Reading HDF5 with dynamic filters

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Ben Dichter
Ben Dichter 2022-3-20
回答： Ninad 2024-1-19
I am trying to read an HDF5 file that uses a zstd filter, and I am having trouble setting the HDF5_PLUGIN_PATH variable. Here is what I have tried:
>> !export HDF5_PLUGIN_PATH=/Users/bendichter/opt/miniconda3/lib/python3.9/site-packages/hdf5plugin/plugins
>> !echo $HDF5_PLUGIN_PATH
/Users/bendichter/opt/miniconda3/lib/python3.9/site-packages/hdf5plugin/plugins
>> setenv("HDF5_PLUGIN_PATH", "/Users/bendichter/opt/miniconda3/lib/python3.9/site-packages/hdf5plugin/plugins")
>> getenv("HDF5_PLUGIN_PATH")
'/Users/bendichter/opt/miniconda3/lib/python3.9/site-packages/hdf5plugin/plugins'
>> h5read("zstd.h5","/data")
Error using h5readc
The HDF5 library encountered an error and produced the following stack trace information:
H5PL__find_plugin_in_path can't open directory: /usr/local/hdf5/lib/plugin
Error in h5read (line 93)
[data,var_class] = h5readc(Filename,Dataset,start,count,stride);
Why is MATLAB looking in /usr/local/hdf5/lib/plugin? That directory does not exist, and I have tried two different ways to tell MATLAB to look an a different directory. What am I doing wrong?
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Ben Dichter
Ben Dichter 2022-3-23
@Benjamin Thompson so do you have any ideas how I might fix this? I am not trying to read a .mat file
Science Machine
Science Machine 2023-4-18
try loading path before starting matlab?

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回答（1 个）

Ninad
Ninad 2024-1-19
Hi Ben,
As per my understanding you want to read an HDF5 file in MATLAB and you are unable to set HDF5_PLUGIN_PATH variable using the "setenv()" function.
Please go through the latest version of MATLAB documentation "Import HDF5 Files":
https://in.mathworks.com/help/matlab/import_export/import-hdf5-files.html
It clearly states that you need to set the HDF5_PLUGIN_PATH environment variable to the folder containing the installed plugin binary file before you start MATLAB.
On Windows® — Set the environment variable using System Properties > Advanced > Environment Variables, and then start MATLAB.
Hope this helps.
Regards
Ninad

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