Extracting data from bench output bin files

Question

This is probably a naive question.  I would like to extract the data for Ca_i from the bin file produced when I use --validate option with bench.  But, I can't find any information about the file format and I am not currently using carputils or any of the visualization tools provided with open carp.  Is there a straightforward way to translate or extract data from the <problem_name>.Cai.bin file?

If it makes a difference, I am using both the Gaur and OHara models in this study.  Gaur includes Cai in the trace file output, OHara does not.

Answer 1

I think this script can be helpful: https://git.opencarp.org/openCARP/carputils/-/blob/master/bin/bin2h5.py?ref_type=heads

Indeed, the format is not documented in the manual currently. I've opened an issue and of course we welcome contributions: https://git.opencarp.org/openCARP/openCARP/-/issues/371

What is included in the trace depends on which quantities are labeled with .trace() in the .model file. See here for the Gaur example: https://git.opencarp.org/openCARP/openCARP/-/blob/master/physics/limpet/models/Gaur.model?ref_type=heads#L454 

Comments

Thanks!  The bin2h5 script was exactly what I needed.  I can now import data quickly into my MATLAB data analysis with their h5read() function.  I'll try to explore more in the carputils package as I continue working with openCARP.