Added data persistence for lesion measurements and timepoints

LesionTracker/.meteor/packages

@@ -16,7 +16,6 @@ standard-minifiers      # JS/CSS minifiers run for production mode
 es5-shim                # ECMAScript 5 compatibility for older browsers.
 ecmascript              # Enable ECMAScript2015+ syntax in app code
 
-autopublish             # Publish all data to the clients (for prototyping)
 insecure                # Allow all DB writes from clients (for prototyping)
 cornerstone
 worklist

LesionTracker/.meteor/versions

@@ -2,7 +2,6 @@ accounts-base@1.2.2
 accounts-password@1.1.4
 anti:i18n@0.4.3
 arsnebula:reactive-promise@0.9.1
-autopublish@1.0.4
 autoupdate@1.2.4
 babel-compiler@5.8.24_1
 babel-runtime@0.1.4

LesionTracker/client/components/viewer.js

@@ -16,12 +16,8 @@ function resizeViewports() {
     }, 1);
 }
 
-Template.viewer.helpers({
-    'studyDateIsShown':function(){
-        return {studyDateIsShown: true};
-    }
-});
 Template.viewer.onCreated(function() {
+    var self = this;
     log.info("viewer onCreated");
 
     OHIF = {
@@ -88,6 +84,7 @@ Template.viewer.onCreated(function() {
 
     Session.set('activeViewport', ViewerData[contentId].activeViewport || 0);
 
+
     // Update the ViewerStudies collection with the loaded studies
     ViewerStudies = new Meteor.Collection(null);
     this.data.studies.forEach(function(study) {
@@ -95,9 +92,53 @@ Template.viewer.onCreated(function() {
         ViewerStudies.insert(study);
     });
 
+    var patientId = this.data.studies[0].patientId;
+    Session.set('patientId', patientId);
+
+    timepointsAdded = false;
+    self.autorun(function() {
+        var patientId = Session.get('patientId');
+        self.subscribe('timepoints', patientId);
+        self.subscribe('measurements', patientId);
+
+        if (!self.subscriptionsReady()) {
+            return;
+        }
+
+        if (timepointsAdded === true) {
+            return;
+        }
+
+        ViewerStudies.find().forEach(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
+            });
+        });
+
+        timepointsAdded = true;
+    });
+
     OHIF.viewer.updateImageSynchronizer = new cornerstoneTools.Synchronizer("CornerstoneNewImage", cornerstoneTools.updateImageSynchronizer);
 });
 
+
 Template.viewer.onDestroyed(function() {
     log.info("onDestroyed");
     OHIF.viewer.updateImageSynchronizer.destroy();

Packages/lesiontracker/both/collections.js

@@ -0,0 +1,2 @@
+Timepoints = new Meteor.Collection('timepoints');
+Measurements = new Meteor.Collection('measurements');

Packages/lesiontracker/compatibility/lesionTool.js

@@ -1,5 +1,4 @@
 var activeLesionMeasurementData;
-var timepointID;
 var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneTools) {
 
     "use strict";
@@ -40,7 +39,7 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
         var measurementData = createNewMeasurement(mouseEventData);
 
         var eventData = {
-            mouseButtonMask: mouseEventData.which,
+            mouseButtonMask: mouseEventData.which
         };
         
         // associate this data with this imageId so we can render it and manipulate it
@@ -188,10 +187,6 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
             return;
         }
 
-        updateLesions(toolData, eventData);
-    }
-
-    function updateLesions(toolData, eventData) {
         // we have tool data for this element - iterate over each one and draw it
         var context = eventData.canvasContext.canvas.getContext('2d');
         context.setTransform(1, 0, 0, 1, 0, 0);

Packages/lesiontracker/compatibility/measurementManagerDAL.js

@@ -9,6 +9,10 @@ var measurementManagerDAL = (function() {
     // Add timepoint data to Measurements collection
     function addTimepointData(lesionData) {
         var timepoints = Timepoints.find().fetch();
+
+        var study = cornerstoneTools.metaData.get('study', lesionData.imageId);
+        var series = cornerstoneTools.metaData.get('study', lesionData.imageId);
+
         var timepointsObject = {};
 
         for (var i = 0; i < timepoints.length; i++) {
@@ -17,10 +21,12 @@ var measurementManagerDAL = (function() {
 
             var timepointObject;
             if (timepointId === lesionTimepointId) {
-                // Add real mesurement
+                // Add real measurement
                 timepointObject = {
                     longestDiameter: lesionData.measurementText,
                     imageId: lesionData.imageId,
+                    studyInstanceUid: study.instanceUid,
+                    seriesInstanceUid: series.instanceUid
                 };
             } else {
                 // Add null measurement
@@ -33,6 +39,7 @@ var measurementManagerDAL = (function() {
         }
 
         var lesionDataObject = {
+            patientId: timepoints[0].patientId,
             lesionUID: uuid.v4(),
             number: Measurements.find().count() + 1,
             lesionNumber: lesionData.lesionNumber,
@@ -47,10 +54,10 @@ var measurementManagerDAL = (function() {
     // Update timepoint data in Measurements collection
     function updateTimepointData(lesionData) {
         // Find the specific lesion to be updated
-        var measurement = Measurements.find({
+        var measurement = Measurements.findOne({
             lesionNumber: lesionData.lesionNumber,
             isTarget: lesionData.isTarget
-        }).fetch()[0];
+        });
 
         // If no such lesion exists, stop here
         if (!measurement) {
@@ -65,10 +72,7 @@ var measurementManagerDAL = (function() {
         timepoints[timepointID].longestDiameter = lesionData.measurementText;
         timepoints[timepointID].imageId = lesionData.imageId;
 
-        Measurements.update({
+        Measurements.update(measurement._id, {
-            lesionNumber: lesionData.lesionNumber,
-            isTarget: lesionData.isTarget
-        }, {
             $set: {
                 timepoints: timepoints
             }
@@ -81,13 +85,14 @@ var measurementManagerDAL = (function() {
             lesionNumber: lesionData.lesionNumber,
             isTarget: lesionData.isTarget
         });
+
         if (timepointData) {
             return true;
         }
         return false;
     }
 
-    // Adds new timepoint item to tiemepoints array
+    // Adds new timepoint item to timepoints array
     function addLesionData(lesionData) {
         if (hasTimepointData(lesionData)) {
             // Update data
@@ -115,6 +120,10 @@ var measurementManagerDAL = (function() {
             var measurement = measurements[i];
             var timepoints = measurement.timepoints;
 
+            if (!timepoints[timepointID]) {
+                return;
+            }
+
             if (timepoints[timepointID].longestDiameter === '') {
                 return measurement.lesionNumber;
             } else {
@@ -130,10 +139,10 @@ var measurementManagerDAL = (function() {
             return;
         }
 
-        var measurement = Measurements.find({
+        var measurement = Measurements.findOne({
             lesionNumber: lesionData.lesionNumber,
             isTarget: lesionData.isTarget
-        }).fetch()[0];
+        });
 
         return measurement.locationUID;
     }

Packages/lesiontracker/components/lesionLocationDialog/lesionLocationDialog.js

@@ -174,20 +174,6 @@ LesionLocations.insert({
     description: ""
 });
 
-var lastAddedLesionData;
-
-Template.lesionLocationDialog.onRendered(function() {
-    // Observe Measurements Collection Changes
-    Measurements.find().observe({
-        added: function(lesionData) {
-            lastAddedLesionData = lesionData;
-        },
-        changed: function(lesionData) {
-            console.log("lesionData has changed!");
-        }
-    });
-});
-
 Template.lesionLocationDialog.helpers({
     'lesionLocations': function() {
         return LesionLocations.find();

Packages/lesiontracker/components/lesionTable/lesionTable.js

@@ -1,17 +1,20 @@
-Measurements = new Meteor.Collection(null);
-Timepoints = new Meteor.Collection(null);
-
 // Activate selected lesions when lesion table row is clicked
 function updateLesions(e) {
     // lesionNumber of measurement = id of row
     var lesionNumber = parseInt($(e.currentTarget).attr("id"), 10);
+
+    // TODO= Clarify this
     var isTarget = $(e.currentTarget).find('td').eq(2).html().trim() === 'N'?false:true;
 
     // Find data for specific lesion
-    var measurementData = Measurements.find({
+    var measurementData = Measurements.findOne({
         lesionNumber: lesionNumber,
         isTarget: isTarget
-    }).fetch()[0];
+    });
+
+    if (!measurementData) {
+        return;
+    }
 
     var timepoints = measurementData.timepoints;
 
@@ -19,7 +22,14 @@ function updateLesions(e) {
         // Get the timepointID related to the image viewer viewport
         // from the DOM itself. This will be changed later when a
         // real association between viewports and timepoints is created.
-        var timepointID = $(element).data('timepointID');
+        var enabledElement = cornerstone.getEnabledElement(element);
+        var study = cornerstoneTools.metaData.get('study', enabledElement.image.imageId);
+        var timepoint = Timepoints.findOne({timepointName: study.date});
+        if (!timepoint) {
+            return;
+        }
+        var timepointID = timepoint.timepointID;
+
         var timepointObject = timepoints[timepointID];
 
         // Defines event data
@@ -54,28 +64,6 @@ function updateLesions(e) {
     });
 }
 
-Template.lesionTable.onRendered(function() {
-    // Observe ViewerStudies Collection Changes
-    // Note: This may not be the best place for this
-    ViewerStudies.find().observe({
-        added: function(study) {
-            log.info('ViewerStudies added to');
-            var timepointID = uuid.v4();
-
-            var timepoint = Timepoints.findOne({timepointName: study.studyDate});
-            if (timepoint) {
-                log.warn("A timepoint with that study date already exists!");
-                return;
-            }
-
-            Timepoints.insert({
-                timepointID: timepointID,
-                timepointName: study.studyDate
-            });
-        }
-    });
-});
-
 Template.lesionTable.helpers({
     'measurement': function() {
         return Measurements.find();

Packages/lesiontracker/components/lesionTableTimepointCell/lesionTableTimepointCell.js

@@ -2,6 +2,12 @@ Template.lesionTableTimepointCell.helpers({
     'longestDiameter': function() {
         // Search Measurements by lesion and timepoint
         var lesionData = Template.parentData(1);
+        if (!lesionData ||
+            !lesionData.timepoints ||
+            !lesionData.timepoints[this.timepointID]) {
+            return;
+        }
+
         return lesionData.timepoints[this.timepointID].longestDiameter;
     }
 });

Packages/lesiontracker/components/nonTargetLesionDialog/nonTargetLesionDialog.js

@@ -1,8 +1,16 @@
 // This event sets lesion number for new lesion
 
 function setLesionNumberCallback(measurementData, eventData, doneCallback) {
+    // Get the current element's timepointID from the study date metadata
+    var element = eventData.element;
+    var enabledElement = cornerstone.getEnabledElement(element);
+    var study = cornerstoneTools.metaData.get('study', enabledElement.image.imageId);
+    var timepoint = Timepoints.findOne({timepointName: study.date});
+    if (!timepoint) {
+        return;
+    }
+    measurementData.timepointID = timepoint.timepointID;
 
-    measurementData.timepointID = $(eventData.element).data('timepointID');
     // 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);
@@ -16,7 +24,7 @@ function setLesionNumberCallback(measurementData, eventData, doneCallback) {
 // If there already exists a lesion with this specific lesion number,
 // related to the chosen location.
 
-function getNonTargetLesionLocationCallback(measurementData, eventData, doneCallback) {
+function getNonTargetLesionLocationCallback(measurementData, eventData) {
 
     // Get the non-target lesion location dialog
     var nonTargetlesionDialog = $("#nonTargetLesionLocationDialog");

Packages/lesiontracker/components/studyDateList/studyDateList.js

@@ -83,6 +83,27 @@ Template.studyDateList.events({
             // with the value True, and insert it into the ViewerStudies Collection
             study.selected = true;
             ViewerStudies.insert(study);
+
+            var timepointID = uuid.v4();
+
+            var timepoint = Timepoints.findOne({timepointName: study.studyDate});
+            if (timepoint) {
+                log.warn("A timepoint with that study date already exists!");
+                return;
+            }
+
+            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
+            });
         });
     }
 });

Packages/lesiontracker/log.js

@@ -0,0 +1,3 @@
+// Create package logger using loglevel
+// https://atmospherejs.com/spacejamio/loglevel
+log = loglevel.createPackageLogger('lesiontracker', defaultLevel = 'info');

Packages/lesiontracker/package.js

@@ -10,10 +10,13 @@ Package.onUse(function (api) {
     api.use('standard-app-packages');
     api.use('jquery');
     api.use('stylus');
+    api.use('practicalmeteor:loglevel');
 
     // Our custom package
     api.use('cornerstone');
 
+    api.addFiles('log.js', ['client', 'server']);
+
     api.addFiles('compatibility/lesionTool.js', 'client', {bare: true});
     api.addFiles('compatibility/nonTargetTool.js', 'client', {bare: true});
     api.addFiles('compatibility/measurementManagerDAL.js', 'client', {bare: true});
@@ -43,14 +46,15 @@ Package.onUse(function (api) {
     api.addFiles('components/studyDateList/studyDateList.styl', 'client');
     api.addFiles('components/studyDateList/studyDateList.js', 'client');
 
+    // Server functions
+    api.addFiles('server/collections.js', 'server');
 
-
+    // Both client and server functions
-
+    api.addFiles('both/collections.js', ['client', 'server']);
 
     // Library functions
     api.addFiles('lib/uuid.js', 'client');
 
-    api.export('Measurements', 'client');
+    api.export('Measurements', ['client', 'server']);
-    api.export('Timepoints', 'client');
+    api.export('Timepoints', ['client', 'server']);
-
 });

Packages/lesiontracker/server/collections.js

@@ -0,0 +1,24 @@
+Meteor.publish('timepoints', function(patientId) {
+    console.log('Publish timepoints');
+    console.log('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});
+});
+
+
+// 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){
+            object.remove({});
+        }
+    }
+});

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

@@ -190,7 +190,6 @@ function thumbnailDragEndHandler(e, target) {
 }
 
 Template.thumbnailEntry.onRendered(function() {
-    console.log(this.data);
     var entry = this.find('.thumbnailEntry');
     $(entry).data('seriesInstanceUid', Template.parentData(0).seriesInstanceUid);
     $(entry).data('studyInstanceUid', Template.parentData(1).studyInstanceUid);