Merge pull request #215 from yagni/callback-all-tags

Use vr callback on all tags, not just to determine sequence.
cornerstonejs · Oct 11, 2022 · 98e991d · 98e991d
2 parents 2c9ee43 + 6ed4f2c
commit 98e991d
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Showing 8 changed files with 40 additions and 19 deletions.
diff --git a/.../dumpWithDataDictionary/dataDictionary.js → examples/dataDictionary.js b/.../dumpWithDataDictionary/dataDictionary.js → examples/dataDictionary.js
diff --git a/examples/dumpWithDataDictionary/index.html b/examples/dumpWithDataDictionary/index.html
@@ -123,7 +123,7 @@ <h1>DICOM Dump with Data Dictionary v<span id="version"></span></h1>
 <script src="../pako.min.js"></script>
 
 <!-- include the data dictionary -->
-<script src="dataDictionary.js"></script>
+<script src="../dataDictionary.js"></script>
 
 <!-- include the uids -->
 <script src="uids.js"></script>
@@ -626,11 +626,15 @@ <h1>DICOM Dump with Data Dictionary v<span id="version"></span></h1>
         setTimeout(function() {
             var sha1Hash = sha1(byteArray, 0, byteArray.length);
 
-            // Invoke the paresDicom function and get back a DataSet object with the contents
+            // Invoke the parseDicom function and get back a DataSet object with the contents
             try {
                 var start = new Date().getTime();
                 var options = {
-                    untilTag: untilTag
+                    untilTag: untilTag,
+                    vrCallback(tag) {
+                        const formatted = `(${tag.substring(1, 5).toUpperCase()},${tag.substring(5, 9).toUpperCase()})`;
+                        return !!TAG_DICT[formatted] ? TAG_DICT[formatted].vr : undefined;
+                    }
                 };
 
                 dataSet = dicomParser.parseDicom(byteArray, options);

diff --git a/examples/explicitDataSetToJS/index.html b/examples/explicitDataSetToJS/index.html
@@ -29,7 +29,9 @@ <h1>DICOM Dump using explicitDataSetToJS</h1>
         </p>
         <p>
             This example illustrates how to recursively iterate over a parsed data set to dump all data elements
-            into a tree like structure using the explicitDataSetToJS utility function.  Note that DICOM files dropped here are not uploaded anywhere, all processing
+            into a tree like structure using the explicitDataSetToJS utility function.  This example parses using 
+            a data dictionary via the vrCallback option in order to use explicitDataSetToJS even with implicit 
+            VR data sets.  Note that DICOM files dropped here are not uploaded anywhere, all processing
             is done inside your web browser in Javascript.
         </p>
         <strong>Use of this example require IE10+ or any other modern browser.</strong>
@@ -59,6 +61,7 @@ <h1>DICOM Dump using explicitDataSetToJS</h1>
 
 <!-- include the dicomParser library -->
 <script src="../../dist/dicomParser.js"></script>
+<script src="../dataDictionary.js"></script>
 <script>window.dicomParser || document.write('<script src="https://unpkg.com/dicom-parser">\x3C/script>')</script>
 
 <!-- jquery - included to make things easier to demo, not needed by dicomParser -->
@@ -138,11 +141,14 @@ <h1>DICOM Dump using explicitDataSetToJS</h1>
             // set a short timeout to do the parse so the DOM has time to update itself with the above message
             setTimeout(function() {
 
-                // Invoke the paresDicom function and get back a DataSet object with the contents
+                // Invoke the parseDicom function and get back a DataSet object with the contents
                 var dataSet;
                 try {
                     var start = new Date().getTime();
-                    dataSet = dicomParser.parseDicom(byteArray);
+                    dataSet = dicomParser.parseDicom(byteArray, { vrCallback(tag) {
+                        const formatted = `(${tag.substr(1, 4).toUpperCase()},${tag.substr(5,9).toUpperCase()})`;
+                        return !!TAG_DICT[formatted] ? TAG_DICT[formatted].vr : undefined;
+                    }});
 
                     var options = {
                         omitPrivateAttibutes :false ,

diff --git a/examples/explicitDataSetToJson/index.html b/examples/explicitDataSetToJson/index.html
@@ -28,7 +28,9 @@ <h1>DICOM Dump to JSON</h1>
             Drag and drop a DICOM Part 10 file into the light gray region below for a json version of it
         </p>
         <p>
-            This example illustrates how to generate a JSON string from a DICOM SOP Instance.
+            This example illustrates how to generate a JSON string from a DICOM SOP Instance.  This example parses using 
+            a data dictionary via the vrCallback option in order to use explicitDataSetToJS even with implicit 
+            VR data sets.
             Note that DICOM files dropped here are not uploaded anywhere, all processing
             is done inside your web browser in Javascript.
         </p>
@@ -65,6 +67,7 @@ <h1>DICOM Dump to JSON</h1>
 
 <!-- include the dicomParser library -->
 <script src="../../dist/dicomParser.js"></script>
+<script src="../dataDictionary.js"></script>
 <script>window.dicomParser || document.write('<script src="https://unpkg.com/dicom-parser">\x3C/script>')</script>
 
 <!-- jquery - included to make things easier to demo, not needed by dicomParser -->
@@ -102,11 +105,14 @@ <h1>DICOM Dump to JSON</h1>
             // set a short timeout to do the parse so the DOM has time to update itself with the above message
             setTimeout(function() {
 
-                // Invoke the paresDicom function and get back a DataSet object with the contents
+                // Invoke the parseDicom function and get back a DataSet object with the contents
                 var dataSet;
                 try {
                     var start = new Date().getTime();
-                    dataSet = dicomParser.parseDicom(byteArray);
+                    dataSet = dicomParser.parseDicom(byteArray, { vrCallback(tag) {
+                        const formatted = `(${tag.substr(1, 4).toUpperCase()},${tag.substr(5,9).toUpperCase()})`;
+                        return !!TAG_DICT[formatted] ? TAG_DICT[formatted].vr : undefined;
+                    }});
 
                     var options = {
                         omitPrivateAttibutes :false ,

diff --git a/src/readDicomElementImplicit.js b/src/readDicomElementImplicit.js
@@ -7,13 +7,9 @@ import { isPrivateTag } from './util/util.js';
  * Internal helper functions for for parsing DICOM elements
  */
 
-const isSequence = (element, byteStream, vrCallback) => {
-  // if a data dictionary callback was provided, use that to verify that the element is a sequence.
-  if (vrCallback !== undefined) {
-    const callbackValue = vrCallback(element.tag);
-    if (callbackValue !== undefined) {
-      return (callbackValue === 'SQ');
-    }
+const isSequence = (element, byteStream) => {
+  if (element.vr !== undefined) {
+    return (element.vr === 'SQ');
   }
 
   if ((byteStream.position + 4) <= byteStream.byteArray.length) {
@@ -38,8 +34,11 @@ export default function readDicomElementImplicit (byteStream, untilTag, vrCallba
     throw 'dicomParser.readDicomElementImplicit: missing required parameter \'byteStream\'';
   }
 
+  const tag = readTag(byteStream);
+
   const element = {
-    tag: readTag(byteStream),
+    tag,
+    vr: (vrCallback !== undefined ? vrCallback(tag) : undefined),
     length: byteStream.readUint32(),
     dataOffset: byteStream.position
   };
@@ -53,9 +52,9 @@ export default function readDicomElementImplicit (byteStream, untilTag, vrCallba
   }
 
   // always parse sequences with undefined lengths, since there's no other way to know how long they are.
-  if (isSequence(element, byteStream, vrCallback) && (!isPrivateTag(element.tag) || element.hadUndefinedLength)) {
+  if (isSequence(element, byteStream) && (!isPrivateTag(element.tag) || element.hadUndefinedLength)) {
     // parse the sequence
-    readSequenceItemsImplicit(byteStream, element);
+    readSequenceItemsImplicit(byteStream, element, vrCallback);
 
     if (isPrivateTag(element.tag)) {
       element.items = undefined;

diff --git a/test/parseDicomDataSet_test.js b/test/parseDicomDataSet_test.js
@@ -104,6 +104,7 @@ describe('parseDicomDataSet', () => {
 
       expect(element).to.be.ok;
       expect(element.items).to.be.undefined;
+      expect(element.vr).to.equal('OW');
       expect(element.length).to.equal(8);
     });
 

diff --git a/test/readDicomElementImplicit_test.js b/test/readDicomElementImplicit_test.js
@@ -178,6 +178,7 @@ describe('readDicomElementImplicit', () => {
     // Assert
     expect(element.tag).to.equal('x7fe00010');
     expect(element.items).to.equal(undefined);
+    expect(element.vr).to.equal('OW');
     expect(element.length).to.equal(8);
   });
 
@@ -235,6 +236,7 @@ describe('readDicomElementImplicit', () => {
     // Assert
     expect(element.tag).to.equal('x7fe00010');
     expect(element.items).to.equal(undefined);
+    expect(element.vr).to.equal('OW');
     expect(element.length).to.equal(11);
   });
 

diff --git a/test/readSequenceItemsImplicit_test.js b/test/readSequenceItemsImplicit_test.js
@@ -48,6 +48,7 @@ describe('readSequenceItemsImplicit', () => {
 
     expect(pixelData).to.be.ok;
     expect(pixelData.length).to.equal(8);
+    expect(pixelData.vr).to.equal('OW');
     expect(sequenceItem.dataSet.elements['xfffee00d']).to.be.ok;
     expect(byteStream.warnings.length).to.equal(0);
   });
@@ -115,6 +116,7 @@ describe('readSequenceItemsImplicit', () => {
 
     expect(pixelData).to.be.ok;
     expect(pixelData.length).to.equal(8);
+    expect(pixelData.vr).to.equal('OW');
     expect(byteStream.warnings.length).to.equal(0);
   });
 
@@ -148,6 +150,7 @@ describe('readSequenceItemsImplicit', () => {
 
     expect(pixelData).to.be.ok;
     expect(pixelData.length).to.equal(8);
+    expect(pixelData.vr).to.equal('OW');
     expect(byteStream.warnings.length).to.equal(0);
   });