From 5bbe81e2f9d24fc0cf59188830d4d592c78b81a7 Mon Sep 17 00:00:00 2001
From: Eugene Katrukha <katpyxa@gmail.com>
Date: Tue, 23 Apr 2024 16:24:57 +0200
Subject: [PATCH] zero iterations case

---
 pom.xml                                       |  2 +-
 .../java/averagingND/IterativeAveraging.java  | 23 ++++++++++++++-----
 src/main/java/averagingND/MiscUtils.java      |  1 +
 .../java/averagingND/RegisterSingleND.java    |  4 ++--
 4 files changed, 21 insertions(+), 9 deletions(-)

diff --git a/pom.xml b/pom.xml
index bbbf399..cd12e75 100644
--- a/pom.xml
+++ b/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>
diff --git a/src/main/java/averagingND/IterativeAveraging.java b/src/main/java/averagingND/IterativeAveraging.java
index 339bf28..cd798aa 100644
--- a/src/main/java/averagingND/IterativeAveraging.java
+++ b/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..");
diff --git a/src/main/java/averagingND/MiscUtils.java b/src/main/java/averagingND/MiscUtils.java
index ee42942..d431079 100644
--- a/src/main/java/averagingND/MiscUtils.java
+++ b/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() )
diff --git a/src/main/java/averagingND/RegisterSingleND.java b/src/main/java/averagingND/RegisterSingleND.java
index 27652cd..0e9a817 100644
--- a/src/main/java/averagingND/RegisterSingleND.java
+++ b/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();