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;
}
}
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");
}
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;
}
