[ome-users] Loading one series only

[Melissa Linkert]

Hi Thomas,

> > Is this the same problem as discussed a few weeks ago?  See:
> > http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-March/005145.html
> 
> Not really, though it looks similar: 
> - what iI was trying to do in the previous thread was to open only the first time points of a dataset (typically to ask the user to draw some ROI)
> - now I’m concerned by the fact that whenever I open one position from a dataset with several ones, the metadata of all positions are parsed before image data is loaded (in BF, positions are seen as series).

OK, thank you for clarifying (and my apologies for the delay).

> > Could you please confirm which of the following you have already tried:
> > - upgrading to 5.1.0 (released today)
> 
> What I reported earlier today is with 5.1.0-dev (March 31st). Previous stable 5.0 was not able to load a dataset from any file that was not the first position (for micro-manager datasets at least; this is why I upgraded).
> 
> > - calling ‘options.setUngroupFiles(true);'
> 
> Well, this is not what I want here. This might help for my previous question.
> 
> > - checking the length of 'imps' to verify that the number of ImagePlus objects returned
> 
> By default it’s 1. I can load all positions at once by using options.setOpenAllSeries(true), then imps.length equals the number of positions (btw this doesn’t take longer).
> 
> Again, my question is really whether it’s possible to disable parsing metadata from other series (here positions, in order to reduce the loading time for a single series) or whether this is not supported by BF.
> Thank you very much for your help. Best,

In that case, no, it is not currently possible to do this in general.
If each series/position is in a single separate file, then you can do this by
disabling file grouping, but otherwise the metadata from the whole
dataset must be parsed first.

Regards,
-Melissa

On Thu, Apr 02, 2015 at 11:55:40PM +0200, Thomas Julou wrote:
> Hi Melissa,
> 
> > Is this the same problem as discussed a few weeks ago?  See:
> > http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-March/005145.html
> 
> Not really, though it looks similar: 
> - what iI was trying to do in the previous thread was to open only the first time points of a dataset (typically to ask the user to draw some ROI)
> - now I’m concerned by the fact that whenever I open one position from a dataset with several ones, the metadata of all positions are parsed before image data is loaded (in BF, positions are seen as series).
> 
> > Could you please confirm which of the following you have already tried:
> > - upgrading to 5.1.0 (released today)
> 
> What I reported earlier today is with 5.1.0-dev (March 31st). Previous stable 5.0 was not able to load a dataset from any file that was not the first position (for micro-manager datasets at least; this is why I upgraded).
> 
> > - calling ‘options.setUngroupFiles(true);'
> 
> Well, this is not what I want here. This might help for my previous question.
> 
> > - checking the length of 'imps' to verify that the number of ImagePlus objects returned
> 
> By default it’s 1. I can load all positions at once by using options.setOpenAllSeries(true), then imps.length equals the number of positions (btw this doesn’t take longer).
> 
> Again, my question is really whether it’s possible to disable parsing metadata from other series (here positions, in order to reduce the loading time for a single series) or whether this is not supported by BF.
> Thank you very much for your help. Best,
> 
> Thomas
> 
> --
> Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21
> 

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