Merge with Tristan's fork

.gitattributes

@@ -0,0 +1 @@
+*.ih linguist-language=C++

deformations/.gitignore

@@ -0,0 +1,2 @@
+build*/
+**/*.swp

deformations/3dVolProjector.cpp

@@ -0,0 +1,273 @@
+/**
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **/
+/**
+ * @file visuDistanceTransform.cpp
+ * @ingroup Examples
+ * @author Bertrand Kerautret (\c [email protected] )
+ * LORIA (CNRS, UMR 7503), University of Nancy, France
+ *
+ * @date 2011/01/04
+ *
+ * An example file named qglViewer.
+ *
+ * This file is part of the DGtal library.
+ */
+
+///////////////////////////////////////////////////////////////////////////////
+#include <iostream>
+#include <sstream>
+#include <iomanip>
+
+// Qt
+#include <QApplication>
+#include <QCoreApplication>
+
+#include "DGtal/base/Common.h"
+#include "DGtal/io/readers/VolReader.h"
+#include "DGtal/io/viewers/Viewer3D.h"
+#include "DGtal/io/DrawWithDisplay3DModifier.h"
+
+
+using namespace std;
+using namespace DGtal;
+using namespace Z3i;
+
+#include "deformationDisplay3d.h"
+
+/////////////////////
+#include <boost/program_options/options_description.hpp>
+#include <boost/program_options/parsers.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+namespace po = boost::program_options;
+
+int displayOneFile( 
+		   const string& inputFilename, 
+		   const string& outputBasename,
+		   const int& offset = 0, const double& step = 0)
+{
+  //image reading
+  typedef ImageSelector<Domain, unsigned char>::Type Image;
+  Image image = VolReader<Image>::importVol( inputFilename );
+
+  QCoreApplication* application = QCoreApplication::instance();
+  Viewer3D<> viewer;
+
+  //display
+  //  displayPartition(viewer, image); 
+  Domain domain(image.domain());
+
+  GradientColorMap<long> colorMap( 0, 510 );
+  colorMap.addColor(Color::Yellow);
+  colorMap.addColor(Color::Blue);
+  colorMap.addColor(Color::Red);
+  colorMap.addColor(Color::Green);
+
+  for(Domain::ConstIterator it = domain.begin(), itend=domain.end(); it!=itend; ++it){
+    unsigned char  val= image( *it );     
+    Color c = colorMap( val );
+    if(val > 0){
+      viewer << CustomColors3D(c, c);     
+      viewer << *it;     
+    }     
+  }
+
+  viewer.show();
+  viewer << Viewer3D<>::updateDisplay;
+
+  // Prepare snapshot and connect it to drawFinished signal
+  // Ref: http://www.libqglviewer.com/refManual/classQGLViewer.html#a1cf2ffb973b096b249dc7e90327a2a8e
+  viewer.setSnapshotFileName(outputBasename.c_str());  
+  viewer.setSnapshotFormat("PNG");  
+  QObject::connect( &viewer, SIGNAL(drawFinished(bool)), &viewer, SLOT(saveSnapshot(bool)) );
+
+  // Camera Configuration
+  if (!viewer.restoreStateFromFile())
+    {
+      string s = viewer.stateFileName().toStdString(); 
+      trace.emphase() << " file " << s 
+		      << " not found " 
+		      << std::endl;
+    }
+
+  if ( (offset != 0)&&(step != 0) )
+    {
+      viewer.camera()->setOrientation( -(offset*step), 0.0);
+      viewer.showEntireScene(); 
+    }
+
+  // Render
+  viewer.updateGL();
+
+
+  {//rename snapshot
+    std::stringstream olds;
+    olds << viewer.snapshotFileName().toStdString()
+	 << "-" << setfill('0') << std::setw(4) 
+	 << (viewer.snapshotCounter()-1) << ".png"; 
+    string oldf = olds.str(); 
+    std::stringstream news; 
+    news << outputBasename << ".png";
+    string newf = news.str();  
+    if (rename (oldf.c_str(), newf.c_str()) == -1) 
+      trace.info() << "renaming " << oldf << " into " 
+		   << newf << " failed " << std::endl; 
+  }
+
+  /*
+  {//rename state file
+    string oldf = viewer.stateFileName().toStdString();
+    std::stringstream news; 
+    news << ".qglviewer" << (QGLViewer::QGLViewerIndex(&viewer)+1) << ".xml";
+    string newf = news.str();  
+    if (rename (oldf.c_str(), newf.c_str()) == -1) 
+      trace.info() << "renaming " << oldf << " into " 
+		   << newf << " failed " << std::endl; 
+  }
+  */
+
+  return 0; 
+}
+
+int main( int argc, char** argv )
+{
+  // Init Qt with command-line parameters
+  QApplication application(argc, argv);
+
+  // parse command line ----------------------------------------------
+  po::options_description general_opt("Allowed options are: ");
+  general_opt.add_options()
+    ("help,h", "display this message")
+    ("output-file,o",   po::value<string>()->default_value("interface"), "output file(s) basename" )
+    ("input-file,i", po::value<std::string>(), "volume file" )
+    ("multi-input,mi", po::value<std::string>(), "volume files basename " )
+    ("start,s",  po::value<int>()->default_value(1), "starting number (for option -mi)" )
+    ("end,e",  po::value<int>()->default_value(2), "ending number, not included (for option -mi)" )
+    ("angle-step,a",  po::value<int>()->default_value(360), "angle step as a fraction of 2PI (0 disables this feature)" )
+    ("number,n",  po::value<int>()->default_value(90), "number of angle steps when moving camera" );
+  po::variables_map vm;
+  po::store(po::parse_command_line(argc, argv, general_opt), vm);  
+  po::notify(vm);    
+  if(vm.count("help")||argc<=1)
+    {
+      std::cout << "Usage: " << argv[0] << " [input-file]\n"
+		<< "Display volume file as a set of digital frontiers"
+		<< general_opt << "\n";
+      return 0;
+    }
+
+  //files
+  if (!(vm.count("output-file"))) 
+    trace.info() << "output file begin with : interface" << std::endl;
+  string outputBasename = vm["output-file"].as<std::string>();
+
+
+  if(vm.count("input-file"))
+    {
+      if (vm.count("multi-input"))
+	{
+	  trace.error() << " Cannot use both input options in the same time " 
+			<< endl;      
+	  return 1;
+	}
+      string inputFilename = vm["input-file"].as<std::string>();
+
+      if(vm.count("angle-step"))
+	{
+	  int den = vm["angle-step"].as<int>(); 
+	  double angleStep = (den == 0)?0.0:( (2.0*M_PI)/((double) den) );
+	  int n = vm["number"].as<int>(); 
+	  for (int i = 0; i < n; ++i)
+	    {
+	      trace.info() << i << std::endl; 
+	      std::stringstream so;
+	      so << outputBasename << setfill('0') << std::setw(4) 
+		 << i; 
+
+	      displayOneFile(inputFilename, so.str(), i+1, angleStep); 
+	    }
+
+	  {//rename state file
+	    std::stringstream olds;
+	    olds << ".qglviewer" << n << ".xml"; 
+	    string oldf = olds.str();
+	    string newf = ".qglviewer.xml";  
+	    if (rename (oldf.c_str(), newf.c_str()) == -1) 
+	      trace.info() << "renaming " << oldf << " into " 
+			   << newf << " failed " << std::endl; 
+	  }
+
+	}
+      else 
+	{
+	  displayOneFile(inputFilename, outputBasename); 
+
+	  {//rename state file
+	    string oldf = ".qglviewer1.xml";
+	    string newf = ".qglviewer.xml";  
+	    if (rename (oldf.c_str(), newf.c_str()) == -1) 
+	      trace.info() << "renaming " << oldf << " into " 
+			   << newf << " failed " << std::endl; 
+	  }
+	}
+    }
+  else
+    {
+      if (vm.count("multi-input"))
+	{
+	  string inputBasename = vm["multi-input"].as<std::string>();
+
+	  int den = vm["angle-step"].as<int>(); 
+	  double angleStep = (den == 0)?0.0:( (2.0*M_PI)/((double) den) );
+
+	  int start = vm["start"].as<int>();
+	  int end = vm["end"].as<int>();
+	  for (int i = start; i != end; ++i)
+	    {
+	      std::stringstream si;
+	      si << inputBasename << setfill('0') << std::setw(4) 
+		 << i << ".vol"; 
+	      trace.info() << si.str() << std::endl; 
+	      std::stringstream so;
+	      so << outputBasename << setfill('0') << std::setw(4) 
+		 << i; 
+
+	      displayOneFile(si.str(), so.str(), i+1, angleStep); 
+
+	    }
+
+
+	  {//rename state file
+	    std::stringstream olds;
+	    olds << ".qglviewer" << (end-start) << ".xml"; 
+	    string oldf = olds.str();
+	    string newf = ".qglviewer.xml";  
+	    if (rename (oldf.c_str(), newf.c_str()) == -1) 
+	      trace.info() << "renaming " << oldf << " into " 
+			   << newf << " failed " << std::endl; 
+	  }
+
+	}
+      else
+	{
+	  trace.error() << " No file name defined" << endl;      
+	  return 1;
+	}
+    }
+
+
+  return 0; 
+}

deformations/3dVolViewer.cpp

@@ -31,6 +31,7 @@
 #include <QtGui/qapplication.h>
 
 #include "DGtal/base/Common.h"
+#include "DGtal/helpers/StdDefs.h"
 #include "DGtal/io/readers/VolReader.h"
 #include "DGtal/io/viewers/Viewer3D.h"
 #include "DGtal/io/DrawWithDisplay3DModifier.h"
@@ -53,6 +54,9 @@ namespace po = boost::program_options;
 
 int main( int argc, char** argv )
 {
+  // Qt init with command-line parameters
+  QApplication application(argc, argv);
+
   // parse command line ----------------------------------------------
   po::options_description general_opt("Allowed options are: ");
   general_opt.add_options()
@@ -82,8 +86,7 @@ int main( int argc, char** argv )
   int thresholdMax = vm["thresholdMax"].as<int>();
   unsigned char transp = vm["transparency"].as<uint>();
 
-  QApplication application(argc,argv);
-  Viewer3D viewer;
+  Viewer3D<> viewer;
   viewer.setWindowTitle("simple Volume Viewer");
   viewer.show();
 
@@ -108,6 +111,6 @@ int main( int argc, char** argv )
       viewer << *it;     
     }     
   }
-  viewer << Viewer3D::updateDisplay;
+  viewer << Viewer3D<>::updateDisplay;
   return application.exec();
 }