Skip to content

Instantly share code, notes, and snippets.

@ctrueden

ctrueden/gist:f960d3d7e67b957d4d9e

Created May 15, 2015 20:18
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save ctrueden/f960d3d7e67b957d4d9e to your computer and use it in GitHub Desktop.
Save ctrueden/f960d3d7e67b957d4d9e to your computer and use it in GitHub Desktop.
Download ZIP
Woes when uploading multichannel data to OMERO
Raw
gistfile1.txt
---=== NEW EXCEPTION ===---
When calling createImage with a multi-element list with values 1...sizeC:
[ERROR] Exception
java.io.IOException: io.scif.img.ImgIOException: io.scif.FormatException: Error writing to OMERO: imageIndex=0, planeIndex=0
at io.scif.services.DefaultDatasetIOService.save(DefaultDatasetIOService.java:157) ~[scifio-0.23.0.jar:0.23.0]
at io.scif.services.DefaultDatasetIOService.save(DefaultDatasetIOService.java:142) ~[scifio-0.23.0.jar:0.23.0]
at net.imagej.omero.commands.SaveImageToOMERO.run(SaveImageToOMERO.java:70) ~[imagej-omero-0.3.0-SNAPSHOT.jar:0.3.0-SNAPSHOT]
at org.scijava.command.CommandModule.run(CommandModule.java:201) [scijava-common-2.41.0.jar:2.41.0]
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) [scijava-common-2.41.0.jar:2.41.0]
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) [scijava-common-2.41.0.jar:2.41.0]
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) [scijava-common-2.41.0.jar:2.41.0]
at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181) [scijava-common-2.41.0.jar:2.41.0]
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) [na:1.6.0_65]
at java.util.concurrent.FutureTask.run(FutureTask.java:138) [na:1.6.0_65]
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895) [na:1.6.0_65]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918) [na:1.6.0_65]
at java.lang.Thread.run(Thread.java:695) [na:1.6.0_65]
Caused by: io.scif.img.ImgIOException: io.scif.FormatException: Error writing to OMERO: imageIndex=0, planeIndex=0
at io.scif.img.ImgSaver.writePlanes(ImgSaver.java:688) ~[scifio-0.23.0.jar:0.23.0]
at io.scif.img.ImgSaver.writeImg(ImgSaver.java:542) ~[scifio-0.23.0.jar:0.23.0]
at io.scif.img.ImgSaver.writeImg(ImgSaver.java:528) ~[scifio-0.23.0.jar:0.23.0]
at io.scif.img.ImgSaver.writeImg(ImgSaver.java:497) ~[scifio-0.23.0.jar:0.23.0]
at io.scif.img.ImgSaver.writeImg(ImgSaver.java:459) ~[scifio-0.23.0.jar:0.23.0]
at io.scif.img.ImgSaver.saveImg(ImgSaver.java:174) ~[scifio-0.23.0.jar:0.23.0]
at io.scif.img.ImgSaver.saveImg(ImgSaver.java:158) ~[scifio-0.23.0.jar:0.23.0]
at io.scif.services.DefaultDatasetIOService.save(DefaultDatasetIOService.java:154) ~[scifio-0.23.0.jar:0.23.0]
... 12 common frames omitted
Caused by: io.scif.FormatException: Error writing to OMERO: imageIndex=0, planeIndex=0
at net.imagej.omero.OMEROFormat.writerException(OMEROFormat.java:659) ~[imagej-omero-0.3.0-SNAPSHOT.jar:0.3.0-SNAPSHOT]
at net.imagej.omero.OMEROFormat.access$300(OMEROFormat.java:74) ~[imagej-omero-0.3.0-SNAPSHOT.jar:0.3.0-SNAPSHOT]
at net.imagej.omero.OMEROFormat$Writer.writePlane(OMEROFormat.java:513) ~[imagej-omero-0.3.0-SNAPSHOT.jar:0.3.0-SNAPSHOT]
at io.scif.AbstractWriter.savePlane(AbstractWriter.java:168) ~[scifio-0.23.0.jar:0.23.0]
at io.scif.AbstractWriter.savePlane(AbstractWriter.java:159) ~[scifio-0.23.0.jar:0.23.0]
at io.scif.img.ImgSaver.writePlanes(ImgSaver.java:685) ~[scifio-0.23.0.jar:0.23.0]
... 19 common frames omitted
Caused by: omero.ResourceError: null
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.6.0_65]
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) ~[na:1.6.0_65]
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) ~[na:1.6.0_65]
at java.lang.reflect.Constructor.newInstance(Constructor.java:513) ~[na:1.6.0_65]
at java.lang.Class.newInstance0(Class.java:357) ~[na:1.6.0_65]
at java.lang.Class.newInstance(Class.java:310) ~[na:1.6.0_65]
at IceInternal.BasicStream.createUserException(BasicStream.java:2615) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at IceInternal.BasicStream.access$300(BasicStream.java:12) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3099) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at IceInternal.BasicStream.throwException(BasicStream.java:2077) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at IceInternal.Outgoing.throwUserException(Outgoing.java:538) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at omero.api._RawPixelsStoreDelM.setPlane(_RawPixelsStoreDelM.java:1668) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at omero.api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java:8082) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at omero.api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java:8044) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at net.imagej.omero.OMEROFormat$Writer.writePlane(OMEROFormat.java:510) ~[imagej-omero-0.3.0-SNAPSHOT.jar:0.3.0-SNAPSHOT]
... 22 common frames omitted
---=== ORIGINAL EXCEPTION ===---
When calling createImage with a single-element list with value 0:
[ERROR] Exception
java.io.IOException: io.scif.img.ImgIOException: io.scif.FormatException: Error writing to OMERO: imageIndex=0, planeIndex=1
at io.scif.services.DefaultDatasetIOService.save(DefaultDatasetIOService.java:157) ~[scifio-0.22.0.jar:0.22.0]
at io.scif.services.DefaultDatasetIOService.save(DefaultDatasetIOService.java:142) ~[scifio-0.22.0.jar:0.22.0]
at net.imagej.omero.commands.SaveImageToOMERO.run(SaveImageToOMERO.java:70) ~[imagej-omero-0.3.0-SNAPSHOT.jar:0.3.0-SNAPSHOT]
at org.scijava.command.CommandModule.run(CommandModule.java:201) [scijava-common-2.40.0.jar:2.40.0]
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) [scijava-common-2.40.0.jar:2.40.0]
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) [scijava-common-2.40.0.jar:2.40.0]
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) [scijava-common-2.40.0.jar:2.40.0]
at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181) [scijava-common-2.40.0.jar:2.40.0]
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) [na:1.6.0_65]
at java.util.concurrent.FutureTask.run(FutureTask.java:138) [na:1.6.0_65]
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895) [na:1.6.0_65]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918) [na:1.6.0_65]
at java.lang.Thread.run(Thread.java:695) [na:1.6.0_65]
Caused by: io.scif.img.ImgIOException: io.scif.FormatException: Error writing to OMERO: imageIndex=0, planeIndex=1
at io.scif.img.ImgSaver.writePlanes(ImgSaver.java:688) ~[scifio-0.22.0.jar:0.22.0]
at io.scif.img.ImgSaver.writeImg(ImgSaver.java:542) ~[scifio-0.22.0.jar:0.22.0]
at io.scif.img.ImgSaver.writeImg(ImgSaver.java:528) ~[scifio-0.22.0.jar:0.22.0]
at io.scif.img.ImgSaver.writeImg(ImgSaver.java:497) ~[scifio-0.22.0.jar:0.22.0]
at io.scif.img.ImgSaver.writeImg(ImgSaver.java:459) ~[scifio-0.22.0.jar:0.22.0]
at io.scif.img.ImgSaver.saveImg(ImgSaver.java:174) ~[scifio-0.22.0.jar:0.22.0]
at io.scif.img.ImgSaver.saveImg(ImgSaver.java:158) ~[scifio-0.22.0.jar:0.22.0]
at io.scif.services.DefaultDatasetIOService.save(DefaultDatasetIOService.java:154) ~[scifio-0.22.0.jar:0.22.0]
... 12 common frames omitted
Caused by: io.scif.FormatException: Error writing to OMERO: imageIndex=0, planeIndex=1
at net.imagej.omero.OMEROFormat.writerException(OMEROFormat.java:659) ~[imagej-omero-0.3.0-SNAPSHOT.jar:0.3.0-SNAPSHOT]
at net.imagej.omero.OMEROFormat.access$300(OMEROFormat.java:74) ~[imagej-omero-0.3.0-SNAPSHOT.jar:0.3.0-SNAPSHOT]
at net.imagej.omero.OMEROFormat$Writer.writePlane(OMEROFormat.java:513) ~[imagej-omero-0.3.0-SNAPSHOT.jar:0.3.0-SNAPSHOT]
at io.scif.AbstractWriter.savePlane(AbstractWriter.java:168) ~[scifio-0.22.0.jar:0.22.0]
at io.scif.AbstractWriter.savePlane(AbstractWriter.java:159) ~[scifio-0.22.0.jar:0.22.0]
at io.scif.img.ImgSaver.writePlanes(ImgSaver.java:685) ~[scifio-0.22.0.jar:0.22.0]
... 19 common frames omitted
Caused by: omero.ApiUsageException: null
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.6.0_65]
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) ~[na:1.6.0_65]
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) ~[na:1.6.0_65]
at java.lang.reflect.Constructor.newInstance(Constructor.java:513) ~[na:1.6.0_65]
at java.lang.Class.newInstance0(Class.java:357) ~[na:1.6.0_65]
at java.lang.Class.newInstance(Class.java:310) ~[na:1.6.0_65]
at IceInternal.BasicStream.createUserException(BasicStream.java:2615) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at IceInternal.BasicStream.access$300(BasicStream.java:12) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3099) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at IceInternal.BasicStream.throwException(BasicStream.java:2077) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at IceInternal.Outgoing.throwUserException(Outgoing.java:538) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at omero.api._RawPixelsStoreDelM.setPlane(_RawPixelsStoreDelM.java:1668) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at omero.api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java:8082) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at omero.api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java:8044) ~[omero-client-dev_5_0-ice35-b287.jar:na]
at net.imagej.omero.OMEROFormat$Writer.writePlane(OMEROFormat.java:510) ~[imagej-omero-0.3.0-SNAPSHOT.jar:0.3.0-SNAPSHOT]
... 22 common frames omitted
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment