package edu.stanford.rsl.tutorial.motion.compensation;
import ij.IJ;
import java.io.IOException;
import java.nio.FloatBuffer;
import java.nio.IntBuffer;
import java.util.ArrayList;
import java.util.Arrays;
import com.jogamp.opencl.CLBuffer;
import com.jogamp.opencl.CLCommandQueue;
import com.jogamp.opencl.CLContext;
import com.jogamp.opencl.CLDevice;
import com.jogamp.opencl.CLImage2d;
import com.jogamp.opencl.CLImageFormat;
import com.jogamp.opencl.CLKernel;
import com.jogamp.opencl.CLProgram;
import com.jogamp.opencl.CLImageFormat.ChannelOrder;
import com.jogamp.opencl.CLImageFormat.ChannelType;
import com.jogamp.opencl.CLMemory.Mem;
import edu.stanford.rsl.apps.gui.Citeable;
import edu.stanford.rsl.conrad.data.numeric.Grid2D;
import edu.stanford.rsl.conrad.data.numeric.Grid3D;
import edu.stanford.rsl.conrad.numerics.SimpleMatrix;
import edu.stanford.rsl.conrad.opencl.OpenCLUtil;
import edu.stanford.rsl.conrad.reconstruction.VOIBasedReconstructionFilter;
import edu.stanford.rsl.conrad.utils.CONRAD;
import edu.stanford.rsl.conrad.utils.Configuration;
import edu.stanford.rsl.conrad.utils.ImageGridBuffer;
/**
* DO NOT USE IN LARGEVOLUMEMODE
* @author Marco
*
*/
public class OpenCLCompensatedBackProjector extends VOIBasedReconstructionFilter implements Runnable, Citeable{
/**
*
*/
private static final long serialVersionUID = -8615490043940236889L;
private ImageGridBuffer inputQueue = new ImageGridBuffer();
static int bpBlockSize[] = {32, 16};
private static boolean debug = false;
/**
* The OpenCL context
*/
private CLContext context;
/**
* The OpenCL program
*/
private CLProgram program;
/**
* The OpenCL device
*/
private CLDevice device;
/**
* The OpenCL kernel function binding
*/
private CLKernel kernelFunction;
/**
* The OpenCL command queue
*/
private CLCommandQueue commandQueue;
/**
* The 2D projection texture reference
*/
private CLImage2d<FloatBuffer> projectionTex = null;
/**
* The volume data that is to be reconstructed
*/
protected float h_volume[];
/**
* The global variable of the module which stores the
* view matrix.
*/
private CLBuffer<FloatBuffer> projectionMatrix = null;
private CLBuffer<IntBuffer> volStride = null;
private CLBuffer<FloatBuffer> volumePointer = null;
private CLBuffer<FloatBuffer> projectionArray = null;
protected ImageGridBuffer projections = new ImageGridBuffer();
protected ArrayList<Integer> projectionsAvailable;
protected ArrayList<Integer> projectionsDone;
private boolean largeVolumeMode = false;
private int nSteps = 1;
private int subVolumeZ = 0;
private boolean initialized = false;
public OpenCLCompensatedBackProjector () {
super();
}
@Override
public void prepareForSerialization(){
super.prepareForSerialization();
projectionMatrix = null;
volStride = null;
volumePointer = null;
projectionArray = null;
projections = null;
projectionsAvailable =null;
projectionsDone = null;
h_volume = null;
initialized = false;
// JOCL members
program = null;
device = null;
kernelFunction = null;
commandQueue = null;
projectionTex = null;
context = null;
}
@Override
public void configure() throws Exception{
configured = true;
}
protected void init(){
if (!initialized) {
largeVolumeMode = false;
int reconDimensionX = getGeometry().getReconDimensionX();
int reconDimensionY = getGeometry().getReconDimensionY();
int reconDimensionZ = getGeometry().getReconDimensionZ();
projectionsAvailable = new ArrayList<Integer>();
projectionsDone = new ArrayList<Integer>();
// Initialize JOCL.
context = OpenCLUtil.createContext();
try {
// get the fastest device
device = context.getMaxFlopsDevice();
// create the command queue
commandQueue = device.createCommandQueue();
// initialize the program
if (program==null || !program.getContext().equals(this.context)){
program = context.createProgram(OpenCLCompensatedBackProjector.class.getResourceAsStream("compensatedBackprojectCL.cl")).build();
}
} catch (Exception e) {
if (commandQueue != null)
commandQueue.release();
if (kernelFunction != null)
kernelFunction.release();
if (program != null)
program.release();
// destory context
if (context != null)
context.release();
// TODO: handle exception
e.printStackTrace();
}
// check space on device:
long memory = device.getMaxMemAllocSize();
long availableMemory = (memory);
long requiredMemory = (long)(((
((double) reconDimensionX) * reconDimensionY * ((double) reconDimensionZ) * 4)
+ (((double)Configuration.getGlobalConfiguration().getGeometry().getDetectorHeight()) * Configuration.getGlobalConfiguration().getGeometry().getDetectorWidth() * 4)));
if (debug) {
System.out.println("Total available Memory on OpenCL card:" + availableMemory);
System.out.println("Required Memory on OpenCL card:" + requiredMemory);
}
if (requiredMemory > availableMemory){
nSteps = (int)OpenCLUtil.iDivUp (requiredMemory, availableMemory);
if (debug) System.out.println("Switching to large volume mode with nSteps = " + nSteps);
largeVolumeMode = true;
}
if (debug) {
//TODO replace
/*
CUdevprop prop = new CUdevprop();
JCudaDriver.cuDeviceGetProperties(prop, dev);
System.out.println(prop.toFormattedString());
*/
}
// create the computing kernel
kernelFunction = program.createCLKernel("backprojectKernel");
// create the reconstruction volume;
int memorysize = reconDimensionX * reconDimensionY * reconDimensionZ * 4;
if (largeVolumeMode){
subVolumeZ = OpenCLUtil.iDivUp(reconDimensionZ, nSteps);
if(debug) System.out.println("SubVolumeZ: " + subVolumeZ);
h_volume = new float[reconDimensionX * reconDimensionY * subVolumeZ];
memorysize = reconDimensionX * reconDimensionY * subVolumeZ * 4;
if(debug)System.out.println("Memory: " + memorysize);
} else {
h_volume = new float[reconDimensionX * reconDimensionY * reconDimensionZ];
}
// compute adapted volume size
// volume size in x = multiple of bpBlockSize[0]
// volume size in y = multiple of bpBlockSize[1]
int adaptedVolSize[] = new int[3];
if ((reconDimensionX % bpBlockSize[0] ) == 0){
adaptedVolSize[0] = reconDimensionX;
} else {
adaptedVolSize[0] = ((reconDimensionX / bpBlockSize[0]) + 1) * bpBlockSize[0];
}
if ((reconDimensionY % bpBlockSize[1] ) == 0){
adaptedVolSize[1] = reconDimensionY;
} else {
adaptedVolSize[1] = ((reconDimensionY / bpBlockSize[1]) + 1) * bpBlockSize[1];
}
adaptedVolSize[2] = reconDimensionZ;
int volStrideHost [] = new int[2];
// compute volstride and copy it to constant memory
volStrideHost[0] = adaptedVolSize[0];
volStrideHost[1] = adaptedVolSize[0] * adaptedVolSize[1];
// copy volume to device
volumePointer = context.createFloatBuffer(h_volume.length, Mem.WRITE_ONLY);
volumePointer.getBuffer().put(h_volume);
volumePointer.getBuffer().rewind();
// copy volume stride to device
volStride = context.createIntBuffer(volStrideHost.length, Mem.READ_ONLY);
volStride.getBuffer().put(volStrideHost);
volStride.getBuffer().rewind();
commandQueue.
putWriteBuffer(volumePointer, true).
putWriteBuffer(volStride, true).
finish();
initialized = true;
}
}
private synchronized void unload(){
if (initialized) {
if ((projectionVolume != null) && (!largeVolumeMode)) {
commandQueue.putReadBuffer(volumePointer, true).finish();
volumePointer.getBuffer().rewind();
volumePointer.getBuffer().get(h_volume);
volumePointer.getBuffer().rewind();
int width = projectionVolume.getSize()[0];
int height = projectionVolume.getSize()[1];
if (this.useVOImap) {
for (int k = 0; k < projectionVolume.getSize()[2]; k++){
for (int j = 0; j < height; j++){
for (int i = 0; i < width; i++){
float value = h_volume[(((height * k) + j) * width) + i];
if (voiMap[i][j][k]) {
projectionVolume.setAtIndex(i, j, k, value);
} else {
projectionVolume.setAtIndex(i, j, k, 0);
}
}
}
}
} else {
for (int k = 0; k < projectionVolume.getSize()[2]; k++){
for (int j = 0; j < height; j++){
for (int i = 0; i < width; i++){
float value = h_volume[(((height * k) + j) * width) + i];
projectionVolume.setAtIndex(i, j, k, value);
}
}
}
}
} else {
System.out.println("Check ProjectionVolume. It seems null.");
}
h_volume = null;
// free memory on device
commandQueue.release();
if (projectionTex != null)
projectionTex.release();
if (projectionMatrix != null)
projectionMatrix.release();
if (volStride != null)
volStride.release();
if (projectionArray != null)
projectionArray.release();
if (volumePointer != null)
volumePointer.release();
kernelFunction.release();
program.release();
// destory context
context.release();
commandQueue = null;
projectionArray = null;
projectionMatrix = null;
projectionTex = null;
volStride = null;
volumePointer = null;
kernelFunction = null;
program = null;
context = null;
initialized = false;
}
}
private synchronized void initProjectionMatrix(int projectionNumber){
// load projection Matrix for current Projection.
SimpleMatrix pMat = getGeometry().getProjectionMatrix(projectionNumber).computeP();
float [] pMatFloat = new float[pMat.getCols() * pMat.getRows()];
for (int j = 0; j< pMat.getRows(); j++) {
for (int i = 0; i< pMat.getCols(); i++) {
pMatFloat[(j * pMat.getCols()) + i] = (float) pMat.getElement(j, i);
}
}
// Obtain the global pointer to the view matrix from
// the module
if (projectionMatrix == null)
projectionMatrix = context.createFloatBuffer(pMatFloat.length, Mem.READ_ONLY);
projectionMatrix.getBuffer().put(pMatFloat);
projectionMatrix.getBuffer().rewind();
commandQueue.putWriteBuffer(projectionMatrix, true).finish();
}
private synchronized void initProjectionData(Grid2D projection){
initialize(projection);
if (projection != null){
float [] proj= new float[projection.getWidth() * projection.getHeight()];
for(int i = 0; i< projection.getWidth(); i++){
for (int j =0; j < projection.getHeight(); j++){
proj[(j*projection.getWidth()) + i] = projection.getPixelValue(i, j);
}
}
if (projectionArray == null) {
// Create the array that will contain the
// projection data.
projectionArray = context.createFloatBuffer(projection.getWidth()*projection.getHeight(), Mem.READ_ONLY);
}
// Copy the projection data to the array
projectionArray.getBuffer().put(proj);
projectionArray.getBuffer().rewind();
// set the texture
CLImageFormat format = new CLImageFormat(ChannelOrder.INTENSITY, ChannelType.FLOAT);
projectionTex = context.createImage2d(projectionArray.getBuffer(), projection.getWidth(), projection.getHeight(), format, Mem.READ_ONLY);
//projectionArray.release();
} else {
System.out.println("Projection was null!!");
}
}
@Override
public String getBibtexCitation() {
String bibtex = "@inproceedings{Rohkohl08-CCR,\n" +
" author = {{Scherl}, H. and {Keck}, B. and {Kowarschik}, M. and {Hornegger}, J.},\n" +
" title = {{Fast GPU-Based CT Reconstruction using the Common Unified Device Architecture (CUDA)}},\n" +
" booktitle = {{Nuclear Science Symposium, Medical Imaging Conference 2007}},\n" +
" publisher = {IEEE},\n" +
" volume={6},\n" +
" address = {Honolulu, HI, United States},\n" +
" year = {2007}\n" +
" pages= {4464--4466},\n" +
"}";
return bibtex;
}
@Override
public String getMedlineCitation() {
return "Scherl H, Keck B, Kowarschik M, Hornegger J. Fast GPU-Based CT Reconstruction using the Common Unified Device Architecture (CUDA). In Nuclear Science Symposium, Medical Imaging Conference Record, IEEE, Honolulu, HI, United States, 2008 6:4464-6.";
}
public void waitForResult(double[] motionfield) {
OpenCLRun(motionfield);
}
@Override
public void backproject(Grid2D projection, int projectionNumber)
{
appendProjection(projection, projectionNumber);
}
private void appendProjection(Grid2D projection, int projectionNumber){
projections.add(projection, projectionNumber);
projectionsAvailable.add(new Integer(projectionNumber));
}
private synchronized void projectSingleProjection(int projectionNumber, int dimz, float respoffset){
// load projection matrix
initProjectionMatrix(projectionNumber);
// load projection
Grid2D projection = projections.get(projectionNumber);
initProjectionData(projection);
if (!largeVolumeMode) {
//projections.remove(projectionNumber);
}
// backproject for each slice
// OpenCL Grids are only two dimensional!
int reconDimensionZ = dimz;
double voxelSpacingX = getGeometry().getVoxelSpacingX();
double voxelSpacingY = getGeometry().getVoxelSpacingY();
double voxelSpacingZ = getGeometry().getVoxelSpacingZ();
// write kernel parameters
kernelFunction.rewind();
kernelFunction
.putArg(volumePointer)
.putArg(respoffset)
.putArg((int) lineOffset)
.putArg(reconDimensionZ)
.putArg((float) voxelSpacingX)
.putArg((float) voxelSpacingY)
.putArg((float) voxelSpacingZ)
.putArg((float) offsetX)
.putArg((float) offsetY)
.putArg((float) offsetZ)
.putArg(projectionTex)
.putArg(volStride)
.putArg(projectionMatrix);
int[] realLocalSize = {Math.min(device.getMaxWorkGroupSize(),bpBlockSize[0]), Math.min(device.getMaxWorkGroupSize(),bpBlockSize[1])};
// rounded up to the nearest multiple of localWorkSize
int[] globalWorkSize = {getGeometry().getReconDimensionX(), getGeometry().getReconDimensionY()};
// Call the OpenCL kernel, writing the results into the volume which is pointed at
commandQueue
.putWriteImage(projectionTex, false)
.finish()
.put2DRangeKernel(kernelFunction, 0, 0, globalWorkSize[0], globalWorkSize[1], realLocalSize[0], realLocalSize[1])
//.finish()
//.putReadBuffer(dOut, true)
.finish();
}
public void OpenCLRun(double[] motionfield) {
try {
while (projectionsAvailable.size() > 0) {
Thread.sleep(CONRAD.INVERSE_SPEEDUP);
if (showStatus) {
float status = (float) (1.0 / projections.size());
if (largeVolumeMode) {
IJ.showStatus("Streaming Projections to OpenCL Buffer");
} else {
IJ.showStatus("Backprojecting with OpenCL");
}
IJ.showProgress(status);
}
if (!largeVolumeMode) {
workOnProjectionData(motionfield);
} else {
checkProjectionData();
}
}
// System.out.println("large Volume " + largeVolumeMode);
if (largeVolumeMode){
// we have collected all projections.
// now we can reconstruct subvolumes and stich them together.
int reconDimensionZ = getGeometry().getReconDimensionZ();
double voxelSpacingX = getGeometry().getVoxelSpacingX();
double voxelSpacingY = getGeometry().getVoxelSpacingY();
double voxelSpacingZ = getGeometry().getVoxelSpacingZ();
useVOImap = false;
initialize(projections.get(0));
double originalOffsetZ = offsetZ;
double originalReconDimZ = reconDimensionZ;
reconDimensionZ = subVolumeZ;
int maxProjectionNumber = projections.size();
float all = nSteps * maxProjectionNumber*2;
for (int n =0; n < nSteps; n++){ // For each subvolume
// set all to 0;
Arrays.fill(h_volume, 0);
volumePointer.getBuffer().rewind();
volumePointer.getBuffer().put(h_volume);
volumePointer.getBuffer().rewind();
commandQueue.putWriteBuffer(volumePointer, true).finish();
offsetZ = originalOffsetZ - (reconDimensionZ*voxelSpacingZ*n);
for (int p = 0; p < maxProjectionNumber; p ++){ // For all projections
float currentStep = (n*maxProjectionNumber*2) + p;
if (showStatus) {
IJ.showStatus("Backprojecting with OpenCL");
IJ.showProgress(currentStep/all);
}
//System.out.println("Current: " + p);
float respoffset = (float) Math.round(motionfield[p]/voxelSpacingZ);
try {
projectSingleProjection(p, reconDimensionZ, respoffset);
} catch (Exception e){
System.out.println("Backprojection of projection " + p + " was not successful.");
e.printStackTrace();
}
}
// Gather volume
commandQueue.putReadBuffer(volumePointer, true).finish();
volumePointer.getBuffer().rewind();
volumePointer.getBuffer().get(h_volume);
volumePointer.getBuffer().rewind();
// move data to ImagePlus;
if (projectionVolume != null) {
for (int k = 0; k < reconDimensionZ; k++){
int index = (n*subVolumeZ) + k;
if (showStatus) {
float currentStep = (n*maxProjectionNumber*2) + maxProjectionNumber + k;
IJ.showStatus("Fetching Volume from OpenCL");
IJ.showProgress(currentStep/all);
}
if (index < originalReconDimZ) {
for (int j = 0; j < projectionVolume.getSize()[1]; j++){
for (int i = 0; i < projectionVolume.getSize()[0]; i++){
float value = h_volume[(((projectionVolume.getSize()[1] * k) + j) * projectionVolume.getSize()[0]) + i];
double[][] voxel = new double [4][1];
voxel[0][0] = (voxelSpacingX * i) - offsetX;
voxel[1][0] = (voxelSpacingY * j) - offsetY;
voxel[2][0] = (voxelSpacingZ * index) - originalOffsetZ;
// exception for the case "interestedInVolume == null" and largeVolume is enabled
if (interestedInVolume == null) {
projectionVolume.setAtIndex(i, j, index, value);
} else {
if (interestedInVolume.contains(voxel[0][0], voxel[1][0], voxel[2][0])) {
projectionVolume.setAtIndex(i, j, index, value);
} else {
projectionVolume.setAtIndex(i, j, index, 0);
}
}
}
}
}
}
}
}
}
} catch (InterruptedException e) {
e.printStackTrace();
}
if (showStatus) IJ.showProgress(1.0);
unload();
if (debug) System.out.println("Unloaded");
}
private synchronized void workOnProjectionData(double[] motionfield){
if (projectionsAvailable.size() > 0){
Integer current = projectionsAvailable.get(0);
projectionsAvailable.remove(0);
int p = current.intValue();
projectSingleProjection(p,
getGeometry().getReconDimensionZ(), (float)(motionfield[p]/getGeometry().getVoxelSpacingZ()));
projectionsDone.add(current);
}
}
private synchronized void checkProjectionData(){
if (projectionsAvailable.size() > 0){
Integer current = projectionsAvailable.get(0);
projectionsAvailable.remove(current);
projectionsDone.add(current);
}
}
protected Grid3D reconstructCL(double[] motionfield){
init();
int n = inputQueue.size();
for (int i = 0; i < n; i++){
backproject(inputQueue.get(i), i);
}
waitForResult(motionfield);
if (Configuration.getGlobalConfiguration().getUseHounsfieldScaling()) applyHounsfieldScaling();
//projectionVolume.show();
return projectionVolume;
}
public void loadInputQueue(ImageGridBuffer inp) throws IOException {
inputQueue = inp;
projections = inp;
}
}
/*
* Copyright (C) 2010-2014 Marco B�gel
* CONRAD is developed as an Open Source project under the GNU General Public License (GPL).
*/