// 1P Calcium Imaging Toolset

macro "Developer Menu Tool - C037T0b11DT7b09eTcb09v" {
	cmd = getArgument();
	if (cmd=="ImageJ Website")
		run("URL...", "url=http://rsbweb.nih.gov/ij/");
	else if (cmd=="Macro and Record Windows...") {
		run("Macro");
		run("Record...");}
	else if (cmd=="News")
		run("URL...", "url=http://rsbweb.nih.gov/ij/notes.html");
	else if (cmd=="Documentation")
		run("URL...", "url=http://rsbweb.nih.gov/ij/docs/");
	else if (cmd=="ImageJ Wiki")
		run("URL...", "url=http://imagejdocu.tudor.lu/imagej-documentation-wiki/");
	else if (cmd=="Resources")
		run("URL...", "url=http://rsbweb.nih.gov/ij/developer/");
	else if (cmd=="Macro Language")
		run("URL...", "url=http://rsbweb.nih.gov/ij/developer/macro/macros.html");
	else if (cmd=="Macros")
		run("URL...", "url=http://rsbweb.nih.gov/ij/macros/");
	else if (cmd=="Macro Functions")
		run("URL...", "url=http://rsbweb.nih.gov/ij/developer/macro/functions.html");
	else if (cmd=="Plugins")
		run("URL...", "url=http://rsbweb.nih.gov/ij/plugins/");
	else if (cmd=="Source Code")
		run("URL...", "url=http://rsbweb.nih.gov/ij/developer/source/");
	else if (cmd=="Mailing List Archives")
		run("URL...", "url=https://list.nih.gov/archives/imagej.html");
	else if (cmd=="Debug Mode")
		setOption("DebugMode", true);
	else if (cmd!="-")
		run(cmd);
}

var sCmds = newMenu("Stacks Menu Tool",
	newArray("Add Slice", "Delete Slice", "Next Slice [>]", "Previous Slice [<]", "Set Slice...", "-",
		"Convert Images to Stack", "Convert Stack to Images", "Make Montage...", "Reslice [/]...", "Z Project...",
		"3D Project...", "Plot Z-axis Profile", "-", "Start Animation", "Stop Animation", "Animation Options...",
		"-", "MRI Stack (528K)"));
macro "Stacks Menu Tool - C037T0b11ST8b09tTcb09k" {
	cmd = getArgument();
	if (cmd!="-") run(cmd);
}

var luts = getLutMenu();
var lCmds = newMenu("LUT Menu Tool", luts);
macro "LUT Menu Tool - C037T0b11LT6b09UTcb09T" {
	cmd = getArgument();
	if (cmd!="-") run(cmd);
}
function getLutMenu() {
	list = getLutList();
	menu = newArray(16+list.length);
	menu[0] = "Invert LUT"; menu[1] = "Apply LUT"; menu[2] = "-";
	menu[3] = "Fire"; menu[4] = "Grays"; menu[5] = "Ice";
	menu[6] = "Spectrum"; menu[7] = "3-3-2 RGB"; menu[8] = "Red";
	menu[9] = "Green"; menu[10] = "Blue"; menu[11] = "Cyan";
	menu[12] = "Magenta"; menu[13] = "Yellow"; menu[14] = "Red/Green";
	menu[15] = "-";
	for (i=0; i<list.length; i++)
		menu[i+16] = list[i];
	return menu;
}

function getLutList() {
	lutdir = getDirectory("luts");
	list = newArray("No LUTs in /ImageJ/luts");
	if (!File.exists(lutdir))
		return list;
	rawlist = getFileList(lutdir);
	if (rawlist.length==0)
		return list;
	count = 0;
	for (i=0; i< rawlist.length; i++)
		if (endsWith(rawlist[i], ".lut")) count++;
	if (count==0)
		return list;
	list = newArray(count);
	index = 0;
	for (i=0; i< rawlist.length; i++) {
		if (endsWith(rawlist[i], ".lut"))
			list[index++] = substring(rawlist[i], 0, lengthOf(rawlist[i])-4);
	}
	return list;
}

macro "Raw Image Importer (Bioformats) Action Tool - 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" {
	run("Bio-Formats Importer");
	// Rename images after importing to file parent name - PMT1, SRS, PMT3
	runMacro("SicLab_imgrename_ext.ijm");
}

macro "Open Virtual Stack Action Tool - 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" {
	run("Bio-Formats Importer");
	// Rename images after importing to file parent name - PMT1, SRS, PMT3
	runMacro("SicLab_imgrename_ext.ijm");
}