resetImageJ();

if (roiManager("count") > 0) {
	roiManager("Delete"); // resetting ROI manager again... seems buggy, leaves old ROIs
}
// you can't run in batchmode if you're asking the user to select something
// they will see nothing when it is time to select
//setBatchMode(false);


open();
ori = getTitle();



// get image dimensions

hgt = getHeight();

wth = getWidth();


print(wth);

//Selecting nothing just in case

run("Select None");



// set line tool

setTool(4);                     //Line Tool



// get user input

message= "Line Selection Required\n Please create a break line";

waitForUser(message);

getLine(x1, y1, x2, y2, lineWidth);


dx = x2-x1; // change in x

dy = y2-y1; // change in y


if (dx == 0) {

	// slope is infinity

	// y intercept is impossible

	// x is always the same

	xAty0point = x1;

	xAtyMaxpoint =  x1;

} else {

	// calculate slope and intercept

	slope = dy / dx;

	intercept = slope * x1 - y1;

	// calculate x at y=0 and y=imgheight


	xAty0point = abs((0-intercept) / slope); // -y = 0
	xAtyMaxpoint =  ((hgt+intercept) / slope); // -y = hgt
}


// make polygon to the right of main line

makePolygon(xAty0point, 0, xAtyMaxpoint, hgt, wth, hgt, wth, 0);



// add to manager and its inverse

roiManager("Add");

run("Make Inverse");

roiManager("Add");

run("Make Inverse");



// ROI[0] should be right side of line

// ROI[1] should be left side

run("Select None");


// duplicate image
run("Duplicate...", "title=Right");


// fill in left side of line with blue and segment on right side
roiManager("Select", 1);

setForegroundColor(0, 0, 255);

run("Fill", "slice");

run("Select None");

// find "black" pixels 
selectWindow("Right");
findblackpixels();

run("Create Selection");

roiManager("Add");

selectWindow("Right");
run("Close");


// fill in right side and focus on left
selectWindow(ori);
run("Duplicate...", "title=Left");

roiManager("Select", 0);

setForegroundColor(0, 0, 255);

run("Fill", "slice");
run("Select None");

// find "black" pixels 
findblackpixels();

run("Create Selection");
roiManager("Add");

selectWindow("Left");
run("Close");

// get measurements
selectWindow(ori);
run("Select None");
roiManager("Select", 2); // Right side
run("Measure");
run("Select None");
roiManager("Select", 3); // Left side
run("Measure");
run("Select None");



///////////////////////////////////////
function resetImageJ() {
	run("Options...", "iterations=1 count=1 edm=Overwrite");
	run("Line Width...", "line=1");
	run("Colors...", "foreground=black background=white selection=yellow");
	run("Clear Results");
	run("Close All");
	print("\\Clear");
	run("ROI Manager...");
	run("Input/Output...", "jpeg=75 gif=-1 file=.csv use_file copy_row save_column save_row");
	run("Set Measurements...", "area mean standard modal min centroid center perimeter bounding fit shape feret's integrated median skewness kurtosis area_fraction stack redirect=None decimal=3");
}
///////////////////////////////////////

///////////////////////////////////////
function findblackpixels() {
	// Color Thresholder 1.48v
	// Autogenerated macro, single images only!
	min=newArray(3);
	max=newArray(3);
	filter=newArray(3);
	a=getTitle();
	run("HSB Stack");
	run("Convert Stack to Images");
	selectWindow("Hue");
	rename("0");
	selectWindow("Saturation");
	rename("1");
	selectWindow("Brightness");
	rename("2");
	min[0]=0;
	max[0]=75;
	filter[0]="pass";
	min[1]=0;
	max[1]=255;
	filter[1]="pass";
	min[2]=0;
	max[2]=150;
	filter[2]="pass";
	for (i=0;i<3;i++){
	  selectWindow(""+i);
	  setThreshold(min[i], max[i]);
	  run("Convert to Mask");
	  if (filter[i]=="stop")  run("Invert");
	}
	imageCalculator("AND create", "0","1");
	imageCalculator("AND create", "Result of 0","2");
	for (i=0;i<3;i++){
	  selectWindow(""+i);
	  close();
	}
	selectWindow("Result of 0");
	close();
	selectWindow("Result of Result of 0");
	rename(a);
	// Colour Thresholding-------------
}
///////////////////////////////////////

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