Re: Fiji Cookbook

[Curtis Rueden]

Hi Lori,

[CCing fiji-devel, since it always better to discuss publicly; see http://imagej.net/Help]

> I am writing about FIJI Cookbook app for Mac (10.7.5).  I recently

> downloaded this app so I can modify images away from the microscope

> (aka at home) and apparently took the wrong fork in the road when

> installing.

The Cookbook is actually an update site for ImageJ. You can install it as follows:

1) Download Fiji from:

    http://imagej.net/Downloads

2) Launch Fiji.

3) Choose Help > Update... from the menus.

4) Click the Manage Update Sites button.

5) Tick the "Cookbook" box.

6) Click OK, do the updates, and restart Fiji.

7) Enjoy the Cookbook plugins. Note that you can press the L key to bring up the quick launch window (a.k.a. "Command Finder") to execute commands more quickly.

Regards,

Curtis

On Wed, Oct 7, 2015 at 10:13 AM, Curtis Rueden <ctru...@gmail.com> wrote:

Hi Curtis,

Greetings from Missouri! I am writing about FIJI Cookbook app for Mac (10.7.5).  I recently downloaded this app so I can modify images away from the microscope (aka at home) and apparently took the wrong fork in the road when installing. I am a mini-geek but this is beyond my abilities.

It gives me this but I have NO clue how to fix it:

Compiling 1 file in /var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java2324506789338012098

/var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java2324506789338012098/src/main/java/Microscope_Scale.java:9: cannot access java.lang.Object

bad class file: ZipFileIndexFileObject[/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/rt.jar(java/lang/Object.class)]

class file has wrong version 52.0, should be 50.0

Please remove or make sure it appears in the correct subdirectory of the classpath.

public class Microscope_Scale implements  PlugInFilter {

       ^

org.scijava.minimaven.JavaCompiler$CompileError: Compile error: 1

at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:80)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:477)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:406)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:391)

at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:211)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)

at org.scijava.script.ScriptModule.run(ScriptModule.java:173)

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$2.call(DefaultThreadService.java:191)

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)

Compiling 1 file in /var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java1086872129514413040

/var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java1086872129514413040/src/main/java/Nucleus_Counter.java:5: cannot access java.awt.List

bad class file: ZipFileIndexFileObject[/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/rt.jar(java/awt/List.class)]

class file has wrong version 52.0, should be 50.0

Please remove or make sure it appears in the correct subdirectory of the classpath.

import java.awt.List;

               ^

org.scijava.minimaven.JavaCompiler$CompileError: Compile error: 1

at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:80)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:477)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:406)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:391)

at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:211)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)

at org.scijava.script.ScriptModule.run(ScriptModule.java:173)

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$2.call(DefaultThreadService.java:191)

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)

Compiling 1 file in /var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java3600938544457906897

/var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java3600938544457906897/src/main/java/Microscope_Scale.java:9: cannot access java.lang.Object

bad class file: ZipFileIndexFileObject[/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/rt.jar(java/lang/Object.class)]

class file has wrong version 52.0, should be 50.0

Please remove or make sure it appears in the correct subdirectory of the classpath.

public class Microscope_Scale implements  PlugInFilter {

       ^

org.scijava.minimaven.JavaCompiler$CompileError: Compile error: 1

at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:80)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:477)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:406)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:391)

at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:211)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)

at org.scijava.script.ScriptModule.run(ScriptModule.java:173)

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$2.call(DefaultThreadService.java:191)

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)

Compiling 1 file in /var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java6946191068023720967

/var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java6946191068023720967/src/main/java/Microscope_Scale.java:9: cannot access java.lang.Object

bad class file: ZipFileIndexFileObject[/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/rt.jar(java/lang/Object.class)]

class file has wrong version 52.0, should be 50.0

Please remove or make sure it appears in the correct subdirectory of the classpath.

public class Microscope_Scale implements  PlugInFilter {

       ^

org.scijava.minimaven.JavaCompiler$CompileError: Compile error: 1

at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:80)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:477)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:406)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:391)

at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:211)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)

at org.scijava.script.ScriptModule.run(ScriptModule.java:173)

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$2.call(DefaultThreadService.java:191)

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)

Compiling 1 file in /var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java7747243777116287890

/var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java7747243777116287890/src/main/java/Nucleus_Counter.java:5: cannot access java.awt.List

bad class file: ZipFileIndexFileObject[/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/rt.jar(java/awt/List.class)]

class file has wrong version 52.0, should be 50.0

Please remove or make sure it appears in the correct subdirectory of the classpath.

import java.awt.List;

               ^

org.scijava.minimaven.JavaCompiler$CompileError: Compile error: 1

at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:80)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:477)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:406)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:391)

at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:211)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)

at org.scijava.script.ScriptModule.run(ScriptModule.java:173)

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$2.call(DefaultThreadService.java:191)

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)

Compiling 1 file in /var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java6918330709112967131

/var/folders/lr/pcmxp04d3jg27yft5rwhmfdc0000gn/T/java6918330709112967131/src/main/java/Microscope_Scale.java:9: cannot access java.lang.Object

bad class file: ZipFileIndexFileObject[/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/rt.jar(java/lang/Object.class)]

class file has wrong version 52.0, should be 50.0

Please remove or make sure it appears in the correct subdirectory of the classpath.

public class Microscope_Scale implements  PlugInFilter {

       ^

org.scijava.minimaven.JavaCompiler$CompileError: Compile error: 1

at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:80)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:477)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:406)

at org.scijava.minimaven.MavenProject.build(MavenProject.java:391)

at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:211)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)

at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)

at org.scijava.script.ScriptModule.run(ScriptModule.java:173)

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$2.call(DefaultThreadService.java:191)

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)

can you help?

Lori D. Gutzmann, DVM, MS
Pfizer-Morris Animal Foundation Fellow
University of Missouri-Columbia
Department of Biomedical Sciences
1600 E. Rollins
Veterinary Medicine Building
Columbia, MO 65211

[Curtis Rueden]

Hi Lori,

> I do not speak Java or C++ or whatever, and though there was a

> promising response posted i do not know how to implement it (set

> fork=true).

You are just trying to _use_ the Cookbook plugins within Fiji, correct? Then you only need to enable the Cookbook update site, and find the plugins in the Cookbook menu.

If that is what you are doing, and you are seeing this error message, can you please give instructions on exactly what steps you took to produce this problem? For details, please see:

   http://imagej.net/Bug_reporting_best_practices

> Others reported a similar problem

Can you please provide links to those discussions?

Thanks,

Curtis

On Wed, Oct 7, 2015 at 1:24 PM, Gutzmann, Lori (MU-Student) <lorigu...@mail.missouri.edu> wrote:

Hi , I looked at the imageJ message boards before mailing you and searched there but found nothing i can use. Others reported a similar problem, but I do not speak Java or C++ or whatever, and though there was a promising response posted i do not know how to implement it (set fork=true).   Sigh. 

Lori

[Curtis Rueden]

Hi Lori,

Please use "reply all" to keep the list in CC. Or switch to the ImageJ forum (http://forum.imagej.net/). Then you won't be stuck waiting for a personal reply from me, and the discussion will benefit others in the community.

> Yes, am trying to use the Cookbook plugin within Fiji.  The problem is

> that when I installed it, there was a question of updating to a newer

> version (presumably of javaApplet version 50 to 52).

To clarify some terminology:

- A Java applet is something that runs in a web browser. They are unlikely to be relevant to this discussion, which is about the ImageJ standalone application, and Cookbook suite of plugins for that application.

- The versions "50" and "52" are internal code indicating version of Java. We will soon update ImageJ to give a nicer error message when Java-version-related errors arise. But for now, see this page: http://imagej.net/Troubleshooting#UnsupportedClassVersionError

The places you linked are about issues much more technical than this problem with the Cookbook. Normal usage of the Cookbook plugins should not require compiling any Java classes, cloning any GitHub repositories, or similarly technical "developer" actions.

Did you follow the directions at http://imagej.net/Cookbook to install? Or do something else?

I ask because from the error message, it looks like ImageJ is trying to compile a Java source file.

What action specifically do you take within the program to trigger that error message? Which plugin are you trying to run? Or does the error appear in some other circumstance?

If you have not already done so, you could try installing Java 6 from:

https://support.apple.com/kb/DL1572

Regards,

Curtis

On Wed, Oct 7, 2015 at 5:26 PM, Gutzmann, Lori (MU-Student) <lorigu...@mail.missouri.edu> wrote:

Yes, am trying to use the Cookbook plugin within Fiji.  The problem is that when I installed it, there was a question of updating to a newer version (presumably of javaApplet version 50 to 52).  The applet worked once after installing, then not at all.  I uninstalled and re-installed but didn't get the option to change my choice, and the applet is not working properly.

This is one of the places I looked for answers:

http://stackoverflow.com/questions/28180915/class-file-has-wrong-version-52-0-should-be-50-0

and this:

https://github.com/fiji/fiji/issues/119

But like I said, I do not understand.  I wouldn't have bothered you unless I was completely stumped. I can't report a bug because the steps I took to cause the initial problem aren't repeatable but the cookbook repeatably does not work on my mac.  At work, on the pc, it works fine and didn't give options when installed.

Lori

---

From: ctrued...@gmail.com <ctrued...@gmail.com> on behalf of Curtis Rueden <ctru...@wisc.edu>
Sent: Wednesday, October 7, 2015 1:52 PM
To: Gutzmann, Lori (MU-Student)
Cc: Fiji Developers
Subject: Re: Fiji Cookbook

 

Hi Lori,

> I do not speak Java or C++ or whatever, and though there was a

> promising response posted i do not know how to implement it (set

> fork=true).

You are just trying to _use_ the Cookbook plugins within Fiji, correct? Then you only need to enable the Cookbook update site, and find the plugins in the Cookbook menu.

If that is what you are doing, and you are seeing this error message, can you please give instructions on exactly what steps you took to produce this problem? For details, please see:

   http://imagej.net/Bug_reporting_best_practices

Bug reporting best practices - ImageJ TL;DR Summary. Report the issue using the Report a Bug plugin (in the Help menu). Provide a minimal, complete, verifiable example. Describe what you already tried. Read more...