Sources not released from HDD when removed from Fiji #77

martinschorb · 2020-01-27T15:31:50Z

Hi,

When I run SpimDataset > Open XML/HDF5 files it always add these to the existing sources list.
This is a bit annoying if I want to look at two different experiments at the same time. I have to do a full Fiji restart to get rid of the previous sources. When I try to delete all of them to get an empty sources list I get the following crash:

java.lang.IllegalArgumentException: node does not have a parent.
	at javax.swing.tree.DefaultTreeModel.removeNodeFromParent(DefaultTreeModel.java:254)
	at sc.fiji.bdvpg.scijava.services.ui.BdvSourceServiceUI.lambda$updateSpimDataFilterNodes$10(BdvSourceServiceUI.java:329)
	at java.util.ArrayList.forEach(ArrayList.java:1257)
	at sc.fiji.bdvpg.scijava.services.ui.BdvSourceServiceUI.updateSpimDataFilterNodes(BdvSourceServiceUI.java:327)
	at sc.fiji.bdvpg.scijava.services.ui.BdvSourceServiceUI.remove(BdvSourceServiceUI.java:418)
	at sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterService.remove(BdvSourceAndConverterService.java:162)
	at sc.fiji.bdvpg.scijava.command.source.SourcesRemoverCommand.run(SourcesRemoverCommand.java:23)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

killing the whole BDV and requiring a Fiji restart.

The text was updated successfully, but these errors were encountered:

NicoKiaru · 2020-01-27T17:13:41Z

Thanks for reporting. Removing all sources should work indeed. I can have a look on wednesday.

NicoKiaru · 2020-01-30T08:01:06Z

Found the bug. I'll try to release to the update site today. Again, thanks for reporting

NicoKiaru · 2020-02-04T15:03:56Z

When Imagej.net will be up, I'll release v0.1.1 that solves this issue -> all sources can be deleted

martinschorb · 2020-02-05T14:21:21Z

I just updated from the Fiji update site and still get an error:

[ERROR] Module threw exception
java.lang.IllegalArgumentException: node does not have a parent.
	at javax.swing.tree.DefaultTreeModel.removeNodeFromParent(DefaultTreeModel.java:254)
	at sc.fiji.bdvpg.scijava.services.ui.BdvSourceServiceUI.lambda$updateSpimDataFilterNodes$10(BdvSourceServiceUI.java:329)
	at java.util.ArrayList.forEach(ArrayList.java:1257)
	at sc.fiji.bdvpg.scijava.services.ui.BdvSourceServiceUI.updateSpimDataFilterNodes(BdvSourceServiceUI.java:327)
	at sc.fiji.bdvpg.scijava.services.ui.BdvSourceServiceUI.remove(BdvSourceServiceUI.java:418)
	at sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterService.remove(BdvSourceAndConverterService.java:162)
	at sc.fiji.bdvpg.scijava.command.source.SourcesRemoverCommand.run(SourcesRemoverCommand.java:23)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

NicoKiaru · 2020-02-05T14:21:51Z

Hum weird, which version do you have ? If you go to jars folder ?

martinschorb · 2020-02-05T14:24:37Z

that's
fiji-plugin-bigDataProcessor2-0.3.10
bigdataviewer-playground-0.1.1

NicoKiaru · 2020-02-05T14:32:14Z

I can't reproduce it. Check that you take bigdataviewer-playground-0.1.1 from the update site (test with a fresh fiji if necessary). Maybe upload the dataset somewhere, to share it with me (one where you are sure it's failing).

What I do exactly:

I open 2 xml hdf5 files
show them in a window
select with ctrl + a all sources in the tree
right-click select Delete Sources

And that works in my hands

Otherewise we can try to schedule a small skype session. Maybe tomorrow ?

NicoKiaru · 2020-02-06T15:23:16Z

@martinschorb I've pushed a new version to the update site . Please try it and let me know.

Just FYI : there was really a version issue because the line mentioned in your error is not correct. It was the correct line in version 0.1.0 but not in 0.1.1.

After FIJI update you should have the version 0.1.2 of bdv-playground.

Please check this and if you still have this error, please report.

martinschorb · 2020-02-06T16:07:31Z

It seems to go further now. All sources are deleted,

however I still get errors for some...

SourceAndConverterBdvDisplayService:Removing converter setup ...
SourceAndConverterBdvDisplayService:Remove source bdv.viewer.SourceAndConverter@71f53dd2 indexed 1 in BdvHandle null
SourceAndConverterBdvDisplayService:Removing converter setup ...
Exception in thread "AWT-EventQueue-0" SourceAndConverterBdvDisplayService:Remove source bdv.viewer.SourceAndConverter@39eb197 indexed 1 in BdvHandle null
java.lang.ArrayIndexOutOfBoundsException: 14 >= 14
SourceAndConverterBdvDisplayService:Removing converter setup ...	at java.util.Vector.elementAt(Vector.java:477)

	at javax.swing.tree.DefaultMutableTreeNode.getChildAt(DefaultMutableTreeNode.java:245)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.updateNextIndex(VariableHeightLayoutCache.java:1758)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.updateNextObject(VariableHeightLayoutCache.java:1708)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.nextElement(VariableHeightLayoutCache.java:1699)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.nextElement(VariableHeightLayoutCache.java:1653)
	at javax.swing.plaf.basic.BasicTreeUI.paint(BasicTreeUI.java:1183)
	at javax.swing.plaf.metal.MetalTreeUI.paint(MetalTreeUI.java:169)
	at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
	at javax.swing.JComponent.paintComponent(JComponent.java:780)
	at javax.swing.JComponent.paint(JComponent.java:1056)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	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.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	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)
SourceAndConverterBdvDisplayService:Remove source bdv.viewer.SourceAndConverter@7c106b1a indexed 1 in BdvHandle null
SourceAndConverterBdvDisplayService:Removing converter setup ...
SourceAndConverterBdvDisplayService:Remove source bdv.viewer.SourceAndConverter@71292e43 indexed 1 in BdvHandle null
SourceAndConverterBdvDisplayService:Removing converter setup ...
SourceAndConverterBdvDisplayService:Remove source bdv.viewer.SourceAndConverter@1f4dfc00 indexed 1 in BdvHandle null
SourceAndConverterBdvDisplayService:Removing converter setup ...
SourceAndConverterBdvDisplayService:Remove source bdv.viewer.SourceAndConverter@23c8f346 indexed 1 in BdvHandle null
SourceAndConverterBdvDisplayService:Removing converter setup ...
SourceAndConverterBdvDisplayService:Remove source bdv.viewer.SourceAndConverter@225f1870 indexed 1 in BdvHandle null
SourceAndConverterBdvDisplayService:Removing converter setup ...

NicoKiaru · 2020-02-06T16:19:09Z

Thanks for testing.

If the sources are not displayed, do you still get the error ?

Can you share a minimal dataset making this bug or is it too complicated ?

martinschorb · 2020-02-07T14:22:06Z

OK,

add two sources, https://oc.embl.de/index.php/s/fFxYlIqFmULJspK
show sources
close bdv window
select sources in list
right click - delete sources

SourceAndConverterBdvDisplayService:Create locations display of sourceandconverter of m_120
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 1 >= 1
	at java.util.Vector.elementAt(Vector.java:477)
	at javax.swing.tree.DefaultMutableTreeNode.getChildAt(DefaultMutableTreeNode.java:245)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.updateNextIndex(VariableHeightLayoutCache.java:1758)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.updateNextObject(VariableHeightLayoutCache.java:1708)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.nextElement(VariableHeightLayoutCache.java:1699)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.nextElement(VariableHeightLayoutCache.java:1653)
	at javax.swing.plaf.basic.BasicTreeUI.paint(BasicTreeUI.java:1183)
	at javax.swing.plaf.metal.MetalTreeUI.paint(MetalTreeUI.java:169)
	at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
	at javax.swing.JComponent.paintComponent(JComponent.java:780)
	at javax.swing.JComponent.paint(JComponent.java:1056)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	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.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	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)

martinschorb · 2020-02-07T14:31:49Z

Hold on,

does not happen with a naked Fiji.

I need to test which other Plugin causes the Problem. I hope it's none of @tischi 's

NicoKiaru · 2020-02-07T14:47:34Z

It's one of those terrible random bug. I think it still comes from the playground. I experience some issues also.

I think it's a problem of synchronization between the rendering and the data modification.

I'll try to see what can be done.

martinschorb · 2020-02-07T14:50:18Z

Well,
at least I had it working for once ;-) without an error. So there is progress...

NicoKiaru · 2020-02-17T07:59:43Z

I've done some modifications and pushed to the update site @martinschorb . Let me know how that goes!

Best

martinschorb · 2020-02-17T13:15:38Z

Hi,

no huge progress...

java.lang.ArrayIndexOutOfBoundsException: 2 >= 2
	at java.util.Vector.elementAt(Vector.java:477)
	at javax.swing.tree.DefaultMutableTreeNode.getChildAt(DefaultMutableTreeNode.java:245)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.updateNextIndex(VariableHeightLayoutCache.java:1758)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.updateNextObject(VariableHeightLayoutCache.java:1708)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.nextElement(VariableHeightLayoutCache.java:1699)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.nextElement(VariableHeightLayoutCache.java:1653)
	at javax.swing.plaf.basic.BasicTreeUI.paint(BasicTreeUI.java:1183)
	at javax.swing.plaf.metal.MetalTreeUI.paint(MetalTreeUI.java:169)
	at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
	at javax.swing.JComponent.paintComponent(JComponent.java:780)
	at javax.swing.JComponent.paint(JComponent.java:1056)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:290)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	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.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	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)

NicoKiaru · 2020-02-17T13:17:53Z

Just make sure that you restarted FIJI after the update and that you have version 0.1.4. I encounteered some errors, but not of this kind. weird.

martinschorb · 2020-02-17T13:24:47Z

OK,

tried now several times including restarts...

It seems to work now without errors.

However, if I delete the sources while they are still shown in a bdv window, I get:

Exception in thread "PainterThread" java.lang.IndexOutOfBoundsException: Index: 2, Size: 2
	at java.util.ArrayList.rangeCheck(ArrayList.java:657)
	at java.util.ArrayList.get(ArrayList.java:433)
	at java.util.Collections$UnmodifiableList.get(Collections.java:1311)
	at bdv.viewer.render.MultiResolutionRenderer.createProjector(MultiResolutionRenderer.java:648)
	at bdv.viewer.render.MultiResolutionRenderer.paint(MultiResolutionRenderer.java:496)
	at bdv.viewer.ViewerPanel.paint(ViewerPanel.java:485)
	at net.imglib2.ui.PainterThread.run(PainterThread.java:86)

or when I delete the sources with the right click inside the bdv window:

Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 3 >= 3
	at java.util.Vector.elementAt(Vector.java:477)
	at javax.swing.tree.DefaultMutableTreeNode.getChildAt(DefaultMutableTreeNode.java:245)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.updateNextIndex(VariableHeightLayoutCache.java:1758)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.updateNextObject(VariableHeightLayoutCache.java:1708)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.nextElement(VariableHeightLayoutCache.java:1699)
	at javax.swing.tree.VariableHeightLayoutCache$VisibleTreeStateNodeEnumeration.nextElement(VariableHeightLayoutCache.java:1653)
	at javax.swing.plaf.basic.BasicTreeUI.paint(BasicTreeUI.java:1183)
	at javax.swing.plaf.metal.MetalTreeUI.paint(MetalTreeUI.java:169)
	at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
	at javax.swing.JComponent.paintComponent(JComponent.java:780)
	at javax.swing.JComponent.paint(JComponent.java:1056)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:290)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	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.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	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)

NicoKiaru · 2020-02-17T13:34:50Z

But you can still continue to work ?

Indeed I have been struggling to avoid this issue, but I couldn't find a proper (or even a dirty) solution. But if you can continue to work, I think I will let it like that and hopefully this will be solved with the new interface by Tobias.

martinschorb · 2020-02-17T13:48:41Z

That's OK I guess...

NicoKiaru · 2020-03-31T10:32:24Z

Now so the new interface is there, can you check if this but still occurs @martinschorb ?

I don't remember exactly what was the issue, but with a bit of luck this should be solved now

NicoKiaru · 2020-04-15T15:52:38Z

Closing this, just reopen it if it occurs again, I hope the new UI and state solved it

martinschorb · 2020-04-28T12:32:03Z

One slightly annoying behaviour:

it crashes when sources are deleted that are still shown in a BDV window.

Can you check this before deleting and then show a warning?

NicoKiaru · 2020-04-28T12:35:20Z

One slightly annoying behaviour:
😄

Yep I will maintain this open because it's not nice.

NicoKiaru · 2020-04-28T12:35:48Z

And the new UI and state didn't solve it, it's the tree UI in bdv playground which is the issue

martinschorb · 2020-04-30T07:46:07Z

Hi,

I also noticed that deleting sources from BDV does not remove the data from memory.

I delete all sources
I cannot delete the h5 file, because ImageJ/Java is still accessing it
I can however modify the h5 (weird..?) and write new stuff into it.
When I then try to load the modified file, BDV crashes (full Java freeze), because it tries to read from the old structure that no longer exists.

So deleting sources from the BDV sources lists needs to make sure that the file is released/closed from Java.

martinschorb · 2020-04-30T07:49:25Z

Only fully closing Fiji releases the files btw...

NicoKiaru · 2020-05-19T10:09:50Z

Hi @martinschorb ,

Can you try to see if you have the same behaviour with a fresh Fiji and using the original BigDataViewer plugin ? If yes, that's something we need to report in bigdataviewer-core.

Thanks!

martinschorb · 2020-05-19T13:44:58Z

I don't quite understand how I can add multiple source to "traditional" BDV. I had a thorough look. Also there is no option of deleting them...

NicoKiaru · 2020-05-19T14:21:39Z

Sorry, just a single dataset. Just open it and close the window. Are the files released then ?

If the window is closed, the files should be released, but I fear they aren't released, even in such a simple case.

martinschorb · 2020-05-20T07:35:58Z

Hi,

I did some testing...

On Mac it looks like release is not important. (deleting works with both built-in BDV and Playground).
On Windows, you are right. Even "normal" BDV does not release the file when you close the window.

NicoKiaru · 2020-05-20T07:38:42Z

Good to know! That's something we need to mention in bdv-core. I'll post an issue

NicoKiaru · 2020-05-20T08:00:18Z

bigdataviewer/bigdataviewer-core#93

NicoKiaru closed this as completed Feb 4, 2020

NicoKiaru reopened this Feb 5, 2020

NicoKiaru closed this as completed Apr 15, 2020

NicoKiaru reopened this Apr 30, 2020

NicoKiaru mentioned this issue May 20, 2020

Hdf5 files not being released on bigdataviewer window closing (Windows) bigdataviewer/bigdataviewer-core#93

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NicoKiaru changed the title ~~adding/deleting sources~~ Sources not released from HDD when removed from Fiji Sep 27, 2021

NicoKiaru added the bug Something isn't working label Jun 7, 2024

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Sources not released from HDD when removed from Fiji #77

Sources not released from HDD when removed from Fiji #77

martinschorb commented Jan 27, 2020

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Sources not released from HDD when removed from Fiji #77

Sources not released from HDD when removed from Fiji #77

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martinschorb commented Jan 27, 2020

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martinschorb commented Apr 30, 2020

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