http://imagej.273.s1.nabble.com/Apply-WEKA-segmentation-script-tp5022890p5022892.html
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
>