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();
}
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();
}
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 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;
}
}
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;
}
}
public Grid2D add(OpenCLGrid2D image1, OpenCLGrid2D image2) {
// create context
if (context == null) {
context = OpenCLUtil.getStaticContext();
}
// select device
if (device == null) {
device = context.getMaxFlopsDevice();
}
// define local and global sizes
int width = Math.min(image1.getWidth(), image2.getWidth());
int height = Math.min(image1.getHeight(), image2.getHeight());
int imageSize = width * height;
int localWorkSize = Math.min(device.getMaxWorkGroupSize(), 8);
int globalWorkSizeW =
OpenCLUtil.roundUp(
localWorkSize, width); // rounded up to the nearest multiple of localWorkSize
int globalWorkSizeH = OpenCLUtil.roundUp(localWorkSize, height);
// load sources, create and build programm
if (program == null) {
try {
program =
context.createProgram(this.getClass().getResourceAsStream("exercise4.cl")).build();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
System.exit(-1);
}
}
// create output image
CLBuffer<FloatBuffer> output = context.createFloatBuffer(imageSize, Mem.WRITE_ONLY);
if (kernel == null) {
kernel = program.createCLKernel("addImages");
}
// createCommandQueue
CLCommandQueue queue = device.createCommandQueue();
image1.getDelegate().prepareForDeviceOperation();
image2.getDelegate().prepareForDeviceOperation();
// put memory on the graphics card
kernel
.putArg(image1.getDelegate().getCLBuffer())
.putArg(image2.getDelegate().getCLBuffer())
.putArg(output)
.putArg(width)
.putArg(height);
kernel.rewind();
queue
.put2DRangeKernel(
kernel, 0, 0, globalWorkSizeW, globalWorkSizeH, localWorkSize, localWorkSize)
.putBarrier()
// put memory from graphic card to host
.putReadBuffer(output, true)
.finish();
Grid2D result = new Grid2D(image1);
output.getBuffer().rewind();
for (int i = 0; i < result.getSize()[1]; ++i) {
for (int j = 0; j < result.getSize()[0]; j++) {
result.setAtIndex(j, i, output.getBuffer().get());
}
}
output.release();
queue.release();
return result;
}
public Grid2D openCLBackprojection(
OpenCLGrid2D filteredSinogramm,
int widthPhantom,
int heightPhantom,
int worksize,
float detectorSpacing,
int numberOfPixel,
int numberProjections,
float scanAngle,
double[] spacing,
double[] origin) {
// create context
CLContext context = OpenCLUtil.getStaticContext();
// select device
CLDevice device = context.getMaxFlopsDevice();
// define local and global sizes
double spacingAngle = (double) (scanAngle / numberProjections);
double originDetector = -(detectorSpacing * numberOfPixel) / 2.0;
int imageSize = widthPhantom * heightPhantom;
int localWorkSize = Math.min(device.getMaxWorkGroupSize(), worksize);
int globalWorkSizeW =
OpenCLUtil.roundUp(
localWorkSize, widthPhantom); // rounded up to the nearest multiple of localWorkSize
int globalWorkSizeH = OpenCLUtil.roundUp(localWorkSize, heightPhantom);
// load sources, create and build programm
try {
this.program =
context.createProgram(this.getClass().getResourceAsStream("exercise4.cl")).build();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
System.exit(-1);
}
// create image from input grid
// CLImageFormat format = new CLImageFormat(ChannelOrder.INTENSITY, ChannelType.FLOAT);
// create output image
CLBuffer<FloatBuffer> output = context.createFloatBuffer(imageSize, Mem.WRITE_ONLY);
if (kernel == null) {
kernel = program.createCLKernel("parallelBackProjection");
}
// createCommandQueue
CLCommandQueue queue = device.createCommandQueue();
filteredSinogramm.getDelegate().prepareForDeviceOperation();
// put memory on the graphics card
kernel
.putArg(filteredSinogramm.getDelegate().getCLBuffer())
.putArg(output)
.putArg(numberProjections)
.putArg(numberOfPixel)
.putArg(scanAngle)
.putArg(widthPhantom)
.putArg(heightPhantom)
.putArg(spacing[0])
.putArg(spacing[1])
.putArg(origin[0])
.putArg(origin[1])
.putArg(detectorSpacing)
.putArg(spacingAngle)
.putArg(originDetector)
.putArg(0.d);
kernel.rewind();
queue
.put2DRangeKernel(
kernel, 0, 0, globalWorkSizeW, globalWorkSizeH, localWorkSize, localWorkSize)
.putBarrier()
.finish();
// put memory from graphic card to host
queue.putReadBuffer(output, true).finish();
output.getBuffer().rewind();
for (int i = 0; i < image.getSize()[1]; ++i) {
for (int j = 0; j < image.getSize()[0]; j++) {
image.setAtIndex(j, i, output.getBuffer().get());
}
}
output.release();
queue.release();
return image;
}