Big Warp on HDF5 files

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bigdataviewer
bigwarp
#1

Is there a way to use Big Warp on images that have been exported as the BigDataViewer hdf5/xml file format? I can open the files well in BigDataViewer, but cannot perform Big Warp on the images (it looks for open images and doesn’t find any since they aren’t ImageJ proper windows).

The reason I am trying to do this is that I am encountering the following error when trying to warp tif files that are opened through imageJ proper:

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52n; Java 1.8.0_66 [64-bit]; Mac OS X 10.13.6; 68210MB of 88889MB (76%)
 
java.lang.ArrayIndexOutOfBoundsException: 3
	at bigwarp.BigWarpInit.namesFromImagePluses(BigWarpInit.java:513)
	at bigwarp.BigWarpInit.createBigWarpDataFromImages(BigWarpInit.java:406)
	at bdv.ij.BigWarpImagePlusPlugIn.run(BigWarpImagePlusPlugIn.java:82)
	at ij.IJ.runUserPlugIn(IJ.java:229)
	at ij.IJ.runPlugIn(IJ.java:193)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)

When I try this with just one of the channels from each image I don’t have any trouble with Big Warp so this seems to be a size issue. Thanks for any advice!

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#2

@boonepeter,

Thanks for reporting this, I’ve been dealing with little bugs here and there in prep for the next release of bigwarp. Would you mind trying the latest version and reporting back?

Just replace the bigwarp jar in your Fiji plugins folder with this one.

It is possible to open xml / h5 files, but I’ll answer than in another post in a moment…
John

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#3

Thanks @bogovicj! Trying the same exact thing but with your updated bigwarp worked. Keep me posted on the xml/h5…haven’t been able to find that info anywhere.

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#4

@boonepeter,

Awesome, thanks for trying that.

That’s my bad, there’s been a bit less need for that, so my work on that front has been limited…

You can use this script to open xml / h5 files with bigwarp.

  • Download the script
  • Open it with the fiji script editor (drag / drop into fiji works).
  • Change line 48 to point to your xml file.
  • Click Run and it will open the active image (moving) and the xml/h5 (as fixed).

John

Edit:
Below are how to modify that script to deal with different image / xml and moving / fixed combinations…

// to open two xml/h5's, change line 55 to:
data = BigWarpInit.createBigWarpDataFromXML( movingXml, fixedXml );

// to open with an xml as moving and current image as target
data = BigWarpInit.createBigWarpDataFromXMLImagePlus( movingXml, IJ.getImage() );

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#5

Thanks a lot! I will check that out soon.

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#6

Hey just to follow up and maybe clarify, when I go to use big warp on tiff files I get the warning log:

WARNING:
Opening <SpimData> dataset that is not suited for interactive browsing.
Consider resaving as HDF5 for better performance.

It would be nice if big warp made it easy to open HDF5 files to deal with that message.

Really not that big of an issue, and I really appreciate all of the work you have put into it. It has worked well for my needs!

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