Change version number, add contributors, other small changes

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>de.csbdresden</groupId>
 	<artifactId>StarDist_</artifactId>
-	<version>0.1.1</version>
+	<version>0.2.0</version>
 
 	<name>StarDist</name>
 	<description>StarDist - Object Detection with Star-convex Shapes</description>
@@ -69,6 +69,16 @@
 			<url>https://github.com/frauzufall</url>
 			<roles><role>reviewer</role></roles>
 		</contributor>
+		<contributor>
+			<name>Olivier Burri</name>
+			<url>https://github.com/lacan</url>
+			<roles><role>developer</role></roles>
+		</contributor>
+		<contributor>
+			<name>Romain Guiet</name>
+			<url>https://github.com/romainGuiet</url>
+			<roles><role>developer</role></roles>
+		</contributor>
 	</contributors>
 
 	<mailingLists>
@@ -79,14 +89,14 @@
 	</mailingLists>
 
 	<scm>
-		<connection>scm:git:git://github.com/uschmidt83/stardist-imagej</connection>
-		<developerConnection>scm:git:git://github.com/uschmidt83/stardist-imagej</developerConnection>
+		<connection>scm:git:git://github.com/mpicbg-csbd/stardist-imagej</connection>
+		<developerConnection>scm:git:git://github.com/mpicbg-csbd/stardist-imagej</developerConnection>
 		<tag>HEAD</tag>
-		<url>https://github.com/uschmidt83/stardist-imagej</url>
+		<url>https://github.com/mpicbg-csbd/stardist-imagej</url>
 	</scm>
 	<issueManagement>
 		<system>GitHub Issues</system>
-		<url>https://github.com/uschmidt83/stardist-imagej/issues</url>
+		<url>https://github.com/mpicbg-csbd/stardist-imagej/issues</url>
 	</issueManagement>
 	<ciManagement>
 		<system>None</system>

src/main/java/de/csbdresden/stardist/Candidates.java

@@ -32,7 +32,9 @@ public class Candidates {
     private final boolean[] suppressed;
     private final boolean verbose;
     private final LogService log;
-    public static final long S = 100;
+
+    // scale all coordinates by this value and divide later to get subpixel resolution
+    private static final long S = 100;
 
     public Candidates(RandomAccessibleInterval<FloatType> prob, RandomAccessibleInterval<FloatType> dist) {
         this(prob, dist, 0.4);

src/main/java/de/csbdresden/stardist/StarDist2D.java

@@ -210,7 +210,7 @@ public void run() {
         checkForCSBDeep();
         if (!checkInputs()) return;
 
-        if (roiPosition == Opt.ROI_POSITION_AUTO)
+        if (roiPosition.equals(Opt.ROI_POSITION_AUTO))
             roiPositionActive = input.numDimensions() > 3 ? Opt.ROI_POSITION_HYPERSTACK : Opt.ROI_POSITION_STACK;
         else
             roiPositionActive = roiPosition;

src/main/java/de/csbdresden/stardist/StarDist2DBase.java

@@ -98,16 +98,16 @@ protected void exportROIs(Candidates polygons, int framePosition, long numFrames
         for (final int i : polygons.getWinner()) {
             final PolygonRoi polyRoi = polygons.getPolygonRoi(i);
             if (framePosition > 0) setRoiPosition(polyRoi, framePosition, roiPosition);
-            roiManager.addRoi(polyRoi);
+            roiManager.add(polyRoi, -1);
             if (exportPointRois) {
                 final PointRoi pointRoi = polygons.getOriginRoi(i);
                 if (framePosition > 0) setRoiPosition(pointRoi, framePosition, roiPosition);
-                roiManager.addRoi(pointRoi);
+                roiManager.add(pointRoi, -1);
             }
             if (exportBboxRois) {
                 final Roi bboxRoi = polygons.getBboxRoi(i);
                 if (framePosition > 0) setRoiPosition(bboxRoi, framePosition, roiPosition);
-                roiManager.addRoi(bboxRoi);
+                roiManager.add(bboxRoi, -1);
             }
         }