JSON-schema: overhaul accepted coordinate keywords (#1149)

* overhaul accepted coordinate keywords * run yarn lint --fix * remove typo
bids-standard · Feb 1, 2021 · 1bcf51a · 1bcf51a
1 parent 0e3bcee
commit 1bcf51a
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Showing 5 changed files with 106 additions and 11 deletions.
diff --git a/bids-validator/tests/json.spec.js b/bids-validator/tests/json.spec.js
@@ -156,7 +156,7 @@ describe('JSON', function() {
       MEGCoordinateSystem: 'CTF',
       MEGCoordinateUnits: 'mm',
       MEGCoordinateSystemDescription: 'this is the usual ...',
-      EEGCoordinateSystem: 'Other',
+      EEGCoordinateSystem: 'CapTrak',
       EEGCoordinateSystemDescription: 'RAS orientation ...',
       HeadCoilCoordinateSystem: 'Other',
       HeadCoilCoordinates: {
@@ -223,11 +223,15 @@ describe('JSON', function() {
     }
     jsonDict[eeg_coordsystem_file.relativePath] = jsonObj
     validate.JSON(eeg_coordsystem_file, jsonDict, function(issues) {
-      assert(issues.length === 1)
+      assert(issues.length === 5)
       assert(
         issues[0].evidence ==
           '.EEGCoordinateSystem should be equal to one of the allowed values',
       )
+      assert(
+        issues[4].evidence ==
+          '.EEGCoordinateSystem should match some schema in anyOf',
+      )
     })
   })
 

diff --git a/bids-validator/validators/json/schemas/common_definitions.json b/bids-validator/validators/json/schemas/common_definitions.json
@@ -4,6 +4,53 @@
     "CogAtlasID": { "type": "string", "format": "uri" },
     "CogPOID": { "type": "string", "format": "uri" },
     "CoordUnits": { "type": "string", "enum": ["m", "mm", "cm", "n/a"] },
+    "MEGCoordSys": { "type": "string", "enum": ["CTF", "ElektaNeuromag", "4DBti", "KitYokogawa", "ChietiItab", "Other"] },
+    "EEGCoordSys": { "type": "string", "enum": ["CapTrak", "Other"] },
+    "iEEGCoordSys": { "type": "string", "enum": ["Pixels", "ACPC", "Other"] },
+    "StandardTemplateCoordSys" :{
+      "type": "string",
+      "enum": [
+        "ICBM452AirSpace",
+        "ICBM452Warp5Space",
+        "IXI549Space",
+        "fsaverage",
+        "fsaverageSym",
+        "fsLR",
+        "MNIColin27",
+        "MNI152Lin",
+        "MNI152NLin2009aSym",
+        "MNI152NLin2009bSym",
+        "MNI152NLin2009cSym",
+        "MNI152NLin2009aAsym",
+        "MNI152NLin2009bAsym",
+        "MNI152NLin2009cAsym",
+        "MNI152NLin6Sym",
+        "MNI152NLin6ASym",
+        "MNI305",
+        "NIHPD",
+        "OASIS30AntsOASISAnts",
+        "OASIS30Atropos",
+        "Talairach",
+        "UNCInfant"
+        ] },
+    "StandardTemplateDeprecatedCoordSys" :{
+      "type": "string",
+      "enum": [
+        "fsaverage3",
+        "fsaverage4",
+        "fsaverage5",
+        "fsaverage6",
+        "fsaveragesym",
+        "UNCInfant0V21",
+        "UNCInfant1V21",
+        "UNCInfant2V21",
+        "UNCInfant0V22",
+        "UNCInfant1V22",
+        "UNCInfant2V22",
+        "UNCInfant0V23",
+        "UNCInfant1V23",
+        "UNCInfant2V23"
+        ] },
     "DeviceSerialNumber": { "type": "string" },
     "ECGChannelCount": { "type": "integer", "minimum": 0 },
     "EEGChannelCount": { "type": "integer", "minimum": 0 },

diff --git a/bids-validator/validators/json/schemas/coordsystem_eeg.json b/bids-validator/validators/json/schemas/coordsystem_eeg.json
@@ -4,14 +4,29 @@
     "IntendedFor": { "type": "string", "minLength": 1 },
     "FiducialsDescription": { "type": "string", "minLength": 1 },
     "FiducialsCoordinates": { "$ref": "common_definitions.json#/definitions/LandmarkCoordinates" },
-    "FiducialsCoordinateSystem": { "type": "string", "enum": ["CapTrak", "Other"] },
+    "FiducialsCoordinateSystem": { "anyOf": [
+      { "$ref": "common_definitions.json#/definitions/MEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/EEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateDeprecatedCoordSys" }
+    ]},
     "FiducialsCoordinateSystemDescription": { "type": "string", "minLength": 1 },
     "FiducialsCoordinateUnits": { "$ref": "common_definitions.json#/definitions/CoordUnits" },
-    "EEGCoordinateSystem": { "type": "string", "enum": ["CapTrak", "Other"] },
+    "EEGCoordinateSystem": { "anyOf": [
+      { "$ref": "common_definitions.json#/definitions/MEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/EEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateDeprecatedCoordSys" }
+    ]},
     "EEGCoordinateUnits": { "$ref": "common_definitions.json#/definitions/CoordUnits" },
     "EEGCoordinateSystemDescription": { "type": "string", "minLength": 1 },
     "AnatomicalLandmarkCoordinates": { "$ref": "common_definitions.json#/definitions/LandmarkCoordinates" },
-    "AnatomicalLandmarkCoordinateSystem": { "type": "string", "enum": ["CapTrak", "Other"] },
+    "AnatomicalLandmarkCoordinateSystem": { "anyOf": [
+      { "$ref": "common_definitions.json#/definitions/MEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/EEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateDeprecatedCoordSys" }
+    ]},
     "AnatomicalLandmarkCoordinateUnits": { "$ref": "common_definitions.json#/definitions/CoordUnits" },
     "AnatomicalLandmarkCoordinateSystemDescription": { "type": "string", "minLength": 1 }
   },

diff --git a/bids-validator/validators/json/schemas/coordsystem_ieeg.json b/bids-validator/validators/json/schemas/coordsystem_ieeg.json
@@ -2,7 +2,11 @@
   "type": "object",
   "properties": {
     "IntendedFor": { "type": "string", "minLength": 1 },
-    "iEEGCoordinateSystem": { "type": "string", "enum": ["Pixels", "ACPC", "Other"] },
+    "iEEGCoordinateSystem": { "anyOf": [
+      { "$ref": "common_definitions.json#/definitions/iEEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateDeprecatedCoordSys" }
+    ]},
     "iEEGCoordinateUnits":  { "type": "string", "enum": ["m", "mm", "cm", "pixels", "n/a"] },
     "iEEGCoordinateSystemDescription": { "type": "string", "minLength": 1 },
     "iEEGCoordinateProcessingDescription": { "type": "string", "minLength": 1 },

diff --git a/bids-validator/validators/json/schemas/coordsystem_meg.json b/bids-validator/validators/json/schemas/coordsystem_meg.json
@@ -1,10 +1,20 @@
 {
   "type": "object",
   "properties": {
-    "MEGCoordinateSystem": { "type": "string", "enum": ["CTF", "ElektaNeuromag", "4DBti", "KitYokogawa", "ChietiItab", "Other"] },
+    "MEGCoordinateSystem": { "anyOf": [
+      { "$ref": "common_definitions.json#/definitions/MEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/EEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateDeprecatedCoordSys" }
+    ]},
     "MEGCoordinateUnits": { "$ref": "common_definitions.json#/definitions/CoordUnits" },
     "MEGCoordinateSystemDescription": { "type": "string", "minLength": 1 },
-    "EEGCoordinateSystem": { "type": "string", "enum": ["CTF", "ElektaNeuromag", "4DBti", "KitYokogawa", "ChietiItab", "Other"] },
+    "EEGCoordinateSystem": { "anyOf": [
+      { "$ref": "common_definitions.json#/definitions/MEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/EEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateDeprecatedCoordSys" }
+    ]},
     "EEGCoordinateUnits": { "$ref": "common_definitions.json#/definitions/CoordUnits" },
     "EEGCoordinateSystemDescription": { "type": "string", "minLength": 1 },
     "IntendedFor": {
@@ -21,15 +31,30 @@
     },
     "FiducialsDescription": { "type": "string", "minLength": 1 },
     "HeadCoilCoordinates": { "$ref": "common_definitions.json#/definitions/LandmarkCoordinates" },
-    "HeadCoilCoordinateSystem": { "type": "string", "enum": ["CTF", "ElektaNeuromag", "4DBti", "KitYokogawa", "ChietiItab", "Other"] },
+    "HeadCoilCoordinateSystem": { "anyOf": [
+      { "$ref": "common_definitions.json#/definitions/MEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/EEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateDeprecatedCoordSys" }
+    ]},
     "HeadCoilCoordinateUnits": { "$ref": "common_definitions.json#/definitions/CoordUnits" },
     "HeadCoilCoordinateSystemDescription": { "type": "string", "minLength": 1 },
     "AnatomicalLandmarkCoordinates": { "$ref": "common_definitions.json#/definitions/LandmarkCoordinates" },
-    "AnatomicalLandmarkCoordinateSystem": { "type": "string", "enum": ["CTF", "ElektaNeuromag", "4DBti", "KitYokogawa", "ChietiItab", "Other"] },
+    "AnatomicalLandmarkCoordinateSystem": { "anyOf": [
+      { "$ref": "common_definitions.json#/definitions/MEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/EEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateDeprecatedCoordSys" }
+    ]},
     "AnatomicalLandmarkCoordinateUnits": { "$ref": "common_definitions.json#/definitions/CoordUnits" },
     "AnatomicalLandmarkCoordinateSystemDescription": { "type": "string", "minLength": 1 },
     "DigitizedHeadPoints": { "type": "string" },
-    "DigitizedHeadPointsCoordinateSystem": { "type": "string", "enum": ["CTF", "ElektaNeuromag", "4DBti", "KitYokogawa", "ChietiItab", "Other"] },
+    "DigitizedHeadPointsCoordinateSystem": { "anyOf": [
+      { "$ref": "common_definitions.json#/definitions/MEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/EEGCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateCoordSys" },
+      { "$ref": "common_definitions.json#/definitions/StandardTemplateDeprecatedCoordSys" }
+    ]},
     "DigitizedHeadPointsCoordinateUnits": { "$ref": "common_definitions.json#/definitions/CoordUnits" },
     "DigitizedHeadPointsCoordinateSystemDescription": { "type": "string", "minLength": 1 }
   },