// CCD_Help.txt
//
// FVH (2010-03-18)
// Changes: ccd.ron in counts but aperture.ccdnoise in e- !!!

// MENU OPTIONS

menunix = " ";
menubias = "Create Master Bias Image";
menudark = "Create Master Dark Image";
menuflat = "Create Master Flatfield Image";
menuproc = "Process Images";
menugain = "gain Calculation";
menuron  = "RON Calculation";
menuexp  = "Exposure correction";

// GET PREFERENCES

gain = call("ij.Prefs.get","aperture.ccdgain","1.0");
ron = call("ij.Prefs.get","aperture.ccdnoise","0.0");
dark = call("ij.Prefs.get","aperture.ccddark","0.0");

biasimage = call("ij.Prefs.get","ccd.biasimage","BIAS");
darkimage = call("ij.Prefs.get","ccd.darkimage","DARK");
flatimage = call("ij.Prefs.get","ccd.flatimage","FLATFIELD");
roncts = call("ij.Prefs.get","ccd.ron","0.0");

biascorr = call("ij.Prefs.get","ccd.biascorr",false);
darkcorr = call("ij.Prefs.get","ccd.darkcorr",false);
flatcorr = call("ij.Prefs.get","ccd.flatcorr",false);
expcorr = call("ij.Prefs.get","ccd.expcorr",false);

// ASK FOR TOPIC

Dialog.create("CCD Help Menu");
Dialog.addMessage("The CCD macros/plugins are for calibrating and processing raw CCD images.");
Dialog.addMessage("Each requires the previous input of specific image/stack data.");
Dialog.addMessage("Current Aperture preferences :");
Dialog.addString("          gain [e-/count] : ",gain);
Dialog.addString("          read-out noise [e-] : ",ron);
Dialog.addString("          dark level [e-] : ",dark);
Dialog.addMessage("Current CCD preferences :");
Dialog.addString("          bias image : ",biasimage,20);
Dialog.addString("          dark-current image : ",darkimage,20);
Dialog.addString("          flatfield image : ",flatimage,20);
Dialog.addString("          raw read-out noise [counts] : ",roncts);
Dialog.addMessage("Current Reduction preferences : correct for...");
Dialog.addCheckbox("          _bias",biascorr);
Dialog.addCheckbox("          _dark current",darkcorr);
Dialog.addCheckbox("          _flatfield(s)",flatcorr);
Dialog.addCheckbox("          _using exposure time",expcorr);
Dialog.addMessage("Select one of the topics below for more information.");
choices = newArray(8);
choices[0] = menunix;
choices[1] = menubias;
choices[2] = menudark;
choices[3] = menuflat;
choices[4] = menuexp;
choices[5] = menuproc;
choices[6] = menugain;
choices[7] = menuron;

Dialog.addChoice("     Help topic",choices,choices[0]);
Dialog.show();

// SAVE USER INPUT

gain = Dialog.getString();
ron = Dialog.getString();
dark = Dialog.getString();

biasimage = Dialog.getString();
darkimage = Dialog.getString();
flatimage = Dialog.getString();
roncts = Dialog.getString();

biascorr = Dialog.getCheckbox();
darkcorr = Dialog.getCheckbox();
flatcorr = Dialog.getCheckbox();
expcorr = Dialog.getCheckbox();
call("ij.Prefs.set","ccd.biasimage",biasimage);
call("ij.Prefs.set","ccd.flatimage",flatimage);
call("ij.Prefs.set","ccd.darkimage",darkimage);
call("ij.Prefs.set","ccd.ron",roncts);

call("ij.Prefs.set","ccd.biascorr",biascorr);
call("ij.Prefs.set","ccd.darkcorr",darkcorr);
call("ij.Prefs.set","ccd.flatcorr",flatcorr);
call("ij.Prefs.set","ccd.expcorr",expcorr);

call("ij.Prefs.set","aperture.ccdron",ron);
call("ij.Prefs.set","aperture.ccdgain",gain);
call("ij.Prefs.set","aperture.ccddark",dark);

// TOPIC TEXT

topic = Dialog.getChoice();
answer = "";
if        (topic == menugain) {
	answer = answer+"INPUT:\n          stack of very similar exposed raw images, minus bias and dark\n";
	answer = answer+"OUTPUT:\n          mean gain\n";
	answer = answer+"DESCRIPTION:\n          compares mean level with noise to estimate gain";
} else if (topic == menuron)  {
	answer = answer+"INPUT:\n          stack of raw bias images\n";
	answer = answer+"OUTPUT:\n          image of RON values, mean RON\n";
	answer = answer+"DESCRIPTION:\n          computes standard deviation of bias images";
} else if (topic == menubias) {
	answer = answer+"INPUT:\n          stack of raw bias images\n";
	answer = answer+"OUTPUT:\n          median bias image\n";
	answer = answer+"DESCRIPTION:\n          uses median to remove cosmic rays";
} else if (topic == menudark) {
	answer = answer+"INPUT:\n          stack of raw dark images\n          optional bias image to be subtracted\n";
	answer = answer+"OUTPUT:\n          median dark image\n";
	answer = answer+"DESCRIPTION:\n          uses median to remove cosmic rays; does not adjust effective exposure time";
} else if (topic == menuflat) {
	answer = answer+"INPUT:\n          stack of raw dome/twilight/sky images\n          optional bias/dark images to be subtracted\n";
	answer = answer+"OUTPUT:\n          median flatfield image, normalized to 1\n";
	answer = answer+"DESCRIPTION:\n          uses median to remove cosmic rays, stars; does not remove gradients";
} else if (topic == menuproc) {
	answer = answer+"INPUT:\n          raw image\n          optional bias/dark/flat images for calibration\n";
	answer = answer+"OUTPUT:\n          calibrated images\n";
	answer = answer+"DESCRIPTION:\n          only works on an image";
}

// SHOW HELP

if (answer != "") {
	print("CCD Help for "+topic+"\n"+answer);
	Dialog.create(topic);
	Dialog.addMessage(answer);
	Dialog.show();
}