[ImageJ-bugs] [Bug 856] New: Phantom windows remain in windows list when none are open

bugzilla at fiji.sc bugzilla at fiji.sc
Tue Jul 15 17:03:31 CDT 2014 

http://fiji.sc/bugzilla/show_bug.cgi?id=856

            Bug ID: 856
           Summary: Phantom windows remain in windows list when none are
                    open
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: vbindoka at bsd.uchicago.edu
                CC: vbindoka at bsd.uchicago.edu

This test macro leave two windows called Mask in the WiINDOW listing when none
are present.
THe macro also illustrates a problem with creating binary masks from stacks--
fixed thresholds seem impossible.

run("Fluorescent Cells (400K)");
rename("countme");
run("Channels Tool...");
Stack.setDisplayMode("color");
setAutoThreshold("Otsu dark stack");
getThreshold(lower, upper);
for (i=1; i<=nSlices; i++){
    setSlice(i);
    setThreshold(lower, upper);
    run("Create Mask");
    selectWindow("mask");    //this name changes from mask to Mask at i>1 !
    run("Select All");
    run("Copy");
    wait(1111);
    run("Close");
    selectWindow("countme");
    run("Paste");
 }

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:\FEB201~1/java/win64/jdk1.6.0_24//jre
  imagej.dir => E:\FEB201~1

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140711170647)
Fiji: http://fiji.sc/update/ (last check:20140709153742)
Archipelago: http://sites.imagej.net/Lindsey/ (last check:20140409134334)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20140711202658)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140711035200)
OpenSPIM: http://openspim.org/update/ (last check:20140630085101)

Files not up-to-date:
  6e9d50db (LOCAL_ONLY) 20140320051924 plugins/Adjustable_Watershed.class
  12ec0761 (LOCAL_ONLY) 20120224100622 plugins/Align_RGB_planes.class
  55de57f2 (LOCAL_ONLY) 20050408121420 plugins/DecCredits$1.class
  66a64476 (LOCAL_ONLY) 20050408121420 plugins/DecCredits.class
  fd4ce3cd (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionFFT.class
  8d9bdfa0 (LOCAL_ONLY) 20090703162900
plugins/DeconvolutionLab/DeconvolutionLab_.jar
  8866a3cd (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionSolution.class
  ce989b93 (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionWavelets.class
  13072662 (LOCAL_ONLY) 20050408121420 plugins/Deconvolution_.class
  11326750 (LOCAL_ONLY) 20050408103628 plugins/FFT1D.class
  18f23277 (LOCAL_ONLY) 20050408103628 plugins/FourierSpace.class
  71b76f0a (LOCAL_ONLY) 20140702072831 plugins/Frac_Lac.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
  d27e0bc5 (LOCAL_ONLY) 20140501133448
plugins/Intensity_Correlation_Analysis2.class
  71ae5c42 (LOCAL_ONLY) 20140509130342 plugins/KalmanOpenStackFilter_.class
  44f1acfa (LOCAL_ONLY) 20121128135145 plugins/Mexican_Hat_Filter.class
  d84cc2bb (LOCAL_ONLY) 20121012091604 plugins/Morphology/Add_Borders.class
  5cccefae (LOCAL_ONLY) 20121012091606 plugins/Morphology/AnnularClosing.txt
  763870ef (LOCAL_ONLY) 20121012091604 plugins/Morphology/AnnularDilation.txt
  5d777e5e (LOCAL_ONLY) 20121012091604
plugins/Morphology/BinaryConditionalDilate_.class
  6cfae168 (LOCAL_ONLY) 20121012091606
plugins/Morphology/BinaryConditionalErode_.class
  877be8e6 (LOCAL_ONLY) 20121012091606
plugins/Morphology/BinaryConnectivity_.class
  ebe4d9b0 (LOCAL_ONLY) 20121012091606
plugins/Morphology/BinaryDilateNoMerge4_.class
  65b35fcd (LOCAL_ONLY) 20121012091606
plugins/Morphology/BinaryDilateNoMerge8_.class
  da5dc033 (LOCAL_ONLY) 20121012091604 plugins/Morphology/BinaryDilateTest.txt
  fe9208a2 (LOCAL_ONLY) 20121012091605 plugins/Morphology/BinaryDilate_.class
  9f2b4ef9 (LOCAL_ONLY) 20121012091604 plugins/Morphology/BinaryErodeTest.txt
  b38e2aa0 (LOCAL_ONLY) 20121012091605 plugins/Morphology/BinaryErode_.class
  3f39caaf (LOCAL_ONLY) 20121012091605
plugins/Morphology/BinaryFilterReconstruct.txt
  76eb6799 (LOCAL_ONLY) 20121012091605
plugins/Morphology/BinaryFilterReconstruct_.class
  6a2c8b7a (LOCAL_ONLY) 20121012091606
plugins/Morphology/BinaryGeodesicDilateNoMerge8_.class
  14c67860 (LOCAL_ONLY) 20121012091605
plugins/Morphology/BinaryHitOrMiss_.class
  33b507c2 (LOCAL_ONLY) 20121012091604
plugins/Morphology/BinaryKillBorders_.class
  4204c1c6 (LOCAL_ONLY) 20121012091606 plugins/Morphology/BinaryLabel8_.class
  d3c84f8c (LOCAL_ONLY) 20121012091606 plugins/Morphology/BinaryLabelMacro.txt
  59e1afe9 (LOCAL_ONLY) 20121012091606 plugins/Morphology/BinaryLabel_.class
  36e4a042 (LOCAL_ONLY) 20121012091605 plugins/Morphology/BinaryPrune.txt
  c8c66f92 (LOCAL_ONLY) 20121012091605
plugins/Morphology/BinaryReconstruct_.class
  3ff298c7 (LOCAL_ONLY) 20121012091606 plugins/Morphology/BinaryThick2_.class
  b73f68f4 (LOCAL_ONLY) 20121012091605 plugins/Morphology/BinaryThick_.class
  2c4c813e (LOCAL_ONLY) 20121012091606 plugins/Morphology/BinaryThin2_.class
  d8a5d664 (LOCAL_ONLY) 20121012091604 plugins/Morphology/BinaryThin_.class
  3e83cc61 (LOCAL_ONLY) 20121012091605 plugins/Morphology/Boundary4.txt
  9d64440e (LOCAL_ONLY) 20121012091604 plugins/Morphology/Boundary8_.txt
  e9fc745d (LOCAL_ONLY) 20121012091606
plugins/Morphology/Catalogue_Particles.txt
  4d0095a2 (LOCAL_ONLY) 20121012091605
plugins/Morphology/Classify_Particles.class
  f53a898e (LOCAL_ONLY) 20121012091604
plugins/Morphology/CloseByReconstructionTopHat.txt
  2c7f38f5 (LOCAL_ONLY) 20121012091606
plugins/Morphology/CloseByReconstruction_.txt
  1c33105a (LOCAL_ONLY) 20121012091605 plugins/Morphology/ConvexHull1.txt
  7cb69fdf (LOCAL_ONLY) 20121012091605 plugins/Morphology/ConvexHull2.txt
  b19cb415 (LOCAL_ONLY) 20121012091604 plugins/Morphology/ConvexHull3.txt
  bd22187f (LOCAL_ONLY) 20121012091605 plugins/Morphology/Corners.txt
  55c709bf (LOCAL_ONLY) 20121012091604
plugins/Morphology/Correlate_Results.class
  d463ee86 (LOCAL_ONLY) 20121012091605 plugins/Morphology/Delete_ZeroArea.txt
  8df2eb76 (LOCAL_ONLY) 20121012091604 plugins/Morphology/Diagonal8to4.txt
  61193e21 (LOCAL_ONLY) 20121012091605 plugins/Morphology/Domes_.class
  e428a0f5 (LOCAL_ONLY) 20121012091604 plugins/Morphology/Domes_stack.txt
  1be944ae (LOCAL_ONLY) 20121012091606 plugins/Morphology/DoubleWaterfall.txt
  925d3d8c (LOCAL_ONLY) 20121012091605 plugins/Morphology/DrawBoundingBox.txt
  63c4cd27 (LOCAL_ONLY) 20121012091605
plugins/Morphology/DrawBoundingCircle.txt
  b97f945a (LOCAL_ONLY) 20121012091606 plugins/Morphology/DrawConvexHulls.txt
  2adcfe94 (LOCAL_ONLY) 20121012091605 plugins/Morphology/DrawFeret&Breadth.txt
  b60f4365 (LOCAL_ONLY) 20121012091605 plugins/Morphology/DrawMinR&MaxR.txt
  288ace7a (LOCAL_ONLY) 20121012091605 plugins/Morphology/EDM_16bits.txt
  71d10273 (LOCAL_ONLY) 20121012091605 plugins/Morphology/Euler.txt
  63757672 (LOCAL_ONLY) 20121012091604 plugins/Morphology/Extended_Maxima.txt
  285e4c16 (LOCAL_ONLY) 20121012091606 plugins/Morphology/Extended_Minima.txt
  2b80b381 (LOCAL_ONLY) 20121012091605
plugins/Morphology/FillHolesReconstruct.txt
  205b6052 (LOCAL_ONLY) 20121012091604 plugins/Morphology/Fill_Border_Holes.txt
  54d7ef21 (LOCAL_ONLY) 20121012091604
plugins/Morphology/Fill_Greyscale_Holes.txt
  75041650 (LOCAL_ONLY) 20121012091604
plugins/Morphology/GreyBlackTopHatByReconstruction_.txt
  6f716dcc (LOCAL_ONLY) 20121012091605
plugins/Morphology/GreyWhiteTopHatByReconstruction_.txt
  579b5383 (LOCAL_ONLY) 20121012091605
plugins/Morphology/GreyscaleCentreFilter.txt
  ee023f37 (LOCAL_ONLY) 20121012114130
plugins/Morphology/GreyscaleDilate_.class
  965f297a (LOCAL_ONLY) 20121012091605 plugins/Morphology/GreyscaleErode_.class
  0a50379d (LOCAL_ONLY) 20121012091605
plugins/Morphology/GreyscaleKillBorders.txt
  d3047959 (LOCAL_ONLY) 20121012091604
plugins/Morphology/GreyscaleProperAutomedian.txt
  b4d94111 (LOCAL_ONLY) 20121012091605
plugins/Morphology/GreyscaleProperClose.txt
  44d81a95 (LOCAL_ONLY) 20121012091604
plugins/Morphology/GreyscaleProperOpen.txt
  9aadbae0 (LOCAL_ONLY) 20121012091604
plugins/Morphology/GreyscaleReconstruct_.class
  4d7e6035 (LOCAL_ONLY) 20121012091604 plugins/Morphology/GreyscaleTopHat.txt
  cb2dc22a (LOCAL_ONLY) 20121012091606 plugins/Morphology/GreyscaleWell.txt
  282495a6 (LOCAL_ONLY) 20121012091604 plugins/Morphology/H-break.txt
  a73d2279 (LOCAL_ONLY) 20121012091605 plugins/Morphology/HMaxima_Transform.txt
  f1c1b630 (LOCAL_ONLY) 20121012091606 plugins/Morphology/HMinima_Transform.txt
  af3183b2 (LOCAL_ONLY) 20121012091606 plugins/Morphology/Hole_Counter.txt
  930ee9e1 (LOCAL_ONLY) 20121012091605 plugins/Morphology/HomotopicMarking.txt
  3429c4f3 (LOCAL_ONLY) 20121012091604 plugins/Morphology/Hysteresis.txt
  2511df4c (LOCAL_ONLY) 20121012091606 plugins/Morphology/Impose_Minimum.txt
  6be72748 (LOCAL_ONLY) 20121012091604 plugins/Morphology/Influence_Zones.txt
  5859277c (LOCAL_ONLY) 20121012091604
plugins/Morphology/KeepLargestParticle.txt
  559e475f (LOCAL_ONLY) 20121012091604
plugins/Morphology/KeepLargestParticlePixels_.txt
  4605ad0a (LOCAL_ONLY) 20121012091605
plugins/Morphology/KeepParticlesInRange.txt
  b46b2695 (LOCAL_ONLY) 20121012091606 plugins/Morphology/Lines8_.class
  43259a0b (LOCAL_ONLY) 20121012091605 plugins/Morphology/LocalMaxima.txt
  c0207001 (LOCAL_ONLY) 20121012091605 plugins/Morphology/LocalMinMax.txt
  b2139bd8 (LOCAL_ONLY) 20121012091605 plugins/Morphology/LocalMinima.txt
  05f0502d (LOCAL_ONLY) 20121012091605 plugins/Morphology/MCentroids.txt
  b3ea5e05 (LOCAL_ONLY) 20121012091605 plugins/Morphology/MinimaDynamic.txt
  57e4bbaa (LOCAL_ONLY) 20121012091605
plugins/Morphology/Morphological2Derivative1.txt
  35b51e7e (LOCAL_ONLY) 20121012091604
plugins/Morphology/Morphological2Derivative2.txt
  ef809632 (LOCAL_ONLY) 20121012091605
plugins/Morphology/Morphological2Derivative3.txt
  73902be6 (LOCAL_ONLY) 20121012091605
plugins/Morphology/MorphologicalContrastTopHat.txt
  86d43a13 (LOCAL_ONLY) 20121012091605
plugins/Morphology/MorphologicalExternalGradient.txt
  66d657f2 (LOCAL_ONLY) 20121012091605
plugins/Morphology/MorphologicalGradient3.txt
  2cd67873 (LOCAL_ONLY) 20121012091604
plugins/Morphology/MorphologicalGradientBeucher.txt
  b141cc35 (LOCAL_ONLY) 20121012091605
plugins/Morphology/MorphologicalInternalGradient.txt
  babf8d91 (LOCAL_ONLY) 20121012091605
plugins/Morphology/MorphologicalSharpGradient.txt
  7e05ec43 (LOCAL_ONLY) 20121012091605
plugins/Morphology/MorphologicalSmoothing1.txt
  df30c851 (LOCAL_ONLY) 20121012091604
plugins/Morphology/MorphologicalSmoothing2.txt
  b4232d82 (LOCAL_ONLY) 20121012091604
plugins/Morphology/Morphological_Clustering.txt
  c4024220 (LOCAL_ONLY) 20121012091604 plugins/Morphology/Morphological_PCA.txt
  44b58573 (LOCAL_ONLY) 20121012091604
plugins/Morphology/Morphological_SelfDualCentre.txt
  d20caeeb (LOCAL_ONLY) 20121012091604
plugins/Morphology/Morphological_contrast.txt
  c40dcb5d (LOCAL_ONLY) 20121012091606
plugins/Morphology/MultiscaleGradient.txt
  7fa60ae6 (LOCAL_ONLY) 20121012091606 plugins/Morphology/NumberParticles8_.txt
  cd6cf4de (LOCAL_ONLY) 20121012091606
plugins/Morphology/OpenByReconstructionTopHat.txt
  5f844fa9 (LOCAL_ONLY) 20121012091606
plugins/Morphology/OpenByReconstruction_.txt
  8fdf1b15 (LOCAL_ONLY) 20121012091605 plugins/Morphology/Parameter_Matrix.txt
  65c22a1e (LOCAL_ONLY) 20121012091605 plugins/Morphology/ParticleHoleArea.txt
  9a713d79 (LOCAL_ONLY) 20121012091605
plugins/Morphology/ParticleHoleNumber.txt
  9c0a7763 (LOCAL_ONLY) 20121012091606 plugins/Morphology/Particle_Data_Map.txt
  85b99ff0 (LOCAL_ONLY) 20121012091605 plugins/Morphology/Particles4_.class
  583118b2 (LOCAL_ONLY) 20121012091604 plugins/Morphology/Particles8_.class
  ac25812c (LOCAL_ONLY) 20121012091604
plugins/Morphology/Plot_BivariateGraphs.txt
  e8ea53cb (LOCAL_ONLY) 20121012091605 plugins/Morphology/Plot_Histograms.txt
  ce077644 (LOCAL_ONLY) 20121012091605 plugins/Morphology/Prune1.txt
  c4126534 (LOCAL_ONLY) 20121012091604 plugins/Morphology/PruneAll.txt
  916ac5a4 (LOCAL_ONLY) 20121012091604 plugins/Morphology/RegionalMinMax.txt
  3dcf6fa2 (LOCAL_ONLY) 20121012091604 plugins/Morphology/Regional_Maxima.txt
  bc61499e (LOCAL_ONLY) 20121012091605 plugins/Morphology/Regional_Minima.txt
  358d5270 (LOCAL_ONLY) 20121012091606
plugins/Morphology/SelfComplementaryTopHat.txt
  36e7e0b4 (LOCAL_ONLY) 20121012091604
plugins/Morphology/SelfDualReconstruction_.txt
  64886ac9 (LOCAL_ONLY) 20121012091605 plugins/Morphology/Skeleton1.txt
  64fa451e (LOCAL_ONLY) 20121012091604 plugins/Morphology/Skeleton2.txt
  809a6770 (LOCAL_ONLY) 20121012091606 plugins/Morphology/Skeleton3.txt
  16447730 (LOCAL_ONLY) 20121012091605 plugins/Morphology/Skeleton4.txt
  b2242712 (LOCAL_ONLY) 20121012091606 plugins/Morphology/SkeletonFiltering.txt
  5d0400a0 (LOCAL_ONLY) 20121012091606 plugins/Morphology/Summarize_Results.txt
  ab0b29c3 (LOCAL_ONLY) 20121012091605
plugins/Morphology/Thin_Results_Table.txt
  090f96c1 (LOCAL_ONLY) 20121012091605 plugins/Morphology/UnbiasedCounting.txt
  fecf6a46 (LOCAL_ONLY) 20121012091604
plugins/Morphology/UnbiasedParticleArea.txt
  19a9433c (LOCAL_ONLY) 20121012091605
plugins/Morphology/Viscous_Geodesic_Reconstruction.txt
  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
  5a3abd78 (LOCAL_ONLY) 20050408150536 plugins/PSF_Gibson_.class
  65b190f7 (LOCAL_ONLY) 20121002063426 plugins/PSF_Simple_.class
  0c89ccf5 (LOCAL_ONLY) 20140507100709 plugins/PoissonNMF_.jar
  12289f6e (LOCAL_ONLY) 20110916093010 plugins/PureDenoise_.jar
  0eb97953 (LOCAL_ONLY) 20120921142744 plugins/RGB_Profiler.class
  a75d3b5e (LOCAL_ONLY) 20140416070711 plugins/Shape_Descriptor1u.class
  69b16199 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4.class
  f0990b22 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4Filter.class
  27901023 (LOCAL_ONLY) 20050408152652 plugins/Wavelet_Deconvolution_.class
  b2afde18 (LOCAL_ONLY) 20140325152012 plugins/cell_counter.jar
  e42576de (LOCAL_ONLY) 20140328082513 plugins/gdsc_.jar
  5c303bf7 (LOCAL_ONLY) 20140328082514 plugins/gdsc_smlm.jar
  71331805 (LOCAL_ONLY) 20140314082430 plugins/jacop_.jar
  16e7eed3 (LOCAL_ONLY) 20140228132323 plugins/jars/Compiler.jar
  9bbfb280 (LOCAL_ONLY) 20140225135257 plugins/octane2_.jar

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