inImage = getDirectory("Choose the images input folder");
outImage1 = getDirectory("Choose the images output folder");
inResult1 = getDirectory("Choose the morpho results folder");
inResult2 = getDirectory("Choose the siliques results folder");
images = getFileList(inImage);



// START NEW OR CONTINUE SELECTION
pathContinued = inResult1 + "Log.txt";
if(File.exists(pathContinued)) {
	filestring=File.openAsString(pathContinued);
	rows=split(filestring, "\n");
	x=newArray(rows.length);
	for(b=0; b<rows.length; b++)
	{
	columns=split(rows[b],"\t");
	g=parseInt(columns[0]) + 1;
	} 
		}
	else
		{
		g = 0;
		}

Date = "yyyymmdd";

// CORE
for (i = g ; i < images.length; i++)
{
	inputPath = inImage + images[i];       
	n = split(images[i],".");
	name = n[0];
	open(inputPath);
	rename("pic");




//----------------------------------
// Extract pot id
//----------------------------------

run("Duplicate...", "title=Pot.JPG");
run("Canvas Size...", "width=2200 height=2800 position=Top-Right");
run("Rotate 90 Degrees Right");

Dialog.create("RAPA_macro");
Dialog.addString("Pot: ", "");
Dialog.show();
pot = Dialog.getString();

Dialog.create("RAPA_macro");
Dialog.addString("Date: ", Date);
Dialog.show();
Date = Dialog.getString();

nameOfPlant = "pot" + pot;
nameOfTray = nameOfPlant + "_" + Date;
print(nameOfPlant);
print(Date);
propres = (i / images.length) * 100;
imI = i + 1;
print("image " + imI + " out of " + images.length + " (" + propres + "% done)");



//----------------------------------
// Extract rosette area data
//----------------------------------
selectWindow("Pot.JPG");
setTool(1);
Dialog.create("Rosette selection");
selectionString = "Select rosette and press OK.";
waitForUser(selectionString);
run("Duplicate...", "title=Rosette.JPG");
rename("Rosette.JPG");

selectWindow("Rosette.JPG");
run("Duplicate...", "title=Rosette0.JPG");
rename(nameOfPlant);
run("Clear Outside");
setOption("BlackBackground", true);
setBackgroundColor(0, 0, 0);
run("Invert");

// Color Thresholder 2.0.0-rc-8/1.49c
// Autogenerated macro, single images only!
setBatchMode(true);
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]=155;
max[0]=255;
filter[0]="pass";
min[1]=20;
max[1]=255;
filter[1]="pass";
min[2]=86;
max[2]=255;
filter[2]="pass";
for (l=0;l<3;l++){
  selectWindow(""+l);
  setThreshold(min[l], max[l]);
  run("Convert to Mask");
  if (filter[l]=="stop")  run("Invert");
}
imageCalculator("AND create", "0","1");
imageCalculator("AND create", "Result of 0","2");
for (l=0;l<3;l++){
  selectWindow(""+l);
  close();
}

selectWindow("Result of Result of 0");
rename(a);
setBatchMode(false);
// Colour Thresholding-------------

run("Remove Outliers...", "radius=5 threshold=50 which=Bright");
run("Remove Outliers...", "radius=5 threshold=50 which=Dark");

setOption("BlackBackground", true);
run("Make Binary");
run("Create Selection");
run("Add to Manager");
roiManager("Show All with labels");
selectWindow("Rosette.JPG");
roiManager("Select", 0);
run("Clear Outside");
roiManager("Show All with labels");


		rename(nameOfPlant + "_rosette_" + Date);	
		saveAs("tiff" , outImage1 + nameOfPlant + "_rosette_" + Date);
			
		selectWindow(nameOfPlant + "_rosette_" + Date + ".tif");	
		roiManager("Select", 0);
		run("Set Measurements...", "area perimeter shape display redirect=None decimal=6");
		run("Measure");							
		nbr = nResults;
		for (inc=0; inc<nbr; inc++)
		{
			setResult("Solidity", inc, 0);				
		}		
	
		roiManager("Select", 0);
		roiManager("Delete");
		
	pathContinued2 = inResult1 + "Morphological_data.xls";
	if(File.exists(pathContinued2)) 
	{
	u = nResults;
	lineseparator = "\n";
	cellseparator = ",\t";
	lines=split(File.openAsString(pathContinued2), lineseparator);
	v = lines.length;	
	
	for (o=1; o<v; o++)
	{
		items=split(lines[o], cellseparator);
		setResult("Label", o + u - 1, items[1]);
		setResult("Area", o + u - 1, items[2]);
		setResult("Perim.", o + u - 1, items[3]);
		setResult("Circ.", o + u - 1, items[4]);
		setResult("AR", o + u - 1, items[5]);
		setResult("Round", o + u - 1, items[6]);
		setResult("Solidity", o + u - 1, 0);				
	}
	     	
		updateResults();
		saveAs("Results", inResult1 + "Morphological_data.xls");	
		saveAs("Results", inResult1 + nameOfPlant + "_rosette_" + Date + "_Morphological_data.xls");	
		selectWindow("Results");
		run("Close");
	}
	else
	{
		saveAs("Results", inResult1 + "Morphological_data.xls");
		saveAs("Results", inResult1 + nameOfPlant + "_rosette_" + Date + "_Morphological_data.xls");	
		selectWindow("Results");
		run("Close");
	}		

selectWindow(nameOfPlant);
run("Close");
selectWindow(nameOfPlant + "_rosette_" + Date + ".tif");
run("Close");
selectWindow("Pot" + ".JPG");
run("Close");
selectWindow("pic");
saveAs("tiff" , outImage1 + nameOfPlant + "_" + Date);









//----------------------------------
// Extract inflorescence data
//----------------------------------

selectWindow(nameOfPlant + "_" + Date + ".tif");
setTool(0);
Dialog.create("Inflorescence selection");
selectionString = "Select inflorescence and press OK.";
waitForUser(selectionString);

setBatchMode(true);
run("Clear Outside");
run("Duplicate...", "title=Inflo.JPG");
rename("Inflo.JPG");
run("Rotate 90 Degrees Right");

run("Set Measurements...", "  display redirect=None decimal=6");
run("Measure");
run("Clear Results");

//selectWindow("Inflo.JPG");
//setTool("point");
//run("Point Tool...", "mark=10 auto-measure label selection=magenta");
//Dialog.create("RAPA_macro");
//selectionString = "Mark all siliques and press OK.";
//waitForUser(selectionString);

//nbr = nResults;
//run("Clear Results");
//setResult("Label", 0, nameOfTray);
//setResult("X", 0, 0);
//setResult("Y", 0, 0);
//setResult("Count", 0, nbr);		
//updateResults();
	
//pathContinued2 = inResult + "Siliques_count.xls";
//	if(File.exists(pathContinued2)) 
//	{
//	u = nResults;
//	lineseparator = "\n";
//	cellseparator = ",\t";
//	lines=split(File.openAsString(pathContinued2), lineseparator);
//	v = lines.length;		
//	for (o=1; o<v; o++)
//	{
//		items=split(lines[o], cellseparator);
//		setResult("Label", o + u - 1, items[1]);
//		setResult("X", o + u - 1, items[2]);
//		setResult("Y", o + u - 1, items[3]);
//		setResult("Count", o + u - 1, items[4]);				
//	}
//
//	     	
//		updateResults();
//		saveAs("Results", inResult + "Siliques_count.xls");	
//		saveAs("Results", inResult + nameOfTray + "_Siliques_count.xls");	
//		selectWindow("Results");
//		run("Close");
//	}
//	else
//	{
//
//saveAs("Results", inResult + "Siliques_count.xls");
//		saveAs("Results", inResult + nameOfTray + "_Siliques_count.xls");	
//		selectWindow("Results");
//		run("Close");
//	}		



//run("Clear Results");

selectWindow("Inflo.JPG");
run("Duplicate...", "title=Inflo0.JPG");
rename(nameOfTray);
run("Invert");

// Color Thresholder 2.0.0-rc-8/1.49c
// Autogenerated macro, single images only!
//setBatchMode(true);
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]=185;
max[0]=255;
filter[0]="pass";
min[1]=20;
max[1]=255;
filter[1]="pass";
min[2]=86;
max[2]=255;
filter[2]="pass";
for (ll=0;ll<3;ll++){
  selectWindow(""+ll);
  setThreshold(min[ll], max[ll]);
  run("Convert to Mask");
  if (filter[ll]=="stop")  run("Invert");
}
imageCalculator("AND create", "0","1");
imageCalculator("AND create", "Result of 0","2");
for (ll=0;ll<3;ll++){
  selectWindow(""+ll);
  close();
}

selectWindow("Result of Result of 0");
rename(a);
//setBatchMode(false);
// Colour Thresholding-------------


//run("Remove Outliers...", "radius=6 threshold=50 which=Bright");
run("Remove Outliers...", "radius=2 threshold=50 which=Bright");
run("Remove Outliers...", "radius=4 threshold=50 which=Dark");

setOption("BlackBackground", true);
run("Make Binary");
run("Create Selection");
run("Add to Manager");
//roiManager("Show All with labels");
//selectWindow("Inflo.JPG");
roiManager("Select", 0);
run("Clear Outside");
roiManager("Show All with labels");
selectWindow(nameOfTray);
rename(nameOfPlant + "_rosette_" + Date + ".tif");	
//saveAs("tiff" , outImage1 + Date + "_inflo_" + nameOfPlant);
//setBatchMode(false);

//setBatchMode(true);
selectWindow(nameOfPlant + "_rosette_" + Date + ".tif");	
run("8-bit");		
run("Make Binary");
run("Skeletonize");
run("Duplicate...", "title=skeleton.JPG");
rename(nameOfPlant + "_" + Date + "_InfloSkeleton");
//run("Rotate 90 Degrees Right");
//saveAs("tiff" , outImage1 + Date + "_InfloSkeleton_" + nameOfPlant);

selectWindow(nameOfPlant + "_" + Date + "_InfloSkeleton");
run("Analyze Skeleton (2D/3D)", "prune=none");

saveAs("Results", inResult2 + nameOfPlant + "_Siliques_data_aut.xls");

nbr0 = nResults;
for (incr=0; incr<nbr0; incr++)
{
	setResult("Label", incr, nameOfTray);				
}	

updateResults();
saveAs("Results", inResult2 + nameOfPlant + "_Siliques_data_aut.xls");	
selectWindow("Results");
run("Close");


setBatchMode(false);




//////////////////////////////////////////////
//		End of the tray analysis
//////////////////////////////////////////////

roiManager("reset");
selectWindow("ROI Manager");
run("Close");
selectWindow("Log");
run("Close");
run("Close All");

	tray = i;
	print(tray);
	selectWindow("Log");
    saveAs("text", inResult1 + "Log.txt");
	run("Close");
}