Running a macro with the Scale command headless fails
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Running a macro with the Scale command headless fails
 
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Hello,
I'd like to run an IJ1 macro headless. It uses the Scale command. This fails apparently because the Scale dialog box cannot be run headless. Can anyone suggest a workaround? Minimal example below. With many thanks, Greg. PS I tried to sign up for http://forum.imagej.net/ using both GitHub & google authentication (gmail address) and directly with my @cam.ac.uk email. I never received a confirmation email. A repeat of this? http://forum.imagej.net/t/forum-server-issues-registration-and-notification-emails-not-sent/3371 --- simple_scale.ijm --- run("Bat Cochlea Volume (19K)"); run("Scale...", "x=.5 y=.5 z=.5 width=60 height=77 depth=57 interpolation=Bilinear average process"); --- snip --- $ /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --run simple_scale.ijm -batch Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release $ /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run simple_scale.ijm -batch Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release java.lang.NullPointerException at ij.plugin.Scaler.showDialog(Scaler.java:253) at ij.plugin.Scaler.run(Scaler.java:42) at ij.IJ.runPlugIn(IJ.java:187) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at ij.IJ.run(IJ.java:297) at ij.macro.Functions.doRun(Functions.java:601) at ij.macro.Functions.doFunction(Functions.java:96) at ij.macro.Interpreter.doStatement(Interpreter.java:230) at ij.macro.Interpreter.doStatements(Interpreter.java:218) at ij.macro.Interpreter.run(Interpreter.java:115) at ij.macro.Interpreter.run(Interpreter.java:85) at ij.macro.Interpreter.run(Interpreter.java:96) at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155) at ij.IJ.runMacro(IJ.java:134) at ij.IJ.runMacro(IJ.java:123) at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1052) at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1048) at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:999) at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1048) at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:136) at org.scijava.script.ScriptModule.run(ScriptModule.java:159) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:237) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) -- Gregory Jefferis, PhD Tel: +44 1223 267048 Division of Neurobiology MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge, CB2 OQH, UK http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis http://jefferislab.org http://www.zoo.cam.ac.uk/departments/connectomics -- Gregory Jefferis, PhD Division of Neurobiology MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge, CB2 OQH, UK http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis http://jefferislab.org http://www.zoo.cam.ac.uk/departments/connectomics -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Running a macro with the Scale command headless fails
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Hi Gregory,
You could try to use: setVoxelSize(width, height, depth, unit) Defines the voxel dimensions and unit of length ("pixel", "mm", etc.) for the current image or stack. A "um" unit will be converted to "µm". The depth argument is ignored if the current image is not a stack. See also: getVoxelSize<https://imagej.nih.gov/ij/developer/macro/functions.html#getVoxelSize>. Hope this helps, Volko ________________________________ From: Gregory Jefferis <[hidden email]> Sent: 31 December 2017 09:15:38 To: [hidden email] Subject: Running a macro with the Scale command headless fails Hello, I'd like to run an IJ1 macro headless. It uses the Scale command. This fails apparently because the Scale dialog box cannot be run headless. Can anyone suggest a workaround? Minimal example below. With many thanks, Greg. PS I tried to sign up for http://forum.imagej.net/ using both GitHub & google authentication (gmail address) and directly with my @cam.ac.uk email. I never received a confirmation email. A repeat of this? http://forum.imagej.net/t/forum-server-issues-registration-and-notification-emails-not-sent/3371 --- simple_scale.ijm --- run("Bat Cochlea Volume (19K)"); run("Scale...", "x=.5 y=.5 z=.5 width=60 height=77 depth=57 interpolation=Bilinear average process"); --- snip --- $ /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --run simple_scale.ijm -batch Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release $ /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run simple_scale.ijm -batch Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release java.lang.NullPointerException at ij.plugin.Scaler.showDialog(Scaler.java:253) at ij.plugin.Scaler.run(Scaler.java:42) at ij.IJ.runPlugIn(IJ.java:187) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at ij.IJ.run(IJ.java:297) at ij.macro.Functions.doRun(Functions.java:601) at ij.macro.Functions.doFunction(Functions.java:96) at ij.macro.Interpreter.doStatement(Interpreter.java:230) at ij.macro.Interpreter.doStatements(Interpreter.java:218) at ij.macro.Interpreter.run(Interpreter.java:115) at ij.macro.Interpreter.run(Interpreter.java:85) at ij.macro.Interpreter.run(Interpreter.java:96) at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155) at ij.IJ.runMacro(IJ.java:134) at ij.IJ.runMacro(IJ.java:123) at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1052) at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1048) at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:999) at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1048) at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:136) at org.scijava.script.ScriptModule.run(ScriptModule.java:159) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:237) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) -- Gregory Jefferis, PhD Tel: +44 1223 267048 Division of Neurobiology MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge, CB2 OQH, UK http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis http://jefferislab.org http://www.zoo.cam.ac.uk/departments/connectomics -- Gregory Jefferis, PhD Division of Neurobiology MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge, CB2 OQH, UK http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis http://jefferislab.org http://www.zoo.cam.ac.uk/departments/connectomics -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Running a macro with the Scale command headless fails
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Thanks a lot for the response however I don't think that will help, so let me clarify. I need to resample the image (reducing the number of pixels on each axis) not change the spatial calibration. Many thanks, Greg.
Sent from my iPhone > On 31 Dec 2017, at 09:37, Straub, Volko A. (Dr.) <[hidden email]> wrote: > > setVoxelSize(width, height, depth, unit) > Defines the voxel dimensions and unit of length ("pixel", "mm", etc.) for the current image or stack. A "um" unit will be converted to "µm". The depth argument is ignored if the current image is not a stack. See also: getVoxelSize<https://imagej.nih.gov/ij/developer/macro/functions.html#getVoxelSize>. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Good day Gregory,
not being a specialist for non-GUI operation of ImageJ but this call works for me (_plain_ ImageJ-1.51t under macOS 10.11.6, Java 1.6.0): ////////// macro "testMacro.txt" path = getArgument(); open(path); run("Scale...", "x=0.5 y=0.5 z=0.5 width=60 height=77 depth=57 interpolation=Bilinear average process"); print("success"); ////////// _Terminal (with result, i.e. ImageJ launched and running)_: java -jar /Applications/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar -macro /Applications/ImageJ/macros/testMacro.txt /Applications/ImageJ/testimages/bat-cochlea-volume.tif _Terminal (result not shown and not saved, i.e. ImageJ doesn't launch)_: java -jar /Applications/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar -batch /Applications/ImageJ/macros/testMacro.txt /Applications/ImageJ/testimages/bat-cochlea-volume.tif HTH Herbie :::::::::::::::::::::::::::::::::::::::::::::: Am 31.12.17 um 15:05 schrieb Gregory Jefferis: > Thanks a lot for the response however I don't think that will help, so let me clarify. I need to resample the image (reducing the number of pixels on each axis) not change the spatial calibration. Many thanks, Greg. > > Sent from my iPhone > >> On 31 Dec 2017, at 09:37, Straub, Volko A. (Dr.) <[hidden email]> wrote: >> >> setVoxelSize(width, height, depth, unit) >> Defines the voxel dimensions and unit of length ("pixel", "mm", etc.) for the current image or stack. A "um" unit will be converted to "µm". The depth argument is ignored if the current image is not a stack. See also: getVoxelSize<https://imagej.nih.gov/ij/developer/macro/functions.html#getVoxelSize>. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Running a macro with the Scale command headless fails
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Dear Herbie,
Thanks a lot for your response. However, I specifically need to be able to run this script headless on a cluster (see https://imagej.net/Headless <https://imagej.net/Headless>) and for that I need to use the --headless switch to the Fiji/ImageJ launcher. At your suggestion, I did try using the plain ImageJ 1.50 distribution (http://wsr.imagej.net/distros/linux/ij150-linux64-java8.zip) on the target Linux cluster but I got the early error pasted below. Further testing revealed that headless support is broken within ImageJ itself before it even tries to run a script, so that is not going to help me. So the question remains, if I use the Fiji/ImageJ launcher, is there a way to get round the fact that the Scale... command does not work headless? This could be another way of resampling images in x,y,z that does not depend on a GUI element that cannot be run headless. Many thanks, Greg. [jefferis@hex ImageJ]$ ./ImageJ --headless -batch simple_scale.ijm Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release Exception in thread "main" java.awt.HeadlessException at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204) at java.awt.MenuComponent.<init>(MenuComponent.java:159) at java.awt.MenuItem.<init>(MenuItem.java:214) at java.awt.MenuItem.<init>(MenuItem.java:198) at java.awt.Menu.<init>(Menu.java:157) at java.awt.Menu.<init>(Menu.java:137) at ij.Menus.getMenu(Menus.java:775) at ij.Menus.getMenu(Menus.java:765) at ij.Menus.addMenuBar(Menus.java:105) at ij.IJ.init(IJ.java:362) at ij.IJ.runMacroFile(IJ.java:146) at ij.ImageJ.main(ImageJ.java:716) I > On 31 Dec 2017, at 17:38, Herbie <[hidden email]> wrote: > > Good day Gregory, > > not being a specialist for non-GUI operation of ImageJ but this call works for me (_plain_ ImageJ-1.51t under macOS 10.11.6, Java 1.6.0): > > ////////// macro "testMacro.txt" > path = getArgument(); > open(path); > run("Scale...", "x=0.5 y=0.5 z=0.5 width=60 height=77 depth=57 interpolation=Bilinear average process"); > print("success"); > ////////// > > _Terminal (with result, i.e. ImageJ launched and running)_: > java -jar /Applications/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar -macro /Applications/ImageJ/macros/testMacro.txt /Applications/ImageJ/testimages/bat-cochlea-volume.tif > > _Terminal (result not shown and not saved, i.e. ImageJ doesn't launch)_: > java -jar /Applications/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar -batch /Applications/ImageJ/macros/testMacro.txt /Applications/ImageJ/testimages/bat-cochlea-volume.tif > > HTH > > Herbie > > :::::::::::::::::::::::::::::::::::::::::::::: > Am 31.12.17 um 15:05 schrieb Gregory Jefferis: >> Thanks a lot for the response however I don't think that will help, so let me clarify. I need to resample the image (reducing the number of pixels on each axis) not change the spatial calibration. Many thanks, Greg. >> Sent from my iPhone >>> On 31 Dec 2017, at 09:37, Straub, Volko A. (Dr.) <[hidden email]> wrote: >>> >>> setVoxelSize(width, height, depth, unit) >>> Defines the voxel dimensions and unit of length ("pixel", "mm", etc.) for the current image or stack. A "um" unit will be converted to "µm". The depth argument is ignored if the current image is not a stack. See also: getVoxelSize<https://imagej.nih.gov/ij/developer/macro/functions.html#getVoxelSize>. >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- Gregory Jefferis, PhD Division of Neurobiology MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge, CB2 OQH, UK http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis http://jefferislab.org http://www.zoo.cam.ac.uk/departments/connectomics -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Sorry Greg,
of being of no help with this issue! The meaning of "headless" and "without GUI" appears not being well-defined. I have no experience with running applications on clusters but I remember some posts on this list and on the Forum that deal with similar problems. As far as I remember things may improve with ImageJ-2 but as the great software architect recently mentioned: "[...] some of the IJ2 API is not yet fully stabilized." The interpretation of this statement is left to experts like you. Good luck and have a successful New Year Herbie :::::::::::::::::::::::::::::::::::::::::::::: Am 02.01.18 um 14:50 schrieb Gregory Jefferis: > Dear Herbie, > > Thanks a lot for your response. However, I specifically need to be able to run this script headless on a cluster (see https://imagej.net/Headless <https://imagej.net/Headless>) and for that I need to use the --headless switch to the Fiji/ImageJ launcher. > > At your suggestion, I did try using the plain ImageJ 1.50 distribution (http://wsr.imagej.net/distros/linux/ij150-linux64-java8.zip) on the target Linux cluster but I got the early error pasted below. Further testing revealed that headless support is broken within ImageJ itself before it even tries to run a script, so that is not going to help me. > > So the question remains, if I use the Fiji/ImageJ launcher, is there a way to get round the fact that the Scale... command does not work headless? This could be another way of resampling images in x,y,z that does not depend on a GUI element that cannot be run headless. > > Many thanks, > > Greg. > > [jefferis@hex ImageJ]$ ./ImageJ --headless -batch simple_scale.ijm > Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 > Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release > Exception in thread "main" java.awt.HeadlessException > at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204) > at java.awt.MenuComponent.<init>(MenuComponent.java:159) > at java.awt.MenuItem.<init>(MenuItem.java:214) > at java.awt.MenuItem.<init>(MenuItem.java:198) > at java.awt.Menu.<init>(Menu.java:157) > at java.awt.Menu.<init>(Menu.java:137) > at ij.Menus.getMenu(Menus.java:775) > at ij.Menus.getMenu(Menus.java:765) > at ij.Menus.addMenuBar(Menus.java:105) > at ij.IJ.init(IJ.java:362) > at ij.IJ.runMacroFile(IJ.java:146) > at ij.ImageJ.main(ImageJ.java:716) > > I > > >> On 31 Dec 2017, at 17:38, Herbie <[hidden email]> wrote: >> >> Good day Gregory, >> >> not being a specialist for non-GUI operation of ImageJ but this call works for me (_plain_ ImageJ-1.51t under macOS 10.11.6, Java 1.6.0): >> >> ////////// macro "testMacro.txt" >> path = getArgument(); >> open(path); >> run("Scale...", "x=0.5 y=0.5 z=0.5 width=60 height=77 depth=57 interpolation=Bilinear average process"); >> print("success"); >> ////////// >> >> _Terminal (with result, i.e. ImageJ launched and running)_: >> java -jar /Applications/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar -macro /Applications/ImageJ/macros/testMacro.txt /Applications/ImageJ/testimages/bat-cochlea-volume.tif >> >> _Terminal (result not shown and not saved, i.e. ImageJ doesn't launch)_: >> java -jar /Applications/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar -batch /Applications/ImageJ/macros/testMacro.txt /Applications/ImageJ/testimages/bat-cochlea-volume.tif >> >> HTH >> >> Herbie >> >> :::::::::::::::::::::::::::::::::::::::::::::: >> Am 31.12.17 um 15:05 schrieb Gregory Jefferis: >>> Thanks a lot for the response however I don't think that will help, so let me clarify. I need to resample the image (reducing the number of pixels on each axis) not change the spatial calibration. Many thanks, Greg. >>> Sent from my iPhone >>>> On 31 Dec 2017, at 09:37, Straub, Volko A. (Dr.) <[hidden email]> wrote: >>>> >>>> setVoxelSize(width, height, depth, unit) >>>> Defines the voxel dimensions and unit of length ("pixel", "mm", etc.) for the current image or stack. A "um" unit will be converted to "µm". The depth argument is ignored if the current image is not a stack. See also: getVoxelSize<https://imagej.nih.gov/ij/developer/macro/functions.html#getVoxelSize>. >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > Gregory Jefferis, PhD > Division of Neurobiology > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge, CB2 OQH, UK > > http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis > http://jefferislab.org > http://www.zoo.cam.ac.uk/departments/connectomics > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Running a macro with the Scale command headless fails
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In reply to this post by Gregory Jefferis-2
Hi Greg,
instead of Image>Scale you can also try Image>Adjust>Size. Internally, these two built-in plugins (Scaler and Resizer) are quite similar, so chances are not too high that the Resizer will work in Headless mode if the Scaler does not. The only difference that gives you a slight chance for a headless 'Size' command is the absence of a FocusListener in the Resizer. If you are happy with just averaging adjacent pixels (1/2, 1/3, 1/4 etc. of the original size, just averaging, no bilinear/bicubic kernel), there is also Image>Transform>Bin. This one has a somewhat simpler dialog, with a better chance to work in headless mode. You could also try JavaScript (or Java, BeanShell) instead of the Macro language; then you can directly access a few public methods of the Resizer (z direction) or ImageProcessor and Binner(x&y direction, unfortunately for single images only) without a dialog (the 'scale' has no suitable method): ImagePlus Resizer.zScale(ImagePlus imp, int newDepth, int interpolationMethod) ImageProcessor Binner.shrink(ImageProcessor ip, int xshrink, int yshrink, int method) ImageProcessor ImageProcessor.resize(int dstWidth, int dstHeight) As far as I remember, the 'headless' mode in ImageJ2/Fiji is quite a hack - it applies some patches to the compiled ImageJ1 code (ImageJ1 heavily depends on the user interface)... See also http://imagej.net/Headless http://imagej.net/Scripting_Headless Michael ________________________________________________________________ On 02/01/2018 14:50, Gregory Jefferis wrote: > Dear Herbie, > > Thanks a lot for your response. However, I specifically need to be able to run this script headless on a cluster (see https://imagej.net/Headless <https://imagej.net/Headless>) and for that I need to use the --headless switch to the Fiji/ImageJ launcher. > > At your suggestion, I did try using the plain ImageJ 1.50 distribution (http://wsr.imagej.net/distros/linux/ij150-linux64-java8.zip) on the target Linux cluster but I got the early error pasted below. Further testing revealed that headless support is broken within ImageJ itself before it even tries to run a script, so that is not going to help me. > > So the question remains, if I use the Fiji/ImageJ launcher, is there a way to get round the fact that the Scale... command does not work headless? This could be another way of resampling images in x,y,z that does not depend on a GUI element that cannot be run headless. > > Many thanks, > > Greg. > > [jefferis@hex ImageJ]$ ./ImageJ --headless -batch simple_scale.ijm > Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 > Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release > Exception in thread "main" java.awt.HeadlessException > at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204) > at java.awt.MenuComponent.<init>(MenuComponent.java:159) > at java.awt.MenuItem.<init>(MenuItem.java:214) > at java.awt.MenuItem.<init>(MenuItem.java:198) > at java.awt.Menu.<init>(Menu.java:157) > at java.awt.Menu.<init>(Menu.java:137) > at ij.Menus.getMenu(Menus.java:775) > at ij.Menus.getMenu(Menus.java:765) > at ij.Menus.addMenuBar(Menus.java:105) > at ij.IJ.init(IJ.java:362) > at ij.IJ.runMacroFile(IJ.java:146) > at ij.ImageJ.main(ImageJ.java:716) > > I > > >> On 31 Dec 2017, at 17:38, Herbie <[hidden email]> wrote: >> >> Good day Gregory, >> >> not being a specialist for non-GUI operation of ImageJ but this call works for me (_plain_ ImageJ-1.51t under macOS 10.11.6, Java 1.6.0): >> >> ////////// macro "testMacro.txt" >> path = getArgument(); >> open(path); >> run("Scale...", "x=0.5 y=0.5 z=0.5 width=60 height=77 depth=57 interpolation=Bilinear average process"); >> print("success"); >> ////////// >> >> _Terminal (with result, i.e. ImageJ launched and running)_: >> java -jar /Applications/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar -macro /Applications/ImageJ/macros/testMacro.txt /Applications/ImageJ/testimages/bat-cochlea-volume.tif >> >> _Terminal (result not shown and not saved, i.e. ImageJ doesn't launch)_: >> java -jar /Applications/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar -batch /Applications/ImageJ/macros/testMacro.txt /Applications/ImageJ/testimages/bat-cochlea-volume.tif >> >> HTH >> >> Herbie >> >> :::::::::::::::::::::::::::::::::::::::::::::: >> Am 31.12.17 um 15:05 schrieb Gregory Jefferis: >>> Thanks a lot for the response however I don't think that will help, so let me clarify. I need to resample the image (reducing the number of pixels on each axis) not change the spatial calibration. Many thanks, Greg. >>> Sent from my iPhone >>>> On 31 Dec 2017, at 09:37, Straub, Volko A. (Dr.) <[hidden email]> wrote: >>>> >>>> setVoxelSize(width, height, depth, unit) >>>> Defines the voxel dimensions and unit of length ("pixel", "mm", etc.) for the current image or stack. A "um" unit will be converted to "µm". The depth argument is ignored if the current image is not a stack. See also: getVoxelSize<https://imagej.nih.gov/ij/developer/macro/functions.html#getVoxelSize>. >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > Gregory Jefferis, PhD > Division of Neurobiology > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge, CB2 OQH, UK > > http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis > http://jefferislab.org > http://www.zoo.cam.ac.uk/departments/connectomics > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Running a macro with the Scale command headless fails
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> On 2 Jan 2018, at 18:16, Michael Schmid <[hidden email]> wrote:
> > instead of Image>Scale you can also try Image>Adjust>Size. > > Internally, these two built-in plugins (Scaler and Resizer) are quite similar, so chances are not too high that the Resizer will work in Headless mode if the Scaler does not. The only difference that gives you a slight chance for a headless 'Size' command is the absence of a FocusListener in the Resizer. This worked! Thanks so much, Michael. In my example it would be called: run("Size...", "width=60 height=76 depth=57 average interpolation=Bilinear"); There is a minor inconvenience of having to calculate the new size explicitly rather than just asking for 0.5x smaller, which is what I wanted, but that is a small price to pay. > You could also try JavaScript (or Java, BeanShell) instead of the Macro language; In future I might go for JavaScript or Groovy (sounds like this might be a better switch than BeanShell) but I have a few fairly complex macros that I don't want to rewrite from scratch for now. Thanks again, Greg. -- Gregory Jefferis, PhD Division of Neurobiology MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge, CB2 OQH, UK http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis http://jefferislab.org http://www.zoo.cam.ac.uk/departments/connectomics -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Gregory Jefferis-2
Hi Greg,
> This fails apparently because the Scale dialog box cannot be run > headless. Indeed, it does not work, because that command has hardcoded assumptions about having a certain number of text fields: https://github.com/imagej/ImageJA/blob/v1.51s/src/main/java/ij/plugin/Scaler.java#L257-L258 It might be possible to change ImageJ2's headless mode to still return actual AWT components (as long as they are not java.awt.Window objects). But I unfortunately cannot investigate it now. If you are interested in attempting that, I could give some pointers. > Can anyone suggest a workaround? Did you try using xvfb? http://imagej.net/Headless#Xvfb > PS I tried to sign up for http://forum.imagej.net/ using both GitHub & > google authentication (gmail address) and directly with my @cam.ac.uk > email. I never received a confirmation email. Your "jefferis" account was already activated, but "gjefferis" was not. I have now activated it. I also increased both accounts to trust level 2. So choose the one you like better and we can merge/delete the other one. Regards, Curtis -- Curtis Rueden LOCI software architect - https://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Sun, Dec 31, 2017 at 3:15 AM, Gregory Jefferis <[hidden email]> wrote: > Hello, > > I'd like to run an IJ1 macro headless. It uses the Scale command. This > fails apparently because the Scale dialog box cannot be run headless. > > Can anyone suggest a workaround? Minimal example below. > > With many thanks, > > Greg. > > PS I tried to sign up for http://forum.imagej.net/ using both GitHub & > google authentication (gmail address) and directly with my @cam.ac.uk > email. I never received a confirmation email. A repeat of this? > http://forum.imagej.net/t/forum-server-issues- > registration-and-notification-emails-not-sent/3371 > > --- simple_scale.ijm --- > run("Bat Cochlea Volume (19K)"); > run("Scale...", "x=.5 y=.5 z=.5 width=60 height=77 depth=57 > interpolation=Bilinear average process"); > --- snip --- > > > $ /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --run > simple_scale.ijm -batch > Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; > support was removed in 8.0 > Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is > deprecated and will likely be removed in a future release > > $ /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless > --run simple_scale.ijm -batch > Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; > support was removed in 8.0 > Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is > deprecated and will likely be removed in a future release > java.lang.NullPointerException > at ij.plugin.Scaler.showDialog(Scaler.java:253) > at ij.plugin.Scaler.run(Scaler.java:42) > at ij.IJ.runPlugIn(IJ.java:187) > at ij.Executer.runCommand(Executer.java:137) > at ij.Executer.run(Executer.java:66) > at ij.IJ.run(IJ.java:297) > at ij.macro.Functions.doRun(Functions.java:601) > at ij.macro.Functions.doFunction(Functions.java:96) > at ij.macro.Interpreter.doStatement(Interpreter.java:230) > at ij.macro.Interpreter.doStatements(Interpreter.java:218) > at ij.macro.Interpreter.run(Interpreter.java:115) > at ij.macro.Interpreter.run(Interpreter.java:85) > at ij.macro.Interpreter.run(Interpreter.java:96) > at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155) > at ij.IJ.runMacro(IJ.java:134) > at ij.IJ.runMacro(IJ.java:123) > at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1052) > at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1048) > at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper. > java:999) > at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1048) > at net.imagej.legacy.plugin.IJ1MacroEngine.eval( > IJ1MacroEngine.java:136) > at org.scijava.script.ScriptModule.run(ScriptModule.java:159) > at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) > at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) > at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) > at org.scijava.thread.DefaultThreadService$3.call( > DefaultThreadService.java:237) > at java.util.concurrent.FutureTask.run(FutureTask.java:266) > at java.util.concurrent.ThreadPoolExecutor.runWorker( > ThreadPoolExecutor.java:1142) > at java.util.concurrent.ThreadPoolExecutor$Worker.run( > ThreadPoolExecutor.java:617) > at java.lang.Thread.run(Thread.java:745) > > > > -- > Gregory Jefferis, PhD Tel: +44 1223 267048 > Division of Neurobiology > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge, CB2 OQH, UK > > http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis > http://jefferislab.org > http://www.zoo.cam.ac.uk/departments/connectomics > > > -- > Gregory Jefferis, PhD > Division of Neurobiology > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge, CB2 OQH, UK > > http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis > http://jefferislab.org > http://www.zoo.cam.ac.uk/departments/connectomics > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Running a macro with the Scale command headless fails
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In reply to this post by Gregory Jefferis-2
> On Dec 31, 2017, at 4:15 AM, Gregory Jefferis <[hidden email]> wrote:
> > Hello, > > I'd like to run an IJ1 macro headless. It uses the Scale command. This fails apparently because the Scale dialog box cannot be run headless. > > Can anyone suggest a workaround? Minimal example below. This bug is fixed in the latest ImageJ daily build (1.51u4). -wayne > With many thanks, > > Greg. > > PS I tried to sign up for http://forum.imagej.net/ using both GitHub & google authentication (gmail address) and directly with my @cam.ac.uk email. I never received a confirmation email. A repeat of this? http://forum.imagej.net/t/forum-server-issues-registration-and-notification-emails-not-sent/3371 > > --- simple_scale.ijm --- > run("Bat Cochlea Volume (19K)"); > run("Scale...", "x=.5 y=.5 z=.5 width=60 height=77 depth=57 interpolation=Bilinear average process"); > --- snip --- > > > $ /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --run simple_scale.ijm -batch > Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 > Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release > > $ /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run simple_scale.ijm -batch > Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 > Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release > java.lang.NullPointerException > at ij.plugin.Scaler.showDialog(Scaler.java:253) > at ij.plugin.Scaler.run(Scaler.java:42) > at ij.IJ.runPlugIn(IJ.java:187) > at ij.Executer.runCommand(Executer.java:137) > at ij.Executer.run(Executer.java:66) > at ij.IJ.run(IJ.java:297) > at ij.macro.Functions.doRun(Functions.java:601) > at ij.macro.Functions.doFunction(Functions.java:96) > at ij.macro.Interpreter.doStatement(Interpreter.java:230) > at ij.macro.Interpreter.doStatements(Interpreter.java:218) > at ij.macro.Interpreter.run(Interpreter.java:115) > at ij.macro.Interpreter.run(Interpreter.java:85) > at ij.macro.Interpreter.run(Interpreter.java:96) > at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155) > at ij.IJ.runMacro(IJ.java:134) > at ij.IJ.runMacro(IJ.java:123) > at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1052) > at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1048) > at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:999) > at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1048) > at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:136) > at org.scijava.script.ScriptModule.run(ScriptModule.java:159) > at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) > at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) > at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) > at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:237) > at java.util.concurrent.FutureTask.run(FutureTask.java:266) > at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) > at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) > at java.lang.Thread.run(Thread.java:745) > > > > -- > Gregory Jefferis, PhD Tel: +44 1223 267048 > Division of Neurobiology > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge, CB2 OQH, UK > > http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis > http://jefferislab.org > http://www.zoo.cam.ac.uk/departments/connectomics > > > -- > Gregory Jefferis, PhD > Division of Neurobiology > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge, CB2 OQH, UK > > http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis > http://jefferislab.org > http://www.zoo.cam.ac.uk/departments/connectomics -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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