exposed blending option to volume import. closes #35. Resets BBox on …

…new mesh.

src/cli/mesher/main.cpp

@@ -83,6 +83,7 @@ const double kDefaultLipschitz = 0.2;
 const double kDefaultMultiplier = 1.0;
 const int    kDefaultPadding = 0;
 const int    kDefaultMaxIterations = 1000;
+const double kDefaultSigma = 1.;
 
 namespace po = boost::program_options;
 
@@ -111,6 +112,7 @@ int main(int argc, char* argv[])
   bool strip_exterior = false;
   enum cleaver::MeshType mesh_mode = cleaver::Structured;
   cleaver::MeshFormat output_format = kDefaultOutputFormat;
+  double sigma = kDefaultSigma;
 
   double sizing_field_time = 0;
   double   background_time = 0;
@@ -145,6 +147,7 @@ int main(int argc, char* argv[])
       ("output_format,f", po::value<std::string>(), "output mesh format (tetgen [default], scirun, matlab, vtkUSG, vtkPoly, ply [Surface mesh only])")
       ("strict,t", "warnings become errors")
       ("segmentation,S", "The input file is a segmentation file.")
+      ("blend_sigma,B", po::value<double>(), "blending sigma for input(s) to remove alias artifacts.")
       ;
 
     boost::program_options::variables_map variables_map;
@@ -242,6 +245,9 @@ int main(int argc, char* argv[])
     if (variables_map.count("alpha_long")) {
       alpha_long = variables_map["alpha_long"].as<double>();
     }
+    if (variables_map.count("blend_sigma")) {
+      sigma = variables_map["blend_sigma"].as<double>();
+    }
 
     if (variables_map.count("background_mesh")) {
       have_background_mesh = true;
@@ -343,7 +349,7 @@ int main(int argc, char* argv[])
       std::cerr << "WARNING: More than 1 input provided for segmentation." <<
         " Only the first input will be used." << std::endl;
     }
-    NRRDTools::segmentationToIndicatorFunctions(material_fields[0]);
+    NRRDTools::segmentationToIndicatorFunctions(material_fields[0], sigma);
   } else if (material_fields.size() == 1) {
     add_inverse = true;
   } else {

src/gui/Application/MainWindow.cpp

@@ -7,8 +7,11 @@
 #include <QProgressDialog>
 #include <QApplication>
 #include <QCheckBox>
+#include <QDoubleSpinBox>
 #include <NRRDTools.h>
 #include <QStatusBar>
+#include <QLayoutItem>
+#include <QLabel>
 
 MainWindow::MainWindow(QWidget *parent) :
   QMainWindow(parent) {}
@@ -319,15 +322,21 @@ class MyFileDialog : public QFileDialog
     MyFileDialog(QWidget *, const QString& a,
         const QString& b, const QString& c);
     bool isSegmentation();
+    double sigma();
     QSize sizeHint() const;
   private:
-    QCheckBox *segmentation_check_;
+    QCheckBox * segmentation_check_;
+    QDoubleSpinBox * sigmaValue_;
 };
 
 bool MyFileDialog::isSegmentation() {
   return !this->segmentation_check_->isChecked();
 }
 
+double MyFileDialog::sigma() {
+  return this->sigmaValue_->value();
+}
+
 MyFileDialog::MyFileDialog( QWidget *parent, const QString& a,
     const QString& b, const QString& c) :
   QFileDialog( parent, a, b, c),
@@ -342,7 +351,15 @@ MyFileDialog::MyFileDialog( QWidget *parent, const QString& a,
   // add some widgets
   segmentation_check_ = new QCheckBox("These are individual indicator functions", this);
   segmentation_check_->setChecked(false);
+  sigmaValue_ = new QDoubleSpinBox(this);
+  sigmaValue_->setValue(1.);
+  sigmaValue_->setMinimum(0.);
+  sigmaValue_->setMaximum(64.);
+  sigmaValue_->setSingleStep(1.);
   hbl->addWidget(segmentation_check_);
+  hbl->addItem(new QSpacerItem(30, 20, QSizePolicy::Expanding, QSizePolicy::Minimum));
+  hbl->addWidget(new QLabel("Blending Function Sigma", this));
+  hbl->addWidget(sigmaValue_);
 
   int numRows = mainLayout->rowCount();
 
@@ -393,6 +410,7 @@ bool MainWindow::checkSaved() {
   }
   return true;
 }
+
 void MainWindow::importVolume() {
   if (!this->checkSaved()) {
     return;
@@ -403,6 +421,7 @@ void MainWindow::importVolume() {
   if (dialog.exec())
     fileNames = dialog.selectedFiles();
   bool segmentation = dialog.isSegmentation();
+  double sigma = dialog.sigma();
   if(!fileNames.isEmpty()) {
     std::string file1 = (*fileNames.begin()).toStdString();
     auto pos = file1.find_last_of('/');
@@ -431,7 +450,7 @@ void MainWindow::importVolume() {
         std::cerr << "WARNING: More than one inputs provided for segmentation." <<
           " Only the first input will be used." << std::endl;
       }
-      fields = NRRDTools::segmentationToIndicatorFunctions(inputs[0]);
+      fields = NRRDTools::segmentationToIndicatorFunctions(inputs[0], sigma);
       status.setValue(90);
       QApplication::processEvents();
     } else {

src/gui/Application/ViewWidgets/MeshWindow.cpp

@@ -1173,7 +1173,7 @@ void MeshWindow::closeEvent(QCloseEvent *event)
 void MeshWindow::setMesh(cleaver::TetMesh *mesh)
 {
   this->mesh_ = mesh;
-  m_dataBounds = cleaver::BoundingBox::merge(m_dataBounds, mesh->bounds);
+  m_dataBounds = cleaver::BoundingBox::merge(cleaver::BoundingBox(), mesh->bounds);
 
   if (mesh->imported) {
 

src/lib/nrrd2cleaver/NRRDTools.cc

@@ -61,7 +61,7 @@ typedef itk::DiscreteGaussianImageFilter<
 typedef itk::ApproximateSignedDistanceMapImageFilter
 <ImageType, ImageType> DMapType;
 std::vector<cleaver::AbstractScalarField*>
-NRRDTools::segmentationToIndicatorFunctions(std::string filename) {
+NRRDTools::segmentationToIndicatorFunctions(std::string filename, double sigma) {
   // read file using ITK
   if (filename.find(".nrrd") != std::string::npos) {
     itk::NrrdImageIOFactory::RegisterOneFactory();
@@ -98,7 +98,7 @@ NRRDTools::segmentationToIndicatorFunctions(std::string filename) {
     //do some blurring
     GaussianBlurType::Pointer blur = GaussianBlurType::New();
     blur->SetInput(multiplyImageFilter->GetOutput());
-    blur->SetVariance(1.);
+    blur->SetVariance(sigma * sigma);
     blur->Update();
     //find the average value between
     ImageCalculatorFilterType::Pointer calc =
@@ -155,7 +155,8 @@ NRRDTools::segmentationToIndicatorFunctions(std::string filename) {
 }
 
 std::vector<cleaver::AbstractScalarField*>
-NRRDTools::loadNRRDFiles(std::vector<std::string> files) {
+NRRDTools::loadNRRDFiles(std::vector<std::string> files,
+  double sigma) {
   std::vector<cleaver::AbstractScalarField*> fields;
   size_t num = 0;
   for (auto file : files) {
@@ -168,7 +169,12 @@ NRRDTools::loadNRRDFiles(std::vector<std::string> files) {
     ReaderType::Pointer reader = ReaderType::New();
     reader->SetFileName(file);
     reader->Update();
-    ImageType::Pointer img = reader->GetOutput();
+    //do some blurring
+    GaussianBlurType::Pointer blur = GaussianBlurType::New();
+    blur->SetInput(reader->GetOutput());
+    blur->SetVariance(sigma * sigma);
+    blur->Update();
+    ImageType::Pointer img = blur->GetOutput();
     //convert the image to a cleaver "abstract field"
     auto region = img->GetLargestPossibleRegion();
     auto numPixel = region.GetNumberOfPixels();

src/lib/nrrd2cleaver/NRRDTools.h

@@ -35,10 +35,10 @@
 
 class NRRDTools {
 public:
-  static std::vector<cleaver::AbstractScalarField*> 
-    segmentationToIndicatorFunctions(std::string file);
   static std::vector<cleaver::AbstractScalarField*>
-    loadNRRDFiles(std::vector<std::string> files);
+    segmentationToIndicatorFunctions(std::string file, double sigma = 1.);
+  static std::vector<cleaver::AbstractScalarField*>
+    loadNRRDFiles(std::vector<std::string> files, double sigma = 1.);
   static void saveNRRDFile(cleaver::AbstractScalarField* field,
     std::string name);
 };