macro "Split to Strips" {
/* 
	A simple macro to split a large file into smaller blocks
	v220728: 1st version  f1-f2: updated stripKnownExtensionFromString function.
	v230803: Replaced get for 1.54g10 f1: 	function pathOverwriteCheck fix
	v231128: Removed "!" from showStatus for stability. F1 updated function pathOverwriteCheck
*/
	macroL = "Split_To_Strips_v231128-f1.ijm";
	t = stripKnownExtensionFromString(getTitle());
	defPath = getDirectory("image");
	if (defPath=="") defPath = getDirectory("file");
	iMMagickPath = findAppPath("ImageMagick","magick.exe","not found");
	if (File.exists(iMMagickPath)) iMMagick = true;
	else iMMagick = false;
	getDimensions(imageWidth, imageHeight, channels, slices, frames);
	selEType = selectionType;
	if (selEType>=0) {
		getSelectionBounds(selEX, selEY, selEWidth, selEHeight);
		if ((selEWidth + selEHeight)<6) selEType=-1; /* Ignore junk selections that are suspiciously small */
		if (selEType==5) getSelectionCoordinates(selLX, selLY);
		leftLimit = selEX;
		rightLimit = selEX + selEWidth;
		topLimit = selEY;
		bottomLimit = selEY + selEHeight;
		maxHeight = selEHeight;
	}
	else {
		leftLimit = 0;
		rightLimit = imageWidth;
		topLimit = selEY;
		bottomLimit = imageHeight;
		maxHeight = imageHeight;
	}
	run("Select None");
	activeImage = getTitle();
	Dialog.create("Strip Parameters: " + macroL);
		Dialog.addNumber("Left coordinate limit", leftLimit, 0, 10, "pixels");
		Dialog.addNumber("Right coordinate limit", rightLimit, 0, 10, "pixels");
		Dialog.addNumber("Top coordinate limit", topLimit, 0, 10, "pixels");
		Dialog.addNumber("Bottom coordinate limit", bottomLimit, 0, 10, "pixels");
		Dialog.addNumber("Block width", imageWidth/10, 0, 10, "pixels");
		Dialog.addNumber("Block height", maxHeight, 0, 10, "pixels");
		Dialog.addNumber("Overlap", 0, 0, 10, "pixels");
		Dialog.addDirectory("Export directory", defPath);
		Dialog.setInsets(0,68,10);
		Dialog.addMessage("Export directory above: " + defPath);
		Dialog.addString("Filename \(prefix, counter and '_lzw.tif' will be added\)", t,30);
		if (iMMagick) Dialog.addString("ImageMagick settings", " -compress lzw ",30);
	Dialog.show();
		leftLimit = Dialog.getNumber;
		rightLimit = Dialog.getNumber;
		topLimit = Dialog.getNumber;
		bottomLimit = Dialog.getNumber;
		blockWidth = Dialog.getNumber;
		blockHeight = Dialog.getNumber;
		overlap = Dialog.getNumber;
		newPath = Dialog.getString();
		prefix = Dialog.getString();
		if (iMMagick) tiffSettings = Dialog.getString();
	totalWidth	 = abs(rightLimit-leftLimit);
	blockPixelCount = blockWidth * blockHeight;
	rows = 1; columns = 1;
	if (blockHeight<maxHeight) rows = round(maxHeight/(blockHeight-overlap));
	if (blockWidth<totalWidth) columns = round(totalWidth/(blockWidth-overlap));
	fileSaves = newArray();
	for(i=0,yStart=topLimit;i<rows;i++){
		if (yStart + blockHeight > bottomLimit) blockHeight = bottomLimit-yStart;
		for(j=0,xStart=leftLimit;j<columns;j++){
			if (xStart+blockWidth>rightLimit) blockWidth = rightLimit-xStart;
			makeRectangle(xStart, yStart, blockWidth, blockHeight);
			newName = prefix+"_C"+j+1;
			if(rows>1) newName += "R" + i+1;
			run("Duplicate...", newName);
			saveTIFFPath = newPath + newName  + "_lzw.tif";
			showStatus("Saving uncompressed TIFF using ImageJ to be used by IM");
			saveTIFFPath = pathOverwriteCheck(saveTIFFPath);
			saveAs("TIFF",saveTIFFPath);
			fileSaves = Array.concat(fileSaves,saveTIFFPath);
			xStart += blockWidth - overlap;
			close();
		}
		if (rows>1) yStart +=  blockHeight - overlap;
	}
	if(selEType==0) makeRectangle(selEX, selEY, selEWidth, selEHeight);
	else if(selEType==1) makeOval(selEX, selEY, selEWidth, selEHeight);
	savedFiles = lengthOf(fileSaves);
	if (savedFiles<1) exit("Fail: no saved files");
	delayTime = 500 + 	blockPixelCount/4E4;
	wait(delayTime);
	if (iMMagick) {
		for (i=0; i<savedFiles; i++){
			execString = "\"" + iMMagickPath + "\" " + "\"" + fileSaves[i] + "\" " +  tiffSettings + " \"" + fileSaves[i] + "\"";
			showStatus("Re-saving using ImageMagick: " + execString);
			exec(execString);
			// print(execString);
			if(!File.exists(fileSaves[i]))	print ("Failed to save:\n",fileSaves[i],"\nFailed command line: \n" + fileSaves[i]);
			else {
				// print ("Saved ",savePath);
				call("ij.Prefs.set", "asc.lastsaved.compressedtiff.path", fileSaves[i]);
				lzwSaved = true;
			}
		}
	}
	beep();beep();beep();
	call("java.lang.System.gc");
	showStatus("Strip Export Completed");
}
	/*
		( 8(|)  ( 8(|)  Functions	@@@@@:-)	@@@@@:-)
	*/
	function findAppPath(appName,appEx,defaultPath) {
		/* v210921 1st version: appName is assumed to be the app folder name, appEx is the executable, default is the default return value
			v211018: assumes specific executable path stored in prefs Prints message rather than exits when app not found
			v211213: fixed defaultPath error
			v211214: Adds additional location as packaged within a Fiji/IJ distribution
			v220121: Changed fS line
			v230803: Replaced getDir with getDirectory for ImageJ 1.54g10 
		*/
		functionL = "findAppPath_v230803";
		fS = File.separator;
		ijPath = getDirectory("imagej");
		appsPath = substring(ijPath,0,lengthOf(ijPath)-1);
		appsPath = substring(appsPath,0,lastIndexOf(appsPath,fS));
		appFound = false;
		prefsName = "asc.external.paths." + toLowerCase(appName) + "." + appEx;
		appPath = call("ij.Prefs.get", prefsName, defaultPath);
		appLoc = ""+fS+appName+fS+appEx;
		cProg = "C:"+fS+"Program Files";		
		defAppPaths = newArray(cProg+fS+"Utilities"+appLoc,cProg+" \(x86\)"+fS+"Utilities"+appLoc,cProg+appLoc,cProg+" \(x86\)"+appLoc,appsPath+appLoc,ijPath+"Apps"+appLoc);
		if (!File.exists(appPath)) { 
			for(i=0;i<lengthOf(defAppPaths);i++){
				if (File.exists(defAppPaths[i])){
					appPath = defAppPaths[i];
					call("ij.Prefs.set", prefsName, appPath);
					appFound = true;
					i = lengthOf(defAppPaths);
				}
			}
		}
		else appFound = true;
		if (appFound==false){
			Dialog.create("Find location of " + appEx + " version: " + functionL);
			Dialog.addMessage(appEx + " can provide additional functionality to this macro\nbut has not been found in the expected locations");
			Dialog.addCheckbox("Get me out of here, I don't want to try and find " + appName + ", whatever that is",false);
			Dialog.addFile("Locate " + appEx + ":","C:"+fS+"Program Files");
			Dialog.addMessage("If found, the location will be saved in prefs for future use:\n" + prefsName);
			Dialog.show;
			if (Dialog.getCheckbox) appFound = false;
			else {
				appPath = Dialog.getString();
				if (!File.exists(appPath)) print(appEx + " not found");
				else {
					call("ij.Prefs.set", prefsName, appPath);
					appFound = true;
				}
			}
		}
		if (appFound) return appPath;
		else return defaultPath;
	}
	function pathOverwriteCheck(path){
		/* v220615: 1st version reworked 061622
			v230811: Fixed to avoid unnecessary loop
			v240118: Fixed path not being updated
			*/
		if (File.exists(path)) saveFlag = false;
		else saveFlag = true;
		while(saveFlag==false){
			newPath = getString("Overwite existing file \(leave\) or rename:", path);
			if (newPath==path || !File.exists(newPath)) saveFlag = true;
			path = newPath;
		}
		return path;
	}
	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;
	}