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Bugzilla – Bug 719 |
Compiles right first time, then restart is necessary |
Last modified: 2014-04-29 11:21:40 CDT |
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NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug. The Fiji project now uses GitHub Issues for issue tracking. Please file all new issues there. |
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Dear Fiji-team, when I write a code and then Compile and Run it the first time after i start Fiji, everything works fine. However the second time, after I add some code, it doesn't apply the new code. Example: ImagePlus imp_copy = new ImagePlus("Hallo", ip); imp_copy.show(); When I first time comlipe and run this a second image appears on my screen. Then I comment out the show-method like this: //imp_copy.show(); But still when I compile and run the second image appears thew it shouldn't. At this point I have to restart Fiji and compile again for the change to apply, but again it works only the first time after restart. Same goes to the normal ImageJ without Fiji. I have worked with fiji for about three months without problems, the strange behaviour started yesterday.(18.03.14) What should I do is that a bug ? If you have further questions just contact me via e-mail. Thank you very much. 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: UP_TO_DATE Information relevant to JAVA_HOME related problems: JAVA_HOME is set to: D:\PROGRA~1\Fiji.app/java/win64/jdk1.6.0_24//jre ij.dir => D:\PROGRA~1\Fiji.app Information about the version of each plugin: 2c93d9a6:2d9d2593:be71a9c0 20140201185146 :00efaa6 426d64f4:be49972e:be49972e 20140201185144 :0307564 8c8f6d33:ac4c137b:ac4c137b 20140201185144 :0326851 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plugins/Fiji_Package_Maker-2.0.0-SNAPSHOT.jar aa889b53 20140201185144 plugins/Fiji_Plugins-2.0.0-SNAPSHOT.jar aa0fa91d 20140201185144 plugins/Fiji_Updater.jar ce69e79a 20140201185144 plugins/FlowJ_-1.29.1-SNAPSHOT.jar f942a886 20140201185144 plugins/Graph_Cut-0.1.1-SNAPSHOT.jar bf032087 20140201185144 plugins/Gray_Morphology-2.3.2-SNAPSHOT.jar f48de7ae 20140201185144 plugins/Helmholtz_Analysis-2.0.1-SNAPSHOT.jar dc5df090 20140201185144 plugins/IJ_Robot-2.0.0-SNAPSHOT.jar eb581ab4 20140201185144 plugins/IO_-2.0.0-SNAPSHOT.jar 8b85c6b0 20140201185144 plugins/Image_5D.jar dc5e4695 20140201185144 plugins/Image_Expression_Parser-2.0.0-SNAPSHOT.jar 65b42030 20140201185144 plugins/Interactive_3D_Surface_Plot-2.31.1-SNAPSHOT.jar b483961e 20140201185144 plugins/IsoData_Classifier-2.0.0-SNAPSHOT.jar 28582f55 20140201185144 plugins/JRuby/imagej.rb 9a5d6894 20140201185144 plugins/JRuby_Interpreter-2.0.0-SNAPSHOT.jar 7d22f08d 20140201185144 plugins/Javascript_-2.0.0-SNAPSHOT.jar a7edca68 20140201185144 plugins/Jython_Interpreter-2.0.0-SNAPSHOT.jar 542ef100 20140201185144 plugins/LSM_Reader.jar 6566ced8 20140201185144 plugins/LSM_Toolbox.jar 5830f8ee 20140201185144 plugins/Lasso_and_Blow_Tool-2.0.0-SNAPSHOT.jar c10ee505 20140201185144 plugins/Linear_Kuwahara-2.0.0-SNAPSHOT.jar cf4ad6ab 20140201185144 plugins/LocalThickness_-3.1.1-SNAPSHOT.jar 587c9f4b 20140201185144 plugins/MTrack2_-2.0.0-SNAPSHOT.jar f6a6a497 20140201185144 plugins/MTrackJ_-1.5.1-SNAPSHOT.jar 64ccfd05 20140201185144 plugins/M_I_P-2.0.0-SNAPSHOT.jar 65a2dd78 20140201185144 plugins/Macros/About_Plugin_Macros.txt dff5642d 20140201185144 plugins/Macros/Bulls_Eye.txt e7ffe8ba 20140201185144 plugins/Macros/Polygon_.txt 39f7ffcd 20140201185144 plugins/Macros/RGB_Histogram.txt 3ee0edfa 20140201185144 plugins/Macros/batch_convert_any_to_tif.txt 55f5b6a0 20140201185144 plugins/Manual_Tracking-2.0.0-SNAPSHOT.jar 9c541ad9 20140201185144 plugins/MosaicJ_-2.0.0-SNAPSHOT.jar 04a4a5c1 20140201185144 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plugins/Scripts/Image/Color/Set_Color_By_Wavelength.ijm 1de6c712 20140201185144 plugins/Scripts/Image/Hyperstacks/Temporal-Color_Code.ijm af064f17 20140201185144 plugins/Scripts/Plugins/Registration/Correct_3D_drift.py a6e496fc 20140201185144 plugins/Scripts/Plugins/Utilities/Create_Desktop_Icon.bsh b5ee58a2 20140201185144 plugins/Scripts/Plugins/Utilities/Find_Jar_For_Class.bsh fc46bd40 20140201185144 plugins/Scripts/Plugins/Utilities/Record_Desktop.py 9d4d012a 20140201185144 plugins/Scripts/Plugins/Utilities/Record_Window.py 8cb22fe2 20140303084553 plugins/Series_Labeler-2.0.0-SNAPSHOT.jar 7c62b5c5 20140201185144 plugins/SheppLogan_-2.0.0-SNAPSHOT.jar 259df97d 20140201185144 plugins/Sholl_Analysis-3.4.0.jar 95dc5b19 20140201185144 plugins/Simple_Neurite_Tracer-2.0.2-SNAPSHOT.jar 0bd5f179 20140201185144 plugins/Siox_Segmentation-1.0.1-SNAPSHOT.jar 52fecf09 20140201185144 plugins/Skeletonize3D_-1.0.1-SNAPSHOT.jar b0820703 20140201185144 plugins/Snakuscule_-2.0.0-SNAPSHOT.jar 33b6af85 20140201185144 plugins/SplineDeformationGenerator_-2.0.0-SNAPSHOT.jar 27de591e 20140201185144 plugins/StackReg_-2.0.0-SNAPSHOT.jar 736bb192 20140201185144 plugins/Stack_Manipulation-2.0.0-SNAPSHOT.jar 59f36299 20140201185144 plugins/Statistical_Region_Merging-2.0.0-SNAPSHOT.jar 08a4daec 20140316150534 plugins/Stitching_-2.0.0-SNAPSHOT.jar 30100de7 20140201185144 plugins/Sync_Win-1.7-fiji2-SNAPSHOT.jar f412ba89 20140316180156 plugins/Test/Frame_Test.class 685ca9dc 20140201185144 plugins/Thread_Killer-2.0.0-SNAPSHOT.jar 2cee6c37 20140201185144 plugins/Threshold_Colour-2.0.1-SNAPSHOT.jar d822b123 20140201185144 plugins/Time_Stamper-2.0.0-SNAPSHOT.jar 584cb5b9 20140201185144 plugins/ToAST_-25.0.1-SNAPSHOT.jar 4cf59217 20140201185144 plugins/TopoJ_-2.0.0-SNAPSHOT.jar a2b2409b 20140201185144 plugins/TrackMate_-2.1.1-SNAPSHOT.jar 279a86b1 20140212125426 plugins/Trainable_Segmentation-2.0.0-SNAPSHOT.jar 59124982 20140201185144 plugins/TrakEM2_-1.0b-SNAPSHOT.jar 8e7f3b79 20140201185144 plugins/TransformJ_-2.8.1-SNAPSHOT.jar c4e87a76 20140201185144 plugins/TurboReg_-2.0.0-SNAPSHOT.jar 9558400d 20140201185144 plugins/UnwarpJ_.jar a32dfe46 20140201185144 plugins/Utilities/Close_All_Without_Saving.txt 253c6df4 20140201185144 plugins/VIB_-2.0.0-SNAPSHOT.jar baa78901 20140201185144 plugins/Vaa3d_Reader-2.0.0-SNAPSHOT.jar 81279d21 20140201185144 plugins/Video_Editing-2.0.0-SNAPSHOT.jar 73396eef 20140201185144 plugins/View5D_-1.3.1-SNAPSHOT.jar 980c0ed9 20140201185144 plugins/Volume_Calculator-1.0.1-SNAPSHOT.jar 2ef6f1eb 20140317145831 plugins/Volume_Viewer-2.01.1-SNAPSHOT.jar 2079ca32 20140201185144 plugins/bUnwarpJ_-2.6.1-SNAPSHOT.jar 5d479ffe 20140316150550 plugins/bio-formats_plugins-5.0.0.jar 0307564a 20140201185144 plugins/blockmatching_-2.0.0-SNAPSHOT.jar 659ad6a3 20140201185144 plugins/ij-ImageIO_.jar 82f900ac 20140201185144 plugins/level_sets-1.0.1-SNAPSHOT.jar df2af815 20140201185144 plugins/mpicbg_-0.6.1-SNAPSHOT.jar 5e32d936 20140201185144 plugins/panorama_.jar 96b34801 20140201185144 plugins/readme.txt 4bd07822 20140218120456 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar 16012d5a 20140201185144 plugins/registration_3d-2.0.0-SNAPSHOT.jar 34b7341d 20140201185150 retro/backport-util-concurrent-3.1.jar 8759ba20 20140201185150 retro/retrotranslator-runtime-1.2.9.jar a6d5a3b2 20140201185150 retro/retrotranslator-transformer-1.2.9.jar d7160d38 20140201185150 scripts/InstallJava3D.m 05a92a3c 20140201185150 scripts/IsJava3DInstalled.m ff34d026 20140201185150 scripts/Matlab3DViewerDemo_1.m 25be149f 20140201185150 scripts/Matlab3DViewerDemo_2.m cb529b6c 20140201185150 scripts/Matlab3DViewerDemo_3.m 53d2da73 20140201185150 scripts/Matlab3DViewerIntroduction.m 4bb342fa 20140201185150 scripts/Miji.m 868cd434 20140201185150 scripts/Miji_Test.m dc94c3a3 20140201185150 scripts/bfopen.m a77cab39 20140201185150 scripts/importTrackMateTracks.mSorry, I cannot reproduce the issue. Here is what I did before I started experimenting: 1. Help>Update Fiji 2. Advanced mode 3. View Options: View all files 4. Click on the "Status/Action" column header to make sure that the only files not "Up-to-date" are the launchers for different platforms Then, I 1. fired up the script editor via File>New>Script 2. Templates>Java>Bare PlugIn 3. inserted the statement ij.IJ.log("Hello"); into the run() method 4. File>Save directly into the Fiji.app/ directory 5. Run>Compile and Run 6. verified that the Log window displays a line "Hello" 7. edited the statement to read ij.IJ.log("Bello"); instead 8. File>Save 9. File>Compile and Run 10. verified that the Log window has a line "Bello", too 11. back in the main Fiji window, clicked Plugins>Compile and Run... and selected the just-saved Bare_PlugIn.java 12. verified that there is yet another "Bello" line in the Log window 13. switched back to the script editor 14. modified the statement to read ij.IJ.log("Cello"); 15. File>Save 16. switched back to the main Fiji window, clicked Plugins>Compile and Run... again and selected the newly-saved Bare_PlugIn.java 17. verified that the Log window now sports "Cello" as new last line For your interest: I saved the file outside of plugins/ or jars/ to avoid problems with ImageJ 1.x' plugin class loader. Could you follow those steps and tell me where it breaks for you?