From 44491c639d48e74089fc4381b30ac243692254d4 Mon Sep 17 00:00:00 2001
From: Erik Ziegler <erik.ziegler@ulg.ac.be>
Date: Sat, 9 Jan 2016 18:41:33 +0100
Subject: [PATCH] Fixes for keydown event detection for dialogs. Updated
 cornerstoneTools to latest master

---
 .../cornerstone/client/cornerstoneTools.js    | 23 +++++++++---------
 .../confirmDeleteDialog.html                  |  2 +-
 .../confirmDeleteDialog.js                    | 11 +++++++--
 .../lesionLocationDialog.html                 |  4 ++--
 .../lesionLocationDialog.js                   | 10 ++++++--
 .../lesionTableTimepointCell.html             |  2 +-
 .../nonTargetLesionDialog.html                |  4 ++--
 .../nonTargetLesionDialog.js                  |  9 +++++--
 .../nonTargetResponseDialog.html              |  2 +-
 .../nonTargetResponseDialog.js                |  9 +++++--
 .../imageViewerViewport.js                    | 24 +++++++++++--------
 Packages/viewerbase/package.js                |  2 ++
 12 files changed, 65 insertions(+), 37 deletions(-)

diff --git a/Packages/cornerstone/client/cornerstoneTools.js b/Packages/cornerstone/client/cornerstoneTools.js
index 1fbb0db70..0024b331c 100644
--- a/Packages/cornerstone/client/cornerstoneTools.js
+++ b/Packages/cornerstone/client/cornerstoneTools.js
@@ -1,4 +1,4 @@
-/*! cornerstoneTools - v0.7.7 - 2015-12-18 | (c) 2014 Chris Hafey | https://github.com/chafey/cornerstoneTools */
+/*! cornerstoneTools - v0.7.7 - 2016-01-09 | (c) 2014 Chris Hafey | https://github.com/chafey/cornerstoneTools */
 // Begin Source: src/header.js
 if (typeof cornerstone === 'undefined') {
     cornerstone = {};
@@ -901,7 +901,7 @@ if (typeof cornerstoneTools === 'undefined') {
             }
 
             var preventHandleOutsideImage;
-            if (mouseToolInterface.options.preventHandleOutsideImage !== undefined) {
+            if (mouseToolInterface.options && mouseToolInterface.options.preventHandleOutsideImage !== undefined) {
                 preventHandleOutsideImage = mouseToolInterface.options.preventHandleOutsideImage;
             } else {
                 preventHandleOutsideImage = false;
@@ -1608,7 +1608,7 @@ if (typeof cornerstoneTools === 'undefined') {
             if (toolData) {
                 for (i = 0; i < toolData.data.length; i++) {
                     data = toolData.data[i];
-                    var distanceSq = 75; // Should probably make this a settable property later
+                    var distanceSq = 25; // Should probably make this a settable property later
                     var handle = cornerstoneTools.getHandleNearImagePoint(element, data.handles, coords, distanceSq);
                     if (handle) {
                         $(element).off('CornerstoneToolsTouchStartActive', touchToolInterface.touchDownActivateCallback || touchDownActivateCallback);
@@ -1674,7 +1674,7 @@ if (typeof cornerstoneTools === 'undefined') {
 
             // now check to see if there is a handle we can move
             var distanceFromTouch = cornerstoneTools.touchSettings.getToolDistanceFromTouch();
-            var distanceSq = Math.pow(Math.max(Math.abs(distanceFromTouch.x), Math.abs(distanceFromTouch.y)), 2);
+            var distanceSq = Math.max(Math.abs(distanceFromTouch.x), Math.abs(distanceFromTouch.y));
             if (toolData) {
                 for (i = 0; i < toolData.data.length; i++) {
                     data = toolData.data[i];
@@ -5415,7 +5415,7 @@ if (typeof cornerstoneTools === 'undefined') {
             return {
                 min: globalMin,
                 max: globalMax,
-                mean: globalMin
+                mean: (globalMin + globalMax) / 2
             };
         }
 
@@ -6739,7 +6739,6 @@ if (typeof cornerstoneTools === 'undefined') {
             handle.active = false;
             $(element).off('CornerstoneToolsTouchDrag', touchDragCallback);
             $(element).off('CornerstoneToolsTouchPinch', touchEndCallback);
-            $(element).off('CornerstoneToolsTouchPress', touchEndCallback);
             $(element).off('CornerstoneToolsTouchEnd', touchEndCallback);
             $(element).off('CornerstoneToolsDragEnd', touchEndCallback);
             $(element).off('CornerstoneToolsTap', touchEndCallback);
@@ -6751,7 +6750,6 @@ if (typeof cornerstoneTools === 'undefined') {
         }
 
         $(element).on('CornerstoneToolsTouchPinch', touchEndCallback);
-        $(element).on('CornerstoneToolsTouchPress', touchEndCallback);
         $(element).on('CornerstoneToolsTouchEnd', touchEndCallback);
         $(element).on('CornerstoneToolsDragEnd', touchEndCallback);
         $(element).on('CornerstoneToolsTap', touchEndCallback);
@@ -10031,17 +10029,18 @@ Display scroll progress bar across bottom of image.
         x = Math.round(x);
         y = Math.round(y);
         var enabledElement = cornerstone.getEnabledElement(element);
+        var image = enabledElement.image;
         var luminance = [];
         var index = 0;
-        var pixelData = enabledElement.image.getPixelData();
+        var pixelData = image.getPixelData();
         var spIndex,
             row,
             column;
 
-        if (enabledElement.image.color) {
+        if (image.color) {
             for (row = 0; row < height; row++) {
                 for (column = 0; column < width; column++) {
-                    spIndex = (((row + y) * enabledElement.image.columns) + (column + x)) * 4;
+                    spIndex = (((row + y) * image.columns) + (column + x)) * 4;
                     var red = pixelData[spIndex];
                     var green = pixelData[spIndex + 1];
                     var blue = pixelData[spIndex + 2];
@@ -10051,8 +10050,8 @@ Display scroll progress bar across bottom of image.
         } else {
             for (row = 0; row < height; row++) {
                 for (column = 0; column < width; column++) {
-                    spIndex = ((row + y) * enabledElement.image.columns) + (column + x);
-                    luminance[index++] = pixelData[spIndex];
+                    spIndex = ((row + y) * image.columns) + (column + x);
+                    luminance[index++] = pixelData[spIndex] * image.slope + image.intercept;
                 }
             }
         }
diff --git a/Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.html b/Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.html
index 978fd1fe5..947939ce9 100644
--- a/Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.html
+++ b/Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.html
@@ -1,5 +1,5 @@
 <template name="confirmDeleteDialog">
-    <div id="confirmDeleteDialog">
+    <div id="confirmDeleteDialog" tabindex="0">
         <h5>Remove Measurement?</h5>
         <p>Are you sure you would like to remove this measurement?</p>
         <button id="cancel" class="btn btn-link" tabindex="1">Cancel</button>
diff --git a/Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.js b/Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.js
index 946f9e28f..b05c0d2a9 100644
--- a/Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.js
+++ b/Packages/lesiontracker/client/components/confirmDeleteDialog/confirmDeleteDialog.js
@@ -7,6 +7,9 @@ function closeHandler() {
 
     // Remove the callback from the template data
     delete Template.confirmDeleteDialog.doneCallback;
+
+    // Restore the focus to the active viewport
+    setFocusToActiveViewport();
 }
 
 showConfirmDialog = function(doneCallback, options) {
@@ -19,14 +22,17 @@ showConfirmDialog = function(doneCallback, options) {
         closeHandler();
     });
 
-    $("#confirmDeleteDialog").css('display', 'block');
+    var confirmDeleteDialog = $("#confirmDeleteDialog");
+    confirmDeleteDialog.css('display', 'block');
+    confirmDeleteDialog.focus();
 
     if (doneCallback && typeof doneCallback === 'function') {
         Template.confirmDeleteDialog.doneCallback = doneCallback;
     }
 };
 
-var keys = {
+// Global object of key names (TODO: put this somewhere else)
+keys = {
     ESC: 27,
     ENTER: 13
 };
@@ -46,6 +52,7 @@ Template.confirmDeleteDialog.events({
     'keydown #confirmDeleteDialog': function(e) {
         if (e.which === keys.ESC) {
             closeHandler();
+            return false;
         }
 
         if (this.keyPressAllowed === false) {
diff --git a/Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.html b/Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.html
index ed3b15d86..c4288714a 100644
--- a/Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.html
+++ b/Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.html
@@ -1,5 +1,5 @@
 <template name="lesionLocationDialog">
-    <div id="lesionLocationDialog">
+    <div id="lesionLocationDialog" tabindex="0">
         <div class="dialogHeader">
             <h4>Select Lesion Location</h4>
         </div>
@@ -16,7 +16,7 @@
         </div>
     </div>
 
-    <div id="lesionLocationRelabelDialog">
+    <div id="lesionLocationRelabelDialog" tabindex="0">
         <div class="dialogHeader">
             <h4>Change Lesion Location</h4>
         </div>
diff --git a/Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.js b/Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.js
index cd2a5fbe8..9db3fae22 100644
--- a/Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.js
+++ b/Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.js
@@ -4,6 +4,9 @@ function closeHandler(dialog) {
 
     // Remove the backdrop
     $(".removableBackdrop").remove();
+
+    // Restore the focus to the active viewport
+    setFocusToActiveViewport();
 }
 
 // This event sets lesion number for new lesion
@@ -96,6 +99,7 @@ function getLesionLocationCallback(measurementData, eventData) {
     }
 
     dialog.css(dialogProperty);
+    dialog.focus();
 }
 
 changeLesionLocationCallback = function(measurementData, eventData, doneCallback) {
@@ -134,6 +138,7 @@ changeLesionLocationCallback = function(measurementData, eventData, doneCallback
     }
 
     dialog.css(dialogProperty);
+    dialog.focus();
 
     var measurement = Measurements.findOne(measurementData.id);
     if (!measurement) {
@@ -249,9 +254,10 @@ Template.lesionLocationDialog.events({
     'keydown #lesionLocationDialog, keydown #lesionLocationRelabelDialog': function(e) {
         var dialog = Template.lesionLocationDialog.dialog;
 
-        // If Enter is pressed, close the dialog
-        if (e.which === 13) {
+        // If Esc or Enter are pressed, close the dialog
+        if (e.which === keys.ESC || e.which === keys.ENTER) {
             closeHandler(dialog);
+            return false;
         }
     }
 });
diff --git a/Packages/lesiontracker/client/components/lesionTableTimepointCell/lesionTableTimepointCell.html b/Packages/lesiontracker/client/components/lesionTableTimepointCell/lesionTableTimepointCell.html
index 1467c21b0..83a4afa7a 100644
--- a/Packages/lesiontracker/client/components/lesionTableTimepointCell/lesionTableTimepointCell.html
+++ b/Packages/lesiontracker/client/components/lesionTableTimepointCell/lesionTableTimepointCell.html
@@ -3,7 +3,7 @@
         {{ #if isTarget }}
             <td class="lesionTableTimepointCell targetCell" tabindex="1">{{displayData}}</td>
         {{ else }}
-            <td class="lesionTableTimepointCell nonTargetCell" tabindex="2">{{displayData}}</td>
+            <td class="lesionTableTimepointCell nonTargetCell" tabindex="1">{{displayData}}</td>
         {{ /if }}
     {{ else }}
     <td class="lesionTableTimepointCell empty"></td>
diff --git a/Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.html b/Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.html
index d1b3487eb..3cdf5dd2a 100644
--- a/Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.html
+++ b/Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.html
@@ -1,5 +1,5 @@
 <template name="nonTargetLesionDialog">
-    <div id="nonTargetLesionLocationDialog">
+    <div id="nonTargetLesionLocationDialog" tabindex="0">
         <div class="dialogHeader">
             <h4>Select Lesion Location</h4>
         </div>
@@ -32,7 +32,7 @@
         </div>
     </div>
 
-    <div id="nonTargetLesionRelabelDialog">
+    <div id="nonTargetLesionRelabelDialog" tabindex="0">
         <div class="dialogHeader">
             <h4>Select Lesion Location</h4>
         </div>
diff --git a/Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.js b/Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.js
index ac7f82e63..29d503739 100644
--- a/Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.js
+++ b/Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.js
@@ -4,6 +4,9 @@ function closeHandler(dialog) {
 
     // Remove the backdrop
     $(".removableBackdrop").remove();
+
+    // Restore the focus to the active viewport
+    setFocusToActiveViewport();
 }
 
 // This event sets lesion number for new lesion
@@ -168,6 +171,7 @@ changeNonTargetLocationCallback = function(measurementData, eventData, doneCallb
     }
 
     dialog.css(dialogProperty);
+    dialog.focus();
 
     var measurement = Measurements.findOne(measurementData.id);
     if (!measurement) {
@@ -311,9 +315,10 @@ Template.nonTargetLesionDialog.events({
     'keydown #lesionLocationDialog, keydown #lesionLocationRelabelDialog': function(e) {
         var dialog = Template.nonTargetLesionDialog.dialog;
 
-        // If Enter is pressed, close the dialog
-        if (e.which === 13) {
+        // If Esc or Enter are pressed, close the dialog
+        if (e.which === keys.ESC || e.which === keys.ENTER) {
             closeHandler(dialog);
+            return false;
         }
     }
 });
diff --git a/Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.html b/Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.html
index 787f021c5..1b8ee9807 100644
--- a/Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.html
+++ b/Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.html
@@ -1,5 +1,5 @@
 <template name="nonTargetResponseDialog">
-    <div id="nonTargetResponseDialog">
+    <div id="nonTargetResponseDialog" tabindex="0">
         <div class="dialogHeader">
             <h5>Select Response</h5>
         </div>
diff --git a/Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.js b/Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.js
index 6498ee652..cd7eb4a65 100644
--- a/Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.js
+++ b/Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.js
@@ -4,6 +4,9 @@ function closeHandler(dialog) {
 
     // Remove the backdrop
     $(".removableBackdrop").remove();
+
+    // Restore the focus to the active viewport
+    setFocusToActiveViewport();
 }
 
 changeNonTargetResponse = function(measurementData, eventData, doneCallback) {
@@ -55,6 +58,7 @@ changeNonTargetResponse = function(measurementData, eventData, doneCallback) {
     }
 
     dialog.css(dialogProperty);
+    dialog.focus();
 
     var measurement = Measurements.findOne(measurementData.id);
     if (!measurement) {
@@ -136,9 +140,10 @@ Template.nonTargetResponseDialog.events({
     'keydown #nonTargetResponseDialog': function(e) {
         var dialog = Template.nonTargetResponseDialog.dialog;
 
-        // If Enter is pressed, close the dialog
-        if (e.which === 13) {
+        // If Esc or Enter are pressed, close the dialog
+        if (e.which === keys.ESC || e.which === keys.ENTER) {
             closeHandler(dialog);
+            return false;
         }
     }
 });
diff --git a/Packages/viewerbase/client/components/viewer/imageViewerViewport/imageViewerViewport.js b/Packages/viewerbase/client/components/viewer/imageViewerViewport/imageViewerViewport.js
index 8defd4cbd..6e66182ed 100644
--- a/Packages/viewerbase/client/components/viewer/imageViewerViewport/imageViewerViewport.js
+++ b/Packages/viewerbase/client/components/viewer/imageViewerViewport/imageViewerViewport.js
@@ -25,7 +25,7 @@ function loadSeriesIntoViewport(data, templateData) {
     // Get the contentID of the current worklist tab, if the viewport is running
     // alongside the worklist package
     var contentId = Session.get('activeContentId');
-    
+
     // If the viewer is inside a tab, create an object related to the specified viewport
     // This data will be saved so that the tab can be reloaded to the same state after tabs
     // are switched
@@ -113,7 +113,7 @@ function loadSeriesIntoViewport(data, templateData) {
     // image is currently being loaded into them. This is useful so that we can
     // place progress (download %) for each image inside the proper viewports.
     ViewportLoading[viewportIndex] = imageId;
-    
+
     // Enable Cornerstone for the viewport element
     //
     // NOTE: This uses the experimental WebGL renderer for Cornerstone!
@@ -131,7 +131,7 @@ function loadSeriesIntoViewport(data, templateData) {
         var enabledElement;
         try {
             enabledElement = cornerstone.getEnabledElement(element);
-        } catch(error) {
+        } catch (error) {
             log.warn('Viewport destroyed before loaded image could be displayed');
             return;
         }
@@ -150,7 +150,7 @@ function loadSeriesIntoViewport(data, templateData) {
         // Remove the data for this viewport from the ViewportLoading object
         // This will stop the loading percentage complete from being displayed.
         delete ViewportLoading[viewportIndex];
-        
+
         // Call the handler function that represents the end of the image loading phase
         // (e.g. hide the progress text box)
         endLoadingHandler(element);
@@ -168,7 +168,7 @@ function loadSeriesIntoViewport(data, templateData) {
         $(element).siblings('.imageViewerViewportOverlay').show();
 
         // Add stack state managers for the stack tool, CINE tool, and reference lines
-        cornerstoneTools.addStackStateManager(element, [ 'stack', 'playClip', 'referenceLines' ]);
+        cornerstoneTools.addStackStateManager(element, ['stack', 'playClip', 'referenceLines']);
 
         // Get the current viewport settings
         var viewport = cornerstone.getViewport(element);
@@ -305,7 +305,7 @@ function loadSeriesIntoViewport(data, templateData) {
             viewport: viewport
         };
         ViewerData[contentId].loadedSeriesData = OHIF.viewer.loadedSeriesData;
-        
+
         // Check if image plane (orientation / loction) data is present for the current image
         var imagePlane = cornerstoneTools.metaData.get('imagePlane', image.imageId);
 
@@ -340,8 +340,12 @@ function loadSeriesIntoViewport(data, templateData) {
  * @param templateData currentData of Template
  *
  */
-function setSeries(data, seriesInstanceUid, templateData){
+function setSeries(data, seriesInstanceUid, templateData) {
     var study = data.study;
+    if (!study || !study.seriesList) {
+        return;
+    }
+
     study.seriesList.every(function(series) {
         if (series.seriesInstanceUid === seriesInstanceUid) {
             data.series = series;
@@ -451,7 +455,7 @@ Template.imageViewerViewport.onRendered(function() {
         Meteor.call('GetStudyMetadata', this.data.studyInstanceUid, function(error, study) {
             // Once we have retrieved the data, we sort the series' by series
             // and instance number in ascending order
-            if(!study){
+            if (!study) {
                 return;
             }
             sortStudy(study);
@@ -470,12 +474,12 @@ Template.imageViewerViewport.onDestroyed(function() {
 
     // When a viewport element is being destroyed
     var element = this.find(".imageViewerViewport");
-    
+
     // Try to stop any currently playing clips
     // Otherwise the interval will continuously throw errors
     try {
         cornerstoneTools.stopClip(element);
-    } catch(error) {
+    } catch (error) {
         log.warn(error);
     }
 
diff --git a/Packages/viewerbase/package.js b/Packages/viewerbase/package.js
index 8b3b739fb..a3f622361 100644
--- a/Packages/viewerbase/package.js
+++ b/Packages/viewerbase/package.js
@@ -122,6 +122,7 @@ Package.onUse(function (api) {
     api.addFiles('lib/viewportFunctions.js', 'client');
     api.addFiles('lib/WLPresets.js', 'client');
     api.addFiles('lib/resizeViewportElements.js', 'client');
+    api.addFiles('lib/setFocusToActiveViewport.js', 'client');
     api.addFiles('lib/encodeQueryData.js', 'server');
 
     //api.export('accountsConfig', 'client');
@@ -139,6 +140,7 @@ Package.onUse(function (api) {
     api.export('rerenderViewportWithNewSeries', 'client');
     api.export('sortStudy', 'client');
     api.export('updateOrientationMarkers', 'client');
+    api.export('setFocusToActiveViewport', 'client');
     api.export('encodeQueryData', 'server');
 
     // Viewer management objects