Fix1441

ChangeLog.md

@@ -82,6 +82,12 @@
  (Adrien Krähenbühl,
  [#1325](https:/DGtal-team/DGtal/pull/1426))
 
+- *DEC*
+ - Fix issue (https:/DGtal-team/DGtal/issues/1441))
+ related to bad link in DEC/moduleAT documentation and missing
+ associated example exampleSurfaceATnormals.cpp (Jacques-Olivier
+ Lachaud,[#1442](https:/DGtal-team/DGtal/pull/1442))
+
 - *doc*
  - Promoting the `Shortcuts` documentation page on the main page. (David
  Coeurjolly [#1417](https:/DGtal-team/DGtal/pull/1417))

examples/dec/CMakeLists.txt

@@ -18,10 +18,11 @@ endif(WITH_CAIRO AND WITH_EIGEN AND WITH_QGLVIEWER)
 if (WITH_EIGEN)
  set(DGTAL_EXAMPLES_SRC2_DEC
  examplePropagation
+ exampleSurfaceATNormals
  )
 
  foreach(FILE ${DGTAL_EXAMPLES_SRC2_DEC})
  add_executable(${FILE} ${FILE})
  target_link_libraries (${FILE} DGtal ${DGtalLibDependencies})
  endforeach(FILE)
-endif()
+endif()

examples/dec/exampleSurfaceATNormals.cpp

@@ -0,0 +1,142 @@
+/**
+ * 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 exampleSurfaceATNormals.cpp
+ * @ingroup Examples
+ * @author Jacques-Olivier Lachaud (\c [email protected] )
+ * Laboratory of Mathematics (CNRS, UMR 5127), University of Savoie, France
+ *
+ * @date 2019/06/09
+ *
+ * An example file named exampleSurfaceATNormals.
+ *
+ * This file is part of the DGtal library.
+ */
+
+/////////////////////////////////////////////////////////////////////
+//! [AT-surface-includes]
+#include <iostream>
+#include "ConfigExamples.h"
+#include "DGtal/base/Common.h"
+#include "DGtal/helpers/StdDefs.h"
+#include "DGtal/helpers/Shortcuts.h"
+#include "DGtal/helpers/ShortcutsGeometry.h"
+#include "DGtal/dec/ATSolver2D.h"
+#include "DGtal/dec/DiscreteExteriorCalculusFactory.h"
+//! [AT-surface-includes]
+///////////////////////////////////////////////////////////////////////////////
+
+using namespace std;
+using namespace DGtal;
+
+///////////////////////////////////////////////////////////////////////////////
+
+int main( int argc, char** argv )
+{
+ typedef Z3i::KSpace KSpace;
+ typedef Shortcuts< KSpace > SH3;
+ typedef ShortcutsGeometry< KSpace > SHG3;
+ typedef SH3::Surfel Surfel;
+ typedef SH3::Cell Cell;
+ typedef SHG3::RealVector RealVector;
+
+ const double alpha_at = 0.1;
+ const double lambda_at = 0.01;
+ const double e1 = 2.0;
+ const double e2 = 0.25;
+ const double er = 2.0;
+
+ const string volfile = argc > 1 ? argv[ 1 ] : examplesPath + "samples/Al.100.vol";
+ const double threshold = argc > 2 ? atof( argv[ 2 ] ) : 0.5;
+ trace.beginBlock ( "Load vol file -> build digital surface -> estimate II normals." );
+ //! [AT-surface-init]
+ auto params = SH3::defaultParameters() | SHG3::defaultParameters();
+ auto bimage = SH3::makeBinaryImage( volfile, params );
+ auto K = SH3::getKSpace( bimage, params );
+ auto surface = SH3::makeDigitalSurface( bimage, K, params );
+ auto surfels = SH3::getSurfelRange( surface, params );
+ auto linels = SH3::getCellRange( surface, 1 );
+ auto ii_normals= SHG3::getIINormalVectors( bimage, surfels, params );
+ auto uembedder = SH3::getCellEmbedder( K );
+ auto embedder = SH3::getSCellEmbedder( K );
+ //! [AT-surface-init]
+ trace.endBlock();
+
+ trace.beginBlock ( "Creating AT solver for digital surface" );
+ //! [AT-surface-calculus]
+ typedef DiscreteExteriorCalculusFactory<EigenLinearAlgebraBackend> CalculusFactory;
+ const auto calculus = CalculusFactory::createFromNSCells<2>( surfels.begin(), surfels.end() );
+ //! [AT-surface-calculus]
+ //! [AT-surface-solve]
+ ATSolver2D< KSpace > at_solver(calculus, 1);
+ at_solver.initInputVectorFieldU2( ii_normals, surfels.cbegin(), surfels.cend() );
+ at_solver.setUp( alpha_at, lambda_at );
+ at_solver.solveGammaConvergence( e1, e2, er );
+ //! [AT-surface-solve]
+ trace.endBlock();
+
+ trace.beginBlock ( "Save AT normals as OBJ file" );
+ //! [AT-surface-getU2]
+ auto at_normals = ii_normals;
+ at_solver.getOutputVectorFieldU2( at_normals, surfels.cbegin(), surfels.cend() );
+ //! [AT-surface-getU2]
+ SH3::RealPoints positions( surfels.size() );
+ std::transform( surfels.cbegin(), surfels.cend(), positions.begin(),
+ [&] (const SH3::SCell& c) { return embedder( c ); } );
+ SH3::Colors colors( surfels.size() );
+ for ( size_t i = 0; i < surfels.size(); i++ )
+ colors[ i ] = SH3::Color( (unsigned char) 255.0*fabs( at_normals[ i ][ 0 ] ),
+ (unsigned char) 255.0*fabs( at_normals[ i ][ 1 ] ),
+ (unsigned char) 255.0*fabs( at_normals[ i ][ 2 ] ) );
+ std::transform( surfels.cbegin(), surfels.cend(), positions.begin(),
+ [&] (const SH3::SCell& c) { return embedder( c ); } );
+
+ bool ok1 = SH3::saveOBJ( surface, at_normals, SH3::Colors(),
+ "output-surface.obj" );
+ bool ok2 = SH3::saveOBJ( surface, at_normals, colors,
+ "output-surface-at-normals.obj" );
+ bool ok3 = SH3::saveVectorFieldOBJ( positions, at_normals, 0.05, SH3::Colors(),
+ "output-vf-at-normals.obj",
+ SH3::Color( 0, 0, 0 ), SH3::Color::Red );
+ //! [AT-surface-getV0]
+ SH3::Scalars features( linels.size() );
+ at_solver.getOutputScalarFieldV0( features, linels.cbegin(), linels.cend(),
+ at_solver.Maximum );
+ //! [AT-surface-getV0]
+ SH3::RealPoints f0;
+ SH3::RealVectors f1;
+ for ( size_t i = 0; i < linels.size(); i++ )
+ {
+ if ( features[ i ] < threshold )
+ {
+ const Cell linel = linels[ i ];
+ const Dimension d = * K.uDirs( linel );
+ const Cell p0 = K.uIncident( linel, d, false );
+ const Cell p1 = K.uIncident( linel, d, true );
+ f0.push_back( uembedder( p0 ) );
+ f1.push_back( uembedder( p1 ) - uembedder( p0 ) );
+ }
+ }
+ bool ok4 = SH3::saveVectorFieldOBJ( f0, f1, 0.1, SH3::Colors(),
+ "output-features.obj",
+ SH3::Color( 0, 0, 0 ), SH3::Color::Red );
+
+ trace.endBlock();
+ return 0;
+}
+// //
+///////////////////////////////////////////////////////////////////////////////

src/DGtal/dec/doc/moduleAT.dox

@@ -12,7 +12,7 @@
 
 namespace DGtal {
 /*!
-@page moduleAT Piecewise-smooth approximation using a discrete calculus model of Ambrosio-Tortorelli functional
+@page moduleGenericAT Piecewise-smooth approximation using a discrete calculus model of Ambrosio-Tortorelli functional
 
 @writers Jacques-Olivier Lachaud, Marion Foare, David Coeurjolly, Pierre Gueth
 

src/DGtal/dec/doc/packageDEC.dox

@@ -56,7 +56,7 @@ Basic operators, such as Hodge duality operator or exterior derivative, can be c
 - \ref moduleDECHelmoltz (Pierre Gueth)
 - \ref moduleDECPropagation (Pierre Gueth)
 - \ref moduleHeatLaplaceOperator (Thomas Caissard)
-- \ref moduleAT (Jacques-Olivier Lachaud, Marion Foare, David Coeurjolly, Pierre Gueth)
+- \ref moduleGenericAT (Jacques-Olivier Lachaud, Marion Foare, David Coeurjolly, Pierre Gueth)
 
 @b Package @b Concepts @b Overview
 - \ref packageDECConcepts