_DKR_Batch_defineSpindleMidzone.txt

// created by Dan Rozelle 20091110
//used to quickly open each  movie, select the category, write results to table and close



macro "_DKR_Batch_defineSpindleMidzone"{

if(nImages>0) exit ("close all images before proceeding");

	if(isOpen("Results")){
		selectWindow("Results");
		run("Close");
		}
	if(isOpen("Log")){
		selectWindow("Log");
		run("Close");
		}

//list auto functions here, adjust mode as necessary
function batchfunction();
mode           = newArray("AUTO", "MANUAL", "BOTH");
filter_choices = newArray('NO', '.dv', 'D3D.dv', 'R3D.dv', '.tif');

/**********************************************************/

Dialog.create("Select Options");
 	Dialog.addChoice("Method",mode,"AUTO");
 	Dialog.addChoice("Filter",filter_choices,"dv");
	
	Dialog.show();

	mode=Dialog.getChoice();
	filter=Dialog.getChoice();
	
/**********************************************************/




dir1 = getDirectory("Choose source directory");
if (dir1=="")
      exit("No directory available");

if(filter == "NO"){
	list = getFileList(dir1);
	}
else{
	
//get a list of all the files in this folder 
	preList = getFileList(dir1);
	size=0;
	
	//count each '*filter*' files
	for(place=0;place<preList.length;place++){
		if(endsWith(preList[place],filter)){
			size++;
		}
	}
	//create a new array and populate with filtered images
	list=newArray(size);
	position=0;
	for(place=0;place<preList.length;place++){
		if(endsWith(preList[place],filter)){
			list[position]=preList[place];
			position++;
			}
		}
	}


/********************************************************************/
/* allows the user to type in the appropriate experiment identifiers*/

Dialog.create("Movie Identifiers");
	Dialog.addMessage(dir1);
 	Dialog.addMessage(list[0]);

 	Dialog.addString("Experiment","48.01");
 	 	
	Dialog.show();
	
	expname= Dialog.getString();

/*******************************************************************/

	

//starting with the first image, we increment through each image until we have done 6, or finish our list, whichever comes first
  for(i=0; i<list.length; i++) {
	//open a two color image in separate channel stacks

	
	if(filter == 'dv' || filter == 'D3D.dv' || filter ==  'R3D.dv'){
		run("Bio-Formats Importer", "open="+dir1+list[i]+" view=Hyperstack stack_order=XYCZT");
		}
	else{
		open(dir1+list[i]);
		}
		
	run("Enhance Contrast", "saturated=0.35");

//	run("Set... ", "zoom=300");
//	waitForUser("adjust your image");
	
		
	if(mode == "MANUAL"){
		wait(100);
		run("Install...", "install=C:\\ImageJ\\macros\\_DKR_AutoScaleBrightestSlice.txt");
		waitForUser("click OK \nto proceed"); 
		}
	
	else if(mode == "AUTO"){
		selectWindow(list[i]);
		run("Set... ", "zoom=300");
		batchfunction(list[i]);
		
		}

	
	
	//close the window after dialog box is closed
	selectWindow(list[i]);
	close();
	}
}


function batchfunction(name)
{
	setResult("Label",nResults,name);
	setResult("Exp",nResults-1,expname);
	setTool("point");
	
	waitForUser("put a point on the midzone");
	
	/**/
Dialog.create("Select Categories");
	choices = newArray("defined","abnormal","metaphase");

 	Dialog.addChoice("This midzone is:",choices,"well defined");
	
	Dialog.show();
	
	choice = Dialog.getChoice();		
	/**/
		
	pointbool = selectionType();
	if(pointbool == 10){
		getSelectionBounds(x,y,width,height);
		wide = getWidth();
		
		midzone_px  = x;
		midzone_pct = midzone_px/wide; 
		
		setResult("midzone_px", nResults-1,midzone_px );
		setResult("total_px",   nResults-1,wide       );
		setResult("midzone_pct",nResults-1,midzone_pct);
		
			if(choice == "defined")     {setResult("defined",nResults-1,1);}
			else if(choice == "abnormal"){setResult("abnormal",nResults-1,1);}
			else if(choice == "metaphase"){setResult("metaphase",nResults-1,1);}
			else{};

		updateResults();
		}
	else{
		print("you f-d up");
		}


}