Bio format error (file serie batch)

[jkm...@gmail.com]

Hello,

I currently trying to run spot detector (km017 protocol) to get MFI on every channel of large images (z stacks + tilling + positions) using the attached batch protocol (km017...002) but I get the following error :

java.lang.NullPointerException

at ome.units.quantity.Length.compareTo(Length.java:150)

at ome.units.quantity.Length.compareTo(Length.java:35)

at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:320)

at java.util.ComparableTimSort.sort(ComparableTimSort.java:188)

at java.util.Arrays.sort(Arrays.java:1246)

at loci.formats.TileStitcher.setId(TileStitcher.java:290)

at plugins.kernel.importer.LociImporterPlugin.openReader(LociImporterPlugin.java:916)

at plugins.kernel.importer.LociImporterPlugin.open(LociImporterPlugin.java:833)

at icy.file.Loader.getOMEXMLMetaData(Loader.java:1102)

at icy.file.Loader.getOMEXMLMetaData(Loader.java:1131)

at plugins.adufour.blocks.lang.SequenceSeriesBatch.initializeLoop(SequenceSeriesBatch.java:71)

at plugins.adufour.blocks.lang.Loop.run(Loop.java:127)

at plugins.adufour.blocks.lang.BlockDescriptor.run(BlockDescriptor.java:541)

at plugins.adufour.blocks.lang.WorkFlow.run(WorkFlow.java:837)

at plugins.adufour.blocks.lang.BlockDescriptor.run(BlockDescriptor.java:541)

at java.lang.Thread.run(Thread.java:748)

Is it a Bio-Format error or is it the way I designed the batch analysis ? I am not sure which batch block I should embed my protocol in.

I got the same results with the other sequence blocks except the Region batch block for which I got :

Unable to insert block: plugins.tprovoost.sequenceblocks.loop.SequenceRegionBatch

Reason: java.lang.NullPointerException: null

Stack trace:

java.lang.NullPointerException

at plugins.adufour.blocks.lang.BlockDescriptor.variableAdded(BlockDescriptor.java:581)

at plugins.adufour.blocks.util.VarList.add(VarList.java:116)

at plugins.adufour.blocks.util.VarList.add(VarList.java:65)

at plugins.tprovoost.sequenceblocks.loop.SequenceRegionBatch.declareInput(SequenceRegionBatch.java:88)

at plugins.adufour.blocks.lang.BlockDescriptor.<init>(BlockDescriptor.java:144)

at plugins.adufour.blocks.lang.WorkFlow.<init>(WorkFlow.java:39)

at plugins.adufour.blocks.lang.Loop.<init>(Loop.java:37)

at plugins.adufour.blocks.lang.Batch.<init>(Batch.java:22)

at plugins.tprovoost.sequenceblocks.loop.SequenceRegionBatch.<init>(SequenceRegionBatch.java:32)

at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)

at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

at java.lang.reflect.Constructor.newInstance(Constructor.java:423)

at java.lang.Class.newInstance(Class.java:442)

at plugins.adufour.protocols.gui.block.WorkFlowContainer.doEmbedWorkflow(WorkFlowContainer.java:501)

at plugins.adufour.protocols.gui.block.WorkFlowContainer.embedWorkFlow(WorkFlowContainer.java:486)

at plugins.adufour.blocks.util.BlocksFinder$4.actionPerformed(BlocksFinder.java:623)

at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)

at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)

at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)

at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)

at javax.swing.AbstractButton.doClick(AbstractButton.java:376)

at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)

at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)

at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)

at java.awt.Component.processMouseEvent(Component.java:6539)

at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)

at java.awt.Component.processEvent(Component.java:6304)

at java.awt.Container.processEvent(Container.java:2239)

at java.awt.Component.dispatchEventImpl(Component.java:4889)

at java.awt.Container.dispatchEventImpl(Container.java:2297)

at java.awt.Component.dispatchEvent(Component.java:4711)

at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)

at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)

at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)

at java.awt.Container.dispatchEventImpl(Container.java:2283)

at java.awt.Window.dispatchEventImpl(Window.java:2746)

at java.awt.Component.dispatchEvent(Component.java:4711)

at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)

at java.awt.EventQueue.access$500(EventQueue.java:97)

at java.awt.EventQueue$3.run(EventQueue.java:709)

at java.awt.EventQueue$3.run(EventQueue.java:703)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)

at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)

at java.awt.EventQueue$4.run(EventQueue.java:733)

at java.awt.EventQueue$4.run(EventQueue.java:731)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)

at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)

at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)

at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

 Let me know if you want a sample image / file (250 to 1000 Mo)

Karim.

[Stephane]

Hi Karim,

Indeed it would be useful if you can share both your protocol and an image sample reproducing the error.

From what i read here, i'm afraid that we meet an error with Bio-Formats but i can make some tests to verify it.

Best,

- Stephane

[jkm...@gmail.com]

Hello ! Thanks for the answer,

Attached are the protocols I used (V001 without batch processing).
And below a link to a sample picture :
https://drive.google.com/file/d/11gYYwcdW4ZZcmtVwtAe-7ymnAoqyBOOf/view?usp=sharing

Let me know if you need another sample image.

Karim