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Bugzilla – Bug 1242 |
We are running a batch files and seem to get the occasional zero-intensity value image when using run("RGB Color") |
Last modified: 2016-03-10 17:02:44 CST |
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| We are running a batch files and seem to get the occasional zero-intensity va... | |
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We use Process-Batch-Marco: path=File.directory+File.name; run("Brightness/Contrast..."); setMinAndMax(500, 20000); run("RGB Color"); The resulting files have occasional (0,0,0) files when they should be non-black. There is no reproducibility that we can find on which files will be written as "black." It seems to be random. We have tested this on 3 Mac laptops (2 running El Cap and one running Yosemite with the the El Cap running latest version of FIJI as of today) while the Yosemite is using 1.50e. The PC seems to be fine- no black images. I am sending this bug report from Yosemite 10.8.5 Please note that we tested the same data set when trouble-shooting though it happens with all data sets. We also tried: -pausing after the RGB command: waitForUser( "Pause","Some \n Dialog"); -one one laptop running Yosemite, there seemed to be a correlation with slowing down the process and better results (few black images) -we are reading and writing directly from the computers- no external drives Information about your version of Java: os.arch => x86_64 os.name => Mac OS X os.version => 10.8.5 java.version => 1.6.0_65 java.vendor => Apple Inc. java.runtime.name => Java(TM) SE Runtime Environment java.runtime.version => 1.6.0_65-b14-462-11M4609 java.vm.name => Java HotSpot(TM) 64-Bit Server VM java.vm.version => 20.65-b04-462 java.vm.vendor => Apple Inc. java.vm.info => mixed mode java.awt.graphicsenv => apple.awt.CGraphicsEnvironment java.specification.name => Java Platform API Specification java.specification.version => 1.6 sun.cpu.endian => little sun.desktop => null file.separator => / The up-to-date check says: CHECK_TURNED_OFF Information relevant to JAVA_HOME related problems: JAVA_HOME is set to: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/ imagej.dir => /Applications/Fiji.app Information about the version of each plugin: Activated update sites: ImageJ: http://update.imagej.net/ (last check:20151221191554) Fiji: http://update.fiji.sc/ (last check:20151221212403) Files not up-to-date: c295a4c5 (OBSOLETE_UNINSTALLED) 20140702174714 jars/jdom-2.0.2.jar 64241209 (OBSOLETE_UNINSTALLED) 20140702174714 jars/jdom-contrib.jar 1ad3be0d (LOCAL_ONLY) 20140703084714 jars/jpedalSTD.jar d2af3ac9 (OBSOLETE_UNINSTALLED) 20140702174714 jars/kryo-2.21-shaded.jar e3f588d6 (LOCAL_ONLY) 20160310183321 macros/BatchMacro.ijm 7f373f94 (LOCAL_ONLY) 20140708115900 macros/MicroTubBleachTool.txt 77d1ae42 (LOCAL_ONLY) 20140707003705 plugins/EMBL_sampleimages-1.0.0.jar 3960cab8 (LOCAL_ONLY) 20140708115900 plugins/MicroTubBleachTool.txt f84c20e3 (LOCAL_ONLY) 20140706091027 plugins/Mosaic_ToolSuite.jar 4fe1cfd7 (LOCAL_ONLY) 20140714081951 plugins/SNR_.jar 12f0acc6 (OBSOLETE_UNINSTALLED) 20150213222520 plugins/Threshold_Colour-2.0.1.jar 71331805 (LOCAL_ONLY) 20160309095328 plugins/jacop_.jar 739a58eb (LOCAL_ONLY) 20140706082321 plugins/mser/MSER$1.class 3595fc8b (LOCAL_ONLY) 20140706082321 plugins/mser/MSER$ConnectedComponent.class b0fd6d19 (LOCAL_ONLY) 20140706082321 plugins/mser/MSER$GrowHistory.class 74ed5b1e (LOCAL_ONLY) 20140706082321 plugins/mser/MSER$OffsetsPostions.class 7d2d0830 (LOCAL_ONLY) 20140706082321 plugins/mser/MSER$Parameters.class f42c66b1 (LOCAL_ONLY) 20140706082321 plugins/mser/MSER.class 1b4b766b (LOCAL_ONLY) 20140706082321 plugins/mser/Region.class ff26cb9f (LOCAL_ONLY) 20140706082321 plugins/mser/RegionFactory.class