""" MicroscopeXport v2.3 Owner: TMG Yenilik v2.3: - Batch mode: birden fazla ND2/CZI dosyası seç - Tek dosyada LUT ayarla + önizle, sonra tüm batch'e uygula - Her dosya ayrı klasöre kaydedilir - Klasör adında hangi channel renkleri varsa onlar yazar - Canlı preview (LUT kaydırınca anlık güncelleme) - Merged PNG + TIFF TRIAL: 10 dosya, XY pozisyon kilitli FULL ($9.99): Sınırsız, XY pozisyon açık Kurulum: pip install nd2 czifile numpy tifffile Pillow EXE: pyinstaller --onefile --windowed --hidden-import=nd2 --hidden-import=czifile --hidden-import=tifffile --hidden-import=PIL biosplit_app.py """ import tkinter as tk from tkinter import ttk, filedialog, messagebox import threading, os, json, hashlib, sys try: import nd2, numpy as np, tifffile from PIL import Image, ImageTk DEPS_OK = True except ImportError as _e: DEPS_OK = False; _ERR = str(_e) try: import czifile; DEPS_CZI = True except ImportError: DEPS_CZI = False APP = "MicroscopeXport" OWNER = "TMG" VER = "2.3" LIMIT = 10 SALT = "biosplit_tugba_secret_2024" PRICE = "$9.99" PREVIEW_SIZE = 120 BG = "#1a1a2e"; SURF = "#12122a"; CARD = "#16162a" ACC = "#6c63ff"; ACC2 = "#00e5cc"; TEXT = "#ddddf5" MUTED = "#7070a0"; RED = "#ff6060"; GREEN = "#22dd88" COLORS = { # ── En yaygın 3 kanal ────────────────────────────────────── "DAPI (405nm)": (0, 0, 255), # mavi "GFP (488nm)": (0, 255, 0), # yeşil "AF594 (594nm)": (255, 60, 0), # kırmızı-turuncu # ── Yaygın ──────────────────────────────────────────────── "mCherry (561nm)": (255, 30, 30), # parlak kırmızı "CY3 (550nm)": (255, 165, 0), # turuncu "CY5 (647nm)": (255, 0, 200), # mor-kırmızı "TRITC (555nm)": (255, 80, 0), # kırmızı-turuncu "FITC (490nm)": (0, 230, 50), # yeşil "CFP (440nm)": (0, 255, 255), # cyan "YFP (514nm)": (255, 255, 0), # sarı "RFP (555nm)": (255, 0, 0), # kırmızı # ── Alexa Fluor serisi ───────────────────────────────────── "AF488 (488nm)": (0, 220, 80), # yeşil "AF555 (555nm)": (255, 140, 0), # turuncu "AF647 (647nm)": (220, 0, 180), # mor "AF750 (750nm)": (160, 0, 255), # koyu mor # ── Az kullanılan ───────────────────────────────────────── "CY2 (492nm)": (0, 255, 100), # yeşilimsi "CY3.5 (581nm)": (255, 100, 0), # koyu turuncu "CY5.5 (675nm)": (200, 0, 255), # mor "CY7 (743nm)": (140, 0, 255), # koyu mor "DAPI2 (405nm)": (100, 100, 255), # ikinci mavi "Custom": (255, 255, 255), # beyaz } # ── Lisans ──────────────────────────────────────────────────────────────────── def _spath(): d = os.path.join(os.environ.get("LOCALAPPDATA") or os.path.expanduser("~"), "MicroscopeXport") os.makedirs(d, exist_ok=True); return os.path.join(d, "state.json") def _load_state(): try: with open(_spath()) as f: return json.load(f) except: return {"count": 0, "licensed": False} def _save_state(s): with open(_spath(), "w") as f: json.dump(s, f) def make_key(email): h = hashlib.sha256(f"{email.lower().strip()}||{SALT}".encode()).hexdigest().upper() return "-".join(h[i:i+4] for i in range(0, 16, 4)) def verify_key(email, k): return k.strip().upper().replace(" ", "") == make_key(email).replace(" ", "") # ── Görüntü işleme ───────────────────────────────────────────────────────────── def apply_lut(arr, lo, hi, gm): a = arr.astype(np.float32); hi = max(hi, lo + 1) a = np.clip((a - lo) / (hi - lo), 0, 1) if gm != 1.0: a = np.power(a, 1.0 / gm) return (a * 255).astype(np.uint8) def colorize(g, rgb): h, w = g.shape; o = np.zeros((h, w, 3), dtype=np.uint8); f = g.astype(np.float32) for i, c in enumerate(rgb): o[:, :, i] = (f * c / 255).astype(np.uint8) return o def colorize_16bit(arr16, lo, hi, gm, rgb): """16-bit array'i LUT uygulayarak 16-bit renkli TIFF'e çevirir.""" a = arr16.astype(np.float32) hi = max(hi, lo + 1) a = np.clip((a - lo) / (hi - lo), 0, 1) if gm != 1.0: a = np.power(a, 1.0 / gm) a = (a * 65535).astype(np.uint16) h, w = a.shape o = np.zeros((h, w, 3), dtype=np.uint16) for i, c in enumerate(rgb): o[:, :, i] = (a.astype(np.float32) * c / 255).astype(np.uint16) return o def arr16_normalize(arr16, lo, hi, gm): """16-bit array'i LUT ile normalize eder, 16-bit grayscale döner.""" a = arr16.astype(np.float32) hi = max(hi, lo + 1) a = np.clip((a - lo) / (hi - lo), 0, 1) if gm != 1.0: a = np.power(a, 1.0 / gm) return (a * 65535).astype(np.uint16) def to_2d(a): while a.ndim > 2: a = a.max(axis=0) return a def make_thumb(arr2d, lo, hi, gm, rgb, size=PREVIEW_SIZE): g = apply_lut(arr2d, lo, hi, gm) img = Image.fromarray(colorize(g, rgb)) img.thumbnail((size, size), Image.LANCZOS) bg = Image.new("RGB", (size, size), (8, 8, 18)) bg.paste(img, ((size - img.width)//2, (size - img.height)//2)) return bg def make_merged_thumb(ch_arrays, luts, size=PREVIEW_SIZE): merged = None for i, arr in enumerate(ch_arrays): lut = luts[i] if i < len(luts) else None if lut and not lut["enabled"].get(): continue lo = lut["min"].get() if lut else 0 hi = lut["max"].get() if lut else 65535 gm = lut["gamma"].get() if lut else 1.0 cn = lut["color"].get() if lut else list(COLORS.keys())[i % len(COLORS)] g = apply_lut(arr, lo, hi, gm) c = colorize(g, COLORS.get(cn, (255,255,255))) merged = c.astype(np.float32) if merged is None else np.clip(merged + c.astype(np.float32), 0, 255) if merged is None: return Image.new("RGB", (size, size), (8, 8, 18)) img = Image.fromarray(merged.astype(np.uint8)) img.thumbnail((size, size), Image.LANCZOS) bg = Image.new("RGB", (size, size), (8, 8, 18)) bg.paste(img, ((size - img.width)//2, (size - img.height)//2)) return bg def read_czi(path): if not DEPS_CZI: raise ImportError("pip install czifile") with czifile.CziFile(path) as czi: data = czi.asarray().squeeze() axes = [a for a in czi.axes if a not in ('B','0')] sh = data.shape sizes = {a: s for a, s in zip(axes, sh) if len(axes) == len(sh)} if not sizes: for a, s in zip(czi.axes, czi.shape): if a not in ('B','0'): sizes[a] = s ch = [] try: import xml.etree.ElementTree as ET root = ET.fromstring(czi.metadata()) for c in root.iter("Channel"): n = c.get("Name") or c.findtext("Name") or "" if n: ch.append(n) except: pass return data, sizes, ch def auto_detect_color(ch_name: str) -> str: """ Channel isminden veya dalga boyundan otomatik renk profili seç. Önce emission dalga boyu sayısını arar, sonra isim eşleşmesi dener. """ import re name_upper = ch_name.upper().replace(" ", "").replace("-", "").replace("_", "") # Dalga boyu bazlı eşleştirme — sayı varsa önce bunu dene wavelength_map = [ ((340, 425), "DAPI (405nm)"), ((426, 465), "CFP (440nm)"), ((466, 515), "GFP (488nm)"), ((516, 535), "YFP (514nm)"), ((536, 575), "CY3 (550nm)"), ((576, 610), "AF594 (594nm)"), ((611, 645), "mCherry (561nm)"), ((646, 680), "CY5 (647nm)"), ((681, 725), "CY5.5 (675nm)"), ((726, 800), "CY7 (743nm)"), ] nums = re.findall(r'\d+', ch_name) for num_str in nums: num = int(num_str) if 340 <= num <= 800: for (lo, hi), color in wavelength_map: if lo <= num <= hi: return color # İsim bazlı eşleştirme name_map = [ (["DAPI", "HOECHST", "DRAQ5"], "DAPI (405nm)"), (["GFP", "EGFP", "FITC", "AF488"], "GFP (488nm)"), (["YFP", "EYFP", "VENUS"], "YFP (514nm)"), (["CFP", "ECFP", "CERULEAN"], "CFP (440nm)"), (["MCHERRY", "CHERRY", "DSRED", "MRFP"], "mCherry (561nm)"), (["RFP", "RED"], "RFP (555nm)"), (["CY3", "TRITC", "AF555"], "CY3 (550nm)"), (["AF594", "TEXASRED"], "AF594 (594nm)"), (["CY5", "AF647"], "CY5 (647nm)"), (["CY55", "CY5.5", "AF680"], "CY5.5 (675nm)"), (["CY7", "AF750"], "CY7 (743nm)"), (["CY2"], "CY2 (492nm)"), (["BF", "BRIGHTFIELD", "DIC", "TRANS", "PH", "PHASE"], "Custom"), ] for keywords, color in name_map: for kw in keywords: if kw in name_upper: return color return "" # Tespit edilemedi — çağıran sıraya göre atar def load_first_pos_channels(path): """Dosyadan ilk pozisyonun tüm channel 2D array'lerini döner.""" ext = os.path.splitext(path)[1].lower() try: if ext == ".nd2": f = nd2.ND2File(path); data = f.asarray(); sz = dict(f.sizes); f.close() print(f"[ND2] sizes={sz} data.shape={data.shape}") ao = list(sz.keys()); pk = "P" if "P" in sz else "M" nch = sz.get("C", 1) if pk in ao and sz.get(pk, 1) > 1: data = np.take(data, 0, axis=ao.index(pk)); ao = [k for k in ao if k != pk] if "T" in ao: data = data.max(axis=ao.index("T")); ao = [k for k in ao if k != "T"] else: data, sz, _ = read_czi(path) ao = [k for k in ("T","S","M","Z","C","Y","X") if k in sz] pk = "S" if "S" in sz else "M"; nch = sz.get("C", 1) if pk in ao and sz.get(pk, 1) > 1: data = np.take(data, 0, axis=ao.index(pk)); ao = [k for k in ao if k != pk] if "T" in ao: data = data.max(axis=ao.index("T")); ao = [k for k in ao if k != "T"] ci = ao.index("C") if "C" in ao else None result = [] for i in range(nch): ch = np.take(data, i, axis=ci) if ci is not None else data ch2d = to_2d(ch) print(f"[CH{i+1}] before to_2d={ch.shape} after={ch2d.shape}") result.append(ch2d) return result except Exception as e: print(f"[LOAD] {e}"); return [] # ── Ana Uygulama ─────────────────────────────────────────────────────────────── class App(tk.Tk): def __init__(self): super().__init__() self.title(f"{APP} v{VER}"); self.geometry("1280x860") self.configure(bg=BG); self.resizable(True, True) self.state = _load_state() self.odir = tk.StringVar() self.do_pos = tk.BooleanVar(value=False) self.do_ch = tk.BooleanVar(value=True) self.do_mpng = tk.BooleanVar(value=False) self.do_mtif = tk.BooleanVar(value=True) self.do_sub = tk.BooleanVar(value=True) self.do_tif = tk.BooleanVar(value=True) # TIFF — varsayılan açık self.do_png = tk.BooleanVar(value=False) # PNG — varsayılan kapalı self.do_jpg = tk.BooleanVar(value=False) # JPG — varsayılan kapalı self.do_16bit= tk.BooleanVar(value=False) # 16-bit renkli TIFF self.upscale = tk.StringVar(value="1x") self.status = tk.StringVar(value="Add files to batch list…") self.prog = tk.DoubleVar(value=0) # Batch listesi self.batch_files = [] # [(path, label), ...] self.preview_idx = 0 # hangi dosya önizleniyor # LUT state self.luts = [] self.nch = 0 self._ch_2d = [] self._build_ui() self._refresh_banner() # ── UI ──────────────────────────────────────────────────────────────────── def _build_ui(self): s = ttk.Style(self); s.theme_use("clam") for n, bg, fg, fo in [ ("TFrame", BG, TEXT, ("Segoe UI",10)), ("TLabel", BG, TEXT, ("Segoe UI",10)), ("M.TLabel", BG, MUTED, ("Segoe UI",9)), ("H.TLabel", BG, ACC, ("Segoe UI",12,"bold")), ("TButton", None, None, ("Segoe UI",10)), ("TCheckbutton", BG, TEXT, ("Segoe UI",10)), ]: kw = {"font": fo} if bg: kw["background"] = bg if fg: kw["foreground"] = fg s.configure(n, **kw) s.configure("TButton", padding=5) s.configure("TCheckbutton", selectcolor=SURF) s.configure("TProgressbar", troughcolor=SURF, background=ACC, thickness=7) # Başlık hdr = ttk.Frame(self, padding=(16,10,16,6)); hdr.pack(fill="x") ttk.Label(hdr, text=APP, style="H.TLabel").pack(side="left") ttk.Label(hdr, text=f" v{VER} • Nikon ND2 + Zeiss CZI • Batch Analysis", style="M.TLabel").pack(side="left", padx=8) ttk.Label(hdr, text=f"© {OWNER}", style="M.TLabel").pack(side="right") tk.Frame(self, bg="#2a2a4a", height=1).pack(fill="x") # Banner self.bframe = tk.Frame(self, pady=6); self.bframe.pack(fill="x") self.blabel = tk.Label(self.bframe, text="", font=("Segoe UI",9,"bold"), anchor="w", padx=14) self.blabel.pack(side="left") self.bbtn = tk.Button(self.bframe, text="Get License / Buy →", bg=ACC, fg="#fff", font=("Segoe UI",9,"bold"), bd=0, padx=10, pady=2, cursor="hand2", command=self._lic_dlg) self.bbtn.pack(side="right", padx=14) # Output klasörü of = ttk.Frame(self, padding=(16,6)); of.pack(fill="x") ttk.Label(of, text="Output Folder:").grid(row=0, column=0, sticky="w", padx=(0,6)) ttk.Entry(of, textvariable=self.odir, width=52).grid(row=0, column=1, sticky="ew") ttk.Button(of, text="Browse", command=self._bout).grid(row=0, column=2, padx=6) of.columnconfigure(1, weight=1) # Seçenekler opt = ttk.Frame(self, padding=(16,4)); opt.pack(fill="x") row = ttk.Frame(opt); row.pack(fill="x") self.pos_cb = ttk.Checkbutton(row, text="XY Position Split 🔒 (Full)", variable=self.do_pos, command=self._guard) self.pos_cb.pack(side="left", padx=(0,12)) ttk.Checkbutton(row, text="Subfolders", variable=self.do_sub).pack(side="left", padx=(0,12)) ttk.Checkbutton(row, text="Channel Files", variable=self.do_ch).pack(side="left", padx=(0,12)) ttk.Checkbutton(row, text="Merged", variable=self.do_mtif).pack(side="left", padx=(0,12)) # Format seçimi row2 = ttk.Frame(opt); row2.pack(fill="x", pady=(4,0)) ttk.Label(row2, text="Output Format:", style="M.TLabel").pack(side="left", padx=(0,8)) ttk.Checkbutton(row2, text="TIFF (8-bit)", variable=self.do_tif).pack(side="left", padx=(0,10)) ttk.Checkbutton(row2, text="TIFF (16-bit color)", variable=self.do_16bit).pack(side="left", padx=(0,10)) ttk.Checkbutton(row2, text="PNG", variable=self.do_png).pack(side="left", padx=(0,10)) ttk.Checkbutton(row2, text="JPG", variable=self.do_jpg).pack(side="left", padx=(0,20)) tk.Frame(self, bg="#2a2a4a", height=1).pack(fill="x", padx=16, pady=3) # 2 sütunlu ana alan: sol=batch, sağ=LUT+preview inline main = ttk.Frame(self); main.pack(fill="both", expand=True, padx=16, pady=4) main.columnconfigure(0, weight=1) # batch listesi main.columnconfigure(1, weight=3) # LUT + inline preview main.rowconfigure(0, weight=1) # SOL: Batch listesi bl = ttk.Frame(main); bl.grid(row=0, column=0, sticky="nsew", padx=(0,8)) hf = ttk.Frame(bl); hf.pack(fill="x") ttk.Label(hf, text="Batch Files", style="H.TLabel").pack(side="left") ttk.Button(hf, text="+ Files", command=self._add_files).pack(side="right") ttk.Button(hf, text="+ Folder", command=self._add_folder).pack(side="right", padx=3) ttk.Button(hf, text="✕", command=self._remove_file).pack(side="right", padx=3) self.batch_lb = tk.Listbox(bl, bg=SURF, fg=TEXT, selectbackground=ACC, selectforeground="#fff", font=("Segoe UI",9), activestyle="none", relief="flat", borderwidth=0) self.batch_lb.pack(fill="both", expand=True, pady=(4,0)) self.batch_lb.bind("<>", self._on_batch_select) self.file_info = tk.Label(bl, text="", bg=SURF, fg=ACC2, font=("Segoe UI",8), anchor="w", padx=4, pady=3) self.file_info.pack(fill="x") # SAĞ: LUT paneli (preview her channel'ın yanında inline) lp = ttk.Frame(main); lp.grid(row=0, column=1, sticky="nsew") lh = ttk.Frame(lp); lh.pack(fill="x") ttk.Label(lh, text="Channel LUT Settings", style="H.TLabel").pack(side="left") ttk.Button(lh, text="↓ Apply to All Files", command=self._apply_lut_to_all).pack(side="right") cv = tk.Canvas(lp, bg=SURF, highlightthickness=0) sb = ttk.Scrollbar(lp, orient="vertical", command=cv.yview) self.li = ttk.Frame(cv) self.li.bind("", lambda e: cv.configure(scrollregion=cv.bbox("all"))) cv.create_window((0,0), window=self.li, anchor="nw") cv.configure(yscrollcommand=sb.set) cv.pack(side="left", fill="both", expand=True); sb.pack(side="right", fill="y") # Preview frame (LUT panelinin içinde, self.li'ye eklenecek) # Her channel için _build_luts_and_preview'da preview label oluşturulacak # Alt bar bot = ttk.Frame(self, padding=(16,6)); bot.pack(fill="x", side="bottom") ttk.Button(bot, text="▶ Process All Files", command=self._start).pack(side="left", ipadx=16, ipady=3) ttk.Button(bot, text="▶ Process Selected", command=self._start_selected).pack(side="left", padx=8, ipadx=8, ipady=3) tk.Frame(self, bg="#2a2a4a", height=1).pack(fill="x", side="bottom") pb = ttk.Frame(self, padding=(16,4)); pb.pack(fill="x", side="bottom") ttk.Progressbar(pb, variable=self.prog, maximum=100, style="TProgressbar", length=440).pack(side="left", padx=(0,10)) ttk.Label(pb, textvariable=self.status, style="M.TLabel").pack(side="left") # ── Banner ──────────────────────────────────────────────────────────────── def _refresh_banner(self): lic = self.state.get("licensed", False) if lic: em = self.state.get("email","") self.bframe.config(bg="#0a2a18") self.blabel.config(bg="#0a2a18", fg=GREEN, text=f"✓ Full Version — {em} | Unlimited + XY Position active") self.bbtn.pack_forget() self.pos_cb.config(text="XY Position Split") else: left = max(0, LIMIT - self.state.get("count",0)) self.bframe.config(bg="#2a0a0a") self.blabel.config(bg="#2a0a0a", fg=RED, text=f"⚠ Trial — {left}/{LIMIT} files remaining | XY locked | Full: {PRICE}") self.bbtn.pack(side="right", padx=14) def _guard(self): if not self.state.get("licensed") and self.do_pos.get(): self.do_pos.set(False) messagebox.showinfo("Full Version Required", f"XY Position splitting requires the full version.\n{PRICE}") # ── Lisans ──────────────────────────────────────────────────────────────── def _lic_dlg(self): w = tk.Toplevel(self); w.title("License Activation") w.geometry("480x390"); w.configure(bg=BG); w.grab_set(); w.resizable(False,False) tk.Label(w, text=f"🔬 {APP} — License", bg=BG, fg=ACC, font=("Segoe UI",13,"bold")).pack(pady=(22,4)) tk.Label(w, text=f"Full version: {PRICE} • Unlimited • XY Position", bg=BG, fg=TEXT, font=("Segoe UI",10)).pack() tk.Frame(w, bg="#2a2a4a", height=1).pack(fill="x", padx=22, pady=12) tk.Label(w, text="➜ microscopexport.gumroad.com/l/qghmob", bg=BG, fg=ACC2, font=("Segoe UI",10,"bold")).pack(anchor="w", padx=26, pady=(0,12)) tk.Label(w, text="Your purchase email:", bg=BG, fg=TEXT, font=("Segoe UI",9)).pack(anchor="w", padx=26) ev = tk.StringVar() tk.Entry(w, textvariable=ev, bg=CARD, fg="#fff", insertbackground="white", font=("Segoe UI",11), bd=0).pack(padx=26, pady=(4,10), ipady=5, fill="x") tk.Label(w, text="License Key:", bg=BG, fg=TEXT, font=("Segoe UI",9)).pack(anchor="w", padx=26) kv = tk.StringVar() ke = tk.Entry(w, textvariable=kv, bg=CARD, fg="#fff", insertbackground="white", font=("Courier New",12), bd=0, justify="center") ke.pack(padx=26, pady=(4,0), ipady=6, fill="x"); ke.focus() msg = tk.Label(w, text="", bg=BG, fg=RED, font=("Segoe UI",9)); msg.pack(pady=6) def act(): em = ev.get().strip().lower(); k = kv.get().strip() if not em or "@" not in em: msg.config(fg=RED, text="✗ Enter a valid email."); return if verify_key(em, k): self.state.update({"licensed":True,"license_key":k,"email":em}) _save_state(self.state); self._refresh_banner() msg.config(fg=GREEN, text="✓ Activated!") self.after(1800, w.destroy) else: msg.config(fg=RED, text="✗ Key does not match this email.") tk.Button(w, text=" Activate ", bg=ACC, fg="#fff", font=("Segoe UI",11,"bold"), bd=0, padx=20, pady=7, cursor="hand2", command=act).pack(pady=(0,4)) # ── Batch yönetimi ──────────────────────────────────────────────────────── def _add_files(self): paths = filedialog.askopenfilenames( filetypes=[("Microscopy","*.nd2 *.czi"),("ND2","*.nd2"),("CZI","*.czi"),("All","*.*")]) self._add_paths(paths) def _add_folder(self): folder = filedialog.askdirectory(title="Select folder with ND2/CZI files") if not folder: return found = [] for root, dirs, files in os.walk(folder): for f in sorted(files): if f.lower().endswith((".nd2", ".czi")): found.append(os.path.join(root, f)) if not found: messagebox.showinfo("No Files", "No .nd2 or .czi files found in this folder.") return self._add_paths(found) self.status.set(f"{len(found)} file(s) found in folder.") def _add_paths(self, paths): existing = [f for f, _ in self.batch_files] added = 0 for p in paths: if p not in existing: lbl = os.path.basename(p) self.batch_files.append((p, lbl)) self.batch_lb.insert(tk.END, lbl) added += 1 if added and not self.luts: self.batch_lb.selection_set(0) self._load_preview(0) def _remove_file(self): sel = self.batch_lb.curselection() if not sel: return idx = sel[0] self.batch_lb.delete(idx) self.batch_files.pop(idx) def _on_batch_select(self, event): sel = self.batch_lb.curselection() if not sel: return idx = sel[0] if idx != self.preview_idx or not self.luts: self.preview_idx = idx self._load_preview(idx) def _load_preview(self, idx): if idx >= len(self.batch_files): return path, _ = self.batch_files[idx] self.status.set(f"Loading preview: {os.path.basename(path)}…") threading.Thread(target=self._load_preview_thread, args=(path,), daemon=True).start() def _load_preview_thread(self, path): try: ext = os.path.splitext(path)[1].lower() if ext == ".nd2": f = nd2.ND2File(path) sz = dict(f.sizes) chs = f.metadata.channels or [] f.close() nch = sz.get("C", 1) # Her channel için hem isim hem emission wavelength al ch_info = [] for c in chs: name = c.channel.name or "" # Emission wavelength metadata'da varsa al em_wave = "" try: em = c.channel.emissionLambdaNm if em and em > 0: em_wave = str(int(em)) except: pass # excitation da dene if not em_wave: try: ex = c.channel.excitationLambdaNm if ex and ex > 0: em_wave = str(int(ex)) except: pass # İsim + dalga boyu birleştir — ikisi de yoksa sadece isim combined = f"{name} {em_wave}".strip() if em_wave else name ch_info.append(combined) ch_names = ch_info if ch_info else [f"CH{i+1}" for i in range(nch)] else: _, sz, ch_names = read_czi(path) nch = sz.get("C", 1) arrays = load_first_pos_channels(path) self.after(0, lambda: self._build_luts_and_preview(nch, ch_names, arrays, sz, path)) except Exception as e: self.after(0, lambda: self.status.set(f"Error loading: {e}")) def _build_luts_and_preview(self, nch, ch_names, arrays, sz, path): self.nch = nch self._ch_2d = arrays cn = list(COLORS.keys()) # Eğer luts zaten var ve channel sayısı aynıysa değerleri koru if len(self.luts) != nch: self.luts = [] default_colors = [ "DAPI (405nm)", "GFP (488nm)", "AF594 (594nm)", "CY5 (647nm)", "mCherry (561nm)", "CY3 (550nm)", "Custom", ] for i in range(nch): nm = ch_names[i] if i < len(ch_names) else f"CH{i+1}" auto_color = auto_detect_color(nm) # Tespit edilemezse channel sırasına göre varsayılan ata if not auto_color: auto_color = default_colors[i % len(default_colors)] self.luts.append({ "min": tk.IntVar(value=0), "max": tk.IntVar(value=65535), "gamma": tk.DoubleVar(value=1.0), "color": tk.StringVar(value=auto_color), "enabled": tk.BooleanVar(value=True), }) # LUT widget'larını yeniden oluştur for w in self.li.winfo_children(): w.destroy() for i in range(nch): nm = ch_names[i] if i < len(ch_names) else f"CH{i+1}" lut = self.luts[i] # Her channel için: LUT sol + preview sağ yan yana ch_row = tk.Frame(self.li, bg=SURF) ch_row.pack(fill="x", padx=4, pady=3) # Sol: LUT kontrolleri frm = tk.LabelFrame(ch_row, text=f" {nm} (CH{i+1}) ", bg=SURF, fg=ACC, font=("Segoe UI",10,"bold"), bd=1, relief="groove", padx=8, pady=5) frm.pack(side="left", fill="both", expand=True) tk.Checkbutton(frm, text="Active", variable=lut["enabled"], bg=SURF, fg=TEXT, selectcolor=CARD, font=("Segoe UI",9), command=lambda idx=i: self._upd_prev(idx)).grid( row=0, column=4, padx=(10,0)) tk.Label(frm, text="Color:", bg=SURF, fg=MUTED).grid(row=0, column=0, sticky="w") cb = ttk.Combobox(frm, textvariable=lut["color"], values=list(COLORS.keys()), width=10, state="readonly") cb.grid(row=0, column=1, padx=(4,10)) cb.bind("<>", lambda e, idx=i: self._upd_prev(idx)) for ri, (key, label, lo, hi, res) in enumerate([ ("min","Min",0,65535,100),("max","Max",0,65535,100),("gamma","Gamma",0.1,4.0,0.05)],1): tk.Label(frm, text=f"{label}:", bg=SURF, fg=MUTED).grid( row=ri, column=0, sticky="w", pady=(3,0)) tk.Scale(frm, from_=lo, to=hi, resolution=res, variable=lut[key], orient="horizontal", bg=SURF, fg=TEXT, troughcolor=CARD, highlightthickness=0, length=200, command=lambda v, idx=i: self._upd_prev(idx)).grid( row=ri, column=1, columnspan=3, sticky="ew", pady=(3,0)) tk.Entry(frm, textvariable=lut[key], width=6, bg=CARD, fg="#fff", insertbackground="white").grid(row=ri, column=4, padx=(5,0), pady=(3,0)) # Sağ: Küçük preview thumbnail — LUT frame ile aynı yükseklik pf = tk.Frame(ch_row, bg=SURF, padx=2) pf.pack(side="right", fill="y") lbl = tk.Label(pf, bg="#08080f") lbl.pack(expand=True, fill="both") lut["_plbl"] = lbl # Merged preview — en altta tam genişlik mf = tk.LabelFrame(self.li, text=" MERGED ", bg=SURF, fg=ACC2, font=("Segoe UI",10,"bold"), bd=1, relief="groove") mf.pack(fill="x", padx=4, pady=(6,2)) self._mlbl = tk.Label(mf, bg=SURF) self._mlbl.pack(pady=4) # Dosya bilgisi ext = os.path.splitext(path)[1].upper().lstrip(".") npos = sz.get("P", sz.get("S", sz.get("M", 1))) self.file_info.config( text=f"{ext} | CH:{nch} | Pos:{npos} | Z:{sz.get('Z',1)} | {sz.get('Y','?')}×{sz.get('X','?')}") self.status.set(f"Preview: {os.path.basename(path)}") self.after(100, self._upd_all_prev) def _upd_prev(self, idx): if idx >= len(self._ch_2d) or idx >= len(self.luts): return lut = self.luts[idx]; arr = self._ch_2d[idx] lo = lut["min"].get(); hi = lut["max"].get(); gm = lut["gamma"].get() cn = lut["color"].get() thumb = make_thumb(arr, lo, hi, gm, COLORS.get(cn,(255,255,255))) itk = ImageTk.PhotoImage(thumb) lut["_plbl"].config(image=itk); lut["_pimg"] = itk self._upd_merged() def _upd_merged(self): if not self._ch_2d: return thumb = make_merged_thumb(self._ch_2d, self.luts) itk = ImageTk.PhotoImage(thumb) self._mlbl.config(image=itk); self._mimg = itk def _upd_all_prev(self): for i in range(len(self.luts)): self._upd_prev(i) def _apply_lut_to_all(self): """Mevcut LUT değerlerini tüm batch dosyalarına uygula (state koru).""" messagebox.showinfo("LUT Applied", f"Current LUT settings will be applied to all {len(self.batch_files)} files when processing.") # ── Output ───────────────────────────────────────────────────────────────── def _bout(self): p = filedialog.askdirectory() if p: self.odir.set(p) # ── İşlem ───────────────────────────────────────────────────────────────── def _start(self): self._process_files(self.batch_files) def _start_selected(self): sel = self.batch_lb.curselection() if not sel: messagebox.showwarning("Warning","Select a file from the list first."); return # Seçili dosya preview'daki dosya mı? idx = sel[0] if idx == self.preview_idx and self._ch_2d: # Preview array'leri hazır — direkt kullan lut_snapshot = [] for lut in self.luts: lut_snapshot.append({ "min": lut["min"].get(), "max": lut["max"].get(), "gamma": lut["gamma"].get(), "color": lut["color"].get(), "enabled": lut["enabled"].get(), }) path, _ = self.batch_files[idx] threading.Thread( target=self._run_single_from_preview, args=(path, self._ch_2d.copy(), lut_snapshot), daemon=True).start() else: self._process_files([self.batch_files[idx]]) def _process_files(self, files): if not DEPS_OK: messagebox.showerror("Missing","pip install nd2 numpy tifffile Pillow"); return if not files: messagebox.showwarning("Warning","Add files to the batch list first."); return if not self.odir.get(): p = filedialog.askdirectory(title="Select Output Folder") if not p: return self.odir.set(p) if not self.luts: messagebox.showwarning("Warning","Select a file first to set LUT values."); return if not self.state.get("licensed"): used = self.state.get("count",0) remaining = LIMIT - used if len(files) > remaining: if messagebox.askyesno("Trial Limit", f"Trial allows {remaining} more file(s), you selected {len(files)}.\n\n" f"Full version: {PRICE}\nPurchase now?"): self._lic_dlg() return # LUT değerlerini ANA THREAD'de oku — thread içinde tkinter var'ları güvenilmez lut_snapshot = [] for lut in self.luts: lut_snapshot.append({ "min": lut["min"].get(), "max": lut["max"].get(), "gamma": lut["gamma"].get(), "color": lut["color"].get(), "enabled": lut["enabled"].get(), }) threading.Thread(target=self._run_batch, args=(files, lut_snapshot), daemon=True).start() def _run_single_from_preview(self, path, ch_arrays, lut_snapshot): """Preview'daki array'leri direkt export eder — dosyadan tekrar okumaz.""" try: self.prog.set(5) base = os.path.splitext(os.path.basename(path))[0] out_root = self.odir.get() active_colors = [lut_snapshot[i]["color"] for i in range(min(len(lut_snapshot), len(ch_arrays))) if lut_snapshot[i]["enabled"]] color_suffix = "_".join(c.split(" ")[0] for c in active_colors) if active_colors else "all" out_dir = os.path.join(out_root, f"{base}_{color_suffix}") os.makedirs(out_dir, exist_ok=True) mrgb = None for ci, c2 in enumerate(ch_arrays): lut = lut_snapshot[ci] if ci < len(lut_snapshot) else None if lut and not lut["enabled"]: continue cl = f"CH{ci+1:02d}" if lut: lo = lut["min"]; hi = lut["max"]; gm = lut["gamma"] cn = lut["color"] else: lo, hi, gm = 0, 65535, 1.0 cn = list(COLORS.keys())[ci % len(COLORS)] print(f"[EXPORT-PREVIEW] CH{ci+1}: min={lo} max={hi} gamma={gm} color={cn}") print(f"[ARRAY] CH{ci+1}: shape={c2.shape} dtype={c2.dtype} min={c2.min()} max={c2.max()}") g8 = apply_lut(c2, lo, hi, gm) col_rgb = COLORS.get(cn, (255,255,255)) colored = colorize(g8, col_rgb) cn_safe = cn.replace(" ","_").replace("(","").replace(")","").replace("/","") g8_save = g8 col_save = colored if self.do_ch.get(): if self.do_tif.get(): tifffile.imwrite(os.path.join(out_dir, f"{base}_{cl}.tif"), g8_save) tifffile.imwrite(os.path.join(out_dir, f"{base}_{cl}_{cn_safe}.tif"), col_save) if self.do_16bit.get(): # 16-bit grayscale — ham array, LUT uygulanmış normalize a16 = arr16_normalize(c2, lo, hi, gm) tifffile.imwrite(os.path.join(out_dir, f"{base}_{cl}_16bit.tif"), a16) # 16-bit renkli col16 = colorize_16bit(c2, lo, hi, gm, col_rgb) tifffile.imwrite(os.path.join(out_dir, f"{base}_{cl}_{cn_safe}_16bit.tif"), col16) if self.do_png.get(): Image.fromarray(g8_save).save(os.path.join(out_dir, f"{base}_{cl}.png")) Image.fromarray(col_save).save(os.path.join(out_dir, f"{base}_{cl}_{cn_safe}.png")) if self.do_jpg.get(): Image.fromarray(g8_save).save(os.path.join(out_dir, f"{base}_{cl}.jpg"), quality=95) Image.fromarray(col_save).save(os.path.join(out_dir, f"{base}_{cl}_{cn_safe}.jpg"), quality=95) if self.do_mtif.get(): mrgb = (colored.astype(np.float32) if mrgb is None else np.clip(mrgb + colored.astype(np.float32), 0, 255)) if not hasattr(self, '_mgray') or self._mgray is None: self._mgray = g8.astype(np.float32) else: self._mgray = np.clip(self._mgray + g8.astype(np.float32), 0, 255) # 16-bit merged için ham değerleri birleştir if self.do_16bit.get(): col16 = colorize_16bit(c2, lo, hi, gm, col_rgb) a16 = arr16_normalize(c2, lo, hi, gm) if not hasattr(self, '_mrgb16') or self._mrgb16 is None: self._mrgb16 = col16.astype(np.float32) self._mgray16 = a16.astype(np.float32) else: self._mrgb16 = np.clip(self._mrgb16 + col16.astype(np.float32), 0, 65535) self._mgray16 = np.clip(self._mgray16 + a16.astype(np.float32), 0, 65535) self.prog.set(5 + 90 * (ci+1) / len(ch_arrays)) if mrgb is not None: m8 = mrgb.astype(np.uint8) mg = self._mgray.astype(np.uint8) if hasattr(self,'_mgray') and self._mgray is not None else None if self.do_tif.get(): tifffile.imwrite(os.path.join(out_dir, f"{base}_MERGED.tif"), m8) if mg is not None: tifffile.imwrite(os.path.join(out_dir, f"{base}_MERGED_gray.tif"), mg) if self.do_16bit.get() and hasattr(self,'_mrgb16') and self._mrgb16 is not None: m16 = self._mrgb16.astype(np.uint16) tifffile.imwrite(os.path.join(out_dir, f"{base}_MERGED_16bit.tif"), m16) if hasattr(self,'_mgray16') and self._mgray16 is not None: tifffile.imwrite(os.path.join(out_dir, f"{base}_MERGED_gray_16bit.tif"), self._mgray16.astype(np.uint16)) self._mrgb16 = None; self._mgray16 = None if self.do_png.get(): Image.fromarray(m8).save(os.path.join(out_dir, f"{base}_MERGED.png")) if mg is not None: Image.fromarray(mg).save(os.path.join(out_dir, f"{base}_MERGED_gray.png")) if self.do_jpg.get(): Image.fromarray(m8).save(os.path.join(out_dir, f"{base}_MERGED.jpg"), quality=95) if mg is not None: Image.fromarray(mg).save(os.path.join(out_dir, f"{base}_MERGED_gray.jpg"), quality=95) self._mgray = None if not self.state.get("licensed"): self.state["count"] = self.state.get("count",0) + 1 _save_state(self.state) self.after(0, self._refresh_banner) self.prog.set(100) self.status.set(f"✓ Done! {base}") messagebox.showinfo("Done", f"Saved to:\n{out_dir}") except Exception as e: self.status.set(f"Error: {e}"); messagebox.showerror("Error", str(e)) def _run_batch(self, files, lut_snapshot): try: self.prog.set(2) out_root = self.odir.get() total_files = len(files) for fi, (path, label) in enumerate(files): base = os.path.splitext(os.path.basename(path))[0] ext = os.path.splitext(path)[1].lower() self.status.set(f"Loading {fi+1}/{total_files}: {base}…") # Dosya metadata if ext == ".nd2": f = nd2.ND2File(path); sz = dict(f.sizes) f.close() nch = sz.get("C", 1) npos = sz.get("P", sz.get("M", 1)) pk = "P" if "P" in sz else "M" else: _, sz, _ = read_czi(path) nch = sz.get("C", 1) npos = sz.get("S", sz.get("M", 1)) pk = "S" if "S" in sz else "M" dp = self.do_pos.get() and npos > 1 # Klasör adı: dosya adı + aktif channel renkleri active_colors = [lut_snapshot[i]["color"] for i in range(min(len(lut_snapshot), nch)) if lut_snapshot[i]["enabled"]] color_suffix = "_".join(c.split(" ")[0] for c in active_colors) if active_colors else "all" total_ops = (npos if dp else 1) * nch op = 0 pos_range = range(npos) if dp else [None] for pi in pos_range: plbl = f"Pos{pi+1:03d}" if pi is not None else None # Her pozisyon için channel array'lerini yükle ch_arrays = self._load_pos_channels(path, ext, sz, pk, pi) if not ch_arrays: self.status.set(f"Skipping {base} — could not read channels") continue # Çıktı klasörü pos_label = f"{base}_{color_suffix}" if plbl: out_dir = os.path.join(out_root, pos_label, plbl) else: out_dir = os.path.join(out_root, pos_label) os.makedirs(out_dir, exist_ok=True) mrgb = None for ci, c2 in enumerate(ch_arrays): lut = lut_snapshot[ci] if ci < len(lut_snapshot) else None if lut and not lut["enabled"]: op += 1; continue pfx = f"{base}_{plbl}" if plbl else base cl = f"CH{ci+1:02d}" if lut: lo = lut["min"]; hi = lut["max"]; gm = lut["gamma"] cn = lut["color"] else: lo, hi, gm = 0, 65535, 1.0 cn = list(COLORS.keys())[ci % len(COLORS)] # DEBUG — terminalde görünür print(f"[EXPORT] CH{ci+1}: min={lo} max={hi} gamma={gm} color={cn}") g8 = apply_lut(c2, lo, hi, gm) col_rgb = COLORS.get(cn, (255, 255, 255)) colored = colorize(g8, col_rgb) if self.do_ch.get(): tifffile.imwrite(os.path.join(out_dir, f"{pfx}_{cl}.tif"), c2) cn_safe = cn.replace(" ", "_").replace("(", "").replace(")", "").replace("/", "") Image.fromarray(colored).save( os.path.join(out_dir, f"{pfx}_{cl}_{cn_safe}.png")) if self.do_mpng.get() or self.do_mtif.get(): mrgb = (colored.astype(np.float32) if mrgb is None else np.clip(mrgb + colored.astype(np.float32), 0, 255)) op += 1 self.prog.set(5 + 90 * ((fi * total_ops + op) / (total_files * total_ops))) self.status.set(f"{fi+1}/{total_files}: {base} CH{ci+1}/{nch}") if mrgb is not None: m8 = mrgb.astype(np.uint8) pfx = f"{base}_{plbl}" if plbl else base if self.do_mpng.get(): Image.fromarray(m8).save(os.path.join(out_dir, f"{pfx}_MERGED.png")) if self.do_mtif.get(): tifffile.imwrite(os.path.join(out_dir, f"{pfx}_MERGED.tif"), m8) if not self.state.get("licensed"): self.state["count"] = self.state.get("count", 0) + 1 _save_state(self.state) self.after(0, self._refresh_banner) self.prog.set(100) self.status.set(f"✓ Done! {total_files} file(s) processed.") messagebox.showinfo("Done", f"{total_files} file(s) processed.\n\nOutput:\n{out_root}") except Exception as e: self.status.set(f"Error: {e}"); messagebox.showerror("Error", str(e)) def _load_pos_channels(self, path, ext, sz, pk, pos_idx): """Belirli bir pozisyonun tüm channel 2D array'lerini döner.""" try: if ext == ".nd2": f = nd2.ND2File(path); data = f.asarray(); ao = list(dict(f.sizes).keys()); f.close() nch = sz.get("C", 1) else: data, _, _ = read_czi(path) ao = [k for k in ("T","S","M","Z","C","Y","X") if k in sz] nch = sz.get("C", 1) # Pozisyon eksenini kes if pk in ao and sz.get(pk, 1) > 1 and pos_idx is not None: pi_ax = ao.index(pk) data = np.take(data, pos_idx, axis=pi_ax) ao = [k for k in ao if k != pk] # T projeksiyonu if "T" in ao: data = data.max(axis=ao.index("T")) ao = [k for k in ao if k != "T"] # Z projeksiyonu if "Z" in ao: data = data.max(axis=ao.index("Z")) ao = [k for k in ao if k != "Z"] # Channel ayır ci_ax = ao.index("C") if "C" in ao else None result = [] for i in range(nch): ch = np.take(data, i, axis=ci_ax) if ci_ax is not None else data # Kalan ekstra eksenler varsa max projeksiyon while ch.ndim > 2: ch = ch.max(axis=0) result.append(ch) return result except Exception as e: print(f"[LOAD_POS] {e}") return [] if __name__ == "__main__": if len(sys.argv) == 3 and sys.argv[1] == "--genkey": email = sys.argv[2]; key = make_key(email) print(f"\n{'='*50}\n {APP} — License Key Generator\n{'='*50}") print(f" Email : {email}\n Key : {key}") print(f"{'='*50}\n Send this key to the customer by email.\n{'='*50}\n") else: App().mainloop()