[ome-users] TIFF pyramid pixels are zero intensity.

[Josh Moore]

On Dec 11, 2012, at 7:22 PM, Wood, Christopher wrote:

> Hello,

Hi Chris,

> I have a large in XY 3 channel (RGB) image:10484 x 9072.
> 
> When I import it, it imports and archive fine.
> The PixelData log show the pyramid creation, and output the the pyramid
> was created successfully.
> 
> When I view the image, the min and max has been set to zero, and it seem
> all of the pixels are zero. The log file confirms this:
> 
> -bash-4.1$ grep "Added StatsInfo" ~/OMERO.server/var/log/PixelData-0.log
> 2012-12-11 11:07:47,320 INFO [ ome.services.pixeldata.PixelDataHandler]
> (2-thread-5) Added StatsInfo:198266 for ome.model.core.Channel:Id_203708 -
> C:0 Max:0.0 Min:0.0
> 2012-12-11 11:07:47,322 INFO [ ome.services.pixeldata.PixelDataHandler]
> (2-thread-5) Added StatsInfo:198267 for ome.model.core.Channel:Id_203709 -
> C:1 Max:0.0 Min:0.0
> 2012-12-11 11:07:47,324 INFO [ ome.services.pixeldata.PixelDataHandler]
> (2-thread-5) Added StatsInfo:198268 for ome.model.core.Channel:Id_203710 -
> C:2 Max:0.0 Min:0.0

Would it be possible to get Blitz-0.log and PixelData-0.log for the 11th?


> Doing an ls -l on the file in /OMERO/Pixels/Dir-069, it is only 1.1 MB
> compared to another file that is smaller but is ~ 68 MB (and displays
> fine). I converted this image to an ome-tiff in FIJI and imported it, the
> it is 97 MB in /OMERO/Pixels/Dir-069/69012_pyramid.
> 
> And I notice that the ome-tiff and the tiff do not go through the same
> import process (ome-tiff does not log to PixelData). What is the reason
> for this?

The following file formats are configured (in 4.4) to be uploaded as are:

  https://github.com/openmicroscopy/openmicroscopy/blob/dev_4_4/etc/omero.properties#L121

Other files, like OME-TIFF, are being parsed on the client and uploaded block by block.


> Below is some output from the PixelData.log, notice the error at
> 11:07:47,328
> 
> The tiff file is available if needed.

It certainly couldn't hurt to upload the file via http://qa.openmicroscopy.org.uk/qa/upload/

Thanks,
~Josh


> Thanks,
> Chris
> 
> ------------------
> 2012-12-11 11:03:33,471 INFO  [                ome.io.nio.PixelsService]
> (2-thread-5) Pyramid creation for Pixels:69000 3979/4428 (89%).2012-12-11
> 11:07:36,119 INFO  [                ome.io.nio.PixelsService] (2-thread-5)
> Pyramid creation for Pixels:69000 4421/4428 (99%).
> 2012-12-11 11:07:40,506 INFO  [                ome.io.nio.PixelsService]
> (2-thread-5) SUCCESS -- Pyramid created for pixels id:69000
> 2012-12-11 11:07:40,509 INFO  [       loci.formats.in.MinimalTiffReader]
> (2-thread-5) Reading IFDs
> 2012-12-11 11:07:40,510 INFO  [       loci.formats.in.MinimalTiffReader]
> (2-thread-5) Populating metadata
> 2012-12-11 11:07:40,531 INFO  [              loci.formats.in.TiffReader]
> (2-thread-5) Checking comment style
> 2012-12-11 11:07:40,531 INFO  [          loci.formats.in.BaseTiffReader]
> (2-thread-5) Populating OME metadata
> 2012-12-11 11:07:40,535 WARN  [          loci.formats.in.BaseTiffReader]
> (2-thread-5) Expected positive value for PhysicalSizeX; got Infinity
> 2012-12-11 11:07:40,535 WARN  [          loci.formats.in.BaseTiffReader]
> (2-thread-5) Expected positive value for PhysicalSizeY; got Infinity
> 2012-12-11 11:07:47,320 INFO  [ ome.services.pixeldata.PixelDataHandler]
> (2-thread-5) Added StatsInfo:198266 for ome.model.core.Channel:Id_203708 -
> C:0 Max:0.0 Min:0.0
> 2012-12-11 11:07:47,322 INFO  [ ome.services.pixeldata.PixelDataHandler]
> (2-thread-5) Added StatsInfo:198267 for ome.model.core.Channel:Id_203709 -
> C:1 Max:0.0 Min:0.0
> 2012-12-11 11:07:47,324 INFO  [ ome.services.pixeldata.PixelDataHandler]
> (2-thread-5) Added StatsInfo:198268 for ome.model.core.Channel:Id_203710 -
> C:2 Max:0.0 Min:0.0
> 2012-12-11 11:07:47,325 INFO  [ ome.services.pixeldata.PixelDataHandler]
> (2-thread-5) HANDLED EventLog:4472709(entityId=69000) [2543285 ms.]
> 2012-12-11 11:07:47,328 ERROR [        ome.services.util.ServiceHandler]
> (2-thread-5) Method interface ome.services.util.Executor$Work.doWork
> invocation took 2543314
> 2012-12-11 11:07:47,341 INFO  [             ome.io.nio.FilePathResolver]
> (2-thread-2) Metadata only file, resulting path:
> /OMERO/Files/Dir-119/119739
> 2012-12-11 11:07:47,343 ERROR [        ome.services.util.ServiceHandler]
> (2-thread-2) Method interface ome.services.util.Executor$Work.doWork
> invocation took 2543328
> 2012-12-11 11:07:47,375 INFO  [       ome.security.basic.CurrentDetails]
> (2-thread-1) Adding log:INSERT,class ome.model.meta.Session,224420
> 2012-12-11 11:07:47,404 INFO  [             ome.io.nio.FilePathResolver]
> (2-thread-5) Metadata only file, resulting path:
> /OMERO/Files/Dir-119/119739
> 2012-12-11 11:07:47,412 INFO  [             ome.io.nio.FilePathResolver]
> (2-thread-4) Metadata only file, resulting path:
> /OMERO/Files/Dir-119/119739
> 2012-12-11 11:07:48,025 INFO  [             ome.io.nio.FilePathResolver]
> (2-thread-5) Metadata only file, resulting path:
> /OMERO/Files/Dir-119/119739
> 2012-12-11 11:07:48,039 INFO  [             ome.io.nio.FilePathResolver]
> (2-thread-3) Metadata only file, resulting path:
> /OMERO/Files/Dir-119/119739
>