Merge pull request #2036 from effigies/fix/nifti_reading

fix(nifti): Load NIfTI headers

bids-validator/src/deps/nifti.ts

@@ -0,0 +1 @@
+export { isCompressed, readHeader } from 'https://esm.sh/[email protected]'

bids-validator/src/files/nifti.test.ts

@@ -0,0 +1,26 @@
+import { assert } from '../deps/asserts.ts'
+import { FileIgnoreRules } from './ignore.ts'
+import { BIDSFileDeno } from './deno.ts'
+
+import { loadHeader } from './nifti.ts'
+
+Deno.test('Test loading nifti header', async (t) => {
+  const ignore = new FileIgnoreRules([])
+  await t.step('Load header from compressed file', async () => {
+    const path = "sub-01/func/sub-01_task-rhymejudgment_bold.nii.gz"
+    const root = "./tests/data/valid_headers"
+    const file = new BIDSFileDeno(root, path, ignore)
+    const header = await loadHeader(file)
+    assert(header !== undefined)
+    assert(header['pixdim'].length === 8)
+  })
+  await t.step('Fail on non-nifti file', async () => {
+    const path = "sub-01/func/sub-01_task-rhymejudgment_events.tsv"
+    const root = "./tests/data/valid_headers"
+    const file = new BIDSFileDeno(root, path, ignore)
+    const header = await loadHeader(file)
+    assert(header !== undefined)
+    assert(header === null)
+  })
+
+})

bids-validator/src/files/nifti.ts

@@ -1,19 +1,46 @@
-import 'https://raw.githubusercontent.com/rii-mango/NIFTI-Reader-JS/v0.6.4/release/current/nifti-reader-min.js'
+import { isCompressed, readHeader } from '../deps/nifti.ts'
 import { BIDSFile } from '../types/filetree.ts'
 import { logger } from '../utils/logger.ts'
+import { ContextNiftiHeader } from '../types/context.ts'
 
-export async function loadHeader(file: BIDSFile) {
+async function extract(buffer: Uint8Array, nbytes: number): Promise<Uint8Array> {
+  // The fflate decompression that is used in nifti-reader does not like
+  // truncated data, so pretend that we have a stream and stop reading
+  // when we have enough bytes.
+  const result = new Uint8Array(nbytes)
+  const stream = new ReadableStream({
+    start(controller) {
+      controller.enqueue(buffer)
+    },
+  })
+  const reader = stream.pipeThrough(new DecompressionStream('gzip')).getReader()
+  let offset = 0
+  while (offset < nbytes) {
+    const { value, done } = await reader.read()
+    if (done) {
+      break
+    }
+    result.set(value.subarray(0, Math.min(value.length, nbytes - offset)), offset)
+    offset += value.length
+  }
+  await reader.cancel()
+  return result
+}
+
+export async function loadHeader(file: BIDSFile): Promise<ContextNiftiHeader | undefined> {
   try {
     const buf = await file.readBytes(1024)
-    // @ts-expect-error NIFTI-Reader-JS required mangling globals
-    const header = globalThis.nifti.readHeader(buf.buffer)
+    const data = isCompressed(buf.buffer) ? await extract(buf, 540) : buf
+    const header = readHeader(data.buffer)
     // normalize between nifti-reader and spec schema
     // https://github.com/bids-standard/bids-specification/blob/master/src/schema/meta/context.yaml#L200
     if (header) {
+      // @ts-expect-error
       header.pixdim = header.pixDims
+      // @ts-expect-error
       header.dim = header.dims
     }
-    return header
+    return header as unknown as ContextNiftiHeader
   } catch (err) {
     logger.warning(`NIfTI file could not be opened or read ${file.path}`)
     logger.debug(err)