Python-based OverlappingAMR HDF5 reader and writer

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:

1. 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.
2. Arrays with character datatype are silently skipped (vtk numpy_support does not handle character arrays very good).
3. Arrays with zero elements are silently skipped.
4. 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.

Installation

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 ..

Running testcases

In the main directory of the repository, run flake8 and python3 -m pytest.