int main() {
// Import CT image
ImageFileImporter::pointer importer = ImageFileImporter::New();
importer->setFilename(Config::getTestDataPath() + "CT/CT-Abdomen.mhd");
// Extract surface mesh from the CT image
SurfaceExtraction::pointer extraction = SurfaceExtraction::New();
extraction->setInputConnection(importer->getOutputPort());
extraction->setThreshold(400);
// Export mesh to disk
VTKMeshFileExporter::pointer exporter = VTKMeshFileExporter::New();
exporter->setInputConnection(extraction->getOutputPort());
exporter->setFilename("region_growing_result.vtk");
exporter->setWriteNormals(true);
exporter->update(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");
// 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() {
// 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();
}
#include "FAST/Streamers/ImageFileStreamer.hpp"
#include "FAST/Testing.hpp"
#include "FAST/Importers/ImageFileImporter.hpp"
#include "ImageRenderer.hpp"
#include "FAST/Visualization/SimpleWindow.hpp"
using namespace fast;
TEST_CASE("ImageRenderer with single 2D image in 2D mode", "[fast][ImageRenderer][visual]") {
ImageFileImporter::pointer importer = ImageFileImporter::New();
importer->setFilename(std::string(FAST_TEST_DATA_DIR)+"US-2D.jpg");
ImageRenderer::pointer renderer = ImageRenderer::New();
renderer->setInputConnection(importer->getOutputPort());
SimpleWindow::pointer window = SimpleWindow::New();
window->addRenderer(renderer);
window->set2DMode();
window->setTimeout(500);
CHECK_NOTHROW(window->start());
}
TEST_CASE("ImageRenderer with dynamic 2D image in 2D mode", "[fast][ImageRenderer][visual]") {
ImageFileStreamer::pointer streamer = ImageFileStreamer::New();
streamer->setFilenameFormat(std::string(FAST_TEST_DATA_DIR)+"US-2Dt/US-2Dt_#.mhd");
ImageRenderer::pointer renderer = ImageRenderer::New();
renderer->setInputConnection(streamer->getOutputPort());
SimpleWindow::pointer window = SimpleWindow::New();
window->addRenderer(renderer);
window->set2DMode();
window->setTimeout(1000);
void ImageFileStreamer::producerStream() {
Streamer::pointer pointerToSelf = mPtr.lock(); // try to avoid this object from being destroyed until this function is finished
uint i = mStartNumber;
while(true) {
std::string filename = mFilenameFormat;
std::string frameNumber = boost::lexical_cast<std::string>(i);
if(mZeroFillDigits > 0 && frameNumber.size() < mZeroFillDigits) {
std::string zeroFilling = "";
for(uint z = 0; z < mZeroFillDigits-frameNumber.size(); z++) {
zeroFilling += "0";
}
frameNumber = zeroFilling + frameNumber;
}
filename.replace(
filename.find("#"),
1,
frameNumber
);
try {
ImageFileImporter::pointer importer = ImageFileImporter::New();
importer->setFilename(filename);
importer->setMainDevice(getMainDevice());
importer->update();
Image::pointer image = importer->getOutputData<Image>();
DynamicData::pointer ptr = getOutputData<Image>();
if(ptr.isValid()) {
try {
ptr->addFrame(image);
if(mSleepTime > 0)
boost::this_thread::sleep(boost::posix_time::milliseconds(mSleepTime));
} catch(NoMoreFramesException &e) {
throw e;
} catch(Exception &e) {
std::cout << "streamer has been deleted, stop" << std::endl;
break;
}
if(!mFirstFrameIsInserted) {
{
boost::lock_guard<boost::mutex> lock(mFirstFrameMutex);
mFirstFrameIsInserted = true;
}
mFirstFrameCondition.notify_one();
}
} else {
std::cout << "DynamicImage object destroyed, stream can stop." << std::endl;
break;
}
mNrOfFrames++;
i += mStepSize;
} catch(FileNotFoundException &e) {
if(i > 0) {
std::cout << "Reached end of stream" << std::endl;
// If there where no files found at all, we need to release the execute method
if(!mFirstFrameIsInserted) {
{
boost::lock_guard<boost::mutex> lock(mFirstFrameMutex);
mFirstFrameIsInserted = true;
}
mFirstFrameCondition.notify_one();
}
if(mLoop) {
// Restart stream
i = mStartNumber;
continue;
}
mHasReachedEnd = true;
// Reached end of stream
break;
} else {
throw e;
}
}
}
}
NLMGUI2D::NLMGUI2D() {
viewOrig = createView();
viewOrig->set2DMode();
//viewOrig->set3DMode();
// Create a 3D view
//View* view = createView();
view = createView();
//view->set3DMode();
view->set2DMode();
//enableFullscreen();
// Import image
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");
// Smooth images
nlmSmoothing = NonLocalMeans::New();
nlmSmoothing->setInputConnection(importer->getOutputPort());
nlmSmoothing->setSigma(0.65f);
nlmSmoothing->setGroupSize(5);
nlmSmoothing->setWindowSize(11);
nlmSmoothing->setDenoiseStrength(0.300);
nlmSmoothing->setK(1);
nlmSmoothing->setEuclid(1);
nlmSmoothing->enableRuntimeMeasurements();
//mSmoothing = GaussianSmoothingFilter::New();
//mSmoothing->setInputConnection(importer->getOutputPort());
//mSmoothing->setStandardDeviation(1);
// Set up surface extraction
//mSurfaceExtraction = SurfaceExtraction::New();
//mSurfaceExtraction->setInputConnection(nlmSmoothing->getOutputPort());
//mSurfaceExtraction->setThreshold(100);
// Set up rendering
renderer = ImageRenderer::New();
//ImageRenderer::pointer renderer = ImageRenderer::New();
renderer->addInputConnection(nlmSmoothing->getOutputPort());
//MeshRenderer::pointer renderer = MeshRenderer::New();
//renderer->addInputConnection(mSurfaceExtraction->getOutputPort());
view->addRenderer(renderer);
rendererOrig = ImageRenderer::New();
rendererOrig->addInputConnection(importer->getOutputPort());
viewOrig->addRenderer(rendererOrig);
// Create and add GUI elements
// First create the menu layout
QVBoxLayout* menuLayout = new QVBoxLayout;
// Menu items should be aligned to the top
menuLayout->setAlignment(Qt::AlignTop);
// Title label
QLabel* title = new QLabel;
title->setText("Menu");
QFont font;
font.setPointSize(28);
title->setFont(font);
menuLayout->addWidget(title);
// Quit button
QPushButton* quitButton = new QPushButton;
quitButton->setText("Quit");
quitButton->setFixedWidth(200);
menuLayout->addWidget(quitButton);
// Connect the clicked signal of the quit button to the stop method for the window
QObject::connect(quitButton, &QPushButton::clicked, boost::bind(&Window::stop, this));
// Smoothing parameter label
//mSmoothingLabel = new QLabel;
//mSmoothingLabel->setText("DenoiseStrength: 300");
//menuLayout->addWidget(mSmoothingLabel);
nlmStrengthLabel = new QLabel;
std::string text1 = "Denoise Strength: " + boost::lexical_cast<std::string>(0.3) + " ";
nlmStrengthLabel->setText(text1.c_str());
menuLayout->addWidget(nlmStrengthLabel);
// Smoothing parameter slider
QSlider* slider = new QSlider(Qt::Horizontal);
slider->setMinimum(10);
slider->setMaximum(3000);
slider->setValue(300);
slider->setFixedWidth(300);
menuLayout->addWidget(slider);
// Connect the value changed signal of the slider to the updateSmoothingParameter method
QObject::connect(slider, &QSlider::valueChanged, boost::bind(&NLMGUI2D::updateDenoiseParameter, this, _1));
// Threshold label
//mThresholdLabel = new QLabel;
//mThresholdLabel->setText("Threshold: 100 HU");
//menuLayout->addWidget(mThresholdLabel);
nlmSigmaLabel = new QLabel;
std::string text2 = "Sigma: " + boost::lexical_cast<std::string>(0.65) + " ";
nlmSigmaLabel->setText(text2.c_str());
menuLayout->addWidget(nlmSigmaLabel);
// Sigma slider
QSlider* slider2 = new QSlider(Qt::Horizontal);
slider2->setMinimum(10);
slider2->setMaximum(3000);
slider2->setValue(650);
slider2->setFixedWidth(300);
menuLayout->addWidget(slider2);
// Connect the value changed signal of the slider to the updateSigma method
QObject::connect(slider2, &QSlider::valueChanged, boost::bind(&NLMGUI2D::updateSigma, this, _1));
//GroupSize Label + Slider
nlmGroupSizeLabel = new QLabel;
std::string text3 = "Group Size: " + boost::lexical_cast<std::string>(3) + " ";
nlmGroupSizeLabel->setText(text3.c_str());
menuLayout->addWidget(nlmGroupSizeLabel);
QSlider* slider3 = new QSlider(Qt::Horizontal);
slider3->setMinimum(3);
slider3->setMaximum(30);
slider3->setValue(3);
slider3->setFixedWidth(300);
menuLayout->addWidget(slider3);
QObject::connect(slider3, &QSlider::valueChanged, boost::bind(&NLMGUI2D::updateGroupSize, this, _1));
//WindowSize Label + Slider
nlmWindowSizeLabel = new QLabel;
std::string text4 = "Window Size: " + boost::lexical_cast<std::string>(5) + " ";
nlmWindowSizeLabel->setText(text4.c_str());
menuLayout->addWidget(nlmWindowSizeLabel);
QSlider* slider4 = new QSlider(Qt::Horizontal);
slider4->setMinimum(5);
slider4->setMaximum(100);
slider4->setValue(5);
slider4->setFixedWidth(300);
menuLayout->addWidget(slider4);
QObject::connect(slider4, &QSlider::valueChanged, boost::bind(&NLMGUI2D::updateWindowSize, this, _1));
//K Label + Slider
nlmKLabel = new QLabel;
std::string text5 = "K Version: " + boost::lexical_cast<std::string>(0) + " ";
nlmKLabel->setText(text5.c_str());
menuLayout->addWidget(nlmKLabel);
QSlider* slider5 = new QSlider(Qt::Horizontal);
slider5->setMinimum(0);
slider5->setMaximum(5);
slider5->setValue(0);
slider5->setFixedWidth(300);
menuLayout->addWidget(slider5);
QObject::connect(slider5, &QSlider::valueChanged, boost::bind(&NLMGUI2D::updateK, this, _1));
nlmELabel = new QLabel;
std::string text7 = "Euclid Version: " + boost::lexical_cast<std::string>(0) + " ";
nlmELabel->setText(text7.c_str());
menuLayout->addWidget(nlmELabel);
QSlider* slider6 = new QSlider(Qt::Horizontal);
slider6->setMinimum(0);
slider6->setMaximum(2);
slider6->setValue(0);
slider6->setFixedWidth(300);
menuLayout->addWidget(slider6);
QObject::connect(slider6, &QSlider::valueChanged, boost::bind(&NLMGUI2D::updateE, this, _1));
timerLabel = new QLabel;
std::string text6 = "Kernal time: -- ms" ;
timerLabel->setText(text6.c_str());
menuLayout->addWidget(timerLabel);
// Add menu and view to main layout
QHBoxLayout* layout = new QHBoxLayout;
layout->addLayout(menuLayout);
layout->addWidget(viewOrig);
layout->addWidget(view);
mWidget->setLayout(layout);
}
