PWV-3: Creating ohif:log package and partially refactoring ohif:measurements

LesionTracker/.meteor/versions

@@ -95,6 +95,7 @@ ohif:cornerstone@0.0.1
 ohif:dicom-services@0.0.1
 ohif:hanging-protocols@0.0.1
 ohif:lesiontracker@0.0.1
+ohif:log@0.0.1
 ohif:measurements@0.0.1
 ohif:study-list@0.0.1
 ohif:user-management@0.0.1

LesionTracker/client/components/viewer/viewer.js

@@ -37,11 +37,11 @@ Template.viewer.onCreated(() => {
     OHIF.viewer.defaultHotkeys.nonTarget = 'N'; // Non-target
 
     if (ViewerData[contentId].loadedSeriesData) {
-        log.info('Reloading previous loadedSeriesData');
+        OHIF.log.info('Reloading previous loadedSeriesData');
         OHIF.viewer.loadedSeriesData = ViewerData[contentId].loadedSeriesData;
 
     } else {
-        log.info('Setting default ViewerData');
+        OHIF.log.info('Setting default ViewerData');
         OHIF.viewer.loadedSeriesData = {};
         ViewerData[contentId].loadedSeriesData = {};
         Session.set('ViewerData', ViewerData);

OHIFViewer/client/components/viewer/viewer.js

@@ -33,10 +33,10 @@ Template.viewer.onCreated(() => {
     const contentId = instance.data.contentId;
 
     if (ViewerData[contentId] && ViewerData[contentId].loadedSeriesData) {
-        log.info('Reloading previous loadedSeriesData');
+        OHIF.log.info('Reloading previous loadedSeriesData');
         OHIF.viewer.loadedSeriesData = ViewerData[contentId].loadedSeriesData;
     } else {
-        log.info('Setting default ViewerData');
+        OHIF.log.info('Setting default ViewerData');
         OHIF.viewer.loadedSeriesData = {};
         ViewerData[contentId] = {};
         ViewerData[contentId].loadedSeriesData = OHIF.viewer.loadedSeriesData;

PETSUVMeasurements/client/components/viewer/viewer.js

@@ -16,11 +16,11 @@ Template.viewer.onCreated(() => {
     const contentId = instance.data.contentId;
 
     if (ViewerData[contentId].loadedSeriesData) {
-        log.info('Reloading previous loadedSeriesData');
+        OHIF.log.info('Reloading previous loadedSeriesData');
         OHIF.viewer.loadedSeriesData = ViewerData[contentId].loadedSeriesData;
 
     } else {
-        log.info('Setting default ViewerData');
+        OHIF.log.info('Setting default ViewerData');
         OHIF.viewer.loadedSeriesData = {};
         ViewerData[contentId].loadedSeriesData = {};
         Session.set('ViewerData', ViewerData);

Packages/ohif-core/client/index.js

@@ -1,6 +1,6 @@
 import './lib';
-import './components';
 import './helpers';
+import './components';
 import './ui';
 
 import './routes.js';

Packages/ohif-core/main.js

@@ -3,6 +3,7 @@
  */
 
 const OHIF = {
+    log: {},
     viewer: {},
     measurements: {}
 };

Packages/ohif-cornerstone/main.js

@@ -0,0 +1,24 @@
+// TODO: stop exposing the libraries below and start using imports
+
+import { cornerstone } from './client/cornerstone.js';
+import { dicomParser } from './client/dicomParser.js';
+import { cornerstoneMath } from './client/cornerstoneMath.js';
+import { cornerstoneTools } from './client/cornerstoneTools.js';
+import { cornerstoneWADOImageLoader } from './client/cornerstoneWADOImageLoader.js';
+
+// Expose the cornerstone objects to the client if it is on development mode
+if (Meteor.isDevelopment) {
+    window.cornerstone = cornerstone;
+    window.cornerstoneMath = cornerstoneMath;
+    window.cornerstoneTools = cornerstoneTools;
+    window.cornerstoneWADOImageLoader = cornerstoneWADOImageLoader;
+    window.dicomParser = dicomParser;
+}
+
+export {
+    cornerstone,
+    cornerstoneMath,
+    cornerstoneTools,
+    cornerstoneWADOImageLoader,
+    dicomParser
+};

Packages/ohif-cornerstone/package.js

@@ -41,5 +41,5 @@ Package.onUse(function(api) {
     api.export('cornerstoneMath', 'client');
     api.export('cornerstoneTools', 'client');
     api.export('cornerstoneWADOImageLoader', 'client');
-    api.export('dicomParser', ['client', 'server']);
+    api.export('dicomParser', 'client');
-});
+});

Packages/ohif-hanging-protocols/client/components/ruleEntryDialog/ruleEntryDialog.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 var keys = {
     ESC: 27
 };
@@ -118,7 +120,7 @@ function getActiveViewportImageId() {
             return;
         }
     } catch(error) {
-        log.warn(error);
+        OHIF.log.warn(error);
         return;
     }
     // Return the enabled element's imageId
@@ -141,7 +143,7 @@ function getAbstractPriorValue(imageId) {
     if (!priorStudy) {
         return;
     }
-    
+
     var studies = StudyListStudies.find({
         patientId: currentStudy.patientId,
         studyDate: {
@@ -184,7 +186,7 @@ function getCurrentAttributeValue(attribute, level) {
     if (level === 'protocol') {
         level = 'study';
     }
-    
+
     if (attribute === 'abstractPriorValue') {
         return getAbstractPriorValue(imageId);
     }

Packages/ohif-hanging-protocols/log.js

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

Packages/ohif-hanging-protocols/package.js

@@ -12,7 +12,6 @@ Package.onUse(function(api) {
     api.use('jquery');
     api.use('stylus');
     api.use('random');
-    api.use('practicalmeteor:loglevel');
     api.use('templating');
     api.use('natestrauser:select2@4.0.1', 'client');
     api.use('clinical:router');
@@ -22,11 +21,6 @@ Package.onUse(function(api) {
     // Our custom packages
     api.use('ohif:viewerbase');
 
-    // This sets the default logging level of the package using the
-    // loglevel package. It can be overridden in the JavaScript
-    // console for debugging purposes
-    api.addFiles('log.js');
-
     api.addAssets('assets/dots.svg', 'client');
 
     // Both client & server

Packages/ohif-lesiontracker/client/components/optionsModal/optionsModal.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 TrialCriteriaTypes = new Meteor.Collection(null);
 
 TrialCriteriaTypes.insert({
@@ -54,7 +56,7 @@ Template.optionsModal.events({
     'click a.clearAllStudyTimepointAssociations': function() {
         Meteor.call('clearAllTimepoints', function(error) {
             if (error) {
-                log.warn(error);
+                OHIF.log.warn(error);
             }
         });
     }

Packages/ohif-lesiontracker/lib/MeasurementValidation.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 // Create a client-only Collection to store our Validation Errors
 ValidationErrors = new Meteor.Collection(null);
 ValidationErrors._debugName = 'ValidationErrors';
@@ -55,7 +57,7 @@ function addValidationErrorsToCollection(validationErrors, prefix, type) {
  * @returns {Array} Array of error messages related to the input conformance checks
  */
 function assessGroupOfMeasurements(constraints) {
-    log.info('assessGroupOfMeasurements');
+    OHIF.log.info('assessGroupOfMeasurements');
 
     // Retrieve the group-level constraints
     var groupConstraints = constraints.group;
@@ -95,7 +97,7 @@ function assessGroupOfMeasurements(constraints) {
  * @returns {Array} Array of error messages related to the input conformance checks
  */
 function assessMeasurementPerOrgan(constraints) {
-    log.info('assessMeasurementPerOrgan');
+    OHIF.log.info('assessMeasurementPerOrgan');
 
     // Retrieve the per-organ constraints
     var perOrganConstraints = constraints.perOrgan;
@@ -154,7 +156,7 @@ function assessMeasurementPerOrgan(constraints) {
  * @returns {Array} Array of error messages related to the input conformance checks
  */
 function assessSingleMeasurement(constraints, measurementData) {
-    log.info('assessSingleMeasurement');
+    OHIF.log.info('assessSingleMeasurement');
 
     // Check whether this is a Target or Non-Target Measurement
     var targetType = measurementData.isTarget ? 'target' : 'nonTarget';
@@ -262,7 +264,7 @@ function validateSingleMeasurement(measurementData) {
 }
 
 function validateGroups() {
-    log.info('validateGroups');
+    OHIF.log.info('validateGroups');
 
     // Obtain the names of the current TrialResponseAssessmentCriteria that
     // we are using.
@@ -281,7 +283,7 @@ function validateGroups() {
     // TODO: Revisit this! We can't use the Timepoints collection inside ANY
     // of these functions, since it causes an infinite loop, since Measurement
     // validation is performed inside the observe:added hook for the Measurements
-    // Collection. 
+    // Collection.
 
     var timepointTypes = ['baseline', 'followup'];
     timepointTypes.forEach(function(timepointType) {

Packages/ohif-lesiontracker/lib/TrialCriteriaConstraints.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 // Define the Trial Criteria Structure
 TrialCriteriaConstraints = {
     RECIST: RECIST,
@@ -148,7 +150,7 @@ function RECIST(image) {
 
 /**
  * irRC Trial Criteria Definition
- * 
+ *
  * Baseline Checks:
  * - Target lesions must be >/= 10 X 10 mm
  * - Up to a max of 5 target lesions per organ
@@ -376,7 +378,7 @@ getTrialCriteriaConstraints = function(criteriaTypes, imageId) {
 
         const timepoint = timepointApi.study(studyMetaData.studyInstanceUid)[0];
         if (!timepoint) {
-            log.warn('Timepoint related to study is missing.');
+            OHIF.log.warn('Timepoint related to study is missing.');
             return;
         }
 

Packages/ohif-lesiontracker/lib/clearMeasurementTimepointData.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 clearMeasurementTimepointData = function(measurementId, timepointId) {
     var data = Measurements.findOne(measurementId);
 
@@ -16,7 +18,7 @@ clearMeasurementTimepointData = function(measurementId, timepointId) {
 };
 
 function removeToolDataWithMeasurementId(imageId, toolType, measurementId) {
-    log.info('removeToolDataWithMeasurementId');
+    OHIF.log.info('removeToolDataWithMeasurementId');
     var toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
 
     // Find any related toolData
@@ -39,8 +41,8 @@ function removeToolDataWithMeasurementId(imageId, toolType, measurementId) {
         }
     });
 
-    log.info('Removing Indices: ');
+    OHIF.log.info('Removing Indices: ');
-    log.info(toRemove);
+    OHIF.log.info(toRemove);
 
     // If any toolData entries need to be removed, splice them from
     // the toolData array

Packages/ohif-lesiontracker/lib/convertNonTarget.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 var responseTypes = {
     crTool: 'CR',
     exTool: 'EX',
@@ -16,7 +18,7 @@ convertNonTarget = function(measurementApi, measurementData, newTooltype) {
     });
 
     if (timepoint && timepoint.timepointType !== 'followup') {
-        log.warn('Not a followup');
+        OHIF.log.warn('Not a followup');
         return;
     }
 

Packages/ohif-lesiontracker/lib/getTimepointName.js

@@ -1,44 +0,0 @@
-/**
- * Calculates a Timepoint's name based on how many timepoints exist between it
- * and the latest Baseline. Names returned are in the form of 'Baseline', or
- * 'Follow-up 1', 'Follow-up 2', and so on.
- *
- * @param timepoint
- * @returns {*} The timepoint name
- */
-getTimepointName = function(timepoint) {
-    // Check if this is a Baseline timepoint, if it is, return 'Baseline'
-    if (timepoint.timepointType === 'baseline') {
-        return 'Baseline';
-    }
-
-    // Retrieve all of the relevant follow-up timepoints for this patient
-    var followupTimepoints = Timepoints.find({
-        patientId: timepoint.patientId,
-        timepointType: timepoint.timepointType
-    }, {
-        sort: {
-            latestDate: 1
-        }
-    });
-
-    // Create an array of just timepointIds, so we can use indexOf
-    // on it to find the current timepoint's relative position
-    var followupTimepointIds = followupTimepoints.map(function(timepoint) {
-        return timepoint.timepointId;
-    });
-
-    // Calculate the index of the current timepoint in the array of all
-    // relevant follow-up timepoints
-    var index = followupTimepointIds.indexOf(timepoint.timepointId) + 1;
-
-    // If index is 0, it means that the current timepoint was not in the list
-    // Log a warning and return here
-    if (!index) {
-        log.warn('Current follow-up was not in the list of relevant follow-ups?');
-        return;
-    }
-
-    // Return the timepoint name as 'Follow-up N'
-    return 'Follow-up ' + index;
-};

Packages/ohif-lesiontracker/lib/pixelSpacingAutorunCheck.js

@@ -1,5 +1,7 @@
+import { OHIF } from 'meteor/ohif:core';
+
 pixelSpacingAutorunCheck = function() {
-    log.info('lesionTool button change autorun');
+    OHIF.log.info('lesionTool button change autorun');
 
     // Get oncology tools
     var oncologyTools = $('button#lesion, button#nonTarget');
@@ -33,4 +35,4 @@ pixelSpacingAutorunCheck = function() {
         oncologyTools.prop('disabled', false);
     }
 
-};
+};

Packages/ohif-lesiontracker/lib/studylist/openNewTabWithTimepoint.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 /**
  * Opens a new tab in the tabbed studylist environment using
  * a given timepoint and new tab title.
@@ -12,7 +14,7 @@ openNewTabWithTimepoint = function(timepointId, title) {
     const timepoint = Timepoints.findOne({
         timepointId: timepointId
     });
-    
+
     if (!timepoint) {
         throw 'No such timepoint exists';
     }
@@ -73,7 +75,7 @@ function getDataFromTimepoint(timepoint) {
         relatedStudies = relatedStudies.concat(baseline.studyInstanceUids[0]);
         timepointIds.push(baseline.timepointId);
     } else {
-        log.warn('No Baseline found while opening a Follow-up Timepoint');
+        OHIF.log.warn('No Baseline found while opening a Follow-up Timepoint');
     }
 
     timepointIds.push(timepoint.timepointId);

Packages/ohif-lesiontracker/lib/syncMeasurementAndToolData.js

@@ -1,10 +1,12 @@
+import { OHIF } from 'meteor/ohif:core';
+
 function toolDataExists(toolState, imageId, toolType) {
     const currentToolState = toolState[imageId][toolType];
     return (currentToolState && currentToolState.data && currentToolState.data.length);
 }
 
 syncMeasurementAndToolData = function(measurement) {
-    log.info('syncMeasurementAndToolData');
+    OHIF.log.info('syncMeasurementAndToolData');
 
     const toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
     const imageId = measurement.imageId;
@@ -57,4 +59,4 @@ syncMeasurementAndToolData = function(measurement) {
 
     // Add the MeasurementData into the toolData for this imageId
     toolState[imageId][toolType].data.push(measurement);
-};
+};

Packages/ohif-lesiontracker/log.js

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

Packages/ohif-lesiontracker/package.js

@@ -15,9 +15,6 @@ Package.onUse(function(api) {
 
     api.use('validatejs');
 
-    // Control over logging
-    api.use('practicalmeteor:loglevel');
-
     // Template overriding
     api.use('aldeed:template-extension@4.0.0');
 
@@ -28,14 +25,12 @@ Package.onUse(function(api) {
     api.use('ohif:cornerstone');
     api.use('ohif:measurements');
 
-    api.addFiles('log.js', [ 'client', 'server' ]);
-
     api.addFiles('both/configuration/bidirectional.js', [ 'client', 'server' ]);
     api.addFiles('both/configuration/nonTarget.js', [ 'client', 'server' ]);
     api.addFiles('both/configuration/ellipse.js', [ 'client', 'server' ]);
     api.addFiles('both/configuration/length.js', [ 'client', 'server' ]);
     api.addFiles('both/configuration/measurementTools.js', [ 'client', 'server' ]);
-    
+
     api.addFiles('both/configuration/dataExchange.js', [ 'client', 'server' ]);
     api.addFiles('both/configuration/dataValidation.js', [ 'client', 'server' ]);
     api.addFiles('both/configuration/configuration.js', [ 'client', 'server' ]);
@@ -72,7 +67,7 @@ Package.onUse(function(api) {
     api.addFiles('client/components/measurementLocationDialog/measurementLocationDialog.html', 'client');
     api.addFiles('client/components/measurementLocationDialog/measurementLocationDialog.js', 'client');
     api.addFiles('client/components/measurementLocationDialog/measurementLocationDialog.styl', 'client');
-    
+
     api.addFiles('client/components/nonTargetLesionDialog/nonTargetLesionDialog.html', 'client');
     api.addFiles('client/components/nonTargetLesionDialog/nonTargetLesionDialog.styl', 'client');
     api.addFiles('client/components/nonTargetLesionDialog/nonTargetLesionDialog.js', 'client');
@@ -92,7 +87,7 @@ Package.onUse(function(api) {
     // Library functions
     api.addFiles('lib/TrialCriteriaConstraints.js', 'client');
     api.addFiles('lib/MeasurementValidation.js', 'client');
-    
+
     api.addFiles('lib/pixelSpacingAutorunCheck.js', 'client');
     api.addFiles('lib/toggleLesionTrackerTools.js', 'client');
     api.addFiles('lib/clearMeasurementTimepointData.js', 'client');
@@ -106,9 +101,6 @@ Package.onUse(function(api) {
     api.export('syncMeasurementAndToolData', 'client');
     api.export('syncImageMeasurementAndToolData', 'client');
     api.export('openNewTabWithTimepoint', 'client');
-    api.export('activateLesion', 'client');
-    api.export('activateMeasurements', 'client');
-    api.export('deactivateAllToolData', 'client');
     api.export('toggleLesionTrackerTools', 'client');
     api.export('clearMeasurementTimepointData', 'client');
     api.export('getTrialCriteriaConstraints', 'client');

Packages/ohif-log/main.js

@@ -0,0 +1,7 @@
+import { OHIF } from 'meteor/ohif:core';
+import { loglevel } from 'meteor/practicalmeteor:loglevel';
+
+const defaultLevel = Meteor.isProduction ? 'error' : 'trace';
+
+// Create package logger using loglevel
+OHIF.log = loglevel.createLogger('', defaultLevel);

Packages/ohif-log/package.js

@@ -0,0 +1,20 @@
+Package.describe({
+    name: 'ohif:log',
+    summary: 'OHIF Logging',
+    version: '0.0.1'
+});
+
+Package.onUse(function(api) {
+    api.versionsFrom('1.4');
+
+    api.use('ecmascript');
+    api.use('standard-app-packages');
+
+    // Control over logging
+    api.use('practicalmeteor:loglevel');
+
+    // Our custom packages
+    api.use('ohif:core');
+
+    api.addFiles('main.js', [ 'client', 'server' ]);
+});

Packages/ohif-measurements/both/configuration/measurements.js

@@ -41,7 +41,6 @@ class MeasurementApi {
 
         return new Promise((resolve, reject) => {
             retrievalFn().then(measurementData => {
-                // TODO: implement converter here
 
                 console.log('Measurement data retrieval');
                 console.log(measurementData);

Packages/ohif-measurements/both/configuration/timepoints.js

@@ -21,7 +21,7 @@ class TimepointApi {
             this.currentTimepointId = currentTimepointId;
         }
 
-        this.config = configuration || MeasurementApi.getConfiguration();
+        this.config = configuration || OHIF.measurements.MeasurementApi.getConfiguration();
     }
 
     retrieveTimepoints() {
@@ -38,7 +38,7 @@ class TimepointApi {
             retrievalFn().then(timepointData => {
                 console.log('Timepoint data retrieval');
                 console.log(timepointData);
-                timepointData.forEach(timepoint => {
+                _.each(timepointData, timepoint => {
                     delete timepoint._id;
                     this.timepoints.insert(timepoint);
                 });
@@ -191,7 +191,7 @@ class TimepointApi {
         // If index is 0, it means that the current timepoint was not in the list
         // Log a warning and return here
         if (!index) {
-            log.warn('Current follow-up was not in the list of relevant follow-ups?');
+            OHIF.log.warn('Current follow-up was not in the list of relevant follow-ups?');
             return;
         }
 

Packages/ohif-measurements/client/components/association/associationModal/associationModal.js

@@ -1,6 +1,8 @@
+import { OHIF } from 'meteor/ohif:core';
+
 Template.associationModal.events({
     'click #saveAssociations': function(e) {
-        log.info('Saving associations');
+        OHIF.log.info('Saving associations');
         const Timepoints = StudyList.timepointApi.timepoints;
 
         // Close the modal

Packages/ohif-measurements/client/components/longitudinal/longitudinalStudyListContextMenu/longitudinalStudyListContextMenu.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 // Use Aldeed's meteor-template-extension package to replace the
 // default StudyListStudy template.
 // See https://github.com/aldeed/meteor-template-extension
@@ -68,7 +70,7 @@ function removeTimepointAssociations() {
             // from the Timepoints Collection via a server call
             Meteor.call('removeTimepoint', timepoint._id, function(error) {
                 if (error) {
-                    log.warn(error);
+                    OHIF.log.warn(error);
                     return;
                 }
 

Packages/ohif-measurements/client/components/measurementTable/measurementTable.js

@@ -57,7 +57,7 @@ Template.measurementTable.onRendered(() => {
 
     // Activate the first lesion
     if (firstLesion) {
-        activateLesion(firstLesion._id, templateData);
+        OHIF.measurements.activateLesion(firstLesion._id, templateData);
     }
 });
 
@@ -67,7 +67,7 @@ Template.measurementTable.events({
      */
     /*'click table#tblLesion tbody tr': function(e, template) {
           var measurementId = $(e.currentTarget).data('measurementid');
-          activateLesion(measurementId, template.data);
+          OHIF.measurements.activateLesion(measurementId, template.data);
     },*/
 });
 

Packages/ohif-measurements/client/components/measurementTable/measurementTableRow/measurementTableRow.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 function doneCallback(measurementData, deleteTool) {
     // If a Lesion or Non-Target is removed via a dialog
     // opened by the Lesion Table, we should clear the data for
@@ -5,7 +7,7 @@ function doneCallback(measurementData, deleteTool) {
     if (deleteTool === true) {
         Meteor.call('removeMeasurement', measurementData.id, function(error, response) {
             if (error) {
-                log.warn(error);
+                OHIF.log.warn(error);
             }
         });
     }
@@ -25,7 +27,7 @@ Template.measurementTableRow.events({
     },
 
     'dblclick .location': function() {
-        log.info('Double clicked on Lesion Location cell');
+        OHIF.log.info('Double clicked on Lesion Location cell');
 
         var measurementData = this;
 
@@ -50,7 +52,7 @@ Template.measurementTableRow.events({
             showConfirmDialog(() => {
                 Meteor.call('removeMeasurement', currentMeasurement._id, (error, response) => {
                     if (error) {
-                        log.warn(error);
+                        OHIF.log.warn(error);
                     }
                 });
             }, options);

Packages/ohif-measurements/client/components/measurementTable/measurementTableTimepointCell/measurementTableTimepointCell.js

@@ -43,7 +43,7 @@ function doneCallback(measurementData, deleteTool) {
     // opened by the Lesion Table, we should clear the data for
     // the specified Timepoint Cell
     if (deleteTool === true) {
-        log.info('Confirm clicked!');
+        OHIF.log.info('Confirm clicked!');
         clearMeasurementTimepointData(measurementData.id, measurementData.timepointId);
     }
 }
@@ -56,7 +56,7 @@ const keys = {
 
 Template.measurementTableTimepointCell.events({
     'dblclick .measurementTableTimepointCell': function() {
-        log.info('Double clicked on a timepoint cell');
+        OHIF.log.info('Double clicked on a timepoint cell');
         // Search Measurements by lesion and timepoint
         const currentMeasurement = Template.parentData(1).rowItem;
 

Packages/ohif-measurements/client/components/measurementTable/measurementTableView/measurementTableView.html

@@ -1,8 +1,8 @@
 <template name="measurementTableView">
     <div class="measurementTableView scrollArea">
-        {{ #let config=measurementConfiguration}}
+        {{#let config=measurementConfiguration}}
-            {{ #each measurementType in config.measurementTools}}
+            {{#each measurementType in config.measurementTools}}
-                {{#if measurementType.options.showInMeasurementTable }}
+                {{#if measurementType.options.showInMeasurementTable}}
                     {{#let collection=(groupByMeasurementNumber measurementType.id)}}
                         {{>measurementTableHeaderRow
                             measurementType=measurementType
@@ -16,11 +16,11 @@
                         {{/each}}
                     {{/let}}
                 {{/if}}
-            {{ /each }}
+            {{/each}}
 
-            {{#if config.newMeasurementTool }}
+            {{#if config.newMeasurementTool}}
-                {{ #let new=newMeasurements }}
+                {{#let new=newMeasurements}}
-                    {{#if new }}
+                    {{#if new}}
                         {{#let collection=new tool=config.newMeasurementTool}}
                             {{>measurementTableHeaderRow
                                 measurementType=tool.measurementType

Packages/ohif-measurements/client/helpers/index.js

@@ -0,0 +1 @@
+import './measurements.js';

Packages/ohif-measurements/client/helpers/measurements.js

@@ -1,21 +1,7 @@
 import { OHIF } from 'meteor/ohif:core';
 
+// Get the current measurement API configuration with information about tools, data exchange
+// and data validation.
 Template.registerHelper('measurementConfiguration', () => {
-	//console.log('helper:measurementTools');
+    return OHIF.measurements.MeasurementApi.getConfiguration();
-    if (!OHIF.measurements.MeasurementApi) {
-        return;
-    }
-
-    const config = OHIF.measurements.MeasurementApi.getConfiguration();
-    return config;
-});
-
-Template.registerHelper('measurementApiCollection', measurementTypeId => {
-	//console.log('helper:measurementApiCollection');
-    if (!measurementTypeId) {
-        return;
-    }
-
-    const api = Template.instance().data.measurementApi;
-    return api[measurementTypeId].find();
 });

Packages/ohif-measurements/client/helpers/timepoints.js

@@ -1,5 +0,0 @@
-Template.registerHelper('getTimepointName', timepoint => {
-	const instance = Template.instance()
-	const timepointApi = instance.data.timepointApi;
-	return timepointApi.name(timepoint);
-});

Packages/ohif-measurements/client/index.js

@@ -0,0 +1,4 @@
+import './lib';
+import './helpers';
+// import './components';
+// import './ui';

Packages/ohif-measurements/client/lib/MeasurementHandlers.js

@@ -38,7 +38,7 @@ MeasurementHandlers.onAdded = (e, instance, eventData) => {
     const sopInstanceUid = sopInstance.sopInstanceUid;
     const frameIndex = sopInstance.frame || 0;
 
-    log.info('CornerstoneToolsMeasurementAdded');
+    OHIF.log.info('CornerstoneToolsMeasurementAdded');
 
     let measurement = $.extend({
         userId: Meteor.userId(),
@@ -108,7 +108,7 @@ MeasurementHandlers.onModified = (e, instance, eventData) => {
     const sopInstanceUid = sopInstance.sopInstanceUid;
     const frameIndex = sopInstance.frame || 0;
 
-    log.info('CornerstoneToolsMeasurementModified');
+    OHIF.log.info('CornerstoneToolsMeasurementModified');
 
     let measurement = Collection.findOne(measurementData.id);
 
@@ -141,7 +141,7 @@ MeasurementHandlers.onRemoved = (e, instance, eventData) => {
         return;
     }
 
-    log.info('CornerstoneToolsMeasurementRemoved');
+    OHIF.log.info('CornerstoneToolsMeasurementRemoved');
 
     const measurementToolConfiguration = config.measurementTools[index];
     const measurementApi = instance.data.measurementApi;

Packages/ohif-measurements/client/lib/activateLesion.js

@@ -1,3 +1,5 @@
+import { $ } from 'meteor/jquery';
+
 import { OHIF } from 'meteor/ohif:core';
 
 /**
@@ -5,35 +7,34 @@ import { OHIF } from 'meteor/ohif:core';
  *
  * @param measurementId The unique key for a specific Measurement
  */
-activateLesion = function(measurementId, templateData) {
+OHIF.measurements.activateLesion = (measurementId, templateData) => {
-
     // Set background color of selected row
-    $('tr[data-measurementid=' + measurementId + ']').addClass('selectedRow').siblings().removeClass('selectedRow');
+    $(`tr[data-measurementid=${measurementId}]`).addClass('selectedRow')
+        .siblings().removeClass('selectedRow');
 
-    var measurementData = Measurements.findOne(measurementId);
+    // Get the data for current measurement
+    const measurementData = Measurements.findOne(measurementId);
 
     // If there is no measurement with this ID, stop here
     if (!measurementData) {
-        log.warn('No Measurements entry associated to an ID in a lesion table row');
+        OHIF.OHIF.log.warn('No Measurements entry associated to an ID in a lesion table row');
         return;
     }
 
-    // Create an empty array to store the ordered timepoint data for this
+    // Create an empty array to store the ordered timepoint data for this measurement
-    // measurement
+    const orderedTimepointEntries = [];
-    var orderedTimepointEntries = [];
 
     // Retrieve the Cursor for this patient's Timepoints in ascending order by studyDate
-    var sortedTimepoints = Timepoints.find({}, {
+    const sortedTimepoints = Timepoints.find({}, {
         sort: {
             latestDate: 1
         }
     });
 
-    // Loop through each timepoint and populate the orderTimepointEntries array with
+    // Loop through each timepoint and populate the orderTimepointEntries array with the
-    // The measurement data at each timepoint. The most recent measurements will be first in
+    // measurement data at each timepoint. The most recent measurements will be first in the array.
-    // the array.
+    sortedTimepoints.forEach(timepoint => {
-    sortedTimepoints.forEach(function(timepoint) {
+        const measurementDataAtTimepoint = measurementData.timepoints[timepoint.timepointId];
-        var measurementDataAtTimepoint = measurementData.timepoints[timepoint.timepointId];
         if (!measurementDataAtTimepoint) {
             return;
         }
@@ -47,24 +48,24 @@ activateLesion = function(measurementId, templateData) {
     }
 
     // Retrieve the list of available viewports
-    var viewports = $('.imageViewerViewport').not('.empty');
+    const $viewports = $('.imageViewerViewport').not('.empty');
 
     // Remove earlier timepoint data entries
-    if (orderedTimepointEntries.length > viewports.length) {
+    if (orderedTimepointEntries.length > $viewports.length) {
-        var difference = orderedTimepointEntries.length - viewports.length;
+        const difference = orderedTimepointEntries.length - $viewports.length;
         orderedTimepointEntries.splice(0, difference);
     }
 
     // Loop through the viewports and display each timepoint
-    viewports.each(function(viewportIndex, element) {
+    $viewports.each((viewportIndex, element) => {
         // Stop if we run out of timepoints before viewports
         if (viewportIndex >= orderedTimepointEntries.length) {
             // Update the element anyway, to remove any other highlights that are present
-            deactivateAllToolData(element, 'bidirectional');
+            OHIF.measurements.deactivateAllToolData(element, 'bidirectional');
-            deactivateAllToolData(element, 'nonTarget');
+            OHIF.measurements.deactivateAllToolData(element, 'nonTarget');
-            deactivateAllToolData(element, 'crTool');
+            OHIF.measurements.deactivateAllToolData(element, 'crTool');
-            deactivateAllToolData(element, 'unTool');
+            OHIF.measurements.deactivateAllToolData(element, 'unTool');
-            deactivateAllToolData(element, 'exTool');
+            OHIF.measurements.deactivateAllToolData(element, 'exTool');
 
             return false;
         }
@@ -72,7 +73,7 @@ activateLesion = function(measurementId, templateData) {
         // Find measurements related to the Nth timepoint
         // TODO=Re-evaluate this approach to populating viewports with timepoints
         // What is the desired behaviour here?
-        var measurementAtTimepoint = orderedTimepointEntries[viewportIndex];
+        const measurementAtTimepoint = orderedTimepointEntries[viewportIndex];
 
         // Find the image that is currently in this viewport
         var enabledElement = cornerstone.getEnabledElement(element);
@@ -83,23 +84,24 @@ activateLesion = function(measurementId, templateData) {
         // If there is no measurement data to display, stop here
         if (!measurementAtTimepoint) {
             // Update the element anyway, to remove any other highlights that are present
-            deactivateAllToolData(element, 'bidirectional');
+            OHIF.measurements.deactivateAllToolData(element, 'bidirectional');
-            deactivateAllToolData(element, 'nonTarget');
+            OHIF.measurements.deactivateAllToolData(element, 'nonTarget');
-            deactivateAllToolData(element, 'crTool');
+            OHIF.measurements.deactivateAllToolData(element, 'crTool');
-            deactivateAllToolData(element, 'unTool');
+            OHIF.measurements.deactivateAllToolData(element, 'unTool');
-            deactivateAllToolData(element, 'exTool');
+            OHIF.measurements.deactivateAllToolData(element, 'exTool');
             cornerstone.updateImage(element);
             return;
         }
 
         // Check which study and series are required to display the measurement at this timepoint
-        var requiredSeriesData = {
+        const requiredSeriesData = {
             seriesInstanceUid: measurementAtTimepoint.seriesInstanceUid,
             studyInstanceUid: measurementAtTimepoint.studyInstanceUid
         };
 
         // Check if the study / series we need is already the one in the viewport
-        var currentSeriesData = OHIF.viewer.loadedSeriesData[viewportIndex];
+        const currentSeriesData = OHIF.viewer.loadedSeriesData[viewportIndex];
+        const activateMeasurements = OHIF.measurements.activateMeasurements;
         if (currentSeriesData.seriesInstanceUid === measurementAtTimepoint.seriesInstanceUid &&
             currentSeriesData.studyInstanceUid === measurementAtTimepoint.studyInstanceUid) {
             // If it is, activate the measurements in this viewport and stop here
@@ -109,7 +111,7 @@ activateLesion = function(measurementId, templateData) {
 
         // Otherwise, re-render the viewport with the required study/series, then
         // add an onRendered callback to activate the measurements
-        layoutManager.rerenderViewportWithNewDisplaySet(element, requiredSeriesData, function(element) {
+        layoutManager.rerenderViewportWithNewDisplaySet(element, requiredSeriesData, element => {
             activateMeasurements(element, measurementId, templateData, viewportIndex);
         });
     });

Packages/ohif-measurements/client/lib/activateMeasurements.js

@@ -1,22 +1,24 @@
+import { OHIF } from 'meteor/ohif:core';
+
 /**
  * Switch to the image of the correct image index
  * Activate the selected measurement on the switched image (color to be green)
  * Deactivate all other measurements on the switched image (color to be white)
  */
-activateMeasurements = function(element, measurementId, templateData, viewportIndex) {
+OHIF.measurements.activateMeasurements = (element, measurementId, templateData, viewportIndex) => {
     // TODO=Switch this to use the new CornerstoneToolMeasurementModified event,
     // Once it has 'modified on activation' set up
 
-    var enabledElement = cornerstone.getEnabledElement(element);
+    const enabledElement = cornerstone.getEnabledElement(element);
-    var imageId = enabledElement.image.imageId;
+    const imageId = enabledElement.image.imageId;
-    var timepointData = getTimepointObject(imageId);
+    const timepointData = getTimepointObject(imageId);
-    var measurementData = Measurements.findOne(measurementId);
+    const measurementData = Measurements.findOne(measurementId);
 
     if (!timepointData) {
         return;
     }
 
-    var measurementAtTimepoint = measurementData.timepoints[timepointData.timepointId];
+    const measurementAtTimepoint = measurementData.timepoints[timepointData.timepointId];
     if (!measurementAtTimepoint) {
         return;
     }
@@ -25,68 +27,25 @@ activateMeasurements = function(element, measurementId, templateData, viewportIn
     // If type is inactive, update lesions of enabledElement as inactive
     //TODO: !stackData.currentImageIdIndex returns incorrect value
     // Get loadedSeriesData currentImageIdIndex from ViewerData
-    var contentId = templateData.contentId;
+    const viewerData = ViewerData[templateData.contentId];
-    var viewerData = ViewerData[contentId];
+    const loadedSeriesData = viewerData.loadedSeriesData[viewportIndex];
-    var elementCurrentImageIdIndex = viewerData.loadedSeriesData[viewportIndex].currentImageIdIndex;
+    const elementCurrentImageIdIndex = loadedSeriesData.currentImageIdIndex;
 
-    var stackToolDataSource = cornerstoneTools.getToolState(element, 'stack');
+    const stackToolDataSource = cornerstoneTools.getToolState(element, 'stack');
-    var stackData = stackToolDataSource.data[0];
+    const stackData = stackToolDataSource.data[0];
-    var imageIds = stackData.imageIds;
+    const imageIds = stackData.imageIds;
-    var imageIdIndex = imageIds.indexOf(measurementAtTimepoint.imageId);
+    const imageIdIndex = imageIds.indexOf(measurementAtTimepoint.imageId);
 
     if (imageIdIndex < 0) {
         return;
     }
 
     if (imageIdIndex === elementCurrentImageIdIndex) {
-        activateTool(element, measurementData, timepointData.timepointId);
+        OHIF.measurements.activateTool(element, measurementData, timepointData.timepointId);
     } else {
-        cornerstone.loadAndCacheImage(imageIds[imageIdIndex]).then(function(image) {
+        cornerstone.loadAndCacheImage(measurementAtTimepoint.imageId).then(image => {
             cornerstone.displayImage(element, image);
-            activateTool(element, measurementData, timepointData.timepointId);
+            OHIF.measurements.activateTool(element, measurementData, timepointData.timepointId);
         });
     }
 };
-
-/**
- * Activates a specific tool data instance and deactivates all other
- * target and non-target measurement data
- *
- * @param element
- * @param measurementData
- * @param timepointId
- */
-function activateTool(element, measurementData, timepointId) {
-    deactivateAllToolData(element, 'bidirectional');
-    deactivateAllToolData(element, 'nonTarget');
-
-    // Deactivate CRUNEX Tools
-    deactivateAllToolData(element, 'crTool');
-    deactivateAllToolData(element, 'unTool');
-    deactivateAllToolData(element, 'exTool');
-
-    var toolType = measurementData.toolType;
-    var toolData = cornerstoneTools.getToolState(element, toolType);
-    if (!toolData) {
-        return;
-    }
-
-    var measurementAtTimepoint = measurementData.timepoints[timepointId];
-
-    for (var i = 0; i < toolData.data.length; i++) {
-        data = toolData.data[i];
-
-        // When click a row of table measurements, measurement will be active and color will be green
-        // TODO= Remove this with the measurementId once it is in the tool data
-        if (data.seriesInstanceUid === measurementAtTimepoint.seriesInstanceUid &&
-            data.studyInstanceUid === measurementAtTimepoint.studyInstanceUid &&
-            data.lesionNumber === measurementData.lesionNumber &&
-            data.isTarget == measurementData.isTarget) {
-
-            data.active = true;
-            break;
-        }
-    }
-
-    cornerstone.updateImage(element);
-}

Packages/ohif-measurements/client/lib/activateTool.js

@@ -0,0 +1,44 @@
+import { OHIF } from 'meteor/ohif:core';
+
+/**
+ * Activates a specific tool data instance and deactivates all other
+ * target and non-target measurement data
+ *
+ * @param element
+ * @param measurementData
+ * @param timepointId
+ */
+OHIF.measurements.activateTool = (element, measurementData, timepointId) => {
+    OHIF.measurements.deactivateAllToolData(element, 'bidirectional');
+    OHIF.measurements.deactivateAllToolData(element, 'nonTarget');
+
+    // Deactivate CRUNEX Tools
+    OHIF.measurements.deactivateAllToolData(element, 'crTool');
+    OHIF.measurements.deactivateAllToolData(element, 'unTool');
+    OHIF.measurements.deactivateAllToolData(element, 'exTool');
+
+    var toolType = measurementData.toolType;
+    var toolData = cornerstoneTools.getToolState(element, toolType);
+    if (!toolData) {
+        return;
+    }
+
+    var measurementAtTimepoint = measurementData.timepoints[timepointId];
+
+    for (var i = 0; i < toolData.data.length; i++) {
+        data = toolData.data[i];
+
+        // When click a row of table measurements, measurement will be active and color will be green
+        // TODO= Remove this with the measurementId once it is in the tool data
+        if (data.seriesInstanceUid === measurementAtTimepoint.seriesInstanceUid &&
+            data.studyInstanceUid === measurementAtTimepoint.studyInstanceUid &&
+            data.lesionNumber === measurementData.lesionNumber &&
+            data.isTarget == measurementData.isTarget) {
+
+            data.active = true;
+            break;
+        }
+    }
+
+    cornerstone.updateImage(element);
+};

Packages/ohif-measurements/client/lib/clearTools.js

@@ -1,60 +0,0 @@
-import { OHIF } from 'meteor/ohif:core';
-
-export const clearTools = () => {
-    const config = OHIF.measurements.MeasurementApi.getConfiguration();
-    const toolTypes = config.measurementTools.map(tool => {
-        return tool.cornerstoneToolType;
-    });
-
-    const $viewportElements = $('.imageViewerViewport').not('.empty');
-
-    let seriesInstanceUids = []; // Holds seriesInstanceUid of imageViewerViewport elements
-    $viewportElements.each((index, element) => {
-        const enabledElement = cornerstone.getEnabledElement(element);
-        const study = cornerstoneTools.metaData.get('study', enabledElement.image.imageId);
-        if (!study) {
-            return;
-        }
-
-        const series = cornerstoneTools.metaData.get('series', enabledElement.image.imageId);
-        if (!series) {
-            return;
-        }
-
-        seriesInstanceUids.push(series.seriesInstanceUid);
-    });
-
-    // Set null array for toolState data found by imageId and toolType
-    const toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
-    const toolStateKeys = Object.keys(toolState).slice(0);
-    toolStateKeys.forEach(imageId => {
-        toolTypes.forEach(toolType => {
-            const toolTypeData = toolState[imageId][toolType];
-            if (!toolTypeData || !toolTypeData.data.length) {
-                return;
-            }
-
-            const series = cornerstoneTools.metaData.get('series', imageId);
-            if (!series) {
-                return;
-            }
-
-            if (seriesInstanceUids.indexOf(series.seriesInstanceUid) === -1) {
-                return;
-            }
-
-            // If seriesInstanceUid is found in seriesInstanceUids, set toolState data as null
-            toolState[imageId][toolType] = {
-                data: []
-            };
-        });
-    });
-
-    // Update imageViewerViewport elements to remove lesions on current image
-    $viewportElements.each((index, element) => {
-        cornerstone.updateImage(element);
-    });
-
-    // Clear all validation errors
-    ValidationErrors.remove({});
-};

Packages/ohif-measurements/client/lib/deactivateAllToolData.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 /**
  * Sets all tool data entries value for 'active' to false
  * This is used to remove the active color on entire sets of tools
@@ -5,7 +7,7 @@
  * @param element The Cornerstone element that is being used
  * @param toolType The tooltype of the tools that will be deactivated
  */
-deactivateAllToolData = function(element, toolType) {
+OHIF.measurements.deactivateAllToolData = (element, toolType) => {
     var toolData = cornerstoneTools.getToolState(element, toolType);
     if (!toolData) {
         return;

Packages/ohif-measurements/client/lib/getTimepointName.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 /**
  * Calculates a Timepoint's name based on how many timepoints exist between it
  * and the latest Baseline. Names returned are in the form of 'Baseline', or
@@ -6,7 +8,7 @@
  * @param timepoint
  * @returns {*} The timepoint name
  */
-getTimepointName = function(timepoint) {
+OHIF.measurements.getTimepointName = (timepoint) => {
     // Check if this is a Baseline timepoint, if it is, return 'Baseline'
     if (timepoint.timepointType === 'baseline') {
         return 'Baseline';
@@ -35,7 +37,7 @@ getTimepointName = function(timepoint) {
     // If index is 0, it means that the current timepoint was not in the list
     // Log a warning and return here
     if (!index) {
-        log.warn('Current follow-up was not in the list of relevant follow-ups?');
+        OHIF.log.warn('Current follow-up was not in the list of relevant follow-ups?');
         return;
     }
 

Packages/ohif-measurements/client/lib/hangingProtocolCustomizations.js

@@ -1,3 +1,5 @@
+// TODO: [LT-refactor] move this to ohif:hanging-protocols package
+
 getTimepointType = function(study) {
     const timepointApi = Template.instance().timepointApi;
     if (!timepointApi) {
@@ -12,8 +14,8 @@ getTimepointType = function(study) {
     return timepoint.timepointType;
 };
 
-const HP = HP || false;
+HP = HP || false;
 
 if (HP) {
-	HP.addCustomAttribute('timepointType', 'Timepoint Type', getTimepointType);	
+    HP.addCustomAttribute('timepointType', 'Timepoint Type', getTimepointType);
-}
+}

Packages/ohif-measurements/client/lib/index.js

@@ -0,0 +1,10 @@
+import './activateLesion.js';
+import './activateMeasurements.js';
+import './activateTool.js';
+import './deactivateAllToolData.js';
+import './getTimepointName.js';
+import './getTimepointObject.js';
+import './hangingProtocolCustomizations.js';
+import './MeasurementHandlers.js';
+import './MeasurementManager.js';
+import './syncMeasurementAndToolData.js';

Packages/ohif-measurements/client/lib/syncMeasurementAndToolData.js

@@ -1,10 +1,12 @@
+import { OHIF } from 'meteor/ohif:core';
+
 function toolDataExists(toolState, imageId, toolType) {
     const currentToolState = toolState[imageId][toolType];
     return (currentToolState && currentToolState.data && currentToolState.data.length);
 }
 
 syncMeasurementAndToolData = function(measurement) {
-    log.info('syncMeasurementAndToolData');
+    OHIF.log.info('syncMeasurementAndToolData');
 
     const toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
     const imageId = measurement.imageId;
@@ -57,4 +59,4 @@ syncMeasurementAndToolData = function(measurement) {
 
     // Add the MeasurementData into the toolData for this imageId
     toolState[imageId][toolType].data.push(measurement);
-};
+};

Packages/ohif-measurements/log.js

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

Packages/ohif-measurements/package.js

@@ -19,19 +19,15 @@ Package.onUse(function(api) {
     api.use('aldeed:simple-schema');
     api.use('aldeed:collection2');
 
-    // Control over logging
-    api.use('practicalmeteor:loglevel');
-
     // Template overriding
     api.use('aldeed:template-extension@4.0.0');
 
     // Our custom packages
+    api.use('ohif:cornerstone');
     api.use('design');
     api.use('ohif:core');
+    api.use('ohif:log');
     api.use('ohif:study-list');
-    api.use('ohif:cornerstone');
-
-    api.addFiles('log.js', [ 'client', 'server' ]);
 
     api.addFiles('both/schema/measurements.js', ['client', 'server']);
     api.addFiles('both/schema/timepoints.js', ['client', 'server']);
@@ -39,11 +35,8 @@ Package.onUse(function(api) {
     api.addFiles('both/configuration/measurements.js', ['client', 'server']);
     api.addFiles('both/configuration/timepoints.js', ['client', 'server']);
 
-    api.addFiles('client/helpers/measurements.js', ['client']);
+    // Client imports and routes
-    api.addFiles('client/helpers/timepoints.js', ['client']);
+    api.addFiles('client/index.js', 'client');
-
-    api.addFiles('client/lib/hangingProtocolCustomizations.js');
-    api.addFiles('client/lib/syncMeasurementAndToolData.js', 'client');
 
     // Measurement Table Components
     api.addFiles('client/components/measurementTable/measurementTable.html', 'client');
@@ -106,14 +99,5 @@ Package.onUse(function(api) {
     api.addFiles('client/components/association/confirmRemoveTimepointAssociation/confirmRemoveTimepointAssociation.html', 'client');
     api.addFiles('client/components/association/confirmRemoveTimepointAssociation/confirmRemoveTimepointAssociation.js', 'client');
 
-    // Client Library functions
-    api.addFiles('client/lib/activateMeasurements.js', 'client');
-    api.addFiles('client/lib/activateLesion.js', 'client');
-    api.addFiles('client/lib/deactivateAllToolData.js', 'client');
-    api.addFiles('client/lib/MeasurementHandlers.js', 'client');
-    api.addFiles('client/lib/MeasurementManager.js', 'client');
-    api.addFiles('client/lib/getTimepointName.js', 'client');
-    api.addFiles('client/lib/getTimepointObject.js', 'client');
-
     api.export('MeasurementSchemaTypes', ['client', 'server']);
 });

Packages/ohif-petsuv/log.js

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

Packages/ohif-petsuv/package.js

@@ -15,9 +15,6 @@ Package.onUse(function(api) {
 
     api.use('validatejs');
 
-    // Control over logging
-    api.use('practicalmeteor:loglevel');
-
     // Template overriding
     api.use('aldeed:template-extension@4.0.0');
 
@@ -28,11 +25,9 @@ Package.onUse(function(api) {
     api.use('ohif:cornerstone');
     api.use('ohif:measurements');
 
-    api.addFiles('log.js', [ 'client', 'server' ]);
-
     api.addFiles('both/configuration/ellipse.js', [ 'client', 'server' ]);
     api.addFiles('both/configuration/measurementTools.js', [ 'client', 'server' ]);
-    
+
     api.addFiles('both/configuration/dataExchange.js', [ 'client', 'server' ]);
     api.addFiles('both/configuration/dataValidation.js', [ 'client', 'server' ]);
     api.addFiles('both/configuration/configuration.js', [ 'client', 'server' ]);

Packages/ohif-study-list/client/components/studylistResult/studylistResult.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 Session.setDefault('showLoadingText', true);
 
 Template.studylistResult.helpers({
@@ -149,7 +151,7 @@ function search() {
     Meteor.call('StudyListSearch', filter, (error, studies) => {
         console.log('StudyListSearch');
         if (error) {
-            log.warn(error);
+            OHIF.log.warn(error);
             return;
         }
 

Packages/ohif-study-list/client/components/studylistStudy/studylistStudy.js

@@ -1,9 +1,11 @@
+import { OHIF } from 'meteor/ohif:core';
+
 // Maybe we should use regular StudyList collection?
 StudyListSelectedStudies = new Meteor.Collection(null);
 StudyListSelectedStudies._debugName = 'StudyListSelectedStudies';
 
 function handleShiftClick(studyRow, data) {
-    //log.info('shiftKey');
+    //OHIF.log.info('shiftKey');
     var studyInstanceUid = studyRow.attr('studyInstanceUid');
 
     // Select all rows in between these two rows
@@ -60,7 +62,7 @@ function handleShiftClick(studyRow, data) {
 }
 
 function handleCtrlClick(studyRow, data) {
-    //log.info('ctrlKey');
+    //OHIF.log.info('ctrlKey');
     var studyInstanceUid = studyRow.attr('studyInstanceUid');
 
     if (studyRow.hasClass('active')) {
@@ -78,7 +80,7 @@ function handleCtrlClick(studyRow, data) {
         // Set this as the previously selected row, so the user can
         // use Shift to select from this point onwards
         StudyList.previouslySelected = studyRow;
-        log.info('StudyList PreviouslySelected set: ' + studyRow.index());
+        OHIF.log.info('StudyList PreviouslySelected set: ' + studyRow.index());
     }
 }
 
@@ -113,7 +115,7 @@ Template.studylistStudy.events({
             handleCtrlClick(studyRow, data);
         } else {
             // Select a single study
-            //log.info('Regular click');
+            //OHIF.log.info('Regular click');
 
             // Clear all selected studies
             StudyListSelectedStudies.remove({});
@@ -121,7 +123,7 @@ Template.studylistStudy.events({
 
             // Set the previous study to the currently clicked-on study
             StudyList.previouslySelected = studyRow;
-            //log.info('StudyList PreviouslySelected set: ' + studyRow.index());
+            //OHIF.log.info('StudyList PreviouslySelected set: ' + studyRow.index());
 
             // Set the current study as selected
             StudyListSelectedStudies.insert(data);
@@ -163,4 +165,4 @@ Template.studylistStudy.events({
         }
     }
 
-});
+});

Packages/ohif-study-list/client/lib/getStudiesMetadata.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 /**
  * Retrieves metaData for multiple studies at once.
  *
@@ -50,9 +52,9 @@ getStudiesMetadata = function(studyInstanceUids, doneCallback, failCallback) {
             doneCallback(studies);
         }
     }).fail(function(error) {
-        log.warn(error);
+        OHIF.log.warn(error);
         if (failCallback && typeof failCallback === 'function') {
             failCallback(error);
         }
     });
-};
+};

Packages/ohif-study-list/client/lib/getStudyMetadata.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 // Define the StudyMetaData object. This is used as a cache
 // to store study meta data information to prevent unnecessary
 // calls to the server
@@ -20,7 +22,7 @@ getStudyMetadata = function(studyInstanceUid, doneCallback, failCallback) {
         doneCallback(study);
         return;
     }
-    
+
     console.time('getStudyMetadata');
 
     // If no study metadata is in the cache variable, we need to retrieve it from
@@ -42,7 +44,7 @@ getStudyMetadata = function(studyInstanceUid, doneCallback, failCallback) {
         }
 
         if (error) {
-            log.warn(error);
+            OHIF.log.warn(error);
             failCallback(error);
             return;
         }

Packages/ohif-study-list/client/lib/importStudies.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 /**
  * Imports selected studies from local into studylist
  * @param filesToImport Files located in the client machine to import
@@ -44,7 +46,7 @@ importStudies = function(filesToImport, importCallback) {
 
                 if (fileUploadStatus.numberOfFilesFailed > 0) {
                     //TODO: Some files failed to upload, so let user know
-                    log.info("Failed to upload " + fileUploadStatus.numberOfFilesFailed + " of " + numberOfFilesToUpload + " files");
+                    OHIF.log.info("Failed to upload " + fileUploadStatus.numberOfFilesFailed + " of " + numberOfFilesToUpload + " files");
                 }
             }
         };
@@ -128,4 +130,4 @@ function importStudiesInternal(studiesToImport, importCallback) {
         //  Import studies with study import status id to get callbacks
         Meteor.call("importStudies", studiesToImport, studyImportStatusId);
     });
-}
+}

Packages/ohif-study-list/client/lib/switchToTab.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 /**
  *  Switches to a new tab in the tabbed studylist container
  *  This function renders either the StudyList or the Viewer template with new data.
@@ -9,7 +11,7 @@ switchToTab = function(contentId) {
         return;
     }
 
-    log.info('Switching to tab: ' + contentId);
+    OHIF.log.info('Switching to tab: ' + contentId);
 
     $('.tabTitle').removeClass('active');
     $('.tabTitle a[data-target="#' + contentId + '"]').addClass('active');
@@ -78,7 +80,7 @@ switchToTab = function(contentId) {
 function viewStudiesInTab(contentId, studies) {
     // Tab closed while study data was being retrieved, stop here
     if (!ViewerData[contentId]) {
-        log.warn('Tab closed while study data was being retrieved');
+        OHIF.log.warn('Tab closed while study data was being retrieved');
         return;
     }
 

Packages/ohif-study-list/log.js

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

Packages/ohif-study-list/package.js

@@ -12,7 +12,6 @@ Package.onUse(function (api) {
     api.use('jquery');
     api.use('stylus');
     api.use('http');
-    api.use('practicalmeteor:loglevel');
     api.use('random');
     api.use('silentcicero:jszip');
     api.use('aldeed:simple-schema');
@@ -35,11 +34,6 @@ Package.onUse(function (api) {
     // TODO: Replace with NPM dependency
     api.use('ohif:cornerstone'); // Only for HammerJS
 
-    // This sets the default logging level of the package using the
-    // loglevel package. It can be overridden in the JavaScript
-    // console for debugging purposes
-    api.addFiles('log.js');
-
     api.addFiles('both/collections.js', ['client', 'server']);
     api.addFiles('both/schema/servers.js', ['client', 'server']);
     api.addFiles('both/lib/getCurrentServer.js', ['client', 'server']);

Packages/ohif-study-list/server/methods/getStudyMetadata.js

@@ -1,10 +1,12 @@
+import { OHIF } from 'meteor/ohif:core';
+
 Meteor.methods({
     /**
      * Retrieves Study metadata given a Study Instance UID
      * This Meteor method is available from both the client and the server
      */
     GetStudyMetadata: function(studyInstanceUid) {
-        log.info('GetStudyMetadata(%s)', studyInstanceUid);
+        OHIF.log.info('GetStudyMetadata(%s)', studyInstanceUid);
 
         // Get the server data. This is user-defined in the config.json files or through servers
         // configuration modal

Packages/ohif-study-list/server/services/dimse/retrieveMetadata.js

@@ -1,4 +1,20 @@
-import { parseFloatArray } from '../../lib/parseFloatArray';
+import { OHIF } from 'meteor/ohif:core';
+import { parseFloatArray } from 'meteor/ohif:study-list/server/lib/parseFloatArray';
+
+/**
+ * Returns the value of the element (e.g. '00280009')
+ *
+ * @param element - The group/element of the element (e.g. '00280009')
+ * @param defaultValue - The default value to return if the element does not exist
+ * @returns {*}
+ */
+function getValue(element, defaultValue) {
+    if (!element || !element.value) {
+        return defaultValue;
+    }
+
+    return element.value;
+}
 
 /**
  * Parses the SourceImageSequence, if it exists, in order
@@ -18,21 +34,6 @@ function getSourceImageInstanceUid(instance) {
     }
 }
 
-/**
- * Returns the value of the element (e.g. '00280009')
- *
- * @param element - The group/element of the element (e.g. '00280009')
- * @param defaultValue - The default value to return if the element does not exist
- * @returns {*}
- */
-function getValue(element, defaultValue) {
-    if (!element || !element.value) {
-        return defaultValue;
-    }
-
-    return element.value;
-}
-
 /**
  * Parses result data from a DIMSE search into Study MetaData
  * Returns an object populated with study metadata, including the
@@ -43,7 +44,7 @@ function getValue(element, defaultValue) {
  * @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
  */
 function resultDataToStudyMetadata(studyInstanceUid, resultData) {
-    log.info('resultDataToStudyMetadata');
+    OHIF.log.info('resultDataToStudyMetadata');
     var seriesMap = {};
     var seriesList = [];
 
@@ -161,4 +162,4 @@ Services.DIMSE.RetrieveMetadata = function(studyInstanceUid) {
     }
 
     return resultDataToStudyMetadata(studyInstanceUid, results);
-};
+};

Packages/ohif-study-list/server/services/dimse/studies.js

@@ -1,59 +1,59 @@
-import { moment } from 'meteor/mrt:moment';
+import { OHIF } from 'meteor/ohif:core';
-
+
-/**
+/**
- * Parses resulting data from a QIDO call into a set of Study MetaData
+ * Parses resulting data from a QIDO call into a set of Study MetaData
- *
+ *
- * @param resultData
+ * @param resultData
- * @returns {Array} An array of Study MetaData objects
+ * @returns {Array} An array of Study MetaData objects
- */
+ */
-function resultDataToStudies(resultData) {
+function resultDataToStudies(resultData) {
-    var studies = [];
+    var studies = [];
-
+
-    resultData.forEach(function(studyRaw) {
+    resultData.forEach(function(studyRaw) {
-        var study = studyRaw.toObject();
+        var study = studyRaw.toObject();
-        studies.push({
+        studies.push({
-            studyInstanceUid: study[0x0020000D],
+            studyInstanceUid: study[0x0020000D],
-            // 00080005 = SpecificCharacterSet
+            // 00080005 = SpecificCharacterSet
-            studyDate: study[0x00080020],
+            studyDate: study[0x00080020],
-            studyTime: study[0x00080030],
+            studyTime: study[0x00080030],
-            accessionNumber: study[0x00080050],
+            accessionNumber: study[0x00080050],
-            referringPhysicianName: study[0x00080090],
+            referringPhysicianName: study[0x00080090],
-            // 00081190 = URL
+            // 00081190 = URL
-            patientName: study[0x00100010],
+            patientName: study[0x00100010],
-            patientId: study[0x00100020],
+            patientId: study[0x00100020],
-            patientBirthdate: study[0x00100030],
+            patientBirthdate: study[0x00100030],
-            patientSex: study[0x00100040],
+            patientSex: study[0x00100040],
-            imageCount: study[0x00201208],
+            imageCount: study[0x00201208],
-            studyId: study[0x00200010],
+            studyId: study[0x00200010],
-            studyDescription: study[0x00081030],
+            studyDescription: study[0x00081030],
-            modalities: study[0x00080061]
+            modalities: study[0x00080061]
-        });
+        });
-    });
+    });
-    return studies;
+    return studies;
-}
+}
-
+
-Services.DIMSE.Studies = function(filter) {
+Services.DIMSE.Studies = function(filter) {
-    log.info('Services.DIMSE.Studies');
+    OHIF.log.info('Services.DIMSE.Studies');
-
+
-    let filterStudyDate = '';
+    let filterStudyDate = '';
-    if (filter.studyDateFrom && filter.studyDateTo) {
+    if (filter.studyDateFrom && filter.studyDateTo) {
-        const convertDate = date => moment(date, 'MM/DD/YYYY').format('YYYYMMDD');
+        const convertDate = date => moment(date, 'MM/DD/YYYY').format('YYYYMMDD');
-        const dateFrom = convertDate(filter.studyDateFrom);
+        const dateFrom = convertDate(filter.studyDateFrom);
-        const dateTo = convertDate(filter.studyDateTo);
+        const dateTo = convertDate(filter.studyDateTo);
-        filterStudyDate = `${dateFrom}-${dateTo}`;
+        filterStudyDate = `${dateFrom}-${dateTo}`;
-    }
+    }
-
+
-    var parameters = {
+    var parameters = {
-        0x00100010: filter.patientName,
+        0x00100010: filter.patientName,
-        0x00100020: filter.patientId,
+        0x00100020: filter.patientId,
-        0x00080050: filter.accessionNumber,
+        0x00080050: filter.accessionNumber,
-        0x00080020: filterStudyDate,
+        0x00080020: filterStudyDate,
-        0x00081030: filter.studyDescription,
+        0x00081030: filter.studyDescription,
-        0x00100040: '',
+        0x00100040: '',
-        0x00201208: '',
+        0x00201208: '',
-        0x00080061: filter.modalitiesInStudy
+        0x00080061: filter.modalitiesInStudy
-    };
+    };
-
+
-    var results = DIMSE.retrieveStudies(parameters);
+    var results = DIMSE.retrieveStudies(parameters);
-    return resultDataToStudies(results);
+    return resultDataToStudies(results);
-};
+};

Packages/ohif-user-management/log.js

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

Packages/ohif-user-management/package.js

@@ -17,9 +17,6 @@ Package.onUse(function(api) {
     api.use('aldeed:simple-schema');
     api.use('aldeed:collection2');
 
-    // Control over logging
-    api.use('practicalmeteor:loglevel');
-
     // Template overriding
     api.use('aldeed:template-extension@4.0.0');
 
@@ -28,8 +25,6 @@ Package.onUse(function(api) {
     api.use('ohif:core');
     api.use('ohif:study-list');
 
-    api.addFiles('log.js', [ 'client', 'server' ]);
-
     api.addFiles('both/collections.js', ['client', 'server']);
     //api.addFiles('both/schema/reviewers.js', ['client', 'server']);
 

Packages/ohif-viewerbase/client/components/viewer/imageViewerViewport/imageViewerViewport.js

@@ -12,11 +12,11 @@ var allCornerstoneEvents = 'CornerstoneToolsMouseDown CornerstoneToolsMouseDownA
  * @param data {object} Object containing the study, series, and viewport element to be used
  */
 function loadDisplaySetIntoViewport(data, templateData) {
-    log.info('imageViewerViewport loadDisplaySetIntoViewport');
+    OHIF.log.info('imageViewerViewport loadDisplaySetIntoViewport');
 
     // Make sure we have all the data required to render the series
     if (!data.study || !data.displaySet || !data.element) {
-        log.warn('loadDisplaySetIntoViewport: No Study, Display Set, or Element provided');
+        OHIF.log.warn('loadDisplaySetIntoViewport: No Study, Display Set, or Element provided');
         return;
     }
 
@@ -66,7 +66,7 @@ function loadDisplaySetIntoViewport(data, templateData) {
 
         var numFrames = image.numFrames;
         if (numFrames > 1) {
-            log.info('Multiframe image detected');
+            OHIF.log.info('Multiframe image detected');
             for (var i = 0; i < numFrames; i++) {
                 metaData.frame = i;
                 imageId = getImageId(image, i);
@@ -136,7 +136,7 @@ function loadDisplaySetIntoViewport(data, templateData) {
         try {
             enabledElement = cornerstone.getEnabledElement(element);
         } catch (error) {
-            log.warn('Viewport destroyed before loaded image could be displayed');
+            OHIF.log.warn('Viewport destroyed before loaded image could be displayed');
             return;
         }
 
@@ -239,10 +239,10 @@ function loadDisplaySetIntoViewport(data, templateData) {
         // Define a function to run whenever the Cornerstone viewport is rendered
         // (e.g. following a change of window or zoom)
         function onImageRendered(e, eventData) {
-            log.info('imageViewerViewport onImageRendered');
+            OHIF.log.info('imageViewerViewport onImageRendered');
 
             if (!layoutManager.viewportData[viewportIndex]) {
-                log.warn("onImageRendered: LayoutManager has no viewport data for this viewport index?: " + viewportIndex);
+                OHIF.log.warn("onImageRendered: LayoutManager has no viewport data for this viewport index?: " + viewportIndex);
             }
 
             // Use Session to trigger reactive updates in the viewportOverlay helper functions
@@ -267,7 +267,7 @@ function loadDisplaySetIntoViewport(data, templateData) {
         // Define a function to run whenever the Cornerstone viewport changes images
         // (e.g. during scrolling)
         function onNewImage(e, eventData) {
-            log.info('imageViewerViewport onNewImage');
+            OHIF.log.info('imageViewerViewport onNewImage');
 
             // Update the metaData for missing fields
             updateMetaData(eventData.enabledElement.image);
@@ -323,7 +323,7 @@ function loadDisplaySetIntoViewport(data, templateData) {
                 return;
             }
 
-            log.info('imageViewerViewport sendActivationTrigger');
+            OHIF.log.info('imageViewerViewport sendActivationTrigger');
 
             // Otherwise, trigger an 'ActivateViewport' event to be handled by the Template event
             // handler
@@ -448,7 +448,7 @@ Meteor.startup(function() {
 
 Template.imageViewerViewport.onRendered(function() {
     var templateData = Template.currentData();
-    log.info('imageViewerViewport onRendered');
+    OHIF.log.info('imageViewerViewport onRendered');
 
     // When the imageViewerViewport template is rendered
     var element = this.find('.imageViewerViewport');
@@ -493,7 +493,7 @@ Template.imageViewerViewport.onRendered(function() {
 });
 
 Template.imageViewerViewport.onDestroyed(function() {
-    log.info('imageViewerViewport onDestroyed');
+    OHIF.log.info('imageViewerViewport onDestroyed');
 
     // When a viewport element is being destroyed
     var element = this.find('.imageViewerViewport');
@@ -509,7 +509,7 @@ Template.imageViewerViewport.onDestroyed(function() {
             cornerstoneTools.stopClip(element);
         }
     } catch (error) {
-        log.warn(error);
+        OHIF.log.warn(error);
     }
 
     // Disable the viewport element with Cornerstone
@@ -520,7 +520,7 @@ Template.imageViewerViewport.onDestroyed(function() {
 
 Template.imageViewerViewport.events({
     'ActivateViewport .imageViewerViewport'(event) {
-        log.info('imageViewerViewport ActivateViewport');
+        OHIF.log.info('imageViewerViewport ActivateViewport');
         setActiveViewport(event.currentTarget);
     },
 

Packages/ohif-viewerbase/client/components/viewer/toolbarSectionButton/toolbarSectionButton.js

@@ -29,10 +29,10 @@ Template.toolbarSectionButton.events({
         const activeTool = toolManager.getActiveTool();
         if (tool === activeTool) {
             const defaultTool = toolManager.getDefaultTool();
-            log.info('Setting active tool to: ' + defaultTool);
+            OHIF.log.info('Setting active tool to: ' + defaultTool);
             toolManager.setActiveTool(defaultTool, elements);
         } else {
-            log.info('Setting active tool to: ' + tool);
+            OHIF.log.info('Setting active tool to: ' + tool);
             toolManager.setActiveTool(tool, elements);
         }
     },

Packages/ohif-viewerbase/client/components/viewer/viewerMain/viewerMain.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 Template.viewerMain.onCreated(() => {
     // Attach the Window resize listener
     // Don't use jQuery here. "window.onresize" will always be null
@@ -28,8 +30,8 @@ Template.viewerMain.onRendered(() => {
 });
 
 Template.viewerMain.onDestroyed(() => {
-    log.info('viewerMain onDestroyed');
+    OHIF.log.info('viewerMain onDestroyed');
-    
+
     // Remove the Window resize listener
     window.removeEventListener('resize', handleResize);
 

Packages/ohif-viewerbase/lib/WLPresets.js

@@ -1,7 +1,7 @@
 import { OHIF } from 'meteor/ohif:core';
 
 applyWLPreset = function(presetName, element) {
-    log.info("Applying WL Preset: " + presetName);
+    OHIF.log.info("Applying WL Preset: " + presetName);
     var viewport = cornerstone.getViewport(element);
 
     if (presetName === 'Default') {

Packages/ohif-viewerbase/lib/displayReferenceLines.js

@@ -8,7 +8,7 @@ import { OHIF } from 'meteor/ohif:core';
  * @param element {node} DOM Node representing the viewport element
  */
 displayReferenceLines = element => {
-    log.info("imageViewerViewport displayReferenceLines");
+    OHIF.log.info("imageViewerViewport displayReferenceLines");
 
     // Check if image plane (orientation / loction) data is present for the current image
     const enabledElement = cornerstone.getEnabledElement(element);

Packages/ohif-viewerbase/lib/enableHotkeys.js

@@ -214,7 +214,7 @@ Meteor.startup(function() {
 $.fn.reverse = [].reverse;
 
 function previousActivePanel() {
-    log.info('nextActivePanel');
+    OHIF.log.info('nextActivePanel');
     var currentIndex = Session.get('activeViewport');
     currentIndex--;
 
@@ -233,7 +233,7 @@ function previousActivePanel() {
 }
 
 function nextActivePanel() {
-    log.info('nextActivePanel');
+    OHIF.log.info('nextActivePanel');
     var currentIndex = Session.get('activeViewport');
     currentIndex++;
 

Packages/ohif-viewerbase/lib/enablePrefetchOnElement.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 /**
  * This function enables stack prefetching for a specified element (viewport)
  * It first disables any prefetching currently occurring on any other viewports.
@@ -5,7 +7,7 @@
  * @param element {node} DOM Node representing the viewport element
  */
 enablePrefetchOnElement = function(element) {
-    log.info("imageViewerViewport enablePrefetchOnElement");
+    OHIF.log.info("imageViewerViewport enablePrefetchOnElement");
 
     // Loop through all viewports and disable stackPrefetch
     $('.imageViewerViewport').each(function() {
@@ -20,4 +22,4 @@ enablePrefetchOnElement = function(element) {
     if (stack && stack.data.length && stack.data[0].imageIds.length > 1) {
         cornerstoneTools.stackPrefetch.enable(element);
     }
-};
+};

Packages/ohif-viewerbase/lib/getWADORSImageId.js

@@ -1,3 +1,5 @@
+import { OHIF } from 'meteor/ohif:core';
+
 /**
  * Obtain an imageId for Cornerstone based on the WADO-RS scheme
  *
@@ -55,6 +57,6 @@ getWADORSImageId = function(instance) {
 
     var imageId = cornerstoneWADOImageLoader.imageManager.add(image);
 
-    log.info('WADO-RS ImageID: ' + imageId);
+    OHIF.log.info('WADO-RS ImageID: ' + imageId);
     return imageId;
 };

Packages/ohif-viewerbase/lib/layoutManager.js

@@ -3,7 +3,7 @@ import { OHIF } from 'meteor/ohif:core';
 // Displays Series in Viewports given a Protocol and list of Studies
 LayoutManager = class LayoutManager {
     constructor(parentNode, studies) {
-        log.info('LayoutManager');
+        OHIF.log.info('LayoutManager');
 
         this.parentNode = parentNode;
         this.studies = studies;
@@ -99,7 +99,7 @@ LayoutManager = class LayoutManager {
     }
 
     updateViewports() {
-        log.info('updateViewports');
+        OHIF.log.info('updateViewports');
 
         if (!this.viewportData ||
             !this.viewportData.length ||
@@ -176,7 +176,7 @@ LayoutManager = class LayoutManager {
     }
 
     enlargeViewport(viewportIndex) {
-        log.info('Zooming Into Viewport: ' + viewportIndex);
+        OHIF.log.info('Zooming Into Viewport: ' + viewportIndex);
 
         if (!this.viewportData ||
             !this.viewportData.length) {

Packages/ohif-viewerbase/log.js

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

Packages/ohif-viewerbase/package.js

@@ -12,7 +12,6 @@ Package.onUse(function(api) {
     api.use('http');
     api.use('jquery');
     api.use('stylus');
-    api.use('practicalmeteor:loglevel');
     api.use('momentjs:moment');
     api.use('validatejs');
 
@@ -21,8 +20,6 @@ Package.onUse(function(api) {
     api.use('ohif:core');
     api.use('ohif:cornerstone');
 
-    api.addFiles('log.js');
-
     api.addAssets('assets/icons.svg', 'client');
 
     // TODO: Use NPM depends for these

StandaloneViewer/SampleClientOnlyBuild/099fe52d37f20fa59c58ba61e783d73eb2b4db91.js

@@ -250,7 +250,6 @@ o.parent(".dropdown-menu").length&&(o=o.closest("li.dropdown").addClass("active"
 
 Mongo=Package.mongo.Mongo,ReactiveVar=Package["reactive-var"].ReactiveVar,$=Package.jquery.$,jQuery=Package.jquery.jQuery,Tracker=Package.tracker.Tracker,Deps=Package.tracker.Deps,cornerstone=Package.cornerstone.cornerstone,cornerstoneMath=Package.cornerstone.cornerstoneMath,cornerstoneTools=Package.cornerstone.cornerstoneTools,cornerstoneWADOImageLoader=Package.cornerstone.cornerstoneWADOImageLoader,dicomParser=Package.cornerstone.dicomParser,DICOMWeb=Package.dicomweb.DICOMWeb,resizeViewportElements=Package.viewerbase.resizeViewportElements,handleResize=Package.viewerbase.handleResize,enableHotkeys=Package.viewerbase.enableHotkeys,enablePrefetchOnElement=Package.viewerbase.enablePrefetchOnElement,displayReferenceLines=Package.viewerbase.displayReferenceLines,setActiveViewport=Package.viewerbase.setActiveViewport,createStacks=Package.viewerbase.createStacks,getImageId=Package.viewerbase.getImageId,getWADORSImageId=Package.viewerbase.getWADORSImageId,metaDataProvider=Package.viewerbase.metaDataProvider,sortStudy=Package.viewerbase.sortStudy,updateOrientationMarkers=Package.viewerbase.updateOrientationMarkers,setFocusToActiveViewport=Package.viewerbase.setFocusToActiveViewport,updateAllViewports=Package.viewerbase.updateAllViewports,queryStudies=Package.viewerbase.queryStudies,getNumberOfFilesInStudy=Package.viewerbase.getNumberOfFilesInStudy,exportStudies=Package.viewerbase.exportStudies,importStudies=Package.viewerbase.importStudies,getActiveViewportElement=Package.viewerbase.getActiveViewportElement,getInstanceClassDefaultViewport=Package.viewerbase.getInstanceClassDefaultViewport,showConfirmDialog=Package.viewerbase.showConfirmDialog,applyWLPreset=Package.viewerbase.applyWLPreset,toggleDialog=Package.viewerbase.toggleDialog,isImage=Package.viewerbase.isImage,sopClassDictionary=Package.viewerbase.sopClassDictionary,addMetaData=Package.viewerbase.addMetaData,toolManager=Package.viewerbase.toolManager,LayoutManager=Package.viewerbase.LayoutManager,ClientId=Package.viewerbase.ClientId,ViewerStudies=Package.viewerbase.ViewerStudies,formatPN=Package.viewerbase.formatPN,isTouchDevice=Package.viewerbase.isTouchDevice,toggleCineDialog=Package.viewerbase.toggleCineDialog,toggleCinePlay=Package.viewerbase.toggleCinePlay,clearTools=Package.viewerbase.clearTools,resetViewport=Package.viewerbase.resetViewport,invert=Package.viewerbase.invert,getStudyMetadata=Package.worklist.getStudyMetadata,getStudiesMetadata=Package.worklist.getStudiesMetadata,openNewTab=Package.worklist.openNewTab,switchToTab=Package.worklist.switchToTab,progressDialog=Package.worklist.progressDialog,Worklist=Package.worklist.Worklist,ViewerData=Package.worklist.ViewerData,WorklistTabs=Package.worklist.WorklistTabs,WorklistStudies=Package.worklist.WorklistStudies,WorklistSelectedStudies=Package.worklist.WorklistSelectedStudies,WADOProxy=Package.wadoproxy.WADOProxy,SimpleSchema=Package["aldeed:simple-schema"].SimpleSchema,MongoObject=Package["aldeed:simple-schema"].MongoObject,Router=Package["clinical:router"].Router,RouteController=Package["clinical:router"].RouteController,Session=Package.session.Session,loglevel=Package["practicalmeteor:loglevel"].loglevel,ObjectLogger=Package["practicalmeteor:loglevel"].ObjectLogger,ReactiveDict=Package["reactive-dict"].ReactiveDict,moment=Package["mrt:moment"].moment,FastClick=Package.fastclick.FastClick,Modal=Package["peppelg:bootstrap-3-modal"].Modal,Random=Package.random.Random,Meteor=Package.meteor.Meteor,global=Package.meteor.global,meteorEnv=Package.meteor.meteorEnv,WebApp=Package.webapp.WebApp,_=Package.underscore._,DDP=Package["ddp-client"].DDP,LaunchScreen=Package["launch-screen"].LaunchScreen,Blaze=Package.ui.Blaze,UI=Package.ui.UI,Handlebars=Package.ui.Handlebars,Spacebars=Package.spacebars.Spacebars,Template=Package["templating-runtime"].Template,meteorInstall=Package.modules.meteorInstall,Buffer=Package.modules.Buffer,process=Package.modules.process,Symbol=Package["ecmascript-runtime"].Symbol,Map=Package["ecmascript-runtime"].Map,Set=Package["ecmascript-runtime"].Set,meteorBabelHelpers=Package["babel-runtime"].meteorBabelHelpers,Promise=Package.promise.Promise,Iron=Package["iron:core"].Iron,Autoupdate=Package.autoupdate.Autoupdate,Reload=Package.reload.Reload,HTML=Package.htmljs.HTML;
 
-var require=meteorInstall({client:{components:{flexboxLayout:{"template.flexboxLayout.js":function(){Template.__checkName("flexboxLayout"),Template.flexboxLayout=new Template("Template.flexboxLayout",function(){var e=this;return HTML.DIV({class:"viewerSection"},"\n        ",HTML.DIV({class:function(){return["sidebarMenu sidebar-left ",Blaze.If(function(){return Spacebars.call(e.lookup("leftSidebarOpen"))},function(){return"sidebar-open"})]}},"\n            ",Blaze._TemplateWith(function(){return Spacebars.dataMustache(e.lookup("clone"),e.lookup("."))},function(){return Spacebars.include(e.lookupTemplate("studyBrowser"))}),"\n        "),"\n        ",HTML.DIV({class:function(){return["mainContent ",Blaze.If(function(){return Spacebars.call(e.lookup("leftSidebarOpen"))},function(){return"sidebar-left-open"})]}},"\n            ",Blaze._TemplateWith(function(){return Spacebars.dataMustache(e.lookup("clone"),e.lookup("."))},function(){return Spacebars.include(e.lookupTemplate("standaloneViewerMain"))}),"\n        "),"\n    ")})},"flexboxLayout.js":function(){Template.flexboxLayout.events({"transitionend .sidebarMenu":function(){function e(e){e.target.classList.contains("sidebarMenu")&&handleResize()}return e}()}),Template.flexboxLayout.helpers({leftSidebarOpen:function(){function e(){return Template.instance().data.state.get("leftSidebar")}return e}()})}},standaloneViewer:{"template.standaloneViewer.js":function(){Template.__checkName("standaloneViewer"),Template.standaloneViewer=new Template("Template.standaloneViewer",function(){var e=this;return[HTML.DIV({class:"topBar noselect"},"\n        ",HTML.DIV({class:"clearfix p-x-1 p-t-1"},"\n            ",HTML.A({target:"_blank",class:"brandSection pull-left",href:"http://ohif.org"},"\n                ",HTML.SVG({class:"logoImage"},"\n                    ",HTML.USE({"xlink:href":"/packages/viewerbase/assets/icons.svg#icon-ohif-logo"}),"\n                "),"\n                ",HTML.Raw('<div class="logoText">\n                    Open Health Imaging Foundation\n                </div>'),"\n            "),"\n        "),"\n    "),"\n    ",Spacebars.include(e.lookupTemplate("viewer"))]})},"standaloneViewer.js":function(){Template.standaloneViewer.onCreated(function(){ViewerData=Session.get("ViewerData")||{}})}},standaloneViewerMain:{"template.standaloneViewerMain.js":function(){Template.__checkName("standaloneViewerMain"),Template.standaloneViewerMain=new Template("Template.standaloneViewerMain",function(){var e=this;return HTML.Raw('<div class="viewerMain">\n        <div id="layoutManagerTarget">\n        </div>\n    </div>')})},"standaloneViewerMain.js":["meteor/ohif:core",function(e,t,a){var n;a.import("meteor/ohif:core",{OHIF:function(e){n=e}}),Template.standaloneViewerMain.onCreated(function(){Meteor.defer(function(){$(window).on("resize",handleResize)}),n.viewer.updateImageSynchronizer=new cornerstoneTools.Synchronizer("CornerstoneNewImage",cornerstoneTools.updateImageSynchronizer)}),Template.standaloneViewerMain.onRendered(function(){var e=Template.instance(),t=e.data.studies,a=e.$("#layoutManagerTarget").get(0);window.layoutManager=new LayoutManager(a,t),window.layoutManager.updateViewports(),enableHotkeys()}),Template.standaloneViewerMain.onDestroyed(function(){$(window).off("resize",handleResize),n.viewer.updateImageSynchronizer.destroy(),delete window.layoutManager})}]},toolbarSection:{"template.toolbarSection.js":function(){Template.__checkName("toolbarSection"),Template.toolbarSection=new Template("Template.toolbarSection",function(){var e=this;return HTML.DIV({class:"toolbarSection noselect p-x-2"},"\n        ",HTML.DIV({class:"clearfix"},"\n            ",HTML.DIV({class:"pull-left m-t-1"},"\n                ",Blaze._TemplateWith(function(){return Spacebars.call(e.lookup("leftSidebarToggleButtonData"))},function(){return Spacebars.include(e.lookupTemplate("roundedButtonGroup"))}),"\n            "),"\n            ",Blaze._TemplateWith(function(){return{toolbarButtons:Spacebars.call(e.lookup("toolbarButtons")),extraToolbarButtons:Spacebars.call(e.lookup("extraToolbarButtons"))}},function(){return Spacebars.include(e.lookupTemplate("toolbarSectionTools"))}),"\n        "),"\n    ")})},"toolbarSection.js":["meteor/ohif:core",function(e,t,a){var n;a.import("meteor/ohif:core",{OHIF:function(e){n=e}}),Template.toolbarSection.helpers({leftSidebarToggleButtonData:function(){function e(){var e=Template.instance();return{toggleable:!0,key:"leftSidebar",value:e.data.state,options:[{value:"studies",svgLink:"/packages/viewerbase/assets/icons.svg#icon-studies",svgWidth:15,svgHeight:13,bottomLabel:"Series"}]}}return e}(),toolbarButtons:function(){function e(){var e=[];return e.push({id:"zoom",title:"Zoom",classes:"imageViewerTool",svgLink:"/packages/viewerbase/assets/icons.svg#icon-tools-zoom"}),e.push({id:"wwwc",title:"Levels",classes:"imageViewerTool",svgLink:"/packages/viewerbase/assets/icons.svg#icon-tools-levels"}),e.push({id:"pan",title:"Pan",classes:"imageViewerToolLine truncated
+var require=meteorInstall({client:{components:{flexboxLayout:{"template.flexboxLayout.js":function(){Template.__checkName("flexboxLayout"),Template.flexboxLayout=new Template("Template.flexboxLayout",function(){var e=this;return HTML.DIV({class:"viewerSection"},"\n        ",HTML.DIV({class:function(){return["sidebarMenu sidebar-left ",Blaze.If(function(){return Spacebars.call(e.lookup("leftSidebarOpen"))},function(){return"sidebar-open"})]}},"\n            ",Blaze._TemplateWith(function(){return Spacebars.dataMustache(e.lookup("clone"),e.lookup("."))},function(){return Spacebars.include(e.lookupTemplate("studyBrowser"))}),"\n        "),"\n        ",HTML.DIV({class:function(){return["mainContent ",Blaze.If(function(){return Spacebars.call(e.lookup("leftSidebarOpen"))},function(){return"sidebar-left-open"})," ",Blaze.If(function(){return Spacebars.call(e.lookup("rightSidebarOpen"))},function(){return"sidebar-right-open"})]}},"\n            ",Blaze._TemplateWith(function(){return Spacebars.dataMustache(e.lookup("clone"),e.lookup("."))},function(){return Spacebars.include(e.lookupTemplate("standaloneViewerMain"))}),"\n        "),"\n    ")})},"flexboxLayout.js":function(){Template.flexboxLayout.events({"transitionend .sidebarMenu":function(){function e(e){e.target.classList.contains("sidebarMenu")&&handleResize()}return e}()}),Template.flexboxLayout.helpers({leftSidebarOpen:function(){function e(){return Template.instance().data.state.get("leftSidebar")}return e}(),rightSidebarOpen:function(){function e(){return Template.instance().data.state.get("rightSidebar")}return e}()})}},standaloneViewer:{"template.standaloneViewer.js":function(){Template.__checkName("standaloneViewer"),Template.standaloneViewer=new Template("Template.standaloneViewer",function(){var e=this;return[HTML.DIV({class:"topBar noselect"},"\n        ",HTML.DIV({class:"clearfix p-x-1 p-t-1"},"\n            ",HTML.A({target:"_blank",class:"brandSection pull-left",href:"http://ohif.org"},"\n                ",HTML.SVG({class:"logoImage"},"\n                    ",HTML.USE({"xlink:href":"/packages/viewerbase/assets/icons.svg#icon-ohif-logo"}),"\n                "),"\n                ",HTML.Raw('<div class="logoText">\n                    Open Health Imaging Foundation\n                </div>'),"\n            "),"\n        "),"\n    "),"\n    ",Spacebars.include(e.lookupTemplate("viewer"))]})},"standaloneViewer.js":function(){Template.standaloneViewer.onCreated(function(){ViewerData=Session.get("ViewerData")||{}})}},standaloneViewerMain:{"template.standaloneViewerMain.js":function(){Template.__checkName("standaloneViewerMain"),Template.standaloneViewerMain=new Template("Template.standaloneViewerMain",function(){var e=this;return HTML.Raw('<div class="viewerMain">\n        <div id="layoutManagerTarget">\n        </div>\n    </div>')})},"standaloneViewerMain.js":["meteor/ohif:core",function(e,t,a){var n;a.import("meteor/ohif:core",{OHIF:function(e){n=e}}),Template.standaloneViewerMain.onCreated(function(){$(window).on("resize",handleResize),n.viewer.updateImageSynchronizer=new cornerstoneTools.Synchronizer("CornerstoneNewImage",cornerstoneTools.updateImageSynchronizer)}),Template.standaloneViewerMain.onRendered(function(){var e=Template.instance(),t=e.data.studies,a=e.$("#layoutManagerTarget").get(0);window.layoutManager=new LayoutManager(a,t),window.layoutManager.updateViewports(),enableHotkeys()}),Template.standaloneViewerMain.onDestroyed(function(){$(window).off("resize",handleResize),n.viewer.updateImageSynchronizer.destroy(),delete window.layoutManager})}]},toolbarSection:{"template.toolbarSection.js":function(){Template.__checkName("toolbarSection"),Template.toolbarSection=new Template("Template.toolbarSection",function(){var e=this;return HTML.DIV({class:"toolbarSection noselect p-x-2"},"\n        ",HTML.DIV({class:"clearfix"},"\n            ",HTML.DIV({class:"pull-left m-t-1"},"\n                ",Blaze._TemplateWith(function(){return Spacebars.call(e.lookup("leftSidebarToggleButtonData"))},function(){return Spacebars.include(e.lookupTemplate("roundedButtonGroup"))}),"\n            "),"\n            ",Blaze._TemplateWith(function(){return{toolbarButtons:Spacebars.call(e.lookup("toolbarButtons")),extraToolbarButtons:Spacebars.call(e.lookup("extraToolbarButtons"))}},function(){return Spacebars.include(e.lookupTemplate("toolbarSectionTools"))}),"\n        "),"\n    ")})},"toolbarSection.js":["meteor/ohif:core",function(e,t,a){var n;a.import("meteor/ohif:core",{OHIF:function(e){n=e}}),Template.toolbarSection.helpers({leftSidebarToggleButtonData:function(){function e(){var e=Template.instance();return{toggleable:!0,key:"leftSidebar",value:e.data.state,options:[{value:"studies",svgLink:"/packages/viewerbase/assets/icons.svg#icon-studies",svgWidth:15,svgHeight:13,bottomLabel:"Series"}]}}return e}(),rightSidebarToggleButtonData:function(){function e(){var e=Template.instance();return{toggleable:!0,key:"rightSidebar",value:e.data.state,options:[{value:"hLine truncated
 
 !function(){var e=Package.meteor.Meteor,r=Package.meteor.global,a=Package.meteor.meteorEnv,t=Package["aldeed:simple-schema"].SimpleSchema,o=Package["aldeed:simple-schema"].MongoObject,i=Package.modules.meteorInstall,n=Package.modules.Buffer,l=Package.modules.process,s=Package["ecmascript-runtime"].Symbol,c=Package["ecmascript-runtime"].Map,m=Package["ecmascript-runtime"].Set,u=Package["babel-runtime"].meteorBabelHelpers,d=Package.promise.Promise,p,g=i({node_modules:{meteor:{"mdg:validation-error":{"validation-error.js":["babel-runtime/helpers/classCallCheck","babel-runtime/helpers/possibleConstructorReturn","babel-runtime/helpers/inherits",function(r,a,o){var i;o.import("babel-runtime/helpers/classCallCheck",{default:function(e){i=e}});var n;o.import("babel-runtime/helpers/possibleConstructorReturn",{default:function(e){n=e}});var l;o.import("babel-runtime/helpers/inherits",{default:function(e){l=e}});var s=new t({name:{type:String},type:{type:String},details:{type:Object,blackbox:!0,optional:!0}}),c=new t({errors:{type:Array},"errors.$":{type:s}});p=function(e){function r(a){var t=arguments.length<=1||void 0===arguments[1]?"Validation Failed":arguments[1];i(this,r),c.validate({errors:a});var o=n(this,e.call(this,p.ERROR_CODE,t,a));return o.errors=a,o}return l(r,e),r}(e.Error),p.ERROR_CODE="validation-error"}]}}}},{extensions:[".js",".json"]});g("./node_modules/meteor/mdg:validation-error/validation-error.js"),"undefined"==typeof Package&&(Package={}),function(e,r){for(var a in r)a in e||(e[a]=r[a])}(Package["mdg:validation-error"]={},{ValidationError:p})}();
-

StandaloneViewer/StandaloneViewer/client/components/viewer/viewer.js

@@ -34,10 +34,10 @@ Template.viewer.onCreated(() => {
     const contentId = instance.data.contentId;
 
     if (ViewerData[contentId] && ViewerData[contentId].loadedSeriesData) {
-        log.info('Reloading previous loadedSeriesData');
+        OHIF.log.info('Reloading previous loadedSeriesData');
         OHIF.viewer.loadedSeriesData = ViewerData[contentId].loadedSeriesData;
     } else {
-        log.info('Setting default ViewerData');
+        OHIF.log.info('Setting default ViewerData');
         OHIF.viewer.loadedSeriesData = {};
         ViewerData[contentId] = {};
         ViewerData[contentId].loadedSeriesData = OHIF.viewer.loadedSeriesData;