liblinear-ruby 0.0.1

data/liblinear-1.93/python/Makefile

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+all = lib
+
+lib:
+	make -C .. lib

data/liblinear-1.93/python/README

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+-------------------------------------
+--- Python interface of LIBLINEAR ---
+-------------------------------------
+
+Table of Contents
+=================
+
+- Introduction
+- Installation
+- Quick Start
+- Design Description
+- Data Structures
+- Utility Functions
+- Additional Information
+
+Introduction
+============
+
+Python (http://www.python.org/) is a programming language suitable for rapid
+development. This tool provides a simple Python interface to LIBLINEAR, a library
+for support vector machines (http://www.csie.ntu.edu.tw/~cjlin/liblinear). The
+interface is very easy to use as the usage is the same as that of LIBLINEAR. The
+interface is developed with the built-in Python library "ctypes."
+
+Installation
+============
+
+On Unix systems, type
+
+> make
+
+The interface needs only LIBLINEAR shared library, which is generated by
+the above command. We assume that the shared library is on the LIBLINEAR
+main directory or in the system path.
+
+For windows, the shared library liblinear.dll is ready in the directory
+`..\windows'. You can also copy it to the system directory (e.g.,
+`C:\WINDOWS\system32\' for Windows XP). To regenerate the shared library,
+please follow the instruction of building windows binaries in LIBLINEAR README.
+
+Quick Start
+===========
+
+There are two levels of usage. The high-level one uses utility functions
+in liblinearutil.py and the usage is the same as the LIBLINEAR MATLAB interface.
+
+>>> from liblinearutil import *
+# Read data in LIBSVM format
+>>> y, x = svm_read_problem('../heart_scale')
+>>> m = train(y[:200], x[:200], '-c 4')
+>>> p_label, p_acc, p_val = predict(y[200:], x[200:], m)
+
+# Construct problem in python format
+# Dense data
+>>> y, x = [1,-1], [[1,0,1], [-1,0,-1]]
+# Sparse data
+>>> y, x = [1,-1], [{1:1, 3:1}, {1:-1,3:-1}]
+>>> prob  = problem(y, x)
+>>> param = parameter('-c 4 -B 1')
+>>> m = train(prob, param)
+
+# Other utility functions
+>>> save_model('heart_scale.model', m)
+>>> m = load_model('heart_scale.model')
+>>> p_label, p_acc, p_val = predict(y, x, m, '-b 1')
+>>> ACC, MSE, SCC = evaluations(y, p_label)
+
+# Getting online help
+>>> help(train)
+
+The low-level use directly calls C interfaces imported by liblinear.py. Note that
+all arguments and return values are in ctypes format. You need to handle them
+carefully.
+
+>>> from liblinear import *
+>>> prob = problem([1,-1], [{1:1, 3:1}, {1:-1,3:-1}])
+>>> param = parameter('-c 4')
+>>> m = liblinear.train(prob, param) # m is a ctype pointer to a model
+# Convert a Python-format instance to feature_nodearray, a ctypes structure
+>>> x0, max_idx = gen_feature_nodearray({1:1, 3:1})
+>>> label = liblinear.predict(m, x0)
+
+Design Description
+==================
+
+There are two files liblinear.py and liblinearutil.py, which respectively correspond to
+low-level and high-level use of the interface.
+
+In liblinear.py, we adopt the Python built-in library "ctypes," so that
+Python can directly access C structures and interface functions defined
+in linear.h.
+
+While advanced users can use structures/functions in liblinear.py, to
+avoid handling ctypes structures, in liblinearutil.py we provide some easy-to-use
+functions. The usage is similar to LIBLINEAR MATLAB interface.
+
+Data Structures
+===============
+
+Three data structures derived from linear.h are node, problem, and
+parameter. They all contain fields with the same names in
+linear.h. Access these fields carefully because you directly use a C structure
+instead of a Python object. The following description introduces additional
+fields and methods.
+
+Before using the data structures, execute the following command to load the
+LIBLINEAR shared library:
+
+    >>> from liblinear import *
+
+- class feature_node:
+
+    Construct a feature_node.
+
+    >>> node = feature_node(idx, val)
+
+    idx: an integer indicates the feature index.
+
+    val: a float indicates the feature value.
+
+    Show the index and the value of a node.
+
+    >>> print(node) 
+
+- Function: gen_feature_nodearray(xi [,feature_max=None [,issparse=True]])
+
+    Generate a feature vector from a Python list/tuple or a dictionary:
+
+    >>> xi, max_idx = gen_feature_nodearray({1:1, 3:1, 5:-2})
+
+    xi: the returned feature_nodearray (a ctypes structure)
+
+    max_idx: the maximal feature index of xi
+
+    issparse: if issparse == True, zero feature values are removed. The default
+              value is True for the sparsity.
+
+    feature_max: if feature_max is assigned, features with indices larger than
+                 feature_max are removed.
+
+- class problem:
+
+    Construct a problem instance
+
+    >>> prob = problem(y, x [,bias=-1])
+
+    y: a Python list/tuple of l labels (type must be int/double).
+
+    x: a Python list/tuple of l data instances. Each element of x must be
+       an instance of list/tuple/dictionary type.
+
+    bias: if bias >= 0, instance x becomes [x; bias]; if < 0, no bias term 
+          added (default -1)
+
+    You can also modify the bias value by
+
+    >>> prob.set_bias(1)
+
+    Note that if your x contains sparse data (i.e., dictionary), the internal
+    ctypes data format is still sparse.
+
+- class parameter:
+
+    Construct a parameter instance
+
+    >>> param = parameter('training_options')
+
+    If 'training_options' is empty, LIBLINEAR default values are applied.
+
+    Set param to LIBLINEAR default values.
+
+    >>> param.set_to_default_values()
+
+    Parse a string of options.
+
+    >>> param.parse_options('training_options')
+
+    Show values of parameters.
+
+    >>> print(param)
+
+- class model:
+
+    There are two ways to obtain an instance of model:
+
+    >>> model_ = train(y, x)
+    >>> model_ = load_model('model_file_name')
+
+    Note that the returned structure of interface functions
+    liblinear.train and liblinear.load_model is a ctypes pointer of
+    model, which is different from the model object returned
+    by train and load_model in liblinearutil.py. We provide a
+    function toPyModel for the conversion:
+
+    >>> model_ptr = liblinear.train(prob, param)
+    >>> model_ = toPyModel(model_ptr)
+
+    If you obtain a model in a way other than the above approaches,
+    handle it carefully to avoid memory leak or segmentation fault.
+
+    Some interface functions to access LIBLINEAR models are wrapped as
+    members of the class model:
+
+    >>> nr_feature =  model_.get_nr_feature()
+    >>> nr_class = model_.get_nr_class()
+    >>> class_labels = model_.get_labels()
+    >>> is_prob_model = model_.is_probability_model()
+
+Utility Functions
+=================
+
+To use utility functions, type
+
+    >>> from liblinearutil import *
+
+The above command loads
+    train()            : train a linear model
+    predict()          : predict testing data
+    svm_read_problem() : read the data from a LIBSVM-format file.
+    load_model()       : load a LIBLINEAR model.
+    save_model()       : save model to a file.
+    evaluations()      : evaluate prediction results.
+
+- Function: train
+
+    There are three ways to call train()
+
+    >>> model = train(y, x [, 'training_options'])
+    >>> model = train(prob [, 'training_options'])
+    >>> model = train(prob, param)
+
+    y: a list/tuple of l training labels (type must be int/double).
+
+    x: a list/tuple of l training instances. The feature vector of
+       each training instance is an instance of list/tuple or dictionary.
+
+    training_options: a string in the same form as that for LIBLINEAR command
+                      mode.
+
+    prob: a problem instance generated by calling
+          problem(y, x).
+
+    param: a parameter instance generated by calling
+           parameter('training_options')
+
+    model: the returned model instance. See linear.h for details of this
+           structure. If '-v' is specified, cross validation is
+           conducted and the returned model is just a scalar: cross-validation
+           accuracy for classification and mean-squared error for regression.
+
+    To train the same data many times with different
+    parameters, the second and the third ways should be faster..
+
+    Examples:
+
+    >>> y, x = svm_read_problem('../heart_scale')
+    >>> prob = problem(y, x)
+    >>> param = parameter('-s 3 -c 5 -q')
+    >>> m = train(y, x, '-c 5')
+    >>> m = train(prob, '-w1 5 -c 5')
+    >>> m = train(prob, param)
+    >>> CV_ACC = train(y, x, '-v 3')
+
+- Function: predict
+
+    To predict testing data with a model, use
+
+    >>> p_labs, p_acc, p_vals = predict(y, x, model [,'predicting_options'])
+
+    y: a list/tuple of l true labels (type must be int/double). It is used
+       for calculating the accuracy. Use [] if true labels are
+       unavailable.
+
+    x: a list/tuple of l predicting instances. The feature vector of
+       each predicting instance is an instance of list/tuple or dictionary.
+
+    predicting_options: a string of predicting options in the same format as
+                        that of LIBLINEAR.
+
+    model: a model instance.
+
+    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.
+
+    Example:
+
+    >>> m = train(y, x, '-c 5')
+    >>> p_labels, p_acc, p_vals = predict(y, x, m)
+
+- Functions: svm_read_problem/load_model/save_model
+
+    See the usage by examples:
+
+    >>> y, x = svm_read_problem('data.txt')
+    >>> m = load_model('model_file')
+    >>> save_model('model_file', m)
+
+- Function: evaluations
+
+    Calculate some evaluations using the true values (ty) and predicted
+    values (pv):
+
+    >>> (ACC, MSE, SCC) = evaluations(ty, pv)
+
+    ty: a list of true values.
+
+    pv: a list of predict values.
+
+    ACC: accuracy.
+
+    MSE: mean squared error.
+
+    SCC: squared correlation coefficient.
+
+
+Additional Information
+======================
+
+This interface was written by Hsiang-Fu Yu from Department of Computer
+Science, National Taiwan University. If you find this tool useful, please
+cite LIBLINEAR as follows
+
+R.-E. Fan, K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin.
+LIBLINEAR: A Library for Large Linear Classification, Journal of
+Machine Learning Research 9(2008), 1871-1874. Software available at
+http://www.csie.ntu.edu.tw/~cjlin/liblinear
+
+For any question, please contact Chih-Jen Lin <cjlin@csie.ntu.edu.tw>,
+or check the FAQ page:
+
+http://www.csie.ntu.edu.tw/~cjlin/liblinear/faq.html

data/liblinear-1.93/python/liblinear.py

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+#!/usr/bin/env python
+
+from ctypes import *
+from ctypes.util import find_library
+from os import path
+import sys
+
+try:
+	dirname = path.dirname(path.abspath(__file__))
+	if sys.platform == 'win32':
+		liblinear = CDLL(path.join(dirname, r'..\windows\liblinear.dll'))
+	else:
+		liblinear = CDLL(path.join(dirname, '../liblinear.so.1'))
+except:
+# For unix the prefix 'lib' is not considered.
+	if find_library('linear'):
+		liblinear = CDLL(find_library('linear'))
+	elif find_library('liblinear'):
+		liblinear = CDLL(find_library('liblinear'))
+	else:
+		raise Exception('LIBLINEAR library not found.')
+
+# Construct constants
+SOLVER_TYPE = ['L2R_LR', 'L2R_L2LOSS_SVC_DUAL', 'L2R_L2LOSS_SVC', 'L2R_L1LOSS_SVC_DUAL',\
+		'MCSVM_CS', 'L1R_L2LOSS_SVC', 'L1R_LR', 'L2R_LR_DUAL', \
+		None, None, None, \
+		'L2R_L2LOSS_SVR', 'L2R_L2LOSS_SVR_DUAL', 'L2R_L1LOSS_SVR_DUAL']
+for i, s in enumerate(SOLVER_TYPE): 
+	if s is not None: exec("%s = %d" % (s , i))
+
+PRINT_STRING_FUN = CFUNCTYPE(None, c_char_p)
+def print_null(s): 
+	return 
+
+def genFields(names, types): 
+	return list(zip(names, types))
+
+def fillprototype(f, restype, argtypes): 
+	f.restype = restype
+	f.argtypes = argtypes
+
+class feature_node(Structure):
+	_names = ["index", "value"]
+	_types = [c_int, c_double]
+	_fields_ = genFields(_names, _types)
+
+	def __str__(self):
+		return '%d:%g' % (self.index, self.value)
+
+def gen_feature_nodearray(xi, feature_max=None, issparse=True):
+	if isinstance(xi, dict):
+		index_range = xi.keys()
+	elif isinstance(xi, (list, tuple)):
+		xi = [0] + xi  # idx should start from 1
+		index_range = range(1, len(xi))
+	else:
+		raise TypeError('xi should be a dictionary, list or tuple')
+
+	if feature_max:
+		assert(isinstance(feature_max, int))
+		index_range = filter(lambda j: j <= feature_max, index_range)
+	if issparse: 
+		index_range = filter(lambda j:xi[j] != 0, index_range)
+
+	index_range = sorted(index_range)
+	ret = (feature_node * (len(index_range)+2))()
+	ret[-1].index = -1 # for bias term
+	ret[-2].index = -1
+	for idx, j in enumerate(index_range):
+		ret[idx].index = j
+		ret[idx].value = xi[j]
+	max_idx = 0
+	if index_range : 
+		max_idx = index_range[-1]
+	return ret, max_idx
+
+class problem(Structure):
+	_names = ["l", "n", "y", "x", "bias"]
+	_types = [c_int, c_int, POINTER(c_double), POINTER(POINTER(feature_node)), c_double]
+	_fields_ = genFields(_names, _types)
+
+	def __init__(self, y, x, bias = -1):
+		if len(y) != len(x) :
+			raise ValueError("len(y) != len(x)")
+		self.l = l = len(y)
+		self.bias = -1
+
+		max_idx = 0
+		x_space = self.x_space = []
+		for i, xi in enumerate(x):
+			tmp_xi, tmp_idx = gen_feature_nodearray(xi)
+			x_space += [tmp_xi]
+			max_idx = max(max_idx, tmp_idx)
+		self.n = max_idx
+
+		self.y = (c_double * l)()
+		for i, yi in enumerate(y): self.y[i] = y[i]
+
+		self.x = (POINTER(feature_node) * l)() 
+		for i, xi in enumerate(self.x_space): self.x[i] = xi
+
+		self.set_bias(bias)
+
+	def set_bias(self, bias):
+		if self.bias == bias:
+			return 
+		if bias >= 0 and self.bias < 0: 
+			self.n += 1
+			node = feature_node(self.n, bias)
+		if bias < 0 and self.bias >= 0: 
+			self.n -= 1
+			node = feature_node(-1, bias)
+
+		for xi in self.x_space:
+			xi[-2] = node
+		self.bias = bias
+
+
+class parameter(Structure):
+	_names = ["solver_type", "eps", "C", "nr_weight", "weight_label", "weight", "p"]
+	_types = [c_int, c_double, c_double, c_int, POINTER(c_int), POINTER(c_double), c_double]
+	_fields_ = genFields(_names, _types)
+
+	def __init__(self, options = None):
+		if options == None:
+			options = ''
+		self.parse_options(options)
+
+	def __str__(self):
+		s = ''
+		attrs = parameter._names + list(self.__dict__.keys())
+		values = map(lambda attr: getattr(self, attr), attrs) 
+		for attr, val in zip(attrs, values):
+			s += (' %s: %s\n' % (attr, val))
+		s = s.strip()
+
+		return s
+
+	def set_to_default_values(self):
+		self.solver_type = L2R_L2LOSS_SVC_DUAL
+		self.eps = float('inf')
+		self.C = 1
+		self.p = 0.1
+		self.nr_weight = 0
+		self.weight_label = (c_int * 0)()
+		self.weight = (c_double * 0)()
+		self.bias = -1
+		self.cross_validation = False
+		self.nr_fold = 0
+		self.print_func = None
+
+	def parse_options(self, options):
+		if isinstance(options, list):
+			argv = options
+		elif isinstance(options, str):
+			argv = options.split()
+		else:
+			raise TypeError("arg 1 should be a list or a str.")
+		self.set_to_default_values()
+		self.print_func = cast(None, PRINT_STRING_FUN)
+		weight_label = []
+		weight = []
+
+		i = 0
+		while i < len(argv) :
+			if argv[i] == "-s":
+				i = i + 1
+				self.solver_type = int(argv[i])
+			elif argv[i] == "-c":
+				i = i + 1
+				self.C = float(argv[i])
+			elif argv[i] == "-p":
+				i = i + 1
+				self.p = float(argv[i])
+			elif argv[i] == "-e":
+				i = i + 1
+				self.eps = float(argv[i])
+			elif argv[i] == "-B":
+				i = i + 1
+				self.bias = float(argv[i])
+			elif argv[i] == "-v":
+				i = i + 1
+				self.cross_validation = 1
+				self.nr_fold = int(argv[i])
+				if self.nr_fold < 2 :
+					raise ValueError("n-fold cross validation: n must >= 2")
+			elif argv[i].startswith("-w"):
+				i = i + 1
+				self.nr_weight += 1
+				nr_weight = self.nr_weight
+				weight_label += [int(argv[i-1][2:])]
+				weight += [float(argv[i])]
+			elif argv[i] == "-q":
+				self.print_func = PRINT_STRING_FUN(print_null)
+			else :
+				raise ValueError("Wrong options")
+			i += 1
+
+		liblinear.set_print_string_function(self.print_func)
+		self.weight_label = (c_int*self.nr_weight)()
+		self.weight = (c_double*self.nr_weight)()
+		for i in range(self.nr_weight): 
+			self.weight[i] = weight[i]
+			self.weight_label[i] = weight_label[i]
+
+		if self.eps == float('inf'):
+			if self.solver_type in [L2R_LR, L2R_L2LOSS_SVC]:
+				self.eps = 0.01
+			elif self.solver_type in [L2R_L2LOSS_SVR]:
+				self.eps = 0.001
+			elif self.solver_type in [L2R_L2LOSS_SVC_DUAL, L2R_L1LOSS_SVC_DUAL, MCSVM_CS, L2R_LR_DUAL]:
+				self.eps = 0.1
+			elif self.solver_type in [L1R_L2LOSS_SVC, L1R_LR]:
+				self.eps = 0.01
+			elif self.solver_type in [L2R_L2LOSS_SVR_DUAL, L2R_L1LOSS_SVR_DUAL]:
+				self.eps = 0.1
+
+class model(Structure):
+	_names = ["param", "nr_class", "nr_feature", "w", "label", "bias"]
+	_types = [parameter, c_int, c_int, POINTER(c_double), POINTER(c_int), c_double]
+	_fields_ = genFields(_names, _types)
+
+	def __init__(self):
+		self.__createfrom__ = 'python'
+
+	def __del__(self):
+		# free memory created by C to avoid memory leak
+		if hasattr(self, '__createfrom__') and self.__createfrom__ == 'C':
+			liblinear.free_and_destroy_model(pointer(self))
+
+	def get_nr_feature(self):
+		return liblinear.get_nr_feature(self)
+
+	def get_nr_class(self):
+		return liblinear.get_nr_class(self)
+
+	def get_labels(self):
+		nr_class = self.get_nr_class()
+		labels = (c_int * nr_class)()
+		liblinear.get_labels(self, labels)
+		return labels[:nr_class]
+
+	def is_probability_model(self):
+		return (liblinear.check_probability_model(self) == 1)
+
+def toPyModel(model_ptr):
+	"""
+	toPyModel(model_ptr) -> model
+
+	Convert a ctypes POINTER(model) to a Python model
+	"""
+	if bool(model_ptr) == False:
+		raise ValueError("Null pointer")
+	m = model_ptr.contents
+	m.__createfrom__ = 'C'
+	return m
+
+fillprototype(liblinear.train, POINTER(model), [POINTER(problem), POINTER(parameter)])
+fillprototype(liblinear.cross_validation, None, [POINTER(problem), POINTER(parameter), c_int, POINTER(c_double)])
+
+fillprototype(liblinear.predict_values, c_double, [POINTER(model), POINTER(feature_node), POINTER(c_double)])
+fillprototype(liblinear.predict, c_double, [POINTER(model), POINTER(feature_node)])
+fillprototype(liblinear.predict_probability, c_double, [POINTER(model), POINTER(feature_node), POINTER(c_double)])
+
+fillprototype(liblinear.save_model, c_int, [c_char_p, POINTER(model)])
+fillprototype(liblinear.load_model, POINTER(model), [c_char_p])
+
+fillprototype(liblinear.get_nr_feature, c_int, [POINTER(model)])
+fillprototype(liblinear.get_nr_class, c_int, [POINTER(model)])
+fillprototype(liblinear.get_labels, None, [POINTER(model), POINTER(c_int)])
+
+fillprototype(liblinear.free_model_content, None, [POINTER(model)])
+fillprototype(liblinear.free_and_destroy_model, None, [POINTER(POINTER(model))])
+fillprototype(liblinear.destroy_param, None, [POINTER(parameter)])
+fillprototype(liblinear.check_parameter, c_char_p, [POINTER(problem), POINTER(parameter)])
+fillprototype(liblinear.check_probability_model, c_int, [POINTER(model)])
+fillprototype(liblinear.set_print_string_function, None, [CFUNCTYPE(None, c_char_p)])