Merge pull request #2579 from iglesias/clean_sgvector

Substitute randperm in SGVector for permute in Math.

examples/undocumented/libshogun/features_subset_labels.cpp

@@ -38,8 +38,9 @@ void test()
 	SGVector<float64_t>::display_vector(labels_data.vector, labels_data.vlen, "labels");
 
 	/* create subset indices */
-	SGVector<index_t> subset_idx(SGVector<index_t>::randperm(num_subset_idx),
-			num_subset_idx);
+	SGVector<index_t> subset_idx(num_subset_idx);
+	subset_idx.range_fill();
+	CMath::permute(subset_idx);
 
 	/* print subset indices */
 	SGVector<index_t>::display_vector(subset_idx.vector, subset_idx.vlen, "subset indices");

examples/undocumented/libshogun/features_subset_simple_features.cpp

@@ -11,6 +11,7 @@
 #include <shogun/base/init.h>
 #include <shogun/features/DenseFeatures.h>
 #include <shogun/features/Subset.h>
+#include <shogun/mathematics/Math.h>
 
 using namespace shogun;
 
@@ -69,8 +70,9 @@ void test()
 			"feature matrix");
 
 	/* create subset indices */
-	SGVector<index_t> subset_idx(SGVector<index_t>::randperm(num_subset_idx),
-			num_subset_idx);
+	SGVector<index_t> subset_idx(num_subset_idx);
+	subset_idx.range_fill();
+	CMath::permute(subset_idx);
 
 	/* print subset indices */
 	SGVector<index_t>::display_vector(subset_idx.vector, subset_idx.vlen, "subset indices");

examples/undocumented/libshogun/kernel_custom.cpp

@@ -13,6 +13,7 @@
 #include <shogun/features/DenseFeatures.h>
 #include <shogun/features/DataGenerator.h>
 #include <shogun/features/IndexFeatures.h>
+#include <shogun/mathematics/Math.h>
 
 using namespace shogun;
 
@@ -36,7 +37,7 @@ void test_custom_kernel_subsets()
 	for (index_t run=0; run<100; ++run)
 	{
 		subset.range_fill();
-		subset.permute();
+		CMath::permute(subset);
 //		subset.display_vector("permutation");
 		features->add_subset(subset);
 		k->init(features, features);

examples/undocumented/libshogun/kernel_custom_index.cpp

@@ -58,9 +58,9 @@ void test_custom_kernel_index_subsets()
 	SGVector<index_t> row_subset(num_sub_row);
 	SGVector<index_t> col_subset(num_sub_col);
 	row_subset.range_fill();
-	row_subset.permute();
+	CMath::permute(row_subset);
 	col_subset.range_fill();
-	col_subset.permute();
+	CMath::permute(col_subset);
 
 	/* create index features */
 	CIndexFeatures* row_idx_feat=new CIndexFeatures(row_subset);

examples/undocumented/libshogun/kernel_custom_kernel.cpp

@@ -35,7 +35,7 @@ void test_custom_kernel_subsets()
 	for (index_t run=0; run<100; ++run)
 	{
 		subset.range_fill();
-		subset.permute();
+		CMath::permute(subset);
 //		subset.display_vector("permutation");
 		features->add_subset(subset);
 		k->init(features, features);

examples/undocumented/libshogun/statistics_quadratic_time_mmd.cpp

@@ -97,7 +97,7 @@ void quadratic_time_mmd()
 	for (index_t i=0; i<num_trials; ++i)
 	{
 		/* this effectively means that p=q - rejecting is tpye I error */
-		inds.permute();
+		CMath::permute(inds);
 		precomputed->add_row_subset(inds);
 		precomputed->add_col_subset(inds);
 		type_I_errors[i]=mmd->perform_test()>alpha;

src/shogun/evaluation/CrossValidationSplitting.cpp

@@ -35,7 +35,7 @@ void CCrossValidationSplitting::build_subsets()
 	/* permute indices */
 	SGVector<index_t> indices(m_labels->get_num_labels());
 	indices.range_fill();
-	indices.permute(m_rng);
+	CMath::permute(indices, m_rng);
 
 	index_t num_subsets=m_subset_indices->get_num_elements();
 

src/shogun/lib/SGVector.cpp

@@ -185,14 +185,6 @@ void SGVector<T>::random(T min_value, T max_value)
 
 COMPLEX128_ERROR_TWOARGS(random)
 
-template<class T>
-void SGVector<T>::randperm()
-{
-	randperm(vector, vlen);
-}
-
-COMPLEX128_ERROR_NOARG(randperm)
-
 template <class T>
 void SGVector<T>::qsort()
 {
@@ -689,88 +681,6 @@ void SGVector<complex128_t>::random_vector(complex128_t* vec, int32_t len,
 	SG_SNOTIMPLEMENTED
 }
 
-template <class T>
-SGVector<T> SGVector<T>::randperm_vec(int32_t n)
-{
-	return SGVector<T>(randperm(n), n);
-}
-
-template <>
-SGVector<complex128_t> SGVector<complex128_t>::randperm_vec(int32_t n)
-{
-	SG_SNOTIMPLEMENTED
-	SGVector<complex128_t> perm(n);
-	return perm;
-}
-
-template <class T>
-T* SGVector<T>::randperm(int32_t n)
-{
-	T* perm = SG_MALLOC(T, n);
-	randperm(perm, n);
-
-	return perm;
-}
-
-template <>
-complex128_t* SGVector<complex128_t>::randperm(int32_t n)
-{
-	SG_SNOTIMPLEMENTED
-	SGVector<complex128_t> perm(n);
-	return perm.vector;
-}
-
-template <class T>
-void SGVector<T>::randperm(T* perm, int32_t n)
-{
-	for (int32_t i = 0; i < n; i++)
-		perm[i] = i;
-	permute(perm,n);
-}
-
-template <>
-void SGVector<complex128_t>::randperm(complex128_t* perm, int32_t n)
-{
-	SG_SNOTIMPLEMENTED
-}
-
-/** permute */
-template <class T>
-void SGVector<T>::permute(T* vec, int32_t n)
-{
-	for (int32_t i = 0; i < n; i++)
-		CMath::swap(vec[i], vec[CMath::random(i, n-1)]);
-}
-
-template <class T>
-void SGVector<T>::permute(T* vec, int32_t n, CRandom * rand)
-{
-	for (int32_t i = 0; i < n; i++)
-		CMath::swap(vec[i], vec[rand->random(i, n-1)]);
-}
-
-template<class T>
-void SGVector<T>::permute()
-{
-	SGVector<T>::permute(vector, vlen);
-}
-
-template<class T>
-void SGVector<T>::permute(CRandom * rand)
-{
-        SGVector<T>::permute(vector, vlen, rand);
-}
-
-template <class T>
-void SGVector<T>::permute_vector(SGVector<T> vec)
-{
-	for (index_t i=0; i<vec.vlen; ++i)
-	{
-		CMath::swap(vec.vector[i],
-				vec.vector[CMath::random(i, vec.vlen-1)]);
-	}
-}
-
 template <>
 bool SGVector<bool>::twonorm(const bool* x, int32_t len)
 {

src/shogun/lib/SGVector.h

@@ -116,20 +116,6 @@ template<class T> class SGVector : public SGReferencedData
 		 */
 		void random(T min_value, T max_value);
 
-		/** Returns a random permutation of number from 0 to len-1 */
-		void randperm();
-
-		/** Returns a random permutation of number from 0 to n-1 */
-		static SGVector<T> randperm_vec(int32_t n);
-
-		/** Returns a random permutation of number from 0 to n-1.
-		 * Caller has to free memory.
-		 *
-		 * @param n range of permutation
-		 * @return random permutation of number from 0 to n-1
-		 */
-		static T* randperm(int32_t n);
-
 		/** Returns a vector with n linearly spaced elements between start and end.
 		 *
 		 * @param start beginning of the interval to divide
@@ -190,15 +176,6 @@ template<class T> class SGVector : public SGReferencedData
 		/** Random vector */
 		static void random_vector(T* vec, int32_t len, T min_value, T max_value);
 
-		/** Random permatutaion */
-		static void randperm(T* perm, int32_t n);
-
-		/** Permute */
-		static void permute(T* vec, int32_t n);
-
-		/** Permute with given CRandom state */
-		static void permute(T* vec, int32_t n, CRandom * rand);
-
 		/**
 		 * Get the vector (no copying is done here)
 		 *
@@ -353,15 +330,6 @@ template<class T> class SGVector : public SGReferencedData
 		 */
 		bool equals(SGVector<T>& other);
 
-		/** Permute vector */
-		static void permute_vector(SGVector<T> vec);
-
-		/** Create a random permutation in place */
-		void permute();
-
-		/** Create a random permutation with given CRandom state */
-		void permute(CRandom * rand);
-
 		/// || x ||_2
 		static T twonorm(const T* x, int32_t len);
 

src/shogun/machine/StochasticGBMachine.cpp

@@ -30,6 +30,7 @@
 
 #include <shogun/machine/StochasticGBMachine.h>
 #include <shogun/optimization/lbfgs/lbfgs.h>
+#include <shogun/mathematics/Math.h>
 
 using namespace shogun;
 
@@ -275,8 +276,8 @@ void CStochasticGBMachine::apply_subset(CDenseFeatures<float64_t>* f, CLabels* i
 {
 	int32_t subset_size=m_subset_frac*(f->get_num_vectors());
 	SGVector<index_t> idx(f->get_num_vectors());
-	idx.range_fill(0);
-	idx.randperm();
+	idx.range_fill();
+	CMath::permute(idx);
 
 	SGVector<index_t> subset(subset_size);
 	memcpy(subset.vector,idx.vector,subset.vlen*sizeof(index_t));

src/shogun/machine/gp/EPInferenceMethod.cpp

@@ -169,7 +169,8 @@ void CEPInferenceMethod::update()
 	}
 
 	// create vector of the random permutation
-	SGVector<index_t> randperm=SGVector<index_t>::randperm_vec(n);
+	SGVector<index_t> v(n);
+	v.range_fill();
 
 	// cavity tau and nu vectors
 	SGVector<float64_t> tau_n(n);
@@ -189,11 +190,11 @@ void CEPInferenceMethod::update()
 		sweep++;
 
 		// shuffle random permutation
-		randperm.permute();
+		CMath::permute(v);
 
 		for (index_t j=0; j<n; j++)
 		{
-			index_t i=randperm[j];
+			index_t i=v[j];
 
 			// find cavity paramters
 			tau_n[i]=1.0/m_Sigma(i,i)-m_ttau[i];

src/shogun/mathematics/Math.h

@@ -27,6 +27,7 @@
 #include <shogun/io/SGIO.h>
 #include <shogun/base/Parallel.h>
 #include <shogun/mathematics/Random.h>
+#include <shogun/lib/SGVector.h>
 
 #ifndef _USE_MATH_DEFINES
 #define _USE_MATH_DEFINES
@@ -694,6 +695,27 @@ class CMath : public CSGObject
 			return sg_rand->std_normal_distrib();
 		}
 
+		/** Permute randomly the elements of the vector. If provided, use the
+		 *  random object to generate the permutations.
+		 *
+		 * @param v the vector to permute.
+		 * @param rand random object that might be used to generate the permutations.
+		 */
+		template <class T>
+			static void permute(SGVector<T> v, CRandom* rand=NULL)
+			{
+				if (rand)
+				{
+					for (index_t i=0; i<v.vlen; ++i)
+						swap(v[i], v[rand->random(i, v.vlen-1)]);
+				}
+				else
+				{
+					for (index_t i=0; i<v.vlen; ++i)
+						swap(v[i], v[random(i, v.vlen-1)]);
+				}
+			}
+
 		template <class T>
 			static int32_t get_num_nonzero(T* vec, int32_t len)
 			{
@@ -1659,9 +1681,9 @@ void CMath::nmin(float64_t* output, T* index, int32_t size, int32_t n)
 {
 	if (6*n*size<13*size*CMath::log(size))
 		for (int32_t i=0; i<n; i++)
-			min(&output[i], &index[i], size-i) ;
+			min(&output[i], &index[i], size-i);
 	else
-		qsort_index(output, index, size) ;
+		qsort_index(output, index, size);
 }
 
 /* move the smallest entry in the array to the beginning */

src/shogun/multiclass/tree/RandomCARTree.cpp

@@ -28,8 +28,8 @@
  * either expressed or implied, of the Shogun Development Team.
  */
 
-#include <shogun/mathematics/Math.h>
 #include <shogun/multiclass/tree/RandomCARTree.h>
+#include <shogun/mathematics/Math.h>
 
 using namespace shogun;
 
@@ -95,8 +95,8 @@ int32_t CRandomCARTree::compute_best_attribute(SGMatrix<float64_t> mat, SGVector
 	// randomly choose w/o replacement the attributes from which best will be chosen
 	// randomly permute and choose 1st randsubset_size elements
 	SGVector<index_t> idx(num_feats);
-	idx.range_fill(0);
-	idx.randperm();
+	idx.range_fill();
+	CMath::permute(idx);
 
 	float64_t max_gain=MIN_SPLIT_GAIN;
 	int32_t best_attribute=-1;

src/shogun/statistics/IndependenceTest.cpp

@@ -90,7 +90,7 @@ SGVector<float64_t> CIndependenceTest::sample_null()
 		 * and compute statistic. This is done using subsets here */
 
 		/* create index permutation and add as subset to features from p */
-		SGVector<index_t>::permute_vector(ind_permutation);
+		CMath::permute(ind_permutation);
 
 		/* compute statistic for this permutation of mixed samples */
 		m_p->add_subset(ind_permutation);

src/shogun/statistics/KernelIndependenceTest.cpp

@@ -33,6 +33,7 @@
 #include <shogun/features/Features.h>
 #include <shogun/kernel/Kernel.h>
 #include <shogun/kernel/CustomKernel.h>
+#include <shogun/mathematics/Math.h>
 
 using namespace shogun;
 
@@ -102,7 +103,7 @@ SGVector<float64_t> CKernelIndependenceTest::sample_null()
 			 * and compute statistic. This is done using subsets here. add to
 			 * custom kernel since it has no features to subset. CustomKernel
 			 * has not to be re-initialised after each subset setting */
-			SGVector<index_t>::permute_vector(ind_permutation);
+			CMath::permute(ind_permutation);
 
 			custom_kernel_p->add_row_subset(ind_permutation);
 			custom_kernel_p->add_col_subset(ind_permutation);

src/shogun/statistics/KernelTwoSampleTest.cpp

@@ -11,6 +11,7 @@
 #include <shogun/features/Features.h>
 #include <shogun/kernel/Kernel.h>
 #include <shogun/kernel/CustomKernel.h>
+#include <shogun/mathematics/Math.h>
 
 using namespace shogun;
 
@@ -91,7 +92,7 @@ SGVector<float64_t> CKernelTwoSampleTest::sample_null()
 			 * This is done using subsets here. add to custom kernel since
 			 * it has no features to subset. CustomKernel has not to be
 			 * re-initialised after each subset setting */
-			SGVector<int32_t>::permute_vector(ind_permutation);
+			CMath::permute(ind_permutation);
 
 			custom_kernel->add_row_subset(ind_permutation);
 			custom_kernel->add_col_subset(ind_permutation);