Fix for RC

src/main/java/mosaic/plugins/RegionCompetition.java

@@ -5,6 +5,7 @@ import java.awt.GraphicsEnvironment;
 import org.apache.log4j.Logger;
 
 import ij.IJ;
+import ij.ImageJ;
 import ij.ImagePlus;
 import ij.Macro;
 import ij.macro.Interpreter;
@@ -244,4 +245,20 @@ public class RegionCompetition implements PlugInFilter {
             MosaicUtils.reorganize(iOutputFileNamesSuffixes, fileNameNoExt, directory, 1);
         }
     }
+    
+    public static void main(String[] args) {
+        // set the plugins.dir property to make the plugin appear in the Plugins menu
+        Class<?> clazz = RegionCompetition.class;
+        String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
+        String pluginsDir = url.substring("file:".length(), url.length() - clazz.getName().length() - ".class".length());
+        System.setProperty("plugins.dir", pluginsDir);
+
+        new ImageJ();
+
+//        ImagePlus image = IJ.openImage("https://upload.wikimedia.org/wikipedia/commons/3/3f/Bikesgray.jpg");
+//        image.show();
+
+        // run the plugin
+        IJ.runPlugIn(clazz.getName(), "");
+    }
 }

src/main/java/mosaic/regions/GUI/GuiRC.java

@@ -172,7 +172,7 @@ public class GuiRC  {
         for (int i = 0; i < energyValues.length; ++i) {
             energyItems[i] = energyValues[i].toString();
         }
-        gd.addChoice("E_data", energyItems, iSettings.energyFunctional.name());
+        gd.addChoice("E_data", energyItems, iSettings.energyFunctional.toString());
         Choice choiceEnergy = (Choice) gd.getChoices().lastElement();
         {
             Button optionButton = new Button("Options");
@@ -200,7 +200,7 @@ public class GuiRC  {
         for (int i = 0; i < regularizationValues.length; ++i) {
             regularizationItems[i] = regularizationValues[i].toString();
         }
-        gd.addChoice("E_length", regularizationItems, iSettings.regularizationType.name());
+        gd.addChoice("E_length", regularizationItems, iSettings.regularizationType.toString());
         
         Choice choiceRegularization = (Choice) gd.getChoices().lastElement();
         {
@@ -227,9 +227,9 @@ public class GuiRC  {
         final InitializationType[] initTypes = InitializationType.values();
         final String[] initializationItems = new String[initTypes.length];
         for (int i = 0; i < initTypes.length; ++i) {
-            initializationItems[i] = initTypes[i].name();
+            initializationItems[i] = initTypes[i].toString();
         }
-        gd.addChoice("Initialization", initializationItems, iSettings.initType.name());
+        gd.addChoice("Initialization", initializationItems, iSettings.initType.toString());
         
         // save reference to this choice, so we can handle it
         Choice initializationChoice = (Choice) gd.getChoices().lastElement();

src/test/java/mosaic/bregman/segmentation/SquasshSegmentationTest.java

@@ -9,23 +9,40 @@ public class SquasshSegmentationTest extends CommonBase {
 
     @Test
     public void testGenerateSeriesOfSquassh() {
-//        String path = "/Users/gonciarz/Documents/MOSAIC/work/testInputs/Crop_12-12.tif";
+//        String path = "/Users/gonciarz/small.tif";
 //        ImagePlus ip = loadImagePlus(path);
 //        
 //        double[][][] img = ImgUtils.ImgToZXYarray(ip);
 //        short[][] blank = new short[img[0].length][img[0][0].length];
 //        
-//        int numOfSteps = 256;
-//        short[][][] out = new short[numOfSteps][][];
+//        int numOfSteps = 20;
+//        float fromVal = 0;
+//        float toVal = 0.2f;
+//        float fromValInt = 0.2f;
+//        float toValInt = 0.8f;
+//        short[][][] out = new short[numOfSteps *numOfSteps][][];
+//        for (int j = 0; j < numOfSteps; j++) {
 //        for (int i = 0; i < numOfSteps; i++) {
 //            System.out.println(i * (1.0/(numOfSteps)));
-//            SegmentationParameters sp = new SegmentationParameters(4, 1, 0.1, i * (1.0/(numOfSteps-1)), true, SegmentationParameters.IntensityMode.AUTOMATIC, SegmentationParameters.NoiseModel.GAUSS, 1, 1, 0);
+//            SegmentationParameters sp = new SegmentationParameters(
+//                    4, // num threads
+//                    1, // interpolation (multiplication factor)
+//                    i * (toVal - fromVal) / numOfSteps,  // regularization
+//                    j * (toValInt - fromValInt) / numOfSteps, // min obj intensity
+//                    true, // exclude z edges
+//                    SegmentationParameters.IntensityMode.AUTOMATIC, // intensity mode 
+//                    SegmentationParameters.NoiseModel.GAUSS, // noise model
+//                    1, // sigma xy
+//                    1, // sigma z
+//                    0, // min regions intensity
+//                    2); // min region size
 //            SquasshSegmentation ss = new SquasshSegmentation(img, sp, 0, 255);
 //            ss.run();
-//            out[i] = (ss.iRegionsList.size() > 0) ? ss.iLabeledRegions[0] : blank;
-//        }
+//            out[i +j * numOfSteps] = (ss.iRegionsList.size() > 0) ? ss.iLabeledRegions[0] : blank;
+//        }}
 //        ImagePlus outImg = ImgUtils.ZXYarrayToImg(ConvertArray.toDouble(out), "Output");
 //        IJ.saveAsTiff(outImg, "/tmp/out.tif");
+//        System.out.println("Range: " +fromVal +"-"+toVal + "   step: " + (toVal - fromVal) / numOfSteps);
     }
 
     @Test

src/test/java/mosaic/plugins/BackgroundSubtractor2_Test.java

 package mosaic.plugins;
 
-import static org.junit.Assert.*;
-
 import org.junit.Test;
 
 import mosaic.test.framework.CommonBase;