Measurements and Timepoint interaction in Lesion Table and tools

Packages/lesiontracker/compatibility/lesionTool.js

@@ -1,26 +1,24 @@
-var lineIndex = 0; //This holds drawn line index
 var activeLesionMeasurementData;
 var timepointID;
-var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTools) {
+var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneTools) {
 
     "use strict";
 
-    if(cornerstoneTools === undefined) {
+    if (cornerstoneTools === undefined) {
         cornerstoneTools = {};
     }
 
     var toolType = "lesion";
 
     ///////// BEGIN ACTIVE TOOL ///////
-    function createNewMeasurement(mouseEventData)
-    {
+    function createNewMeasurement(mouseEventData) {
         var element = mouseEventData.element;
-        timepointID = getActiveTimepointID(element);
-        var lesionNumber = measurementManagerDAL.getLesionNumber(timepointID);
+        timepointID = $(element).data('timepointID');
+        var lesionNumber = measurementManagerDAL.getNewLesionNumber(timepointID);
         var lesionCounter = "";
 
         // Subscribe CornerstoneMouseup event, when mouse is up, call lesionDialog
-        $(element).on("CornerstoneToolsMouseUp", function (e) {
+        $(element).on("CornerstoneToolsMouseUp", function(e) {
 
             // Unsubscribe CornerstoneToolsMouseUp event
             $(element).off("CornerstoneToolsMouseUp");
@@ -31,11 +29,10 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
 
             // Show LesionDialog
             $(document).trigger("ShowLesionDialog", [e, activeLesionMeasurementData]);
-
         });
 
         // Set Lesion Name
-        $(element).on("LesionNameSet", function(e,lesionName){
+        $(element).on("LesionNameSet", function(e, lesionName) {
             lesionCounter = lesionName;
         });
 
@@ -45,55 +42,52 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
         console.log(mouseEventData.image.imageId);
         // create the measurement data for this tool with the end handle activated
         var measurementData = {
-            visible : true,
-            active : true,
-            handles : {
-                start : {
-                    x : mouseEventData.currentPoints.image.x,
-                    y : mouseEventData.currentPoints.image.y,
+            visible: true,
+            active: true,
+            handles: {
+                start: {
+                    x: mouseEventData.currentPoints.image.x,
+                    y: mouseEventData.currentPoints.image.y,
                     highlight: true,
                     active: false
                 },
                 end: {
-                    x : mouseEventData.currentPoints.image.x,
-                    y : mouseEventData.currentPoints.image.y,
+                    x: mouseEventData.currentPoints.image.x,
+                    y: mouseEventData.currentPoints.image.y,
                     highlight: true,
                     active: true
                 }
             },
-            index: lineIndex,
             imageId: mouseEventData.image.imageId,
-            measurementText: "",
+            measurementText: 0,
             linkedTextCoords: {
-                start : {
-                    x : mouseEventData.currentPoints.image.x,
-                    y : mouseEventData.currentPoints.image.y,
+                start: {
+                    x: mouseEventData.currentPoints.image.x,
+                    y: mouseEventData.currentPoints.image.y,
                     highlight: true,
                     active: false
                 },
                 end: {
-                    x : mouseEventData.currentPoints.image.x,
-                    y : mouseEventData.currentPoints.image.y,
+                    x: mouseEventData.currentPoints.image.x,
+                    y: mouseEventData.currentPoints.image.y,
                     highlight: true,
                     active: true
                 },
                 init: false
             },
-            lesionName: "Target "+lesionNumber,
+            lesionName: "Target " + lesionNumber,
             isDeleted: false,
-            lineNumber:"", //Indicates line number on image
             lesionNumber: lesionNumber,
             uid: uuid.v4()
         };
-        lineIndex++;
         return measurementData;
     }
     ///////// END ACTIVE TOOL ///////
 
-    function pointNearTool(element, data, coords)
-    {
+    function pointNearTool(element, data, coords) {
         var lineSegment = {
-            start: cornerstone.pixelToCanvas(element, data.handles.start), end: cornerstone.pixelToCanvas(element, data.handles.end)
+            start: cornerstone.pixelToCanvas(element, data.handles.start),
+            end: cornerstone.pixelToCanvas(element, data.handles.end)
         };
         var distanceToPoint = cornerstoneMath.lineSegment.distanceToPoint(lineSegment, coords);
         return (distanceToPoint < 25);
@@ -101,7 +95,8 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
 
     function pointNearToolForText(element, data, coords) {
         var lineSegment = {
-            start: cornerstone.pixelToCanvas(element, data.linkedTextCoords.start), end: cornerstone.pixelToCanvas(element, data.linkedTextCoords.end)
+            start: cornerstone.pixelToCanvas(element, data.linkedTextCoords.start),
+            end: cornerstone.pixelToCanvas(element, data.linkedTextCoords.end)
         };
 
         var distanceToPoint = cornerstoneMath.lineSegment.distanceToPoint(lineSegment, coords);
@@ -109,8 +104,8 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
 
     }
 
-    function suscribeLesionToolModifiedEvent (element) {
-        var elementEvents = $._data(element, "events" );
+    function suscribeLesionToolModifiedEvent(element) {
+        var elementEvents = $._data(element, "events");
         var index = Object.keys(elementEvents).indexOf("LesionToolModified");
         if (index < 0) {
             // Subscribe LesionToolModified and calls measurementModified function when lesion measurement is changed or updated.
@@ -125,7 +120,7 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
 
         // if we have no toolData for this element, return immediately as there is nothing to do
         var toolData = cornerstoneTools.getToolState(e.currentTarget, toolType);
-        if (toolData === undefined) {
+        if (!toolData) {
             return;
         }
 
@@ -146,7 +141,7 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
     function updateLesionCollection(lesionData, currentElement) {
 
         if (lesionData.active) {
-            if(lesionData.timepointID !== undefined && lesionData.timepointID !== "") {
+            if (lesionData.timepointID !== undefined && lesionData.timepointID !== "") {
                 // Update Measurements Collection
                 measurementManagerDAL.updateTimepointData(lesionData);
 
@@ -156,13 +151,13 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
         }
     }
 
-    function renderLesion(lesion, context, eventData){
+    function renderLesion(lesion, context, eventData) {
         context.save();
 
         var color;
         var lineWidth = cornerstoneTools.toolStyle.getToolWidth();
         var font = cornerstoneTools.textStyle.getFont();
-        var config = cornerstoneTools.length.getConfiguration();
+        var config = cornerstoneTools.lesion.getConfiguration();
 
         // configurable shadow from CornerstoneTools
         if (config && config.shadow) {
@@ -194,7 +189,7 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
         //Set coordinates of text
         var linkedTextStartCanvas = cornerstone.pixelToCanvas(eventData.element, lesion.linkedTextCoords.start);
         var linkedTextEndCanvas = cornerstone.pixelToCanvas(eventData.element, lesion.linkedTextCoords.end);
-        if(!lesion.linkedTextCoords.init){
+        if (!lesion.linkedTextCoords.init) {
             lesion.linkedTextCoords.start.x = lesion.handles.start.x + 50;
             lesion.linkedTextCoords.start.y = lesion.handles.start.y + 40;
             linkedTextStartCanvas = cornerstone.pixelToCanvas(eventData.element, lesion.linkedTextCoords.start);
@@ -209,12 +204,13 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
         }
 
         //Draw linked line as dashed
-        context.setLineDash([2,3]);
+        context.setLineDash([2, 3]);
         context.beginPath();
         context.strokeStyle = color;
         context.lineWidth = 1 / eventData.viewport.scale;
         var mid = {
-            x:(handleStartCanvas.x + handleEndCanvas.x) / 2, y:(handleStartCanvas.y + handleEndCanvas.y) / 2
+            x: (handleStartCanvas.x + handleEndCanvas.x) / 2,
+            y: (handleStartCanvas.y + handleEndCanvas.y) / 2
         };
 
         context.moveTo(mid.x, mid.y);
@@ -235,17 +231,18 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
 
         var text = '' + length.toFixed(2) + suffix;
         var textCoords = {
-            x:  linkedTextStartCanvas.x, y: linkedTextStartCanvas.y
+            x: linkedTextStartCanvas.x,
+            y: linkedTextStartCanvas.y
         };
 
         cornerstoneTools.drawTextBox(context, lesion.lesionName, textCoords.x, textCoords.y, color);
         cornerstoneTools.drawTextBox(context, text, textCoords.x, textCoords.y + 20, color);
 
-        //Set measurement text to show lesion table
-        lesion.measurementText = length.toFixed(2);
+        // Set measurement text to show lesion table
+        lesion.measurementText = length.toFixed(1);
 
         // Lesion Measurement is changed
-        $(eventData.enabledElement.element).trigger("LesionTextChanged",lesion);
+        $(eventData.enabledElement.element).trigger("LesionTextChanged", lesion);
 
         context.restore();
     }
@@ -266,7 +263,7 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
         }
 
         //If type is delete, remove measurement
-        if(type === "delete") {
+        if (type === "delete") {
             var deletedDataIndex = -1;
 
             for (var i = 0; i < toolData.data.length; i++) {
@@ -282,17 +279,17 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
             if (deletedDataIndex >= 0 && deletedDataIndex < toolData.data.length) {
                 toolData.data.splice(deletedDataIndex, 1);
             }
-        } else if(type === "active") {
+        } else if (type === "active") {
             for (var i = 0; i < toolData.data.length; i++) {
                 var data = toolData.data[i];
                 //When click a row of table measurements, measurement will be active and color will be green
                 if (data.lesionNumber === eventObject.lesionData.lesionNumber && eventObject.type === "active") {
                     data.active = true;
-                } else{
+                } else {
                     data.active = false;
                 }
             }
-        } else if(type === "inactive") {
+        } else if (type === "inactive") {
             for (var i = 0; i < toolData.data.length; i++) {
                 var data = toolData.data[i];
                 // Make inactive all lesions for the timepoint
@@ -310,15 +307,15 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
         //console.log(diff + ' ms');
 
         var eventData = {
-            viewport : enabledElement.viewport,
-            element : enabledElement.element,
-            image : enabledElement.image,
-            enabledElement : enabledElement,
+            viewport: enabledElement.viewport,
+            element: enabledElement.element,
+            image: enabledElement.image,
+            enabledElement: enabledElement,
             canvasContext: context,
             measurementText: "",
-            renderTimeInMs : diff,
-            lesionNumber : lesionNumber,
-            type : type //Holds image will be deleted or active
+            renderTimeInMs: diff,
+            lesionNumber: lesionNumber,
+            type: type //Holds image will be deleted or active
         };
 
         enabledElement.invalid = false;
@@ -339,11 +336,11 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
             var indexOfImage = imageIdsArr.indexOf(eventObject.lesionData.imageId);
             if (indexOfImage > -1) {
                 cornerstone.loadAndCacheImage(stackData.imageIds[indexOfImage]).then(function(image) {
-                    cornerstone.displayImage(eventObject.enabledElement.element,image);
+                    cornerstone.displayImage(eventObject.enabledElement.element, image);
                     updateLesion(e, eventObject);
                 });
             }
-        } else if(eventObject.type === "inactive") {
+        } else if (eventObject.type === "inactive") {
             updateLesion(e, eventObject);
         }
 
@@ -351,17 +348,17 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
     }
 
     //This function is called from cornerstone-viewport.html and updates lesion measurement and makes the lesion active
-    function measurementModified(e, eventObject){
-        loadImage(e,eventObject);
+    function measurementModified(e, eventObject) {
+        loadImage(e, eventObject);
     }
 
     // module exports
     cornerstoneTools.lesion = cornerstoneTools.mouseButtonTool({
-        createNewMeasurement : createNewMeasurement,
+        createNewMeasurement: createNewMeasurement,
         onImageRendered: onImageRendered,
-        pointNearTool : pointNearTool,
+        pointNearTool: pointNearTool,
         pointNearToolForText: pointNearToolForText,
-        toolType : toolType
+        toolType: toolType
     });
     cornerstoneTools.lesionTouch = cornerstoneTools.touchTool({
         createNewMeasurement: createNewMeasurement,
@@ -371,4 +368,5 @@ var cornerstoneTools = (function ($, cornerstone, cornerstoneMath, cornerstoneTo
         toolType: toolType
     });
     return cornerstoneTools;
+
 }($, cornerstone, cornerstoneMath, cornerstoneTools));

Packages/lesiontracker/compatibility/measurementManagerDAL.js

@@ -1,203 +1,165 @@
-var measurementManagerDAL =  (function () {
+var measurementManagerDAL = (function() {
     var trialPatientLocations = [];
-    var timepoints = [];
 
     // Returns trialPatientLocations array
-    function getPatientLocations () {
+    function getPatientLocations() {
         return trialPatientLocations;
     }
 
-    function getLocationName (locationUID) {
-        for(var i = 0; i< trialPatientLocations.length; i++) {
+    function getLocationName(locationUID) {
+        for (var i = 0; i < trialPatientLocations.length; i++) {
             var locationObject = trialPatientLocations[i];
-            if(locationObject.uid === locationUID) {
+            if (locationObject.uid === locationUID) {
                 return locationObject.location.location;
             }
         }
-
         return "";
     }
 
-    function getTimepoints() {
-        return timepoints;
-    }
-
     // Adds new location to trialPatientLocations array
-    function addPatientLocation (location) {
-        var contentId = getContentId();
+    function addPatientLocation(location) {
         var locationUID = uuid.v4();
-        var locationObject = {contentId: contentId, uid: locationUID, location: location};
+        var locationObject = {
+            uid: locationUID,
+            location: location
+        };
         trialPatientLocations.push(locationObject);
-
         return locationUID;
     }
 
-    function getContentId () {
-        return Session.get("activeContentId");
-    }
-
-    function getTimepointsOfTab (){
-        var contentId = getContentId();
-        var tabData = TabsTimepoints.find({contentId: contentId}).fetch();
-        return tabData[0].timepoints;
-    }
-
     // Add timepoint data to Measurements collection
     function addTimepointData(lesionData) {
+        var timepoints = Timepoints.find().fetch();
+        var timepointsObject = {};
 
-        var contentId = getContentId();
-        var timepointsOfTab = getTimepointsOfTab();
-        var timepointsArr = [];
-        for(var i=0; i< timepointsOfTab.length; i++) {
-            var timepointId = timepointsOfTab[i].timepointID;
+        for (var i = 0; i < timepoints.length; i++) {
+            var timepointId = timepoints[i].timepointID;
             var lesionTimepointId = lesionData.timepointID;
 
+            var timepointObject;
             if (timepointId === lesionTimepointId) {
                 // Add real mesurement
-                var timepointObject =  {};
-                timepointObject[timepointId] = {longestDiameter: lesionData.measurementText, imageId: lesionData.imageId};
-                timepointsArr.push(timepointObject);
+                timepointObject = {
+                    longestDiameter: lesionData.measurementText,
+                    imageId: lesionData.imageId
+                };
             } else {
                 // Add null measurement
-                var timepointObject =  {};
-                timepointObject[timepointId] = {longestDiameter: "", imageId: ""};
-                timepointsArr.push(timepointObject);
-
+                timepointObject = {
+                    longestDiameter: "",
+                    imageId: ""
+                };
             }
+            timepointsObject[timepointId] = timepointObject;
         }
 
-        var lesionDataCollectionObject = {
+        var lesionDataObject = {
             lesionNumber: lesionData.lesionNumber,
             isTarget: true,
             locationUID: lesionData.locationUID,
             location: getLocationName(lesionData.locationUID),
-            timepoints: timepointsArr
+            timepoints: timepointsObject
         };
-
-        Measurements.insert({contentId: contentId, lesionData: lesionDataCollectionObject});
+        Measurements.insert(lesionDataObject);
     }
 
     // Update timepoint data in Measurements collection
-    function updateTimepointData (lesionData) {
-        var contentId = getContentId();
-        var timepointID = lesionData.timepointID;
-        var tabMeasurements = Measurements.find({contentId: contentId, "lesionData.lesionNumber": lesionData.lesionNumber}).fetch();
-        var tabMeasurementsData = tabMeasurements[0];
-        if (tabMeasurements != undefined && tabMeasurements.length > 0) {
-
-            // Update timepoint
-            var timepointArr = tabMeasurementsData.lesionData.timepoints;
-            for(var i=0; i< timepointArr.length; i++) {
-                var timepoint = timepointArr[i];
-                if(timepoint[timepointID] != undefined) {
-                    timepoint[timepointID].longestDiameter = lesionData.measurementText;
-                    timepoint[timepointID].imageId = lesionData.imageId;
-
-                }
-            }
-            Measurements.update(
-                { contentId: contentId, "lesionData.lesionNumber": lesionData.lesionNumber},
-                {
-                    $set: {
-                        "lesionData.timepoints": timepointArr
-                    }
-                }, {multi: true}
-            );
+    function updateTimepointData(lesionData) {
+        // Find the specific lesion to be updated
+        var measurement = Measurements.find({
+            lesionNumber: lesionData.lesionNumber
+        }).fetch()[0];
 
+        // 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;
+        timepoints[timepointID].longestDiameter = lesionData.measurementText;
+        timepoints[timepointID].imageId = lesionData.imageId;
+
+        Measurements.update({
+            lesionNumber: lesionData.lesionNumber
+        }, {
+            $set: {
+                timepoints: timepoints
+            }
+        });
     }
 
     // Check timepointData is found in Measurements collection
-    function timepointDataIsFound (lesionNumber) {
-        var contentId = getContentId();
-        var timepointData = Measurements.findOne({contentId: contentId, "lesionData.lesionNumber": lesionNumber});
-        if (timepointData != undefined) {
+    function timepointDataIsFound(lesionNumber) {
+        var timepointData = Measurements.findOne({
+            lesionNumber: lesionNumber
+        });
+        if (timepointData) {
             return true;
-        } else {
-            return false;
         }
+        return false;
     }
 
     // Adds new timepoint item to tiemepoints array
-    function addLesionData (lesionData) {
-        if(timepointDataIsFound(lesionData)) {
+    function addLesionData(lesionData) {
+        if (timepointDataIsFound(lesionData)) {
             // Update data
             updateTimepointData(lesionData);
-        } else{
+        } else {
             // Insert data
             addTimepointData(lesionData);
         }
-
-        // TODO: This code block will be removed
-        // Populate timepoints array
-        var roi = {
-            uid: lesionData.uid,
-            number: lesionData.lesionNumber,
-            measurement: lesionData.measurementText,
-            locationUID: lesionData.locationUID
-        };
-        if (timepoints.length) {
-            timepoints.forEach(function(timepoint) {
-                if(timepoint.timepointID === timepointID) {
-                    timepoint.rois.push(roi);
-                }
-            });
-        } else {
-            timepoints.push({timepointID: timepointID, rois: [roi]});
-        }
-
     }
 
     // Returns new lesion number according to timepointID
-    function getNewLesionNumber (timepointID) {
-        var contentId = getContentId();
-        var lesionNumberCounter = 0;
-        var timepointsData = Measurements.find({contentId: contentId}).fetch();
-        if(timepointsData.length > 0) {
-            for(var i=0; i< timepointsData.length; i++) {
-                var timepointData = timepointsData[i];
-                var timepoints = timepointData.lesionData.timepoints;
-                for(var j=0; j< timepoints.length; j++) {
-                    var timepoint = timepoints[j];
-                    var key = Object.keys(timepoint);
-                    if(key == timepointID) {
-                        if (timepoint[key].longestDiameter === "") {
-                            return timepointData.lesionData.lesionNumber;
+    function getNewLesionNumber(timepointID) {
+        // Get all current lesion measurements
+        var measurements = Measurements.find().fetch();
 
-                        } else {
-                            lesionNumberCounter = lesionNumberCounter + 1;
-                        }
-                    }
-                }
-            }
-            console.log(lesionNumberCounter + 1);
-
-            return lesionNumberCounter + 1;
+        // If no measurements exist yet, start at 1
+        if (!measurements.length) {
+            return 1;
         }
 
-        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].longestDiameter === '') {
+                return measurement.lesionNumber;
+            } else {
+                lesionNumberCounter = lesionNumberCounter + 1;
+            }
+        }
+        console.log(lesionNumberCounter + 1);
+        return lesionNumberCounter + 1;
     }
 
     // If lesion number is added for any timepoint, returns lesion locationUID
-    function isLesionNumberAdded (lesionNumber) {
-        if (timepointDataIsFound(lesionNumber)){
-            var contentId = getContentId();
-            var timepointData = Measurements.find({contentId: contentId, "lesionData.lesionNumber": lesionNumber}).fetch();
-            return timepointData[0].lesionData.locationUID;
-
+    function isLesionNumberAdded(lesionNumber) {
+        if (!timepointDataIsFound(lesionNumber)) {
+            return;
         }
-        return null
 
+        var measurement = Measurements.find({
+            lesionNumber: lesionNumber
+        }).fetch()[0];
+
+        return measurement.locationUID;
     }
 
     return {
         addNewLocation: addPatientLocation,
         getLocations: getPatientLocations,
         addLesionData: addLesionData,
-        getLesionNumber: getNewLesionNumber,
+        getNewLesionNumber: getNewLesionNumber,
         isLesionNumberAdded: isLesionNumberAdded,
-        getTimepoints: getTimepoints,
         updateTimepointData: updateTimepointData
-
     };
 })();