Support ASYNC functions (#52)

Author: neurolabusc

__tests__/nifti1-little-async.spec.ts

@@ -0,0 +1,57 @@
+import { isCompressed, readHeaderAsync, decompressAsync, isNIFTI1, readImage } from '../src/nifti.js'
+import { NIFTI1 } from '../src/nifti1.js'
+import { describe, it, assert, beforeEach } from 'vitest'
+import * as fs from 'fs'
+import { Utils } from '../src/utilities.js'
+import { NIFTI2 } from '../src/nifti2.js'
+
+let data: ArrayBuffer
+let nifti1: NIFTI1 | NIFTI2 | null = null
+
+beforeEach(async () => {
+  const buf = fs.readFileSync('./data/little.nii.gz')
+  data = Utils.toArrayBuffer(buf)
+  if (isCompressed(data)) {
+    data = await decompressAsync(data)
+  }
+  nifti1 = await readHeaderAsync(data)
+})
+
+describe('NIFTI-Reader-JS', function () {
+  describe('nifti-1 little endian test', function () {
+    it('should have a valid NIFTI header', async function () {
+      assert.notEqual(nifti1, null)
+      console.log(nifti1)
+    })
+
+    it('isNIFTI1() should return true', async function () {
+      assert.equal(true, isNIFTI1(data))
+    })
+
+    it('numBitsPerVoxel should be 32', async function () {
+      assert.equal(32, nifti1!.numBitsPerVoxel)
+    })
+
+    it('littleEndian should be true', async function () {
+      assert.equal(true, nifti1!.littleEndian)
+    })
+
+    it('dims[1] should be 64', async function () {
+      assert.equal(64, nifti1!.dims[1])
+    })
+
+    it('dims[2] should be 64', async function () {
+      assert.equal(64, nifti1!.dims[2])
+    })
+
+    it('dims[3] should be 21', async function () {
+      assert.equal(21, nifti1!.dims[3])
+    })
+
+    it('image data checksum should equal 4006845507', async function () {
+      const imageData = readImage(nifti1!, data)
+      const checksum = Utils.crc32(new DataView(imageData))
+      assert.equal(checksum, 4006845507)
+    })
+  })
+})

__tests__/nifti2-extension-async.spec.ts

@@ -0,0 +1,45 @@
+import { readHeaderAsync } from '../src/nifti.js'
+import { NIFTI1 } from '../src/nifti1.js'
+import * as fs from 'fs'
+import { Utils } from '../src/utilities.js'
+import { NIFTI2 } from '../src/nifti2.js'
+import { NIFTIEXTENSION } from '../src/nifti.js'
+import { describe, it, assert, beforeEach } from 'vitest'
+
+let nifti2 = null
+
+beforeEach(async () => {
+  const buf = fs.readFileSync('./data/avg152T1_LR_nifti2.nii.gz')
+  const data = Utils.toArrayBuffer(buf)
+  nifti2 = await readHeaderAsync(data)
+})
+
+describe('NIFTI-Reader-JS', function () {
+  const EXPECTED_EXTENSION_LENGTH = 376
+
+  describe('nifti-2 extension test', function () {
+    it('should not throw error when reading header', async function () {
+      assert.doesNotThrow(() => {
+        if (!nifti2) {
+          throw new Error('Failed to read NIFTI header')
+        }
+      })
+    })
+
+    it('extensions can be added and serialized', async function () {
+      let edata = new Int32Array(6)
+      edata.fill(8)
+      let newExtension = new NIFTIEXTENSION(32, 4, edata.buffer, true)
+      nifti2!.addExtension(newExtension)
+
+      assert.equal(1, nifti2!.extensions.length)
+
+      let bytes = nifti2!.toArrayBuffer(true)
+      let copy = await readHeaderAsync(bytes)
+
+      assert.equal(1, copy!.extensions.length)
+      assert.equal(4, copy!.extensions[0].ecode)
+      assert.equal(24, copy!.extensions[0].edata.byteLength)
+    })
+  })
+})

__tests__/nifti2-extension-asyncGZ.spec.ts

@@ -0,0 +1,65 @@
+import { readHeaderAsync } from '../src/nifti.js'
+import { NIFTI1 } from '../src/nifti1.js'
+import * as fs from 'fs'
+import { Utils } from '../src/utilities.js'
+import { NIFTI2 } from '../src/nifti2.js'
+import { NIFTIEXTENSION } from '../src/nifti.js'
+import { describe, it, assert, beforeEach } from 'vitest'
+
+let nifti2 = null
+
+async function compress(data: ArrayBuffer): Promise<ArrayBuffer> {
+  const uint8Data = new Uint8Array(data)
+  const format = 'gzip' // Changed to gzip as requested
+  const stream = new CompressionStream(format)
+  const writer = stream.writable.getWriter()
+
+  await writer.write(uint8Data)
+  await writer.close()
+
+  const response = new Response(stream.readable)
+  return await response.arrayBuffer()
+}
+
+beforeEach(async () => {
+  const buf = fs.readFileSync('./data/avg152T1_LR_nifti2.nii.gz')
+  const data = Utils.toArrayBuffer(buf)
+  nifti2 = await readHeaderAsync(data)
+})
+
+describe('NIFTI-Reader-JS', function () {
+  const EXPECTED_EXTENSION_LENGTH = 376
+
+  describe('nifti-2 extension test', function () {
+    it('should not throw error when reading header', async function () {
+      assert.doesNotThrow(() => {
+        if (!nifti2) {
+          throw new Error('Failed to read NIFTI header')
+        }
+      })
+    })
+
+    it('extensions can be added, compressed, and serialized', async function () {
+      let edata = new Int32Array(6)
+      edata.fill(8)
+      let newExtension = new NIFTIEXTENSION(32, 4, edata.buffer, true)
+      nifti2!.addExtension(newExtension)
+
+      assert.equal(1, nifti2!.extensions.length)
+
+      let bytes = nifti2!.toArrayBuffer(true)
+      console.log('Original bytes length:', bytes.byteLength)
+
+      // Compress the arrayBuffer bytes using gzip
+      let compressedBytes = await compress(bytes)
+      console.log('Compressed bytes length:', compressedBytes.byteLength)
+
+      // Decompress and read the header
+      let copy = await readHeaderAsync(compressedBytes)
+
+      assert.equal(1, copy!.extensions.length)
+      assert.equal(4, copy!.extensions[0].ecode)
+      assert.equal(24, copy!.extensions[0].edata.byteLength)
+    })
+  })
+})

dist/nifti-extension.d.ts

@@ -18,6 +18,6 @@ export declare class NIFTIEXTENSION {
      * Returns extension as ArrayBuffer.
      * @returns {ArrayBuffer}
      */
-    toArrayBuffer(): ArrayBufferLike;
+    toArrayBuffer(): ArrayBuffer;
 }
 //# sourceMappingURL=nifti-extension.d.ts.map

dist/nifti-extension.js

@@ -35,12 +35,26 @@ export declare function isCompressed(data: ArrayBuffer): boolean;
  * @returns {ArrayBuffer}
  */
 export declare function decompress(data: ArrayBuffer): ArrayBufferLike;
+/**
+ * Returns promise of decompressed data.
+ * @param {ArrayBuffer} data
+ * @returns {Promise<ArrayBuffer>}
+ */
+export declare function decompressAsync(data: ArrayBuffer): Promise<ArrayBuffer>;
+/**
+ * Returns promise of decompressed initial portion of data, reads at least minOutputBytes or entire file.
+ * @param {ArrayBuffer} data
+ * @param {number } minOutputBytes
+ * @returns {Promise<ArrayBuffer>}
+ */
+export declare function decompressHeaderAsync(data: ArrayBuffer, minOutputBytes?: number): Promise<ArrayBufferLike>;
 /**
  * Reads and returns the header object.
  * @param {ArrayBuffer} data
  * @returns {NIFTI1|NIFTI2}
  */
 export declare function readHeader(data: ArrayBuffer, isHdrImgPairOK?: boolean): NIFTI1 | NIFTI2;
+export declare function readHeaderAsync(data: ArrayBuffer, isHdrImgPairOK?: boolean): Promise<NIFTI1 | NIFTI2>;
 /**
  * Returns true if this header contains an extension.
  * @param {NIFTI1|NIFTI2} header