/* "Create transparent overlay from selection
	v231206:	1st Version  Peter J. Lee, Applied Superconductivity Center
	v231207:	Added stroke options. b: Names overlays.
	v231208:	Expanded selections recognized to include composite ROIs. Changed naming from transparency to opacity to match # name. Added add/replace options if there are already overlays on the image.
	v231209:	Removed redundant code leftover from earlier versions. F1: Updated getColorFromColorName function (012324).
 */
macro "Create transparent overlay from selection" {
	macroL = "Create_Transparent_Overlay_v231209-f2.ijm";
	prefsNameKey = "ascTranspOverlay.";
	lastBox = call("ij.Prefs.get", prefsNameKey + "roi.box", "");
	selType = selectionType;
	/* Returns the selection type, where 0=rectangle, 1=oval, 2=polygon, 3=freehand, 4=traced, 5=straight line, 6=segmented line, 7=freehand line, 8=angle, 9=composite and 10=point. Returns -1 if there is no selection. */
	if ((selType<0 || selType>4) && selType!=9){
		usePreviousBox = false;
		if (lastBox!=""){
			previousBox = split(lastBox,",");
			if (lengthOf(previousBox)==4) usePreviousBox = getBoolean("There is no selection, do you want to use the previously saved bounding box?");
		}
		if (usePreviousBox)
			  makeRectangle(parseInt(previousBox[0]), parseInt(previousBox[1]), parseInt(previousBox[2]), parseInt(previousBox[3]));
		selType = selectionType;
	}
	if ((selType<0 || selType>4) && selType!=9){
		msg = "Draw a bounding box around the ROIs to be selected";
		waitForUser("Please select the ROIs", msg);
		selType = selectionType;
	}
	if (selType>=0 && (selType<4 || selType==9)){
		getSelectionBounds(selPosStartX, selPosStartY, originalSelEWidth, originalSelEHeight);
		call("ij.Prefs.set", prefsNameKey + "roi.box","" + selPosStartX + "," + selPosStartY + "," + originalSelEWidth + "," + originalSelEHeight);
	}
	overlayN = Overlay.size();
	Dialog.create("Overlay options \(" + macroL + "\)");
		grayChoices = newArray("white", "black", "off-white", "off-black", "lightGray", "gray", "darkGray");
		colorChoicesStd = newArray("red", "green", "blue", "cyan", "magenta", "yellow", "pink", "orange", "violet");
		colorChoicesMaterials = newArray("bronze", "antique_bronze", "brass", "dull_brass", "chrome", "copper", "aged_copper", "dusky_copper", "light_copper", "garnet", "burnished_gold", "gold", "slate_gray", "titanium", "vault_garnet", "plaza_brick", "vault_gold");
		colorChoicesMod = newArray("aqua_modern", "blue_accent_modern", "blue_dark_modern", "blue_modern", "blue_honolulu", "gray_modern", "green_dark_modern", "green_modern", "green_modern_accent", "green_spring_accent", "orange_modern", "pink_modern", "purple_modern", "red_n_modern", "red_modern", "tan_modern", "violet_modern", "yellow_modern");
		colorChoicesNeon = newArray("jazzberry_jam", "radical_red", "wild_watermelon", "outrageous_orange", "supernova_orange", "atomic_tangerine", "neon_carrot", "sunglow", "laser_lemon", "electric_lime", "screamin'_green", "magic_mint", "blizzard_blue", "dodger_blue", "shocking_pink", "razzle_dazzle_rose", "hot_magenta");
		colorChoices = Array.concat(grayChoices, colorChoicesStd, colorChoicesMaterials, colorChoicesMod, colorChoicesNeon);
		colorFillChoice = call("ij.Prefs.get", prefsNameKey + "colorFillChoice", "white");
		Dialog.addChoice("Select Fill color", colorChoices, colorFillChoice);
		opacFillN = parseInt(call("ij.Prefs.get", prefsNameKey + "opacFillN", "50"));
		Dialog.addSlider("Fill opacity \(0 = No Fill\)", 0, 100, opacFillN);
		colorStrokeChoice = call("ij.Prefs.get", prefsNameKey + "colorStrokeChoice", "white");
		Dialog.addChoice("Select color", colorChoices, colorStrokeChoice);
		opacStrokeN = parseInt(call("ij.Prefs.get", prefsNameKey + "opacStrokeN", "50"));
		Dialog.addSlider("Stroke opacity", 0, 100, opacStrokeN);
		strokeWidth = parseInt(call("ij.Prefs.get", prefsNameKey + "strokeWidth", "0"));
		Dialog.addNumber("Stroke width \(0 = No stroke \)", strokeWidth, 0, 4, "pixels");
		if (overlayN>0){
			replaceOverlay = call("ij.Prefs.get", prefsNameKey + "replaceOverlay", true);
			Dialog.addCheckbox("Replace current with new overlay", replaceOverlay);
		}
		flattenIt = call("ij.Prefs.get", prefsNameKey + "flattenIt", true);
		Dialog.addCheckbox("Create flattened copy of image after overlay creation", flattenIt);
		removeOv = call("ij.Prefs.get", prefsNameKey + "removeOv", true);
		Dialog.addCheckbox("Remove overlay from original image", removeOv);
		Dialog.addMessage("The non-destructive overlays will be saved in the TIFF header\nif you save the image as an uncompressed TIFF file");
	Dialog.show();
		colorFillChoice = Dialog.getChoice();
		call("ij.Prefs.set", prefsNameKey + "colorFillChoice", colorFillChoice);
		opacFillN = parseInt(Dialog.getNumber());
		call("ij.Prefs.set", prefsNameKey + "opacFillN", opacFillN);
		colorStrokeChoice = Dialog.getChoice();
		call("ij.Prefs.set", prefsNameKey + "colorStrokeChoice", colorStrokeChoice);
		opacStrokeN = parseInt(Dialog.getNumber());
		call("ij.Prefs.set", prefsNameKey + "opacStrokeN", opacStrokeN);
		strokeWidth = parseInt(Dialog.getNumber());
		call("ij.Prefs.set", prefsNameKey + "strokeWidth", strokeWidth);
		if (overlayN>0){
			replaceOverlay = Dialog.getCheckbox();
			call("ij.Prefs.set", prefsNameKey + "replaceOverlay", replaceOverlay);
		}
		else replaceOverlay = false;
		flattenIt = Dialog.getCheckbox();
		call("ij.Prefs.set", prefsNameKey + "flattenIt", flattenIt);
		removeOv = Dialog.getCheckbox();
		call("ij.Prefs.set", prefsNameKey + "removeOv", removeOv);
	ovName = "";
	if (opacFillN==0 && (strokeWidth==0 || opacStrokeN==0)) exit ("It is 'transparent' that there is nothing to do here!");
	else {
		colFillHex = getHexColorFromColorName(colorFillChoice);
		if (opacFillN>0) opacFillHex = String.pad(toHex(255 * opacFillN/100), 2);
		else opacFillHex = "";
		ovName += "" + colorFillChoice + " fill ";
		colFillHex = replace(colFillHex, "#", opacFillHex);
		ovOptions = "fill=" + colFillHex;
	}
	if (strokeWidth>0 && opacStrokeN>0){
		colStrokeHex = getHexColorFromColorName(colorStrokeChoice);
		if (opacStrokeN>0) opacStrokeHex =  String.pad(toHex(255 * opacStrokeN/100), 2);
		else opacStrokeHex = "";
		colStrokeHex = replace(colStrokeHex, "#", opacStrokeHex);
		ovName += "" + colorStrokeChoice + " border";
		ovOptions += " width=" + strokeWidth + " stroke=" + colStrokeHex;
	}
	if (replaceOverlay) ovOptions += " new";
	setSelectionName(ovName);	/* Makes it easier to identify colors vs # in overlay descriptions in the overlay manager */
	run("Add Selection...", ovOptions);
	run("Select None");
	wait(100);
	overlayedID = getImageID();
	if (flattenIt){
		run("Flatten");
		flatID = getImageID();
	}
	if (removeOv){
		selectImage(overlayedID);
		run("Remove Overlay");
		if (flattenIt)
			selectImage(flatID);
	} 
	showStatus(macroL + " macro finished", "flash green");
}
	/*
	ASC Modified BAR Color Functions
	*/
	function getColorArrayFromColorName(colorName) {
		/* v180828 added Fluorescent Colors
		   v181017-8 added off-white and off-black for use in gif transparency and also added safe exit if no color match found
		   v191211 added Cyan
		   v211022 all names lower-case, all spaces to underscores v220225 Added more hash value comments as a reference v220706 restores missing magenta
		   v230130 Added more descriptions and modified order.
		   v230908: Returns "white" array if not match is found and logs issues without exiting.
		   v240123: Removed duplicate entries: Now 53 unique colors.
		   v240709: Added 2024 FSU-Branding Colors. Some reorganization. Now 60 unique colors.
		   v260202: Added 12 (mostly metallic) "Materials" colors. Now 72 unique colors.
		*/
		functionL = "getColorArrayFromColorName_v260203";
		cA = newArray(255, 255, 255); /* defaults to white */
		if (colorName == "white") cA = newArray(255, 255, 255);
		else if (colorName == "black") cA = newArray(0, 0, 0);
		else if (colorName == "off-white") cA = newArray(245, 245, 245);
		else if (colorName == "off-black") cA = newArray(10, 10, 10);
		else if (colorName == "lightGray") cA = newArray(192, 192, 192);
		else if (colorName == "gray") cA = newArray(127, 127, 127);
		else if (colorName == "darkGray") cA = newArray(64, 64, 64);
		else if (colorName == "red") cA = newArray(255, 0, 0);
		else if (colorName == "green") cA = newArray(0, 255, 0);						/* #00FF00 AKA Lime green */
		else if (colorName == "blue") cA = newArray(0, 0, 255);
		else if (colorName == "cyan") cA = newArray(0, 255, 255);
		else if (colorName == "yellow") cA = newArray(255, 255, 0);
		else if (colorName == "magenta") cA = newArray(255, 0, 255);					/* #FF00FF */
		else if (colorName == "pink") cA = newArray(255, 192, 203);
		else if (colorName == "violet") cA = newArray(127, 0, 255);
		else if (colorName == "orange") cA = newArray(255, 165, 0);
			/* Excel Modern  + */
		else if (colorName == "aqua_modern") cA = newArray(75, 172, 198);			/* #4bacc6 AKA "Viking" aqua */
		else if (colorName == "blue_accent_modern") cA = newArray(79, 129, 189);	/* #4f81bd */
		else if (colorName == "blue_dark_modern") cA = newArray(31, 73, 125);		/* #1F497D */
		else if (colorName == "blue_honolulu") cA = newArray(0, 118, 182);			/* Honolulu Blue #006db0 */
		else if (colorName == "blue_modern") cA = newArray(58, 93, 174);			/* #3a5dae */
		else if (colorName == "gray_modern") cA = newArray(83, 86, 90);				/* bright gray #53565A */
		else if (colorName == "green_dark_modern") cA = newArray(121, 133, 65);		/* Wasabi #798541 */
		else if (colorName == "green_modern") cA = newArray(155, 187, 89);			/* #9bbb59 AKA "Chelsea Cucumber" */
		else if (colorName == "green_modern_accent") cA = newArray(214, 228, 187); 	/* #D6E4BB AKA "Gin" */
		else if (colorName == "green_spring_accent") cA = newArray(0, 255, 102);	/* #00FF66 AKA "Spring Green" */
		else if (colorName == "orange_modern") cA = newArray(247, 150, 70);			/* #f79646 tan hide, light orange */
		else if (colorName == "pink_modern") cA = newArray(255, 105, 180);			/* hot pink #ff69b4 */
		else if (colorName == "purple_modern") cA = newArray(128, 100, 162);		/* blue-magenta, purple paradise #8064A2 */
		else if (colorName == "red_n_modern") cA = newArray(227, 24, 55);
		else if (colorName == "red_modern") cA = newArray(192, 80, 77);
		else if (colorName == "tan_modern") cA = newArray(238, 236, 225);
		else if (colorName == "violet_modern") cA = newArray(76, 65, 132);
		else if (colorName == "yellow_modern") cA = newArray(247, 238, 69);
			/* FSU */
		else if (colorName == "garnet") cA = newArray(120, 47, 64);					/* #782F40 */
		else if (colorName == "gold") cA = newArray(206, 184, 136);					/* #CEB888 */
		else if (colorName == "gulf_sands") cA = newArray(223, 209, 167);				/* #DFD1A7 */
		else if (colorName == "stadium_night") cA = newArray(16, 24, 32);				/* #101820 */
		else if (colorName == "westcott_water") cA = newArray(92, 184, 178);			/* #5CB8B2 */
		else if (colorName == "vault_garnet") cA = newArray(166, 25, 46);				/* #A6192E */
		else if (colorName == "legacy_blue") cA = newArray(66, 85, 99);				/* #425563 */
		else if (colorName == "plaza_brick") cA = newArray(66, 85, 99);				/* #572932 */
		else if (colorName == "vault_gold") cA = newArray(255, 199, 44);				/* #FFC72C */
			/* Materials */
		else if (colorName == "bronze") cA = newArray(205, 127, 50);					/* #CD7F32 */
		else if (colorName == "antique_bronze") cA = newArray(102, 93, 30);			/* #665D1E */
		else if (colorName == "brass") cA = newArray(181, 166, 66);					/* #B5A642 */
		else if (colorName == "dull_brass") cA = newArray(142, 124, 80);				/* #8E7C50 */
		else if (colorName == "burnished_gold") cA = newArray(133, 109, 77);			/* #856D4D */
		else if (colorName == "chrome") cA = newArray(229, 228, 226);					/* #E5E4E2 */
		else if (colorName == "copper") cA = newArray(184, 115, 51);					/* #B87333 */
		else if (colorName == "aged_copper") cA = newArray(110, 58, 7);				/* #6E3A07 */
		else if (colorName == "dusky_copper") cA = newArray(110, 59, 59);				/* #6E3B3B */
		else if (colorName == "light_copper") cA = newArray(218, 138, 103);			/* #DA8A67 */
		else if (colorName == "slate_gray") cA = newArray(112, 128, 144);				/* #708090 */
		else if (colorName == "titanium") cA = newArray(135, 134, 129);				/* #878681 */
		   /* Fluorescent Colors https://www.w3schools.com/colors/colors_crayola.asp   */
		else if (colorName == "radical_red") cA = newArray(255, 53, 94);			/* #FF355E */
		else if (colorName == "jazzberry_jam") cA = newArray(165, 11, 94);
		else if (colorName == "wild_watermelon") cA = newArray(253, 91, 120);		/* #FD5B78 */
		else if (colorName == "shocking_pink") cA = newArray(255, 110, 255);		/* #FF6EFF Ultra Pink */
		else if (colorName == "razzle_dazzle_rose") cA = newArray(238, 52, 210);	/* #EE34D2 */
		else if (colorName == "hot_magenta") cA = newArray(255, 0, 204);			/* #FF00CC AKA Purple Pizzazz */
		else if (colorName == "outrageous_orange") cA = newArray(255, 96, 55);		/* #FF6037 */
		else if (colorName == "supernova_orange") cA = newArray(255, 191, 63);		/* FFBF3F Supernova Neon Orange*/
		else if (colorName == "sunglow") cA = newArray(255, 204, 51);				/* #FFCC33 */
		else if (colorName == "neon_carrot") cA = newArray(255, 153, 51);			/* #FF9933 */
		else if (colorName == "atomic_tangerine") cA = newArray(255, 153, 102);		/* #FF9966 */
		else if (colorName == "laser_lemon") cA = newArray(255, 255, 102);			/* #FFFF66 "Unmellow Yellow" */
		else if (colorName == "electric_lime") cA = newArray(204, 255, 0);			/* #CCFF00 */
		else if (colorName == "screamin'_green") cA = newArray(102, 255, 102);		/* #66FF66 */
		else if (colorName == "magic_mint") cA = newArray(170, 240, 209);			/* #AAF0D1 */
		else if (colorName == "blizzard_blue") cA = newArray(80, 191, 230);		/* #50BFE6 Malibu */
		else if (colorName == "dodger_blue") cA = newArray(9, 159, 255);			/* #099FFF Dodger Neon Blue */
		else IJ.log(colorName + " not found in " + functionL + ": Color defaulted to white");
		return cA;
	}
	/* Hex conversion below adapted from T.Ferreira, 20010.01 https://imagej.net/doku.php?id=macro:rgbtohex */
	function getHexColorFromColorName(colorNameString) {
		/* v231207: Uses IJ String.pad instead of function: pad */
		colorArray = getColorArrayFromColorName(colorNameString);
		 r = toHex(colorArray[0]); g = toHex(colorArray[1]); b = toHex(colorArray[2]);
		 hexName= "#" + "" + String.pad(r, 2) + "" + String.pad(g, 2) + "" + String.pad(b, 2);
		 return hexName;
	}