Merge pull request #1166 from kerautret/DocExamplesListing

Doc examples listing

ChangeLog.md

@@ -37,6 +37,8 @@
  - Add cmake configuration file NeighborhoodTablesConfig to
    decompress and install look up tables. (Pablo Hernandez-Cerdan,
    [#1155](https://github.com/DGtal-team/DGtal/pull/1155))
+ - Check and add all DGtal examples in the Examples listing section.
+   (Bertrand Kerautret,[#1166](https://github.com/DGtal-team/DGtal/pull/1166))))
 
 - *Base Package*
  - Alias and ConstAlias now raise compilation error when using invalid

examples/io/viewDualSurface.cpp

@@ -20,7 +20,7 @@
  *
  * @date 2011/03/25
  *
- * An example file named digitalSetFromVol.
+ * An example file named viewDualSurface.
  *
  * This file is part of the DGtal library.
  */
@@ -393,7 +393,7 @@ int main( int argc, char** argv )
 {
   typedef KSpace::CellSet CellSet;
   QApplication application(argc,argv);
-  //! [ExampleDisplay3DToOFF]
+
   KSpace KS;
 
   Viewer3D<Z3i::Space,Z3i::KSpace> viewer(KS);
@@ -444,6 +444,6 @@ int main( int argc, char** argv )
             }
       }
   viewer << Viewer3D<>::updateDisplay;
-  //! [ExampleDisplay3DToOFF]
+
   return application.exec();
 }

examples/tutorial-examples/2DSliceImageFromVol.cpp

@@ -0,0 +1,87 @@
+/**
+ *  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 2DSliceImageFromVol.cpp
+ * @ingroup tutorial-examples
+ * @author Bertrand Kerautret (\c [email protected] )
+ * LORIA (CNRS, UMR 7503), University of Lorraine, France
+ * 
+ *
+ * @date 2016/05/09
+ *
+ * @brief Example associated to the tutorial 5 on Image adapter
+ *
+ * This file is part of the DGtal library.
+ */
+
+#include <iostream>
+#include <DGtal/base/Common.h>
+#include "DGtal/io/readers/GenericReader.h"
+#include "DGtal/io/writers/GenericWriter.h"
+
+#include <DGtal/helpers/StdDefs.h>
+#include <DGtal/images/ImageContainerBySTLVector.h>
+#include <DGtal/images/ConstImageAdapter.h>
+
+
+#include "DGtal/kernel/BasicPointFunctors.h"
+
+using namespace std;
+using namespace DGtal;
+using namespace Z2i;
+
+
+
+int main(int argc, char ** argv)
+{
+
+  typedef ImageContainerBySTLVector<Z2i::Domain, unsigned char>  Image2D;
+  typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char>  Image3D;
+
+  if(argc < 3)
+    {
+      trace.error() << "You need to indicate the volumetric image name and slice number as parameters." << std::endl;
+      trace.error() << std::endl;
+      return 1;
+    }
+  std::string filename(argv[1]);  
+  std::string outputFileName = "sliceImage.pgm";
+
+  unsigned int numSlice = atoi(argv[2]);
+
+  trace.beginBlock("Loading file");
+  Image3D  image3d = GenericReader< Image3D >::import ( filename );
+
+
+  functors::Identity id;  
+  typedef ConstImageAdapter<Image3D, Image2D::Domain, functors::Projector<Z3i::Space>,
+                            Image3D::Value,  functors::Identity >  SliceImageAdapter;
+  functors::Projector<Z2i::Space >  proj(2);
+  Z2i::Domain domain2D(proj(image3d.domain().lowerBound()),
+                              proj(image3d.domain().upperBound()));
+
+  DGtal::functors::Projector<Z3i::Space> aSliceFunctor(numSlice); 
+  aSliceFunctor.initAddOneDim(2);
+  SliceImageAdapter sliceImageZ(image3d, domain2D, aSliceFunctor, id);
+
+  trace.endBlock();
+
+  trace.beginBlock("Exporting...");
+  sliceImageZ >> outputFileName; 
+  trace.endBlock();
+  return 0;
+}

examples/tutorial-examples/CMakeLists.txt

@@ -6,6 +6,7 @@ SET(DGTAL_TUTO_EXAMPLES_SRC
   shapeGridCurveEstimator
   freemanChainFromImage
   FMMErosion
+  2DSliceImageFromVol
 )
 
 

examples/tutorial-examples/volDTGranulo.cpp

@@ -180,10 +180,6 @@ int main(int argc, char ** argv)
   trace.info() << "Got "<<cpt<<" points."<<std::endl;
   viewer3 << DGtal::Viewer3D<>::updateDisplay;
   trace.info() << "viewer3  launched..."<<std::endl;
-  res = res&& application3.exec();
+ return application3.exec();
 
-  if (res)
-    return 0;
-  else
-    return 1;
 }

src/DGtal/dec/doc/packageDEC.dox

@@ -47,6 +47,8 @@ namespace DGtal {
 Discrete exterior calculus (DEC) provides an easy and efficient way to describe linear operator over various structure.
 Basic operators, such as Hodge duality operator or exterior derivative, can be combined to create classical vector analysis operator such as gradient, curl and divergence.
 
+@note To use this package, you have to build DGtal with the Eigen option (and with Cairo option to have the examples compiled). By using cmake you have to use these options:  -DWITH_EIGEN=true -DWITH_CAIRO=true.
+
 @b Modules
 - \ref moduleDECIntroduction
 - \ref moduleDECEmbedding
@@ -60,14 +62,55 @@ Basic operators, such as Hodge duality operator or exterior derivative, can be c
 @b Related @b documentation @b pages
 
 @b Related @b examples
-- testDiscreteExteriorCalculus.cpp
+- exampleDECSurface.cpp
+- examplePropagation.cpp
 - exampleDiscreteExteriorCalculusUsage.cpp
 - exampleDiscreteExteriorCalculusSolve.cpp
-- examplePropagation.cpp
-- testLinearStructure.cpp
-- testEmbedding.cpp
-- exampleDECSurface.cpp
+- exampleDiscreteExteriorCalculusChladni.cpp
 
 */
 
+
+
+/**
+   Example of Discrete Exterior Calculus with Chladni.
+   @see \ref sectDECHelmoltzProblem
+   \image  html  exampleDECChladni.png "Primal Helmoltz decomposition harmonic component."
+   \example dec/exampleDiscreteExteriorCalculusChladni.cpp
+**/
+
+
+/**
+   Example of primal and dual Helmoltz decomposition in 2D and 3D using Discrete Exterior Calculus.
+   @see \ref sectDECHelmoltzProblem
+   \image  html  solve_2d_primal_decomposition_calculusSmall.png "Primal Helmoltz decomposition harmonic component."
+   \example dec/exampleDiscreteExteriorCalculusSolve.cpp
+**/
+
+
+
+/**
+   Example of vector field manipulation using Discrete Exterior Calculus.
+   @see \ref sectDECIntroduction
+   \image html usage_primal_one_form_sharp_flat.png "Flat sharped primal gradient vector field."
+   \example dec/exampleDiscreteExteriorCalculusUsage.cpp
+**/
+
+
+
+/**
+   Example of solving Poisson equation using the DEC package.
+    @see \ref sectDECPoissonProblem
+   \image html alcapone_phi.png "Solution dual 0-form."
+   \example dec/exampleDECSurface.cpp
+**/
+
+
+/**
+   Example of 2D wave propagation using the DEC package.
+    @see \ref moduleDECPropagation
+   \image html  propagation_time_wave_ii.gif  "You should obtain such wave propagation (by converting svg files)."
+   \example dec/examplePropagation.cpp
+**/
+
 }

src/DGtal/doc/tutorials/tutoAreaSurface.dox

@@ -123,4 +123,10 @@ VoronoiCovarianceMeasureLocalEstimator.
 
 */
 
+
+/**
+ Example of tutorial 4: Surface area estimation
+ @see @ref tutoAreaSurface
+ \example tutorial-examples/AreaSurfaceEstimation-final.cpp
+**/
 }

src/DGtal/doc/tutorials/tutoFMMErosion.dox

@@ -174,4 +174,13 @@ Once these types are defined, you can construct your new point predicate as foll
 
 */
 
+/**
+Example of tutorial 1: Local morphological opening of a 3d volume by the Fast Marching Method
+@see @ref tutoFMMErosion
+\image html tutoFMMerode.png  "erosion using FMM."
+@example tutorial-examples/FMMErosion.cpp
+
+*/
+
+
 }

src/DGtal/doc/tutorials/tutoImageManipulations.dox

@@ -140,12 +140,12 @@ To apply the extraction you can follow these steps:
   - type of the source Image (Image3D).
   - the domain type of the resulting image (Image2D::Domain).
   - the functor taking in input 2D data and return 3D
-  points (DGtal::Projector<Z3i::Space>) to access to source image data.
+  points ( DGtal::functors::Projector<Z3i::Space>) to access to source image data.
   - the type of value of the 3D image (Image3D::Value)
   - the functor type to be applied on the source image value during the reading process.
-\code 
- typedef DGtal::ConstImageAdapter<Image3D, Image2D::Domain, DGtal::Projector<Z3i::Space>,
-                                   Image3D::Value,  DGtal::DefaultFunctor >  SliceImageAdapter;
+\code
+ typedef ConstImageAdapter<Image3D, Image2D::Domain, functors::Projector<Z3i::Space>,
+                            Image3D::Value,  functors::Identity >  SliceImageAdapter;
 \endcode
 
 
@@ -167,7 +167,7 @@ should obtain the following image:
 @subsubsection subsubsectHintsImageExtractionIntroTutoImageManipulations Hints:
 - To construct the domain of the resulting image you can use a projector:
 \code 
-  DGtal::Projector<Z2i::Space >  proj(2);
+  DGtal::functors::Projector<Z2i::Space >  proj(2);
   DGtal::Z2i::Domain domain2D(proj(image3d.domain().lowerBound()),
                               proj(image3d.domain().upperBound()));
 \endcode
@@ -214,6 +214,15 @@ the previous image you should obtain:
 
 */
 
+/**
+  Example of tutorial 5: ImageAdapter: some simple image manipulations
+   @see @ref tutoImageManipulations
+  \image html slice20Lobster.png " Result of slice image number 20 on Z axis."  
+  @example tutorial-examples/2DSliceImageFromVol.cpp
+**/
+
+
+
 }
 
 

src/DGtal/doc/tutorials/tutoPolyhedralisation.dox

@@ -587,5 +587,12 @@ $ ./examples/tutorial-examples/polyhedralizer
 \example examples/tutorial-examples/polyhedralizer.cpp
 */
 
+/**
+Example of tutorial 2: making a polyhedron from a digital object
+   @see @ref tutoPolyhedralisation
+   \image html polyhedral-al-finished-w3.png "The polyhedral surface approaching Al Capone digital object, for width=3/1."
+   @example tutorial-examples/polyhedralizer.cpp
+
+*/
 
 }

src/DGtal/doc/tutorials/tutoVolDTGranulometry.dox

@@ -198,4 +198,13 @@ propagation based granulometric/thickness function from the PowerMap
 
 */
 
+/**
+Example of tutorial 3: Volumetric analysis and Granulometry
+@see @ref  tutoVolDTGranulometry
+\image html tutoVolDTGranulometry.png  "result on obtained examples/samples/Al.100.vol."
+@example tutorial-examples/volDTGranulo.cpp
+
+*/
+
+
 }

src/DGtal/geometry/doc/moduleVolumetric.dox

@@ -298,17 +298,17 @@ ExactPredicateLpPowerSeparableMetric, see @ref moduleMetrics
    Example of a Voronoi map construction in dimension 2 for the
    Eucldiean metric.
 
-@see \ref voronoiSect
-
-\example geometry/volumes/distance/voronoimap2D.cpp
+   @see \ref voronoiSect
+   \image html voronoimap-dt.png "Distance transformation for the l_2 metric."
+   \example geometry/volumes/distance/voronoimap2D.cpp
 */
 
 /**
    Example of distance transformation in dimension 2.
 
-@see \ref moduleVolumetric
-
-\example geometry/volumes/distance/distancetransform2D.cpp
+   @see \ref moduleVolumetric
+   \image  html  example-DT-L2.png "Distance transform with L2 norm."
+   \example geometry/volumes/distance/distancetransform2D.cpp
 */
 
 /**

src/DGtal/geometry/doc/packageGeometry.dox

@@ -88,11 +88,39 @@ of arbitrary dimension, by the means of separable and incremental distance trans
 @b Related @b documentation @b pages
 
 @b Related @b examples
-
+- exampleCurvature.cpp
 - voronoimap2D.cpp, distancetransform3D.cpp, distancetransform2D.cpp
 - viewer3D-7-planes.cpp , viewer3D-7bis-planes.cpp , viewer3D-7-stdplane.cpp , viewer3D-7bis-stdplane.cpp , greedy-plane-segmentation.cpp  , greedy-plane-segmentation-ex2.cpp
 - exampleConvexHull2D.cpp, exampleAlphaShape.cpp
 
 */
 
 }
+
+/**
+  Example of geometric predicates.
+  @see @ref moduleGeometricPredicates
+  \example geometry/tools/determinant/exampleInHalfPlane.cpp
+**/
+
+
+/**
+   Example of curvature estimation based on Digital Circular Arc (DCA) estimator.
+   \image  html  exampleCurvature.png "Curvature estimated using DCA estimator on a flower shape."
+   \example geometry/curves/estimation/exampleCurvature.cpp
+**/
+
+
+/**
+   Example of DSLSubsegment.
+   \example geometry/curves/exampleDSLSubsegment.cpp
+**/
+
+
+
+/**
+   Example of Preimage2D.
+   \image  html  preimageExample2.png "Example of preimage based arc recognition."
+   \example geometry/tools/examplePreimage.cpp
+**/
+

src/DGtal/images/doc/moduleBigImages.dox

@@ -273,3 +273,13 @@ And finally, here is the modified original image after the two writings.
 */
 
 }
+
+
+/**
+*  Example of HDF5 ImageFactory.
+   @see @ref dgtalBigImagesAbstract   
+
+   \image html TiledImageFromImage-11-write.png "Example of writing in cache. "
+*  \example images/exampleImageFactoryFromHDF5.cpp
+**/
+