confusionmatrix.py

import numpy as np


class ConfusionMatrix:
    """
       Simple confusion matrix class
       row is the true class, column is the predicted class
    """
    def __init__(self, num_classes, class_names=None):
        self.n_classes = num_classes
        if class_names is None:
            self.class_names = map(str, range(num_classes))
        else:
            self.class_names = class_names

        # find max class_name and pad
        max_len = max(map(len, self.class_names))
        self.max_len = max_len
        for idx, name in enumerate(self.class_names):
            if len(self.class_names) < max_len:
                self.class_names[idx] = name + " "*(max_len-len(name))

        self.mat = np.zeros((num_classes,num_classes),dtype='int')

    def __str__(self):
        # calucate row and column sums
        col_sum = np.sum(self.mat, axis=1)
        row_sum = np.sum(self.mat, axis=0)

        s = []

        mat_str = self.mat.__str__()
        mat_str = mat_str.replace('[','').replace(']','').split('\n')

        for idx, row in enumerate(mat_str):
            if idx == 0:
                pad = " "
            else:
                pad = ""
            class_name = self.class_names[idx]
            class_name = " " + class_name + " |"
            row_str = class_name + pad + row
            row_str += " |" + str(col_sum[idx])
            s.append(row_str)

        row_sum = [(self.max_len+4)*" "+" ".join(map(str, row_sum))]
        hline = [(1+self.max_len)*" "+"-"*len(row_sum[0])]

        s = hline + s + hline + row_sum

        # add linebreaks
        s_out = [line+'\n' for line in s]
        return "".join(s_out)

    def batch_add(self, targets, preds):
        assert targets.shape == preds.shape
        assert len(targets) == len(preds)
        assert max(targets) < self.n_classes
        assert max(preds) < self.n_classes
        targets = targets.flatten()
        preds = preds.flatten()
        for i in range(len(targets)):
                self.mat[targets[i], preds[i]] += 1

    def get_errors(self):
        tp = np.asarray(np.diag(self.mat).flatten(),dtype='float')
        fn = np.asarray(np.sum(self.mat, axis=1).flatten(),dtype='float') - tp
        fp = np.asarray(np.sum(self.mat, axis=0).flatten(),dtype='float') - tp
        tn = np.asarray(np.sum(self.mat)*np.ones(self.n_classes).flatten(),
                        dtype='float') - tp - fn - fp
        return tp, fn, fp, tn

    def accuracy(self):
        """
        Calculates global accuracy
        :return: accuracy
        :example: >>> conf = ConfusionMatrix(3)
                  >>> conf.batchAdd([0,0,1],[0,0,2])
                  >>> print conf.accuracy()
        """
        tp, _, _, _ = self.get_errors()
        n_samples = np.sum(self.mat)
        return np.sum(tp) / n_samples

    def sensitivity(self):
        tp, tn, fp, fn = self.get_errors()
        res = tp / (tp + fn)
        res = res[~np.isnan(res)]
        return res

    def specificity(self):
        tp, tn, fp, fn = self.get_errors()
        res = tn / (tn + fp)
        res = res[~np.isnan(res)]
        return res

    def positive_predictive_value(self):
        tp, tn, fp, fn = self.get_errors()
        res = tp / (tp + fp)
        res = res[~np.isnan(res)]
        return res

    def negative_predictive_value(self):
        tp, tn, fp, fn = self.get_errors()
        res = tn / (tn + fn)
        res = res[~np.isnan(res)]
        return res

    def false_positive_rate(self):
        tp, tn, fp, fn = self.get_errors()
        res = fp / (fp + tn)
        res = res[~np.isnan(res)]
        return res

    def false_discovery_rate(self):
        tp, tn, fp, fn = self.get_errors()
        res = fp / (tp + fp)
        res = res[~np.isnan(res)]
        return res

    def F1(self):
        tp, tn, fp, fn = self.get_errors()
        res = (2*tp) / (2*tp + fp + fn)
        res = res[~np.isnan(res)]
        return res

    def matthews_correlation(self):
        tp, tn, fp, fn = self.get_errors()
        numerator = tp*tn - fp*fn
        denominator = np.sqrt((tp + fp)*(tp + fn)*(tn + fp)*(tn + fn))
        res = numerator / denominator
        res = res[~np.isnan(res)]
        return res