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Hi Felix,
<div class=""><br class="">
</div>
<div class="">Thank you for providing the sample file and carrying out additional testing. I was able to reproduce the issue as reported using the latest Bio-Formats release and the file provided.</div>
<div class="">This looks like it may be the same as a previous issue which had been reported on GitHub - <a href="https://github.com/openmicroscopy/bioformats/issues/2544" class="">https://github.com/openmicroscopy/bioformats/issues/2544</a></div>
<div class="">I have updated the existing Trello card with the details of this report and I will try to spend some further time debugging the issue. You can follow the progress on the Trello card at <a href="https://trello.com/c/YMsm1dzp/64-ndpi-to-tiff-conversion-is-failling" class="">https://trello.com/c/YMsm1dzp/64-ndpi-to-tiff-conversion-is-failling</a></div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 30 Jan 2018, at 18:18, MEYENHOFER Felix <<a href="mailto:felix.meyenhofer@unifr.ch" class="">felix.meyenhofer@unifr.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hello <br class="">
<br class="">
when accessing a certain magnification (one that requires to access the lowest pixels of the resolution pyramid), with the omero viewer, the server fails to generate and consequently cannot deliver the tiles.<br class="">
<br class="">
OMERO.web.log contains the following error:<br class="">
<br class="">
2018-01-30 17:47:58,730 WARNI [ omero.gateway] (proc.08522) debug():4507 InternalException on <class 'omeroweb.webclient.webclient_gateway.OmeroWebSafeCallWrapper'> to <6febc192-51e6-4901-a08d-1d6fdb91698bomero.api.RenderingEngine>
renderCompressed((object #0 (::omero::romio::PlaneDef)<br class="">
{<br class="">
slice = 0<br class="">
x = 0<br class="">
y = 0<br class="">
z = 0<br class="">
t = 0<br class="">
region = object #1 (::omero::romio::RegionDef)<br class="">
{<br class="">
x = 15360<br class="">
y = 44032<br class="">
width = 1024<br class="">
height = 1024<br class="">
}<br class="">
stride = 0<br class="">
}, <ServiceOptsDict: [...]<br class="">
Traceback [...]<br class="">
File "[...]OMERO.server/lib/python/omero_api_RenderingEngine_ice.py", line 905, in renderCompressed<br class="">
return _M_omero.api.RenderingEngine._op_renderCompressed.invoke(self, ((_def, ), _ctx))<br class="">
InternalException: exception ::omero::InternalException<br class="">
{<br class="">
serverStackTrace = ome.conditions.InternalException: Wrapped Exception: (java.lang.RuntimeException):<br class="">
java.io.IOException<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:223)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:104)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:284)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:380)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:344)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:557)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:522)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ome.services.RenderingBean.renderCompressed(RenderingBean.java:552)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.GeneratedMethodAccessor979.invoke(Unknown Source)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.reflect.Method.invoke(Method.java:498)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at com.sun.proxy.$Proxy103.renderCompressed(Unknown Source)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.GeneratedMethodAccessor979.invoke(Unknown Source)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.reflect.Method.invoke(Method.java:498)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at com.sun.proxy.$Proxy103.renderCompressed(Unknown Source)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.GeneratedMethodAccessor1019.invoke(Unknown Source)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.reflect.Method.invoke(Method.java:498)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ome.services.throttling.Callback.run(Callback.java:56)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ome.services.blitz.impl.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:352)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.GeneratedMethodAccessor1018.invoke(Unknown Source)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.reflect.Method.invoke(Method.java:498)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at omero.cmd.CallContext.invoke(CallContext.java:78)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at com.sun.proxy.$Proxy104.renderCompressed_async(Unknown Source)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:298)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:998)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2363)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at IceInternal.Incoming.invoke(Incoming.java:221)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at Ice.ConnectionI.dispatch(ConnectionI.java:1145)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at Ice.ConnectionI.message(ConnectionI.java:1056)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at IceInternal.ThreadPool.run(ThreadPool.java:395)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at IceInternal.ThreadPool.access$300(ThreadPool.java:12)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Thread.run(Thread.java:748)<br class="">
<br class="">
serverExceptionClass = ome.conditions.InternalException<br class="">
message = Wrapped Exception: (java.lang.RuntimeException):<br class="">
java.io.IOException<br class="">
}<br class="">
<br class="">
So I took the file [1] and checked how the bio-formats library deals with it using fiji. When trying to open series-1 I got:<br class="">
"java.lang.IllegalArgumentException: Array size too large: 35304 x 86184 x 1".<br class="">
Nothing new here [2]. So I try cropping on opening (which seem how RenderingEngine is accessing the data anyway) using a bounding box: 0,0,1000,1000. This fails telling me via dialog: "sorry, there was an I/O problem during import. switching scijava log level
DEBUG I get:<br class="">
<br class="">
java.io.IOException<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.services.JPEGTurboServiceImpl.getTile(JPEGTurboServiceImpl.java:329)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.services.JPEGTurboServiceImpl.getTile(JPEGTurboServiceImpl.java:235)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:191)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:148)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:159)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:422)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:387)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:282)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:243)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:221)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:116)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.readPixels(Importer.java:149)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.run(Importer.java:86)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.LociImporter.run(LociImporter.java:78)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runUserPlugIn(IJ.java:221)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:185)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.runCommand(Executer.java:137)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.run(Executer.java:66)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Thread.run(Thread.java:745)<br class="">
Caused by: java.lang.NegativeArraySizeException<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at org.libjpegturbo.turbojpeg.TJDecompressor.decompress(TJDecompressor.java:338)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.services.JPEGTurboServiceImpl.getTile(JPEGTurboServiceImpl.java:322)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>... 25 more<br class="">
<br class="">
So before drilling deeper. Does anyone already have a guess about what this might be?<br class="">
<br class="">
[1]<a href="https://drive.switch.ch/index.php/s/xYo5nzkEflj04eT" class="">https://drive.switch.ch/index.php/s/xYo5nzkEflj04eT</a>
<br class="">
[2]<a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-March/005142.html" class="">http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-March/005142.html</a><br class="">
<br class="">
Best regards,<br class="">
<br class="">
Felix <br class="">
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http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
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