Saving to OME-Zarr from virtual stack does not work

[oanegros]

I downloaded the most recent fiji version for windows 10, and was not able to save to OME-Zarr when opening a .tif as virtual stack.
With this:

• it makes the .zarr directory with .zgroup
• (sometimes) makes an s0 directory, and .zattrs

When loading the full stack into memory the OME-Zarr saving seems to work on this same dataset.

I'm not very adept with Fiji so never get how to get a good full log (without the '6 more ...') but i got this output:

(Fiji Is Just) ImageJ 2.16.0/1.54p; Java 1.8.0_322 [64-bit]; Windows 10 10.0; 5824MB of 195584MB (2%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
    at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:308)
    at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:160)
    at ij.IJ.runPlugIn(IJ.java)
    at ij.Executer.runCommand(Executer.java:152)
    at ij.Executer.run(Executer.java:70)
    at java.lang.Thread.run(Thread.java:750)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
    at java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.util.concurrent.FutureTask.get(FutureTask.java:192)
    at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:304)
    ... 5 more
Caused by: java.lang.RuntimeException: Module threw exception
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:128)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    ... 1 more
Caused by: java.lang.NullPointerException
    at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1334)
    at loci.formats.FormatReader.setSeries(FormatReader.java:972)
    at loci.formats.DelegateReader.setSeries(DelegateReader.java:123)
    at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:407)
    at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:407)
    at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:407)
    at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:407)
    at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:407)
    at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:407)
    at loci.plugins.util.BFVirtualStack.getProcessor(BFVirtualStack.java:159)
    at net.imglib2.img.imageplus.ByteImagePlus.<init>(ByteImagePlus.java:98)
    at net.imglib2.img.ImagePlusAdapter.wrapByte(ImagePlusAdapter.java:157)
    at net.imglib2.img.ImagePlusAdapter.wrapLocal(ImagePlusAdapter.java:101)
    at net.imglib2.img.ImagePlusAdapter.wrap(ImagePlusAdapter.java:75)
    at net.imglib2.img.display.imagej.ImageJFunctions.wrap(ImageJFunctions.java:94)
    at org.janelia.saalfeldlab.n5.metadata.imagej.ImageplusMetadata.datasetAttributes(ImageplusMetadata.java:77)
    at org.janelia.saalfeldlab.n5.metadata.imagej.NgffToImagePlus.readMetadata(NgffToImagePlus.java:153)
    at org.janelia.saalfeldlab.n5.metadata.imagej.NgffToImagePlus.readMetadata(NgffToImagePlus.java:15)
    at org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter.initializeBaseMetadata(N5ScalePyramidExporter.java:647)
    at org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter.processMultiscale(N5ScalePyramidExporter.java:549)
    at org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter.run(N5ScalePyramidExporter.java:1494)
    at org.scijava.command.CommandModule.run(CommandModule.java:196)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
    ... 6 more

Please let me know if you need more info :)

[oanegros]

I'm also having other virtual stacking issues on this machine for some reason, even with this fresh fiji install, so it might also be something else? Can you all reproduce this?

[bogovicj]

Thanks @oanegros ,

So far, I have not been able to reproduce this so far (i.e. saving a virtual stack worked for me as expected).

This part

Caused by: java.lang.NullPointerException
    at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1334)
    at loci.formats.FormatReader.setSeries(FormatReader.java:972)
...
    at loci.plugins.util.BFVirtualStack.getProcessor(BFVirtualStack.java:159)

is suggestive that its a bio formats thing.
So my follow up questions:

• what kind of file are you opening?
• how are you using fiji to open it?

[oanegros]

Ah okay; i was opening an imagej-tif made from fiji itself, using the bioformats importer with virtual stack on

[bogovicj]

thanks, I'll investigate