Issue #3 array out of bound error fixed.

The reason was that anchor point array for affine was defined only for
singele point, not three points. At the same time, anchors for the
translation was excessively defined to be three points, so these two
definitions were swapped.

Author: miura

pom.xml

@@ -15,7 +15,7 @@
 
 	<groupId>de.embl.cmci</groupId>
 	<artifactId>MultiStackRegistration_</artifactId>
-	<version>1.46.0</version>
+	<version>1.46.1</version>
 
 	<name>plugins/MultiStackRegistration_.jar</name>
 	<description>A Maven project implementing an ImageJ 1.x plugin. MultiStackRegistration plugin written by Brad Busse.</description>
@@ -37,6 +37,11 @@
 			<groupId>net.imagej</groupId>
 			<artifactId>ij</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>sc.fiji</groupId>
+			<artifactId>TurboReg_</artifactId>
+			<version>2.0.1-SNAPSHOT</version>
+		</dependency>
 	</dependencies>
 
 	<build>

src/main/java/de/embl/cmci/registration/MultiStackReg_.java

@@ -237,6 +237,7 @@ public void run ( final String arg) {
   loadPath="";
   loadFile="None";
 
+  //@TODO show help with a help button, rather than a radio button. 
   if (viewManual){ //they just want to read the manual.  Do so and quit.
     final MultiStackRegCredits dialog = new MultiStackRegCredits(IJ.getInstance());
     GUI.center(dialog);
@@ -433,14 +434,14 @@ public int processDirectives(ImagePlus imp, boolean loadBool){
 	};
 	double[][] anchorPoints = null;
 	switch (transformation) {
-		case AFFINE: {
+		case TRANSLATION: {	//AFFINE: { //should be three points, not one. 
 			anchorPoints = new double[1][3];
 			anchorPoints[0][0] = (double)(width / 2);
 			anchorPoints[0][1] = (double)(height / 2);
 			anchorPoints[0][2] = 1.0;
 			break;
 		}
-		case RIGID_BODY: {
+		case RIGID_BODY: { //three points
 			anchorPoints = new double[3][3];
 			anchorPoints[0][0] = (double)(width / 2);
 			anchorPoints[0][1] = (double)(height / 2);
@@ -453,7 +454,7 @@ public int processDirectives(ImagePlus imp, boolean loadBool){
 			anchorPoints[2][2] = 1.0;
 			break;
 		}
-		case SCALED_ROTATION: {
+		case SCALED_ROTATION: { //two points
 			anchorPoints = new double[2][3];
 			anchorPoints[0][0] = (double)(width / 4);
 			anchorPoints[0][1] = (double)(height / 2);
@@ -463,7 +464,7 @@ public int processDirectives(ImagePlus imp, boolean loadBool){
 			anchorPoints[1][2] = 1.0;
 			break;
 		}
-		case TRANSLATION: {
+		case AFFINE: {//TRANSLATION: { //should be one point, not three. 
 			anchorPoints = new double[3][3];
 			anchorPoints[0][0] = (double)(width / 2);
 			anchorPoints[0][1] = (double)(height / 4);
@@ -1578,7 +1579,7 @@ private void QRdecomposition (
 } /* end QRdecomposition */
 
 /*------------------------------------------------------------------*/
-@SuppressWarnings({ "rawtypes", "rawtypes" })
+@SuppressWarnings({ })
 private ImagePlus registerSlice (
 	ImagePlus source,
 	ImagePlus target,
@@ -2351,10 +2352,16 @@ private ImagePlus registerSlice (
 							sourcePoints[0][i] = 0.0;
 							sourcePoints[1][i] = 0.0;
 							sourcePoints[2][i] = 0.0;
+							IJ.log("sourcePoints rows:" + Integer.toString(sourcePoints.length));
+							IJ.log("sourcePoints cols:" + Integer.toString(sourcePoints[0].length));
+							IJ.log("globalTransform rows:" + Integer.toString(globalTransform.length));
+							IJ.log("globalTransform cols:" + Integer.toString(globalTransform[0].length));
+							IJ.log("anchorPoints rows:" + Integer.toString(anchorPoints.length));
+							IJ.log("anchorPoints cols:" + Integer.toString(anchorPoints[0].length));
 							for (int j = 0; (j < 3); j++) {
 								sourcePoints[0][i] += globalTransform[i][j]
 									* anchorPoints[0][j];
-								sourcePoints[1][i] += globalTransform[i][j]
+								sourcePoints[1][i] += globalTransform[i][j] //java.lang.ArrayIndexOutOfBoundsException: 1
 									* anchorPoints[1][j];
 								sourcePoints[2][i] += globalTransform[i][j]
 									* anchorPoints[2][j];
@@ -2533,5 +2540,18 @@ public void setSavePath(String savePath) {
 	this.savePath = savePath;
 }
 
+public static void main(String[] args) {
+	MultiStackReg_ msr = new MultiStackReg_();
+	ImagePlus srcimp = new ImagePlus("/Users/miura/Dropbox/sampleImages/RegistrationExample/translation/MAX_reference.tif");
+	ImagePlus tgtimp = new ImagePlus("/Users/miura/Dropbox/sampleImages/RegistrationExample/translation/MAX_30-pixel-translation-along-x.tif");
+	msr.setSrcImg(srcimp);
+	msr.setTgtImg(tgtimp);
+	msr.setSrcAction("Use as Reference");
+	msr.setTgtAction("Align to First Stack");
+	msr.setTransformation(0);
+	msr.setSaveTransform(true);
+	msr.core("", "");
+}
+
 } /* end class StackReg_ */