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cheminfo / hdf5

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What is hdf5 #1

Open lpatiny opened 1 year ago

lpatiny commented 1 year ago

https://www.neonscience.org/resources/learning-hub/tutorials/about-hdf5

Example of file from: https://ic.bbp.epfl.ch/icproject

rCell23970.nwb.zip

targos commented 1 year ago

Example of file from: https://ic.bbp.epfl.ch/icproject

This link is not public.

targos commented 1 year ago

HDF5 is very similar to NetCDF, so maybe we should keep only one parser for less maintenance cost.

lpatiny commented 1 year ago

Yes indeed we need to check if it can be added in the netCDF parser.

There is a java code that read this file format https://www.hdfgroup.org/downloads/hdfview/

On the website https://ic.bbp.epfl.ch/icproject they say it is public ;)

image

ghost commented 1 year ago

Interesting, I've seen it in python for ML, I think to store images. I'll read about it.

ghost commented 1 year ago

I've read part of the specification manual here, and wrote just some code to test, it seems possible to write it. We may shortcut / save time using the source code of the viewer, from the link you send previously as well.

But is there any reason why jsfive isn't useful? The license says it is in the public domain. Looking in the code is based off (pyfive) is BSD3.0 which still can be embedded anywhere I think.

Let me know just to know whether I should keep reading it or not.

lpatiny commented 1 year ago

Example of file

Data_2023.05.19_15h01m27s.h5.zip