rec_to_nwb.processing.builder.nwb_file_builder

Module Contents

Classes

NWBFileBuilder(data_path: str, animal_name: str, date: str, nwb_metadata: MetadataManager, process_dio: bool = True, process_mda: bool = True, process_analog: bool = True, process_pos_timestamps: bool = True, video_path: str = '', output_file: str = 'output.nwb', reconfig_header: str = '')

Unpack data from preprocessing folder specified by arguments, and write those data into NWB file format
path
logger
class NWBFileBuilder(data_path: str, animal_name: str, date: str, nwb_metadata: MetadataManager, process_dio: bool = True, process_mda: bool = True, process_analog: bool = True, process_pos_timestamps: bool = True, video_path: str = '', output_file: str = 'output.nwb', reconfig_header: str = '')

Unpack data from preprocessing 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

  • date (string) – date of experiment

  • nwb_metadata (MetadataManager) – object contains metadata about experiment

  • process_dio (boolean) – flag if dio data should be processed

  • process_mda (boolean) – flag if mda data should be processed

  • process_analog (boolean) – flag if analog data should be processed

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

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

build()
write()
build_and_append_to_nwb()
__extract_datasets(self, animal_name, date)
build(self)

Build NWBFile

Returns

Return NWBFile content

Return type

NWBFile

write(self, content)

Write nwb file handler with colected data into actual file

__build_corrupted_data_manager(self)
build_and_append_to_nwb(self, process_mda_valid_time=True, process_mda_invalid_time=True, process_pos_valid_time=True, process_pos_invalid_time=True)

Create and append to existing nwb. Set flag to add it to nwb

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)

Raises

ElementExistException – If element already exist in NWB

Returns

Return NWBFile content

Return type

NWBFile