Open Microscopy Environment

achessel wrote:where do I upload again?

I am having issues opening some images using the omero imagej plugin. It just ends with 'an error occurred while loading the image'. They are rather big plain tiff file saved in fiji (12kx3k for example).

It imported all right in omero, and can be opened fine in insight, the original file can be opened fine in imagej with bioformats and other image in omero can be opened fine in fiji. Additionally omero logs seems fine as well, with the relevant calls seemingly finishing with a successful call to getPlane.

There is just a lot of 'File is a raw codestream not a JP2.' and 'Unknown JPEG 2000 box'.

Any Idea of what is happening or how I could debug? is there a log in the omero imagej plugin side for example?

Code: Select all

2016-01-15 15:34:57,717 INFO  [          loci.formats.in.BaseTiffReader] (2-thread-4) Populating OME metadata
2016-01-15 15:34:58,032 ERROR [ ome.services.pixeldata.PixelDataHandler] (2-thread-4) Failed to handle pixels 31051
java.lang.NullPointerException: null
   at loci.common.RandomAccessInputStream.getFilePointer(RandomAccessInputStream.java:198) ~[formats-common.jar:5.1.4]
   at loci.formats.tiff.OnDemandLongArray.toArray(OnDemandLongArray.java:79) ~[formats-bsd.jar:5.1.4]
   at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:858) ~[formats-bsd.jar:5.1.4]
   at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:785) ~[formats-bsd.jar:5.1.4]
   at loci.formats.in.OMETiffReader.openBytes(OMETiffReader.java:314) ~[formats-bsd.jar:5.1.4]
   at loci.formats.ImageReader.openBytes(ImageReader.java:453) ~[formats-api.jar:5.1.4]
   at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156) ~[formats-bsd.jar:5.1.4]
   at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:225) ~[formats-bsd.jar:5.1.4]
   at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349) ~[formats-api.jar:5.1.4]
   at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349) ~[formats-api.jar:5.1.4]
   at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269) ~[formats-bsd.jar:5.1.4]
   at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:345) ~[romio.jar:na]
   at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:475) ~[romio.jar:na]
   at ome.io.nio.PixelsService$1.run(PixelsService.java:418) ~[romio.jar:na]
   at ome.io.nio.Utils.forEachTile(Utils.java:88) ~[romio.jar:na]
   at ome.io.nio.Utils.forEachTile(Utils.java:39) ~[romio.jar:na]
   at ome.io.nio.PixelsService.performWrite(PixelsService.java:402) ~[romio.jar:na]
   at ome.io.nio.PixelsService.makePyramid(PixelsService.java:306) ~[romio.jar:na]
   at ome.services.pixeldata.PixelDataHandler.process(PixelDataHandler.java:146) [server.jar:na]
   at ome.services.pixeldata.PixelDataHandler.handleEventLog(PixelDataHandler.java:113) [server.jar:na]
   at ome.services.pixeldata.PixelDataThread$HandleEventLog.doWork(PixelDataThread.java:246) [server.jar:na]
   at sun.reflect.GeneratedMethodAccessor118.invoke(Unknown Source) ~[na:na]
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_66]
   at java.lang.reflect.Method.invoke(Method.java:497) ~[na:1.8.0_66]
   at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:566) [server.jar:na]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at ome.security.basic.NullEventHandler.invoke(NullEventHandler.java:39) [server.jar:na]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) [org.springframework.orm.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) [org.springframework.transaction.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) [server.jar:na]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) [server.jar:na]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at com.sun.proxy.$Proxy73.doWork(Unknown Source) [na:na]
   at ome.services.util.Executor$Impl.execute(Executor.java:447) [server.jar:na]
   at ome.services.util.Executor$Impl.execute(Executor.java:391) [server.jar:na]
   at ome.services.pixeldata.PixelDataThread.go(PixelDataThread.java:255) [server.jar:na]
   at ome.services.pixeldata.PixelDataThread.access$000(PixelDataThread.java:52) [server.jar:na]
   at ome.services.pixeldata.PixelDataThread$1.call(PixelDataThread.java:203) [server.jar:na]
   at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_66]
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [na:1.8.0_66]
   at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_66]
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_66]
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_66]
   at java.lang.Thread.run(Thread.java:745) [na:1.8.0_66]


I had those messages, and increased the Ice.MessageSizeMax, and stoped having them (the master.err log file is not updated when that error occurs). Just in case I increased it again to above 500mb, which is more than the size of the whole image (is there a way to check that it was taken into account? I could not see a way to get the CLI to spit it the actual value of that parameter out), and the error is still occurring, with no master.err log...

Did it solve the issue on your end to increase that parameter?

On a related point: I tried to save the image as OME.tiff, in case it would change something (it does not).
But I also tried to save it as OME.btf (ome big tiff?), which is not needed for that one plane but would be for the whole 80Gb stack, and import failed at pyramid generation, with the following error in PixelData log: