Merge pull request #101 from wjp/composite

 Add CompositeGeometryManager

4 files changed, 378 insertions, 82 deletions

diff --git a/cuda/3d/astra3d.cu b/cuda/3d/astra3d.cu
index 3815a1a..8328229 100644
--- a/cuda/3d/astra3d.cu
+++ b/cuda/3d/astra3d.cu
@@ -58,88 +58,6 @@ enum CUDAProjectionType3d {
 };
 
 
-static SConeProjection* genConeProjections(unsigned int iProjAngles,
-                                           unsigned int iProjU,
-                                           unsigned int iProjV,
-                                           double fOriginSourceDistance,
-                                           double fOriginDetectorDistance,
-                                           double fDetUSize,
-                                           double fDetVSize,
-                                           const float *pfAngles)
-{
-	SConeProjection base;
-	base.fSrcX = 0.0f;
-	base.fSrcY = -fOriginSourceDistance;
-	base.fSrcZ = 0.0f;
-
-	base.fDetSX = iProjU * fDetUSize * -0.5f;
-	base.fDetSY = fOriginDetectorDistance;
-	base.fDetSZ = iProjV * fDetVSize * -0.5f;
-
-	base.fDetUX = fDetUSize;
-	base.fDetUY = 0.0f;
-	base.fDetUZ = 0.0f;
-
-	base.fDetVX = 0.0f;
-	base.fDetVY = 0.0f;
-	base.fDetVZ = fDetVSize;
-
-	SConeProjection* p = new SConeProjection[iProjAngles];
-
-#define ROTATE0(name,i,alpha) do { p[i].f##name##X = base.f##name##X * cos(alpha) - base.f##name##Y * sin(alpha); p[i].f##name##Y = base.f##name##X * sin(alpha) + base.f##name##Y * cos(alpha); p[i].f##name##Z = base.f##name##Z; } while(0)
-
-	for (unsigned int i = 0; i < iProjAngles; ++i) {
-		ROTATE0(Src, i, pfAngles[i]);
-		ROTATE0(DetS, i, pfAngles[i]);
-		ROTATE0(DetU, i, pfAngles[i]);
-		ROTATE0(DetV, i, pfAngles[i]);
-	}
-
-#undef ROTATE0
-
-	return p;
-}
-
-static SPar3DProjection* genPar3DProjections(unsigned int iProjAngles,
-                                             unsigned int iProjU,
-                                             unsigned int iProjV,
-                                             double fDetUSize,
-                                             double fDetVSize,
-                                             const float *pfAngles)
-{
-	SPar3DProjection base;
-	base.fRayX = 0.0f;
-	base.fRayY = 1.0f;
-	base.fRayZ = 0.0f;
-
-	base.fDetSX = iProjU * fDetUSize * -0.5f;
-	base.fDetSY = 0.0f;
-	base.fDetSZ = iProjV * fDetVSize * -0.5f;
-
-	base.fDetUX = fDetUSize;
-	base.fDetUY = 0.0f;
-	base.fDetUZ = 0.0f;
-
-	base.fDetVX = 0.0f;
-	base.fDetVY = 0.0f;
-	base.fDetVZ = fDetVSize;
-
-	SPar3DProjection* p = new SPar3DProjection[iProjAngles];
-
-#define ROTATE0(name,i,alpha) do { p[i].f##name##X = base.f##name##X * cos(alpha) - base.f##name##Y * sin(alpha); p[i].f##name##Y = base.f##name##X * sin(alpha) + base.f##name##Y * cos(alpha); p[i].f##name##Z = base.f##name##Z; } while(0)
-
-	for (unsigned int i = 0; i < iProjAngles; ++i) {
-		ROTATE0(Ray, i, pfAngles[i]);
-		ROTATE0(DetS, i, pfAngles[i]);
-		ROTATE0(DetU, i, pfAngles[i]);
-		ROTATE0(DetV, i, pfAngles[i]);
-	}
-
-#undef ROTATE0
-
-	return p;
-}
-
 
 
 
diff --git a/cuda/3d/astra3d.h b/cuda/3d/astra3d.h
index 6c3fcfb..2782994 100644
--- a/cuda/3d/astra3d.h
+++ b/cuda/3d/astra3d.h
@@ -281,6 +281,15 @@ protected:
 	AstraCGLS3d_internal *pData;
 };
 
+bool convertAstraGeometry_dims(const CVolumeGeometry3D* pVolGeom,
+                               const CProjectionGeometry3D* pProjGeom,
+                               astraCUDA3d::SDimensions3D& dims);
+
+bool convertAstraGeometry(const CVolumeGeometry3D* pVolGeom,
+                          const CProjectionGeometry3D* pProjGeom,
+                          SPar3DProjection*& pParProjs,
+                          SConeProjection*& pConeProjs,
+                          float& fOutputScale);
 
 _AstraExport bool astraCudaFP(const float* pfVolume, float* pfProjections,
                       const CVolumeGeometry3D* pVolGeom,
diff --git a/cuda/3d/mem3d.cu b/cuda/3d/mem3d.cu
new file mode 100644
index 0000000..6d81dc0
--- /dev/null
+++ b/cuda/3d/mem3d.cu
@@ -0,0 +1,270 @@
+/*
+-----------------------------------------------------------------------
+Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
+           2014-2015, CWI, Amsterdam
+
+Contact: astra@uantwerpen.be
+Website: http://sf.net/projects/astra-toolbox
+
+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/>.
+
+-----------------------------------------------------------------------
+$Id$
+*/
+
+#include <cstdio>
+#include <cassert>
+
+#include "util3d.h"
+
+#include "mem3d.h"
+
+#include "astra3d.h"
+#include "cone_fp.h"
+#include "cone_bp.h"
+#include "par3d_fp.h"
+#include "par3d_bp.h"
+
+#include "astra/Logging.h"
+
+
+namespace astraCUDA3d {
+
+
+struct SMemHandle3D_internal
+{
+	cudaPitchedPtr ptr;
+	unsigned int nx;
+	unsigned int ny;
+	unsigned int nz;
+};
+
+size_t availableGPUMemory()
+{
+	size_t free, total;
+	cudaError_t err = cudaMemGetInfo(&free, &total);
+	if (err != cudaSuccess)
+		return 0;
+	return free;
+}
+
+MemHandle3D allocateGPUMemory(unsigned int x, unsigned int y, unsigned int z, Mem3DZeroMode zero)
+{
+	SMemHandle3D_internal hnd;
+	hnd.nx = x;
+	hnd.ny = y;
+	hnd.nz = z;
+
+	size_t free = availableGPUMemory();
+
+	cudaError_t err;
+	err = cudaMalloc3D(&hnd.ptr, make_cudaExtent(sizeof(float)*x, y, z));
+
+	if (err != cudaSuccess) {
+		return MemHandle3D();
+	}
+
+	size_t free2 = availableGPUMemory();
+
+	ASTRA_DEBUG("Allocated %d x %d x %d on GPU. (Pre: %lu, post: %lu)", x, y, z, free, free2);
+
+
+
+	if (zero == INIT_ZERO) {
+		err = cudaMemset3D(hnd.ptr, 0, make_cudaExtent(sizeof(float)*x, y, z));
+		if (err != cudaSuccess) {
+			cudaFree(hnd.ptr.ptr);
+			return MemHandle3D();
+		}
+	}
+
+	MemHandle3D ret;
+	ret.d = boost::shared_ptr<SMemHandle3D_internal>(new SMemHandle3D_internal);
+	*ret.d = hnd;
+
+	return ret;
+}
+
+bool freeGPUMemory(MemHandle3D handle)
+{
+	size_t free = availableGPUMemory();
+	cudaError_t err = cudaFree(handle.d->ptr.ptr);
+	size_t free2 = availableGPUMemory();
+
+	ASTRA_DEBUG("Freeing memory. (Pre: %lu, post: %lu)", free, free2);
+
+	return err == cudaSuccess;
+}
+
+bool copyToGPUMemory(const float *src, MemHandle3D dst, const SSubDimensions3D &pos)
+{
+	ASTRA_DEBUG("Copying %d x %d x %d to GPU", pos.subnx, pos.subny, pos.subnz);
+	ASTRA_DEBUG("Offset %d,%d,%d", pos.subx, pos.suby, pos.subz);
+	cudaPitchedPtr s;
+	s.ptr = (void*)src; // const cast away
+	s.pitch = pos.pitch * sizeof(float);
+	s.xsize = pos.nx * sizeof(float);
+	s.ysize = pos.ny;
+	ASTRA_DEBUG("Pitch %d, xsize %d, ysize %d", s.pitch, s.xsize, s.ysize);
+
+	cudaMemcpy3DParms p;
+	p.srcArray = 0;
+	p.srcPos = make_cudaPos(pos.subx * sizeof(float), pos.suby, pos.subz);
+	p.srcPtr = s;
+
+	p.dstArray = 0;
+	p.dstPos = make_cudaPos(0, 0, 0);
+	p.dstPtr = dst.d->ptr;
+
+	p.extent = make_cudaExtent(pos.subnx * sizeof(float), pos.subny, pos.subnz);
+
+	p.kind = cudaMemcpyHostToDevice;
+
+	cudaError_t err = cudaMemcpy3D(&p);
+
+	return err == cudaSuccess;
+}
+
+
+bool copyFromGPUMemory(float *dst, MemHandle3D src, const SSubDimensions3D &pos)
+{
+	ASTRA_DEBUG("Copying %d x %d x %d from GPU", pos.subnx, pos.subny, pos.subnz);
+	ASTRA_DEBUG("Offset %d,%d,%d", pos.subx, pos.suby, pos.subz);
+	cudaPitchedPtr d;
+	d.ptr = (void*)dst;
+	d.pitch = pos.pitch * sizeof(float);
+	d.xsize = pos.nx * sizeof(float);
+	d.ysize = pos.ny;
+	ASTRA_DEBUG("Pitch %d, xsize %d, ysize %d", d.pitch, d.xsize, d.ysize);
+
+	cudaMemcpy3DParms p;
+	p.srcArray = 0;
+	p.srcPos = make_cudaPos(0, 0, 0);
+	p.srcPtr = src.d->ptr;
+
+	p.dstArray = 0;
+	p.dstPos = make_cudaPos(pos.subx * sizeof(float), pos.suby, pos.subz);
+	p.dstPtr = d;
+
+	p.extent = make_cudaExtent(pos.subnx * sizeof(float), pos.subny, pos.subnz);
+
+	p.kind = cudaMemcpyDeviceToHost;
+
+	cudaError_t err = cudaMemcpy3D(&p);
+
+	return err == cudaSuccess;
+
+}
+
+
+bool FP(const astra::CProjectionGeometry3D* pProjGeom, MemHandle3D projData, const astra::CVolumeGeometry3D* pVolGeom, MemHandle3D volData, int iDetectorSuperSampling, astra::Cuda3DProjectionKernel projKernel)
+{
+	SDimensions3D dims;
+
+	bool ok = convertAstraGeometry_dims(pVolGeom, pProjGeom, dims);
+	if (!ok)
+		return false;
+
+#if 1
+	dims.iRaysPerDetDim = iDetectorSuperSampling;
+	if (iDetectorSuperSampling == 0)
+		return false;
+#else
+	dims.iRaysPerDetDim = 1;
+	astra::Cuda3DProjectionKernel projKernel = astra::ker3d_default;
+#endif
+
+
+	SPar3DProjection* pParProjs;
+	SConeProjection* pConeProjs;
+
+	float outputScale = 1.0f;
+
+	ok = convertAstraGeometry(pVolGeom, pProjGeom,
+	                          pParProjs, pConeProjs,
+	                          outputScale);
+
+	if (pParProjs) {
+#if 0
+		for (int i = 0; i < dims.iProjAngles; ++i) {
+			ASTRA_DEBUG("Vec: %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f\n",
+			    pParProjs[i].fRayX, pParProjs[i].fRayY, pParProjs[i].fRayZ,
+			    pParProjs[i].fDetSX, pParProjs[i].fDetSY, pParProjs[i].fDetSZ,
+			    pParProjs[i].fDetUX, pParProjs[i].fDetUY, pParProjs[i].fDetUZ,
+			    pParProjs[i].fDetVX, pParProjs[i].fDetVY, pParProjs[i].fDetVZ);
+		}
+#endif
+
+		switch (projKernel) {
+		case astra::ker3d_default:
+			ok &= Par3DFP(volData.d->ptr, projData.d->ptr, dims, pParProjs, outputScale);
+			break;
+		case astra::ker3d_sum_square_weights:
+			ok &= Par3DFP_SumSqW(volData.d->ptr, projData.d->ptr, dims, pParProjs, outputScale*outputScale);
+			break;
+		default:
+			ok = false;
+		}
+	} else {
+		switch (projKernel) {
+		case astra::ker3d_default:
+			ok &= ConeFP(volData.d->ptr, projData.d->ptr, dims, pConeProjs, outputScale);
+			break;
+		default:
+			ok = false;
+		}
+	}
+
+	return ok;
+}
+
+bool BP(const astra::CProjectionGeometry3D* pProjGeom, MemHandle3D projData, const astra::CVolumeGeometry3D* pVolGeom, MemHandle3D volData, int iVoxelSuperSampling)
+{
+	SDimensions3D dims;
+
+	bool ok = convertAstraGeometry_dims(pVolGeom, pProjGeom, dims);
+	if (!ok)
+		return false;
+
+#if 1
+	dims.iRaysPerVoxelDim = iVoxelSuperSampling;
+#else
+	dims.iRaysPerVoxelDim = 1;
+#endif
+
+	SPar3DProjection* pParProjs;
+	SConeProjection* pConeProjs;
+
+	float outputScale = 1.0f;
+
+	ok = convertAstraGeometry(pVolGeom, pProjGeom,
+	                          pParProjs, pConeProjs,
+	                          outputScale);
+
+	if (pParProjs)
+		ok &= Par3DBP(volData.d->ptr, projData.d->ptr, dims, pParProjs, outputScale);
+	else
+		ok &= ConeBP(volData.d->ptr, projData.d->ptr, dims, pConeProjs, outputScale);
+
+	return ok;
+
+}
+
+
+
+
+}
diff --git a/cuda/3d/mem3d.h b/cuda/3d/mem3d.h
new file mode 100644
index 0000000..82bad19
--- /dev/null
+++ b/cuda/3d/mem3d.h
@@ -0,0 +1,99 @@
+/*
+-----------------------------------------------------------------------
+Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
+           2014-2015, CWI, Amsterdam
+
+Contact: astra@uantwerpen.be
+Website: http://sf.net/projects/astra-toolbox
+
+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_MEM3D_H
+#define _CUDA_MEM3D_H
+
+#include <boost/shared_ptr.hpp>
+
+#include "astra3d.h"
+
+namespace astra {
+class CVolumeGeometry3D;
+class CProjectionGeometry3D;	
+}
+
+namespace astraCUDA3d {
+
+// TODO: Make it possible to delete these handles when they're no longer
+// necessary inside the FP/BP
+//
+// TODO: Add functions for querying capacity
+
+struct SMemHandle3D_internal;
+
+struct MemHandle3D {
+	boost::shared_ptr<SMemHandle3D_internal> d;
+	operator bool() const { return (bool)d; }
+};
+
+struct SSubDimensions3D {
+	unsigned int nx;
+	unsigned int ny;
+	unsigned int nz;
+	unsigned int pitch;
+	unsigned int subnx;
+	unsigned int subny;
+	unsigned int subnz;
+	unsigned int subx;
+	unsigned int suby;
+	unsigned int subz;
+};
+
+/*
+// Useful or not?
+enum Mem3DCopyMode {
+	MODE_SET,
+	MODE_ADD
+};
+*/
+
+enum Mem3DZeroMode {
+	INIT_NO,
+	INIT_ZERO
+};
+
+size_t availableGPUMemory();
+
+MemHandle3D allocateGPUMemory(unsigned int x, unsigned int y, unsigned int z, Mem3DZeroMode zero);
+
+bool copyToGPUMemory(const float *src, MemHandle3D dst, const SSubDimensions3D &pos);
+
+bool copyFromGPUMemory(float *dst, MemHandle3D src, const SSubDimensions3D &pos);
+
+bool freeGPUMemory(MemHandle3D handle);
+
+
+bool FP(const astra::CProjectionGeometry3D* pProjGeom, MemHandle3D projData, const astra::CVolumeGeometry3D* pVolGeom, MemHandle3D volData, int iDetectorSuperSampling, astra::Cuda3DProjectionKernel projKernel);
+
+bool BP(const astra::CProjectionGeometry3D* pProjGeom, MemHandle3D projData, const astra::CVolumeGeometry3D* pVolGeom, MemHandle3D volData, int iVoxelSuperSampling);
+
+
+
+}
+
+#endif