[ome-users] OMERO 5.0 .nd import question
Melissa Linkert
melissa at glencoesoftware.com
Fri Feb 7 20:10:24 GMT 2014
Hi Christophe,
You may have already seen this, but just in case (and for everyone
else's benefit) there is now a ticket for this issue:
http://trac.openmicroscopy.org.uk/ome/ticket/11968
Regards,
-Melissa
On Tue, Feb 04, 2014 at 03:32:10AM -0600, Melissa Linkert wrote:
> Hi Christophe,
>
> > Why does it seem when importing a Metamorph .nd stack, that only 2 pixels by 2 pixels are being read in ?
> > A TileHeight of 2 seems to be extremely inefficient.
>
> From the log:
>
> > 2014-02-04 05:10:50,663 DEBUG [ o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:0 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
>
> it looks like it is reading 1392x2 tiles at a time. In general, tiles are read
> as they are stored in the file, though it's certainly possible that
> something is going wrong in this case.
>
> > If anybody knows what could be going on here that would be great.
> >
> > Just as an info, but a .nd linking to ~70 MB of images, is taking more than 40 mins to still not finish importing...
>
> Is it correct to assume that this is using a 5.0.0-rc1 server? If so,
> would you be willing to send the dataset that exhibits this behavior so
> that we can verify the problem (and any potential solution)? The
> dataset can be uploaded to:
>
> http://qa.openmicroscopy.org.uk/qa/upload/
>
> Regards,
> -Melissa
>
> On Tue, Feb 04, 2014 at 10:27:14AM +0000, Christophe TREFOIS wrote:
> > Dear all,
> >
> > Why does it seem when importing a Metamorph .nd stack, that only 2 pixels by 2 pixels are being read in ?
> > A TileHeight of 2 seems to be extremely inefficient.
> >
> > If anybody knows what could be going on here that would be great.
> >
> > Just as an info, but a .nd linking to ~70 MB of images, is taking more than 40 mins to still not finish importing...
> >
> > Thank you,
> >
> > 2014-02-04 05:10:50,663 DEBUG [ o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:0 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
> > 2014-02-04 05:10:50,666 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
> > 2014-02-04 05:10:50,679 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
> > 2014-02-04 05:10:51,017 INFO [ loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
> > 2014-02-04 05:10:51,024 DEBUG [ o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:2 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
> > 2014-02-04 05:10:51,027 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
> > 2014-02-04 05:10:51,041 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
> > 2014-02-04 05:10:51,377 INFO [ loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
> > 2014-02-04 05:10:51,382 DEBUG [ o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:4 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
> > 2014-02-04 05:10:51,384 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
> > 2014-02-04 05:10:51,398 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
> > 2014-02-04 05:10:51,721 INFO [ loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
> > 2014-02-04 05:10:51,727 DEBUG [ o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:6 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
> > 2014-02-04 05:10:51,729 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
> > 2014-02-04 05:10:51,743 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
> > 2014-02-04 05:10:52,100 INFO [ loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
> > 2014-02-04 05:10:52,106 DEBUG [ o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:8 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
> > 2014-02-04 05:10:52,109 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
> > 2014-02-04 05:10:52,125 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
> > 2014-02-04 05:10:52,530 INFO [ loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
> > 2014-02-04 05:10:52,624 DEBUG [ o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:10 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
> > 2014-02-04 05:10:52,628 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
> > 2014-02-04 05:10:52,649 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
> > 2014-02-04 05:10:53,021 INFO [ loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
> > 2014-02-04 05:10:53,027 DEBUG [ o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:12 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
> > 2014-02-04 05:10:53,030 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
> > 2014-02-04 05:10:53,044 INFO [ loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
> > 2014-02-04 05:10:53,458 INFO [ loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
> > 2014-02-04 05:10:53,464 DEBUG [ o.s.blitz.repo.ManagedImportRequestI] (3-thread-1) Plane:0 X:0 Y:14 TileWidth:1392 TileHeight:2 arrayBuf.length:5568
> >
> >
> > ................................................................................
> >
> > Dipl.-Ing. Christophe TREFOIS
> > Ing. Sys. Com. Dipl. EPF
> >
> > PhD Candidate
> >
> >
> > Université du Luxembourg | University of Luxembourg
> >
> > Campus Belval | House of Biomedicine
> >
> > 7, avenue des Hauts-Fourneaux
> >
> > L-4362 Esch-sur-Alzette
> >
> > T +352 46 66 44 6124
> > F +352 46 66 44 6949
> > www.uni.lu/lcsb<http://www.uni.lu/lcsb>
> >
> >
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>
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