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

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

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

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)
^

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

In progress...

seems to me that voltools subfolder can be removed

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

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

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

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

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

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

actually all slices are extracted...

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.

due to changes in LocalFunctor init() ?

cc @jlevallois

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

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 ?

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

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

• 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

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

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

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.

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).

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

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

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

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

...

With 3 axis image view

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 {

And perhaps then remove the convertVol too generic...

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

like binvox tool