nwbinspector fails

[grg2rsr]

@h-mayorquin
wrote you an email about this, just putting it here as well for documentation. Will start to tackle the easier looking ones and will let you know how far I got

**************************************************
NWBInspector Report Summary

Timestamp: 2024-12-17 14:52:01.905102+01:00
Platform: Linux-6.11.0-12-generic-x86_64-with-glibc2.40
NWBInspector version: 0.6.1

Found 16 issues over 2 files:
       3 - BEST_PRACTICE_VIOLATION
      13 - BEST_PRACTICE_SUGGESTION
**************************************************


0  BEST_PRACTICE_VIOLATION
==========================

0.0  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb: check_compass_direction_unit - 'CompassDirection' object with name 'CompassDirection'
       Message: SpatialSeries objects inside a CompassDirection object should be angular and should have a unit of 'degrees' or 'radians', but 'WheelPositionSeries' has units 'rad'.

0.1  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw.nwb: check_large_dataset_compression - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesAPImec1'
       Message: data is a large uncompressed dataset! Please enable compression.

0.2  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw.nwb: check_large_dataset_compression - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesAPImec0'
       Message: data is a large uncompressed dataset! Please enable compression.

1  BEST_PRACTICE_SUGGESTION
===========================

1.3  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb: check_description - 'VectorData' object with name 'probe_name'
       Message: Description ('No description.') is a placeholder.

1.4  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb and 1 other file: check_experimenter_exists - 'NWBFile' object at location '/'
       Message: Experimenter is missing.

1.5  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb and 1 other file: check_keywords - 'NWBFile' object at location '/'
       Message: Metadata /general/keywords is missing.

1.6  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb: check_processing_module_name - 'ProcessingModule' object with name 'wheel'
       Message: Processing module is named wheel. It is recommended to use the schema module names: ophys, ecephys, icephys, behavior, misc, ogen, retinotopy

1.7  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb: check_processing_module_name - 'ProcessingModule' object with name 'camera'
       Message: Processing module is named camera. It is recommended to use the schema module names: ophys, ecephys, icephys, behavior, misc, ogen, retinotopy

1.8  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb: check_column_binary_capability - 'Units' object with name 'units'
       Message: Column 'sliding_refractory_period_violation' uses 'floats' but has binary values [0. 1.]. Consider making it boolean instead and renaming the column to start with 'is_'; doing so will save 9.51KB.

1.9  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw.nwb: check_description - 'VectorData' object with name 'inter_sample_shift'
       Message: Description ('no description') is a placeholder.

1.10  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw.nwb: check_timestamp_of_the_first_sample_is_not_negative - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesLFImec1'
        Message: Timestamps should not be negative. It is recommended to align the `session_start_time` or `timestamps_reference_time` to be the earliest time value that occurs in the data, and shift all other signals accordingly.

1.11  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw.nwb: check_timestamp_of_the_first_sample_is_not_negative - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesLFImec0'
        Message: Timestamps should not be negative. It is recommended to align the `session_start_time` or `timestamps_reference_time` to be the earliest time value that occurs in the data, and shift all other signals accordingly.

1.12  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw.nwb: check_timestamp_of_the_first_sample_is_not_negative - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesAPImec1'
        Message: Timestamps should not be negative. It is recommended to align the `session_start_time` or `timestamps_reference_time` to be the earliest time value that occurs in the data, and shift all other signals accordingly.

1.13  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw.nwb: check_timestamp_of_the_first_sample_is_not_negative - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesAPImec0'
        Message: Timestamps should not be negative. It is recommended to align the `session_start_time` or `timestamps_reference_time` to be the earliest time value that occurs in the data, and shift all other signals accordingly.

[grg2rsr]

**************************************************
NWBInspector Report Summary

Timestamp: 2024-12-18 15:00:01.531213+01:00
Platform: Linux-6.11.0-12-generic-x86_64-with-glibc2.40
NWBInspector version: 0.6.1

Found 15 issues over 2 files:
       2 - BEST_PRACTICE_VIOLATION
      13 - BEST_PRACTICE_SUGGESTION
**************************************************


0  BEST_PRACTICE_VIOLATION
==========================

0.0  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw_ecephys+raw_video.nwb: check_large_dataset_compression - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesAPImec1'
       Message: data is a large uncompressed dataset! Please enable compression.

0.1  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw_ecephys+raw_video.nwb: check_large_dataset_compression - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesAPImec0'
       Message: data is a large uncompressed dataset! Please enable compression.

1  BEST_PRACTICE_SUGGESTION
===========================

1.2  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb: check_description - 'VectorData' object with name 'probe_name'
       Message: Description ('No description.') is a placeholder.

1.3  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb and 1 other file: check_experimenter_exists - 'NWBFile' object at location '/'
       Message: Experimenter is missing.

1.4  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb and 1 other file: check_keywords - 'NWBFile' object at location '/'
       Message: Metadata /general/keywords is missing.

1.5  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb: check_processing_module_name - 'ProcessingModule' object with name 'wheel'
       Message: Processing module is named wheel. It is recommended to use the schema module names: ophys, ecephys, icephys, behavior, misc, ogen, retinotopy

1.6  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb: check_processing_module_name - 'ProcessingModule' object with name 'camera'
       Message: Processing module is named camera. It is recommended to use the schema module names: ophys, ecephys, icephys, behavior, misc, ogen, retinotopy

1.7  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed.nwb: check_column_binary_capability - 'Units' object with name 'units'
       Message: Column 'sliding_refractory_period_violation' uses 'floats' but has binary values [0. 1.]. Consider making it boolean instead and renaming the column to start with 'is_'; doing so will save 9.51KB.

1.8  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw_ecephys+raw_video.nwb: check_description - 'VectorData' object with name 'inter_sample_shift'
       Message: Description ('no description') is a placeholder.

1.9  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw_ecephys+raw_video.nwb: check_timestamp_of_the_first_sample_is_not_negative - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesLFImec1'
       Message: Timestamps should not be negative. It is recommended to align the `session_start_time` or `timestamps_reference_time` to be the earliest time value that occurs in the data, and shift all other signals accordingly.

1.10  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw_ecephys+raw_video.nwb: check_timestamp_of_the_first_sample_is_not_negative - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesLFImec0'
        Message: Timestamps should not be negative. It is recommended to align the `session_start_time` or `timestamps_reference_time` to be the earliest time value that occurs in the data, and shift all other signals accordingly.

1.11  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw_ecephys+raw_video.nwb: check_timestamp_of_the_first_sample_is_not_negative - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesAPImec1'
        Message: Timestamps should not be negative. It is recommended to align the `session_start_time` or `timestamps_reference_time` to be the earliest time value that occurs in the data, and shift all other signals accordingly.

1.12  sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw_ecephys+raw_video.nwb: check_timestamp_of_the_first_sample_is_not_negative - 'ElectricalSeries' object at location '/acquisition/ElectricalSeriesAPImec0'
        Message: Timestamps should not be negative. It is recommended to align the `session_start_time` or `timestamps_reference_time` to be the earliest time value that occurs in the data, and shift all other signals accordingly.

[h-mayorquin]

Can you re-run this with the latest versions of the inspector and neuroconv to see if we are clear so we can close this @grg2rsr ?

[h-mayorquin]

Also, as discussed, probably we should write the times such that the start timestamps are negative:

https://nwbinspector.readthedocs.io/en/dev/best_practices/time_series.html#avoid-negative-timestamps