Introduced converters module, moved DR preprocessors to it, fixed exa…

…mples, updated other classes according to changes
shogun-toolbox · Oct 13, 2011 · 04b6de9 · 04b6de9
1 parent 78c8694
commit 04b6de9
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Showing 75 changed files with 734 additions and 736 deletions.
diff --git a/...rp_modular/preprocessor_isomap_modular.cs → ...sharp_modular/converter_isomap_modular.cs b/...rp_modular/preprocessor_isomap_modular.cs → ...sharp_modular/converter_isomap_modular.cs
@@ -1,6 +1,6 @@
 using System;
 
-public class preprocessor_classicisomap_modular {
+public class converter_classicisomap_modular {
 	public static void Main() {
 		modshogun.init_shogun_with_defaults();
 
@@ -10,7 +10,7 @@ public class preprocessor_classicisomap_modular {
 
 		Isomap preprocessor = new Isomap();
 		preprocessor.set_target_dim(1);
-		preprocessor.apply_to_feature_matrix(features);
+		preprocessor.apply(features);
 
 		modshogun.exit_shogun();
 	}

diff --git a/...ocessor_locallylinearembedding_modular.cs → ...nverter_locallylinearembedding_modular.cs b/...ocessor_locallylinearembedding_modular.cs → ...nverter_locallylinearembedding_modular.cs
@@ -1,6 +1,6 @@
 using System;
 
-public class preprocessor_locallylinearembedding_modular {
+public class converter_locallylinearembedding_modular {
 	public static void Main() {
 
 		modshogun.init_shogun_with_defaults();
@@ -10,7 +10,7 @@ public class preprocessor_locallylinearembedding_modular {
 		RealFeatures features = new RealFeatures(data);
 		LocallyLinearEmbedding preprocessor = new LocallyLinearEmbedding();
 		preprocessor.set_target_dim(1);
-		preprocessor.apply_to_feature_matrix(features);
+		preprocessor.apply(features);
 
 		modshogun.exit_shogun();
 	}

diff --git a/...cessor_multidimensionalscaling_modular.cs → ...verter_multidimensionalscaling_modular.cs b/...cessor_multidimensionalscaling_modular.cs → ...verter_multidimensionalscaling_modular.cs
@@ -1,6 +1,6 @@
 using System;
 
-public class preprocessor_multidimensionalscaling_modular {
+public class converter_multidimensionalscaling_modular {
 	public static void Main() {
 		modshogun.init_shogun_with_defaults();
 
@@ -11,7 +11,7 @@ public class preprocessor_multidimensionalscaling_modular {
 		mds.set_target_dim(1);
 		mds.set_landmark(false);
 
-		mds.apply_to_feature_matrix(features);
+		mds.apply(features);
 
 		modshogun.exit_shogun();
 	}

diff --git a/..._modular/preprocessor_isomap_modular.java → ...ava_modular/converter_isomap_modular.java b/..._modular/preprocessor_isomap_modular.java → ...ava_modular/converter_isomap_modular.java
@@ -1,7 +1,7 @@
 import org.shogun.*;
 import org.jblas.*;
 
-public class preprocessor_isomap_modular {
+public class converter_isomap_modular {
 	static {
 		System.loadLibrary("modshogun");
 	}
@@ -16,7 +16,7 @@ public static void main(String argv[]) {
 		isomap.set_target_dim(1);
 		isomap.set_k(6);
 		isomap.set_landmark(false);
-		isomap.apply_to_feature_matrix(features);
+		isomap.apply(features);
 
 		modshogun.exit_shogun();
 	}

diff --git a/...essor_locallylinearembedding_modular.java → ...nverter_locallylinearembedding_modular.py b/...essor_locallylinearembedding_modular.java → ...nverter_locallylinearembedding_modular.py
@@ -1,7 +1,7 @@
 import org.shogun.*;
 import org.jblas.*;
 
-public class preprocessor_locallylinearembedding_modular {
+public class converter_locallylinearembedding_modular {
 	static {
 		System.loadLibrary("modshogun");
 	}
@@ -14,7 +14,7 @@ public static void main(String argv[]) {
 		RealFeatures features = new RealFeatures(data);
 		LocallyLinearEmbedding preprocessor = new LocallyLinearEmbedding();
 		preprocessor.set_target_dim(1);
-		preprocessor.apply_to_feature_matrix(features);
+		preprocessor.apply(features);
 
 		modshogun.exit_shogun();
 	}

diff --git a/...ssor_multidimensionalscaling_modular.java → ...rter_multidimensionalscaling_modular.java b/...ssor_multidimensionalscaling_modular.java → ...rter_multidimensionalscaling_modular.java
@@ -1,7 +1,7 @@
 import org.shogun.*;
 import org.jblas.*;
 
-public class preprocessor_multidimensionalscaling_modular {
+public class converter_multidimensionalscaling_modular {
 	static {
 		System.loadLibrary("modshogun");
 	}
@@ -16,7 +16,7 @@ public static void main(String argv[]) {
 		mds.set_target_dim(1);
 		mds.set_landmark(false);
 
-		mds.apply_to_feature_matrix(features);
+		mds.apply(features);
 
 		modshogun.exit_shogun();
 	}

diff --git a/examples/undocumented/libshogun/Makefile b/examples/undocumented/libshogun/Makefile
@@ -38,15 +38,15 @@ TARGETS =	  basic_minimal classifier_libsvm classifier_minimal_svm \
 		  library_fibonacci_heap \
 		  library_hashset \
 		  mathematics_lapack \
-		  preprocessor_locallylinearembedding \
-		  preprocessor_localtangentspacealignment \
-		  preprocessor_hessianlocallylinearembedding \
-		  preprocessor_kernellocallylinearembedding \
-		  preprocessor_kernellocaltangentspacealignment \
-		  preprocessor_multidimensionalscaling \
-		  preprocessor_isomap \
-		  preprocessor_diffusionmaps \
-		  preprocessor_laplacianeigenmaps \
+		  converter_locallylinearembedding \
+		  converter_localtangentspacealignment \
+		  converter_hessianlocallylinearembedding \
+		  converter_kernellocallylinearembedding \
+		  converter_kernellocaltangentspacealignment \
+		  converter_multidimensionalscaling \
+		  converter_isomap \
+		  converter_diffusionmaps \
+		  converter_laplacianeigenmaps \
 
 all: $(TARGETS)
 

diff --git a/.../libshogun/preprocessor_diffusionmaps.cpp → ...ted/libshogun/converter_diffusionmaps.cpp b/.../libshogun/preprocessor_diffusionmaps.cpp → ...ted/libshogun/converter_diffusionmaps.cpp
@@ -10,7 +10,7 @@
 
 #include <shogun/base/init.h>
 #include <shogun/features/SimpleFeatures.h>
-#include <shogun/preprocessor/DiffusionMaps.h>
+#include <shogun/converter/DiffusionMaps.h>
 
 using namespace shogun;
 
@@ -30,7 +30,8 @@ int main(int argc, char** argv)
 	dmaps->set_target_dim(2);
 	dmaps->set_t(10);
 	dmaps->parallel->set_num_threads(4);
-	dmaps->apply_to_feature_matrix(features);
+	CSimpleFeatures<double>* embedding = dmaps->apply(features);
+	SG_UNREF(embedding);
 	SG_UNREF(dmaps);
 	SG_UNREF(features);
 	exit_shogun();

diff --git a/...ocessor_hessianlocallylinearembedding.cpp → ...nverter_hessianlocallylinearembedding.cpp b/...ocessor_hessianlocallylinearembedding.cpp → ...nverter_hessianlocallylinearembedding.cpp
@@ -10,7 +10,7 @@
 
 #include <shogun/base/init.h>
 #include <shogun/features/SimpleFeatures.h>
-#include <shogun/preprocessor/HessianLocallyLinearEmbedding.h>
+#include <shogun/converter/HessianLocallyLinearEmbedding.h>
 
 using namespace shogun;
 
@@ -29,8 +29,9 @@ int main(int argc, char** argv)
 	CHessianLocallyLinearEmbedding* hlle = new CHessianLocallyLinearEmbedding();
 	hlle->set_target_dim(2);
 	hlle->set_k(8);
-	hlle->apply_to_feature_matrix(features);
 	hlle->parallel->set_num_threads(4);
+	CSimpleFeatures<double>* embedding = hlle->apply(features);
+	SG_UNREF(embedding);
 	SG_UNREF(hlle);
 	SG_UNREF(features);
 	exit_shogun();

diff --git a/...umented/libshogun/preprocessor_isomap.cpp → ...documented/libshogun/converter_isomap.cpp b/...umented/libshogun/preprocessor_isomap.cpp → ...documented/libshogun/converter_isomap.cpp
@@ -10,8 +10,7 @@
 
 #include <shogun/base/init.h>
 #include <shogun/features/SimpleFeatures.h>
-#include <shogun/preprocessor/DimensionReductionPreprocessor.h>
-#include <shogun/preprocessor/Isomap.h>
+#include <shogun/converter/Isomap.h>
 
 using namespace shogun;
 
@@ -32,7 +31,8 @@ int main(int argc, char** argv)
 	isomap->set_landmark(true);
 	isomap->set_k(4);
 	isomap->parallel->set_num_threads(4);
-	isomap->apply_to_feature_matrix(features);
+	CSimpleFeatures<double>* embedding = isomap->apply(features);
+	SG_UNREF(embedding);
 	SG_UNREF(isomap);
 	SG_UNREF(features);
 	exit_shogun();

diff --git a/...rocessor_kernellocallylinearembedding.cpp → ...onverter_kernellocallylinearembedding.cpp b/...rocessor_kernellocallylinearembedding.cpp → ...onverter_kernellocallylinearembedding.cpp
@@ -10,7 +10,7 @@
 
 #include <shogun/base/init.h>
 #include <shogun/features/SimpleFeatures.h>
-#include <shogun/preprocessor/KernelLocallyLinearEmbedding.h>
+#include <shogun/converter/KernelLocallyLinearEmbedding.h>
 #include <shogun/kernel/LinearKernel.h>
 
 using namespace shogun;
@@ -33,7 +33,8 @@ int main(int argc, char** argv)
 	klle->set_k(4);
 	klle->set_kernel(kernel);
 	klle->parallel->set_num_threads(4);
-	klle->apply_to_feature_matrix(features);
+	CSimpleFeatures<double>* embedding = klle->apply(features);
+	SG_UNREF(embedding);
 	SG_UNREF(klle);
 	SG_UNREF(features);
 	exit_shogun();

diff --git a/...ssor_kernellocaltangentspacealignment.cpp → ...rter_kernellocaltangentspacealignment.cpp b/...ssor_kernellocaltangentspacealignment.cpp → ...rter_kernellocaltangentspacealignment.cpp
@@ -10,7 +10,7 @@
 
 #include <shogun/base/init.h>
 #include <shogun/features/SimpleFeatures.h>
-#include <shogun/preprocessor/KernelLocalTangentSpaceAlignment.h>
+#include <shogun/converter/KernelLocalTangentSpaceAlignment.h>
 #include <shogun/kernel/LinearKernel.h>
 
 using namespace shogun;
@@ -33,7 +33,8 @@ int main(int argc, char** argv)
 	kltsa->set_k(4);
 	kltsa->set_kernel(kernel);
 	kltsa->parallel->set_num_threads(4);
-	kltsa->apply_to_feature_matrix(features);
+	CSimpleFeatures<double>* embedding = kltsa->apply(features);
+	SG_UNREF(embedding);
 	SG_UNREF(kltsa);
 	SG_UNREF(features);
 	exit_shogun();

diff --git a/...hogun/preprocessor_laplacianeigenmaps.cpp → ...ibshogun/converter_laplacianeigenmaps.cpp b/...hogun/preprocessor_laplacianeigenmaps.cpp → ...ibshogun/converter_laplacianeigenmaps.cpp
@@ -10,7 +10,7 @@
 
 #include <shogun/base/init.h>
 #include <shogun/features/SimpleFeatures.h>
-#include <shogun/preprocessor/LaplacianEigenmaps.h>
+#include <shogun/converter/LaplacianEigenmaps.h>
 
 using namespace shogun;
 
@@ -30,7 +30,8 @@ int main(int argc, char** argv)
 	lem->set_target_dim(2);
 	lem->set_k(10);
 	lem->parallel->set_num_threads(4);
-	lem->apply_to_feature_matrix(features);
+	CSimpleFeatures<double>* embedding = lem->apply(features);
+	SG_UNREF(embedding);
 	SG_UNREF(lem);
 	SG_UNREF(features);
 	exit_shogun();

diff --git a/...n/preprocessor_locallylinearembedding.cpp → ...ogun/converter_locallylinearembedding.cpp b/...n/preprocessor_locallylinearembedding.cpp → ...ogun/converter_locallylinearembedding.cpp
@@ -10,7 +10,7 @@
 
 #include <shogun/base/init.h>
 #include <shogun/features/SimpleFeatures.h>
-#include <shogun/preprocessor/LocallyLinearEmbedding.h>
+#include <shogun/converter/LocallyLinearEmbedding.h>
 
 using namespace shogun;
 
@@ -30,7 +30,8 @@ int main(int argc, char** argv)
 	lle->set_target_dim(2);
 	lle->set_k(4);
 	lle->parallel->set_num_threads(4);
-	lle->apply_to_feature_matrix(features);
+	CSimpleFeatures<double>* embedding = lle->apply(features);
+	SG_UNREF(embedding);
 	SG_UNREF(lle);
 	SG_UNREF(features);
 	exit_shogun();

diff --git a/...eprocessor_localtangentspacealignment.cpp → .../converter_localtangentspacealignment.cpp b/...eprocessor_localtangentspacealignment.cpp → .../converter_localtangentspacealignment.cpp
@@ -10,7 +10,7 @@
 
 #include <shogun/base/init.h>
 #include <shogun/features/SimpleFeatures.h>
-#include <shogun/preprocessor/LocalTangentSpaceAlignment.h>
+#include <shogun/converter/LocalTangentSpaceAlignment.h>
 
 using namespace shogun;
 
@@ -30,7 +30,8 @@ int main(int argc, char** argv)
 	ltsa->set_target_dim(2);
 	ltsa->set_k(4);
 	ltsa->parallel->set_num_threads(4);
-	ltsa->apply_to_feature_matrix(features);
+	CSimpleFeatures<double>* embedding = ltsa->apply(features);
+	SG_UNREF(embedding);
 	SG_UNREF(ltsa);
 	SG_UNREF(features);
 	exit_shogun();

diff --git a/.../preprocessor_multidimensionalscaling.cpp → ...gun/converter_multidimensionalscaling.cpp b/.../preprocessor_multidimensionalscaling.cpp → ...gun/converter_multidimensionalscaling.cpp
@@ -10,8 +10,7 @@
 
 #include <shogun/base/init.h>
 #include <shogun/features/SimpleFeatures.h>
-#include <shogun/preprocessor/DimensionReductionPreprocessor.h>
-#include <shogun/preprocessor/MultidimensionalScaling.h>
+#include <shogun/converter/MultidimensionalScaling.h>
 
 using namespace shogun;
 
@@ -31,7 +30,8 @@ int main(int argc, char** argv)
 	mds->set_target_dim(2);
 	mds->set_landmark(true);
 	mds->parallel->set_num_threads(4);
-	mds->apply_to_feature_matrix(features);
+	CSimpleFeatures<double>* embedding = mds->apply(features);
+	SG_UNREF(embedding);
 	SG_UNREF(mds);
 	SG_UNREF(features);
 	exit_shogun();

diff --git a/examples/undocumented/python_modular/converter_diffusionmaps_modular.py b/examples/undocumented/python_modular/converter_diffusionmaps_modular.py
@@ -0,0 +1,27 @@
+from tools.load import LoadMatrix
+
+lm=LoadMatrix()
+data = lm.load_numbers('../data/fm_train_real.dat')
+
+parameter_list = [[data,10],[data,20]]
+
+def converter_diffusionmaps_modular(data,t):
+	from shogun.Features import RealFeatures
+	from shogun.Converter import DiffusionMaps
+	from shogun.Kernel import GaussianKernel
+
+	features = RealFeatures(data)
+
+	converter = DiffusionMaps()
+	converter.set_target_dim(1)
+	converter.set_kernel(GaussianKernel(10,10.0))
+	converter.set_t(t)
+	converter.apply(features)
+
+	return features
+
+
+if __name__=='__main__':
+	print 'DiffusionMaps'
+	converter_diffusionmaps_modular(*parameter_list[0])
+
diff --git a/examples/undocumented/python_modular/converter_hessianlocallylinearembedding_modular.py b/examples/undocumented/python_modular/converter_hessianlocallylinearembedding_modular.py
@@ -0,0 +1,25 @@
+from tools.load import LoadMatrix
+
+lm=LoadMatrix()
+data = lm.load_numbers('../data/fm_train_real.dat')
+
+parameter_list = [[data,10],[data,20]]
+
+def converter_hessianlocallylinearembedding_modular(data,k):
+	from shogun.Features import RealFeatures
+	from shogun.Converter import HessianLocallyLinearEmbedding
+
+	features = RealFeatures(data)
+
+	converter = HessianLocallyLinearEmbedding()
+	converter.set_target_dim(1)
+	converter.set_k(k)
+	converter.apply(features)
+
+	return features
+
+
+if __name__=='__main__':
+	print 'HessianLocallyLinearEmbedding'
+	converter_hessianlocallylinearembedding_modular(*parameter_list[0])
+
diff --git a/examples/undocumented/python_modular/converter_isomap_modular.py b/examples/undocumented/python_modular/converter_isomap_modular.py
@@ -0,0 +1,27 @@
+from tools.load import LoadMatrix
+
+lm=LoadMatrix()
+data = lm.load_numbers('../data/fm_train_real.dat')
+
+parameter_list = [[data]]
+
+def converter_isomap_modular(data):
+	from shogun.Features import RealFeatures
+	from shogun.Converter import Isomap
+
+	features = RealFeatures(data)
+
+	converter = Isomap()
+	converter.set_landmark(True)
+	converter.set_landmark_number(5)
+	converter.set_k(6)
+	converter.set_target_dim(1)
+	converter.apply(features)
+
+	return features
+
+
+if __name__=='__main__':
+	print 'Isomap'
+	converter_isomap_modular(*parameter_list[0])
+