Instance metadata/metadata providers overhaul (#1481)

* Instance metadata plus metadata provider overhaul.

Fix consumption of wado-uri urls

fallbacks + datatype agnosticism.

WIP DICOMify things.

fix various issues with naturalized variable naming migration.

Remove metadata provider.

Fix consumption of multiframe images and addition of CWIL metadata.

Fix strange build issues.

Fix CWIL style windowWidth to array from naturalized DICOM.

Fix PT, CT, CR and DX issues for cornerstone + DX issues for vtkjs.

Move color palette fetching down to the natuaralized JSON level.

Remove unused StudyMetadataSummary

Remove redundant dicom metadata dictionary.

Working local + json routes.

Fix SR read.

Finished first round of testing + cleaned up debugging etc.

* data => metadata for instance naturalizedJSON

* Update dcmjs version

* Correct github isssues.

* Fix erroneously replaced files.

* Danny's recommended changes.

* Instance metadata plus metadata provider overhaul.

Fix consumption of wado-uri urls

fallbacks + datatype agnosticism.

WIP DICOMify things.

fix various issues with naturalized variable naming migration.

Remove metadata provider.

Fix consumption of multiframe images and addition of CWIL metadata.

Fix strange build issues.

Fix CWIL style windowWidth to array from naturalized DICOM.

Fix PT, CT, CR and DX issues for cornerstone + DX issues for vtkjs.

Move color palette fetching down to the natuaralized JSON level.

Remove unused StudyMetadataSummary

Remove redundant dicom metadata dictionary.

Working local + json routes.

Fix SR read.

Finished first round of testing + cleaned up debugging etc.

* data => metadata for instance naturalizedJSON

* Update dcmjs version

* Correct github isssues.

* Fix erroneously replaced files.

* Danny's recommended changes.

* Update JSON CI

* Update casing of import.

* Fix jump for SR.

* Fix unit tests for measurements service

* Fix json CI test.

* fix: update yarn lock

* Fix local non-encapsulated pdf view

* CI updated to new sucess message.

Co-authored-by: Danny <danny.ri.brown@gmail.com>

platform/core/src/utils/StackManager.js

@@ -1,9 +1,9 @@
 import OHIFError from '../classes/OHIFError.js';
 import getImageId from './getImageId';
+import metadataProvider from '../classes/MetadataProvider.js';
 
 let stackMap = {};
 let configuration = {};
-let stackManagerMetaDataProvider;
 const stackUpdatedCallbacks = [];
 
 /**
@@ -15,13 +15,7 @@ const stackUpdatedCallbacks = [];
  * @param  {Object} displaySet            The set of images to make the stack from
  * @return {Array}                        Array with image IDs
  */
-function createAndAddStack(
-  stackMap,
-  study,
-  displaySet,
-  stackUpdatedCallbacks,
-  metadataProvider
-) {
+function createAndAddStack(stackMap, study, displaySet, stackUpdatedCallbacks) {
   const images = displaySet.images;
   if (!images) {
     return;
@@ -41,31 +35,56 @@ function createAndAddStack(
       imageIndex: imageIndex + 1,
     };
 
-    const numberOfFrames = image.numberOfFrames;
-    if (numberOfFrames > 1) {
-      for (let i = 0; i < numberOfFrames; i++) {
+    const NumberOfFrames = image.NumberOfFrames;
+
+    if (NumberOfFrames > 1) {
+      for (let i = 0; i < NumberOfFrames; i++) {
         metaData.frameNumber = i;
         imageId = getImageId(image, i);
         imageIds.push(imageId);
-        metadataProvider.addMetadata(imageId, metaData);
+
+        const {
+          StudyInstanceUID,
+          SeriesInstanceUID,
+          SOPInstanceUID,
+        } = instance.getData().metadata;
+
+        metadataProvider.addImageIdToUIDs(imageId, {
+          StudyInstanceUID,
+          SeriesInstanceUID,
+          SOPInstanceUID,
+        });
       }
     } else {
       metaData.frameNumber = 1;
       imageId = getImageId(image);
       imageIds.push(imageId);
-      metadataProvider.addMetadata(imageId, metaData);
+
+      const naturalizedInstance = instance.getData().metadata;
+
+      const {
+        StudyInstanceUID,
+        SeriesInstanceUID,
+        SOPInstanceUID,
+      } = naturalizedInstance;
+
+      metadataProvider.addImageIdToUIDs(imageId, {
+        StudyInstanceUID,
+        SeriesInstanceUID,
+        SOPInstanceUID,
+      });
     }
   });
 
   const stack = {
-    studyInstanceUid: study.studyInstanceUid,
-    displaySetInstanceUid: displaySet.displaySetInstanceUid,
+    StudyInstanceUID: study.StudyInstanceUID,
+    displaySetInstanceUID: displaySet.displaySetInstanceUID,
     imageIds,
     frameRate: displaySet.frameRate,
     isClip: displaySet.isClip,
   };
 
-  stackMap[displaySet.displaySetInstanceUid] = stack;
+  stackMap[displaySet.displaySetInstanceUID] = stack;
 
   return stack;
 }
@@ -80,9 +99,6 @@ configuration = {
  * come in, you can register a callback with addStackUpdatedCallback.
  */
 const StackManager = {
-  setMetadataProvider(provider) {
-    stackManagerMetaDataProvider = provider;
-  },
   /**
    * Removes all current stacks
    */
@@ -96,27 +112,20 @@ const StackManager = {
    * @return {Array} Array with image IDs
    */
   makeAndAddStack(study, displaySet) {
-    if (!stackManagerMetaDataProvider) {
-      throw new Error(
-        'Please call StackManager.setMetadataProvider(provider) first.'
-      );
-    }
-
     return configuration.createAndAddStack(
       stackMap,
       study,
       displaySet,
-      stackUpdatedCallbacks,
-      stackManagerMetaDataProvider
+      stackUpdatedCallbacks
     );
   },
   /**
    * Find a stack from the currently created stacks.
-   * @param displaySetInstanceUid The UID of the stack to find.
+   * @param displaySetInstanceUID The UID of the stack to find.
    * @returns {*} undefined if not found, otherwise the stack object is returned.
    */
-  findStack(displaySetInstanceUid) {
-    return stackMap[displaySetInstanceUid];
+  findStack(displaySetInstanceUID) {
+    return stackMap[displaySetInstanceUID];
   },
   /**
    * Find a stack or reate one if it has not been created yet
@@ -125,7 +134,7 @@ const StackManager = {
    * @return {Array} Array with image IDs
    */
   findOrCreateStack(study, displaySet) {
-    let stack = this.findStack(displaySet.displaySetInstanceUid);
+    let stack = this.findStack(displaySet.displaySetInstanceUID);
 
     if (!stack || !stack.imageIds) {
       stack = this.makeAndAddStack(study, displaySet);
@@ -134,9 +143,9 @@ const StackManager = {
     return stack;
   },
   /**
-   * Gets the underlying map of displaySetInstanceUid to stack object.
+   * Gets the underlying map of displaySetInstanceUID to stack object.
    * WARNING: Do not change this object. It directly affects the manager.
-   * @returns {{}} map of displaySetInstanceUid -> stack.
+   * @returns {{}} map of displaySetInstanceUID -> stack.
    */
   getAllStacks() {
     return stackMap;