Add setWorldBaseTransform function to KinDynComputations and high-level Matlab wrappers

[LoreMoretti]

This PR addresses #1082.

[LoreMoretti]

Now, I will try to generate the Matlab bindings following generating-idyntree-matlab-bindings.md

[LoreMoretti]

Now, I will try to generate the Matlab bindings following generating-idyntree-matlab-bindings.md

I am getting the following error when running make:

[ 99%] Built target iDynTreeMEX_swig_compilation
[ 99%] Building CXX object bindings/matlab/CMakeFiles/iDynTreeMEX.dir/autogenerated/iDynTreeMATLAB_wrap.cxx.o
/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/bindings/matlab/autogenerated/iDynTreeMATLAB_wrap.cxx:171:10: fatal error: mex.h: No such file or directory
  171 | #include <mex.h>
      |          ^~~~~~~
compilation terminated.
make[2]: *** [bindings/matlab/CMakeFiles/iDynTreeMEX.dir/build.make:76: bindings/matlab/CMakeFiles/iDynTreeMEX.dir/autogenerated/iDynTreeMATLAB_wrap.cxx.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:954: bindings/matlab/CMakeFiles/iDynTreeMEX.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

[traversaro]

Do you have MATLAB installed in the system? What is the CMakeCache.txt of your build?

[LoreMoretti]

Do you have MATLAB installed in the system? What is the CMakeCache.txt of your build?

Yes, here the CMakeCache.txt

CMakeCache.txt

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[traversaro]

Ok, somehow is not finding the mex.h file, not sure why. I think we can:

• Check that the mex.h file is indeed there, for example with find /usr/local/MATLAB/R2023b/extern/include | grep mex.h
• Verify that the include directory is correctly passed to the compile that is trying to compile iDynTreeMATLAB_wrap.cxx, to get the exact command used to compile iDynTreeMATLAB_wrap.cxx, you can either compile with make VERBOSE=1 or ninja -vv, or simply search for iDynTreeMATLAB_wrap.cxx in your compile_command.json . You should find a -I<path> or -Isystem<path> option that points to the folder that contains the mex.h file.

[LoreMoretti]

The mex.h file exists:

(robsub) lomoretti@IITICUBLAP226:~/robotology/robotology-superbuild/build/src/iDynTree (master)$ find /usr/local/MATLAB/R2023b/extern/include | grep mex.h
/usr/local/MATLAB/R2023b/extern/include/mex.h

Then I tried with make VERBOSE=1 as you suggested. I am reporting just the chunk related to the error:

[ 99%] Building CXX object bindings/matlab/CMakeFiles/iDynTreeMEX.dir/autogenerated/iDynTreeMATLAB_wrap.cxx.o
cd /home/lomoretti/robotology/robotology-superbuild/build/src/iDynTree/bindings/matlab && /home/lomoretti/mambaforge/envs/robsub/bin/x86_64-conda-linux-gnu-c++ -DiDynTreeMEX_EXPORTS -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/core/include -I/home/lomoretti/robotology/robotology-superbuild/build/src/iDynTree/src/core -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/model/include -I/home/lomoretti/robotology/robotology-superbuild/build/src/iDynTree/src/model -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/model_io/xml/include -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/model_io/xml/include/iDynTree -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/model_io/codecs/include -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/model_io/codecs/include/private -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/estimation/include -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/solid-shapes/include -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/high-level/include -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/inverse-kinematics/include -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/optimalcontrol/include -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/yarp/include -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/icub/include -I/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/src/visualization/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/lomoretti/mambaforge/envs/robsub/include -g -fPIC   -Wno-deprecated-declarations -Wno-deprecated -MD -MT bindings/matlab/CMakeFiles/iDynTreeMEX.dir/autogenerated/iDynTreeMATLAB_wrap.cxx.o -MF CMakeFiles/iDynTreeMEX.dir/autogenerated/iDynTreeMATLAB_wrap.cxx.o.d -o CMakeFiles/iDynTreeMEX.dir/autogenerated/iDynTreeMATLAB_wrap.cxx.o -c /home/lomoretti/robotology/robotology-superbuild/src/iDynTree/bindings/matlab/autogenerated/iDynTreeMATLAB_wrap.cxx
/home/lomoretti/robotology/robotology-superbuild/src/iDynTree/bindings/matlab/autogenerated/iDynTreeMATLAB_wrap.cxx:171:10: fatal error: mex.h: No such file or directory
  171 | #include <mex.h>

And indeed there is not the /usr/local/MATLAB/R2023b/extern/include/ among the directories.

[traversaro]

And indeed there is not the /usr/local/MATLAB/R2023b/extern/include/ among the directories.

That is interesting, by looking into

idyntree/bindings/matlab/CMakeLists.txt

Line 118 in d6af7ff

target_link_libraries(${target_name} ${IDYNTREE_LIBRARIES} ${Matlab_MEX_LIBRARY} ${Matlab_MX_LIBRARY})

I could not understand which command should actually ensure that is the case. Probably it is a bug of the combination of trying to generate+compile the source code in the same step, while typically we (and the CI) generate the source code in one build, and compile in another.

Can you try to add:

target_include_directories(${target_name} PRIVATE ${Matlab_INCLUDE_DIRS})

right before

idyntree/bindings/matlab/CMakeLists.txt

Line 118 in d6af7ff

target_link_libraries(${target_name} ${IDYNTREE_LIBRARIES} ${Matlab_MEX_LIBRARY} ${Matlab_MX_LIBRARY})

?

Thanks! Note that in general this is not required as setting the include directories is handled by passing to target_link_libraries the correct imported targets, however to be compatible with CMake 3.16 we can't use the imported targets Matlab::mex and Matlab::mx, there are available since CMake 3.22 (see https://cmake.org/cmake/help/v3.29/module/FindMatlab.html#imported-targets).

[LoreMoretti]

Awesome, it worked!

I have included the line target_include_directories(${target_name} PRIVATE ${Matlab_INCLUDE_DIRS}) in this PR.

[traversaro]

Minor comments, thanks!

[traversaro]

Thanks @LoreMoretti !