first commit

Author: ekatrukha

radiality_script_v1_20170221.ijm

@@ -0,0 +1,106 @@
+
+imHeight=getHeight();
+imWidth=getWidth();
+//rtype = Roi.getType();
+imName=getTitle();
+origID=getImageID();
+dWidth=1;
+
+if(selectionType() ==10)
+{
+Roi.getCoordinates(xpoints, ypoints);
+
+Dialog.create("Analysis parameters");
+Dialog.addMessage("OrientationJ parameters");
+Dialog.addNumber("Gaussian window (sigma, line width):", 1) 
+items=newArray("Cubic Spline Gradient","Finite Difference Gradient","Fourier Gradient","Riesz Filters","Gaussian Gradient","Finite Difference Hessian");
+Dialog.addChoice("Map calculation method:", items);
+Dialog.show();
+dWidth=Dialog.getNumber();	
+dMethod=Dialog.getChoice();
+dMethodN=0;
+if(startsWith(dMethod,"Cubic Spline Gradien"))
+	dMethodN=0;
+if(startsWith(dMethod,"Finite Difference Gradien"))
+	dMethodN=1;
+if(startsWith(dMethod,"Fourier Gradien"))
+	dMethodN=2;
+if(startsWith(dMethod,"Riesz Filter"))
+	dMethodN=3;
+if(startsWith(dMethod,"Gaussian Gradien"))
+	dMethodN=4;
+if(startsWith(dMethod,"Finite Difference Hessia"))
+	dMethodN=5;
+runstring="log=0.0 tensor="+toString(dWidth)+" gradient="+toString(dMethodN)+" harris-index=on color-survey=off s-distribution=off orientation=on hue=Gradient-X sat=Gradient-X bri=Gradient-X ";
+//run("OrientationJ Analysis", "log=0.0 tensor=5.0 gradient=0 harris-index=on color-survey=off s-distribution=off orientation=on hue=Gradient-X sat=Gradient-X bri=Gradient-X ");
+run("OrientationJ Analysis",runstring);
+rename(imName+"_orientantion_map_width="+toString(dWidth));
+
+centx=xpoints[0];	
+centy=ypoints[0];	
+//IJ.log(toString(centx));
+//IJ.log(toString(centy));
+
+
+//convert to radians
+for(i=0;i<imWidth;i++)
+	for(j=0;j<imHeight;j++)
+	{
+			val=getPixel(i,j)*PI/180;
+			setPixel(i,j,val);
+	}
+orientmapID=getImageID();
+run("Enhance Contrast", "saturated=0.35");
+//polarity map
+run("Duplicate...", "title=["+imName+"_radiality_map_width="+toString(dWidth)+"]");
+for(i=0;i<imWidth;i++)
+	for(j=0;j<imHeight;j++)
+	{
+		val=getPixel(i,j);
+		//dl=sqrt(px*px+py*py);
+		vx=i-centx;
+		vy=centy-j;		
+		vangle=atan(vy/vx);
+		newval=abs(cos(vangle-val));
+		setPixel(i,j,newval);		
+	}
+run("Enhance Contrast", "saturated=0.35");
+polaritymapID=getImageID();
+polarityTitle=getTitle();
+
+imageCalculator("Multiply create 32-bit", imName,polarityTitle);
+rename(imName+"_mult_radiality_map_width="+toString(dWidth));
+run("Fire");
+
+selectImage(orientmapID);
+
+run("Enhance Contrast", "saturated=0.35");
+//polarity map
+run("Duplicate...", "title=["+imName+"_nonradiality_map_width="+toString(dWidth)+"]");
+for(i=0;i<imWidth;i++)
+	for(j=0;j<imHeight;j++)
+	{
+		val=getPixel(i,j);
+		//dl=sqrt(px*px+py*py);
+		vx=i-centx;
+		vy=centy-j;		
+		vangle=atan(vy/vx);
+		newval=1-abs(cos(vangle-val));
+		setPixel(i,j,newval);
+		
+		
+	}
+run("Enhance Contrast", "saturated=0.35");
+nonpolaritymapID=getImageID();
+nonpolarityTitle=getTitle();
+
+imageCalculator("Multiply create 32-bit", imName,nonpolarityTitle);
+rename(imName+"_mult_nonradiality_map_width="+toString(dWidth));
+run("Fire");
+
+
+}
+else
+{
+	exit("Need to choose a point ROI first");
+}