Update version to 1.3

1 files changed, 428 insertions, 0 deletions

diff --git a/cuda/3d/cgls3d.cu b/cuda/3d/cgls3d.cu
new file mode 100644
index 0000000..72bb9cd
--- /dev/null
+++ b/cuda/3d/cgls3d.cu
@@ -0,0 +1,428 @@
+/*
+-----------------------------------------------------------------------
+Copyright 2012 iMinds-Vision Lab, University of Antwerp
+
+Contact: astra@ua.ac.be
+Website: http://astra.ua.ac.be
+
+
+This file is part of the
+All Scale Tomographic Reconstruction Antwerp Toolbox ("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 "cgls3d.h"
+#include "util3d.h"
+#include "arith3d.h"
+#include "cone_fp.h"
+
+#ifdef STANDALONE
+#include "testutil.h"
+#endif
+
+namespace astraCUDA3d {
+
+CGLS::CGLS() : ReconAlgo3D()
+{
+	D_maskData.ptr = 0;
+	D_smaskData.ptr = 0;
+
+	D_sinoData.ptr = 0;
+	D_volumeData.ptr = 0;
+
+	D_r.ptr = 0;
+	D_w.ptr = 0;
+	D_z.ptr = 0;
+	D_p.ptr = 0;
+
+	useVolumeMask = false;
+	useSinogramMask = false;
+}
+
+
+CGLS::~CGLS()
+{
+	reset();
+}
+
+void CGLS::reset()
+{
+	cudaFree(D_r.ptr);
+	cudaFree(D_w.ptr);
+	cudaFree(D_z.ptr);
+	cudaFree(D_p.ptr);
+
+	D_maskData.ptr = 0;
+	D_smaskData.ptr = 0;
+
+	D_sinoData.ptr = 0;
+	D_volumeData.ptr = 0;
+
+	D_r.ptr = 0;
+	D_w.ptr = 0;
+	D_z.ptr = 0;
+	D_p.ptr = 0;
+
+	useVolumeMask = false;
+	useSinogramMask = false;
+
+	sliceInitialized = false;
+
+	ReconAlgo3D::reset();
+}
+
+bool CGLS::enableVolumeMask()
+{
+	useVolumeMask = true;
+	return true;
+}
+
+bool CGLS::enableSinogramMask()
+{
+	useSinogramMask = true;
+	return true;
+}
+
+
+bool CGLS::init()
+{
+	D_z = allocateVolumeData(dims);
+	D_p = allocateVolumeData(dims);
+	D_r = allocateProjectionData(dims);
+	D_w = allocateProjectionData(dims);
+
+	// TODO: check if allocations succeeded
+	return true;
+}
+
+bool CGLS::setVolumeMask(cudaPitchedPtr& _D_maskData)
+{
+	assert(useVolumeMask);
+
+	D_maskData = _D_maskData;
+
+	return true;
+}
+
+bool CGLS::setSinogramMask(cudaPitchedPtr& _D_smaskData)
+{
+	return false;
+#if 0
+	// TODO: Implement this
+	assert(useSinogramMask);
+
+	D_smaskData = _D_smaskData;
+	return true;
+#endif
+}
+
+bool CGLS::setBuffers(cudaPitchedPtr& _D_volumeData,
+                      cudaPitchedPtr& _D_projData)
+{
+	D_volumeData = _D_volumeData;
+	D_sinoData = _D_projData;
+
+	fprintf(stderr, "Reconstruction buffer: %p\n", (void*)D_volumeData.ptr);
+
+	sliceInitialized = false;
+
+	return true;
+}
+
+bool CGLS::iterate(unsigned int iterations)
+{
+	shouldAbort = false;
+
+	if (!sliceInitialized) {
+
+		// copy sinogram
+		duplicateProjectionData(D_r, D_sinoData, dims);
+
+		// r = sino - A*x
+		if (useVolumeMask) {
+				duplicateVolumeData(D_z, D_volumeData, dims);
+				processVol3D<opMul>(D_z, D_maskData, dims);
+				callFP(D_z, D_r, -1.0f);
+		} else {
+				callFP(D_volumeData, D_r, -1.0f);
+		}
+
+		// p = A'*r
+		zeroVolumeData(D_p, dims);
+		callBP(D_p, D_r);
+		if (useVolumeMask)
+			processVol3D<opMul>(D_p, D_maskData, dims);
+
+		gamma = dotProduct3D(D_p, dims.iVolX, dims.iVolY, dims.iVolZ);
+
+		sliceInitialized = true;
+
+	}
+
+
+	// iteration
+	for (unsigned int iter = 0; iter < iterations && !shouldAbort; ++iter) {
+
+		// w = A*p
+		zeroProjectionData(D_w, dims);
+		callFP(D_p, D_w, 1.0f);
+
+		// alpha = gamma / <w,w>
+		float ww = dotProduct3D(D_w, dims.iProjU, dims.iProjAngles, dims.iProjV);
+		float alpha = gamma / ww;
+
+		// x += alpha*p
+		processVol3D<opAddScaled>(D_volumeData, D_p, alpha, dims);
+
+		// r -= alpha*w
+		processSino3D<opAddScaled>(D_r, D_w, -alpha, dims);
+
+		// z = A'*r
+		zeroVolumeData(D_z, dims);
+		callBP(D_z, D_r);
+		if (useVolumeMask)
+			processVol3D<opMul>(D_z, D_maskData, dims);
+
+		float beta = 1.0f / gamma;
+		gamma = dotProduct3D(D_z, dims.iVolX, dims.iVolY, dims.iVolZ);
+
+		beta *= gamma;
+
+		// p = z + beta*p
+		processVol3D<opScaleAndAdd>(D_p, D_z, beta, dims);
+	}
+
+	return true;
+}
+
+float CGLS::computeDiffNorm()
+{
+	// We can use w and z as temporary storage here since they're not
+	// used outside of iterations.
+
+	// copy sinogram to w
+	duplicateProjectionData(D_w, D_sinoData, dims);
+
+	// do FP, subtracting projection from sinogram
+	if (useVolumeMask) {
+			duplicateVolumeData(D_z, D_volumeData, dims);
+			processVol3D<opMul>(D_z, D_maskData, dims);
+			callFP(D_z, D_w, -1.0f);
+	} else {
+			callFP(D_volumeData, D_w, -1.0f);
+	}
+
+	float s = dotProduct3D(D_w, dims.iProjU, dims.iProjAngles, dims.iProjV);
+	return sqrt(s);
+}
+
+
+bool doCGLS(cudaPitchedPtr& D_volumeData, 
+            cudaPitchedPtr& D_sinoData,
+            cudaPitchedPtr& D_maskData,
+            const SDimensions3D& dims, const SConeProjection* angles,
+            unsigned int iterations)
+{
+	CGLS cgls;
+	bool ok = true;
+
+	ok &= cgls.setConeGeometry(dims, angles);
+	if (D_maskData.ptr)
+		ok &= cgls.enableVolumeMask();
+
+	if (!ok)
+		return false;
+
+	ok = cgls.init();
+	if (!ok)
+		return false;
+
+	if (D_maskData.ptr)
+		ok &= cgls.setVolumeMask(D_maskData);
+
+	ok &= cgls.setBuffers(D_volumeData, D_sinoData);
+	if (!ok)
+		return false;
+
+	ok = cgls.iterate(iterations);
+
+	return ok;
+}
+
+}
+
+#ifdef STANDALONE
+
+using namespace astraCUDA3d;
+
+int main()
+{
+	SDimensions3D dims;
+	dims.iVolX = 256;
+	dims.iVolY = 256;
+	dims.iVolZ = 256;
+	dims.iProjAngles = 100;
+	dims.iProjU = 512;
+	dims.iProjV = 512;
+	dims.iRaysPerDet = 1;
+
+	SConeProjection angle[100];
+	angle[0].fSrcX = -2905.6;
+	angle[0].fSrcY = 0;
+	angle[0].fSrcZ = 0;
+
+	angle[0].fDetSX = 694.4;
+	angle[0].fDetSY = -122.4704;
+	angle[0].fDetSZ = -122.4704;
+
+	angle[0].fDetUX = 0;
+	angle[0].fDetUY = .4784;
+	//angle[0].fDetUY = .5;
+	angle[0].fDetUZ = 0;
+
+	angle[0].fDetVX = 0;
+	angle[0].fDetVY = 0;
+	angle[0].fDetVZ = .4784;
+
+#define ROTATE0(name,i,alpha) do { angle[i].f##name##X = angle[0].f##name##X * cos(alpha) - angle[0].f##name##Y * sin(alpha); angle[i].f##name##Y = angle[0].f##name##X * sin(alpha) + angle[0].f##name##Y * cos(alpha); } while(0)
+	for (int i = 1; i < 100; ++i) {
+		angle[i] = angle[0];
+		ROTATE0(Src, i, i*2*M_PI/100);
+		ROTATE0(DetS, i, i*2*M_PI/100);
+		ROTATE0(DetU, i, i*2*M_PI/100);
+		ROTATE0(DetV, i, i*2*M_PI/100);
+	}
+#undef ROTATE0
+
+
+	cudaPitchedPtr volData = allocateVolumeData(dims);
+	cudaPitchedPtr projData = allocateProjectionData(dims);
+	zeroProjectionData(projData, dims);
+
+	float* pbuf = new float[100*512*512];
+	copyProjectionsFromDevice(pbuf, projData, dims);
+	copyProjectionsToDevice(pbuf, projData, dims);
+	delete[] pbuf;
+
+#if 0
+	float* slice = new float[256*256];
+	cudaPitchedPtr ptr;
+	ptr.ptr = slice;
+	ptr.pitch = 256*sizeof(float);
+	ptr.xsize = 256*sizeof(float);
+	ptr.ysize = 256;
+
+	for (unsigned int i = 0; i < 256; ++i) {
+		for (unsigned int y = 0; y < 256; ++y)
+			for (unsigned int x = 0; x < 256; ++x)
+				slice[y*256+x] = (i-127.5)*(i-127.5)+(y-127.5)*(y-127.5)+(x-127.5)*(x-127.5) < 4900 ? 1.0f : 0.0f;
+
+		cudaExtent extentS;
+		extentS.width = dims.iVolX*sizeof(float);
+		extentS.height = dims.iVolY;
+		extentS.depth = 1;
+		cudaPos sp = { 0, 0, 0 };
+		cudaPos dp = { 0, 0, i };
+		cudaMemcpy3DParms p;
+		p.srcArray = 0;
+		p.srcPos = sp;
+		p.srcPtr = ptr;
+		p.dstArray = 0;
+		p.dstPos = dp;
+		p.dstPtr = volData;
+		p.extent = extentS;
+		p.kind = cudaMemcpyHostToDevice;
+		cudaMemcpy3D(&p);
+	}
+	astraCUDA3d::ConeFP(volData, projData, dims, angle, 1.0f);
+
+#else
+
+	for (int i = 0; i < 100; ++i) {
+		char fname[32];
+		sprintf(fname, "Tiffs/%04d.png", 4*i);
+		unsigned int w,h;
+		float* bufp = loadImage(fname, w,h);
+
+		for (int j = 0; j < 512*512; ++j) {
+			float v = bufp[j];
+			if (v > 236.0f) v = 236.0f;
+			v = logf(236.0f / v);
+			bufp[j] = 256*v;
+		}
+
+		for (int j = 0; j < 512; ++j) {
+			cudaMemcpy(((float*)projData.ptr)+100*512*j+512*i, bufp+512*j, 512*sizeof(float), cudaMemcpyHostToDevice);
+		}
+
+		delete[] bufp;
+
+	}
+#endif
+
+#if 0
+	float* bufs = new float[100*512];
+
+	for (int i = 0; i < 512; ++i) {
+		cudaMemcpy(bufs, ((float*)projData.ptr)+100*512*i, 100*512*sizeof(float), cudaMemcpyDeviceToHost);
+
+		printf("%d %d %d\n", projData.pitch, projData.xsize, projData.ysize);
+
+		char fname[20];
+		sprintf(fname, "sino%03d.png", i);
+		saveImage(fname, 100, 512, bufs);
+	}
+
+	float* bufp = new float[512*512];
+
+	for (int i = 0; i < 100; ++i) {
+		for (int j = 0; j < 512; ++j) {
+			cudaMemcpy(bufp+512*j, ((float*)projData.ptr)+100*512*j+512*i, 512*sizeof(float), cudaMemcpyDeviceToHost);
+		}
+
+		char fname[20];
+		sprintf(fname, "proj%03d.png", i);
+		saveImage(fname, 512, 512, bufp);
+	}
+#endif
+
+	zeroVolumeData(volData, dims);
+
+	cudaPitchedPtr maskData;
+	maskData.ptr = 0;
+
+	astraCUDA3d::doCGLS(volData, projData, maskData, dims, angle, 50);
+#if 1
+	float* buf = new float[256*256];
+
+	for (int i = 0; i < 256; ++i) {
+		cudaMemcpy(buf, ((float*)volData.ptr)+256*256*i, 256*256*sizeof(float), cudaMemcpyDeviceToHost);
+
+		char fname[20];
+		sprintf(fname, "vol%03d.png", i);
+		saveImage(fname, 256, 256, buf);
+	}
+#endif
+
+	return 0;
+}
+#endif
+