Merge pull request #1797 from effigies/enh/associations

ENH: Finish populating associations

bids-validator/src/files/dwi.ts

@@ -0,0 +1,29 @@
+/*
+ * DWI
+ * Module for parsing DWI-associated files
+ */
+const normalizeEOL = (str: string): string =>
+  str.replace(/\r\n/g, '\n').replace(/\r/g, '\n')
+
+export function parseBval(contents: string): number[][] {
+  // BVAL files are a single row of numbers, and may contain
+  // trailing whitespace
+  return [contents
+    .split(/\s+/)
+    .filter((x) => x !== '')
+    .map((x) => Number(x))]
+}
+
+export function parseBvec(contents: string): number[][] {
+  // BVEC files are a matrix of numbers, with each row being
+  // a different axis
+  return normalizeEOL(contents)
+    .split(/\s*\n/)
+    .filter((x) => x !== '')
+    .map((row) =>
+      row
+        .split(/\s+/)
+        .filter((x) => x !== '')
+        .map((x) => Number(x)),
+    )
+}

bids-validator/src/schema/associations.ts

@@ -7,6 +7,7 @@ import { FileTree } from '../types/filetree.ts'
 import { BIDSContext } from './context.ts'
 import { readEntities } from './entities.ts'
 import { parseTSV } from '../files/tsv.ts'
+import { parseBval, parseBvec } from '../files/dwi.ts'
 
 // type AssociationsLookup = Record<keyof ContextAssociations, { extensions: string[], inherit: boolean, load: ... }
 
@@ -23,63 +24,104 @@ import { parseTSV } from '../files/tsv.ts'
  */
 const associationLookup = {
   events: {
+    suffix: 'events',
     extensions: ['.tsv'],
     inherit: true,
-    load: (file: BIDSFile): Promise<ContextAssociations['events']> => {
-      return file
-        .text()
-        .then((text) => parseTSV(text) as ContextAssociationsEvents)
+    load: async (file: BIDSFile): Promise<ContextAssociations['events']> => {
+      const text = await file.text()
+      const columns = parseTSV(text)
+      return {
+        path: file.path,
+        onset: columns.get('onset') || [],
+      }
     },
   },
   aslcontext: {
+    suffix: 'aslcontext',
     extensions: ['.tsv'],
     inherit: true,
-    load: (file: BIDSFile): Promise<ContextAssociations['aslcontext']> => {
-      return Promise.resolve({ path: file.path, n_rows: 0, volume_type: [] })
+    load: async (
+      file: BIDSFile,
+    ): Promise<ContextAssociations['aslcontext']> => {
+      const contents = await file.text()
+      const columns = parseTSV(contents)
+      return {
+        path: file.path,
+        n_rows: columns.get('volume_type')?.length || 0,
+        volume_type: columns.get('volume_type') || [],
+      }
     },
   },
   m0scan: {
+    suffix: 'm0scan',
     extensions: ['.nii', '.nii.gz'],
     inherit: false,
     load: (file: BIDSFile): Promise<ContextAssociations['m0scan']> => {
       return Promise.resolve({ path: file.path })
     },
   },
   magnitude: {
+    suffix: 'magnitude',
     extensions: ['.nii', '.nii.gz'],
     inherit: false,
     load: (file: BIDSFile): Promise<ContextAssociations['magnitude']> => {
-      return Promise.resolve({ path: file.path, onset: 'silly' })
+      return Promise.resolve({ path: file.path })
     },
   },
   magnitude1: {
+    suffix: 'magnitude1',
     extensions: ['.nii', '.nii.gz'],
     inherit: false,
     load: (file: BIDSFile): Promise<ContextAssociations['magnitude1']> => {
       return Promise.resolve({ path: file.path })
     },
   },
   bval: {
-    extensions: ['.nii', '.nii.gz'],
+    suffix: 'dwi',
+    extensions: ['.bval'],
     inherit: true,
-    load: (file: BIDSFile): Promise<ContextAssociations['bval']> => {
-      return Promise.resolve({ path: file.path, n_cols: 0 })
+    load: async (file: BIDSFile): Promise<ContextAssociations['bval']> => {
+      const contents = await file.text()
+      const columns = parseBval(contents)
+      return {
+        path: file.path,
+        n_cols: columns ? columns[0].length : 0,
+      }
     },
   },
   bvec: {
-    extensions: ['.nii', '.nii.gz'],
+    suffix: 'dwi',
+    extensions: ['.bvec'],
     inherit: true,
-    load: (file: BIDSFile): Promise<ContextAssociations['bvec']> => {
-      return Promise.resolve({ path: file.path, n_cols: 0 })
+    load: async (file: BIDSFile): Promise<ContextAssociations['bvec']> => {
+      const contents = await file.text()
+      const columns = parseBvec(contents)
+      return {
+        path: file.path,
+        n_cols: columns ? columns[0].length : 0,
+      }
     },
   },
   channels: {
+    suffix: 'channels',
     extensions: ['.tsv'],
     inherit: true,
-    load: (file: BIDSFile): Promise<ContextAssociations['events']> => {
-      return file
-        .text()
-        .then((text) => parseTSV(text) as ContextAssociationsEvents)
+    load: async (file: BIDSFile): Promise<ContextAssociations['channels']> => {
+      const contents = await file.text()
+      const columns = parseTSV(contents)
+      return {
+        path: file.path,
+        type: columns.get('type') || [],
+        short_channel: columns.get('short_channel') || [],
+      }
+    },
+  },
+  coordsystem: {
+    suffix: 'coordsystem',
+    extensions: ['.json'],
+    inherit: true,
+    load: (file: BIDSFile): Promise<ContextAssociations['coordsystem']> => {
+      return Promise.resolve({ path: file.path })
     },
   },
 }
@@ -90,9 +132,9 @@ export async function buildAssociations(
 ): Promise<ContextAssociations> {
   const associations: ContextAssociations = {}
   for (const key in associationLookup as typeof associationLookup) {
-    const { extensions, inherit } =
+    const { suffix, extensions, inherit } =
       associationLookup[key as keyof typeof associationLookup]
-    const paths = getPaths(fileTree, source, key, extensions)
+    const paths = getPaths(fileTree, source, suffix, extensions)
     if (paths.length === 0) {
       continue
     }

bids-validator/src/schema/context.ts

@@ -5,13 +5,15 @@ import {
   ContextSubject,
   ContextAssociations,
   ContextNiftiHeader,
+  ContextData,
 } from '../types/context.ts'
 import { BIDSFile } from '../types/file.ts'
 import { FileTree } from '../types/filetree.ts'
 import { ColumnsMap } from '../types/columns.ts'
 import { BIDSEntities, readEntities } from './entities.ts'
 import { DatasetIssues } from '../issues/datasetIssues.ts'
 import { parseTSV } from '../files/tsv.ts'
+import { parseBval, parseBvec } from '../files/dwi.ts'
 import { loadHeader } from '../files/nifti.ts'
 import { buildAssociations } from './associations.ts'
 import { ValidatorOptions } from '../setup/options.ts'
@@ -66,6 +68,7 @@ export class BIDSContext implements Context {
   columns: ColumnsMap
   associations: ContextAssociations
   nifti_header?: ContextNiftiHeader
+  data?: ContextData
 
   constructor(
     fileTree: FileTree,
@@ -171,6 +174,27 @@ export class BIDSContext implements Context {
     }
   }
 
+  // Currently un-specified bit of context needed for bval/bvec
+  async loadData(): Promise<void> {
+    let parser
+    if (this.file.path.endsWith('.bval')) {
+      parser = parseBval
+    } else if (this.file.path.endsWith('.bvec')) {
+      parser = parseBvec
+    }
+    if (parser) {
+      this.data = await this.file
+        .text()
+        .then(parser as (value: string) => number[][])
+        .then((data) => {
+          return {
+            n_rows: data.length,
+            n_cols: data ? data[0].length : 0,
+          }
+        }).then((ret) => {console.log(ret); return ret})
+    }
+  }
+
   async loadColumns(): Promise<void> {
     if (this.extension !== '.tsv') {
       return
@@ -198,6 +222,7 @@ export class BIDSContext implements Context {
       this.loadSidecar(),
       this.loadColumns(),
       this.loadAssociations(),
+      this.loadData(),
     ])
     this.loadNiftiHeader()
   }

bids-validator/src/types/context.ts

@@ -48,6 +48,14 @@ export interface ContextAssociationsBvec {
   path: string
   n_cols: number
 }
+export interface ContextAssociationsChannels {
+  path?: string
+  type?: string[]
+  short_channel?: string[]
+}
+export interface ContextAssociationsCoordsystem {
+  path: string
+}
 export interface ContextAssociations {
   events?: ContextAssociationsEvents
   aslcontext?: ContextAssociationsAslcontext
@@ -56,6 +64,8 @@ export interface ContextAssociations {
   magnitude1?: ContextAssociationsMagnitude1
   bval?: ContextAssociationsBval
   bvec?: ContextAssociationsBvec
+  channels?: ContextAssociationsChannels
+  coordsystem?: ContextAssociationsCoordsystem
 }
 export interface ContextNiftiHeaderDimInfo {
   freq: number
@@ -74,6 +84,10 @@ export interface ContextNiftiHeader {
   qform_code: number
   sform_code: number
 }
+export interface ContextData {
+  n_cols?: number
+  n_rows?: number
+}
 export interface Context {
   dataset: ContextDataset
   subject: ContextSubject
@@ -88,4 +102,5 @@ export interface Context {
   columns: object
   json: object
   nifti_header?: ContextNiftiHeader
+  data?: ContextData
 }