Analyzer.py

import numpy as np
from scipy import stats
from scipy.stats import chi2

from config import project_name
from helper_scripts.results_helper import add_result


class Analyzer:
    def analyze_results(self, name, smelling_co_changing_pairs, all_smelly_pairs, co_changed_pairs, all_pairs):
        # All pairs formed from all files changed in the relevant time frame.

        # Only keep the smelly pairs that are part of 'all_pairs'
        relevant_smelly_pairs = all_smelly_pairs.intersection(all_pairs)

        # Calculate sets for contingency table
        non_smelling_non_co_changing_pairs = all_pairs.difference(relevant_smelly_pairs).difference(co_changed_pairs)
        non_smelling_co_changing_pairs = co_changed_pairs.difference(relevant_smelly_pairs)
        smelling_non_co_changing_pairs = relevant_smelly_pairs.difference(smelling_co_changing_pairs)

        # Calculate values of the contingency table cells
        non_smelling_non_co_changing_pairs_size = len(non_smelling_non_co_changing_pairs)
        non_smelling_co_changing_pairs_size = len(non_smelling_co_changing_pairs)
        smelling_non_co_changing_pairs_size = len(smelling_non_co_changing_pairs)
        smelling_co_changing_pairs_size = len(smelling_co_changing_pairs)

        # total amount of observations
        n = non_smelling_non_co_changing_pairs_size + non_smelling_co_changing_pairs_size + smelling_non_co_changing_pairs_size + smelling_co_changing_pairs_size
        print("general information:")
        print("all changed pairs during the history: " + str(len(all_pairs)))
        print("smells in project: " + str(len(all_smelly_pairs)))
        print("smells contained in all pairs: " + str(len(relevant_smelly_pairs)))
        print("all co changes in project: " + str(len(co_changed_pairs)))
        print("\n")

        self.perform_chi2_analysis(name, non_smelling_non_co_changing_pairs_size, non_smelling_co_changing_pairs_size, smelling_non_co_changing_pairs_size, smelling_co_changing_pairs_size, n)
        self.perform_fisher(name, non_smelling_non_co_changing_pairs_size, non_smelling_co_changing_pairs_size, smelling_non_co_changing_pairs_size, smelling_co_changing_pairs_size)

    # Executes Fisher's test on the passed contingency table values.
    @staticmethod
    def perform_fisher(name, non_smelling_non_co_changing_pairs, non_smelling_co_changing_pairs, smelling_non_co_changing_pairs, smelling_co_changing_pairs):
        oddsratio, pvalue = stats.fisher_exact([[non_smelling_non_co_changing_pairs, non_smelling_co_changing_pairs], [smelling_non_co_changing_pairs, smelling_co_changing_pairs]])
        print("Fisher values:")
        print("oddsratio: " + str(oddsratio))
        print("p-value: " + str(pvalue))
        print("\n")

        add_result(project_name, name + "_fisher_odds", oddsratio)
        add_result(project_name, name + "_fisher_pvalue", pvalue)

    # Executes the chi squared test on the passed contingency table values.
    def perform_chi2_analysis(self, name, non_smelling_non_co_changing_pairs, non_smelling_co_changing_pairs, smelling_non_co_changing_pairs, smelling_co_changing_pairs, n):
        print("chi2 values:")
        print("non_smelling_non_co_changing_pairs: " + str(non_smelling_non_co_changing_pairs))
        print("non_smelling_co_changing_pairs: " + str(non_smelling_co_changing_pairs))
        print("smelling_non_co_changing_pairs: " + str(smelling_non_co_changing_pairs))
        print("smelling_co_changing_pairs: " + str(smelling_co_changing_pairs))

        if non_smelling_non_co_changing_pairs == 0 or non_smelling_co_changing_pairs == 0 or smelling_non_co_changing_pairs == 0 or smelling_co_changing_pairs == 0:
            print('Cannot calculate chi2 due to zero in table')
            return

        # Calculate chi2
        chi2_stat, p_val, dof, ex = stats.chi2_contingency([[non_smelling_non_co_changing_pairs, non_smelling_co_changing_pairs], [smelling_non_co_changing_pairs, smelling_co_changing_pairs]])
        # calculate critical value
        significance = 0.05
        p = 1 - significance
        critical_value = chi2.ppf(p, dof)
        # calculate phi value
        phi = np.sqrt(chi2_stat / n)
        odds = self.odds_ratio(non_smelling_non_co_changing_pairs, non_smelling_co_changing_pairs, smelling_non_co_changing_pairs, smelling_co_changing_pairs)
        print("===Chi2 Stat vs critical value===")
        print('chi=%.6f, critical value=%.6f\n' % (chi2_stat, critical_value))
        print('oddsratio: %.6f' % odds)
        print("\n")
        print("===Phi value[0.1: small | 0.3: average | 0.5: large]===")
        print(phi)
        print("\n")
        print("===Degrees of Freedom===")
        print(dof)
        print("\n")
        print("===P-Value===")
        print(p_val)
        print("\n")
        print("===Contingency Table===")
        print(ex)

        add_result(project_name, name + "_chi_phi", phi)
        add_result(project_name, name + "_chi_dof", dof)
        add_result(project_name, name + "_chi_pvalue", p_val)
        add_result(project_name, name + "_chi_odds", odds)
        add_result(project_name, name + "_chi_chi", chi2_stat)
        add_result(project_name, name + "_chi_crit", critical_value)

    # Calculates the odds ratio on the passed contingency table values.
    @staticmethod
    def odds_ratio(non_smelling_non_co_changing_pairs, non_smelling_co_changing_pairs, smelling_non_co_changing_pairs, smelling_co_changing_pairs):
        if non_smelling_co_changing_pairs*smelling_non_co_changing_pairs == 0:
            return 0
        return (non_smelling_non_co_changing_pairs*smelling_co_changing_pairs)/(non_smelling_co_changing_pairs*smelling_non_co_changing_pairs)