Link to existing OME-Zarr images in Fiji project creator

[tischi]

@K-Meech

You had:

            gd.addMessage( "Note: You can only 'link' to images outside the project folder \n" +
                    " for local projects. 'copy' or 'move' if you wish to upload to s3" );

I don't see why one could not link to OME-Zarr from and to S3? In fact, I would think in the future it could be a major use-case to link to OME-Zarr hosted on S3 at the BioImage Archive.

[tischi]

Same question here:

            if ( imageDataFormat == ImageDataFormat.OmeZarr && addMethod == ProjectCreator.AddMethod.link )
            {
                IJ.log( "link is currently unsupported for ome-zarr. Please choose copy or move instead for this file format." );
                return;
            }

Why is that? We could just store the absolutePath to the linked OME-Zarr; I don't see the problem....

[K-Meech]

            gd.addMessage( "Note: You can only 'link' to images outside the project folder \n" +
                    " for local projects. 'copy' or 'move' if you wish to upload to s3" );

This message was about people linking to images stored on the filesystem outside of their project. It's useful to be able to do this so people don't have to copy large images around when they just want to view their mobie project locally. The issue is that when this project is then uploaded to S3, these links will break and the images will no longer be available.

I agree - it should be possible to link to ome-zarr images that are already hosted on S3. This just hasn't been implemented yet, and would need to be some kind of new option.

            if ( imageDataFormat == ImageDataFormat.OmeZarr && addMethod == ProjectCreator.AddMethod.link )
            {
                IJ.log( "link is currently unsupported for ome-zarr. Please choose copy or move instead for this file format." );
                return;
            }

For this one, it's just that this hasn't been implemented yet. So far all linking has been done by placing an XML file inside the MoBIE project that internally contains a link to the position of the file elsewhere on the filesystem. I agree that using absolute path is probably a better way to do this - and would mean that n5 + ome-zarr could be handled in the same way.

[tischi]

@K-Meech would you have some time to look into the new-n5 branch to see how we could add support linking to existing OME-Zarr datasets in the ProjectCreator via the absolute path mechanism?

[K-Meech]

@tischi I probably wouldn't have time until next week or the week after. Do you need it done before then?

[tischi]

There is no deadline for any of the issues that I posted today; I just had time travelling to work on this. Maybe you could check the issues once you have time and if you feel like working on something you can do it. In case I will do something I will try to keep the issues up to date such that we don't both work on the same thing.

[tischi]

The ImagesCreatorTests are running now, but:

//    @Test
//    void linkImage() throws IOException {
//        testLinkingImages( false );
//    }

...this needs work and is thus commented out for now.

[tischi]

Hi @K-Meech, little ping :-)

And please use the new-n5-merge-main branch.

[K-Meech]

Sorry for the delay in getting back to you @tischi ! I should have time to take a look at this next week.

[K-Meech]

@tischi I'm starting to look into this, but I'm having trouble getting it to build. Just to check, you're using:

• new-n5-merge-main branch of this repo
• new-n5 branch of mobie-io
• master branch of imagej-utils

[tischi]

Yes, that's correct.

[K-Meech]

Thanks @tischi - I'm getting cannot find symbol from this line in MOBIE.java. I couldn't see the corresponding method in ImageDataFormat on that branch of mobie-io?

[tischi]

@K-Meech

Could you please pull everything again and re-built?

[K-Meech]

Thanks @tischi - everything builds now.

[K-Meech]

@tischi I couldn't find absolutePath in the current mobie schema. Can the absolute path be a file path or a remote S3 link? Do you have an example of a project that uses it?

[tischi]

You are right, we would need to discuss this.

I will sent a mail around.

[tischi]

Hmm, I have it in the Java code, though:

public class StorageLocation
{
    // for data on disk:
    // either
    public String relativePath;
    // or
    public String absolutePath;

    // for data on s3:
    public String s3Address;
    public String signingRegion;

My proposal would be adding a new way of referring to the storage location, called uri, which would combine all of those: relativePath, absolutePath, and s3Address. Relative paths would be discovered by the uri starting with a ., e.g. ./image_data/image.tiff. S3 locations would be discovered by the http and s3 in the address.

[K-Meech]

In the spec there's currently two different ways of specifying ome-zarr files: ome.zarr with a relativePath, and ome.zarr.s3 with an s3address. To keep compatibility with previous mobie projects it might be easier to just add an absolutePath option to ome.zarr which has to be a file path?

For the project creator, you could then have three options for adding images: adding the currently open image from imageJ, adding an ome-zarr file from the file system (link or copy, using absolute or relative path), then adding an ome-zarr file from s3 (where you can type in the s3 path)?

[tischi]

adding an ome-zarr file from the file system (link or copy, using absolute or relative path), then adding an ome-zarr file from s3 (where you can type in the s3 path)

We can still keep those separate on the UI level, but internally we could use uri for both.

OK, but what I think you could do right now is to implement what you proposed, because it should just work, given the current code in MoBIE.class:

    public synchronized String getImageLocation( ImageDataFormat imageDataFormat, StorageLocation storageLocation )
    {
        switch (imageDataFormat) {
            case OpenOrganelleS3:
            case OmeZarrS3:
                if ( storageLocation.s3Address != null )
                    return storageLocation.s3Address;
                else
                    return storageLocation.absolutePath; // works now, too
            default:
                if ( storageLocation.absolutePath != null  )
                    return storageLocation.absolutePath;
                else
                    return combinePath( imageRoot, dataset.getName(), storageLocation.relativePath );
        }
    }

Could you please try this?

We can then, as a second step, discuss what we do on the spec level, where absolutePath simply seems to be missing...?!

[K-Meech]

Ok - sounds good! I should hopefully have time to look at this tomorrow.

[normanrz]

Fwiw, in OME-Zarr this attribute is called path.

[tischi]

I was trying to anticipate the collection spec, where I think you proposed uri...

[normanrz]

I initially had uri but then switched to path because that is also used in the multiscale metadata.

[K-Meech]

@tischi I'm trying to get linking images to work, but having issues reading/writing ome-zarr with the current code in the project creator. For example, running:

void testZarrReadWrite() {
        ImagePlus imp = IJ.createImage( "test", "8-bit noise", 186, 226, 27 );
        String filePath = "C:\\Users\\kimme\\Documents\\Temp\\test.ome.zarr";
        OMEZarrWriter.write( imp, filePath, OMEZarrWriter.ImageType.Intensities, true );
        ImageData< ? > imageData = ImageDataOpener.open( filePath );
        int numSetups = imageData.getNumDatasets();
    }

throws a bunch of errors:

N5ImageData: Error opening C:\Users\kimme\Documents\Temp\test.ome.zarr
java.lang.NullPointerException
    at org.janelia.saalfeldlab.n5.bdv.N5Viewer.buildN5Sources(N5Viewer.java:522)
    at org.janelia.saalfeldlab.n5.bdv.N5Viewer.buildN5Sources(N5Viewer.java:497)
    at org.embl.mobie.io.imagedata.N5ImageData.open(N5ImageData.java:153)
    at org.embl.mobie.io.imagedata.N5ImageData.getNumDatasets(N5ImageData.java:88)
    at org.embl.mobie.lib.create.ImagesCreatorTest.testZarrReadWrite(ImagesCreatorTest.java:248)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:628)
    at org.junit.jupiter.engine.execution.ExecutableInvoker.invoke(ExecutableInvoker.java:117)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:184)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:180)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:127)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:68)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$5(NodeTestTask.java:135)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$7(NodeTestTask.java:125)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:135)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:123)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:122)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:80)
    at java.util.ArrayList.forEach(ArrayList.java:1259)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:38)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$5(NodeTestTask.java:139)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$7(NodeTestTask.java:125)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:135)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:123)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:122)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:80)
    at java.util.ArrayList.forEach(ArrayList.java:1259)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:38)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$5(NodeTestTask.java:139)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$7(NodeTestTask.java:125)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:135)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:123)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:122)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:80)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:32)
    at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57)
    at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:51)
    at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:229)
    at org.junit.platform.launcher.core.DefaultLauncher.lambda$execute$6(DefaultLauncher.java:197)
    at org.junit.platform.launcher.core.DefaultLauncher.withInterceptedStreams(DefaultLauncher.java:211)
    at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:191)
    at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:128)
    at com.intellij.junit5.JUnit5IdeaTestRunner.startRunnerWithArgs(JUnit5IdeaTestRunner.java:57)
    at com.intellij.rt.junit.IdeaTestRunner$Repeater$1.execute(IdeaTestRunner.java:38)
    at com.intellij.rt.execution.junit.TestsRepeater.repeat(TestsRepeater.java:11)
    at com.intellij.rt.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:35)
    at com.intellij.rt.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:232)
    at com.intellij.rt.junit.JUnitStarter.main(JUnitStarter.java:55)

java.lang.RuntimeException: java.lang.NullPointerException

    at org.embl.mobie.io.imagedata.N5ImageData.open(N5ImageData.java:168)
    at org.embl.mobie.io.imagedata.N5ImageData.getNumDatasets(N5ImageData.java:88)
    at org.embl.mobie.lib.create.ImagesCreatorTest.testZarrReadWrite(ImagesCreatorTest.java:248)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:628)
    at org.junit.jupiter.engine.execution.ExecutableInvoker.invoke(ExecutableInvoker.java:117)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:184)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:180)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:127)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:68)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$5(NodeTestTask.java:135)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$7(NodeTestTask.java:125)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:135)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:123)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:122)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:80)
    at java.util.ArrayList.forEach(ArrayList.java:1259)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:38)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$5(NodeTestTask.java:139)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$7(NodeTestTask.java:125)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:135)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:123)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:122)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:80)
    at java.util.ArrayList.forEach(ArrayList.java:1259)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:38)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$5(NodeTestTask.java:139)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$7(NodeTestTask.java:125)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:135)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:123)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:122)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:80)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:32)
    at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57)
    at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:51)
    at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:229)
    at org.junit.platform.launcher.core.DefaultLauncher.lambda$execute$6(DefaultLauncher.java:197)
    at org.junit.platform.launcher.core.DefaultLauncher.withInterceptedStreams(DefaultLauncher.java:211)
    at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:191)
    at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:128)
    at com.intellij.junit5.JUnit5IdeaTestRunner.startRunnerWithArgs(JUnit5IdeaTestRunner.java:57)
    at com.intellij.rt.junit.IdeaTestRunner$Repeater$1.execute(IdeaTestRunner.java:38)
    at com.intellij.rt.execution.junit.TestsRepeater.repeat(TestsRepeater.java:11)
    at com.intellij.rt.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:35)
    at com.intellij.rt.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:232)
    at com.intellij.rt.junit.JUnitStarter.main(JUnitStarter.java:55)
Caused by: java.lang.NullPointerException
    at org.janelia.saalfeldlab.n5.bdv.N5Viewer.buildN5Sources(N5Viewer.java:522)
    at org.janelia.saalfeldlab.n5.bdv.N5Viewer.buildN5Sources(N5Viewer.java:497)
    at org.embl.mobie.io.imagedata.N5ImageData.open(N5ImageData.java:153)
    ... 55 more

Does the same happen on your system? Potentially it's windows specific.

[tischi]

Hi @K-Meech,

I added an OMEZarrWriterTest to mobie-io and that works for me...

If you pull that and run the test, does it work for you?

If not, we 'd probably need to ask the Janelia folks...

[K-Meech]

Thanks @tischi - I just tried and this test fails on my Windows 11 computer. The ome-zarr file is written successfully, but can't be opened again:

N5ImageData: Error opening src/test/tmp/test.zarr
java.lang.NullPointerException
    at org.janelia.saalfeldlab.n5.bdv.N5Viewer.buildN5Sources(N5Viewer.java:522)
    at org.janelia.saalfeldlab.n5.bdv.N5Viewer.buildN5Sources(N5Viewer.java:497)
    at org.embl.mobie.io.imagedata.N5ImageData.open(N5ImageData.java:153)
    at org.embl.mobie.io.imagedata.N5ImageData.getSourcePair(N5ImageData.java:70)
    at org.embl.mobie.io.OMEZarrWriterTest.writeAndReadOMEZarr(OMEZarrWriterTest.java:25)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:727)
    at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60)
    at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131)
    at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156)
    at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147)
    at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86)
    at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103)
    at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93)
    at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106)
    at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64)
    at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45)
    at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37)
    at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92)
    at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:217)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:213)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:138)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:68)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95)
    at java.util.ArrayList.forEach(ArrayList.java:1259)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95)
    at java.util.ArrayList.forEach(ArrayList.java:1259)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35)
    at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57)
    at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:147)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:127)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:90)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:55)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:102)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:54)
    at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:114)
    at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:86)
    at org.junit.platform.launcher.core.DefaultLauncherSession$DelegatingLauncher.execute(DefaultLauncherSession.java:86)
    at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:53)
    at com.intellij.junit5.JUnit5IdeaTestRunner.startRunnerWithArgs(JUnit5IdeaTestRunner.java:57)
    at com.intellij.rt.junit.IdeaTestRunner$Repeater$1.execute(IdeaTestRunner.java:38)
    at com.intellij.rt.execution.junit.TestsRepeater.repeat(TestsRepeater.java:11)
    at com.intellij.rt.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:35)
    at com.intellij.rt.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:232)
    at com.intellij.rt.junit.JUnitStarter.main(JUnitStarter.java:55)

java.lang.RuntimeException: java.lang.NullPointerException

    at org.embl.mobie.io.imagedata.N5ImageData.open(N5ImageData.java:168)
    at org.embl.mobie.io.imagedata.N5ImageData.getSourcePair(N5ImageData.java:70)
    at org.embl.mobie.io.OMEZarrWriterTest.writeAndReadOMEZarr(OMEZarrWriterTest.java:25)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:727)
    at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60)
    at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131)
    at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156)
    at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147)
    at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86)
    at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103)
    at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93)
    at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106)
    at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64)
    at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45)
    at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37)
    at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92)
    at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:217)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:213)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:138)
    at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:68)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95)
    at java.util.ArrayList.forEach(ArrayList.java:1259)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95)
    at java.util.ArrayList.forEach(ArrayList.java:1259)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141)
    at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139)
    at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138)
    at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95)
    at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35)
    at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57)
    at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:147)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:127)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:90)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:55)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:102)
    at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:54)
    at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:114)
    at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:86)
    at org.junit.platform.launcher.core.DefaultLauncherSession$DelegatingLauncher.execute(DefaultLauncherSession.java:86)
    at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:53)
    at com.intellij.junit5.JUnit5IdeaTestRunner.startRunnerWithArgs(JUnit5IdeaTestRunner.java:57)
    at com.intellij.rt.junit.IdeaTestRunner$Repeater$1.execute(IdeaTestRunner.java:38)
    at com.intellij.rt.execution.junit.TestsRepeater.repeat(TestsRepeater.java:11)
    at com.intellij.rt.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:35)
    at com.intellij.rt.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:232)
    at com.intellij.rt.junit.JUnitStarter.main(JUnitStarter.java:55)
Caused by: java.lang.NullPointerException
    at org.janelia.saalfeldlab.n5.bdv.N5Viewer.buildN5Sources(N5Viewer.java:522)
    at org.janelia.saalfeldlab.n5.bdv.N5Viewer.buildN5Sources(N5Viewer.java:497)
    at org.embl.mobie.io.imagedata.N5ImageData.open(N5ImageData.java:153)
    ... 72 more

[tischi]

Hi,

@k-dominik (on your Mac) and @constantinpape (on your Linux) could you please do us a favour and please try whether this works for you?

• git pull https://github.com/mobie/mobie-io.git
• git checkout new-n5
• mvn test

For Kimberly the OMEZarrWriter test fails, for me it works.

[k-dominik]

Seems to work for me:

[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.601 s -- in org.embl.mobie.io.OMEZarrWriterTest
[INFO]
[INFO] Results:
[INFO]
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  03:08 min
[INFO] Finished at: 2024-04-15T09:57:49+02:00
[INFO] ------------------------------------------------------------------------
╭─ ~/scratch/mobie-io  new-n5 ························································································ ✔  3m 15s  java   09:57:49
╰─ git log -1
commit 44fab8ace6b1a786eadb01b9787455025c6349eb (HEAD -> new-n5, origin/new-n5)
Author: Christian Tischer 
Date:   Fri Apr 12 23:18:09 2024 +0200

    Add OMEZarrWriterTest

[tischi]

@K-Meech would you mind asking for help here? https://imagesc.zulipchat.com/#narrow/stream/328251-NGFF

[K-Meech]

Done!

[k-dominik]

I've also confirmed an issue on windows 10, albeit a different one?

[ERROR] org.embl.mobie.io.imagedata.N5ImageDataTest.openOMEZarrFromEBIS3

``` [ERROR] org.embl.mobie.io.imagedata.N5ImageDataTest.openOMEZarrFromEBIS3 -- Time elapsed: 5.569 s <<< ERROR! java.lang.RuntimeException: java.lang.NullPointerException: Cannot invoke "org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata.getName()" because "metadata" is null at org.embl.mobie.io.imagedata.N5ImageData.open(N5ImageData.java:168) at org.embl.mobie.io.imagedata.N5ImageData.getSourcePair(N5ImageData.java:70) at org.embl.mobie.io.imagedata.N5ImageDataTest.openOMEZarrFromEBIS3(N5ImageDataTest.java:33) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:727) at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60) at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147) at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86) at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103) at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:217) at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:213) at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:138) at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:68) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:147) at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:127) at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:90) at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:55) at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:102) at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:54) at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:114) at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:86) at org.junit.platform.launcher.core.DefaultLauncherSession$DelegatingLauncher.execute(DefaultLauncherSession.java:86) at org.apache.maven.surefire.junitplatform.LazyLauncher.execute(LazyLauncher.java:56) at org.apache.maven.surefire.junitplatform.JUnitPlatformProvider.execute(JUnitPlatformProvider.java:184) at org.apache.maven.surefire.junitplatform.JUnitPlatformProvider.invokeAllTests(JUnitPlatformProvider.java:148) at org.apache.maven.surefire.junitplatform.JUnitPlatformProvider.invoke(JUnitPlatformProvider.java:122) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162) at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495) Caused by: java.lang.NullPointerException: Cannot invoke "org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata.getName()" because "metadata" is null at org.janelia.saalfeldlab.n5.bdv.N5Viewer.buildN5Sources(N5Viewer.java:522) at org.janelia.saalfeldlab.n5.bdv.N5Viewer.buildN5Sources(N5Viewer.java:497) at org.embl.mobie.io.imagedata.N5ImageData.open(N5ImageData.java:153) ... 71 more [INFO] Running org.embl.mobie.io.OMEZarrWriterTest 18:24:02.194 [pool-10-thread-3] DEBUG org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer - parsed metadata for: /s1: found: N5SingleScaleMetadata 18:24:02.194 [pool-10-thread-2] DEBUG org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer - parsed metadata for: /s0: found: N5SingleScaleMetadata 18:24:02.198 [main] DEBUG org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer - parsed metadata for: /: found: OmeNgffMetadata [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.653 s -- in org.embl.mobie.io.OMEZarrWriterTest [INFO] [INFO] Results: [INFO] [ERROR] Errors: [ERROR] N5ImageDataTest.openOMEZarrFromEBIS3:33 ┬╗ Runtime java.lang.NullPointerException: Cannot invoke "org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata.getName()" because "metadata" is null [INFO] [ERROR] Tests run: 9, Failures: 0, Errors: 1, Skipped: 0 ```

[constantinpape]

I tried on Ubuntu @tischi. I had to do a mvn clean install before the mvn test, but then everything seems to work.

[axtimwalde]

I traced the first two lines in the exception trace and the outcome is that selectedMetaData[i] must be null but set. The data comes from

org.embl.mobie.io.imagedata.N5ImageData.open(N5ImageData.java:153

Please follow up from here.

Reference with stream of thought https://imagesc.zulipchat.com/#narrow/stream/328251-NGFF/topic/Making.20it.20easy.20to.20read.20.2B.20write.20ome-zarr.20in.20Fiji

[tischi]

Thanks @axtimwalde for the analysis!

@K-Meech could you try the following on your Windows machine:

After this line of code: Running in debug mode, could you check what the group variable is? I wonder whether the "/" is wrong and should rather be File.separator..?

[K-Meech]

@tischi - I just checked and group is "/"

[tischi]

Time for a short zoom now?

[tischi]

Does it help if you change the code to:

String group = n5URI.getGroupPath() != null ? n5URI.getGroupPath() : File.separator;

?

[K-Meech]

Sorry @tischi - I'm just about to head out! Using File.separator didn't fix it unfortunately. Are you around on Friday? I could do a zoom call then?

[K-Meech]

Ok - so looking in to this more, it seems to be an issue with how the path inside datasets and multiscales is written in the top .zattrs file. For the ome-zarr file created in the test (which has two datasets s0 and s1), they are written as "path":"..\\..s0" and "path":"..\\..s1". Manually changing these to just "s0" and "s1" allows it to be opened correctly.

There are probably a number of places that contribute to this - but for example, canoncialPath gets called with parent of "" and child of ..\s0 and ends up returning /..s0

[tischi]

@K-Meech could you please try whether that also happens when you are using the Fiji UI:

You could run this macro, but just adapt the containerroot to point to a folder on your computer.

run("Blobs (25K)");
run("Scale...", "x=8 y=8 width=2048 height=2032 interpolation=Bilinear average create");
run("HDF5/N5/Zarr/OME-NGFF ...", "containerroot=/Users/tischer/Desktop dataset=image storageformat=Zarr chunksizearg=100 createpyramidifpossible=true downsamplemethod=Sample compressionarg=gzip metadatastyle=OME-NGFF nthreads=1 overwrite=true");

[K-Meech]

@tischi The same doesn't happen in Fiji. Running this macro writes the image successfully with paths like "path":"s0" in the .zattrs file

[tischi]

Ha, that's interesting...then we need to look into the OME-Zarr writing code in mobie-io and n5-viewer and find the difference. I will have a look right now, however due to lack of access to a Windows computer I can only do educated guessing. So, if you could also have a look that would be ❤️ !

[tischi]

@K-Meech could you please try whether it makes a different if you put a non-empty string here?

For instance, replace that line with String n5Dataset = "image";...

---

Along similar lines, could you please also test writing an image from the Fiji GUI and then leaving the dataset empty (instead of "image")?

In fact I don't know how to do this in the macro.....?

run("Blobs (25K)");
run("Scale...", "x=8 y=8 width=2048 height=2032 interpolation=Bilinear average create");
run("HDF5/N5/Zarr/OME-NGFF ...", "containerroot=/Users/tischer/Desktop dataset=???? storageformat=Zarr chunksizearg=100 createpyramidifpossible=true downsamplemethod=Sample compressionarg=gzip metadatastyle=OME-NGFF nthreads=1 overwrite=true");

[K-Meech]

@tischi - yes, changing n5Dataset to a non-empty string fixes the paths (now "path":"s0" etc). It couldn't then open it from the test though, I guess because the location is now "src/test/tmp/test.zarr/image"

[tischi]

And what happens if you put an empty string into the Fiji UI and save it there?

[K-Meech]

If the dataset is empty in Fiji, then it writes an ome-zarr with wrong paths again "path":"..\\..s0"

[axtimwalde]

containerroot=/Users/tischer/Desktop means that /Users/tischer/Desktop is your Zarr container. This works but is likely not what you want. dataset being empty creating ..\\..s0 would be a bug. @bogovicj will have a look.

[bogovicj]

I'm testing this now, but it will be tricky (for me right now) because I'm not on a windows machine, and @cmhulbert has an idea of what's causing this.

A side comment: overwrite=true is pretty dangerous especially if the containing you're writing into is your desktop. (It will delete any folders that it will write into)

p.s. thanks for identifying this issue

[tischi]

A side comment: overwrite=true is pretty dangerous especially if the containing you're writing into is your desktop. (It will delete any folders that it will write into)

Oh wow...thanks for letting me know!

[bogovicj]

This issue on windows might be (probably is?) fixed by the latest n5-universe (1.4.3-SNAPSHOT). I made a test that was failing on the windows build but not the ubuntu build that now works for both (see this PR.

@K-Meech , if you have a chance to try it, please let me know if it behaves better

[K-Meech]

All tests pass on Windows now - thanks @bogovicj ! The paths are written correctly now like "path":"s0"