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Re: [h5md-user] Particle tracking
From: |
Peter Colberg |
Subject: |
Re: [h5md-user] Particle tracking |
Date: |
Sun, 1 Sep 2013 11:02:34 -0400 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
Hello Mathieu,
Welcome to the H5MD mailing list :-).
On Sun, Sep 01, 2013 at 12:43:18AM +0200, Mathieu Leocmach wrote:
> I like very much the H5MD initiative and I wonder if I could use this
> format to output and share my experimental data.
>
> I track particles, usually colloids via confocal microscopy. Contrary to
> simulations, I observe only a small portion of the system and particles
> always come in and out of the field of view. Therefore the number of
> particles in a frame is not constant in time and the number of particles
> seen at least once is increasing with time.
>
> Do you think your file structure can accommodate this type of data?
I think the H5MD file format would be well suited for this data. As
Olaf mentioned, however, the specification currently specifies data
groups for fixed particle number only.
A while ago I proposed [1] an extension to extend the step/time/value
scheme with a range dataset to accommodate variable particle numbers.
Now would be the right time to finalize this proposal.
[1] http://thread.gmane.org/gmane.science.simulation.h5md.user/76
Regards,
Peter
- [h5md-user] Particle tracking, Mathieu Leocmach, 2013/09/01
- Re: [h5md-user] Particle tracking, Pierre de Buyl, 2013/09/01
- Re: [h5md-user] Particle tracking, Peter Colberg, 2013/09/01
- Re: [h5md-user] Particle tracking, Pierre de Buyl, 2013/09/01
- Re: [h5md-user] Particle tracking, Peter Colberg, 2013/09/01
- Re: [h5md-user] Particle tracking, Peter Colberg, 2013/09/01
- Re: [h5md-user] Particle tracking, Felix Höfling, 2013/09/02
- Re: [h5md-user] Particle tracking, Peter Colberg, 2013/09/02
- Re: [h5md-user] Particle tracking, Peter Colberg, 2013/09/02
- Re: [h5md-user] Particle tracking, Olaf Lenz, 2013/09/03