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https://github.com/tierra-colada/h5geo

C++17 and python API to work with geo-data (seismic, wells, maps, other in process) based on HDF5. Aimed at geoscientists and developers.
https://github.com/tierra-colada/h5geo

cpp geo-data hdf5 python seismic surfaces wells

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C++17 and python API to work with geo-data (seismic, wells, maps, other in process) based on HDF5. Aimed at geoscientists and developers.

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README 

        
![h5geo](docs/logo_126x51.png?raw=true)

 

[![][build-img]][build-status]

[![][docs-dev-img]][docs-dev-status]



C++ and python API to work with geo-data based on [HDF5](https://www.hdfgroup.org/solutions/hdf5/) containers through [h5gt](https://travis-ci.com/tierra-colada/h5geo) 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](https://github.com/pybind/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***



## Documentation

Common documentation: [h5geo.readthedocs.io](https://h5geo.readthedocs.io/)



C++ API documentation: [tierra-colada.github.io/h5geo](https://tierra-colada.github.io/h5geo/)



## Building h5geo with h5geopy support

**h5geo** depends on:

* [HDF5](https://github.com/HDFGroup/hdf5)

* [h5gt](https://github.com/tierra-colada/h5gt) (header only)

* [Eigen3](https://gitlab.com/libeigen/eigen) (header only)

* [magic-enum](https://github.com/Neargye/magic_enum) (header only)

* [units](https://github.com/LLNL/units)

* [mio](https://github.com/mandreyel/mio) (header only)

* optionally: [TBB](https://github.com/oneapi-src/oneTBB)

* optionally: [GDAL](https://github.com/OSGeo/gdal)

* optionally: [h5gtpy](https://github.com/tierra-colada/h5gt) (needed only when building with python support `-DH5GEO_BUILD_h5geopy=ON`)



You can use superbuild or build every dependency by yourself. Then do:

```cmake

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 `_ROOT` path (root directory of every package) you can pass `_DIR` path containing some `-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**.



## Installation h5geo with h5geopy



`h5geo` installation is done the same way one usually installs cmake project:

```cmake

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!**



## Build & Install using `pip`

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.



## Usage

Importing is done via:

```python

from h5gtpy import h5gt

from h5geopy import h5geo

```



You can find tests in `site-packages/h5geopy`.

To run them:

```python

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.



## Integrating with VS Code

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:

```shell

pip install pybind11-stubgen

pybind11-stubgen --no-setup-py h5geopy._h5geo

```



## Integrating with PyCharm

You don't need to provide stub file to PyCharm as it handles this by its own.



## Supported HDF5 versions

1.10, 1.12 (recommended)



## Supported platforms

Windows 10/11, Linux, OSX



[build-img]:https://img.shields.io/travis/com/tierra-colada/h5geo?style=plastic

[build-status]:https://app.travis-ci.com/tierra-colada/h5geo



[docs-dev-img]:https://img.shields.io/badge/docs-dev-blue.svg?style=plastic

[docs-dev-status]:https://h5geo.readthedocs.io/en/latest/?badge=latest