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[Best Practices] Add check for TimeSeries unit follows CMIXF-12 convention #281

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[Best Practices] Add check for TimeSeries unit follows CMIXF-12 convention #281

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0ab683b
add check for unit formatting complies with CMIXF-12
weiglszonja Oct 3, 2022
257e292
add cmixf to requirements.txt
weiglszonja Oct 3, 2022
ac22c09
add unittests for check_unit_formatting
weiglszonja Oct 3, 2022
a9f5e90
add units formatting as new section with examples
weiglszonja Oct 3, 2022
5641e1a
extend best practice for TimeSeries with unit formatting
weiglszonja Oct 3, 2022
842e0f1
add unit formatting to appear at the end of best practices
weiglszonja Oct 3, 2022
82329ac
Merge branch 'dev' into add_check_for_unit_follows_CMIXF-12
weiglszonja Oct 3, 2022
2dfb82b
fix derived unit test
weiglszonja Oct 3, 2022
ac5888c
Merge remote-tracking branch 'origin/add_check_for_unit_follows_CMIXF…
weiglszonja Oct 3, 2022
bba0820
Apply suggestions from code review
weiglszonja Oct 3, 2022
f4aad15
fix unittest
weiglszonja Oct 4, 2022
1d1e0c8
use CMIXFLexer instead of parser
weiglszonja Oct 4, 2022
8964521
move CMIXF-12 into Units of Measurement
weiglszonja Oct 4, 2022
f2f7017
fix reference for best_practice_unit_of_measurement
weiglszonja Oct 4, 2022
655a97f
extend examples
weiglszonja Oct 4, 2022
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1 change: 0 additions & 1 deletion docs/best_practices/best_practices_index.rst
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Expand Up @@ -29,4 +29,3 @@ Authors: Oliver Ruebel, Andrew Tritt, Ryan Ly, Cody Baker and Ben Dichter
image_series
simulated_data
extensions
units
71 changes: 69 additions & 2 deletions docs/best_practices/time_series.rst
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Expand Up @@ -37,8 +37,75 @@ measurement for that data, using the appropriate type from the

Check function: :py:meth:`~nwbinspector.checks.time_series.check_missing_unit`

It is recommended that the **formatting** of SI units be `CMIXF-12 <https://people.csail.mit.edu/jaffer/MIXF/CMIXF-12>`_ compliant.
See :ref:`units` for more information.
For **formatting** of SI units, the `CMIXF-12 <https://people.csail.mit.edu/jaffer/MIXF/CMIXF-12>`_
convention is recommended to minimize the variability of representation of unit values.

If the unit of measurement is unknown or unavailable, the unit can be declared as "a.u."
which stands for arbitrary units.
Please note the appropriate upper- or lower- casing when using CMIXF-12.

The `cmixf <https://github.com/sensein/cmixf>`_ Python package is used to check whether
the formatting of unit is compliant.

Examples for CMIXF-12 representation of units:

.. list-table::
:widths: 25 25 50
:align: center
:header-rows: 1

* - Neurodata type
- Unit in CMIXF-12
- Unit Name
* - :py:class:`~pynwb.behavior.SpatialSeries`
- "m"
- Meters (e.g. position)
* - :py:class:`~pynwb.behavior.SpatialSeries`
- "m/s"
- Meters per second (speed, velocity)
* - :py:class:`~pynwb.behavior.SpatialSeries`
- "m/s^2"
- Meters per second squared (acceleration)
* - :py:class:`~pynwb.ecephys.ElectricalSeries`
- "V"
- Volts
* - :py:class:`~pynwb.ecephys.SpikeEventSeries`
- "V"
- Volts
* - :py:class:`~pynwb.icephys.PatchClampSeries`
- "V"
- Volts
* - :py:class:`~pynwb.icephys.CurrentClampSeries`
- "V"
- Volts
* - :py:class:`~pynwb.icephys.IZeroClampSeries`
- "V"
- Volts
* - :py:class:`~pynwb.icephys.CurrentClampStimulusSeries`
- "A"
- Amperes
* - :py:class:`~pynwb.icephys.VoltageClampSeries`
- "A"
- Amperes
* - :py:class:`~pynwb.icephys.VoltageClampStimulusSeries`
- "V"
- Volts
* - :py:class:`~pynwb.image.ImageSeries`
- "a.u."
- Arbitrary Units (unknown)
* - :py:class:`~pynwb.image.IndexSeries`
- "a.u."
- Arbitrary Units (unknown)
* - :py:class:`~pynwb.image.ImageMaskSeries`
- "a.u."
- Arbitrary Units (unknown)
* - :py:class:`~pynwb.image.OpticalSeries`
- "a.u."
- Arbitrary Units (unknown)
* - :py:class:`~pynwb.retinotopy.AxisMap`
- "o"
- Degrees
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@weiglszonja weiglszonja Oct 4, 2022 •
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This is not TimeSeries but I thought could be good to include for example for representing degrees?

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@CodyCBakerPhD CodyCBakerPhD Oct 4, 2022

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CompassDirection is more typical for that as an example (be sure to include radians as well)



Check function: :py:meth:`~nwbinspector.checks.time_series.check_unit_formatting`

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66 changes: 0 additions & 66 deletions docs/best_practices/units.rst
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