pd_parser Command Line Interface (CLI)

Here we list the pd_parser tools that you can use from the command line.

add_events_to_raw

usage: add_events_to_raw raw [-h] [--out_fname OUT_FNAME] [--keep_pd_channels] [-v] [-o]

positional arguments

raw

The electrophysiology filepath

options

-h, --help

show this help message and exit

--out_fname OUT_FNAME

The name to save out the new raw file out to

--keep_pd_channels

Whether to keep the channels with the photodiode data.

-v, --verbose

Whether to print function progress.

-o, --overwrite

Pass this flag to overwrite an existing file

add_pd_off_events

usage: add_pd_off_events raw [-h] [--off_event_name OFF_EVENT_NAME] [--max_len MAX_LEN] [--zscore ZSCORE] [--max_flip_i MAX_FLIP_I] [--baseline BASELINE] [-v] [-o]

positional arguments

raw

The electrophysiology raw object or filepath

options

-h, --help

show this help message and exit

--off_event_name OFF_EVENT_NAME

The name of the photodiode event

--max_len MAX_LEN

The length of the longest photodiode event

--zscore ZSCORE

The same zscore as used for parse_pd.

--max_flip_i MAX_FLIP_I

The same max_flip_i as used for parse_pd.

--baseline BASELINE

The same baseline as used for parse_pd.

-v, --verbose

Whether to print function progress.

-o, --overwrite

Pass this flag to overwrite an existing file

add_relative_events

usage: add_relative_events raw [-h] [--beh BEH] [--relative_event_keys [RELATIVE_EVENT_KEYS ...]] [--relative_event_names [RELATIVE_EVENT_NAMES ...]] [-v] [-o]

positional arguments

raw

The electrophysiology raw object or filepath

options

-h, --help

show this help message and exit

--beh BEH

The behavioral tsv filepath

–relative_event_keys [RELATIVE_EVENT_KEYS …] A behavioral key (column) in the tsv file that has the time relative to the photodiode events on the same trial as in the beh_key event.

–relative_event_names [RELATIVE_EVENT_NAMES …] The name of the corresponding relative_event_keys events

-v, --verbose

Whether to print function progress.

-o, --overwrite

Pass this flag to overwrite an existing file

find_pd_params

usage: find_pd_params raw [-h] [--pd_ch_names [PD_CH_NAMES ...]] [-v]

positional arguments

raw

The electrophysiology raw object or filepath

options

-h, --help

show this help message and exit

–pd_ch_names [PD_CH_NAMES …] The name(s) of the channels with the photodiode data. Can be one channel for common referenced recording or two for a bipolar recording. If not provided, the data will be plotted for the user to pick

-v, --verbose

Whether to print function progress.

parse_audio

usage: parse_audio raw [-h] [--audio_event_name AUDIO_EVENT_NAME] [--beh BEH] [--beh_key BEH_KEY] [--audio_ch_names [AUDIO_CH_NAMES ...]] [--exclude_shift EXCLUDE_SHIFT] [--resync RESYNC] [--max_len MAX_LEN] [--zscore ZSCORE] [--add_events] [--recover] [-v] [-o]

positional arguments

raw

TThe electrophysiology raw object or filepath

options

-h, --help

show this help message and exit

--audio_event_name AUDIO_EVENT_NAME

The name of the audio event

--beh BEH

The behavioral dictionary or tsv filepath

--beh_key BEH_KEY

The name of the behavioral key (column) corresponding to the audio event timing

–audio_ch_names [AUDIO_CH_NAMES …] The name(s) of the channels with the audio data. Note that they will be if thereare two channels they will be bipolar referenced

--exclude_shift EXCLUDE_SHIFT

How many seconds off to exclude an audio-behavioral event difference

--resync RESYNC

How large of a difference to use to resynchronize events. See pd_parser.parse_pd for more information

--max_len MAX_LEN

The length of the longest audio event

--zscore ZSCORE

How many standard deviations larger than the baseline the correlation of the audio is. If None, zscore is found interactively.

--add_events

Whether to run the parser a second time to add more events from deflections corresponding to multiple events on the same channel

--recover

Whether to recover corrupted events manually.

-v, --verbose

Whether to print function progress.

-o, --overwrite

Pass this flag to overwrite an existing file

parse_pd

usage: parse_pd raw [-h] [--pd_event_name PD_EVENT_NAME] [--beh BEH] [--beh_key BEH_KEY] [--pd_ch_names [PD_CH_NAMES ...]] [--exclude_shift EXCLUDE_SHIFT] [--resync RESYNC] [--max_len MAX_LEN] [--zscore ZSCORE] [--max_flip_i MAX_FLIP_I] [--baseline BASELINE] [--add_events] [--recover] [-v] [-o]

positional arguments

raw

The electrophysiology raw object or filepath

options

-h, --help

show this help message and exit

--pd_event_name PD_EVENT_NAME

The name of the photodiode event

--beh BEH

The behavioral dictionary or tsv filepath

--beh_key BEH_KEY

The name of the behavioral key (column) corresponding to the photodiode event timing

–pd_ch_names [PD_CH_NAMES …] The name(s) of the channels with the photodiode data. Can be one channel for common referenced recording or two for a bipolar recording. If not provided, the data will be plotted for the user to pick

--exclude_shift EXCLUDE_SHIFT

How many seconds off to exclude a photodiode- behavioral event difference

--resync RESYNC

How large of a difference to use to resynchronize events. This is for when events are off but not by much and so they should be excluded but are still needed to fit an alignment.Increase if the alignment is failing because too many events are being excluded, decrease to speed up execution.

--max_len MAX_LEN

The length of the longest photodiode event

--zscore ZSCORE

How many standard deviations larger than the baseline the photodiode event is. Decrease if too many events are being found and increase if too few. Use find_pd_params to determine if unsure.

--max_flip_i MAX_FLIP_I

The maximum number of samples the photodiode event takes to transition. Increase if the transitions are not being found, decrease for fewer false positives.

--baseline BASELINE

How much relative to the max_lento use to idenify the time before the photodiode event. Probably don’t change but increasing will reduce false-positives and decreasing will reduce false-negatives.

--add_events

Whether to run the parser a second time to add more events from deflections corresponding to multiple events on the same channel

--recover

Whether to recover corrupted events manually.

-v, --verbose

Whether to print function progress.

-o, --overwrite

Pass this flag to overwrite an existing file