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saalfeldlab / n5-ij

ImageJ convenience layer for N5
BSD 2-Clause "Simplified" License
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Opening zarr files with .zattrs #46

Closed jingxuanlim closed 6 months ago

jingxuanlim commented 2 years ago

Hello. I noticed that opening .zarr directories that contain .zattrs is not possible. This is the exception:

Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedOperationException: JsonNull
    at com.google.gson.JsonElement.getAsString(JsonElement.java:179)
    at org.janelia.saalfeldlab.n5.zarr.N5ZarrReader.getZArraryAttributes(N5ZarrReader.java:258)
    at org.janelia.saalfeldlab.n5.zarr.N5ZarrReader.getDatasetAttributes(N5ZarrReader.java:267)
    at org.janelia.saalfeldlab.n5.zarr.N5ZarrReader.datasetExists(N5ZarrReader.java:275)
    at org.janelia.saalfeldlab.n5.zarr.N5ZarrReader.exists(N5ZarrReader.java:287)
    at org.janelia.saalfeldlab.n5.N5FSReader.<init>(N5FSReader.java:118)
    at org.janelia.saalfeldlab.n5.zarr.N5ZarrReader.<init>(N5ZarrReader.java:100)
    at org.janelia.saalfeldlab.n5.ij.N5Factory.openZarrReader(N5Factory.java:214)
    at org.janelia.saalfeldlab.n5.ij.N5Factory.openReader(N5Factory.java:383)
    at org.janelia.saalfeldlab.n5.ij.N5Importer$N5ViewerReaderFun.apply(N5Importer.java:691)
    at org.janelia.saalfeldlab.n5.ij.N5Importer$N5ViewerReaderFun.apply(N5Importer.java:672)
    at org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog.openContainer(DatasetSelectorDialog.java:548)
    at org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog.openContainer(DatasetSelectorDialog.java:527)
    at org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog.lambda$run$2(DatasetSelectorDialog.java:309)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
    at javax.swing.AbstractButton$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)
bogovicj commented 2 years ago

Thanks @jingxlim, What is the contents of your .zattrs? Is it empty?

jingxuanlim commented 2 years ago

It's currently empty.

$ cat .zattrs
{}
bogovicj commented 6 months ago

A new release should fix this issue:

ZarrKeyValueReader zarr = (ZarrKeyValueReader)new N5Factory().openReader("mri-test.zarr");
ZArrayAttributes a = zarr.getZArrayAttributes("a");
System.out.println(a);

will no longer throw an exception.