[WIP] Standardize units of measurement to use CMIXF-12

core/nwb.base.yaml

@@ -128,8 +128,8 @@ groups:
       doc: Sampling rate, in Hz.
     - name: unit
       dtype: text
-      value: seconds
-      doc: Unit of measurement for time, which is fixed to 'seconds'.
+      value: s
+      doc: Unit of measurement for time, which is fixed to 's'.
   - name: timestamps
     dtype: float64
     dims:
@@ -146,8 +146,8 @@ groups:
       doc: Value is '1'
     - name: unit
       dtype: text
-      value: seconds
-      doc: Unit of measurement for timestamps, which is fixed to 'seconds'.
+      value: s
+      doc: Unit of measurement for timestamps, which is fixed to 's'.
   - name: control
     dtype: uint8
     dims:

core/nwb.behavior.yaml

@@ -25,9 +25,9 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      default_value: meters
+      default_value: m
       doc: Base unit of measurement for working with the data. The default value
-        is 'meters'. Actual stored values are not necessarily stored in these units.
+        is 'm'. Actual stored values are not necessarily stored in these units.
         To access the data in these units, multiply 'data' by 'conversion'.
       required: false
   - name: reference_frame

core/nwb.ecephys.yaml

@@ -26,9 +26,9 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      value: volts
+      value: V
       doc: Base unit of measurement for working with the data. This value is fixed to
-        'volts'. Actual stored values are not necessarily stored in these units. To
+        'V'. Actual stored values are not necessarily stored in these units. To
         access the data in these units, multiply 'data' by 'conversion' and
         'channel_conversion' (if present).
   - name: electrodes
@@ -84,8 +84,8 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      value: volts
-      doc: Unit of measurement for waveforms, which is fixed to 'volts'.
+      value: V
+      doc: Unit of measurement for waveforms, which is fixed to 'V'.
   - name: timestamps
     dtype: float64
     dims:
@@ -103,8 +103,8 @@ groups:
       doc: Value is '1'
     - name: unit
       dtype: text
-      value: seconds
-      doc: Unit of measurement for timestamps, which is fixed to 'seconds'.
+      value: s
+      doc: Unit of measurement for timestamps, which is fixed to 's'.
 
 - neurodata_type_def: FeatureExtraction
   neurodata_type_inc: NWBDataInterface
@@ -170,8 +170,8 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      value: seconds
-      doc: Unit of measurement for event times, which is fixed to 'seconds'.
+      value: s
+      doc: Unit of measurement for event times, which is fixed to 's'.
   links:
   - name: source_electricalseries
     target_type: ElectricalSeries

core/nwb.file.yaml

@@ -7,7 +7,7 @@ groups:
   attributes:
   - name: nwb_version
     dtype: text
-    value: 2.2.5
+    value: 2.3.0-alpha
     doc: File version string. Use semantic versioning, e.g. 1.2.1. This will be the
       name of the format with trailing major, minor and patch numbers.
   datasets:

core/nwb.icephys.yaml

@@ -46,22 +46,37 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      value: volts
-      doc: Base unit of measurement for working with the data. which is fixed to 'volts'.
+      value: V
+      doc: Base unit of measurement for working with the data. which is fixed to 'V'.
         Actual stored values are not necessarily stored in these units. To access the data in these units,
         multiply 'data' by 'conversion'.
   - name: bias_current
     dtype: float32
     doc: Bias current, in amps.
     quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: A
+      doc: Unit of measurement for bias_current, which is fixed to 'A'.
   - name: bridge_balance
     dtype: float32
     doc: Bridge balance, in ohms.
     quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: Ohm
+      doc: Unit of measurement for bridge_balance, which is fixed to 'Ohm'.
   - name: capacitance_compensation
     dtype: float32
     doc: Capacitance compensation, in farads.
     quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: F
+      doc: Unit of measurement for capacitance_compensation, which is fixed to 'F'.
 
 - neurodata_type_def: IZeroClampSeries
   neurodata_type_inc: CurrentClampSeries
@@ -92,8 +107,8 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      value: amperes
-      doc: Base unit of measurement for working with the data. which is fixed to 'amperes'.
+      value: A
+      doc: Base unit of measurement for working with the data. which is fixed to 'A'.
         Actual stored values are not necessarily stored in these units. To access the data in these units,
         multiply 'data' by 'conversion'.
 
@@ -108,8 +123,8 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      value: amperes
-      doc: Base unit of measurement for working with the data. which is fixed to 'amperes'.
+      value: A
+      doc: Base unit of measurement for working with the data. which is fixed to 'A'.
         Actual stored values are not necessarily stored in these units. To access the data in these units,
         multiply 'data' by 'conversion'.
   - name: capacitance_fast
@@ -119,62 +134,62 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      value: farads
-      doc: Unit of measurement for capacitance_fast, which is fixed to 'farads'.
+      value: F
+      doc: Unit of measurement for capacitance_fast, which is fixed to 'F'.
   - name: capacitance_slow
     dtype: float32
     doc: Slow capacitance, in farads.
     quantity: '?'
     attributes:
     - name: unit
       dtype: text
-      value: farads
-      doc: Unit of measurement for capacitance_fast, which is fixed to 'farads'.
+      value: F
+      doc: Unit of measurement for capacitance_fast, which is fixed to 'F'.
   - name: resistance_comp_bandwidth
     dtype: float32
     doc: Resistance compensation bandwidth, in hertz.
     quantity: '?'
     attributes:
     - name: unit
       dtype: text
-      value: hertz
-      doc: Unit of measurement for resistance_comp_bandwidth, which is fixed to 'hertz'.
+      value: Hz
+      doc: Unit of measurement for resistance_comp_bandwidth, which is fixed to 'Hz'.
   - name: resistance_comp_correction
     dtype: float32
     doc: Resistance compensation correction, in percent.
     quantity: '?'
     attributes:
     - name: unit
       dtype: text
-      value: percent
-      doc: Unit of measurement for resistance_comp_correction, which is fixed to 'percent'.
+      value: '%'
+      doc: Unit of measurement for resistance_comp_correction, which is fixed to '%'.
   - name: resistance_comp_prediction
     dtype: float32
     doc: Resistance compensation prediction, in percent.
     quantity: '?'
     attributes:
     - name: unit
       dtype: text
-      value: percent
-      doc: Unit of measurement for resistance_comp_prediction, which is fixed to 'percent'.
+      value: '%'
+      doc: Unit of measurement for resistance_comp_prediction, which is fixed to '%'.
   - name: whole_cell_capacitance_comp
     dtype: float32
     doc: Whole cell capacitance compensation, in farads.
     quantity: '?'
     attributes:
     - name: unit
       dtype: text
-      value: farads
-      doc: Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'farads'.
+      value: F
+      doc: Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'F'.
   - name: whole_cell_series_resistance_comp
     dtype: float32
     doc: Whole cell series resistance compensation, in ohms.
     quantity: '?'
     attributes:
     - name: unit
       dtype: text
-      value: ohms
-      doc: Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'ohms'.
+      value: Ohm
+      doc: Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'Ohm'.
 
 - neurodata_type_def: VoltageClampStimulusSeries
   neurodata_type_inc: PatchClampSeries
@@ -185,8 +200,8 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      value: volts
-      doc: Base unit of measurement for working with the data. which is fixed to 'volts'.
+      value: V
+      doc: Base unit of measurement for working with the data. which is fixed to 'V'.
         Actual stored values are not necessarily stored in these units. To access the data in these units,
         multiply 'data' by 'conversion'.
 

core/nwb.misc.yaml

@@ -25,17 +25,17 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      default_value: see 'feature_units'
+      default_value: n/a
       doc: Since there can be different units for different features, store the units
-        in 'feature_units'. The default value for this attribute is "see 'feature_units'".
+        in 'feature_units'. The default value for this attribute is "n/a".
       required: false
   - name: feature_units
     dtype: text
     dims:
     - num_features
     shape:
     - null
-    doc: Units of each feature.
+    doc: Units of measurement of each feature.
     quantity: '?'
   - name: features
     dtype: text
@@ -115,13 +115,6 @@ groups:
     - null
     - null
     doc: Data decomposed into frequency bands.
-    attributes:
-    - name: unit
-      dtype: text
-      default_value: no unit
-      doc: Base unit of measurement for working with the data. Actual stored values are
-        not necessarily stored in these units. To access the data in these units,
-        multiply 'data' by 'conversion'.
   - name: metric
     dtype: text
     doc: The metric used, e.g. phase, amplitude, power.
@@ -247,8 +240,8 @@ groups:
       required: false
     - name: unit
       dtype: text
-      value: volts
-      doc: Unit of measurement. This value is fixed to 'volts'.
+      value: V
+      doc: Unit of measurement. This value is fixed to 'V'.
       required: false
   - name: waveform_sd
     neurodata_type_inc: VectorData
@@ -274,6 +267,6 @@ groups:
       required: false
     - name: unit
       dtype: text
-      value: volts
-      doc: Unit of measurement. This value is fixed to 'volts'.
+      value: V
+      doc: Unit of measurement. This value is fixed to 'V'.
       required: false

core/nwb.namespace.yaml

@@ -57,4 +57,4 @@ namespaces:
   - doc: This source module contains neurodata_type for retinotopy data.
     source: nwb.retinotopy.yaml
     title: Retinotopy
-  version: 2.2.5
+  version: 2.3.0-alpha

core/nwb.ogen.yaml

@@ -13,8 +13,8 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      value: watts
-      doc: Unit of measurement for data, which is fixed to 'watts'.
+      value: W
+      doc: Unit of measurement for data, which is fixed to 'W'.
   links:
   - name: site
     target_type: OptogeneticStimulusSite

core/nwb.ophys.yaml

@@ -226,8 +226,8 @@ groups:
       required: false
     - name: unit
       dtype: text
-      default_value: meters
-      doc: Base unit of measurement for working with the data. The default value is 'meters'.
+      default_value: m
+      doc: Base unit of measurement for working with the data. The default value is 'm'.
       required: false
   - name: origin_coords
     dtype: float32
@@ -243,8 +243,8 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      default_value: meters
-      doc: Measurement units for origin_coords. The default value is 'meters'.
+      default_value: m
+      doc: Measurement units for origin_coords. The default value is 'm'.
   - name: grid_spacing
     dtype: float32
     dims:
@@ -259,8 +259,8 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      default_value: meters
-      doc: Measurement units for grid_spacing. The default value is 'meters'.
+      default_value: m
+      doc: Measurement units for grid_spacing. The default value is 'm'.
   - name: reference_frame
     dtype: text
     doc: Describes reference frame of origin_coords and grid_spacing.

core/nwb.retinotopy.yaml

@@ -39,7 +39,7 @@ groups:
       doc: Size of viewing area, in meters.
     - name: unit
       dtype: text
-      doc: Unit that axis data is stored in (e.g., degrees).
+      doc: Unit of measurement for axis data, e.g., "o" for degrees.
   - name: axis_1_power_map
     dtype: float32
     dims:
@@ -69,7 +69,7 @@ groups:
       doc: Size of viewing area, in meters.
     - name: unit
       dtype: text
-      doc: Unit that axis data is stored in (e.g., degrees).
+      doc: Unit of measurement for axis data, e.g., "o" for degrees.
   - name: axis_2_phase_map
     dtype: float32
     dims:
@@ -97,7 +97,7 @@ groups:
       doc: Size of viewing area, in meters.
     - name: unit
       dtype: text
-      doc: Unit that axis data is stored in (e.g., degrees).
+      doc: Unit of measurement for axis data, e.g., "o" for degrees.
   - name: axis_2_power_map
     dtype: float32
     dims:
@@ -127,7 +127,7 @@ groups:
       doc: Size of viewing area, in meters.
     - name: unit
       dtype: text
-      doc: Unit that axis data is stored in (e.g., degrees).
+      doc: Unit of measurement for axis data, e.g., "o" for degrees.
   - name: axis_descriptions
     dtype: text
     dims:

docs/format/source/conf.py

@@ -83,7 +83,7 @@ def setup(app):
 # built documents.
 #
 # The short X.Y version.
-version = 'v2.2.5'
+version = 'v2.3.0-alpha'
 # The full version, including alpha/beta/rc tags.
 release = version