zero iterations case

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>nl.uu.science.cellbiology</groupId>
 	<artifactId>AveragingND</artifactId>
-	<version>0.0.4-SNAPSHOT</version>
+	<version>0.1.0-SNAPSHOT</version>
 
 	<name>AveragingND</name>
 	<description>Averaging of ND images using normalized cross-correlation. </description>

src/main/java/averagingND/IterativeAveraging.java

@@ -301,7 +301,7 @@ public void run(String paramString) {
 		sumAndCount = AverageWithoutZero.sumAndCountArray(imgs_shift);
 
 		IntervalView<FloatType> currAverageImg;
-		if(bIntermediateAverage)
+		if(bIntermediateAverage && nIterN>0)
 		{		
 			processIntermediate(0);
 		}
@@ -341,9 +341,21 @@ public void run(String paramString) {
 			maxAverCCshifts.add(new long[nDimReg]);
 		}
 
+		//initial iteration
+		int iterBeg = 0;
+		//for zero iterations we want to do one without shifts
+		if(nIterN == 0)
+		{
+			iterBeg=-1;
+			lim_fractions = null;
+			limInterval = new FinalInterval(new long [nDimReg], new long [nDimReg]);
+			//no need to save, since they are the same
+			bOutputInput = false;
+		}
+
 		long iterStartT, iterEndT;
 
-		for(iter=0;(iter<nIterN && !bConverged);iter++)
+		for(iter=iterBeg;(iter<nIterN && !bConverged);iter++)
 		{
 			IJ.showStatus("Averaging iteration "+Integer.toString(iter+1)+"...");
 			avrgCC = 0.0;
@@ -453,15 +465,14 @@ public void run(String paramString) {
 		{
 			IJ.log("Best result: iteration #" + Integer.toString(nIterMax) + " with average CC " + df.format(maxAverCC));
 
-			ptable.show("Results");
-			ptableCC.show("Average CC");
-			shifts = maxAverCCshifts;
 		}
 		else
 		{
 			IJ.log("Iteration count is equal to zero, no registration was done, just averaging.");
 		}
-
+		ptable.show("Results");
+		ptableCC.show("Average CC");
+		shifts = maxAverCCshifts;
 
 		//calculate final average image		
 		IJ.log("calculating final average image..");

src/main/java/averagingND/MiscUtils.java

@@ -66,6 +66,7 @@ public static < T extends Comparable< T > & Type< T > > T computeMaxLocation(
 			// initialize min and max with the first image value
 			T type = cursor.next();
 			T max = type.copy();
+			maxLocation.setPosition( cursor );
 
 			// loop over the rest of the data and determine min and max value
 			while ( cursor.hasNext() )

src/main/java/averagingND/RegisterSingleND.java

@@ -359,8 +359,8 @@ public static void main( final String[] args ) throws ImgIOException, Incompatib
 
 		//IJ.open("/home/eugene/Desktop/projects/RegisterNDFFT/4d/HyperStack.tif");
 		//IJ.open("/home/eugene/Desktop/projects/RegisterNDFFT/4d/HyperStack-1.tif");
-		IJ.open("/home/eugene/Desktop/projects/RegisterNDFFT/centered/full.tif");
-		IJ.open("/home/eugene/Desktop/projects/RegisterNDFFT/centered/center.tif");
+		IJ.open("/home/eugene/Desktop/projects/RegisterNDFFT/center/full.tif");
+		IJ.open("/home/eugene/Desktop/projects/RegisterNDFFT/center/center.tif");
 
 
 		RegisterSingleND test = new RegisterSingleND();