Add transformer::apply(features, inplace) api

shogun-toolbox · Jul 12, 2018 · b47d428 · b47d428
1 parent ed287db
commit b47d428
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Showing 52 changed files with 67 additions and 56 deletions.
diff --git a/src/shogun/converter/Converter.h b/src/shogun/converter/Converter.h
@@ -37,7 +37,7 @@ class CConverter : public CTransformer
 	 * @param features features to convert
 	 * @return converted features
 	 */
-	virtual CFeatures* apply(CFeatures* features) = 0;
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true) = 0;
 };
 }
 #endif /* CONVERTER_H_ */

diff --git a/src/shogun/converter/DiffusionMaps.cpp b/src/shogun/converter/DiffusionMaps.cpp
@@ -58,7 +58,7 @@ const char* CDiffusionMaps::get_name() const
 	return "DiffusionMaps";
 };
 
-CFeatures* CDiffusionMaps::apply(CFeatures* features)
+CFeatures* CDiffusionMaps::apply(CFeatures* features, bool inplace)
 {
 	ASSERT(features)
 	// shorthand for simplefeatures

diff --git a/src/shogun/converter/DiffusionMaps.h b/src/shogun/converter/DiffusionMaps.h
@@ -45,7 +45,7 @@ class CDiffusionMaps: public CEmbeddingConverter
 	/** apply preprocessor to features
 	 * @param features
 	 */
-	virtual CFeatures* apply(CFeatures* features);
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 	/** embed distance
 	 * @param distance to use for embedding

diff --git a/src/shogun/converter/EmbeddingConverter.h b/src/shogun/converter/EmbeddingConverter.h
@@ -40,7 +40,7 @@ class CEmbeddingConverter: public CConverter
 	 * @param features features to embed
 	 * @return embedding features
 	 */
-	virtual CFeatures* apply(CFeatures* features) = 0;
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true) = 0;
 
 	/** embed given features, acts the same as apply, but returns
 	 * DenseFeatures

diff --git a/src/shogun/converter/FactorAnalysis.cpp b/src/shogun/converter/FactorAnalysis.cpp
@@ -54,7 +54,7 @@ float64_t CFactorAnalysis::get_epsilon() const
 	return m_epsilon;
 }
 
-CFeatures* CFactorAnalysis::apply(CFeatures* features)
+CFeatures* CFactorAnalysis::apply(CFeatures* features, bool inplace)
 {
 	TAPKEE_PARAMETERS_FOR_SHOGUN parameters;
 	parameters.max_iteration = m_max_iteration;

diff --git a/src/shogun/converter/FactorAnalysis.h b/src/shogun/converter/FactorAnalysis.h
@@ -60,7 +60,7 @@ class CFactorAnalysis : public CEmbeddingConverter
 	 *
 	 * @param features features to embed
 	 */
-	virtual CFeatures* apply(CFeatures* features);
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 	/** setter for the maximum number of iterations
 	 *

diff --git a/src/shogun/converter/HashedDocConverter.cpp b/src/shogun/converter/HashedDocConverter.cpp
@@ -73,7 +73,7 @@ const char* CHashedDocConverter::get_name() const
 	return "HashedDocConverter";
 }
 
-CFeatures* CHashedDocConverter::apply(CFeatures* features)
+CFeatures* CHashedDocConverter::apply(CFeatures* features, bool inplace)
 {
 	ASSERT(features);
 	if (strcmp(features->get_name(), "StringFeatures")!=0)

diff --git a/src/shogun/converter/HashedDocConverter.h b/src/shogun/converter/HashedDocConverter.h
@@ -68,7 +68,7 @@ class CHashedDocConverter : public CConverter
 	 * @param features the strings to be hashed. Must be an instance of CStringFeatures.
 	 * @return a CSparseFeatures object containing the hashes of the strings.
 	 */
-	virtual CFeatures* apply(CFeatures* features);
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 	/** Hashes the tokens contained in document
 	 *

diff --git a/src/shogun/converter/HessianLocallyLinearEmbedding.cpp b/src/shogun/converter/HessianLocallyLinearEmbedding.cpp
@@ -25,7 +25,8 @@ const char* CHessianLocallyLinearEmbedding::get_name() const
 	return "HessianLocallyLinearEmbedding";
 };
 
-CFeatures* CHessianLocallyLinearEmbedding::apply(CFeatures* features)
+CFeatures*
+CHessianLocallyLinearEmbedding::apply(CFeatures* features, bool inplace)
 {
 	CKernel* kernel = new CLinearKernel((CDotFeatures*)features,(CDotFeatures*)features);
 	TAPKEE_PARAMETERS_FOR_SHOGUN parameters;

diff --git a/src/shogun/converter/HessianLocallyLinearEmbedding.h b/src/shogun/converter/HessianLocallyLinearEmbedding.h
@@ -48,7 +48,7 @@ class CHessianLocallyLinearEmbedding: public CLocallyLinearEmbedding
 	virtual const char* get_name() const;
 
 	/** apply */
-	virtual CFeatures* apply(CFeatures* features);
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 };
 }
 

diff --git a/src/shogun/converter/KernelLocallyLinearEmbedding.cpp b/src/shogun/converter/KernelLocallyLinearEmbedding.cpp
@@ -31,7 +31,8 @@ CKernelLocallyLinearEmbedding::~CKernelLocallyLinearEmbedding()
 {
 }
 
-CFeatures* CKernelLocallyLinearEmbedding::apply(CFeatures* features)
+CFeatures*
+CKernelLocallyLinearEmbedding::apply(CFeatures* features, bool inplace)
 {
 	ASSERT(features)
 	SG_REF(features);

diff --git a/src/shogun/converter/KernelLocallyLinearEmbedding.h b/src/shogun/converter/KernelLocallyLinearEmbedding.h
@@ -52,7 +52,7 @@ class CKernelLocallyLinearEmbedding: public CLocallyLinearEmbedding
 	virtual ~CKernelLocallyLinearEmbedding();
 
 	/** apply */
-	virtual CFeatures* apply(CFeatures* features);
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 	/** embed kernel (kernel should be inited)
 	 * @param kernel kernel to construct embed

diff --git a/src/shogun/converter/LaplacianEigenmaps.cpp b/src/shogun/converter/LaplacianEigenmaps.cpp
@@ -57,7 +57,7 @@ const char* CLaplacianEigenmaps::get_name() const
 	return "LaplacianEigenmaps";
 };
 
-CFeatures* CLaplacianEigenmaps::apply(CFeatures* features)
+CFeatures* CLaplacianEigenmaps::apply(CFeatures* features, bool inplace)
 {
 	// shorthand for simplefeatures
 	SG_REF(features);

diff --git a/src/shogun/converter/LaplacianEigenmaps.h b/src/shogun/converter/LaplacianEigenmaps.h
@@ -46,7 +46,7 @@ class CLaplacianEigenmaps: public CEmbeddingConverter
 	 * @param features to embed
 	 * @return embedded features
 	 */
-	virtual CFeatures* apply(CFeatures* features);
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 	/** embed distance
 	 * @param distance to use for embedding

diff --git a/src/shogun/converter/LinearLocalTangentSpaceAlignment.cpp b/src/shogun/converter/LinearLocalTangentSpaceAlignment.cpp
@@ -26,7 +26,8 @@ const char* CLinearLocalTangentSpaceAlignment::get_name() const
 	return "LinearLocalTangentSpaceAlignment";
 }
 
-CFeatures* CLinearLocalTangentSpaceAlignment::apply(CFeatures* features)
+CFeatures*
+CLinearLocalTangentSpaceAlignment::apply(CFeatures* features, bool inplace)
 {
 	CKernel* kernel = new CLinearKernel((CDotFeatures*)features,(CDotFeatures*)features);
 	TAPKEE_PARAMETERS_FOR_SHOGUN parameters;

diff --git a/src/shogun/converter/LinearLocalTangentSpaceAlignment.h b/src/shogun/converter/LinearLocalTangentSpaceAlignment.h
@@ -49,8 +49,7 @@ class CLinearLocalTangentSpaceAlignment: public CLocalTangentSpaceAlignment
 	virtual const char* get_name() const;
 
 	/** apply */
-	virtual CFeatures* apply(CFeatures* features);
-
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 };
 }
 

diff --git a/src/shogun/converter/LocalTangentSpaceAlignment.cpp b/src/shogun/converter/LocalTangentSpaceAlignment.cpp
@@ -26,7 +26,7 @@ const char* CLocalTangentSpaceAlignment::get_name() const
 	return "LocalTangentSpaceAlignment";
 };
 
-CFeatures* CLocalTangentSpaceAlignment::apply(CFeatures* features)
+CFeatures* CLocalTangentSpaceAlignment::apply(CFeatures* features, bool inplace)
 {
 	CKernel* kernel = new CLinearKernel((CDotFeatures*)features,(CDotFeatures*)features);
 	TAPKEE_PARAMETERS_FOR_SHOGUN parameters;

diff --git a/src/shogun/converter/LocalTangentSpaceAlignment.h b/src/shogun/converter/LocalTangentSpaceAlignment.h
@@ -47,8 +47,7 @@ class CLocalTangentSpaceAlignment: public CLocallyLinearEmbedding
 	virtual const char* get_name() const;
 
 	/** apply */
-	virtual CFeatures* apply(CFeatures* features);
-
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 };
 }
 

diff --git a/src/shogun/converter/LocalityPreservingProjections.cpp b/src/shogun/converter/LocalityPreservingProjections.cpp
@@ -26,7 +26,8 @@ const char* CLocalityPreservingProjections::get_name() const
 	return "LocalityPreservingProjections";
 };
 
-CFeatures* CLocalityPreservingProjections::apply(CFeatures* features)
+CFeatures*
+CLocalityPreservingProjections::apply(CFeatures* features, bool inplace)
 {
 	TAPKEE_PARAMETERS_FOR_SHOGUN parameters;
 	m_distance->init(features,features);

diff --git a/src/shogun/converter/LocalityPreservingProjections.h b/src/shogun/converter/LocalityPreservingProjections.h
@@ -44,8 +44,7 @@ class CLocalityPreservingProjections: public CLaplacianEigenmaps
 	virtual const char* get_name() const;
 
 	/** apply */
-	virtual CFeatures* apply(CFeatures* features);
-
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 };
 }
 

diff --git a/src/shogun/converter/LocallyLinearEmbedding.cpp b/src/shogun/converter/LocallyLinearEmbedding.cpp
@@ -74,7 +74,7 @@ const char* CLocallyLinearEmbedding::get_name() const
 	return "LocallyLinearEmbedding";
 }
 
-CFeatures* CLocallyLinearEmbedding::apply(CFeatures* features)
+CFeatures* CLocallyLinearEmbedding::apply(CFeatures* features, bool inplace)
 {
 	// oh my let me dirty cast it
 	CKernel* kernel = new CLinearKernel((CDotFeatures*)features,(CDotFeatures*)features);

diff --git a/src/shogun/converter/LocallyLinearEmbedding.h b/src/shogun/converter/LocallyLinearEmbedding.h
@@ -52,7 +52,7 @@ class CLocallyLinearEmbedding: public CEmbeddingConverter
 	/** apply preprocessor to features
 	 * @param features
 	 */
-	virtual CFeatures* apply(CFeatures* features);
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 	/** setter for k parameter
 	 * @param k k value

diff --git a/src/shogun/converter/ManifoldSculpting.cpp b/src/shogun/converter/ManifoldSculpting.cpp
@@ -72,7 +72,7 @@ int32_t CManifoldSculpting::get_max_iteration() const
 	return m_max_iteration;
 }
 
-CFeatures* CManifoldSculpting::apply(CFeatures* features)
+CFeatures* CManifoldSculpting::apply(CFeatures* features, bool inplace)
 {
 	CDenseFeatures<float64_t>* feats = (CDenseFeatures<float64_t>*)features;
 	SG_REF(feats);

diff --git a/src/shogun/converter/ManifoldSculpting.h b/src/shogun/converter/ManifoldSculpting.h
@@ -37,7 +37,7 @@ class CManifoldSculpting : public CEmbeddingConverter
 	 *
 	 * @param features features to embed
 	 */
-	virtual CFeatures* apply(CFeatures* features);
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 	/** setter for the k
 	 *

diff --git a/src/shogun/converter/MultidimensionalScaling.cpp b/src/shogun/converter/MultidimensionalScaling.cpp
@@ -96,7 +96,7 @@ CDenseFeatures<float64_t>* CMultidimensionalScaling::embed_distance(CDistance* d
 	return embedding;
 }
 
-CFeatures* CMultidimensionalScaling::apply(CFeatures* features)
+CFeatures* CMultidimensionalScaling::apply(CFeatures* features, bool inplace)
 {
 	SG_REF(features);
 	ASSERT(m_distance)

diff --git a/src/shogun/converter/MultidimensionalScaling.h b/src/shogun/converter/MultidimensionalScaling.h
@@ -75,7 +75,7 @@ class CMultidimensionalScaling: public CEmbeddingConverter
 	 * @param features features which feature matrix should be processed
 	 * @return new feature matrix
 	 */
-	virtual CFeatures* apply(CFeatures* features);
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 	/** get name */
 	const char* get_name() const;

diff --git a/src/shogun/converter/NeighborhoodPreservingEmbedding.cpp b/src/shogun/converter/NeighborhoodPreservingEmbedding.cpp
@@ -27,7 +27,8 @@ const char* CNeighborhoodPreservingEmbedding::get_name() const
 	return "NeighborhoodPreservingEmbedding";
 }
 
-CFeatures* CNeighborhoodPreservingEmbedding::apply(CFeatures* features)
+CFeatures*
+CNeighborhoodPreservingEmbedding::apply(CFeatures* features, bool inplace)
 {
 	CKernel* kernel = new CLinearKernel((CDotFeatures*)features,(CDotFeatures*)features);
 	TAPKEE_PARAMETERS_FOR_SHOGUN parameters;

diff --git a/src/shogun/converter/NeighborhoodPreservingEmbedding.h b/src/shogun/converter/NeighborhoodPreservingEmbedding.h
@@ -49,8 +49,7 @@ class CNeighborhoodPreservingEmbedding: public CLocallyLinearEmbedding
 	virtual const char* get_name() const;
 
 	/** apply */
-	virtual CFeatures* apply(CFeatures* features);
-
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 };
 }
 

diff --git a/src/shogun/converter/StochasticProximityEmbedding.cpp b/src/shogun/converter/StochasticProximityEmbedding.cpp
@@ -105,7 +105,8 @@ const char * CStochasticProximityEmbedding::get_name() const
 	return "StochasticProximityEmbedding";
 }
 
-CFeatures* CStochasticProximityEmbedding::apply(CFeatures* features)
+CFeatures*
+CStochasticProximityEmbedding::apply(CFeatures* features, bool inplace)
 {
 	if ( !features )
 		SG_ERROR("Features are required to apply SPE\n")

diff --git a/src/shogun/converter/StochasticProximityEmbedding.h b/src/shogun/converter/StochasticProximityEmbedding.h
@@ -72,7 +72,7 @@ class CStochasticProximityEmbedding : public CEmbeddingConverter
 		 * @param features features to embed
 		 * @return embedding features
 		 */
-		virtual CFeatures* apply(CFeatures* features);
+		virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 		/** setter for number of neighbors k in local strategy
 		 *

diff --git a/src/shogun/converter/TDistributedStochasticNeighborEmbedding.cpp b/src/shogun/converter/TDistributedStochasticNeighborEmbedding.cpp
@@ -55,7 +55,8 @@ float64_t CTDistributedStochasticNeighborEmbedding::get_perplexity() const
 	return m_perplexity;
 }
 
-CFeatures* CTDistributedStochasticNeighborEmbedding::apply(CFeatures* features)
+CFeatures* CTDistributedStochasticNeighborEmbedding::apply(
+    CFeatures* features, bool inplace)
 {
 	TAPKEE_PARAMETERS_FOR_SHOGUN parameters;
 	parameters.sne_theta = m_theta;

diff --git a/src/shogun/converter/TDistributedStochasticNeighborEmbedding.h b/src/shogun/converter/TDistributedStochasticNeighborEmbedding.h
@@ -38,7 +38,7 @@ class CTDistributedStochasticNeighborEmbedding : public CEmbeddingConverter
 	 *
 	 * @param features features to embed
 	 */
-	virtual CFeatures* apply(CFeatures* features);
+	virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 	/** setter for the learning rate
 	 *

diff --git a/src/shogun/converter/ica/FFSep.cpp b/src/shogun/converter/ica/FFSep.cpp
@@ -52,7 +52,7 @@ SGNDArray<float64_t> CFFSep::get_covs() const
 	return m_covs;
 }
 
-CFeatures* CFFSep::apply(CFeatures* features)
+CFeatures* CFFSep::apply(CFeatures* features, bool inplace)
 {
 	ASSERT(features);
 	SG_REF(features);

diff --git a/src/shogun/converter/ica/FFSep.h b/src/shogun/converter/ica/FFSep.h
@@ -42,7 +42,7 @@ class CFFSep: public CICAConverter
 		/** apply to features
 		 * @param features features to embed
 		 */
-		virtual CFeatures* apply(CFeatures* features);
+		virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 		/** getter for tau parameter
 		 * @return tau vector

diff --git a/src/shogun/converter/ica/FastICA.cpp b/src/shogun/converter/ica/FastICA.cpp
@@ -66,7 +66,7 @@ bool CFastICA::get_whiten() const
 	return whiten;
 }
 
-CFeatures* CFastICA::apply(CFeatures* features)
+CFeatures* CFastICA::apply(CFeatures* features, bool inplace)
 {
 	ASSERT(features);
 	SG_REF(features);

diff --git a/src/shogun/converter/ica/FastICA.h b/src/shogun/converter/ica/FastICA.h
@@ -38,7 +38,7 @@ class CFastICA: public CICAConverter
 		/** apply to features
 		 * @param features features to embed
 		 */
-		virtual CFeatures* apply(CFeatures* features);
+		virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 		/** setter for whiten flag
 		 * whether to whiten the data or not

diff --git a/src/shogun/converter/ica/ICAConverter.h b/src/shogun/converter/ica/ICAConverter.h
@@ -33,7 +33,7 @@ class CICAConverter: public CConverter
 		/** apply to features
 		 * @param features features to embed
 		 */
-		virtual CFeatures* apply(CFeatures* features) = 0;
+		virtual CFeatures* apply(CFeatures* features, bool inplace = true) = 0;
 
 		/** setter for mixing matrix, if the mixing matrix is set it will be
 		 * used as an initial guess if supported by the algorithm

diff --git a/src/shogun/converter/ica/Jade.cpp b/src/shogun/converter/ica/Jade.cpp
@@ -40,7 +40,7 @@ SGMatrix<float64_t> CJade::get_cumulant_matrix() const
 	return m_cumulant_matrix;
 }
 
-CFeatures* CJade::apply(CFeatures* features)
+CFeatures* CJade::apply(CFeatures* features, bool inplace)
 {
 	ASSERT(features);
 	SG_REF(features);

diff --git a/src/shogun/converter/ica/Jade.h b/src/shogun/converter/ica/Jade.h
@@ -43,7 +43,7 @@ class CJade: public CICAConverter
 		/** apply to features
 		 * @param features features to embed
 		 */
-		virtual CFeatures* apply(CFeatures* features);
+		virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 		/** getter for cumulant_matrix
 		 * @return cumulant_matrix

diff --git a/src/shogun/converter/ica/JediSep.cpp b/src/shogun/converter/ica/JediSep.cpp
@@ -52,7 +52,7 @@ SGNDArray<float64_t> CJediSep::get_covs() const
 	return m_covs;
 }
 
-CFeatures* CJediSep::apply(CFeatures* features)
+CFeatures* CJediSep::apply(CFeatures* features, bool inplace)
 {
 	REQUIRE(features, "features is null");
 	SG_REF(features);

diff --git a/src/shogun/converter/ica/JediSep.h b/src/shogun/converter/ica/JediSep.h
@@ -41,7 +41,7 @@ class CJediSep: public CICAConverter
 		/** apply to features
 		 * @param features features to embed
 		 */
-		virtual CFeatures* apply(CFeatures* features);
+		virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 		/** getter for tau parameter
 		 * @return tau vector

diff --git a/src/shogun/converter/ica/SOBI.cpp b/src/shogun/converter/ica/SOBI.cpp
@@ -52,7 +52,7 @@ SGNDArray<float64_t> CSOBI::get_covs() const
 	return m_covs;
 }
 
-CFeatures* CSOBI::apply(CFeatures* features)
+CFeatures* CSOBI::apply(CFeatures* features, bool inplace)
 {
 	ASSERT(features);
 	SG_REF(features);

diff --git a/src/shogun/converter/ica/SOBI.h b/src/shogun/converter/ica/SOBI.h
@@ -43,7 +43,7 @@ class CSOBI: public CICAConverter
 		/** apply to features
 		 * @param features features to embed
 		 */
-		virtual CFeatures* apply(CFeatures* features);
+		virtual CFeatures* apply(CFeatures* features, bool inplace = true);
 
 		/** getter for tau parameter
 		 * @return tau vector