/*
 * Chris Gell
 * Dec 2018
 * 
 * Semi-automated analysis of kymographs.
 * Load a red-green kymoe, when prompted 
Mark ROIS for bg
Mark ROI for non-ends
Mark roi for ends

Then correct the ROIs - at the moment can only delete I think.


TO DO NEXT!!!!!!!!!!
Revisit the structure where all of the data is saved and make sure summary, latice and end events go into seperate folders
these should be grouped otgether for analysis as appropriate - i.e. all of the streams for the same experiment on a given
day etc...



TO DO Write an igor routine that filters out unwanted events (i.e. only one wide).
TO DO Extend the ROI tools so that you remove AND edit and create ROIs

DONE Need to make sure all ori are saved
DONE Need the MT length
DONE Need total number sof each event
DONE Best to put these in a log window and save all into a folder with same name as the kymo 






*/

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

//waitForUser( "Pause","Set options");

//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 add");
//Rename the ROIs

n=roiManager("count");
startRenameFrom=4;
tempEventName=1;

    for (p=startRenameFrom; p<n; p++) { 
		roiManager("select", p);
		roiManager("rename", "C"+tempEventName);
		tempEventName++;    
    } 


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; 
    eventHeightLat = newArray(n);
    eventLabelLat = newArray(n);
 

    eventCount=1;
    for (k=0; k<n-4; k++) { 
        eventHeightLat[k] = frameInt*getResult("Height", count);
        eventLabelLat[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", eventLabelLat, eventHeightLat);
   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 add");
selectWindow(kymoImageName);
roiManager("show all");
n=roiManager("count");
startRenameFrom=4;
tempEventName=1;

    for (p=startRenameFrom; p<n; p++) { 
		roiManager("select", p);
		roiManager("rename", "L"+tempEventName);
		tempEventName++;    
    } 
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; 
    eventHeightLE = newArray(n);
    eventLabelLE = newArray(n);
 

    eventCount=1;
    for (k=0; k<n-4; k++) { 
        eventHeightLE[k] = frameInt*getResult("Height", count);
        eventLabelLE[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", eventLabelLE, eventHeightLE);
   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 add");
selectWindow(kymoImageName);
roiManager("show all");
n=roiManager("count");
startRenameFrom=4;
tempEventName=1;

    for (p=startRenameFrom; p<n; p++) { 
		roiManager("select", p);
		roiManager("rename", "R"+tempEventName);
		tempEventName++;    
    } 
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; 
    eventHeightRE = newArray(n);
    eventLabelRE = newArray(n);
 

    eventCount=1;
    for (k=0; k<n-4; k++) { 
        eventHeightRE[k] = frameInt*getResult("Height", count);
        eventLabelRE[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", eventLabelRE, eventHeightRE);
   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"); 
   }

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