Source code for immuneML.dev_util.util

import numpy as np
import pandas as pd
import yaml

from immuneML.data_model.encoded_data.EncodedData import EncodedData

[docs]def load_encoded_data(labels_path: str, encoding_details_path: str, design_matrix_path: str) -> EncodedData: """ Utility function for adding ML methods; if one encodes data using immuneML through YAML specification and exports the encoded data using DesignMatrixExporter, this function can be used to import the data and return it in the format it would be available if the ML method was called from within immuneML Args: labels_path (str): path to labels file as exported by the DesignMatrixExporter encoding_details_path (str): path to the details file, where example_ids, feature_names and the encoding name will be imported from design_matrix_path (str): path to csv or npy file where the design matrix is stored Returns: EncodedData object as it would be provided to an ML method within immuneML """ # read the data from these files # TODO: support H5py examples = pd.read_csv(design_matrix_path).values if design_matrix_path.endswith(".csv") else np.load(design_matrix_path, allow_pickle=True) labels = pd.read_csv(labels_path).to_dict('list') with open(encoding_details_path, "r") as file: encoding_details = yaml.safe_load(file) # create an EncodedData object which can be used as an input argument for the fit or predict functions encoded_data = EncodedData(examples=examples, labels=labels, example_ids=encoding_details['example_ids'], feature_names=encoding_details['feature_names'], encoding=encoding_details['encoding']) return encoded_data