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Bugzilla – Bug 707 |
run("Image sequence ...") opens unwanted dialog window |
Last modified: 2014-03-03 20:58:06 CST |
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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 All, I have a directory with two subdirectories (named dir1 and dir2) containing image series and I would like to open both series within a macro. When I start Fiji and run the macro (code see below) for the first time, stack1 is opened fine without the Image Sequence dialog popping up. But stack2 does´t. Instead the Image sequence dialog pops up. The options given in the macro, e.g. scale=50) are not automatically taken in this dialog. When I run the macro for a second time, also the first stack is not opened automatically. The bug seems to be Fiji specific since the macro runs fine with plain ImageJ (1.48r) source_dir = getDirectory("Source Directory"); stack1=source_dir+"dir1"+File.separator; run("Image Sequence...", "open=&stack1 scale=50 convert sort"); stack2=source_dir+"dir2"+File.separator; run("Image Sequence...", "open=&stack2 scale=50 convert sort"); Thank you, Martin 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: CHECK_TURNED_OFF Information relevant to JAVA_HOME related problems: JAVA_HOME is set to: C:\Users\martin\Desktop\FIJI~2.APP\Fiji.app/java/win64/jdk1.6.0_24//jre ij.dir => C:\Users\martin\Desktop\FIJI~2.APP\Fiji.app Information about the version of each plugin: 2c93d9a6:2d9d2593:be71a9c0 20131204180458 :00efaa6 bdf6dc82:91b262e7:09001cd1 20130715055040 :019970f 13ce586a:be23db6b:315fb93c 20131204180457 :02ea642 3e2f1199:e01e63c7:e01e63c7 20070515132330 :030038e 426d64f4:be49972e:be49972e 20131204180518 :0307564 8c8f6d33:ac4c137b:ac4c137b 20130715055038 :0326851 dc0a9d07:01345c54:3449bd49 20140107142259 :034fe21 6cfb774f:b8f734bb:b8f734bb 20131204180515 :04478f7 58ca5c05:3f4f326a:3f4f326a 20131204181233 :0449e3e 6738a701:d6932866:d6932866 20130715055038 :04a4a5c e8f2c736:013da83a:f76888cb 20131204181233 :04f8e59 6bd9ca65:0954132b:637e808e 20140226105252 :05b1de4 30420365:5a23ed73:5a23ed73 20130715055038 :069ebf3 738cf583:36e9a80a:bca93bda 20140107142257 :087a0a0 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20130715055042 :fc6c041 6b5ff8b0:e81b757e:5ad0451e 20140107142300 :fc7638b e39a6824:1e2967fd:59fc158f 20131204180447 :fc9dc6d 889b108a:91cf7904:d2d3fa13 20130715055038 :fcc28a5 4685bacc:30ee9e13:f380bd40 20140226105239 :fd69038 01c74ba1:65e68950:8e461112 20130715055038 :fd9b13d 4ba3c76b:a2e8cdd8:a2e8cdd8 20130715055038 :ff0e448 5fb422d7:5bab7768:5bab7768 20130715055038 :ff131d4 a15791e0:723fa207:2510e060 20131204180504 :ffff0cc 7c30c48a 20130715055038 Contents/Info.plist 6b82c620 20130715055038 Contents/Resources/Fiji.icns 992807f6 20130715055038 Contents/Resources/ImageJ.icns 0f7817ae 20131204180457 ImageJ-win64.exe 1faaeed6 20130715055044 images/icon-flat.png a02d5340 20130715055044 images/icon.png 91ece67d 20131219131210 jars/JWlz.jar c3f8675e 20130715055038 jars/Jama.jar ad44ab73 20130715055038 jars/VIB-lib-2.0.0-SNAPSHOT.jar bd573380 20130715055038 jars/VectorString.jar 5cf0711e 20131204181231 jars/akutan-1.0.jar 8e160955 20130715055038 jars/ant-junit.jar 4124ed0d 20130715055038 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20130715055040 jars/jacl.jar 8c636e50 20130715055040 jars/jai_codec.jar 717dd8e0 20130715055040 jars/jai_core.jar e5852db5 20131204180445 jars/jai_imageio-1.0.1.jar ac77c0f5 20140226105255 jars/jama-1.0.3.jar e4ac596e 20130715055040 jars/java-cup-0.11a.jar 15f34947 20130715055040 jars/javac.jar fb25609e 20130715055040 jars/javassist-3.16.1-GA.jar ccf6c908 20130715055040 jars/jcommon-1.0.17.jar efe2e903 20131204180502 jars/jdatepicker-1.3.2.jar c295a4c5 20130715055040 jars/jdom-2.0.2.jar 64241209 20130715055040 jars/jdom-contrib.jar 166036ab 20130715055040 jars/jep.jar 55d8499c 20130715055040 jars/jfreechart-1.0.14.jar 0e15c072 20130715055040 jars/jgrapht-0.8.3.jar 0b768690 20130715055040 jars/jgraphx-1.10.4.1.jar 242749dc 20130715055040 jars/jhotdraw-7.6.0.jar 90915f54 20130715055040 jars/jna.jar 4c09d41c 20131219131210 jars/joda-time-2.2.jar 1ad3be0d 20130715055040 jars/jpedalSTD.jar da499a7d 20130715055040 jars/jruby.jar 65f86378 20130715055040 jars/js.jar 2ce2c00a 20130715055042 jars/jsch-0.1.49.jar 24d47d70 20130715055042 jars/junit-4.8.1.jar c480d491 20131204181229 jars/jxlayer.jar f5968a72 20130715055042 jars/jython.jar 5ce5840c 20130715055042 jars/jzlib.jar d2af3ac9 20131219131204 jars/kryo-2.21-shaded.jar 5a6f6f25 20131204180530 jars/legacy-imglib1-2.0.0-SNAPSHOT.jar 8523861f 20131204181234 jars/lma-1.3.jar 561c8afa 20140214145529 jars/loci-common.jar 35c256ae 20131204180447 jars/log4j-1.2.17.jar d1d9b590 20140107142259 jars/mapdb-0.9.7.jar 1daf5806 20130715055042 jars/markdownj-0.3.0-1.0.2b4.jar e8d453ec 20131204180511 jars/mdbtools-java-4.4.9.jar 70e68706 20131204180503 jars/metakit-4.4.9.jar 7f0caa5d 20130715055042 jars/miglayout-3.7.3.1-swing.jar a11cfc71 20130715055042 jars/mij-1.3.6-fiji2-SNAPSHOT.jar b6bf3817 20140107142300 jars/mines-jtk-20100113.jar 5bd64fbe 20131204180504 jars/mpicbg-0.6.1-SNAPSHOT.jar e1a35a80 20140214145529 jars/native-lib-loader-2.0-SNAPSHOT.jar 04f8e59b 20131204181233 jars/native-library-util-2.0-SNAPSHOT.jar 8b4b4a32 20131204180534 jars/netcdf-4.0.03.jar f41603bf 20130715055042 jars/object-inspector-0.1.jar 5da6834c 20131210095019 jars/ome-formats-0.3.0.jar 7e0e5ad8 20140206232602 jars/ome-xml.jar e0088259 20130715055042 jars/pal-optimization.jar 82577709 20130715055042 jars/pentaho-package-manager-1.0.0.jar 096abf51 20131219131205 jars/poi-loci.jar c586a356 20130715055042 jars/postgresql.jar 72184439 20131204180459 jars/rsyntaxtextarea-2.0.4.1.jar fd690387 20140226105239 jars/scifio-0.9.2.jar 4792fc4e 20131210095019 jars/scifio-bf-compat-1.3.2.jar af5808fb 20131210095018 jars/scifio-lifesci-0.2.2.jar 38772153 20140226105142 jars/scijava-common-2.9.0.jar eedc0cd9 20130715055042 jars/serializer-2.7.1.jar 572a727b 20131204180454 jars/slf4j-api-1.7.2.jar 9ae3dd1b 20131204180452 jars/slf4j-log4j12-1.7.2.jar 1dedefe8 20130715055042 jars/tools-1.4.2.jar 68c26a79 20131204180502 jars/udunits-4.3.18.jar 7d5ba6c5 20130715055042 jars/wavelets.jar fc6c0417 20130715055042 jars/weave_jy2java.jar 9a71e194 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luts/glasbey.lut 325c01f3 20130715055044 luts/glow.lut f2b7e781 20131204181229 luts/lifetime.lut 1f99f07e 20130715055044 luts/phase.lut 52a3c399 20130715055044 luts/physics.lut 49f5e48a 20130715055044 luts/royal.lut 898954dd 20130715055044 luts/sepia.lut ebd4ed6b 20130715055044 luts/smart.lut 36e7ca9e 20130715055044 luts/thal.lut 940b38f9 20130715055044 luts/thallium.lut 17243681 20130715055044 luts/unionjack.lut 49b0a061 20130802090211 macros/AutoRun/install-shortcuts.ijm 324fc6ad 20130618175153 macros/BatchMacro.ijm 25abcd0c 20130715055044 macros/StartupMacros.fiji.ijm cc9e8f22 20120927102535 macros/StartupMacros.ijm 727cfd08 20130801152017 macros/StartupMacros.txt cc9d1580 20130808103222 macros/_old_StartupMacros.txt a97e1da9 20130715055044 macros/listManagement.txt ace7fa1a 20131014093918 macros/my-shortcuts.ijm 732db46b 20121005130507 macros/overlay_example_macros.ijm a6ee6b6b 20140226105306 macros/toolsets/BioVoxxel_Toolbox.ijm 1785bbbf 20130715055044 macros/toolsets/Clear Custom Tools.txt 54200f47 20130715055044 macros/toolsets/Drawing Tools.txt cb6970ee 20131204183807 macros/toolsets/LineAndProfileTool.txt 9bd39ac4 20130715055044 macros/toolsets/Lookup Tables.txt 93050a3f 20111117192504 macros/toolsets/MBF_StartupMacros.txt 6264ce63 20111115185109 macros/toolsets/Magic_Montage.txt 545b95ef 20130605195721 macros/toolsets/Nearest_Neighbor_Indicator.ijm 5c7af901 20130625111729 macros/toolsets/ROI Manager Tools.txt 8fbab9f6 20130715055038 plugins/3D_Blob_Segmentation-2.0.0-SNAPSHOT.jar d5c84beb 20130715055038 plugins/3D_Objects_Counter-2.0.0-SNAPSHOT.jar f42bdae5 20130715055038 plugins/3D_Viewer.jar 02a52ea2 20131204181229 plugins/ActionBar/BioVoxxel_bar.txt 547dbaf3 20130618160202 plugins/ActionBar/Shared Bars/BIOP_PSF_Quality.ijm e9bf0b0f 20130625084935 plugins/ActionBar/Shared Bars/BIOP_SIMAssess.ijm 88a76b5c 20131114210659 plugins/ActionBar/Shared Bars/BIOP_VSI_Reader.ijm 68175df5 20130715055038 plugins/Algorithm_Launcher.jar 9274f337 20130715055038 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