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Bug 820 - Macro fails to run from the plugins menu
Macro fails to run from the plugins menu
Status: ASSIGNED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-25 14:30 CDT by Kaitlin Snider
Modified: 2014-06-26 00:08 CDT
3 users (show)

See Also:
Description Kaitlin Snider 2014-06-25 14:30:38 CDT 
I've been working on a macro to automate selection of 3D ROIs.  The macro itself is working great; I can pull it up in the script editor and it runs correctly.  However, I'm going to need to call it from the plugin menu, and that isn't working. Right now I have it saved under Fiji ->  Fiji.app -> plugins as "Cell_nuclei_macro_x.ijm".  It shows up in the plugins menu as "Cell nuclei macro x".  If I click on that, the "status bar" on the Fiji main window reads "Command finished: cell nuclei macro x", but nothing actually happens.

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: D:\GOOGLE~1\Fiji\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => D:\GOOGLE~1\Fiji\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140623162553)
Fiji: http://fiji.sc/update/ (last check:20140625145538)

Files not up-to-date:
  df5c2e64 (LOCAL_ONLY) 20120118165120 jars/Fiji_Plugins.jar
  a63eaea9 (LOCAL_ONLY) 20140607174541 macros/BatchMacro.ijm
  5674bd16 (LOCAL_ONLY) 20140621115152 macros/Cell nuclei macro x.ijm
  e2a23def (LOCAL_ONLY) 20140621111348 macros/Cell_nuclei_macro_x.ijm
  8dc8d7c1 (LOCAL_ONLY) 20140607124947 macros/GetDirectoryExampleNotWorking.ijm
  33a3d239 (LOCAL_ONLY) 20140110165131 macros/SpineDraft1.ijm
  a8456198 (LOCAL_ONLY) 20131105150819 macros/batch convert 2.txt
  8784cdeb (LOCAL_ONLY) 20140514170744 plugins/Add_Borders.class
  03d40fa2 (LOCAL_ONLY) 20140514170744 plugins/AnnularClosing.txt
  fdadf615 (LOCAL_ONLY) 20140514170744 plugins/AnnularDilation.txt
  3f800c5d (LOCAL_ONLY) 20140514170744 plugins/BinaryConditionalDilate_.class
  aaa03c9c (LOCAL_ONLY) 20140514170744 plugins/BinaryConditionalErode_.class
  ddb1bfb1 (LOCAL_ONLY) 20140514170650 plugins/BinaryConnectivity_.class
  ec3c3b29 (LOCAL_ONLY) 20140514170659 plugins/BinaryDilateNoMerge4_.class
  82393254 (LOCAL_ONLY) 20140514170700 plugins/BinaryDilateNoMerge8_.class
  a1396723 (LOCAL_ONLY) 20140514170704 plugins/BinaryDilateTest.txt
  c1356312 (LOCAL_ONLY) 20140514170657 plugins/BinaryDilate_.class
  85f9e350 (LOCAL_ONLY) 20140514170709 plugins/BinaryErodeTest.txt
  664fd92a (LOCAL_ONLY) 20140514170706 plugins/BinaryErode_.class
  6e5b8ba8 (LOCAL_ONLY) 20140514170709 plugins/BinaryFilterReconstruct.txt
  f232af18 (LOCAL_ONLY) 20140514170710 plugins/BinaryFilterReconstruct_.class
  be79e621 (LOCAL_ONLY) 20140514170711 plugins/BinaryGeodesicDilateNoMerge8_.class
  f43826e0 (LOCAL_ONLY) 20140514170712 plugins/BinaryHitOrMiss_.class
  2ecaa3ea (LOCAL_ONLY) 20140514170714 plugins/BinaryKillBorders_.class
  8a1a4414 (LOCAL_ONLY) 20140514170722 plugins/BinaryLabel8_.class
  483d2b7c (LOCAL_ONLY) 20140514170723 plugins/BinaryLabelMacro.txt
  3c091943 (LOCAL_ONLY) 20140514170716 plugins/BinaryLabel_.class
  e5775afd (LOCAL_ONLY) 20140514170723 plugins/BinaryPrune.txt
  a3aa5e2d (LOCAL_ONLY) 20140514170724 plugins/BinaryReconstruct_.class
  3471da4e (LOCAL_ONLY) 20140514170728 plugins/BinaryThick2_.class
  868814e7 (LOCAL_ONLY) 20140514170727 plugins/BinaryThick_.class
  2d4c9dd1 (LOCAL_ONLY) 20140514170730 plugins/BinaryThin2_.class
  5b8b2aa2 (LOCAL_ONLY) 20140514170730 plugins/BinaryThin_.class
  c0f5f8c9 (LOCAL_ONLY) 20140505173840 plugins/BoneJ_.jar
  24a94be4 (LOCAL_ONLY) 20140514170730 plugins/Boundary4.txt
  f5dfa5aa (LOCAL_ONLY) 20140514170730 plugins/Boundary8_.txt
  e8e919dc (LOCAL_ONLY) 20140514170731 plugins/Catalogue_Particles.txt
  4347fc42 (LOCAL_ONLY) 20140625123459 plugins/Cell_nuclei_macro_x.ijm
  90fb6e35 (LOCAL_ONLY) 20140514170732 plugins/Classify_Particles.class
  bc68dd30 (LOCAL_ONLY) 20140514170732 plugins/CloseByReconstructionTopHat.txt
  77fb6dfa (LOCAL_ONLY) 20140514170732 plugins/CloseByReconstruction_.txt
  b91c6eeb (LOCAL_ONLY) 20140514170732 plugins/ConvexHull1.txt
  25286882 (LOCAL_ONLY) 20140514170732 plugins/ConvexHull2.txt
  19fa9756 (LOCAL_ONLY) 20140514170732 plugins/ConvexHull3.txt
  e4dfc67d (LOCAL_ONLY) 20140514170732 plugins/Corners.txt
  ffbe6a82 (LOCAL_ONLY) 20140514170732 plugins/Correlate_Results.class
  83fb5738 (LOCAL_ONLY) 20140514170732 plugins/Delete_ZeroArea.txt
  9e56311b (LOCAL_ONLY) 20140514170733 plugins/Diagonal8to4.txt
  84e003bc (LOCAL_ONLY) 20140514170733 plugins/Domes_.class
  61d3e5ff (LOCAL_ONLY) 20140514170733 plugins/Domes_stack.txt
  09765271 (LOCAL_ONLY) 20140514170733 plugins/DoubleWaterfall.txt
  4317920e (LOCAL_ONLY) 20140514170733 plugins/DrawBoundingBox.txt
  292ac1a5 (LOCAL_ONLY) 20140514170733 plugins/DrawBoundingCircle.txt
  a9d0fa61 (LOCAL_ONLY) 20140514170733 plugins/DrawConvexHulls.txt
  972eb519 (LOCAL_ONLY) 20140514170733 plugins/DrawFeret&Breadth.txt
  d6952718 (LOCAL_ONLY) 20140514170734 plugins/DrawMinR&MaxR.txt
  26b1cf1f (LOCAL_ONLY) 20140514170734 plugins/EDM_16bits.txt
  95e08cc6 (LOCAL_ONLY) 20140514170734 plugins/Euler.txt
  d59dd4ca (LOCAL_ONLY) 20140514170734 plugins/Extended_Maxima.txt
  fefc89c2 (LOCAL_ONLY) 20140514170734 plugins/Extended_Minima.txt
  b6e2898f (LOCAL_ONLY) 20140514170734 plugins/FillHolesReconstruct.txt
  fcada02c (LOCAL_ONLY) 20140514170734 plugins/Fill_Border_Holes.txt
  9942bf2d (LOCAL_ONLY) 20140514170734 plugins/Fill_Greyscale_Holes.txt
  2bba06c9 (LOCAL_ONLY) 20140514170734 plugins/GreyBlackTopHatByReconstruction_.txt
  147f99bf (LOCAL_ONLY) 20140514170736 plugins/GreyWhiteTopHatByReconstruction_.txt
  6c2d736e (LOCAL_ONLY) 20140514170734 plugins/GreyscaleCentreFilter.txt
  23770dd0 (LOCAL_ONLY) 20140514170735 plugins/GreyscaleDilate_.class
  570921ba (LOCAL_ONLY) 20140514170735 plugins/GreyscaleErode_.class
  aa8dfc54 (LOCAL_ONLY) 20140514170735 plugins/GreyscaleKillBorders.txt
  50596252 (LOCAL_ONLY) 20140514170735 plugins/GreyscaleProperAutomedian.txt
  9cf40048 (LOCAL_ONLY) 20140514170736 plugins/GreyscaleProperClose.txt
  ceccf07c (LOCAL_ONLY) 20140514170736 plugins/GreyscaleProperOpen.txt
  bae0507a (LOCAL_ONLY) 20140514170736 plugins/GreyscaleReconstruct_.class
  38c07c14 (LOCAL_ONLY) 20140514170736 plugins/GreyscaleTopHat.txt
  9e6d0f71 (LOCAL_ONLY) 20140514170736 plugins/GreyscaleWell.txt
  f933f17a (LOCAL_ONLY) 20131101160723 plugins/Grid_.class
  484a6906 (LOCAL_ONLY) 20140514170736 plugins/H-break.txt
  ca3a48ac (LOCAL_ONLY) 20140514170736 plugins/HMaxima_Transform.txt
  f74c924a (LOCAL_ONLY) 20140514170736 plugins/HMinima_Transform.txt
  8e0fe1d0 (LOCAL_ONLY) 20140514170737 plugins/Hole_Counter.txt
  1c0c855a (LOCAL_ONLY) 20140514170737 plugins/HomotopicMarking.txt
  b1539cbc (LOCAL_ONLY) 20140514170737 plugins/Hysteresis.txt
  20e2cec7 (LOCAL_ONLY) 20131102175325 plugins/ICTN_1_6_.jar
  2a05fa37 (LOCAL_ONLY) 20140514170737 plugins/Impose_Minimum.txt
  3fa60268 (LOCAL_ONLY) 20140514170738 plugins/Influence_Zones.txt
  729354c2 (LOCAL_ONLY) 20140514170738 plugins/KeepLargestParticle.txt
  19e2cec5 (LOCAL_ONLY) 20140514170738 plugins/KeepLargestParticlePixels_.txt
  b29da12e (LOCAL_ONLY) 20140514170738 plugins/KeepParticlesInRange.txt
  d08c07ab (LOCAL_ONLY) 20140514170738 plugins/Lines8_.class
  75b56606 (LOCAL_ONLY) 20140514170738 plugins/LocalMaxima.txt
  aaf95163 (LOCAL_ONLY) 20140514170739 plugins/LocalMinMax.txt
  46a25fab (LOCAL_ONLY) 20140514170738 plugins/LocalMinima.txt
  6b22836f (LOCAL_ONLY) 20140514170739 plugins/MCentroids.txt
  be5418e3 (LOCAL_ONLY) 20140621113024 plugins/Macros/Cell_nuclei_macro_x.ijm
  5b4b4fbb (LOCAL_ONLY) 20140514170739 plugins/MinimaDynamic.txt
  d8614f50 (LOCAL_ONLY) 20140514170739 plugins/Morphological2Derivative1.txt
  60301798 (LOCAL_ONLY) 20140514170740 plugins/Morphological2Derivative2.txt
  09a83645 (LOCAL_ONLY) 20140514170740 plugins/Morphological2Derivative3.txt
  0997e864 (LOCAL_ONLY) 20140514170740 plugins/MorphologicalContrastTopHat.txt
  cf65f2a1 (LOCAL_ONLY) 20140514170740 plugins/MorphologicalExternalGradient.txt
  78aef0f1 (LOCAL_ONLY) 20140514170740 plugins/MorphologicalGradient3.txt
  dee63a68 (LOCAL_ONLY) 20140514170740 plugins/MorphologicalGradientBeucher.txt
  b0e77e8d (LOCAL_ONLY) 20140514170740 plugins/MorphologicalInternalGradient.txt
  edbaef60 (LOCAL_ONLY) 20140514170740 plugins/MorphologicalSharpGradient.txt
  c235cdc8 (LOCAL_ONLY) 20140514170740 plugins/MorphologicalSmoothing1.txt
  c19df699 (LOCAL_ONLY) 20140514170741 plugins/MorphologicalSmoothing2.txt
  0f607ae2 (LOCAL_ONLY) 20140514170739 plugins/Morphological_Clustering.txt
  644fa5f2 (LOCAL_ONLY) 20140514170739 plugins/Morphological_PCA.txt
  3cf5195c (LOCAL_ONLY) 20140514170739 plugins/Morphological_SelfDualCentre.txt
  10712b1d (LOCAL_ONLY) 20140514170739 plugins/Morphological_contrast.txt
  d5a239b2 (LOCAL_ONLY) 20140514170741 plugins/MultiscaleGradient.txt
  cd3c1f6c (LOCAL_ONLY) 20140514170741 plugins/NumberParticles8_.txt
  0cf4b4fa (LOCAL_ONLY) 20140514170741 plugins/OpenByReconstructionTopHat.txt
  968d13fe (LOCAL_ONLY) 20140514170741 plugins/OpenByReconstruction_.txt
  3d964f7f (LOCAL_ONLY) 20140514170741 plugins/Parameter_Matrix.txt
  8402fa18 (LOCAL_ONLY) 20140514170741 plugins/ParticleHoleArea.txt
  b409ff83 (LOCAL_ONLY) 20140514170742 plugins/ParticleHoleNumber.txt
  61a2c46a (LOCAL_ONLY) 20140514170741 plugins/Particle_Data_Map.txt
  c677631a (LOCAL_ONLY) 20140514170742 plugins/Particles4_.class
  8ffb4cda (LOCAL_ONLY) 20140514170742 plugins/Particles8_.class
  b1135d5c (LOCAL_ONLY) 20140514170742 plugins/Plot_BivariateGraphs.txt
  cbbcc54c (LOCAL_ONLY) 20140514170742 plugins/Plot_Histograms.txt
  2f4c9d20 (LOCAL_ONLY) 20140514170742 plugins/Prune1.txt
  5171e5b9 (LOCAL_ONLY) 20140514170742 plugins/PruneAll.txt
  d2c7cb77 (LOCAL_ONLY) 20140514170742 plugins/RegionalMinMax.txt
  6a14d6c7 (LOCAL_ONLY) 20140514170742 plugins/Regional_Maxima.txt
  cb2dbb5e (LOCAL_ONLY) 20140514170742 plugins/Regional_Minima.txt
  db83e76c (LOCAL_ONLY) 20140619152728 plugins/Sample_Binary.ijm
  9abeefc6 (LOCAL_ONLY) 20140514170742 plugins/SelfComplementaryTopHat.txt
  49c4e43f (LOCAL_ONLY) 20140514170742 plugins/SelfDualReconstruction_.txt
  c89f017a (LOCAL_ONLY) 20140514170742 plugins/Skeleton1.txt
  5d028adb (LOCAL_ONLY) 20140514170743 plugins/Skeleton2.txt
  0f400b57 (LOCAL_ONLY) 20140514170743 plugins/Skeleton3.txt
  61705b77 (LOCAL_ONLY) 20140514170743 plugins/Skeleton4.txt
  e9eae17e (LOCAL_ONLY) 20140514170743 plugins/SkeletonFiltering.txt
  dbb6ca65 (LOCAL_ONLY) 20140514170743 plugins/Summarize_Results.txt
  9003c507 (LOCAL_ONLY) 20140514170743 plugins/Thin_Results_Table.txt
  3ab9a05e (LOCAL_ONLY) 20140514170743 plugins/UnbiasedCounting.txt
  ac9543a1 (LOCAL_ONLY) 20140514170743 plugins/UnbiasedParticleArea.txt
  54c73267 (LOCAL_ONLY) 20140514170743 plugins/Viscous_Geodesic_Reconstruction.txt
  b2afde18 (LOCAL_ONLY) 20131107133335 plugins/cell_counter.jar
  fc868626 (LOCAL_ONLY) 20140605183507 plugins/jars/Jython.jar
  86bf5a23 (LOCAL_ONLY) 20140505181325 plugins/mcib3d-core2.71.jar
  86bf5a23 (LOCAL_ONLY) 20140505181325 plugins/mcib3d-suite2.71 (1)/mcib3d-suite/mcib3d-core2.71.jar
  859549db (LOCAL_ONLY) 20140505181324 plugins/mcib3d-suite2.71 (1)/mcib3d-suite/mcib3d_plugins2.71.jar
  8cb8d89b (LOCAL_ONLY) 20140505181325 plugins/mcib3d-suite2.71 (1)/mcib3d-suite/quickhull3d.jar
  859549db (LOCAL_ONLY) 20140505180947 plugins/mcib3d_plugins2.71.jar
Comment 1 Johannes Schindelin 2014-06-25 16:50:22 CDT 
Thank you for opening a bug report. This makes it easy to see the information about the versions of files you have installed.

However, it also makes things awkward because there are now *two* places where the bug is discussed, since there is already a thread going on on the mailing list: http://thread.gmane.org/gmane.comp.java.imagej/33330.

Since that thread is already in full swing, I will continue to comment there.
Comment 2 Wayne Rasband 2014-06-26 00:08:16 CDT 
Try adding

   print("macro starting");

to the beginning of Fiji.app/plugins/Cell_nuclei_macro_x.ijm, restart Fiji and select "Cell nuclei macro x" from the Plugins menu. When I do this, I see "macro starting" displayed in the Log window. You should probably also remove the file with the same name in Fiji.app/plugins/Macros.