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() {
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();
}
#include "FAST/Tests/catch.hpp"
#include "FAST/DeviceManager.hpp"
#include <boost/thread.hpp>
#include "FAST/Streamers/ImageFileStreamer.hpp"
#include "FAST/Tests/DummyObjects.hpp"
#include "FAST/Data/Image.hpp"
using namespace fast;
TEST_CASE("No filename format given to ImageFileStreamer", "[fast][ImageFileStreamer]") {
ImageFileStreamer::pointer mhdStreamer = ImageFileStreamer::New();
CHECK_THROWS(mhdStreamer->update());
}
TEST_CASE("No hash tag in filename format given to ImageFileStreamer", "[fast][ImageFileStreamer]") {
ImageFileStreamer::pointer mhdStreamer = ImageFileStreamer::New();
CHECK_THROWS(mhdStreamer->setFilenameFormat("asd"));
}
TEST_CASE("Default streaming mode is NEWEST_FRAME_ONLY", "[fast][ImageFileStreamer]") {
ImageFileStreamer::pointer mhdStreamer = ImageFileStreamer::New();
CHECK(mhdStreamer->getStreamingMode() == STREAMING_MODE_NEWEST_FRAME_ONLY);
}
/*
// TODO fix this, will not work because it is another thread that throws the exception
TEST_CASE("Wrong filename format given to ImageFileStreamer", "[fast][ImageFileStreamer]") {
ImageFileStreamer::pointer mhdStreamer = ImageFileStreamer::New();
mhdStreamer->setFilenameFormat("asd#asd");
DynamicData::pointer image = mhdStreamer->getOutput();
std::cout << "asd" << std::endl;
TriangleRenderer->setInputConnection(segmentation->getOutputPort());
ImageRenderer::pointer imageRenderer = ImageRenderer::New();
imageRenderer->setInputConnection(streamer->getOutputPort());
SimpleWindow::pointer window = SimpleWindow::New();
window->addRenderer(imageRenderer);
window->addRenderer(TriangleRenderer);
window->set2DMode();
window->start();
}
*/
TEST_CASE("Model based segmentation with spline model on 2D cardiac US data", "[fast][ModelBasedSegmentation][2d][cardiac][visual]") {
ImageFileStreamer::pointer streamer = ImageFileStreamer::New();
//streamer->setFilenameFormat(Config::getTestDataPath()+"US/Heart/ApicalTwoChamber/US-2D_#.mhd");
//streamer->setFilenameFormat(Config::getTestDataPath()+"US/Heart/ApicalLongAxis/US-2D_#.mhd");
streamer->setFilenameFormat(Config::getTestDataPath()+"US/Heart/ApicalFourChamber/US-2D_#.mhd");
//streamer->setFilenameFormat("/home/smistad/data/ultrasound_smistad_heart/1234/H1ADBNGK/US-2D_#.mhd");
//streamer->setFilenameFormat("/home/smistad/data/ultrasound_smistad_heart/1234/H1ADCKOO/US-2D_#.mhd");
//streamer->setFilenameFormat("/home/smistad/data/ultrasound_smistad_heart/1234/H1ADCL8Q/US-2D_#.mhd");
streamer->enableLooping();
//streamer->setStreamingMode(STREAMING_MODE_PROCESS_ALL_FRAMES);
streamer->setSleepTime(50);
// Control points for spline model
std::vector<Vector2f> controlPoints = {
Vector2f(89,22), // Apex
Vector2f(100,31),
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();
}