diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 6fd0a78128..502901f1f8 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -166,10 +166,11 @@ depth__probes: name: depth display_name: Depth description: | - Physical depth of the probe, for example, '0.3'. + Physical depth of the probe in mm, for example, '0.3'. This dimension should be omitted or set to 0 for two-dimensional (shank-type) probes. This dimension corresponds to the z-axis of the probe's local coordinate frame. type: number + unit: mm coordinate_system: name: coordinate_system display_name: Coordinate System @@ -244,15 +245,6 @@ dimension: Size of the group (grid/strip/probe) that this electrode belongs to. Must be of form `[AxB]` with the smallest dimension first (for example, `[1x8]`). type: string -# TODO: Add unit enums if everyone agrees to keep this column. -dimension_unit: - name: dimension_unit - display_name: Dimension unit - description: | - Spatial units for a position or a physical dimension of electrodes, such as - 'width', 'height' or 'depth' of the probe. - For example, `um`. - type: string duration: name: duration display_name: Event duration @@ -297,7 +289,6 @@ filename: Relative paths to files. type: string format: participant_relative -# TODO: Figure out and add rule for default values. gain: name: gain display_name: Gain @@ -306,7 +297,6 @@ gain: to the signal stored in the data file. If no gain factor is provided it is assumed to be 1. type: number -# TODO: Clarify if the optionality of the column be defined here or as an addendum in the rules. ground: name: ground display_name: Ground @@ -369,10 +359,11 @@ height__probes: name: height display_name: Probe height description: | - Physical height of the probe, for example, '0.3'. + Physical height of the probe in mm, for example, '0.3'. This dimension should be omitted or set to 0 for one-dimensional (linear) probes. This dimension corresponds to the y-axis of the probe's local coordinate frame. type: number + unit: mm hemisphere: name: hemisphere display_name: Electrode hemisphere @@ -382,7 +373,7 @@ hemisphere: enum: - $ref: objects.enums.left_hemisphere.value - $ref: objects.enums.right_hemisphere.value -# TODO: Should the hemisphere details be unified for electrodes and probes or will it break other modality? +# consider unifying with base `hemisphere` column between electrodes and probes hemisphere__probes: name: hemisphere display_name: Hemisphere @@ -453,7 +444,7 @@ manufacturer: The manufacturer for each electrode. Can be used if electrodes were manufactured by more than one company. type: string -# TODO: Should the manufacturer details be unified for electrodes and probes? +# consider unifying with base `manufacturer` column between electrodes and probes manufacturer__probes: name: manufacturer display_name: Manufacturer @@ -466,6 +457,7 @@ mapping: description: | Corresponding integer label in the standard BIDS label lookup. type: integer +# consider unifying with base `material` column between electrodes and probes material: name: material display_name: Electrode material @@ -834,7 +826,6 @@ short_channel: The total number of channels listed as short channels SHOULD be stored in `ShortChannelCount` in `*_nirs.json`. type: boolean -# TODO: might need to dup for microephys__size and have it um^2 signal_electrode: name: signal_electrode display_name: Signal electrode @@ -849,6 +840,13 @@ size: Surface area of the electrode, units MUST be in `mm^2`. type: number unit: 'mm^2' +size__microephys: + name: size + display_name: Electrode size + description: | + Surface area of the electrode, units MUST be in `um^2`. + type: number + unit: 'um^2' software_filters: name: software_filters display_name: Software filters @@ -956,16 +954,6 @@ stream_id: description: | Data stream of the recording the signal. type: string -# TODO: Clarify if column values can be arrays. -surgery_date: - name: surgery_date - display_name: Surgery date - description: | - Date(s) of surgery. Datetime format and their anonymization - are described in [Units](SPEC_ROOT/common-principles.md#units). - The details of the surgery should be described in the sidecar json file. - type: string - format: datetime target_muscle: name: target_muscle display_name: Target muscle @@ -1132,15 +1120,6 @@ units: (see [Units](SPEC_ROOT/common-principles.md#units)). type: string format: unit -units__channels: - name: units - display_name: Units - description: | - Physical unit of the value represented in this channel, - for example, `V` for Volt, or `uV` for micro Volt - (see [Units](SPEC_ROOT/common-principles.md#units)). - type: string - format: unit units__nirs: name: units display_name: Units @@ -1208,9 +1187,10 @@ width__probes: name: width display_name: Width description: | - Physical width of the probe, for example, '5'. + Physical width of the probe in mm, for example, '5'. This dimension corresponds to the x-axis of the probe's local coordinate frame. type: number + unit: mm whole_blood_radioactivity: name: whole_blood_radioactivity display_name: Whole blood radioactivity @@ -1267,54 +1247,6 @@ z__optodes: - type: string enum: - n/a -# TODO: Remove the overspecified entries for electrode positions if not used in microephys -# TODO: finish up setup below -x__electrodes: - name: x - display_name: Electrode X position - description: | - When no [`space-