Jama/.jar incompatibility

[Joachim Wesner]

Hi list,

I was going to take a look at Michael Doube´s Circle-Fitting library and
test plugin. The library requires Jama .jar which I copied in the latest
version 1.0.2 to the plugins folder.

I can compile Micheal´s library but it will not run (using the internal
ImageJ editor and compile-and-run mechamism): (javaclassnotfounderror:
Matrix, i.e in Jama)

On another website I found the hint that there might occur an
incompatibilty to the JRE that ImageJ uses (I use the built-in 1.6.0_02 and
ImageJ 1.43h), and indeed I can get the code
to run if I get the Jama sources and copy those to a subdirectory Jama of
"plugins" (I have "plugins" in the Imagej class path) and recompile all
classes localy.

Nevertheless, I do not seem to be able to recreate a working Jama.jar (The
plugin and library compile when using the new jar but later again i get:
javaclassnotfounderror: Matrix

What is the reason for the incompatibilty and how to create a valid on? Any
hint would be appreciated!

Joachim


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[Michael Doube]

Hi Joachim

Thanks for your interest in the class.

Check out the compiled plugin I sent off-list.

I use Sun JRE 1.6.0_10 (on XP) and _15 (on Ubuntu) and _16 (on Vista)
and all work fine.

I'd really appreciate it if some of the more mathematically-inclined
list members could take a look at the error-estimating method
getErrors() and tell me how to get a better estimate of error in the
estimated parameters (x, y) and R.

http://github.com/mdoube/BoneJ/blob/master/src/org/doube/bonej/FitCircle.java

Cheers,

Michael

Joachim Wesner wrote:

> Hi list,
>
> I was going to take a look at Michael Doube´s Circle-Fitting library and
> test plugin. The library requires Jama .jar which I copied in the latest
> version 1.0.2 to the plugins folder.
>
> I can compile Micheal´s library but it will not run (using the internal
> ImageJ editor and compile-and-run mechamism): (javaclassnotfounderror:
> Matrix, i.e in Jama)
>
> On another website I found the hint that there might occur an
> incompatibilty to the JRE that ImageJ uses (I use the built-in 1.6.0_02 and
> ImageJ 1.43h), and indeed I can get the code
> to run if I get the Jama sources and copy those to a subdirectory Jama of
> "plugins" (I have "plugins" in the Imagej class path) and recompile all
> classes localy.
>
> Nevertheless, I do not seem to be able to recreate a working Jama.jar (The
> plugin and library compile when using the new jar but later again i get:
> javaclassnotfounderror: Matrix
>
> What is the reason for the incompatibilty and how to create a valid on? Any
> hint would be appreciated!
>
> Joachim
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email 
> ______________________________________________________________________

[David Webster]

Joachim,

I downloaded FitCircle.java and Test_Circle.java from
http://doube.org/plugins.html. I copied my copy of Jama-1.0.2.jar into  
the same folder with these 2 and was able to get ImageJ's compile and load
to work. Is this what you were talking about? The biggest problem with
this approach is that the jar file must be in the same folder as the java
files so you can't use it elsewhere. Maybe compiling from the command line
will work. I'll give it shot sometime.

David Webster

[Joachim Wesner]

Hi David

thanx for trying,

no, not exactly, what I did was to copy jama.1.02.jar from the website and
the java files into the plugins folder and was able to compile but not run
(class Matrix not found). This must be a problem with my particular
installation, 1.6.0.2 JRE, I can give it a try on another computer that has
the latest from the ImageJ website with 1.6.0.10 or something...

Interestingly, Konen at his site reports about the same problem
(unfortunatelly for some of you in German....)

      http://www.gm.fh-koeln.de/~konen/WPF-BV/aufgaben_IJ2.htm

"Jama-Installation: Jama-1.0.2.zip (Version mit Sourcen) herunterladen,
entpacken ins Verzeichnis, das das eigene Plugin enthält, dann alle
.class-Files löschen (damit erzwingen wir Re-Compile, denn die .class-Files
aus dem Download funktionieren nicht mit ImageJ's JRE). Dann eigenes Plugin
compilieren."

i.e. that one needs to unpack the sources from the ZIP file, delete all old
class files to force a recompilation, because "the class files from the
download do not work with the ImageJ JRE" (However, he forgets to mention
that this means one willl need to remove the package statements in this
case!)

So I thought I stumbeld on just the same problem....

I will later check with the other computer, strange...

Joachim



                                                                           
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Joachim,

I downloaded FitCircle.java and Test_Circle.java from
http://doube.org/plugins.html. I copied my copy of Jama-1.0.2.jar into
the same folder with these 2 and was able to get ImageJ's compile and load
to work. Is this what you were talking about? The biggest problem with
this approach is that the jar file must be in the same folder as the java
files so you can't use it elsewhere. Maybe compiling from the command line
will work. I'll give it shot sometime.

David Webster



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