void SeededRegionGrowing::recompileOpenCLCode(Image::pointer input) {
// Check if there is a need to recompile OpenCL code
if(input->getDimensions() == mDimensionCLCodeCompiledFor &&
input->getDataType() == mTypeCLCodeCompiledFor)
return;
OpenCLDevice::pointer device = getMainDevice();
std::string buildOptions = "";
if(input->getDataType() == TYPE_FLOAT) {
buildOptions = "-DTYPE_FLOAT";
} else if(input->getDataType() == TYPE_INT8 || input->getDataType() == TYPE_INT16) {
buildOptions = "-DTYPE_INT";
} else {
buildOptions = "-DTYPE_UINT";
}
std::string filename;
if(input->getDimensions() == 2) {
filename = "Algorithms/SeededRegionGrowing/SeededRegionGrowing2D.cl";
} else {
filename = "Algorithms/SeededRegionGrowing/SeededRegionGrowing3D.cl";
}
int programNr = device->createProgramFromSource(std::string(FAST_SOURCE_DIR) + filename, buildOptions);
mKernel = cl::Kernel(device->getProgram(programNr), "seededRegionGrowing");
mDimensionCLCodeCompiledFor = input->getDimensions();
mTypeCLCodeCompiledFor = input->getDataType();
}
void NoneLocalMeans::recompileOpenCLCode(Image::pointer input) {
// Check if there is a need to recompile OpenCL code
if(input->getDimensions() == mDimensionCLCodeCompiledFor &&
input->getDataType() == mTypeCLCodeCompiledFor && !recompile)
return;
recompile = false;
OpenCLDevice::pointer device = getMainDevice();
std::string buildOptions = "";
if(!device->isWritingTo3DTexturesSupported()) {
buildOptions = "-DTYPE=" + getCTypeAsString(mOutputType);
}
buildOptions += " -D WINDOW=";
buildOptions += std::to_string((windowSize-1)/2);
buildOptions += " -D GROUP=";
buildOptions += std::to_string((groupSize-1)/2);
buildOptions += " -D KVERSION=";
buildOptions += std::to_string(k);
buildOptions += " -D EUCLID=";
buildOptions += std::to_string(k);
cl::Program program;
if(input->getDimensions() == 2) {
program = getOpenCLProgram(device, "2D", buildOptions);
} else {
//createOpenCLProgram(std::string(FAST_SOURCE_DIR) + "Algorithms/NoneLocalMeans/NoneLocalMeans3Dgs.cl", "3D");
program = getOpenCLProgram(device, "3D", buildOptions);
}
mKernel = cl::Kernel(program, "noneLocalMeans");
mDimensionCLCodeCompiledFor = input->getDimensions();
mTypeCLCodeCompiledFor = input->getDataType();
}
void BinaryThresholding::execute() {
if(!mLowerThresholdSet && !mUpperThresholdSet) {
throw Exception("BinaryThresholding need at least one threshold to be set.");
}
Image::pointer input = getStaticInputData<Image>(0);
Segmentation::pointer output = getStaticOutputData<Segmentation>(0);
output->createFromImage(input);
if(getMainDevice()->isHost()) {
throw Exception("Not implemented yet.");
} else {
OpenCLDevice::pointer device = OpenCLDevice::pointer(getMainDevice());
cl::Program program;
if(input->getDimensions() == 3) {
program = getOpenCLProgram(device, "3D");
} else {
program = getOpenCLProgram(device, "2D");
}
cl::Kernel kernel;
if(mLowerThresholdSet && mUpperThresholdSet) {
kernel = cl::Kernel(program, "tresholding");
kernel.setArg(3, mLowerThreshold);
kernel.setArg(4, mUpperThreshold);
} else if(mLowerThresholdSet) {
kernel = cl::Kernel(program, "thresholdingWithOnlyLower");
kernel.setArg(3, mLowerThreshold);
} else {
kernel = cl::Kernel(program, "thresholdingWithOnlyUpper");
kernel.setArg(3, mUpperThreshold);
}
cl::NDRange globalSize;
OpenCLImageAccess::pointer access = input->getOpenCLImageAccess(ACCESS_READ, device);
if(input->getDimensions() == 2) {
OpenCLImageAccess::pointer access2 = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
kernel.setArg(0, *access->get2DImage());
kernel.setArg(1, *access2->get2DImage());
globalSize = cl::NDRange(output->getWidth(), output->getHeight());
} else {
// TODO no 3d image write support
OpenCLImageAccess::pointer access2 = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
kernel.setArg(0, *access->get3DImage());
kernel.setArg(1, *access2->get3DImage());
globalSize = cl::NDRange(output->getWidth(), output->getHeight(), output->getDepth());
}
kernel.setArg(2, (uchar)mLabel);
cl::CommandQueue queue = device->getCommandQueue();
queue.enqueueNDRangeKernel(
kernel,
cl::NullRange,
globalSize,
cl::NullRange
);
}
}
void Dilation::execute() {
Image::pointer input = getInputData<Image>();
if(input->getDataType() != TYPE_UINT8) {
throw Exception("Data type of image given to Dilation must be UINT8");
}
Image::pointer output = getOutputData<Image>();
output->createFromImage(input);
SceneGraph::setParentNode(output, input);
output->fill(0);
OpenCLDevice::pointer device = std::dynamic_pointer_cast<OpenCLDevice>(getMainDevice());
cl::CommandQueue queue = device->getCommandQueue();
cl::Program program = getOpenCLProgram(device);
cl::Kernel dilateKernel(program, "dilate");
Vector3ui size = input->getSize();
OpenCLImageAccess::pointer access = input->getOpenCLImageAccess(ACCESS_READ, device);
dilateKernel.setArg(0, *access->get3DImage());
dilateKernel.setArg(2, mSize/2);
if(!device->isWritingTo3DTexturesSupported()) {
OpenCLBufferAccess::pointer access2 = output->getOpenCLBufferAccess(ACCESS_READ_WRITE, device);
dilateKernel.setArg(1, *access2->get());
queue.enqueueNDRangeKernel(
dilateKernel,
cl::NullRange,
cl::NDRange(size.x(), size.y(), size.z()),
cl::NullRange
);
} else {
OpenCLImageAccess::pointer access2 = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
dilateKernel.setArg(1, *access2->get3DImage());
queue.enqueueNDRangeKernel(
dilateKernel,
cl::NullRange,
cl::NDRange(size.x(), size.y(), size.z()),
cl::NullRange
);
}
}
void NoneLocalMeans::waitToFinish() {
if (!getMainDevice()->isHost()) {
OpenCLDevice::pointer device = getMainDevice();
device->getCommandQueue().finish();
}
}
/*
void NoneLocalMeans::recompileOpenCLCode(Image::pointer input) {
// Check if there is a need to recompile OpenCL code
if (input->getDimensions() == mDimensionCLCodeCompiledFor &&
input->getDataType() == mTypeCLCodeCompiledFor && !recompile)
return;
OpenCLDevice::pointer device = getMainDevice();
recompile = false;
std::string buildOptions = "";
const bool writingTo3DTextures = device->getDevice().getInfo<CL_DEVICE_EXTENSIONS>().find("cl_khr_3d_image_writes") != std::string::npos;
if (!writingTo3DTextures) {
switch (mOutputType) {
case TYPE_FLOAT:
buildOptions += " -DTYPE=float";
break;
case TYPE_INT8:
buildOptions += " -DTYPE=char";
break;
case TYPE_UINT8:
buildOptions += " -DTYPE=uchar";
break;
case TYPE_INT16:
buildOptions += " -DTYPE=short";
break;
case TYPE_UINT16:
buildOptions += " -DTYPE=ushort";
break;
}
}
buildOptions += " -D WINDOW=";
buildOptions += std::to_string((windowSize-1)/2);
buildOptions += " -D GROUP=";
buildOptions += std::to_string((groupSize-1)/2);
std::string filename;
//might have to seperate color vs gray here, for better runtime
if (input->getDimensions() == 2) {
if(k == 0){
filename = "Algorithms/NoneLocalMeans/NoneLocalMeans2Dconstant.cl";
}else if(k == 1){
filename = "Algorithms/NoneLocalMeans/NoneLocalMeans2Dgaussian.cl";
}else{
filename = "Algorithms/NoneLocalMeans/NoneLocalMeans2Dconstant.cl";
}
//filename = "Algorithms/NoneLocalMeans/NoneLocalMeans2DgsPixelWise.cl";
//filename = "Algorithms/NoneLocalMeans/NoneLocalMeans2Dgs.cl";
//filename = "Algorithms/NoneLocalMeans/NoneLocalMeans2Dc.cl";
}
else {
filename = "Algorithms/NoneLocalMeans/NoneLocalMeans3Dgs.cl";
}
int programNr = device->createProgramFromSource(std::string(FAST_SOURCE_DIR) + filename, buildOptions);
mKernel = cl::Kernel(device->getProgram(programNr), "noneLocalMeans");
mDimensionCLCodeCompiledFor = input->getDimensions();
mTypeCLCodeCompiledFor = input->getDataType();
}*/
void NoneLocalMeans::execute() {
Image::pointer input = getStaticInputData<Image>(0);
Image::pointer output = getStaticOutputData<Image>(0);
// Initialize output image
ExecutionDevice::pointer device = getMainDevice();
if(mOutputTypeSet) {
output->create(input->getSize(), mOutputType, input->getNrOfComponents());
output->setSpacing(input->getSpacing());
} else {
output->createFromImage(input);
}
mOutputType = output->getDataType();
SceneGraph::setParentNode(output, input);
if(device->isHost()) {
switch(input->getDataType()) {
fastSwitchTypeMacro(executeAlgorithmOnHost<FAST_TYPE>(input, output, groupSize, windowSize, denoiseStrength, sigma));
}
} else {
OpenCLDevice::pointer clDevice = device;
recompileOpenCLCode(input);
cl::NDRange globalSize;
OpenCLImageAccess::pointer inputAccess = input->getOpenCLImageAccess(ACCESS_READ, device);
if(input->getDimensions() == 2) {
OpenCLImageAccess::pointer outputAccess = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
mKernel.setArg(2, (denoiseStrength*denoiseStrength));
mKernel.setArg(3, (sigma*sigma));
globalSize = cl::NDRange(input->getWidth(),input->getHeight());
mKernel.setArg(0, *inputAccess->get2DImage());
mKernel.setArg(1, *outputAccess->get2DImage());
clDevice->getCommandQueue().enqueueNDRangeKernel(
mKernel,
cl::NullRange,
globalSize,
cl::NullRange
);
} else {
// Create an auxilliary image
//Image::pointer output2 = Image::New();
//output2->createFromImage(output);
globalSize = cl::NDRange(input->getWidth(),input->getHeight(),input->getDepth());
if(clDevice->isWritingTo3DTexturesSupported()) {
mKernel.setArg(2, (denoiseStrength*denoiseStrength));
mKernel.setArg(3, (sigma*sigma));
OpenCLImageAccess::pointer outputAccess = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
//OpenCLImageAccess::pointer outputAccess2 = output2->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
//cl::Image3D* image2;
cl::Image3D* image;
image = outputAccess->get3DImage();
//image2 = outputAccess->get3DImage();
mKernel.setArg(0, *inputAccess->get3DImage());
mKernel.setArg(1, *image);
clDevice->getCommandQueue().enqueueNDRangeKernel(
mKernel,
cl::NullRange,
globalSize,
cl::NullRange
);
}else{
mKernel.setArg(2, (denoiseStrength*denoiseStrength));
mKernel.setArg(3, (sigma*sigma));
OpenCLBufferAccess::pointer outputAccess = output->getOpenCLBufferAccess(ACCESS_READ_WRITE, device);
mKernel.setArg(0, *inputAccess->get3DImage());
mKernel.setArg(1, *outputAccess->get());
clDevice->getCommandQueue().enqueueNDRangeKernel(
mKernel,
cl::NullRange,
globalSize,
cl::NullRange
);
}
}
}
}
void MeshRenderer::draw2D(
cl::BufferGL PBO,
uint width,
uint height,
Eigen::Transform<float, 3, Eigen::Affine> pixelToViewportTransform,
float PBOspacing,
Vector2f translation
) {
boost::lock_guard<boost::mutex> lock(mMutex);
OpenCLDevice::pointer device = getMainDevice();
cl::CommandQueue queue = device->getCommandQueue();
std::vector<cl::Memory> v;
v.push_back(PBO);
queue.enqueueAcquireGLObjects(&v);
// Map would probably be better here, but doesn't work on NVIDIA, segfault surprise!
//float* pixels = (float*)queue.enqueueMapBuffer(PBO, CL_TRUE, CL_MAP_WRITE, 0, width*height*sizeof(float)*4);
boost::shared_array<float> pixels(new float[width*height*sizeof(float)*4]);
queue.enqueueReadBuffer(PBO, CL_TRUE, 0, width*height*4*sizeof(float), pixels.get());
boost::unordered_map<uint, Mesh::pointer>::iterator it;
for(it = mMeshToRender.begin(); it != mMeshToRender.end(); it++) {
Mesh::pointer mesh = it->second;
if(mesh->getDimensions() != 2) // Mesh must be 2D
continue;
Color color = mDefaultColor;
ProcessObjectPort port = getInputPort(it->first);
if(mInputColors.count(port) > 0) {
color = mInputColors[port];
}
MeshAccess::pointer access = mesh->getMeshAccess(ACCESS_READ);
std::vector<VectorXui> lines = access->getLines();
std::vector<MeshVertex> vertices = access->getVertices();
// Draw each line
for(int i = 0; i < lines.size(); ++i) {
Vector2ui line = lines[i];
Vector2f a = vertices[line.x()].getPosition();
Vector2f b = vertices[line.y()].getPosition();
Vector2f direction = b - a;
float lengthInPixels = ceil(direction.norm() / PBOspacing);
// Draw the line
for(int j = 0; j <= lengthInPixels; ++j) {
Vector2f positionInMM = a + direction*((float)j/lengthInPixels);
Vector2f positionInPixels = positionInMM / PBOspacing;
int x = round(positionInPixels.x());
int y = round(positionInPixels.y());
y = height - 1 - y;
if(x < 0 || y < 0 || x >= width || y >= height)
continue;
pixels[4*(x + y*width)] = color.getRedValue();
pixels[4*(x + y*width) + 1] = color.getGreenValue();
pixels[4*(x + y*width) + 2] = color.getBlueValue();
}
}
}
//queue.enqueueUnmapMemObject(PBO, pixels);
queue.enqueueWriteBuffer(PBO, CL_TRUE, 0, width*height*4*sizeof(float), pixels.get());
queue.enqueueReleaseGLObjects(&v);
}
void BinaryThresholding::waitToFinish() {
OpenCLDevice::pointer device = OpenCLDevice::pointer(getMainDevice());
device->getCommandQueue().finish();
}
void DoubleFilter::execute() {
if(!mInput.isValid()) {
throw Exception("No input supplied to GaussianSmoothingFilter");
}
Image::pointer input = mInput;
Image::pointer output = mOutput;
// Initialize output image
output->createFromImage(input, mDevice);
if(mDevice->isHost()) {
// Execution device is Host, use the executeAlgorithmOnHost function with the given data type
switch(input->getDataType()) {
// This macro creates a case statement for each data type and sets FAST_TYPE to the correct C++ data type
fastSwitchTypeMacro(executeAlgorithmOnHost<FAST_TYPE>(input, output));
}
} else {
// Execution device is an OpenCL device
OpenCLDevice::pointer device = boost::static_pointer_cast<OpenCLDevice>(mDevice);
// Set build options based on the data type of the data
std::string buildOptions = "";
switch(input->getDataType()) {
case TYPE_FLOAT:
buildOptions = "-DTYPE=float";
break;
case TYPE_INT8:
buildOptions = "-DTYPE=char";
break;
case TYPE_UINT8:
buildOptions = "-DTYPE=uchar";
break;
case TYPE_INT16:
buildOptions = "-DTYPE=short";
break;
case TYPE_UINT16:
buildOptions = "-DTYPE=ushort";
break;
}
// Compile the code
int programNr = device->createProgramFromSource(std::string(FAST_SOURCE_DIR) + "Tests/Algorithms/DoubleFilter.cl", buildOptions);
cl::Kernel kernel = cl::Kernel(device->getProgram(programNr), "doubleFilter");
// Get global size for the kernel
cl::NDRange globalSize(input->getWidth()*input->getHeight()*input->getDepth()*input->getNrOfComponents());
// Set the arguments for the kernel
OpenCLBufferAccess inputAccess = input->getOpenCLBufferAccess(ACCESS_READ, device);
OpenCLBufferAccess outputAccess = output->getOpenCLBufferAccess(ACCESS_READ_WRITE, device);
kernel.setArg(0, *inputAccess.get());
kernel.setArg(1, *outputAccess.get());
// Execute the kernel
device->getCommandQueue().enqueueNDRangeKernel(
kernel,
cl::NullRange,
globalSize,
cl::NullRange
);
}
// Update timestamp of the output data
output->updateModifiedTimestamp();
}
void NonLocalMeans::waitToFinish() {
if (!getMainDevice()->isHost()) {
OpenCLDevice::pointer device = std::dynamic_pointer_cast<OpenCLDevice>(getMainDevice());
device->getCommandQueue().finish();
}
}
void getIntensitySumFromOpenCLImage(OpenCLDevice::pointer device, cl::Image2D image, DataType type, float* sum) {
// Get power of two size
unsigned int powerOfTwoSize = getPowerOfTwoSize(std::max(image.getImageInfo<CL_IMAGE_WIDTH>(), image.getImageInfo<CL_IMAGE_HEIGHT>()));
// Create image levels
unsigned int size = powerOfTwoSize;
size /= 2;
std::vector<cl::Image2D> levels;
while(size >= 4) {
cl::Image2D level = cl::Image2D(device->getContext(), CL_MEM_READ_WRITE, getOpenCLImageFormat(device, CL_MEM_OBJECT_IMAGE2D, TYPE_FLOAT, 1), size, size);
levels.push_back(level);
size /= 2;
}
// Compile OpenCL code
std::string buildOptions = "";
switch(type) {
case TYPE_FLOAT:
buildOptions = "-DTYPE_FLOAT";
break;
case TYPE_UINT8:
buildOptions = "-DTYPE_UINT8";
break;
case TYPE_INT8:
buildOptions = "-DTYPE_INT8";
break;
case TYPE_UINT16:
buildOptions = "-DTYPE_UINT16";
break;
case TYPE_INT16:
buildOptions = "-DTYPE_INT16";
break;
}
std::string sourceFilename = std::string(FAST_SOURCE_DIR) + "/ImageSum.cl";
std::string programName = sourceFilename + buildOptions;
// Only create program if it doesn't exist for this device from before
if(!device->hasProgram(programName))
device->createProgramFromSourceWithName(programName, sourceFilename, buildOptions);
cl::Program program = device->getProgram(programName);
cl::CommandQueue queue = device->getCommandQueue();
// Fill first level
size = powerOfTwoSize/2;
cl::Kernel firstLevel(program, "createFirstSumImage2DLevel");
firstLevel.setArg(0, image);
firstLevel.setArg(1, levels[0]);
queue.enqueueNDRangeKernel(
firstLevel,
cl::NullRange,
cl::NDRange(size,size),
cl::NullRange
);
// Fill all other levels
cl::Kernel createLevel(program, "createSumImage2DLevel");
int i = 0;
size /= 2;
while(size >= 4) {
createLevel.setArg(0, levels[i]);
createLevel.setArg(1, levels[i+1]);
queue.enqueueNDRangeKernel(
createLevel,
cl::NullRange,
cl::NDRange(size,size),
cl::NullRange
);
i++;
size /= 2;
}
// Get result from the last level
unsigned int nrOfElements = 4*4;
unsigned int nrOfComponents = getOpenCLImageFormat(device, CL_MEM_OBJECT_IMAGE2D, TYPE_FLOAT, 1).image_channel_order == CL_RGBA ? 4 : 1;
float* result = (float*)allocateDataArray(nrOfElements,TYPE_FLOAT,nrOfComponents);
queue.enqueueReadImage(levels[levels.size()-1],CL_TRUE,createOrigoRegion(),createRegion(4,4,1),0,0,result);
*sum = getSumFromOpenCLImageResult<float>(result, nrOfElements, nrOfComponents);
delete[] result;
}
void getMaxAndMinFromOpenCLBuffer(OpenCLDevice::pointer device, cl::Buffer buffer, unsigned int size, DataType type, float* min, float* max) {
// Compile OpenCL code
std::string buildOptions = "";
switch(type) {
case TYPE_FLOAT:
buildOptions = "-DTYPE_FLOAT";
break;
case TYPE_UINT8:
buildOptions = "-DTYPE_UINT8";
break;
case TYPE_INT8:
buildOptions = "-DTYPE_INT8";
break;
case TYPE_UINT16:
buildOptions = "-DTYPE_UINT16";
break;
case TYPE_INT16:
buildOptions = "-DTYPE_INT16";
break;
}
std::string sourceFilename = std::string(FAST_SOURCE_DIR) + "/ImageMinMax.cl";
std::string programName = sourceFilename + buildOptions;
// Only create program if it doesn't exist for this device from before
if(!device->hasProgram(programName))
device->createProgramFromSourceWithName(programName, sourceFilename, buildOptions);
cl::Program program = device->getProgram(programName);
cl::CommandQueue queue = device->getCommandQueue();
// Nr of work groups must be set so that work-group size does not exceed max work-group size (256 on AMD)
int length = size;
cl::Kernel reduce(program, "reduce");
cl::Buffer current = buffer;
cl::Buffer clResult;
int workGroupSize = 256;
int workGroups = 256;
int X = ceil((float)length / (workGroups*workGroupSize));
clResult = cl::Buffer(device->getContext(), CL_MEM_READ_WRITE, getSizeOfDataType(type,1)*workGroups*2);
reduce.setArg(0, current);
reduce.setArg(1, workGroupSize * getSizeOfDataType(type,1), NULL);
reduce.setArg(2, workGroupSize * getSizeOfDataType(type,1), NULL);
reduce.setArg(3, size);
reduce.setArg(4, X);
reduce.setArg(5, clResult);
queue.enqueueNDRangeKernel(
reduce,
cl::NullRange,
cl::NDRange(workGroups*workGroupSize),
cl::NDRange(workGroupSize)
);
length = workGroups;
void* result = allocateDataArray(length, type, 2);
unsigned int nrOfElements = length;
queue.enqueueReadBuffer(clResult,CL_TRUE,0,getSizeOfDataType(type,1)*workGroups*2,result);
switch(type) {
case TYPE_FLOAT:
getMaxAndMinFromOpenCLImageResult<float>(result, nrOfElements, 2, min, max);
break;
case TYPE_INT8:
getMaxAndMinFromOpenCLImageResult<char>(result, nrOfElements, 2, min, max);
break;
case TYPE_UINT8:
getMaxAndMinFromOpenCLImageResult<uchar>(result, nrOfElements, 2, min, max);
break;
case TYPE_INT16:
getMaxAndMinFromOpenCLImageResult<short>(result, nrOfElements, 2, min, max);
break;
case TYPE_UINT16:
getMaxAndMinFromOpenCLImageResult<ushort>(result, nrOfElements, 2, min, max);
break;
}
deleteArray(result, type);
}
void SeededRegionGrowing::waitToFinish() {
if(!getMainDevice()->isHost()) {
OpenCLDevice::pointer device = getMainDevice();
device->getCommandQueue().finish();
}
}
void SeededRegionGrowing::execute() {
if(mSeedPoints.size() == 0)
throw Exception("No seed points supplied to SeededRegionGrowing");
Image::pointer input = getStaticInputData<Image>();
if(input->getNrOfComponents() != 1)
throw Exception("Seeded region growing currently doesn't support images with several components.");
Segmentation::pointer output = getStaticOutputData<Segmentation>();
// Initialize output image
output->createFromImage(input, getMainDevice());
if(getMainDevice()->isHost()) {
ImageAccess::pointer inputAccess = input->getImageAccess(ACCESS_READ);
void* inputData = inputAccess->get();
switch(input->getDataType()) {
fastSwitchTypeMacro(executeOnHost<FAST_TYPE>((FAST_TYPE*)inputData, output));
}
} else {
OpenCLDevice::pointer device = getMainDevice();
recompileOpenCLCode(input);
ImageAccess::pointer access = output->getImageAccess(ACCESS_READ_WRITE);
uchar* outputData = (uchar*)access->get();
// Initialize to all 0s
memset(outputData,0,sizeof(uchar)*output->getWidth()*output->getHeight()*output->getDepth());
// Add sedd points
for(int i = 0; i < mSeedPoints.size(); i++) {
Vector3ui pos = mSeedPoints[i];
// Check if seed point is in bounds
if(pos.x() < 0 || pos.y() < 0 || pos.z() < 0 ||
pos.x() >= output->getWidth() || pos.y() >= output->getHeight() || pos.z() >= output->getDepth())
throw Exception("One of the seed points given to SeededRegionGrowing was out of bounds.");
outputData[pos.x() + pos.y()*output->getWidth() + pos.z()*output->getWidth()*output->getHeight()] = 2;
}
access->release();
cl::NDRange globalSize;
if(output->getDimensions() == 2) {
globalSize = cl::NDRange(input->getWidth(),input->getHeight());
OpenCLImageAccess2D::pointer inputAccess = input->getOpenCLImageAccess2D(ACCESS_READ, device);
mKernel.setArg(0, *inputAccess->get());
} else {
globalSize = cl::NDRange(input->getWidth(),input->getHeight(), input->getDepth());
OpenCLImageAccess3D::pointer inputAccess = input->getOpenCLImageAccess3D(ACCESS_READ, device);
mKernel.setArg(0, *inputAccess->get());
}
OpenCLBufferAccess::pointer outputAccess = output->getOpenCLBufferAccess(ACCESS_READ_WRITE, device);
cl::Buffer stopGrowingBuffer = cl::Buffer(
device->getContext(),
CL_MEM_READ_WRITE,
sizeof(char));
cl::CommandQueue queue = device->getCommandQueue();
mKernel.setArg(1, *outputAccess->get());
mKernel.setArg(2, stopGrowingBuffer);
mKernel.setArg(3, mMinimumIntensity);
mKernel.setArg(4, mMaximumIntensity);
bool stopGrowing = false;
char stopGrowingInit = 1;
char * stopGrowingResult = new char;
int iterations = 0;
do {
iterations++;
queue.enqueueWriteBuffer(stopGrowingBuffer, CL_TRUE, 0, sizeof(char), &stopGrowingInit);
queue.enqueueNDRangeKernel(
mKernel,
cl::NullRange,
globalSize,
cl::NullRange
);
queue.enqueueReadBuffer(stopGrowingBuffer, CL_TRUE, 0, sizeof(char), stopGrowingResult);
if(*stopGrowingResult == 1)
stopGrowing = true;
} while(!stopGrowing);
}
}
void ImageSlicer::orthogonalSlicing(Image::pointer input, Image::pointer output) {
OpenCLDevice::pointer device = getMainDevice();
// Determine slice nr and width and height
unsigned int sliceNr;
if(mOrthogonalSliceNr < 0) {
switch(mOrthogonalSlicePlane) {
case PLANE_X:
sliceNr = input->getWidth()/2;
break;
case PLANE_Y:
sliceNr = input->getHeight()/2;
break;
case PLANE_Z:
sliceNr = input->getDepth()/2;
break;
}
} else {
// Check that mSliceNr is valid
sliceNr = mOrthogonalSliceNr;
switch(mOrthogonalSlicePlane) {
case PLANE_X:
if(sliceNr >= input->getWidth())
sliceNr = input->getWidth()-1;
break;
case PLANE_Y:
if(sliceNr >= input->getHeight())
sliceNr = input->getHeight()-1;
break;
case PLANE_Z:
if(sliceNr >= input->getDepth())
sliceNr = input->getDepth()-1;
break;
}
}
unsigned int slicePlaneNr, width, height;
Vector3f spacing(0,0,0);
switch(mOrthogonalSlicePlane) {
case PLANE_X:
slicePlaneNr = 0;
width = input->getHeight();
height = input->getDepth();
spacing.x() = input->getSpacing().y();
spacing.y() = input->getSpacing().z();
break;
case PLANE_Y:
slicePlaneNr = 1;
width = input->getWidth();
height = input->getDepth();
spacing.x() = input->getSpacing().x();
spacing.y() = input->getSpacing().z();
break;
case PLANE_Z:
slicePlaneNr = 2;
width = input->getWidth();
height = input->getHeight();
spacing.x() = input->getSpacing().x();
spacing.y() = input->getSpacing().y();
break;
}
output->create(width, height, input->getDataType(), input->getNrOfComponents());
output->setSpacing(spacing);
OpenCLImageAccess::pointer inputAccess = input->getOpenCLImageAccess(ACCESS_READ, device);
OpenCLImageAccess::pointer outputAccess = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
cl::CommandQueue queue = device->getCommandQueue();
cl::Program program = getOpenCLProgram(device);
cl::Kernel kernel(program, "orthogonalSlicing");
kernel.setArg(0, *inputAccess->get3DImage());
kernel.setArg(1, *outputAccess->get2DImage());
kernel.setArg(2, sliceNr);
kernel.setArg(3, slicePlaneNr);
queue.enqueueNDRangeKernel(
kernel,
cl::NullRange,
cl::NDRange(width, height),
cl::NullRange
);
// TODO set scene graph transformation
}
void
SegmentationRenderer::draw(Matrix4f perspectiveMatrix, Matrix4f viewingMatrix, float zNear, float zFar, bool mode2D) {
std::lock_guard<std::mutex> lock(mMutex);
OpenCLDevice::pointer device = std::dynamic_pointer_cast<OpenCLDevice>(getMainDevice());
if(mColorsModified) {
// Transfer colors to device (this doesn't have to happen every render call..)
std::unique_ptr<float[]> colorData(new float[3*mLabelColors.size()]);
std::unordered_map<int, Color>::iterator it;
for(it = mLabelColors.begin(); it != mLabelColors.end(); it++) {
colorData[it->first*3] = it->second.getRedValue();
colorData[it->first*3+1] = it->second.getGreenValue();
colorData[it->first*3+2] = it->second.getBlueValue();
}
mColorBuffer = cl::Buffer(
device->getContext(),
CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR,
sizeof(float)*3*mLabelColors.size(),
colorData.get()
);
}
if(mFillAreaModified) {
// Transfer colors to device (this doesn't have to happen every render call..)
std::unique_ptr<char[]> fillAreaData(new char[mLabelColors.size()]);
std::unordered_map<int, Color>::iterator it;
for(it = mLabelColors.begin(); it != mLabelColors.end(); it++) {
if(mLabelFillArea.count(it->first) == 0) {
// Use default value
fillAreaData[it->first] = mFillArea;
} else {
fillAreaData[it->first] = mLabelFillArea[it->first];
}
}
mFillAreaBuffer = cl::Buffer(
device->getContext(),
CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR,
sizeof(char)*mLabelColors.size(),
fillAreaData.get()
);
}
mKernel = cl::Kernel(getOpenCLProgram(device), "renderToTexture");
mKernel.setArg(2, mColorBuffer);
mKernel.setArg(3, mFillAreaBuffer);
mKernel.setArg(4, mBorderRadius);
mKernel.setArg(5, mOpacity);
for(auto it : mDataToRender) {
Image::pointer input = std::static_pointer_cast<Image>(it.second);
uint inputNr = it.first;
if(input->getDimensions() != 2)
throw Exception("SegmentationRenderer only supports 2D images. Use ImageSlicer to extract a 2D slice from a 3D image.");
if(input->getDataType() != TYPE_UINT8)
throw Exception("SegmentationRenderer only support images with dat type uint8.");
// Check if a texture has already been created for this image
if(mTexturesToRender.count(inputNr) > 0 && mImageUsed[inputNr] == input)
continue; // If it has already been created, skip it
// If it has not been created, create the texture
OpenCLImageAccess::pointer access = input->getOpenCLImageAccess(ACCESS_READ, device);
cl::Image2D *clImage = access->get2DImage();
// Run kernel to fill the texture
cl::CommandQueue queue = device->getCommandQueue();
if (mTexturesToRender.count(inputNr) > 0) {
// Delete old texture
glDeleteTextures(1, &mTexturesToRender[inputNr]);
mTexturesToRender.erase(inputNr);
glDeleteVertexArrays(1, &mVAO[inputNr]);
mVAO.erase(inputNr);
}
cl::Image2D image;
cl::ImageGL imageGL;
std::vector<cl::Memory> v;
GLuint textureID;
// TODO The GL-CL interop here is causing glClear to not work on AMD systems and therefore disabled
/*
if(DeviceManager::isGLInteropEnabled()) {
// Create OpenGL texture
glGenTextures(1, &textureID);
glBindTexture(GL_TEXTURE_2D, textureID);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);
glTexImage2D(GL_TEXTURE_2D, 0, GL_RGBA32F, input->getWidth(), input->getHeight(), 0, GL_RGBA, GL_FLOAT, 0);
// Create CL-GL image
imageGL = cl::ImageGL(
device->getContext(),
CL_MEM_READ_WRITE,
GL_TEXTURE_2D,
0,
textureID
);
glBindTexture(GL_TEXTURE_2D, 0);
glFinish();
mKernel.setArg(1, imageGL);
v.push_back(imageGL);
queue.enqueueAcquireGLObjects(&v);
} else {
*/
image = cl::Image2D(
device->getContext(),
CL_MEM_READ_WRITE,
cl::ImageFormat(CL_RGBA, CL_FLOAT),
input->getWidth(), input->getHeight()
);
mKernel.setArg(1, image);
//}
mKernel.setArg(0, *clImage);
queue.enqueueNDRangeKernel(
mKernel,
cl::NullRange,
cl::NDRange(input->getWidth(), input->getHeight()),
cl::NullRange
);
/*if(DeviceManager::isGLInteropEnabled()) {
queue.enqueueReleaseGLObjects(&v);
} else {*/
// Copy data from CL image to CPU
auto data = make_uninitialized_unique<float[]>(input->getWidth() * input->getHeight() * 4);
queue.enqueueReadImage(
image,
CL_TRUE,
createOrigoRegion(),
createRegion(input->getWidth(), input->getHeight(), 1),
0, 0,
data.get()
);
// Copy data from CPU to GL texture
glGenTextures(1, &textureID);
glBindTexture(GL_TEXTURE_2D, textureID);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);
glTexImage2D(GL_TEXTURE_2D, 0, GL_RGBA32F, input->getWidth(), input->getHeight(), 0, GL_RGBA, GL_FLOAT, data.get());
glBindTexture(GL_TEXTURE_2D, 0);
glFinish();
//}
mTexturesToRender[inputNr] = textureID;
mImageUsed[inputNr] = input;
queue.finish();
}
glEnable(GL_BLEND);
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
drawTextures(perspectiveMatrix, viewingMatrix, mode2D);
glDisable(GL_BLEND);
}
