lattice-sub 1.2.2__tar.gz → 1.3.1__tar.gz

{lattice_sub-1.2.2/src/lattice_sub.egg-info → lattice_sub-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lattice-sub
-Version: 1.2.2
+Version: 1.3.1
 Summary: Lattice subtraction for cryo-EM micrographs - removes periodic crystal signals to reveal non-periodic features
 Author-email: George Stephenson <george.stephenson@colorado.edu>, Vignesh Kasinath <vignesh.kasinath@colorado.edu>
 License: MIT
@@ -94,7 +94,17 @@ lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56
 lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56 --vis comparisons/
 ```
 
-This creates side-by-side PNG images showing before/after/difference for each micrograph.
+This creates 4-panel PNG comparison images for each micrograph showing:
+1. **Original** - Input micrograph
+2. **Subtracted** - Lattice-removed result  
+3. **Difference** - What was removed (5x amplified)
+4. **Threshold Curve** - Threshold vs lattice removal efficacy
+
+**Limit the number of visualizations:**
+```bash
+# Generate visualizations for first 10 images only
+lattice-sub batch input_folder/ output_folder/ -p 0.56 --vis comparisons/ -n 10
+```
 
 ---
 
@@ -105,6 +115,8 @@ This creates side-by-side PNG images showing before/after/difference for each mi
 | `-p, --pixel-size` | **Required.** Pixel size in Ångstroms |
 | `-o, --output` | Output file path (default: `sub_<input>`) |
 | `-t, --threshold` | Peak detection sensitivity (default: **auto** - optimized per image) |
+| `--vis DIR` | Generate 4-panel comparison PNGs in DIR |
+| `-n, --num-vis N` | Limit visualizations to first N images |
 | `--cpu` | Force CPU processing (GPU is used by default) |
 | `-q, --quiet` | Hide the banner and progress messages |
 | `-v, --verbose` | Show detailed processing information |
@@ -207,7 +219,7 @@ lattice-sub batch input/ output/ -p 0.56
 
 **Output:**
 ```
-Phase-preserving FFT inpainting for cryo-EM  |  v1.2.2
+Phase-preserving FFT inpainting for cryo-EM  |  v1.3.0
 
   Configuration
   -------------

{lattice_sub-1.2.2 → lattice_sub-1.3.1}/README.md

@@ -53,7 +53,17 @@ lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56
 lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56 --vis comparisons/
 ```
 
-This creates side-by-side PNG images showing before/after/difference for each micrograph.
+This creates 4-panel PNG comparison images for each micrograph showing:
+1. **Original** - Input micrograph
+2. **Subtracted** - Lattice-removed result  
+3. **Difference** - What was removed (5x amplified)
+4. **Threshold Curve** - Threshold vs lattice removal efficacy
+
+**Limit the number of visualizations:**
+```bash
+# Generate visualizations for first 10 images only
+lattice-sub batch input_folder/ output_folder/ -p 0.56 --vis comparisons/ -n 10
+```
 
 ---
 
@@ -64,6 +74,8 @@ This creates side-by-side PNG images showing before/after/difference for each mi
 | `-p, --pixel-size` | **Required.** Pixel size in Ångstroms |
 | `-o, --output` | Output file path (default: `sub_<input>`) |
 | `-t, --threshold` | Peak detection sensitivity (default: **auto** - optimized per image) |
+| `--vis DIR` | Generate 4-panel comparison PNGs in DIR |
+| `-n, --num-vis N` | Limit visualizations to first N images |
 | `--cpu` | Force CPU processing (GPU is used by default) |
 | `-q, --quiet` | Hide the banner and progress messages |
 | `-v, --verbose` | Show detailed processing information |
@@ -166,7 +178,7 @@ lattice-sub batch input/ output/ -p 0.56
 
 **Output:**
 ```
-Phase-preserving FFT inpainting for cryo-EM  |  v1.2.2
+Phase-preserving FFT inpainting for cryo-EM  |  v1.3.0
 
   Configuration
   -------------

{lattice_sub-1.2.2 → lattice_sub-1.3.1}/examples/config.yaml

@@ -1,9 +1,9 @@
-# Lattice Subtraction - Example Configuration (v1.1.0)
+# Lattice Subtraction - Example Configuration
 # 
 # This file contains all available configuration options.
 # Copy and modify for your specific dataset.
 #
-# NEW in v1.1.0: Auto-threshold and Kornia GPU acceleration are now defaults!
+# Auto-threshold and Kornia GPU acceleration are defaults.
 # Just run `lattice-sub process image.mrc -p 0.56` for optimal results.
 
 # ============================================

{lattice_sub-1.2.2 → lattice_sub-1.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "lattice-sub"
-version = "1.2.2"
+version = "1.3.1"
 description = "Lattice subtraction for cryo-EM micrographs - removes periodic crystal signals to reveal non-periodic features"
 readme = "README.md"
 license = {text = "MIT"}

{lattice_sub-1.2.2 → lattice_sub-1.3.1/src/lattice_sub.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lattice-sub
-Version: 1.2.2
+Version: 1.3.1
 Summary: Lattice subtraction for cryo-EM micrographs - removes periodic crystal signals to reveal non-periodic features
 Author-email: George Stephenson <george.stephenson@colorado.edu>, Vignesh Kasinath <vignesh.kasinath@colorado.edu>
 License: MIT
@@ -94,7 +94,17 @@ lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56
 lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56 --vis comparisons/
 ```
 
-This creates side-by-side PNG images showing before/after/difference for each micrograph.
+This creates 4-panel PNG comparison images for each micrograph showing:
+1. **Original** - Input micrograph
+2. **Subtracted** - Lattice-removed result  
+3. **Difference** - What was removed (5x amplified)
+4. **Threshold Curve** - Threshold vs lattice removal efficacy
+
+**Limit the number of visualizations:**
+```bash
+# Generate visualizations for first 10 images only
+lattice-sub batch input_folder/ output_folder/ -p 0.56 --vis comparisons/ -n 10
+```
 
 ---
 
@@ -105,6 +115,8 @@ This creates side-by-side PNG images showing before/after/difference for each mi
 | `-p, --pixel-size` | **Required.** Pixel size in Ångstroms |
 | `-o, --output` | Output file path (default: `sub_<input>`) |
 | `-t, --threshold` | Peak detection sensitivity (default: **auto** - optimized per image) |
+| `--vis DIR` | Generate 4-panel comparison PNGs in DIR |
+| `-n, --num-vis N` | Limit visualizations to first N images |
 | `--cpu` | Force CPU processing (GPU is used by default) |
 | `-q, --quiet` | Hide the banner and progress messages |
 | `-v, --verbose` | Show detailed processing information |
@@ -207,7 +219,7 @@ lattice-sub batch input/ output/ -p 0.56
 
 **Output:**
 ```
-Phase-preserving FFT inpainting for cryo-EM  |  v1.2.2
+Phase-preserving FFT inpainting for cryo-EM  |  v1.3.0
 
   Configuration
   -------------

{lattice_sub-1.2.2 → lattice_sub-1.3.1}/src/lattice_subtraction/__init__.py

@@ -19,7 +19,7 @@ Example:
     >>> result.save("output.mrc")
 """
 
-__version__ = "1.2.2"
+__version__ = "1.3.1"
 __author__ = "George Stephenson & Vignesh Kasinath"
 
 from .config import Config

{lattice_sub-1.2.2 → lattice_sub-1.3.1}/src/lattice_subtraction/cli.py

@@ -153,9 +153,12 @@ def main():
         # Batch process directory (GPU handles parallelism)
         lattice-sub batch input_dir/ output_dir/ --pixel-size 0.56
         
-        # Batch with visualizations
+        # Batch with visualizations (4-panel with threshold curve)
         lattice-sub batch input_dir/ output_dir/ -p 0.56 --vis viz_dir/
         
+        # Batch with limited visualizations (only first 10)
+        lattice-sub batch input_dir/ output_dir/ -p 0.56 --vis viz_dir/ -n 10
+        
         # CPU batch with parallel workers (use -j only with --cpu)
         lattice-sub batch input_dir/ output_dir/ -p 0.56 --cpu -j 8
         
@@ -502,6 +505,12 @@ def process(
     default=None,
     help="Generate comparison visualizations in this directory",
 )
+@click.option(
+    "-n", "--num-vis",
+    type=int,
+    default=None,
+    help="Number of visualizations to generate (default: all)",
+)
 @click.option(
     "-v", "--verbose",
     is_flag=True,
@@ -528,6 +537,7 @@ def batch(
     config: Optional[str],
     recursive: bool,
     vis: Optional[str],
+    num_vis: Optional[int],
     verbose: bool,
     quiet: bool,
     cpu: bool,
@@ -617,7 +627,8 @@ def batch(
     
     # Generate visualizations if requested
     if vis:
-        logger.info(f"Generating visualizations in: {vis}")
+        limit_msg = f" (limit: {num_vis})" if num_vis else ""
+        logger.info(f"Generating visualizations in: {vis}{limit_msg}")
         viz_success, viz_total = generate_visualizations(
             input_dir=input_dir,
             output_dir=output_dir,
@@ -625,6 +636,8 @@ def batch(
             prefix=prefix,
             pattern=pattern,
             show_progress=True,
+            limit=num_vis,
+            config=cfg,
         )
         logger.info(f"Visualizations: {viz_success}/{viz_total} created")
 

lattice_sub-1.3.1/src/lattice_subtraction/visualization.py

@@ -0,0 +1,370 @@
+"""
+Visualization utilities for lattice subtraction results.
+
+This module provides functions to create comparison visualizations
+showing original, processed, difference images, and threshold optimization curves.
+"""
+
+import logging
+from pathlib import Path
+from typing import Optional, Tuple, List
+
+import numpy as np
+
+# Silence matplotlib's verbose debug logging
+logging.getLogger('matplotlib').setLevel(logging.WARNING)
+logging.getLogger('matplotlib.font_manager').setLevel(logging.WARNING)
+
+# Silence PIL/Pillow debug logging (PNG chunk messages)
+logging.getLogger('PIL').setLevel(logging.WARNING)
+logging.getLogger('PIL.PngImagePlugin').setLevel(logging.WARNING)
+
+logger = logging.getLogger(__name__)
+
+
+def compute_threshold_curve(
+    image: np.ndarray,
+    config,
+    n_points: int = 21,
+) -> Tuple[np.ndarray, np.ndarray, float, float]:
+    """
+    Compute quality scores across a range of thresholds.
+    
+    Args:
+        image: Original image array
+        config: Config object with processing parameters
+        n_points: Number of threshold points to evaluate
+        
+    Returns:
+        Tuple of (thresholds, quality_scores, optimal_threshold, optimal_quality)
+    """
+    from .threshold_optimizer import ThresholdOptimizer
+    
+    optimizer = ThresholdOptimizer(config)
+    
+    # Prepare FFT data once
+    subtracted, radial_mask, box_size = optimizer._prepare_fft_data(image)
+    
+    # Evaluate across threshold range
+    thresholds = np.linspace(
+        optimizer.min_threshold, 
+        optimizer.max_threshold, 
+        n_points
+    )
+    
+    # Use GPU batch if available
+    if optimizer.use_gpu:
+        qualities, peak_counts = optimizer._compute_quality_batch_gpu(
+            subtracted, radial_mask, thresholds
+        )
+    else:
+        qualities = []
+        for t in thresholds:
+            q, _ = optimizer._compute_quality(subtracted, radial_mask, t)
+            qualities.append(q)
+        qualities = np.array(qualities)
+    
+    # Find optimal
+    best_idx = np.argmax(qualities)
+    optimal_threshold = thresholds[best_idx]
+    optimal_quality = qualities[best_idx]
+    
+    return thresholds, qualities, optimal_threshold, optimal_quality
+
+
+def create_comparison_figure(
+    original: np.ndarray,
+    processed: np.ndarray,
+    title: str = "Lattice Subtraction Comparison",
+    figsize: Tuple[int, int] = (18, 6),
+    dpi: int = 150,
+):
+    """
+    Create a comparison figure showing original, processed, and difference images.
+    
+    Args:
+        original: Original image array
+        processed: Processed (lattice-subtracted) image array
+        title: Figure title
+        figsize: Figure size in inches (width, height)
+        dpi: Resolution for saving
+        
+    Returns:
+        matplotlib Figure object
+    """
+    import matplotlib.pyplot as plt
+    
+    # Compute difference
+    difference = original - processed
+    
+    # Create figure
+    fig, axes = plt.subplots(1, 3, figsize=figsize)
+    
+    # Contrast limits from original
+    vmin, vmax = np.percentile(original, [1, 99])
+    
+    # Original
+    axes[0].imshow(original, cmap='gray', vmin=vmin, vmax=vmax)
+    axes[0].set_title(f'Original\n{original.shape}')
+    axes[0].axis('off')
+    
+    # Lattice Subtracted
+    axes[1].imshow(processed, cmap='gray', vmin=vmin, vmax=vmax)
+    axes[1].set_title(f'Lattice Subtracted\n{processed.shape}')
+    axes[1].axis('off')
+    
+    # Difference (removed lattice)
+    diff_std = np.std(difference)
+    axes[2].imshow(
+        difference, 
+        cmap='RdBu_r',
+        vmin=-diff_std * 3, 
+        vmax=diff_std * 3
+    )
+    axes[2].set_title('Difference (Removed Lattice)')
+    axes[2].axis('off')
+    
+    # Title
+    plt.suptitle(title, fontsize=14)
+    plt.tight_layout()
+    
+    return fig
+
+
+def create_comparison_figure_with_threshold(
+    original: np.ndarray,
+    processed: np.ndarray,
+    thresholds: np.ndarray,
+    quality_scores: np.ndarray,
+    optimal_threshold: float,
+    optimal_quality: float,
+    title: str = "Lattice Subtraction Comparison",
+    figsize: Tuple[int, int] = (14, 12),
+    dpi: int = 150,
+):
+    """
+    Create a 4-panel comparison figure with threshold optimization curve.
+    
+    Layout (2x2 grid):
+        [Original]        [Subtracted]
+        [Difference]      [Threshold Curve]
+    
+    Args:
+        original: Original image array
+        processed: Processed (lattice-subtracted) image array
+        thresholds: Array of threshold values tested
+        quality_scores: Array of quality scores for each threshold
+        optimal_threshold: The optimal threshold that was selected
+        optimal_quality: Quality score at optimal threshold
+        title: Figure title
+        figsize: Figure size in inches (width, height)
+        dpi: Resolution for saving
+        
+    Returns:
+        matplotlib Figure object
+    """
+    import matplotlib.pyplot as plt
+    
+    # Compute difference
+    difference = original - processed
+    
+    # Create figure with 4 panels (2 rows, 2 columns)
+    fig, axes = plt.subplots(2, 2, figsize=figsize)
+    
+    # Contrast limits from original
+    vmin, vmax = np.percentile(original, [1, 99])
+    
+    # Panel 1 (top-left): Original
+    axes[0, 0].imshow(original, cmap='gray', vmin=vmin, vmax=vmax)
+    axes[0, 0].set_title(f'Original\n{original.shape}')
+    axes[0, 0].axis('off')
+    
+    # Panel 2 (top-right): Lattice Subtracted
+    axes[0, 1].imshow(processed, cmap='gray', vmin=vmin, vmax=vmax)
+    axes[0, 1].set_title(f'Lattice Subtracted\n{processed.shape}')
+    axes[0, 1].axis('off')
+    
+    # Panel 3 (bottom-left): Difference (removed lattice)
+    diff_std = np.std(difference)
+    axes[1, 0].imshow(
+        difference, 
+        cmap='RdBu_r',
+        vmin=-diff_std * 3, 
+        vmax=diff_std * 3
+    )
+    axes[1, 0].set_title('Difference (Removed Lattice)')
+    axes[1, 0].axis('off')
+    
+    # Panel 4 (bottom-right): Threshold vs Quality Score curve
+    axes[1, 1].plot(thresholds, quality_scores, 'b-', linewidth=2, label='Quality Score')
+    axes[1, 1].axvline(x=optimal_threshold, color='r', linestyle='--', linewidth=2, 
+                    label=f'Optimal: {optimal_threshold:.3f}')
+    axes[1, 1].scatter([optimal_threshold], [optimal_quality], color='r', s=100, zorder=5)
+    axes[1, 1].set_xlabel('Threshold', fontsize=11)
+    axes[1, 1].set_ylabel('Lattice Removal Efficacy', fontsize=11)
+    axes[1, 1].set_title(f'Threshold Optimization\nOptimal = {optimal_threshold:.3f}')
+    axes[1, 1].legend(loc='best', fontsize=9)
+    axes[1, 1].grid(True, alpha=0.3)
+    axes[1, 1].set_xlim(thresholds.min(), thresholds.max())
+    
+    # Title
+    plt.suptitle(title, fontsize=14)
+    plt.tight_layout()
+    
+    return fig
+
+
+def save_comparison_visualization(
+    original_path: Path,
+    processed_path: Path,
+    output_path: Path,
+    config = None,
+    dpi: int = 150,
+) -> None:
+    """
+    Create and save a 4-panel comparison visualization for a single image pair.
+    
+    Includes threshold optimization curve showing how the optimal threshold
+    was selected based on lattice removal efficacy.
+    
+    Args:
+        original_path: Path to original MRC file
+        processed_path: Path to processed MRC file
+        output_path: Path for output PNG file
+        config: Config object for threshold computation (optional, will use defaults)
+        dpi: Resolution for output images
+    """
+    import matplotlib.pyplot as plt
+    import mrcfile
+    
+    # Load images
+    with mrcfile.open(original_path, 'r') as f:
+        original = f.data.copy()
+    with mrcfile.open(processed_path, 'r') as f:
+        processed = f.data.copy()
+    
+    # Create title
+    name = original_path.name
+    short_name = name[:50] + "..." if len(name) > 50 else name
+    title = f"Lattice Subtraction: {short_name}"
+    
+    # Try to compute threshold curve if config available
+    try:
+        if config is None:
+            # Create default config for threshold computation
+            from .config import Config
+            config = Config(pixel_ang=0.56)  # Default K3 pixel size
+        
+        # Compute threshold optimization curve
+        thresholds, quality_scores, optimal_threshold, optimal_quality = \
+            compute_threshold_curve(original, config)
+        
+        # Create 4-panel figure with threshold curve
+        fig = create_comparison_figure_with_threshold(
+            original, processed,
+            thresholds, quality_scores,
+            optimal_threshold, optimal_quality,
+            title=title, dpi=dpi
+        )
+    except Exception as e:
+        # Fallback to 3-panel if threshold computation fails
+        logger.debug(f"Could not compute threshold curve: {e}, using 3-panel view")
+        fig = create_comparison_figure(original, processed, title=title, dpi=dpi)
+    
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    fig.savefig(output_path, dpi=dpi, bbox_inches='tight')
+    plt.close(fig)
+
+
+def generate_visualizations(
+    input_dir: Path,
+    output_dir: Path,
+    viz_dir: Path,
+    prefix: str = "sub_",
+    pattern: str = "*.mrc",
+    dpi: int = 150,
+    show_progress: bool = True,
+    limit: Optional[int] = None,
+    config = None,
+) -> Tuple[int, int]:
+    """
+    Generate comparison visualizations for processed images in a directory.
+    
+    Args:
+        input_dir: Directory containing original MRC files
+        output_dir: Directory containing processed MRC files
+        viz_dir: Directory for output visualization PNG files
+        prefix: Prefix used for processed files (default: "sub_")
+        pattern: Glob pattern for finding processed files
+        dpi: Resolution for output images
+        show_progress: Show progress bar
+        limit: Maximum number of visualizations to generate (None = all)
+        config: Config object for threshold computation (optional)
+        
+    Returns:
+        Tuple of (successful_count, total_count)
+    """
+    import matplotlib.pyplot as plt
+    
+    viz_dir = Path(viz_dir)
+    viz_dir.mkdir(parents=True, exist_ok=True)
+    
+    # Find all processed files
+    output_files = sorted(Path(output_dir).glob(f"{prefix}{pattern}"))
+    
+    if not output_files:
+        logger.warning(f"No processed files found matching '{prefix}{pattern}' in {output_dir}")
+        return 0, 0
+    
+    # Apply limit if specified
+    total_available = len(output_files)
+    if limit is not None and limit > 0:
+        output_files = output_files[:limit]
+        logger.info(f"Limiting to {limit} visualizations (of {total_available} available)")
+    
+    successful = 0
+    total = len(output_files)
+    
+    # Setup iterator with optional progress bar
+    if show_progress:
+        try:
+            from tqdm import tqdm
+            iterator = tqdm(output_files, desc="Generating visualizations", unit="file")
+        except ImportError:
+            iterator = output_files
+    else:
+        iterator = output_files
+    
+    for processed_path in iterator:
+        try:
+            # Get corresponding input file
+            input_name = processed_path.name.replace(prefix, "", 1)
+            input_path = Path(input_dir) / input_name
+            
+            if not input_path.exists():
+                logger.debug(f"Original not found: {input_path}")
+                continue
+            
+            # Output path
+            viz_name = input_name.replace(".mrc", ".png")
+            viz_path = viz_dir / viz_name
+            
+            # Skip if already exists
+            if viz_path.exists():
+                successful += 1
+                continue
+            
+            # Generate visualization with 4-panel layout
+            save_comparison_visualization(
+                original_path=input_path,
+                processed_path=processed_path,
+                output_path=viz_path,
+                config=config,
+                dpi=dpi,
+            )
+            successful += 1
+            
+        except Exception as e:
+            logger.error(f"Failed to create visualization for {processed_path.name}: {e}")
+    
+    return successful, total

lattice_sub-1.2.2/src/lattice_subtraction/visualization.py

@@ -1,199 +0,0 @@
-"""
-Visualization utilities for lattice subtraction results.
-
-This module provides functions to create comparison visualizations
-showing original, processed, and difference images.
-"""
-
-import logging
-from pathlib import Path
-from typing import Optional, Tuple
-
-import numpy as np
-
-# Silence matplotlib's verbose debug logging
-logging.getLogger('matplotlib').setLevel(logging.WARNING)
-logging.getLogger('matplotlib.font_manager').setLevel(logging.WARNING)
-
-# Silence PIL/Pillow debug logging (PNG chunk messages)
-logging.getLogger('PIL').setLevel(logging.WARNING)
-logging.getLogger('PIL.PngImagePlugin').setLevel(logging.WARNING)
-
-logger = logging.getLogger(__name__)
-
-
-def create_comparison_figure(
-    original: np.ndarray,
-    processed: np.ndarray,
-    title: str = "Lattice Subtraction Comparison",
-    figsize: Tuple[int, int] = (18, 6),
-    dpi: int = 150,
-):
-    """
-    Create a comparison figure showing original, processed, and difference images.
-    
-    Args:
-        original: Original image array
-        processed: Processed (lattice-subtracted) image array
-        title: Figure title
-        figsize: Figure size in inches (width, height)
-        dpi: Resolution for saving
-        
-    Returns:
-        matplotlib Figure object
-    """
-    import matplotlib.pyplot as plt
-    
-    # Compute difference
-    difference = original - processed
-    
-    # Create figure
-    fig, axes = plt.subplots(1, 3, figsize=figsize)
-    
-    # Contrast limits from original
-    vmin, vmax = np.percentile(original, [1, 99])
-    
-    # Original
-    axes[0].imshow(original, cmap='gray', vmin=vmin, vmax=vmax)
-    axes[0].set_title(f'Original\n{original.shape}')
-    axes[0].axis('off')
-    
-    # Lattice Subtracted
-    axes[1].imshow(processed, cmap='gray', vmin=vmin, vmax=vmax)
-    axes[1].set_title(f'Lattice Subtracted\n{processed.shape}')
-    axes[1].axis('off')
-    
-    # Difference (removed lattice)
-    diff_std = np.std(difference)
-    axes[2].imshow(
-        difference, 
-        cmap='RdBu_r',
-        vmin=-diff_std * 3, 
-        vmax=diff_std * 3
-    )
-    axes[2].set_title('Difference (Removed Lattice)')
-    axes[2].axis('off')
-    
-    # Title
-    plt.suptitle(title, fontsize=14)
-    plt.tight_layout()
-    
-    return fig
-
-
-def save_comparison_visualization(
-    original_path: Path,
-    processed_path: Path,
-    output_path: Path,
-    dpi: int = 150,
-) -> None:
-    """
-    Create and save a comparison visualization for a single image pair.
-    
-    Args:
-        original_path: Path to original MRC file
-        processed_path: Path to processed MRC file
-        output_path: Path for output PNG file
-    """
-    import matplotlib.pyplot as plt
-    import mrcfile
-    
-    # Load images
-    with mrcfile.open(original_path, 'r') as f:
-        original = f.data.copy()
-    with mrcfile.open(processed_path, 'r') as f:
-        processed = f.data.copy()
-    
-    # Create title
-    name = original_path.name
-    short_name = name[:60] + "..." if len(name) > 60 else name
-    title = f"Lattice Subtraction Comparison: {short_name}"
-    
-    # Create and save figure
-    fig = create_comparison_figure(original, processed, title=title, dpi=dpi)
-    output_path.parent.mkdir(parents=True, exist_ok=True)
-    fig.savefig(output_path, dpi=dpi, bbox_inches='tight')
-    plt.close(fig)
-
-
-def generate_visualizations(
-    input_dir: Path,
-    output_dir: Path,
-    viz_dir: Path,
-    prefix: str = "sub_",
-    pattern: str = "*.mrc",
-    dpi: int = 150,
-    show_progress: bool = True,
-) -> Tuple[int, int]:
-    """
-    Generate comparison visualizations for all processed images in a directory.
-    
-    Args:
-        input_dir: Directory containing original MRC files
-        output_dir: Directory containing processed MRC files
-        viz_dir: Directory for output visualization PNG files
-        prefix: Prefix used for processed files (default: "sub_")
-        pattern: Glob pattern for finding processed files
-        dpi: Resolution for output images
-        show_progress: Show progress bar
-        
-    Returns:
-        Tuple of (successful_count, total_count)
-    """
-    import matplotlib.pyplot as plt
-    
-    viz_dir = Path(viz_dir)
-    viz_dir.mkdir(parents=True, exist_ok=True)
-    
-    # Find all processed files
-    output_files = sorted(Path(output_dir).glob(f"{prefix}{pattern}"))
-    
-    if not output_files:
-        logger.warning(f"No processed files found matching '{prefix}{pattern}' in {output_dir}")
-        return 0, 0
-    
-    successful = 0
-    total = len(output_files)
-    
-    # Setup iterator with optional progress bar
-    if show_progress:
-        try:
-            from tqdm import tqdm
-            iterator = tqdm(output_files, desc="Generating visualizations", unit="file")
-        except ImportError:
-            iterator = output_files
-    else:
-        iterator = output_files
-    
-    for processed_path in iterator:
-        try:
-            # Get corresponding input file
-            input_name = processed_path.name.replace(prefix, "", 1)
-            input_path = Path(input_dir) / input_name
-            
-            if not input_path.exists():
-                logger.debug(f"Original not found: {input_path}")
-                continue
-            
-            # Output path
-            viz_name = input_name.replace(".mrc", ".png")
-            viz_path = viz_dir / viz_name
-            
-            # Skip if already exists
-            if viz_path.exists():
-                successful += 1
-                continue
-            
-            # Generate visualization
-            save_comparison_visualization(
-                original_path=input_path,
-                processed_path=processed_path,
-                output_path=viz_path,
-                dpi=dpi,
-            )
-            successful += 1
-            
-        except Exception as e:
-            logger.error(f"Failed to create visualization for {processed_path.name}: {e}")
-    
-    return successful, total