<div dir="ltr">You can grab a small test slide here: <a href="http://medtech.med.wayne.edu/test/SG09-599.zip">http://medtech.med.wayne.edu/test/SG09-599.zip</a><div><br></div><div>You would then change into that directory and import SlideScan.ini or any of the other .ini files.</div><div><br></div><div>Here is the crucial part of the import log after all the jpg files are uploaded:</div><div><br></div><div><div>2017-03-08 16:32:28,615 19727      [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END</div><div>2017-03-08 16:32:28,753 19865      [      main] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4000</div><div>2017-03-08 16:32:28,980 20092      [l.Client-1] ERROR     ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/SG09-599/SlideScan.ini</div><div>java.lang.RuntimeException: Failure response on import!</div><div>Category: ::omero::grid::ImportRequest</div><div>Name: import-request-failure</div><div>Parameters: {stacktrace=java.lang.NullPointerException</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at ome.formats.model.ChannelProcessor.process(ChannelProcessor.java:469)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:1752)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at ome.services.blitz.repo.ManagedImportRequestI.importMetadata(ManagedImportRequestI.java:623)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:501)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">  </span>at omero.cmd.HandleI.steps(HandleI.java:438)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at omero.cmd.HandleI$1.doWork(HandleI.java:366)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at omero.cmd.HandleI$1.doWork(HandleI.java:362)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at sun.reflect.GeneratedMethodAccessor291.invoke(Unknown Source)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at java.lang.reflect.Method.invoke(Method.java:498)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">  </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at ome.security.basic.EventHandler.invoke(EventHandler.java:154)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">  </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">      </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at com.sun.proxy.$Proxy72.doWork(Unknown Source)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at ome.services.util.Executor$Impl.execute(Executor.java:443)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">  </span>at omero.cmd.HandleI.run(HandleI.java:360)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at ome.services.util.Executor$Impl$1.call(Executor.java:484)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at java.util.concurrent.FutureTask.run(FutureTask.java:266)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at java.lang.Thread.run(Thread.java:745)</div><div>, message=}</div><div><br></div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:665)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">      </span>at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at IceInternal.Incoming.invoke(Incoming.java:222)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">      </span>at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at Ice.ConnectionI.dispatch(ConnectionI.java:1258)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at Ice.ConnectionI.message(ConnectionI.java:1213)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">      </span>at IceInternal.ThreadPool.run(ThreadPool.java:321)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at IceInternal.ThreadPool.access$300(ThreadPool.java:12)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">  </span>at java.lang.Thread.run(Thread.java:745)</div><div><br></div><div>java.lang.RuntimeException: Failure response on import!</div><div>Category: ::omero::grid::ImportRequest</div><div>Name: import-request-failure</div><div>Parameters: {stacktrace=java.lang.NullPointerException</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at ome.formats.model.ChannelProcessor.process(ChannelProcessor.java:469)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:1752)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at ome.services.blitz.repo.ManagedImportRequestI.importMetadata(ManagedImportRequestI.java:623)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:501)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">  </span>at omero.cmd.HandleI.steps(HandleI.java:438)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at omero.cmd.HandleI$1.doWork(HandleI.java:366)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at omero.cmd.HandleI$1.doWork(HandleI.java:362)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at sun.reflect.GeneratedMethodAccessor291.invoke(Unknown Source)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at java.lang.reflect.Method.invoke(Method.java:498)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">  </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at ome.security.basic.EventHandler.invoke(EventHandler.java:154)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">  </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">      </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at com.sun.proxy.$Proxy72.doWork(Unknown Source)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at ome.services.util.Executor$Impl.execute(Executor.java:443)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">  </span>at omero.cmd.HandleI.run(HandleI.java:360)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at ome.services.util.Executor$Impl$1.call(Executor.java:484)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">   </span>at java.util.concurrent.FutureTask.run(FutureTask.java:266)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at java.lang.Thread.run(Thread.java:745)</div><div>, message=}</div><div><br></div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:665) ~[blitz.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) [blitz.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) [blitz.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) [blitz.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at IceInternal.Incoming.invoke(Incoming.java:222) [ice.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre"> </span>at Ice.ConnectionI.invokeAll(ConnectionI.java:2482) [ice.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">       </span>at Ice.ConnectionI.dispatch(ConnectionI.java:1258) [ice.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at Ice.ConnectionI.message(ConnectionI.java:1213) [ice.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre"> </span>at IceInternal.ThreadPool.run(ThreadPool.java:321) [ice.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">        </span>at IceInternal.ThreadPool.access$300(ThreadPool.java:12) [ice.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">  </span>at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693) [ice.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at java.lang.Thread.run(Thread.java:745) [na:1.8.0_121]</div><div>2017-03-08 16:32:28,985 20097      [      main] ERROR        ome.formats.importer.ImportLibrary - Error on import</div><div>java.lang.Exception: Import failure</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">    </span>at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:560) ~[blitz.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">      </span>at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289) ~[blitz.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre"> </span>at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:293) [blitz.jar:na]</div><div><span class="gmail-Apple-tab-span" style="white-space:pre">     </span>at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:950) [blitz.jar:na]</div><div>2017-03-08 16:32:28,985 20097      [      main] INFO         ome.formats.importer.ImportLibrary - Exiting on error</div><div><br></div><div>==> Summary</div><div>494 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:17.810</div></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 8, 2017 at 4:55 PM, Paul Richards <span dir="ltr"><<a href="mailto:paulrichards321@gmail.com" target="_blank">paulrichards321@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>I have successfully developed a separate open source C++ program to convert Olympus SlideScan.ini pyramid images into big tiff format. I have since been working on a open microscopy version of this importer, but keep running into a java NullPointer exception on import. I have been debugging this for about a week with no luck. I can import the images fine if I do not assign resolutionCount > 1, but then I do not see the pyramid view. Attached is the log with the java runtime error. I have tried different version of bioformats, and grabbed yesterday's git version of the open microscopy source code and also tried 5.2.7 with no luck. I keep getting the same NullPointer error. I know I must be doing something wrong!</div><div><br></div><div>Here is the source code of the import module: </div><div><br></div><div><a href="http://medtech.med.wayne.edu/test/OlympusINIReader.java" target="_blank">http://medtech.med.wayne.edu/<wbr>test/OlympusINIReader.java</a></div><div><br></div><div>(just plop this file into bioformats-5.3.4/components/<wbr>formats-gpl/src/loci/in and run ant in the formats-gpl directory)</div><div><br></div><div><a href="http://medtech.med.wayne.edu/test/readers.txt" target="_blank">http://medtech.med.wayne.edu/<wbr>test/readers.txt</a></div><div><br></div><div>(this file goes into bioformats-5.3.4/components/<wbr>formats-api/src/loci/<wbr>formatsats-api/src/)</div><div><br></div><div>Please let me know if you would like me to use the git tree for these, I didn't include them since they are not working properly.</div><div><br></div><div>Any help is greatly appreciated!</div><div><br></div><div>Best Regards,</div><div><br></div><div>Paul Richards</div><div>Web Developer</div><div>Wayne State University School of Medicine</div></div>
</blockquote></div><br></div>