TCossaLabABFReader

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

Bases: MetaReader

Subclass of MetaReader for reading ABF2 files

Public Methods

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

Perform any actions necessary to gracefully close resources before app exit

Parameters:

channel (Optional[int]) – channel ID

TCossaLabABFReader.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 Axon Binary Format 2 .abf file to read. The ABF header carries the sample rate and scaling.

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]]

TCossaLabABFReader.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

TCossaLabABFReader._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]

TCossaLabABFReader._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]

Raises:

  • NotImplementedError – If the file type is not ABF2 specifically

  • TypeError – If one of the channels does not have an “I” in its header label

  • ValueError – If any number of channels other than 2 is found in the data file

TCossaLabABFReader._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]

Raises:

ValueError – If the filename does not match the expected pattern

TCossaLabABFReader._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

Raises:

ValueError – If the base naming pattern cannot be ascertained.

TCossaLabABFReader._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]

Raises:

ValueError – If the filename does not match the expected pattern

TCossaLabABFReader._init() → None

called at the start of base class initialization

TCossaLabABFReader._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.

TCossaLabABFReader._set_file_extension() → str

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

TCossaLabABFReader._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

TCossaLabABFReader._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.