Esempio n. 1
0
int main() {
    Reporter::setGlobalReportMethod(Reporter::COUT);

    ImageFileStreamer::pointer streamer = ImageFileStreamer::New();
    streamer->setFilenameFormat(Config::getTestDataPath() + "US/JugularVein/US-2D_#.mhd");
    streamer->setTimestampFilename(Config::getTestDataPath() + "US/JugularVein/timestamps.fts");
    streamer->enableLooping();

    PixelClassifier::pointer segmentation = PixelClassifier::New();
    segmentation->setNrOfClasses(3);
    segmentation->setScaleFactor(1.0f / 255.0f);
    const auto engine = segmentation->getInferenceEngine()->getName();
    if(engine == "TensorFlow") {
        // TensorFlow needs to know what the output node is called
        segmentation->addOutputNode(0, "conv2d_23/truediv");
    } else if(engine == "TensorRT") {
        // TensorRT needs to know everything about the input and output nodes
        segmentation->addInputNode(0, "input_image", NodeType::IMAGE, TensorShape({-1, 1, 256, 256}));
        segmentation->addOutputNode(0, "permute_2/transpose");
    }
    segmentation->load(join(Config::getTestDataPath(),
                            "NeuralNetworkModels/jugular_vein_segmentation." + segmentation->getInferenceEngine()->getDefaultFileExtension()));
    segmentation->setInputConnection(streamer->getOutputPort());
    segmentation->enableRuntimeMeasurements();

    SegmentationRenderer::pointer segmentationRenderer = SegmentationRenderer::New();
    segmentationRenderer->addInputConnection(segmentation->getOutputPort());
    segmentationRenderer->setOpacity(0.25);
    segmentationRenderer->setColor(Segmentation::LABEL_FOREGROUND, Color::Red());
    segmentationRenderer->setColor(Segmentation::LABEL_BLOOD, Color::Blue());

    ImageRenderer::pointer imageRenderer = ImageRenderer::New();
    imageRenderer->setInputConnection(streamer->getOutputPort());

    SimpleWindow::pointer window = SimpleWindow::New();
    window->addRenderer(imageRenderer);
    window->addRenderer(segmentationRenderer);
    window->set2DMode();
    window->getView()->setBackgroundColor(Color::Black());
    window->start();
    segmentation->getAllRuntimes()->printAll();
}
Esempio n. 2
0
int main() {
    // Import two point sets A and B
    VTKPointSetFileImporter::pointer importerA = VTKPointSetFileImporter::New();
    importerA->setFilename(Config::getTestDataPath() + "Surface_LV.vtk");

    VTKPointSetFileImporter::pointer importerB = VTKPointSetFileImporter::New();
    importerB->setFilename(Config::getTestDataPath() + "Surface_LV.vtk");

    // Apply a transformation to point set B
    Vector3f translation(0.01, 0, 0.01);
    Vector3f rotation(0.5, 0, 0);
    AffineTransformation::pointer transformation = AffineTransformation::New();
    transformation->getTransform().translate(translation);
    Matrix3f R;
    R = Eigen::AngleAxisf(rotation.x(), Vector3f::UnitX())
    * Eigen::AngleAxisf(rotation.y(), Vector3f::UnitY())
    * Eigen::AngleAxisf(rotation.z(), Vector3f::UnitZ());
    transformation->getTransform()->rotate(R);
    importerB->update();
    importerB->getOutputData<PointSet>()->getSceneGraphNode()->setTransformation(transformation);

    // Perform the registration
    IterativeClosestPoint::pointer icp = IterativeClosestPoint::New();
    icp->setMovingPointSetPort(importerA->getOutputPort());
    icp->setFixedPointSetPort(importerB->getOutputPort());
    icp->update();

    // Apply transformation to A
    importerA->getOutputData<PointSet>()->getSceneGraphNode()->setTransformation(icp->getOutputTransformation());

    Reporter::info() << "Registration result: " << Reporter::end();
    Reporter::info() << "Rotation: " << icp->getOutputTransformation()->getEulerAngles().transpose() << Reporter::end();
    Reporter::info() << "Translation:" << icp->getOutputTransformation()->getTransform().translation().transpose() << Reporter::end();

    // Visualize the two point sets
    VertexRenderer::pointer renderer = VertexRenderer::New();
    renderer->addInputConnection(importerA->getOutputPort(), Color::Blue(), 10);
    renderer->addInputConnection(importerB->getOutputPort(), Color::Green(), 5);
    renderer->setDefaultDrawOnTop(true);

    SimpleWindow::pointer window = SimpleWindow::New();
    window->addRenderer(renderer);
#ifdef FAST_CONTINUOUS_INTEGRATION
	// This will automatically close the window after 5 seconds, used for CI testing
    window->setTimeout(5*1000);
#endif
    window->start();
}
int main() {
    // Import images from files using the ImageFileStreamer
    ImageFileStreamer::pointer streamer = ImageFileStreamer::New();
    // The hashtag here will be replaced with an integer, starting with 0 as default
    streamer->setFilenameFormat(std::string(FAST_TEST_DATA_DIR)+"/US-2Dt/US-2Dt_#.mhd");

    // Renderer image
    ImageRenderer::pointer renderer = ImageRenderer::New();
    renderer->addInputConnection(streamer->getOutputPort());
    SimpleWindow::pointer window = SimpleWindow::New();
    window->addRenderer(renderer);
    window->set2DMode();
#ifdef FAST_CONTINUOUS_INTEGRATION
	// This will automatically close the window after 5 seconds, used for CI testing
    window->setTimeout(5*1000);
#endif
    window->start();
}
Esempio n. 4
0
int main(int argc, char** argv) {
    CommandLineParser parser("Import triangle mesh from file");
    parser.addPositionVariable(1, "filename", Config::getTestDataPath()+"/Surface_LV.vtk");
    parser.parse(argc, argv);

    // Import a triangle mesh from vtk file using the VTKMeshFileImporter
    VTKMeshFileImporter::pointer importer = VTKMeshFileImporter::New();
    importer->setFilename(parser.get("filename"));

    // Renderer mesh
    TriangleRenderer::pointer renderer = TriangleRenderer::New();
    renderer->addInputConnection(importer->getOutputPort());

    // Setup window
    SimpleWindow::pointer window = SimpleWindow::New();
    window->addRenderer(renderer);
#ifdef FAST_CONTINUOUS_INTEGRATION
    window->setTimeout(5*1000); // automatically close window after 5 seconds
#endif
    window->start();
}
int main() {
    // Import image from file using the ImageFileImporter
    ImageFileImporter::pointer importer = ImageFileImporter::New();
    importer->setFilename(std::string(FAST_TEST_DATA_DIR)+"/US-2D.jpg");

    // Smooth image
    GaussianSmoothingFilter::pointer filter = GaussianSmoothingFilter::New();
    filter->setInputConnection(importer->getOutputPort());
    filter->setStandardDeviation(2.0);
    filter->setMaskSize(7);

    // Renderer image
    ImageRenderer::pointer renderer = ImageRenderer::New();
    renderer->addInputConnection(filter->getOutputPort());
    SimpleWindow::pointer window = SimpleWindow::New();
    window->addRenderer(renderer);
#ifdef FAST_CONTINUOUS_INTEGRATION
	// This will automatically close the window after 5 seconds, used for CI testing
    window->setTimeout(5*1000);
#endif
    window->start();
}
Esempio n. 6
0
int main(int argc, char** argv) {
    CommandLineParser parser("Import point set from file");
    parser.addPositionVariable(1, "filename", Config::getTestDataPath() + "Surface_LV.vtk");
    parser.parse(argc, argv);

    // Import line set from vtk file
    VTKMeshFileImporter::pointer importer = VTKMeshFileImporter::New();
    importer->setFilename(parser.get("filename"));

    // Render vertices
    VertexRenderer::pointer renderer = VertexRenderer::New();
    renderer->addInputConnection(importer->getOutputPort());

    // Setup window
    SimpleWindow::pointer window = SimpleWindow::New();
    window->addRenderer(renderer);
#ifdef FAST_CONTINUOUS_INTEGRATION
	// This will automatically close the window after 5 seconds, used for CI testing
    window->setTimeout(5*1000);
#endif
    window->start();
}
int main() {
    // Import CT image
    ImageFileImporter::pointer importer = ImageFileImporter::New();
    importer->setFilename(std::string(FAST_TEST_DATA_DIR) + "CT-Abdomen.mhd");

    // Extract surface mesh using a threshold value
    SurfaceExtraction::pointer extraction = SurfaceExtraction::New();
    extraction->setInputConnection(importer->getOutputPort());
    extraction->setThreshold(300);

    // Render and visualize the mesh
    MeshRenderer::pointer surfaceRenderer = MeshRenderer::New();
    surfaceRenderer->setInputConnection(extraction->getOutputPort());

	SimpleWindow::pointer window = SimpleWindow::New();
    window->addRenderer(surfaceRenderer);
#ifdef FAST_CONTINUOUS_INTEGRATION
	// This will automatically close the window after 5 seconds, used for CI testing
    window->setTimeout(5*1000);
#endif
    window->start();
}
Esempio n. 8
0
int main() {
    // Import image from file using the ImageFileImporter
    ImageFileImporter::pointer importer = ImageFileImporter::New();
    importer->setFilename(std::string(FAST_TEST_DATA_DIR)+"/US-2D.jpg");
    //importer->setFilename(std::string(FAST_TEST_DATA_DIR) + "/US-1-2D.png");
    
    /*
    //K = 1, dvs K = gamle versjonen, M_PI gaus
    int groupSize = 5;
    int windowSize = 51;
    float sigma = 1.65f;
    float dS = 0.5f;
    */
    /*
    //K = 0, dvs K = 1/2d
    int groupSize = 5;
    int windowSize = 51;
    float sigma = 0.65f;
    float dS = 0.135f;
    */
    //K = 3 dvs ny gauss
    int groupSize = 17;
    int windowSize = 17;
    float sigma = 5.000f;
    //float dS = 0.03999f;
    float dS = 5.0f;
    
    // Smooth image
    NoneLocalMeans::pointer filter = NoneLocalMeans::New();
    filter->setInputConnection(importer->getOutputPort());
    //filter->setGroupSize(15);
    //filter->setWindowSize(51);
    //filter->setSigma(0.15f);
    //filter->setDenoiseStrength(0.15f);
    filter->setGroupSize(groupSize);
    filter->setWindowSize(windowSize);
    filter->setSigma(sigma);
    filter->setDenoiseStrength(dS);
    filter->setEuclid(1);
    filter->setK(2);
    //filter->setOutputType(TYPE_FLOAT);
    
    //Export img
    ImageExporter::pointer exporter = ImageExporter::New();
    std::string text = "";
    //text += std::to_string( groupSize );
    //text += "WS_";
    //text += std::to_string( windowSize );
    //text += "S_";
    //text += std::to_string( sigma );
    //text += "DS_";
    //text += std::to_string( dS );
    text += "TIME_";
    time_t seconds;
    seconds = time (NULL);
    text += std::to_string( seconds );
    text += ".jpg";
    exporter->setFilename(text);
    exporter->setInputConnection(filter->getOutputPort());
    exporter->update();
    
    // Renderer image
    ImageRenderer::pointer renderer = ImageRenderer::New();
    renderer->addInputConnection(filter->getOutputPort());
    SimpleWindow::pointer window = SimpleWindow::New();
    window->addRenderer(renderer);
    window->setTimeout(200*1000); // automatically close window after 5 seconds
    window->start();
}
int main(int argc, char** argv) {
	std::vector<std::string> recordings = {
	"/home/smistad/AssistantTestData/1/US-Acq_03_20150608T103739/Acquisition/US-Acq_03_20150608T103739_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/1/US-Acq_04_20150608T103837/Acquisition/US-Acq_04_20150608T103837_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/1/US-Acq_07_20150608T104148/Acquisition/US-Acq_07_20150608T104148_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/1/US-Acq_08_20150608T104238/Acquisition/US-Acq_08_20150608T104238_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/0/US-Acq_03_20150608T102144/Acquisition/US-Acq_03_20150608T102144_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/0/US-Acq_04_20150608T102242/Acquisition/US-Acq_04_20150608T102242_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/0/US-Acq_07_20150608T102703/Acquisition/US-Acq_07_20150608T102703_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/0/US-Acq_08_20150608T102854/Acquisition/US-Acq_08_20150608T102854_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/2/US-Acq_03_20150608T104805/Acquisition/US-Acq_03_20150608T104805_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/2/US-Acq_04_20150608T104910/Acquisition/US-Acq_04_20150608T104910_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/2/US-Acq_07_20150608T105549/Acquisition/US-Acq_07_20150608T105549_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/2/US-Acq_08_20150608T105649/Acquisition/US-Acq_08_20150608T105649_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/3/US-Acq_03_20150608T113646/Acquisition/US-Acq_03_20150608T113646_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/3/US-Acq_04_20150608T113750/Acquisition/US-Acq_04_20150608T113750_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/3/US-Acq_07_20150608T114115/Acquisition/US-Acq_07_20150608T114115_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/3/US-Acq_08_20150608T114217/Acquisition/US-Acq_08_20150608T114217_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/4/US-Acq_03_20150608T112610/Acquisition/US-Acq_03_20150608T112610_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/4/US-Acq_04_20150608T112656/Acquisition/US-Acq_04_20150608T112656_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/4/US-Acq_08_20150608T113129/Acquisition/US-Acq_08_20150608T113129_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/4/US-Acq_09_20150608T113245/Acquisition/US-Acq_09_20150608T113245_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/5/US-Acq_03_20150608T111610/Acquisition/US-Acq_03_20150608T111610_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/5/US-Acq_04_20150608T111701/Acquisition/US-Acq_04_20150608T111701_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/5/US-Acq_07_20150608T111940/Acquisition/US-Acq_07_20150608T111940_Image_Transducer_#.mhd",
	"/home/smistad/AssistantTestData/6/0/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/6/1/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/6/2/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/6/3/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/6/4/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/7/0/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/7/1/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/7/2/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/7/3/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/8/0/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/8/1/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/8/2/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/8/3/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/9/0/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/9/1/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/9/2/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/9/3/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/10/0/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/10/1/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/10/2/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/10/3/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/11/0/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/11/1/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/11/2/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/11/3/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/12/0/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/12/1/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/12/2/US-2D_#.mhd",
	"/home/smistad/AssistantTestData/12/3/US-2D_#.mhd",
	"/media/smistad/New Volume/Carotis/Erik/2016-06-02-140622/US-2D_#.mhd",
	"/media/smistad/New Volume/Carotis/Erik/2016-06-02-140721/US-2D_#.mhd",
	"/media/smistad/New Volume/Carotis/Erik/2016-06-02-140846/US-2D_#.mhd",
	"/media/smistad/New Volume/Carotis/Erik/2016-06-02-140923/US-2D_#.mhd"
	};
	uint recordingID = 0;
	if(argc != 2) {
		std::cout << "Usage: " << argv[0] << "<recording-id: 0-" << recordings.size() << ">" << std::endl;
		return 0;
	} else {
		recordingID = atoi(argv[1]);
	}


	ImageFileStreamer::pointer streamer = ImageFileStreamer::New();
	streamer->setStreamingMode(STREAMING_MODE_PROCESS_ALL_FRAMES);
	streamer->setFilenameFormat(recordings[recordingID]);
	streamer->update();

	UltrasoundVesselDetection::pointer detector = UltrasoundVesselDetection::New();
	detector->setInputConnection(streamer->getOutputPort());
	detector->enableRuntimeMeasurements();

	SegmentationRenderer::pointer segmentationRenderer = SegmentationRenderer::New();
	segmentationRenderer->addInputConnection(detector->getOutputSegmentationPort());
	segmentationRenderer->setFillArea(false);

	ImageRenderer::pointer imageRenderer = ImageRenderer::New();
	imageRenderer->addInputConnection(streamer->getOutputPort());

	SimpleWindow::pointer window = SimpleWindow::New();
	window->addRenderer(imageRenderer);
	window->addRenderer(segmentationRenderer);
	window->set2DMode();
	window->setWidth(1920);
	window->setHeight(1080);
	window->start();
	detector->getRuntime("ellipse fitting")->print();
	detector->getRuntime("candidate selection")->print();
	detector->getRuntime("classifier")->print();
	detector->getRuntime("segmentation")->print();
}