#!/usr/bin/env python from __future__ import absolute_import from __future__ import unicode_literals from __future__ import print_function from __future__ import division from builtins import str, bytes, dict, int from builtins import object, range from builtins import map, zip, filter import os import sys sys.path = [os.path.dirname(os.path.abspath(__file__))] + sys.path from liblinear import * from liblinear import __all__ as liblinear_all from liblinear import scipy, sparse from ctypes import c_double __all__ = ['svm_read_problem', 'load_model', 'save_model', 'evaluations', 'train', 'predict'] + liblinear_all def svm_read_problem(data_file_name, return_scipy=False): """ svm_read_problem(data_file_name, return_scipy=False) -> [y, x], y: list, x: list of dictionary svm_read_problem(data_file_name, return_scipy=True) -> [y, x], y: ndarray, x: csr_matrix Read LIBSVM-format data from data_file_name and return labels y and data instances x. """ prob_y = [] prob_x = [] row_ptr = [0] col_idx = [] for i, line in enumerate(open(data_file_name)): line = line.split(None, 1) # In case an instance with all zero features if len(line) == 1: line += [''] label, features = line prob_y += [float(label)] if scipy is not None and return_scipy: nz = 0 for e in features.split(): ind, val = e.split(":") val = float(val) if val != 0: col_idx += [int(ind) - 1] prob_x += [val] nz += 1 row_ptr += [row_ptr[-1] + nz] else: xi = {} for e in features.split(): ind, val = e.split(":") if val != 0: xi[int(ind)] = float(val) prob_x += [xi] if scipy is not None and return_scipy: prob_y = scipy.array(prob_y) prob_x = scipy.array(prob_x) col_idx = scipy.array(col_idx) row_ptr = scipy.array(row_ptr) prob_x = sparse.csr_matrix((prob_x, col_idx, row_ptr)) return (prob_y, prob_x) def load_model(model_file_name): """ load_model(model_file_name) -> model Load a LIBLINEAR model from model_file_name and return. """ model = liblinear.load_model(model_file_name.encode()) if not model: print("can't open model file %s" % model_file_name) return None model = toPyModel(model) return model def save_model(model_file_name, model): """ save_model(model_file_name, model) -> None Save a LIBLINEAR model to the file model_file_name. """ liblinear.save_model(model_file_name.encode(), model) def evaluations_scipy(ty, pv): """ evaluations_scipy(ty, pv) -> (ACC, MSE, SCC) ty, pv: ndarray Calculate accuracy, mean squared error and squared correlation coefficient using the true values (ty) and predicted values (pv). """ if not (scipy is not None and isinstance(ty, scipy.ndarray) and isinstance(pv, scipy.ndarray)): raise TypeError("type of ty and pv must be ndarray") if len(ty) != len(pv): raise ValueError("len(ty) must be equal to len(pv)") ACC = 100.0 * (ty == pv).mean() MSE = ((ty - pv)**2).mean() l = len(ty) sumv = pv.sum() sumy = ty.sum() sumvy = (pv * ty).sum() sumvv = (pv * pv).sum() sumyy = (ty * ty).sum() with scipy.errstate(all = 'raise'): try: SCC = ((l * sumvy - sumv * sumy) * (l * sumvy - sumv * sumy)) / ((l * sumvv - sumv * sumv) * (l * sumyy - sumy * sumy)) except: SCC = float('nan') return (float(ACC), float(MSE), float(SCC)) def evaluations(ty, pv, useScipy = True): """ evaluations(ty, pv, useScipy) -> (ACC, MSE, SCC) ty, pv: list, tuple or ndarray useScipy: convert ty, pv to ndarray, and use scipy functions for the evaluation Calculate accuracy, mean squared error and squared correlation coefficient using the true values (ty) and predicted values (pv). """ if scipy is not None and useScipy: return evaluations_scipy(scipy.asarray(ty), scipy.asarray(pv)) if len(ty) != len(pv): raise ValueError("len(ty) must be equal to len(pv)") total_correct = total_error = 0 sumv = sumy = sumvv = sumyy = sumvy = 0 for v, y in zip(pv, ty): if y == v: total_correct += 1 total_error += (v - y) * (v - y) sumv += v sumy += y sumvv += v * v sumyy += y * y sumvy += v * y l = len(ty) ACC = 100.0 * total_correct / l MSE = total_error / l try: SCC = ((l * sumvy - sumv * sumy) * (l * sumvy - sumv * sumy)) / ((l * sumvv - sumv * sumv) * (l * sumyy - sumy * sumy)) except: SCC = float('nan') return (float(ACC), float(MSE), float(SCC)) def train(arg1, arg2=None, arg3=None): """ train(y, x [, options]) -> model | ACC y: a list/tuple/ndarray of l true labels (type must be int/double). x: 1. a list/tuple of l training instances. Feature vector of each training instance is a list/tuple or dictionary. 2. an l * n numpy ndarray or scipy spmatrix (n: number of features). train(prob [, options]) -> model | ACC train(prob, param) -> model | ACC Train a model from data (y, x) or a problem prob using 'options' or a parameter param. If '-v' is specified in 'options' (i.e., cross validation) either accuracy (ACC) or mean-squared error (MSE) is returned. options: -s type : set type of solver (default 1) for multi-class classification 0 -- L2-regularized logistic regression (primal) 1 -- L2-regularized L2-loss support vector classification (dual) 2 -- L2-regularized L2-loss support vector classification (primal) 3 -- L2-regularized L1-loss support vector classification (dual) 4 -- support vector classification by Crammer and Singer 5 -- L1-regularized L2-loss support vector classification 6 -- L1-regularized logistic regression 7 -- L2-regularized logistic regression (dual) for regression 11 -- L2-regularized L2-loss support vector regression (primal) 12 -- L2-regularized L2-loss support vector regression (dual) 13 -- L2-regularized L1-loss support vector regression (dual) -c cost : set the parameter C (default 1) -p epsilon : set the epsilon in loss function of SVR (default 0.1) -e epsilon : set tolerance of termination criterion -s 0 and 2 |f'(w)|_2 <= eps*min(pos,neg)/l*|f'(w0)|_2, where f is the primal function, (default 0.01) -s 11 |f'(w)|_2 <= eps*|f'(w0)|_2 (default 0.001) -s 1, 3, 4, and 7 Dual maximal violation <= eps; similar to liblinear (default 0.) -s 5 and 6 |f'(w)|_inf <= eps*min(pos,neg)/l*|f'(w0)|_inf, where f is the primal function (default 0.01) -s 12 and 13 |f'(alpha)|_1 <= eps |f'(alpha0)|, where f is the dual function (default 0.1) -B bias : if bias >= 0, instance x becomes [x; bias]; if < 0, no bias term added (default -1) -wi weight: weights adjust the parameter C of different classes (see README for details) -v n: n-fold cross validation mode -q : quiet mode (no outputs) """ prob, param = None, None if isinstance(arg1, (list, tuple)) or (scipy and isinstance(arg1, scipy.ndarray)): assert isinstance(arg2, (list, tuple)) or (scipy and isinstance(arg2, (scipy.ndarray, sparse.spmatrix))) y, x, options = arg1, arg2, arg3 prob = problem(y, x) param = parameter(options) elif isinstance(arg1, problem): prob = arg1 if isinstance(arg2, parameter): param = arg2 else: param = parameter(arg2) if prob is None or param is None: raise TypeError("Wrong types for the arguments") prob.set_bias(param.bias) liblinear.set_print_string_function(param.print_func) err_msg = liblinear.check_parameter(prob, param) if err_msg: raise ValueError('Error: %s' % err_msg) if param.flag_find_C: nr_fold = param.nr_fold best_C = c_double() best_rate = c_double() max_C = 1024 if param.flag_C_specified: start_C = param.C else: start_C = -1.0 liblinear.find_parameter_C(prob, param, nr_fold, start_C, max_C, best_C, best_rate) print("Best C = %lf CV accuracy = %g%%\n" % (best_C.value, 100.0 * best_rate.value)) return best_C.value, best_rate.value elif param.flag_cross_validation: l, nr_fold = prob.l, param.nr_fold target = (c_double * l)() liblinear.cross_validation(prob, param, nr_fold, target) ACC, MSE, SCC = evaluations(prob.y[:l], target[:l]) if param.solver_type in [L2R_L2LOSS_SVR, L2R_L2LOSS_SVR_DUAL, L2R_L1LOSS_SVR_DUAL]: print("Cross Validation Mean squared error = %g" % MSE) print("Cross Validation Squared correlation coefficient = %g" % SCC) return MSE else: print("Cross Validation Accuracy = %g%%" % ACC) return ACC else: m = liblinear.train(prob, param) m = toPyModel(m) return m def predict(y, x, m, options=""): """ predict(y, x, m [, options]) -> (p_labels, p_acc, p_vals) y: a list/tuple/ndarray of l true labels (type must be int/double). It is used for calculating the accuracy. Use [] if true labels are unavailable. x: 1. a list/tuple of l training instances. Feature vector of each training instance is a list/tuple or dictionary. 2. an l * n numpy ndarray or scipy spmatrix (n: number of features). Predict data (y, x) with the SVM model m. options: -b probability_estimates: whether to output probability estimates, 0 or 1 (default 0); currently for logistic regression only -q quiet mode (no outputs) The return tuple contains p_labels: a list of predicted labels p_acc: a tuple including accuracy (for classification), mean-squared error, and squared correlation coefficient (for regression). p_vals: a list of decision values or probability estimates (if '-b 1' is specified). If k is the number of classes, for decision values, each element includes results of predicting k binary-class SVMs. if k = 2 and solver is not MCSVM_CS, only one decision value is returned. For probabilities, each element contains k values indicating the probability that the testing instance is in each class. Note that the order of classes here is the same as 'model.label' field in the model structure. """ def info(s): print(s) if scipy and isinstance(x, scipy.ndarray): x = scipy.ascontiguousarray(x) # enforce row-major elif sparse and isinstance(x, sparse.spmatrix): x = x.tocsr() elif not isinstance(x, (list, tuple)): raise TypeError("type of x: {0} is not supported!".format(type(x))) if (not isinstance(y, (list, tuple))) and (not (scipy and isinstance(y, scipy.ndarray))): raise TypeError("type of y: {0} is not supported!".format(type(y))) predict_probability = 0 argv = options.split() i = 0 while i < len(argv): if argv[i] == '-b': i += 1 predict_probability = int(argv[i]) elif argv[i] == '-q': info = print_null else: raise ValueError("Wrong options") i += 1 solver_type = m.param.solver_type nr_class = m.get_nr_class() nr_feature = m.get_nr_feature() is_prob_model = m.is_probability_model() bias = m.bias if bias >= 0: biasterm = feature_node(nr_feature + 1, bias) else: biasterm = feature_node(-1, bias) pred_labels = [] pred_values = [] if scipy and isinstance(x, sparse.spmatrix): nr_instance = x.shape[0] else: nr_instance = len(x) if predict_probability: if not is_prob_model: raise TypeError('probability output is only supported for logistic regression') prob_estimates = (c_double * nr_class)() for i in range(nr_instance): if scipy and isinstance(x, sparse.spmatrix): indslice = slice(x.indptr[i], x.indptr[i + 1]) xi, idx = gen_feature_nodearray((x.indices[indslice], x.data[indslice]), feature_max=nr_feature) else: xi, idx = gen_feature_nodearray(x[i], feature_max=nr_feature) xi[-2] = biasterm label = liblinear.predict_probability(m, xi, prob_estimates) values = prob_estimates[:nr_class] pred_labels += [label] pred_values += [values] else: if nr_class <= 2: nr_classifier = 1 else: nr_classifier = nr_class dec_values = (c_double * nr_classifier)() for i in range(nr_instance): if scipy and isinstance(x, sparse.spmatrix): indslice = slice(x.indptr[i], x.indptr[i + 1]) xi, idx = gen_feature_nodearray((x.indices[indslice], x.data[indslice]), feature_max=nr_feature) else: xi, idx = gen_feature_nodearray(x[i], feature_max=nr_feature) xi[-2] = biasterm label = liblinear.predict_values(m, xi, dec_values) values = dec_values[:nr_classifier] pred_labels += [label] pred_values += [values] if len(y) == 0: y = [0] * nr_instance ACC, MSE, SCC = evaluations(y, pred_labels) if m.is_regression_model(): info("Mean squared error = %g (regression)" % MSE) info("Squared correlation coefficient = %g (regression)" % SCC) else: info("Accuracy = %g%% (%d/%d) (classification)" % (ACC, int(round(nr_instance * ACC / 100)), nr_instance)) return pred_labels, (ACC, MSE, SCC), pred_values