lattice-sub 1.2.2__py3-none-any.whl → 1.3.1__py3-none-any.whl

{lattice_sub-1.2.2.dist-info → lattice_sub-1.3.1.dist-info}/METADATA

@@ -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.dist-info → lattice_sub-1.3.1.dist-info}/RECORD

@@ -1,7 +1,7 @@
-lattice_sub-1.2.2.dist-info/licenses/LICENSE,sha256=2kPoH0cbEp0cVEGqMpyF2IQX1npxdtQmWJB__HIRSb0,1101
-lattice_subtraction/__init__.py,sha256=UkIWBvAFMQ3YgK1t8DwHaGqufsArImuHhBAp5iCBC2E,1737
+lattice_sub-1.3.1.dist-info/licenses/LICENSE,sha256=2kPoH0cbEp0cVEGqMpyF2IQX1npxdtQmWJB__HIRSb0,1101
+lattice_subtraction/__init__.py,sha256=KL12LDW3dzz_JSBMGIo6UJ3_9vw7oooF7z7EG5P3i4Y,1737
 lattice_subtraction/batch.py,sha256=zJzvUnr8dznvxE8jaPKDLJ7AcJg8Cbfv5nVo0FzZz1I,20891
-lattice_subtraction/cli.py,sha256=fWZ3ueahQXPQ_ApzS345AdslsMF0-6HIAIvan2IFHkk,23597
+lattice_subtraction/cli.py,sha256=W99XQClUMKaaFQxle0W-ILQ6UuYRFXZVJWD4qXpcIj4,24063
 lattice_subtraction/config.py,sha256=uzwKb5Zi3phHUk2ZgoiLsQdwFdN-rTiY8n02U91SObc,8426
 lattice_subtraction/core.py,sha256=VzcecSZHRuBuHUc2jHGv8LalINL75RH0aTpABI708y8,16265
 lattice_subtraction/io.py,sha256=uHku6rJ0jeCph7w-gOIDJx-xpNoF6PZcLfb5TBTOiw0,4594
@@ -9,9 +9,9 @@ lattice_subtraction/masks.py,sha256=HIamrACmbQDkaCV4kXhnjMDSwIig4OtQFLig9A8PMO8,
 lattice_subtraction/processing.py,sha256=tmnj5K4Z9HCQhRpJ-iMd9Bj_uTRuvDEWyUenh8MCWEM,8341
 lattice_subtraction/threshold_optimizer.py,sha256=yEsGM_zt6YjgEulEZqtRy113xOFB69aHJIETm2xSS6k,15398
 lattice_subtraction/ui.py,sha256=Sp_a-yNmBRZJxll8h9T_H5-_KsI13zGYmHcbcpVpbR8,9176
-lattice_subtraction/visualization.py,sha256=pMZKcz6Xgs98lLaZbvGjoMIyEYA_MLRracVxpQStC3w,5935
-lattice_sub-1.2.2.dist-info/METADATA,sha256=u8Fy9n7k3bXazhftD4Zl4_yPgY3Aki9Jv3Sm4EjzBUk,14419
-lattice_sub-1.2.2.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
-lattice_sub-1.2.2.dist-info/entry_points.txt,sha256=o8PzJR8kFnXlKZufoYGBIHpiosM-P4PZeKZXJjtPS6Y,61
-lattice_sub-1.2.2.dist-info/top_level.txt,sha256=BOuW-sm4G-fQtsWPRdeLzWn0WS8sDYVNKIMj5I3JXew,20
-lattice_sub-1.2.2.dist-info/RECORD,,
+lattice_subtraction/visualization.py,sha256=noRhBXi_Xd1b5deBfVo0Bk0f3d2kqlf3_SQwAPJC0E0,12032
+lattice_sub-1.3.1.dist-info/METADATA,sha256=qN0VzkEJyNbBe_AN5tKcUXh4VjDzaL1COQCk0W83ZiM,14901
+lattice_sub-1.3.1.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+lattice_sub-1.3.1.dist-info/entry_points.txt,sha256=o8PzJR8kFnXlKZufoYGBIHpiosM-P4PZeKZXJjtPS6Y,61
+lattice_sub-1.3.1.dist-info/top_level.txt,sha256=BOuW-sm4G-fQtsWPRdeLzWn0WS8sDYVNKIMj5I3JXew,20
+lattice_sub-1.3.1.dist-info/RECORD,,

{lattice_sub-1.2.2.dist-info → lattice_sub-1.3.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.10.1)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

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_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_subtraction/visualization.py

@@ -2,12 +2,12 @@
 Visualization utilities for lattice subtraction results.
 
 This module provides functions to create comparison visualizations
-showing original, processed, and difference images.
+showing original, processed, difference images, and threshold optimization curves.
 """
 
 import logging
 from pathlib import Path
-from typing import Optional, Tuple
+from typing import Optional, Tuple, List
 
 import numpy as np
 
@@ -22,6 +22,56 @@ 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,
@@ -81,19 +131,108 @@ def create_comparison_figure(
     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 comparison visualization for a single image pair.
+    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
@@ -106,11 +245,32 @@ def save_comparison_visualization(
     
     # Create title
     name = original_path.name
-    short_name = name[:60] + "..." if len(name) > 60 else name
-    title = f"Lattice Subtraction Comparison: {short_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)
     
-    # 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)
@@ -124,9 +284,11 @@ def generate_visualizations(
     pattern: str = "*.mrc",
     dpi: int = 150,
     show_progress: bool = True,
+    limit: Optional[int] = None,
+    config = None,
 ) -> Tuple[int, int]:
     """
-    Generate comparison visualizations for all processed images in a directory.
+    Generate comparison visualizations for processed images in a directory.
     
     Args:
         input_dir: Directory containing original MRC files
@@ -136,6 +298,8 @@ def generate_visualizations(
         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)
@@ -152,6 +316,12 @@ def generate_visualizations(
         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)
     
@@ -184,11 +354,12 @@ def generate_visualizations(
                 successful += 1
                 continue
             
-            # Generate visualization
+            # 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