Merge pull request #92 from effigies/fix/bval-bvec

fix(bval): Handle trailing whitespace without newlines

Author: rwblair

src/files/deno.ts

@@ -159,7 +159,7 @@ export async function readFileTree(rootPath: string): Promise<FileTree> {
     )
     ignore.add(await readBidsIgnore(ignoreFile))
   } catch (err) {
-    if (err && typeof err === 'object' && !('code' in err && err.code !== 'ENOENT')) {
+    if (err && typeof err === 'object' && !('code' in err && err.code === 'ENOENT')) {
       logger.error(`Failed to read '.bidsignore' file with the following error:\n${err}`)
     }
   }

src/files/dwi.test.ts

@@ -0,0 +1,35 @@
+import { assertEquals } from '@std/assert'
+
+import { parseBvalBvec } from './dwi.ts'
+
+Deno.test('Test bval/bvec parsing', async (t) => {
+  await t.step('Load 3 bvals', async () => {
+    const bvals = parseBvalBvec('0 1 2 \n')  // Typically ends with " \n"
+    assertEquals(bvals, [['0', '1', '2']])
+  })
+  await t.step('Load 3 bvals - missing newline', async () => {
+    const bvals = parseBvalBvec('0 1 2 ')
+    assertEquals(bvals, [['0', '1', '2']])
+  })
+  await t.step('Load 3 bvals - no spaces', async () => {
+    const bvals = parseBvalBvec('0 1 2')
+    assertEquals(bvals, [['0', '1', '2']])
+  })
+  await t.step('Load 3 bvecs', async () => {
+    const bvecs = parseBvalBvec('0 1 2 \n0 1 2 \n0 1 2 \n')
+    assertEquals(bvecs, [['0', '1', '2'], ['0', '1', '2'], ['0', '1', '2']])
+  })
+  await t.step('Load 3 bvals - missing newline', async () => {
+    const bvecs = parseBvalBvec('0 1 2 \n0 1 2 \n0 1 2 ')
+    assertEquals(bvecs, [['0', '1', '2'], ['0', '1', '2'], ['0', '1', '2']])
+  })
+  await t.step('Load 3 bvals - no spaces', async () => {
+    const bvecs = parseBvalBvec('0 1 2\n0 1 2\n0 1 2\n')
+    assertEquals(bvecs, [['0', '1', '2'], ['0', '1', '2'], ['0', '1', '2']])
+  })
+  await t.step('Load 3 bvals - no spaces, missing newline', async () => {
+    const bvecs = parseBvalBvec('0 1 2\n0 1 2\n0 1 2')
+    assertEquals(bvecs, [['0', '1', '2'], ['0', '1', '2'], ['0', '1', '2']])
+  })
+})
+

src/files/dwi.ts

@@ -10,7 +10,7 @@ export function parseBvalBvec(contents: string): string[][] {
   // BVAL files are a single row of numbers, and may contain
   // trailing whitespace
   return normalizeEOL(contents)
-    .split(/\s*\n/) // Split on newlines, ignoring trailing whitespace
+    .split(/\n/) // Split on newlines
     .filter((x) => x.match(/\S/)) // Remove empty lines
-    .map((row) => row.split(/\s+/))
+    .map((row) => row.trimEnd().split(/\s+/)) // Split on whitespace, ignoring trailing
 }