[ome-users] OMERO 5.0 .nd import question

Tue Feb 4 09:32:10 GMT 2014

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
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> T +352 46 66 44 6124
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> 
> 
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