[ome-users] Loading a subset of a stack

[Roger Leigh]

On 11/03/15 12:49, Thomas Julou wrote:
> Dear Roger,
>
> Thank you very much for your answer and help.
>
>>> 2. or to create a reader and then load the plane I want only.
>>> but the metadata of all frames are still loaded during the reader
>>> creation?
>>>
>>>> IFormatReader reader = new ImageReader();
>>
>> Try adding here:
>>
>> MetadataOptions options = reader.getMetadataOptions();
>> options.setMetadataLevel(MetadataLevel.MINIMUM);
>>
>>>> reader.setId(id);
>>>> //seriesCount = reader.getSeriesCount();
>>>> sizeZ = reader.getSizeZ();
>>>> sizeC = reader.getSizeC();
>>>> sizeT = reader.getSizeT();
>>>> imageCount = reader.getImageCount();
>>>> IJ.log(sizeT + " frames.");
>
> This looks like exactly what I was after. Unfortunately, when I tried it
> with a 5gb dataset produced by micromanager (supposably ome.tif stacks),
> I don’t get any significant change in performance. I guess it is due to
> how this specific reader is implemented :(
>
>> The default behaviour is to read all metadata.  The above two lines
>> should set it to read a minimum amount of metadata.  However, please
>> note that this is dependent upon the implementation details of the
>> individual readers and file formats; you may or many not see any
>> difference in speed.  It will also mean if you need the extra metadata
>> you'll need to reopen the image since it's parsed once when you
>> initialise the reader.
>
> Thanks for the detailed explanation.
>
>> I should also point out that recent work has been done to improve the
>> performance of Bio-Formats with files on network storage which should be
>> in the upcoming 5.1 release.  You may find that this will provide
>> significant improvements, though it will depend upon the file
>> format/reader in question.
>
> As mentionned above, I’m mostly using micro-manager dataset. Do you know
> whether any work has been done on this?
> Or can you explain me where to find the corresponding files in the
> source code? (then I could track to check the changes on github).

The Micro-Manager reader is in
components/formats-bsd/src/loci/formats/in/MicromanagerReader.java

To view the changes with git (the github interface won't show it--there
are too many other changes):

   git diff origin/dev_5_0..origin/develop --
components/formats-bsd/src/loci/formats/in/MicromanagerReader.java

Summary: there are no significant changes other than some annotations
and support for units in the data model; nothing that would obviously
improve performance.  Any other changes have already been backported to
5.0.x (dev_5_0).

Looking at the reader, it does appear that the slowness is likely due to
the nature of the file format.  In the initFile method, it's required to
trawl through the directory tree to find additional positions, and this
may be quite slow on networked storage.  It's possible that this could
be updated to improve performance, but that's making the assumption that
this hasn't already been done which I'm not certain of (I'll
double-check this and open a ticket for it if not).


Kind regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096