/* 
 *  This script provides an instantaneous conversion from reciprocal space to real  
 *  space for selected area diffraction (SAD) pattern measurements. 
 *  
 *  It assumes that your diffraction pattern was collected using Gatan's 
 *  Digital Micrograph software, and that your image is properly calibrated in 
 *  reciprocal space, i.e. scale bar units display as 1/nm in DM. 
 *  
 *  It also assumes that you have used imageJ's circle tool to measure the spot/ring 
 *  patterns concentric to the (000) direct beam. From the area measurement, the radius
 *  (G) is found. From G = 1/d in reciprocal space, the d-spacing is calculated for  
 *  each measurement made.
 *  
 *  Written by: Mak Koten, Ph.D. (2018)
 */

// Make sure the right measurements are set (for next time plugin is run).
setMeasurements();

// Read the area from the results window into an area array.
area=getArray("Area");

// Calculate G and d from Area measurements.
G=calcG(area);
d=calcD(area);
e=dError(d);

// Print the values of d as a list in a text window. [[Un-comment next line to enable]].
//printToText("d-Spacing List","d (A)", d); 

// Update the results table.
updateResults();

/*
 *************************
 * * * * FUNCTIONS * * * *
 *************************
 */

// This ensures that Area and centroid will be measured the next time, if they weren't already...
function setMeasurements() {
	run("Set Measurements...", "area centroid redirect=None decimal=3");
}

// This will return an array created from a column in the Results window.
function getArray(resultsHeader) {
	array = newArray();
	for (i=0; i<nResults; i++) {
		value=getResult(resultsHeader, i);
		array=Array.concat(array, value);
	}
	return array;
}

// For each area measurement, a value of G (1/nm) is calculated, the results table is set, and a G array is returned.
function calcG(area) {
	G = newArray();
	for (i=0; i<area.length; i++) {
		g=sqrt(area[i]/3.141593);
		G=Array.concat(G, g);
		setResult("  G (1/nm)", i, g);
	}
	return G;
}

// For each area measurement, a value of d (Angstroms) is calculated, the results table is set, and a d array is returned.
function calcD(area) {
	d = newArray();
	for (i=0; i<area.length; i++) {
		g=sqrt(area[i]/3.141593);
		D=10/g;
		d=Array.concat(d, D);
		setResult("  d (A)", i, D);
	}
	return d;
}

// Multiply a number times every element in an array.
function dError(array1) {
	array2 = newArray();
	for (i=0; i<array1.length; i++) {
		array2=Array.concat(array2, 0.02*array1[i]);
		setResult("  2% error", i, 0.02*array1[i]);
	}
	return array2;
}

// Prints an array to a new Text Window.
function printToText(title, name, array) {
	f = "["+title+"]";
	run("Text Window...", "name="+f+" width=72 height=4 menu");
	print(f, "\\Update:"); // clears the window
	print(f, name);
	for (i=0; i<array.length; i++) {
		if (i==0) {
			print(f, ": ");
		}
		if (i==array.length-1) {
			print(f, d2s(array[i],2)+".");
			exit;
		}
		print(f, d2s(array[i],2)+", ");
	}
}

// Sometimes useful for troubleshooting.
function list(name, a) {
    print(name); 
    Array.print(a);
}