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();
}
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();
}
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();
}
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();
}
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();
}