// This macro generates kymographs and movies for each microtubule marked by a line ROI
// The macro requires that the plugin KymographMin is installed (https://biop.epfl.ch/TOOL_KYMOGRAPH.html).
// it's possible to use other kymograph plugins, just make sure you call the plugin correctly (line 30)
// The macro runs in patch mode where no images are displayed during processing but instead kymographs and movies are saved to the chosen folder
//
// how to use this macro//
//1. using the line tool select the microtubules and add the selection to the ROI manager by pressing "t" 
//2. run the macro
//3. for each microtubule a movie and a kymograph are generated with unique identifiers and the ROIs are saved in a zip file
// 
// by Mohammed Mahamdeh (Mohammed.mahamdeh@gmail.com)
// 2018-12-08


setBatchMode(true); // if true then no images or kymos will be displayed, instead all will be saved to the folder

id = getImageID(); //get active image Id, in this case the stack 
t  = getTitle(); // get image title (used to get the path)
N = roiManager("count"); //number of MTs in ROI to analyze 
path = getDirectory(t); // set the directory for saving 

// case: ROIs in the ROI manager 
if (Overlay.size==0){

for (i=0 ; i<roiManager("count"); i++) {
	selectImage(id); //select stack
    roiManager("select", i); // select line ROIs 
	
	// generate kymograph
	ROIname = call("ij.plugin.frame.RoiManager.getName", i);
	run("KymographMin", "linewidth=23");
	KymoID = getImageID ();
	selectImage(KymoID);
	rename(ROIname);
	saveAs("tiff", path+ROIname);
	close();
	
	// save kymo movie
	selectImage(id); //select stack
	roiManager("select", i);
	run("To Bounding Box");
	run("Enlarge...", "enlarge=10 pixel");
	run("Duplicate...", "duplicate");
	//run("Straighten...", "line=60 process title=" + ROIname);
	saveAs("tiff", path+ROIname+"movie");
	close();
}
};


// case: ROI are saved in an overlay
else{
	run("To ROI Manager");

for (i=0 ; i<roiManager("count"); i++) {
	selectImage(id); //select stack
    roiManager("select", i); 
	
	// generate kymograph
	ROIname = call("ij.plugin.frame.RoiManager.getName", i);
	run("KymographMin", "linewidth=23");
	KymoID = getImageID ();
	selectImage(KymoID);
	rename(ROIname);
	saveAs("tiff", path+ROIname);
	close();
	
	// save kymo movie
	selectImage(id); //select stack
	roiManager("select", i);
	run("To Bounding Box");
	run("Enlarge...", "enlarge=10 pixel");
	run("Duplicate...", "duplicate");
	//run("Straighten...", "line=60 process title=" + ROIname);
	saveAs("tiff", path+ROIname+"movie");
	close();
}
};

showMessage("Process completed, all kymos and related movies are saved");
roiManager("save", path+"ROI.zip");