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BouchardLab / nsds_lab_to_nwb

Python package to convert NSDS Lab data to NWB files.
https://nsds-lab-to-nwb.readthedocs.io/en/latest/
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check, and possibly drop, legacy contents in stimulus metadata #54

Closed jihyunbak closed 3 years ago

jihyunbak commented 3 years ago

I know this is legacy stuff. I don't think it's useful information so maybe get rid off it's not being used for anything? stim_values: np.ones(60) baseline_start: 0.3 baseline_end: 0.5 first_mark: 0.0 luigi_cls: WhiteNoiseAnalysis tokenizer: wn_tokenize

_Originally posted by @jthermiz in https://github.com/BouchardLab/nsds_lab_to_nwb/issues/46#issuecomment-859986965_

jihyunbak commented 3 years ago

@VBaratham Which of the fields in the stimulus metadata (file in this folder in the metadata repo) are actually useful for HTK processing and which ones are no longer relevant?

Example file that we were looking at: wn2.yaml

name: wn
2type: discrete
mark_offset: 0.25
mark_threshold: 0.3
mark_sampling_rate: 12207.03125
nsamples: 60
duration: 0.1
stim_values: np.ones(60)
baseline_start: 0.3
baseline_end: 0.5
first_mark: 0.0
luigi_cls: WhiteNoiseAnalysis
tokenizer: wn_tokenize
VBaratham commented 3 years ago

I believe these are the only ones needed:

mark_offset: 0.25

mark_sampling_rate: 12207.03125

On Mon, Jun 14, 2021 at 9:34 AM Ji Hyun Bak @.***> wrote:

@VBaratham https://github.com/VBaratham Which of the fields in the stimulus metadata (file in this folder in the metadata repo https://github.com/BouchardLab/NSDSLab-NWB-metadata/tree/main/auditory/yaml/stimulus) are actually useful for HTK processing and which ones are no longer relevant?

Example file that we were looking at: wn2.yaml

name: wn2type: discretemark_offset: 0.25mark_threshold: 0.3mark_sampling_rate: 12207.03125nsamples: 60duration: 0.1stim_values: np.ones(60)baseline_start: 0.3baseline_end: 0.5first_mark: 0.0luigi_cls: WhiteNoiseAnalysistokenizer: wn_tokenize

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jihyunbak commented 3 years ago

Update: we are actually using most of the stimulus metadata items. For the wn2.yaml example above, these fields are being used:

name: wn2
type: discrete
mark_offset: 0.25
mark_threshold: 0.3
mark_sampling_rate: 12207.03125
nsamples: 60
duration: 0.1
baseline_start: 0.3
baseline_end: 0.5
first_mark: 0.0

whereas these are no longer used.

# stim_values: np.ones(60)
# luigi_cls: WhiteNoiseAnalysis
# tokenizer: wn_tokenize

Closing this issue with this note.