Add spatio_temporal_voxel_layer

[Ericsii]

WIP.

• Fix error: custom srv files cannot be generated

Reference issue: #270

[Ericsii]

I noticed that the openvdb_vender package builds the OpenVDB from source rather than finding the package from the system. I don't know if this is the proper way not to install openvdb with conda-forge.

[traversaro]

I noticed that the openvdb_vender package builds the OpenVDB from source rather than finding the package from the system. I don't know if this is the proper way not to install openvdb with conda-forge.

Good catch. Typically we patch vendor packages and add the missing vendor dependency to use the conda-forge version. I am now on the phone, but you can probably find examples of this pattern in the repo, I can provide links as soon as I am on a laptop.

[Tobias-Fischer]

For reference, here is the vendor package - it looks like all we need to do is to make sure openvdb=10 is available.

[Ericsii]

I tried to set openvdb=10.0.1 in dependencies.yaml. Unfortunately, this cannot pass the dependency checking.

[traversaro]

For reference, here is the vendor package -

I guess it is https://github.com/SteveMacenski/spatio_temporal_voxel_layer/blob/616690db7011178014d2c096cf6d56d1c7dfd5f3/openvdb_vendor/CMakeLists.txt .

OpenVDB does not seem to contain a lot of breaking changes (even if the major version changes), could it make sense to give it a short with openvdb 12? A patch with
SteveMacenski/spatio_temporal_voxel_layer@b69c109 should be sufficient. You also need to add openvdb host dependency in https://github.com/RoboStack/ros-humble/pull/275/files#diff-c7f3123b8b51a41cb7205f2d7819ab151c25c473aaebbcebe0f71ffa1b1fc605R187-R188 .

[Ericsii]

I have updated openvdb-vendor to use openvdb in conda-forge. It works. However, I don't know how to solve the linking error with SaveGrid.srv. Could you guys give me any advice? @traversaro @Tobias-Fischer

[Ericsii]

Here is the build log. It looks like something wrong with rosidl_generator_py

build.log

[traversaro]

@Ericsii can you please rebase on top of latest main? Thanks! I do not think this will solve your build failure, but at least we will build on a working base.

[traversaro]

Ok, thanks for the rebase, back to the build error, that is the same on linux-64 and linux-aarch64:

 │ │ [32/41] Linking C shared library rosidl_generator_py/spatio_temporal_voxel_layer/spatio_temporal_voxel_layer_s__rosidl_typesupport_fastrtps_c.cpython-311-x
 │ │ 86_64-linux-gnu.so
 │ │ FAILED: rosidl_generator_py/spatio_temporal_voxel_layer/spatio_temporal_voxel_layer_s__rosidl_typesupport_fastrtps_c.cpython-311-x86_64-linux-gnu.so 
 │ │ : && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -fPIC -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction
 │ │ -sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ros-humble-spatio-temporal-voxel-layer-2.3.3 -fdebug-prefix-map=$
 │ │ PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS=1 -O3 -DNDEBUG  -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-n
 │ │ ew-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -Wl,--no-undefined -Wl,--dependency
 │ │ -file=CMakeFiles/spatio_temporal_voxel_layer__rosidl_typesupport_fastrtps_c__pyext.dir/link.d -shared -Wl,-soname,spatio_temporal_voxel_layer_s__rosidl_typ
 │ │ esupport_fastrtps_c.cpython-311-x86_64-linux-gnu.so -o rosidl_generator_py/spatio_temporal_voxel_layer/spatio_temporal_voxel_layer_s__rosidl_typesupport_fa
 │ │ strtps_c.cpython-311-x86_64-linux-gnu.so CMakeFiles/spatio_temporal_voxel_layer__rosidl_typesupport_fastrtps_c__pyext.dir/rosidl_generator_py/spatio_tempor
 │ │ al_voxel_layer/_spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_fastrtps_c.c.o  -Wl,-rpath,$SRC_DIR/build/rosidl_generator_py/spatio_temporal_voxel_lay
 │ │ er:$SRC_DIR/build:  rosidl_generator_py/spatio_temporal_voxel_layer/libspatio_temporal_voxel_layer__rosidl_generator_py.so  libspatio_temporal_voxel_layer_
 │ │ _rosidl_typesupport_fastrtps_c.so  libspatio_temporal_voxel_layer__rosidl_typesupport_c.so  $PREFIX/lib/libstd_msgs__rosidl_typesupport_fastrtps_c.so  $PRE
 │ │ FIX/lib/libstd_msgs__rosidl_typesupport_fastrtps_cpp.so  $PREFIX/lib/libstd_msgs__rosidl_typesupport_introspection_c.so  $PREFIX/lib/libstd_msgs__rosidl_ty
 │ │ pesupport_introspection_cpp.so  $PREFIX/lib/libstd_msgs__rosidl_typesupport_cpp.so  $PREFIX/lib/libstd_msgs__rosidl_generator_py.so  $PREFIX/lib/librmw.so 
 │ │  $PREFIX/lib/libbuiltin_interfaces__rosidl_generator_py.so  $PREFIX/lib/libstd_msgs__rosidl_typesupport_c.so  $PREFIX/lib/libbuiltin_interfaces__rosidl_typ
 │ │ esupport_c.so  $PREFIX/lib/libbuiltin_interfaces__rosidl_typesupport_fastrtps_c.so  $PREFIX/lib/librosidl_typesupport_fastrtps_c.so  libspatio_temporal_vox
 │ │ el_layer__rosidl_generator_c.so  $PREFIX/lib/libbuiltin_interfaces__rosidl_typesupport_fastrtps_cpp.so  $PREFIX/lib/librosidl_typesupport_fastrtps_cpp.so  
 │ │ $PREFIX/lib/libfastcdr.so.1.0.24  $PREFIX/lib/librmw.so  $PREFIX/lib/libbuiltin_interfaces__rosidl_typesupport_introspection_c.so  $PREFIX/lib/libstd_msgs_
 │ │ _rosidl_generator_c.so  $PREFIX/lib/libbuiltin_interfaces__rosidl_generator_c.so  $PREFIX/lib/libbuiltin_interfaces__rosidl_typesupport_introspection_cpp.s
 │ │ o  $PREFIX/lib/librosidl_typesupport_introspection_cpp.so  $PREFIX/lib/librosidl_typesupport_introspection_c.so  $PREFIX/lib/libbuiltin_interfaces__rosidl_
 │ │ typesupport_cpp.so  $PREFIX/lib/librosidl_typesupport_c.so  $PREFIX/lib/librosidl_runtime_c.so  $PREFIX/lib/librcutils.so  -ldl  -lrt && :
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: CMakeFiles/spatio_temporal_voxel_layer__rosidl_typesu
 │ │ pport_fastrtps_c__pyext.dir/rosidl_generator_py/spatio_temporal_voxel_layer/_spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_fastrtps_c.c.o: in functio
 │ │ n `_register_msg_type__srv__save_grid__request':
 │ │ _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0x14): undefined reference to `PyCapsu
 │ │ le_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0x33): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0x5d): undefined reference to `PyCapsule_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0x7c): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0x94): undefined reference to `PyCapsule_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0xb3): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0xcb): undefined reference to `PyCapsule_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0xe6): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0x106): undefined reference to `PyCapsule_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0x121): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__request+0x13d): undefined reference to `_Py_Dealloc'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: CMakeFiles/spatio_temporal_voxel_layer__rosidl_typesu
 │ │ pport_fastrtps_c__pyext.dir/rosidl_generator_py/spatio_temporal_voxel_layer/_spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_fastrtps_c.c.o: in functio
 │ │ n `_register_msg_type__srv__save_grid__response':
 │ │ _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0x14): undefined reference to `PyCaps
 │ │ ule_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0x33): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0x5d): undefined reference to `PyCapsule_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0x7c): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0x94): undefined reference to `PyCapsule_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0xb3): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0xcb): undefined reference to `PyCapsule_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0xe6): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0x106): undefined reference to `PyCapsule_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0x121): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_msg_type__srv__save_grid__response+0x13d): undefined reference to `_Py_Dealloc'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: CMakeFiles/spatio_temporal_voxel_layer__rosidl_typesu
 │ │ pport_fastrtps_c__pyext.dir/rosidl_generator_py/spatio_temporal_voxel_layer/_spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_fastrtps_c.c.o: in functio
 │ │ n `_register_srv_type__srv__save_grid':
 │ │ _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_fastrtps_c.c:(.text._register_srv_type__srv__save_grid+0x1a): undefined reference to `PyCapsule_New'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_srv_type__srv__save_grid+0x35): undefined reference to `PyModule_AddObject'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text._register_srv_type__srv__save_grid+0x5a): undefined reference to `_Py_Dealloc'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: CMakeFiles/spatio_temporal_voxel_layer__rosidl_typesu
 │ │ pport_fastrtps_c__pyext.dir/rosidl_generator_py/spatio_temporal_voxel_layer/_spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_fastrtps_c.c.o: in functio
 │ │ n `PyInit_spatio_temporal_voxel_layer_s__rosidl_typesupport_fastrtps_c':
 │ │ _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_fastrtps_c.c:(.text.PyInit_spatio_temporal_voxel_layer_s__rosidl_typesupport_fastrtps_c+0xf): undefine
 │ │ d reference to `PyModule_Create2'
 │ │ $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: _spatio_temporal_voxel_layer_s.ep.rosidl_typesupport_
 │ │ fastrtps_c.c:(.text.PyInit_spatio_temporal_voxel_layer_s__rosidl_typesupport_fastrtps_c+0x67): undefined reference to `_Py_Dealloc'
 │ │ collect2: error: ld returned 1 exit status
 │ │ [33/41] Building CXX object CMakeFiles/spatio_temporal_voxel_layer_core.dir/src/frustum_models/depth_camera_frustum.cpp.o
 │ │ [34/41] Building CXX object CMakeFiles/spatio_temporal_voxel_layer_core.dir/src/vdb2pc.cpp.o
 │ │ [35/41] Building CXX object CMakeFiles/spatio_temporal_voxel_layer_core.dir/src/measurement_buffer.cpp.o
 │ │ [36/41] Building CXX object CMakeFiles/spatio_temporal_voxel_layer_core.dir/src/spatio_temporal_voxel_grid.cpp.o
 │ │ $SRC_DIR/ros-humble-spatio-temporal-voxel-layer/src/work/src/spatio_temporal_voxel_grid.cpp: In member function 'void volume_grid::SpatioTemporalVoxelGrid:
 │ │ :ResetGridArea(const volume_grid::occupany_cell&, const volume_grid::occupany_cell&, bool)':
 │ │ $SRC_DIR/ros-humble-spatio-temporal-voxel-layer/src/work/src/spatio_temporal_voxel_grid.cpp:404:8: warning: statement has no effect [-Wunused-value]
 │ │   404 |   for (cit_grid; cit_grid.test(); ++cit_grid)
 │ │       |        ^~~~~~~~
 │ │ $SRC_DIR/ros-humble-spatio-temporal-voxel-layer/src/work/src/spatio_temporal_voxel_grid.cpp: In member function 'void volume_grid::SpatioTemporalVoxelGrid:
 │ │ :ClearFrustums(const std::vector<observation::MeasurementReading>&, std::unordered_set<volume_grid::occupany_cell>&)':
 │ │ $SRC_DIR/ros-humble-spatio-temporal-voxel-layer/src/work/src/spatio_temporal_voxel_grid.cpp:136:14: warning: 'frustum' may be used uninitialized [-Wmaybe-u
 │ │ ninitialized]
 │ │   136 |       delete frustum;
 │ │       |              ^~~~~~~
 │ │ $SRC_DIR/ros-humble-spatio-temporal-voxel-layer/src/work/src/spatio_temporal_voxel_grid.cpp:125:25: note: 'frustum' declared here
 │ │   125 |     geometry::Frustum * frustum;
 │ │       |                         ^~~~~~~
 │ │ [37/41] Building CXX object CMakeFiles/spatio_temporal_voxel_layer_core.dir/src/spatio_temporal_voxel_layer.cpp.o
 │ │ ninja: build stopped: subcommand failed.
 │ │ × error Script failed with status 1
 │ │ × error Work directory: '/home/runner/work/ros-humble/ros-humble/output/bld/rattler-build_ros-humble-spatio-temporal-voxel-layer_1744168604/work'
 │ │ × error To debug the build, run it manually in the work directory (execute the `./conda_build.sh` or `conda_build.bat` script)
 │ │

[traversaro]

So, it is a bit surprising that the linker complains about missing symbols, as in general it is perfectly fine for a shared library on ELF platform not to resolve all it symbols at link time, as long as those symbols are then eventually present in the binary that loads the shared library (in case of Python extensions, the Python interpreter itself).

Indeed, with recent version of CMake if you link with Python::Module imported library the Python shared library is not linked to the libpython shared library, to provide support for the Python interpreters that statically link the libpython (see astral-sh/python-build-standalone#540 and ros2/rclpy#1305).

What is different in this project w.r.t. to other projects is these CMake line: https://github.com/SteveMacenski/spatio_temporal_voxel_layer/blob/7801267acfd63d9845c0e581ec3b652ea11c1aa3/spatio_temporal_voxel_layer/CMakeLists.txt#L82-L83 . Patching it out everything should work fine.

[traversaro]

I suggested an upstream solution in SteveMacenski/spatio_temporal_voxel_layer#325 and add it locally as a patch.

[traversaro]

Thanks @Ericsii !