Cannot open version 3 .zarr files #106
Description
I'm using dasks to_zarr-function to save large-ish tomographic datasets to .zarr files.
I use something along the lines of VOI[:, :, :, 0].rechunk('auto').to_zarr(row['OutputNameVOI']) to do so.
Recently, the zarr library by default switched to it's version 3 for saving files, see https://zarr.readthedocs.io/en/stable/api/zarr/api/asynchronous/index.html#zarr.api.asynchronous.save, where they several times mention 'default is 3'.
The resulting files cannot be read with your library, and produce the exception pasted below.
If I specify the 'old' output format with CroppedReconstructions.rechunk(chunks=(250,250,250)).to_zarr(Data['OutputNameZarrCrop'][whichscan], zarr_format=2), then all is fine and dandy and I can load the files with ImageJ.
Would it be possible to somehow support the new format directly?
If helpful, I can share .zarr files written with both formats and more information that might be needed.
(Fiji Is Just) ImageJ 2.16.0/1.54p; Java 1.8.0_322 [64-bit]; Linux 6.8.0-57-generic; 1369MB of 268999MB (<1%)
org.janelia.saalfeldlab.n5.N5Exception$N5IOException: No container exists at /media/habi/Fast_SSD/REDACTED/REDACTED/B1_01A/B1_01A.rec.cropped_0251-2674_0682-2098_0450-2072.zarr
at org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader.<init>(ZarrKeyValueReader.java:189)
at org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader.<init>(ZarrKeyValueReader.java:152)
at org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader.<init>(ZarrKeyValueReader.java:228)
at org.janelia.saalfeldlab.n5.universe.N5Factory.openReader(N5Factory.java:408)
at org.janelia.saalfeldlab.n5.universe.N5Factory.openN5Container(N5Factory.java:604)
at org.janelia.saalfeldlab.n5.universe.N5Factory.openReader(N5Factory.java:368)
at org.janelia.saalfeldlab.n5.universe.N5Factory.openReader(N5Factory.java:342)
at org.janelia.saalfeldlab.n5.ij.N5Importer$N5ViewerReaderFun.apply(N5Importer.java:1070)
at org.janelia.saalfeldlab.n5.ij.N5Importer$N5ViewerReaderFun.apply(N5Importer.java:1042)
at org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog.openContainer(DatasetSelectorDialog.java:665)
at org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog.openContainer(DatasetSelectorDialog.java:634)
at org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog.lambda$run$2(DatasetSelectorDialog.java:348)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
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)
```