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PhotoshopTiffReader pyramid file creation fails

PostPosted: Thu Mar 14, 2019 3:32 pm
by sukunis
Hi,

i try to import a tif-file generated by photoshop merge. According to the importer the file will be successfully imported and processed. But at the web-client/insight-client it doesn't show thumbnails and i can't open the file with a viewer in OMERO.
The PixelData.log shows a NullPointerException in PhotoshopTiffReader.openBytes:

2019-03-14 11:44:04,129 INFO [ ome.io.nio.PixelsService] (2-thread-4) Creating BfPixelBuffer: /OMERO/ManagedRepository/Kunis_52/2019-03/14/11-43-58.932/0017_Fix21__Embryo_Mtgarz137_Kardioolasten12000_Ubersicht_Herz_langsames_speichern.TIF Series: 0
2019-03-14 11:44:04,129 INFO [ ome.io.nio.PixelsService] (2-thread-4) Destination pyramid tile size: java.awt.Dimension[width=256,height=256]
2019-03-14 11:44:04,129 INFO [ ome.io.nio.PixelsService] (2-thread-4) Pyramid creation for Pixels:368240 1/630 (0%).
2019-03-14 11:44:04,130 INFO [ ome.io.nio.PixelsService] (2-thread-3) Creating BfPixelBuffer: /OMERO/ManagedRepository/Kunis_52/2019-03/14/11-43-58.932/0017_Fix21__Embryo_Mtgarz137_Kardioolasten12000_Ubersicht_Herz_langsames_speichern.TIF Series: 1
2019-03-14 11:44:04,130 INFO [ ome.io.nio.PixelsService] (2-thread-3) Destination pyramid tile size: java.awt.Dimension[width=256,height=256]
2019-03-14 11:44:04,130 INFO [ ome.io.nio.PixelsService] (2-thread-3) Pyramid creation for Pixels:368241 1/840 (0%).
2019-03-14 11:44:04,137 ERROR [ ome.services.pixeldata.PixelDataHandler] (2-thread-3) Failed to handle pixels 368241
java.lang.NullPointerException: null
at loci.formats.in.PhotoshopTiffReader.openBytes(PhotoshopTiffReader.java:104) ~[formats-gpl.jar:5.9.2-c1]
at loci.formats.ImageReader.openBytes(ImageReader.java:460) ~[formats-api.jar:5.9.2-c1]
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156) ~[formats-bsd.jar:5.9.2-c1]
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:148) ~[formats-bsd.jar:5.9.2-c1]
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198) ~[formats-bsd.jar:5.9.2-c1]
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348) ~[formats-api.jar:5.9.2-c1]
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348) ~[formats-api.jar:5.9.2-c1]
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269) ~[formats-bsd.jar:5.9.2-c1]
at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:350) ~[romio.jar:na]
at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:499) ~[romio.jar:na]
at ome.io.nio.PixelsService$1.run(PixelsService.java:461) ~[romio.jar:na]
at ome.io.nio.Utils.forEachTile(Utils.java:90) ~[romio.jar:na]
at ome.io.nio.Utils.forEachTile(Utils.java:40) ~[romio.jar:na]
at ome.io.nio.PixelsService.performWrite(PixelsService.java:445) ~[romio.jar:na]
at ome.io.nio.PixelsService.makePyramid(PixelsService.java:349) ~[romio.jar:na]
at ome.services.pixeldata.PixelDataHandler.process(PixelDataHandler.java:144) [server.jar:na]
at ome.services.pixeldata.PixelDataHandler.handleEventLog(PixelDataHandler.java:111) [server.jar:na]
at ome.services.pixeldata.PixelDataThread$HandleEventLog.doWork(PixelDataThread.java:293) [server.jar:na]
at sun.reflect.GeneratedMethodAccessor128.invoke(Unknown Source) ~[na:na]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_201]
at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_201]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [spring-aop.jar:3.0.1.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [spring-aop.jar:3.0.1.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [spring-aop.jar:3.0.1.RELEASE]
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:573) [server.jar:na]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
at ome.security.basic.NullEventHandler.invoke(NullEventHandler.java:39) [server.jar:na]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) [spring-orm.jar:3.0.1.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]


Opening the image with FIJI->Bio-Formats Import works.

Regards,
Susanne

Re: PhotoshopTiffReader pyramid file creation fails

PostPosted: Fri Mar 15, 2019 10:35 am
by mtbc
Dear Susanne,

Sorry to hear you've run into this one: we heard about something like it a couple of years ago but have never had a sample file that reproduced the issue clearly. Would you be able to upload one for us to http://qa.openmicroscopy.org.uk/qa/upload/ so we can take a look?

Cheers,
Mark

Re: PhotoshopTiffReader pyramid file creation fails

PostPosted: Mon Mar 18, 2019 9:00 am
by sukunis
Dear Mark,

sorry, i tried to upload a sample file, but the OMERO.qa shows me: Cannot upload Zero Byte files. I checked my shockwave version - that's not the problem. Is there another way to upload the sample file (file size: 35MB).

Regards,
Susanne

Re: PhotoshopTiffReader pyramid file creation fails

PostPosted: Mon Mar 18, 2019 12:10 pm
by jmoore
Uploaded to inbox/sukunis out-of-band.
~Josh