[ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation

[Yellen, Gary]

Hi Andrew - I do realize that this is a ridiculously long Experiment Description string.  It contains unparsed metadata strings from MATLAB - I'll take care of the parsing if and when I can establish the practicality of my storing acquired data in the OME-TIFF format.

I mentioned it in the context of the excessive file size being produced by the LOCI calls, simply because eliminating it was an easy way to rule out the wholesale duplication of all the XML metadata. 
Thanks - Gary 


> On Oct 27, 2014, at 11:54 AM, Andrew Patterson <ajpatterson at lifesci.dundee.ac.uk> wrote:
> 
> Hello Gary,
> 
> I am coming to this discussion late and you may only be talking about dummy test data, but I was wonder why your Experiment Description would be that large?
> 
> This is normally used for a few lines of text that can be displayed to the user, perhaps in a tool-tip, to help then tell similarly named experiments apart.
> http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/ome_xsd.html#Experiment_Description
> 
> If you have a quantity of data you wish to store the better location might be an annotation on a Dataset, Project, Experimenter, or Image.
> CommentAnnotation can store a long string.
> http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/SA_xsd.html#CommentAnnotation
> Or XMLAnnotation more structured data.
> http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/SA_xsd.html#XMLAnnotation
> 
> Hope this helps,
> 
> Andrew
> 
> 
>> On 27 Oct 2014, at 15:20, "Yellen, Gary" <gary_yellen at hms.harvard.edu> wrote:
>> 
>> Ian – I did give this a try and it did not fix either the file size or the slow speed problem. 
>> Also, I reduced the size of the metadata (at least, of the ExperimentDescription string) by 5 KB, and the file size was reduced only by this amount.  So at least this particular metadata item is not being duplicated.
>> Best,
>> Gary
>> 
>> From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Munro, Ian
>> Sent: Monday, October 27, 2014 9:02 AM
>> Cc: ome-devel at lists.openmicroscopy.org.uk
>> Subject: Re: [ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation
>> 
>> Hi Again Gary 
>> 
>> Good to know that you’ve found a solution. However,  I find it puzzling that the files are different sizes.
>> We had a problem where bio-formats was writing multiple copies of the xml when called from Matlab.
>> The work-around was to add the following line:
>> 
>> java.lang.System.setProperty('javax.xml.transform.TransformerFactory', 'com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl’);
>> 
>> to the Matlab code as in the example that I sent.
>> Perhaps this might help.
>> 
>> Regards
>> 
>> Ian 
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>