/*

Mark ROIS for bg
Mark ROI for non-ends
Mark roi for ends


Need to make sure all ori are saved
Need the MT length
Need total number sof each event
Best to put these in a log window and save all into a folder with same name as the kymo 
Write an igor routine that filters out unwanted events (i.e. only one wide).



*/

//Need to make sure that a bounding rectangle is fit for the measurements
run("Set Measurements...", "bounding redirect=None decimal=3");

//Time spacing
frameInt=0.1;
pxSize=0.1;


//clear the ROI manager
if (roiManager("count") !=0)  {
roiManager("deselect");
roiManager("delete");
}

roiManager("show all");



 //create an array with a list of open window names
 n = nImages; 
    list = newArray(n); 
    //setBatchMode(true); 
    for (i=1; i<=n; i++) { 
        selectImage(i); 
        list[i-1] = getTitle; 
    } 
// create a dialog to get the user to give us the kymo to be analysed
title = "Choose Kymo";
width=1024; height=1024;
Dialog.create("Choose Kymo");
Dialog.addChoice("Type:", list);
Dialog.show();
kymoImageName = Dialog.getChoice();
selectWindow(kymoImageName);
kymoID=getImageID();





//going to have the user choose the 4 ROI
selectWindow(kymoImageName);
run("Select None");
imgHeight=getHeight();
imgWidth=getWidth();



//wait for the user
makeRectangle(0, 0, 6, imgHeight);
waitForUser( "Pause","Draw the ROI bg, click OK.");
roiManager("add");
roiManager("select", 0)
roiManager("rename", "BG");
roiManager("Set Color", "blue");
roiManager("Set Line Width", 1);

selectWindow(kymoImageName);
run("Select None");
//wait for the user
makeRectangle(10, 0, 6, imgHeight);
waitForUser( "Pause","Draw the ROI left end, click OK.");
roiManager("add");
roiManager("select", 1)
roiManager("rename", "LeftEnd");
roiManager("Set Color", "red");
roiManager("Set Line Width", 1);

selectWindow(kymoImageName);
run("Select None");
//wait for the user
makeRectangle(imgWidth-20, 0, 6, imgHeight);
waitForUser( "Pause","Draw the ROI right end, click OK.");
roiManager("add");
roiManager("select", 2)
roiManager("rename", "RightEnd");
roiManager("Set Color", "red");
roiManager("Set Line Width", 1);

selectWindow(kymoImageName);
run("Select None");
//wait for the user
imgCent=round(imgWidth/2);
makeRectangle(imgCent, 0, 20, imgHeight);
waitForUser( "Pause","Draw the ROI lattice, click OK.");
roiManager("add");
roiManager("select", 3)
roiManager("rename", "Lattice");
roiManager("Set Color", "blue");
roiManager("Set Line Width", 1);
roiManager("show none");
run("Select None");



//create a dir to store everything
dir = getDirectory("Choose a Directory");
//File.makeDirectory(dir); 
newDir=dir;

/*make sure these are recorded
roiManager("deselect");
roiManager("save", newDir +kymoImageName+"areas.zip");
selectWindow(kymoImageName);
roiManager("show none");
*/


//could use the ROI to calculate the MT length.
//Would put that here.

setBatchMode(false);

//copy out the GFP data
selectImage(kymoID);
//selectWindow(kymoImageName);
run("Duplicate...", "title=gfpOnly duplicate channels=1");
gfpOnlyID=getImageID();



//get bg value
roiManager("select", 0);

getStatistics(area, mean, min, max);
backGround=max;



//run("Threshold...");
selectImage(gfpOnlyID);
setThreshold(max, 3.4e38);
setOption("BlackBackground", false);
run("Convert to Mask");

//this simulate the joning conditions - this is the really hard bit to do quickly though.
run("Dilate");
run("Erode");



//measure each of the 3 areas
//*****************************************************************************************************************
//Lattice events
//*****************************************************************************************************************
selectImage(gfpOnlyID);
roiManager("select", 3)
run("Analyze Particles...", "size=2-Infinity show=Outlines add");
selectWindow(kymoImageName);
roiManager("show all");
waitForUser( "Pause","Please edit ROIs as necessary, click OK.");

//make sure these are recorded
roiManager("deselect");
roiManager("save", newDir +kymoImageName+"areas_lattice.zip");
selectWindow(kymoImageName);
roiManager("show all");

//Run the measurement
numRois=roiManager("count");
roiManager("deselect");
roiManager("Measure");

//Read out the data you need and put it in a new table
	count=4;
	n = numRois; 
    eventHeight = newArray(n);
    eventLabel = newArray(n);
 

    eventCount=1;
    for (k=0; k<n-4; k++) { 
        eventHeight[k] = frameInt*getResult("Height", count);
        eventLabel[k] = eventCount;
        eventCount++;
        count++; 
    } 
    
//close the results of the calc
   if (isOpen("Results")) { 
       selectWindow("Results"); 
      run("Close"); 
   } 

 	//Generate a results window with the selected values
   Array.show("ResultsTest", eventLabel, eventHeight);
   selectWindow("ResultsTest"); 
   saveAs("ResultsTest", dir+"Results"+"_Lattice_"+kymoImageName+"_.txt");

   //close the changed results
   if (isOpen("Results"+"_Lattice_"+kymoImageName+"_.txt")) { 
       selectWindow("Results"+"_Lattice_"+kymoImageName+"_.txt"); 
       run("Close"); 
   }


   //need to clear the ROIs (except the first 4).
       numRois=roiManager("count");
       n = numRois; 
       for (p=n-1; p>3; p--) { 
        roiManager("select", p);
        roiManager("delete");
    } 
    
numLatticeEvents=0;
numLatticeEvents=numRois-4;
   
//*****************************************************************************************************************    
//End of lattice results data collection
//*****************************************************************************************************************







//*****************************************************************************************************************
//Left End events
//*****************************************************************************************************************
selectImage(gfpOnlyID);
roiManager("select", 1)
run("Analyze Particles...", "size=2-Infinity show=Outlines add");
selectWindow(kymoImageName);
roiManager("show all");
waitForUser( "Pause","Please edit ROIs as necessary, click OK.");

//make sure these are recorded
roiManager("deselect");
roiManager("save", newDir +kymoImageName+"areas_left_end.zip");
selectWindow(kymoImageName);
roiManager("show all");

//Run the measurement
numRois=roiManager("count");
roiManager("deselect");
roiManager("Measure");

//Read out the data you need and put it in a new table
	count=4;
	n = numRois; 
    eventHeight = newArray(n);
    eventLabel = newArray(n);
 

    eventCount=1;
    for (k=0; k<n-4; k++) { 
        eventHeight[k] = frameInt*getResult("Height", count);
        eventLabel[k] = eventCount;
        eventCount++;
        count++; 
    } 
    
//close the results of the calc
   if (isOpen("Results")) { 
       selectWindow("Results"); 
      run("Close"); 
   } 

 	//Generate a results window with the selected values
   Array.show("ResultsTest", eventLabel, eventHeight);
   selectWindow("ResultsTest"); 
   saveAs("ResultsTest", dir+"Results"+"_Left_End_"+kymoImageName+"_.txt");

   //close the changed results
   if (isOpen("Results"+"_Left_End_"+kymoImageName+"_.txt")) { 
       selectWindow("Results"+"_Left_End_"+kymoImageName+"_.txt"); 
       run("Close"); 
   }

   //need to clear the ROIs (except the first 4).
       numRois=roiManager("count");
       n = numRois; 
       for (p=n-1; p>3; p--) { 
        roiManager("select", p);
        roiManager("delete");
    }    

numEndBindings=0;
numEndBindings=numRois-4;
    
//*****************************************************************************************************************    
//End of left-end results data collection
//*****************************************************************************************************************


//*****************************************************************************************************************
//Right End events
//*****************************************************************************************************************
selectImage(gfpOnlyID);
roiManager("select", 2)
run("Analyze Particles...", "size=2-Infinity show=Outlines add");
selectWindow(kymoImageName);
roiManager("show all");
waitForUser( "Pause","Please edit ROIs as necessary, click OK.");

//make sure these are recorded
roiManager("deselect");
roiManager("save", newDir +kymoImageName+"areas_right_end.zip");
selectWindow(kymoImageName);
roiManager("show all");

//Run the measurement
numRois=roiManager("count");
roiManager("deselect");
roiManager("Measure");

//Read out the data you need and put it in a new table
	count=4;
	n = numRois; 
    eventHeight = newArray(n);
    eventLabel = newArray(n);
 

    eventCount=1;
    for (k=0; k<n-4; k++) { 
        eventHeight[k] = frameInt*getResult("Height", count);
        eventLabel[k] = eventCount;
        eventCount++;
        count++; 
    } 
    
//close the results of the calc
   if (isOpen("Results")) { 
       selectWindow("Results"); 
      run("Close"); 
   } 

 	//Generate a results window with the selected values
   Array.show("ResultsTest", eventLabel, eventHeight);
   selectWindow("ResultsTest"); 
   saveAs("ResultsTest", dir+"Results"+"_Right_End_"+kymoImageName+"_.txt");

   //close the changed results
   if (isOpen("Results"+"_Right_End_"+kymoImageName+"_.txt")) { 
       selectWindow("Results"+"_Right_End_"+kymoImageName+"_.txt"); 
       run("Close"); 
   }

   //need to clear the ROIs (except the first 4).
       numRois=roiManager("count");
       n = numRois; 
       for (p=n-1; p>3; p--) { 
        roiManager("select", p);
        roiManager("delete");
    }

numEndBindings=numEndBindings+numRois-4;        
//*****************************************************************************************************************    
//End of right-end results data collection
//*****************************************************************************************************************

//Write some summary information to a file.

/*

Threshold used (in backGround)
MT length
Num End bindings
Mean End binding time
Num lattice events
Mean lattice time

*/
//*************************************************************************
//Measure MT length
roiManager("deselect");
roiManager("select", 1);
 Roi.getBounds(x,y,w,h);
 left=x;
 roiManager("select", 2);
 Roi.getBounds(x,y,w,h);
 right=x+w;
 mtLength=right-left;
 mtLength=mtLength*pxSize;


 // backGround

// numLatticeEvents 
 
 // numEndBindings


 	backGroundRes = newArray(1);
    numLatticeEventsRes = newArray(1);
    numEndBindingsRes = newArray(1);
    mtLengthRes = newArray(1);

    backGroundRes[0] = backGround;
    numLatticeEventsRes[0] = numLatticeEvents;
    numEndBindingsRes[0] = numEndBindings;
    mtLengthRes[0] = mtLength;
   
    
	//Generate a results window with the selected values
   Array.show("ResultsSummary", backGroundRes, numLatticeEventsRes, numEndBindingsRes, mtLengthRes);
   selectWindow("ResultsSummary"); 
   saveAs("ResultsSummary", dir+"Results"+"_Summary_"+kymoImageName+"_.txt");




//Very end of the experiment

//Tidy up a few windows no longer needed, should really run this in batch mode.
   //close the changed results
   if (isOpen("gfpOnly")) { 
       selectWindow("gfpOnly"); 
       run("Close"); 
   }
      if (isOpen("Drawing of gfpOnly")) { 
       selectWindow("Drawing of gfpOnly"); 
       run("Close"); 
   }