[ome-devel] MetaVue 7.7.9.0 timestamps not read correctly

[Melissa Linkert]

Hi Christoffer,

> First of all, apologise if this has been addressed before, but I couldn't
> find anything reported on this topic prior.
> 
> I am trying to use the BioFormats library to read the timestamps from a
> file produced by MetaVue version 7.7.0.0. I am (currently) using the
> BioFormats Importer in Fiji for this purpose, but that should not be source
> of (at least not both of) my problems.

Thank you for reporting these problems.

> 1. The first issue I am facing is that a time-stamp which should be
> "2015-03-12 16:43:45:753" is returned as "1426178625753" when viewing the
> "Original Metadata". I am not sure if that is an ImageJ/Fiji issue or stems
> from the BioFormats library. In the actual TIF file, it is correctly
> written as "20150312 16:43:45.753" which is also what I can see when
> opening the file in the original MetaVue software.

Is the "1426178625753" value recorded in the "timestamp" field?  If so,
that is expected; the nicely formatted date should be present in an
"acquisition-time-local" and/or "DateTime" entry.

> 2. My second, and more important, issue is that the milliseconds part of
> the time-stamps are incorrectly read. This is due to the strange way the
> time-stamps are stored in the file, whereas the BioFormats library attempts
> to read them in a more "sane" way.
> 
> The problem is the following: While the date-time March 12 2015
> 16:43:45:753 is stored in the file as "2015-03-12 16:43:45:753", the
> date-time March 12 2015 16:43:46:003 is stored as "2015-03-12 16:43:45:03".
> That is, notice that "003" is just stored as "03". I have confirmed this
> with several different time-points, looking at what is written in the file
> and comparing with what I can see in the original MetaVue software.
> 
> The solution is, thus, simply to pad the millisecond field with zeros from
> the left, rather than from the right. This should be a very simple
> correction and I would do it myself, were it not for that I do not write
> Java and I am afraid to break something which is otherwise working
> (especially given that this does not seem to have been reported before).

A ticket for this is now open on our issue tracking system:

http://trac.openmicroscopy.org/ome/ticket/12810

You will be automatically notified of updates to the ticket; if you
prefer not to receive updates, please let us know.

Regards,
-Melissa

On Thu, Mar 26, 2015 at 05:30:42PM +0100, Christoffer Aberg wrote:
> Dear all,
> 
> First of all, apologise if this has been addressed before, but I couldn't
> find anything reported on this topic prior.
> 
> I am trying to use the BioFormats library to read the timestamps from a
> file produced by MetaVue version 7.7.0.0. I am (currently) using the
> BioFormats Importer in Fiji for this purpose, but that should not be source
> of (at least not both of) my problems.
> 
> 1. The first issue I am facing is that a time-stamp which should be
> "2015-03-12 16:43:45:753" is returned as "1426178625753" when viewing the
> "Original Metadata". I am not sure if that is an ImageJ/Fiji issue or stems
> from the BioFormats library. In the actual TIF file, it is correctly
> written as "20150312 16:43:45.753" which is also what I can see when
> opening the file in the original MetaVue software.
> 
> 2. My second, and more important, issue is that the milliseconds part of
> the time-stamps are incorrectly read. This is due to the strange way the
> time-stamps are stored in the file, whereas the BioFormats library attempts
> to read them in a more "sane" way.
> 
> The problem is the following: While the date-time March 12 2015
> 16:43:45:753 is stored in the file as "2015-03-12 16:43:45:753", the
> date-time March 12 2015 16:43:46:003 is stored as "2015-03-12 16:43:45:03".
> That is, notice that "003" is just stored as "03". I have confirmed this
> with several different time-points, looking at what is written in the file
> and comparing with what I can see in the original MetaVue software.
> 
> The solution is, thus, simply to pad the millisecond field with zeros from
> the left, rather than from the right. This should be a very simple
> correction and I would do it myself, were it not for that I do not write
> Java and I am afraid to break something which is otherwise working
> (especially given that this does not seem to have been reported before).
> 
> I am more than willing to help out with further tests, should they be
> needed, and also to supply test image files with known metadata to improve
> the fidelity with which the library reads these files.
> 
> Best,
> Christoffer

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