v.0.0.4

Author: ekatrukha

Correlescence_v_0.0.4.jar

@@ -4,6 +4,7 @@
 import ij.ImagePlus;
 import ij.Prefs;
 import ij.gui.GenericDialog;
+import ij.measure.Calibration;
 import ij.plugin.PlugIn;
 
 public class Corr1DSTICS implements PlugIn {
@@ -30,6 +31,7 @@ public void run(String arg)
 		int nStackSize;
 		int imHeight;
 		String sTitle;
+		ImagePlus finalImp;
 
 		imp = IJ.getImage();		
 		imHeight= imp.getHeight();
@@ -72,7 +74,11 @@ else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &
 		else
 			sTitle=sTitle+"_1Dxt_fft";
 
-		new ImagePlus(sTitle,x1D.xCorrSpaceTime(imp.getProcessor(), nMaxUserDelay1D,nCalcMethod,nNormMethod)).show();
+		finalImp = new ImagePlus(sTitle,x1D.xCorrSpaceTime(imp.getProcessor(), nMaxUserDelay1D,nCalcMethod,nNormMethod));
+		Calibration cal = finalImp.getCalibration();
+	    cal.xOrigin=Math.round(imp.getWidth()*0.5)-1;
+	    cal.yOrigin=0;
+		finalImp.show();
 			//x1D.xCorrSpaceTimeFFT();
 	}
 

bin/Correlescence/Corr1DSTICS.class

@@ -96,6 +96,7 @@ else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &
 	sTitle=imp.getTitle();
 	IJ.showStatus("2D STICS calculation done.");
 	finalImp=new ImagePlus(sTitle+"_2D_STICS", stSTICS);
+	//calibration
 	Calibration cal = finalImp.getCalibration();
     cal.xOrigin=Math.round(origW*0.5);
     cal.yOrigin=Math.round(origH*0.5);

bin/Correlescence/Corr2DSTICS.class

@@ -48,6 +48,7 @@ public void run(String arg) {
     int [] xymax;
     String sTitle;
     String sImTitle;
+    String sInTitle;
     ImageStack crosscorrstack;
     int [][] xydrifttable;
     boolean bAutoCorr =false;
@@ -78,6 +79,7 @@ else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &
 	    IJ.log("Only one image in stack, limiting choice to autocorrelation");
 	    	bAutoCorr=true;
 	}
+	sInTitle = imp.getTitle();
 
 	if(!x2Dialog(bAutoCorr))
 		return;
@@ -101,7 +103,7 @@ else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &
     if(sChoice.equals("consecutive images"))
     {
     	sImTitle =sImTitle +sChoice;
-    	sImTitle = sImTitle+"_delay_"+Integer.toString(nImNumber);
+    	sImTitle = sImTitle+"_delay_"+Integer.toString(nImNumber)+"_"+sInTitle;
     	if (bDrift)
     	{
     		xydrifttable[0][0]=0;
@@ -162,8 +164,9 @@ else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &
     //current image in stack and all others
     if(sChoice.equals("current image in stack and all others"))
     {
-    	sImTitle =sImTitle +"vs_current_image";
+    	
     	i=imp.getCurrentSlice();
+    	sImTitle =sImTitle +"vs_frame"+Integer.toString(i)+"_"+sInTitle;
     	ip1=getFloatversion(imp);
     	//subtract average intensity value
 		ip1.subtract(ImageStatistics.getStatistics(ip1,Measurements.MEAN,null).mean);
@@ -205,7 +208,7 @@ else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &
     //autocorrelation
     if(sChoice.equals("autocorrelation"))
     {	
-    	sImTitle =sImTitle +"autocorrelation_";
+    	sImTitle =sImTitle +"autocorrelation_"+sInTitle;
 
 		//i=imp.getCurrentSlice();
 		//ip1=getFloatversion(imp);
@@ -223,7 +226,8 @@ else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &
 				{ip = x2D.calcFFTCorrelationImage(ip2, ip2);}
 
 			sTitle = String.format("corr_%d_x_%d", j,j);
-			xymax = getmaxpositions(ip);
+			xymax = getmaxpositionscenterlimit(ip);
+			//xymax = getmaxpositions(ip);
 
 			ptable.incrementCounter();
 			ptable.addLabel(sTitle);
@@ -299,7 +303,7 @@ public boolean x2Dialog(boolean bAutoOn)
 	else
 	{	x2DDial.addRadioButtonGroup("Calculate 2D cross correlation between:", items, 3, 1, Prefs.get("Correlescence.2Dcorr", "consecutive images"));}
 
-	x2DDial.addNumericField("for consecutive, distance between images", Prefs.get("Correlescence.2Ddist", 1), 0, 4, " ");
+	x2DDial.addNumericField("for consecutive, interval between images", Prefs.get("Correlescence.2Ddist", 1), 0, 4, "frames (or slices) ");
 	x2DDial.addChoice("Calculation method:", itemsC, Prefs.get("Correlescence.2Dcorrmethod", "FFT cross-correlation (fast)"));
 
 	x2DDial.addCheckbox("Correct drift (max of corr)?", Prefs.get("Correlescence.2Ddrift", false));