/*
 * Toolset for quickly rename and save ROIs
 * It was thought for brain autoradiograms (in situ hybridization/receptor binding experiments)
 * where typically measurements need to be performed manually in multiple regions.
 * 
 * For a faster workflow create first all ROIs (press [t] to add them to the ROI Manager),
 * and then use the 'Group Labeling' tools to rename them.
 * Default labels can be modified below...
 *
 * Tiago Ferreira  ferreira <at> embl.de - 10.2007
 */

// --------------- These are the default settings: -------------------
// Regions:
	var l1 ="CA1";
	var l2 ="CA3";
	var l3 ="DG";
	var l4 ="Cortex";
	var l5 ="Striatum";
	var l6 ="Amigdala";
	var l7 ="Raphe";
	var l8 ="Ce";
	var l9 ="-";
	var l10 ="-";

// Groups:
	var g1 ="WT";
	var g2 ="Het";
	var g3 ="KO";

// --------------- QuicklyRename&SaveRoiSets Macro: ---------------
var labels =getLabelList();
var groups =getGroupList();
var i =roiManager("index");
var aCmds =newMenu("Group 1 labeling Menu Tool", labels);
var bCmds =newMenu("Group 2 labeling Menu Tool", labels);
var cCmds =newMenu("Group 3 labeling Menu Tool", labels);
var xx = requires138b(); // check version at install
function requires138b() {requires("1.38b"); return 0; }
}
macro "Unused Tool - " {
}
macro "Group 1 labeling Menu Tool - C000T0b121" {
	cmd = getArgument();
	if (roiManager("count")==0) exit("Before renaming a region\n    you need to create it!");
	else
	roiManager('Rename',i+" "+cmd+" "+groups[0]);
	MoveToNext();
}
macro "Group 2 labeling Menu Tool - C000T0b122" {
	cmd = getArgument();
	if (roiManager("count")==0) exit("Before renaming a region\n    you need to create it!");
	else
	roiManager('Rename',i+" "+cmd+" "+groups[1]);
	MoveToNext();
}
macro "Group 3 labeling Menu Tool - C000T0b123" {
	cmd = getArgument();
	if (roiManager("count")==0) exit("Before renaming a region\n    you need to create it!");
	else
	roiManager('Rename',i+" "+cmd+" "+groups[2]);
	MoveToNext();
}
macro "Previous Region Action Tool -  C000D57D58D67D68D76D77D78D79D86D87D88D89D95D96D97D98D99D9aDa5Da6Da7Da8Da9DaaC000C111C222C333C444C555C666C777C888C999CaaaCbbbCcccCdddCeeeCfff" {
	if (roiManager("count")==0) exit ("ROI Manager is empty.\nCannot cycle through.");
	else
	MoveToPrevious();
}
macro "Next Region Action Tool -  C000D55D56D57D58D59D5aD65D66D67D68D69D6aD76D77D78D79D86D87D88D89D97D98Da7Da8C000C111C222C333C444C555C666C777C888C999CaaaCbbbCcccCdddCeeeCfff" {
	if (roiManager("count")==0) exit ("ROI Manager is empty.\nCannot cycle through.");
	else
	MoveToNext();
}
macro "Save All Regions Action Tool - C000D00D01D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD10D14D15D16D17D18D19D1aD1bD1cD1dD1eD1fD20D24D25D26D27D28D29D2aD2bD2cD2dD2eD2fD30D34D35D36D37D38D39D3aD3bD3cD3dD3eD3fD40D44D45D46D47D48D49D4aD4bD4cD4dD4eD4fD50D54D55D5aD5bD5cD5dD5eD5fD60D64D6bD6cD6dD6eD6fD70D74D7bD80D81D82D83D84D8bD90D91D92D93D94D9bD9cD9dD9eD9fDa0Da1Da2Da3Da4Da5DaaDabDacDadDaeDafDb0Db1Db2Db3Db4Db5Db6Db7Db8Db9DbaDbbDbcDbdDbeDbfDc0Dc1Dc2Dc3Dc4Dc5Dc6Dc8Dc9DcaDcbDccDcdDceDcfDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8Dd9DdaDdbDdcDddDdeDdfDe0De1De2De3De4De5De6De7De8De9DeaDebDecDedDeeDefDf0Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC000D0fC000D02C000C111C222C333C444C555C666C777C888C999CaaaCbbbCcccCdddCeeeCfff"{
	options=newArray('Same folder as Image', "Another location");
	
	if (roiManager("count")==0) exit ("ROI Manager is empty.\n     No ROIs to save.");
	else
	if (nImages==0 && roiManager("count")!=0) exit ("This tool requires an open image");
	else
	if (getDirectory("image")==""){
	options=newArray("Another location");
	foot =getTitle+' is either on a remote server'+'\n'+'or it has not been saved yet...';}
	else 
	if (File.exists(getDirectory("image")+getTitle+'-RoiSet.zip')==1)
	foot ="Attention!\nA similar .zip file already exists at\n"+getDirectory("image")+"\nIf you don't want to overwritte it choose 'Another location'";
	else 
	foot ='Current image location:'+'\n'+getDirectory("image");
	roiManager('Deselect');
	setOption("Show All", true);
	Dialog.create("Save Session");
	Dialog.addChoice('Save '+getTitle()+'-RoiSet.zip'+' in:',options);
	Dialog.addMessage(foot);
	Dialog.show();
	target = Dialog.getChoice();
			
	if (target=="Same folder as Image")
	roiManager('save',getDirectory("image")+getTitle()+'-RoiSet.zip');
	else
	roiManager('save', getDirectory("Select a Directory")+getTitle()+'-RoiSet.zip');

	setOption("Show All", false);
}
function getLabelList() {
	if (nImages>0) a=bitDepth; else a=24;
	Dialog.create("Settings (I)");
	Dialog.addMessage('Labels Definition:')
	Dialog.addString("Label 01", l1, 10);
	Dialog.addString("Label 02", l2, 10);
	Dialog.addString("Label 03", l3, 10);
	Dialog.addString("Label 04", l4, 10);
	Dialog.addString("Label 05", l5, 10);
	Dialog.addString("Label 06", l6, 10);
	Dialog.addString("Label 07", l7, 10);
	Dialog.addString("Label 08", l8, 10);
	Dialog.addString("Label 09", l9, 10);
	Dialog.addString("Label 10", l10, 10);
	Dialog.addMessage("Labels defined by '-'\n    will be ignored");
	Dialog.addCheckbox("Invert gray values", false);
	Dialog.show();
	l1 =Dialog.getString(); 
	l2 =Dialog.getString();
	l3 =Dialog.getString(); 
	l4 =Dialog.getString();
	l5 =Dialog.getString(); 
	l6 =Dialog.getString(); 
	l7 =Dialog.getString();
	l8 =Dialog.getString(); 
	l9 =Dialog.getString();
	l10 =Dialog.getString();
	inv =Dialog.getCheckbox();
	if(inv==true && nImages>0 && a!=24) {run("Invert");run("Invert LUT");}
	tags =newArray(""+l1,""+l2,""+l3,""+l4,""+l5,""+l6,""+l7,""+l8,""+l9,""+l10,"-","Background");
	return tags;
}
function getGroupList() {
	Dialog.create("Settings (II)");
	Dialog.addMessage('Groups definition:')
	Dialog.addString("Group 1", g1, 7);
	Dialog.addString("Group 2", g2, 7);
	Dialog.addString("Group 3", g3, 7);
	Dialog.show();
	g1 =Dialog.getString(); 
	g2 =Dialog.getString();
	g3 =Dialog.getString(); 
	groups =newArray(""+g1,""+g2,""+g3);
	return groups;
}
function MoveToNext() {
	n =roiManager("count");
	i =roiManager("index");
	if(n==i+1) roiManager('select', 0);
	else roiManager('select', i+1);
}
function MoveToPrevious() {
	n =roiManager("count");
	i =roiManager("index");
	if (i<=0) roiManager('select', n-1);
	else roiManager('select', i-1);
}