[SCHEMA] Add remaining enum definitions

src/schema/meta/context.yaml

@@ -300,17 +300,19 @@ context:
               name: 'XYZ Units'
               description: 'String representing the unit of voxel spacing.'
               type: string
+              # TODO: Add definitions for these values. (perhaps don't specify)
               enum:
-                - 'unknown'
+                - $ref: objects.enums.unknown.value
                 - 'meter'
                 - 'mm'
                 - 'um'
             t:
               name: 'Time Unit'
               description: 'String representing the unit of inter-volume intervals.'
               type: string
+              # TODO: Add definitions for these values. (perhaps don't specify)
               enum:
-                - 'unknown'
+                - $ref: objects.enums.unknown.value
                 - 'sec'
                 - 'msec'
                 - 'usec'

src/schema/objects/columns.yaml

@@ -64,13 +64,13 @@ component:
     or `quat_x`, `quat_y`, `quat_z`, `quat_w` for quaternion orientation channels.
   type: string
   enum:
-    - x
-    - y
-    - z
-    - quat_x
-    - quat_y
-    - quat_z
-    - quat_w
+    - $ref: objects.enums.x.value
+    - $ref: objects.enums.y.value
+    - $ref: objects.enums.z.value
+    - $ref: objects.enums.quat_x.value
+    - $ref: objects.enums.quat_y.value
+    - $ref: objects.enums.quat_z.value
+    - $ref: objects.enums.quat_w.value
     - n/a
 detector__channels:
   name: detector
@@ -162,6 +162,7 @@ handedness:
     For "ambidextrous", use one of these values: `ambidextrous`, `a`, `A`, `AMBIDEXTROUS`,
     `Ambidextrous`.
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - left
     - l
@@ -424,6 +425,7 @@ sample_type:
     Biosample type defined by
     [ENCODE Biosample Type](https://www.encodeproject.org/profiles/biosample_type).
   type: string
+  # TODO: Add definitions for these values.
   enum:
     - cell line
     - in vitro differentiated cells
@@ -461,6 +463,7 @@ sex:
 
     For "other", use one of these values: `other`, `o`, `O`, `OTHER`, `Other`.
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - male
     - m
@@ -543,6 +546,7 @@ status:
     If quality is unknown, then a value of `n/a` may be used.
     Description of noise type SHOULD be provided in `[status_description]`.
   type: string
+  # TODO: Add definitions for these values.
   enum:
     - good
     - bad
@@ -686,8 +690,8 @@ type__optodes:
     The type of the optode.
   type: string
   enum:
-    - source
-    - detector
+    - $ref: objects.enums.source
+    - $ref: objects.enums.detector
     - n/a
 units:
   name: units
@@ -730,6 +734,7 @@ volume_type:
     The `*_aslcontext.tsv` table consists of a single column of labels identifying
     the `volume_type` of each volume in the corresponding `*_asl.nii[.gz]` file.
   type: string
+  # TODO: Add definitions for these values.
   enum:
     - control
     - label

src/schema/objects/enums.yaml

@@ -322,6 +322,22 @@ ChietiItab:
   display_name: Chieti ITAB
   description: |
     RAS orientation and the origin between the ears.
+calibration:
+  value: calibration
+  display_name: calibration
+  description: |
+    The fine-calibration file, is produced by the MaxFilter software and the work of
+    Neuromag/Elekta/MEGIN engineers during maintenance of the MEG acquisition system.
+    It is specific to the site of recording and may change in the process of regular system maintenance.
+    it is usually shared with a crosstalk file.
+crosstalk:
+  value: crosstalk
+  display_name: crosstalk
+  description: |
+    The crosstalk file, is produced by the MaxFilter software and the work of
+    Neuromag/Elekta/MEGIN engineers during maintenance of the MEG acquisition system.
+    It is specific to the site of recording and may change in the process of regular system maintenance.
+    it is usually shared with a fine-calibration file.
 individual:
   value: individual
   display_name: individual
@@ -1087,3 +1103,63 @@ NIRSCWMUA:
     - fnirs
   description: |
     Continuous wave optical absorption measurements. Equivalent to dataTypeLabel mua in SNIRF.
+source:
+  value: source
+  display_name: source
+  description: |
+    A light emitting device, sometimes called a transmitter.
+detector:
+  value: detector
+  display_name: detector
+  description: |
+    A photoelectric transducer, sometimes called a receiver.
+mixed:
+  value: mixed
+  display_name: mixed
+  description: |
+    Mixed detector types were used for this NIRS recording, specify in `optodes.tsv`.
+x:
+  value: x
+  display_name: x
+  description: |
+    The x dimension of the coordinate system.
+y:
+  value: y
+  display_name: y
+  description: |
+    The y dimension of the coordinate system.
+z:
+  value: z
+  display_name: z
+  description: |
+    The z dimension of the coordinate system.
+quat_x:
+  value: quat_x
+  display_name: quat_x
+  description: |
+    The quaternion x dimension of the coordinate system.
+quat_y:
+  value: quat_y
+  display_name: quat_y
+  description: |
+    The quaternion y dimension of the coordinate system.
+quat_z:
+  value: quat_z
+  display_name: quat_z
+  description: |
+    The quaternion z dimension of the coordinate system.
+quat_w:
+  value: quat_w
+  display_name: quat_w
+  description: |
+    The quaternion w dimension of the coordinate system.
+unknown:
+  value: 'unknown'
+  display_name: unknown
+  description: |
+    An unknown unit.
+pixels:
+  value: pixels
+  display_name: pixels
+  description: |
+    A dimension specified in pixels.

src/schema/objects/metadata.yaml

@@ -98,6 +98,7 @@ AnatomicalLandmarkCoordinateUnits:
   description: |
     Units of the coordinates of `"AnatomicalLandmarkCoordinateSystem"`.
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - m
     - mm
@@ -363,6 +364,7 @@ CASLType:
   description: |
     Describes if a separate coil is used for labeling.
   type: string
+  # TODO: Add definitions for these values.
   enum:
     - single-coil
     - double-coil
@@ -488,6 +490,7 @@ ContrastBolusIngredient:
     Active ingredient of agent.
     Corresponds to DICOM Tag 0018, 1048 `Contrast/Bolus Ingredient`.
   type: string
+  # TODO: Add definitions for these values.
   enum:
     - IODINE
     - GADOLINIUM
@@ -534,6 +537,7 @@ DatasetType:
     The interpretation of the dataset.
     For backwards compatibility, the default value is `"raw"`.
   type: string
+  # TODO: Add definitions for these values.
   enum:
     - raw
     - derivative
@@ -610,7 +614,7 @@ DetectorType:
       format: unit
     - type: string
       enum:
-        - mixed
+        - $ref: objects.enums.mixed.value
 DeviceSerialNumber:
   name: DeviceSerialNumber
   display_name: Device Serial Number
@@ -673,6 +677,7 @@ DigitizedHeadPointsCoordinateUnits:
   description: |
     Units of the coordinates of `"DigitizedHeadPointsCoordinateSystem"`.
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - m
     - mm
@@ -774,6 +779,7 @@ EEGCoordinateUnits:
   description: |
     Units of the coordinates of `EEGCoordinateSystem`.
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - m
     - mm
@@ -982,6 +988,7 @@ FiducialsCoordinateUnits:
     Units in which the coordinates that are  listed in the field
     `"FiducialsCoordinateSystem"` are represented.
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - m
     - mm
@@ -1280,6 +1287,7 @@ HeadCoilCoordinateUnits:
   description: |
     Units of the coordinates of `HeadCoilCoordinateSystem`.
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - m
     - mm
@@ -1803,6 +1811,7 @@ MEGCoordinateUnits:
   description: |
     Units of the coordinates of `"MEGCoordinateSystem"`.
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - m
     - mm
@@ -2143,6 +2152,7 @@ NIRSCoordinateUnits:
   description: |
     Units of the coordinates of `NIRSCoordinateSystem`.
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - m
     - mm
@@ -2398,6 +2408,7 @@ PixelSizeUnits:
     Unit format of the specified `"PixelSize"`. MUST be one of: `"mm"` (millimeter), `"um"`
     (micrometer) or `"nm"` (nanometer).
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - mm
     - um
@@ -2714,6 +2725,7 @@ RotationOrder:
   description: |
     Specify the sequence in which the elemental 3D extrinsic rotations are applied around the three distinct axes.
   type: string
+  # TODO: Add definitions for these values.
   enum:
     - XYZ
     - XZY
@@ -2730,6 +2742,7 @@ RotationRule:
     clockwise around an axis when seen from the positive direction (left-hand rule) or
     counter-clockwise (right-hand rule). Must be one of: "left-hand", "right-hand".
   type: string
+  # TODO: Add definitions for these values.
   enum:
     - left-hand
     - right-hand
@@ -2754,6 +2767,7 @@ SampleEnvironment:
     Environment in which the sample was imaged. MUST be one of: `"in vivo"`, `"ex vivo"`
     or `"in vitro"`.
   type: string
+  # TODO: Add definitions for these values.
   enum:
     - in vivo
     - ex vivo
@@ -3638,11 +3652,12 @@ iEEGCoordinateUnits:
     Units of the `*_electrodes.tsv`.
     MUST be `"pixels"` if `iEEGCoordinateSystem` is `Pixels`.
   type: string
+  # TODO: Add definitions for these values. (perhaps don't specify)
   enum:
     - m
     - mm
     - cm
-    - pixels
+    - $ref: objects.enums.pixels.value
     - n/a
 iEEGElectrodeGroups:
   name: iEEGElectrodeGroups

src/schema/rules/files/raw/meg.yaml

@@ -39,9 +39,8 @@ calibration:
     session: optional
     acquisition:
       level: required
-      # TODO: Add definitions for these values.
       enum:
-        - calibration
+        - $ref: objects.enums.calibration.value
 
 crosstalk:
   suffixes:
@@ -55,9 +54,8 @@ crosstalk:
     session: optional
     acquisition:
       level: required
-      # TODO: Add definitions for these values.
       enum:
-        - crosstalk
+        - $ref: objects.enums.crosstalk.value
 
 headshape:
   suffixes: