Source code for omnigenbench.src.abc.abstract_metric

# -*- coding: utf-8 -*-
# file: abstract_metric.py
# time: 12:58 09/04/2024
# author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
# github: https://github.com/yangheng95
# huggingface: https://huggingface.co/yangheng
# google scholar: https://scholar.google.com/citations?user=NPq5a_0AAAAJ&hl=en
# Copyright (C) 2019-2024. All Rights Reserved.
import numpy as np
import sklearn.metrics as metrics

from ..misc.utils import env_meta_info




class OmniMetric:
    """
    This class provides a unified interface for evaluation metrics in the OmniGenome
    framework. It integrates with scikit-learn's metric functions and provides
    additional functionality for handling genomic data evaluation. The class automatically exposes all scikit-learn metrics as attributes,
    making them easily accessible for evaluation tasks.

    Attributes:
        metric_func (callable): A callable metric function from `sklearn.metrics`.
        ignore_y (any): A value in the ground truth labels to be ignored during
                       metric computation.
        metadata (dict): Metadata about the metric including version info.
    """

    def __init__(self, metric_func=None, ignore_y=None, *args, **kwargs):
        """
        Initializes the metric.

        Args:
            metric_func (callable, optional): A callable metric function from
                                            `sklearn.metrics`. If None, subclasses
                                            should implement their own compute method.
            ignore_y (any, optional): A value in the ground truth labels to be
                                    ignored during metric computation.
            *args: Additional positional arguments.
            **kwargs: Additional keyword arguments.

        Example:
            >>> # Initialize with a specific metric function
            >>> metric = OmniMetric(metrics.accuracy_score)

            >>> # Initialize with ignore value
            >>> metric = OmniMetric(ignore_y=-100)
        """
        self.metric_func = metric_func
        self.ignore_y = ignore_y

        # Expose all scikit-learn metrics as attributes
        for metric in metrics.__dict__.keys():
            setattr(self, metric, metrics.__dict__[metric])

        self.metadata = env_meta_info()



    def compute(self, y_true, y_pred) -> dict:
        """
        Computes the metric. This method must be implemented by subclasses.

        Args:
            y_true: Ground truth labels.
            y_pred: Predicted labels.

        Returns:
            dict: A dictionary with the metric name as key and its value.

        Raises:
            NotImplementedError: If the method is not implemented by the subclass.

        Example:
            >>> # In a classification metric
            >>> result = metric.compute(y_true, y_pred)
            >>> print(result)  # {'accuracy': 0.85}
        """
        raise NotImplementedError(
            "Method compute() is not implemented in the child class. "
            "This function returns a dict containing the metric name and value."
            "e.g. {'accuracy': 0.9}"
        )




    @staticmethod
    def flatten(y_true, y_pred):
        """
        Flattens the ground truth and prediction arrays. It handles various input formats and converts
        them to 1D numpy arrays.

        Args:
            y_true: Ground truth labels in any format that can be converted to numpy array.
            y_pred: Predicted labels in any format that can be converted to numpy array.

        Returns:
            tuple: A tuple of flattened `y_true` and `y_pred` as numpy arrays.

        Example:
            >>> y_true = [[1, 2], [3, 4]]
            >>> y_pred = [[1, 2], [3, 4]]
            >>> flat_true, flat_pred = OmniMetric.flatten(y_true, y_pred)
            >>> print(flat_true.shape)  # (4,)
        """
        y_true = np.array(y_true).flatten()
        y_pred = np.array(y_pred).flatten()
        return y_true, y_pred