+        dialogProperty.left = eventData.currentPoints.page.x - dialog.outerWidth() / 2;
     }
 
     dialog.css(dialogProperty);
-}
+
+    var measurement = Measurements.findOne(measurementData.id);
+    if (!measurement) {
+        return;
+    }
+
+    LesionLocations.update({},
+        {$set: {selected: false}},
+        { multi: true });
+
+    var currentLocation = LesionLocations.findOne({
+        id: measurement.locationId
+    });
+
+    if (!currentLocation) {
+        return;
+    }
+
+    LesionLocations.update(currentLocation._id, {
+        $set: {
+            selected: true
+        }
+    });
+
+    LocationResponses.update({},
+        {$set: {selected: false}},
+        { multi: true });
+
+    var response = measurement.timepoints[measurementData.timepointID].response;
+
+    // TODO = Standardize this. Searching by code probably isn't the best, we should use
+    // some sort of UID
+    var currentResponse = LocationResponses.findOne({
+        code: response
+    });
+
+    if (!currentResponse) {
+        return;
+    }
+
+    LocationResponses.update(currentResponse._id, {
+        $set: {
+            selected: true
+        }
+    });
+};
 
 var config = {
     setLesionNumberCallback: setLesionNumberCallback,
     getLesionLocationCallback: getLesionLocationCallback,
-    changeLesionLocationCallback: changeLesionLocationCallback
+    changeLesionLocationCallback: changeNonTargetLocationCallback
 };
 
 cornerstoneTools.nonTarget.setConfiguration(config);
@@ -205,22 +251,8 @@ Template.nonTargetLesionDialog.events({
             id = PatientLocations.insert({location: locationObj.location});
         }
 
-        if (!measurementData.id) {
-            // Add an ID value to the tool data to link it to the Measurements collection
-            measurementData.id = 'notready';
-
-            // Link locationUID with active lesion measurementData
-            measurementData.locationUID = id;
-
-            /// Set the isTarget value to true, since this is the target-lesion dialog callback
-            measurementData.isTarget = false;
-
-            // measurementText is set from location response list
-            measurementData.measurementText = responseOptionId;
-
-            // Adds lesion data to timepoints array
-            measurementManagerDAL.addLesionData(measurementData);
-        } else {
+        if (measurementData.id) {
+            // Update the location data
             Measurements.update(measurementData.id, {
                 $set: {
                     location: locationObj.location,
@@ -228,8 +260,24 @@ Template.nonTargetLesionDialog.events({
                     locationUID: id
                 }
             });
+        } else {
+            // Add an ID value to the tool data to link it to the Measurements collection
+            measurementData.id = 'notready';
         }
 
+        // Link locationUID with active lesion measurementData
+        measurementData.locationUID = id;
+
+        /// Set the isTarget value to true, since this is the target-lesion dialog callback
+        measurementData.isTarget = false;
+
+        // measurementText is set from location response list
+        measurementData.measurementText = responseOptionId;
+        measurementData.response = responseOptionId;
+
+        // Adds lesion data to timepoints array
+        LesionManager.updateLesionData(measurementData);
+
         // Close the dialog
         closeHandler(dialog);
     },
@@ -238,10 +286,12 @@ Template.nonTargetLesionDialog.events({
         var doneCallback = Template.nonTargetLesionDialog.doneCallback;
         var dialog = Template.nonTargetLesionDialog.dialog;
 
-        if (doneCallback && typeof doneCallback === 'function') {
-            var deleteTool = true;
-            doneCallback(measurementData, deleteTool);
-        }
+        showConfirmDialog(function() {
+            if (doneCallback && typeof doneCallback === 'function') {
+                var deleteTool = true;
+                doneCallback(measurementData, deleteTool);
+            }
+        });
 
         closeHandler(dialog);
     },

Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.html

@@ -0,0 +1,26 @@
+<template name="nonTargetResponseDialog">
+    <div id="nonTargetResponseDialog">
+        <div class="dialogHeader">
+            <h5>Select Response</h5>
+        </div>
+        <div class="dialogContent">
+            <div class="locationResponse">
+                <label>Response</label>
+                <select id="selectNonTargetLesionLocationResponse">
+                    <option value="-1"></option>
+                    {{ #each locationResponses}}
+                    {{ #if code }}
+                    <option value={{code}} selected={{selected}}>{{code}} - {{text}}</option>
+                    {{ else }}
+                    <option value={{text}} selected={{selected}}>{{text}}</option>
+                    {{ /if }}
+                    {{ /each}}
+                </select>
+            </div>
+            <div class="locationOK">
+                <button class="btn btn-link" id="removeLesion">Remove</button>
+                <button class="btn btn-primary" id="nonTargetLesionOK">OK</button>
+            </div>
+        </div>
+    </div>
+</template>

Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.js

@@ -0,0 +1,143 @@
+function closeHandler(dialog) {
+    // Hide the lesion dialog
+    $(dialog).css('display', 'none');
+
+    // Remove the backdrop
+    $(".removableBackdrop").remove();
+}
+
+changeNonTargetResponse = function(measurementData, eventData, doneCallback) {
+    Template.nonTargetResponseDialog.measurementData = measurementData;
+    Template.nonTargetResponseDialog.doneCallback = doneCallback;
+
+    // Get the non-target lesion location dialog
+    var dialog = $("#nonTargetResponseDialog");
+    Template.nonTargetResponseDialog.dialog = dialog;
+
+    // Show the backdrop
+    UI.render(Template.removableBackdrop, document.body);
+
+    // Make sure the context menu is closed when the user clicks away
+    $(".removableBackdrop").one('mousedown touchstart', function() {
+        closeHandler(dialog);
+
+        if (doneCallback && typeof doneCallback === 'function') {
+            var deleteTool = true;
+            doneCallback(measurementData, deleteTool);
+        }
+    });
+
+    // Show the nonTargetLesion dialog above
+    var dialogProperty =  {
+        display: 'block'
+    };
+
+    // Device is touch device or not
+    // If device is touch device, set position center of screen vertically and horizontally
+    if (!eventData || isTouchDevice()) {
+        // add dialogMobile class to provide a black,transparent background
+        dialog.addClass("dialogMobile");
+        dialogProperty.top = 0;
+        dialogProperty.left = 0;
+        dialogProperty.right = 0;
+        dialogProperty.bottom = 0;
+    } else {
+        dialogProperty.top = eventData.currentPoints.page.y - dialog.outerHeight() - 40;
+        dialogProperty.left = eventData.currentPoints.page.x - dialog.outerWidth() / 2;
+    }
+
+    dialog.css(dialogProperty);
+
+    var measurement = Measurements.findOne(measurementData.id);
+    if (!measurement) {
+        return;
+    }
+
+    var response = measurement.timepoints[measurementData.timepointID].response;
+
+    // TODO = Standardize this. Searching by code probably isn't the best, we should use
+    // some sort of UID
+    var currentResponse = LocationResponses.findOne({
+        code: response
+    });
+
+    if (!currentResponse) {
+        return;
+    }
+
+    LocationResponses.update(currentResponse._id, {
+        $set: {
+            selected: true
+        }
+    });
+};
+
+Template.nonTargetResponseDialog.events({
+    'click #nonTargetLesionOK': function() {
+        var dialog = Template.nonTargetResponseDialog.dialog;
+        var measurementData = Template.nonTargetResponseDialog.measurementData;
+
+        // Find the select option box
+        var selectorResponse = dialog.find("select#selectNonTargetLesionLocationResponse");
+
+        // Get the current value of the selector
+        var responseOptionId = selectorResponse.find("option:selected").val();
+
+        // If the selected response option is still the default (-1)
+        // then stop here
+        if (responseOptionId < 0) {
+            return;
+        }
+
+        if (!measurementData.id) {
+            // Add an ID value to the tool data to link it to the Measurements collection
+            measurementData.id = 'notready';
+        }
+
+        /// Set the isTarget value to true, since this is the target-lesion dialog callback
+        measurementData.isTarget = false;
+
+        // measurementText is set from location response list
+        measurementData.measurementText = responseOptionId;
+        measurementData.response = responseOptionId;
+
+        // Adds lesion data to timepoints array
+        LesionManager.updateLesionData(measurementData);
+
+        // Close the dialog
+        closeHandler(dialog);
+    },
+    'click #removeLesion': function() {
+        var measurementData = Template.nonTargetResponseDialog.measurementData;
+        var doneCallback = Template.nonTargetResponseDialog.doneCallback;
+        var dialog = Template.nonTargetResponseDialog.dialog;
+
+        showConfirmDialog(function() {
+            if (doneCallback && typeof doneCallback === 'function') {
+                var deleteTool = true;
+                doneCallback(measurementData, deleteTool);
+            }
+        });
+
+        closeHandler(dialog);
+    },
+    'click #btnCloseLesionPopup': function() {
+        var dialog = Template.nonTargetResponseDialog.dialog;
+        closeHandler(dialog);
+    },
+    'keypress #nonTargetResponseDialog': function(e) {
+        var dialog = Template.nonTargetResponseDialog.dialog;
+
+        // If Enter is pressed, close the dialog
+        if (e.which === 13) {
+            closeHandler(dialog);
+        }
+    }
+});
+
+
+Template.nonTargetResponseDialog.helpers({
+    'locationResponses': function() {
+        return LocationResponses.find();
+    }
+});

Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.styl

@@ -0,0 +1,23 @@
+#nonTargetResponseDialog
+  display: none
+  position: absolute
+  top: 0
+  bottom: 0
+  left: 0
+  right: 0
+  z-index: 100
+  width: 300px
+  height: 150px
+  border-radius: 5px
+  padding: 10px 20px 10px 20px
+  background-color: rgba(255,255,255,1)
+
+  #selectNonTargetLesionLocationResponse
+    width: 100%
+
+  .dialogContent, .locationResponse
+    margin-bottom: 20px
+
+  .locationOK
+    text-align: center
+    

Packages/lesiontracker/lib/activateLesion.js

@@ -0,0 +1,96 @@
+/**
+ * Activates a set of lesions when lesion table row is clicked
+ *
+ * @param measurementId The unique key for a specific Measurement
+ */
+activateLesion = function(measurementId, templateData) {
+
+    // Set background color of selected row
+    $("tr[data-measurementid=" + measurementId + "]").addClass("selectedRow").siblings().removeClass("selectedRow");
+
+    var measurementData = Measurements.findOne(measurementId);
+
+    // 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;
+
+    // Get all non-dummy timepoint entries in the Measurement
+    // TODO=Re-evaluate this approach to populating viewports with timepoints
+    // What is the desired behaviour here?
+    var timepointsWithEntries = [];
+    Object.keys(timepoints).forEach(function(key) {
+        var timepoint = timepoints[key];
+
+        if (timepoint.imageId === "" ||
+            timepoint.studyInstanceUid === "" ||
+            timepoint.seriesInstanceUid === "") {
+            return;
+        }
+
+        timepointsWithEntries.push(timepoint);
+    });
+
+    // If there are no non-dummy timepoint entries, stop here
+    if (!timepointsWithEntries.length) {
+        return;
+    }
+
+    // Loop through the viewports and display each timepoint
+    $(".imageViewerViewport").each(function(viewportIndex, element) {
+        // Stop if we run out of timepoints before viewports
+        if (viewportIndex >= timepointsWithEntries.length) {
+            // Update the element anyway, to remove any other highlights that are present
+            deactivateAllToolData(element, 'lesion');
+            deactivateAllToolData(element, 'nonTarget');
+            cornerstone.updateImage(element);
+
+            return false;
+        }
+
+        // Find measurements related to the Nth timepoint
+        // TODO=Re-evaluate this approach to populating viewports with timepoints
+        // What is the desired behaviour here?
+        var measurementAtTimepoint = timepointsWithEntries[viewportIndex];
+
+        // Find the image that is currently in this viewport
+        var enabledElement = cornerstone.getEnabledElement(element);
+        if (!enabledElement || !enabledElement.image) {
+            return;
+        }
+
+        // If there is no measurement data to display, stop here
+        if (!measurementAtTimepoint) {
+            // Update the element anyway, to remove any other highlights that are present
+            deactivateAllToolData(element, 'lesion');
+            deactivateAllToolData(element, 'nonTarget');
+            cornerstone.updateImage(element);
+            return;
+        }
+
+        // Check which study and series are required to display the measurement at this timepoint
+        var requiredSeriesData = {
+            seriesInstanceUid: measurementAtTimepoint.seriesInstanceUid,
+            studyInstanceUid: measurementAtTimepoint.studyInstanceUid
+        };
+
+        // Check if the study / series we need is already the one in the viewport
+        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, templateData, viewportIndex);
+            return;
+        }
+
+        // Otherwise, re-render the viewport with the required study/series, then
+        // add an onRendered callback to activate the measurements
+        rerenderViewportWithNewSeries(element, requiredSeriesData, function(element) {
+            activateMeasurements(element, measurementId, templateData, viewportIndex);
+        });
+    });
+};

Packages/lesiontracker/lib/activateMeasurements.js

@@ -0,0 +1,83 @@
+/**
+ * Switch to the image of the correct image index
+ * Activate the selected measurement on the switched image (color to be green)
+ * Deactivate all other measurements on the switched image (color to be white)
+ */
+activateMeasurements = function(element, measurementId, templateData, viewportIndex) {
+    // TODO=Switch this to use the new CornerstoneToolMeasurementModified event,
+    // Once it has 'modified on activation' set up
+
+    var enabledElement = cornerstone.getEnabledElement(element);
+    var imageId = enabledElement.image.imageId;
+    var timepointData = getTimepointObject(imageId);
+    var measurementData = Measurements.findOne(measurementId);
+
+    var measurementAtTimepoint = measurementData.timepoints[timepointData.timepointID];
+    if (!measurementAtTimepoint) {
+        return;
+    }
+
+    // If type is active, load image and activate lesion
+    // If type is inactive, update lesions of enabledElement as inactive
+    //TODO: !stackData.currentImageIdIndex returns incorrect value
+    // Get loadedSeriesData currentImageIdIndex from ViewerData
+    var contentId = templateData.contentId;
+    var viewerData = ViewerData[contentId];
+    var elementCurrentImageIdIndex = viewerData.loadedSeriesData[viewportIndex].currentImageIdIndex;
+
+    var stackToolDataSource = cornerstoneTools.getToolState(element, 'stack');
+    var stackData = stackToolDataSource.data[0];
+    var imageIds = stackData.imageIds;
+    var imageIdIndex = imageIds.indexOf(measurementAtTimepoint.imageId);
+
+    if (imageIdIndex < 0) {
+        return;
+    }
+
+    if (imageIdIndex === elementCurrentImageIdIndex) {
+        activateTool(element, measurementData, timepointData.timepointID);
+    } else {
+        cornerstone.loadAndCacheImage(imageIds[imageIdIndex]).then(function(image) {
+            cornerstone.displayImage(element, image);
+            activateTool(element, measurementData, timepointData.timepointID);
+        });
+    }
+};
+
+/**
+ * Activates a specific tool data instance and deactivates all other
+ * target and non-target measurement data
+ *
+ * @param element
+ * @param measurementData
+ * @param timepointID
+ */
+function activateTool(element, measurementData, timepointID) {
+    deactivateAllToolData(element, 'lesion');
+    deactivateAllToolData(element, 'nonTarget');
+
+    var toolType = measurementData.isTarget ? 'lesion' : 'nonTarget';
+    var toolData = cornerstoneTools.getToolState(element, toolType);
+    if (!toolData) {
+        return;
+    }
+
+    var measurementAtTimepoint = measurementData.timepoints[timepointID];
+
+    for (var i = 0; i < toolData.data.length; i++) {
+        data = toolData.data[i];
+
+        // When click a row of table measurements, measurement will be active and color will be green
+        // TODO= Remove this with the measurementId once it is in the tool data
+        if (data.seriesInstanceUid === measurementAtTimepoint.seriesInstanceUid &&
+            data.studyInstanceUid === measurementAtTimepoint.studyInstanceUid &&
+            data.lesionNumber === measurementData.lesionNumber &&
+            data.isTarget == measurementData.isTarget) {
+
+            data.active = true;
+            break;
+        }
+    }
+
+    cornerstone.updateImage(element);
+}

Packages/lesiontracker/lib/clearMeasurementTimepointData.js

@@ -0,0 +1,34 @@
+clearMeasurementTimepointData = function(measurementId, timepointId) {
+    var data = Measurements.findOne(measurementId);
+
+    // Check that this Measurement actually contains data for this timepoint
+    if (!data || !data.timepoints[timepointId]) {
+        return;
+    }
+
+    // Clear the Measurement data for this timepoint
+    var imageId = data.timepoints[timepointId].imageId;
+    var toolType = data.isTarget ? 'lesion' : 'nonTarget';
+    removeToolDataWithMeasurementId(imageId, toolType, measurementId);
+
+    // Update any viewports that are currently displaying this imageId
+    var enabledElements = cornerstone.getEnabledElementsByImageId(imageId);
+    enabledElements.forEach(function(enabledElement) {
+        cornerstone.updateImage(enabledElement.element);
+    });
+
+    delete data.timepoints[timepointId];
+
+    if (Object.keys(data.timepoints).length === 0) {
+        Meteor.call("removeMeasurement", measurementId, function(error, response) {
+            console.log('Removed!');
+        });
+    } else {
+        // Update the Timepoint object of the Measurement document
+        Measurements.update(measurementId, {
+            $set: {
+                timepoints: data.timepoints
+            }
+        });
+    }
+};

Packages/lesiontracker/lib/deactivateAllToolData.js

@@ -0,0 +1,18 @@
+/**
+ * Sets all tool data entries value for 'active' to false
+ * This is used to remove the active color on entire sets of tools
+ *
+ * @param element The Cornerstone element that is being used
+ * @param toolType The tooltype of the tools that will be deactivated
+ */
+deactivateAllToolData = function(element, toolType) {
+    var toolData = cornerstoneTools.getToolState(element, toolType);
+    if (!toolData) {
+        return;
+    }
+
+    for (var i = 0; i < toolData.data.length; i++) {
+        var data = toolData.data[i];
+        data.active = false;
+    }
+};

Packages/lesiontracker/lib/getTimepointObject.js

@@ -0,0 +1,13 @@
+/**
+ * Returns timepoint object given a specified imageId
+ *
+ * @param imageId
+ * @returns {*|{}} Timepoint object
+ */
+getTimepointObject = function(imageId) {
+    var study = cornerstoneTools.metaData.get('study', imageId);
+    if (!study) {
+        return;
+    }
+    return Timepoints.findOne({timepointName: study.studyDate});
+};

Packages/lesiontracker/lib/removeToolDataWithMeasurementId.js

@@ -0,0 +1,28 @@
+removeToolDataWithMeasurementId = function(imageId, toolType, measurementId) {
+    var toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
+    
+    // Find any related toolData
+    if (!toolState[imageId] || !toolState[imageId][toolType]) {
+        return;
+    }
+    
+    var toolData = toolState[imageId][toolType].data;
+    if (!toolData.length) {
+        return;
+    }
+
+    // Search toolData for entries linked to the specified Measurement
+    var toRemove = [];
+    toolData.forEach(function(measurement, index) {
+        if (measurement.id === measurementId) {
+            toRemove.push(index);
+            return false;
+        }
+    });
+
+    // If any toolData entries need to be removed, splice them from
+    // the toolData array
+    toRemove.forEach(function(index) {
+        toolData.splice(index, 1);
+    });
+};

Packages/lesiontracker/lib/toggleLesionTrackerTools.js

@@ -15,7 +15,7 @@ toggleLesionTrackerTools = function() {
 
         // Hide the tools (set them all to disabled)
         var toolDefaultStates = {
-            activate: [],
+            activate: ['deleteLesionKeyboardTool'],
             deactivate: [],
             enable: [],
             disable: ['lesion', 'nonTarget', 'biDirectional']

Packages/lesiontracker/package.js

@@ -23,7 +23,8 @@ Package.onUse(function (api) {
     api.addFiles('client/compatibility/lesionTool.js', 'client', {bare: true});
     api.addFiles('client/compatibility/nonTargetTool.js', 'client', {bare: true});
     api.addFiles('client/compatibility/biDirectionalTool.js', 'client', {bare: true});
-    api.addFiles('client/compatibility/measurementManagerDAL.js', 'client', {bare: true});
+    api.addFiles('client/compatibility/deleteLesionKeyboardTool.js', 'client', {bare: true});
+    api.addFiles('client/compatibility/LesionManager.js', 'client', {bare: true});
 
     api.addFiles('client/components/lesionLocationDialog/lesionLocationDialog.html', 'client');
     api.addFiles('client/components/lesionLocationDialog/lesionLocationDialog.js', 'client');
@@ -37,6 +38,7 @@ Package.onUse(function (api) {
     api.addFiles('client/components/lesionTableRow/lesionTableRow.js', 'client');
 
     api.addFiles('client/components/lesionTableTimepointCell/lesionTableTimepointCell.html', 'client');
+    api.addFiles('client/components/lesionTableTimepointCell/lesionTableTimepointCell.styl', 'client');
     api.addFiles('client/components/lesionTableTimepointCell/lesionTableTimepointCell.js', 'client');
 
     api.addFiles('client/components/lesionTableTimepointHeader/lesionTableTimepointHeader.html', 'client');
@@ -51,6 +53,14 @@ Package.onUse(function (api) {
     api.addFiles('client/components/studyDateList/studyDateList.styl', 'client');
     api.addFiles('client/components/studyDateList/studyDateList.js', 'client');
 
+    api.addFiles('client/components/confirmDeleteDialog/confirmDeleteDialog.html', 'client');
+    api.addFiles('client/components/confirmDeleteDialog/confirmDeleteDialog.styl', 'client');
+    api.addFiles('client/components/confirmDeleteDialog/confirmDeleteDialog.js', 'client');
+
+    api.addFiles('client/components/nonTargetResponseDialog/nonTargetResponseDialog.html', 'client');
+    api.addFiles('client/components/nonTargetResponseDialog/nonTargetResponseDialog.styl', 'client');
+    api.addFiles('client/components/nonTargetResponseDialog/nonTargetResponseDialog.js', 'client');
+
     api.addFiles('client/components/timepointTextDialog/timepointTextDialog.html', 'client');
     api.addFiles('client/components/timepointTextDialog/timepointTextDialog.styl', 'client');
 
@@ -64,15 +74,26 @@ Package.onUse(function (api) {
     // Library functions
     api.addFiles('lib/uuid.js', 'client');
     api.addFiles('lib/toggleLesionTrackerTools.js', 'client');
+    api.addFiles('lib/clearMeasurementTimepointData.js', 'client');
+    api.addFiles('lib/removeToolDataWithMeasurementId.js', 'client');
+    api.addFiles('lib/getTimepointObject.js', 'client');
+    api.addFiles('lib/activateMeasurements.js', 'client');
+    api.addFiles('lib/activateLesion.js', 'client');
+    api.addFiles('lib/deactivateAllToolData.js', 'client');
     api.addFiles('lib/clearTools.js', 'client');
     api.addFiles('lib/mathUtils.js', 'client');
 
 
     // Export lesionTable function for activate measurements
     api.export('activateLesion','client');
+    api.export('activateMeasurements','client');
+    api.export('deactivateAllToolData','client');
     api.export('toggleLesionTrackerTools', 'client');
+    api.export('clearMeasurementTimepointData', 'client');
+    api.export('removeToolDataWithMeasurementId', 'client');
+    api.export('getTimepointObject', 'client');
     api.export('clearTools', 'client');
-    api.export('measurementManagerDAL', 'client');
+    api.export('LesionManager', 'client');
 
     // Export mathUtils functions
     api.export('sign','client');
@@ -80,7 +101,6 @@ Package.onUse(function (api) {
     api.export('getDistance','client');
     api.export('getDistanceFromPointToLine','client');
 
-
     // Export client-side collections
     api.export('LesionLocations', 'client');
     api.export('LocationResponses', 'client');

Packages/lesiontracker/server/collections.js

@@ -1,23 +1,27 @@
 Meteor.publish('timepoints', function(patientId) {
     console.log('Publish timepoints');
     console.log('patientId ' + patientId);
-    return Timepoints.find({patientId: patientId});
+    return Timepoints.find({
+        patientId: patientId
+    });
 });
 
 Meteor.publish('measurements', function(patientId) {
     console.log('Publish measurements');
     console.log('patientId ' + patientId);
-    return Measurements.find({patientId: patientId});
+    return Measurements.find({
+        patientId: patientId
+    });
 });
 
 
 // Temporary fix to drop all Collections on server restart
 // http://stackoverflow.com/questions/23891631/meteor-how-can-i-drop-all-mongo-collections-and-clear-all-data-on-startup
-Meteor.startup(function(){
-    var globalObject=Meteor.isClient?window:global;
-    for(var property in globalObject){
-        var object=globalObject[property];
-        if(object instanceof Meteor.Collection){
+Meteor.startup(function() {
+    var globalObject = Meteor.isClient ? window : global;
+    for (var property in globalObject) {
+        var object = globalObject[property];
+        if (object instanceof Meteor.Collection) {
             object.remove({});
         }
     }

Packages/lesiontracker/server/removeCollections.js

@@ -1,21 +1,21 @@
-
 Meteor.methods({
-    "removeMeasurementsByPatientId": function(patientId) {
-        Measurements.remove(
-            {patientId: patientId}
-        );
+    "removeMeasurement": function(id) {
+        console.log(Measurements.find().fetch());
+        console.log("Removing: " + id);
+        Measurements.remove(id);
+        console.log(Measurements.find().fetch());
     },
-
+    "removeMeasurementsByPatientId": function(patientId) {
+        Measurements.remove({patientId: patientId});
+    },
+    // TODO= Check where this is used? Seems like nowhere.. 
     "removePatientMeasurement": function(lesionObject) {
-
         // Find patient data
-        var measurementData = Measurements.findOne(
-            {
-                patientId: lesionObject.patientId,
-                isTarget: lesionObject.isTarget,
-                lesionNumber: lesionObject.lesionNumber
-            }
-        );
+        var measurementData = Measurements.findOne({
+            patientId: lesionObject.patientId,
+            isTarget: lesionObject.isTarget,
+            lesionNumber: lesionObject.lesionNumber
+        });
 
         // Get timepoints
         var timepoints = measurementData.timepoints;
@@ -23,41 +23,32 @@ Meteor.methods({
         // Create an array to hold keys of timepoints
         var timepointsIds = Object.keys(timepoints).slice(0);
 
-          timepointsIds.forEach(function(timepointId){
-              if(timepointId === lesionObject.timepointId) {
-                  delete timepoints[timepointId];
-              }
-          });
+        timepointsIds.forEach(function(timepointId) {
+            if (timepointId === lesionObject.timepointId) {
+                delete timepoints[timepointId];
+            }
+        });
 
         var newTimepointsIds = Object.keys(timepoints);
         // If there is no timepoints object, remove measurement data
-        if(newTimepointsIds.length) {
+        if (newTimepointsIds.length) {
             //Update measurement timepoints
-            Measurements.update(
-                {
-                    patientId: lesionObject.patientId,
-                    isTarget: lesionObject.isTarget,
-                    lesionNumber: lesionObject.lesionNumber
-                 },
-                {
-                    $set: {
-                        timepoints: timepoints
-                    }
+            Measurements.update({
+                patientId: lesionObject.patientId,
+                isTarget: lesionObject.isTarget,
+                lesionNumber: lesionObject.lesionNumber
+            }, {
+                $set: {
+                    timepoints: timepoints
                 }
-            );
-        }else {
+            });
+        } else {
             // Remove all data
-            Measurements.remove(
-                {
-                    patientId: lesionObject.patientId,
-                    isTarget: lesionObject.isTarget,
-                    lesionNumber: lesionObject.lesionNumber
-                }
-            );
+            Measurements.remove({
+                patientId: lesionObject.patientId,
+                isTarget: lesionObject.isTarget,
+                lesionNumber: lesionObject.lesionNumber
+            });
         }
-
-
     }
-
-});
-
+});

Packages/viewerbase/client/components/viewer/imageViewerViewport/imageViewerViewport.html

@@ -2,7 +2,8 @@
     <div class='imageViewerViewport'
         oncontextmenu='return false;'
         unselectable='on'
-        onselectstart='return false;'>
+        onselectstart='return false;'
+        tabindex='0'>
     </div>
     <div class='viewportInstructions'>
         Please drag a stack here to view images.

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

@@ -180,10 +180,11 @@ function loadSeriesIntoViewport(data, templateData) {
         cornerstoneTools.clearToolState(element, 'stack');
         cornerstoneTools.addToolState(element, 'stack', stack);
 
-        // Enable mouse, mouseWheel, and touch input on the element
+        // Enable mouse, mouseWheel, touch, and keyboard input on the element
         cornerstoneTools.mouseInput.enable(element);
         cornerstoneTools.touchInput.enable(element);
         cornerstoneTools.mouseWheelInput.enable(element);
+        cornerstoneTools.keyboardInput.enable(element);
 
         // Use the tool manager to enable the currently active tool for this
         // newly rendered element
@@ -210,102 +211,6 @@ function loadSeriesIntoViewport(data, templateData) {
         $(element).off('CornerstoneImageRendered', onImageRendered);
         $(element).on('CornerstoneImageRendered', onImageRendered);
 
-        //TODO: ********************************************
-        //TODO: Delete a lesion, if ctrl+d or del is pressed after lesion selected
-        //TODO: getTimepointObject should be global function to use everywhere
-
-        function getTimepointObject(imageId) {
-            var study = cornerstoneTools.metaData.get('study', imageId);
-            return Timepoints.findOne({timepointName: study.studyDate});
-        }
-
-        // ctrl+d is used to detect delete event if del key is not found on keyboard.
-        // Id key is down
-        var keyMap = {17: false, 68: false, 46: false};
-        function keyPressDownHandler(e, lesionData){
-            if (e.keyCode in keyMap) {
-                keyMap[e.keyCode] = true;
-                if (keyMap[46] || keyMap[17] && keyMap[68]) {
-                    var toolType = lesionData.isTarget ? 'lesion' : 'nonTarget';
-                    var imageId = lesionData.imageId;
-                    var toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
-                    Object.keys(toolState).forEach(function(imageIdKey){
-                        if(imageIdKey === imageId) {
-                            var toolStateArray = toolState[imageId][toolType].data;
-                            toolStateArray.forEach(function(data, index) {
-                                if(data.lesionNumber === lesionData.lesionNumber){
-                                    toolState[imageId][toolType].data.splice(index, 1);
-
-                                    // Remove from collection
-                                    var patientId = data.patientId;
-                                    var enabledElement = cornerstone.getEnabledElement(element);
-                                    var elementImageId = enabledElement.image.imageId;
-                                    var timepointData = getTimepointObject(elementImageId);
-                                    var lesionObject = {
-                                        patientId: patientId,
-                                        lesionNumber: lesionData.lesionNumber,
-                                        isTarget: lesionData.isTarget,
-                                        timepointId: timepointData.timepointID
-                                    };
-
-                                    // Remove patient measurement
-                                    Meteor.call('removePatientMeasurement', lesionObject);
-
-                                    //Update element
-                                    cornerstone.updateImage(element);
-                                }
-                            });
-
-
-                        }
-                    });
-
-                }
-            }
-        }
-
-        // When key is up
-        function keyPressUpHandler(e){
-            if (e.keyCode in keyMap) {
-                keyMap[e.keyCode] = false;
-            }
-        }
-
-        // CornerstoneToolsMouseDown event callback
-        function onMouseDown(e,eventData) {
-            var element = e.currentTarget;
-            var distanceSq = 5;
-            var coords = eventData.startPoints.canvas;
-            var toolTypes = ["lesion", "nonTarget"];
-            toolTypes.forEach(function(toolType){
-                var toolData = cornerstoneTools.getToolState(element, toolType);
-
-                // now check to see if there is a handle we can move
-                if (toolData) {
-                    for (var i = 0; i < toolData.data.length; i++) {
-                        var data = toolData.data[i];
-                        var handle = cornerstoneTools.getHandleNearImagePoint(element, data.handles, coords, distanceSq);
-                        if(handle) {
-                            $(document).off("keydown");
-                            $(document).on('keydown', function(e){
-                                keyPressDownHandler(e,data);
-                                return;
-                            });
-                            $(document).off("keyup");
-                            $(document).on('keyup',keyPressUpHandler);
-                            return;
-                        }
-                    }
-                }
-            });
-        }
-
-        $(element).on('CornerstoneToolsMouseDown', onMouseDown);
-        $(element).on('CornerstoneToolsMouseDown', onMouseDown);
-
-        //TODO: Delete a lesion ends
-        //TODO: ********************************************
-
         // Set a random value for the Session variable in order to trigger an overlay update
         Session.set('CornerstoneImageRendered' + viewportIndex, Random.id());
 
@@ -365,8 +270,13 @@ function loadSeriesIntoViewport(data, templateData) {
             // Check if the current active viewport in the Meteor Session
             // Is the same as the viewport in which the activation event was fired.
             // If it was, no changes are necessary, so stop here.
+            var element = eventData.element;
             var activeViewportIndex = Session.get('activeViewport');
-            var viewportIndex = $(".imageViewerViewport").index(eventData.element);
+            var viewportIndex = $(".imageViewerViewport").index(element);
+
+            // Reset the focus, even if we don't need to re-enable reference lines or prefetching
+            $(element).focus();
+
             if (viewportIndex === activeViewportIndex) {
                 return;
             }
@@ -403,11 +313,13 @@ function loadSeriesIntoViewport(data, templateData) {
         // that is used for updating reference lines, and enable reference lines for this viewport.
         if (OHIF.viewer.refLinesEnabled && imagePlane && imagePlane.frameOfReferenceUID) {
             OHIF.viewer.updateImageSynchronizer.add(element);
-            displayReferenceLines(element);
         }
 
+        // Set the active viewport based on the Session variable
+        // This is done to ensure that the active element has the current
+        // focus, so that keyboard events are triggered.
         if (viewportIndex === Session.get('activeViewport')) {
-            enablePrefetchOnElement(element);
+            setActiveViewport(element);
         }
 
         // Run any renderedCallback that exists in the data context
@@ -428,7 +340,7 @@ function loadSeriesIntoViewport(data, templateData) {
  * @param templateData currentData of Template
  *
  */
-function setSeries(data,seriesInstanceUid, templateData){
+function setSeries(data, seriesInstanceUid, templateData){
     var study = data.study;
     study.seriesList.every(function(series) {
         if (series.seriesInstanceUid === seriesInstanceUid) {
@@ -493,24 +405,18 @@ Meteor.startup(function() {
 });
 
 Template.imageViewerViewport.onRendered(function() {
-
     var templateData = Template.currentData();
     log.info("imageViewerViewport onRendered");
 
     // When the imageViewerViewport template is rendered
     var element = this.find(".imageViewerViewport");
 
-
     // Display the loading indicator for this element
     $(element).siblings('.imageViewerLoadingIndicator').css('display', 'block');
 
     // Get the current active viewport index, if this viewport has the same index,
     // add the CSS 'active' class to highlight this viewport.
     var activeViewport = Session.get('activeViewport');
-    if (activeViewport === this.data.viewportIndex) {
-        $('#imageViewerViewports .viewportContainer').removeClass('active');
-        $(element).parents('.viewportContainer').addClass('active');
-    }
 
     // Create a data object to pass to the series loading function (loadSeriesIntoViewport)
     var data = {
@@ -550,14 +456,13 @@ Template.imageViewerViewport.onRendered(function() {
             }
             sortStudy(study);
             data.study = study;
+
             setSeries(data, seriesInstanceUid, templateData);
-            return;
         });
     }
 
     data.study = study;
     setSeries(data, seriesInstanceUid, templateData);
-
 });
 
 Template.imageViewerViewport.onDestroyed(function() {

Packages/viewerbase/lib/createStacks.js

@@ -16,7 +16,7 @@ createStacks = function(study) {
 
     // TODO: Split by multi-frame, modality, image size, etc
     study.seriesList.forEach(function(series) {
-        // If the series has no instanced, skip it
+        // If the series has no instances, skip it
         if (!series.instances) {
             return;
         }

Packages/viewerbase/lib/displayReferenceLines.js

@@ -8,6 +8,15 @@
 displayReferenceLines = function(element) {
     log.info("imageViewerViewport displayReferenceLines");
 
+    // Check if image plane (orientation / loction) data is present for the current image
+    var enabledElement = cornerstone.getEnabledElement(element);
+    var imageId = enabledElement.image.imageId;
+    var imagePlane = cornerstoneTools.metaData.get('imagePlane', imageId);
+
+    if (!OHIF.viewer.refLinesEnabled || !imagePlane || !imagePlane.frameOfReferenceUID) {
+        return;
+    }
+
     // Disable reference lines for the current element
     cornerstoneTools.referenceLines.tool.disable(element);
 

Packages/viewerbase/lib/setActiveViewport.js

@@ -17,4 +17,7 @@ setActiveViewport = function(element) {
     // the newly activated viewport
     enablePrefetchOnElement(element);
     displayReferenceLines(element);
+
+    // Set the div to focused, so keypress events are handled
+    $(element).focus();
 };

Packages/viewerbase/lib/toolManager.js

@@ -83,6 +83,9 @@ toolManager = {
     addTool: function(name, base) {
         tools[name] = base;
     },
+    getTools: function() {
+        return tools;
+    },
     setToolDefaultStates: function(states) {
         toolDefaultStates = states;
     },