- Fix for the SlopeOverlapResolver (by Mark Hiner)

- Saves the settings now
- Release 1.1.2

src/main/java/de/biomedical_imaging/ij/steger/Lines_.java

@@ -32,6 +32,7 @@
 
 import ij.IJ;
 import ij.ImagePlus;
+import ij.Prefs;
 import ij.gui.DialogListener;
 import ij.gui.GenericDialog;
 import ij.gui.Overlay;
@@ -58,26 +59,47 @@ public class Lines_ implements ExtendedPlugInFilter, DialogListener {
 	double contrastLow = contrastLowDefault;
 
 	final static double sigmaDefault = 1.51;
-	double sigma = 1.5;
+	double sigma = sigmaDefault;
 
 	final static double lowerThreshDefault = 3.06;
 	double lowerThresh = lowerThreshDefault;
 
 	final static double upperThreshDefault = 7.99;
 	double upperThresh = upperThreshDefault;
-	boolean isDarkLine = false;
-	boolean doCorrectPosition = false;
-	boolean doEstimateWidth = false;
-	boolean doExtendLine = true;
-	boolean showJunctionPoints = false;
-	boolean isPreview = false;
-	boolean displayResults = true;
-	boolean addToRoiManager = true;
+
+	final static boolean isDarkLineDefault = false;
+	boolean isDarkLine = isDarkLineDefault;
+
+	final static boolean doCorrectPositionDefault = false;
+	boolean doCorrectPosition = doCorrectPositionDefault;
+
+	final static boolean doEstimateWidthDefault = false;
+	boolean doEstimateWidth = doEstimateWidthDefault;
+
+	final static boolean doExtendLineDefault = true;
+	boolean doExtendLine = doExtendLineDefault;
+
+	final static boolean showJunctionPointsDefault = false;
+	boolean showJunctionPoints = showJunctionPointsDefault;
+
+	final static boolean displayResultsDefault = true;
+	boolean displayResults = displayResultsDefault;
+
+	final static boolean addToRoiManagerDefault = true;
+	boolean addToRoiManager = addToRoiManagerDefault;
+
 	OverlapOption overlapOption = OverlapOption.NONE;
+
+	final static boolean showIDsDefault = false;
+	boolean showIDs = showIDsDefault;
+
+	final static boolean verboseDefault = false;
+	boolean verbose = verboseDefault;
+
+	boolean isPreview = false;
 	boolean contrastOrLineWidthChangedOnce = false;
 	boolean doStack = false;
-	boolean showIDs = false;
-	boolean verbose = false;
+
 	private Options usedOptions = null;
 	private static Lines_ instance = null;
 
@@ -148,7 +170,7 @@ public int setup(String arg, ImagePlus imp) {
 		this.imp = imp;
 		result = new ArrayList<Lines>();
 		resultJunction = new ArrayList<Junctions>();
-
+		readSettings();
 		return DOES_8G + DOES_STACKS + FINAL_PROCESSING + PARALLELIZE_STACKS;
 	}
 
@@ -235,16 +257,58 @@ public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
 		displayResults = gd.getNextBoolean();
 		addToRoiManager = gd.getNextBoolean();
 		overlapOption = OverlapOption.valueOf(gd.getNextChoice());
+		saveSettings();
+
 		result = new ArrayList<Lines>();
 		resultJunction = new ArrayList<Junctions>();
 
 		int labels =  IJ.setupDialog(imp, DOES_8G + FINAL_PROCESSING
 				+ PARALLELIZE_STACKS);
 		doStack = (labels!=DOES_8G + FINAL_PROCESSING
 				+ PARALLELIZE_STACKS);
+
 		return labels;
 	}
 
+	private void readSettings(){
+		lineWidth = Prefs.get("RidgeDetection.lineWidth", lineWidthDefault);
+		contrastHigh = Prefs.get("RidgeDetection.contrastHigh", contrastHighDefault);
+		contrastLow = Prefs.get("RidgeDetection.contrastLow", contrastLowDefault);
+		sigma = Prefs.get("RidgeDetection.sigma",sigmaDefault);
+		lowerThresh = Prefs.get("RidgeDetection.lowerThresh", lowerThreshDefault);
+		upperThresh = Prefs.get("RidgeDetection.upperThresh", upperThreshDefault);
+		isDarkLine = Prefs.get("RidgeDetection.isDarkLine", isDarkLineDefault);
+		doCorrectPosition = Prefs.get("RidgeDetection.doCorrectPosition", doCorrectPositionDefault);
+		doEstimateWidth = Prefs.get("RidgeDetection.doEstimateWidth", doEstimateWidthDefault);
+		doExtendLine = Prefs.get("RidgeDetection.doExtendLine", doExtendLineDefault);
+		showJunctionPoints = Prefs.get("RidgeDetection.showJunctionPoints", showJunctionPointsDefault);
+		showIDs = Prefs.get("RidgeDetection.showIDs", showIDsDefault);
+		verbose = Prefs.get("RidgeDetection.verbose", verboseDefault);
+		displayResults = Prefs.get("RidgeDetection.displayResults", displayResultsDefault);
+		addToRoiManager = Prefs.get("RidgeDetection.addToRoiManager", addToRoiManagerDefault);
+		String overlapOptionString = Prefs.get("RidgeDetection.overlapOption", OverlapOption.NONE.name());
+		overlapOption = OverlapOption.valueOf(overlapOptionString);
+	}
+
+	private void saveSettings(){
+		Prefs.set("RidgeDetection.lineWidth", lineWidth);
+		Prefs.set("RidgeDetection.contrastHigh", contrastHigh);
+		Prefs.set("RidgeDetection.contrastLow", contrastLow);
+		Prefs.set("RidgeDetection.sigma", sigma);
+		Prefs.set("RidgeDetection.lowerThresh", lowerThresh);
+		Prefs.set("RidgeDetection.upperThresh", upperThresh);
+		Prefs.set("RidgeDetection.isDarkLine", isDarkLine);
+		Prefs.set("RidgeDetection.doCorrectPosition", doCorrectPosition);
+		Prefs.set("RidgeDetection.doEstimateWidth", doEstimateWidth);
+		Prefs.set("RidgeDetection.doExtendLine", doExtendLine);
+		Prefs.set("RidgeDetection.showJunctionPoints", showJunctionPoints);
+		Prefs.set("RidgeDetection.showIDs", showIDs);
+		Prefs.set("RidgeDetection.verbose", verbose);
+		Prefs.set("RidgeDetection.displayResults", displayResults);
+		Prefs.set("RidgeDetection.addToRoiManager", addToRoiManager);
+		Prefs.set("RidgeDetection.overlapOption", overlapOption.name());
+	}
+
 	public void addToRoiManager(){
 		RoiManager rm = RoiManager.getInstance();
 		if(rm==null){

src/main/java/de/biomedical_imaging/ij/steger/ResetToDefaultListener.java

@@ -23,6 +23,8 @@
 
 import ij.IJ;
 
+import java.awt.Checkbox;
+import java.awt.Choice;
 import java.awt.TextField;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -62,6 +64,18 @@ public void actionPerformed(ActionEvent arg0) {
 		textUppThresh.setText("" + IJ.d2s(Lines_.upperThreshDefault, 2));
 		textUppThresh.setEditable(true);
 
+		((Checkbox)gd.getCheckboxes().get(0)).setState(Lines_.isDarkLineDefault);
+		((Checkbox)gd.getCheckboxes().get(1)).setState(Lines_.doCorrectPositionDefault);
+		((Checkbox)gd.getCheckboxes().get(2)).setState(Lines_.doEstimateWidthDefault);
+		((Checkbox)gd.getCheckboxes().get(3)).setState(Lines_.doExtendLineDefault);
+		((Checkbox)gd.getCheckboxes().get(4)).setState(Lines_.showJunctionPointsDefault);
+		((Checkbox)gd.getCheckboxes().get(5)).setState(Lines_.showIDsDefault);
+		((Checkbox)gd.getCheckboxes().get(6)).setState(Lines_.verboseDefault);
+		((Checkbox)gd.getCheckboxes().get(7)).setState(Lines_.displayResultsDefault);
+		((Checkbox)gd.getCheckboxes().get(8)).setState(Lines_.addToRoiManagerDefault);
+
+		((Choice)gd.getChoices().get(0)).select(0);
+
 	}
 
 }

src/main/java/de/biomedical_imaging/ij/steger/SlopeOverlapResolver.java

@@ -179,24 +179,36 @@ private void findOverlap(final Set<Line> enclosed,
 
 		// clean up enclosed lines.. any enclosed line that intersects with another
 		// enclosed line at BOTH ends should be removed.
-		final Set<Line> toRemove = new HashSet<Line>();
 
-		for (final Line l1 : enclosed) {
-			boolean foundStartMatch = false;
-			boolean foundEndMatch = false;
+		boolean pruneEnclosed = true;
 
-			for (final Line l2 : enclosed) {
-				if (l2 == l1) continue;
-				else if (intersectsStart(l1, l2, SIGMA)) foundStartMatch = true;
-				else if (intersectsEnd(l1, l2, SIGMA)) foundEndMatch = true;
+		while (pruneEnclosed) {
+			pruneEnclosed = false;
+			Line toRemove = null;
+
+			for (final Line l1 : enclosed) {
+				boolean foundStartMatch = false;
+				boolean foundEndMatch = false;
+
+				for (final Line l2 : enclosed) {
+					if (l2 == l1) continue;
+					else if (intersectsStart(l1, l2, SIGMA)) foundStartMatch = true;
+					else if (intersectsEnd(l1, l2, SIGMA)) foundEndMatch = true;
+
+					if (foundStartMatch && foundEndMatch) break;
+				}
+
+				// found a line to prune
+				// remove it and restart
+				if (foundStartMatch && foundEndMatch) {
+					toRemove = l1;
+					pruneEnclosed = true;
+				}
 			}
 
-			if (foundStartMatch && foundEndMatch) toRemove.add(l1);
+			if (toRemove != null) enclosed.remove(toRemove);
 		}
 
-		for (final Line l : toRemove)
-			enclosed.remove(l);
-
 		if (verbose) {
 			for (final Line l : enclosed)
 				IJ.log("Found enclosed line: " + l.getID());
@@ -648,4 +660,4 @@ private boolean matchesEnd(final Junction junction, final Line line) {
 		return line.getXCoordinates()[count] == junction.getX() && line
 			.getYCoordinates()[count] == junction.getY();
 	}
-}
+}