Add fNIRS support

bids-validator/bids_validator/rules/file_level_rules.json

@@ -505,6 +505,24 @@
     "regexp": "^[\\/\\\\](?:stimuli)[\\/\\\\](?:.*)$"
   },
 
+  "nirs": {
+    "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?nirs\\/\\1(_\\2)?(?:_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_@@@))$",
+    "tokens": {
+      "@@@_nirs_type_@@@": ["snirf"],
+      "@@@_nirs_ext_@@@": [
+        "_events\\.json",
+        "_events\\.tsv",
+        "_optodes\\.json",
+        "_optodes\\.tsv",
+        "_channels\\.json",
+        "_channels\\.tsv",
+        "_nirs\\.json",
+        "_coordsystem\\.json",
+        "_photo\\.jpg"
+      ]
+    }
+  },
+
   "pet": {
     "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?pet[\\/\\\\](sub-[a-zA-Z0-9]+)(?:(_ses-[a-zA-Z0-9]+))?(?:_task-[a-zA-Z0-9]+)?(?:_trc-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(@@@_pet_ext_@@@)$",
     "tokens": {

bids-validator/bids_validator/rules/session_level_rules.json

@@ -226,5 +226,19 @@
         "_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/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

@@ -127,6 +127,23 @@
       ]
     }
   },
+  "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_@@@)$",
+    "tokens": {
+      "@@@_nirs_top_ext_@@@": [
+        "_nirs\\.json",
+        "_channels\\.tsv",
+        "_optodes\\.tsv",
+        "_photo\\.jpg",
+        "_coordsystem\\.json"
+      ]
+    }
+  "meg_calibration_top": {
+    "regexp": "^[\\/\\\\](?:(ses-[a-zA-Z0-9]+_)?)acq-calibration_meg\\.fif$"
+  },
+  "meg_crosstalk_top": {
+    "regexp": "^[\\/\\\\](?:(ses-[a-zA-Z0-9]+_)?)acq-crosstalk_meg\\.dat$"
+  },
   "multi_dir_fieldmap": {
     "regexp": "^[\\/\\\\](?:acq-[a-zA-Z0-9]+_)?(?:dir-[a-zA-Z0-9]+_)epi\\.json$"
   },

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/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) ||
@@ -118,6 +122,7 @@ export default {
       this.file.isPETBlood(path) ||
       this.file.isMicroscopy(path) ||
       this.file.isMicroscopyJSON(path)
+
     )
   },
 
@@ -142,6 +147,7 @@ export default {
           eegTop.test(path) ||
           ieegTop.test(path) ||
           petTop.test(path) ||
+          nirsTop.test(path) ||
           microscopyTop.test(path)
         )
       } else {
@@ -157,6 +163,7 @@ export default {
           eegTop.test(path) ||
           ieegTop.test(path) ||
           petTop.test(path) ||
+          nirsTop.test(path) ||
           microscopyTop.test(path)
         )
       }
@@ -210,6 +217,9 @@ export default {
         conditionalMatch(anatSes, path) ||
         conditionalMatch(dwiSes, path) ||
         conditionalMatch(megSes, path) ||
+        conditionalMatch(nirsSes, path) ||
+        conditionalMatch(megCalibrationSes, path) ||
+        conditionalMatch(megCrosstalkSes, path) ||
         conditionalMatch(eegSes, path) ||
         conditionalMatch(ieegSes, path) ||
         conditionalMatch(petSes, path) ||
@@ -333,6 +343,10 @@ 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 +395,7 @@ 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')) {
@@ -131,6 +133,10 @@ const selectSchema = file => {
       file.name.endsWith('coordsystem.json')
     ) {
       schema = require('./schemas/coordsystem_eeg.json')
+    } else if (file.name.endsWith('pet.json')) {
+      schema = require('./schemas/pet.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')

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 },

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

@@ -0,0 +1,105 @@
+{
+  "type": "object",
+  "properties": {
+    "TaskName": { "$ref": "common_definitions.json#/definitions/TaskName" },
+    "TaskDescription": {
+      "$ref": "common_definitions.json#/definitions/TaskDescription"
+    },
+    "Instructions": {
+      "$ref": "common_definitions.json#/definitions/Instructions"
+    },
+    "CogAtlasID": { "$ref": "common_definitions.json#/definitions/CogAtlasID" },
+    "CogPOID": { "$ref": "common_definitions.json#/definitions/CogPOID" },
+    "InstitutionName": {
+      "$ref": "common_definitions.json#/definitions/InstitutionName"
+    },
+    "InstitutionalDepartmentName": { "type": "string" },
+    "InstitutionAddress": {
+      "$ref": "common_definitions.json#/definitions/InstitutionAddress"
+    },
+    "Manufacturer": {
+      "$ref": "common_definitions.json#/definitions/Manufacturer"
+    },
+    "ManufacturersModelName": { "type": "string", "minLength": 1 },
+    "DeviceSerialNumber": {
+      "$ref": "common_definitions.json#/definitions/DeviceSerialNumber"
+    },
+    "SoftwareVersions": {
+      "$ref": "common_definitions.json#/definitions/SoftwareVersions"
+    },
+    "PowerLineFrequency": {
+      "$ref": "common_definitions.json#/definitions/PowerLineFrequency"
+    },
+    "SamplingFrequency": {
+      "anyOf": [
+        { "$ref": "common_definitions.json#/definitions/SamplingFrequency" },
+        { "enum": ["n/a"] }
+      ]
+    },
+    "NIRSChannelCount": {
+      "$ref": "common_definitions.json#/definitions/NIRSChannelCount"
+    },
+    "NIRSSourceOptodeCount": {
+      "$ref": "common_definitions.json#/definitions/NIRSSourceOptodeCount"
+    },
+    "NIRSDetectorOptodeCount": {
+      "$ref": "common_definitions.json#/definitions/NIRSDetectorOptodeCount"
+    },
+    "EEGChannelCount": {
+      "$ref": "common_definitions.json#/definitions/EEGChannelCount"
+    },
+    "EOGChannelCount": {
+      "$ref": "common_definitions.json#/definitions/EOGChannelCount"
+    },
+    "ECGChannelCount": {
+      "$ref": "common_definitions.json#/definitions/ECGChannelCount"
+    },
+    "EMGChannelCount": {
+      "$ref": "common_definitions.json#/definitions/EMGChannelCount"
+    },
+    "MiscChannelCount": {
+      "$ref": "common_definitions.json#/definitions/MiscChannelCount"
+    },
+    "TriggerChannelCount": {
+      "$ref": "common_definitions.json#/definitions/TriggerChannelCount"
+    },
+    "NIRSPlacementScheme": { "type": "string" },
+    "CapManufacturer": { "type": "string" },
+    "CapManufacturersModelName": { "type": "string" },
+    "HeadCircumference": { "type": "number", "exclusiveMinimum": 0 },
+    "ShortChannelCount": {
+      "type": "number",
+      "exclusiveMinimum": 0,
+      "recommends_tsv_non_custom_columns": ["short_channel"]
+    },
+    "HardwareFilters": {
+      "$ref": "common_definitions.json#/definitions/HardwareFilters"
+    },
+    "SoftwareFilters": {
+      "$ref": "common_definitions.json#/definitions/SoftwareFilters"
+    },
+    "RecordingDuration": {
+      "$ref": "common_definitions.json#/definitions/RecordingDuration"
+    },
+    "RecordingType": {
+      "$ref": "common_definitions.json#/definitions/RecordingType"
+    },
+    "SubjectArtefactDescription": { "type": "string" },
+    "ACCELChannelCount": { "type": "number" },
+    "GYROChannelCount": { "type": "number" },
+    "MAGNChannelCount": { "type": "number" }
+  },
+  "required": [
+    "TaskName",
+    "SamplingFrequency",
+    "NIRSChannelCount",
+    "NIRSSourceOptodeCount",
+    "NIRSDetectorOptodeCount"
+  ],
+  "required_if_tsv_value_present": {
+    "ACCELChannelCount": { "header": "type", "value": "ACC" },
+    "MAGNChannelCount": { "header": "type", "value": "MAGN" },
+    "GYROChannelCount": { "header": "type", "value": "GYRO" }
+  },
+  "additionalProperties": false
+}