macro "Erode and Prune to Fully(4)-Connected Skeleton" {
	/*	Uses Gabriel Landini's skeletonization algorithm, different from the one in ImageJ similar to skeleton1 but 4-connected
		3 Dec 2003 uses BinaryThin2_.class available from http://www.mecourse.com/landinig/software/software.html assumes a white object on a black background 
		v171108 
		v180305 added option to keep white background - useful for creating skeletonized backgrounds
		v190325 fixed missing zero in coordinates.
		v200424 changed to adapt to black or white background based on mean intensity v200428 tweaked final filename
		v200428 added a bit more complexity to auto-file naming v200506 Just added a couple of show status updates
		v200512 added broken diagonals and trapped squares cleanup options
		v210727 changed to non-inverting.
		v211103 Adds median smoothing and autoSave options.
		v211104: Updated stripKnownExtensionFromString function    211112+220616+230505: Again.  Updated functions: 5/16/2022 2:09 PM and 8/18/2022 11:06 AM + 6/7/2023 1:41 PM
		v220818: Auto-thresholds, no longer uses restoreExit.
		v240731: Pruning is now optional. "Trapped squares" now include 8-pixel trap (one corner missing). Better organization of dialogs. Restores selections and LUT condition.
		v250625: Fixed "tSkel" to fName.
		v250626: Additional options.
	*/
	macroL = "4(fully)-Cnctd_Skeleton_v250626.ijm";
	if (!checkForPlugin("morphology_collection")) exit("Exiting: Gabriel Landini's morphology suite is needed to run this function.");
	fullFName = getInfo("image.filename");
	if (fullFName == "") {
		fName = stripKnownExtensionFromString(getTitle());
		extension = "";
	} else {
		path = getInfo("image.directory");
		fName = File.getNameWithoutExtension(path + fullFName);
		extension = substring(fullFName, lengthOf(fName));
	}
	fName += "_skel";
	orID = getImageID();
	selType = selectionType;
	if (selType >= 0) run("Select None");
	run("Duplicate...", "title=&fName slice");
	run("8-bit");
	if (!is("binary")) {
		/* Quick-n-dirty threshold if not previously thresholded */
		getThreshold(t1, t2);
		if (t1 == -1) {
			run("Auto Threshold", "method=Default");
			setOption("BlackBackground", false);
			run("Make Binary");
			IJ.log("Default auto-threshold applied to " + fName);
		}
	}
	if (is("Inverting LUT")) {
		hadInvertedLUT = true;
		run("Invert LUT");
	} else hadInvertedLUT = false;
	getStatistics(null, meanI, null, null, null, null);
	getDimensions(imageWidth, imageHeight, imageChannels, imageSlices, imageFrames);
	if (meanI < 128) blackSkel = false;
	else blackSkel = true;
	dFixes = 0;
	sFixes = 0;
	skelInt = 255;
	bgInt = 0;
	dFixes = 0;
	sFixes = 0;
	semiPixels = 0;
	zoomOPC = 100 * getZoom();
	/* ASC message theme */
	infoColor = "#006db0"; /* Honolulu blue */
	instructionColor = "#798541"; /* green_dark_modern (121,133,65) AKA Wasabi */
	infoWarningColor = "#ff69b4"; /* pink_modern AKA hot pink */
	infoFontSize = 12;
	getLocationAndSize(xW, yW, widthW, heightW);
	Dialog.create(macroL + ": Erosion limits");
	Dialog.addMessage("File: " + fullFName, infoFontSize * maxOf(0.5, minOf(1, 80 / lengthOf(fullFName))), infoColor);
	Dialog.addMessage("Directory: " + path, infoFontSize * maxOf(0.5, minOf(1, 80 / lengthOf(path))), infoColor);
	Dialog.addNumber("Denoise with median filter first:", 0, 1, 4, "radius in pixels");
	Dialog.addNumber("Limit number of erosions?", -1, 0, 3, "-1 = until idempotence reached");
	if (imageWidth * imageHeight > 4000000) Dialog.addMessage("The following fixes can take a long time on large images:");
	if (blackSkel) Dialog.addCheckbox("Black skeleton recognized; is this true?", true);
	else Dialog.addCheckbox("White skeleton recognized; is this true?", true);
	Dialog.addCheckbox("Fix broken diagonals for full connection?", true);
	Dialog.addCheckbox("Fix trapped solid squares by clearing top and bottom pixels?", true);
	Dialog.addCheckbox("Fill open squares with single pixel diagonal disconnect?", false);
	Dialog.addCheckbox("Rerun erosions after diagonal and solid square fixes?", true);
	Dialog.addCheckbox("Prune \(performed after erosions and fixes\)?", true);
	Dialog.addCheckbox("Output fix report to log window?", false);
	Dialog.show();
	medianRadius = Dialog.getNumber();
	erosionN = Dialog.getNumber();
	if (blackSkel){
		if (!Dialog.getCheckbox()) blackSkel = false;
	}	
	else if (!Dialog.getCheckbox()) blackSkel = true;	
	dFix = Dialog.getCheckbox();
	sFix = Dialog.getCheckbox();
	semiPixel = Dialog.getCheckbox();
	reErode = Dialog.getCheckbox();
	pruneIt = Dialog.getCheckbox();
	report = Dialog.getCheckbox();
	xMax = imageWidth - 1;
	yMax = imageHeight - 1;
	/* Based on skeleton3.txt by G. Landini: a skeletonization algorithm, different from the one in ImageJ similar to skeleton1 but 4-connected
	3 Dec 2003 uses BinaryThin2_.class available from http://www.mecourse.com/landinig/software/software.html assumes a white object on a black background */
	setBatchMode(true);
	if (blackSkel) run("Invert");
	showStatus("Creating Skeleton");
	if (medianRadius > 0) run("Median...", "radius=" + medianRadius);
	run("BinaryThin2 ", "kernel_a='1 1 1 2 1 2 0 0 0 ' kernel_b='2 1 1 0 1 1 0 0 2 ' rotations='rotate 45' iterations=&erosionN white");
	if (dFix) {
		for (i = 1; i < imageWidth - 1; i++) {
			/* start 2nd column, end penultimate column */
			showStatus("Fixing broken diagonals: " + dFixes + " fixes");
			showProgress(i, imageWidth - 1);
			for (j = bgInt; j < imageHeight - 1; j++) {
				/* start 1st row, end penultimate row */
				if ((getPixel(i, j)) == skelInt) {
					if ((getPixel(i + 1, j)) == bgInt) {
						if ((getPixel(i, j + 1)) == bgInt) {
							if ((getPixel(i + 1, j + 1)) == skelInt) {
								setPixel(i + 1, j, skelInt);
								dFixes += 1;
							}
						}
					} /* conditions end iteration at first exception */
					/* assume right and left fill-ins will balance out */
					if ((getPixel(i - 1, j)) == bgInt) {
						if ((getPixel(i, j + 1)) == bgInt) {
							if ((getPixel(i - 1, j + 1)) == skelInt) {
								setPixel(i - 1, j, skelInt);
								dFixes += 1;
							}
						}
					} /* conditions end iteration at first exception */
				}
			}
		}
	}
	if (sFix) {
		/* next open up trapped squares */
		for (i = 1; i < imageWidth - 2; i++) {
			/* start 2nd column, end penultimate but one column */
			showStatus("Fixing trapped squares: " + sFixes + " fixes");
			showProgress(i, imageWidth - 1);
			for (j = 1; j < imageHeight - 3; j++) {
				/* start 2nd row, end penultimate but two row */
				coreInt = getPixel(i, j);
				if (coreInt == bgInt) coreOpen = true;
				else coreOpen = false;
				skelN = 0;
				diagN = 0;
				for (k = 0; k < 3; k++) {
					for (l = 0; l < 3; l++) {
						pixInt = getPixel(i + k, j + l);
						if (pixInt == skelInt) skelN++;
						if (k != 1 && l != 1 && pixInt == bgInt) diagN++;
					}
				}
				if (skelN >= 8) {
					/* trapped square */
					if ((getPixel(i + 1, j - 1)) == bgInt) {
						setPixel(i + 1, j, bgInt);
						sFixes += 1;
					}
					if ((getPixel(i + 1, j + 3)) == bgInt) {
						setPixel(i + 1, j + 2, bgInt);
						sFixes += 1;
					}
				} else if (coreOpen && semiPixel && skelN == 7 && diagN == 1) {
					setPixel(i, j, skelInt);
					semiPixels++;
				}
			}
		}
	}
	if ((dFix || sFix) && reErode) run("BinaryThin2 ", "kernel_a='1 1 1 2 1 2 0 0 0 ' kernel_b='2 1 1 0 1 1 0 0 2 ' rotations='rotate 45' iterations=&erosionN white");
	if (blackSkel) run("Invert");
	if (pruneIt) {
		setBatchMode("exit & display"); /* Probably not necessary if exiting gracefully but otherwise harmless */
		Dialog.create("Save before pruning: Options");
		Dialog.addNumber("Limit number of pruning iterations?", -1, 0, 3, "0 = No pruning, -1 = until idempotence reached");
		Dialog.addCheckbox("Pin edge of image?", false);
		Dialog.addCheckbox("Apply to duplicate of image or active selection", false);
		Dialog.addRadioButtonGroup("Save before pruning?", newArray("Yes", "No", "Exit"), 1, 3, "No");
		if (medianRadius > 0) fName += "_M" + medianRadius + "Smth";
		fName += extension;
		Dialog.addString("Autosave directory:", path, lengthOf(path) + 5);
		Dialog.addString("Autosave filename:", fName, lengthOf(fName) + 5);
		Dialog.show();
		pruneN = Dialog.getNumber();
		pinEdge = Dialog.getCheckbox();
		if (Dialog.getCheckbox()) {
			run("Duplicate...", " ");
			if (pinEdge) run("Canvas Size...", "width=" + imageWidth + 2 + " height=" imageHeight + 2 + " position=Center");
			xW += 20;
			xY += 20;
			run("Set... ", "zoom=&zoomOPC x=&xW y=&xY");
		}
		else if (pinEdge) run("Canvas Size...", "width=" + imageWidth + 2 + " height=" + imageHeight + 2 + " position=Center");
		saveOpt = Dialog.getRadioButton();
		path = Dialog.getString();
		if (!endsWith(path, File.separator)) path += File.separator;
		autoPath = path + Dialog.getString;
		if (saveOpt == "Yes") save(autoPath);
		if (saveOpt == "Exit") exit("Bye bye");
		/* Based on PruneAll by G. Landini: a pruning algorithm, different from the one in ImageJ. Prunes all branches of a skeleton leaving only the closed loops 8-connected
		4 Dec 2003: uses BinaryThin_.class available from https://blog.bham.ac.uk/intellimic/g-landini-software assumes a white object on a black background */
		setBatchMode(true);
		if (blackSkel) run("Invert");
		showStatus("Pruning Skeleton");
		run("BinaryThin ", "kernel_a='0 2 2 0 1 0 0 0 0'  rotations='rotate 45' iterations=&pruneN white");
		if (blackSkel) run("Invert");
	}
	if (hadInvertedLUT)
		run("Invert LUT");
	if (pinEdge) run("Canvas Size...", "width=&imageWidth height=&imageHeight position=Center");
	if (selType >= 0) {
		finalID = getImageID();
		selectImage(orID);
		run("Restore Selection");
		selectImage(finalID);
	}
	setBatchMode("exit & display"); /* Probably not necessary if exiting gracefully but otherwise harmless */
	beep();
	wait(300);
	beep();
	wait(300);
	beep();
	if (report) IJ.log(dFixes + " diagonal fixes and " + sFixes + " trapped square fixes applied");
	call("java.lang.System.gc"); /* force a garbage collection */
	showStatus(macroL + " completed: " + dFixes + " diagonal fixes and " + sFixes + " trapped square fixes applied", "flash green");
}
/*
( 8(|)  ( 8(|)  All ASC Functions    @@@@@:-)  @@@@@:-)
*/
function checkForPlugin(pluginName) {
	/* v161102 changed to true-false
		v180831 some cleanup
		v210429 Expandable array version
		v220510 Looks for both class and jar if no extension is given
		v220818 Mystery issue fixed, no longer requires restoreExit	*/
	pluginCheck = false;
	if (getDirectory("plugins") == "") print("Failure to find any plugins!");
	else {
		pluginDir = getDirectory("plugins");
		if (lastIndexOf(pluginName, ".") == pluginName.length - 1) pluginName = substring(pluginName, 0, pluginName.length - 1);
		pExts = newArray(".jar", ".class");
		knownExt = false;
		for (j = 0; j < lengthOf(pExts); j++)
			if (endsWith(pluginName, pExts[j])) knownExt = true;
		pluginNameO = pluginName;
		for (j = 0; j < lengthOf(pExts) && !pluginCheck; j++) {
			if (!knownExt) pluginName = pluginName + pExts[j];
			if (File.exists(pluginDir + pluginName)) {
				pluginCheck = true;
				showStatus(pluginName + "found in: " + pluginDir);
			} else {
				pluginList = getFileList(pluginDir);
				subFolderList = newArray;
				for (i = 0, subFolderCount = 0; i < lengthOf(pluginList); i++) {
					if (endsWith(pluginList[i], "/")) {
						subFolderList[subFolderCount] = pluginList[i];
						subFolderCount++;
					}
				}
				for (i = 0; i < lengthOf(subFolderList); i++) {
					if (File.exists(pluginDir + subFolderList[i] + "\\" + pluginName)) {
						pluginCheck = true;
						showStatus(pluginName + " found in: " + pluginDir + subFolderList[i]);
						i = lengthOf(subFolderList);
					}
				}
			}
		}
	}
	return pluginCheck;
}

function stripKnownExtensionFromString(string) {
	/*	Note: Do not use on path as it may change the directory names
	v210924: Tries to make sure string stays as string.	v211014: Adds some additional cleanup.	v211025: fixes multiple 'known's issue.	v211101: Added ".Ext_" removal.
	v211104: Restricts cleanup to end of string to reduce risk of corrupting path.	v211112: Tries to fix trapped extension before channel listing. Adds xlsx extension.
	v220615: Tries to fix the fix for the trapped extensions ...	v230504: Protects directory path if included in string. Only removes doubled spaces and lines.
	v230505: Unwanted dupes replaced by unusefulCombos.	v230607: Quick fix for infinite loop on one of while statements.
	v230614: Added AVI.	v230905: Better fix for infinite loop. v230914: Added BMP and "_transp" and rearranged
	*/
	fS = File.separator;
	string = "" + string;
	protectedPathEnd = lastIndexOf(string, fS) + 1;
	if (protectedPathEnd > 0) {
		protectedPath = substring(string, 0, protectedPathEnd);
		string = substring(string, protectedPathEnd);
	}
	unusefulCombos = newArray("-", "_", " ");
	for (i = 0; i < lengthOf(unusefulCombos); i++) {
		for (j = 0; j < lengthOf(unusefulCombos); j++) {
			combo = unusefulCombos[i] + unusefulCombos[j];
			while (indexOf(string, combo) >= 0) string = replace(string, combo, unusefulCombos[i]);
		}
	}
	if (lastIndexOf(string, ".") > 0 || lastIndexOf(string, "_lzw") > 0) {
		knownExts = newArray(".avi", ".csv", ".bmp", ".dsx", ".gif", ".jpg", ".jpeg", ".jp2", ".png", ".tif", ".txt", ".xlsx");
		knownExts = Array.concat(knownExts, knownExts, "_transp", "_lzw");
		kEL = knownExts.length;
		for (i = 0; i < kEL / 2; i++) knownExts[i] = toUpperCase(knownExts[i]);
		chanLabels = newArray(" \(red\)", " \(green\)", " \(blue\)", "\(red\)", "\(green\)", "\(blue\)");
		for (i = 0, k = 0; i < kEL; i++) {
			for (j = 0; j < chanLabels.length; j++) {
				/* Looking for channel-label-trapped extensions */
				iChanLabels = lastIndexOf(string, chanLabels[j]) - 1;
				if (iChanLabels > 0) {
					preChan = substring(string, 0, iChanLabels);
					postChan = substring(string, iChanLabels);
					while (indexOf(preChan, knownExts[i]) > 0) {
						preChan = replace(preChan, knownExts[i], "");
						string = preChan + postChan;
					}
				}
			}
			while (endsWith(string, knownExts[i])) string = "" + substring(string, 0, lastIndexOf(string, knownExts[i]));
		}
	}
	unwantedSuffixes = newArray(" ", "_", "-");
	for (i = 0; i < unwantedSuffixes.length; i++) {
		while (endsWith(string, unwantedSuffixes[i])) string = substring(string, 0, string.length - lengthOf(unwantedSuffixes[i])); /* cleanup previous suffix */
	}
	if (protectedPathEnd > 0) {
		if (!endsWith(protectedPath, fS)) protectedPath += fS;
		string = protectedPath + string;
	}
	return string;
}