ChimeraReader20240501¶

class ChimeraReader20240501(settings: Optional[dict] = None)

Subclass of MetaReader for reading chimera VC400 .log files using the 2024-05 specification that uses a separate json file for metadata

Attributes:: datafile (str): Path to the data file. logger (logging.Logger): Logger instance for logging messages. datafiles (List[List[str]]): List of sorted data files grouped by channel and time. configs (List[List[dict]]): List of sorted configuration dictionaries grouped by channel and time. datamaps (List[List[numpy.ndarray]]): List of sorted data maps (memmaps or numpy arrays) grouped by channel and time. file_start_indices (List[List[int]]): List of starting indices for each data map in each channel. total_channel_samples (List[int]): List of total number of samples in each channel. samplerate (float): Sampling rate for data acquisition.

Public Methods¶

ChimeraReader20240501.close_resources(channel: int | None = None) → None¶

Perform any actions necessary to gracefully close resources before app exit

Parameters:: channel (Optional[int]) – channel ID

ChimeraReader20240501.get_empty_settings(globally_available_plugins: Dict[str, List[str]] | None = None, standalone: bool = False) → Dict[str, Dict[str, Any]]¶

Get a dict populated with keys needed to initialize the filter if they are not set yet. This dict must have the following structure, but Min, Max, and Options can be skipped or explicitly set to None if they are not used. Type is required; Value may be omitted or set to None, both meaning there is no default and the user must supply one. All values provided must be consistent with Type.

settings = {'Parameter 1': {'Type': <int, float, str, bool>,
                                 'Value': <value> or None,
                                 'Options': [<option_1>, <option_2>, ... ] or None,
                                 'Min': <min_value> or None,
                                 'Max': <max_value> or None,
                                 'Units': <unit str> or None
                                },
                ...
                }

Several parameter keywords are reserved: these are

‘Input File’ ‘Output File’ ‘Folder’

These must have Type str and will cause the GUI to generate widgets to allow selection of these elements when used

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]]

ChimeraReader20240501.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¶

ChimeraReader20240501._convert_data(data: ndarray[tuple[int, ...], dtype[int16]], config: dict, raw_data: bool = False) → Tuple[ndarray, float, float] | ndarray¶

Scale or otherwise transform and return requested data. Applies the tia_gain/i_offset/filter_gain scale and offset recovered from the companion .json settings file to convert raw ADC codes to pA. if raw_data is true, return also scale and offset

Parameters:

data (npt.NDArray[np.int16]) – Data to convert.
config (dict) – Configuration dictionary for data conversion.
raw_data (bool) – Decide whether to rescale data or return raw adc codes

Returns:

Converted data, and scale and offset if and only if raw_data is True

Return type:

Union[Tuple[np.ndarray, float, float], np.ndarray]

ChimeraReader20240501._get_configs(datafiles: List[str]) → List[dict]¶

Load configuration files as dictionaries, corresponding to datamaps as needed. Parses each file’s companion .json settings file (same stem, .json extension) to build a per-file configuration dict; unlike ChimeraReader20240101, this format has no embedded header.

Parameters:: datafiles (List[str]) – List of data file paths.
Returns:: List of configuration dictionaries.
Return type:: List[dict]

ChimeraReader20240501._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]

ChimeraReader20240501._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.

ChimeraReader20240501._get_file_time_stamps(file_names: List[str], configs: List[dict]) → List[datetime]¶

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[datetime]

ChimeraReader20240501._init() → None¶: called at the start of base class initialization

ChimeraReader20240501._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.

ChimeraReader20240501._set_file_extension() → str¶: Set the expected file extension for files read using this reader subclass

ChimeraReader20240501._set_raw_dtype(configs: List[dict]) → dtype¶

Set the data type for the raw data in files of this type

Parameters:: configs (List[dict]) – List of configuration dictionaries corresponding to data files.
Returns:: the dtype of the raw data in your data files
Return type:: np.dtype

ChimeraReader20240501._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

ChimeraReader20240501._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.