code cleanup

Author: dlegland

src/main/java/inra/ijpb/measure/region2d/RegionBoundaries.java

@@ -243,6 +243,8 @@ public final static Map<Integer, ArrayList<Point2D>> runLengthsCornersMap(ImageP
      * <li><i>(x+0.5, y+1)</i>: bottom boundary</li>
      * </ul>
      * 
+     * Method used for computation of convexity.
+     * 
      * @param binaryImage
      *            the image processor containing the binary region
      * @return an array of Point2D, located on the boundary of the region.
@@ -303,6 +305,8 @@ public static final ArrayList<Point2D> boundaryPixelsMiddleEdges(ImageProcessor
      * <li><i>(x+0.5, y+1)</i>: bottom boundary</li>
      * </ul>
      * 
+     * Method used for computation of convexity.
+     * 
      * @param labelImage
      *            the image processor containing the region labels
      * @param labels

src/main/java/inra/ijpb/measure/region3d/GeodesicDiameter3D.java

@@ -71,11 +71,6 @@ public class GeodesicDiameter3D extends RegionAnalyzer3D<GeodesicDiameter3D.Resu
 	 */
 	ChamferMask3D chamferMask;
 
-	/**
-	 * The string used for indicating the current step in algo events.
-	 */
-	String currentStep = "";
-	
 
 	// ==================================================
 	// Constructors 
@@ -198,10 +193,10 @@ public Result[] analyzeRegions(ImageStack labelImage, int[] labels,
 
 		this.fireStatusChanged(this, "Computing first geodesic extremities...");
 
-		// Second distance propagation from first maximum
+		// Distance propagation from initial markers
 		distanceMap = gdt.geodesicDistanceMap(marker, labelImage);
 
-		// find position of maximal value for each label
+		// find position of maximum value for each label
 		// this is expected to correspond to a geodesic extremity 
 		Cursor3D[] firstGeodesicExtremities = LabelValues.findPositionOfMaxValues(distanceMap, labelImage, labels);
 
@@ -250,25 +245,15 @@ public Result[] analyzeRegions(ImageStack labelImage, int[] labels,
 			result[i] = res;
 		}
 
-		//		// calibrate the results
-		//		if (calib.scaled())
-		//		{
-		//			this.fireStatusChanged(this, "Re-calibrating results");
-		//			for (int i = 0; i < nLabels; i++)
-		//			{
-		//				result[i] = result[i].recalibrate(calib);
-		//			}
-		//		}
-
 		// returns the results
 		return result;
 	}
 
 
-		// ==================================================
-		// Implementation of AlgoListener interface 
+	// ==================================================
+	// Implementation of AlgoListener interface 
 
-		@Override
+	@Override
 	public void algoProgressChanged(AlgoEvent evt) 
 	{
 		fireProgressChanged(new Event(this, evt));
@@ -289,10 +274,6 @@ class Event extends AlgoEvent
 		public Event(GeodesicDiameter3D source, AlgoEvent evt)
 		{
 			super(source, "(GeodDiam3d) " + evt.getStatus(), evt.getCurrentProgress(), evt.getTotalProgress());
-			if (!currentStep.isEmpty())
-			{
-				this.status = "(GeodDiam3d-" + currentStep + ") " + evt.getStatus();
-			}
 		}
 	}
 

src/main/java/inra/ijpb/plugins/AnalyzeRegions.java

@@ -274,40 +274,58 @@ public ResultsTable process(ImagePlus imagePlus)
     public static final class Features
     {
         /** The boolean flag for computing pixel count.*/
-        public boolean pixelCount = false;
+        @Deprecated
+		public boolean pixelCount = false;
         /** The boolean flag for computing area.*/
+        @Deprecated
         public boolean area = true;
         /** The boolean flag for computing perimeter.*/
+        @Deprecated
         public boolean perimeter = true;
         /** The boolean flag for computing circularity.*/
+        @Deprecated
         public boolean circularity = true;
         /** The boolean flag for computing Euler number.*/
+        @Deprecated
         public boolean eulerNumber = true;
         /** The boolean flag for computing bounding box.*/
+        @Deprecated
         public boolean boundingBox = true;
         /** The boolean flag for computing centroid.*/
+        @Deprecated
         public boolean centroid = true;
         /** The boolean flag for computing equivalent ellipse.*/
+        @Deprecated
         public boolean equivalentEllipse = true;
         /** The boolean flag for computing ellipse elongation.*/
+        @Deprecated
         public boolean ellipseElongation = true;
         /** The boolean flag for computing convexity.*/
+        @Deprecated
         public boolean convexity = true;
         /** The boolean flag for computing maximum Feret diameter.*/
+        @Deprecated
         public boolean maxFeretDiameter = true;
         /** The boolean flag for computing oriented box.*/
+        @Deprecated
         public boolean orientedBox = true;
         /** The boolean flag for computing elongation of oriented box.*/
+        @Deprecated
         public boolean orientedBoxElongation = true;
         /** The boolean flag for computing geodesic diameter.*/
+        @Deprecated
         public boolean geodesicDiameter = true;
         /** The boolean flag for computing tortuosity.*/
+        @Deprecated
         public boolean tortuosity = true;
         /** The boolean flag for computing largest inscribed disc.*/
+        @Deprecated
         public boolean maxInscribedDisc = true;
         /** The boolean flag for computing average thickness.*/
+        @Deprecated
         public boolean averageThickness = true;
         /** The boolean flag for computing geodesic elongation.*/
+        @Deprecated
         public boolean geodesicElongation = true;
 
         /**
@@ -316,6 +334,7 @@ public static final class Features
          * @param state
          *            the state to set.
          */
+        @Deprecated
         public void setAll(boolean state)
         {
             this.pixelCount = state;