src/gui.py

@@ -88,18 +88,6 @@ class AppGUI:
             on_mosaic_updated=self._on_mosaic_updated
         )
     
-        # Update initial memory estimate
-        self._update_memory_estimate()
-    
-    def _update_memory_estimate(self):
-        """Update memory estimate label"""
-        bytes_per_pixel = 3
-        mem_mb = (self.stitch_config.max_mosaic_width * 
-                  self.stitch_config.max_mosaic_height * 
-                  bytes_per_pixel) / (1024 * 1024)
-        if hasattr(self, 'memory_label'):
-            self.memory_label.config(text=f"~{mem_mb:.0f} MB")
-    
     def _on_command_sent(self, cmd):
         self.log_message(f"> {cmd}")
     
@@ -289,54 +277,63 @@ class AppGUI:
                   command=self._show_mosaic_window).pack(side=tk.RIGHT, padx=2)
     
     def _build_row2_stitch_settings(self, parent):
-        """Row 2: Stitching settings with max dimensions"""
+        """Row 2: Stitching settings"""
         row = ttk.LabelFrame(parent, text="Stitch Settings")
         row.pack(fill=tk.X, pady=(0, 3))
         
-        # First row: Threshold, Speed, Overlap
-        inner1 = ttk.Frame(row)
-        inner1.pack(fill=tk.X, padx=5, pady=3)
+        inner = ttk.Frame(row)
+        inner.pack(fill=tk.X, padx=5, pady=3)
         
         # Displacement threshold
-        ttk.Label(inner1, text="Threshold:").pack(side=tk.LEFT)
+        ttk.Label(inner, text="Threshold:").pack(side=tk.LEFT)
         self.disp_threshold_var = tk.DoubleVar(value=0.10)
         self.disp_threshold_spinbox = ttk.Spinbox(
-            inner1, from_=0.05, to=0.30, increment=0.01, width=5,
+            inner, from_=0.05, to=0.30, increment=0.01, width=5,
             textvariable=self.disp_threshold_var,
             command=self._update_stitch_config
         )
         self.disp_threshold_spinbox.pack(side=tk.LEFT, padx=(2, 10))
         
-        # Scan speed
-        ttk.Label(inner1, text="Speed:").pack(side=tk.LEFT)
-        self.scan_speed_var = tk.IntVar(value=3)
-        self.scan_speed_spinbox = ttk.Spinbox(
-            inner1, from_=1, to=6, width=3,
-            textvariable=self.scan_speed_var,
+        # Number of rows
+        ttk.Label(inner, text="Rows:").pack(side=tk.LEFT)
+        self.num_rows_var = tk.IntVar(value=3)
+        self.num_rows_spinbox = ttk.Spinbox(
+            inner, from_=1, to=10, width=3,
+            textvariable=self.num_rows_var,
             command=self._update_stitch_config
         )
-        self.scan_speed_spinbox.pack(side=tk.LEFT, padx=(2, 10))
+        self.num_rows_spinbox.pack(side=tk.LEFT, padx=(2, 10))
         
         # Row overlap
-        ttk.Label(inner1, text="Overlap:").pack(side=tk.LEFT)
+        ttk.Label(inner, text="Overlap:").pack(side=tk.LEFT)
         self.row_overlap_var = tk.DoubleVar(value=0.15)
         self.row_overlap_spinbox = ttk.Spinbox(
-            inner1, from_=0.05, to=0.50, increment=0.05, width=5,
+            inner, from_=0.05, to=0.50, increment=0.05, width=5,
             textvariable=self.row_overlap_var,
             command=self._update_stitch_config
         )
         self.row_overlap_spinbox.pack(side=tk.LEFT, padx=(2, 10))
         
+        # Scan speed
+        ttk.Label(inner, text="Speed:").pack(side=tk.LEFT)
+        self.scan_speed_var = tk.IntVar(value=3)
+        self.scan_speed_spinbox = ttk.Spinbox(
+            inner, from_=1, to=6, width=3,
+            textvariable=self.scan_speed_var,
+            command=self._update_stitch_config
+        )
+        self.scan_speed_spinbox.pack(side=tk.LEFT, padx=(2, 10))
+        
         # Autofocus toggle
         self.af_every_row_var = tk.BooleanVar(value=True)
         ttk.Checkbutton(
-            inner1, text="AF each row",
+            inner, text="AF each row",
             variable=self.af_every_row_var,
             command=self._update_stitch_config
         ).pack(side=tk.LEFT, padx=(10, 0))
         
         # Row/Direction status on right
-        status_frame = ttk.Frame(inner1)
+        status_frame = ttk.Frame(inner)
         status_frame.pack(side=tk.RIGHT)
         
         ttk.Label(status_frame, text="Row:").pack(side=tk.LEFT)
@@ -347,49 +344,6 @@ class AppGUI:
         self.direction_label = ttk.Label(status_frame, text="--", width=6, font=('Arial', 9))
         self.direction_label.pack(side=tk.LEFT)
     
-        # Second row: Max dimensions and test buttons
-        inner2 = ttk.Frame(row)
-        inner2.pack(fill=tk.X, padx=5, pady=(0, 3))
-        
-        # Max Width
-        ttk.Label(inner2, text="Max W:").pack(side=tk.LEFT)
-        self.max_width_var = tk.IntVar(value=5000)
-        self.max_width_entry = ttk.Entry(inner2, textvariable=self.max_width_var, width=7)
-        self.max_width_entry.pack(side=tk.LEFT, padx=(2, 5))
-        self.max_width_entry.bind('<Return>', lambda e: self._update_stitch_config())
-        
-        # Max Height
-        ttk.Label(inner2, text="Max H:").pack(side=tk.LEFT)
-        self.max_height_var = tk.IntVar(value=5000)
-        self.max_height_entry = ttk.Entry(inner2, textvariable=self.max_height_var, width=7)
-        self.max_height_entry.pack(side=tk.LEFT, padx=(2, 5))
-        self.max_height_entry.bind('<Return>', lambda e: self._update_stitch_config())
-        
-        # Apply button
-        ttk.Button(inner2, text="Apply", width=5,
-                  command=self._update_stitch_config).pack(side=tk.LEFT, padx=(5, 10))
-        
-        ttk.Separator(inner2, orient=tk.VERTICAL).pack(side=tk.LEFT, fill=tk.Y, padx=5)
-        
-        # Test buttons
-        ttk.Label(inner2, text="Test:").pack(side=tk.LEFT)
-        
-        ttk.Button(inner2, text="Row↓", width=5,
-                  command=self._test_row_transition).pack(side=tk.LEFT, padx=2)
-        
-        ttk.Button(inner2, text="Scan→", width=5,
-                  command=lambda: self._test_horizontal('right')).pack(side=tk.LEFT, padx=2)
-        
-        ttk.Button(inner2, text="Scan←", width=5,
-                  command=lambda: self._test_horizontal('left')).pack(side=tk.LEFT, padx=2)
-        
-        ttk.Button(inner2, text="Est", width=4,
-                  command=self._show_scan_estimate).pack(side=tk.LEFT, padx=2)
-        
-        # Memory estimate label
-        self.memory_label = ttk.Label(inner2, text="~-- MB", font=('Arial', 9))
-        self.memory_label.pack(side=tk.RIGHT)
-    
     def _build_row3_movement(self, parent):
         """Row 3: Movement controls for all axes"""
         row = ttk.LabelFrame(parent, text="Movement")
@@ -557,15 +511,11 @@ class AppGUI:
     def _update_stitch_config(self):
         """Update stitching scanner config from GUI values"""
         self.stitch_config.displacement_threshold = self.disp_threshold_var.get()
-        self.stitch_config.max_mosaic_width = self.max_width_var.get()
-        self.stitch_config.max_mosaic_height = self.max_height_var.get()
+        self.stitch_config.rows = self.num_rows_var.get()
         self.stitch_config.row_overlap = self.row_overlap_var.get()
         self.stitch_config.scan_speed_index = self.scan_speed_var.get()
         self.stitch_config.autofocus_every_row = self.af_every_row_var.get()
         
-        # Update memory estimate
-        self._update_memory_estimate()
-        
         # Reinitialize stitching scanner with new config
         self.stitch_scanner = StitchingScanner(
             camera=self.camera,
@@ -577,54 +527,6 @@ class AppGUI:
             on_mosaic_updated=self._on_mosaic_updated
         )
     
-        self.log_message(f"Config updated: {self.stitch_config.max_mosaic_width}x{self.stitch_config.max_mosaic_height}")
-    
-    def _test_row_transition(self):
-        """Test row transition without full scan"""
-        if not self.stitch_scanner:
-            self._update_stitch_config()
-        
-        self.log_message("Testing row transition...")
-        
-        def run_test():
-            result = self.stitch_scanner.test_row_transition()
-            self.root.after(0, lambda: self.log_message(
-                f"Row transition: {'SUCCESS' if result['success'] else 'FAILED'}, "
-                f"Y moved: {result['y_moved']:.1f}px"))
-            self.root.after(0, self._update_mosaic_window)
-        
-        threading.Thread(target=run_test, daemon=True).start()
-    
-    def _test_horizontal(self, direction: str):
-        """Test single row scan"""
-        if not self.stitch_scanner:
-            self._update_stitch_config()
-        
-        self.log_message(f"Testing single row scan ({direction})...")
-        
-        def run_test():
-            result = self.stitch_scanner.test_single_row(direction)
-            self.root.after(0, lambda: self.log_message(
-                f"Row scan: {result['stop_reason']}, {result['appends']} appends, "
-                f"mosaic: {result['mosaic_after'][0]}x{result['mosaic_after'][1]}"))
-            self.root.after(0, self._update_mosaic_window)
-        
-        threading.Thread(target=run_test, daemon=True).start()
-    
-    def _show_scan_estimate(self):
-        """Show memory estimate based on current settings"""
-        if not self.stitch_scanner:
-            self._update_stitch_config()
-        
-        est = self.stitch_scanner.get_memory_estimate()
-        
-        msg = (f"Memory Estimate:\n"
-               f"  Current: {est['current_size'][0]}x{est['current_size'][1]} = {est['current_mb']:.1f} MB\n"
-               f"  Max: {est['max_size'][0]}x{est['max_size'][1]} = {est['max_mb']:.0f} MB")
-        
-        self.log_message(msg)
-        self.memory_label.config(text=f"~{est['max_mb']:.0f} MB")
-    
     # =========================================================================
     # Overlay Drawing
     # =========================================================================
@@ -1024,16 +926,10 @@ class AppGUI:
             text=f"X: {state.cumulative_x:.1f} Y: {state.cumulative_y:.1f}"
         )
         
-        # Update row/direction and size
+        # Update row/direction
         if state.is_scanning:
-            # Show current row and progress percentage
-            width_pct = min(100, (state.mosaic_width / self.stitch_config.max_mosaic_width) * 100)
-            height_pct = min(100, (state.mosaic_height / self.stitch_config.max_mosaic_height) * 100)
-            self.row_label.config(text=f"R{state.current_row + 1}")
+            self.row_label.config(text=f"{state.current_row + 1}/{state.total_rows}")
             self.direction_label.config(text=state.direction)
-            # Update mosaic size label with progress
-            self.mosaic_size_label.config(
-                text=f"{state.mosaic_width}x{state.mosaic_height} ({height_pct:.0f}%)")
         else:
             self.row_label.config(text="--")
             self.direction_label.config(text="--")

src/stitching_scanner.py

@@ -1,59 +1,84 @@
 """
-Stitching Scanner v2 - Simplified unified approach
+Stitching Scanner v2 - Fixed displacement tracking
 
-Same displacement-based stitching for both horizontal rows and vertical row transitions.
-No complex visual matching - just track displacement and append strips.
+Key fix: Track displacement since last APPEND, not just cumulative.
+The strip width must match actual movement since we last added to the mosaic.
 """
 
 import cv2
 import numpy as np
 import time
 import threading
-from dataclasses import dataclass
-from typing import Optional, Callable, Tuple
+from dataclasses import dataclass, field
+from typing import List, Optional, Callable, Tuple
 from enum import Enum
 
 
 class ScanDirection(Enum):
-    RIGHT = 'right'
-    LEFT = 'left'
-    DOWN = 'down'
-    UP = 'up'
+    """Scan direction constants"""
+    RIGHT = 'right'   # X+ (E command)
+    LEFT = 'left'     # X- (W command)
+    DOWN = 'down'     # Y- (N command)
+    UP = 'up'         # Y+ (S command)
 
 
 @dataclass
 class StitchConfig:
-    displacement_threshold: float = 0.10  # 10% of frame triggers append
-    movement_interval: float = 0.001
-    frame_interval: float = 1.00
-    settle_time: float = 0.75
-    max_scan_time: float = 300.0
+    """Stitching scanner configuration"""
+    # Displacement threshold (percentage of frame size)
+    displacement_threshold: float = 0.10  # 10% of frame dimension
+    
+    # Movement timing
+    movement_interval: float = 0.001  # Seconds of motor on time
+    frame_interval: float = 0.25  # Seconds between frame captures (settle time)
+    settle_time: float = 0.5  # Seconds to wait after stopping
+    max_scan_time: float = 2400.0  # Safety timeout (5 minutes)
+    
+    # Scan pattern
+    rows: int = 3
     row_overlap: float = 0.15
-    max_mosaic_width: int = 15000
-    max_mosaic_height: int = 12000
+    
+    # Speed setting for scanning
     scan_speed_index: int = 3
+    
+    # Focus
     autofocus_every_row: bool = True
     
+    # Memory management
+    max_mosaic_width: int = 11000
+    max_mosaic_height: int = 11000
+# 11000, 24500, 450000
 
 @dataclass
 class StitchState:
+    """Current state for visualization"""
     is_scanning: bool = False
     direction: str = ''
+    
+    # Displacement tracking
     cumulative_x: float = 0.0
     cumulative_y: float = 0.0
     last_displacement: Tuple[float, float] = (0.0, 0.0)
+    
+    # Progress
     current_row: int = 0
     total_rows: int = 0
+    
+    # Mosaic size
     mosaic_width: int = 0
     mosaic_height: int = 0
+    
+    # Debug
     frame_count: int = 0
     append_count: int = 0
 
 
 class StitchingScanner:
     """
-    Slide scanner using continuous stitching.
-    Unified approach for horizontal and vertical movement.
+    Slide scanner using continuous stitching with correct displacement tracking.
+    
+    Key insight: We must track displacement since the LAST APPEND, and the
+    strip we append must exactly match that displacement.
     """
     
     def __init__(self, camera, motion_controller, autofocus_controller=None,
@@ -66,25 +91,32 @@ class StitchingScanner:
         self.autofocus = autofocus_controller
         self.config = config or StitchConfig()
         
+        # Callbacks
         self.on_log = on_log
         self.on_progress = on_progress
         self.on_mosaic_updated = on_mosaic_updated
         
+        # State
         self.running = False
         self.paused = False
         self.state = StitchState()
         self._state_lock = threading.Lock()
         
+        # Mosaic data
         self.mosaic: Optional[np.ndarray] = None
         self._mosaic_lock = threading.Lock()
         
-        self._prev_frame: Optional[np.ndarray] = None
-        self._displacement_since_append_x: float = 0.0
+        # Frame tracking - KEY CHANGE: separate reference for displacement calc vs append
+        self._prev_frame: Optional[np.ndarray] = None  # For frame-to-frame displacement
+        self._append_ref_frame: Optional[np.ndarray] = None  # Reference from last append
+        self._displacement_since_append_x: float = 0.0  # Accumulated since last append
         self._displacement_since_append_y: float = 0.0
         
+        # Thread
         self._thread: Optional[threading.Thread] = None
     
     def log(self, message: str):
+        """Log a message"""
         if self.on_log:
             self.on_log(f"[Stitch] {message}")
         print(f"[Stitch] {message}")
@@ -94,12 +126,17 @@ class StitchingScanner:
     # =========================================================================
     
     def _to_grayscale(self, frame: np.ndarray) -> np.ndarray:
+        """Convert frame to grayscale"""
         if len(frame.shape) == 3:
             return cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
         return frame
     
     def _detect_displacement(self, prev_frame: np.ndarray, 
                              curr_frame: np.ndarray) -> Tuple[float, float]:
+        """
+        Detect displacement between two frames using phase correlation.
+        Returns (dx, dy) in pixels.
+        """
         prev_gray = self._to_grayscale(prev_frame)
         curr_gray = self._to_grayscale(curr_frame)
         
@@ -109,16 +146,20 @@ class StitchingScanner:
         prev_f = prev_gray.astype(np.float32)
         curr_f = curr_gray.astype(np.float32)
         
+        # Apply window function to reduce edge effects
         h, w = prev_gray.shape
         window = cv2.createHanningWindow((w, h), cv2.CV_32F)
         prev_f = prev_f * window
         curr_f = curr_f * window
         
-        shift, _ = cv2.phaseCorrelate(prev_f, curr_f)
-        return shift
+        shift, response = cv2.phaseCorrelate(prev_f, curr_f)
+        dx, dy = shift
+        
+        return (dx, dy)
     
     def _detect_displacement_robust(self, prev_frame: np.ndarray,
                                    curr_frame: np.ndarray) -> Tuple[float, float]:
+        """Displacement detection with sanity checks"""
         dx, dy = self._detect_displacement(prev_frame, curr_frame)
         
         h, w = prev_frame.shape[:2]
@@ -131,14 +172,17 @@ class StitchingScanner:
         return (dx, dy)
     
     # =========================================================================
-    # Mosaic Building
+    # Mosaic Building - FIXED VERSION
     # =========================================================================
     
     def _init_mosaic(self, frame: np.ndarray):
+        """Initialize mosaic with first frame"""
         with self._mosaic_lock:
             self.mosaic = frame.copy()
         
+        # Set reference frames
         self._prev_frame = frame.copy()
+        self._append_ref_frame = frame.copy()
         self._displacement_since_append_x = 0.0
         self._displacement_since_append_y = 0.0
         
@@ -151,17 +195,20 @@ class StitchingScanner:
         
         self.log(f"Initialized mosaic: {frame.shape[1]}x{frame.shape[0]}")
     
-    def _blend_horizontal(self, base: np.ndarray, strip: np.ndarray, 
+    def _blend_strips_horizontal(self, base: np.ndarray, strip: np.ndarray, 
                                    blend_width: int, append_right: bool) -> np.ndarray:
+        """Blend strip onto base with gradient at seam to hide discontinuities."""
         if blend_width <= 0 or blend_width >= strip.shape[1]:
             if append_right:
                 return np.hstack([base, strip])
+            else:
                 return np.hstack([strip, base])
         
         h_base, w_base = base.shape[:2]
         h_strip, w_strip = strip.shape[:2]
         
         if h_strip != h_base:
+            # Height mismatch - can't blend properly
             if append_right:
                 return np.hstack([base, strip])
             return np.hstack([strip, base])
@@ -169,80 +216,53 @@ class StitchingScanner:
         blend_w = min(blend_width, w_strip, w_base)
         
         if append_right:
+            # base | blend_zone | rest_of_strip
             result_width = w_base + w_strip - blend_w
             result = np.zeros((h_base, result_width, 3), dtype=np.uint8)
+            
+            # Copy base
             result[:, :w_base] = base
             
+            # Create gradient: 1->0 for base weight
             alpha = np.linspace(1, 0, blend_w, dtype=np.float32)[np.newaxis, :, np.newaxis]
+            
             base_overlap = base[:, -blend_w:].astype(np.float32)
             strip_overlap = strip[:, :blend_w].astype(np.float32)
             blended = (base_overlap * alpha + strip_overlap * (1 - alpha)).astype(np.uint8)
             
             result[:, w_base - blend_w:w_base] = blended
             result[:, w_base:] = strip[:, blend_w:]
+            
             return result
         else:
+            # rest_of_strip | blend_zone | base
             result_width = w_base + w_strip - blend_w
             result = np.zeros((h_base, result_width, 3), dtype=np.uint8)
+            
             result[:, :w_strip] = strip
             
             alpha = np.linspace(0, 1, blend_w, dtype=np.float32)[np.newaxis, :, np.newaxis]
+            
             strip_overlap = strip[:, -blend_w:].astype(np.float32)
             base_overlap = base[:, :blend_w].astype(np.float32)
             blended = (strip_overlap * (1 - alpha) + base_overlap * alpha).astype(np.uint8)
             
             result[:, w_strip - blend_w:w_strip] = blended
             result[:, w_strip:] = base[:, blend_w:]
+            
             return result
 
-    def _blend_vertical(self, base: np.ndarray, strip: np.ndarray,
-                        blend_height: int, append_below: bool) -> np.ndarray:
-        mh, mw = base.shape[:2]
-        sh, sw = strip.shape[:2]
+    def _append_to_mosaic_fixed(self, frame: np.ndarray, direction: ScanDirection):
+        """
+        FIXED: Append with blending and fractional pixel preservation.
         
-        # Match widths
-        if sw > mw:
-            strip = strip[:, :mw]
-        elif sw < mw:
-            pad = np.zeros((sh, mw - sw, 3), dtype=np.uint8)
-            strip = np.hstack([strip, pad])
-        
-        blend_h = min(blend_height, sh, mh)
-        
-        if blend_h <= 0:
-            if append_below:
-                return np.vstack([base, strip])
-            return np.vstack([strip, base])
-        
-        if append_below:
-            alpha = np.linspace(1, 0, blend_h, dtype=np.float32)[:, np.newaxis, np.newaxis]
-            base_overlap = base[-blend_h:].astype(np.float32)
-            strip_overlap = strip[:blend_h].astype(np.float32)
-            blended = (base_overlap * alpha + strip_overlap * (1 - alpha)).astype(np.uint8)
-            
-            result_h = mh + sh - blend_h
-            result = np.zeros((result_h, mw, 3), dtype=np.uint8)
-            result[:mh - blend_h] = base[:-blend_h]
-            result[mh - blend_h:mh] = blended
-            result[mh:] = strip[blend_h:]
-            return result
-        else:
-            alpha = np.linspace(0, 1, blend_h, dtype=np.float32)[:, np.newaxis, np.newaxis]
-            strip_overlap = strip[-blend_h:].astype(np.float32)
-            base_overlap = base[:blend_h].astype(np.float32)
-            blended = (strip_overlap * (1 - alpha) + base_overlap * alpha).astype(np.uint8)
-            
-            result_h = mh + sh - blend_h
-            result = np.zeros((result_h, mw, 3), dtype=np.uint8)
-            result[:sh - blend_h] = strip[:-blend_h]
-            result[sh - blend_h:sh] = blended
-            result[sh:] = base[blend_h:]
-            return result
-    
-    def _append_strip(self, frame: np.ndarray, direction: ScanDirection):
-        """Append strip to mosaic based on accumulated displacement."""
-        BLEND_WIDTH = 10
-        SAFETY_MARGIN = 2
+        Key improvements:
+        1. Gradient blending at seams to hide color discontinuities
+        2. Preserve fractional pixel remainder to prevent cumulative drift
+        3. Small safety margin for alignment tolerance
+        """
+        BLEND_WIDTH = 10     # Pixels to blend at seam
+        SAFETY_MARGIN = 2    # Extra pixels as tolerance
         
         with self._mosaic_lock:
             if self.mosaic is None:
@@ -255,26 +275,30 @@ class StitchingScanner:
             dy = abs(self._displacement_since_append_y)
             
             if direction in [ScanDirection.RIGHT, ScanDirection.LEFT]:
+                # Round and add safety margin
                 append_width = round(dx) + SAFETY_MARGIN
                 append_width = min(append_width, w - BLEND_WIDTH - 5)
                 
                 if append_width < 1:
                     return
                 
+                # Calculate fractional remainder to preserve
                 pixels_consumed = append_width - SAFETY_MARGIN
                 fractional_remainder = dx - pixels_consumed
                 
                 if direction == ScanDirection.RIGHT:
+                    # Grab strip with extra for blending
                     strip_start = max(0, w - append_width - BLEND_WIDTH)
                     new_strip = frame[:, strip_start:]
-                    self.mosaic = self._blend_horizontal(
+                    self.mosaic = self._blend_strips_horizontal(
                         self.mosaic, new_strip, BLEND_WIDTH, append_right=True)
                 else:
                     strip_end = min(w, append_width + BLEND_WIDTH)
                     new_strip = frame[:, :strip_end]
-                    self.mosaic = self._blend_horizontal(
+                    self.mosaic = self._blend_strips_horizontal(
                         self.mosaic, new_strip, BLEND_WIDTH, append_right=False)
                 
+                # KEEP fractional remainder instead of resetting to 0!
                 self._displacement_since_append_x = fractional_remainder
                 self._displacement_since_append_y = 0.0
                     
@@ -289,34 +313,112 @@ class StitchingScanner:
                 fractional_remainder = dy - pixels_consumed
                 
                 if direction == ScanDirection.DOWN:
-                    strip_end = min(h, append_height + BLEND_WIDTH)
-                    new_strip = frame[:strip_end:, :]
-                    self.mosaic = self._blend_vertical(
-                        self.mosaic, new_strip, BLEND_WIDTH, append_below=False)
-                else:
                     strip_start = max(0, h - append_height - BLEND_WIDTH)
-                    new_strip = frame[:strip_start, :]
-                    self.mosaic = self._blend_vertical(
-                        self.mosaic, new_strip, BLEND_WIDTH, append_below=True)
+                    new_strip = frame[strip_start:, :]
+                    
+                    # Match widths
+                    if new_strip.shape[1] > mw:
+                        new_strip = new_strip[:, :mw]
+                    elif new_strip.shape[1] < mw:
+                        pad = np.zeros((new_strip.shape[0], mw - new_strip.shape[1], 3), dtype=np.uint8)
+                        new_strip = np.hstack([new_strip, pad])
+                    
+                    # Vertical blend
+                    blend_h = min(BLEND_WIDTH, new_strip.shape[0], mh)
+                    alpha = np.linspace(1, 0, blend_h, dtype=np.float32)[:, np.newaxis, np.newaxis]
+                    
+                    base_overlap = self.mosaic[-blend_h:].astype(np.float32)
+                    strip_overlap = new_strip[:blend_h].astype(np.float32)
+                    blended = (base_overlap * alpha + strip_overlap * (1 - alpha)).astype(np.uint8)
+                    
+                    result_h = mh + new_strip.shape[0] - blend_h
+                    result = np.zeros((result_h, mw, 3), dtype=np.uint8)
+                    result[:mh - blend_h] = self.mosaic[:-blend_h]
+                    result[mh - blend_h:mh] = blended
+                    result[mh:] = new_strip[blend_h:]
+                    self.mosaic = result
+                else:
+                    strip_end = min(h, append_height + BLEND_WIDTH)
+                    new_strip = frame[:strip_end, :]
+                    
+                    if new_strip.shape[1] > mw:
+                        new_strip = new_strip[:, :mw]
+                    elif new_strip.shape[1] < mw:
+                        pad = np.zeros((new_strip.shape[0], mw - new_strip.shape[1], 3), dtype=np.uint8)
+                        new_strip = np.hstack([new_strip, pad])
+                    
+                    self.mosaic = np.vstack([new_strip, self.mosaic])
                 
                 self._displacement_since_append_x = 0.0
                 self._displacement_since_append_y = fractional_remainder
             
             new_mh, new_mw = self.mosaic.shape[:2]
         
+        # Update state
         with self._state_lock:
             self.state.mosaic_width = new_mw
             self.state.mosaic_height = new_mh
             self.state.append_count += 1
         
+        # Update reference frame (fractional remainder already set above - don't reset!)
+        self._append_ref_frame = frame.copy()
+        
         if self.on_mosaic_updated:
             self.on_mosaic_updated()
     
+    def _start_new_row(self, frame: np.ndarray, direction: ScanDirection):
+        """Start a new row in the mosaic"""
+        with self._mosaic_lock:
+            if self.mosaic is None:
+                self._init_mosaic(frame)
+                return
+            
+            h, w = frame.shape[:2]
+            mh, mw = self.mosaic.shape[:2]
+            
+            # Calculate overlap
+            overlap_pixels = int(h * self.config.row_overlap)
+            append_height = h - overlap_pixels
+            
+            if direction == ScanDirection.DOWN:
+                new_strip = frame[overlap_pixels:, :]
+                
+                if new_strip.shape[1] < mw:
+                    pad = np.zeros((new_strip.shape[0], mw - new_strip.shape[1], 3), dtype=np.uint8)
+                    new_strip = np.hstack([new_strip, pad])
+                elif new_strip.shape[1] > mw:
+                    new_strip = new_strip[:, :mw]
+                
+                self.mosaic = np.vstack([self.mosaic, new_strip])
+            else:
+                new_strip = frame[:append_height, :]
+                
+                if new_strip.shape[1] < mw:
+                    pad = np.zeros((new_strip.shape[0], mw - new_strip.shape[1], 3), dtype=np.uint8)
+                    new_strip = np.hstack([new_strip, pad])
+                elif new_strip.shape[1] > mw:
+                    new_strip = new_strip[:, :mw]
+                
+                self.mosaic = np.vstack([new_strip, self.mosaic])
+        
+        # Reset all tracking for new row
+        self._prev_frame = frame.copy()
+        self._append_ref_frame = frame.copy()
+        self._displacement_since_append_x = 0.0
+        self._displacement_since_append_y = 0.0
+        
+        with self._state_lock:
+            self.state.mosaic_height = self.mosaic.shape[0]
+            self.state.mosaic_width = self.mosaic.shape[1]
+        
+        self.log(f"New row started, mosaic: {self.mosaic.shape[1]}x{self.mosaic.shape[0]}")
+    
     # =========================================================================
     # Scan Control
     # =========================================================================
     
     def start(self) -> bool:
+        """Start the stitching scan"""
         if self.running:
             self.log("Already running")
             return False
@@ -327,11 +429,13 @@ class StitchingScanner:
         with self._state_lock:
             self.state = StitchState()
             self.state.is_scanning = True
+            self.state.total_rows = self.config.rows
         
         with self._mosaic_lock:
             self.mosaic = None
         
         self._prev_frame = None
+        self._append_ref_frame = None
         self._displacement_since_append_x = 0.0
         self._displacement_since_append_y = 0.0
         
@@ -342,6 +446,7 @@ class StitchingScanner:
         return True
     
     def stop(self):
+        """Stop the scan"""
         self.running = False
         self.paused = False
         self.motion.stop_all()
@@ -352,24 +457,26 @@ class StitchingScanner:
         self.log("Scan stopped")
     
     def pause(self):
+        """Pause the scan"""
         if self.running and not self.paused:
             self.paused = True
             self.motion.stop_all()
             self.log("Scan paused")
     
     def resume(self):
+        """Resume the scan"""
         if self.running and self.paused:
             self.paused = False
             self.log("Scan resumed")
     
     # =========================================================================
-    # Scanning Logic
+    # Main Scan Loop
     # =========================================================================
     
     def _scan_loop(self):
+        """Main scanning loop"""
         try:
             self.log("Starting scan loop")
-            self.log(f"Max dimensions: {self.config.max_mosaic_width}x{self.config.max_mosaic_height}")
             
             self.motion.set_speed(self.config.scan_speed_index)
             time.sleep(0.1)
@@ -377,35 +484,30 @@ class StitchingScanner:
             frame = self._capture_frame()
             self._init_mosaic(frame)
             
-            row = 0
-            while self.running:
+            for row in range(self.config.rows):
+                if not self.running:
+                    break
+                
                 with self._state_lock:
                     self.state.current_row = row
-                    self.state.total_rows = row + 1
                 
-                self.log(f"=== Row {row + 1} ===")
+                self.log(f"=== Row {row + 1}/{self.config.rows} ===")
                 
-                # Serpentine: even rows right, odd rows left
-                h_direction = ScanDirection.RIGHT if row % 2 == 0 else ScanDirection.LEFT
+                # Serpentine pattern
+                if row % 2 == 0:
+                    h_direction = ScanDirection.RIGHT
+                else:
+                    h_direction = ScanDirection.LEFT
                 
-                stop_reason = self._scan_direction(h_direction)
+                self._scan_horizontal(h_direction)
                 
                 if not self.running:
                     break
                 
-                # Check max height
-                if self.state.mosaic_height >= self.config.max_mosaic_height:
-                    self.log(f"Max height reached ({self.state.mosaic_height}px)")
-                    break
+                if row < self.config.rows - 1:
+                    self._move_to_next_row()
             
-                # Move to next row using same stitching approach
-                if not self._move_to_next_row():
-                    self.log("Failed to move to next row")
-                    break
-                
-                row += 1
-            
-            self.log(f"Scan complete! Final: {self.state.mosaic_width}x{self.state.mosaic_height}")
+            self.log("Scan complete!")
             
         except Exception as e:
             self.log(f"Scan error: {e}")
@@ -417,8 +519,8 @@ class StitchingScanner:
             with self._state_lock:
                 self.state.is_scanning = False
     
-    def _scan_direction(self, direction: ScanDirection) -> str:
-        """Scan in a direction until edge or max dimension reached."""
+    def _scan_horizontal(self, direction: ScanDirection):
+        """Scan horizontally with fixed displacement tracking"""
         self.log(f"Scanning {direction.value}...")
         
         with self._state_lock:
@@ -426,51 +528,44 @@ class StitchingScanner:
         
         frame = self._capture_frame()
         h, w = frame.shape[:2]
-        
-        # Setup based on direction
-        if direction in [ScanDirection.RIGHT, ScanDirection.LEFT]:
         threshold_pixels = w * self.config.displacement_threshold
-            max_dim = self.config.max_mosaic_width
-            current_dim = lambda: self.state.mosaic_width
-            start_cmd = 'E' if direction == ScanDirection.RIGHT else 'W'
-            stop_cmd = 'e' if direction == ScanDirection.RIGHT else 'w'
-        else:
-            threshold_pixels = h * self.config.displacement_threshold
-            max_dim = self.config.max_mosaic_height
-            current_dim = lambda: self.state.mosaic_height
-            start_cmd = 'S' if direction == ScanDirection.DOWN else 'N'
-            stop_cmd = 's' if direction == ScanDirection.DOWN else 'n'
         
+        # Initialize tracking
         self._prev_frame = frame.copy()
+        self._append_ref_frame = frame.copy()
         self._displacement_since_append_x = 0.0
         self._displacement_since_append_y = 0.0
         
         start_time = time.time()
         no_movement_count = 0
         max_no_movement = 50
-        stop_reason = 'stopped'
         
         while self.running and not self.paused:
             if time.time() - start_time > self.config.max_scan_time:
                 self.log("Scan timeout")
-                stop_reason = 'timeout'
                 break
             
-            if current_dim() >= max_dim:
-                self.log(f"Max dimension reached ({current_dim()}px)")
-                stop_reason = 'max_dim'
-                break
+            # Pulse the motor
+            if direction == ScanDirection.RIGHT:
+                self.motion.send_command('E')
+            else:
+                self.motion.send_command('W')
             
-            # Pulse motor
-            self.motion.send_command(start_cmd)
             time.sleep(self.config.movement_interval)
-            self.motion.send_command(stop_cmd)
             
+            if direction == ScanDirection.RIGHT:
+                self.motion.send_command('e')
+            else:
+                self.motion.send_command('w')
+            
+            # Wait for settle
             time.sleep(self.config.frame_interval)
             
+            # Capture and measure
             curr_frame = self._capture_frame()
             dx, dy = self._detect_displacement_robust(self._prev_frame, curr_frame)
             
+            # Accumulate displacement SINCE LAST APPEND
             self._displacement_since_append_x += dx
             self._displacement_since_append_y += dy
             
@@ -480,119 +575,78 @@ class StitchingScanner:
                 self.state.last_displacement = (dx, dy)
                 self.state.frame_count += 1
             
-            # Edge detection
-            movement = abs(dx) if direction in [ScanDirection.RIGHT, ScanDirection.LEFT] else abs(dy)
-            if movement < 1.0:
+            # Check for no movement
+            if abs(dx) < 1.0 and abs(dy) < 1.0:
                 no_movement_count += 1
                 if no_movement_count >= max_no_movement:
-                    self.log(f"Edge detected (no movement)")
-                    stop_reason = 'edge'
+                    self.log(f"Edge detected (no movement for {no_movement_count} frames)")
                     break
             else:
                 no_movement_count = 0
             
-            # Append when threshold reached
-            disp = abs(self._displacement_since_append_x) if direction in [ScanDirection.RIGHT, ScanDirection.LEFT] else abs(self._displacement_since_append_y)
-            if disp >= threshold_pixels:
-                self._append_strip(curr_frame, direction)
-                self.log(f"Appended {disp:.1f}px, mosaic: {self.state.mosaic_width}x{self.state.mosaic_height}")
+            # Check threshold and append
+            if abs(self._displacement_since_append_x) >= threshold_pixels:
+                self._append_to_mosaic_fixed(curr_frame, direction)
+                self.log(f"Appended {abs(self._displacement_since_append_x):.1f}px strip, "
+                        f"mosaic: {self.state.mosaic_width}x{self.state.mosaic_height}")
             
+            # Update prev_frame for next displacement calculation
             self._prev_frame = curr_frame.copy()
             
             if self.on_progress:
                 self.on_progress(self.state.append_count, 0)
         
-        self.motion.send_command(stop_cmd)
-        time.sleep(self.config.settle_time)
-        self.log(f"Direction finished: {stop_reason}")
-        return stop_reason
+        # Stop
+        if direction == ScanDirection.RIGHT:
+            self.motion.send_command('e')
+        else:
+            self.motion.send_command('w')
         
-    def _move_to_next_row(self) -> bool:
-        """
-        Move down to next row using displacement-based stitching.
-        Same approach as horizontal scanning.
-        """
+        time.sleep(self.config.settle_time)
+    
+    def _move_to_next_row(self):
+        """Move down to next row"""
         self.log("Moving to next row...")
         
         frame = self._capture_frame()
         h, w = frame.shape[:2]
-        
-        # Target: move (1 - overlap) * frame_height
-        target_displacement = h * (1 - self.config.row_overlap)
-        threshold_pixels = h * self.config.displacement_threshold
-        
-        self.log(f"Target Y: {target_displacement:.0f}px, threshold: {threshold_pixels:.0f}px")
+        move_distance = h * (1 - self.config.row_overlap)
         
         with self._state_lock:
             self.state.direction = 'down'
-            self.state.cumulative_y = 0.0
+        
+        self.motion.send_command('N')
         
         self._prev_frame = frame.copy()
-        self._displacement_since_append_x = 0.0
-        self._displacement_since_append_y = 0.0
+        cumulative_y = 0.0
         
-        total_y = 0.0
-        no_movement_count = 0
-        max_no_movement = 30
-        
-        # Start moving South
-        self.motion.send_command('S')
-        
-        try:
         while self.running:
             time.sleep(self.config.frame_interval)
             
             curr_frame = self._capture_frame()
             dx, dy = self._detect_displacement_robust(self._prev_frame, curr_frame)
             
-                self._displacement_since_append_y += dy
-                total_y += dy
-                
-                with self._state_lock:
-                    self.state.cumulative_y = total_y
-                    self.state.last_displacement = (dx, dy)
-                
-                # Edge detection
-                if abs(dy) < 1.0:
-                    no_movement_count += 1
-                    if no_movement_count >= max_no_movement:
-                        self.log("Edge detected during row transition")
-                        self.motion.send_command('s')
-                        time.sleep(self.config.settle_time)
-                        return False
-                else:
-                    no_movement_count = 0
-                
-                # Append strip when threshold reached
-                if abs(self._displacement_since_append_y) >= threshold_pixels:
-                    self._append_strip(curr_frame, ScanDirection.DOWN)
-                    self.log(f"  Row transition: appended, total Y: {abs(total_y):.1f}px")
-                
-                # Done when we've moved enough
-                if abs(total_y) >= target_displacement:
-                    self.log(f"Row transition complete: {abs(total_y):.1f}px")
-                    self.motion.send_command('s')
-                    time.sleep(self.config.settle_time)
-                    
-                    # Reset for next horizontal row
-                    frame = self._capture_frame()
-                    self._prev_frame = frame.copy()
-                    self._displacement_since_append_x = 0.0
-                    self._displacement_since_append_y = 0.0
-                    return True
-                
+            cumulative_y += dy
             self._prev_frame = curr_frame.copy()
             
-        except Exception as e:
-            self.log(f"Row transition error: {e}")
-            self.motion.send_command('s')
-            return False
+            with self._state_lock:
+                self.state.cumulative_y = cumulative_y
             
-        self.motion.send_command('s')
+            if abs(cumulative_y) >= move_distance:
+                break
+            
+            if abs(cumulative_y) < 5 and self.state.frame_count > 50:
+                self.log("Warning: Minimal Y movement")
+                break
+        
+        self.motion.send_command('n')
         time.sleep(self.config.settle_time)
-        return False
+        
+        frame = self._capture_frame()
+        self._start_new_row(frame, ScanDirection.DOWN)
     
     def _capture_frame(self) -> np.ndarray:
+        """Capture and rotate frame"""
         frame = self.camera.capture_frame()
         frame = cv2.rotate(frame, cv2.ROTATE_90_CLOCKWISE)
         return frame
@@ -602,6 +656,7 @@ class StitchingScanner:
     # =========================================================================
     
     def get_state(self) -> StitchState:
+        """Get current scan state"""
         with self._state_lock:
             return StitchState(
                 is_scanning=self.state.is_scanning,
@@ -618,12 +673,14 @@ class StitchingScanner:
             )
     
     def get_mosaic(self) -> Optional[np.ndarray]:
+        """Get current mosaic (full resolution)"""
         with self._mosaic_lock:
             if self.mosaic is not None:
                 return self.mosaic.copy()
             return None
     
     def get_mosaic_preview(self, max_size: int = 600) -> Optional[np.ndarray]:
+        """Get scaled mosaic for preview"""
         with self._mosaic_lock:
             if self.mosaic is None:
                 return None
@@ -639,9 +696,11 @@ class StitchingScanner:
             return self.mosaic.copy()
     
     def save_mosaic(self, filepath: str) -> bool:
+        """Save mosaic to file"""
         with self._mosaic_lock:
             if self.mosaic is None:
                 return False
+            
             cv2.imwrite(filepath, self.mosaic)
             self.log(f"Saved mosaic to {filepath}")
             return True
@@ -651,106 +710,25 @@ class StitchingScanner:
     # =========================================================================
     
     def test_displacement(self, num_frames: int = 10) -> dict:
-        results = {'frames': [], 'total_dx': 0.0, 'total_dy': 0.0}
+        """Test displacement detection"""
+        results = {
+            'frames': [],
+            'total_dx': 0.0,
+            'total_dy': 0.0
+        }
+        
         prev_frame = self._capture_frame()
         
         for i in range(num_frames):
             time.sleep(0.1)
             curr_frame = self._capture_frame()
+            
             dx, dy = self._detect_displacement(prev_frame, curr_frame)
+            
             results['frames'].append({'frame': i, 'dx': dx, 'dy': dy})
             results['total_dx'] += dx
             results['total_dy'] += dy
+            
             prev_frame = curr_frame
         
         return results
-    
-    def test_row_transition(self) -> dict:
-        """Test row transition using displacement stitching."""
-        results = {
-            'success': False,
-            'y_moved': 0.0,
-            'mosaic_before': (0, 0),
-            'mosaic_after': (0, 0),
-            'error': None
-        }
-        
-        try:
-            self.log("Testing row transition...")
-            
-            if self.mosaic is None:
-                frame = self._capture_frame()
-                self._init_mosaic(frame)
-            
-            results['mosaic_before'] = (self.state.mosaic_width, self.state.mosaic_height)
-            
-            with self._state_lock:
-                self.state.cumulative_y = 0.0
-            
-            self.running = True
-            success = self._move_to_next_row()
-            self.running = False
-            
-            results['success'] = success
-            results['y_moved'] = self.state.cumulative_y
-            results['mosaic_after'] = (self.state.mosaic_width, self.state.mosaic_height)
-            
-            self.log(f"Row transition: {'SUCCESS' if success else 'FAILED'}, Y: {results['y_moved']:.1f}px")
-            
-        except Exception as e:
-            results['error'] = str(e)
-            self.log(f"Test error: {e}")
-            self.running = False
-        
-        return results
-    
-    def test_single_row(self, direction: str = 'right') -> dict:
-        """Test scanning a single row."""
-        results = {
-            'success': False,
-            'stop_reason': None,
-            'appends': 0,
-            'mosaic_before': (0, 0),
-            'mosaic_after': (0, 0),
-            'error': None
-        }
-        
-        try:
-            self.log(f"Testing single row ({direction})...")
-            
-            if self.mosaic is None:
-                frame = self._capture_frame()
-                self._init_mosaic(frame)
-            
-            results['mosaic_before'] = (self.state.mosaic_width, self.state.mosaic_height)
-            appends_before = self.state.append_count
-            
-            self.motion.set_speed(self.config.scan_speed_index)
-            time.sleep(0.1)
-            
-            self.running = True
-            scan_dir = ScanDirection.RIGHT if direction == 'right' else ScanDirection.LEFT
-            stop_reason = self._scan_direction(scan_dir)
-            self.running = False
-            
-            results['success'] = True
-            results['stop_reason'] = stop_reason
-            results['appends'] = self.state.append_count - appends_before
-            results['mosaic_after'] = (self.state.mosaic_width, self.state.mosaic_height)
-            
-        except Exception as e:
-            results['error'] = str(e)
-            self.running = False
-        
-        return results
-    
-    def get_memory_estimate(self) -> dict:
-        current_bytes = self.mosaic.nbytes if self.mosaic is not None else 0
-        max_bytes = self.config.max_mosaic_width * self.config.max_mosaic_height * 3
-        
-        return {
-            'current_size': (self.state.mosaic_width, self.state.mosaic_height),
-            'current_mb': current_bytes / (1024 * 1024),
-            'max_size': (self.config.max_mosaic_width, self.config.max_mosaic_height),
-            'max_mb': max_bytes / (1024 * 1024),
-        }