Add NIRS support to BIDS Validator

.github/workflows/test-bids-examples.yml

@@ -40,7 +40,7 @@ jobs:
 
       - name: Get bids-examples data
         run: |
-          git clone --depth 1 https://github.com/bids-standard/bids-examples -b ${{ matrix.bids-examples-branch }}
+          git clone --depth 1 https://github.com/rob-luke/bids-examples --branch fnirstapping
 
       - name: Display versions and environment information
         run: |

bids-validator/bids_validator/rules/file_level_rules.json

@@ -511,6 +511,25 @@
     "regexp": "^[\\/\\\\](?:stimuli)[\\/\\\\](?:.*)$"
   },
 
+  "nirs": {
+    "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?nirs\\/\\1(_\\2)?@@@_nirs_optodes_@@@|((?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_part-[0-9]+)?(_nirs\\.(@@@_nirs_type_@@@)|(@@@_nirs_ext_@@@)))$",
+    "tokens": {
+      "@@@_nirs_type_@@@": ["snirf"],
+      "@@@_nirs_ext_@@@": [
+        "_events\\.json",
+        "_events\\.tsv",
+        "_channels\\.json",
+        "_channels\\.tsv",
+        "_nirs\\.json",
+        "_photo\\.jpg"
+      ],
+      "@@@_nirs_optodes_@@@": [
+        "_optodes\\.tsv",
+        "_coordsystem\\.json"
+      ]
+    }
+  },
+
   "pet": {
     "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?pet[\\/\\\\](sub-[a-zA-Z0-9]+)(?:(_ses-[a-zA-Z0-9]+))?(?:_task-[a-zA-Z0-9]+)?(?:_trc-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(@@@_pet_ext_@@@)$",
     "tokens": {

bids-validator/bids_validator/rules/session_level_rules.json

@@ -232,5 +232,19 @@
         "_SPIM.json"
       ]
     }
+  },
+
+  "nirs_ses": {
+    "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(@@@_nirs_ses_type_@@@)$",
+    "tokens": {
+      "@@@_nirs_ses_type_@@@": [
+        "_events.tsv",
+        "_channels.tsv",
+        "_optodes.tsv",
+        "_nirs.json",
+        "_coordsystem.json",
+        "_photo.jpg"
+      ]
+    }
   }
 }

bids-validator/bids_validator/rules/top_level_rules.json

@@ -134,6 +134,18 @@
       ]
     }
   },
+  "nirs_top": {
+    "regexp": "^\\/(?:ses-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:@@@_nirs_top_ext_@@@)$",
+    "tokens": {
+      "@@@_nirs_top_ext_@@@": [
+        "_nirs\\.json",
+        "_channels\\.tsv",
+        "_optodes\\.tsv",
+        "_photo\\.jpg",
+        "_coordsystem\\.json"
+      ]
+    }
+  },
   "multi_dir_fieldmap": {
     "regexp": "^[\\/\\\\](?:acq-[a-zA-Z0-9]+_)?(?:dir-[a-zA-Z0-9]+_)epi\\.json$"
   },

bids-validator/bids_validator/tsv/non_custom_columns.json

@@ -5,6 +5,13 @@
     "low_cutoff",
     "name",
     "notch",
+    "source",
+    "detector",
+    "wavelength_actual",
+    "wavelength_nominal",
+    "wavelength_emission_actual",
+    "orientation_component",
+    "short_channel",
     "sampling_frequency",
     "software_filters",
     "status",
@@ -28,6 +35,18 @@
     "impedance",
     "dimension"
   ],
+  "optodes": [
+    "name",
+    "type",
+    "x",
+    "y",
+    "z",
+    "template_x",
+    "template_y",
+    "template_z",
+    "source_type",
+    "detector_type"
+  ],
   "events": [
     "duration",
     "HED",
@@ -44,5 +63,21 @@
   "scans": ["acq_time", "filename"],
   "sessions": ["acq_time", "session_id"],
   "aslcontext": ["volume_type"],
-  "blood": ["time", "plasma_radioactivity", "whole_blood_radioactivity", "metabolite_parent_fraction", "hplc_recovery_fractions"]
+  "blood": ["time", "plasma_radioactivity", "whole_blood_radioactivity", "metabolite_parent_fraction", "hplc_recovery_fractions"],
+  "nirs": [
+    "name",
+    "type",
+    "source",
+    "detector",
+    "wavelength_nominal",
+    "units",
+    "sampling_frequency",
+    "orientation_component",
+    "wavelength_actual",
+    "description",
+    "wavelength_emission_actual",
+    "short_channel",
+    "status",
+    "status_description"
+  ]
 }

bids-validator/tests/json.spec.js

@@ -692,4 +692,62 @@ describe('JSON', function() {
       assert(issues.length === 0)
     })
   })
+
+  var nirs_file = {
+    name: 'sub-01_run-01_nirs.json',
+    relativePath: '/sub-01_run-01_nirs.json',
+  }
+
+  it('*_nirs.json sidecars should have required key/value pairs', function() {
+    var jsonObj = {
+      TaskName: 'Audiovis',
+      SamplingFrequency: 7,
+      NIRSChannelCount: 7,
+      NIRSSourceOptodeCount: 7,
+      NIRSDetectorOptodeCount: 7,
+      CapManufacturer: 'EasyCap',
+      CapManufacturersModelName: 'actiCAP 64 Ch Standard-2',
+    }
+    jsonDict[nirs_file.relativePath] = jsonObj
+    validate.JSON(nirs_file, jsonDict, function(issues) {
+      assert(issues.length === 0)
+    })
+    var jsonObjInval = jsonObj
+    jsonObjInval['BadKey'] = ''
+    jsonDict[nirs_file.relativePath] = jsonObjInval
+    validate.JSON(nirs_file, jsonDict, function(issues) {
+      assert(issues && issues.length === 1)
+    })
+  })
+  var nirs_coordsystem_file = {
+    name: 'sub-01/nirs/sub-01_task-testing_coordsystem.json',
+    relativePath: '/sub-01/nirs/sub-01_task-testing_coordsystem.json',
+  }
+
+  it('NIRS *_coordsystem.json files should have required key/value pairs', function() {
+    var jsonObj = {
+      NIRSCoordinateSystem: 'fsaverage',
+      NIRSCoordinateUnits: 'mm',
+    }
+    jsonDict[nirs_coordsystem_file.relativePath] = jsonObj
+    validate.JSON(nirs_coordsystem_file, jsonDict, function(issues) {
+      assert(issues.length === 0)
+    })
+  })
+
+  it('NIRS *_coordsystem.json schema should require *Description if *Coordsystem is "Other"', function() {
+    var jsonObj = {
+      NIRSCoordinateSystem: 'Other',
+      NIRSCoordinateUnits: 'mm',
+    }
+    jsonDict[nirs_coordsystem_file.relativePath] = jsonObj
+    validate.JSON(nirs_coordsystem_file, jsonDict, function(issues) {
+      assert(issues.length === 2)
+      assert(
+        issues[0].evidence ==
+          " should have required property 'NIRSCoordinateSystemDescription'",
+      )
+      assert(issues[1].evidence == ' should match "then" schema')
+    })
+  })
 })

bids-validator/tests/tsv.spec.js

@@ -582,6 +582,50 @@ describe('TSV', function() {
       assert(issues.length === 0)
     })
   })
+  var channelsFileNIRS = {
+    name: 'sub-01_ses-001_task-rest_run-01_channels.tsv',
+    relativePath:
+      '/sub-01/ses-001/nirs/sub-01_ses-001_task-rest_run-01_channels.tsv',
+  }
+
+  it('NIRS channels.tsv with correct columns should throw no error', function() {
+    var tsv =
+      'name\ttype\tsource\tdetector\twavelength_nominal\tunits\n' +
+      'testch\tNIRSCWAMPLITUDE\tS1\tD1\t760.0\tV'
+    validate.TSV.TSV(channelsFileNIRS, tsv, [], function(issues) {
+      assert(issues.length === 0)
+    })
+  })
+
+  it('should not allow NIRS channels.tsv files without name column', function() {
+    var tsv =
+      'type\tsource\tdetector\twavelength_nominal\tunits\n' +
+      'NIRSCWAMPLITUDE\tS1\tD1\t760.0\tV'
+    validate.TSV.TSV(channelsFileNIRS, tsv, [], function(issues) {
+      assert(issues[0].code === 229)
+    })
+  })
+
+  // optodes checks ---------------------------------------------------------
+  var optodesFileNIRS = {
+    name: 'sub-01_ses-001_task-rest_run-01_optodes.tsv',
+    relativePath:
+      '/sub-01/ses-001/nirs/sub-01_ses-001_task-rest_run-01_optodes.tsv',
+  }
+
+  it('should allow NIRS optodes.tsv files with correct columns', function() {
+    var tsv = 'name\ttype\tx\ty\tz\n' + 'S1\tsource\t-0.04\t0.02\t0.5\n'
+    validate.TSV.TSV(optodesFileNIRS, tsv, [], function(issues) {
+      assert(issues.length === 0)
+    })
+  })
+
+  it('should not allow NIRS optodes.tsv files with out name columns', function() {
+    var tsv = 'type\tx\ty\tz\n' + 'source\t-0.04\t0.02\t0.5\n'
+    validate.TSV.TSV(optodesFileNIRS, tsv, [], function(issues) {
+      assert(issues[0].code === 228)
+    })
+  })
 
   // electrodes checks ---------------------------------------------------------
   var electrodesFileEEG = {

bids-validator/utils/issues/list.js

@@ -1119,4 +1119,16 @@ export default {
     severity: 'error',
     reason: 'Inconsistent TIFF file type and extension',
   },
+  228: {
+    key: 'MISSING_TSV_COLUMN_NIRS_OPTODES',
+    severity: 'error',
+    reason:
+      "The column names of the optodes file must begin with ['name', 'type', 'x', 'y', 'z']",
+  },
+  229: {
+    key: 'MISSING_TSV_COLUMN_NIRS_CHANNELS',
+    severity: 'error',
+    reason:
+      "The column names of the channels file must begin with ['name', 'type', 'source', 'detector', 'wavelength_nominal', 'units':]",
+  },
 }

bids-validator/utils/type.js

@@ -62,6 +62,7 @@ const petBlood = buildRegExp(file_level_rules.pet_blood)
 const microscopyData = buildRegExp(file_level_rules.microscopy)
 const microscopyPhotoData = buildRegExp(file_level_rules.microscopy_photo)
 const microscopyJSON = buildRegExp(file_level_rules.microscopy_json)
+const nirsData = buildRegExp(file_level_rules.nirs)
 // Phenotypic data
 const phenotypicData = buildRegExp(phenotypic_rules.phenotypic_data)
 // Session level
@@ -75,6 +76,7 @@ const megSes = buildRegExp(session_level_rules.meg_ses)
 const scansSes = buildRegExp(session_level_rules.scans)
 const petSes = buildRegExp(session_level_rules.pet_ses)
 const microscopySes = buildRegExp(session_level_rules.microscopy_ses)
+const nirsSes = buildRegExp(session_level_rules.nirs_ses)
 // Subject level
 const subjectLevel = buildRegExp(subject_level_rules.subject_level)
 // Top level
@@ -90,6 +92,7 @@ const otherTopFiles = buildRegExp(top_level_rules.other_top_files)
 const megTop = buildRegExp(top_level_rules.meg_top)
 const petTop = buildRegExp(top_level_rules.pet_top)
 const microscopyTop = buildRegExp(top_level_rules.microscopy_top)
+const nirsTop = buildRegExp(top_level_rules.nirs_top)
 
 export default {
   /**
@@ -109,6 +112,7 @@ export default {
       this.file.isFunc(path) ||
       this.file.isAsl(path) ||
       this.file.isMeg(path) ||
+      this.file.isNIRS(path) ||
       this.file.isIEEG(path) ||
       this.file.isEEG(path) ||
       this.file.isBehavioral(path) ||
@@ -142,6 +146,7 @@ export default {
           eegTop.test(path) ||
           ieegTop.test(path) ||
           petTop.test(path) ||
+          nirsTop.test(path) ||
           microscopyTop.test(path)
         )
       } else {
@@ -157,6 +162,7 @@ export default {
           eegTop.test(path) ||
           ieegTop.test(path) ||
           petTop.test(path) ||
+          nirsTop.test(path) ||
           microscopyTop.test(path)
         )
       }
@@ -210,6 +216,7 @@ export default {
         conditionalMatch(anatSes, path) ||
         conditionalMatch(dwiSes, path) ||
         conditionalMatch(megSes, path) ||
+        conditionalMatch(nirsSes, path) ||
         conditionalMatch(eegSes, path) ||
         conditionalMatch(ieegSes, path) ||
         conditionalMatch(petSes, path) ||
@@ -333,6 +340,10 @@ export default {
       }
     },
 
+    isNIRS: function(path) {
+      return conditionalMatch(nirsData, path)
+    },
+
     isEEG: function(path) {
       if (bids_schema) {
         return bids_schema.datatypes['eeg'].some(regex => regex.exec(path))
@@ -381,6 +392,7 @@ export default {
         this.isFunc(path) ||
         this.isAsl(path) ||
         this.isMeg(path) ||
+        this.isNIRS(path) ||
         this.isEEG(path) ||
         this.isIEEG(path) ||
         this.isBehavioral(path) ||

bids-validator/validators/json/json.js

@@ -88,6 +88,8 @@ const selectSchema = file => {
       schema = require('./schemas/asl.json')
     } else if (file.name.endsWith('pet.json')) {
       schema = require('./schemas/pet.json')
+    } else if (file.name.endsWith('nirs.json')) {
+      schema = require('./schemas/nirs.json')
     } else if (file.relativePath === '/dataset_description.json') {
       schema = require('./schemas/dataset_description.json')
     } else if (file.name.endsWith('meg.json')) {
@@ -131,13 +133,18 @@ const selectSchema = file => {
       file.name.endsWith('coordsystem.json')
     ) {
       schema = require('./schemas/coordsystem_eeg.json')
+    } else if (
+      file.relativePath.includes('/nirs/') &&
+      file.name.endsWith('coordsystem.json')
+    ) {
+      schema = require('./schemas/coordsystem_nirs.json')
+    } else if (file.name.endsWith('genetic_info.json')) {
+      schema = require('./schemas/genetic_info.json')
     } else if (
       file.relativePath.includes('/pet/') &&
       file.name.endsWith('blood.json')
     ) {
       schema = require('./schemas/pet_blood.json')
-    } else if (file.name.endsWith('genetic_info.json')) {
-      schema = require('./schemas/genetic_info.json')
     } else if (
       file.name.endsWith('physio.json') ||
       file.name.endsWith('stim.json')

bids-validator/validators/json/schemas/common_definitions.json

@@ -66,6 +66,9 @@
     "DeviceSerialNumber": { "type": "string" },
     "ECGChannelCount": { "type": "integer", "minimum": 0 },
     "EEGChannelCount": { "type": "integer", "minimum": 0 },
+    "NIRSChannelCount": { "type": "integer", "minimum": 0 },
+    "NIRSSourceOptodeCount": { "type": "integer", "minimum": 0 },
+    "NIRSDetectorOptodeCount": { "type": "integer", "minimum": 0 },
     "EMGChannelCount": { "type": "integer", "minimum": 0 },
     "EOGChannelCount": { "type": "integer", "minimum": 0 },
     "EpochLength": { "type": "number", "minimum": 0 },