scienceimage = getTitle();
call("ij.Prefs.set", "multiaperture.finished","false");
run("Process Images", " subtract bias=bias.fits remove-dark-current dark=dark.fits divide flat=flat.fits");


xlabel="J.D.-2400000";
ylabel="ratio1";
errlabel="ratio1_error";

showErrors=call("ij.Prefs.get", "plot.showErrors","false");
if (showErrors=="true") showErrors = 1;
else showErrors = 0;

lines=call("ij.Prefs.get", "plot.lines", "false");
if (lines=="true") lines = 1;
else lines = 0;

markerIndex=call("ij.Prefs.get", "plot.markerIndex",3);

mmag=call("ij.Prefs.get", "plot.mmag","true");
if (mmag=="true") mmag = 1;
else mmag = 0;


xTics=call("ij.Prefs.get", "plot.xTics", "true");
if (xTics=="true") xTics = 1;
else xTics = 0;


yTics=call("ij.Prefs.get", "plot.yTics", "true");
if (yTics=="true") yTics= 1;
else yTics= 0;

xGrid=call("ij.Prefs.get", "plot.xGrid", "false");
if (xGrid=="true") xGrid = 1;
else xGrid = 0;

yGrid=call("ij.Prefs.get", "plot.yGrid", "true");
if (yGrid =="true") yGrid = 1;
else yGrid = 0;

xNumbers=call("ij.Prefs.get", "plot.xNumbers", "true");
if (xNumbers=="true") xNumbers = 1;
else xNumbers = 0;

yNumbers=call("ij.Prefs.get", "plot.yNumbers", "true");
if (yNumbers=="true") yNumbers = 1;
else yNumbers = 0;

autoScaleX=call("ij.Prefs.get", "plot.autoScaleX","false");
if (autoScaleX=="true") autoScaleX = 1;
else autoScaleX = 0;

autoScaleY=call("ij.Prefs.get", "plot.autoScaleY","false");
if (autoScaleY=="true") autoScaleY = 1;
else autoScaleY = 0;

xMin=call("ij.Prefs.get", "plot.xMin", 55000);
xMax=call("ij.Prefs.get", "plot.xMax", 57000);
yMin=call("ij.Prefs.get", "plot.yMin", -20);
yMax=call("ij.Prefs.get", "plot.yMax", 10);

plotSizeX=call("ij.Prefs.get", "plot.plotSizeX", 600);
plotSizeY=call("ij.Prefs.get", "plot.plotSizeY", 350);

imageDisplayTime=call("ij.Prefs.get", "plot.imagedisplaytime", 1);
minContrast=call("ij.Prefs.get", "plot.mincontrast", 0);  
maxContrast=call("ij.Prefs.get", "plot.maxcontrast", 1000);

setMinAndMax(minContrast, maxContrast);

markers = newArray("box","circle","cross","dot","none","triangle","X");

if (!isOpen("Plot of Measurements")) {

	//ask for option settings if no plot screen is open

	Dialog.create("Auto Plot Options:");
            Dialog.addNumber ("X plot size",plotSizeX,0,4,"pixels");
            Dialog.addNumber ("Y plot size",plotSizeY,0,4,"pixels");
	Dialog.addNumber ("Minimum contrast level",minContrast,0,5,"");
	Dialog.addNumber ("Maximum contrast level",maxContrast,0,5,"");
	Dialog.addNumber ("Image Display Time",imageDisplayTime,0,4,"seconds");
	 
            Dialog.addCheckbox ("Plot Y-data in relative mmag",mmag);
	Dialog.addCheckbox ("Show Y-errors",showErrors);
 	Dialog.addChoice ("Marker", markers, markers[markerIndex]);

            Dialog.addCheckbox ("Connect markers with lines",lines);
            Dialog.addCheckbox ("X tick marks",xTics);
            Dialog.addCheckbox ("Y tick marks",yTics);
            Dialog.addCheckbox ("X grid lines",xGrid);
            Dialog.addCheckbox ("Y grid lines",yGrid);
            Dialog.addCheckbox ("X numbers",xNumbers);
            Dialog.addCheckbox ("Y numbers",yNumbers);

	Dialog.addMessage("");
	Dialog.addCheckbox ("X automatic scaling",autoScaleX);
	Dialog.addNumber ("Minimum X-value",xMin,2,8,"");
	Dialog.addNumber ("Maximum X-value",xMax,2,8,"");
            Dialog.addCheckbox ("Y automatic scaling",autoScaleY);
	Dialog.addNumber ("Minimum Y-value",yMin,2,8,"");
	Dialog.addNumber ("Maximum Y-value",yMax,2,8,"");
	Dialog.show();

	//read in user selections

	plotSizeX=Dialog.getNumber();
	plotSizeY=Dialog.getNumber();
	minContrast=Dialog.getNumber();
	maxContrast=Dialog.getNumber();
	imageDisplayTime=Dialog.getNumber();
            mmag=Dialog.getCheckbox ();
	showErrors=Dialog.getCheckbox ();
 	markerIndex=Dialog.getChoice ();
            lines=Dialog.getCheckbox ();
            xTics=Dialog.getCheckbox ();
            yTics=Dialog.getCheckbox ();
            xGrid=Dialog.getCheckbox ();
            yGrid=Dialog.getCheckbox ();
            xNumbers=Dialog.getCheckbox ();
            yNumbers=Dialog.getCheckbox ();
	autoScaleX=Dialog.getCheckbox ();
	xMin=Dialog.getNumber ();
	xMax=Dialog.getNumber ();
            autoScaleY=Dialog.getCheckbox ();
	yMin=Dialog.getNumber ();
	yMax=Dialog.getNumber ();
 	call("ij.Prefs.set", "plot.mincontrast", minContrast);  
	call("ij.Prefs.set", "plot.maxcontrast", maxContrast);
	call("ij.Prefs.set", "plot.imagedisplaytime", imageDisplayTime);
	}
else {
	markerIndex=markers[markerIndex];
	}

if (mmag == 1) mmag = " plot_y-data_in_relative_mmag ";
else mmag = "";
if (showErrors == 1) showErrors= " show_y-errors ";
else showErrors= "";
if (lines == 1) lines = " connect ";
else lines = "";
if (xTics == 1) xTics= " x_tick_marks ";
else xTics= "";
if (yTics == 1) yTics= " y_tick_marks ";
else yTics= "";
if (xGrid == 1) xGrid= " x_grid_lines ";
else xGrid= "";
if (yGrid == 1) yGrid= " y_grid_lines ";
else yGrid= "";
if (xNumbers == 1) xNumbers= "  x_numbers ";
else xNumbers= "";
if (yNumbers == 1) yNumbers= "  y_numbers ";
else yNumbers= "";
if (autoScaleX == 1) autoScaleX= " x_automatic_scaling ";
else autoScaleX= "";
if (autoScaleY == 1) autoScaleY= " y_automatic_scaling";
else autoScaleY= "";

imageDisplayTime *= 1000;


if (isOpen("Plot of Measurements")) {
	automode = "true";
	call("ij.Prefs.set", "multiaperture.automode",automode);
	run("MultiAperture ");
	automode = "false";
	call("ij.Prefs.set", "multiaperture.automode",automode);
	
} else {
	automode = "false";
	call("ij.Prefs.set", "multiaperture.automode",automode);
	run("MultiAperture ");
	finished=call("ij.Prefs.get", "multiaperture.finished","false");
	while (finished == "false") {
		finished=call("ij.Prefs.get", "multiaperture.finished","false");		
		wait(10);
	}

}
	

wait(imageDisplayTime);

selectWindow(scienceimage);
activeimage = getTitle();
if ((activeimage == scienceimage) && (imageDisplayTime !=0)) {
	close();
	}
if (isOpen("Plot of Measurements")) {
	selectWindow("Plot of Measurements");
	close();
	}


run("Plot Table Columns", "table=Measurements x-data="+xlabel+"  y-data="+ylabel+mmag+showErrors+" y-error="+errlabel+" marker="+markerIndex+" x_plot_size="+plotSizeX+" y_plot_size="+plotSizeY+lines+xTics+yTics+xGrid+yGrid+xNumbers+yNumbers+autoScaleX+" minimum_x-value="+xMin+" maximum_x-value="+xMax+autoScaleY+" minimum_y-value="+yMin+" maximum_y-value="+yMax);