Update instructions for opening OME-Zarrs in BDV and MoBIE#33
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will-moore wants to merge 2 commits intoome:masterfrom
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Update instructions for opening OME-Zarrs in BDV and MoBIE#33will-moore wants to merge 2 commits intoome:masterfrom
will-moore wants to merge 2 commits intoome:masterfrom
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I've removed the Groovy script section as it's not working and I don't know where the script actually is or how to fix it. |
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@will-moore Confused. Do you claim that the script is
How do you know Ad 1. when Ad 2. applies ? |
pwalczysko
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Apr 16, 2025
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Please address comment, thank you
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I downloaded the script so that I could copy the text in it. |
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Error running the script is: |
pwalczysko
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Apr 16, 2025
| #. In the text field, enter the desired URL e.g. | ||
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| #. When the image is displayed in the BigDataViewer, select the dialog and press *P* to display the rendering controls. | ||
| ``https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr`` |
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This does not wfm.
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw error
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.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw error
at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:304)
... 5 more
Caused by: java.lang.RuntimeException: Module threw error
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:131)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
... 1 more
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https://github.com/ome/ome-ngff-tools/pull/26/files#diff-b4d68dc855d0f9476d3f2ee343853bd21bf82ea9960d0cf06661baa244439dd6R9 has the versions of BDV jars that I had when testing.
But otherwise I don't know how to troubleshoot that error.
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BDV? I am commenting on the MoBIE workflow...
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Sorry, yep. Don't know what's going on there. Works for me, with latest MoBIE jars:
$ ls /Applications/Fiji.app/jars | grep mobie
mobie-io-4.0.3.jar
mobie-viewer-fiji-6.3.3.jar
But, the error doesn't seem to come from MoBIE code.
pwalczysko
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Apr 16, 2025
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I have downloaded a fresh Fiji and run the MoBIE manual workflow on it. The same error occurred. |
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The Big Data Viewer workflow errors for me with |
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Update as part of ome/ome-ngff-tools#26
cc @pwalczysko