Self-consistently train the classifier

def trainClassifier(self):
        """
        Self-consistently train the classifier
        """
        
        self.loadPopulationMetadata()
        self.loadSimResults()
        
        cut_geometry, flags_geometry = self.applyGeometry(self.data_population['RA'], self.data_population['DEC'])
        
        cut_detect_sim_results_sig = (np.logical_or(np.logical_and(self.data_sim['SIG'] >=  self.config[self.algorithm]['sig_threshold'], 
                                      self.data_sim['DIFFICULTY'] == 0), np.logical_or(self.data_sim['DIFFICULTY'] == 1, self.data_sim['DIFFICULTY'] == 4)))
        cut_detect_sim_results_ts = (np.logical_or(np.logical_and(self.data_sim['TS'] >=  self.config[self.algorithm]['ts_threshold'], 
                                      self.data_sim['DIFFICULTY'] == 0), np.logical_or(self.data_sim['DIFFICULTY'] == 1, self.data_sim['DIFFICULTY'] == 4)))
        
        mc_source_id_detect = self.data_sim['MC_SOURCE_ID'][cut_detect_sim_results_sig & cut_detect_sim_results_ts]
        cut_detect = np.in1d(self.data_population['MC_SOURCE_ID'], mc_source_id_detect)

        features = []
        for key, operation in self.config['operation']['params_intrinsic']:
            assert operation.lower() in ['linear', 'log'], 'ERROR'
            if operation.lower() == 'linear':
                features.append(self.data_population[key])
            else:
                features.append(np.log10(self.data_population[key]))

        X = np.vstack(features).T
        X = X[cut_geometry]
        Y = cut_detect[cut_geometry]

        # Create training and test sets
        indices = np.arange(len(X))
        X_train, X_test, Y_train, Y_test, cut_train, cut_test = train_test_split(X,Y,indices,test_size=0.2)

        # Train random forest classifier
        if True:
            print 'Training the machine learning classifier. This may take a while ...'
            t_start = time.time()
            parameters = {'n_estimators':(500,1000)}#, 'criterion':["gini","entropy"], "min_samples_leaf": [1,2,4]}
            rf = RandomForestClassifier(oob_score=True)
            rf_tuned = GridSearchCV(rf, parameters, cv=10, verbose=1)
            self.classifier = rf_tuned.fit(X_train, Y_train)
            
            #self.classifier = sklearn.gaussian_process.GaussianProcessClassifier(1.0 * sklearn.gaussian_process.kernels.RBF(0.5))
            #self.classifier = sklearn.neighbors.KNeighborsClassifier(3, weights='uniform')
            #self.classifier = sklearn.neighbors.KNeighborsClassifier(2, weights='distance') 
            #self.classifier = sklearn.svm.SVC(gamma=2, C=1)
            
            # Print the best score and estimator:
            print('Best Score:', self.classifier.best_score_)
            print(self.classifier.best_estimator_)
            print(self.classifier.best_params_)
            t_end = time.time()
            print '  ... training took %.2f seconds'%(t_end - t_start)

            # Save the trained classifier
            classifier_data = pickle.dumps(self.classifier)
            writer = open(self.config[self.algorithm]['classifier'], 'w')
            writer.write(classifier_data)
            writer.close()
            print 'Saving machine learning classifier to %s ...'%(self.config[self.algorithm]['classifier'])
        else:
            self.loadClassifier()

        y_pred = self.classifier.predict_proba(X_test)[:,1]
        
        #Confusion matrix
        y_pred_label = self.classifier.predict(X_test)
        cm = confusion_matrix(Y_test, y_pred_label)
        nondet_frac = cm[0][0]/(1.0*cm[0][0]+1.0*cm[0][1])
        det_frac = cm[1][1]/(1.0*cm[1][0]+1.0*cm[1][1])

        print('Fraction of non-detections test set labeled correctly: %0.2f' % nondet_frac)
        print('Fraction of detections in test set labeled correctly: %0.2f' % det_frac)

        plt.figure(figsize=(8,6))
        plt.matshow(cm)
        plt.title('Confusion Matrix', fontsize=18, position = (0.5,1.1))
        plt.colorbar()
        plt.ylabel('True label', fontsize=16)
        plt.xlabel('Predicted label', fontsize=16, position = (0.5, -10.5))
        plt.tick_params(labelsize=12)
        plt.show()
        
        # Compute ROC curve and area under curve (AUC) for each class:
        BestRFselector = self.classifier.best_estimator_
        y_pred_best = BestRFselector.predict_proba(X_test)
        labels = BestRFselector.classes_
        fpr = dict()
        tpr = dict()
        roc_auc = dict()
        for i,label in enumerate(labels):
            fpr[label], tpr[label], _ = roc_curve(Y_test, y_pred_best[:, i], pos_label=label)
            roc_auc[label] = auc(fpr[label], tpr[label])
            
        plt.figure(figsize=(8,6))
        plt.plot([0, 1], [1, 1], color='red', linestyle='-', linewidth=3, label='Perfect Classifier (AUC = %0.2f)' % (1.0))
        plt.plot(fpr[1], tpr[1], lw=3, label='Random Forest (AUC = %0.2f)' % (roc_auc[1]), color='blue')
        plt.plot([0, 1], [0, 1], color='black', linestyle=':', linewidth=2.5, label='Random Classifier (AUC = %0.2f)' % (0.5))
        plt.xlim([0.0, 1.0])
        plt.ylim([0.0, 1.025])
        plt.tick_params(labelsize=16)
        plt.xlabel('False Positive Rate', fontsize=20, labelpad=8)
        plt.ylabel('True Positive Rate', fontsize=20, labelpad=8)
        plt.legend(loc="lower right", fontsize=16)
        plt.show()

        self.validateClassifier(cut_detect, cut_train, cut_geometry, y_pred)