Program: 22706
Project: 22706
Buggy source:
/** 
 * Apply current classifier to specific image (2D or stack)
 * @param dir input image directory path
 * @param fileName input image name
 * @param showResultsFlag string containing the boolean flag to display results
 * @param storeResultsFlag string containing the boolean flag to store result in a directory
 * @param probabilityMapsFlag string containing the boolean flag to calculate probabilities instead of a binary result
 * @param storeDir directory to store the results
 */
public static void applyClassifier(String dir,String fileName,String showResultsFlag,String storeResultsFlag,String probabilityMapsFlag,String storeDir){
  final ImageWindow iw=WindowManager.getCurrentImage().getWindow();
  if (iw instanceof CustomWindow) {
    final CustomWindow win=(CustomWindow)iw;
    final WekaSegmentation wekaSegmentation=win.getWekaSegmentation();
    ImagePlus testImage=IJ.openImage(dir + File.separator + fileName);
    if (null == testImage) {
      IJ.log("String_Node_Str" + dir + File.separator+ fileName+ "String_Node_Str");
      return;
    }
    boolean probabilityMaps=probabilityMapsFlag.contains("String_Node_Str");
    boolean storeResults=storeResultsFlag.contains("String_Node_Str");
    boolean showResults=showResultsFlag.contains("String_Node_Str");
    IJ.log("String_Node_Str" + dir + File.separator+ fileName);
    ImagePlus segmentation=wekaSegmentation.applyClassifier(testImage,0,probabilityMaps);
    convertTo8bitNoScaling(segmentation);
    segmentation.getProcessor().setColorModel(win.getOverlayLUT());
    segmentation.getImageStack().setColorModel(win.getOverlayLUT());
    segmentation.updateAndDraw();
    if (showResults) {
      segmentation.show();
      testImage.show();
    }
    if (storeResults) {
      String filename=storeDir + File.separator + fileName;
      IJ.log("String_Node_Str" + filename);
      IJ.save(segmentation,filename);
      segmentation.close();
      testImage.close();
    }
  }
}

Fixed version (ground truth):
/** 
 * Apply current classifier to specific image (2D or stack)
 * @param dir input image directory path
 * @param fileName input image name
 * @param showResultsFlag string containing the boolean flag to display results
 * @param storeResultsFlag string containing the boolean flag to store result in a directory
 * @param probabilityMapsFlag string containing the boolean flag to calculate probabilities instead of a binary result
 * @param storeDir directory to store the results
 */
public static void applyClassifier(String dir,String fileName,String showResultsFlag,String storeResultsFlag,String probabilityMapsFlag,String storeDir){
  final ImageWindow iw=WindowManager.getCurrentImage().getWindow();
  if (iw instanceof CustomWindow) {
    final CustomWindow win=(CustomWindow)iw;
    final WekaSegmentation wekaSegmentation=win.getWekaSegmentation();
    ImagePlus testImage=IJ.openImage(dir + File.separator + fileName);
    if (null == testImage) {
      IJ.log("String_Node_Str" + dir + File.separator+ fileName+ "String_Node_Str");
      return;
    }
    boolean probabilityMaps=probabilityMapsFlag.contains("String_Node_Str");
    boolean storeResults=storeResultsFlag.contains("String_Node_Str");
    boolean showResults=showResultsFlag.contains("String_Node_Str");
    IJ.log("String_Node_Str" + dir + File.separator+ fileName);
    ImagePlus segmentation=wekaSegmentation.applyClassifier(testImage,0,probabilityMaps);
    if (!probabilityMaps) {
      convertTo8bitNoScaling(segmentation);
      segmentation.getProcessor().setColorModel(win.getOverlayLUT());
      segmentation.getImageStack().setColorModel(win.getOverlayLUT());
      segmentation.updateAndDraw();
    }
    if (showResults) {
      segmentation.show();
      testImage.show();
    }
    if (storeResults) {
      String filename=storeDir + File.separator + fileName;
      IJ.log("String_Node_Str" + filename);
      IJ.save(segmentation,filename);
      segmentation.close();
      testImage.close();
    }
  }
}