#@ File(label="Input directory", description="Select the directory with input images", style="directory") inputDir
#@ File(label="Output directory", description="Select the output directory", style="directory") outputDir
#@ 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;
  
// starting time
startTime = System.currentTimeMillis();
  
// caculate probabilities?
getProbs = resultMode.equals( "Probabilities" );
 
// create segmentator
segmentator = new WekaSegmentation();
// load classifier
segmentator.loadClassifier( modelPath.getCanonicalPath() );
  
// get list of input images
listOfFiles = inputDir.listFiles();
for ( i = 0; i < listOfFiles.length; i++ )
{
    // process only files (do not go into sub-folders)
    if( listOfFiles[ i ].isFile() )
    {
        // try to read file as image
        image = IJ.openImage( listOfFiles[i].getCanonicalPath() );
        if( image != null )
        {                   
            // 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() );
             
            // save result as TIFF in output folder
            outputFileName = listOfFiles[ i ].getName().replaceFirst("[.][^.]+$", "") + " out.tif";
            new FileSaver( result ).saveAsTiff( outputDir.getPath() + File.separator + outputFileName );
  
            // force garbage collection (important for large images)
            result = null; 
            image = null;
            System.gc();
        }
    }
}
// print elapsed time
estimatedTime = System.currentTimeMillis() - startTime;
IJ.log( "** Finished processing folder in " + estimatedTime + " ms **" );