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Bug 1167 - grid stitching seems broken
grid stitching seems broken
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-09-30 16:58 CDT by vbindoka
Modified: 2015-10-13 10:32 CDT
2 users (show)

See Also:

Description vbindoka 2015-09-30 16:58:37 CDT
tried and true stitiching macro quit working today.
err console reports:
There was a problem with the class net.imglib2.view.Views which can be found here:
/E:/SEP201~1/jars/imglib2-2.0.0-beta-26.jar
java.lang.NoSuchMethodError: net.imglib2.view.Views.extendMirrorSingle(Lnet/imglib2/RandomAccessibleInterval;)Lnet/imglib2/view/ExtendedRandomAccessibleInterval;
	at mpicbg.stitching.fusion.ImageInterpolation.<init>(ImageInterpolation.java:29)
	at mpicbg.stitching.fusion.Fusion.fuse(Fusion.java:154)
	at plugin.Stitching_Grid.run(Stitching_Grid.java:601)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.Executer.runCommand(Executer.java:132)
	at ij.Executer.run(Executer.java:65)
	at java.lang.Thread.run(Thread.java:662)

java.lang.NoSuchMethodException: Could not find method net.imglib2.view.Views.extendMirrorSingle(Lnet/imglib2/RandomAccessibleInterval;)Lnet/imglib2/view/ExtendedRandomAccessibleInterval;
There was a problem with the class net.imglib2.view.Views which can be found here:
/E:/SEP201~1/jars/imglib2-2.0.0-beta-26.jar
java.lang.NoSuchMethodError: net.imglib2.view.Views.extendMirrorSingle(Lnet/imglib2/RandomAccessibleInterval;)Lnet/imglib2/view/ExtendedRandomAccessibleInterval;
	at mpicbg.stitching.fusion.ImageInterpolation.<init>(ImageInterpolation.java:29)
	at mpicbg.stitching.fusion.Fusion.fuse(Fusion.java:154)
	at plugin.Stitching_Grid.run(Stitching_Grid.java:601)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.Executer.runCommand(Executer.java:132)
	at ij.Executer.run(Executer.java:65)
	at java.lang.Thread.run(Thread.java:662)

	at mpicbg.stitching.fusion.ImageInterpolation.<init>(ImageInterpolation.java:29)
	at mpicbg.stitching.fusion.Fusion.fuse(Fusion.java:154)
	at plugin.Stitching_Grid.run(Stitching_Grid.java:601)
	at ij.IJ.runUserPlugIn(IJ.java:212)
	at ij.IJ.runPlugIn(IJ.java:176)
	at ij.Executer.runCommand(Executer.java:132)
	at ij.Executer.run(Executer.java:65)
	at java.lang.Thread.run(Thread.java:662)

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: E:\SEP201~1/java/win64/jdk1.6.0_24//jre
  imagej.dir => E:\SEP201~1

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150915084157)
Fiji: http://update.fiji.sc/ (last check:20150928080247)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20150914000333)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150929202643)
ClearVolume: http://sites.imagej.net/ClearVolume/ (last check:20150703051607)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606102449)
GDSC-SMLM: http://sites.imagej.net/GDSC-SMLM/ (last check:20150327072750)
HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214064119)
LLTT: http://sites.imagej.net/Alex-krull/ (last check:20141018111721)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723095558)
MS-ECS-2D: http://sites.imagej.net/MS-ECS-2D/ (last check:20150821142350)
Stowers: http://research.stowers.org/imagejplugins/updates/ (last check:20150929093505)

Files not up-to-date:
  6d337b7a (LOCAL_ONLY) 20140730142734 plugins/Accurate_Gaussian_Blur.class
  6e9d50db (LOCAL_ONLY) 20140320051924 plugins/Adjustable_Watershed.class
  306ad943 (LOCAL_ONLY) 20150721115948 plugins/Align3_TP.jar
  12ec0761 (LOCAL_ONLY) 20120224100622 plugins/Align_RGB_planes.class
  f98ce4f3 (LOCAL_ONLY) 20150721120238 plugins/Auto_Align_2.jar
  b0398adb (LOCAL_ONLY) 20141028073350 plugins/DeconvolutionLab/DeconvolutionLab_.jar
  11326750 (LOCAL_ONLY) 20050408103628 plugins/FFT1D.class
  18f23277 (LOCAL_ONLY) 20050408103628 plugins/FourierSpace.class
  44693e65 (LOCAL_ONLY) 20150325121214 plugins/Frac_Lac.jar
  348da731 (LOCAL_ONLY) 20141126044659 plugins/GHT_.jar
  15a0aac2 (LOCAL_ONLY) 20050408150536 plugins/GibsonPSF.class
  52861b7c (LOCAL_ONLY) 20050408150244 plugins/GibsonPSFF.class
  f481dc68 (LOCAL_ONLY) 20120817074900 plugins/Hybrid_2D_Filters.class
  6b2de3e5 (LOCAL_ONLY) 20120817084143 plugins/Hybrid_3D_Filters.class
  e9cb6eb7 (LOCAL_ONLY) 20150115083713 plugins/Image_CorrelationJ_1o.class
  077159f3 (LOCAL_ONLY) 20150716125422 plugins/Image_Stabilizer.class
  55624188 (LOCAL_ONLY) 20150716125430 plugins/Image_Stabilizer_Log_Applier.class
  71ae5c42 (LOCAL_ONLY) 20140509130342 plugins/KalmanOpenStackFilter_.class
  d0d470a1 (LOCAL_ONLY) 20150910042624 plugins/MIST_.jar
  53c5c1ad (LOCAL_ONLY) 20141103073745 plugins/NL_Means_.jar
  21927175 (LOCAL_ONLY) 20140808090713 plugins/PIV_.jar
  b3b13b1f (LOCAL_ONLY) 20050408150244 plugins/PSFCredits$1.class
  cb99705d (LOCAL_ONLY) 20050408150244 plugins/PSFCredits.class
  de90b917 (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG$1.class
  e33950eb (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG.class
  9f2412ff (LOCAL_ONLY) 20141028082626 plugins/PSF_Generator.jar
  5a3abd78 (LOCAL_ONLY) 20050408150536 plugins/PSF_Gibson_.class
  65b190f7 (LOCAL_ONLY) 20121002063426 plugins/PSF_Simple_.class
  12289f6e (LOCAL_ONLY) 20110916093010 plugins/PureDenoise_.jar
  2d4a0cba (LOCAL_ONLY) 20150918081935 plugins/Thunder_STORM.jar
  69b16199 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4.class
  f0990b22 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4Filter.class
  27901023 (LOCAL_ONLY) 20050408152652 plugins/Wavelet_Deconvolution_.class
  71331805 (LOCAL_ONLY) 20140314082430 plugins/jacop_.jar
  9bbfb280 (LOCAL_ONLY) 20140225135257 plugins/octane2_.jar
Comment 1 Curtis Rueden 2015-10-13 10:32:36 CDT
You have several update sites enabled. The "NoSuchMethodError" indicates that one (or more) of them is shipping an old version of the core ImgLib2 library. This situation is known as "version skew". See:

  http://imagej.net/Troubleshooting#NoSuchMethodError_or_NoClassDefFoundError

The problem in this case is the Alex-krull update site. Try disabling it.

If you need the functionality available from that update site, you can keep a separate copy of ImageJ with just that one update site enabled, and launch it separately as needed.

You may also want to contact him via email about the problem, and ask him to stop shadowing these old versions of core ImageJ libraries:

  http://imagej.net/User:Alex-krull