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Bugzilla – Bug 369 |
headless: duplication of an image fails |
Last modified: 2011-10-19 20:09:39 CDT |
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Hi, I need to run a macro headless on our cluster which iterates many times over the same image stack. Because the image gets destroyed in that macro (by splitChannels) I keep the original image open and generate working copies via the Duplicate command. This works nicely when I run fiji in normal, interactive (GUI) mode and in batch mode, but it fails when run headless. How can I fix this? in the test suite I put together I call fiji three times with the same task: the first call is headless the second call runs in batch mode the third call is in normal GUI mode the different sections are marked as "headless", "batch" and "GUI" in the standard output below. btw, this behavior is not Mac-specific. I get the same results (with slightly different line numbers) on a Linux node which I run in X-redirect (nxclient to our cluster). when run on the cluster without GUI (ssh) I get the same error in the batch-run as in the headless-run. the Gui-run of course complains about a missing GUI, which is fine. The raw reader is not the problem either. I tested this also with tifs, leading to the same behavior/error messages. Please help, thanks, aRnim --------------- the call --------------- jenetta$ sh callFijiWithImageAndMacro2.sh /Volumes/secondaryHD/secondary-cache/GMR_9E11_AE_01_10-fA01b_C111005_20111005101713843.reg.local.raw /Volumes/rubinlab/aRnim/scripts/ij/macros/cluster/testDuplication.ijm 0 --------------- the shell wrapper: callFijiWithImageAndMacro2.sh --------------- #!/bin/bash # display start date of process date # this script is a subversion of callFijiWithImageAndMacro designed to work with # raw files. due to its proprietary nature this file format is not recognized # correctly by imageJ/fiji but a custom-made reader has to be called from inside # the macro called by this script!!! # macros called with this script can not expect to encounter an open image but # need to call the raw-reader first to open the image which is passed as # macro parameter. to recieve the parameter from within the macro called by this # script use the macro function getArgument(). # due to this fact no parameters can be passed to the macro anymore. # $1 = full (platform dependent) path to image # $2 = full (platform dependent) path to macro # extract basename from image name in $1 # "basename" gave strange results in test, therefore this was constructed from scratch. fn=$(echo $1 |awk -F "/" '{print $NF}') bn=$(echo $fn |awk -F "." '{print $1}') # define local directory to store image files temporarily. user=$(whoami) # define OS-specific parameters. case $(uname) in Linux) img=/tmp/$fn baseString=/groups/rubin/home/rubinlab/ fiji=/groups/rubin/home/jenetta/Desktop/fiji/fiji/Fiji.app/fiji-linux64 ;; Darwin) img=/scratch/$user/$fn baseString=/Volumes/rubinlab/ fiji=/Volumes/secondaryHD/localfiji/fiji${3}/Fiji.app/Contents/MacOS/fiji-macosx ;; *) printf "ERROR: did not recognize platform.\n" ;; esac # tests showed, that fiji loads from a local drive significantly faster, # than over the network. This is why this script copies the image files # it works with to a temporary directory and opens them from there. When # done the script removes the current image from the local drive. # make image local if [ ! -e $img ]; then cp -v $1 $img fi # call fiji headlessly with Image and macro # --headless prevents fiji from rendering any GUI element: no main window, no dialogs, no error messages # --> http://fiji.sc/wiki/index.php/Scripting_Help # disadvantage: if a macro produces dialogs ( maybe left-overs from development) fiji gonna crash, throwing an error message. # -eval 'run("Refresh JRuby Scripts","");' I am not sure why, but this piece is really needed, without the call dies # -Dplugins.dir=${baseString}aRnim/scripts/ij/ this defines the plugins directory # by that location also the macro's dir is defined: macrosdir=$pluginsdir/../macros # $img an image passed to imagej/fiji as a first parameter is automatically opened # -macro $2 this is a macro-call generic to fiji (I think imagej is handeling this the same way). # -batch Runs a macro or script in batch (no GUI) mode, passing it an optional argument. # ImageJ exits when the macro finishes. # --> http://rsbweb.nih.gov/ij/docs/install/linux.html#options if [ -d $baseString ]; then printf "=================\nheadless\n" $fiji --headless -eval 'run("Refresh JRuby Scripts","");' -Dplugins.dir=${baseString}aRnim/scripts/ij/ -macro $2 "$img" -batch; printf "=================\nbatch\n" $fiji -eval 'run("Refresh JRuby Scripts","");' -Dplugins.dir=${baseString}aRnim/scripts/ij/ -macro $2 "$img" -batch; printf "=================\nGUI\n" $fiji -eval 'run("Refresh JRuby Scripts","");' -Dplugins.dir=${baseString}aRnim/scripts/ij/ -macro $2 $img; else printf "ERROR: $baseString is not mounted.\n\n" fi # remove local copy of the image rm $img # display date when process finished. date --------------- the macro: testDuplication.ijm --------------- IID = ""; image=getArgument(); OPEN_FILE(image); orgID=getImageID(); title=getTitle(); fn=split(title, "/"); fn=fn[lengthOf(fn)-1]; if(isOpen(IID) == 0) { Stack.getDimensions(width, height, channels, slices, frames); print("tick", nImages()); run("Duplicate...", "title="+fn+" duplicate channels=1-"+channels+" slices=1-"+slices); print("tack", nImages()); IID=getImageID(); } function OPEN_FILE(fileName) { print("open", fileName); if (endsWith(fileName, "lsm")) { print("lsm recognized. Using bio-formats."); // run("Bio-Formats", "open="+fileName+" color_mode=Default view=Hyperstack stack_order=XYCZT"); run("LSM...", "open="+fileName); } else if (endsWith(fileName, "v3draw") || endsWith(fileName, "raw")) { print("raw recognized.Using raw reader."); run("raw reader", "open="+fileName); fn=split(fileName, "/"); fn=fn[lengthOf(fn)-1]; rename(fn); } else { print("no special file format recognized. using standard opening mechanism."); open(fileName); } fn=split(fileName, "/"); fn=fn[lengthOf(fn)-1]; bn=split(fn, "."); bn=bn[0]; if(endsWith(getTitle(), fn) == 0) { rename(fn); } } --------------- the standard out --------------- ================= headless open /scratch/jenetta/GMR_9E11_AE_01_10-fA01b_C111005_20111005101713843.reg.local.raw raw recognized.Using raw reader. tick 1 java.lang.ClassCastException: java.lang.String cannot be cast to java.awt.TextField at ij.plugin.Duplicator.showHSDialog(Duplicator.java:306) at ij.plugin.Duplicator.duplicateHyperstack(Duplicator.java:247) at ij.plugin.Duplicator.run(Duplicator.java:37) at ij.IJ.runPlugInUnchecked(IJ.java:175) at ij.IJ.runPlugIn(IJ.java:157) at ij.Executer.runCommand(Executer.java:150) at ij.Executer.run(Executer.java:81) at ij.IJ.run(IJ.java:269) at ij.macro.Functions.doRun(Functions.java:569) at ij.macro.Functions.doFunction(Functions.java:80) at ij.macro.Interpreter.doStatement(Interpreter.java:203) at ij.macro.Interpreter.doBlock(Interpreter.java:518) at ij.macro.Interpreter.doStatement(Interpreter.java:239) at ij.macro.Interpreter.doIf(Interpreter.java:852) at ij.macro.Interpreter.doStatement(Interpreter.java:215) at ij.macro.Interpreter.doStatements(Interpreter.java:191) at ij.macro.Interpreter.run(Interpreter.java:102) at ij.macro.Interpreter.run(Interpreter.java:72) at ij.macro.Interpreter.run(Interpreter.java:83) at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:102) at ij.plugin.Macro_Runner.runMacroFile(Macro_Runner.java:87) at ij.IJ.runMacroFile(IJ.java:121) at ij.ImageJ.main(ImageJ.java:647) at fiji.Main.main(Main.java:363) ================= batch open /scratch/jenetta/GMR_9E11_AE_01_10-fA01b_C111005_20111005101713843.reg.local.raw raw recognized.Using raw reader. tick 1 tack 2 ================= GUI (this runs as expected. tick and tack can be found in the Log window.) [end of sermon] Information about your version of Java - this information is useful for the Fiji developers: os.arch => x86_64 os.name => Mac OS X os.version => 10.6.8 java.version => 1.6.0_26 java.vendor => Apple Inc. java.runtime.name => Java(TM) SE Runtime Environment java.runtime.version => 1.6.0_26-b03-384-10M3425 java.vm.name => Java HotSpot(TM) 64-Bit Server VM java.vm.version => 20.1-b02-384 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: You wanted never to be reminded. Information relevant to JAVA_HOME related problems: JAVA_HOME is set to: null fiji.dir => /Volumes/secondaryHD/localfiji/fiji9/Fiji.app Information about the version of each plugin: 7d4fe4018e4eec8eef8d52d0a335ef9a5e076f94 20110307092649 fiji-macosx 0daf9183a73311e50bf0152443cb662d3f74885a 20110307092649 fiji-tiger ca9bc7b44bf9b2b7b91f4aecabf1296634337e99 20110307090953 jars/Fiji.jar 31fc72943db1de218eb827e7ea3becc16d76d851 20110307090953 jars/Jama-1.0.2.jar 83496926787f5d4215cd6a4c54e816014b413f34 20110307091000 jars/VIB-lib.jar bd57338068f48b9ce4c5275544633ba172b0902a 20110307090955 jars/VectorString.jar 68a9e41d2a7cec1ffedd5e38f4c064927b43b3c7 20110303144100 jars/ant-junit.jar 4199e18036ba2020bdcbc733f603564f41cf9009 20110303144100 jars/ant-launcher.jar 92b2335d3a97549b633dbcc3c41381a90f2b924b 20110303144100 jars/ant-nodeps.jar b1492f77c5c13e4f9dc05fe0ba9f95d6ec826660 20110303144100 jars/ant.jar 5bab776822719667a604b8fb2eafc679161aeb0f 20110307090954 jars/autocomplete.jar 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the source code repository. If things go according to plan, I will upload the fixes to the updater tomorrow. FWIW. this was my commandline to reproduce quickly: ./fiji --headless -eval 'newImage("a1", "8-bit", 2, 2, 8);run("Stack to Hyperstack...", "channels=2 slices=2 frames=2");run("Duplicate...", "title=Untitled-1 channels=1-2 slices=1-2 frames=1-2");print(nImages);' -batch and this is the commit with the fix: http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=commitdiff;h=22dc3c8b19dd4d03058a6a4a5d880315a7d1fdf2