From 8f0dae93345b0ab6a1bfe8944897abe2fed9f476 Mon Sep 17 00:00:00 2001
From: Patrice Mascalchi <18047969+pmascalchi@users.noreply.github.com>
Date: Tue, 3 Nov 2020 09:34:30 +0100
Subject: [PATCH] Delete Export-LIF-as-individual-images_1.3.ijm

---
 Export-LIF-as-individual-images_1.3.ijm | 108 ------------------------
 1 file changed, 108 deletions(-)
 delete mode 100644 Export-LIF-as-individual-images_1.3.ijm

diff --git a/Export-LIF-as-individual-images_1.3.ijm b/Export-LIF-as-individual-images_1.3.ijm
deleted file mode 100644
index 3899795..0000000
--- a/Export-LIF-as-individual-images_1.3.ijm
+++ /dev/null
@@ -1,108 +0,0 @@
-// -------------------------------------------------------------------
-// Written by: Patrice Mascalchi
-// Date: 2013
-// Location: Cancer Research Institute, University of Cambridge, UK
-// New Location: Bordeaux Imaging Center, University of Bordeaux-CNRS UMS3420-INSERM US4, France
-// Contact: patrice.mascalchi@gmail.com
-// -------------------------------------------------------------------
-
-// v1.3: - Bug fixed with file separator
-
-requires("1.48a");
-run("Bio-Formats Macro Extensions");
-
-// Dialog window for parameters choice ----------------
-yesno = newArray("no", "yes");
-ftypes = newArray("tif", "jpg", "ics");
-Dialog.create("Settings for all LIF files");
-Dialog.addChoice("Batch process (multiple .LIF files in same folder)", yesno);
-Dialog.addMessage("");
-Dialog.addChoice("for multi-channel images, save merge as RGB? ", yesno);
-Dialog.addChoice("for z-stack images, save maximum projection? ", yesno);
-Dialog.addMessage("");
-Dialog.addChoice("output format: ", ftypes);
-Dialog.addChoice("generate numbers in front of image name: ", yesno, "yes");
-Dialog.show();
-
-batch = Dialog.getChoice;
-merge = Dialog.getChoice;
-maxproj = Dialog.getChoice;
-ftyp = Dialog.getChoice;
-prefix = Dialog.getChoice;
-
-// End of Dialog --------------------------------------
-
-if (batch=="yes") {
-	Mypath = getDirectory("Choose the directory containing .LIF files");
-	Mylist = SortFileList(Mypath, ".lif");
-} else {
-	Mylist = newArray(1);
-	tmppa = File.openDialog("Select .LIF file");
-	if (endsWith(tmppa, ".lif")==0) exit("error while selecting .lif file..."); 
-	Mylist[0] = File.getName(tmppa);
-	Mypath = File.getParent(tmppa) + File.separator;
-}
-setBatchMode(true);
-
-count = 0;
-
-for (i=0; i<Mylist.length; i++) {
-	outdir = Mypath + replace(Mylist[i], ".lif", File.separator);
-	if (!File.exists(outdir)) {
-		File.makeDirectory(outdir);
-	}
-	showProgress(i/(Mylist.length-1));
-	
-	Ext.setGroupFiles("false"); 
-	Ext.setId(Mypath + Mylist[i]);
-	Ext.getSeriesCount(count);
-
-	for (f=1;f<count+1;f++) {
-		Ext.setSeries(f-1);
-		Ext.getSeriesName(sname);
-		proceed = 0;
-		if (indexOf(sname, "TileScan_")==-1) proceed = 1;
-		if (indexOf(sname, "TileScan_") > -1 && indexOf(sname, "Merging") > -1) proceed = 1;
-		if (proceed==1) {
-			print("Processing: "+sname);
-			run("Bio-Formats Importer", "open=[" + Mypath + Mylist[i] +"] autoscale color_mode=Composite view=Hyperstack stack_order=Default series_" + f);
-			getDimensions(wi, he, ch, sl, fr);
-			if (maxproj=="yes" && sl>1) run("Z Project...", "projection=[Max Intensity]");
-			if (merge=="yes" && ch>1) run("Stack to RGB");
-			
-			// Rename images 
-			t = replace(getTitle(),Mylist[i],"");
-			t = substring(t, 3, lengthOf(t));
-			t = replace(t,"/","_");
-			t = replace(t," - ","");
-			if (prefix == "yes") t = IJ.pad(f, 3) +"_"+ t;
-			
-			// Only for multipositions filtering
-			if (indexOf(t, "Pos0") > -1) t = replace(t, "Mark_and_Find_", "");
-			
-			if (ftyp=="tif") saveAs("Tiff", outdir + t + ".tif");
-			if (ftyp=="jpg") saveAs("Jpeg", outdir + t + ".jpg");
-			if (ftyp=="ics") run("Bio-Formats Exporter", "save=["+ outdir + t + ".ids]");
-			
-			run("Close All");
-		}
-	}
-	Ext.close();
-}
-setBatchMode(false);
-print("done!");
-
-// ************************ FUNCTIONS *************************************************
-function SortFileList(path, filter) {		// Sort with endsWith
-	flist = getFileList(path);
-	OutAr = newArray(flist.length);
-	ind = 0;
-	for (f=0; f<flist.length; f++) {
-		//print(flist[f] + " : "+endsWith(flist[f], filter));
-		if (endsWith(flist[f], filter)) {
-			OutAr[ind] = flist[f];
-			ind++;
-		}
-	}
-	return Array.trim(OutAr, ind);
-}