Added persistent single-image measurments (length, ellipse) (LT-37, LT-156)

LesionTracker/client/components/viewer.js

@@ -115,6 +115,7 @@ Template.viewer.onCreated(function() {
         self.subscribe('singlePatientAssociatedStudies', dataContext.studies[0].patientId);
         self.subscribe('singlePatientTimepoints', dataContext.studies[0].patientId);
         self.subscribe('singlePatientMeasurements', dataContext.studies[0].patientId);
+        self.subscribe('singlePatientImageMeasurements', dataContext.studies[0].patientId);
 
         var subscriptionsReady = self.subscriptionsReady();
         log.info('autorun viewer.js. Ready: ' + subscriptionsReady);
@@ -145,6 +146,39 @@ Template.viewer.onCreated(function() {
                 }
             });
 
+            ImageMeasurements.find().observe({
+                added: function(data) {
+                    if (data.clientId === ClientId) {
+                        return;
+                    }
+
+                    syncImageMeasurementAndToolData(data);
+
+                    // Update each displayed viewport
+                    updateAllViewports();
+                },
+                changed: function(data) {
+                    if (data.clientId === ClientId) {
+                        return;
+                    }
+
+                    syncImageMeasurementAndToolData(data);
+
+                    // Update each displayed viewport
+                    updateAllViewports();
+                },
+                removed: function(data) {
+                    if (data.clientId === ClientId) {
+                        return;
+                    }
+
+                    removeToolDataWithMeasurementId(data.imageId, data.toolType, data.id);
+
+                    // Update each displayed viewport
+                    updateAllViewports();
+                }
+            });
+
             Measurements.find().observe({
                 added: function(data) {
                     if (data.clientId === ClientId) {
@@ -170,10 +204,7 @@ Template.viewer.onCreated(function() {
                     }
 
                     // Update each displayed viewport
-                    var viewports = $('.imageViewerViewport').not('.empty');
+                    updateAllViewports();
-                    viewports.each(function(index, element) {
-                        cornerstone.updateImage(element);
-                    });
                 },
                 changed: function(data) {
                     if (data.clientId === ClientId) {
@@ -188,10 +219,7 @@ Template.viewer.onCreated(function() {
                     syncMeasurementAndToolData(data);
 
                     // Update each displayed viewport
-                    var viewports = $('.imageViewerViewport').not('.empty');
+                    updateAllViewports();
-                    viewports.each(function(index, element) {
-                        cornerstone.updateImage(element);
-                    });
 
                     TrialResponseCriteria.validateAllDelayed();
                 },
@@ -235,10 +263,7 @@ Template.viewer.onCreated(function() {
                     });
 
                     // Update each displayed viewport
-                    var viewports = $('.imageViewerViewport').not('.empty');
+                    updateAllViewports();
-                    viewports.each(function(index, element) {
-                        cornerstone.updateImage(element);
-                    });
 
                     ValidationErrors.remove({
                         measurementId: data._id

LesionTracker/client/components/viewerMain/viewerMain.js

@@ -46,6 +46,13 @@ Template.viewerMain.helpers({
             iconClasses: 'fa fa-arrows-v'
         });
 
+        buttonData.push({
+            id: 'ellipticalRoi',
+            title: 'Elliptical ROI Measurement',
+            classes: 'imageViewerTool',
+            iconClasses: 'fa fa-circle-o'
+        });
+
         buttonData.push({
             id: 'lesion',
             title: 'Target Tool',

Packages/cornerstone/client/cornerstoneTools.js

@@ -3136,6 +3136,8 @@ if (typeof cornerstoneTools === 'undefined') {
 
                 if (!isNaN(meanStdDev.mean) && !isNaN(meanStdDev.stdDev)) {
                     data.meanStdDev = meanStdDev;
+                    data.mean = meanStdDev.mean;
+                    data.stdev = meanStdDev.stdev;
                 }
             }
 
@@ -3985,6 +3987,9 @@ if (typeof cornerstoneTools === 'undefined') {
             // Calculate the length, and create the text variable with the millimeters or pixels suffix            
             var length = Math.sqrt(dx * dx + dy * dy);
 
+            // Store the length inside the tool for outside access
+            data.length = length;
+
             // Set the length text suffix depending on whether or not pixelSpacing is available
             var suffix = ' mm';
             if (!eventData.image.rowPixelSpacing || !eventData.image.columnPixelSpacing) {
@@ -6646,7 +6651,7 @@ if (typeof cornerstoneTools === 'undefined') {
             // If any handle is outside the image, delete the tool data
             if (options.deleteIfHandleOutsideImage === true &&
                 cornerstoneTools.anyHandlesOutsideImage(eventData, data.handles)) {
-                cornerstoneTools.toolState.removeToolState(element, toolType, data);
+                cornerstoneTools.removeToolState(element, toolType, data);
             }
 
             cornerstone.updateImage(element);

Packages/lesiontracker/both/collections.js

@@ -1,5 +1,6 @@
 Timepoints = new Meteor.Collection('timepoints');
 Studies = new Meteor.Collection('studies');
 Measurements = new Meteor.Collection('measurements');
+ImageMeasurements = new Meteor.Collection('imageMeasurements');
 
 WorklistSubscriptions = ['studies', 'timepoints'];

Packages/lesiontracker/client/compatibility/lesionTool.js

@@ -99,7 +99,8 @@
             longestDiameter: 0,
             shortestDiameter: 0,
             isDeleted: false,
-            isTarget: true
+            isTarget: true,
+            measurementType: 'bidirectional'
         };
         return measurementData;
     }

Packages/lesiontracker/client/compatibility/nonTargetTool.js

@@ -153,7 +153,8 @@
             studyInstanceUid: studyInstanceUid,
             patientId: patientId,
             response: '',
-            isTarget: false
+            isTarget: false,
+            measurementType: 'nonTarget'
         };
 
         return measurementData;

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

@@ -1,7 +1,14 @@
 Template.lesionTable.helpers({
     measurement: function() {
         // All Targets shall be listed first followed by Non-Targets
-        return Measurements.find({}, {
+        return Measurements.find({
+            measurementType: {
+                $in: [
+                    'bidirectional',
+                    'nonTarget'
+                ]
+            }
+        }, {
             sort: {
                 isTarget: -1,
                 lesionNumberAbsolute: 1

Packages/lesiontracker/lib/LesionManager.js

@@ -1,3 +1,17 @@
+measurementValuesByType = {
+    bidirectional: [
+        'shortestDiameter',
+        'longestDiameter'
+    ],
+    nonTarget: ['response'],
+    length: ['length'],
+    ellipticalRoi: [
+        'area',
+        'mean',
+        'stdev'
+    ]
+};
+
 /**
  * Update the Timepoint object for a specific Measurement.
  * If no measurement exists yet, one will be created.
@@ -46,13 +60,18 @@ function updateLesionData(lesionData) {
         imageId: lesionData.imageId
     };
 
-    if (lesionData.isTarget === true) {
+    if (!lesionData.measurementType) {
-        timepointData.shortestDiameter = lesionData.shortestDiameter;
+        // For debugging
-        timepointData.longestDiameter = lesionData.longestDiameter;
+        log.warn('No MeasurementType available?');
-    } else {
-        timepointData.response = lesionData.response;
     }
 
+    // Populate this timepoint's data with whichever values
+    // are stored for this Measurement type
+    var values = measurementValuesByType[lesionData.measurementType];
+    values.forEach(function(valueName) {
+        timepointData[valueName] = lesionData[valueName];
+    });
+
     // If no such lesion exists, we need to add one
     if (!existingMeasurement) {
         // Create a data structure for the Measurement

Packages/lesiontracker/lib/TrialResponseCriteria.js

@@ -233,7 +233,6 @@ function validateSingleMeasurement(measurementData) {
 
     // If no such Measurement exists, stop here
     if (!measurement) {
-        log.warn('No Measurement found?');
         return;
     }
 

Packages/lesiontracker/lib/clearTools.js

@@ -1,6 +1,6 @@
 clearTools = function() {
     var patientId = Session.get('patientId');
-    var toolTypes = [ 'lesion', 'nonTarget', 'length' ];
+    var toolTypes = [ 'lesion', 'nonTarget', 'length', 'ellipticalRoi'];
     var toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
     var toolStateKeys = Object.keys(toolState).slice(0);
 
@@ -43,6 +43,7 @@ clearTools = function() {
 
     // Remove patient's measurements
     Meteor.call('removeMeasurementsByPatientId', patientId);
+    Meteor.call('removeImageMeasurementsByPatientId', patientId);
 
     // Clear all validation errors
     ValidationErrors.remove({});

Packages/lesiontracker/lib/handleMeasurementAdded.js

@@ -7,6 +7,27 @@ handleMeasurementAdded = function(e, eventData) {
             log.info('CornerstoneToolsMeasurementAdded');
             LesionManager.updateLesionData(measurementData);
             TrialResponseCriteria.validateDelayed(measurementData);
+            break;
+        case 'ellipticalRoi':
+        case 'length':
+            var enabledElement = cornerstone.getEnabledElement(eventData.element);
+            var imageId = enabledElement.image.imageId;
+
+            // Get the studyInstanceUid and series metaData
+            var study = cornerstoneTools.metaData.get('study', imageId);
+            var series = cornerstoneTools.metaData.get('series', imageId);
+
+            // Add the relevant metaData to this ImageMeasurement's toolData
+            measurementData.clientId = ClientId;
+            measurementData.imageId = imageId;
+            measurementData.measurementType = eventData.toolType;
+            measurementData.patientId = study.patientId;
+            measurementData.studyInstanceUid = study.studyInstanceUid;
+            measurementData.seriesInstanceUid = series.seriesInstanceUid;
+
+            // Create the ImageMeasurement in the database
+            measurementData._id = ImageMeasurements.insert(measurementData);
+
             break;
     }
 };

Packages/lesiontracker/lib/handleMeasurementModified.js

@@ -8,5 +8,31 @@ handleMeasurementModified = function(e, eventData) {
             LesionManager.updateLesionData(measurementData);
             TrialResponseCriteria.validateDelayed(measurementData);
             break;
+        case 'ellipticalRoi':
+        case 'length':
+            var enabledElement = cornerstone.getEnabledElement(eventData.element);
+            var imageId = enabledElement.image.imageId;
+
+            // Get the studyInstanceUid and series metaData
+            var study = cornerstoneTools.metaData.get('study', imageId);
+            var series = cornerstoneTools.metaData.get('series', imageId);
+
+            // Add the relevant metaData to this ImageMeasurement's toolData
+            measurementData.clientId = ClientId;
+            measurementData.imageId = imageId;
+            measurementData.measurementType = eventData.toolType;
+            measurementData.patientId = study.patientId;
+            measurementData.studyInstanceUid = study.studyInstanceUid;
+            measurementData.seriesInstanceUid = series.seriesInstanceUid;
+            var toUpdate = $.extend({}, measurementData);
+
+            // Remove the Mongo _id otherwise it will complain when we try to 'mod' it.
+            delete toUpdate._id;
+
+            // Update the ImageMeasurement in the database
+            ImageMeasurements.update(measurementData._id, {
+                $set: toUpdate
+            });
+            break;
     }
 };

Packages/lesiontracker/lib/removeToolDataWithMeasurementId.js

@@ -15,13 +15,14 @@ removeToolDataWithMeasurementId = function(imageId, toolType, measurementId) {
     // Search toolData for entries linked to the specified Measurement
     var toRemove = [];
     toolData.forEach(function(measurement, index) {
-        if (measurement.id === measurementId) {
+        if (measurement.id === measurementId ||
+            measurement._id === measurementId) {
             toRemove.push(index);
             return false;
         }
     });
 
-    log.info("Removing Indices: ");
+    log.info('Removing Indices: ');
     log.info(toRemove);
 
     // If any toolData entries need to be removed, splice them from

Packages/lesiontracker/lib/syncImageMeasurementAndToolData.js

@@ -0,0 +1,59 @@
+syncImageMeasurementAndToolData = function(measurement) {
+    // TODO: Refactor this to merge it with syncMeasurementAndToolData somehow
+    log.info('syncImageMeasurementAndToolData');
+
+    var toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
+
+    var imageId = measurement.imageId;
+    var toolType = measurement.measurementType;
+
+    // If no tool state exists for this imageId, create an empty object to store it
+    if (!toolState[imageId]) {
+        toolState[imageId] = {};
+    }
+
+    // Check if we already have toolData for this imageId and toolType
+    if (toolState[imageId][toolType] &&
+        toolState[imageId][toolType].data &&
+        toolState[imageId][toolType].data.length) {
+        // If we have toolData, we should search it for any toolData
+        // related to the current ImageMeasurement
+        var toolData = toolState[imageId][toolType].data;
+
+        // Create a flag so we know if we have successfully updated
+        // this ImageMeasurement's timepoint data in the toolData
+        var alreadyExists = false;
+
+        // Loop through the toolData to search for this ImageMeasurement
+        toolData.forEach(function(tool) {
+            // Break the loop if this isn't the ImageMeasurement we are looking for
+            if (tool._id !== measurement._id) {
+                return;
+            }
+
+            // If we find the ImageMeasurement, set the flag to True
+            alreadyExists = true;
+
+            // Update the toolData from the ImageMeasurement data
+            $.extend(tool, measurement);
+            return false;
+        });
+
+        // If we found the ImageMeasurement we intended to update, we can stop
+        // this function here
+        if (alreadyExists === true) {
+            return;
+        }
+    } else {
+        // If no toolData exists for this toolType, create an empty array to hold some
+        toolState[imageId][toolType] = {
+            data: []
+        };
+    }
+
+    // If we have reached this point, it means we haven't found the ImageMeasurement we are
+    // looking for in the current toolData. This means we need to add it.
+
+    // Add the ImageMeasurementData into the toolData for this imageId
+    toolState[imageId][toolType].data.push(measurement);
+};

Packages/lesiontracker/package.js

@@ -146,6 +146,7 @@ Package.onUse(function(api) {
     api.addFiles('lib/calculateTotalLesionBurden.js', 'client');
 
     api.addFiles('lib/syncMeasurementAndToolData.js', 'client');
+    api.addFiles('lib/syncImageMeasurementAndToolData.js', 'client');
     api.addFiles('lib/updateRelatedElements.js', 'client');
 
     api.addFiles('lib/handleMeasurementAdded.js', 'client');
@@ -159,6 +160,7 @@ Package.onUse(function(api) {
     api.export('handleMeasurementModified', 'client');
     api.export('handleMeasurementRemoved', 'client');
     api.export('syncMeasurementAndToolData', 'client');
+    api.export('syncImageMeasurementAndToolData', 'client');
     api.export('updateRelatedElements', 'client');
     api.export('openNewTabWithTimepoint', 'client');
     api.export('activateLesion', 'client');
@@ -184,6 +186,7 @@ Package.onUse(function(api) {
     api.export('LocationResponses', 'client');
 
     // Export collections spanning both client and server
+    api.export('ImageMeasurements', [ 'client', 'server' ]);
     api.export('Measurements', [ 'client', 'server' ]);
     api.export('Studies', [ 'client', 'server' ]);
     api.export('Timepoints', [ 'client', 'server' ]);

Packages/lesiontracker/server/collections.js

@@ -24,6 +24,12 @@ Meteor.publish('singlePatientMeasurements', function(patientId) {
     });
 });
 
+Meteor.publish('singlePatientImageMeasurements', function(patientId) {
+    return ImageMeasurements.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() {

Packages/lesiontracker/server/removeCollections.js

@@ -44,6 +44,11 @@ Meteor.methods({
             patientId: patientId
         });
     },
+    removeImageMeasurementsByPatientId: function(patientId) {
+        ImageMeasurements.remove({
+            patientId: patientId
+        });
+    },
     clearAllTimepoints: function() {
         Timepoints.remove({});
     },

Packages/viewerbase/lib/updateAllViewports.js

@@ -0,0 +1,6 @@
+updateAllViewports = function() {
+    var viewports = $('.imageViewerViewport').not('.empty');
+    viewports.each(function(index, element) {
+        cornerstone.updateImage(element);
+    });
+};

Packages/viewerbase/lib/viewportFunctions.js

@@ -1,5 +1,5 @@
 getActiveViewportElement = function() {
-    var viewportIndex = Session.get("activeViewport");
+    var viewportIndex = Session.get("activeViewport") || 0;
     return $('.imageViewerViewport').get(viewportIndex);
 };
 

Packages/viewerbase/package.js

@@ -1,10 +1,10 @@
 Package.describe({
-  name: "viewerbase",
+    name: 'viewerbase',
-  summary: "Shared components and functions for Meteor DICOM Viewers",
+    summary: 'Shared components and functions for Meteor DICOM Viewers',
-  version: '0.0.1'
+    version: '0.0.1'
 });
 
-Package.onUse(function (api) {
+Package.onUse(function(api) {
     api.versionsFrom('1.2.0.2');
 
     api.use('standard-app-packages');
@@ -27,7 +27,6 @@ Package.onUse(function (api) {
     // TODO= Find a meteor package for this
     api.addFiles('client/compatibility/jquery.hotkeys.js', 'client');
 
-
     // ---------- Collections ----------
     api.addFiles('client/collections.js', 'client');
 
@@ -128,12 +127,12 @@ Package.onUse(function (api) {
     api.addFiles('lib/WLPresets.js', 'client');
     api.addFiles('lib/resizeViewportElements.js', 'client');
     api.addFiles('lib/setFocusToActiveViewport.js', 'client');
+    api.addFiles('lib/updateAllViewports.js', 'client');
     api.addFiles('lib/encodeQueryData.js', 'server');
 
-
     //api.export('accountsConfig', 'client');
-    api.export('resizeViewportElements','client');
+    api.export('resizeViewportElements', 'client');
-    api.export('handleResize','client');
+    api.export('handleResize', 'client');
     api.export('enableHotkeys', 'client');
     api.export('enablePrefetchOnElement', 'client');
     api.export('displayReferenceLines', 'client');
@@ -146,6 +145,7 @@ Package.onUse(function (api) {
     api.export('sortStudy', 'client');
     api.export('updateOrientationMarkers', 'client');
     api.export('setFocusToActiveViewport', 'client');
+    api.export('updateAllViewports', 'client');
     api.export('encodeQueryData', 'server');
 
     // Viewer management objects