From 3d850913cdc06925901614cb990facd7a7aa6d12 Mon Sep 17 00:00:00 2001
From: Patrice Mascalchi <18047969+pmascalchi@users.noreply.github.com>
Date: Tue, 3 Nov 2020 09:34:06 +0100
Subject: [PATCH] Add files via upload

---
 Export-as-individual-images_1.6.ijm | 156 ++++++++++++++++++++++++++++
 1 file changed, 156 insertions(+)
 create mode 100644 Export-as-individual-images_1.6.ijm

diff --git a/Export-as-individual-images_1.6.ijm b/Export-as-individual-images_1.6.ijm
new file mode 100644
index 0000000..ad3197b
--- /dev/null
+++ b/Export-as-individual-images_1.6.ijm
@@ -0,0 +1,156 @@
+// -------------------------------------------------------------------
+// Written by: Patrice Mascalchi
+// Date: 2019
+// Location: Cancer Research Institute, University of Cambridge, UK
+// New Location: DRVision Technologies LLC, Bordeaux, France
+// Contact: p.mascalchi@gmail.com
+// -------------------------------------------------------------------
+
+/*
+	Macro to export multi-image (i.e. multi FOV) files such as some .lif, .nd2, .czi, etc.
+	By default, all images embedded in the same input file will be output in an individual subfolder
+*/ 
+
+// v1.3: - Bug fixed with file separator
+// v1.4: - Includes comparison of names to skip multi-scale/pyramidal images
+// v1.5: - For pyramidal images, compares pixel sizes to detect change in field of view
+// v1.6: - Adding a file extension filter for the input + fixed bug with output image naming
+//		 - Added option to save all in the same output folder
+
+requires("1.48a");
+run("Bio-Formats Macro Extensions");
+
+// Dialog window for parameters choice ----------------
+yesno = newArray("no", "yes");
+ftypes = newArray("tif", "jpg", "ics (better compatibility with Aivia)");
+Dialog.create("Settings for all files");
+Dialog.addChoice("Batch process (multiple files in same folder)", yesno);
+Dialog.addString("File extension filter: (leave blank to disable)", ".tif");
+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, "no");
+Dialog.addChoice("Output in a subfolder for each input file", yesno, "yes");
+Dialog.show();
+
+batch = Dialog.getChoice;
+inputType = Dialog.getString;
+merge = Dialog.getChoice;
+maxproj = Dialog.getChoice;
+ftyp = Dialog.getChoice;
+prefix = Dialog.getChoice;
+indivfolder = Dialog.getChoice;
+
+// End of Dialog --------------------------------------
+
+if (batch=="yes") {
+	Mypath = getDirectory("Choose the directory containing files to convert");
+	Mylist = SortFileList(Mypath, inputType);
+} else {
+	Mylist = newArray(1);
+	tmppa = File.openDialog("Select file to convert");
+	if (endsWith(tmppa, inputType)==0) exit("error while selecting "+inputType+" file..."); 
+	Mylist[0] = File.getName(tmppa);
+	Mypath = File.getParent(tmppa);
+	if (!endsWith(Mypath, File.separator)) Mypath = Mypath + File.separator;
+	print(Mypath);
+}
+setBatchMode(true);
+
+count = 0;
+
+for (i=0; i<Mylist.length; i++) {
+	// Setting output folder
+	outdir = Mypath + "converted" + File.separator;
+	if (indivfolder == "yes") outdir = Mypath + replace(Mylist[i], ".", "_") + File.separator;		// TODO
+	if (!File.exists(outdir)) {
+		File.makeDirectory(outdir);
+	}
+	if (!File.exists(outdir)) exit("Cannot create export folder\n" + outdir);
+	
+	showProgress(i/(Mylist.length-1));
+	
+	Ext.setGroupFiles("false"); 
+	Ext.setId(Mypath + Mylist[i]);
+	Ext.getSeriesCount(count);
+	tmpName = "";
+	tmpSizeX = 0;
+	tmpI = 0;
+	pyramidal = false;
+
+	for (f=1;f<count+1;f++) {
+		Ext.setSeries(f-1);
+		Ext.getSeriesName(sname);
+		proceed = 1;
+		if (indexOf(sname, "TileScan_") > -1) proceed = 0;
+		if (indexOf(sname, "TileScan_") > -1 && indexOf(sname, "Merging") > -1) proceed = 1;
+		
+		// pyramidal detection
+		tmpInd = indexOf(sname, "#");
+		snamePart = sname;
+		if (tmpInd > -1) snamePart = substring(sname, 0, tmpInd-1);
+		
+		// pixel size detection for pyramidal comparison
+		Ext.getSizeX(sizeX);
+
+		print("*"+ snamePart +"* // *"+ tmpName +"*,   sizeX="+ sizeX +" // "+tmpSizeX);
+		if (snamePart == tmpName) {
+			if (sizeX < tmpSizeX) {
+				proceed = 0;
+			} else {
+				tmpI++;
+				pyramidal = true;
+			}
+		}
+		tmpSizeX = sizeX;
+		tmpName = snamePart;
+		
+		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 = getTitle();
+			if (lengthOf(t) > lengthOf(Mylist[i])) t = replace(t, Mylist[i], "");
+			t = substring(t, 3, lengthOf(t));
+			t = replace(t,"/","_");
+			t = replace(t," - ","");
+			t = replace(t, " #", "series");
+			if (pyramidal) t = t + "_" + tmpI;
+			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 (better compatibility with Aivia)") 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);
+}
+