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

Thu Dec 13 15:14:27 GMT 2012

Hi Josh,

The log files are attached.

I also converted this tiff file to a png (of the same size, in fiji) and
it imported much faster than the tiff and the pixel values where not zero.

Thanks,
Chris

On 12/13/12 5:29 AM, "Josh Moore" <josh at glencoesoftware.com> wrote:

>
>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.pr
>operties#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
>> 
>

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