var IJPath="C:\\Program Files\\ImageJ-FIJI\\"; //cestu nech v uvozovkach. Mozna budes muset separatory zmenit napriklad ve win z \ na \\.
var original, originalID, name;
var option;
var Sn,Sx,Sy,Sxx,Syy,Sxy,rot2,density,Centrex,Centrey,Theta, R1,R2;
var original, scalar, units, TA, CA, Cx, Cy, Ix, Iy, Imax, Imin, Zx, Zy, Xmaxrad, Ymaxrad, xmin, ymin, xmax, ymax;

macro "Batch measure [n0]" {  //zmeri vsechny pozadovane soubory v adresari
	if (is("Batch Mode")) setBatchMode(false);
	option=getOptions();
	if (!File.isDirectory(option[5])) {
		option[5]=getDirectory("Choose a measurements output directory"); //
		option[4]=false;
		setOptions(option);
		}

	inputPath=getDirectory("Choose a directory with INPUT data");
  	Dialog.create("Input options");
  	Dialog.addMessage("Choose type of data to measure");
	Dialog.addChoice("Image type:", newArray(".TIFF [images]", ".zip [selections]"));
	Dialog.show();
  	dataType = Dialog.getChoice(); //get dataType for analysis;
	if (dataType==".TIFF [images]") dataType=".tif";
	if (dataType==".zip [selections]") dataType=".zip";
	
	fileList=getFileList(inputPath);
	for (i=0; i<fileList.length; i++) {
		if (endsWith(fileList[i], dataType)) {
			roiManager("reset"); 
			open(inputPath+fileList[i]);
			if (dataType==".tif") MomentMacroJ();
			if (dataType==".zip") measureSelection();
			close();
		}
	}
}

macro "MomentMacroJ [n1]" {
	MomentMacroJ();
}

macro "Measure Selection [n2]" {
	measureSelection();
}

macro "Options [n3]"{
  option=getOptions();
  Dialog.create("MomentMacro options");
  Dialog.addMessage("This plugin is considered to analyze\nMRI or Confocal bone sections");
  Dialog.addChoice("Image type:", newArray("Confocal", "MRI"), option[0]);
  Dialog.addChoice("Boundaries creation:", newArray("Semi-Automated", "Automated", "Manual"),option[1]);
  Dialog.addCheckbox("Show selection", option[2]);
  Dialog.addCheckbox("Show principal axes", option[3]);
  Dialog.addCheckbox("Get destination directory", option[4]);
  Dialog.addMessage("Actual output directory:");
  Dialog.addMessage(option[5]);
  Dialog.show();
  option[0] = Dialog.getChoice(); //image Type;
  option[1] = Dialog.getChoice(); //selection method
  option[2] = Dialog.getCheckbox(); //show selection
  option[3] = Dialog.getCheckbox(); //show axes
  option[4] = Dialog.getCheckbox(); //read output directory
// option[5]  - OUTPUT directory
  
  if (option[4]==true) {
	option[5]=getDirectory("Choose an measurements output directory"); //
	option[4]=false;
	}
  if (!File.isDirectory(option[5])) option[5]="None";
  setOptions(option);
} //end of macro Options

//******************************************************************************* FUNCTIONS ***************************************************************************************************************************************
//************************** overiding functions *******************
function MomentMacroJ(){
if (is("Batch Mode")) setBatchMode(false);
option=getOptions();
if (!File.isDirectory(option[5])) {
	option[5]=getDirectory("Choose an measurements output directory"); //
	option[4]=false;
	setOptions(option);
	}
originalID=getImageID();
original=getTitle();
name=replace(original, ".tif", "");
// kontrola kalibrace obrazu na mm
AutoCalibrateImage();
channel=findRelevantChannel();		// pripravi obrazek a relevantni kanal pro analyzu
originalID=getImageID();
run("Select None");
run("Duplicate...", "title=mask1 duplicate channels="+channel); 		//duplikuje relevantni kanal pro vytvoreni ROI
if (option[1]=="Automated") {
	AutoSelectOuter();
	AutoSelectInner();
	}
else if (option[1]=="Semi-Automated"){
	// semi automated method outer selection
	AutoSelectOuter();
	index=roiManager("index");
	run("Fit Spline");
	resetThreshold();
	waitForUser("Outer Selection Adjustment","Now adjust manually outer selection.\n Outer space");
//	roiManager("Select", index);
	roiManager("Update");
	
	// semi-automated method inner selection
	AutoSelectInner();
	index=roiManager("index");
	run("Fit Spline");
	waitForUser("Inner Selection Adjustment","Now adjust manually inner selection.\n");
//	roiManager("Select", index);
	roiManager("Update");
	}
else if (option[1]=="Manual")	waitForUser("Manual Selection","Now adjust manually outer & inner selection.\nSend both to roi Manager by pressing 't'.\nThen press OK");
checkROIs();
selectImage("mask1");
close();
selectImage(originalID);
checkROIs();
measureMoments();
saveResults();
} //end of momentMacroJ....

//*********************** measureSelection ***************************
function measureSelection() {
	if (is("Batch Mode")) setBatchMode(false);
	option=getOptions();
	  if (!File.isDirectory(option[5])) {
		option[5]=getDirectory("Choose an measurements output directory"); //
		option[4]=false;
		setOptions(option);
		}
//	option[2]=1;
//	option[3]=1;
	name=File.nameWithoutExtension;
	name=replace(name, ".tif", "");
	if (roiManager("count")==0) exit("No Selections in ROI Manager!!!");
	newImage("examine", "8-bit Black", 1, 1, 1);
	checkROIs();
	getSelectionBounds(x, y, width, height);
	selectImage("examine"); close();
	newImage(name+".tif", "8-bit Black", (width+1), (height+1), 1);
	original=getTitle();
	AutoCalibrateImage();
	channel=findRelevantChannel();
	originalID=getImageID();
	checkROIs();
	setSelectionLocation(0,0);
	updateSelection();
	setForegroundColor(50, 50,50);
	Stack.setDisplayMode("color");
	run("Fill", "slice");
	Stack.setDisplayMode("composite");
	measureMoments();
	saveResults();
}	



//************************** findRelevantChannel *****************
function findRelevantChannel(){
	if (getMetadata("info")!="prepared" || !Stack.isHyperstack) prepareImage();			// kontrola, ze obrazek je pripraveny
	Stack.getDimensions(width, height, channels, slices, frames);
	if (channels==5 || channels==3) {
		channel=round((channels-2)/2);
		}
	else {
		showMessageWithCancel("unexpected channel number","The number of channels should now be 5 or 3");
		waitForUser("select channel for analysis", "Please, select the channel for analysis (e.g. set slicer on appropriate channel)");
		Stack.getPosition(channel, s, f);
		}
	return(channel);
}
	


//************************** PREPAREIMAGE **********************
// pruzkum obrazku, priprava do compositu

function prepareImage() {
//1 obrazek je RGB
image=getTitle();
if (bitDepth()==24) { 
	run("Make Composite");
	selectImage(image);
	getDimensions(width, height, channels, slices, frames);
	}

hyperstack=Stack.isHyperstack;    //1. je to hyperstack nebo neni
if (hyperstack) {
	Stack.getDimensions(width, height, channels, slices, frames);
	}
if (!hyperstack){ 	// Kdyz neni hyperstack
	getDimensions(width, height, channels, slices, frames);
	if (is("composite")) {
		run("Stack to Hyperstack...", "order=xyczt(default) channels="+channels+" slices="+slices+" frames="+frames+" display=Composite");
		selectImage(image);
		Stack.getDimensions(width, height, channels, slices, frames);
		}
	}
if (slices!=1) {
	//!!!!!! dotaz na projekci !!!!!!!!!!!!!1
	waitForUser("Z-Projection","Now examine your stack and decide which slices to include into Z-projection.\nFirst and Last.");
	run("Z Project...");
	max=getTitle();
	selectImage(image); close();
	selectImage(max); rename(image);
	}
getDimensions(width, height, channels, slices, frames);
if (is("composite")) {	
	run("Stack to Hyperstack...", "order=xyczt(default) channels="+channels+" slices="+slices+" frames="+frames+" display=Composite");
	if (getMetadata("info")!="prepared") {
		setSlice(nSlices);
		run("Add Slice");
		setSlice(nSlices);
		run("Yellow");
		setMetadata("Label", "selection");
		run("Add Slice");
		setSlice(nSlices);
		run("Cyan");
		setMetadata("Label", "principal axes");
		setSlice(2);
		setMetadata("info", "prepared");
		}
	}
else {	getLut(reds, greens, blues);
	run("Add Slice");
	run("Add Slice");
	run("Stack to Hyperstack...", "order=xyczt(default) channels="+channels+2+" slices="+slices+" frames="+frames+" display=Composite");
	setLut(reds, greens, blues);
	setSlice(nSlices-1);
	run("Yellow");
	setMetadata("Label", "selection");
	setSlice(nSlices);
	run("Cyan");
	setMetadata("Label", "principal axes");
	setSlice(1);
	setMetadata("info", "prepared");
	}
}
//************************** RECALIBRATE ************************ 
function recalibrate(){
	getVoxelSize(width, height, depth, unit);
	fail=true;
	if (unit=="pixels") {
		lastName=File.name;
		if (endsWith(lastName,".zip")) {
			lastName=replace(lastName, ".zip", ".tif");
			lastName=replace(lastName, ".txt", ".tif");
			path=File.directory;
			fileName=path+lastName;
			if (File.exists(fileName)) {
				open(fileName);
				getVoxelSize(width, height, depth, unit);
				close();
				setVoxelSize(width, height, depth, unit);
				fail=false;
			} 
		}
		else if  (endsWith(lastName, ".tif")) {
			path=File.directory;
			fileName=path+lastName;
			if (File.exists(fileName)) {
				open(fileName);
				getVoxelSize(width, height, depth, unit);
				close();
				setVoxelSize(width, height, depth, unit);
				fail=false;
			} 
		}
			
	}
	if (unit==getInfo("micrometer.abbreviation") || unit=="um" || unit=="microns") {
		setVoxelSize(width/1000, height/1000, depth/1000, "mm");
		fail=false;
		}
	if (unit=="m" && width!=1){
		run("Properties...", "unit=um");
		fail=false;
		}
	if (unit=="cm"&& width!=1) {
		setVoxelSize(width*10, height*10, depth*10, "mm");
		fail=false;
		}
	if (fail) waitForUser("Automatic calibration failed", "Please, calibrate image manually in mm...\nThen press OK");
}

//************************** AUTOCALBRATEIMAGE ****************
function AutoCalibrateImage() {
	error=false;
	// pokus o automatickou kalibraci obrazku z konfokalu
	lastPath=File.directory;
	lastName=File.name;
	if (indexOf(lastName,"_")!=-1) {
	leiName=substring(lastName,0, indexOf(lastName,"_"));
	if (indexOf(lastName,"_z")==-1 && (indexOf(lastName,"_ch")==-1)) endString=lengthOf(lastName);
	else if (indexOf(lastName,"_z")!=-1) endString=indexOf(lastName, "_z");
	else if (indexOf(lastName,"_z")==-1 && indexOf(lastName,"_ch")!=-1) endString=indexOf(lastName, "_ch");
	imageName=substring(lastName,  indexOf(lastName,"_")+1, endString);
	isThereLei=File.exists(lastPath+leiName+".lei");
	isThereTxt=File.exists(lastPath+leiName+".txt");
	if (isThereLei && isThereTxt){
		TXTfile=File.openAsString(lastPath+leiName+".txt");
		namePos=indexOf(TXTfile, imageName);
		voxPos=indexOf(TXTfile, "Voxel-Width", namePos);
		voxel=substring(TXTfile, voxPos+16, indexOf(TXTfile, "\n", voxPos)-1);
		voxel=parseFloat(voxel);
		zvoxPos=indexOf(TXTfile, "Voxel-Depth", namePos);
		zvoxel=substring(TXTfile, zvoxPos+16, indexOf(TXTfile, "\n", zvoxPos)-1);
		zvoxel=parseFloat(zvoxel);
		if (isNaN(voxel) || isNaN(zvoxel)) error=true;
		else {   
			if (isOpen(lastName)) {
				selectImage(lastName);
				setVoxelSize(voxel, voxel, zvoxel, getInfo("micrometer.abbreviation"));
				}
			}
	}
	} 
	if (error || !calControl()) errorHandle();
}

//************************** ERRORHANDLE ***************************
function errorHandle(){
	cal=false;
while (cal==false) {
	recalibrate();
	cal=calControl();
	}
}

//************************** CALCONTROL ****************************
function calControl() {
	getPixelSize(unit, v, h);
	if (unit=="mm") return true;
	else return false;
}

//***************************GETOPTIONS******************************
function getOptions(){
	keys = getList('java.properties');
//	IJPath=getInfo(keys[1]);
	if (File.exists(IJPath+"MomentMacro.cfg")) {
		options=File.openAsString(IJPath+"MomentMacro.cfg");
		options=split(options, "\n");
		}
	else options=newArray("Confocal", "Semi-Automated", true, true, true, "None");
	return options;
}
//***************************SETOPTIONS******************************
function setOptions(options){
	ent="\n";
	string="";
	for (i=0; i<options.length; i++) string=string+options[i]+ent;
	keys = getList('java.properties');
//	IJPath=getInfo(keys[1]);
	File.saveString(string, IJPath+"MomentMacro.cfg");
}

//***************************estimateSize*********************************
function estimateSize(){
run("Select None");
setAutoThr();
run("Create Selection");
getStatistics(area);
run("Select None");
return area/3;
}

//************************************* AutoSelectInner *****************************************
function AutoSelectInner(){
	getPixelSize(unit, pixelWidth, pixelHeight);
	run("Set Measurements...", "  mean standard centroid redirect=None decimal=3");
  	List.setMeasurements;
	X = List.getValue("X")/pixelWidth;
	Y = List.getValue("Y")/pixelHeight;
	mean = List.getValue("Mean");
	std = List.getValue("StdDev");
	resetThreshold();
	run("Select None");
	if (option[0]=="MRI" || bitDepth()!=8) WandParam=mean;
	if (option[0]=="Confocal" || bitDepth()==8) WandParam=maxOf(mean,std)/minOf(mean,std);
	doWand(X, Y, WandParam, "legacy");
	while (selectionType==-1) waitForUser("Automatic Inner Selection failed", "Please define inner selection manualy.\nThen press OK.");	
	roiManager("Add");
	roiManager("Select", roiManager("count")-1);
	roiManager("Rename", "Inner");
}

function setAutoThr() {
if (option[0]=="MRI") setAutoThreshold("Minimum dark");
if (option[0]=="Confocal") setAutoThreshold("Huang dark");
}

//********************************************AutoSelectOuter() *********************************
function AutoSelectOuter(){
roiManager("reset");
run("Copy");
if (option[0]=="Confocal") run("Gaussian Blur...", "sigma=3");
estSize=estimateSize();
setAutoThr();
run("Analyze Particles...", "size="+estSize+"-Infinity circularity=0.00-1.00 show=Nothing clear add");
do {   //kontrola pochodu vyberu vnejsi selekce
if (roiManager("count")==0) {
	waitForUser("Automatic Outer Selection failed", "Please define inner selection manualy.\nThen press OK.");
	roiManager("Add");
	}
else if (roiManager("count")>1) {
	do {waitForUser("Automatic Outer confused", "Please select manualy appropriate selection in ROI manager.\nAlternatively add new selection  by pressing 't' end select.\nThen press OK.");
	} while (roiManager("index")==-1);
	roiManager("Select", roiManager("index"));
	roiManager("reset");
	roiManager("Add");
	}
}while  (!roiManager("count")==1) 
run("Paste");
setAutoThr();
roiManager("Select", 0);
roiManager("Rename", "Outer");
}
//****************************************CHECKROIS********************************************
function checkROIs() {
	while (roiManager("count")!=2) waitForUser("Too many ROIs in Manager", "Please leave only outer and inner selection in ROI manager.\nThen press OK.");
	roiManager("Deselect");
	resetMinAndMax();
	roiManager("XOR");
}
//*************************************** DRAWAXES ********************************************
function DrawAxis() {
//optional function to draw major/minor axis of ellipse
  run("Select None");
  moveTo(Centrex,Centrey);
  setColor(255,255,255);
  lineTo(Centrex-(cos((0-Theta)*3.141592654/180)*2*R1),
         Centrey+(sin((0-Theta)*3.141592654/180)*2*R1));
  moveTo(Centrex,Centrey);
  lineTo(Centrex-(cos((Theta+90)*3.141592654/180)*2*R2),
         Centrey-(sin((Theta+90)*3.141592654/180)*2*R2));
  moveTo(Centrex,Centrey);
  lineTo(Centrex+(cos((0-Theta)*3.141592654/180)*2*R1),
         Centrey-(sin((0-Theta)*3.141592654/180)*2*R1));
  moveTo(Centrex,Centrey);
  lineTo(Centrex+(cos((Theta+90)*3.141592654/180)*2*R2),
         Centrey+(sin((Theta+90)*3.141592654/180)*2*R2));
  }
//**************************** SQR******************
function sqr(n) {
	return n*n;
  }
//*******************************CALCSUMS*******************************************************
function CalcSums() {
	Sn=0; Sx=0; Sy=0; Sxx=0; Syy=0; Sxy=0;
	vyska=ymin+ymax;
	sirka=xmin+xmax;
	for (y=ymin; y<=vyska; y++)  {
		showStatus("Calculation in progress.....");
		showProgress(y/ymax);
      		for (x=xmin; x<=sirka; x++) {
				if (selectionContains(x, y)==true){
            				Sn=Sn+1;
              				Sx=Sx+(x*cos(rot2)+y*sin(rot2));
              				Sy=Sy+(y*cos(rot2)-x*sin(rot2));
              				Sxx=Sxx+sqr((x*cos(rot2)+y*sin(rot2)));
              				Syy=Syy+sqr((y*cos(rot2)-x*sin(rot2)));
              				Sxy=Sxy+((y*cos(rot2)-x*sin(rot2))*(x*cos(rot2)+y*sin(rot2)));
			}
		}
	}
  }
//************************************ MEASURE MOMENTS*******************************************
function measureMoments(){// This macro calculates the anisometry and bulkiness of binary particles
// based on the dynamically equivalent ellipse as defined by Medalia (1970).
	setBatchMode(true);
	getPixelSize(unit, pixelWidth, pixelHeight);
	scalar=pixelWidth;
	units=unit;
	selectImage(originalID);

	getSelectionBounds(xmin,ymin,xmax,ymax);	//  ymin is measured from top,xmin from left
						//  xmax & ymax= diameters along x & y axes

//Calculate Moments
	CalcSums();
		if (Sn==0) {
			showMessage("Selection too narrow. Exit calculation"); 
			exit; 
		}

	Cx=Sx/Sn-1;		//x-coord. of Centroid
	Cy=Sy/Sn-1;  		//y-coord. of Centroid
	Centrex=Cx;
	Centrey=Cy;
	
// following  code calculates y (dist from neutral axis)
	if (((ymax + ymin) - Cy) > (Cy - ymin)) {
		Ymaxrad= ymax + ymin - Cy;
		Yminrad= Cy - ymin;
		BigY= Ymaxrad;
	}
	else {
		Ymaxrad= Cy - ymin;
		Yminrad= ymax + ymin - Cy;
		BigY= Ymaxrad;
	}

// following code calculates x (dist from neutral axis)
	if (((xmax + xmin) - Cx) > (Cx - xmin)) {
		Xmaxrad= xmax + xmin - Cx;
		Xminrad= Cx - xmin;
		BigX= Xmaxrad;	
	}
	else {
		Xmaxrad= Cx - xmin;
		Xminrad= xmax + xmin - Cx;
		BigX= Xmaxrad;
	}
	
	Xmaxrad= Xmaxrad*scalar;		//calibrating radii
	Xminrad= Xminrad*scalar;
	Ymaxrad= Ymaxrad*scalar;
	Yminrad= Yminrad*scalar;

	Myy=Sxx-(Sx*Sx/Sn);
	Mxx=Syy-(Sy*Sy/Sn);
	Mxy=Sxy-(Sx*Sy/Sn);
	if (Mxy==0) {
		Theta=0;
	}
	else {
		Theta=atan(((Mxx-Myy)+sqrt(sqr(Mxx-Myy)+(4*sqr(Mxy))))/(2*Mxy))*180/3.141592654;
	}

//end CA


  	Cx = Cx*scalar;			//save x-coord of centroid
	Cy= Cy*scalar;			//save y-coord of centroid
	BigX= BigX*scalar;			//calibrating x,y,Cx,Cy
	BigY= BigY*scalar;
	Ix= Mxx*(sqr(sqr(scalar))); 		//save mom about x-axis
	Iy= Myy*(sqr(sqr(scalar)));
	Zx= Ix/BigY;			//save section moduli
	Zy= Iy/BigX;
	
	rot2=Theta*3.141592654/180;
	CalcSums();
	Parea=Sn;
	M1=Sxx-(Sx*Sx/Sn);
	M2=Syy-(Sy*Sy/Sn);
	R1=sqrt(M1/Parea);
	R2=sqrt(M2/Parea);
	Imax= M1*(sqr(sqr(scalar)));
	Imin= M2*(sqr(sqr(scalar )));
	Rmaks= R1*scalar;
	Rmyn= R2*scalar;
	rot2=0;
	//Theta= -Theta; //REMOVED due to no apparent function and gives incorrect principal axes (5/24/2005)

//calculate TA
	roiManager("Deselect");
	roiManager("OR");
	getStatistics(Tarea);
	roiManager("AND");
	getStatistics(Carea);
	TA = Tarea;	
	CA= Tarea-Carea;
//end TA
	setBatchMode(false);
} //  End of main macro "Calculating Moments"

//********************************************save results*******************************************************
function saveResults(){
	setForegroundColor(255, 255, 255);
	setBackgroundColor(0,0,0);
	Stack.getDimensions(width, height, channels, slices, frames);
//Draw selection
		selectImage(originalID);
		Stack.setDisplayMode("color");
		Stack.setChannel(channels-1);
		clearChannel();
		roiManager("Deselect");
		roiManager("XOR");
		run("Draw", "slice");
		resetMinAndMax();

//Draw principal axes
		Stack.setChannel(channels);
		clearChannel();
		DrawAxis();
		resetMinAndMax();
		Stack.setDisplayMode("composite");
		

//displays the results in the upper left corner of the text window

	path=option[5];
	name=indexName(name);

	setFont('Monaco',10);
	tab=fromCharCode(0009);
	if(!isOpen("Log")) {
		print("Name"+tab+"Scale"+tab+"TA"+tab+"CA"+tab+"Xbar"+tab+"Ybar"+tab+"Ix"+tab+"Iy"+tab+"Imax"+tab+"Imin"+tab+"Theta"+tab+"Zx"+tab+"Zy"+tab+"MaxXrad"+tab+"MaxYrad");
	}
	print(name+tab+scalar+units+"/pixel"+tab+TA+tab+CA+tab+Cx+tab+Cy+tab+Ix+tab+Iy+tab+Imax+tab+Imin+tab+Theta+tab+Zx+tab+Zy+tab+Xmaxrad+tab+Ymaxrad);
	
	run("Channels Tool... ");
	selectWindow("Log");
 	saveAs("Text", path+name+".txt"); // File>Save As>Text
	selectImage(originalID);
	activeChannels=activateChannels(channels);
	Stack.setActiveChannels(activeChannels);
	run("Stack to RGB");
	saveAs("Tiff", path+name+".tif");
	close();
	roiManager("Deselect");
	roiManager("Save", path+name+".zip");
	selectImage(originalID);
	rename(name+".tif");
	
} //  End of "saveResults"

//********************** activate channels ********************
function activateChannels(channels) {
	array=newArray(channels);
	Array.fill(array, 1);
	if (!option[2]) array[channels-2]=0;
	if (!option[3]) array[channels-1]=0;
	string="";
	for (i=0; i<array.length; i++) {
		string=string+d2s(array[i],0);
	}
	return string;
}
//********************* updateSelection *******************
function updateSelection(){
	roiManager("Reset");
	roiManager("add");
	roiManager("Split");
	roiManager("Select", 2);
	roiManager("Rename", "Outer");
	roiManager("Select", 1);
	roiManager("Rename", "Inner");
	roiManager("Select", 0);
	roiManager("Delete");
	roiManager("XOR");
}

//************************* indexName ********************
function indexName(name){
	path=option[5];
	i=1;
	iName=name;
	while (File.exists(path+iName+".tif")) {
		iName=name+"_"+toString(i);
		i++;
	}
	return iName;
}
//************************clearChannel*********************
function clearChannel(){
	run("Select All");
	run("Clear", "slice");
	run("Restore Selection");
}