//Define Input Dialog///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
requires("1.45f");
Dialog.create("MoloVideo Setup");
	Dialog.addMessage("MoloVideo generates a video file containing 3 different data sets")
	Dialog.addMessage("Therefore 3 seperate folders with Molographic, Straylight and Fluorescence Images are needed") 
	Dialog.addMessage("MoloVideo Requires ImageJ v.1.45f") 
	Dialog.addMessage("Enter Values for Image Adjustment") 
	Dialog.addSlider("Brightness Min:", 0, 65000, 100);
	Dialog.addSlider("Brightness Max:", 0, 65000, 5000);
	Dialog.addChoice("LUT for Straylight images", newArray("Fire", "Grays", "Ice", "Spectrum"), "Fire") //define colorcode of straylight images
	Dialog.addCheckbox("Delete Original files", false); //if checked "tif" images are deleted further down in the code
	//Dialog.addCheckbox("Molographic files", true); //if checked "tif" images are deleted further down in the code
	Dialog.addCheckbox("Straylight files", true); //if checked "tif" images are deleted further down in the code
	Dialog.addCheckbox("Fluoresence files", true); //if checked "tif" images are deleted further down in the code
Dialog.show();
///////////////////////////////////////////////////////	
	//Save variables of Dialog///////////////////////// transfered in order of apperance in the dialoge
	Min = Dialog.getNumber();
	Max = Dialog.getNumber();
	LUT = Dialog.getChoice();							
	Delete = Dialog.getCheckbox();
	//Files_molo = Dialog.getCheckbox();
	Files_stray = Dialog.getCheckbox();
	Files_fluor = Dialog.getCheckbox();						
		//print("Values:", Min);
		//print("Values:", Max);
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


//Load Molostack ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
path_molo = File.openDialog("Select a Molographic File"); 	//get total file path --> open image Sequence
  	print("Filepath:", path_molo);

parent_molo = File.getParent(path_molo);					//get folder directory where the selected file is 
  	print("Directory:", parent_molo);
  	folder_molo = File.getName(parent_molo);				//get folder name --> stack name (needed for stack combination)
  		print("Foldername:", folder_molo);

run("Image Sequence...", "open="+path_molo+" sort");			//Image Sequence of all Images
	makeRectangle(10, 248, 441, 327);					//Define Crop area
	run("Crop");
	setMinAndMax(Min, Max);								//Set Brightness
	run(LUT);											//Apply coloring to images
	wait(100);											//If no wait the LUT is not applied properly

//open(path);

/*
	//Titel extrahieren/////////////////////////////////
	MetaInfo = getMetadata("Info");						//MetaInfos auslesen
			//print("MetaInfo:", MetaInfo);		
	//Titel_end = indexOf(MetaInfo, ".tif"); 				//Weleche Position hat ".tif"
	//MetaTitel = substring (MetaInfo, 0, Titel_end); 	//Titel extrahieren von Position "0" bis ".tif"
		//print("MetaTitel:", MetaTitel);
	////////////////////////////////////////////////////
	
	//Position extrahieren//////////////////////////////
	//Position_end = indexOf(MetaInfo, "_"); 				
	//Position = substring (MetaInfo, 0, Position_end); 	
	//print("MetaTitel:", Position); 
	////////////////////////////////////////////////////

	/*Emission filter///////////////////////////////////
	Looks in the MetaInfos for the type of Emmsion filter and colors the image accordingly
	Looks for [title="Emission filter" value="Red"] if not present value=-1
	
	Emission = indexOf(MetaInfo, "title=\"Emission filter\" value=\"Red\""); 	
		//print("MetaTitel:", Emission);
		if (Emission!=-1) 
		{
			 run("Red");
			 wait(100);		//If no wait the LUT is not applied properly
 		} 
 	Emission = indexOf(MetaInfo, "title=\"Emission filter\" value=\"Green\""); 	
		//print("MetaTitel:", Emission);
		if (Emission!=-1) 
		{
			 run("Green");
			 wait(100);		//If no wait the LUT is not applied properly
 		} 
	////////////////////////////////////////////////////
*/
	/*Coupling value///////////////////////////////////
	Looks in the MetaInfos for the coupling value
	Looks for [title="Coupling value" value="] if not present value=-1
	
	Coupling_start = indexOf(MetaInfo, "title=\"Coupling value\" value=");
	Coupling_start = Coupling_start + 30;	//increase start index to get rid of text in front of value
		//print("C_start:", Coupling_start);
	Coupling_end = indexOf(MetaInfo, "\"/><CouplingGrayFilter");
		//print("C_end:", Coupling_end);
		Coupling = substring (MetaInfo, Coupling_start, Coupling_end); 	//Titel extrahieren von Position "0" bis ".tif"
		//print("C:", Coupling);
	////////////////////////////////////////////////////
*/
	/*Instrument///////////////////////////////////////
	Looks in the Titel for the Instrument Type
	Looks for [title="Coupling value" value="] if not present value=-1
	*/
	//Instrument_start = indexOf(MetaTitel, "_Z");
	//Instrument_start = Instrument_start + 1;	//increase start index to get rid of text in front of value
		//print("C_start:", Coupling_start);
	//Instrument_end = Instrument_start + 2;
		//print("C_end:", Coupling_end);
		//Instrument = substring (MetaTitel, Instrument_start, Instrument_end); 	//Titel extrahieren von Position "0" bis ".tif"
		//print("Instrument:", Instrument);
	////////////////////////////////////////////////////
//close();		
	/*Draw Infos into image///////////////////////////////////
	*/
	setFont("Sanserif", 24);
	setColor("black");

  	drawString("Molographic", 10, 40, "white");
  	//drawString("Coupling:" + Coupling, 50, 40, "white");
  	drawString("Min-Max:" + Min + "-" + Max, 10, 320, "white");
  	//drawString(Instrument, 10, 80, "white");
  	wait(100);											//waiting for drawing
	////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

	
//Load Straylight-stack ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
if (Files_stray == true) 
{ 
path_stray = File.openDialog("Select a Straylight File"); 	//get total file path --> open image Sequence
  	print("Filepath:", path_stray);

parent_stray = File.getParent(path_stray);					//get folder directory where the selected file is 
  	print("Directory:", parent_stray);
  	folder_stray = File.getName(parent_stray);				//get folder name --> stack name (needed for stack combination)
  		print("Foldername:", folder_stray);

run("Image Sequence...", "open="+path_stray+" sort");		//Image Sequence of all Images
	makeRectangle(10, 248, 441, 327);						//Define Crop area
	run("Crop");
	setMinAndMax(Min, Max);									//Set Brightness
	run(LUT);												//Apply coloring to images
	wait(100);												//If no wait the LUT is not applied properly

	/*Draw Infos into image///////////////////////////////////
	*/
  	drawString("Straylight", 10, 40, "white");
  	wait(100);											//waiting for drawing
	////////////////////////////////////////////////////
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


//Load Fluoresence-stack ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
if (Files_fluor == true) 
{ 
path_fluor = File.openDialog("Select a Fluoresence File"); 	//get total file path --> open image Sequence
  	print("Filepath:", path_fluor);

parent_fluor = File.getParent(path_fluor);					//get folder directory where the selected file is 
  	print("Directory:", parent_fluor);
  	folder_fluor = File.getName(parent_fluor);				//get folder name --> stack name (needed for stack combination)
  		print("Foldername:", folder_fluor);
 		
run("Image Sequence...", "open="+path_fluor+" sort");		//Image Sequence of all Images
	makeRectangle(10, 248, 441, 327);						//Define Crop area
	run("Crop");
	setMinAndMax(Min, Max);									//Set Brightness
	run(LUT);												//Apply coloring to images
	wait(100);												//If no wait the LUT is not applied properly

	/*Draw Infos into image///////////////////////////////////
	*/
  	drawString("Fluoresence", 10, 40, "white");
  	wait(100);											//waiting for drawing
	////////////////////////////////////////////////////
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////



////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

/*Generation of Montage/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
All apen Stacks combined in a single Stack
*/ 	
run("Combine...", "stack1="+folder_molo+" stack2="+folder_stray);
run("Combine...", "stack1=[Combined Stacks] stack2="+folder_fluor);
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

/*Save as Video/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
*/

dir_movie = File.getParent(parent_fluor);					//get folder directory where the selected file is 
  	print("Movie:", dir_movie);
	print("Movie:", dir_movie+"Video.avi");


run("AVI... ", "compression=PNG frame=13.5 save=["+dir_movie+"/Video.avi]");
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


//Cleaning up///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//close();		//close Montage		
//close();		//close Stack
//Closing Log Window/////////////////////////////
/*
if (isOpen("Log")) { 
    selectWindow("Log"); 
    run("Close"); 
    } 
////////////////*Generation of Montage//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////