Installing Threshold Blur plugin for Fiji

[Paul Stutzman-2]

I am trying to install a couple of plugins for Fiji that I have successfully used with ImageJ but am having difficulties.  I am running OS X 10.11.6

The plugin Threshold Blur has been very useful in cleaning up my segmented images but after following the install using the Plugins->Install and a later attempt using Plugins->Install Plugin, I get a message that it was successfully installed however, upon running I get the following error message:


javax.script.ScriptException: Class Thresholded_Blur in invalid directory: /Applications/Fiji.app/plugins/thresholded_blur.java
at org.scijava.plugins.scripting.java.JavaEngine.getMavenProject(JavaEngine.java:520)
at org.scijava.plugins.scripting.java.JavaEngine.access$600(JavaEngine.java:95)
at org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:407)
at org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:369)
at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:198)
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)


What do I need to do to get this plugin running?  I have not found any others to process my images to clean up mis-classified indexed pixels (indexed by mineral component).  The info for an image is reproduced below.


(Fiji Is Just) ImageJ 2.0.0-rc-43/1.51f; Java 1.8.0_111 [64-bit]; Mac OS X 10.11.6; 69MB of 5254MB (1%)

Title: 86_C_12_1MS.tif
Width:  1024   (1024)
Height:  768   (768)
Size:  768K
Resolution:  1 pixels per
Pixel size: 1x1  ^2
ID: -3
Bits per pixel: 8 (color LUT)
No threshold
Uncalibrated
Path: /Users/stutz/Documents/SEM/86c/86_C_12_1MS.tif
Screen location: 1247,229 (2560x1440)
SetMenuBarCount: 8 (0ms)
No overlay
No selection




Paul Stutzman
Materials and Structural Systems Division
100 Bureau Drive
Gaithersburg, MD 20899-8615
301 975-6715, 6645 (lab)
[hidden email]<mailto:[hidden email]>





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[Michael Schmid]

Hi Paul,

Fiji has a problem with 'Compile & Run'.

Please try with the compiled .class file from the distribution page,
 
http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start

Make sure you rename it to Thresholded_Blur.class; uppercase/lowercase
matters.

--

If you have an image with the pixel value really being an index (each
index value corresponding to a different mineral component), I fear that
Thresholded Blur is not the right sort of filter.
Thresholded Blur is fine for edge-preserving blur if you have a
microscope image with different grayscale values corresponding to
different mineral components, so grayscale is still an 'analog' value.
Then you would do the conversion from grayscale to mineral component
type afterwards.

If you really have indexed mineral types (e.g. from some spectroscopy or
other multi-channel input), I guess what you would need is an algorithm
that replaces a pixel if it is different from all of its neighbors. The
replacement would be the value occurring most frequently among the
neighbors. Maybe someone else out there already has such a filter?


Michael
________________________________________________________________

On 2016-11-21 14:53, Stutzman, Paul E. (Fed) wrote:

> I am trying to install a couple of plugins for Fiji that I have successfully used with ImageJ but am having difficulties.  I am running OS X 10.11.6
>
> The plugin Threshold Blur has been very useful in cleaning up my segmented images but after following the install using the Plugins->Install and a later attempt using Plugins->Install Plugin, I get a message that it was successfully installed however, upon running I get the following error message:
>
>
> javax.script.ScriptException: Class Thresholded_Blur in invalid directory: /Applications/Fiji.app/plugins/thresholded_blur.java
> at org.scijava.plugins.scripting.java.JavaEngine.getMavenProject(JavaEngine.java:520)
> at org.scijava.plugins.scripting.java.JavaEngine.access$600(JavaEngine.java:95)
> at org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:407)
> at org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:369)
> at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:198)
> 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)
>
>
> What do I need to do to get this plugin running?  I have not found any others to process my images to clean up mis-classified indexed pixels (indexed by mineral component).  The info for an image is reproduced below.
>
>
> (Fiji Is Just) ImageJ 2.0.0-rc-43/1.51f; Java 1.8.0_111 [64-bit]; Mac OS X 10.11.6; 69MB of 5254MB (1%)
>
> Title: 86_C_12_1MS.tif
> Width:  1024   (1024)
> Height:  768   (768)
> Size:  768K
> Resolution:  1 pixels per
> Pixel size: 1x1  ^2
> ID: -3
> Bits per pixel: 8 (color LUT)
> No threshold
> Uncalibrated
> Path: /Users/stutz/Documents/SEM/86c/86_C_12_1MS.tif
> Screen location: 1247,229 (2560x1440)
> SetMenuBarCount: 8 (0ms)
> No overlay
> No selection
>
>
>
>
> Paul Stutzman
> Materials and Structural Systems Division
> 100 Bureau Drive
> Gaithersburg, MD 20899-8615
> 301 975-6715, 6645 (lab)
> [hidden email]<mailto:[hidden email]>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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