Fix multiframe read/write (#147)

- Use offset table for reading fragments if present, otherwise, loop until end of stream/sequence
- Add option to not fragment encapsulated pixel data (use fragments equal to frame size)

# Conflicts:
#	src/ValueRepresentation.js

src/DicomDict.js

@@ -17,7 +17,7 @@ class DicomDict {
         }
     }
 
-    write() {
+    write(writeOptions = {}) {
         var metaSyntax = EXPLICIT_LITTLE_ENDIAN;
         var fileStream = new WriteBufferStream(4096, true);
         fileStream.writeHex("00".repeat(128));
@@ -30,7 +30,7 @@ class DicomDict {
                 Value: [EXPLICIT_LITTLE_ENDIAN]
             };
         }
-        DicomMessage.write(this.meta, metaStream, metaSyntax);
+        DicomMessage.write(this.meta, metaStream, metaSyntax, writeOptions);
         DicomMessage.writeTagObject(
             fileStream,
             "00020000",
@@ -41,7 +41,7 @@ class DicomDict {
         fileStream.concat(metaStream);
 
         var useSyntax = this.meta["00020010"].Value[0];
-        DicomMessage.write(this.dict, fileStream, useSyntax);
+        DicomMessage.write(this.dict, fileStream, useSyntax, writeOptions);
         return fileStream.getBuffer();
     }
 }

src/DicomMessage.js

@@ -100,7 +100,7 @@ class DicomMessage {
         tag.write(stream, vr, values, syntax);
     }
 
-    static write(jsonObjects, useStream, syntax) {
+    static write(jsonObjects, useStream, syntax, writeOptions) {
         var written = 0;
 
         var sortedTags = Object.keys(jsonObjects).sort();
@@ -110,7 +110,13 @@ class DicomMessage {
                 vrType = tagObject.vr,
                 values = tagObject.Value;
 
-            written += tag.write(useStream, vrType, values, syntax);
+            written += tag.write(
+                useStream,
+                vrType,
+                values,
+                syntax,
+                writeOptions
+            );
         });
 
         return written;

src/Tag.js

@@ -86,7 +86,7 @@ class Tag {
         return Tag.fromNumbers(group, element);
     }
 
-    write(stream, vrType, values, syntax) {
+    write(stream, vrType, values, syntax, writeOptions) {
         var vr = ValueRepresentation.createByTypeString(vrType),
             useSyntax = DicomMessage._normalizeSyntax(syntax);
 
@@ -113,10 +113,16 @@ class Tag {
                 tagStream,
                 values,
                 useSyntax,
-                isEncapsulated
+                isEncapsulated,
+                writeOptions
             );
         } else {
-            valueLength = vr.writeBytes(tagStream, values, useSyntax);
+            valueLength = vr.writeBytes(
+                tagStream,
+                values,
+                useSyntax,
+                writeOptions
+            );
         }
 
         if (vrType == "SQ") {

src/ValueRepresentation.js

@@ -241,9 +241,10 @@ class BinaryRepresentation extends ValueRepresentation {
         super(type);
     }
 
-    writeBytes(stream, value, syntax, isEncapsulated) {
+    writeBytes(stream, value, syntax, isEncapsulated, writeOptions) {
         var i;
         var binaryStream;
+        var { fragmentMultiframe = true } = writeOptions;
         if (isEncapsulated) {
             var fragmentSize = 1024 * 20,
                 frames = value.length,
@@ -253,16 +254,24 @@ class BinaryRepresentation extends ValueRepresentation {
                 1024 * 1024 * 20,
                 stream.isLittleEndian
             );
+
             for (i = 0; i < frames; i++) {
                 startOffset.push(binaryStream.size);
                 var frameBuffer = value[i],
-                    frameStream = new ReadBufferStream(frameBuffer),
+                    frameStream = new ReadBufferStream(frameBuffer);
+
+                var fragmentsLength = 1;
+                if (fragmentMultiframe) {
                     fragmentsLength = Math.ceil(
                         frameStream.size / fragmentSize
                     );
+                }
 
                 for (var j = 0, fragmentStart = 0; j < fragmentsLength; j++) {
-                    var fragmentEnd = fragmentStart + fragmentSize;
+                    var fragmentEnd = fragmentStart + frameStream.size;
+                    if (fragmentMultiframe) {
+                        fragmentEnd = fragmentStart + fragmentSize;
+                    }
                     if (j == fragmentsLength - 1) {
                         fragmentEnd = frameStream.size;
                     }
@@ -318,26 +327,49 @@ class BinaryRepresentation extends ValueRepresentation {
                         offsets.push(stream.readUint32());
                     }
                 } else {
-                    offsets = [0];
+                    offsets = [];
                 }
 
-                for (let i = 0; i < offsets.length; i++) {
-                    const nextTag = Tag.readTag(stream);
+                // If there is an offset table, use that to loop through pixel data sequence
+                // FIX: These two loops contain the exact same code, but I couldn't think of a way
+                // to combine the for and while loops non-confusingly so went with the explicit but
+                // redundant approach.
+                if (offsets.length > 0) {
+                    for (let i = 0; i < offsets.length; i++) {
+                        const nextTag = Tag.readTag(stream);
 
-                    if (!nextTag.is(0xfffee000)) {
-                        break;
+                        if (!nextTag.is(0xfffee000)) {
+                            break;
+                        }
+
+                        const frameItemLength = stream.readUint32();
+                        const fragmentStream = stream.more(frameItemLength);
+
+                        frames.push(fragmentStream.buffer);
                     }
+                }
+                // If no offset table, loop through remainder of stream looking for termination tag
+                else {
+                    while (stream.offset < stream.size) {
+                        const nextTag = Tag.readTag(stream);
+
+                        if (!nextTag.is(0xfffee000)) {
+                            break;
+                        }
 
-                    const frameItemLength = stream.readUint32();
-                    const fragmentStream = stream.more(frameItemLength);
+                        const frameItemLength = stream.readUint32();
+                        const fragmentStream = stream.more(frameItemLength);
 
-                    frames.push(fragmentStream.buffer);
+                        frames.push(fragmentStream.buffer);
+                    }
                 }
 
                 // Read SequenceDelimitationItem Tag
                 stream.readUint32();
                 // Read SequenceDelimitationItem value.
-                stream.readUint32();
+                if (stream.size - stream.offset >= 4) {
+                    stream.readUint32();
+                }
             } else {
                 throw new Error(
                     "Item tag not found after undefined binary length"

test/test_data.js

@@ -2,7 +2,7 @@ const expect = require('chai').expect;
 const dcmjs = require('../build/dcmjs');
 
 const fs = require("fs");
-const {http, https} = require("follow-redirects");
+const { http, https } = require("follow-redirects");
 const os = require("os");
 const path = require("path");
 const unzipper = require("unzipper");
@@ -14,34 +14,34 @@ fileMetaInformationVersionArray[1] = 1;
 
 const metadata = {
   "00020001": {
-      "Value": [
-        fileMetaInformationVersionArray.buffer
-      ],
-      "vr": "OB"
+    "Value": [
+      fileMetaInformationVersionArray.buffer
+    ],
+    "vr": "OB"
   },
   "00020012": {
-      "Value": [
-          "1.2.840.113819.7.1.1997.1.0"
-      ],
-      "vr": "UI"
+    "Value": [
+      "1.2.840.113819.7.1.1997.1.0"
+    ],
+    "vr": "UI"
   },
   "00020002": {
-      "Value": [
-          "1.2.840.10008.5.1.4.1.1.4"
-      ],
-      "vr": "UI"
+    "Value": [
+      "1.2.840.10008.5.1.4.1.1.4"
+    ],
+    "vr": "UI"
   },
   "00020003": {
-      "Value": [
-          DicomMetaDictionary.uid()
-      ],
-      "vr": "UI"
+    "Value": [
+      DicomMetaDictionary.uid()
+    ],
+    "vr": "UI"
   },
   "00020010": {
-      "Value": [
-          "1.2.840.10008.1.2"
-      ],
-      "vr": "UI"
+    "Value": [
+      "1.2.840.10008.1.2"
+    ],
+    "vr": "UI"
   }
 };
 
@@ -74,7 +74,7 @@ const sequenceMetadata = {
 }
 
 function downloadToFile(url, filePath) {
-  return new Promise( (resolve,reject) => {
+  return new Promise((resolve, reject) => {
     const fileStream = fs.createWriteStream(filePath);
     const request = https.get(url, (response) => {
       response.pipe(fileStream);
@@ -152,9 +152,9 @@ const tests = {
     const unzipPath = path.join(os.tmpdir(), "test_multiframe_1");
 
     downloadToFile(url, zipFilePath)
-      .then( () => {
+      .then(() => {
         fs.createReadStream(zipFilePath)
-          .pipe(unzipper.Extract( {path: unzipPath} )
+          .pipe(unzipper.Extract({ path: unzipPath })
             .on('close', () => {
               const mrHeadPath = path.join(unzipPath, "MRHead");
               fs.readdir(mrHeadPath, (err, fileNames) => {
@@ -188,9 +188,9 @@ const tests = {
     const segFilePath = path.join(os.tmpdir(), "Lesion1_onesliceSEG.dcm");
 
     downloadToFile(ctPelvisURL, zipFilePath)
-      .then( () => {
+      .then(() => {
         fs.createReadStream(zipFilePath)
-          .pipe(unzipper.Extract( {path: unzipPath} )
+          .pipe(unzipper.Extract({ path: unzipPath })
             .on('close', () => {
               const ctPelvisPath = path.join(unzipPath, "Series-1.2.840.113704.1.111.1916.1223562191.15");
               fs.readdir(ctPelvisPath, (err, fileNames) => {
@@ -211,7 +211,7 @@ const tests = {
                 expect(roundedSpacing).to.equal(5);
 
                 downloadToFile(segURL, segFilePath)
-                  .then( () => {
+                  .then(() => {
                     const arrayBuffer = fs.readFileSync(segFilePath).buffer;
                     const dicomDict = DicomMessage.readFile(arrayBuffer);
                     const dataset = DicomMetaDictionary.naturalizeDataset(dicomDict.dict);
@@ -225,6 +225,18 @@ const tests = {
           );
       });
   },
+
+  test_multiframe_us: () => {
+    const file = fs.readFileSync(path.join(__dirname, 'cine-test.dcm'));
+    const dicomData = dcmjs.data.DicomMessage.readFile(file.buffer, {
+      // ignoreErrors: true,
+    });
+    const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(dicomData.dict);
+    // eslint-disable-next-line no-underscore-dangle
+    dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
+    expect(dataset.NumberOfFrames).to.equal(117);
+    console.log("Finished test_multiframe_us")
+  }
 }