latimagine / statismo Goto Github PK

Is your feature request related to a problem? Please describe.
When defining landmarks file for cli tools (statismo-fit-image, statismo-posterior), the current csv parser cannot handle comma in escaped string for landmark name

Describe the solution you'd like
Use a tokenizer that can handle comma in landmark name

Describe alternatives you've considered
None.

Additional context
None.

I noticed that since the last time I built Statismo in 2017, many things have changed, including the flags for statismo-build-shape-model. Previously, there was a flag -o for the output file name, but this appears to have been removed and instead the last argument is the filename.

I tried executing statismo-build-shape-model on a dataset (all files are meshed to the same number of vertices, faces, and are aligned to a reference mesh in a .vtk format), and when I run the following, I get no errors or output (including if I try to send any log output to a file via the --log-file flag). However, I also don't get any .h5 files written anywhere on my computer.

statismo-build-shape-model -l C:\path\to\filelist.txt -p reference -r C:\path\to\reference.vtk C:\path\to\mymodel.h5

Not sure what's happening here- maybe my flag usage is incorrect somehow? I tried the suggested test to make sure I built and installed things correctly:

> cd build/Statismo-build
> ctest -C Release

I passed all of these tests.

Any ideas what might be going on? Thanks!

Describe the bug
I was not able to build statismo outside the docker, unfortunately. So i used the docker container. I was able to build and run the docker successfully. Now i wonder how could i debug the examples that are in the docker... is there a way ?

Describe the bug
During the installation of Statismo, the procedure stops with a compilation error once it starts compiling/linking with the HDF5 library.

To Reproduce
Steps to reproduce the behavior:
I followed the cmake procedure with the default options as proposed on the GitHub page. All goes will till the process arrives at the compilation of VTK routines referring to HDF5.

Screenshots/Logs/Console Output

After starting the command: cmake --build . --config Release
[ 4%] Performing build step for 'VTK'
[ 0%] Built target VTKData
Consolidate compiler generated dependencies of target WrappingTools
...
[ 62%] Built target vtkRenderingImage-hierarchy
Consolidate compiler generated dependencies of target H5detect
[ 62%] Built target H5detect
Consolidate compiler generated dependencies of target H5make_libsettings
[ 62%] Built target H5make_libsettings
Consolidate compiler generated dependencies of target vtkhdf5_src
[ 62%] Building C object ThirdParty/hdf5/vtkhdf5/src/CMakeFiles/vtkhdf5_src.dir/H5Fsuper.c.o
/Users/dvdm/Applications/statismo/build/VTK/ThirdParty/hdf5/vtkhdf5/src/H5Fsuper.c:1397:16: error: implicit declaration of function 'vtkhdf5_H5O__fsinfo_set_version' is
invalid in C99 [-Werror,-Wimplicit-function-declaration]
if(H5O__fsinfo_set_version(f, &fsinfo) < 0)
^
/Users/dvdm/Applications/statismo/build/VTK/ThirdParty/hdf5/vtkhdf5/src/vtk_hdf5_mangle.h:1882:33: note: expanded from macro 'H5O__fsinfo_set_version'
#define H5O__fsinfo_set_version vtkhdf5_H5O__fsinfo_set_version
^
1 error generated.

make[5]: *** [ThirdParty/hdf5/vtkhdf5/src/CMakeFiles/vtkhdf5_src.dir/H5Fsuper.c.o] Error 1
make[4]: *** [ThirdParty/hdf5/vtkhdf5/src/CMakeFiles/vtkhdf5_src.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [VTK-prefix/src/VTK-stamp/VTK-build] Error 2
make[1]: *** [CMakeFiles/VTK.dir/all] Error 2
make: *** [all] Error 2

Environment

• OS: 10.15.7 (Catalina)
• Compilation toolchain: clang++
• CMake Version: 3.20.2
• Statismo Version x (the most recent one)
• Statismo Dependencies Version: NOT using system dependencies

VTK & ITK version evolution
Links are not possible with latest version of ITK (5.1.0) or VTK (9.0.1) .

I used external ITK, VTK & Eigen to build Statismo. Although I faced some problems while using external HDF5, I managed to build and run tests using ITK_HDF5 instead.

However, now I'm encountering an error while making a simple Statismo project using cmake. Could you please suggest a solution to resolve this issue?
LNK2019 error: unresolved external symbol "__declspec(dllimport) public: class H5::H5File & __cdecl H5::H5File.

buildshapemodel.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class H5::H5File & __cdecl H5::H5File::operator=(class H5::H5File const &)" (_imp??4H5File@H5@@QEAAAEAV01@AEBV01@@z) referenced in function "public: virtual void __cdecl statismo::DataManagerBase<class itk::Mesh<float,3,class itk::DefaultStaticMeshTraits<float,3,3,float,float,float> >,class statismo::BasicDataManager<class itk::Mesh<float,3,class itk::DefaultStaticMeshTraits<float,3,3,float,float,float> > > >::Save(class std::basic_string<char,struct std::char_traits,class std::allocator > const &)const " (?Save@?$DataManagerBase@V?$Mesh@M$02V?$DefaultStaticMeshTraits@M$02$02MMM@itk@@@itk@@v?$BasicDataManager@V?$Mesh@M$02V?$DefaultStaticMeshTraits@M$02$02MMM@itk@@@itk@@@statismo@@@statismo@@UEBAXAEBV?$basic_string@DU?$char_traits@D@std@@v?$allocator@D@2@@std@@@z)
2>C:\Projects\NahomProjects\Repositories\statismo-build-examples\ITK\build\Release\statismo-app.exe : fatal error LNK1120: 1 unresolved externals

When I am building the statismo, it is giving the following error even if I built the correct version of Eigen library. Can you please help me on this.
CMake Error at C:/Program Files/CMake/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION)
(Required is at least version "3.3.5")
Call Stack (most recent call first):
C:/Program Files/CMake/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE)
cmake/Modules/FindEigen3.cmake:50 (find_package_handle_standard_args)

Describe the bug

In itkStandardMeshRepresenter (line 337), the iteration loop refers to hard-coded constant 3 instead of template arg MESH_DIMENSION, which can cause undefined behavior with 2D meshes:

    for (unsigned d = 0; d < 3; d++)
    {
      vertexMat(d, i) = pt[d];
    }

To Reproduce

NA

Expected behavior
In range pixel access.

Screenshots/Logs/Console Output
Compilation output:

itkStandardMeshRepresenter.hxx:339:7: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations]
       vertexMat(d, i) = pt[d];
       ^~~~~~~~~
statismofetch-src/modules/ITK/include/statismo/ITK/itkStandardMeshRepresenter.hxx:337:28: note: within this loop
     for (unsigned d = 0; d < 3; d++)

Environment

• OS: Linux Ubunut 16.04
• Compilation toolchain: g++-7
• CMake Version: 3.15.3
• Statismo Version: 0.12.0
• Statismo Dependencies Version: ITK 5.1.0

Additional context
None

Describe the bug
The example crash on MacOs.

To Reproduce
Steps to reproduce the behavior:

1. Launch runVTKExample.sh

Expected behavior
The example should succeed.

Screenshots/Logs/Console Output
None.

Environment

• OS: macOS 10.14
• Compilation toolchain: xcode 11.3.1
• Statismo Version: 0.11.0
• Statismo Dependencies Version: VTK 8, ITK 5