Merge pull request #668 from karlnapf/master

new data generator class to generate example data
shogun-toolbox · Jul 22, 2012 · 8e101b7 · 8e101b7
2 parents 9bef2a5 + 1b70388
commit 8e101b7
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Showing 5 changed files with 121 additions and 22 deletions.
diff --git a/examples/undocumented/libshogun/statistics_quadratic_time_mmd.cpp b/examples/undocumented/libshogun/statistics_quadratic_time_mmd.cpp
@@ -12,25 +12,10 @@
 #include <shogun/kernel/GaussianKernel.h>
 #include <shogun/features/DenseFeatures.h>
 #include <shogun/mathematics/Statistics.h>
+#include <shogun/features/DataGenerator.h>
 
 using namespace shogun;
 
-
-void create_mean_data(SGMatrix<float64_t> target, float64_t difference)
-{
-	/* create data matrix for P and Q. P is a standard normal, Q is the same but
-	 * has a mean difference in one dimension */
-	for (index_t i=0; i<target.num_rows; ++i)
-	{
-		for (index_t j=0; j<target.num_cols/2; ++j)
-			target(i,j)=CMath::randn_double();
-
-		/* add mean difference in first dimension of second half of data */
-		for (index_t j=target.num_cols/2; j<target.num_cols; ++j)
-				target(i,j)=CMath::randn_double() + (i==0 ? difference : 0);
-	}
-}
-
 /** tests the quadratic mmd statistic for a single data case and ensures
  * equality with matlab implementation */
 void test_quadratic_mmd_fixed()
@@ -73,8 +58,8 @@ void test_quadratic_mmd_bootstrap()
 	index_t num_iterations=1000;
 	num_iterations=10; //speed up
 
-	SGMatrix<float64_t> data(dimension, 2*m);
-	create_mean_data(data, difference);
+	SGMatrix<float64_t> data=CDataGenerator::generate_mean_data(m, dimension,
+			difference);
 	CDenseFeatures<float64_t>* features=new CDenseFeatures<float64_t>(data);
 
 	/* shoguns kernel width is different */
@@ -112,8 +97,8 @@ void test_quadratic_mmd_spectrum()
 	float64_t difference=0.5;
 	float64_t sigma=2;
 
-	SGMatrix<float64_t> data(dimension, 2*m);
-	create_mean_data(data, difference);
+	SGMatrix<float64_t> data=CDataGenerator::generate_mean_data(m, dimension,
+			difference);
 
 	CDenseFeatures<float64_t>* features=new CDenseFeatures<float64_t>(data);
 
@@ -185,8 +170,8 @@ void test_quadratic_mmd_random()
 	num_runs=10; //speed up
 	SGVector<float64_t> mmds(num_runs);
 
+	/* pre-allocate data matrix and features, just change elements later */
 	SGMatrix<float64_t> data(dimension, 2*m);
-
 	CDenseFeatures<float64_t>* features=new CDenseFeatures<float64_t>(data);
 
 	/* shoguns kernel width is different */
@@ -195,7 +180,9 @@ void test_quadratic_mmd_random()
 	mmd->set_statistic_type(UNBIASED);
 	for (index_t i=0; i<num_runs; ++i)
 	{
-		create_mean_data(data, difference);
+		/* use pre-allocated space for data generation */
+		CDataGenerator::generate_mean_data(m, dimension,
+					difference, data.matrix);
 		kernel->init(features, features);
 		mmds[i]=mmd->compute_statistic();
 	}

diff --git a/src/interfaces/modular/Features.i b/src/interfaces/modular/Features.i
@@ -63,6 +63,7 @@
 %rename(LBPPyrDotFeatures) CLBPPyrDotFeatures;
 %rename(ExplicitSpecFeatures) CExplicitSpecFeatures;
 %rename(ImplicitWeightedSpecFeatures) CImplicitWeightedSpecFeatures;
+%rename(DataGenerator) CDataGenerator;
 
 /* Include Class Headers to make them visible from within the target language */
 %include <shogun/features/FeatureTypes.h>
@@ -75,6 +76,7 @@
 %include <shogun/features/StreamingFeatures.h>
 %include <shogun/features/StreamingDotFeatures.h>
 %include <shogun/features/StreamingVwFeatures.h>
+%include <shogun/features/DataGenerator.h>
 
 /* Templated Class StringFeatures */
 %include <shogun/features/StringFeatures.h>

diff --git a/src/interfaces/modular/Features_includes.i b/src/interfaces/modular/Features_includes.i
@@ -40,4 +40,5 @@
 #include <shogun/features/LBPPyrDotFeatures.h>
 #include <shogun/features/ExplicitSpecFeatures.h>
 #include <shogun/features/ImplicitWeightedSpecFeatures.h>
+#include <shogun/features/DataGenerator.h>
 %}
diff --git a/src/shogun/features/DataGenerator.cpp b/src/shogun/features/DataGenerator.cpp
@@ -0,0 +1,56 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Written (W) 2012 Heiko Strathmann
+ */
+
+#include <shogun/features/DataGenerator.h>
+#include <shogun/mathematics/Math.h>
+
+using namespace shogun;
+
+CDataGenerator::CDataGenerator() : CSGObject()
+{
+	init();
+}
+
+CDataGenerator::~CDataGenerator()
+{
+
+}
+
+void CDataGenerator::init()
+{
+}
+
+SGMatrix<float64_t> CDataGenerator::generate_mean_data(index_t m,
+		index_t dim, float64_t mean_shift, float64_t* target_data)
+{
+	/* evtl use pre-allocated space */
+	SGMatrix<float64_t> result;
+
+	if (target_data)
+	{
+		result.matrix=target_data;
+		result.num_rows=dim;
+		result.num_cols=2*m;
+	}
+	else
+		result=SGMatrix<float64_t>(dim, 2*m);
+
+	/* fill matrix with normal data */
+	for (index_t i=0; i<2*m; ++i)
+	{
+		for (index_t j=0; j<dim; ++j)
+			result(j,i)=CMath::randn_double();
+
+		/* mean shift for second half */
+		if (i>=m)
+			result(0,i)+=mean_shift;
+	}
+
+	return result;
+}
diff --git a/src/shogun/features/DataGenerator.h b/src/shogun/features/DataGenerator.h
@@ -0,0 +1,53 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Written (W) 2012 Heiko Strathmann
+ */
+
+#ifndef __DATAGENERATOR_H_
+#define __DATAGENERATOR_H_
+
+#include <shogun/base/SGObject.h>
+#include <shogun/lib/SGMatrix.h>
+
+namespace shogun
+{
+
+/** @brief Class that is able to generate various data samples, which may be
+ * used for examples in SHOGUN.
+ */
+class CDataGenerator: public CSGObject
+{
+public:
+	CDataGenerator();
+
+	virtual ~CDataGenerator();
+
+	/** Takes each m samples from two distributions p and q, where each element
+	 * is standard normally distributed, except for the first dimension of q,
+	 * where the mean is shifted by a specified value.
+	 *
+	 * @param m number of samples to generate
+	 * @param dim dimension of generated samples
+	 * @param mean_shift is added mean of first dimension
+	 * @target_data if non-NULL then this is used as matrix data storage. Make
+	 * sure that its dimensions fit
+	 * @return matrix with concatenated samples,first p then q
+	 */
+	static SGMatrix<float64_t> generate_mean_data(index_t m, index_t dim,
+			float64_t mean_shift, float64_t* target_data=NULL);
+
+	inline virtual const char* get_name() const { return "DataGenerator"; }
+
+private:
+	/** registers all parameters and initializes variables with defaults */
+	void init();
+
+};
+
+}
+
+#endif /* __DATAGENERATOR_H_ */