rec_to_nwb.processing.builder.raw_to_nwb_builder

Module Contents

Classes

RawToNWBBuilder(data_path: str, animal_name: str, dates: list, nwb_metadata: MetadataManager, output_path: str = '', video_path: str = '', extract_analog: bool = True, extract_spikes: bool = False, extract_lfps: bool = False, extract_dio: bool = True, extract_mda: bool = True, overwrite: bool = True, lfp_export_args: tuple = _DEFAULT_LFP_EXPORT_ARGS, mda_export_args: tuple = _DEFAULT_MDA_EXPORT_ARGS, analog_export_args: tuple = _DEFAULT_ANALOG_EXPORT_ARGS, dio_export_args: tuple = _DEFAULT_DIO_EXPORT_ARGS, time_export_args: tuple = _DEFAULT_TIME_EXPORT_ARGS, spikes_export_args: tuple = _DEFAULT_SPIKE_EXPORT_ARGS, parallel_instances: int = 4, trodes_rec_export_args: tuple = _DEFAULT_TRODES_REC_EXPORT_ARGS)

Unpack data from raw folder specified by arguments, and write those data into NWB file format
path
logger
_DEFAULT_LFP_EXPORT_ARGS = ['-highpass', '0', '-lowpass', '400', '-interp', '0', '-userefs', '0', '-outputrate', '1500']
_DEFAULT_MDA_EXPORT_ARGS = ['-usespikefilters', '0', '-interp', '0', '-userefs', '0']
_DEFAULT_ANALOG_EXPORT_ARGS = []
_DEFAULT_DIO_EXPORT_ARGS = []
_DEFAULT_SPIKE_EXPORT_ARGS = []
_DEFAULT_TIME_EXPORT_ARGS = []
_DEFAULT_TRODES_REC_EXPORT_ARGS = []
class RawToNWBBuilder(data_path: str, animal_name: str, dates: list, nwb_metadata: MetadataManager, output_path: str = '', video_path: str = '', extract_analog: bool = True, extract_spikes: bool = False, extract_lfps: bool = False, extract_dio: bool = True, extract_mda: bool = True, overwrite: bool = True, lfp_export_args: tuple = _DEFAULT_LFP_EXPORT_ARGS, mda_export_args: tuple = _DEFAULT_MDA_EXPORT_ARGS, analog_export_args: tuple = _DEFAULT_ANALOG_EXPORT_ARGS, dio_export_args: tuple = _DEFAULT_DIO_EXPORT_ARGS, time_export_args: tuple = _DEFAULT_TIME_EXPORT_ARGS, spikes_export_args: tuple = _DEFAULT_SPIKE_EXPORT_ARGS, parallel_instances: int = 4, trodes_rec_export_args: tuple = _DEFAULT_TRODES_REC_EXPORT_ARGS)

Unpack data from raw folder specified by arguments, and write those data into NWB file format

Parameters

  • data_path (string) – path to directory containing all experiments data

  • animal_name (string) – directory name which represents animal subject of experiment

  • dates (list of strings) – dates of experiments on above animal

  • nwb_metadata (MetadataManager) – object containig metadata about experiment

  • output_path (string) – path and name specifying where .nwb file gonna be written

  • video_path (string) – path to directory with video files associated to nwb file

  • extract_analog (boolean) – flag if analog data should be extracted and processed from raw data

  • extract_spikes (boolean) – flag if spikes data should be extracted and processed from raw data

  • extract_lfps (boolean) – flag if lfps data should be extracted and processed from raw data

  • extract_dio (boolean) – flag if dio data should be extracted and processed from raw data

  • extract_mda (boolean) – flag if mda data should be extracted and processed from raw data

  • overwrite (boolean) – flag if current extracted data in preprocessed folder content should be overwritten

  • lfp_export_args (tuple of strings) – parameters to launch lfp extraction from spikegadgets

  • mda_export_args (tuple of strings) – parameters to launch mda extraction from spikegadgets

  • dio_export_args (tuple of strings) – parameters to launch dio extraction from spikegadgets

  • analog_export_args (tuple of strings) – parameters to launch analog extraction from spikegadgets

  • spikes_export_args (tuple of strings) – parameters to launch spikes extraction from spikegadgets

  • time_export_args (tuple of strings) – parameters to launch time extraction from spikegadgets

  • trodes_rec_export_args (tuple of strings) – parameters to launch analog extraction from spikegadgets

  • parallel_instances (int) – number of parallel processes used during processing data

build_nwb()
append_to_nwb()
cleanup()
__is_rec_config_valid(self)

Check if XML is valid with XSD file

__get_header_path(self)
build_nwb(self, process_mda_valid_time=True, process_mda_invalid_time=True, process_pos_valid_time=True, process_pos_invalid_time=True)

Builds nwb file for experiments from given dates.

Parameters

  • process_mda_valid_time (boolean) – True if the mda valid times should be build and append to nwb. Need the mda data inside the nwb. (default True)

  • process_mda_invalid_time (boolean) – True if the mda invalid times should be build and append to nwb. Need the mda data inside the nwb. (default True)

  • process_pos_valid_time (boolean) – True if the pos valid times should be build and append to nwb. Need the pos data inside the nwb. (default True)

  • process_pos_invalid_time (boolean) – True if the pos invalid times should be build and append to nwb. Need the pos data inside the nwb. (default True)

__preprocess_data(self)

process data with rec_to_binaries library

static append_to_nwb(nwb_builder, process_mda_valid_time, process_mda_invalid_time, process_pos_valid_time, process_pos_invalid_time)

Append to NWBFile that was build using NWBFileBuilder passed in parameter.

Parameters

  • nwb_builder (NWBFileBuilder) – Builder that created NWBFile you want to append to

  • process_mda_valid_time (boolean) – If true, build and inject into NWB mda valid times

  • process_mda_invalid_time (boolean) – If true, build and inject into NWB mda invalid times

  • process_pos_valid_time (boolean) – If true, build and inject into NWB pos valid times

  • process_pos_invalid_time (boolean) – If true, build and inject into NWB pos invalid times

cleanup(self)

Remove all temporary files structure from preprocessing folder