added support for parsing deflated explicit little endian transfer sy…

…ntax (if pako is loaded at the time of parse)
solidsloth · Nov 2, 2015 · 347fe9a · 347fe9a
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diff --git a/README.md b/README.md
@@ -2,14 +2,18 @@ dicomParser
 ===========
 
 dicomParser is a lightweight library for parsing DICOM P10 byte streams in modern web browsers (IE10+),  Node.js
-and Meteor.  dicomParser is fast, easy to use and has no external dependencies.
+and Meteor.  dicomParser is fast, easy to use and has no required external dependencies
+([pako](https://github.com/nodeca/pako) is required if you support for the Deflated Explicit VR Little Endian
+ transfer syntax)
 
 Live Examples
 ---------------
 
 The best way to see the power of this library is to actually see it in use.  A number of live examples are
 included that are not only useful but also show how to use dicomParser.
 [Click here for a list of all live examples](https://rawgithub.com/chafey/dicomParser/master/examples/index.html)
+Make sure you try out the [DICOM Dump with Data Dictionary](https://rawgit.com/chafey/dicomParser/master/examples/dumpWithDataDictionary/index.html)
+which is a very useful tool and excellent example of most features.
 
 Community
 ---------
@@ -37,6 +41,9 @@ Or install via atmosphere for [Meteor](https://www.meteor.com/) applications
 
 > meteor add chafey:dicom-parser
 
+* Note - make sure you install [pako](https://github.com/nodeca/pako) if you need to support
+the Deflated Explicit VR Little Endian transfer syntax
+
 Usage
 -----
 
@@ -83,6 +90,7 @@ Key Features
 * Parses DICOM Part 10 byte arrays in all encodings
   * Explicit and implicit
   * Little endian and big endian
+  * Deflated Explicit VR Little Endian transfer syntax
 * Supports all VR's including sequences
 * Supports elements with undefined length
 * Supports sequence items with undefined length
@@ -152,6 +160,7 @@ Future:
   * dataSet creation logic could filter out unwanted tags to improve performance of parse
   * dataSet creation logic could defer creation of sequence dataSets to improve performance of parse
 * Function to parse non P10 byte streams given the byte stream and the transfer syntax
+* Support for encrypted dicom
 
 Contributors
 ============================================

diff --git a/bower.json b/bower.json
@@ -1,6 +1,6 @@
 {
     "name": "dicomParser",
-    "version": "1.1.7",
+    "version": "1.2.0",
     "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 - v1.1.7 - 2015-09-18 | (c) 2014 Chris Hafey | https://github.com/chafey/dicomParser */
+/*! dicom-parser - v1.2.0 - 2015-11-02 | (c) 2014 Chris Hafey | https://github.com/chafey/dicomParser */
 (function (root, factory) {
 
     // node.js
@@ -46,49 +46,12 @@ var dicomParser = (function(dicomParser) {
             throw "dicomParser.parseDicom: missing required parameter 'byteArray'";
         }
 
-        var littleEndianByteStream = new dicomParser.ByteStream(dicomParser.littleEndianByteArrayParser, byteArray);
-
-        function readPrefix()
-        {
-            littleEndianByteStream.seek(128);
-            var prefix = littleEndianByteStream.readFixedString(4);
-            if(prefix !== "DICM")
-            {
-                throw "dicomParser.parseDicom: DICM prefix not found at location 132";
-            }
-        }
-
-        function readPart10Header()
-        {
-            // Per the DICOM standard, the header is always encoded in Explicit VR Little Endian (see PS3.10, section 7.1)
-            // so use littleEndianByteStream throughout this method regardless of the transfer syntax
-            readPrefix();
-
-            var warnings = [];
-            var elements = {};
-            while(littleEndianByteStream.position < littleEndianByteStream.byteArray.length) {
-                var position = littleEndianByteStream.position;
-                var element = dicomParser.readDicomElementExplicit(littleEndianByteStream, warnings);
-                if(element.tag > 'x0002ffff') {
-                    littleEndianByteStream.position = position;
-                    break;
-                }
-                // Cache the littleEndianByteArrayParser for meta header elements, since the rest of the data set may be big endian
-                // and this parser will be needed later if the meta header values are to be read.
-                element.parser = dicomParser.littleEndianByteArrayParser;
-                elements[element.tag] = element;
-            }
-            var metaHeaderDataSet = new dicomParser.DataSet(littleEndianByteStream.byteArrayParser, littleEndianByteStream.byteArray, elements);
-            metaHeaderDataSet.warnings = littleEndianByteStream.warnings;
-            return metaHeaderDataSet;
-        }
-
         function readTransferSyntax(metaHeaderDataSet) {
             if(metaHeaderDataSet.elements.x00020010 === undefined) {
                 throw 'dicomParser.parseDicom: missing required meta header attribute 0002,0010';
             }
             var transferSyntaxElement = metaHeaderDataSet.elements.x00020010;
-            return dicomParser.readFixedString(littleEndianByteStream.byteArray, transferSyntaxElement.dataOffset, transferSyntaxElement.length);
+            return dicomParser.readFixedString(byteArray, transferSyntaxElement.dataOffset, transferSyntaxElement.length);
         }
 
         function isExplicit(transferSyntax) {
@@ -100,16 +63,30 @@ var dicomParser = (function(dicomParser) {
             return true;
         }
 
-        function getDataSetByteStream(transferSyntax) {
+        function getDataSetByteStream(transferSyntax, position) {
+            if(transferSyntax === '1.2.840.10008.1.2.1.99')
+            {
+              if(typeof(pako) === "undefined") {
+                throw 'dicomParser.parseDicom: deflated transfer syntax encountered but pako not loaded';
+              }
+              var deflated = byteArray.slice(position);
+              var inflated = pako.inflateRaw(deflated);
+
+              // create a single byte array with the full header bytes and the inflated bytes
+              var fullByteArray = new Uint8Array(inflated.length + position);
+              fullByteArray.set(byteArray.slice(0, position), 0);
+              fullByteArray.set(inflated, position);
+              return new dicomParser.ByteStream(dicomParser.littleEndianByteArrayParser, fullByteArray, 0);
+            }
             if(transferSyntax === '1.2.840.10008.1.2.2') // explicit big endian
             {
-                return new dicomParser.ByteStream(dicomParser.bigEndianByteArrayParser, byteArray, littleEndianByteStream.position);
+                return new dicomParser.ByteStream(dicomParser.bigEndianByteArrayParser, byteArray, position);
             }
             else
             {
                 // all other transfer syntaxes are little endian; only the pixel encoding differs
                 // make a new stream so the metaheader warnings don't come along for the ride
-                return new dicomParser.ByteStream(dicomParser.littleEndianByteArrayParser, byteArray, littleEndianByteStream.position);
+                return new dicomParser.ByteStream(dicomParser.littleEndianByteArrayParser, byteArray, position);
             }
         }
 
@@ -132,7 +109,7 @@ var dicomParser = (function(dicomParser) {
         {
             var transferSyntax = readTransferSyntax(metaHeaderDataSet);
             var explicit = isExplicit(transferSyntax);
-            var dataSetByteStream = getDataSetByteStream(transferSyntax);
+            var dataSetByteStream = getDataSetByteStream(transferSyntax, metaHeaderDataSet.position);
 
             var elements = {};
             var dataSet = new dicomParser.DataSet(dataSetByteStream.byteArrayParser, dataSetByteStream.byteArray, elements);
@@ -159,7 +136,7 @@ var dicomParser = (function(dicomParser) {
 
         // main function here
         function parseTheByteStream() {
-            var metaHeaderDataSet = readPart10Header();
+            var metaHeaderDataSet = dicomParser.readPart10Header(byteArray, options);
 
             var dataSet = readDataSet(metaHeaderDataSet);
 
@@ -1898,6 +1875,75 @@ var dicomParser = (function (dicomParser)
 
     return dicomParser;
 }(dicomParser));
+/**
+ * Parses a DICOM P10 byte array and returns a DataSet object with the parsed elements.  If the options
+ * argument is supplied and it contains the untilTag property, parsing will stop once that
+ * tag is encoutered.  This can be used to parse partial byte streams.
+ *
+ * @param byteArray the byte array
+ * @param options object to control parsing behavior (optional)
+ * @returns {DataSet}
+ * @throws error if an error occurs while parsing.  The exception object will contain a property dataSet with the
+ *         elements successfully parsed before the error.
+ */
+var dicomParser = (function(dicomParser) {
+  if(dicomParser === undefined)
+  {
+    dicomParser = {};
+  }
+
+  dicomParser.readPart10Header = function(byteArray, options) {
+
+    if(byteArray === undefined)
+    {
+      throw "dicomParser.readPart10Header: missing required parameter 'byteArray'";
+    }
+
+    var littleEndianByteStream = new dicomParser.ByteStream(dicomParser.littleEndianByteArrayParser, byteArray);
+
+    function readPrefix()
+    {
+      littleEndianByteStream.seek(128);
+      var prefix = littleEndianByteStream.readFixedString(4);
+      if(prefix !== "DICM")
+      {
+        throw "dicomParser.readPart10Header: DICM prefix not found at location 132";
+      }
+    }
+
+    // main function here
+    function readTheHeader() {
+      // Per the DICOM standard, the header is always encoded in Explicit VR Little Endian (see PS3.10, section 7.1)
+      // so use littleEndianByteStream throughout this method regardless of the transfer syntax
+      readPrefix();
+
+      var warnings = [];
+      var elements = {};
+      while(littleEndianByteStream.position < littleEndianByteStream.byteArray.length) {
+        var position = littleEndianByteStream.position;
+        var element = dicomParser.readDicomElementExplicit(littleEndianByteStream, warnings);
+        if(element.tag > 'x0002ffff') {
+          littleEndianByteStream.position = position;
+          break;
+        }
+        // Cache the littleEndianByteArrayParser for meta header elements, since the rest of the data set may be big endian
+        // and this parser will be needed later if the meta header values are to be read.
+        element.parser = dicomParser.littleEndianByteArrayParser;
+        elements[element.tag] = element;
+      }
+      var metaHeaderDataSet = new dicomParser.DataSet(littleEndianByteStream.byteArrayParser, littleEndianByteStream.byteArray, elements);
+      metaHeaderDataSet.warnings = littleEndianByteStream.warnings;
+      metaHeaderDataSet.position = littleEndianByteStream.position;
+      return metaHeaderDataSet;
+    }
+
+    // This is where we actually start parsing
+    return readTheHeader();
+  };
+
+  return dicomParser;
+})(dicomParser);
+
 /**
  * Internal helper functions for parsing DICOM elements
  */
@@ -2207,7 +2253,7 @@ var dicomParser = (function (dicomParser)
     dicomParser = {};
   }
 
-  dicomParser.version = "1.1.6";
+  dicomParser.version = "1.2.0";
 
   return dicomParser;
 }(dicomParser));

diff --git a/dist/dicomParser.min.js b/dist/dicomParser.min.js
diff --git a/dist/package.js b/dist/package.js
@@ -1,7 +1,7 @@
 Package.describe({
   name: 'chafey:dicom-parser',
   summary: 'Javascript parser for DICOM Part 10 data',
-  version: '1.1.7',
+  version: '1.2.0',
   git: 'https://github.com/chafey/dicomParser.git/',
   documentation: null
 });

diff --git a/examples/dumpWithDataDictionary/index.html b/examples/dumpWithDataDictionary/index.html
@@ -88,6 +88,7 @@ <h1>DICOM Dump with Data Dictionary v<span id="version"></span></h1>
                 <div class="text-center" style="margin-top:225px;"><h3>Drag and drop a DICOM P10 file here to dump its elements</h3></div>
 
             </div>
+
         </div>
     </div>
 
@@ -100,6 +101,9 @@ <h1>DICOM Dump with Data Dictionary v<span id="version"></span></h1>
 <!-- jquery - included to make things easier to demo, not needed by dicomParser -->
 <script src="../jquery.min.js"></script>
 
+<!-- pako - needed to support deflated transfer syntax -->
+<script src="../pako.min.js"></script>
+
 <!-- include the data dictionary -->
 <script src="dataDictionary.js"></script>
 
@@ -269,7 +273,8 @@ <h1>DICOM Dump with Data Dictionary v<span id="version"></span></h1>
             }
             else if (element.fragments) {
                 text += "encapsulated pixel data with " + element.basicOffsetTable.length + " offsets and " + element.fragments.length + " fragments";
-                output.push('<li>' + text + '</li>');
+                title += "; dataOffset=" + element.dataOffset;
+                output.push("<li title='" + title + "'=>" + text + '</li>');
                 /*
                 output.push('<ul>');
 

diff --git a/examples/pako.min.js b/examples/pako.min.js
diff --git a/meteor/dicomParser/package.js b/meteor/dicomParser/package.js
@@ -1,7 +1,7 @@
 Package.describe({
   name: 'chafey:dicom-parser',
   summary: 'Javascript parser for DICOM Part 10 data',
-  version: '1.1.7',
+  version: '1.2.0',
   git: 'https://github.com/chafey/dicomParser.git/',
   documentation: null
 });

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "dicom-parser",
-  "version": "1.1.7",
+  "version": "1.2.0",
   "description": "Javascript parser for DICOM Part 10 data",
   "keywords": [
     "DICOM",