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Bug 893 - Small compiler issue within the Fiji script editor
Small compiler issue within the Fiji script editor
Status: NEW
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-11 02:25 CDT by CARL
Modified: 2014-08-26 03:03 CDT
1 user (show)

See Also:
Description CARL 2014-08-11 02:25:02 CDT 
Dear all/Johannes,
I just figured out that the Fiji Script editor is not anymore compiling a java file when it is calling a library that is linked to the plugin.
In order to try to make myself a little bit clearer, let me try to describe the problem with an example.
in the case you download the Radial Profile Extended plugin (http://rsb.info.nih.gov/ij/plugins/radial-profile-ext.html) and then explode the jar file (http://rsb.info.nih.gov/ij/plugins/download/jars/Radial_Profile_Angle_Ext.jar) in a folder, you end up with a multi_plot folder (containing an extension of the Plot classes) and the Radial_Profile_Angle_Ext .java and .class (as well as the plugins.config) files.
And if you then try to Run the Radial_Profile_Angle_Ext .java file from a Fiji Script editor window you get the following error:
Radial_Profile_Angle_Ext.java:18: package multi_plot does not exist
import multi_plot.*;
As the same file compiled through the Plugins->Compile_and_Run… feature is compiling right.
Am I doing something wrong?
Should I change something within the code so this is still working (as I was still developing code in the same way with success some weeks ago).
I thank you very much in advance for your help and/or suggestions.
My best regards,
Philippe

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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Work\SOFTWA~1\Fiji/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Work\SOFTWA~1\Fiji

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140810142118)
Fiji: http://fiji.sc/update/ (last check:20140808200226)

Files not up-to-date:
  1c354c8b (LOCAL_ONLY) 20000413165800 luts/S_Pet.lut
  07c05d23 (LOCAL_ONLY) 20121217160354 luts/multitxt.lut
  bf66597a (LOCAL_ONLY) 20121218140114 luts/physicsmodtxt.lut
  6e6ad239 (LOCAL_ONLY) 20121217155828 luts/physicstxt.lut
  12fce5aa (LOCAL_ONLY) 20140718101359 plugins/ExtendedDepthField.txt
  7433440a (LOCAL_ONLY) 20130204161151 plugins/Image Stabilizer/Image_Stabilizer.class
  03be9b84 (LOCAL_ONLY) 20130204161218 plugins/Image Stabilizer/Image_Stabilizer_Log_Applier.class
  24c44d4d (LOCAL_ONLY) 20140506160726 plugins/Scripts/Ph_CARL/Close_All....ijm
  f12146b9 (LOCAL_ONLY) 20130206163024 plugins/Scripts/Ph_CARL/Close_All2.ijm
  9b4b29d2 (LOCAL_ONLY) 20140218154016 plugins/Scripts/Ph_CARL/Create_folder.ijm
  85c6344e (LOCAL_ONLY) 20131108164053 plugins/Scripts/Ph_CARL/Extract_coordinates.ijm
  ab3013fb (LOCAL_ONLY) 20131127144746 plugins/Scripts/Ph_CARL/Extract_coordinates2.ijm
  4d456e4f (LOCAL_ONLY) 20131119161132 plugins/Scripts/Ph_CARL/Fast/Reduce_Dimensionality2.ijm
  5110a5ad (LOCAL_ONLY) 20131119152640 plugins/Scripts/Ph_CARL/Fast/Set_slice_and_contrast.ijm
  7588f796 (LOCAL_ONLY) 20140718093041 plugins/Scripts/Ph_CARL/Fiji_always_on_top.js
  afaf85ed (LOCAL_ONLY) 20140718093035 plugins/Scripts/Ph_CARL/Fiji_always_on_top_end.js
  72733ef5 (LOCAL_ONLY) 20140220161413 plugins/Scripts/Ph_CARL/Filter_Images.ijm
  bb04c482 (LOCAL_ONLY) 20140704110222 plugins/Scripts/Ph_CARL/Maximum_Finder_Mod_Ext.class
  cb190657 (LOCAL_ONLY) 20130424162624 plugins/Scripts/Ph_CARL/Measure_ROI_values.ijm
  134592f3 (LOCAL_ONLY) 20121213101213 plugins/Scripts/Ph_CARL/Microscope_Scale_iMIC.class
  cbe8f8c1 (LOCAL_ONLY) 20121218094342 plugins/Scripts/Ph_CARL/Open_Recent_File_0.class
  8ba195e6 (LOCAL_ONLY) 20121218094751 plugins/Scripts/Ph_CARL/Open_Recent_File_1.class
  76008cf7 (LOCAL_ONLY) 20121218094721 plugins/Scripts/Ph_CARL/Open_Recent_File_2.class
  4f38fb08 (LOCAL_ONLY) 20140414135258 plugins/Scripts/Ph_CARL/Particle_Tracker_PIV_Inputs.jar
  b143d1c5 (LOCAL_ONLY) 20131004145906 plugins/Scripts/Ph_CARL/Reduce_Dimensionality.ijm
  8ab755b8 (LOCAL_ONLY) 20130528171542 plugins/Scripts/Ph_CARL/Resize_and_Save_as_TIFF_and_Close.ijm
  48262963 (LOCAL_ONLY) 20140218154016 plugins/Scripts/Ph_CARL/Save_FTTC_Pictures_Full_Experiment.ijm
  5c369cb4 (LOCAL_ONLY) 20130924104247 plugins/Scripts/Ph_CARL/Save_JPG_Traction.ijm
  fb4a4385 (LOCAL_ONLY) 20140218154016 plugins/Scripts/Ph_CARL/Save_JPG_Traction_Full_Experiment.ijm
  d11f8fb2 (LOCAL_ONLY) 20140218154016 plugins/Scripts/Ph_CARL/Save_PIV_FTTC_JPG_Full_Experiment.ijm
  4c3c67b6 (LOCAL_ONLY) 20140217095124 plugins/Scripts/Ph_CARL/Save_PIV_Pictures.ijm
  8bd3841b (LOCAL_ONLY) 20140217092614 plugins/Scripts/Ph_CARL/Save_PIV_Pictures_Full_Experiment.ijm
  f99cafae (LOCAL_ONLY) 20121108104349 plugins/Scripts/Ph_CARL/Save_SCFS_Data.ijm
  4da1c631 (LOCAL_ONLY) 20140207144548 plugins/Scripts/Ph_CARL/Save_SCFS_Data_new.ijm
  01611468 (LOCAL_ONLY) 20130118143346 plugins/Scripts/Ph_CARL/Save_as_TIFF_and_Close.ijm
  f7ff1d43 (LOCAL_ONLY) 20140610102635 plugins/Scripts/Ph_CARL/SegFA_PseudoTIRF.ijm
  3b022ee2 (LOCAL_ONLY) 20121212114323 plugins/Scripts/Ph_CARL/Shift_latéral.ijm
  70e6a55b (LOCAL_ONLY) 20130311151957 plugins/Scripts/Ph_CARL/Stack_to_Hyperstack.ijm
  ff04c0b0 (LOCAL_ONLY) 20140425094242 plugins/Scripts/Ph_CARL/Translation_Alignment.class
  96df2830 (LOCAL_ONLY) 20131007085502 plugins/Scripts/Ph_CARL/test/NumberParticles8_.ijm
  d34b5256 (LOCAL_ONLY) 20140730164535 plugins/Scripts/Ph_CARL/test/Versatile_Wand.class
  83cb8345 (LOCAL_ONLY) 20140723154636 plugins/Scripts/Ph_CARL/test/morphology_collection.jar
  99308836 (LOCAL_ONLY) 20131217165922 plugins/Traction Force 2/FTTC_.jar
  ec703275 (LOCAL_ONLY) 20140416161333 plugins/Traction Force 2/PIV_.jar
  7d5b3965 (LOCAL_ONLY) 20120711154540 plugins/Traction Force 2/javacv.jar
  90915f54 (LOCAL_ONLY) 20120711154548 plugins/Traction Force 2/jna.jar
  9e276f37 (LOCAL_ONLY) 20140610135439 plugins/Traction Force/Traction_Force_Calculation_with_FRAP.class
  1a4c5bdf (LOCAL_ONLY) 20121129112014 plugins/X Shifter/X_Shifter.class
  d198e2f0 (LOCAL_ONLY) 20140702170514 plugins/arf/SegFA_PseudoTIRF_Dialog.ijm
Comment 1 CARL 2014-08-26 03:03:42 CDT 
Dear Curtis,
I will try to adress all your comments and hope not to forget some of your points.
So first I still have the same problem and I get the following error message:

Started Radial_Profile_Angle_Ext.java at Mon Aug 25 14:12:15 CEST 2014 Compiling 1 file in C:\Users\Ph-K\AppData\Local\Temp\java8197273006779848693
C:\Users\Ph-K\AppData\Local\Temp\java8197273006779848693\src\main\java\Radial_Profile_Angle_Ext.java:59: cannot access MultyPlotExt bad class file: RegularFileObject[C:\Work\SOFTWA~1\Fiji\plugins\Radial2\multi_plot\MultyPlotExt.class]
class file contains wrong class: multi_plot.MultyPlotExt Please remove or make sure it appears in the correct subdirectory of the classpath.
	MultyPlotExt plot;
	^
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.eval(JavaEngine.java:154)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
	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$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:662)

Then following the advice of Wayne (it was through a private E-mailing) I had filed in a bug report about this issue one or two days after my first mail.

And by following your description of using the following BeanShell Script in the Editor:
import multi_plot.*;
print(MultyPlotExt.class.getName());
It works perfectly and I get actually the following output:
Started New_.bsh at Mon Aug 25 14:15:50 CEST 2014 multi_plot.MultyPlotExt

> Another possibility is that you made changes to the multi_plot code and then they were not reflected when executing code from the Script Editor until after ImageJ was restarted?

No, I didn't make any changes within the multi_plot code and started Fiji just before trying to compile the code.

> If you could isolate a minimal, complete, verifiable example (MCVE), it would be much appreciated!

I replayed from scratch the action I described in my first mail and it is still not working (and I have an up to date Fiji version).
I may have a hint why there is this problem (just an idea) which is the fact that the compiled files are generated within the following folder:
"C:\Users\Ph-K\AppData\Local\Temp\java8197273006779848693"
and not within the "Fiji\plugins" folder one.
This change came with an update I made (either of Fiji or Java) and is probably the issue, since it is maybe looking for a "C:\Users\Ph-K\AppData\Local\Temp\java8197273006779848693\multi_plot" folder and not a "Fiji\plugins\Radial\multi_plot" one.

I will look into your suggested IDE developing options.

My best regards,

Philippe

-----Message d'origine-----
De : ImageJ Interest Group [mailto:IMAGEJ@list.nih.gov] De la part de Curtis Rueden Envoyé : vendredi 22 août 2014 21:18 À : IMAGEJ@list.nih.gov Objet : Re: Small compiler issue within the Fiji script editor

Hi Philippe,

> Radial_Profile_Angle_Ext.java:18: package multi_plot does not exist

I cannot reproduce the problem you describe. After unpacking the JAR file into my ImageJ's plugins folder, the following BeanShell works in my Script
Editor:

import multi_plot.*;
print(MultyPlotExt.class.getName());

Possibly, this issue was addressed since you wrote the mail. Or else there is something different in the steps we followed. If you still have this problem, please file a bug report using Help > Report a Bug -- it will report exact details of your ImageJ installation including OS, plugin versions, etc.

Another possibility is that you made changes to the multi_plot code and then they were not reflected when executing code from the Script Editor until after ImageJ was restarted? If so, that is an issue I have seen
recently: there are some class loading quirks right now with classes present in the jars or plugins folder which getting repeatedly recompiled without restarting ImageJ. If you could isolate a minimal, complete, verifiable example (MCVE), it would be much appreciated!

> I was still developing code in the same way with success some weeks 
> ago

I would encourage you to try developing plugins in an IDE, since there are many advantages. Once you become proficient with the software it is much faster, with many powerful debugging tools. See:

https://github.com/imagej/minimal-ij1-plugin
https://www.youtube.com/watch?v=Ac-6gJ2eRb0
http://imagej.net/Debugging#Attaching_to_ImageJ_instances
http://imagej.net/Maven

These resources are far from perfect, but hopefully they help get you started.

Regards,
Curtis