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Hi Aryeh,
> Can someone out there tell me how to launch with java 6 without my having to remove java 8? I don't believe it's possible with Fiji right now due to limitations with the --java-home flag; the java 8 installation would have to be removed/renamed. This was alluded to in the FAQ but not stated explicitly. Apologies for that; I updated it to be clearer[1]. Best, Mark [1] http://imagej.net/Frequently_Asked_Questions#On_OS_X On Wed, Jul 22, 2015 at 8:09 AM, Aryeh Weiss <[hidden email]> wrote: > On 7/22/15 1:43 PM, Gabriel Landini wrote: > >> On Tuesday 21 Jul 2015 22:31:01 Wayne wrote: >> >>> ImageJ using Java 8 performs GUI operations, like opening and closing >>> windows, a lot slower on Macs. The macro at >>> >> >> >>> http://imagej.nih.gov/ij/macros/RegressionTests.txt >>> >> For some reason I do not seem to be able to find the "RegressionTest.js" >> file >> which is called in the 2nd line. Where can I download that from? >> >> If I remove that line, sometimes the macro aborts with the embryos image >> under >> java 1.6.0, claiming that there should be a stack to process (there is one >> called embryos-1.jpg) the error is "Convert Stack to Images requires a >> stack". >> Could this be a race condition? >> >> Anyway, the first run of the macro before that error, which shows the >> progress >> bar and stops for some secs shows "filter tester successful" >> >> Java 1.6.0_35: -> 37 sec then if it does not abort, total: 47 sec to the >> end. >> openkdk 1.7 : -> 508 sec total 522 to the end, >> Java 1.8.0_51: -> 703 sec, total: 714 sec to the end. >> >> 15 times slower?? >> >> I have not figured out how to switch between 1.8 and 1.6 when running > Fiji under OSX (10.10.4). > I found this, but it does not work for me (to be fair, it says it will not > work...) > I have Java 1.6 in: > /System/Library/Java/JavaVirtualMachines/1.6.0.jdk > and /usr/bin/java > > and java 1.8 lives in: > /Library/Internet Plug-Ins/JavaAppletPlugin.plugin > > Can someone out there tell me how to launch with java 6 without my having > to remove java 8? > > Thanks in advance > --aryeh > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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On 7/22/15 4:34 PM, Mark Hiner wrote:
> Hi Aryeh, > > > Can someone out there tell me how to launch with java 6 without my > having to remove java 8? > > I don't believe it's possible with Fiji right now due to limitations > with the --java-home flag; the java 8 installation would have to be > removed/renamed. This was alluded to in the FAQ but not stated > explicitly. Apologies for that; I updated it to be clearer[1]. > > Best, > Mark > Hi Mark -- thanks for your quick reply. Being naive -- I tried the following: /Applications/local/fiji/Fiji.app/Contents/MacOS/ImageJ-macosx -- java-home '/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home' And it in fact did not work, in that about imagej informs me that it is using 1.8 . However, a side effect is that the interface looks different -- particular the script editor menus are now in the script editor window (instead of at the top of the screen). Unfortunately, the problems that seem to relate to the ROI manager and window updating are still there. Best regards --aryeh > [1] http://imagej.net/Frequently_Asked_Questions#On_OS_X > > On Wed, Jul 22, 2015 at 8:09 AM, Aryeh Weiss <[hidden email] > <mailto:[hidden email]>> wrote: > > On 7/22/15 1:43 PM, Gabriel Landini wrote: > > On Tuesday 21 Jul 2015 22:31:01 Wayne wrote: > > ImageJ using Java 8 performs GUI operations, like opening > and closing > windows, a lot slower on Macs. The macro at > > > http://imagej.nih.gov/ij/macros/RegressionTests.txt > > For some reason I do not seem to be able to find the > "RegressionTest.js" file > which is called in the 2nd line. Where can I download that from? > > If I remove that line, sometimes the macro aborts with the > embryos image under > java 1.6.0, claiming that there should be a stack to process > (there is one > called embryos-1.jpg) the error is "Convert Stack to Images > requires a stack". > Could this be a race condition? > > Anyway, the first run of the macro before that error, which > shows the progress > bar and stops for some secs shows "filter tester successful" > > Java 1.6.0_35: -> 37 sec then if it does not abort, total: 47 > sec to the end. > openkdk 1.7 : -> 508 sec total 522 to the end, > Java 1.8.0_51: -> 703 sec, total: 714 sec to the end. > > 15 times slower?? > > I have not figured out how to switch between 1.8 and 1.6 when > running Fiji under OSX (10.10.4). > I found this, but it does not work for me (to be fair, it says it > will not work...) > I have Java 1.6 in: > /System/Library/Java/JavaVirtualMachines/1.6.0.jdk > and /usr/bin/java > > and java 1.8 lives in: > /Library/Internet Plug-Ins/JavaAppletPlugin.plugin > > Can someone out there tell me how to launch with java 6 without my > having to remove java 8? > > Thanks in advance > --aryeh > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Aryeh,
> And it in fact did not work, in that about imagej informs me that it is using 1.8 . Indeed, that is expected. Further in that FAQ section it mentions that --java-home will not work with Java 6 on OSX. Curtis updated the FAQ just now adding a command to launch ImageJ with Java 6, even with Java 7/8 installed: export J6="$(/usr/libexec/java_home -v 1.6)" export IJ_HOME=/Applications/Fiji.app $J6/bin/$($IJ_HOME/Contents/MacOS/ImageJ-macosx --dry-run | sed 's/ -Djava.ext.dirs=[^ ]*//') Hope that helps. - Mark On Wed, Jul 22, 2015 at 8:46 AM, Aryeh Weiss <[hidden email]> wrote: > On 7/22/15 4:34 PM, Mark Hiner wrote: > > Hi Aryeh, > > > Can someone out there tell me how to launch with java 6 without my > having to remove java 8? > > I don't believe it's possible with Fiji right now due to limitations with > the --java-home flag; the java 8 installation would have to be > removed/renamed. This was alluded to in the FAQ but not stated explicitly. > Apologies for that; I updated it to be clearer[1]. > > Best, > Mark > > > Hi Mark -- thanks for your quick reply. > > Being naive -- I tried the following: > /Applications/local/fiji/Fiji.app/Contents/MacOS/ImageJ-macosx -- > java-home '/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home' > > And it in fact did not work, in that about imagej informs me that it is > using 1.8 . > > However, a side effect is that the interface looks different -- particular > the script editor menus are now in the script editor window (instead of at > the top of the screen). > > Unfortunately, the problems that seem to relate to the ROI manager and > window updating are still there. > > Best regards > --aryeh > > > > [1] http://imagej.net/Frequently_Asked_Questions#On_OS_X > > On Wed, Jul 22, 2015 at 8:09 AM, Aryeh Weiss <[hidden email]> wrote: > >> On 7/22/15 1:43 PM, Gabriel Landini wrote: >> >>> On Tuesday 21 Jul 2015 22:31:01 Wayne wrote: >>> >>>> ImageJ using Java 8 performs GUI operations, like opening and closing >>>> windows, a lot slower on Macs. The macro at >>>> >>> >>> >>>> http://imagej.nih.gov/ij/macros/RegressionTests.txt >>>> >>> For some reason I do not seem to be able to find the >>> "RegressionTest.js" file >>> which is called in the 2nd line. Where can I download that from? >>> >>> If I remove that line, sometimes the macro aborts with the embryos image >>> under >>> java 1.6.0, claiming that there should be a stack to process (there is >>> one >>> called embryos-1.jpg) the error is "Convert Stack to Images requires a >>> stack". >>> Could this be a race condition? >>> >>> Anyway, the first run of the macro before that error, which shows the >>> progress >>> bar and stops for some secs shows "filter tester successful" >>> >>> Java 1.6.0_35: -> 37 sec then if it does not abort, total: 47 sec to >>> the end. >>> openkdk 1.7 : -> 508 sec total 522 to the end, >>> Java 1.8.0_51: -> 703 sec, total: 714 sec to the end. >>> >>> 15 times slower?? >>> >>> I have not figured out how to switch between 1.8 and 1.6 when running >> Fiji under OSX (10.10.4). >> I found this, but it does not work for me (to be fair, it says it will >> not work...) >> I have Java 1.6 in: >> /System/Library/Java/JavaVirtualMachines/1.6.0.jdk >> and /usr/bin/java >> >> and java 1.8 lives in: >> /Library/Internet Plug-Ins/JavaAppletPlugin.plugin >> >> Can someone out there tell me how to launch with java 6 without my having >> to remove java 8? >> >> Thanks in advance >> --aryeh >> >> -- >> Aryeh Weiss >> Faculty of Engineering >> Bar Ilan University >> Ramat Gan 52900 Israel >> >> Ph: 972-3-5317638 >> FAX: 972-3-7384051 >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Brandon Hurr
On Wednesday 22 Jul 2015 06:23:22 Brandon Hurr wrote:
> I took a guess and the js file is here: > http://imagej.nih.gov/ij/macros/RegressionTests.js Thanks! I had a look and could not see it. I even looked in the js folder... Selectively blind! Cheers Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Mark Hiner
On 7/22/15 9:11 PM, Mark Hiner wrote:
> Hi Aryeh, > > > And it in fact did not work, in that about imagej informs me that it > is using 1.8 . > > Indeed, that is expected. Further in that FAQ section it mentions that > --java-home will not work with Java 6 on OSX. > > Curtis updated the FAQ just now adding a command to launch ImageJ with > Java 6, even with Java 7/8 installed: > export J6="$(/usr/libexec/java_home -v 1.6)" > export IJ_HOME=/Applications/Fiji.app > $J6/bin/$($IJ_HOME/Contents/MacOS/ImageJ-macosx --dry-run | sed 's/ -Djava.ext.dirs=[^ ]*//') > Hope that helps. > > - Mark > Hi Mark -- thank you for your reply. I tried it, modifying IJ_HOME for my system. It produced the following error: Exception in thread "main" java.lang.NoClassDefFoundError: Plug-Ins/JavaAppletPlugin/plugin/Contents/Home/jre/lib/ext:/Library/Internet\ Caused by: java.lang.ClassNotFoundException: Plug-Ins.JavaAppletPlugin.plugin.Contents.Home.jre.lib.ext:.Library.Internet\ at java.net.URLClassLoader$1.run(URLClassLoader.java:202) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:190) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:247) Best regards --aryeh > On Wed, Jul 22, 2015 at 8:46 AM, Aryeh Weiss <[hidden email] > <mailto:[hidden email]>> wrote: > > On 7/22/15 4:34 PM, Mark Hiner wrote: >> Hi Aryeh, >> >> > Can someone out there tell me how to launch with java 6 without >> my having to remove java 8? >> >> I don't believe it's possible with Fiji right now due to >> limitations with the --java-home flag; the java 8 installation >> would have to be removed/renamed. This was alluded to in the FAQ >> but not stated explicitly. Apologies for that; I updated it to be >> clearer[1]. >> >> Best, >> Mark >> > > Hi Mark -- thanks for your quick reply. > > Being naive -- I tried the following: > /Applications/local/fiji/Fiji.app/Contents/MacOS/ImageJ-macosx -- > java-home > '/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home' > > And it in fact did not work, in that about imagej informs me that > it is using 1.8 . > > However, a side effect is that the interface looks different -- > particular the script editor menus are now in the script editor > window (instead of at the top of the screen). > > Unfortunately, the problems that seem to relate to the ROI manager > and window updating are still there. > > Best regards > --aryeh > > > >> [1] http://imagej.net/Frequently_Asked_Questions#On_OS_X >> >> On Wed, Jul 22, 2015 at 8:09 AM, Aryeh Weiss <[hidden email] >> <mailto:[hidden email]>> wrote: >> >> On 7/22/15 1:43 PM, Gabriel Landini wrote: >> >> On Tuesday 21 Jul 2015 22:31:01 Wayne wrote: >> >> ImageJ using Java 8 performs GUI operations, like >> opening and closing >> windows, a lot slower on Macs. The macro at >> >> >> http://imagej.nih.gov/ij/macros/RegressionTests.txt >> >> For some reason I do not seem to be able to find the >> "RegressionTest.js" file >> which is called in the 2nd line. Where can I download >> that from? >> >> If I remove that line, sometimes the macro aborts with >> the embryos image under >> java 1.6.0, claiming that there should be a stack to >> process (there is one >> called embryos-1.jpg) the error is "Convert Stack to >> Images requires a stack". >> Could this be a race condition? >> >> Anyway, the first run of the macro before that error, >> which shows the progress >> bar and stops for some secs shows "filter tester successful" >> >> Java 1.6.0_35: -> 37 sec then if it does not abort, >> total: 47 sec to the end. >> openkdk 1.7 : -> 508 sec total 522 to the end, >> Java 1.8.0_51: -> 703 sec, total: 714 sec to the end. >> >> 15 times slower?? >> >> I have not figured out how to switch between 1.8 and 1.6 when >> running Fiji under OSX (10.10.4). >> I found this, but it does not work for me (to be fair, it >> says it will not work...) >> I have Java 1.6 in: >> /System/Library/Java/JavaVirtualMachines/1.6.0.jdk >> and /usr/bin/java >> >> and java 1.8 lives in: >> /Library/Internet Plug-Ins/JavaAppletPlugin.plugin >> >> Can someone out there tell me how to launch with java 6 >> without my having to remove java 8? >> >> Thanks in advance >> --aryeh >> >> -- >> Aryeh Weiss >> Faculty of Engineering >> Bar Ilan University >> Ramat Gan 52900 Israel >> >> Ph: 972-3-5317638 >> FAX: 972-3-7384051 >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> > > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Aryeh,
Can you post the output of: $IJ_HOME/Contents/MacOS/ImageJ-macosx --dry-run My guess is that the sed pattern did not completely wipe your java.ext.dirs because you have a Java 8 JRE instead of JDK. Thanks! - Mark -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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On 7/22/15 10:14 PM, Mark Hiner wrote:
> Hi Aryeh, > > Can you post the output of: > > $IJ_HOME/Contents/MacOS/ImageJ-macosx --dry-run > > My guess is that the sed pattern did not completely wipe your > java.ext.dirs because you have a Java 8 JRE instead of JDK. > > Thanks! > - Mark > java -Djava.ext.dirs=/Applications/local/fiji/Fiji.app/java/macosx-java3d/Home/lib/ext:/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/jre/lib/ext:/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/ext:/Library/Java/Extensions:/System/Library/Java/Extensions:/System/Library/Frameworks/JavaVM.framework/Home/lib/ext -Dpython.cachedir.skip=true -Dplugins.dir=/Applications/local/fiji/Fiji.app -Xmx12288m -Xincgc -XX:PermSize=128m -Djava.class.path=/Applications/local/fiji/Fiji.app/jars/imagej-launcher-3.1.6.jar -Dimagej.dir=/Applications/local/fiji/Fiji.app -Dij.dir=/Applications/local/fiji/Fiji.app -Dfiji.dir=/Applications/local/fiji/Fiji.app -Dfiji.executable=/Applications/local/fiji/Fiji.app/Contents/MacOS/ImageJ-macosx -Dij.executable=/Applications/local/fiji/Fiji.app/Contents/MacOS/ImageJ-macosx -Djava.library.path=/Applications/local/fiji/Fiji.app/lib/macosx:/Applications/local/fiji/Fiji.app/mm/macosx net.imagej.launcher.ClassLauncher -ijjarpath jars -ijjarpath plugins net.imagej.Main --aryeh -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Thanks Aryeh. Yes, looks like the JRE directory has a space in it.. thus we
can't use space to mark the end of the java.ext.dirs match. So, try this instead: $J6/bin/$($IJ_HOME/Contents/MacOS/ImageJ-macosx --dry-run | perl -pe 's/ -Djava.ext.dirs=.*? -D/ -D/') On Wed, Jul 22, 2015 at 2:25 PM, Aryeh Weiss <[hidden email]> wrote: > On 7/22/15 10:14 PM, Mark Hiner wrote: > > Hi Aryeh, > > Can you post the output of: > > $IJ_HOME/Contents/MacOS/ImageJ-macosx --dry-run > > > My guess is that the sed pattern did not completely wipe your > java.ext.dirs because you have a Java 8 JRE instead of JDK. > > Thanks! > - Mark > > Here it is: > > java > -Djava.ext.dirs=/Applications/local/fiji/Fiji.app/java/macosx-java3d/Home/lib/ext:/Library/Internet\ > Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/jre/lib/ext:/Library/Internet\ > Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/ext:/Library/Java/Extensions:/System/Library/Java/Extensions:/System/Library/Frameworks/JavaVM.framework/Home/lib/ext > -Dpython.cachedir.skip=true -Dplugins.dir=/Applications/local/fiji/Fiji.app > -Xmx12288m -Xincgc -XX:PermSize=128m > -Djava.class.path=/Applications/local/fiji/Fiji.app/jars/imagej-launcher-3.1.6.jar > -Dimagej.dir=/Applications/local/fiji/Fiji.app > -Dij.dir=/Applications/local/fiji/Fiji.app > -Dfiji.dir=/Applications/local/fiji/Fiji.app > -Dfiji.executable=/Applications/local/fiji/Fiji.app/Contents/MacOS/ImageJ-macosx > -Dij.executable=/Applications/local/fiji/Fiji.app/Contents/MacOS/ImageJ-macosx > -Djava.library.path=/Applications/local/fiji/Fiji.app/lib/macosx:/Applications/local/fiji/Fiji.app/mm/macosx > net.imagej.launcher.ClassLauncher -ijjarpath jars -ijjarpath plugins > net.imagej.Main > > --aryeh > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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On 7/22/15 10:42 PM, Mark Hiner wrote:
> Thanks Aryeh. Yes, looks like the JRE directory has a space in it.. > thus we can't use space to mark the end of the java.ext.dirs match. > > So, try this instead: > > $J6/bin/$($IJ_HOME/Contents/MacOS/ImageJ-macosx --dry-run | perl -pe 's/ -Djava.ext.dirs=.*? -D/ -D/') > Thank you -- this appears to work properly. Best regards --aryeh > > > On Wed, Jul 22, 2015 at 2:25 PM, Aryeh Weiss <[hidden email] > <mailto:[hidden email]>> wrote: > > On 7/22/15 10:14 PM, Mark Hiner wrote: >> Hi Aryeh, >> >> Can you post the output of: >> >> $IJ_HOME/Contents/MacOS/ImageJ-macosx --dry-run >> >> My guess is that the sed pattern did not completely wipe your >> java.ext.dirs because you have a Java 8 JRE instead of JDK. >> >> Thanks! >> - Mark >> > Here it is: > > java > -Djava.ext.dirs=/Applications/local/fiji/Fiji.app/java/macosx-java3d/Home/lib/ext:/Library/Internet\ > Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/jre/lib/ext:/Library/Internet\ > Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/ext:/Library/Java/Extensions:/System/Library/Java/Extensions:/System/Library/Frameworks/JavaVM.framework/Home/lib/ext > -Dpython.cachedir.skip=true > -Dplugins.dir=/Applications/local/fiji/Fiji.app -Xmx12288m -Xincgc > -XX:PermSize=128m > -Djava.class.path=/Applications/local/fiji/Fiji.app/jars/imagej-launcher-3.1.6.jar > -Dimagej.dir=/Applications/local/fiji/Fiji.app > -Dij.dir=/Applications/local/fiji/Fiji.app > -Dfiji.dir=/Applications/local/fiji/Fiji.app > -Dfiji.executable=/Applications/local/fiji/Fiji.app/Contents/MacOS/ImageJ-macosx > -Dij.executable=/Applications/local/fiji/Fiji.app/Contents/MacOS/ImageJ-macosx > -Djava.library.path=/Applications/local/fiji/Fiji.app/lib/macosx:/Applications/local/fiji/Fiji.app/mm/macosx > net.imagej.launcher.ClassLauncher -ijjarpath jars -ijjarpath > plugins net.imagej.Main > > --aryeh > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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