Improved lesion removing / renumbering after removal

LesionTracker/client/components/viewer.js

@@ -158,9 +158,7 @@ Template.viewer.onCreated(function() {
                     }
 
                     log.info('Measurement added');
-
+                    syncMeasurementAndToolData(data);
-                    addMeasurementAsToolData(data);
-
                     updateRelatedElements(data.imageId);
                 },
                 removed: function(data) {
@@ -174,34 +172,43 @@ Template.viewer.onCreated(function() {
                     var measurementId = data._id;
                     var toolType = data.isTarget ? 'lesion' : 'nonTarget';
 
-                    // Find the list of imageIds that needs to be updated
+                    // Remove the measurement from all the imageIds on which it exists
-                    var imageIds = [];
+                    // as toolData
                     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
+                    // Update all Measurements to decrement the lesion numbers for those
-                    var enabledElements = [];
+                    // that were created after the current lesion by 1
-                    imageIds.forEach(function(imageId) {
+                    Meteor.call('decrementLesionNumbers', data, function(error, response) {
-                        var elems = cornerstone.getEnabledElementsByImageId(imageId);
+                        if (error) {
-                        enabledElements = enabledElements.concat(elems);
+                            log.warn(error)
-                    });
-
-                    // 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;
                         }
+
+                        // Sync database data with toolData for all the measurements
+                        // that have just been updated
+
+                        // Note that here we need to use greater than and equals to
+                        // find the Measurements, whereas on the server it's
+                        // only "greater than", since inside this callback the
+                        // Measurements have already been decremented.
+                        Measurements.find({
+                            patientId: data.patientId,
+                            lesionNumberAbsolute: {
+                                $gte: data.lesionNumberAbsolute
+                            }
+                        }).forEach(function(measurementData) {
+                            syncMeasurementAndToolData(measurementData);
+                        });
+
+                        // Update each displayed viewport
+                        var viewports = $('.imageViewerViewport').not('.empty');
+                        viewports.each(function(index, element) {
                             cornerstone.updateImage(element);
                         });
+                    });
                 }
             });
         }
@@ -224,7 +231,7 @@ function updateRelatedElements(imageId) {
     });
 }
 
-function addMeasurementAsToolData(data) {
+function syncMeasurementAndToolData(data) {
     // Check what toolType we should be adding this to, based on the isTarget value
     // of the stored Measurement
     var toolType = data.isTarget ? 'lesion' : 'nonTarget';
@@ -266,6 +273,9 @@ function addMeasurementAsToolData(data) {
                 toolState[imageId][toolType].data.forEach(function(measurement) {
                     if (measurement.id === data._id) {
                         alreadyExists = true;
+
+                        // Update the toolData lesionNumber from the Measurement
+                        measurement.lesionNumber = data.lesionNumber;
                         return false;
                     }
                 });
@@ -282,7 +292,6 @@ function addMeasurementAsToolData(data) {
         measurementData.isTarget = data.isTarget;
         measurementData.lesionNumber = data.lesionNumber;
         measurementData.measurementText = data.measurementText;
-        measurementData.lesionName = data.lesionName;
         measurementData.isDeleted = data.isDeleted;
         measurementData.location = data.location;
         measurementData.locationUID = data.locationUID;

Packages/lesiontracker/client/compatibility/lesionTool.js

@@ -1,10 +1,8 @@
-var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneTools) {
+(function($, cornerstone, cornerstoneMath, cornerstoneTools) {
 
     "use strict";
 
-    if (cornerstoneTools === undefined) {
+    var toolType = "lesion";
-        cornerstoneTools = {};
-    }
 
     var configuration = {
         setLesionNumberCallback: setLesionNumberCallback,
@@ -29,15 +27,12 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
         //doneCallback(prompt('Change your lesion location:'));
     }
 
-    var toolType = "lesion";
-
     ///////// BEGIN ACTIVE TOOL ///////
 
     function addNewMeasurement(mouseEventData) {
         var element = mouseEventData.element;
 
         function doneCallback(lesionNumber) {
-            measurementData.lesionName = "Target " + lesionNumber;
             measurementData.lesionNumber = lesionNumber;
             measurementData.active = false;
             cornerstone.updateImage(element);
@@ -82,8 +77,6 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
             $(element).on('CornerstoneToolsMouseDown', eventData, mouseDownCallback);
             $(element).on('CornerstoneToolsMouseDownActivate', eventData, cornerstoneTools.lesion.mouseDownActivateCallback);
             cornerstone.updateImage(element);
-
-            //updateLesionCollection(measurementData);
         });
     }
 
@@ -91,7 +84,6 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
         var element = touchEventData.element;
 
         function doneCallback(lesionNumber) {
-            measurementData.lesionName = "Bi-Directional " + lesionNumber;
             measurementData.lesionNumber = lesionNumber;
             measurementData.active = false;
             cornerstone.updateImage(element);
@@ -199,7 +191,6 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
             measurementText: 0,
             widthMeasurement: 0,
             perpendicularMeasurement: 0,
-            lesionName: 'Target',
             isDeleted: false,
             isTarget: true,
             uid: uuid.v4()
@@ -262,7 +253,10 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
 
         var k = distanceToLineP2 / newLineLength;
 
-        var newIntersection = { x: data.handles.end.x + ((eventData.currentPoints.image.x - data.handles.end.x) * k), y: data.handles.end.y + ((eventData.currentPoints.image.y - data.handles.end.y) * k)};
+        var newIntersection = {
+            x: data.handles.end.x + ((eventData.currentPoints.image.x - data.handles.end.x) * k),
+            y: data.handles.end.y + ((eventData.currentPoints.image.y - data.handles.end.y) * k)
+        };
 
         data.handles.perpendicularStart.x = newIntersection.x - distanceFromPerpendicularP1 * dy;
         data.handles.perpendicularStart.y = newIntersection.y + distanceFromPerpendicularP1 * dx;
@@ -294,7 +288,10 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
 
         var k = distanceToLineP2 / newLineLength;
 
-        var newIntersection = { x: data.handles.start.x + ((eventData.currentPoints.image.x - data.handles.start.x) * k), y: data.handles.start.y + ((eventData.currentPoints.image.y - data.handles.start.y) * k)};
+        var newIntersection = {
+            x: data.handles.start.x + ((eventData.currentPoints.image.x - data.handles.start.x) * k),
+            y: data.handles.start.y + ((eventData.currentPoints.image.y - data.handles.start.y) * k)
+        };
 
         data.handles.perpendicularStart.x = newIntersection.x + distanceFromPerpendicularP1 * dy;
         data.handles.perpendicularStart.y = newIntersection.y - distanceFromPerpendicularP1 * dx;
@@ -330,8 +327,14 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
         var dx = (data.handles.start.x - data.handles.end.x) / length;
         var dy = (data.handles.start.y - data.handles.end.y) / length;
 
-        var adjustedLineP1 = {x: data.handles.start.x - fudgeFactor * dx, y: data.handles.start.y - fudgeFactor * dy};
+        var adjustedLineP1 = {
-        var adjustedLineP2 = {x: data.handles.end.x + fudgeFactor * dx, y: data.handles.end.y + fudgeFactor * dy};
+            x: data.handles.start.x - fudgeFactor * dx,
+            y: data.handles.start.y - fudgeFactor * dy
+        };
+        var adjustedLineP2 = {
+            x: data.handles.end.x + fudgeFactor * dx,
+            y: data.handles.end.y + fudgeFactor * dy
+        };
 
         data.handles.perpendicularStart.x = movedPoint.x;
         data.handles.perpendicularStart.y = movedPoint.y;
@@ -386,8 +389,14 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
         var dx = (data.handles.start.x - data.handles.end.x) / length;
         var dy = (data.handles.start.y - data.handles.end.y) / length;
 
-        var adjustedLineP1 = {x: data.handles.start.x - fudgeFactor * dx, y: data.handles.start.y - fudgeFactor * dy};
+        var adjustedLineP1 = {
-        var adjustedLineP2 = {x: data.handles.end.x + fudgeFactor * dx, y: data.handles.end.y + fudgeFactor * dy};
+            x: data.handles.start.x - fudgeFactor * dx,
+            y: data.handles.start.y - fudgeFactor * dy
+        };
+        var adjustedLineP2 = {
+            x: data.handles.end.x + fudgeFactor * dx,
+            y: data.handles.end.y + fudgeFactor * dy
+        };
 
         data.handles.perpendicularStart.x = movedPoint.x + total * dy;
         data.handles.perpendicularStart.y = movedPoint.y - total * dx;
@@ -729,18 +738,27 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
 
         // Find distances between handles and textBox
         var distanceToStart = getDistance(data.handles.start, data.handles.textBox);
-        distancesArr.push({distance: distanceToStart, point: data.handles.start});
+        distancesArr.push({
+            distance: distanceToStart,
+            point: data.handles.start
+        });
         minDistance = distanceToStart;
 
         var distanceToEnd = getDistance(data.handles.end, data.handles.textBox);
-        distancesArr.push({distance: distanceToEnd, point: data.handles.end});
+        distancesArr.push({
+            distance: distanceToEnd,
+            point: data.handles.end
+        });
         if (distanceToEnd < minDistance) {
             minDistance = distanceToEnd;
         }
 
         if (data.handles.perpendicularStart.x && data.handles.perpendicularStart.y) {
             var distanceToPerpendicularStart = getDistance(data.handles.perpendicularStart, data.handles.textBox);
-            distancesArr.push({distance: distanceToPerpendicularStart, point: data.handles.perpendicularStart});
+            distancesArr.push({
+                distance: distanceToPerpendicularStart,
+                point: data.handles.perpendicularStart
+            });
             if (distanceToPerpendicularStart < minDistance) {
                 minDistance = distanceToPerpendicularStart;
             }
@@ -749,7 +767,10 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
 
         if (data.handles.perpendicularEnd.x && data.handles.perpendicularEnd.y) {
             var distanceToPerpendicularEnd = getDistance(data.handles.perpendicularEnd, data.handles.textBox);
-            distancesArr.push({distance: distanceToPerpendicularEnd, point: data.handles.perpendicularEnd});
+            distancesArr.push({
+                distance: distanceToPerpendicularEnd,
+                point: data.handles.perpendicularEnd
+            });
             if (distanceToPerpendicularEnd < minDistance) {
                 minDistance = distanceToPerpendicularEnd;
             }
@@ -845,7 +866,7 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
 
             var lengthText = ' L ' + length.toFixed(1) + suffix;
             var widthText = ' W ' + width.toFixed(1) + suffix;
-            var textLines = [data.lesionName, lengthText, widthText];
+            var textLines = ['Target ' + data.lesionNumber, lengthText, widthText];
 
             var boundingBox = cornerstoneTools.drawTextBox(context,
                 textLines,
@@ -861,18 +882,6 @@ 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
-            LesionManager.updateLesionData(lesionData);
-        }
-    }
-
     function doubleClickCallback(e, eventData) {
         // Prevent other double click handlers from firing after this one
         //e.stopImmediatePropagation();
@@ -884,16 +893,7 @@ 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)) {
@@ -948,6 +948,4 @@ var cornerstoneTools = (function($, cornerstone, cornerstoneMath, cornerstoneToo
 
     cornerstoneTools.lesion.setConfiguration(configuration);
 
-    return cornerstoneTools;
+})($, cornerstone, cornerstoneMath, cornerstoneTools);
-
-}($, cornerstone, cornerstoneMath, cornerstoneTools));

Packages/lesiontracker/client/compatibility/nonTargetTool.js

@@ -35,7 +35,6 @@
         var element = mouseEventData.element;
 
         function doneCallback(lesionNumber) {
-            measurementData.lesionName = "Non-Target " + lesionNumber;
             measurementData.lesionNumber = lesionNumber;
             measurementData.active = true;
             cornerstone.updateImage(element);
@@ -208,7 +207,7 @@
             }
 
             // Draw the text
-            if (data.lesionName && data.lesionName !== '') {
+            if (data.lesionNumber) {
                 // Draw linked line as dashed
                 var mid = {
                     x: (handleStartCanvas.x + handleEndCanvas.x) / 2,
@@ -224,7 +223,7 @@
                 context.lineTo(canvasTextLocation.x + 20, canvasTextLocation.y + 20);
                 context.stroke();
 
-                var boundingBox = cornerstoneTools.drawTextBox(context, data.lesionName, canvasTextLocation.x, canvasTextLocation.y, color);
+                var boundingBox = cornerstoneTools.drawTextBox(context, 'Non-Target ' + data.lesionNumber, canvasTextLocation.x, canvasTextLocation.y, color);
                 data.handles.textBox.boundingBox = boundingBox;
             }
 
@@ -239,7 +238,6 @@
         var element = touchEventData.element;
 
         function doneCallback(lesionNumber) {
-            measurementData.lesionName = "Non-Target " + lesionNumber;
             measurementData.lesionNumber = lesionNumber;
             measurementData.active = true;
             cornerstone.updateImage(element);

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

@@ -12,9 +12,9 @@
   border-radius: 5px
   padding: 10px 20px 10px 20px
   background-color: rgba(255,255,255,1)
+  outline: none
 
   .btn
-    outline: none
     text-decoration: none
 
   #cancel

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

@@ -11,6 +11,7 @@
   border-radius: 5px
   padding: 10px 20px 10px 20px
   background-color: rgba(255,255,255,1)
+  outline: none
 
   #closeLesionPopup
     outline: none

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

@@ -10,7 +10,9 @@ function doneCallback(measurementData, deleteTool) {
     // the specified Timepoint Cell
     if (deleteTool === true) {
         Meteor.call("removeMeasurement", measurementData.id, function(error, response) {
-            console.log('Removed!');
+            if (error) {
+                log.warn(error);
+            }
         });
     }
 }
@@ -47,7 +49,6 @@ Template.lesionTableRow.events({
                     if (error) {
                         log.warn(error);
                     }
-                    log.info(response);
                 });
             }, options);
         }

Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.styl

@@ -11,6 +11,7 @@
   border-radius: 5px
   padding: 10px 20px 10px 20px
   background-color: rgba(255,255,255,1)
+  outline: none
 
   #selectNonTargetLesionLocation, #selectNonTargetLesionLocationResponse
     width: 100%

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

@@ -11,6 +11,7 @@
   border-radius: 5px
   padding: 10px 20px 10px 20px
   background-color: rgba(255,255,255,1)
+  outline: none
 
   #selectNonTargetLesionLocationResponse
     width: 100%

Packages/lesiontracker/server/collections.js

@@ -1,14 +1,10 @@
 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
     });

Packages/lesiontracker/server/removeCollections.js

@@ -1,54 +1,44 @@
 Meteor.methods({
     "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.. 
+    "decrementLesionNumbers": function(lesionData) {
-    "removePatientMeasurement": function(lesionObject) {
+        // Update all Measurements to decrement the lesion numbers for those
-        // Find patient data
+        // that were created after the current lesion by 1
-        var measurementData = Measurements.findOne({
-            patientId: lesionObject.patientId,
-            isTarget: lesionObject.isTarget,
-            lesionNumber: lesionObject.lesionNumber
-        });
 
-        // Get timepoints
+        // TODO: Update this when we have more criteria than patientId
-        var timepoints = measurementData.timepoints;
+        // Decrement the absolute lesion number of all lesions with
-
+        // absolute lesion numbers greater than the current lesion by 1
-        // 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];
-            }
-        });
-
-        var newTimepointsIds = Object.keys(timepoints);
-        // If there is no timepoints object, remove measurement data
-        if (newTimepointsIds.length) {
-            //Update measurement timepoints
         Measurements.update({
-                patientId: lesionObject.patientId,
+            patientId: lesionData.patientId,
-                isTarget: lesionObject.isTarget,
+            lesionNumberAbsolute: {
-                lesionNumber: lesionObject.lesionNumber
+                $gt: lesionData.lesionNumberAbsolute
+            }
         }, {
-                $set: {
+            $inc: {
-                    timepoints: timepoints
+                lesionNumberAbsolute: -1
             }
+        }, {
+            multi: true
         });
-        } else {
+
-            // Remove all data
+        // Decrement the lesion number of all related (i.e. target or non-target)
-            Measurements.remove({
+        // lesions with lesion numbers greater than the current lesion by 1
-                patientId: lesionObject.patientId,
+        Measurements.update({
-                isTarget: lesionObject.isTarget,
+            patientId: lesionData.patientId,
-                lesionNumber: lesionObject.lesionNumber
+            lesionNumber: {
+                $gt: lesionData.lesionNumber
+            },
+            isTarget: lesionData.isTarget
+        }, {
+            $inc: {
+                lesionNumber: -1
+            }
+        }, {
+            multi: true
         });
     }
-    }
 });

Packages/viewerbase/lib/setFocusToActiveViewport.js

@@ -0,0 +1,19 @@
+/**
+ * Restores the browser focus to the currently specified active viewport
+ * as determined from Meteor's Session variable.
+ *
+ * This is allows keydown events to be captured on the focused element
+ */
+setFocusToActiveViewport = function() {
+    // Get the list of viewports
+    var viewports = $('.imageViewerViewport');
+
+    // Get the current active viewport index from Session
+    var activeViewportIndex = Session.get('activeViewport');
+
+    // Find the div from the list of viewports
+    var activeViewport = viewports.eq(activeViewportIndex);
+
+    // Set the browser focus to this div
+    activeViewport.focus();
+};