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icephys.yaml: Some entries miss unit attribute #410

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t-b opened this issue Feb 9, 2020 · 1 comment · May be fixed by #446
Open

icephys.yaml: Some entries miss unit attribute #410

t-b opened this issue Feb 9, 2020 · 1 comment · May be fixed by #446
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category: bug errors in the code or code behavior priority: medium non-critical problem and/or affecting only a small set of NWB users

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@t-b
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t-b commented Feb 9, 2020

The CurrentClampSeries properties

nwb-schema/core/nwb.icephys.yaml

Lines 53 to 80 in 571bfb0

- name: bias_current
dtype: float32
doc: Bias current, in amps.
quantity: '?'
- name: bridge_balance
dtype: float32
doc: Bridge balance, in ohms.
quantity: '?'
- name: capacitance_compensation
dtype: float32
doc: Capacitance compensation, in farads.
quantity: '?'
- neurodata_type_def: IZeroClampSeries
neurodata_type_inc: CurrentClampSeries
doc: Voltage data from an intracellular recording when all current
and amplifier settings are off (i.e., CurrentClampSeries fields will be zero).
There is no CurrentClampStimulusSeries associated with an IZero series because
the amplifier is disconnected and no stimulus can reach the cell.
datasets:
- name: bias_current
dtype: float32
value: 0.0
doc: Bias current, in amps, fixed to 0.0.
- name: bridge_balance
dtype: float32
value: 0.0
doc: Bridge balance, in ohms, fixed to 0.0.
don't have a units attributes whereas

nwb-schema/core/nwb.icephys.yaml

Lines 115 to 130 in 571bfb0

- name: capacitance_fast
dtype: float32
doc: Fast capacitance, in farads.
quantity: '?'
attributes:
- name: unit
dtype: text
value: farads
doc: Unit of measurement for capacitance_fast, which is fixed to 'farads'.
- name: capacitance_slow
dtype: float32
doc: Slow capacitance, in farads.
quantity: '?'
attributes:
- name: unit
dtype: text
do have unit attributes. This is inconsistent.
@t-b t-b mentioned this issue Feb 9, 2020
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t-b added a commit to AllenInstitute/IPNWB that referenced this issue Feb 9, 2020
@t-b
WriteSingleChannel: Don't output units for CurrentClampSeries entries
63a6fbe 
This is not required, but see
NeurodataWithoutBorders/nwb-schema#410 for an
issue discussing that.
t-b added a commit to AllenInstitute/IPNWB that referenced this issue Feb 9, 2020
@t-b
WriteSingleChannel: Don't output units for CurrentClampSeries entries
815decd 
This is not required, but see
NeurodataWithoutBorders/nwb-schema#410 for an
issue discussing that.
@rly rly linked a pull request May 30, 2020 that will close this issue
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@bendichter
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Thanks, @t-b. It looks like this is being handled in #446

@stephprince stephprince added category: bug errors in the code or code behavior priority: medium non-critical problem and/or affecting only a small set of NWB users labels May 10, 2024
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[WIP] Standardize units of measurement to use CMIXF-12 NeurodataWithoutBorders/nwb-schema
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@bendichter @t-b @stephprince