Beispiel #1
0
static igtl::ImageMessage::Pointer createIGTLImageMessage(Image::pointer image) {
    // size parameters
    int   size[3]     = {(int)image->getWidth(), (int)image->getHeight(), (int)image->getDepth()};       // image dimension
    float spacing[3]  = {image->getSpacing().x(), image->getSpacing().y(), image->getSpacing().z()};     // spacing (mm/pixel)
    int   svoffset[3] = {0, 0, 0};           // sub-volume offset
    int   scalarType;
    size_t totalSize = image->getWidth()*image->getHeight()*image->getDepth()*image->getNrOfChannels();
    switch(image->getDataType()) {
        case TYPE_UINT8:
            scalarType = igtl::ImageMessage::TYPE_UINT8;
            totalSize *= sizeof(unsigned char);
            break;
        case TYPE_INT8:
            scalarType = igtl::ImageMessage::TYPE_INT8;
            totalSize *= sizeof(char);
            break;
        case TYPE_UINT16:
            scalarType = igtl::ImageMessage::TYPE_UINT16;
            totalSize *= sizeof(unsigned short);
            break;
        case TYPE_INT16:
            scalarType = igtl::ImageMessage::TYPE_INT16;
            totalSize *= sizeof(short);
            break;
        case TYPE_FLOAT:
            scalarType = igtl::ImageMessage::TYPE_FLOAT32;
            totalSize *= sizeof(float);
            break;
    }

    //------------------------------------------------------------
    // Create a new IMAGE type message
    igtl::ImageMessage::Pointer imgMsg = igtl::ImageMessage::New();
    imgMsg->SetDimensions(size);
    imgMsg->SetSpacing(spacing);
    imgMsg->SetNumComponents(image->getNrOfChannels());
    imgMsg->SetScalarType(scalarType);
    imgMsg->SetDeviceName("DummyImage");
    imgMsg->SetSubVolume(size, svoffset);
    imgMsg->AllocateScalars();

    ImageAccess::pointer access = image->getImageAccess(ACCESS_READ);
    memcpy(imgMsg->GetScalarPointer(), access->get(), totalSize);

    return imgMsg;
}
Beispiel #2
0
/*
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
                );
            }
            
            
        }
    }
}
Beispiel #3
0
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
}