factories are factories

they are always gonna love :)

examples/meta/src/evaluation/cross_validation_multiple_kernel_learning_weights_storage.sg

@@ -21,8 +21,8 @@ combined_kernel.add("kernel_array", k_3)
 #![create_kernels]
 
 #![create_classifier]
-SVM libsvm = as_svm(machine("LibSVM"))
-Machine svm = machine("MKLClassification", kernel=combined_kernel, interleaved_optimization=False, svm=libsvm)
+SVM libsvm = machine("LibSVM")
+Machine svm = machine("MKLClassification", kernel=combined_kernel, interleaved_optimization=False, svm=as_svm(libsvm))
 #![create_classifier]
 
 #![create_cross_validation]

examples/meta/src/regression/multiple_kernel_learning.sg

@@ -25,8 +25,8 @@ combined_kernel.init(features_train, features_train)
 #![create_combined_train]
 
 #![train_mkl]
-SVM binary_svm_solver = as_svm(machine("SVRLight"))
-Machine mkl = machine("MKLRegression", svm=binary_svm_solver, kernel=combined_kernel, labels=labels_train)
+SVM binary_svm_solver = machine("SVRLight")
+Machine mkl = machine("MKLRegression", svm=as_svm(binary_svm_solver), kernel=combined_kernel, labels=labels_train)
 mkl.train()
 #![train_mkl]
 

src/interfaces/swig/factory.i

@@ -1,3 +1,28 @@
+%newobject shogun::distance(std::string name);
+%newobject shogun::evaluation(const std::string& name);
+%newobject shogun::kernel(const std::string& name);
+%newobject shogun::machine(const std::string& name);
+%newobject shogun::multiclass_strategy(const std::string& name);
+%newobject shogun::ecoc_encoder(const std::string& name);
+%newobject shogun::ecoc_decoder(const std::string& name);
+%newobject shogun::transformer(const std::string& name);
+%newobject shogun::layer(const std::string& name);
+%newobject shogun::splitting_strategy(const std::string& name);
+%newobject shogun::machine_evaluation(const std::string& name);
+%newobject shogun::svm(const std::string& name);
+%newobject shogun::features;
+%newobject shogun::gp_likelihood(const std::string& name);
+%newobject shogun::gp_mean(const std::string& name);
+%newobject shogun::differentiable(const std::string& name);
+%newobject shogun::gp_inference(const std::string& name);
+%newobject shogun::loss(const std::string& name);
+%newobject shogun::string_features(CFile*, EAlphabet alpha = DNA, EPrimitiveType primitive_type = PT_CHAR);
+%newobject shogun::transformer(const std::string&);
+%newobject shogun::csv_file(std::string fname, char rw);
+%newobject shogun::libsvm_file(std::string fname, char rw);
+%newobject shogun::pipeline;
+%newobject shogun::labels;
+
 %{
     #include <shogun/util/factory.h>
 %}
@@ -10,9 +35,3 @@
 #endif //SWIGJAVA
 
 %template(labels) shogun::labels<float64_t>;
-
-%newobject shogun::features(CFile*, EPrimitiveType primitive_type);
-%newobject shogun::string_features(CFile*, EAlphabet alpha = DNA, EPrimitiveType primitive_type = PT_CHAR);
-%newobject shogun::transformer(const std::string&);
-%newobject shogun::csv_file(std::string fname, char rw);
-%newobject shogun::libsvm_file(std::string fname, char rw);

src/shogun/base/class_list.h

@@ -60,8 +60,6 @@ namespace shogun {
 			delete_object(object);
 			throw e;
 		}
-
-		cast->ref();
 		return cast;
 	}
 

src/shogun/clustering/KMeansMiniBatch.cpp

@@ -68,7 +68,7 @@ void CKMeansMiniBatch::minibatch_KMeans()
 
 	CDenseFeatures<float64_t>* lhs=
 		distance->get_lhs()->as<CDenseFeatures<float64_t>>();
-	CDenseFeatures<float64_t>* rhs_mus=new CDenseFeatures<float64_t>(mus);
+	auto rhs_mus=some<CDenseFeatures<float64_t>>(mus);
 	CFeatures* rhs_cache=distance->replace_rhs(rhs_mus);
 	int32_t XSize=lhs->get_num_vectors();
 	int32_t dims=lhs->get_num_features();
@@ -113,7 +113,6 @@ void CKMeansMiniBatch::minibatch_KMeans()
 	}
 	SG_UNREF(lhs);
 	distance->replace_rhs(rhs_cache);
-	delete rhs_mus;
 }
 
 SGVector<int32_t> CKMeansMiniBatch::mbchoose_rand(int32_t b, int32_t num)

src/shogun/converter/ica/FFSep.cpp

@@ -55,7 +55,6 @@ SGNDArray<float64_t> CFFSep::get_covs() const
 void CFFSep::fit_dense(CDenseFeatures<float64_t>* features)
 {
 	ASSERT(features);
-	SG_REF(features);
 
 	auto X = features->get_feature_matrix();
 

src/shogun/converter/ica/ICAConverter.cpp

@@ -72,19 +72,13 @@ void CICAConverter::fit(CFeatures* features)
 	    features->get_feature_type() == F_DREAL,
 	    "ICA converters only work with real features\n");
 
-	SG_REF(features);
-
 	fit_dense(static_cast<CDenseFeatures<float64_t>*>(features));
-
-	SG_UNREF(features);
 }
 
 CFeatures* CICAConverter::transform(CFeatures* features, bool inplace)
 {
 	REQUIRE(m_mixing_matrix.matrix, "ICAConverter has not been fitted.\n");
 
-	SG_REF(features);
-
 	auto X = features->as<CDenseFeatures<float64_t>>()->get_feature_matrix();
 	if (!inplace)
 		X = X.clone();
@@ -97,26 +91,18 @@ CFeatures* CICAConverter::transform(CFeatures* features, bool inplace)
 	// Unmix
 	EX = C.inverse() * EX;
 
-	auto processed = new CDenseFeatures<float64_t>(X);
-	SG_UNREF(features);
-
-	return processed;
+	return new CDenseFeatures<float64_t>(X);
 }
 
 CFeatures* CICAConverter::inverse_transform(CFeatures* features, bool inplace)
 {
 	REQUIRE(m_mixing_matrix.matrix, "ICAConverter has not been fitted.\n");
 
-	SG_REF(features);
-
 	auto X = features->as<CDenseFeatures<float64_t>>()->get_feature_matrix();
 	if (!inplace)
 		X = X.clone();
 
 	linalg::matrix_prod(m_mixing_matrix, X, X);
 
-	auto processed = new CDenseFeatures<float64_t>(X);
-	SG_UNREF(features);
-
-	return processed;
+	return new CDenseFeatures<float64_t>(X);
 }

src/shogun/converter/ica/Jade.cpp

@@ -43,7 +43,6 @@ SGMatrix<float64_t> CJade::get_cumulant_matrix() const
 void CJade::fit_dense(CDenseFeatures<float64_t>* features)
 {
 	ASSERT(features);
-	SG_REF(features);
 
 	auto X = features->get_feature_matrix();
 

src/shogun/kernel/GaussianKernel.cpp

@@ -79,8 +79,7 @@ void CGaussianKernel::cleanup()
 bool CGaussianKernel::init(CFeatures* l, CFeatures* r)
 {
 	cleanup();
-	CShiftInvariantKernel::init(l, r);
-	return init_normalizer();
+	return CShiftInvariantKernel::init(l, r);
 }
 
 void CGaussianKernel::set_width(float64_t w)

src/shogun/kernel/Kernel.cpp

@@ -90,10 +90,6 @@ void CKernel::resize_kernel_cache(KERNELCACHE_IDX size, bool regression_hack)
 
 bool CKernel::init(CFeatures* l, CFeatures* r)
 {
-	/* make sure that features are not deleted if same ones are used */
-	SG_REF(l);
-	SG_REF(r);
-
 	//make sure features were indeed supplied
 	REQUIRE(l, "CKernel::init(%p, %p): Left hand side features required!\n", l, r)
 	REQUIRE(r, "CKernel::init(%p, %p): Right hand side features required!\n", l, r)
@@ -116,7 +112,6 @@ bool CKernel::init(CFeatures* l, CFeatures* r)
 	//remove references to previous features
 	remove_lhs_and_rhs();
 
-	//increase reference counts
 	SG_REF(l);
 	if (l==r)
 		lhs_equals_rhs=true;
@@ -132,10 +127,6 @@ bool CKernel::init(CFeatures* l, CFeatures* r)
 	num_lhs=l->get_num_vectors();
 	num_rhs=r->get_num_vectors();
 
-	/* unref "safety" refs from beginning */
-	SG_UNREF(r);
-	SG_UNREF(l);
-
 	SG_DEBUG("leaving CKernel::init(%p, %p)\n", l, r)
 	return true;
 }

src/shogun/machine/GaussianProcessMachine.cpp

@@ -151,8 +151,6 @@ SGVector<float64_t> CGaussianProcessMachine::get_posterior_variances(
 	else
 		feat=m_method->get_features();
 
-	SG_REF(data);
-
 	// get kernel and compute kernel matrix: K(data, data)*scale^2
 	CKernel* training_kernel=m_method->get_kernel();
 	CKernel* kernel = training_kernel->clone()->as<CKernel>();
@@ -179,7 +177,6 @@ SGVector<float64_t> CGaussianProcessMachine::get_posterior_variances(
 	// cleanup
 	SG_UNREF(kernel);
 	SG_UNREF(feat);
-	SG_UNREF(data);
 
 	// get shogun representation of cholesky and create eigen representation
 	SGMatrix<float64_t> L=m_method->get_cholesky();

src/shogun/machine/Pipeline.cpp

@@ -130,42 +130,43 @@ namespace shogun
 		{
 			REQUIRE(m_labels, "No labels given.\n");
 		}
-
+		auto current_data = data;
 		for (auto&& stage : m_stages)
 		{
 			if (holds_alternative<CTransformer*>(stage.second))
 			{
 				auto transformer = shogun::get<CTransformer*>(stage.second);
 				transformer->train_require_labels()
-				    ? transformer->fit(data, m_labels)
-				    : transformer->fit(data);
+				    ? transformer->fit(current_data, m_labels)
+				    : transformer->fit(current_data);
 
-				data = transformer->transform(data);
+				current_data = wrap(transformer->transform(current_data));
 			}
 			else
 			{
 				auto machine = shogun::get<CMachine*>(stage.second);
 				if (machine->train_require_labels())
 					machine->set_labels(m_labels);
-				machine->train(data);
+				machine->train(current_data);
 			}
 		}
 		return true;
 	}
 
 	CLabels* CPipeline::apply(CFeatures* data)
 	{
+		auto current_data = wrap(data);
 		for (auto&& stage : m_stages)
 		{
 			if (holds_alternative<CTransformer*>(stage.second))
 			{
 				auto transformer = shogun::get<CTransformer*>(stage.second);
-				data = transformer->transform(data);
+				current_data = wrap(transformer->transform(current_data));
 			}
 			else
 			{
 				auto machine = shogun::get<CMachine*>(stage.second);
-				return machine->apply(data);
+				return machine->apply(current_data);
 			}
 		}
 

src/shogun/multiclass/ShareBoost.cpp

@@ -1,7 +1,7 @@
 /*
  * This software is distributed under BSD 3-clause license (see LICENSE file).
  *
- * Authors: Chiyuan Zhang, Soeren Sonnenburg, Pan Deng, Bjoern Esser, 
+ * Authors: Chiyuan Zhang, Soeren Sonnenburg, Pan Deng, Bjoern Esser,
  *          Sanuj Sharma
  */
 
@@ -110,7 +110,6 @@ void CShareBoost::compute_pred()
 {
 	CDenseFeatures<float64_t> *fea = dynamic_cast<CDenseFeatures<float64_t> *>(m_features);
 	CDenseSubsetFeatures<float64_t> *subset_fea = new CDenseSubsetFeatures<float64_t>(fea, m_activeset);
-	SG_REF(subset_fea);
 	for (int32_t i=0; i < m_multiclass_strategy->get_num_classes(); ++i)
 	{
 		CLinearMachine *machine = dynamic_cast<CLinearMachine *>(m_machines->get_element(i));
@@ -120,7 +119,6 @@ void CShareBoost::compute_pred()
 		SG_UNREF(machine);
 		SG_UNREF(lab);
 	}
-	SG_UNREF(subset_fea);
 }
 
 void CShareBoost::compute_pred(const float64_t *W)

src/shogun/preprocessor/DensePreprocessor.cpp

@@ -92,15 +92,11 @@ CFeatures* CDensePreprocessor<ST>::transform(CFeatures* features, bool inplace)
 			"has to be of C_DENSE (%d) class!\n",
 			features->get_feature_class(), C_DENSE);
 
-	SG_REF(features);
 	auto matrix = features->as<CDenseFeatures<ST>>()->get_feature_matrix();
 	if (!inplace)
 		matrix = matrix.clone();
 	auto feat_matrix = apply_to_matrix(matrix);
-	auto preprocessed = new CDenseFeatures<ST>(feat_matrix);
-
-	SG_UNREF(features);
-	return preprocessed;
+	return new CDenseFeatures<ST>(feat_matrix);
 }
 
 template <class ST>
@@ -113,15 +109,11 @@ CDensePreprocessor<ST>::inverse_transform(CFeatures* features, bool inplace)
 		"has to be of C_DENSE (%d) class!\n",
 		features->get_feature_class(), C_DENSE);
 
-	SG_REF(features);
 	auto matrix = features->as<CDenseFeatures<ST>>()->get_feature_matrix();
 	if (!inplace)
 		matrix = matrix.clone();
 	auto feat_matrix = inverse_apply_to_matrix(matrix);
-	auto preprocessed = new CDenseFeatures<ST>(feat_matrix);
-
-	SG_UNREF(features);
-	return preprocessed;
+	return new CDenseFeatures<ST>(feat_matrix);
 }
 
 template <class ST>

src/shogun/regression/GaussianProcessRegression.cpp

@@ -1,7 +1,7 @@
 /*
  * This software is distributed under BSD 3-clause license (see LICENSE file).
  *
- * Authors: Jacob Walker, Roman Votyakov, Sergey Lisitsyn, Soeren Sonnenburg, 
+ * Authors: Jacob Walker, Roman Votyakov, Sergey Lisitsyn, Soeren Sonnenburg,
  *          Heiko Strathmann, Wu Lin
  */
 
@@ -110,10 +110,8 @@ SGVector<float64_t> CGaussianProcessRegression::get_mean_vector(CFeatures* data)
 			"regression\n",	m_method->get_name(), lik->get_name())
 	SG_UNREF(lik);
 
-	SG_REF(data);
 	SGVector<float64_t> mu=get_posterior_means(data);
 	SGVector<float64_t> s2=get_posterior_variances(data);
-	SG_UNREF(data);
 
 	// evaluate mean
 	lik=m_method->get_model();
@@ -133,10 +131,8 @@ SGVector<float64_t> CGaussianProcessRegression::get_variance_vector(
 	REQUIRE(m_method->supports_regression(), "%s with %s doesn't support "
 			"regression\n",	m_method->get_name(), lik->get_name())
 
-	SG_REF(data);
 	SGVector<float64_t> mu=get_posterior_means(data);
 	SGVector<float64_t> s2=get_posterior_variances(data);
-	SG_UNREF(data);
 
 	// evaluate variance
 	s2=lik->get_predictive_variances(mu, s2);

src/shogun/solver/LDASolver.h

@@ -76,21 +76,21 @@ namespace shogun
 		    CDenseFeatures<T>* features, CMulticlassLabels* labels,
 		    float64_t gamma = 0.0)
 		{
+			SG_REF(features);
+			SG_REF(labels);
+
 			m_features = features;
 			m_labels = labels;
 			m_gamma = gamma;
 
-			SG_REF(m_features)
-			SG_REF(m_labels)
-
 			compute_means();
 			compute_within_cov();
 		}
 
 		~LDASolver()
 		{
-			SG_UNREF(m_features)
-			SG_UNREF(m_labels)
+			SG_UNREF(m_features);
+			SG_UNREF(m_labels);
 		}
 
 		/** @return the vector of classes' mean */