http://imagej.273.s1.nabble.com/Apply-WEKA-segmentation-script-tp5022890p5022894.html
thank you for your reply. I've put the script to
> Hello Rainer,
>
> What works for me is to put the .bsh files under
> Fiji.app/plugins/Scripts/Plugins/
>
> Is that what you do? You can also create a folder inside the above path so
> the script shows up in the menu under Plugins > "your folder name".
>
> Cheers!
>
> On Fri, Jan 24, 2020 at 2:01 PM Rainer M. Engel <
[hidden email]> wrote:
>
>> Can somebody help me, why the provided BeanShell-Script below does work
>> nicely from the editor but not when put into ImageJ's 'scripts'-folder
>> to be executed from the menu.
>>
>> That would be great..
>>
>> Kind regards,
>> Rainer
>>
>>
>>
>>
>> Am 23.01.2020 um 10:37 schrieb Rainer M. Engel:
>>> Hey..
>>>
>>> I tried WEKA automation via macro and despite of all the available
>>> commands this seems to be not that ideal, although this is a clear
>>> drawback considering the GUI for a nice way to create robust models,
>>> which shall/could also be applied via macro (batch).
>>>
>>> To wait for the UI to pop up could be enhanced via..
>>>
>>>>> macro language..........................................START
>>> wekaNotReady = true;
>>> c = 0;
>>> while (wekaNotReady && c < 60) {
>>> if (isOpen("Trainable Weka Segmentation v3.2.33") == true) {
>>> wekaNotReady = false; }
>>> wait(50);
>>> c++;
>>> }
>>> << macro language............................................END
>>>
>>> But I could not work with batch mode and WEKA (macro).
>>>
>>> So this BeanShell-Script offers the same functionality like the known
>>> "Apply SIOX segmentator" for SIOX but in this case for WEKA (only a
>>> modification of a script, which was part of the WEKA documentation.
>>>
>>>>> BeanShell language (Apply-saved-WEKA-segmentator.bsh).........START
>>> // @File(label="Weka model", description="Select the Weka model to
>>> apply") modelPath
>>> // @String(label="Result mode",choices={"Labels","Probabilities"})
>>> resultMode
>>>
>>> import trainableSegmentation.WekaSegmentation;
>>> import trainableSegmentation.utils.Utils;
>>> import ij.io.FileSaver;
>>> import ij.IJ;
>>> import ij.ImagePlus;
>>>
>>> // based on the beanshell script found on:
>>> //
https://imagej.net/Scripting_the_Trainable_Weka_Segmentation modified
>>> by rengel, 2020-01
>>>
>>> // starting time
>>> startTime = System.currentTimeMillis();
>>>
>>> // caculate probabilities?
>>> getProbs = resultMode.equals( "Probabilities" );
>>> // create segmentator
>>> segmentator = new WekaSegmentation();
>>> // load classifier
>>> segmentator.loadClassifier( modelPath.getCanonicalPath() );
>>>
>>> // get details from already opened image
>>> image = IJ.getImage();
>>> //IJ.log(""+image);
>>>
>>> // apply classifier and get results (0 indicates number of threads is
>>> auto-detected)
>>> result = segmentator.applyClassifier( image, 0, getProbs );
>>>
>>> if( !getProbs )
>>> // assign same LUT as in GUI
>>> result.setLut( Utils.getGoldenAngleLUT() );
>>>
>>> // show result
>>> result.show();
>>>
>>> // force garbage collection (important for large images)
>>> result = null;
>>> image = null;
>>> System.gc();
>>>
>>> // print elapsed time
>>> estimatedTime = System.currentTimeMillis() - startTime;
>>> IJ.log( "** Finished processing image in " + estimatedTime + " ms **" );
>>> << BeanShell language............................................END
>>>
>>>
>>> I put the "Apply-saved-WEKA-segmentator.bsh" into a sub-folder of
>>> 'scripts' to see this script in the menu of ImageJ, but it is not shown,
>>> although my Python scripts are. Any help on this is much appreciated.
>>>
>>> Kind regards,
>>> Rainer
>>>
>>
>> --
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