And perhaps then remove the convertVol too generic...

Here is the build error:

/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp: In function ‘int main(int, char*)’:
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:116:51: erreur: type/value mismatch at argument 2 in template parameter list for ‘template<class Image, unsigned int p, class IntegerLong> class DGtal::DistanceTransformation’
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:116:51: erreur: expected a constant of type ‘unsigned int’, got ‘Predicate {aka DGtal::SimpleThresholdForegroundPredicate<DGtal::ImageContainerBySTLVector<DGtal::HyperRectDomain<DGtal::SpaceND<3u, int> >, unsigned char> >}’
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:116:51: erreur: type/value mismatch at argument 3 in template parameter list for ‘template<class Image, unsigned int p, class IntegerLong> class DGtal::DistanceTransformation’
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:116:51: erreur: expected a type, got ‘2’
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:116:55: erreur: invalid type in declaration before ‘(’ token
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:116:81: erreur: expression list treated as compound expression in initializer [-fpermissive]
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:116:81: erreur: cannot convert ‘Predicate {aka DGtal::SimpleThresholdForegroundPredicate<DGtal::ImageContainerBySTLVector<DGtal::HyperRectDomain<DGtal::SpaceND<3u, int> >, unsigned char> >}’ to ‘int’ in initialization
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:117:58: erreur: type/value mismatch at argument 2 in template parameter list for ‘template<class Image, unsigned int p, class IntegerLong> class DGtal::DistanceTransformation’
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:117:58: erreur: expected a constant of type ‘unsigned int’, got ‘Predicate {aka DGtal::SimpleThresholdForegroundPredicate<DGtal::ImageContainerBySTLVector<DGtal::HyperRectDomain<DGtal::SpaceND<3u, int> >, unsigned char> >}’
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:117:58: erreur: type/value mismatch at argument 3 in template parameter list for ‘template<class Image, unsigned int p, class IntegerLong> class DGtal::DistanceTransformation’
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:117:58: erreur: expected a type, got ‘2’
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:117:73: erreur: expected initializer before ‘ImageLong’
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:120:3: erreur: ‘ImageLong’ was not declared in this scope
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:120:13: erreur: expected ‘;’ before ‘resultL2’
/home/roussillon/Git/DGtalTools/volumetric/homotopicThinning3D.cpp:153:22: erreur: ‘resultL2’ was not declared in this scope
make[2]: ** [volumetric/CMakeFiles/homotopicThinning3D.dir/homotopicThinning3D.cpp.o] Erreur 1
make[2]: La cible « volumetric/CMakeFiles/homotopicThinning3D.dir/build » n'a pas pu être refabriquée à cause d'erreurs.
make[1]: *** [volumetric/CMakeFiles/homotopicThinning3D.dir/all] Erreur 2

With 3 axis image view

due to changes in LocalFunctor init() ?

cc @jlevallois

when using --exportOnly option, we should make sure that a "--export" is given.

It does not come from my ITK since it works with DGtal install ...

Linking CXX executable 3dVolMarchingCubes
ld: library not found for -litksys
collect2: ld returned 1 exit status
make[2]: *** [volumetric/3dVolMarchingCubes] Error 1
make[1]: *** [volumetric/CMakeFiles/3dVolMarchingCubes.dir/all] Error 2
make: *** [all] Error 2

And use markdown syntax to enhance the readability (with nice rendering in github) ?

Update the url in the description of the project http://liris.cnrs.fr/dgtal with http://libdgtal.org.
@dcoeurjo or @JacquesOlivierLachaud can perhaps do I suppose that it is the setting repository ?

Additionally, 3dCurvatureViewer should compile without QGLviewer thanks to the OBJ export.

By using the generic reader and propose some options to use basic functor

It would be nice to switch the viewer colormap in a set of predefined maps (e.g. {grayscale, hueshade, random}).

I just compiled DGtal from master with no problems with the following options:

ccmake -G"Eclipse CDT4 - Unix Makefiles" -DCMAKE_CXX_COMPILER_ARG1=-std=c++11 -DCMAKE_CXX_FLAGS=-std=c++11 -DWITH_QT5:BOOL=ON -DWITH_CGAL:BOOL=ON -DWITH_ITK:BOOL=ON -DWITH_EIGEN:BOOL=ON -DWITH_HDF5:BOOL=ON -DWITH_MAGICK:BOOL=ON -DWITH_OPENMP:BOOL=ON -DWITH_GMP:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=ON -DBUILD_TESTING:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/home/phc/devtoolset/release/DGtal -DCMAKE_BUILD_TYPE=Release ../DGtal-src

Facing build errors related with CGAL:

[24%] Building CXX object estimators/CMakeFiles/3dLocalEstimators.dir/3dLocalEstimators.cpp.o

In file included from /home/phc/Software/DGtal/DGtalTools-src/estimators/3dLocalEstimators.cpp:69:0:
/home/phc/devtoolset/release/DGtal/include/DGtal/geometry/surfaces/estimation/estimationFunctors/MongeJetFittingMeanCurvatureEstimator.h:101:51: error: wrong number of te
mplate arguments (1, should be 3)
     typedef CGAL::Monge_via_jet_fitting<CGALKernel>  CGALMongeViaJet;
                                                   ^
In file included from /home/phc/devtoolset/release/DGtal/include/DGtal/geometry/surfaces/estimation/estimationFunctors/MongeJetFittingMeanCurvatureEstimator.h:56:0,
                 from /home/phc/Software/DGtal/DGtalTools-src/estimators/3dLocalEstimators.cpp:69:
/usr/include/CGAL/Monge_via_jet_fitting.h:56:9: note: provided for ‘template<class DataKernel, class LocalKernel, class SvdTraits> class CGAL::Monge_via_jet_fitting’
   class Monge_via_jet_fitting {

I have some issues perhaps related to kanugo method of DGtal:
./visualisation/3dCurvatureViewerNoise -i ../../DGtal/examples/samples/cat10.vol --properties mean -r 4 -n 0.7

I have an issue with the sliceViewer tool (see snapshot): the origin of the Vol file is not taken into account correctly in the slice panes (I'll send you the Catenoid vol file by email).

It could be useful to display 3D image with false colors defined from a colormap and from source image intensity level.

When I test the shape generator i obtained the following error:

./shapeGenerator/contourGenerator --shape ball -R 10 -f fc --outputGeometry titi
1 -9 0000100101101011111111121211221212222222223232233232333333333030330030300000
Assertion failed: (isValid()), function eval, file /usr/local/include/DGtal/geometry/curves/estimation/TrueLocalEstimatorOnPoints.ih, line 99.
Abort trap: 6

With the pts format it gives no errors but empty geometric file.

This prog were commented since it implies errors from previous update of DGtal.
Perhaps Tristan could you correct it ?

If not only me thinks that it will be nice to have those converters I am going to add them.

BTW Could not we have some general converter which recognize extension? There is GenericReader and Writer in DGtal so should not be a problem to have something like that.

In progress...

When compiling DGtal without QGLViewer, I get the error (due to missing WITH...)

[ 94%] [ 94%] Built target volCComponentCounter
Built target volSubSample
[100%] Building CXX object surfaceTools/CMakeFiles/ofs2off.dir/ofs2off.cpp.o
/home/dcoeurjo/Sources/DGtalTools/surfaceTools/ofs2off.cpp:31:32: erreur fatale: QtGui/qapplication.h : Aucun fichier ou dossier de ce type
compilation terminée.
make[2]: *** [surfaceTools/CMakeFiles/ofs2off.dir/ofs2off.cpp.o] Erreur 1

Perhaps choose always -i for all input (image, sep, vol etc...)

vol2off and 3dVolMarchingCubes are the same, keep second in volumetric

For me I try it some days ago and it fails to convert any file.
Did it fork for someone ?

seems to me that voltools subfolder can be removed

2D: Uniforms (for instance setParams) between estimators (for length or other estimators)
3D:

like binvox tool

When you apply:
./visualisation/3dCurvatureViewer -i ~/EnCours/DGtal/examples/samples/cat10.vol -r 2 -u 100
It produces:

actually all slices are extracted...

Since perhaps some DGtal updates ...
David it is perhaps related to previous modification of DistanceTransformation ? Can you check it ?

Scanning dependencies of target homotopicThinning3D
[ 15%] Building CXX object volumetric/CMakeFiles/homotopicThinning3D.dir/homotopicThinning3D.cpp.o
/Users/kerautre/EnCours/DGtalTools/volumetric/homotopicThinning3D.cpp:113:42: error: template
argument for template type parameter must be a type
typedef DistanceTransformation<Image, 0> DTL2;
^
/usr/local/include/DGtal/geometry/volumes/distance/DistanceTransformation.h:92:23: note:
template parameter is declared here
typename TPointPredicate,
^
/Users/kerautre/EnCours/DGtalTools/volumetric/homotopicThinning3D.cpp:116:3: error: expected a
class or namespace
DTL2::OutputImage resultL2 = dtL2.compute ( image );
^
/Users/kerautre/EnCours/DGtalTools/volumetric/homotopicThinning3D.cpp:149:8: error: use of
undeclared identifier 'resultL2'
if (resultL2( _it ) <= layer_layer)
^

• the command line should display a message with program usage (instead of an ERROR)
• you should describe what the program does
• add an entry in the README

Like pgm2freeman but for volume from basic threshold or auto with otsu

When displaying 3D vol image obtained from a domain with lower point != 0 is not centered.

• adding curvatureMCMS
• removing curvatureBC tangentBC and curvatureMCMS in favor to a single estimatorcomparator ?
• rename estimatorComparator -> estimatorComparator2d?

• raw2vol
• vol2raw
• longvol2vol
• pgm3d..
• vol2longvol

...