feat(deflated): Added support for reading datasets with deflated tran…

…sfer syntax (#312)

* feat(deflated): Added support for reading datasets with deflated transfer syntax

* Updated deflated tests

README.md

@@ -36,9 +36,9 @@ _Parts of DICOM that dcmjs *will* focus on:_
 
 _Parts of DICOM that dcmjs *will not* focus on:_
 
-- DIMSE (legacy networking like C-STORE, C-FIND, C-MOVE, etc). See the [dcmjs-dimse project](https://github.com/PantelisGeorgiadis/dcmjs-dimse) for that.
+- DIMSE (legacy networking like C-STORE, C-FIND, C-MOVE, etc). See the [dcmjs-dimse](https://github.com/PantelisGeorgiadis/dcmjs-dimse) project for that.
 - Physical Media (optical disks). See [this FAQ](https://www.dclunie.com/medical-image-faq/html/index.html) if you need to work with those.
-- Image processing. See [dcmjs-imaging](https://github.com/PantelisGeorgiadis/dcmjs-imaging) for this.
+- Image rendering. See [dcmjs-imaging](https://github.com/PantelisGeorgiadis/dcmjs-imaging) for this.
 
 # Usage
 

package.json

@@ -53,7 +53,8 @@
     "gl-matrix": "^3.1.0",
     "lodash.clonedeep": "^4.5.0",
     "loglevelnext": "^3.0.1",
-    "ndarray": "^1.0.19"
+    "ndarray": "^1.0.19",
+    "pako": "^2.0.4"
   },
   "husky": {
     "hooks": {

src/BufferStream.js

@@ -1,3 +1,5 @@
+import pako from "pako";
+
 function toInt(val) {
     if (isNaN(val)) {
         throw new Error("Not a number: " + val);
@@ -423,6 +425,15 @@ class ReadBufferStream extends BufferStream {
     }
 }
 
+class DeflatedReadBufferStream extends ReadBufferStream {
+    constructor(stream, options) {
+        const inflatedBuffer = pako.inflateRaw(
+            stream.getBuffer(stream.offset, stream.size)
+        );
+        super(inflatedBuffer.buffer, stream.littleEndian, options);
+    }
+}
+
 class WriteBufferStream extends BufferStream {
     constructor(buffer, littleEndian) {
         super(buffer, littleEndian);
@@ -431,4 +442,5 @@ class WriteBufferStream extends BufferStream {
 }
 
 export { ReadBufferStream };
+export { DeflatedReadBufferStream };
 export { WriteBufferStream };

src/DicomMessage.js

@@ -1,11 +1,13 @@
 import { ReadBufferStream } from "./BufferStream.js";
+import { DeflatedReadBufferStream } from "./BufferStream.js";
 import { Tag } from "./Tag.js";
 import { DicomMetaDictionary } from "./DicomMetaDictionary.js";
 import { DicomDict } from "./DicomDict.js";
 import { ValueRepresentation } from "./ValueRepresentation.js";
 
 const IMPLICIT_LITTLE_ENDIAN = "1.2.840.10008.1.2";
 const EXPLICIT_LITTLE_ENDIAN = "1.2.840.10008.1.2.1";
+const DEFLATED_EXPLICIT_LITTLE_ENDIAN = "1.2.840.10008.1.2.1.99";
 const EXPLICIT_BIG_ENDIAN = "1.2.840.10008.1.2.2";
 const singleVRs = ["SQ", "OF", "OW", "OB", "UN", "LT"];
 
@@ -203,10 +205,18 @@ class DicomMessage {
 
         //read header buffer
         var metaStream = stream.more(metaLength);
-
         var metaHeader = DicomMessage._read(metaStream, useSyntax, options);
+
         //get the syntax
         var mainSyntax = metaHeader["00020010"].Value[0];
+
+        //in case of deflated dataset, decompress and continue
+        if (mainSyntax === DEFLATED_EXPLICIT_LITTLE_ENDIAN) {
+            stream = new DeflatedReadBufferStream(stream, {
+                noCopy: options.noCopy
+            });
+        }
+
         mainSyntax = DicomMessage._normalizeSyntax(mainSyntax);
         var objects = DicomMessage._read(stream, mainSyntax, options);
 

src/index.js

@@ -1,6 +1,7 @@
 // Data
 import { BitArray } from "./bitArray.js";
 import { ReadBufferStream } from "./BufferStream.js";
+import { DeflatedReadBufferStream } from "./BufferStream.js";
 import { WriteBufferStream } from "./BufferStream.js";
 import { DicomDict } from "./DicomDict.js";
 import { DicomMessage } from "./DicomMessage.js";
@@ -46,6 +47,7 @@ import { cleanTags, getTagsNameToEmpty } from "./anonymizer.js";
 let data = {
     BitArray,
     ReadBufferStream,
+    DeflatedReadBufferStream,
     WriteBufferStream,
     DicomDict,
     DicomMessage,

test/data.test.js

@@ -622,6 +622,31 @@ it("Writes encapsulated OB data which has an odd length with a padding byte in i
     ]);
 });
 
+it("test_deflated", async () => {
+    const url =
+        "https://github.com/dcmjs-org/data/releases/download/deflate-transfer-syntax/deflate_tests.zip";
+    const unzipPath = await getZippedTestDataset(url, "deflate_tests.zip", "deflate_tests");
+    const deflatedPath = path.join(unzipPath, "deflate_tests");
+
+    const expected = [
+        { file: "image_dfl", tags: { Modality: "OT", Rows: 512, Columns: 512 }},
+        { file: "report_dfl", tags: { Modality: "SR", VerificationFlag: "UNVERIFIED", ContentDate: "20001110" }},
+        { file: "wave_dfl", tags: { Modality: "ECG", SynchronizationTrigger: "NO TRIGGER", ContentDate: "19991223" }}
+    ];
+
+    expected.forEach(e => {
+        const buffer = fs.readFileSync(path.join(deflatedPath, e.file));
+        const dicomDict = DicomMessage.readFile(buffer.buffer.slice(
+            buffer.byteOffset,
+            buffer.byteOffset + buffer.byteLength
+          ));
+        const dataset = DicomMetaDictionary.naturalizeDataset(dicomDict.dict);
+        Object.keys(e.tags).forEach(t => {
+            expect(dataset[t]).toEqual(e.tags[t]);
+        });
+    });
+});
+
 describe("With a SpecificCharacterSet tag", () => {
     it("Reads a long string in the '' character set", async () => {
         expect(readEncodedLongString("", [0x68, 0x69])).toEqual("hi");