search

PreibischLab / BigStitcher

ImgLib2/BDV implementation of Stitching for large datasets
GNU General Public License v2.0
68 stars 15 forks source link

java.lang.NoClassDefFoundError: net/imglib2/converter/BiConverter #78

Open lacan opened 4 years ago

lacan commented 4 years ago

In an Up-To-Date Fiji the following error occurs when running Interest Point Detection

Exception in thread "Thread-10740" java.lang.NoClassDefFoundError: net/imglib2/converter/BiConverter
    at net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoG.addInterestPoints(DoG.java:159)
    at net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI.findInterestPoints(DifferenceOfGaussianGUI.java:143)
    at net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection.detectInterestPoints(Interest_Point_Detection.java:215)
    at net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection.detectInterestPoints(Interest_Point_Detection.java:109)
    at net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DetectInterestPointsPopup$MyActionListener$1.run(DetectInterestPointsPopup.java:87)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: net.imglib2.converter.BiConverter
    at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 6 more

Probably linked to the big update to Fiji that happened recently?

Best

Oli

lacan commented 4 years ago

Hmmm, this actually is linked to a difference in dependencies between BDV Playground and BigStitcher actually. Disabling BDV Playground fixes the issue, but it's not an ideal solution.... https://github.com/bigdataviewer/bigdataviewer-playground

StephanPreibisch commented 4 years ago

Hi, that means that bigdataviewer-playground uses an older version of imglib2-core than the main Fiji distribution (I assume 5.9.0). It should not use an older version than is shipped with the main Fiji. Who could fix that?

pdd2110 commented 3 years ago

Hi, I was getting this same error yesterday running Interest Point Detection. I did a complete reinstall of FIJI and now am getting this:

[ERROR] java.lang.NoSuchMethodException: Could not find method net.imglib2.cache.img.ReadOnlyCachedCellImgOptions.cellDimensions([I)Ljava/lang/Object; There was a problem with the class net.imglib2.cache.img.ReadOnlyCachedCellImgOptions which can be found here: /G:/[User]/Fiji.app/jars/imglib2-cache-1.0.0-beta-13.jar java.lang.NoSuchMethodError: net.imglib2.cache.img.ReadOnlyCachedCellImgOptions.cellDimensions([I)Ljava/lang/Object; at net.preibisch.mvrecon.process.fusion.FusionTools.cacheRandomAccessibleInterval(FusionTools.java:713) at net.preibisch.mvrecon.process.fusion.FusionTools.cacheRandomAccessibleInterval(FusionTools.java:692) at net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2.computeDoG(DoGImgLib2.java:249) at net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2.computeDoG(DoGImgLib2.java:139) at net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoG.addInterestPoints(DoG.java:163) at net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI.findInterestPoints(DifferenceOfGaussianGUI.java:143) at net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection.detectInterestPoints(Interest_Point_Detection.java:215) at net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection.run(Interest_Point_Detection.java:90) at ij.IJ.runUserPlugIn(IJ.java:241) at ij.IJ.runPlugIn(IJ.java:204) at ij.Executer.runCommand(Executer.java:151) at ij.Executer.run(Executer.java:69) at java.lang.Thread.run(Thread.java:748)

at net.preibisch.mvrecon.process.fusion.FusionTools.cacheRandomAccessibleInterval(FusionTools.java:713) at net.preibisch.mvrecon.process.fusion.FusionTools.cacheRandomAccessibleInterval(FusionTools.java:692) at net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2.computeDoG(DoGImgLib2.java:249) at net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2.computeDoG(DoGImgLib2.java:139) at net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoG.addInterestPoints(DoG.java:163) at net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI.findInterestPoints(DifferenceOfGaussianGUI.java:143) at net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection.detectInterestPoints(Interest_Point_Detection.java:215) at net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection.run(Interest_Point_Detection.java:90) at ij.IJ.runUserPlugIn(IJ.java:241) at ij.IJ.runPlugIn(IJ.java:204) at ij.Executer.runCommand(Executer.java:151) at ij.Executer.run(Executer.java:69) at java.lang.Thread.run(Thread.java:748)

In case its helpful at all, here is the log window:

Using spimdata version: 0.9-revision Using multiview-reconstruction version: 0.10.2 angles selected: 0 channels selected: tdTom-T1, AF488-T2, AF405-T3, AF647-T3 illuminations selected: 0 tiles selected: 0 Timepoints selected: 0 (Tue Mar 30 11:49:45 EDT 2021): Opening and downsampling ... (Tue Mar 30 11:49:45 EDT 2021): Requesting Img from ImgLoader (tp=0, setup=3), downsampling: (1, 1, 1) (Tue Mar 30 11:49:45 EDT 2021): Using precomputed Multiresolution Images [1x1x1], Remaining downsampling [1x1x1] (Tue Mar 30 11:49:49 EDT 2021): Wrapping ImagePlus around input image ... (Tue Mar 30 11:50:16 EDT 2021): Requesting Img from ImgLoader (tp=0, setup=0), downsampling: (1, 1, 1) (Tue Mar 30 11:50:16 EDT 2021): Using precomputed Multiresolution Images [1x1x1], Remaining downsampling [1x1x1] (Tue Mar 30 11:50:19 EDT 2021): min intensity = 144.0, max intensity = 65535.0 (Tue Mar 30 11:50:19 EDT 2021): computing DoG with (sigma=1.8015, threshold=0.007973356, sigma1=(1.7307230234146118, 1.7307230234146118, 1.7307230234146118), sigma2=(2.0831925868988037, 2.0831925868988037, 2.0831925868988037))

I get the same issue whether I call the function through BigStitcher or Multiview Reconstruction.

Unsure if its related, but when I open the xml file via Multiview Reconstruction Application I get the following error:

[ERROR] java.lang.NoSuchMethodException: Could not find method bdv.viewer.ViewerPanel.getDisplay()Lbdv/viewer/InteractiveDisplayCanvas; There was a problem with the class bdv.viewer.ViewerPanel which can be found here: /G:/[User]/Fiji.app/jars/bigdataviewer-core-9.0.6.jar java.lang.NoSuchMethodError: bdv.viewer.ViewerPanel.getDisplay()Lbdv/viewer/InteractiveDisplayCanvas; at net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup.initTransform(BDVPopup.java:341) at net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup.createBDV(BDVPopup.java:303) at net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel.(ViewSetupExplorerPanel.java:169) at net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer.(ViewSetupExplorer.java:47) at net.preibisch.mvrecon.fiji.plugin.Data_Explorer.run(Data_Explorer.java:76) at ij.IJ.runUserPlugIn(IJ.java:235) at ij.IJ.runPlugIn(IJ.java:198) at ij.Executer.runCommand(Executer.java:150) at ij.Executer.run(Executer.java:65) at java.lang.Thread.run(Thread.java:748)

at net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup.initTransform(BDVPopup.java:341) at net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup.createBDV(BDVPopup.java:303) at net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel.(ViewSetupExplorerPanel.java:169) at net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer.(ViewSetupExplorer.java:47) at net.preibisch.mvrecon.fiji.plugin.Data_Explorer.run(Data_Explorer.java:76) at ij.IJ.runUserPlugIn(IJ.java:235) at ij.IJ.runPlugIn(IJ.java:198) at ij.Executer.runCommand(Executer.java:150) at ij.Executer.run(Executer.java:65) at java.lang.Thread.run(Thread.java:748)

Any help is much appreciated!