// ---------- Vorbereitung ----------
if (isOpen("Log")) { selectWindow("Log"); run("Close"); }
close("*");

// ---------- 1. BILDER ÖFFNEN ----------
flatPath = File.openDialog("1. Leerbild (Flatfield) öffnen");
open(flatPath);
rename("FLAT_BASE");
run("32-bit");

origPath = File.openDialog("2. Originalbild (fleckig) öffnen");
open(origPath);
origName = getTitle(); 
rename("ORIG_BASE");
run("32-bit");

// ---------- 2. KANÄLE SPLITTEN ----------
selectWindow("FLAT_BASE"); run("Make Composite"); run("Split Channels"); 
selectWindow("ORIG_BASE"); run("Make Composite"); run("Split Channels"); 

// ---------- 3. PARAMETER & DIVISION ----------
gSigma = 600; 
haloProtectionRadius = 15; 

finalNames = newArray(3);
for (c = 1; c <= 3; c++) {
    fK = "C" + c + "-FLAT_BASE";
    oK = "C" + c + "-ORIG_BASE";
    targetName = "Final_C" + c;
    
    selectWindow(fK); run("Add...", "value=1.0");
    imageCalculator("Divide create 32-bit", oK, fK);
    tempDiv = getTitle(); 
    
    selectWindow(tempDiv);
    run("Duplicate...", "title=BG_Model");
    run("Median...", "radius=" + haloProtectionRadius); 
    run("Gaussian Blur...", "sigma=" + gSigma);
    imageCalculator("Divide 32-bit", tempDiv, "BG_Model");
    
    rename(targetName);
    finalNames[c-1] = targetName;
    close("BG_Model"); 
}

// ---------- 4. ZUSAMMENFÜGEN ----------
run("Merge Channels...", "c1=["+finalNames[0]+"] c2=["+finalNames[1]+"] c3=["+finalNames[2]+"] create");
run("RGB Color"); 
rename("FINAL_ADJUSTMENT");

run("Enhance Contrast", "saturated=0.35");

// ---------- 5. MASKE & GLÄTTUNG ----------
run("Duplicate...", "title=MaskenBasis");
run("8-bit"); run("Median...", "radius=3"); 
setThreshold(0, 255); 
run("Threshold..."); 
setOption("BlackBackground", true); 
waitForUser("Threshold", "Präparat ROT markieren. Dann OK.");

run("Create Selection");
if (selectionType() != -1) {
    close("MaskenBasis");
    selectWindow("FINAL_ADJUSTMENT");
    run("Restore Selection");
    run("Make Inverse"); 
    run("Median...", "radius=4"); 
    run("Select None"); 
}

// Threshold-Fenster sofort schließen
if (isOpen("Threshold")) { selectWindow("Threshold"); run("Close"); }

// ---------- 6. SCHRITTWEISE MANUELLE KORREKTUR ----------
selectWindow("FINAL_ADJUSTMENT");

// --- TEIL A: FARBE ---
run("Color Balance...");
waitForUser("Schritt 1: FARBE", "1. Farbe einstellen.\n2. 'APPLY' klicken!\n3. Dann OK.");
if (isOpen("Color Balance")) { selectWindow("Color Balance"); run("Close"); }

// --- TEIL B: HELLIGKEIT & KONTRAST ---
if (isOpen("B&C")) { selectWindow("B&C"); run("Close"); }
run("Brightness/Contrast...");
waitForUser("Schritt 2: HELLIGKEIT", "1. Helligkeit einstellen.\n2. 'APPLY' klicken!\n3. Dann OK.");
if (isOpen("B&C")) { selectWindow("B&C"); run("Close"); }

// ---------- 7. SPEICHERN ----------
dotIndex = lastIndexOf(origName, ".");
baseName = "";
if (dotIndex >= 0) {
    baseName = substring(origName, 0, dotIndex);
} else {
    baseName = origName;
}

finalFileName = baseName + "_FF.tif";
savePath = File.getParent(origPath) + File.separator + finalFileName;

run("Properties...", "channels=1 slices=1 frames=1 unit=pixel pixel_width=1 pixel_height=1 voxel_depth=1");
saveAs("Tiff", savePath); 

// ---------- 8. RADIKALER CLEANUP ----------
// Wir nutzen einen Trick, um alles außer dem Hauptbild zu schließen
close("*"); 

// Log-Fenster schließen (häufigster Fehlerherd)
if (isOpen("Log")) {
    selectWindow("Log");
    run("Close");
}

// Eventuell verwaiste Tool-Fenster schließen
if (isOpen("Threshold")) { selectWindow("Threshold"); run("Close"); }
if (isOpen("B&C")) { selectWindow("B&C"); run("Close"); }
if (isOpen("Color Balance")) { selectWindow("Color Balance"); run("Close"); }

// Nur das Endergebnis öffnen
open(savePath);
run("Select None");

// Ende ohne Log-Eintrag, um das Log-Fenster nicht wieder zu triggern