fixes for parsing undefined length sequences with zero items

cornerstonejs · Aug 4, 2015 · f63b408 · henryqdineen · Aug 4, 2015 · f63b408
1 parent d32d019
commit f63b408
Show file tree

Hide file tree

Showing 8 changed files with 78 additions and 54 deletions.
diff --git a/bower.json b/bower.json
@@ -1,6 +1,6 @@
 {
     "name": "dicomParser",
-    "version": "1.1.0",
+    "version": "1.1.1",
     "description": "Javascript parser for DICOM Part 10 data",
     "main" : "dist/dicomParser.js",
     "ignore": [

diff --git a/dist/dicomParser.js b/dist/dicomParser.js
@@ -1,4 +1,4 @@
-/*! dicom-parser - v1.1.0 - 2015-08-03 | (c) 2014 Chris Hafey | https://github.com/chafey/dicomParser */
+/*! dicom-parser - v1.1.1 - 2015-08-03 | (c) 2014 Chris Hafey | https://github.com/chafey/dicomParser */
 (function (root, factory) {
 
     // node.js
@@ -1373,7 +1373,7 @@ var dicomParser = (function (dicomParser)
             if(groupNumber === 0xfffe)
             {
                 var elementNumber = byteStream.readUint16();
-                if(elementNumber === 0xe00d || elementNumber === 0xe0dd)
+                if(elementNumber === 0xe00d)
                 {
                     // NOTE: It would be better to also check for the length to be 0 as part of the check above
                     // but we will just log a warning for now
@@ -1782,6 +1782,13 @@ var dicomParser = (function (dicomParser)
             var nextTag = dicomParser.readTag(byteStream);
             byteStream.seek(-4);
 
+            // zero length sequence
+            if (element.hadUndefinedLength && nextTag === 'xfffee0dd') {
+              element.length = 0;
+              byteStream.seek(8);
+              return element;
+            }
+
             if (nextTag === 'xfffee000') {
                 // parse the sequence
                 dicomParser.readSequenceItemsImplicit(byteStream, element);
@@ -1864,21 +1871,20 @@ var dicomParser = (function (dicomParser)
     {
         while(byteStream.position < byteStream.byteArray.length)
         {
+          // end reading this sequence if the next tag is the sequence delimitation item
+          var nextTag = dicomParser.readTag(byteStream);
+          byteStream.seek(-4);
+          if (nextTag === 'xfffee0dd') {
+            // set the correct length
+            element.length = byteStream.position - element.dataOffset;
+            byteStream.seek(8);
+            return element;
+          }
+
             var item = readSequenceItemExplicit(byteStream, warnings);
             element.items.push(item);
-
-            // If this is the sequence delimitation item, return the offset of the next element
-            if(item.tag === 'xfffee0dd')
-            {
-                // sequence delimitation item, update attr data length and return
-                element.length = byteStream.position - element.dataOffset;
-                return;
-            }
         }
-
-        // eof encountered - log a warning and set the length of the element based on the buffer size
-        byteStream.warnings.push('eof encountered before finding sequence delimitation item in sequence element of undefined length with tag ' + element.tag);
-        element.length = byteStream.byteArray.length - element.dataOffset;
+        element.length = byteStream.position - element.dataOffset;
     }
 
     function readSQElementKnownLengthExplicit(byteStream, element, warnings)
@@ -1943,6 +1949,7 @@ var dicomParser = (function (dicomParser)
             // the end of this sequence item
             if(element.tag === 'xfffee00d')
             {
+              console.log('end of sequence item');
                 return new dicomParser.DataSet(byteStream.byteArrayParser, byteStream.byteArray, elements);
             }
         }
@@ -1973,20 +1980,19 @@ var dicomParser = (function (dicomParser)
     {
         while(byteStream.position < byteStream.byteArray.length)
         {
-            var item = readSequenceItemImplicit(byteStream);
-            element.items.push(item);
+          // end reading this sequence if the next tag is the sequence delimitation item
+          var nextTag = dicomParser.readTag(byteStream);
+          byteStream.seek(-4);
+          if (nextTag === 'xfffee0dd') {
+            // set the correct length
+            element.length = byteStream.position - element.dataOffset;
+            byteStream.seek(8);
+            return element;
+          }
 
-            // If this is the sequence delimitation item, return the offset of the next element
-            if(item.tag === 'xfffee0dd')
-            {
-                // sequence delimitation item, update attr data length and return
-                element.length = byteStream.position - element.dataOffset;
-                return;
-            }
+          var item = readSequenceItemImplicit(byteStream);
+          element.items.push(item);
         }
-
-        // eof encountered - log a warning and set the length of the element based on the buffer size
-        byteStream.warnings.push('eof encountered before finding sequence delimitation item in sequence of undefined length');
         element.length = byteStream.byteArray.length - element.dataOffset;
     }
 

diff --git a/examples/dumpWithDataDictionary/index.html b/examples/dumpWithDataDictionary/index.html
@@ -230,7 +230,17 @@ <h1>DICOM Dump with Data Dictionary</h1>
                 // and recursively call this function
                 var itemNumber = 0;
                 element.items.forEach(function (item) {
-                    output.push('<li>Item #' + itemNumber++ + ' ' + item.tag + '</li>')
+                    output.push('<li>Item #' + itemNumber++ + ' ' + item.tag);
+                    var lengthText = " length=" + item.length;
+                    if (item.hadUndefinedLength) {
+                        lengthText += " <strong>(-1)</strong>";
+                    }
+
+                    if(showLength === true) {
+                        text += lengthText + "; ";
+                        output.push(lengthText);
+                    }
+                    output.push('</li>');
                     output.push('<ul>');
                     dumpDataSet(item.dataSet, output);
                     output.push('</ul>');
@@ -382,6 +392,8 @@ <h1>DICOM Dump with Data Dictionary</h1>
                             var elementHexStr = ("0000" + element.toString(16)).substr(-4);
                             text += "x" + groupHexStr + elementHexStr;
                         }
+                        else if(vr === 'SQ') {
+                        }
                         else {
                             // If it is some other length and we have no string
                             text += "<i>no display code for VR " + vr + " yet, sorry!</i>";

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "dicom-parser",
-  "version": "1.1.0",
+  "version": "1.1.1",
   "description": "Javascript parser for DICOM Part 10 data",
   "keywords": [
     "DICOM",

diff --git a/src/findItemDelimitationItem.js b/src/findItemDelimitationItem.js
@@ -32,7 +32,7 @@ var dicomParser = (function (dicomParser)
             if(groupNumber === 0xfffe)
             {
                 var elementNumber = byteStream.readUint16();
-                if(elementNumber === 0xe00d || elementNumber === 0xe0dd)
+                if(elementNumber === 0xe00d)
                 {
                     // NOTE: It would be better to also check for the length to be 0 as part of the check above
                     // but we will just log a warning for now

diff --git a/src/readDicomElementImplicit.js b/src/readDicomElementImplicit.js
@@ -40,6 +40,13 @@ var dicomParser = (function (dicomParser)
             var nextTag = dicomParser.readTag(byteStream);
             byteStream.seek(-4);
 
+            // zero length sequence
+            if (element.hadUndefinedLength && nextTag === 'xfffee0dd') {
+              element.length = 0;
+              byteStream.seek(8);
+              return element;
+            }
+
             if (nextTag === 'xfffee000') {
                 // parse the sequence
                 dicomParser.readSequenceItemsImplicit(byteStream, element);

diff --git a/src/readSequenceElementExplicit.js b/src/readSequenceElementExplicit.js
@@ -56,21 +56,20 @@ var dicomParser = (function (dicomParser)
     {
         while(byteStream.position < byteStream.byteArray.length)
         {
+          // end reading this sequence if the next tag is the sequence delimitation item
+          var nextTag = dicomParser.readTag(byteStream);
+          byteStream.seek(-4);
+          if (nextTag === 'xfffee0dd') {
+            // set the correct length
+            element.length = byteStream.position - element.dataOffset;
+            byteStream.seek(8);
+            return element;
+          }
+
             var item = readSequenceItemExplicit(byteStream, warnings);
             element.items.push(item);
-
-            // If this is the sequence delimitation item, return the offset of the next element
-            if(item.tag === 'xfffee0dd')
-            {
-                // sequence delimitation item, update attr data length and return
-                element.length = byteStream.position - element.dataOffset;
-                return;
-            }
         }
-
-        // eof encountered - log a warning and set the length of the element based on the buffer size
-        byteStream.warnings.push('eof encountered before finding sequence delimitation item in sequence element of undefined length with tag ' + element.tag);
-        element.length = byteStream.byteArray.length - element.dataOffset;
+        element.length = byteStream.position - element.dataOffset;
     }
 
     function readSQElementKnownLengthExplicit(byteStream, element, warnings)

diff --git a/src/readSequenceElementImplicit.js b/src/readSequenceElementImplicit.js
@@ -24,6 +24,7 @@ var dicomParser = (function (dicomParser)
             // the end of this sequence item
             if(element.tag === 'xfffee00d')
             {
+              console.log('end of sequence item');
                 return new dicomParser.DataSet(byteStream.byteArrayParser, byteStream.byteArray, elements);
             }
         }
@@ -54,20 +55,19 @@ var dicomParser = (function (dicomParser)
     {
         while(byteStream.position < byteStream.byteArray.length)
         {
-            var item = readSequenceItemImplicit(byteStream);
-            element.items.push(item);
+          // end reading this sequence if the next tag is the sequence delimitation item
+          var nextTag = dicomParser.readTag(byteStream);
+          byteStream.seek(-4);
+          if (nextTag === 'xfffee0dd') {
+            // set the correct length
+            element.length = byteStream.position - element.dataOffset;
+            byteStream.seek(8);
+            return element;
+          }
 
-            // If this is the sequence delimitation item, return the offset of the next element
-            if(item.tag === 'xfffee0dd')
-            {
-                // sequence delimitation item, update attr data length and return
-                element.length = byteStream.position - element.dataOffset;
-                return;
-            }
+          var item = readSequenceItemImplicit(byteStream);
+          element.items.push(item);
         }
-
-        // eof encountered - log a warning and set the length of the element based on the buffer size
-        byteStream.warnings.push('eof encountered before finding sequence delimitation item in sequence of undefined length');
         element.length = byteStream.byteArray.length - element.dataOffset;
     }