32 files changed, 103 insertions, 1442 deletions
diff --git a/cuda/2d/algo.cu b/cuda/2d/algo.cu
index 02790f0..f809c23 100644
--- a/cuda/2d/algo.cu
+++ b/cuda/2d/algo.cu
@@ -25,16 +25,16 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include <cassert>
+#include "astra/cuda/2d/algo.h"
+#include "astra/cuda/2d/par_fp.h"
+#include "astra/cuda/2d/fan_fp.h"
+#include "astra/cuda/2d/par_bp.h"
+#include "astra/cuda/2d/fan_bp.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/arith.h"
+#include "astra/cuda/2d/astra.h"
 
-#include "algo.h"
-#include "par_fp.h"
-#include "fan_fp.h"
-#include "par_bp.h"
-#include "fan_bp.h"
-#include "util.h"
-#include "arith.h"
-#include "astra.h"
+#include <cassert>
 
 namespace astraCUDA {
 
diff --git a/cuda/2d/algo.h b/cuda/2d/algo.h
deleted file mode 100644
index 2ce929c..0000000
--- a/cuda/2d/algo.h
+++ /dev/null
@@ -1,173 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_ALGO_H
-#define _CUDA_ALGO_H
-
-#include "astra/Globals.h"
-#include "dims.h"
-
-namespace astra {
-
-class CParallelProjectionGeometry2D;
-class CParallelVecProjectionGeometry2D;
-class CFanFlatProjectionGeometry2D;
-class CFanFlatVecProjectionGeometry2D;
-class CVolumeGeometry2D;
-class CProjectionGeometry2D;
-
-}
-
-namespace astraCUDA {
-
-class _AstraExport ReconAlgo {
-public:
-	ReconAlgo();
-	virtual ~ReconAlgo();
-
-	bool setGPUIndex(int iGPUIndex);
-
-	bool setGeometry(const astra::CVolumeGeometry2D* pVolGeom,
-	                 const astra::CProjectionGeometry2D* pProjGeom);
-
-	bool setSuperSampling(int raysPerDet, int raysPerPixelDim);
-
-	void signalAbort() { shouldAbort = true; }
-
-	virtual bool enableVolumeMask();
-	virtual bool enableSinogramMask();
-
-	// init should be called after setting all geometry
-	virtual bool init() = 0;
-
-	// setVolumeMask should be called after init and before iterate,
-	// but only if enableVolumeMask was called before init.
-	// It may be called again after iterate.
-	bool setVolumeMask(float* D_maskData, unsigned int maskPitch);
-
-	// setSinogramMask should be called after init and before iterate,
-	// but only if enableSinogramMask was called before init.
-	// It may be called again after iterate.
-	bool setSinogramMask(float* D_smaskData, unsigned int smaskPitch);
-
-
-	// setBuffers should be called after init and before iterate.
-	// It may be called again after iterate.
-	virtual bool setBuffers(float* D_volumeData, unsigned int volumePitch,
-	                        float* D_projData, unsigned int projPitch);
-
-
-	// instead of calling setBuffers, you can also call allocateBuffers
-	// to let ReconAlgo manage its own GPU memory
-	virtual bool allocateBuffers();
-
-	// copy data to GPU. This must be called after allocateBuffers.
-	// pfSinogram, pfReconstruction, pfVolMask, pfSinoMask are the
-	// sinogram, reconstruction, volume mask and sinogram mask in system RAM,
-	// respectively. The corresponding pitch variables give the pitches
-	// of these buffers, measured in floats.
-	// The sinogram is multiplied by fSinogramScale after uploading it.
-	virtual bool copyDataToGPU(const float* pfSinogram, unsigned int iSinogramPitch, float fSinogramScale,
-	                           const float* pfReconstruction, unsigned int iReconstructionPitch,
-	                           const float* pfVolMask, unsigned int iVolMaskPitch,
-	                           const float* pfSinoMask, unsigned int iSinoMaskPitch);
-
-
-
-	// set Min/Max constraints. They may be called at any time, and will affect
-	// any iterate() calls afterwards.
-	virtual bool setMinConstraint(float fMin);
-	virtual bool setMaxConstraint(float fMax);
-
-
-	// iterate should be called after init and setBuffers.
-	// It may be called multiple times.
-	virtual bool iterate(unsigned int iterations) = 0;
-
-	// Compute the norm of the difference of the FP of the current
-	// reconstruction and the sinogram. (This performs one FP.)
-	// It can be called after iterate.
-	virtual float computeDiffNorm() = 0;
-	// TODO: computeDiffNorm shouldn't be virtual, but for it to be
-	// implemented in ReconAlgo, it needs a way to get a suitable
-	// temporary sinogram buffer.
-
-	bool getReconstruction(float* pfReconstruction,
-                           unsigned int iReconstructionPitch) const;
-
-
-
-protected:
-	void reset();
-
-	bool callFP(float* D_volumeData, unsigned int volumePitch,
-	            float* D_projData, unsigned int projPitch,
-	            float outputScale);
-	bool callBP(float* D_volumeData, unsigned int volumePitch,
-	            float* D_projData, unsigned int projPitch,
-	            float outputScale);
-
-
-	SDimensions dims;
-	SParProjection* parProjs;
-	SFanProjection* fanProjs;
-	float fOutputScale;
-
-	volatile bool shouldAbort;
-
-	bool freeGPUMemory;
-
-	// Input/output
-	float* D_sinoData;
-	unsigned int sinoPitch;
-
-	float* D_volumeData;
-	unsigned int volumePitch;
-
-	// Masks
-	bool useVolumeMask;
-	bool useSinogramMask;
-
-	float* D_maskData;
-	unsigned int maskPitch;
-	float* D_smaskData;
-	unsigned int smaskPitch;
-
-	// Min/max
-	bool useMinConstraint;
-	bool useMaxConstraint;
-	float fMinConstraint;
-	float fMaxConstraint;
-
-
-};
-
-
-}
-
-#endif
-
diff --git a/cuda/2d/arith.cu b/cuda/2d/arith.cu
index 0ff4aa0..62eb8c2 100644
--- a/cuda/2d/arith.cu
+++ b/cuda/2d/arith.cu
@@ -25,8 +25,9 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include "util.h"
-#include "arith.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/arith.h"
+
 #include <cassert>
 
 namespace astraCUDA {
diff --git a/cuda/2d/arith.h b/cuda/2d/arith.h
deleted file mode 100644
index e18bb1b..0000000
--- a/cuda/2d/arith.h
+++ /dev/null
@@ -1,85 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_ARITH_H
-#define _CUDA_ARITH_H
-
-#include <cuda.h>
-
-namespace astraCUDA {
-
-
-struct opAddScaled;
-struct opScaleAndAdd;
-struct opAddMulScaled;
-struct opAddMul;
-struct opAdd;
-struct opAdd2;
-struct opMul;
-struct opDiv;
-struct opMul2;
-struct opDividedBy;
-struct opInvert;
-struct opSet;
-struct opClampMin;
-struct opClampMax;
-struct opClampMinMask;
-struct opClampMaxMask;
-struct opSegmentAndMask;
-struct opSetMaskedValues;
-
-struct opMulMask;
-
-
-template<typename op> void processVolCopy(float* out, const SDimensions& dims);
-template<typename op> void processVolCopy(float* out, float param, const SDimensions& dims);
-template<typename op> void processVolCopy(float* out1, float* out2, float param1, float param2, const SDimensions& dims);
-template<typename op> void processVolCopy(float* out, const float* in, const SDimensions& dims);
-template<typename op> void processVolCopy(float* out, const float* in, float param, const SDimensions& dims);
-template<typename op> void processVolCopy(float* out, const float* in1, const float* in2, const SDimensions& dims);
-template<typename op> void processVolCopy(float* out, const float* in1, const float* in2, float param, const SDimensions& dims);
-
-template<typename op> void processVol(float* out, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processVol(float* out, float fParam, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processVol(float* out1, float* out2, float fParam1, float fParam2, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processVol(float* out, const float* in, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processVol(float* out, const float* in, float fParam, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processVol(float* out, const float* in1, const float* in2, float fParam, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processVol(float* out, const float* in1, const float* in2, unsigned int pitch, const SDimensions& dims);
-
-template<typename op> void processSino(float* out, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processSino(float* out, float fParam, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processSino(float* out1, float* out2, float fParam1, float fParam2, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processSino(float* out, const float* in, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processSino(float* out, const float* in, float fParam, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processSino(float* out, const float* in1, const float* in2, float fParam, unsigned int pitch, const SDimensions& dims);
-template<typename op> void processSino(float* out, const float* in1, const float* in2, unsigned int pitch, const SDimensions& dims);
-
-
-}
-
-#endif
diff --git a/cuda/2d/astra.cu b/cuda/2d/astra.cu
index 2ee469c..ec03517 100644
--- a/cuda/2d/astra.cu
+++ b/cuda/2d/astra.cu
@@ -25,33 +25,31 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include <cstdio>
-#include <cassert>
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/par_fp.h"
+#include "astra/cuda/2d/fan_fp.h"
+#include "astra/cuda/2d/par_bp.h"
+#include "astra/cuda/2d/fan_bp.h"
+#include "astra/cuda/2d/arith.h"
+#include "astra/cuda/2d/astra.h"
+#include "astra/cuda/2d/fft.h"
 
-#include "util.h"
-#include "par_fp.h"
-#include "fan_fp.h"
-#include "par_bp.h"
-#include "fan_bp.h"
-#include "arith.h"
-#include "astra.h"
+// For fan beam FBP weighting
+#include "astra/cuda/3d/fdk.h"
 
-#include "fft.h"
+#include "astra/GeometryUtil2D.h"
+#include "astra/VolumeGeometry2D.h"
+#include "astra/ParallelProjectionGeometry2D.h"
+#include "astra/ParallelVecProjectionGeometry2D.h"
+#include "astra/FanFlatProjectionGeometry2D.h"
+#include "astra/FanFlatVecProjectionGeometry2D.h"
+#include "astra/Logging.h"
 
+#include <cstdio>
+#include <cassert>
 #include <fstream>
-#include <cuda.h>
-
-#include "../../include/astra/GeometryUtil2D.h"
-#include "../../include/astra/VolumeGeometry2D.h"
-#include "../../include/astra/ParallelProjectionGeometry2D.h"
-#include "../../include/astra/ParallelVecProjectionGeometry2D.h"
-#include "../../include/astra/FanFlatProjectionGeometry2D.h"
-#include "../../include/astra/FanFlatVecProjectionGeometry2D.h"
-
-#include "../../include/astra/Logging.h"
 
-// For fan beam FBP weighting
-#include "../3d/fdk.h"
+#include <cuda.h>
 
 using namespace astraCUDA;
 using namespace std;
diff --git a/cuda/2d/astra.h b/cuda/2d/astra.h
deleted file mode 100644
index 6f0e2f0..0000000
--- a/cuda/2d/astra.h
+++ /dev/null
@@ -1,127 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_ASTRA_H
-#define _CUDA_ASTRA_H
-
-#include "fbp_filters.h"
-#include "dims.h"
-#include "algo.h"
-
-using astraCUDA::SFanProjection;
-
-namespace astra {
-
-enum Cuda2DProjectionKernel {
-	ker2d_default = 0
-};
-
-class CParallelProjectionGeometry2D;
-class CParallelVecProjectionGeometry2D;
-class CFanFlatProjectionGeometry2D;
-class CFanFlatVecProjectionGeometry2D;
-class CVolumeGeometry2D;
-class CProjectionGeometry2D;
-
-
-class _AstraExport BPalgo : public astraCUDA::ReconAlgo {
-public:
-	BPalgo();
-	~BPalgo();
-
-	virtual bool init();
-
-	virtual bool iterate(unsigned int iterations);
-
-	virtual float computeDiffNorm();
-};
-
-
-
-
-// TODO: Clean up this interface to FP
-
-// Do a single forward projection
-_AstraExport bool astraCudaFP(const float* pfVolume, float* pfSinogram,
-                 unsigned int iVolWidth, unsigned int iVolHeight,
-                 unsigned int iProjAngles, unsigned int iProjDets,
-                 const SParProjection *pAngles,
-                 unsigned int iDetSuperSampling = 1,
-                 float fOutputScale = 1.0f, int iGPUIndex = 0);
-
-_AstraExport bool astraCudaFanFP(const float* pfVolume, float* pfSinogram,
-                    unsigned int iVolWidth, unsigned int iVolHeight,
-                    unsigned int iProjAngles, unsigned int iProjDets,
-                    const SFanProjection *pAngles,
-                    unsigned int iDetSuperSampling = 1,
-                    float fOutputScale = 1.0f, int iGPUIndex = 0);
-
-
-_AstraExport bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom,
-                    const CParallelProjectionGeometry2D* pProjGeom,
-                    astraCUDA::SParProjection*& pProjs,
-                    float& fOutputScale);
-
-_AstraExport bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom,
-                    const CParallelVecProjectionGeometry2D* pProjGeom,
-                    astraCUDA::SParProjection*& pProjs,
-                    float& fOutputScale);
-
-
-_AstraExport bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom,
-                    const CFanFlatProjectionGeometry2D* pProjGeom,
-                    astraCUDA::SFanProjection*& pProjs,
-                    float& outputScale);
-
-_AstraExport bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom,
-                    const CFanFlatVecProjectionGeometry2D* pProjGeom,
-                    astraCUDA::SFanProjection*& pProjs,
-                    float& outputScale);
-
-_AstraExport bool convertAstraGeometry_dims(const CVolumeGeometry2D* pVolGeom,
-                          const CProjectionGeometry2D* pProjGeom,
-                          astraCUDA::SDimensions& dims);
-
-_AstraExport bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom,
-                          const CProjectionGeometry2D* pProjGeom,
-                          astraCUDA::SParProjection*& pParProjs,
-                          astraCUDA::SFanProjection*& pFanProjs,
-                          float& outputScale);
-}
-
-namespace astraCUDA {
-
-// Return string with CUDA device number, name and memory size.
-// Use device == -1 to get info for the current device.
-_AstraExport std::string getCudaDeviceString(int device);
-
-_AstraExport bool setGPUIndex(int index);
-
-_AstraExport size_t availableGPUMemory();
-
-}
-#endif
diff --git a/cuda/2d/cgls.cu b/cuda/2d/cgls.cu
index f9fd6c1..696a0c1 100644
--- a/cuda/2d/cgls.cu
+++ b/cuda/2d/cgls.cu
@@ -25,17 +25,17 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include <cstdio>
-#include <cassert>
-
-#include "cgls.h"
-#include "util.h"
-#include "arith.h"
+#include "astra/cuda/2d/cgls.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/arith.h"
 
 #ifdef STANDALONE
 #include "testutil.h"
 #endif
 
+#include <cstdio>
+#include <cassert>
+
 namespace astraCUDA {
 
 CGLS::CGLS() : ReconAlgo()
diff --git a/cuda/2d/cgls.h b/cuda/2d/cgls.h
deleted file mode 100644
index 375a425..0000000
--- a/cuda/2d/cgls.h
+++ /dev/null
@@ -1,90 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_CGLS_H
-#define _CUDA_CGLS_H
-
-#include "algo.h"
-
-namespace astraCUDA {
-
-class _AstraExport CGLS : public ReconAlgo {
-public:
-	CGLS();
-	virtual ~CGLS();
-
-	// disable some features
-	virtual bool enableSinogramMask() { return false; }
-	virtual bool setMinConstraint(float) { return false; }
-	virtual bool setMaxConstraint(float) { return false; }
-
-	virtual bool init();
-
-	virtual bool setBuffers(float* D_volumeData, unsigned int volumePitch,
-	                        float* D_projData, unsigned int projPitch);
-
-	virtual bool copyDataToGPU(const float* pfSinogram, unsigned int iSinogramPitch, float fSinogramScale,
-	                           const float* pfReconstruction, unsigned int iReconstructionPitch,
-	                           const float* pfVolMask, unsigned int iVolMaskPitch,
-	                           const float* pfSinoMask, unsigned int iSinoMaskPitch);
-
-
-	virtual bool iterate(unsigned int iterations);
-
-	virtual float computeDiffNorm();
-
-protected:
-	void reset();
-
-	bool sliceInitialized;
-
- 	// Buffers
-	float* D_r;
-	unsigned int rPitch;
-
-	float* D_w;
-	unsigned int wPitch;
-
-	float* D_z;
-	unsigned int zPitch;
-
-	float* D_p;
-	unsigned int pPitch;
-
-
-	float gamma;
-};
-
-
-_AstraExport bool doCGLS(float* D_volumeData, unsigned int volumePitch,
-            float* D_projData, unsigned int projPitch,
-            const SDimensions& dims, const float* angles,
-            const float* TOffsets, unsigned int iterations);
-
-}
-
-#endif
diff --git a/cuda/2d/darthelper.cu b/cuda/2d/darthelper.cu
index 4041d79..b466840 100644
--- a/cuda/2d/darthelper.cu
+++ b/cuda/2d/darthelper.cu
@@ -25,8 +25,9 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include "util.h"
-#include "darthelper.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/darthelper.h"
+
 #include <cassert>
 
 namespace astraCUDA {
diff --git a/cuda/2d/darthelper.h b/cuda/2d/darthelper.h
deleted file mode 100644
index 3c2f83c..0000000
--- a/cuda/2d/darthelper.h
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_ARITH2_H
-#define _CUDA_ARITH2_H
-
-#include "astra/Globals.h"
-
-namespace astraCUDA {
-
-	void roiSelect(float* out, float radius, unsigned int width, unsigned int height);
-	void dartMask(float* out, const float* in, unsigned int conn, unsigned int radius, unsigned int threshold, unsigned int width, unsigned int height);
-	void dartSmoothing(float* out, const float* in, float b, unsigned int radius, unsigned int width, unsigned int height);
-
-}
-
-#endif
diff --git a/cuda/2d/dims.h b/cuda/2d/dims.h
deleted file mode 100644
index 0bdefa9..0000000
--- a/cuda/2d/dims.h
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_DIMS_H
-#define _CUDA_DIMS_H
-
-#include "astra/GeometryUtil2D.h"
-
-
-namespace astraCUDA {
-
-using astra::SParProjection;
-using astra::SFanProjection;
-
-
-
-struct SDimensions {
-	// Width, height of reconstruction volume
-	unsigned int iVolWidth;
-	unsigned int iVolHeight;
-
-	// Number of projection angles
-	unsigned int iProjAngles;
-
-	// Number of detector pixels
-	unsigned int iProjDets;
-
-	// in FP, number of rays to trace per detector pixel.
-	// This should usually be set to 1.
-	// If fDetScale > 1, this should be set to an integer of roughly
-	// the same size as fDetScale.
-	unsigned int iRaysPerDet;
-
-	// in BP, square root of number of rays to trace per volume pixel
-	// This should usually be set to 1.
-	// If fDetScale < 1, this should be set to an integer of roughly
-	// the same size as 1 / fDetScale.
-	unsigned int iRaysPerPixelDim;
-};
-
-}
-
-#endif
-
diff --git a/cuda/2d/em.cu b/cuda/2d/em.cu
index cf67f9b..ca09d31 100644
--- a/cuda/2d/em.cu
+++ b/cuda/2d/em.cu
@@ -25,17 +25,17 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include <cstdio>
-#include <cassert>
-
-#include "em.h"
-#include "util.h"
-#include "arith.h"
+#include "astra/cuda/2d/em.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/arith.h"
 
 #ifdef STANDALONE
 #include "testutil.h"
 #endif
 
+#include <cstdio>
+#include <cassert>
+
 namespace astraCUDA {
 
 
diff --git a/cuda/2d/em.h b/cuda/2d/em.h
deleted file mode 100644
index 3ffe01b..0000000
--- a/cuda/2d/em.h
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_EM_H
-#define _CUDA_EM_H
-
-#include "algo.h"
-
-namespace astraCUDA {
-
-class _AstraExport EM : public ReconAlgo {
-public:
-	EM();
-	virtual ~EM();
-
-	// disable some features
-	virtual bool enableSinogramMask() { return false; }
-	virtual bool enableVolumeMask() { return false; }
-	virtual bool setMinConstraint(float) { return false; }
-	virtual bool setMaxConstraint(float) { return false; }
-
-	virtual bool init();
-
-	virtual bool iterate(unsigned int iterations);
-
-	virtual float computeDiffNorm();
-
-protected:
-	void reset();
-	bool precomputeWeights();
-
- 	// Temporary buffers
-	float* D_projData;
-	unsigned int projPitch;
-
-	float* D_tmpData;
-	unsigned int tmpPitch;
-
-	// Geometry-specific precomputed data
-	float* D_pixelWeight;
-	unsigned int pixelPitch;
-};
-
-_AstraExport bool doEM(float* D_volumeData, unsigned int volumePitch,
-          float* D_projData, unsigned int projPitch,
-          const SDimensions& dims, const float* angles,
-          const float* TOffsets, unsigned int iterations);
-
-}
-
-#endif
diff --git a/cuda/2d/fan_bp.cu b/cuda/2d/fan_bp.cu
index 793b5f4..dac3ac2 100644
--- a/cuda/2d/fan_bp.cu
+++ b/cuda/2d/fan_bp.cu
@@ -25,18 +25,16 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include <cstdio>
-#include <cassert>
-#include <iostream>
-
-#include "util.h"
-#include "arith.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/arith.h"
 
 #ifdef STANDALONE
 #include "testutil.h"
 #endif
 
-#define PIXELTRACE
+#include <cstdio>
+#include <cassert>
+#include <iostream>
 
 
 typedef texture<float, 2, cudaReadModeElementType> texture2D;
diff --git a/cuda/2d/fan_bp.h b/cuda/2d/fan_bp.h
deleted file mode 100644
index 22349b0..0000000
--- a/cuda/2d/fan_bp.h
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_FAN_BP_H
-#define _CUDA_FAN_BP_H
-
-namespace astraCUDA {
-
-_AstraExport bool FanBP(float* D_volumeData, unsigned int volumePitch,
-           float* D_projData, unsigned int projPitch,
-           const SDimensions& dims, const SFanProjection* angles,
-           float fOutputScale);
-
-_AstraExport bool FanBP_SART(float* D_volumeData, unsigned int volumePitch,
-                float* D_projData, unsigned int projPitch,
-                unsigned int angle,
-                const SDimensions& dims, const SFanProjection* angles,
-                float fOutputScale);
-
-_AstraExport bool FanBP_FBPWeighted(float* D_volumeData, unsigned int volumePitch,
-           float* D_projData, unsigned int projPitch,
-           const SDimensions& dims, const SFanProjection* angles,
-           float fOutputScale);
-
-
-}
-
-#endif
diff --git a/cuda/2d/fan_fp.cu b/cuda/2d/fan_fp.cu
index f08a681..3479650 100644
--- a/cuda/2d/fan_fp.cu
+++ b/cuda/2d/fan_fp.cu
@@ -25,18 +25,18 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include <cstdio>
-#include <cassert>
-#include <iostream>
-#include <list>
-
-#include "util.h"
-#include "arith.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/arith.h"
 
 #ifdef STANDALONE
 #include "testutil.h"
 #endif
 
+#include <cstdio>
+#include <cassert>
+#include <iostream>
+#include <list>
+
 
 typedef texture<float, 2, cudaReadModeElementType> texture2D;
 
diff --git a/cuda/2d/fan_fp.h b/cuda/2d/fan_fp.h
deleted file mode 100644
index 3e8f1e4..0000000
--- a/cuda/2d/fan_fp.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_FAN_FP_H
-#define _CUDA_FAN_FP_H
-
-namespace astraCUDA {
-
-_AstraExport bool FanFP(float* D_volumeData, unsigned int volumePitch,
-           float* D_projData, unsigned int projPitch,
-           const SDimensions& dims, const SFanProjection* angles,
-           float outputScale);
-
-}
-
-#endif
diff --git a/cuda/2d/fbp.cu b/cuda/2d/fbp.cu
index ecaf544..48fb7dc 100644
--- a/cuda/2d/fbp.cu
+++ b/cuda/2d/fbp.cu
@@ -25,14 +25,14 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include "fbp.h"
-#include "fft.h"
-#include "par_bp.h"
-#include "fan_bp.h"
-#include "util.h"
+#include "astra/cuda/2d/fbp.h"
+#include "astra/cuda/2d/fft.h"
+#include "astra/cuda/2d/par_bp.h"
+#include "astra/cuda/2d/fan_bp.h"
+#include "astra/cuda/2d/util.h"
 
 // For fan-beam preweighting
-#include "../3d/fdk.h"
+#include "astra/cuda/3d/fdk.h"
 
 #include "astra/Logging.h"
 
diff --git a/cuda/2d/fbp.h b/cuda/2d/fbp.h
deleted file mode 100644
index 8666646..0000000
--- a/cuda/2d/fbp.h
+++ /dev/null
@@ -1,97 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#include "algo.h"
-#include "fbp_filters.h"
-
-namespace astraCUDA {
-
-class _AstraExport FBP : public ReconAlgo {
-public:
-	FBP();
-	~FBP();
-
-	virtual bool useSinogramMask() { return false; }
-	virtual bool useVolumeMask() { return false; }
-
-	// Returns the required size of a filter in the fourier domain
-	// when multiplying it with the fft of the projection data.
-	// Its value is equal to the smallest power of two larger than
-	// or equal to twice the number of detectors in the spatial domain.
-	//
-	// _iDetectorCount is the number of detectors in the spatial domain.
-	static int calcFourierFilterSize(int _iDetectorCount);
-
-	// Sets the filter type. Some filter types require the user to supply an
-	// array containing the filter.
-	// The number of elements in a filter in the fourier domain should be equal
-	// to the value returned by calcFourierFilterSize().
-	// The following types require a filter:
-	//
-	// - FILTER_PROJECTION:
-	// The filter size should be equal to the output of
-	// calcFourierFilterSize(). The filtered sinogram is
-	// multiplied with the supplied filter.
-	//
-	// - FILTER_SINOGRAM:
-	// Same as FILTER_PROJECTION, but now the filter should contain a row for
-	// every projection direction.
-	//
-	// - FILTER_RPROJECTION:
-	// The filter should now contain one kernel (= ifft of filter), with the
-	// peak in the center. The filter width
-	// can be any value. If odd, the peak is assumed to be in the center, if
-	// even, it is assumed to be at floor(filter-width/2).
-	//
-	// - FILTER_RSINOGRAM
-	// Same as FILTER_RPROJECTION, but now the supplied filter should contain a
-	// row for every projection direction.
-	//
-	// A large number of other filters (FILTER_RAMLAK, FILTER_SHEPPLOGAN,
-	// FILTER_COSINE, FILTER_HAMMING, and FILTER_HANN)
-	// have a D variable, which gives the cutoff point in the frequency domain.
-	// Setting this value to 1.0 will include the whole filter
-	bool setFilter(astra::E_FBPFILTER _eFilter,
-                   const float * _pfHostFilter = NULL,
-                   int _iFilterWidth = 0, float _fD = 1.0f, float _fFilterParameter = -1.0f);
-
-	bool setShortScan(bool ss) { m_bShortScan = ss; return true; }
-
-	virtual bool init();
-
-	virtual bool iterate(unsigned int iterations);
-
-	virtual float computeDiffNorm() { return 0.0f; } // TODO
-
-protected:
-	void reset();
-
-	void* D_filter; // cufftComplex*
-	bool m_bShortScan;
-};
-
-}
diff --git a/cuda/2d/fbp_filters.h b/cuda/2d/fbp_filters.h
deleted file mode 100644
index 7c1121a..0000000
--- a/cuda/2d/fbp_filters.h
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef FBP_FILTERS_H
-#define FBP_FILTERS_H
-
-namespace astra {
-
-enum E_FBPFILTER
-{
-	FILTER_NONE,			//< no filter (regular BP)
-	FILTER_RAMLAK,			//< default FBP filter
-	FILTER_SHEPPLOGAN,		//< Shepp-Logan
-	FILTER_COSINE,			//< Cosine
-	FILTER_HAMMING,			//< Hamming filter
-	FILTER_HANN,			//< Hann filter
-	FILTER_TUKEY,			//< Tukey filter
-	FILTER_LANCZOS,			//< Lanczos filter
-	FILTER_TRIANGULAR,		//< Triangular filter
-	FILTER_GAUSSIAN,		//< Gaussian filter
-	FILTER_BARTLETTHANN,	//< Bartlett-Hann filter
-	FILTER_BLACKMAN,		//< Blackman filter
-	FILTER_NUTTALL,			//< Nuttall filter, continuous first derivative
-	FILTER_BLACKMANHARRIS,	//< Blackman-Harris filter
-	FILTER_BLACKMANNUTTALL,	//< Blackman-Nuttall filter
-	FILTER_FLATTOP,			//< Flat top filter
-	FILTER_KAISER,			//< Kaiser filter
-	FILTER_PARZEN,			//< Parzen filter
-	FILTER_PROJECTION,		//< all projection directions share one filter
-	FILTER_SINOGRAM,		//< every projection direction has its own filter
-	FILTER_RPROJECTION,		//< projection filter in real space (as opposed to fourier space)
-	FILTER_RSINOGRAM,		//< sinogram filter in real space
-};
-
-}
-
-#endif /* FBP_FILTERS_H */
diff --git a/cuda/2d/fft.cu b/cuda/2d/fft.cu
index a1b1b93..bd8cab5 100644
--- a/cuda/2d/fft.cu
+++ b/cuda/2d/fft.cu
@@ -25,16 +25,18 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include "fft.h"
-#include "util.h"
+#include "astra/cuda/2d/fft.h"
+#include "astra/cuda/2d/util.h"
+
+#include "astra/Logging.h"
+#include "astra/Fourier.h"
 
-#include <cufft.h>
 #include <iostream>
-#include <cuda.h>
 #include <fstream>
 
-#include "../../include/astra/Logging.h"
-#include "../../include/astra/Fourier.h"
+#include <cufft.h>
+#include <cuda.h>
+
 
 using namespace astra;
 
diff --git a/cuda/2d/fft.h b/cuda/2d/fft.h
deleted file mode 100644
index d36cae2..0000000
--- a/cuda/2d/fft.h
+++ /dev/null
@@ -1,72 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef FFT_H
-#define FFT_H
-
-#include <cufft.h>
-#include <cuda.h>
-
-#include "fbp_filters.h"
-
-namespace astraCUDA {
-
-bool allocateComplexOnDevice(int _iProjectionCount,
-                             int _iDetectorCount,
-                             cufftComplex ** _ppDevComplex);
-
-bool freeComplexOnDevice(cufftComplex * _pDevComplex);
-
-bool uploadComplexArrayToDevice(int _iProjectionCount, int _iDetectorCount,
-                                cufftComplex * _pHostComplexSource,
-                                cufftComplex * _pDevComplexTarget);
-
-bool runCudaFFT(int _iProjectionCount, const float * _pfDevRealSource,
-                int _iSourcePitch, int _iProjDets,
-                int _iFFTRealDetectorCount, int _iFFTFourierDetectorCount,
-                cufftComplex * _pDevTargetComplex);
-
-bool runCudaIFFT(int _iProjectionCount, const cufftComplex* _pDevSourceComplex,
-                 float * _pfRealTarget,
-                 int _iTargetPitch, int _iProjDets,
-                 int _iFFTRealDetectorCount, int _iFFTFourierDetectorCount);
-
-void applyFilter(int _iProjectionCount, int _iFreqBinCount,
-                 cufftComplex * _pSinogram, cufftComplex * _pFilter);
-
-int calcFFTFourierSize(int _iFFTRealSize);
-
-void genFilter(astra::E_FBPFILTER _eFilter, float _fD, int _iProjectionCount,
-               cufftComplex * _pFilter, int _iFFTRealDetectorCount,
-               int _iFFTFourierDetectorCount, float _fParameter = -1.0f);
-
-void genIdenFilter(int _iProjectionCount, cufftComplex * _pFilter,
-                   int _iFFTRealDetectorCount, int _iFFTFourierDetectorCount);
-
-}
-
-#endif /* FFT_H */
diff --git a/cuda/2d/par_bp.cu b/cuda/2d/par_bp.cu
index a894f3f..09a6554 100644
--- a/cuda/2d/par_bp.cu
+++ b/cuda/2d/par_bp.cu
@@ -25,18 +25,16 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include <cstdio>
-#include <cassert>
-#include <iostream>
-
-#include "util.h"
-#include "arith.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/arith.h"
 
 #ifdef STANDALONE
 #include "testutil.h"
 #endif
 
-#define PIXELTRACE
+#include <cstdio>
+#include <cassert>
+#include <iostream>
 
 
 typedef texture<float, 2, cudaReadModeElementType> texture2D;
diff --git a/cuda/2d/par_bp.h b/cuda/2d/par_bp.h
deleted file mode 100644
index c8dfab8..0000000
--- a/cuda/2d/par_bp.h
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_PAR_BP_H
-#define _CUDA_PAR_BP_H
-
-#include "dims.h"
-
-namespace astraCUDA {
-
-_AstraExport bool BP(float* D_volumeData, unsigned int volumePitch,
-        float* D_projData, unsigned int projPitch,
-        const SDimensions& dims, const SParProjection* angles,
-        float fOutputScale);
-
-_AstraExport bool BP_SART(float* D_volumeData, unsigned int volumePitch,
-             float* D_projData, unsigned int projPitch,
-             unsigned int angle, const SDimensions& dims,
-             const SParProjection* angles, float fOutputScale);
-
-}
-
-#endif
diff --git a/cuda/2d/par_fp.cu b/cuda/2d/par_fp.cu
index 427a4e8..0835301 100644
--- a/cuda/2d/par_fp.cu
+++ b/cuda/2d/par_fp.cu
@@ -25,21 +25,18 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include <cstdio>
-#include <cassert>
-#include <iostream>
-#include <list>
-#include <cmath>
-
-#include "util.h"
-#include "arith.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/arith.h"
 
 #ifdef STANDALONE
 #include "testutil.h"
 #endif
 
-#define PIXELTRACE
-
+#include <cstdio>
+#include <cassert>
+#include <iostream>
+#include <list>
+#include <cmath>
 
 typedef texture<float, 2, cudaReadModeElementType> texture2D;
 
diff --git a/cuda/2d/par_fp.h b/cuda/2d/par_fp.h
deleted file mode 100644
index 62277a1..0000000
--- a/cuda/2d/par_fp.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_PAR_FP_H
-#define _CUDA_PAR_FP_H
-
-namespace astraCUDA {
-
-_AstraExport bool FP(float* D_volumeData, unsigned int volumePitch,
-        float* D_projData, unsigned int projPitch,
-        const SDimensions& dims, const SParProjection* angles,
-        float fOutputScale);
-
-}
-
-#endif
diff --git a/cuda/2d/sart.cu b/cuda/2d/sart.cu
index 8b6f50e..cf9babc 100644
--- a/cuda/2d/sart.cu
+++ b/cuda/2d/sart.cu
@@ -25,17 +25,17 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
+#include "astra/cuda/2d/sart.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/arith.h"
+#include "astra/cuda/2d/fan_fp.h"
+#include "astra/cuda/2d/fan_bp.h"
+#include "astra/cuda/2d/par_fp.h"
+#include "astra/cuda/2d/par_bp.h"
+
 #include <cstdio>
 #include <cassert>
 
-#include "sart.h"
-#include "util.h"
-#include "arith.h"
-#include "fan_fp.h"
-#include "fan_bp.h"
-#include "par_fp.h"
-#include "par_bp.h"
-
 namespace astraCUDA {
 
 // FIXME: Remove these functions. (Outdated)
diff --git a/cuda/2d/sart.h b/cuda/2d/sart.h
deleted file mode 100644
index 6c0e547..0000000
--- a/cuda/2d/sart.h
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_SART_H
-#define _CUDA_SART_H
-
-#include "algo.h"
-
-namespace astraCUDA {
-
-class _AstraExport SART : public ReconAlgo {
-public:
-	SART();
-	~SART();
-
-	// disable some features
-	virtual bool enableSinogramMask() { return false; }
-
-	virtual bool init();
-
-	virtual bool setProjectionOrder(int* projectionOrder, int projectionCount);
-
-	virtual bool iterate(unsigned int iterations);
-
-	virtual float computeDiffNorm();
-
-	void setRelaxation(float r) { fRelaxation = r; }
-
-protected:
-	void reset();
-	bool precomputeWeights();
-
-	bool callFP_SART(float* D_volumeData, unsigned int volumePitch,
-	                 float* D_projData, unsigned int projPitch,
-	                 unsigned int angle, float outputScale);
-	bool callBP_SART(float* D_volumeData, unsigned int volumePitch,
-	                 float* D_projData, unsigned int projPitch,
-	                 unsigned int angle, float outputScale);
-
-
-	// projection angle variables
-	bool customOrder;
-	int* projectionOrder;
-	int projectionCount;
-	int iteration;
-
- 	// Temporary buffers
-	float* D_projData;
-	unsigned int projPitch;
-
-	float* D_tmpData; // Only used when there's a volume mask
-	unsigned int tmpPitch;
-
-	// Geometry-specific precomputed data
-	float* D_lineWeight;
-	unsigned int linePitch;
-
-	float fRelaxation;
-};
-
-}
-
-#endif
diff --git a/cuda/2d/sirt.cu b/cuda/2d/sirt.cu
index faba7a7..7ec377c 100644
--- a/cuda/2d/sirt.cu
+++ b/cuda/2d/sirt.cu
@@ -25,17 +25,17 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
-#include <cstdio>
-#include <cassert>
-
-#include "sirt.h"
-#include "util.h"
-#include "arith.h"
+#include "astra/cuda/2d/sirt.h"
+#include "astra/cuda/2d/util.h"
+#include "astra/cuda/2d/arith.h"
 
 #ifdef STANDALONE
 #include "testutil.h"
 #endif
 
+#include <cstdio>
+#include <cassert>
+
 namespace astraCUDA {
 
 SIRT::SIRT() : ReconAlgo()
diff --git a/cuda/2d/sirt.h b/cuda/2d/sirt.h
deleted file mode 100644
index 434a07c..0000000
--- a/cuda/2d/sirt.h
+++ /dev/null
@@ -1,96 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_SIRT_H
-#define _CUDA_SIRT_H
-
-#include "algo.h"
-
-namespace astraCUDA {
-
-class _AstraExport SIRT : public ReconAlgo {
-public:
-	SIRT();
-	~SIRT();
-
-	virtual bool init();
-
-	// Do optional long-object compensation. See the comments in sirt.cu.
-	// Call this after init(). It can not be used in combination with masks.
-	bool doSlabCorrections();
-
-	// Set min/max masks to existing GPU memory buffers
-	bool setMinMaxMasks(float* D_minMaskData, float* D_maxMaskData,
-	                    unsigned int pitch);
-
-	// Set min/max masks from RAM buffers
-	bool uploadMinMaxMasks(const float* minMaskData, const float* maxMaskData,
-	                       unsigned int pitch);
-
-	void setRelaxation(float r) { fRelaxation = r; }
-
-	virtual bool iterate(unsigned int iterations);
-
-	virtual float computeDiffNorm();
-
-protected:
-	void reset();
-	bool precomputeWeights();
-
- 	// Temporary buffers
-	float* D_projData;
-	unsigned int projPitch;
-
-	float* D_tmpData;
-	unsigned int tmpPitch;
-
-	// Geometry-specific precomputed data
-	float* D_lineWeight;
-	unsigned int linePitch;
-
-	float* D_pixelWeight;
-	unsigned int pixelPitch;
-
-	// Masks
-	bool freeMinMaxMasks;
-	float* D_minMaskData;
-	unsigned int minMaskPitch;
-	float* D_maxMaskData;
-	unsigned int maxMaskPitch;
-
-	float fRelaxation;
-};
-
-bool doSIRT(float* D_volumeData, unsigned int volumePitch,
-            float* D_projData, unsigned int projPitch,
-            float* D_maskData, unsigned int maskPitch,
-            const SDimensions& dims, const float* angles,
-            const float* TOffsets, unsigned int iterations);
-
-}
-
-#endif
diff --git a/cuda/2d/util.cu b/cuda/2d/util.cu
index dfc5de9..533b86c 100644
--- a/cuda/2d/util.cu
+++ b/cuda/2d/util.cu
@@ -25,11 +25,12 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 -----------------------------------------------------------------------
 */
 
+#include "astra/cuda/2d/util.h"
+
+#include "astra/Logging.h"
+
 #include <cstdio>
 #include <cassert>
-#include "util.h"
-
-#include "../../include/astra/Logging.h"
 
 namespace astraCUDA {
 
diff --git a/cuda/2d/util.h b/cuda/2d/util.h
deleted file mode 100644
index 70e7c86..0000000
--- a/cuda/2d/util.h
+++ /dev/null
@@ -1,84 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2018, imec Vision Lab, University of Antwerp
-           2014-2018, CWI, Amsterdam
-
-Contact: astra@astra-toolbox.com
-Website: http://www.astra-toolbox.com/
-
-This file is part of the ASTRA Toolbox.
-
-
-The ASTRA Toolbox 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.
-
-The ASTRA Toolbox is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _CUDA_UTIL_H
-#define _CUDA_UTIL_H
-
-#include <cuda.h>
-#include <driver_types.h>
-#include <string>
-
-#include "astra/Globals.h"
-
-#include "dims.h"
-
-#ifndef M_PI
-#define M_PI 3.14159265358979323846
-#endif
-
-#define ASTRA_CUDA_ASSERT(err) do {  if (err != cudaSuccess) { astraCUDA::reportCudaError(err); assert(err == cudaSuccess); } } while(0)
-
-
-namespace astraCUDA {
-
-bool copyVolumeToDevice(const float* in_data, unsigned int in_pitch,
-		const SDimensions& dims,
-		float* outD_data, unsigned int out_pitch);
-bool copyVolumeFromDevice(float* out_data, unsigned int out_pitch,
-		const SDimensions& dims,
-		float* inD_data, unsigned int in_pitch);
-bool copySinogramFromDevice(float* out_data, unsigned int out_pitch,
-		const SDimensions& dims,
-		float* inD_data, unsigned int in_pitch);
-bool copySinogramToDevice(const float* in_data, unsigned int in_pitch,
-		const SDimensions& dims,
-		float* outD_data, unsigned int out_pitch);
-
-bool allocateVolume(float*& D_ptr, unsigned int width, unsigned int height, unsigned int& pitch);
-void zeroVolume(float* D_data, unsigned int pitch, unsigned int width, unsigned int height);
-
-bool allocateVolumeData(float*& D_ptr, unsigned int& pitch, const SDimensions& dims);
-bool allocateProjectionData(float*& D_ptr, unsigned int& pitch, const SDimensions& dims);
-void zeroVolumeData(float* D_ptr, unsigned int pitch, const SDimensions& dims);
-void zeroProjectionData(float* D_ptr, unsigned int pitch, const SDimensions& dims);
-
-void duplicateVolumeData(float* D_dst, float* D_src, unsigned int pitch, const SDimensions& dims);
-void duplicateProjectionData(float* D_dst, float* D_src, unsigned int pitch, const SDimensions& dims);
-
-
-
-bool cudaTextForceKernelsCompletion();
-void reportCudaError(cudaError_t err);
-
-
-
-float dotProduct2D(float* D_data, unsigned int pitch,
-                   unsigned int width, unsigned int height);
-
-}
-
-#endif