C++ and python API to work with geo-data based on HDF5 containers through h5gt header only library.
For now h5geo provides API to work with:
- seismic data
- wells (deviations, logs, welltops)
- maps
- points
- horizons
h5geo also includes h5geopy project wich is a python wrapper.
h5geopy uses pybind11 to make python bindings and there may be some perfomance penalty when copying matrices from C++ Eigen3
matrices to numpy
(or std::vector
to py::list
). I have not done any perfomance testing.
This project is aimed at geoscientists and developers
Common documentation: h5geo.readthedocs.io
C++ API documentation: tierra-colada.github.io/h5geo
h5geo depends on:
- HDF5
- h5gt (header only)
- Eigen3 (header only)
- magic-enum (header only)
- units
- mio (header only)
- optionally: TBB
- optionally: GDAL
- optionally: h5gtpy (needed only when building with python support
-DH5GEO_BUILD_h5geopy=ON
)
You can use superbuild or build every dependency by yourself. Then do:
mkdir build
cd build
cmake ..
-DCMAKE_BUILD_TYPE=Release
-DEigen3_ROOT:PATH=/path/to/eigen
-Dmagic_enum_ROOT:PATH=/path/to/magic_enum
-Dmio_ROOT:PATH=/path/to/mio
-Dh5gt_ROOT:PATH=/path/to/h5gt
-DH5GEO_SUPERBUILD:BOOL=OFF
-DH5GEO_USE_THREADS:BOOL=ON
-DTBB_ROOT:PATH=/path/to/tbb
-DH5GEO_BUILD_SHARED_LIBS:BOOL=ON
-DH5GEO_BUILD_h5geopy:BOOL=ON
-DHDF5_RUNTIME_DIR:PATH=/path/to/dir/containing/hdf5-runtime
-DH5GEOPY_COPY_RUNTIME_DEPS:BOOL=ON
-DPYTHON_EXECUTABLE=/path/to/python.exe
-DH5GEO_BUILD_TESTS:BOOL=OFF
-DCMAKE_INSTALL_PREFIX:PATH=/install/prefix
-G "some generator"
cmake --build .
NOTE: instead of <prefix>_ROOT
path (root directory of every package) you can pass <prefix>_DIR
path containing some <prefix>-config.cmake
file of every package.
NOTE: to run h5geopy python must know where HDF5-runtime, units-runtime, tbb-runtime and h5geo-runtime are located. You may choose whether to copy them to site-packages/h5geopy
dir or add their dirs to PATH
env. By default cmake try to search h5geo-runtime in h5geo-install/lib
folder. Also h5geopy depends on h5gtpy. So you would need to have installed h5gtpy.
h5geo
installation is done the same way one usually installs cmake project:
cmake --install . --prefix /some/path --config Release
Then you can find h5geopy in site-packages
of your python env.
NOTE: cmake tries to find runtime dependencies at install
step. If there are unresolved or conflict dependencies then you need to modify PATH
env, rerun cmake ..
and cmake --install . --prefix /some/path --config Release
. You don't have to rebuild the project!
It is possible to build and install the library using the following command:
pip install git+https://github.com/tierra-colada/[email protected] --verbose
This will automatically run CMake Superbuild to build build h5geo v0.1.0 and its dependencies (without GDAL support) in the site-pakages/h5geopy
dir.
On modern PC this usually takes a couple of minutes.
NOTE: CMake and C++ compiler are needed.
Importing is done via:
from h5gtpy import h5gt
from h5geopy import h5geo
You can find tests in site-packages/h5geopy
.
To run them:
python -m unittest discover h5geopy.tests
Note: h5geopy
(as well as h5geo
) uses fortran memory order (columnwise). Thus you should allocate numpy with numpy.asfortranarray
or order='F'
as numpy uses C
order by default.
There is stub file h5geopy/h5geo.pyi
. You need to set VS Code setting "python.analysis.stubPath": "some/relative/path/to/stub-storage"
: where stub-storage
is supposed to contain folder h5geopy
with h5geo.pyi
file.
I'm some kind of a uncomfortable to distribute stub file, so to be sure that stub file is updated you can generate your own stub file:
pip install pybind11-stubgen
pybind11-stubgen --no-setup-py h5geopy._h5geo
You don't need to provide stub file to PyCharm as it handles this by its own.
1.10, 1.12 (recommended)
Windows 10/11, Linux, OSX