@Override
public void configure() throws Exception {
Configuration config = Configuration.getGlobalConfiguration();
setConfiguration(config);
// double [] minmax = null;
checkDelta();
setNumberOfProjections(config.getGeometry().getPrimaryAngles().length);
double maxRange = (Math.PI + (2 * delta));
if (getPrimaryAngles() != null) {
// minmax = DoubleArrayUtil.minAndMaxOfArray(primaryAngles);
double factor = 15 - (deltaX / Math.PI * 180);
if (factor < 1) factor = 1;
double range =
(computeScanRange() + (factor * config.getGeometry().getAverageAngularIncrement()))
* Math.PI
/ 180.0;
offset = ((maxRange - range) / 2);
offset = factor * config.getGeometry().getAverageAngularIncrement() / 180.0 * Math.PI / 2;
deltaX = range - Math.PI;
if (debug) System.out.println("delta: " + delta * 180 / Math.PI);
if (debug) System.out.println("Angular Offset: " + offset + " " + maxRange + " " + range);
if (debug) System.out.println("deltaX: " + deltaX);
}
if (this.numberOfProjections == 0) {
throw new Exception("Number of projections not known");
}
setConfigured(true);
}
@Override
public void workOnSlice(int sliceNumber) {
PrioritizableScene phantomScene = phantom;
if (phantom instanceof AnalyticPhantom4D) {
AnalyticPhantom4D scene4D = (AnalyticPhantom4D) phantom;
phantomScene = scene4D.getScene(((double) sliceNumber) / trajectory.getProjectionStackSize());
String disableAutoCenterBoolean =
Configuration.getGlobalConfiguration()
.getRegistryEntry(RegKeys.DISABLE_CENTERING_4DPHANTOM_PROJECTION_RENDERING);
boolean disableAutoCenter = false;
if (disableAutoCenterBoolean != null) {
disableAutoCenter = Boolean.parseBoolean(disableAutoCenterBoolean);
}
Translation centerTranslation = new Translation(new SimpleVector(0, 0, 0));
if (!disableAutoCenter) {
SimpleVector center =
SimpleOperators.add(
phantom.getMax().getAbstractVector(), phantom.getMin().getAbstractVector())
.dividedBy(2);
centerTranslation = new Translation(center.negated());
}
for (PhysicalObject o : phantomScene) {
o.getShape().applyTransform(centerTranslation);
// System.out.println(o.getShape().getMax() + " " + o.getShape().getMin());
// Translate a part of XCAT to the center of source & detector for 2D projection (e.g. knee
// at the center of the 2d projection)
String translationString =
Configuration.getGlobalConfiguration()
.getRegistryEntry(RegKeys.GLOBAL_TRANSLATION_4DPHANTOM_PROJECTION_RENDERING);
if (translationString != null) {
// Center b/w RKJC & LKJC: -292.6426 211.7856 440.7783 (subj 5, static60),-401.1700
// 165.9885 478.5600 (subj 2, static60)
// XCAT Center by min & max: -177.73999504606988, 179.8512744259873, 312.19713254613583
// translationVector = (XCAT Center by min & max) - (Center b/w RKJC & LKJC)=>
// 114.9026, -31.9343, -128.5811 (subj5), 120, 3, -110(subj2) Try 114.0568 2.4778
// -106.2550
String[] values = translationString.split(", ");
SimpleVector translationVector =
new SimpleVector(
Double.parseDouble(values[0]),
Double.parseDouble(values[1]),
Double.parseDouble(values[2]));
Translation translationToRotationCenter = new Translation(translationVector);
o.getShape().applyTransform(translationToRotationCenter);
}
}
// System.out.println(phantomScene.getMax() + " " + phantomScene.getMin());
}
Grid2D slice = raytraceScene(phantomScene, trajectory.getProjectionMatrix(sliceNumber));
this.imageBuffer.add(slice, sliceNumber);
}
/**
* feeds the filter from a projection Source.
*
* @param source the source
* @param showStatus displays whether the status should be displayed using ImageJ
* @throws Exception may happen.
*/
public void feedFilter(ProjectionSource source, boolean showStatus) throws Exception {
// Stream data into filter
int stackSize = Configuration.getGlobalConfiguration().getGeometry().getProjectionStackSize();
for (int i = 0; i < stackSize; i++) {
process(source.getNextProjection(), i);
}
}
public void reconstructOffline(ImagePlus imagePlus) throws Exception {
ImagePlusDataSink sink = new ImagePlusDataSink();
configure();
init();
for (int i = 0; i < imagePlus.getStackSize(); i++) {
backproject(ImageUtil.wrapImageProcessor(imagePlus.getStack().getProcessor(i + 1)), i);
}
waitForResult();
if (Configuration.getGlobalConfiguration().getUseHounsfieldScaling()) applyHounsfieldScaling();
int[] size = projectionVolume.getSize();
System.out.println(size[0] + " " + size[1] + " " + size[2]);
for (int k = 0; k < projectionVolume.getSize()[2]; k++) {
FloatProcessor fl =
new FloatProcessor(projectionVolume.getSize()[0], projectionVolume.getSize()[1]);
for (int j = 0; j < projectionVolume.getSize()[1]; j++) {
for (int i = 0; i < projectionVolume.getSize()[0]; i++) {
fl.putPixelValue(i, j, projectionVolume.getAtIndex(i, j, k));
}
}
sink.process(projectionVolume.getSubGrid(k), k);
}
sink.close();
ImagePlus revan =
ImageUtil.wrapGrid3D(sink.getResult(), "Reconstruction of " + imagePlus.getTitle());
revan.setTitle(imagePlus.getTitle() + " reconstructed");
revan.show();
reset();
}
@Test
public void testCreateVolume() {
Configuration.loadConfiguration();
Volume3D vol = op.createVolume(size, dim, 1);
CUDAVolume3D cudaVol = (CUDAVolume3D) cuop.createVolume(size, dim, 1);
cudaVol.fetch();
assertVolumeEquality(vol, cudaVol);
cudaVol.destroy();
vol.destroy();
}
@Test
public void testfilt_gauss() {
Configuration.loadConfiguration();
cuop.initCUDA();
Volume3D one = op.createGaussLowPassFilter(3, size, dim, 2);
CUDAVolume3D cudaVol = (CUDAVolume3D) cuop.createGaussLowPassFilter(3, size, dim, 2);
cudaVol.fetch();
assertVolumeEquality(one, cudaVol);
cudaVol.destroy();
one.destroy();
}
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;
}
@Test
public void testMin() {
Configuration.loadConfiguration();
Volume3D one = createRandomVolume();
cuop.initCUDA();
CUDAVolume3D cudaVol = createCUDACopy(one);
float cpu = op.min(one);
float gpu = cuop.min(cudaVol);
cudaVol.fetch();
org.junit.Assert.assertTrue(cpu == gpu);
cudaVol.destroy();
one.destroy();
}
@Test
public void testDivideScalar() {
Configuration.loadConfiguration();
Volume3D one = createRandomVolume();
cuop.initCUDA();
CUDAVolume3D cudaVol = createCUDACopy(one);
op.divideScalar(one, 3.0f, 0.0f);
cuop.divideScalar(cudaVol, 3.0f, 0.0f);
cudaVol.fetch();
assertVolumeEquality(one, cudaVol);
cudaVol.destroy();
one.destroy();
}
@Test
public void testAbs() {
Configuration.loadConfiguration();
Volume3D one = createRandomVolume();
cuop.initCUDA();
CUDAVolume3D cudaVol = createCUDACopy(one);
op.abs(one);
cuop.abs(cudaVol);
cudaVol.fetch();
assertVolumeEquality(one, cudaVol);
cudaVol.destroy();
one.destroy();
}
public static void main(String[] args) {
CONRAD.setup();
Configuration config = Configuration.getGlobalConfiguration();
CircularTrajectory traj = new CircularTrajectory(config.getGeometry());
double[] startAngles = new double[] {0, 20, 40};
for (int j = 0; j < startAngles.length; j++) {
traj.setTrajectory(
2,
600,
90,
0,
0,
CameraAxisDirection.ROTATIONAXIS_PLUS,
CameraAxisDirection.DETECTORMOTION_PLUS,
new SimpleVector(0, 0, 1),
new PointND(0, 0, 0),
startAngles[j]);
for (int i = 0; i < traj.getNumProjectionMatrices(); i++) {
System.out.println("Matrix: " + traj.getProjectionMatrix(i).toString());
}
System.out.println(" ");
}
}
@Test
public void testMean() {
Configuration.loadConfiguration();
Volume3D one = createRandomVolume();
cuop.initCUDA();
CUDAVolume3D cudaVol = createCUDACopy(one);
float cpu = op.mean(one);
float gpu = cuop.mean(cudaVol);
cudaVol.fetch();
// System.out.println(cpu + " " + gpu);
org.junit.Assert.assertTrue(Math.abs(cpu - gpu) < 0.00001);
cudaVol.destroy();
one.destroy();
}
@Override
protected void reconstruct() throws Exception {
init();
for (int i = 0; i < nImages; i++) {
backproject(inputQueue.get(i), i);
}
waitForResult();
if (Configuration.getGlobalConfiguration().getUseHounsfieldScaling()) applyHounsfieldScaling();
int[] size = projectionVolume.getSize();
for (int k = 0; k < size[2]; k++) {
sink.process(projectionVolume.getSubGrid(k), k);
}
sink.close();
}
@Test
public void testfilt_cos2_quad() {
Configuration.loadConfiguration();
cuop.initCUDA();
float[][] dirs = new float[6][3];
AnisotropicFilterFunction.filt_get_filt_dirs(3, dirs);
Volume3D one =
op.createDirectionalWeights(3, size, dim, dirs[0], 1, VolumeOperator.FILTER_TYPE.QUADRATIC);
CUDAVolume3D cudaVol =
(CUDAVolume3D)
cuop.createDirectionalWeights(
3, size, dim, dirs[0], 1, VolumeOperator.FILTER_TYPE.QUADRATIC);
cudaVol.fetch();
assertVolumeEquality(one, cudaVol);
cudaVol.destroy();
one.destroy();
}
@Test
public void testAddVolumeWeight() {
Configuration.loadConfiguration();
Volume3D one = createRandomVolume();
Volume3D two = createRandomVolume();
cuop.initCUDA();
CUDAVolume3D cudaVol = createCUDACopy(one);
CUDAVolume3D cudaVol2 = createCUDACopy(two);
op.addVolume(one, two, 2.0);
cuop.addVolume(cudaVol, cudaVol2, 2.0);
cudaVol.fetch();
assertVolumeEquality(one, cudaVol);
cudaVol.destroy();
cudaVol2.destroy();
one.destroy();
two.destroy();
}
@Test
public void testfilt_cos2r() {
Configuration.loadConfiguration();
cuop.initCUDA();
float[][] dirs = new float[6][3];
AnisotropicFilterFunction.filt_get_filt_dirs(3, dirs);
Volume3D one =
op.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[0], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.NORMAL);
CUDAVolume3D cudaVol =
(CUDAVolume3D)
cuop.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[0], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.NORMAL);
cudaVol.fetch();
assertVolumeEquality(one, cudaVol);
cudaVol.destroy();
one.destroy();
}
@Test
public void testDivideByVolume() {
Configuration.loadConfiguration();
Volume3D one = createRandomVolume();
Volume3D two = createRandomVolume();
op.multiplyScalar(one, 1000, 0);
op.addScalar(two, 10, 0);
cuop.initCUDA();
CUDAVolume3D cudaVol = createCUDACopy(one);
CUDAVolume3D cudaVol2 = createCUDACopy(two);
op.divideByVolume(one, two);
cuop.divideByVolume(cudaVol, cudaVol2);
cudaVol.fetch();
assertWeakVolumeEquality(one, cudaVol);
cudaVol.destroy();
cudaVol2.destroy();
one.destroy();
two.destroy();
}
public DefrisePhantom() {
Trajectory trajectory = Configuration.getGlobalConfiguration().getGeometry();
double sourceAxisDistance = trajectory.getSourceToAxisDistance();
double sourceDetectorDistance = trajectory.getSourceToDetectorDistance();
double detectorYAxis = trajectory.getDetectorHeight() * trajectory.getPixelDimensionY();
double detectorXAxis = trajectory.getDetectorWidth() * trajectory.getPixelDimensionX();
double fovRadius = detectorXAxis * sourceAxisDistance / sourceDetectorDistance / 2 * 0.95;
double diskRadius = 4.0 / 5.0 * fovRadius;
double fovHeight = detectorYAxis * sourceAxisDistance / sourceDetectorDistance;
double diskHeight = fovHeight / 15.0;
double diskSpacing = fovHeight / 15.0;
int numDisks = 5;
double diskStart =
-(fovHeight / 2.0)
+ ((fovHeight - (numDisks * diskHeight + diskSpacing * (numDisks - 1))) / 2.0)
+ diskHeight / 2.0;
// Water Body
Cylinder cyl = new Cylinder(fovRadius, fovRadius, fovHeight);
cyl.setName("Water-like body of the phantom");
PhysicalObject po = new PhysicalObject();
po.setMaterial(MaterialsDB.getMaterialWithName("Water")); // D = 1.0
po.setShape(cyl);
add(po);
// Disk Inserts
for (int i = 0; i < numDisks; i++) {
cyl = new Cylinder(diskRadius, diskRadius, diskHeight);
cyl.setName("Disk");
cyl.applyTransform(
new Translation(new SimpleVector(0, 0, diskStart + (diskSpacing + diskHeight) * i)));
po = new PhysicalObject();
po.setMaterial(MaterialsDB.getMaterialWithName("Plexiglass")); // D = 1.95
po.setShape(cyl);
add(po);
}
}
@Override
public void configure() throws Exception {
// We will now read this from the Configuration. The detector needs to be preconfigured!
// detector = (XRayDetector) UserUtil.queryObject("Select Detector:", "Detector Selection",
// XRayDetector.class);
// detector.configure();
detector = Configuration.getGlobalConfiguration().getDetector();
detector.init();
phantom = UserUtil.queryPhantom("Select Phantom", "Select Phantom");
Material mat = null;
do {
String materialstr = UserUtil.queryString("Enter Background Medium:", "vacuum");
mat = MaterialsDB.getMaterialWithName(materialstr);
} while (mat == null);
phantom.setBackground(mat);
phantom.configure();
rayTracer.setScene((PrioritizableScene) phantom);
environment.setMaterial(phantom.getBackgroundMaterial());
super.configure();
}
@Override
public void configure() throws Exception {
slope = UserUtil.queryDouble("Enter slope of correction transformatoin", slope);
// offset = UserUtil.queryDouble("Enter offset of correction transformation", offset);
measureHard = UserUtil.queryDouble("Measurement of hard material [HU]", measureHard);
measureSoft = UserUtil.queryDouble("Measurement of soft material [HU]", measureSoft);
projectionXShift = UserUtil.queryDouble("Enter projection x shift", projectionXShift);
projectionYShift = UserUtil.queryDouble("Enter projection y shift", projectionYShift);
lambda0 = VolumeAttenuationFactorCorrectionTool.getLambda0(measureHard, measureSoft);
lut = Configuration.getGlobalConfiguration().getBeamHardeningLookupTable();
ImagePlus[] images = ImageUtil.getAvailableImagePlusAsArray();
hardMaterial =
ImageUtil.wrapImagePlus(
(ImagePlus)
JOptionPane.showInputDialog(
null,
"Select projections with hard material: ",
"Select source",
JOptionPane.PLAIN_MESSAGE,
null,
images,
images[0]));
configured = true;
}
@Test
public void testfilt_solve_max_eigenValue() {
Configuration.loadConfiguration();
cuop.initCUDA();
int[] size = {30, 30, 30};
this.size = size;
float[][] dirs = new float[6][3];
AnisotropicFilterFunction.filt_get_filt_dirs(3, dirs);
Volume3D a11 =
op.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[0], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
Volume3D a12 =
op.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[1], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
Volume3D a13 =
op.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[2], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
Volume3D a22 =
op.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[3], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
Volume3D a23 =
op.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[4], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
Volume3D a33 =
op.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[5], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
op.real(a11);
op.real(a12);
op.real(a13);
op.real(a22);
op.real(a23);
op.real(a33);
Volume3D[][] st = new Volume3D[3][3];
st[0][0] = a11;
st[0][1] = a12;
st[0][2] = a13;
st[1][0] = a12;
st[1][1] = a22;
st[1][2] = a23;
st[2][0] = a13;
st[2][1] = a23;
st[2][2] = a33;
CUDAVolume3D ca11 =
(CUDAVolume3D)
cuop.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[0], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
CUDAVolume3D ca12 =
(CUDAVolume3D)
cuop.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[1], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
CUDAVolume3D ca13 =
(CUDAVolume3D)
cuop.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[2], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
CUDAVolume3D ca22 =
(CUDAVolume3D)
cuop.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[3], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
CUDAVolume3D ca23 =
(CUDAVolume3D)
cuop.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[4], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
CUDAVolume3D ca33 =
(CUDAVolume3D)
cuop.createExponentialDirectionalHighPassFilter(
3, size, dim, dirs[5], 1, 2.0f, 1.5f, VolumeOperator.FILTER_TYPE.QUADRATIC);
cuop.real(ca11);
cuop.real(ca12);
cuop.real(ca13);
cuop.real(ca22);
cuop.real(ca23);
cuop.real(ca33);
CUDAVolume3D[][] cst = new CUDAVolume3D[3][3];
cst[0][0] = ca11;
cst[0][1] = ca12;
cst[0][2] = ca13;
cst[1][1] = ca22;
cst[1][2] = ca23;
cst[2][2] = ca33;
// new ImageJ();
Volume3D one = op.solveMaximumEigenvalue(st);
// one.getImagePlus("CPU Result").show();
CUDAVolume3D cudaVol = (CUDAVolume3D) cuop.solveMaximumEigenvalue(cst);
cudaVol.fetch();
// cudaVol.getImagePlus("CUDA Result").show();
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
assertWeakVolumeEquality(one, cudaVol);
a11.destroy();
a12.destroy();
a13.destroy();
a22.destroy();
a23.destroy();
a33.destroy();
ca11.destroy();
ca12.destroy();
ca13.destroy();
ca22.destroy();
ca23.destroy();
ca33.destroy();
cudaVol.destroy();
one.destroy();
}
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;
}
}
/**
* Projects arbitrarily defined phantoms to a detector using ray casting.<br>
* The pixel value on the detector is determined by the absorption model.<br>
* <br>
* <b>If you change anything in this class, notify the conrad-dev mailing list.</b>
*
* @author Rotimi X Ojo
* @author Andreas Maier
*/
public class AnalyticPhantomProjectorWorker extends SliceWorker {
protected AnalyticPhantom phantom;
protected Trajectory trajectory = Configuration.getGlobalConfiguration().getGeometry();
private XRayDetector detector;
private PriorityRayTracer rayTracer = new PriorityRayTracer();
private static boolean accurate = false;
// First rule of optimization is: Don't optimize!
// Start for speed up
// private StraightLine castLine = new StraightLine(new PointND(0,0,0),new SimpleVector(0,0,0));
// private SimpleVector pixel = new SimpleVector(0, 0);
// private ArrayList<PhysicalObject> segmentsBuff = new ArrayList<PhysicalObject> (1);
private PhysicalObject environment = new PhysicalObject();
// private PointND startPoint = new PointND(0,0);
// private PointND endPoint = new PointND(0,0);
// private Edge environmentEdge = new Edge(startPoint, endPoint);
// private PointND raySource = new PointND(0,0,0);
// End for speed up
@Override
public void workOnSlice(int sliceNumber) {
PrioritizableScene phantomScene = phantom;
if (phantom instanceof AnalyticPhantom4D) {
AnalyticPhantom4D scene4D = (AnalyticPhantom4D) phantom;
phantomScene = scene4D.getScene(((double) sliceNumber) / trajectory.getProjectionStackSize());
String disableAutoCenterBoolean =
Configuration.getGlobalConfiguration()
.getRegistryEntry(RegKeys.DISABLE_CENTERING_4DPHANTOM_PROJECTION_RENDERING);
boolean disableAutoCenter = false;
if (disableAutoCenterBoolean != null) {
disableAutoCenter = Boolean.parseBoolean(disableAutoCenterBoolean);
}
Translation centerTranslation = new Translation(new SimpleVector(0, 0, 0));
if (!disableAutoCenter) {
SimpleVector center =
SimpleOperators.add(
phantom.getMax().getAbstractVector(), phantom.getMin().getAbstractVector())
.dividedBy(2);
centerTranslation = new Translation(center.negated());
}
for (PhysicalObject o : phantomScene) {
o.getShape().applyTransform(centerTranslation);
// System.out.println(o.getShape().getMax() + " " + o.getShape().getMin());
// Translate a part of XCAT to the center of source & detector for 2D projection (e.g. knee
// at the center of the 2d projection)
String translationString =
Configuration.getGlobalConfiguration()
.getRegistryEntry(RegKeys.GLOBAL_TRANSLATION_4DPHANTOM_PROJECTION_RENDERING);
if (translationString != null) {
// Center b/w RKJC & LKJC: -292.6426 211.7856 440.7783 (subj 5, static60),-401.1700
// 165.9885 478.5600 (subj 2, static60)
// XCAT Center by min & max: -177.73999504606988, 179.8512744259873, 312.19713254613583
// translationVector = (XCAT Center by min & max) - (Center b/w RKJC & LKJC)=>
// 114.9026, -31.9343, -128.5811 (subj5), 120, 3, -110(subj2) Try 114.0568 2.4778
// -106.2550
String[] values = translationString.split(", ");
SimpleVector translationVector =
new SimpleVector(
Double.parseDouble(values[0]),
Double.parseDouble(values[1]),
Double.parseDouble(values[2]));
Translation translationToRotationCenter = new Translation(translationVector);
o.getShape().applyTransform(translationToRotationCenter);
}
}
// System.out.println(phantomScene.getMax() + " " + phantomScene.getMin());
}
Grid2D slice = raytraceScene(phantomScene, trajectory.getProjectionMatrix(sliceNumber));
this.imageBuffer.add(slice, sliceNumber);
}
public Grid2D raytraceScene(PrioritizableScene phantomScene, Projection projection) {
Trajectory geom = Configuration.getGlobalConfiguration().getGeometry();
// Grid2D slice = new Grid2D(geom.getDetectorWidth(), geom.getDetectorHeight());
Grid2D slice =
detector.createDetectorGrid(geom.getDetectorWidth(), geom.getDetectorHeight(), projection);
rayTracer.setScene(phantomScene);
// Second rule of optimization is: Optimize later.
PointND raySource = new PointND(0, 0, 0);
raySource.setCoordinates(projection.computeCameraCenter());
StraightLine castLine = new StraightLine(raySource, new SimpleVector(0, 0, 0));
SimpleVector centerPixDir = null;
if (accurate) {
centerPixDir = projection.computePrincipalAxis();
}
// SimpleVector prinpoint = trajectory.getProjectionMatrix(sliceNumber).getPrincipalPoint();
double xcorr = 0; // trajectory.getDetectorWidth()/2 - prinpoint.getElement(0);
double ycorr = 0; // trajectory.getDetectorHeight()/2 - prinpoint.getElement(1);
double length = trajectory.getSourceToDetectorDistance();
Edge environmentEdge = new Edge(new PointND(0), new PointND(length));
ArrayList<PhysicalObject> fallBackBackground = new ArrayList<PhysicalObject>(1);
SimpleVector pixel = new SimpleVector(0, 0);
boolean negate = false;
for (int y = 0; y < trajectory.getDetectorHeight(); y++) {
for (int x = 0; x < trajectory.getDetectorWidth(); x++) {
pixel.setElementValue(0, x - xcorr);
pixel.setElementValue(1, y - ycorr);
SimpleVector dir = projection.computeRayDirection(pixel);
if ((y == 0) && (x == 0)) {
// Check that ray direction is towards origin.
double max = 0;
int index = 0;
for (int i = 0; i < 3; i++) {
if (Math.abs(dir.getElement(i)) > max) {
max = Math.abs(dir.getElement(i));
index = i;
}
}
double t = -raySource.get(index) / dir.getElement(index);
if (t < 0) negate = true;
}
if (negate) dir.negate();
castLine.setDirection(dir);
ArrayList<PhysicalObject> segments = rayTracer.castRay(castLine);
if (accurate) {
double dirCosine = SimpleOperators.multiplyInnerProd(centerPixDir, dir);
length = trajectory.getSourceToDetectorDistance() / dirCosine;
}
if (segments == null) {
fallBackBackground.clear();
segments = fallBackBackground;
} else {
if (accurate) {
environmentEdge =
new Edge(new PointND(0), new PointND(length - getTotalSegmentsLength(segments)));
}
}
environment.setShape(environmentEdge);
segments.add(environment);
/* old code:
double integral = absorptionModel.evaluateLineIntegral(segments);
slice.putPixelValue(x, y, integral);
*/
detector.writeToDetector(slice, x, y, segments);
}
}
return slice;
}
private double getTotalSegmentsLength(ArrayList<PhysicalObject> segments) {
double sum = 0;
Iterator<PhysicalObject> it = segments.iterator();
while (it.hasNext()) {
// sum+=((Edge) it.next().getShape()).getLength();
}
return sum;
}
public SliceWorker clone() {
AnalyticPhantomProjectorWorker newRend = new AnalyticPhantomProjectorWorker();
newRend.phantom = phantom;
newRend.detector = detector;
newRend.environment.setMaterial(phantom.getBackgroundMaterial());
newRend.rayTracer.setScene((PrioritizableScene) phantom);
return newRend;
}
@Override
public void configure() throws Exception {
// We will now read this from the Configuration. The detector needs to be preconfigured!
// detector = (XRayDetector) UserUtil.queryObject("Select Detector:", "Detector Selection",
// XRayDetector.class);
// detector.configure();
detector = Configuration.getGlobalConfiguration().getDetector();
detector.init();
phantom = UserUtil.queryPhantom("Select Phantom", "Select Phantom");
Material mat = null;
do {
String materialstr = UserUtil.queryString("Enter Background Medium:", "vacuum");
mat = MaterialsDB.getMaterialWithName(materialstr);
} while (mat == null);
phantom.setBackground(mat);
phantom.configure();
rayTracer.setScene((PrioritizableScene) phantom);
environment.setMaterial(phantom.getBackgroundMaterial());
super.configure();
}
public void configure(AnalyticPhantom phan, XRayDetector detector) throws Exception {
this.detector = detector;
this.detector.init();
phantom = phan;
if (phantom.getBackgroundMaterial() == null) {
Material mat = null;
String materialstr = "vacuum";
mat = MaterialsDB.getMaterialWithName(materialstr);
phantom.setBackground(mat);
}
rayTracer.setScene((PrioritizableScene) phantom);
environment.setMaterial(phantom.getBackgroundMaterial());
super.configure();
}
@Override
public String getProcessName() {
return "Generic Phantom Projector";
}
@Override
public String getBibtexCitation() {
return CONRAD.CONRADBibtex;
}
@Override
public String getMedlineCitation() {
return CONRAD.CONRADMedline;
}
/** @return the absorptionModel */
public XRayDetector getDetector() {
return detector;
}
/** @param absorptionModel the absorptionModel to set */
public void setDetector(XRayDetector detector) {
this.detector = detector;
}
}
public Grid2D raytraceScene(PrioritizableScene phantomScene, Projection projection) {
Trajectory geom = Configuration.getGlobalConfiguration().getGeometry();
// Grid2D slice = new Grid2D(geom.getDetectorWidth(), geom.getDetectorHeight());
Grid2D slice =
detector.createDetectorGrid(geom.getDetectorWidth(), geom.getDetectorHeight(), projection);
rayTracer.setScene(phantomScene);
// Second rule of optimization is: Optimize later.
PointND raySource = new PointND(0, 0, 0);
raySource.setCoordinates(projection.computeCameraCenter());
StraightLine castLine = new StraightLine(raySource, new SimpleVector(0, 0, 0));
SimpleVector centerPixDir = null;
if (accurate) {
centerPixDir = projection.computePrincipalAxis();
}
// SimpleVector prinpoint = trajectory.getProjectionMatrix(sliceNumber).getPrincipalPoint();
double xcorr = 0; // trajectory.getDetectorWidth()/2 - prinpoint.getElement(0);
double ycorr = 0; // trajectory.getDetectorHeight()/2 - prinpoint.getElement(1);
double length = trajectory.getSourceToDetectorDistance();
Edge environmentEdge = new Edge(new PointND(0), new PointND(length));
ArrayList<PhysicalObject> fallBackBackground = new ArrayList<PhysicalObject>(1);
SimpleVector pixel = new SimpleVector(0, 0);
boolean negate = false;
for (int y = 0; y < trajectory.getDetectorHeight(); y++) {
for (int x = 0; x < trajectory.getDetectorWidth(); x++) {
pixel.setElementValue(0, x - xcorr);
pixel.setElementValue(1, y - ycorr);
SimpleVector dir = projection.computeRayDirection(pixel);
if ((y == 0) && (x == 0)) {
// Check that ray direction is towards origin.
double max = 0;
int index = 0;
for (int i = 0; i < 3; i++) {
if (Math.abs(dir.getElement(i)) > max) {
max = Math.abs(dir.getElement(i));
index = i;
}
}
double t = -raySource.get(index) / dir.getElement(index);
if (t < 0) negate = true;
}
if (negate) dir.negate();
castLine.setDirection(dir);
ArrayList<PhysicalObject> segments = rayTracer.castRay(castLine);
if (accurate) {
double dirCosine = SimpleOperators.multiplyInnerProd(centerPixDir, dir);
length = trajectory.getSourceToDetectorDistance() / dirCosine;
}
if (segments == null) {
fallBackBackground.clear();
segments = fallBackBackground;
} else {
if (accurate) {
environmentEdge =
new Edge(new PointND(0), new PointND(length - getTotalSegmentsLength(segments)));
}
}
environment.setShape(environmentEdge);
segments.add(environment);
/* old code:
double integral = absorptionModel.evaluateLineIntegral(segments);
slice.putPixelValue(x, y, integral);
*/
detector.writeToDetector(slice, x, y, segments);
}
}
return slice;
}
@Override
public Grid2D applyToolToImage(Grid2D imageProcessor) {
FloatProcessor imp = new FloatProcessor(imageProcessor.getWidth(), imageProcessor.getHeight());
imp.setPixels(imageProcessor.getBuffer());
if (!initBead) initializeBead();
ImageProcessor imp1 = imp.duplicate(); // original
double[][] beadMean3D = config.getBeadMeanPosition3D(); // [beadNo][x,y,z]
double[] uv = new double[1];
SimpleMatrix pMatrix = config.getGeometry().getProjectionMatrix(imageIndex).computeP();
// [projection #][bead #][u, v, state[0: initial, 1: registered, 2: updated by hough searching]]
double[][][] beadPosition2D = config.getBeadPosition2D();
int noBeadRegistered = 0;
double[][] xy1 = new double[WeightBearingBeadPositionBuilder.beadNo][2]; // original
double[][] xy2 =
new double[WeightBearingBeadPositionBuilder.beadNo]
[2]; // warped (mapped to the mean), control points, reference
double[][] xy1_hat = new double[WeightBearingBeadPositionBuilder.beadNo][2]; // original
double[][] xy2_hat = new double[WeightBearingBeadPositionBuilder.beadNo][2]; // original
// double distanceReferenceToCurrentBead = 0;
for (int i = WeightBearingBeadPositionBuilder.currentBeadNo; i >= 0; i--) {
if (beadMean3D[i][0] != 0
|| beadMean3D[i][1] != 0
|| beadMean3D[i][2] != 0) { // assume bead 3d is registered.
uv = compute2DCoordinates(beadMean3D[i], pMatrix);
// find bead location if registered by txt: state 1
if (beadPosition2D[imageIndex][i][2] == 1) {
noBeadRegistered++;
if (isDisplay) {
imp1.setValue(2);
imp1.drawLine(
(int) Math.round(beadPosition2D[imageIndex][i][0] - 10),
(int) Math.round(beadPosition2D[imageIndex][i][1] - 10),
(int) Math.round(beadPosition2D[imageIndex][i][0] + 10),
(int) Math.round(beadPosition2D[imageIndex][i][1] + 10));
imp1.drawLine(
(int) Math.round(beadPosition2D[imageIndex][i][0] - 10),
(int) Math.round(beadPosition2D[imageIndex][i][1] + 10),
(int) Math.round(beadPosition2D[imageIndex][i][0] + 10),
(int) Math.round(beadPosition2D[imageIndex][i][1] - 10));
imp1.drawString(
"Bead " + i + " (state:" + (int) beadPosition2D[imageIndex][i][2] + ")",
(int) beadPosition2D[imageIndex][i][0],
(int) beadPosition2D[imageIndex][i][1] - 10);
}
xy1[noBeadRegistered - 1][0] = beadPosition2D[imageIndex][i][0];
xy1[noBeadRegistered - 1][1] = beadPosition2D[imageIndex][i][1];
xy2[noBeadRegistered - 1][0] = uv[0];
xy2[noBeadRegistered - 1][1] = uv[1];
} else if (imageIndex != 0
&& imageIndex != config.getGeometry().getNumProjectionMatrices() - 1) {
if (beadPosition2D[imageIndex - 1][i][2] == 1
&& beadPosition2D[imageIndex + 1][i][2] == 1) {
noBeadRegistered++;
double xMean =
(beadPosition2D[imageIndex - 1][i][0] + beadPosition2D[imageIndex - 1][i][0]) / 2;
double yMean =
(beadPosition2D[imageIndex + 1][i][1] + beadPosition2D[imageIndex + 1][i][1]) / 2;
if (isDisplay) {
imp1.setValue(2);
imp1.drawLine(
(int) Math.round(xMean - 10),
(int) Math.round(yMean - 10),
(int) Math.round(xMean + 10),
(int) Math.round(yMean + 10));
imp1.drawLine(
(int) Math.round(xMean - 10),
(int) Math.round(yMean + 10),
(int) Math.round(xMean + 10),
(int) Math.round(yMean - 10));
imp1.drawString("Bead " + i + " (state:" + "M)", (int) xMean, (int) yMean - 10);
}
xy1[noBeadRegistered - 1][0] = xMean;
xy1[noBeadRegistered - 1][1] = yMean;
xy2[noBeadRegistered - 1][0] = uv[0];
xy2[noBeadRegistered - 1][1] = uv[1];
}
}
// mean projected bead
// imp1.drawLine((int) Math.round(uv[0]-10), (int) Math.round(uv[1]), (int)
// Math.round(uv[0]+10), (int) Math.round(uv[1]));
// imp1.drawLine((int) Math.round(uv[0]), (int) Math.round(uv[1]-10), (int)
// Math.round(uv[0]), (int) Math.round(uv[1]+10));
}
}
if (isDisplay) {
for (int x = 0; x < config.getGeometry().getDetectorWidth(); x += 50)
imp1.drawLine(x, 0, x, config.getGeometry().getDetectorHeight());
for (int y = 0; y < config.getGeometry().getDetectorHeight(); y += 50)
imp1.drawLine(0, y, config.getGeometry().getDetectorWidth(), y);
}
if (isCornerIncluded) {
xy1[noBeadRegistered + 0][0] = 0;
xy1[noBeadRegistered + 0][1] = 0;
xy2[noBeadRegistered + 0][0] = 0;
xy2[noBeadRegistered + 0][1] = 0;
xy1[noBeadRegistered + 1][0] = 0;
xy1[noBeadRegistered + 1][1] = config.getGeometry().getDetectorHeight();
xy2[noBeadRegistered + 1][0] = 0;
xy2[noBeadRegistered + 1][1] = config.getGeometry().getDetectorHeight();
xy1[noBeadRegistered + 2][0] = config.getGeometry().getDetectorWidth();
xy1[noBeadRegistered + 2][1] = 0;
xy2[noBeadRegistered + 2][0] = config.getGeometry().getDetectorWidth();
xy2[noBeadRegistered + 2][1] = 0;
xy1[noBeadRegistered + 3][0] = config.getGeometry().getDetectorWidth();
xy1[noBeadRegistered + 3][1] = config.getGeometry().getDetectorHeight();
xy2[noBeadRegistered + 3][0] = config.getGeometry().getDetectorWidth();
xy2[noBeadRegistered + 3][1] = config.getGeometry().getDetectorHeight();
noBeadRegistered = noBeadRegistered + 4;
}
boolean fScaling = true;
double minX = Double.MAX_VALUE;
double maxX = 0;
double minY = Double.MAX_VALUE;
double maxY = 0;
double c = 0;
if (fScaling) { // ----- scaling to reduce condition # of A matrix
for (int i = 0; i < noBeadRegistered; i++) {
minX = Math.min(minX, xy1[i][0]);
maxX = Math.max(maxX, xy1[i][0]);
minY = Math.min(minY, xy1[i][1]);
maxY = Math.max(maxY, xy1[i][1]);
}
c = Math.max(maxX - minX, maxY - minY);
for (int i = 0; i < noBeadRegistered; i++) {
xy1_hat[i][0] = (xy1[i][0] - minX) / c;
xy1_hat[i][1] = (xy1[i][1] - minY) / c;
xy2_hat[i][0] = (xy2[i][0] - minX) / c;
xy2_hat[i][1] = (xy2[i][1] - minY) / c;
}
} else {
xy1_hat = xy1;
xy2_hat = xy2;
}
ImageProcessor imp2 = imp1.duplicate(); // warped
/*
* A*x = b
* Matrix A = (n + 3) * (n + 3);
* n (noBeadRegistered + 4): # of control points + 4 corner points (assume corner points are static)
*/
int n = noBeadRegistered + 3;
SimpleMatrix A = new SimpleMatrix(n, n);
SimpleVector x_x = new SimpleVector(n);
SimpleVector x_y = new SimpleVector(n);
SimpleVector b_x = new SimpleVector(n);
SimpleVector b_y = new SimpleVector(n);
double rij = 0;
double valA = 0;
double valb_x = 0;
double valb_y = 0;
// Matrix L formation
// alpha: mean of distances between control points' xy-projections) is a constant only present
// on the diagonal of K
// lambda: TPS smoothing regularization coefficient
double alpha = 0.0;
double lambda = 1.6; // 1.6
for (int i = 0; i < noBeadRegistered; i++) { // i= # of row
for (int j = i; j < noBeadRegistered; j++) { // j= # of column
alpha +=
Math.sqrt(
Math.pow(xy2_hat[i][0] - xy2_hat[j][0], 2)
+ Math.pow(xy2_hat[i][1] - xy2_hat[j][1], 2));
}
}
alpha = alpha / Math.pow(noBeadRegistered, 2);
for (int i = 0; i < n; i++) { // i= # of row
for (int j = i; j < n; j++) { // j= # of column
if (i < 3 && j < 3) valA = 0;
else if (i >= 3 && j >= 3 && i == j) {
valA = Math.pow(alpha, 2) * lambda;
// valA = lambda;
if (imageIndex < 10)
System.out.println("Regularization = " + valA + ", lambda= " + lambda);
} else if (i == 0 && j >= 0) valA = 1;
else if (i == 1 && j >= 3) valA = xy1_hat[j - 3][0];
else if (i == 2 && j >= 3) valA = xy1_hat[j - 3][1];
else {
rij =
Math.pow(xy1_hat[j - 3][0] - xy1_hat[i - 3][0], 2)
+ Math.pow(xy1_hat[j - 3][1] - xy1_hat[i - 3][1], 2);
if (rij == 0) valA = 0;
else valA = rij * Math.log(rij);
}
A.setElementValue(i, j, valA);
A.setElementValue(j, i, valA);
}
if (i < 3) {
valb_x = 0;
valb_y = 0;
} else {
// valb_x = xy2_hat[i-3][0]-xy1_hat[i-3][0];
// valb_y = xy2_hat[i-3][1]-xy1_hat[i-3][1];
valb_x = xy2[i - 3][0] - xy1[i - 3][0];
valb_y = xy2[i - 3][1] - xy1[i - 3][1];
// if (imageIndex > 150 && imageIndex < 170)
// System.out.println("Idx" + imageIndex + ",Elevation" + (i-3) + ": " + valb_x + "---"
// + valb_y);
}
b_x.setElementValue(i, valb_x);
b_y.setElementValue(i, valb_y);
}
// System.out.println("A condition number=" + A.conditionNumber(MatrixNormType.MAT_NORM_L1));
// System.out.println("A condition number=" + A.conditionNumber(MatrixNormType.MAT_NORM_LINF));
x_x = Solvers.solveLinearSysytemOfEquations(A, b_x);
x_y = Solvers.solveLinearSysytemOfEquations(A, b_y);
if (fScaling) {
// ----- pixel space coefficients a, b scaling back
double tmpA0 =
x_x.getElement(0) - x_x.getElement(1) * (minX / c) - x_x.getElement(2) * (minY / c);
for (int j = 0; j < noBeadRegistered; j++) {
tmpA0 -=
Math.log(c)
* 2
* x_x.getElement(j + 3)
* (Math.pow(xy1_hat[j][0], 2) + Math.pow(xy1_hat[j][1], 2));
}
x_x.setElementValue(0, tmpA0);
tmpA0 = x_y.getElement(0) - x_y.getElement(1) * (minX / c) - x_y.getElement(2) * (minY / c);
for (int j = 0; j < noBeadRegistered; j++) {
tmpA0 -=
Math.log(c)
* 2
* x_y.getElement(j + 3)
* (Math.pow(xy1_hat[j][0], 2) + Math.pow(xy1_hat[j][1], 2));
}
x_y.setElementValue(0, tmpA0);
x_x.setElementValue(1, x_x.getElement(1) / c);
x_y.setElementValue(1, x_y.getElement(1) / c);
x_x.setElementValue(2, x_x.getElement(2) / c);
x_y.setElementValue(2, x_y.getElement(2) / c);
for (int i = 3; i < n; i++) {
x_x.setElementValue(i, x_x.getElement(i) / Math.pow(c, 2));
x_y.setElementValue(i, x_y.getElement(i) / Math.pow(c, 2));
}
// ----- pixel space coefficients a, b scaling back end
}
double devU = 0;
double devV = 0;
// Do warping
// if (imageIndex == 0) {
for (int y = 0; y < config.getGeometry().getDetectorHeight(); y++) {
// for (int y=252; y<253; y++) {
for (int x = 0; x < config.getGeometry().getDetectorWidth(); x++) {
// for (int x=606; x<607; x++) {
devU = x_x.getElement(0) + x_x.getElement(1) * x + x_x.getElement(2) * y;
devV = x_y.getElement(0) + x_y.getElement(1) * x + x_y.getElement(2) * y;
for (int i = 0; i < noBeadRegistered; i++) {
rij = Math.pow(xy1[i][0] - x, 2) + Math.pow(xy1[i][1] - y, 2);
if (rij > 0) {
devU += x_x.getElement(i + 3) * rij * Math.log(rij);
devV += x_y.getElement(i + 3) * rij * Math.log(rij);
}
}
// devU = 0;
// devV = 0;
imp2.setf(x, y, (float) imp1.getInterpolatedValue(x - devU, y - devV));
// System.out.println("x, y=" + x + ", " + y + "\t" + devU + ", " + devV);
// maxDevU = Math.max(maxDevU, devU);
// maxDevV = Math.max(maxDevV, devV);
}
}
// Error estimate after transformation
// for (int i=0; i<= WeightBearingBeadPositionBuilder.currentBeadNo; i++){
//
// if (beadMean3D[i][0] != 0 || beadMean3D[i][1] != 0 || beadMean3D[i][2] != 0){ // assume
// bead 3d is registered.
//
// // find bead location if registered by txt: state 1
// if (beadPosition2D[imageIndex][i][2] == 1){
//
// // Projected Reference
// uv = compute2DCoordinates(beadMean3D[i], pMatrix);
// double x = uv[0];
// double y = uv[1];
// // bead detected position in 2d
// // Transform to 2D coordinates, time variant position
// //beadPosition2D[imageIndex][i][0];
// //beadPosition2D[imageIndex][i][1];
//
// devU = x_x.getElement(0) + x_x.getElement(1)*x + x_x.getElement(2)*y;
// devV = x_y.getElement(0) + x_y.getElement(1)*x + x_y.getElement(2)*y;
// for (int j=0; j<noBeadRegistered; j++){
// rij = Math.pow(xy1[j][0]-x, 2) + Math.pow(xy1[j][1]-y, 2);
// if (rij > 0) {
// devU += x_x.getElement(j+3)*rij*Math.log(rij);
// devV += x_y.getElement(j+3)*rij*Math.log(rij);
// }
// }
//
// distanceReferenceToCurrentBead +=
// Math.sqrt(Math.pow(uv[0]-(beadPosition2D[imageIndex][i][0]+devU),
// 2)+Math.pow(uv[1]-(beadPosition2D[imageIndex][i][1]+devV), 2));
//
// }
// }
// }
// System.out.println("Euclidean distance\t" + imageIndex + "\t" +
// distanceReferenceToCurrentBead/noBeadRegistered);
// }
if (isDisplay) {
for (int i = WeightBearingBeadPositionBuilder.currentBeadNo; i >= 0; i--) {
if (beadMean3D[i][0] != 0
|| beadMean3D[i][1] != 0
|| beadMean3D[i][2] != 0) { // assume bead 3d is registered.
uv = compute2DCoordinates(beadMean3D[i], pMatrix);
imp2.setValue(2);
// mean projected bead
imp2.drawLine(
(int) Math.round(uv[0] - 10),
(int) Math.round(uv[1]),
(int) Math.round(uv[0] + 10),
(int) Math.round(uv[1]));
imp2.drawLine(
(int) Math.round(uv[0]),
(int) Math.round(uv[1] - 10),
(int) Math.round(uv[0]),
(int) Math.round(uv[1] + 10));
}
}
}
Grid2D result = new Grid2D((float[]) imp2.getPixels(), imp2.getWidth(), imp2.getHeight());
return result;
}
public class ThinPlateSplinesBasedProjectionWarpingTool extends IndividualImageFilteringTool {
/**
* Warping projections using thin plate splines for marker based motion correction
*
* <p>http://elonen.iki.fi/code/tpsdemo/index.html, Based mostly on "Approximation Methods for
* Thin Plate Spline Mappings and Principal Warps" by Gianluca Donato and Serge Belongie, 2002.
* (http://cseweb.ucsd.edu/~sjb/pami_tps.pdf)
*
* @author Jang-Hwan Choi
*/
private static final long serialVersionUID = -3377571138470875648L;
WeightBearingBeadPositionBuilder beadBuilder;
Configuration config = Configuration.getGlobalConfiguration();
private boolean initBead = false;
// display bead indication, horizontal & vertical lines
private boolean isDisplay = false;
private boolean isCornerIncluded = true;
public ThinPlateSplinesBasedProjectionWarpingTool() {
configured = true;
}
protected void initializeBead() {
if (!initBead) {
System.out.println("Read in initial bead positions.");
beadBuilder = new WeightBearingBeadPositionBuilder();
beadBuilder.readInitialBeadPositionFromFile();
beadBuilder.estimateBeadMeanPositionIn3D();
initBead = true;
}
}
@Override
public Grid2D applyToolToImage(Grid2D imageProcessor) {
FloatProcessor imp = new FloatProcessor(imageProcessor.getWidth(), imageProcessor.getHeight());
imp.setPixels(imageProcessor.getBuffer());
if (!initBead) initializeBead();
ImageProcessor imp1 = imp.duplicate(); // original
double[][] beadMean3D = config.getBeadMeanPosition3D(); // [beadNo][x,y,z]
double[] uv = new double[1];
SimpleMatrix pMatrix = config.getGeometry().getProjectionMatrix(imageIndex).computeP();
// [projection #][bead #][u, v, state[0: initial, 1: registered, 2: updated by hough searching]]
double[][][] beadPosition2D = config.getBeadPosition2D();
int noBeadRegistered = 0;
double[][] xy1 = new double[WeightBearingBeadPositionBuilder.beadNo][2]; // original
double[][] xy2 =
new double[WeightBearingBeadPositionBuilder.beadNo]
[2]; // warped (mapped to the mean), control points, reference
double[][] xy1_hat = new double[WeightBearingBeadPositionBuilder.beadNo][2]; // original
double[][] xy2_hat = new double[WeightBearingBeadPositionBuilder.beadNo][2]; // original
// double distanceReferenceToCurrentBead = 0;
for (int i = WeightBearingBeadPositionBuilder.currentBeadNo; i >= 0; i--) {
if (beadMean3D[i][0] != 0
|| beadMean3D[i][1] != 0
|| beadMean3D[i][2] != 0) { // assume bead 3d is registered.
uv = compute2DCoordinates(beadMean3D[i], pMatrix);
// find bead location if registered by txt: state 1
if (beadPosition2D[imageIndex][i][2] == 1) {
noBeadRegistered++;
if (isDisplay) {
imp1.setValue(2);
imp1.drawLine(
(int) Math.round(beadPosition2D[imageIndex][i][0] - 10),
(int) Math.round(beadPosition2D[imageIndex][i][1] - 10),
(int) Math.round(beadPosition2D[imageIndex][i][0] + 10),
(int) Math.round(beadPosition2D[imageIndex][i][1] + 10));
imp1.drawLine(
(int) Math.round(beadPosition2D[imageIndex][i][0] - 10),
(int) Math.round(beadPosition2D[imageIndex][i][1] + 10),
(int) Math.round(beadPosition2D[imageIndex][i][0] + 10),
(int) Math.round(beadPosition2D[imageIndex][i][1] - 10));
imp1.drawString(
"Bead " + i + " (state:" + (int) beadPosition2D[imageIndex][i][2] + ")",
(int) beadPosition2D[imageIndex][i][0],
(int) beadPosition2D[imageIndex][i][1] - 10);
}
xy1[noBeadRegistered - 1][0] = beadPosition2D[imageIndex][i][0];
xy1[noBeadRegistered - 1][1] = beadPosition2D[imageIndex][i][1];
xy2[noBeadRegistered - 1][0] = uv[0];
xy2[noBeadRegistered - 1][1] = uv[1];
} else if (imageIndex != 0
&& imageIndex != config.getGeometry().getNumProjectionMatrices() - 1) {
if (beadPosition2D[imageIndex - 1][i][2] == 1
&& beadPosition2D[imageIndex + 1][i][2] == 1) {
noBeadRegistered++;
double xMean =
(beadPosition2D[imageIndex - 1][i][0] + beadPosition2D[imageIndex - 1][i][0]) / 2;
double yMean =
(beadPosition2D[imageIndex + 1][i][1] + beadPosition2D[imageIndex + 1][i][1]) / 2;
if (isDisplay) {
imp1.setValue(2);
imp1.drawLine(
(int) Math.round(xMean - 10),
(int) Math.round(yMean - 10),
(int) Math.round(xMean + 10),
(int) Math.round(yMean + 10));
imp1.drawLine(
(int) Math.round(xMean - 10),
(int) Math.round(yMean + 10),
(int) Math.round(xMean + 10),
(int) Math.round(yMean - 10));
imp1.drawString("Bead " + i + " (state:" + "M)", (int) xMean, (int) yMean - 10);
}
xy1[noBeadRegistered - 1][0] = xMean;
xy1[noBeadRegistered - 1][1] = yMean;
xy2[noBeadRegistered - 1][0] = uv[0];
xy2[noBeadRegistered - 1][1] = uv[1];
}
}
// mean projected bead
// imp1.drawLine((int) Math.round(uv[0]-10), (int) Math.round(uv[1]), (int)
// Math.round(uv[0]+10), (int) Math.round(uv[1]));
// imp1.drawLine((int) Math.round(uv[0]), (int) Math.round(uv[1]-10), (int)
// Math.round(uv[0]), (int) Math.round(uv[1]+10));
}
}
if (isDisplay) {
for (int x = 0; x < config.getGeometry().getDetectorWidth(); x += 50)
imp1.drawLine(x, 0, x, config.getGeometry().getDetectorHeight());
for (int y = 0; y < config.getGeometry().getDetectorHeight(); y += 50)
imp1.drawLine(0, y, config.getGeometry().getDetectorWidth(), y);
}
if (isCornerIncluded) {
xy1[noBeadRegistered + 0][0] = 0;
xy1[noBeadRegistered + 0][1] = 0;
xy2[noBeadRegistered + 0][0] = 0;
xy2[noBeadRegistered + 0][1] = 0;
xy1[noBeadRegistered + 1][0] = 0;
xy1[noBeadRegistered + 1][1] = config.getGeometry().getDetectorHeight();
xy2[noBeadRegistered + 1][0] = 0;
xy2[noBeadRegistered + 1][1] = config.getGeometry().getDetectorHeight();
xy1[noBeadRegistered + 2][0] = config.getGeometry().getDetectorWidth();
xy1[noBeadRegistered + 2][1] = 0;
xy2[noBeadRegistered + 2][0] = config.getGeometry().getDetectorWidth();
xy2[noBeadRegistered + 2][1] = 0;
xy1[noBeadRegistered + 3][0] = config.getGeometry().getDetectorWidth();
xy1[noBeadRegistered + 3][1] = config.getGeometry().getDetectorHeight();
xy2[noBeadRegistered + 3][0] = config.getGeometry().getDetectorWidth();
xy2[noBeadRegistered + 3][1] = config.getGeometry().getDetectorHeight();
noBeadRegistered = noBeadRegistered + 4;
}
boolean fScaling = true;
double minX = Double.MAX_VALUE;
double maxX = 0;
double minY = Double.MAX_VALUE;
double maxY = 0;
double c = 0;
if (fScaling) { // ----- scaling to reduce condition # of A matrix
for (int i = 0; i < noBeadRegistered; i++) {
minX = Math.min(minX, xy1[i][0]);
maxX = Math.max(maxX, xy1[i][0]);
minY = Math.min(minY, xy1[i][1]);
maxY = Math.max(maxY, xy1[i][1]);
}
c = Math.max(maxX - minX, maxY - minY);
for (int i = 0; i < noBeadRegistered; i++) {
xy1_hat[i][0] = (xy1[i][0] - minX) / c;
xy1_hat[i][1] = (xy1[i][1] - minY) / c;
xy2_hat[i][0] = (xy2[i][0] - minX) / c;
xy2_hat[i][1] = (xy2[i][1] - minY) / c;
}
} else {
xy1_hat = xy1;
xy2_hat = xy2;
}
ImageProcessor imp2 = imp1.duplicate(); // warped
/*
* A*x = b
* Matrix A = (n + 3) * (n + 3);
* n (noBeadRegistered + 4): # of control points + 4 corner points (assume corner points are static)
*/
int n = noBeadRegistered + 3;
SimpleMatrix A = new SimpleMatrix(n, n);
SimpleVector x_x = new SimpleVector(n);
SimpleVector x_y = new SimpleVector(n);
SimpleVector b_x = new SimpleVector(n);
SimpleVector b_y = new SimpleVector(n);
double rij = 0;
double valA = 0;
double valb_x = 0;
double valb_y = 0;
// Matrix L formation
// alpha: mean of distances between control points' xy-projections) is a constant only present
// on the diagonal of K
// lambda: TPS smoothing regularization coefficient
double alpha = 0.0;
double lambda = 1.6; // 1.6
for (int i = 0; i < noBeadRegistered; i++) { // i= # of row
for (int j = i; j < noBeadRegistered; j++) { // j= # of column
alpha +=
Math.sqrt(
Math.pow(xy2_hat[i][0] - xy2_hat[j][0], 2)
+ Math.pow(xy2_hat[i][1] - xy2_hat[j][1], 2));
}
}
alpha = alpha / Math.pow(noBeadRegistered, 2);
for (int i = 0; i < n; i++) { // i= # of row
for (int j = i; j < n; j++) { // j= # of column
if (i < 3 && j < 3) valA = 0;
else if (i >= 3 && j >= 3 && i == j) {
valA = Math.pow(alpha, 2) * lambda;
// valA = lambda;
if (imageIndex < 10)
System.out.println("Regularization = " + valA + ", lambda= " + lambda);
} else if (i == 0 && j >= 0) valA = 1;
else if (i == 1 && j >= 3) valA = xy1_hat[j - 3][0];
else if (i == 2 && j >= 3) valA = xy1_hat[j - 3][1];
else {
rij =
Math.pow(xy1_hat[j - 3][0] - xy1_hat[i - 3][0], 2)
+ Math.pow(xy1_hat[j - 3][1] - xy1_hat[i - 3][1], 2);
if (rij == 0) valA = 0;
else valA = rij * Math.log(rij);
}
A.setElementValue(i, j, valA);
A.setElementValue(j, i, valA);
}
if (i < 3) {
valb_x = 0;
valb_y = 0;
} else {
// valb_x = xy2_hat[i-3][0]-xy1_hat[i-3][0];
// valb_y = xy2_hat[i-3][1]-xy1_hat[i-3][1];
valb_x = xy2[i - 3][0] - xy1[i - 3][0];
valb_y = xy2[i - 3][1] - xy1[i - 3][1];
// if (imageIndex > 150 && imageIndex < 170)
// System.out.println("Idx" + imageIndex + ",Elevation" + (i-3) + ": " + valb_x + "---"
// + valb_y);
}
b_x.setElementValue(i, valb_x);
b_y.setElementValue(i, valb_y);
}
// System.out.println("A condition number=" + A.conditionNumber(MatrixNormType.MAT_NORM_L1));
// System.out.println("A condition number=" + A.conditionNumber(MatrixNormType.MAT_NORM_LINF));
x_x = Solvers.solveLinearSysytemOfEquations(A, b_x);
x_y = Solvers.solveLinearSysytemOfEquations(A, b_y);
if (fScaling) {
// ----- pixel space coefficients a, b scaling back
double tmpA0 =
x_x.getElement(0) - x_x.getElement(1) * (minX / c) - x_x.getElement(2) * (minY / c);
for (int j = 0; j < noBeadRegistered; j++) {
tmpA0 -=
Math.log(c)
* 2
* x_x.getElement(j + 3)
* (Math.pow(xy1_hat[j][0], 2) + Math.pow(xy1_hat[j][1], 2));
}
x_x.setElementValue(0, tmpA0);
tmpA0 = x_y.getElement(0) - x_y.getElement(1) * (minX / c) - x_y.getElement(2) * (minY / c);
for (int j = 0; j < noBeadRegistered; j++) {
tmpA0 -=
Math.log(c)
* 2
* x_y.getElement(j + 3)
* (Math.pow(xy1_hat[j][0], 2) + Math.pow(xy1_hat[j][1], 2));
}
x_y.setElementValue(0, tmpA0);
x_x.setElementValue(1, x_x.getElement(1) / c);
x_y.setElementValue(1, x_y.getElement(1) / c);
x_x.setElementValue(2, x_x.getElement(2) / c);
x_y.setElementValue(2, x_y.getElement(2) / c);
for (int i = 3; i < n; i++) {
x_x.setElementValue(i, x_x.getElement(i) / Math.pow(c, 2));
x_y.setElementValue(i, x_y.getElement(i) / Math.pow(c, 2));
}
// ----- pixel space coefficients a, b scaling back end
}
double devU = 0;
double devV = 0;
// Do warping
// if (imageIndex == 0) {
for (int y = 0; y < config.getGeometry().getDetectorHeight(); y++) {
// for (int y=252; y<253; y++) {
for (int x = 0; x < config.getGeometry().getDetectorWidth(); x++) {
// for (int x=606; x<607; x++) {
devU = x_x.getElement(0) + x_x.getElement(1) * x + x_x.getElement(2) * y;
devV = x_y.getElement(0) + x_y.getElement(1) * x + x_y.getElement(2) * y;
for (int i = 0; i < noBeadRegistered; i++) {
rij = Math.pow(xy1[i][0] - x, 2) + Math.pow(xy1[i][1] - y, 2);
if (rij > 0) {
devU += x_x.getElement(i + 3) * rij * Math.log(rij);
devV += x_y.getElement(i + 3) * rij * Math.log(rij);
}
}
// devU = 0;
// devV = 0;
imp2.setf(x, y, (float) imp1.getInterpolatedValue(x - devU, y - devV));
// System.out.println("x, y=" + x + ", " + y + "\t" + devU + ", " + devV);
// maxDevU = Math.max(maxDevU, devU);
// maxDevV = Math.max(maxDevV, devV);
}
}
// Error estimate after transformation
// for (int i=0; i<= WeightBearingBeadPositionBuilder.currentBeadNo; i++){
//
// if (beadMean3D[i][0] != 0 || beadMean3D[i][1] != 0 || beadMean3D[i][2] != 0){ // assume
// bead 3d is registered.
//
// // find bead location if registered by txt: state 1
// if (beadPosition2D[imageIndex][i][2] == 1){
//
// // Projected Reference
// uv = compute2DCoordinates(beadMean3D[i], pMatrix);
// double x = uv[0];
// double y = uv[1];
// // bead detected position in 2d
// // Transform to 2D coordinates, time variant position
// //beadPosition2D[imageIndex][i][0];
// //beadPosition2D[imageIndex][i][1];
//
// devU = x_x.getElement(0) + x_x.getElement(1)*x + x_x.getElement(2)*y;
// devV = x_y.getElement(0) + x_y.getElement(1)*x + x_y.getElement(2)*y;
// for (int j=0; j<noBeadRegistered; j++){
// rij = Math.pow(xy1[j][0]-x, 2) + Math.pow(xy1[j][1]-y, 2);
// if (rij > 0) {
// devU += x_x.getElement(j+3)*rij*Math.log(rij);
// devV += x_y.getElement(j+3)*rij*Math.log(rij);
// }
// }
//
// distanceReferenceToCurrentBead +=
// Math.sqrt(Math.pow(uv[0]-(beadPosition2D[imageIndex][i][0]+devU),
// 2)+Math.pow(uv[1]-(beadPosition2D[imageIndex][i][1]+devV), 2));
//
// }
// }
// }
// System.out.println("Euclidean distance\t" + imageIndex + "\t" +
// distanceReferenceToCurrentBead/noBeadRegistered);
// }
if (isDisplay) {
for (int i = WeightBearingBeadPositionBuilder.currentBeadNo; i >= 0; i--) {
if (beadMean3D[i][0] != 0
|| beadMean3D[i][1] != 0
|| beadMean3D[i][2] != 0) { // assume bead 3d is registered.
uv = compute2DCoordinates(beadMean3D[i], pMatrix);
imp2.setValue(2);
// mean projected bead
imp2.drawLine(
(int) Math.round(uv[0] - 10),
(int) Math.round(uv[1]),
(int) Math.round(uv[0] + 10),
(int) Math.round(uv[1]));
imp2.drawLine(
(int) Math.round(uv[0]),
(int) Math.round(uv[1] - 10),
(int) Math.round(uv[0]),
(int) Math.round(uv[1] + 10));
}
}
}
Grid2D result = new Grid2D((float[]) imp2.getPixels(), imp2.getWidth(), imp2.getHeight());
return result;
}
private double[] compute2DCoordinates(double[] point3D, SimpleMatrix pMatrix) {
// Compute coordinates in projection data.
SimpleVector homogeneousPoint =
SimpleOperators.multiply(pMatrix, new SimpleVector(point3D[0], point3D[1], point3D[2], 1));
// Transform to 2D coordinates
double coordU = homogeneousPoint.getElement(0) / homogeneousPoint.getElement(2);
double coordV = homogeneousPoint.getElement(1) / homogeneousPoint.getElement(2);
// double pxlSize = config.getGeometry().getPixelDimensionX();
return new double[] {coordU, coordV};
}
@Override
public IndividualImageFilteringTool clone() {
IndividualImageFilteringTool clone = new ThinPlateSplinesBasedProjectionWarpingTool();
clone.configured = configured;
return clone;
}
@Override
public String getToolName() {
return "Projection Warping Using Thin Plate Splines";
}
@Override
public void configure() throws Exception {
setConfigured(true);
}
@Override
public boolean isDeviceDependent() {
return true;
}
@Override
public String getBibtexCitation() {
return "@article{Bookstein89-PWT,\n"
+ " author={Bookstein FL},\n"
+ " title={Principal warps: Thin-plate splines and the decomposition of deformations},\n"
+ " journal={IEEE Transactions on Pattern Analysis and Machine Intelligence},\n"
+ " volume={11},\n"
+ " number={6},\n"
+ " pages={568-585},\n"
+ " year={1989}\n"
+ "}";
}
@Override
public String getMedlineCitation() {
return "Bookstein FL. Principal warps: Thin-plate splines and the decomposition of deformations. IEEE Transactions on Pattern Analysis and Machine Intelligence 11(6):568-585, 1989.";
}
}
protected void init() {
if (!initialized) {
largeVolumeMode = false;
int reconDimensionX = getGeometry().getReconDimensionX();
int reconDimensionY = getGeometry().getReconDimensionY();
int reconDimensionZ = getGeometry().getReconDimensionZ();
projections = new ImageGridBuffer();
projectionsAvailable = new ArrayList<Integer>();
projectionsDone = new ArrayList<Integer>();
// Initialize the JCudaDriver. Note that this has to be done from
// the same thread that will later use the JCudaDriver API.
JCudaDriver.setExceptionsEnabled(true);
JCudaDriver.cuInit(0);
CUdevice dev = CUDAUtil.getBestDevice();
cuCtx = new CUcontext();
JCudaDriver.cuCtxCreate(cuCtx, 0, dev);
// check space on device:
int[] memory = new int[1];
int[] total = new int[1];
JCudaDriver.cuDeviceTotalMem(memory, dev);
JCudaDriver.cuMemGetInfo(memory, total);
int availableMemory = (int) (CUDAUtil.correctMemoryValue(memory[0]) / ((long) 1024 * 1024));
int requiredMemory =
(int)
(((((double) reconDimensionX)
* reconDimensionY
* ((double) reconDimensionZ)
* Sizeof.FLOAT)
+ (((double)
Configuration.getGlobalConfiguration()
.getGeometry()
.getDetectorHeight())
* Configuration.getGlobalConfiguration().getGeometry().getDetectorWidth()
* Sizeof.FLOAT))
/ (1024.0 * 1024));
if (debug) {
System.out.println("Total available Memory on CUDA card:" + availableMemory);
System.out.println("Required Memory on CUDA card:" + requiredMemory);
}
if (requiredMemory > availableMemory) {
nSteps = CUDAUtil.iDivUp(requiredMemory, (int) (availableMemory));
if (debug) System.out.println("Switching to large volume mode with nSteps = " + nSteps);
largeVolumeMode = true;
}
if (debug) {
CUdevprop prop = new CUdevprop();
JCudaDriver.cuDeviceGetProperties(prop, dev);
System.out.println(prop.toFormattedString());
}
// Load the CUBIN file containing the kernel
module = new CUmodule();
JCudaDriver.cuModuleLoad(module, "backprojectWithCuda.ptx");
// Obtain a function pointer to the kernel function. This function
// will later be called.
//
function = new CUfunction();
JCudaDriver.cuModuleGetFunction(function, module, "_Z17backprojectKernelPfiiffffff");
// create the reconstruction volume;
int memorysize = reconDimensionX * reconDimensionY * reconDimensionZ * Sizeof.FLOAT;
if (largeVolumeMode) {
subVolumeZ = CUDAUtil.iDivUp(reconDimensionZ, nSteps);
if (debug) System.out.println("SubVolumeZ: " + subVolumeZ);
h_volume = new float[reconDimensionX * reconDimensionY * subVolumeZ];
memorysize = reconDimensionX * reconDimensionY * subVolumeZ * Sizeof.FLOAT;
if (debug) System.out.println("Memory: " + memorysize);
} else {
h_volume = new float[reconDimensionX * reconDimensionY * reconDimensionZ];
}
// copy volume to device
volumePointer = new CUdeviceptr();
JCudaDriver.cuMemAlloc(volumePointer, memorysize);
JCudaDriver.cuMemcpyHtoD(volumePointer, Pointer.to(h_volume), memorysize);
// 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];
volStride = new CUdeviceptr();
JCudaDriver.cuModuleGetGlobal(volStride, new int[1], module, "gVolStride");
JCudaDriver.cuMemcpyHtoD(volStride, Pointer.to(volStrideHost), Sizeof.INT * 2);
// Calculate new grid size
gridSize =
new dim3(
CUDAUtil.iDivUp(adaptedVolSize[0], bpBlockSize[0]),
CUDAUtil.iDivUp(adaptedVolSize[1], bpBlockSize[1]),
adaptedVolSize[2]);
// Obtain the global pointer to the view matrix from
// the module
projectionMatrix = new CUdeviceptr();
JCudaDriver.cuModuleGetGlobal(projectionMatrix, new int[1], module, "gProjMatrix");
initialized = true;
}
}