SingleBinaryDecoder

class SingleBinaryDecoder(settings: Optional[dict] = None)

Bases: MetaReader

Subclass of MetaReader for reading a single, user-configured raw binary file, with sampling rate, header size, array count, byte order, and data type all specified via settings rather than inferred from a vendor-specific header.

Public Methods

SingleBinaryDecoder.close_resources(channel: int | None = None) → None

Perform any actions necessary to gracefully close resources before app exit

Parameters:

channel (Optional[int]) – channel ID

SingleBinaryDecoder.get_empty_settings(globally_available_plugins: Dict[str, List[str]] | None = None, standalone: bool = False) → Dict[str, Dict[str, Any]]

Declare the settings this reader exposes, on top of the base contract.

Called by poriscope when the plugin is instantiated or reconfigured, to build the settings dialog and to sanity-check whatever the user enters; the accepted values are then readable through self.settings. See get_empty_settings() for the structure of the dict and what Type, Value, Min, Max, Options and Units mean in it, and for the reserved keys the GUI builds file pickers from.

The keys this plugin adds:

  • Input File - the raw binary file to read. Unlike the other readers this one has no header to consult, so every parameter below has to be supplied by hand.

  • Sampling Rate (Hz) - the acquisition rate the file was recorded at.

  • Header Bytes - how many bytes to skip before the first sample.

  • Number of Arrays - how many interleaved channels the file holds.

  • Byte Order - '<' for little-endian, '>' for big-endian.

  • Data Type - Floating Point, Signed Integer or Unsigned Integer.

  • Data Bytes - the width of one sample, 8, 4 or 2 bytes.

  • Bitmask - applied to each integer sample before scaling, for formats that pack status bits into the data word; 0 disables it.

  • Scale and Offset - the affine conversion from raw sample to pA.

Parameters:

  • globally_available_plugins (Optional[Dict[str, List[str]]]) – a dict containing all data plugins that exist to date, keyes by metaclass

  • standalone (bool) – False if this is called as part of a GUI, True otherwise. Default False

Returns:

the dict that must be filled in to initialize the filter

Return type:

Dict[str, Dict[str, Any]]

SingleBinaryDecoder.reset_channel(channel: int | None = None) → None

Perform any actions necessary to gracefully close resources before app exit. If channel is not None, handle only that channel, else close all of them.

Parameters:

channel (Optional[int]) – channel ID

Private Methods

SingleBinaryDecoder._convert_data(data: ndarray[tuple[int, ...], dtype[int16]], config: dict) → ndarray[tuple[int, ...], dtype[float64]]

Convert raw data from disk into rescaled current, in pA.

Parameters:

  • data (npt.NDArray[np.int16]) – Data to convert.

  • config (dict) – Configuration dictionary for data conversion.

Returns:

The data, rescaled to pA.

Return type:

npt.NDArray[np.float64]

SingleBinaryDecoder._get_configs(datafiles: List[str]) → List[dict]

Load configuration files as dictionaries, corresponding to datamaps as needed. Default behavior assumes there are no config files needed.

Parameters:

datafiles (List[str]) – List of data file paths.

Returns:

List of configuration dictionaries.

Return type:

List[dict]

SingleBinaryDecoder._get_file_channel_stamps(file_names: List[str], configs: List[dict]) → List[int]

Get a list of serialization keys used to sort the list of files associated to the experiment.

Parameters:

  • file_names (List[str]) – List of file paths.

  • configs (List[dict]) – List of configuration dictionaries.

Returns:

List of channel numbers parsed from configuration.

Return type:

List[int]

SingleBinaryDecoder._get_file_pattern(file_name: str) → str

Get the base name for matching other files to the same dataset as the initial one provided to the constructor.

Parameters:

file_name (str) – File path.

Returns:

Base name for matching other files.

Return type:

str

SingleBinaryDecoder._get_file_time_stamps(file_names: List[str], configs: List[dict]) → List[int]

Get a list of serialization keys used to sort the list of files associated to the experiment.

Parameters:

  • file_names (List[str]) – List of file paths.

  • configs (List[dict]) – List of configuration dictionaries.

Returns:

List of timestamps parsed from configuration.

Return type:

List[int]

SingleBinaryDecoder._init() → None

called at the start of base class initialization

SingleBinaryDecoder._map_data(datafiles: List[str], configs: List[dict]) → List[ndarray]

Map data files into a set of memmaps or similarly define a way to access the raw data on disk. Returns a list of memmaps corresponding to each datafile/configfile pair.

Parameters:

  • datafiles (List[str]) – List of data file paths.

  • configs (List[dict]) – List of configuration dictionaries.

Returns:

List of memmaps containing raw data.

Return type:

List[np.ndarray]

Raises:

  • FileNotFoundError – If at least one of the input raw data files is missing or renamed.

  • OSError – If the file indicated is inaccessible.

SingleBinaryDecoder._set_file_extension() → str

Set the expected file extension for files read using this reader subclass

SingleBinaryDecoder._validate_file_type(filename: PathLike) → None

Check that the file(s) being opened are of the correct type, and raise IOError if not

Parameters:

filename (os.PathLike) – the path to one of the files to be opened

SingleBinaryDecoder._validate_settings(settings: dict) → None

Validate that the settings dict contains the correct information for use by the subclass.

Parameters:

settings (dict) – Parameters for event detection.

Raises:

ValueError – If the settings dict does not contain the correct information.