add mesh voxelizer

ChangeLog.md

@@ -15,12 +15,15 @@
    [#300](https://github.com/DGtal-team/pull/300))
 
 - *visualisation*:
-  - 2dCompImage : Computes and displays image comparisons (squared and absolute differences)
-   (Bertrand Kerautret, [#313](https://github.com/DGtal-team/DGtalTools/pull/313))
-
-  - Improve visualisation tools (vol2heightfield, vol2obj, vol2raw, vol2sdp, vol2slice, volBoundary2obj, 3dImageViewer,     	3dVolViewer, sliceViewer, Viewer3DImage)
-    allowing to read longvol including rescaling.
-    (Bertrand Kerautret, [#296](https://github.com/DGtal-team/DGtalTools/pull/296))
+  - New tool for mesh voxelization from a mesh in input (.off)
+    to a volumetric output (vol, pgm3d)
+  - 2dCompImage : Computes and displays image comparisons (squared and absolute 
+    differences) 
+    (Bertrand Kerautret, [#313](https://github.com/DGtal-team/DGtalTools/pull/313))
+  - Improve visualisation tools (vol2heightfield, vol2obj, vol2raw, vol2sdp, 
+    vol2slice,volBoundary2obj,3dImageViewer, 3dVolViewer, sliceViewer, Viewer3DImage) 
+    allowing to read longvol including rescaling. (Bertrand Kerautret, 
+    [#296](https://github.com/DGtal-team/DGtalTools/pull/296))
   - Add an option to filter vector displayed in 3dSDPViewer.
    (Bertrand Kerautret, [#297](https://github.com/DGtal-team/DGtalTools/pull/297))
 

converters/CMakeLists.txt

@@ -18,7 +18,8 @@ SET(DGTAL_TOOLS_SRC
   vol2heightfield
   heightfield2vol
   heightfield2shading
-  mesh2heightfield)
+  mesh2heightfield
+  mesh2vol)
 
 if( WITH_HDF5 )
 SET(DGTAL_TOOLS_SRC ${DGTAL_TOOLS_SRC}

converters/mesh2vol.cpp

@@ -0,0 +1,201 @@
+/**
+ *  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 mesh2vol.cpp
+ * @ingroup converters
+ *
+ * @date 2018/01/11
+ *
+ *
+ *
+ * This file is part of the DGtalTools.
+ */
+
+///////////////////////////////////////////////////////////////////////////////
+#include <iostream>
+#include <fstream>
+#include <chrono>
+#include "DGtal/helpers/StdDefs.h"
+#include "DGtal/shapes/MeshVoxelizer.h"
+#include "DGtal/kernel/sets/CDigitalSet.h"
+#include "DGtal/kernel/domains/HyperRectDomain.h"
+#include "DGtal/io/readers/MeshReader.h"
+#include "DGtal/io/Display3D.h"
+#include "DGtal/io/writers/GenericWriter.h"
+#include "DGtal/images/ImageContainerBySTLVector.h"
+#include <boost/program_options/options_description.hpp>
+#include <boost/program_options/parsers.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+using namespace std;
+using namespace DGtal;
+
+///////////////////////////////////////////////////////////////////////////////
+namespace po = boost::program_options;
+
+/**
+ @page mesh2vol
+ @brief Convert a mesh file into a 26-separated or 6-separated voxelization in a given resolution grid.
+
+@b Usage: mesh2vol [input]
+
+@b Allowed @b options @b are:
+
+@code
+  -h [ --help ]                   display this message
+  -i [ --input ] arg              mesh file (.off)
+  -o [ --output ] arg             filename of ouput volumetric file (vol, pgm3d, ...)
+                                  (auto-generated by argument values if empty)
+  -s [ --separation ] arg (=6)    voxelization 6-separated or 26-separated.
+  -r [ --resolution ]             digitization domain size (e.g. 128). The mesh will be scaled such that its bounding box maps to [0,resolution)^3.
+
+@endcode
+
+@b Example:
+@code
+  $ mesh2vol -i ${DGtal}/examples/samples/tref.off --separation 26 --resolution 256 -o output.vol
+@endcode
+
+@see mesh2vol.cpp
+
+*/
+
+template< unsigned int SEP >
+void voxelizeAndExport(const std::string& inputFilename,
+                       const std::string& outputFilename,
+                       const unsigned int resolution)
+{
+  using Domain   = Z3i::Domain;
+  using PointR3  = Z3i::RealPoint;
+  using PointZ3  = Z3i::Point;
+
+  trace.beginBlock("Preparing the mesh");
+  trace.info() << "Reading input file: " << inputFilename;
+  Mesh<PointR3> inputMesh;
+  MeshReader<PointR3>::importOFFFile(inputFilename.c_str(), inputMesh);
+  trace.info() << " [done]" << std::endl;
+  const std::pair<PointR3, PointR3> bbox = inputMesh.getBoundingBox();
+  trace.info()<< "Mesh bounding box: "<<bbox.first <<" "<<bbox.second<<std::endl;
+
+  const double smax = (bbox.second - bbox.first).max();
+  const double factor = resolution / smax;
+  const PointR3 translate = -bbox.first;
+  trace.info() << "Scale = "<<factor<<" translate = "<<translate<<std::endl;
+  for(auto it = inputMesh.vertexBegin(), itend = inputMesh.vertexEnd();
+      it != itend; ++it)
+  {
+    //scale + translation
+    *it += translate;
+    *it *= factor;
+  }
+  trace.endBlock();
+
+  trace.beginBlock("Voxelization");
+  trace.info() << "Voxelization " << SEP << "-separated ; " << resolution << "^3 ";
+  Domain aDomain(PointZ3().diagonal(0), PointZ3().diagonal(resolution));
+
+  //Digitization step
+  Z3i::DigitalSet mySet(aDomain);
+  MeshVoxelizer<Z3i::DigitalSet, SEP> aVoxelizer;
+  aVoxelizer.voxelize(mySet, inputMesh, 1.0);
+  trace.info() << " [done] " << std::endl;
+  trace.endBlock();
+
+  trace.beginBlock("Exporting");
+  // Export the digital set to a vol file
+  trace.info()<<aDomain<<std::endl;
+  ImageContainerBySTLVector<Domain, unsigned char> image(aDomain);
+  for(auto p: mySet)
+    image.setValue(p, 128);
+  image >> outputFilename.c_str();
+  trace.endBlock();
+}
+
+int main( int argc, char** argv )
+{ 
+  // parse command line ----------------------------------------------
+  po::options_description general_opt("\nAllowed options are");
+  general_opt.add_options()
+    ("help,h", "display this message")
+    ("input,i", po::value<std::string>(), "mesh file (.off) " )
+    ("output,o", po::value<std::string>(), "filename of ouput volumetric file (vol, pgm3d, ...).")
+    ("separation,s", po::value<unsigned int>()->default_value(6), "voxelization 6-separated or 26-separated." )
+    ("resolution,r", po::value<unsigned int>(), "digitization domain size (e.g. 128). The mesh will be scaled such that its bounding box maps to [0,resolution)^3." );
+
+  bool parseOK=true;
+  po::variables_map vm;
+  try {
+    po::store(po::parse_command_line(argc, argv, general_opt), vm);
+  } catch(const std::exception& ex) {
+    parseOK=false;
+    trace.info() << "Error checking program options: " << ex.what() << endl;
+  }
+
+  po::notify(vm);
+
+  if(!parseOK || vm.count("help") || argc < 1)
+  {
+    std::cout << "Usage: " << argv[0] << " -i [input]\n"
+              << "Convert a mesh file into a 26-separated or 6-separated volumetric voxelization in a given resolution grid."
+              << general_opt << "\n";
+    std::cout << "Example:\n"
+              << "mesh2vol -i ${DGtal}/examples/samples/tref.off -o output.vol --separation 26 --resolution 256 \n";
+    return -1;
+  }
+
+  if( !vm.count("input") )
+  {
+    trace.error() << " Input filename is needed to be defined" << endl;
+    return -1;
+  }
+
+  if( vm["separation"].as<unsigned int>() != 6 &&
+      vm["separation"].as<unsigned int>() != 26 )
+  {
+    trace.error() << " Separation should be 6 or 26" << endl;
+    return -1;
+  }
+
+  unsigned int separation = vm["separation"].as<unsigned int>();
+  unsigned int resolution;
+  if (vm.count("resolution"))
+    resolution = vm["resolution"].as<unsigned int>();
+  else
+  {
+    trace.error()<<"Missing output parameter '--resolution'"<<std::endl;
+    return -1;
+  }
+
+  string inputFilename = vm["input"].as<std::string>();
+  string outputFilename;
+
+  if( vm.count("output") )
+    outputFilename = vm["output"].as<std::string>();
+  else
+  {
+    trace.error()<<"Missing output parameter '--output'"<<std::endl;
+    return -1;
+  }
+
+
+  if(separation == 6)
+    voxelizeAndExport<6>(inputFilename, outputFilename, resolution);
+  else if(separation == 26)
+    voxelizeAndExport<26>(inputFilename, outputFilename, resolution);
+
+  return 0;
+}
+

doc/converters.dox

@@ -36,6 +36,7 @@ Utilities to convert various simple file formats:
   - @ref itk2vol : converts itk file into a volumetric file (.vol, .pgm3d).
   - @ref longvol2vol : converts a longvol (long int) to a vol file (unsigned char).
   - @ref mesh2heightfield : converts a mesh file into a 2D heightmap (from a normal direction N and from a starting point P).
+  - @ref mesh2vol : converts a mesh file into a 26-separated or 6-separated voxelization in a given resolution grid.
   - @ref ofs2off : converts OFS file into OFF mesh format.
   - @ref raw2HDF5 :  converts a 3D 8-bit raw file to HDF5.
   - @ref raw2vol : converts a  8-bit raw file to vol.