Creating ohif:metadata package with metadata classes and adding it to the viewers

LesionTracker/.meteor/packages

@@ -35,6 +35,7 @@ ohif:dicom-services
 ohif:hanging-protocols
 ohif:user-management
 ohif:lesiontracker
+ohif:metadata
 
 accounts-base@1.2.14
 accounts-password@1.3.3

LesionTracker/.meteor/versions

@@ -95,6 +95,7 @@ ohif:hanging-protocols@0.0.1
 ohif:lesiontracker@0.0.1
 ohif:log@0.0.1
 ohif:measurements@0.0.1
+ohif:metadata@0.0.1
 ohif:study-list@0.0.1
 ohif:user-management@0.0.1
 ohif:viewerbase@0.0.1

OHIFViewer/.meteor/packages

@@ -13,6 +13,7 @@ ohif:study-list
 ohif:dicom-services
 ohif:hanging-protocols
 # ohif:user-management
+ohif:metadata
 
 twbs:bootstrap
 http@1.2.10

OHIFViewer/.meteor/versions

@@ -20,10 +20,6 @@ caching-compiler@1.1.9
 caching-html-compiler@1.0.7
 callback-hook@1.0.10
 check@1.2.4
-clinical:router@2.0.17
-clinical:router-location@2.0.14
-clinical:router-middleware-stack@2.0.13
-clinical:router-url@2.0.15
 coffeescript@1.11.1_4
 ddp@1.2.5
 ddp-client@1.3.2
@@ -81,6 +77,7 @@ ohif:design@0.0.1
 ohif:dicom-services@0.0.1
 ohif:hanging-protocols@0.0.1
 ohif:log@0.0.1
+ohif:metadata@0.0.1
 ohif:study-list@0.0.1
 ohif:viewerbase@0.0.1
 ohif:wadoproxy@0.0.1

OHIFViewer/client/components/toolbarSection/toolbarSection.js

@@ -1,7 +1,8 @@
-import { OHIF } from 'meteor/ohif:core';
 import { Template } from 'meteor/templating';
 import { $ } from 'meteor/jquery';
-import { Viewerbase } from 'meteor/ohif:viewerbase';
+
+import { OHIF } from 'meteor/ohif:core';
+import 'meteor/ohif:viewerbase';
 
 Template.toolbarSection.onCreated(() => {
     const instance = Template.instance();
@@ -182,7 +183,7 @@ Template.toolbarSection.helpers({
                 title: 'CINE',
                 classes: 'imageViewerCommand',
                 iconClasses: 'fa fa-youtube-play',
-                disableFunction: Viewerbase.viewportUtils.hasMultipleFrames
+                disableFunction: OHIF.viewerbase.viewportUtils.hasMultipleFrames
             });
         }
 
@@ -232,11 +233,11 @@ Template.toolbarSection.onRendered(function() {
     instance.$('#layout').dropdown();
 
     if (OHIF.uiSettings.displayEchoUltrasoundWorkflow) {
-        Viewerbase.viewportUtils.toggleCineDialog();
+        toggleCineDialog();
     }
 
     // Set disabled/enabled tool buttons that are set in toolManager
-    const states = Viewerbase.toolManager.getToolDefaultStates();
+    const states = OHIF.viewerbase.toolManager.getToolDefaultStates();
     const disabledToolButtons = states.disabledToolButtons;
     const allToolbarButtons = $('#toolbar').find('button');
     if (disabledToolButtons && disabledToolButtons.length > 0) {

OHIFViewer/client/components/viewer/viewer.js

@@ -1,5 +1,6 @@
 import { OHIF } from 'meteor/ohif:core';
-import { Viewerbase } from 'meteor/ohif:viewerbase';
+import 'meteor/ohif:viewerbase';
+import 'meteor/ohif:metadata';
 
 OHIF.viewer = OHIF.viewer || {};
 OHIF.viewer.defaultTool = 'wwwc';
@@ -54,6 +55,8 @@ Template.viewer.onCreated(() => {
     instance.data.studies.forEach(study => {
         study.selected = true;
         study.displaySets = Viewerbase.createStacks(study);
+        // const studyMetadata = new OHIF.metadata.StudyMetadata(study);
+        // study.displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(studyMetadata);
         ViewerStudies.insert(study);
         ViewerData[contentId].studyInstanceUids.push(study.studyInstanceUid);
     });

Packages/ohif-hanging-protocols/package.js

@@ -26,7 +26,6 @@ Package.onUse(function(api) {
     // Both client & server
     api.addFiles('both/namespace.js');
     api.addFiles('both/collections.js');
-    //api.addFiles('both/dicomTagDescriptions.js');
     api.addFiles('both/schema.js');
     api.addFiles('both/hardcodedData.js');
     api.addFiles('both/testData.js');

Packages/ohif-metadata/client/OHIFInstanceMetadata.js

@@ -0,0 +1,58 @@
+import { Viewerbase } from 'meteor/ohif:viewerbase';
+
+const InstanceMetadata = Viewerbase.metadata.InstanceMetadata;
+
+export class OHIFInstanceMetadata extends InstanceMetadata {
+
+    /**
+     * @param {Object} Instance object.
+     */
+    constructor(data) {
+        super(data);
+        this.init();
+    }
+
+    init() {
+        const data = this.getData();
+        // set protected property...
+        this._sopInstanceUID = data.sopInstanceUid;
+    }
+
+    // Override
+    getRawValue(tagOrProperty, defaultValue) {
+        const propertyName = OHIFInstanceMetadata.getPropertyName(tagOrProperty);
+
+        const data = this.getData();
+        const rawValue = data[propertyName];
+
+        return rawValue !== void 0 ? rawValue : defaultValue;
+    }
+
+    // Override
+    tagExists(tagOrProperty) {
+        const propertyName = OHIFInstanceMetadata.getPropertyName(tagOrProperty);
+
+        const data = this.getData();
+
+        return (propertyName in data);
+    }
+
+    /**
+     * Static methods
+     */
+    
+    static getPropertyName(tagOrProperty) {
+        const tagInfo = InstanceMetadata.getTagInfo(tagOrProperty);
+
+        if(tagInfo.propertyName === null) {
+            return;
+        }
+
+        let propertyName = tagInfo.propertyName.charAt(0).toLowerCase() + tagInfo.propertyName.substr(1);
+        // TODO: Improve this: change retriveMetadata to use dicom standard names (see dicomTagDescriptions.js)
+        propertyName = propertyName.replace(/^sop/, 'SOP');
+        propertyName = propertyName.replace(/uid$/i, 'UID');
+
+        return propertyName;
+    }
+}

Packages/ohif-metadata/client/OHIFSeriesMetadata.js

@@ -0,0 +1,26 @@
+import { Viewerbase } from 'meteor/ohif:viewerbase';
+import { OHIFInstanceMetadata } from './OHIFInstanceMetadata';
+
+export class OHIFSeriesMetadata extends Viewerbase.metadata.SeriesMetadata {
+
+    /**
+     * @param {Object} Series object.
+     */
+    constructor(data) {
+        super(data);
+        this.init();
+    }
+
+    init() {
+        const data = this.getData();
+
+        // set protected property...
+        this._seriesInstanceUID = data.seriesInstanceUid;
+        // populate internal list of instances...
+        data.instances.forEach(instance => {
+            this.addInstance(new OHIFInstanceMetadata(instance));
+        });
+    }
+
+}
+

Packages/ohif-metadata/client/OHIFStudyMetadata.js

@@ -0,0 +1,25 @@
+import { Viewerbase } from 'meteor/ohif:viewerbase';
+import { OHIFSeriesMetadata } from './OHIFSeriesMetadata';
+
+export class OHIFStudyMetadata extends Viewerbase.metadata.StudyMetadata {
+
+    /**
+     * @param {Object} Study object.
+     */
+    constructor(data) {
+        super(data);
+        this.init();
+    }
+
+    init() {
+        const data = this.getData();
+
+        // set protected property...
+        this._studyInstanceUID = data.studyInstanceUid;
+        // populate internal list of series...
+        data.seriesList.forEach(series => {
+            this.addSeries(new OHIFSeriesMetadata(series));
+        });
+    }
+
+}

Packages/ohif-metadata/client/index.js

@@ -0,0 +1,10 @@
+import { Metadata } from '../namespace';
+
+// OHIFStudyMetadata, OHIFSeriesMetadata, OHIFInstanceMetadata
+import { OHIFStudyMetadata } from './OHIFStudyMetadata';
+import { OHIFSeriesMetadata } from './OHIFSeriesMetadata';
+import { OHIFInstanceMetadata } from './OHIFInstanceMetadata';
+
+Metadata.StudyMetadata = OHIFStudyMetadata;
+Metadata.SeriesMetadata = OHIFSeriesMetadata;
+Metadata.InstanceMetadata = OHIFInstanceMetadata;

Packages/ohif-metadata/main.js

@@ -0,0 +1,39 @@
+/**
+ * Import namespace...
+ */
+
+import { OHIF, Metadata } from  './namespace.js';
+
+/**
+ * Import scripts that will populate the Metadata namespace as a side effect only import. This is effectively the public API...
+ */
+
+import './client/'; // which is actually: import './client/index.js';
+
+/**
+ * Export relevant objects...
+ *
+ * With the following export it becomes possible to import "OHIF" from "ohif:core" and "Metadata"
+ * from "ohif:metadata" using a single import (a shorthand), like this:
+ *
+ * import { OHIF } from 'meteor/ohif:metadata';
+ *
+ * Which is equivalent to:
+ *
+ * import { OHIF } from 'meteor/ohif:core';
+ * import 'meteor/ohif:metadata';
+ *
+ * The second (extended) format should be used when other OHIF packages are also to be used within
+ * the current module. This makes it explicit that the following imports will populate their
+ * respective namespaces within the to "OHIF" namespace. Example:
+ *
+ * import { OHIF } from 'meteor/ohif:core';
+ * import 'meteor/ohif:metadata';
+ * import 'meteor/ohif:hanging-protocols';
+ * [ ... ]
+ * OHIF.metadata.setActiveViewport(...);
+ * OHIF.hangingprotocols.doSomething(...);
+ *
+ */
+
+export { OHIF, Metadata };

Packages/ohif-metadata/namespace.js

@@ -0,0 +1,23 @@
+/**
+ * Import main dependency...
+ */
+
+import { OHIF } from 'meteor/ohif:core';
+
+/**
+ * Create Metadata namespace...
+ */
+
+const Metadata = {};
+
+/**
+ * Append Metadata namespace to OHIF namespace...
+ */
+
+OHIF.metadata = Metadata;
+
+/**
+ * Export relevant objects...
+ */
+
+export { OHIF, Metadata };

Packages/ohif-metadata/package.js

@@ -0,0 +1,16 @@
+Package.describe({
+    name: 'ohif:metadata',
+    summary: 'OHIF Metadata classes',
+    version: '0.0.1'
+});
+
+Package.onUse(function(api) {
+    api.versionsFrom('1.4');
+
+    api.use('ecmascript');
+
+    api.use('ohif:core');
+    api.use('ohif:viewerbase');
+
+    api.mainModule('main.js', 'client');
+});

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

@@ -1,5 +1,5 @@
 import { OHIF } from 'meteor/ohif:core';
-import { Viewerbase } from 'meteor/ohif:viewerbase';
+import 'meteor/ohif:viewerbase';
 
 // Define the StudyMetaData object. This is used as a cache
 // to store study meta data information to prevent unnecessary
@@ -56,7 +56,7 @@ getStudyMetadata = function(studyInstanceUid, doneCallback, failCallback) {
 
         // Once we have retrieved the data, we sort the series' by series
         // and instance number in ascending order
-        Viewerbase.sortStudy(study);
+        OHIF.viewerbase.sortStudy(study);
 
         // Add additional metadata to our study from the studylist
         var studylistStudy = StudyListStudies.findOne({

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

@@ -119,7 +119,7 @@ function resultDataToStudyMetadata(studyInstanceUid, resultData) {
             laterality: instance[0x00200062],
             viewPosition: instance[0x00185101],
             acquisitionDatetime: instance[0x0008002A],
-            numFrames: parseFloat(instance[0x00280008]),
+            numberOfFrames: parseFloat(instance[0x00280008]),
             frameIncrementPointer: getValue(instance[0x00280009]),
             frameTime: parseFloat(instance[0x00181063]),
             frameTimeVector: parseFloatArray(instance[0x00181065]),

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

@@ -97,7 +97,7 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
             laterality: remoteGetValue(instance['0020,0062']),
             viewPosition: remoteGetValue(instance['0018,5101']),
             acquisitionDatetime: remoteGetValue(instance['0008,002A']),
-            numFrames: parseFloat(remoteGetValue(instance['0028,0008'])),
+            numberOfFrames: parseFloat(remoteGetValue(instance['0028,0008'])),
             frameIncrementPointer: remoteGetValue(instance['0028,0009']),
             frameTime: parseFloat(remoteGetValue(instance['0018,1063'])),
             frameTimeVector: parseFloatArray(remoteGetValue(instance['0018,1065']))

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

@@ -109,7 +109,7 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
             laterality: DICOMWeb.getString(instance['00200062']),
             viewPosition: DICOMWeb.getString(instance['00185101']),
             acquisitionDatetime: DICOMWeb.getString(instance['0008002A']),
-            numFrames: DICOMWeb.getNumber(instance['00280008']),
+            numberOfFrames: DICOMWeb.getNumber(instance['00280008']),
             frameIncrementPointer: DICOMWeb.getAttribute(instance['00280009']),
             frameTime: DICOMWeb.getNumber(instance['00181063']),
             frameTimeVector: parseFloatArray(DICOMWeb.getString(instance['00181065'])),

Packages/ohif-viewerbase/client/index.js

@@ -163,6 +163,10 @@ Viewerbase.helpers = helpers;
 import { sopClassDictionary } from './lib/sopClassDictionary';
 Viewerbase.sopClassDictionary = sopClassDictionary;
 
+// dicomTagDescriptions
+import { dicomTagDescriptions } from './lib/dicomTagDescriptions';
+Viewerbase.dicomTagDescriptions = dicomTagDescriptions;
+
 /**
  * Exported Classes
  */

Packages/ohif-viewerbase/client/lib/StackManager.js

@@ -30,10 +30,10 @@ function createAndAddStack(stackMap, study, displaySet) {
           imageIndex: imageIndex + 1
       };
 
-      const numFrames = image.numFrames;
-      if (numFrames > 1) {
+      const numberOfFrames = image.numberOfFrames;
+      if (numberOfFrames > 1) {
           OHIF.log.info('Multiframe image detected');
-          for (let i = 0; i < numFrames; i++) {
+          for (let i = 0; i < numberOfFrames; i++) {
               metaData.frame = i;
               imageId = getImageId(image, i);
               imageIds.push(imageId);

Packages/ohif-viewerbase/client/lib/classes/metadata/InstanceMetadata.js

@@ -1,9 +1,10 @@
 import { Metadata } from './Metadata';
+import { dicomTagDescriptions } from '../../dicomTagDescriptions';
 
 const UNDEFINED = 'undefined';
 const NUMBER = 'number';
 const STRING = 'string';
-const REGEX_TAG = /^x[0-9a-f]{8}$/;
+const REGEX_TAG = /^x[0-9a-fx]{8}$/;
 
 export class InstanceMetadata extends Metadata {
 
@@ -132,7 +133,17 @@ export class InstanceMetadata extends Metadata {
             propertyName = tagOrProperty;
         }
 
-        // @TODO: map tagName to propertyName and vice versa
+        // It's a property
+        if (tagName === null) {
+            for (let tag in dicomTagDescriptions) {
+                if (dicomTagDescriptions[tag] === propertyName) {
+                    tagName = tag;
+                    break;
+                }
+            }
+        } else if (propertyName === null) {
+            propertyName = dicomTagDescriptions[tagName] || null;
+        }
 
         return { tagName, propertyName };
     }

Packages/ohif-viewerbase/client/lib/createStacks.js

@@ -44,7 +44,7 @@ function createStacks(study) {
                 displaySet.setAttributes({
                     isClip: true,
                     studyInstanceUid: study.studyInstanceUid, // Include the study instance Uid for drag/drop purposes
-                    numImageFrames: instance.numFrames, // Override the default value of instances.length
+                    numImageFrames: instance.numberOfFrames, // Override the default value of instances.length
                     instanceNumber: instance.instanceNumber, // Include the instance number
                     acquisitionDatetime: instance.acquisitionDatetime // Include the acquisition datetime
                 });
@@ -110,7 +110,7 @@ function isSingleImageModality(modality) {
 }
 
 function isMultiFrame(instance) {
-    return instance.numFrames > 1;
+    return instance.numberOfFrames > 1;
 }
 
 /**

Packages/ohif-viewerbase/client/lib/dicomTagDescriptions.js

@@ -1,4 +1,4 @@
-HP.tagDescriptions = {
+export const dicomTagDescriptions = {
     x00020000: 'FileMetaInfoGroupLength',
     x00020001: 'FileMetaInfoVersion',
     x00020002: 'MediaStorageSOPClassUID',
@@ -3145,4 +3145,4 @@ HP.tagDescriptions = {
     xfffee000: 'StartOfItem',
     xfffee00d: 'EndOfItems',
     xfffee0dd: 'EndOfSequence'
-};
+};

Packages/ohif-viewerbase/client/lib/getSortedData.js

@@ -126,7 +126,6 @@ const stackOfInstancesToDisplaySets = (sopInstances, seriesView) => {
     const groups = _.groupBy(sopInstances, sopInstance => {
         // Create an empty string to store our key
         let result = '';
-        const instanceView = sopInstance.getData();
 
         // For each rule, find out if the tag exists
         seriesSplittingRules.forEach(rule => {
@@ -134,8 +133,8 @@ const stackOfInstancesToDisplaySets = (sopInstances, seriesView) => {
             result += ';'
 
             // If the tag exists, concatenate its value to our key
-            if (instanceView.exists(rule.tag)) {
-                result += instanceView.raw(rule.tag);
+            if (sopInstance.tagExists(rule.tag)) {
+                result += sopInstance.getRawValue(rule.tag);
             }
         });