Paraview Python File Readers

This repository contains some tools and examples to build Python Programmable Filters for ParaView which can act as file readers.

The basic idea is simple. We make a Python programmable filter that can take a list of FileNames as an argument. Then we instruct ParaView to treat it as a FileReader. We must implement the functionality for reading timeseries ourselves, since using this with vtkFileSeriesReader is not supported. This turns out to be not so difficult.

References

• https://blog.kitware.com/easy-customization-of-the-paraview-python-programmable-filter-property-panel
• https://www.paraview.org/Wiki/Python_calculator_and_programmable_filter
• https://public.kitware.com/pipermail/paraview-developers/2017-January/005051.html

Installation

1. Clone this repository
2. Run the python filter generator on your input file

./python_filter_generator paraview_read_npz.py reader.xml

3. Add reader.xml to your ParaView plugin list (Tools > Manage Plugins > Load New) (selecting autoload is useful)

Local packages

Paraview automatically includes ~/.local/lib/python2.7/site-packages if it exists. This is in disregard of the PYTHONNOUSERSITE environment variable when running pvpython. Be sure to not have numpy (or h5py) installed there, as that might cause problems.

pip2 uninstall numpy h5py

Building h5py against python paraview

HDF5 is a common format for

1. First install https://github.com/pyenv/pyenv
2. Then run the following commands to install h5py with the same hdf5 as paraview

export PV_PY_VER=2.7.11
export PV_PY_UCS=2
export PV_NP_VER=1.8.1
export PV_H5_VER=1.8.13

export PYTHON_CONFIGURE_OPTS=--enable-unicode=ucs$PV_PY_UCS
# Install python2 with ucs2 https://stackoverflow.com/questions/38928942/build-python-as-ucs-4-via-pyenv
pyenv install -v $PV_PY_VER
pyenv local $PV_PY_VER

# Install pip
wget https://bootstrap.pypa.io/get-pip.py && ~/.pyenv/versions/$PV_PY_VER/python get-pip.py

# Install the same numpy paraview uses and a not too recent cython
~/.pyenv/versions/$PV_PY_VER/bin/pip uninstall -y numpy cython
~/.pyenv/versions/$PV_PY_VER/bin/pip install --ignore-installed --user numpy==$PV_NP_VER cython==0.29

# Install hdf5 of the same version as paraview (not enough files included in binary paraview distribution to build against)
export PV_H5_MJ_VER=${PV_H5_VER%.*}
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$PV_H5_MJ_VER/hdf5-$PV_H5_VER/src/hdf5-$PV_H5_VER.tar.bz2
tar jxf hdf5-$PV_H5_VER.tar.bz2
cd hdf5-$PV_H5_VER
./configure
make -j
make install

# Install h5py against theis hdf5 library
export HDF5_DIR=`pwd`/hdf5
~/.pyenv/versions/$PV_PY_VER/bin/pip uninstall -y h5py
~/.pyenv/versions/$PV_PY_VER/bin/pip install --no-binary=h5py --user h5py

Known version numbers

You can fill in the version numbers below for your specific version of ParaView.

ParaView version	Python version	Python UCS status	Numpy version	HDF5 version
5.4.1	2.7.11	2	1.8.1	1.8.13
5.5.2	2.7.14	2	1.8.1	1.8.13
5.6.0	2.7.??	4	1.15.1	1.8.13

Known issues

Mismatch in library and header version

Sometimes the h5py installer does not correctly find the hdf5 version number. In that case you can set the HDF5_VERSION enviroment variable (to something like 1.8.13 depending on your version)

h5py failed to build

Cython 0.30a is known not to work. Additionally you can run the pip install h5py in verbose mode with -vvv

ImportError

If you get an error like

ImportError:
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

Original error was: /home/daan/.local/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyUnicodeUCS4_FromObject

you still have a numpy installed in .local/lib/python2.7/site-packages or some other directory in your PYTHONPATH

Undefined symbol: PyUnicodeUCS4_DecodeUTF8

This error occurs when loading a python module which has binary extensions and is compiled for python with Unicode UCS4 support. Trying to run it with the ParaView python interpreter (which has UCS2) will fail with an error like

ImportError: /home/daan/.local/lib/python2.7/site-packages/h5py/_errors.so: undefined symbol: PyUnicodeUCS4_DecodeUTF8

Follow the steps above to install a python with UCS2 and use that to compile your extensions.

License

This work is licensed under the GPLv3 license. See the file LICENSE for more details.

Contributing

Contributions are very welcome. If you use this plugin to make a ParaView reader, please consider submitting it here as an example.