commit cf78f42c15a8a9cff4bf85b50c83026798897281
Author: Shaiv Kamat <shaivkamat@gmail.com>
Date:   Fri Dec 26 16:29:44 2025 -0800

    Base working code with Autofocus

diff --git a/.gitignore b/.gitignore
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+venv
+env
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diff --git a/Workflow.txt b/Workflow.txt
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+++ b/Workflow.txt
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+ cd Autoscope
+  source venv/bin/activate      # Enter environment
+  pip install something         # Installs to this project only
+  python main.py                # Runs with this project's packages
+  deactivate                    # Exit environment
diff --git a/config/settings.py b/config/settings.py
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index 0000000..e69de29
diff --git a/requirements.txt b/requirements.txt
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+++ b/requirements.txt
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+opencv-python>=4.5.0
+pyserial>=3.5
+numpy>=1.20.0
+Pillow>=1.0.0
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diff --git a/src/__init__.py b/src/__init__.py
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diff --git a/src/__pycache__/camera.cpython-39.pyc b/src/__pycache__/camera.cpython-39.pyc
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diff --git a/src/__pycache__/gui.cpython-39.pyc b/src/__pycache__/gui.cpython-39.pyc
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diff --git a/src/__pycache__/vision.cpython-39.pyc b/src/__pycache__/vision.cpython-39.pyc
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diff --git a/src/arduino.py b/src/arduino.py
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index 0000000..ebee2e1
--- /dev/null
+++ b/src/arduino.py
@@ -0,0 +1,120 @@
+import serial
+import serial.tools.list_ports
+import time
+
+class Arduino:
+    # Known Arduino USB vendor/product IDs
+    ARDUINO_IDS = [
+        (0x2341, None),     # Arduino SA
+        (0x2A03, None),     # Arduino SA (alt)
+        (0x1A86, 0x7523),   # CH340 (common clone chip)
+        (0x0403, 0x6001),   # FTDI FT232
+        (0x10C4, 0xEA60),   # CP210x
+        (0x2341, 0x0043),   # Arduino Uno
+        (0x2341, 0x0001),   # Arduino Mega
+        (0x2341, 0x0042),   # Arduino Mega 2560
+    ]
+    
+    def __init__(self, baud=115200):
+        self.port = self.find_arduino()
+        
+        if not self.port:
+            raise RuntimeError("Could not find Arduino")
+        
+        print(f"Connecting to Arduino on {self.port}")
+        
+        try:
+            self.ser = serial.Serial(self.port, baud, timeout=1)
+            time.sleep(2)  # Wait for Arduino reset
+            self.clear_buffer()
+                
+        except FileNotFoundError:
+            print("Shutting down...")
+    
+    @classmethod
+    def find_arduino(cls):
+        """
+        Search available USB ports for an Arduino.
+        Returns port path or None if not found.
+        """
+        print("Searching for Arduino...")
+        
+        ports = serial.tools.list_ports.comports()
+        
+        for port in ports:
+            print(f"  Found: {port.device}")
+            print(f"         VID:PID = {port.vid}:{port.pid}")
+            print(f"         Description: {port.description}")
+            print(f"         Manufacturer: {port.manufacturer}")
+            
+            # Check against known Arduino IDs
+            for vid, pid in cls.ARDUINO_IDS:
+                if port.vid == vid:
+                    if pid is None or port.pid == pid:
+                        print(f"  → Arduino detected on {port.device}")
+                        return port.device
+            
+            # Fallback: check description/manufacturer strings
+            desc = (port.description or "").lower()
+            mfr = (port.manufacturer or "").lower()
+            
+            if any(term in desc or term in mfr for term in 
+                   ["arduino", "ch340", "ftdi", "usb-serial", "cp210"]):
+                print(f"  → Probable Arduino on {port.device}")
+                return port.device
+        
+        print("  No Arduino found")
+        return None
+    
+    def clear_buffer(self):
+        """Clear any pending data in serial buffer"""
+        self.ser.reset_input_buffer()
+        self.ser.reset_output_buffer()
+    
+    def send_command(self, cmd):
+        """Send command to Arduino"""
+        self.ser.write(cmd.encode())
+        self.ser.flush()
+    
+    def read_response(self, timeout=1.0):
+        """Read line from Arduino"""
+        self.ser.timeout = timeout
+        return self.ser.readline().decode().strip()
+    
+    def move(self, axis, direction):
+        """
+        axis: 'X', 'Y', or 'Z'
+        direction: '+' or '-'
+        """
+        cmd = f"MOVE {axis}{direction}"
+        self.send_command(cmd)
+    
+    def stop(self, axis="ALL"):
+        """Stop movement. axis: 'X', 'Y', 'Z', or 'ALL'"""
+        self.send_command(f"STOP {axis}")
+    
+    def home_z(self):
+        """Home Z axis to max limit switch"""
+        self.send_command("HOME Z")
+        while True:
+            response = self.read_response(timeout=10.0)
+            if "LIMIT Z+" in response:
+                return True
+            if not response:
+                raise RuntimeError("Timeout waiting for Z home")
+    
+    def status(self):
+        """Query Arduino status"""
+        self.send_command("STATUS?")
+        return self.read_response()
+    
+    def close(self):
+        """Close serial connection"""
+        if self.ser and self.ser.is_open:
+            self.ser.close()
+    
+    def __enter__(self):
+        return self
+    
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self.close()
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diff --git a/src/camera.py b/src/camera.py
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index 0000000..a2e9f30
--- /dev/null
+++ b/src/camera.py
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+import cv2
+
+class Camera:
+    def __init__(self, device_id=0):
+        self.cap = cv2.VideoCapture(device_id)
+        
+        if not self.cap.isOpened():
+            raise RuntimeError("Could not open camera, stop program")
+        
+        # set resolution
+        # self.cap.set(cv2.CAP_PROP_FRAME_WIDTH, 1920)
+        # self.cap.set(cv2.CAP_PROP_FRAME_HEIGHT, 1080)
+        
+        self.window_name = "AutoScope"
+    
+    def capture_frame(self):
+        ret, frame = self.cap.read()
+        if not ret:
+            raise RuntimeError("Failed to capture frame, stop program")
+        return frame
+    
+    def show_frame(self, frame):
+        """Display frame in window"""
+        cv2.imshow(self.window_name, frame)
+    
+    def wait_key(self, delay_ms=1):
+        """
+        Wait for key press. Required for window to update.
+        Returns key code or -1 if no key pressed.
+        """
+        return cv2.waitKey(delay_ms) & 0xFF
+    
+    def run_preview_frame(self):
+        frame = self.capture_frame()
+        self.show_frame(frame)
+        
+        key = self.wait_key(1)
+        
+    def close_window(self):
+        """Close the preview window"""
+        cv2.destroyWindow(self.window_name)
+    
+    def release(self):
+        """Release camera and close windows"""
+        self.cap.release()
+        cv2.destroyAllWindows()
+    
+    def __enter__(self):
+        return self
+    
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self.release()
+
+
+    # Unusued
+    def run_preview(self):
+        """
+        Run live preview loop.
+        Press 'q' to quit.
+        """
+        print("Starting preview. Press 'q' to quit.")
+        
+        while True:
+            frame = self.capture_frame()
+            self.show_frame(frame)
+            
+            key = self.wait_key(1)
+            if key == ord('q'):
+                break
+        
+        self.close_window()
+    
\ No newline at end of file
diff --git a/src/gui.py b/src/gui.py
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--- /dev/null
+++ b/src/gui.py
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+import tkinter as tk
+from tkinter import ttk, scrolledtext
+from PIL import Image, ImageTk
+import cv2
+import threading
+import queue
+
+class AppGUI:
+    def __init__(self, camera, arduino):
+        self.camera = camera
+        self.arduino = arduino
+        self.running = True
+        self._updating_slider = False 
+        self.autofocus_running = False
+        self.autofocus_speed_range = (1, 6)  # Speed indices 1-6 (values: 2, 5, 10, 30, 50, 70)
+        
+        # Track movement state for toggle buttons
+        self.axis_direction = {'X': 1, 'Y': 1, 'Z': 1}  # 1 = positive, -1 = negative
+        self.axis_moving = {'X': False, 'Y': False, 'Z': False}
+        
+        # Queue for thread-safe serial log updates
+        self.serial_queue = queue.Queue()
+        
+        # Build the window
+        self.root = tk.Tk()
+        self.root.title("AutoScope")
+        self.root.geometry("1080x1080") 
+        self.root.minsize(1080, 1080)
+        self.root.protocol("WM_DELETE_WINDOW", self.on_close)
+        
+        self._build_ui()
+        
+        # Start serial reader thread
+        self.serial_thread = threading.Thread(target=self._serial_reader, daemon=True)
+        self.serial_thread.start()
+    
+    def _build_ui(self):
+        # Main container
+        main_frame = ttk.Frame(self.root)
+        main_frame.pack(fill=tk.BOTH, expand=True, padx=5, pady=5)
+        
+        # Left: Camera view
+        self.camera_label = ttk.Label(main_frame)
+        self.camera_label.pack(side=tk.LEFT, padx=(0, 5))
+        
+        # Right: Control panel
+        right_frame = ttk.Frame(main_frame, width=320)
+        right_frame.pack(side=tk.RIGHT, fill=tk.BOTH, expand=True)
+        right_frame.pack_propagate(False)
+        
+        # === EMERGENCY STOP (prominent at top) ===
+        emergency_frame = ttk.Frame(right_frame)
+        emergency_frame.pack(fill=tk.X, pady=(0, 10))
+        
+        self.emergency_btn = tk.Button(
+            emergency_frame, 
+            text="⚠ EMERGENCY STOP ⚠", 
+            command=lambda: self.send_command("!"),
+            bg='red', fg='white', font=('Arial', 12, 'bold'),
+            height=2
+        )
+        self.emergency_btn.pack(fill=tk.X)
+        
+        # === SPEED CONTROL ===
+        speed_frame = ttk.LabelFrame(right_frame, text="Speed")
+        speed_frame.pack(fill=tk.X, pady=(0, 10))
+        
+        speed_btn_frame = ttk.Frame(speed_frame)
+        speed_btn_frame.pack(fill=tk.X, padx=5, pady=5)
+        
+        self.speed_var = tk.StringVar(value="Medium")
+        
+        ttk.Radiobutton(speed_btn_frame, text="Slow", variable=self.speed_var, 
+                        value="Slow", command=lambda: self.send_command("L")).pack(side=tk.LEFT, padx=5)
+        ttk.Radiobutton(speed_btn_frame, text="Medium", variable=self.speed_var, 
+                        value="Medium", command=lambda: self.send_command("M")).pack(side=tk.LEFT, padx=5)
+        ttk.Radiobutton(speed_btn_frame, text="Fast", variable=self.speed_var, 
+                        value="Fast", command=lambda: self.send_command("F")).pack(side=tk.LEFT, padx=5)
+        # === FINE SPEED CONTROL ===
+        fine_speed_frame = ttk.LabelFrame(right_frame, text="Fine Speed Control")
+        fine_speed_frame.pack(fill=tk.X, pady=(0, 10))
+
+        # Speed values matching Arduino speedArr (index 0-5) plus 0 for stop
+        self.speed_values = [0, 2, 5, 10, 30, 50, 70, 100]
+
+        fine_inner = ttk.Frame(fine_speed_frame)
+        fine_inner.pack(fill=tk.X, padx=5, pady=5)
+
+        # Current speed display
+        self.fine_speed_label = ttk.Label(fine_inner, text="Speed: 50", font=('Arial', 10, 'bold'))
+        self.fine_speed_label.pack(anchor=tk.W)
+
+        # Slider
+        self.speed_slider = ttk.Scale(
+            fine_inner, 
+            from_=0, 
+            to=6,
+            orient=tk.HORIZONTAL,
+            command=self._on_speed_slider_change
+        )
+        self.speed_slider.set(5)  # Default to middle
+        self.speed_slider.pack(fill=tk.X, pady=(5, 0))
+
+        # Number buttons for direct selection
+        btn_row = ttk.Frame(fine_inner)
+        btn_row.pack(fill=tk.X, pady=(5, 0))
+
+        for i in range(7):
+            btn = ttk.Button(
+                btn_row, 
+                text=str(i), 
+                width=2,
+                command=lambda x=i: self._set_fine_speed(x)
+            )
+            btn.pack(side=tk.LEFT, padx=1)
+        # === MOVEMENT CONTROLS ===
+        move_frame = ttk.LabelFrame(right_frame, text="Movement Control")
+        move_frame.pack(fill=tk.X, pady=(0, 10))
+        
+        # Command mapping for each axis
+        self.axis_commands = {
+            'X': {'pos': 'E', 'neg': 'W', 'stop': 'e'},
+            'Y': {'pos': 'N', 'neg': 'S', 'stop': 'n'},
+            'Z': {'pos': 'U', 'neg': 'D', 'stop': 'u'}
+        }
+        
+        self.dir_labels = {}
+        self.move_buttons = {}
+        
+        for axis in ["X", "Y", "Z"]:
+            row = ttk.Frame(move_frame)
+            row.pack(fill=tk.X, pady=3, padx=5)
+            
+            # Axis label
+            ttk.Label(row, text=f"{axis}:", width=3, font=('Arial', 10, 'bold')).pack(side=tk.LEFT)
+            
+            # Direction toggle button
+            dir_btn = ttk.Button(row, text="+ →", width=5, 
+                                command=lambda a=axis: self.toggle_direction(a))
+            dir_btn.pack(side=tk.LEFT, padx=2)
+            self.dir_labels[axis] = dir_btn
+            
+            # Start/Stop movement toggle
+            move_btn = tk.Button(row, text="Move", width=8, bg='green', fg='white',
+                                command=lambda a=axis: self.toggle_movement(a))
+            move_btn.pack(side=tk.LEFT, padx=2)
+            self.move_buttons[axis] = move_btn
+            
+            # Quick stop for this axis
+            ttk.Button(row, text="Stop", width=6, 
+                      command=lambda a=axis: self.stop_axis(a)).pack(side=tk.LEFT, padx=2)
+        
+        # Stop All button
+        ttk.Button(move_frame, text="Stop All Axes", 
+                  command=lambda: self.send_command("X")).pack(fill=tk.X, padx=5, pady=5)
+        
+        # === AUTOFOCUS CONTROL ===
+        af_frame = ttk.LabelFrame(right_frame, text="Autofocus")
+        af_frame.pack(fill=tk.X, pady=(0, 10))
+
+        af_inner = ttk.Frame(af_frame)
+        af_inner.pack(fill=tk.X, padx=5, pady=5)
+
+        # Focus score display
+        self.focus_score_label = ttk.Label(af_inner, text="Focus: --", font=('Arial', 10))
+        self.focus_score_label.pack(anchor=tk.W)
+
+        # Autofocus buttons
+        af_btn_row = ttk.Frame(af_inner)
+        af_btn_row.pack(fill=tk.X, pady=(5, 0))
+
+        self.af_button = ttk.Button(af_btn_row, text="Autofocus", command=self.start_autofocus)
+        self.af_button.pack(side=tk.LEFT, padx=2)
+
+        ttk.Button(af_btn_row, text="Coarse AF", command=lambda: self.start_autofocus(coarse=True)).pack(side=tk.LEFT, padx=2)
+        ttk.Button(af_btn_row, text="Fine AF", command=lambda: self.start_autofocus(fine=True)).pack(side=tk.LEFT, padx=2)
+        ttk.Button(af_btn_row, text="Stop AF", command=self.stop_autofocus).pack(side=tk.LEFT, padx=2)
+
+        # Live focus monitoring toggle
+        self.live_focus_var = tk.BooleanVar(value=True)
+        ttk.Checkbutton(af_inner, text="Show live focus score", 
+                        variable=self.live_focus_var).pack(anchor=tk.W, pady=(5, 0))
+
+
+        # === POSITION & STATUS ===
+        pos_frame = ttk.LabelFrame(right_frame, text="Status")
+        pos_frame.pack(fill=tk.X, pady=(0, 10))
+        
+        pos_btn_frame = ttk.Frame(pos_frame)
+        pos_btn_frame.pack(fill=tk.X, padx=5, pady=5)
+        
+        ttk.Button(pos_btn_frame, text="Status", command=lambda: self.send_command("?")).pack(side=tk.LEFT, padx=2)
+        ttk.Button(pos_btn_frame, text="Zero All", command=lambda: self.send_command("Z")).pack(side=tk.LEFT, padx=2)
+        ttk.Button(pos_btn_frame, text="Go Origin", command=lambda: self.send_command("G")).pack(side=tk.LEFT, padx=2)
+        
+        # === MODE CONTROL ===
+        mode_frame = ttk.LabelFrame(right_frame, text="Control Mode")
+        mode_frame.pack(fill=tk.X, pady=(0, 10))
+        
+        mode_btn_frame = ttk.Frame(mode_frame)
+        mode_btn_frame.pack(fill=tk.X, padx=5, pady=5)
+        
+        self.mode_label = ttk.Label(mode_btn_frame, text="Mode: Serial", font=('Arial', 9))
+        self.mode_label.pack(side=tk.LEFT, padx=5)
+        
+        ttk.Button(mode_btn_frame, text="Toggle Mode", command=lambda: self.send_command("T")).pack(side=tk.RIGHT, padx=2)
+        
+        # === SERIAL LOG ===
+        ttk.Label(right_frame, text="Serial Log:").pack(anchor=tk.W)
+        self.serial_log = scrolledtext.ScrolledText(right_frame, height=10, width=35, state=tk.DISABLED)
+        self.serial_log.pack(fill=tk.BOTH, expand=True, pady=(0, 10))
+        
+        # === CUSTOM COMMAND ===
+        ttk.Label(right_frame, text="Send Command:").pack(anchor=tk.W)
+        cmd_frame = ttk.Frame(right_frame)
+        cmd_frame.pack(fill=tk.X)
+        
+        self.cmd_entry = ttk.Entry(cmd_frame)
+        self.cmd_entry.pack(side=tk.LEFT, fill=tk.X, expand=True)
+        self.cmd_entry.bind("<Return>", lambda e: self.send_custom_command())
+        
+        ttk.Button(cmd_frame, text="Send", command=self.send_custom_command).pack(side=tk.RIGHT, padx=(5, 0))
+    
+    def toggle_direction(self, axis):
+        """Toggle direction for an axis"""
+        self.axis_direction[axis] *= -1
+        direction = "+" if self.axis_direction[axis] == 1 else "-"
+        arrow = "→" if self.axis_direction[axis] == 1 else "←"
+        self.dir_labels[axis].config(text=f"{direction} {arrow}")
+        
+        # If currently moving, restart in new direction
+        if self.axis_moving[axis]:
+            self.stop_axis(axis)
+            self.start_movement(axis)
+    
+    def toggle_movement(self, axis):
+        """Toggle movement on/off for an axis"""
+        if self.axis_moving[axis]:
+            self.stop_axis(axis)
+        else:
+            self.start_movement(axis)
+    
+    def start_movement(self, axis):
+        """Start continuous movement on an axis"""
+        commands = self.axis_commands[axis]
+        cmd = commands['pos'] if self.axis_direction[axis] == 1 else commands['neg']
+        self.send_command(cmd)
+        self.axis_moving[axis] = True
+        self.move_buttons[axis].config(text="Moving", bg='orange')
+    
+    def stop_axis(self, axis):
+        """Stop movement on a specific axis"""
+        commands = self.axis_commands[axis]
+        self.send_command(commands['stop'])
+        self.axis_moving[axis] = False
+        self.move_buttons[axis].config(text="Move", bg='green')
+    
+    def send_command(self, cmd):
+        """Send a command and log it"""
+        self.log_message(f"> {cmd}")
+        if self.arduino:
+            self.arduino.send_command(cmd)
+    
+    def send_custom_command(self):
+        """Send command from entry box"""
+        cmd = self.cmd_entry.get().strip()
+        if cmd:
+            self.send_command(cmd)
+            self.cmd_entry.delete(0, tk.END)
+
+    def _on_speed_slider_change(self, value):
+        """Handle slider movement"""
+        if self._updating_slider:
+            return
+        # Round to nearest integer
+        index = round(float(value))
+        self._set_fine_speed(index)
+
+    def _set_fine_speed(self, index):
+        """Set fine speed by index (0-10)"""
+        # Prevent recursion
+        self._updating_slider = True
+        # Update slider position
+        self.speed_slider.set(index)
+        
+        # Update label with actual speed value
+        speed_val = self.speed_values[index]
+        self.fine_speed_label.config(text=f"Speed: {speed_val}")
+        self._updating_slider = False
+        
+        # Send command - '0' for index 0, '1'-'9' for 1-9, 'a' for 10
+        if index == 0:
+            self.send_command("0")
+        elif index <= 9:
+            self.send_command(str(index))
+        else:
+            # For index 10 (speed 300), you'd need to add a handler on Arduino
+            # For now, send '9' as max or add a new command
+            self.send_command("9")
+
+    
+
+
+
+
+
+
+
+    def get_focus_score(self):
+        """Get current focus score from camera"""
+        try:
+            frame = self.camera.capture_frame()
+            from vision import calculate_focus_score_sobel
+            score = calculate_focus_score_sobel(frame)
+            return score
+        except Exception as e:
+            print(f"Focus score error: {e}")
+            return 0
+
+    def start_autofocus(self, coarse=False, fine=False):
+        """Start autofocus routine in background thread"""
+        if self.autofocus_running:
+            self.log_message("Autofocus already running")
+            return
+        
+        self.autofocus_running = True
+        self.af_button.config(state='disabled')
+        
+        # Determine speed range based on mode
+        if coarse:
+            speed_range = (4, 6)  # Faster speeds: 30, 50, 70
+        elif fine:
+            speed_range = (1, 3)  # Slower speeds: 2, 5, 10
+        else:
+            speed_range = (1, 6)  # Full range
+        
+        af_thread = threading.Thread(
+            target=self._autofocus_routine, 
+            args=(speed_range,),
+            daemon=True
+        )
+        af_thread.start()
+
+    def stop_autofocus(self):
+        """Stop autofocus routine"""
+        self.autofocus_running = False
+        self.send_command('u')  # Stop Z axis
+        self.af_button.config(state='normal')
+        self.log_message("Autofocus stopped")
+
+    def _get_averaged_focus(self, samples=5, delay_between=0.05):
+        """
+        Get averaged focus score from multiple samples.
+        Reduces noise in focus measurements.
+        """
+        import time
+        scores = []
+        for _ in range(samples):
+            scores.append(self.get_focus_score())
+            time.sleep(delay_between)
+        
+        # Remove outliers (optional - take middle 60%)
+        scores.sort()
+        trim = len(scores) // 5  # Remove top and bottom 20%
+        if trim > 0:
+            scores = scores[trim:-trim]
+        
+        return sum(scores) / len(scores)
+
+    def _autofocus_routine(self, speed_range):
+        """
+        Autofocus using sweep search + hill climbing.
+        Phase 1: Sweep across range to find approximate peak
+        Phase 2: Fine tune from best position found
+        """
+        import time
+        
+        self.log_message(f"Starting autofocus (speed range: {speed_range})")
+        
+        min_speed_idx, max_speed_idx = speed_range
+        
+        # Timing settings
+        SWEEP_MOVE_TIME = 2      # Movement time per sweep step
+        SWEEP_SETTLE_TIME = 0.25     # Settle time during sweep
+        SWEEP_SAMPLES = 10
+        
+        FINE_MOVE_TIME = 0.15
+        FINE_SETTLE_TIME = 0.25
+        FINE_SAMPLES = 10
+        
+        # Number of steps in each direction for sweep
+        SWEEP_STEPS = 15  # Total sweep = 2 * SWEEP_STEPS positions
+        
+        # ========================================
+        # Phase 1: Sweep search
+        # ========================================
+        self.log_message("Phase 1: Sweep search")
+        
+        # Use medium speed for sweep
+        sweep_speed = (min_speed_idx + max_speed_idx) // 2
+        self._set_fine_speed_no_send(sweep_speed)
+        self.send_command(str(sweep_speed))
+        time.sleep(0.1)
+        
+        # Record starting position score
+        time.sleep(SWEEP_SETTLE_TIME)
+        start_score = self._get_averaged_focus(samples=SWEEP_SAMPLES)
+        self._update_focus_display(start_score)
+        
+        # Data structure: (steps_from_start, score)
+        # Positive = up from start, negative = down from start
+        sweep_data = [(0, start_score)]
+        self.log_message(f"Start position: {start_score:.1f}")
+        
+        if not self.autofocus_running:
+            return
+        
+        # Sweep DOWN first tyo avoid objective / slide contact
+        self.log_message(f"Sweeping down {SWEEP_STEPS} steps...")
+        for i in range(1, SWEEP_STEPS + 1):
+            if not self.autofocus_running:
+                return
+            
+            self.send_command('D')
+            time.sleep(SWEEP_MOVE_TIME)
+            self.send_command('d')
+            time.sleep(SWEEP_SETTLE_TIME)
+            
+            score = self._get_averaged_focus(samples=SWEEP_SAMPLES)
+            sweep_data.append((-i, score))
+            self._update_focus_display(score)
+            
+            if i % 5 == 0:
+                self.log_message(f"  Step -{i}: {score:.1f}")
+        
+        if not self.autofocus_running:
+            return
+        
+        # Return to start
+        self.log_message("Returning to start...")
+        for _ in range(SWEEP_STEPS):
+            if not self.autofocus_running:
+                return
+            self.send_command('U')
+            time.sleep(SWEEP_MOVE_TIME)
+            self.send_command('u')
+            time.sleep(0.1)  # Faster return, no need to sample
+        
+        time.sleep(SWEEP_SETTLE_TIME)
+        
+        if not self.autofocus_running:
+            return
+        
+        # Sweep UP
+        self.log_message(f"Sweeping up {SWEEP_STEPS} steps...")
+        for i in range(1, SWEEP_STEPS + 1):
+            if not self.autofocus_running:
+                return
+            
+            self.send_command('U')
+            time.sleep(SWEEP_MOVE_TIME)
+            self.send_command('u')
+            time.sleep(SWEEP_SETTLE_TIME)
+            
+            score = self._get_averaged_focus(samples=SWEEP_SAMPLES)
+            sweep_data.append((i, score))
+            self._update_focus_display(score)
+            
+            if i % 5 == 0:
+                self.log_message(f"  Step +{i}: {score:.1f}")
+        
+        if not self.autofocus_running:
+            return
+        
+        # ========================================
+        # Find best position from sweep
+        # ========================================
+        best_step, best_score = max(sweep_data, key=lambda x: x[1])
+        self.log_message(f"Best found at step {best_step}: {best_score:.1f}")
+        
+        # Log the full sweep curve for debugging
+        self.log_message("Sweep curve:")
+        sorted_data = sorted(sweep_data, key=lambda x: x[0])
+        curve_str = " ".join([f"{s[1]:.0f}" for s in sorted_data])
+        self.log_message(f"  {curve_str}")
+        
+        # ========================================
+        # Move to best position
+        # ========================================
+        # Currently at +SWEEP_STEPS, need to go to best_step
+        steps_to_move = SWEEP_STEPS - best_step  # Positive = move down
+        
+        if steps_to_move > 0:
+            self.log_message(f"Moving down {steps_to_move} steps to best position")
+            move_cmd, stop_cmd = 'D', 'd'
+        else:
+            self.log_message(f"Moving up {abs(steps_to_move)} steps to best position")
+            move_cmd, stop_cmd = 'U', 'u'
+            steps_to_move = abs(steps_to_move)
+        
+        for _ in range(steps_to_move):
+            if not self.autofocus_running:
+                return
+            self.send_command(move_cmd)
+            time.sleep(SWEEP_MOVE_TIME)
+            self.send_command(stop_cmd)
+            time.sleep(0.1)
+        
+        time.sleep(SWEEP_SETTLE_TIME)
+        current_score = self._get_averaged_focus(samples=SWEEP_SAMPLES)
+        self.log_message(f"At best position: {current_score:.1f}")
+        
+        if not self.autofocus_running:
+            return
+        
+        # ========================================
+        # Phase 2: Fine hill-climbing from best position
+        # ========================================
+        self.log_message("Phase 2: Fine tuning")
+        
+        fine_speed = min_speed_idx
+        self._set_fine_speed_no_send(fine_speed)
+        self.send_command(str(fine_speed))
+        time.sleep(0.1)
+        
+        best_score = current_score
+        
+        # Try both directions to find which improves
+        # Try UP first
+        self.send_command('D')
+        time.sleep(FINE_MOVE_TIME)
+        self.send_command('d')
+        time.sleep(FINE_SETTLE_TIME)
+        
+        down_score = self._get_averaged_focus(samples=FINE_SAMPLES)
+        
+        if down_score > best_score:
+            fine_direction = 0  # DOWN
+            best_score = down_score
+            self.log_message(f"Fine direction: UP ({down_score:.1f})")
+        else:
+            # Go back down and try down
+            self.send_command('U')
+            time.sleep(FINE_MOVE_TIME)
+            self.send_command('u')
+            time.sleep(FINE_SETTLE_TIME)
+            
+            self.send_command('U')
+            time.sleep(FINE_MOVE_TIME)
+            self.send_command('u')
+            time.sleep(FINE_SETTLE_TIME)
+            
+            up_score = self._get_averaged_focus(samples=FINE_SAMPLES)
+            
+            if up_score > best_score:
+                fine_direction = 1  # UP
+                best_score = up_score
+                self.log_message(f"Fine direction: DOWN ({up_score:.1f})")
+            else:
+                # We're already at the peak
+                self.log_message("Already at peak, minor adjustment only")
+                fine_direction = 1  # Try up anyway
+                # Go back to center
+                self.send_command('U')
+                time.sleep(FINE_MOVE_TIME)
+                self.send_command('u')
+                time.sleep(FINE_SETTLE_TIME)
+        
+        if not self.autofocus_running:
+            return
+        
+        # Fine search
+        move_cmd = 'U' if fine_direction else 'D'
+        stop_cmd = 'u' if fine_direction else 'd'
+        reverse_cmd = 'D' if fine_direction else 'U'
+        reverse_stop = 'd' if fine_direction else 'u'
+        
+        no_improvement_count = 0
+        max_fine_no_improvement = 5
+        best_position_offset = 0
+        
+        while self.autofocus_running and no_improvement_count < max_fine_no_improvement:
+            self.send_command(move_cmd)
+            time.sleep(FINE_MOVE_TIME)
+            self.send_command(stop_cmd)
+            time.sleep(FINE_SETTLE_TIME)
+            
+            current_score = self._get_averaged_focus(samples=FINE_SAMPLES)
+            self._update_focus_display(current_score)
+            
+            if current_score > best_score:
+                best_score = current_score
+                no_improvement_count = 0
+                best_position_offset = 0
+                self.log_message(f"Fine better: {current_score:.1f}")
+            else:
+                no_improvement_count += 1
+                best_position_offset += 1
+        
+        if not self.autofocus_running:
+            return
+        
+        # Return to best fine position
+        if best_position_offset > 0:
+            self.log_message(f"Returning {best_position_offset} steps")
+            for _ in range(best_position_offset):
+                self.send_command(reverse_cmd)
+                time.sleep(FINE_MOVE_TIME)
+                self.send_command(reverse_stop)
+                time.sleep(0.1)
+        
+        # Final reading
+        time.sleep(FINE_SETTLE_TIME)
+        final_score = self._get_averaged_focus(samples=FINE_SAMPLES)
+        self._update_focus_display(final_score)
+        
+        self.autofocus_running = False
+        self.log_message(f"Autofocus complete. Final: {final_score:.1f}")
+        
+        self.root.after(0, lambda: self.af_button.config(state='normal'))
+
+    
+    
+    def _set_fine_speed_no_send(self, index):
+        """Update slider/label without sending command (for internal use)"""
+        self._updating_slider = True
+        self.speed_slider.set(index)
+        speed_val = self.speed_values[index]
+        self.fine_speed_label.config(text=f"Speed: {speed_val}")
+        self._updating_slider = False
+
+    def _update_focus_display(self, score):
+        """Update focus score display (thread-safe)"""
+        self.root.after(0, lambda: self.focus_score_label.config(text=f"Focus: {score:.1f}"))
+        
+    def log_message(self, msg):
+        """Add message to serial log"""
+        if not hasattr(self, 'serial_log'):
+            return
+        self.serial_log.config(state=tk.NORMAL)
+        self.serial_log.insert(tk.END, msg + "\n")
+        self.serial_log.see(tk.END)
+        self.serial_log.config(state=tk.DISABLED)
+        print(f"  Log: {msg}")
+        
+        # Check for mode changes in received messages
+        if msg.startswith("< MODE:"):
+            mode = msg.split(":")[-1]
+            self.mode_label.config(text=f"Mode: {mode.capitalize()}")
+    
+    def _serial_reader(self):
+        """Background thread to read serial data"""
+        while self.running:
+            if self.arduino and self.arduino.ser.in_waiting:
+                try:
+                    line = self.arduino.ser.readline().decode().strip()
+                    if line:
+                        self.serial_queue.put(line)
+                except Exception as e:
+                    self.serial_queue.put(f"[Error: {e}]")
+            threading.Event().wait(0.05)
+    
+    def _process_serial_queue(self):
+        """Process queued serial messages (call from main thread)"""
+        while not self.serial_queue.empty():
+            msg = self.serial_queue.get_nowait()
+            self.log_message(f"< {msg}")
+    
+    def update_camera(self):
+        """Capture and display one frame"""
+        try:
+            frame = self.camera.capture_frame()
+            
+            # Show live focus score if enabled
+            if self.live_focus_var.get():
+                score = self._get_averaged_focus()
+                self.focus_score_label.config(text=f"Focus: {score:.1f}")
+            
+            frame = cv2.cvtColor(frame, cv2.COLOR_BGR2RGB)
+            
+            # Resize if needed
+            h, w = frame.shape[:2]
+            max_width = 640
+            if w > max_width:
+                scale = max_width / w
+                frame = cv2.resize(frame, (int(w * scale), int(h * scale)))
+            
+            img = Image.fromarray(frame)
+            imgtk = ImageTk.PhotoImage(image=img)
+            
+            self.camera_label.imgtk = imgtk
+            self.camera_label.configure(image=imgtk)
+        except Exception as e:
+            print(f"Camera error: {e}")
+    
+    def run(self):
+        """Main loop"""
+        def update():
+            if self.running:
+                self.update_camera()
+                self._process_serial_queue()
+                self.root.after(33, update)
+        
+        update()
+        self.root.mainloop()
+    
+    def on_close(self):
+        """Clean shutdown"""
+        self.running = False
+        self.root.destroy()
\ No newline at end of file
diff --git a/src/main.py b/src/main.py
new file mode 100644
index 0000000..82358c5
--- /dev/null
+++ b/src/main.py
@@ -0,0 +1,27 @@
+from camera import Camera
+from arduino import Arduino
+from gui import AppGUI
+
+def main():
+    camera = Camera(device_id=0)
+    
+    # Arduino is optional - GUI still works without it
+    try:
+        arduino = Arduino()
+    except RuntimeError as e:
+        print(f"Arduino not found: {e}")
+        arduino = None
+    
+    try:
+        app = AppGUI(camera, arduino)
+        app.run()
+        
+    except KeyboardInterrupt:
+        print("Shutting down...")
+    finally:
+        if arduino:
+            arduino.close()
+        camera.release()
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file
diff --git a/src/scanner.py b/src/scanner.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/vision.py b/src/vision.py
new file mode 100644
index 0000000..879b47e
--- /dev/null
+++ b/src/vision.py
@@ -0,0 +1,21 @@
+import cv2
+import numpy as np
+
+def calculate_focus_score(frame):
+    """
+    Calculate focus score using Laplacian variance.
+    """
+    gray = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
+    laplacian = cv2.Laplacian(gray, cv2.CV_64F)
+    score = laplacian.var()
+    return score
+
+def calculate_focus_score_sobel(frame):
+    """
+    Focus score using Sobel gradients.
+    """
+    gray = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
+    sobel_x = cv2.Sobel(gray, cv2.CV_64F, 1, 0, ksize=3)
+    sobel_y = cv2.Sobel(gray, cv2.CV_64F, 0, 1, ksize=3)
+    score = np.mean(sobel_x**2 + sobel_y**2)
+    return score
\ No newline at end of file