0.0.3

README.md

@@ -1,4 +1,40 @@
 # RegisterNDFFT
 
-Registration of ND images using FFT. 
-Work in progress.
+Registration of ND (2/3/4D) images using FFT.   
+Work in progress, use at your own risk.  
+
+This plugin uses masked normalized cross-correlation calculation according to the paper:  
+_D. Padfield, “[Masked object registration in the Fourier domain](https://doi.org/10.1109/TIP.2011.2181402)” IEEE Transactions on Image Processing (2012)._  
+So basically it can account (exclude) image values that are zero and does not need arbitrary image padding during fast CC calculation using FFT.  
+
+To install it, you need to copy jar file from the [latest release](https://github.com/ekatrukha/RegisterNDFFT/releases) to jar folder of your [FIJI](https://fiji.sc/) installation. The plugin commands should appear in the _Plugins->ARegisterNDFFT_ menu (it starts with an extra A letter).   
+
+The plugin works with 2D/3D/multichannel images.  
+
+## Single template registration
+
+This command registers template image(dataset) to the reference image using rigid translation (in all axis).  
+The precision of registration is up to one voxel (subpixel is not available).   
+It is possible to limit the maximum shift of the template by a fraction of its size (in all dimensions).  
+In case of multi-channel images, only one user selected channel from each image will be used for the registration.  
+
+
+## Iterative registration
+
+Provided with a set of opened in FIJI or stored on hard drive images of the same dimensions, the plugin will perform iterative registration/averaging.  
+At the initial step it will create an reference image as an average of input images (depending on initial template settings).  
+After that it will iteratively register input images to this average, update it, register again.   
+Depending on the number of iterations or convergence of average CC it will stop and show the final image.
+
+## Pairwise CC
+
+Given a set of input images, the plugin will pairwise calculate the maximum of cross-correlation among them.  
+
+----------
+
+Developed in <a href='http://cellbiology.science.uu.nl/'>Cell Biology group</a> of Utrecht University.  
+<a href="mailto:katpyxa@gmail.com">E-mail</a> for any questions.
+
+
+
+

pom.xml

@@ -5,13 +5,13 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>30.0.0</version>
+		<version>34.0.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>RegisterNDFFT</artifactId>
-	<version>0.0.1-SNAPSHOT</version>
+	<version>0.0.3</version>
 
 	<name>RegisterNDFFT</name>
 	<description>Registration of ND images using FFT and imglib2. </description>
@@ -108,10 +108,7 @@
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2-realtransform</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>net.imglib2</groupId>
-			<artifactId>imglib2-ui</artifactId>
-		</dependency>
+
 
 		<!-- ImageJ dependencies -->
 		<dependency>

src/main/java/fiji/plugin/RegisterNDFFT/AverageWithoutZero.java

@@ -3,7 +3,7 @@
 import java.util.ArrayList;
 
 import ij.IJ;
-import ij.ImagePlus;
+
 import ij.WindowManager;
 import ij.plugin.PlugIn;
 import net.imglib2.Cursor;
@@ -62,6 +62,7 @@ public void run(String arg0) {
 		averagedIP.show();
 		*/
 	}
+	/** returns an interval that encompasses all RAIs in the input ArrayList **/
 	public static FinalInterval getIntervalAverageArray(ArrayList<RandomAccessibleInterval< FloatType >> imgs)
 	{
 		int i,j;
@@ -100,7 +101,7 @@ public static FinalInterval getIntervalAverageArray(ArrayList<RandomAccessibleIn
 	public static IntervalView<FloatType> averageArray(ArrayList<RandomAccessibleInterval< FloatType >> imgs)
 	{
 		int i;
-		int nDim = imgs.get(0).numDimensions();
+		//int nDim = imgs.get(0).numDimensions();
 
 		FinalInterval intervalMax = getIntervalAverageArray(imgs);
 
@@ -147,7 +148,11 @@ public static IntervalView<FloatType> averageArray(ArrayList<RandomAccessibleInt
 
 	}
 
-
+	/** Provided with an ArrayList of RAI, returns a new ArrayList with two RAIs:
+	 * the first contains sum of all intensities at a current voxel/pixel location,
+	 * the second contains an integer equal to how many RAIs have a pixel at this location. 
+	 * Since input RAIs could be of different sizeslocations, the output size is made to include
+	 * all of them, i.e. hyper box that includes them all **/
 
 	public static ArrayList<IntervalView<FloatType>> sumAndCountArray(ArrayList<RandomAccessibleInterval< FloatType >> imgs)
 	{
@@ -207,7 +212,9 @@ public static ArrayList<IntervalView<FloatType>> sumAndCountArray(ArrayList<Rand
 		return 	finalSumCnt;
 
 	}
-
+	/** returns an average RAI provided ArrayList with two RAIs:
+	 * first being intensity values and the second is count number.
+	 * Checks for zero counts and returned RAI origin is at zeros. **/
 	public static IntervalView<FloatType> averageFromSumAndCount(ArrayList<IntervalView<FloatType>> alSumCnt)
 	{
 

src/main/java/fiji/plugin/RegisterNDFFT/GenNormCC.java

@@ -39,10 +39,13 @@ public class GenNormCC {
 	/** whether to log results to IJ.log window **/
 	public boolean bVerbose = true;
 
-	/** **/
-
+	/** whether to exclude/ignore voxels that are zeros **/	
 	public boolean bExcludeZeros = false;
 
+	/** whether to look for the zero with X shift = 0,
+	 * needed for rotation registration **/
+	public boolean bZeroX = false;
+
 
 	/** 
 	 * @param image
@@ -293,7 +296,33 @@ public boolean caclulateGenNormCC(final RandomAccessibleInterval< FloatType > im
 
 		//now find max value
 		Point shift = new Point(nDim);
-		FloatType fCCvalue = MiscUtils.computeMaxLocation(ivCCswapped,shift);
+		FloatType fCCvalue;
+		if(!bZeroX)
+		{
+			fCCvalue = MiscUtils.computeMaxLocation(ivCCswapped,shift);
+		}
+		else
+		{
+			//Point shiftZeroX =new Point(nDim-1);
+			long [] minX = ivCCswapped.minAsLongArray();
+			long [] maxX = ivCCswapped.maxAsLongArray();
+			minX[0]=0;
+			maxX[0]=0;
+			//minX[1]=-179;
+			//maxX[1]=180;
+			FinalInterval valX = new FinalInterval(minX,maxX);
+			//ImageJFunctions.show(Views.interval(ivCCswapped, valX)).setTitle( "XZero" );
+
+			fCCvalue = MiscUtils.computeMaxLocation(Views.interval(ivCCswapped, valX),shift);
+			/*
+			//ImageJFunctions.show(Views.hyperSlice(ivCCswapped, 0, 0)).setTitle( "XZero" );
+			//fCCvalue = MiscUtils.computeMaxLocation(Views.hyperSlice(ivCCswapped, 0, 0),shiftZeroX);
+			for(i=1;i<nDim;i++)
+			{
+				shift.setPosition(shiftZeroX.getLongPosition(i-1), i);
+			}
+			*/
+		}
 
 		if (bVerbose)
 		{