From b14fb531ad9ae3d565f2cf28f5506408ab10dbed Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 18 Nov 2015 11:26:15 +0100
Subject: Add CompositeGeometryManager
This handles FP and BP operations on multiple data objects at once,
splitting them to fit in GPU memory where necessary.
---
cuda/3d/astra3d.cu | 82 ----------------
cuda/3d/astra3d.h | 9 ++
cuda/3d/mem3d.cu | 270 +++++++++++++++++++++++++++++++++++++++++++++++++++++
cuda/3d/mem3d.h | 99 ++++++++++++++++++++
4 files changed, 378 insertions(+), 82 deletions(-)
create mode 100644 cuda/3d/mem3d.cu
create mode 100644 cuda/3d/mem3d.h
(limited to 'cuda/3d')
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
--
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