Merge pull request #1053 from sappelhoff/crosstalk

Extend validator for crosstalk+finecalib for FIF

.gitignore

@@ -16,3 +16,5 @@ bids-validator-web/.next/
 # Only use global yarn.lock
 bids-validator/yarn.lock
 bids-validator-web/yarn.lock
+
+.vscode/

bids-validator/bids_validator/rules/file_level_rules.json

@@ -248,6 +248,14 @@
     }
   },
 
+  "meg_calbibration": {
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?meg[\\/]\\1(_\\2)?_acq-calibration_meg\\.fif$"
+  },
+
+  "meg_crosstalk": {
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?meg[\\/]\\1(_\\2)?_acq-crosstalk_meg\\.dat$"
+  },
+
   "stimuli": {
     "regexp": "^[\\/\\\\](?:stimuli)[\\/\\\\](?:.*)$"
   }

bids-validator/bids_validator/rules/subject_level_rules.json

@@ -2,7 +2,10 @@
   "subject_level": {
     "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\]\\1(@@@_subject_level_ext_@@@)$",
     "tokens": {
-      "@@@_subject_level_ext_@@@": ["_sessions\\.tsv", "_sessions\\.json"]
+      "@@@_subject_level_ext_@@@": [
+        "_sessions\\.tsv",
+        "_sessions\\.json"
+      ]
     }
   }
 }

bids-validator/bids_validator/rules/top_level_rules.json

@@ -101,7 +101,6 @@
   "multi_dir_fieldmap": {
     "regexp": "^[\\/\\\\](?:acq-[a-zA-Z0-9]+_)?(?:dir-[a-zA-Z0-9]+_)epi\\.json$"
   },
-
   "other_top_files": {
     "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:recording-[a-zA-Z0-9]+_)?(?:task-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(@@@_other_top_files_ext_@@@)$",
     "tokens": {

bids-validator/tests/type.spec.js

@@ -108,6 +108,10 @@ describe('utils.type.file.isTopLevel', function() {
     '/_T1w.json',
     '/_dwi.json',
     '/_task-test_physio.json',
+    // cross-talk and fine-calibration files for Neuromag/Elekta/MEGIN data (.fif)
+    // must be defined at file level.
+    '/acq-calibration_meg.fif',
+    '/acq-crosstalk_meg.dat',
   ]
 
   badFilenames.forEach(function(path) {
@@ -118,6 +122,37 @@ describe('utils.type.file.isTopLevel', function() {
   })
 })
 
+describe('utils.type.file.isSubjectLevel', () => {
+  const goodFilenames = [] // to be extended in the future...
+
+  goodFilenames.forEach(path => {
+    it("isSubjectLevel('" + path + "') === true", function(isdone) {
+      assert.equal(utils.type.file.isSubjectLevel(path), true)
+      isdone()
+    })
+  })
+
+  const badFilenames = [
+    // cross-talk and fine-calibration files for Neuromag/Elekta/MEGIN data (.fif)
+    // must be placed on file level.
+    '/sub-12/sub-12_acq-calibration_meg.fif',
+    '/sub-12/sub-12_acq-crosstalk_meg.dat',
+    '/sub-12/sub-12_acq-calibration_meg.dat',
+    '/sub-12/sub-12_acq-crosstalk_meg.fif',
+    '/sub-12/acq-calibration_meg.fif',
+    '/sub-12/acq-crosstalk_meg.dat',
+    '/sub-12/acq-calibration.fif',
+    '/sub-12/acq-crosstalk.dat',
+  ]
+
+  badFilenames.forEach(path => {
+    it("isSubjectLevel('" + path + "') === false", function(isdone) {
+      assert.equal(utils.type.file.isSubjectLevel(path), false)
+      isdone()
+    })
+  })
+})
+
 describe('utils.type.file.isSessionLevel', function() {
   const goodFilenames = [
     '/sub-12/sub-12_scans.tsv',
@@ -136,6 +171,12 @@ describe('utils.type.file.isSessionLevel', function() {
   const badFilenames = [
     '/sub-12/sub-12.tsv',
     '/sub-12/ses-pre/sub-12_ses-pre_scan.tsv',
+    // cross-talk and fine-calibration files for Neuromag/Elekta/MEGIN data (.fif)
+    // must be placed at file level.
+    '/sub-12/sub-12_acq-calibration_meg.fif',
+    '/sub-12/sub-12_acq-crosstalk_meg.dat',
+    '/sub-12/ses-pre/sub-12_ses-pre_acq-calibration_meg.fif',
+    '/sub-12/ses-pre/sub-12_ses-pre_acq-crosstalk_meg.dat',
   ]
 
   badFilenames.forEach(function(path) {
@@ -206,6 +247,11 @@ describe('utils.type.file.isMEG', function() {
     // NO father dir: fif data
     '/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_split-01_meg.fif',
     '/sub-01/ses-001/meg/sub-01_ses-001_task-rest_acq-TEST_run-01_split-01_meg.fif',
+    // cross-talk and fine-calibration files for Neuromag/Elekta/MEGIN data (.fif)
+    '/sub-01/meg/sub-01_acq-calibration_meg.fif',
+    '/sub-01/meg/sub-01_acq-crosstalk_meg.dat',
+    '/sub-01/ses-001/meg/sub-01_ses-001_acq-calibration_meg.fif',
+    '/sub-01/ses-001/meg/sub-01_ses-001_acq-crosstalk_meg.dat',
   ]
 
   goodFilenames.forEach(function(path) {
@@ -241,6 +287,10 @@ describe('utils.type.file.isMEG', function() {
     '/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.kdf',
     '/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.trg',
     '/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.chn',
+    // cross-talk and fine-calibration files for Neuromag/Elekta/MEGIN data (.fif)
+    // .dat in MEG only allowed for "acq-crosstalk"
+    '/acq-notcrosstalk_meg.dat',
+    '/sub-01/ses-001/meg/sub-01_ses-001_acq-notcrosstalk_meg.dat',
   ]
 
   badFilenames.forEach(function(path) {

bids-validator/utils/type.js

@@ -31,6 +31,8 @@ const funcData = buildRegExp(file_level_rules.func)
 const funcBoldData = buildRegExp(file_level_rules.func_bold)
 const ieegData = buildRegExp(file_level_rules.ieeg)
 const megData = buildRegExp(file_level_rules.meg)
+const megCalibrationData = buildRegExp(file_level_rules.meg_calbibration)
+const megCrosstalkData = buildRegExp(file_level_rules.meg_crosstalk)
 const stimuliData = buildRegExp(file_level_rules.stimuli)
 // Phenotypic data
 const phenotypicData = buildRegExp(phenotypic_rules.phenotypic_data)
@@ -196,7 +198,11 @@ export default {
     },
 
     isMeg: function(path) {
-      return conditionalMatch(megData, path)
+      return (
+        conditionalMatch(megData, path) ||
+        conditionalMatch(megCalibrationData, path) ||
+        conditionalMatch(megCrosstalkData, path)
+      )
     },
 
     isEEG: function(path) {