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Bugzilla – Bug 1030 |
long pauses when launching macro script on virtual stack |
Last modified: 2015-03-19 14:12:21 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. |
| long pauses when launching macro script on virtual stack | |
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Odd stuff last two days-- I am running a macro to align large Z stacks using max projections to get offsets and angular changes, then apply to a slice from a virtual stack with full data. 40-50megapixels per image, 2 Ch, 16bits. On launch, the IJ tool bar shows the progress bar flashing and the text "computing min/max complete" after some time, then the first user dialog opens sometimes after 5-10 MINUTES! Whatever fiji is doing is NOT part of the script! I can run the same code in imagej and the dialog pops up in a second or two, as expected. If I kill the hang and relaunch, fiji can sometimes behave as if imagej, otherwise it can be coffee break. I never ask for min/max. The first few lines of macro are: /* open a max projection of reference and then of a 2CH stack to register *open the to-do Z-stack as virtual (use bioformats import), then follow instructions */ run("Set Measurements...", "centroid center feret's display redirect=None decimal=3"); if (isOpen("Results")) { selectWindow("Results"); run("Close");} waitForUser("click on REFerence projection, then hit OK"); c0=getImageID(); selectImage(c0); getDimensions(width, height, channels, slices, frames); rW=width; rH=height; best regards, 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:\DEC201~1/java/win64/jdk1.6.0_24//jre imagej.dir => E:\DEC201~1 Information about the version of each plugin: Activated update sites: ImageJ: http://update.imagej.net/ (last check:20150319121059) Fiji: http://fiji.sc/update/ (last check:20150318151552) 3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20141208015245) FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606102449) GDSC-SMLM: http://sites.imagej.net/GDSC-SMLM/ (last check:20150312115558) HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214064119) IJPB-plugins: http://sites.imagej.net/IJPB-plugins/ (last check:20150219043515) Morphology: http://sites.imagej.net/Landini/ (last check:20140723095558) OpenSPIM: http://openspim.org/update/ (last check:20140630085101) Files not up-to-date: 1ad3be0d (LOCAL_ONLY) 20141222042830 jars/jpedalSTD.jar 6d337b7a (LOCAL_ONLY) 20140730142734 plugins/Accurate_Gaussian_Blur.class 6e9d50db (LOCAL_ONLY) 20140320051924 plugins/Adjustable_Watershed.class 12ec0761 (LOCAL_ONLY) 20120224100622 plugins/Align_RGB_planes.class 0c575fd1 (LOCAL_ONLY) 20141209160514 plugins/BioVoxxel_Plugins.jar 52ff6766 (LOCAL_ONLY) 20150115075008 plugins/Create_Template.jar 55de57f2 (LOCAL_ONLY) 20050408121420 plugins/DecCredits$1.class 66a64476 (LOCAL_ONLY) 20050408121420 plugins/DecCredits.class fd4ce3cd (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionFFT.class b0398adb (LOCAL_ONLY) 20141028073350 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 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 d6bc39b9 (LOCAL_ONLY) 20141023044548 plugins/Jay_Plugins.jar 04b38ca7 (LOCAL_ONLY) 20141023044548 plugins/Jay_Plugins2.jar 71ae5c42 (LOCAL_ONLY) 20140509130342 plugins/KalmanOpenStackFilter_.class 44f1acfa (LOCAL_ONLY) 20121128135145 plugins/Mexican_Hat_Filter.class 53c5c1ad (LOCAL_ONLY) 20141103073745 plugins/NL_Means_.jar 4ed208ff (LOCAL_ONLY) 20140929064046 plugins/NanoTrackJ_.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 0c89ccf5 (LOCAL_ONLY) 20140507100709 plugins/PoissonNMF_.jar 12289f6e (LOCAL_ONLY) 20110916093010 plugins/PureDenoise_.jar 33ca5f87 (LOCAL_ONLY) 20141215122204 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_.jarVytas wrote via private mail: > I did NOT enable those options AND they are not checked on in the GUI > on looking just now. Could the GUI be broken and ON by default? -- > strange! The GUI is very unlikely to be broken, though you could confirm for certain by running this BeanShell script in the Script Editor: // @ImageJ ij // @OptionsService options ij2opts = ij.options().getOptions(net.imagej.legacy.ImageJ2Options.class); ij.ui().showDialog( "Enable ImageJ2 data structures? " + ij2opts.isSyncEnabled() + "\n" + "Use SCIFIO when opening files? " + ij2opts.isSciJavaIO());