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

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;