mzpkl

Overview

This module defines the structure of the mzpkl file format, which is a temporary file format used to store the raw MS data for faster reloading. The mzpkl file format is a pickle file that is organized this way:

{
    "name": str, # the name of the file
    "ion_mode": str, # the ion mode of the file
    "ms1_time_arr": np.ndarray, # the time array of the MS1 scans
    "ms1_idx": np.ndarray, # the index array of the MS1 scans
    "ms2_idx": np.ndarray, # the index array of the MS2 scans
    "scans": list of 2D np.ndarray # MS1 and MS2 scans in the file. Each scan is a 2D np.ndarray with shape (n, 2), [[m/z, intensity], ...]
}

Functions

Convert MS Data object to mzpkl

convert_MSData_to_mzpkl(d, output_dir: str = None)

Converts an MSData object to an mzpkl file.

Parameters:

d (MSData): The MSData object to be converted.
output_dir (str): The directory where the mzpkl file will be saved.

Output:

the converted mzpkl file will be saved in the specified directory.
if the output directory is not specified, the mzpkl file will be returned as a dictionary.

Read mzpkl to MS Data object

read_mzpkl_to_MSData(d, file_path: str)

Reads an mzpkl file to an MSData object.

Parameters:

d (MSData): The initiated MSData object without scans data.
file_path (str): The path to the mzpkl file.

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