BigWarp does not load XML / h5 files

Hello, I have two image stacks to warp and find corresponding points between, and would like to use an HDF5 representation to speed viewing and zooming. Stack 1 = serial EM data (~ 21 GB .h5) and stack 2 = 2 photon 2 channel data (~4 GB .h5). Original TIFF stacks were exported as XML/HDF5 using BigDataViewer. Also tried downsampling and cropping stacks to make smaller HDF5 files, but same errors occur. Machine has lots of RAM (128 GB)

I have re-installed and upgraded Fiji, and bigwarp is at the most recent version (5.0.0).

Also downloaded the BigWarp_ImagePlus_or_Xml.groovy script and tried to open the XMLs from there. Here are the errors I get:

Blockquote
[ERROR] java.lang.ArrayIndexOutOfBoundsException: 2
at bigwarp.BigWarpInit.wrapSourcesAsRenamable(BigWarpInit.java:490)
at bigwarp.BigWarpInit.createBigWarpData(BigWarpInit.java:472)
at bigwarp.BigWarpInit.createBigWarpData(BigWarpInit.java:598)
at bigwarp.BigWarpInit.createBigWarpDataFromXML(BigWarpInit.java:627)
at bigwarp.BigWarpInit$createBigWarpDataFromXML.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
at Script1.run(Script1.groovy:16)
at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:303)
at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:122)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

I’ve looked at solutions to @MariaZ’s issues

and @boonepeter (though this was solved with a newer bigwarp plugin, which I seem to have)

and other related topics, but I still get the errors. Thanks for any help.

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_202 [64-bit]; Windows 10

Hi @mtakeno,

Thanks for reporting this issue.

Idea 1

Can you try the newest (not yet in Fiji) bigwarp?

That should provide you a new Bigwarp option:
Plugins > BigDataViewer > Bigwarp XML/HDF5
that might behave better.

Idea 2

If that doesn’t work, there may just be a bug. :-/
Do your data xml/s have multiple channels? I’m not sure bigwarp handles that correctly.
If you describe your data in more detail, it’ll help me track down the issue.
Specifically, how big are your data in x,y,z,t,c. What is the data type. Anything else of note?

Thanks for reporting,
John

Hi John @bogovicj ,

Voila! Idea 1 (newest bigwarp 5.0.1 build) seems to work! Thank you.

About Idea 2 - one of the xml’s did have multiple channels (2 channels) but it does seem to open and allow brightness and color changes correctly with the new 5.0.1 build.

Thank you -
Marc

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