Using the connected_component feature with the CLI

[KillianBabilotte]

Hi,

I'm working on Connected Component Labeling (CCL) in massive distributed setting and I have found your work https://arxiv.org/abs/2003.02351 very interesting. So I wanted to try ftk via the CLI before trying to use it as a library to perform CCL, but I'm stumbling into some minor issues that you could may be help me to solve.

I have installed the master version of ftk with spack:

$ spack install --add ftk@master +mpi +vtk ^[email protected]

I have a file my_file.vti that contain 3D data with 4 scalar fields and a vector field of 3 components. One of this scalars field is named "contribution" and I want to identify each group of voxels that have a value above 1.

This look like an undocumented use of ftk so I have try several options of ftk that look promising to me such as: -f connected_component, --threshold 1.0, --var contribution, --output-type discrete|sliced but none of the combination that have tried seams to work.

Here are the two most illustrative examples of my problem:

$ ftk -f connected_component -i my_file.vti -n 1 --var contribution --output test.vtp

produced the following output:

[FTK FATAL] VTK variable not found
Obtained 7 stack frames.
ftk(_ZN3ftk15print_backtraceEv+0x2c) [0x55f680772acc]
ftk(_ZN3ftk5fatalEiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x81) [0x55f680777c21]
ftk(+0x19790b) [0x55f68089a90b]
ftk(+0x59bd7) [0x55f68075cbd7]
ftk(+0x3236a) [0x55f68073536a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f0c056d9083]
ftk(+0x3266e) [0x55f68073566e]

and without the option --var:

$ ftk -f connected_component -i my_file.vti -n 1 --output test.vtp

I have this output:

terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_M_construct null not valid
*** Process received signal ***
Signal: Aborted (6)
Signal code:  (-6)
[ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x14420)[0x7f181c636420]
[ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcb)[0x7f181bdf700b]
[ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x12b)[0x7f181bdd6859]
[ 3] /home/user/software/spack/opt/spack/linux/gcc-9.4.0/gcc-runtime-9.4.0-tu4d4s4qlhsu3r73sgs2ta7gkecvv24m/lib/libstdc++.so.6(+0x9e8d1)[0x7f181c1b08d1]
[ 4] /home/user/software/spack/opt/spack/linux/gcc-9.4.0/gcc-runtime-9.4.0-tu4d4s4qlhsu3r73sgs2ta7gkecvv24m/lib/libstdc++.so.6(+0xaa37c)[0x7f181c1bc37c]
[ 5] /home/user/software/spack/opt/spack/linux/gcc-9.4.0/gcc-runtime-9.4.0-tu4d4s4qlhsu3r73sgs2ta7gkecvv24m/lib/libstdc++.so.6(+0xaa3e7)[0x7f181c1bc3e7]
[ 6] /home/user/software/spack/opt/spack/linux/gcc-9.4.0/gcc-runtime-9.4.0-tu4d4s4qlhsu3r73sgs2ta7gkecvv24m/lib/libstdc++.so.6(+0xaa699)[0x7f181c1bc699]
[ 7] /home/user/software/spack/opt/spack/linux/gcc-9.4.0/gcc-runtime-9.4.0-tu4d4s4qlhsu3r73sgs2ta7gkecvv24m/lib/libstdc++.so.6(_ZSt19__throw_logic_errorPKc+0x41)[0x7f181c1b31dc]
[ 8] ftk(+0x3387b)[0x56181c1ac87b]
[ 9] ftk(+0x1971de)[0x56181c3101de]
[10] ftk(+0x59bd7)[0x56181c1d2bd7]
[11] ftk(+0x3236a)[0x56181c1ab36a]
[12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f181bdd8083]
[13] ftk(+0x3266e)[0x56181c1ab66e]
*** End of error message ***
Abandon (core dumped)

Thanks in advance,
Killian