This is an pure Python (using numpy and h5py only) implementation for
the HDF5-based vtkOverlappingAMR file format reader and writer. The official
C++ VTK library contains a reader for the same format in the
vtkHDFReader class
but there are no corresponding writer in the VTK library.
The code can either be imported as a module in a Python program, used as a
command line converter or used as a Python-plugin in recent Paraview
versions (given support for Python is present and the packages h5py and
numpy is installed).
The implementation has the following limitations:
- Only the first grid on the first level is interrogated to find which data arrays to write out. All arrays must be present on all grids on all levels.
- Arrays with character datatype are silently skipped (vtk
numpy_supportdoes not handle character arrays very good). - Arrays with zero elements are silently skipped.
- The implementation create a memory buffer for each data array, fills this buffer completely and flushes it to disk for each complete array and level for maximum performance. This might consume a lot of memory.
See also the VTK forum discussion thread and the associated merge request.
The only thing you need is the file PythonAMRHDF.py. This file serve
both as a Python module that can be imported (import PythonAMRHDF),
a Paraview plugin ("Tools" -> "Manage Plugins..." -> "Load New") and a
standalone CLI converter tool ("./PythonAMRHDF.py --help").
It is also possible to install it as a Python package. In that case you need
setuptools version 61.0 or greater, and the easiest is to install it directly
from Github:
pip install git+https://github.com/kmturbulenz/PythonAMRHDF.git
If you checkout the repository you can also install it in editable mode:
pip install -e . or as an ordinary package with pip install ..
In the main directory of the repository, run flake8 and
python3 -m pytest.