[ome-users] TIFF pyramid pixels are zero intensity.
Josh Moore
josh at glencoesoftware.com
Tue Dec 18 10:38:32 GMT 2012
On Dec 13, 2012, at 4:14 PM, Wood, Christopher wrote:
> Hi Josh,
Hi Chris,
> 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 for the logs and the file. When I import the file locally I see the same 0 size stats info objects:
2012-12-18 08:19:44,048 INFO [ ome.io.nio.FilePathResolver] (2-thread-1) Metadata only file, resulting path: /OMERO/Files/Dir-013/13102
...
2012-12-18 08:19:44,503 INFO [ ome.io.nio.PixelsService] (2-thread-1) Creating BfPixelBuffer: /OMERO/Files/Dir-013/13102 Series: 0
2012-12-18 08:19:44,503 INFO [ ome.io.nio.PixelsService] (2-thread-1) Destination pyramid tile size: java.awt.Dimension[width=256,height=256]
2012-12-18 08:19:44,505 INFO [ ome.io.nio.PixelsService] (2-thread-1) Pyramid creation for Pixels:8651 1/4428 (0%).
2012-12...
2012-12-18 09:16:44,576 INFO [ ome.io.nio.PixelsService] (2-thread-1) Pyramid creation for Pixels:8651 3979/4428 (89%).
2012-12-18 09:22:57,325 INFO [ ome.io.nio.PixelsService] (2-thread-1) Pyramid creation for Pixels:8651 4421/4428 (99%).
2012-12-18 09:23:04,019 INFO [ ome.io.nio.PixelsService] (2-thread-1) SUCCESS -- Pyramid created for pixels id:8651
...
2012-12-18 09:23:10,907 INFO [ ome.services.pixeldata.PixelDataHandler] (2-thread-1) Added StatsInfo:17049 for ome.model.core.Channel:Id_18251 - C:0 Max:0.0 Min:0.0
2012-12-18 09:23:10,909 INFO [ ome.services.pixeldata.PixelDataHandler] (2-thread-1) Added StatsInfo:17050 for ome.model.core.Channel:Id_18252 - C:1 Max:0.0 Min:0.0
2012-12-18 09:23:10,910 INFO [ ome.services.pixeldata.PixelDataHandler] (2-thread-1) Added StatsInfo:17051 for ome.model.core.Channel:Id_18253 - C:2 Max:0.0 Min:0.0
as well as the same 1MB pyramid file:
-rw-r--r-- 1 hudson hudson 1147663 2012-12-18 09:23 8651_pyramid
I've CC'd you on ticket https://trac.openmicroscopy.org.uk/ome/ticket/10050
Thanks for all your feedback.
~Josh
> 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
>>>
>>
>
> <cjw12-11-2012.logs.tgz>
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