예제 #1
0
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);

    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;
        OpenCLImageAccess::pointer inputAccess = input->getOpenCLImageAccess(ACCESS_READ, device);
        if(output->getDimensions() == 2) {
            globalSize = cl::NDRange(input->getWidth(),input->getHeight());
            mKernel.setArg(0, *inputAccess->get2DImage());
        } else {
            globalSize = cl::NDRange(input->getWidth(),input->getHeight(), input->getDepth());
            mKernel.setArg(0, *inputAccess->get3DImage());
        }

        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);
    }

}
예제 #2
0
#include "VTKImageImporter.hpp"
#include "VTKImageExporter.hpp"
#include "ImageImporter.hpp"

using namespace fast;

// TODO rewrite this test so that it doesn't use the vtk exporter
TEST_CASE("Import an image from VTK to FAST", "[fast][VTK]") {
    ImageImporter::pointer importer = ImageImporter::New();
    importer->setFilename(std::string(FAST_TEST_DATA_DIR) + "US-2D.jpg");
    Image::pointer fastImage = importer->getOutput();

    // VTK Export
    vtkSmartPointer<VTKImageExporter> vtkExporter = VTKImageExporter::New();
    vtkExporter->SetInput(fastImage);
    vtkSmartPointer<vtkImageData> vtkImage = vtkExporter->GetOutput();
    vtkExporter->Update();

    // VTK Import example
    VTKImageImporter::pointer vtkImporter = VTKImageImporter::New();
    vtkImporter->setInput(vtkImage);
    Image::pointer importedImage = vtkImporter->getOutput();
    vtkImporter->update();

    CHECK(fastImage->getWidth() == importedImage->getWidth());
    CHECK(fastImage->getHeight() == importedImage->getHeight());
    CHECK(fastImage->getDepth() == 1);
    CHECK(fastImage->getDimensions() == 2);
    CHECK(fastImage->getDataType() == TYPE_FLOAT);
}
예제 #3
0
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);
}