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Re: [h5md-user] Particle tracking

From: Pierre de Buyl
Subject: Re: [h5md-user] Particle tracking
Date: Sun, 01 Sep 2013 14:15:41 -0400
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Hi Mathieu, and welcome!

Peter Colberg <address@hidden> a écrit :
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?

As of now, it is possible but implies to pick a solution such as using
the "id" data (see Olaf Lenz's post - btw, the thread has split) and
tagging "empty" particle slots with an id of -1, for instance.

As Olaf and Peter mentioned, you should still set a maximum number Nmax of
particles to be considered but if you enable chunking on your dataset you
do not need to store Nmax. Empty chunks do not need storage.

Example: say Nmax=10^6, chunk size=1000.

For 1 to 1000 particles, you only store one chunk (1000 points), for
i*1000 to i+1*1000 particles, you store only i+1 chunks.

This allows to set Nmax to large values without wasting disk space.

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

Did you consider variable length datatypes? It would allow to keep
the first dimension of datasets the time.


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