lattice-sub 1.3.0__py3-none-any.whl → 1.3.1__py3-none-any.whl

{lattice_sub-1.3.0.dist-info → lattice_sub-1.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lattice-sub
-Version: 1.3.0
+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

{lattice_sub-1.3.0.dist-info → lattice_sub-1.3.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
-lattice_sub-1.3.0.dist-info/licenses/LICENSE,sha256=2kPoH0cbEp0cVEGqMpyF2IQX1npxdtQmWJB__HIRSb0,1101
-lattice_subtraction/__init__.py,sha256=TNaJXvSgCQdvYUYJfS5scn92YjORiGfLot9WadZ8u28,1737
+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=W99XQClUMKaaFQxle0W-ILQ6UuYRFXZVJWD4qXpcIj4,24063
 lattice_subtraction/config.py,sha256=uzwKb5Zi3phHUk2ZgoiLsQdwFdN-rTiY8n02U91SObc,8426
@@ -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=hWFz49NBBrS7d6ofO0VyJ6-v8Q6hPG1dijbDtecMOQs,11890
-lattice_sub-1.3.0.dist-info/METADATA,sha256=pKwt8TcftbZGm1gvWZGO1n3iQiI4JB3E_ix3InB-4D0,14901
-lattice_sub-1.3.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-lattice_sub-1.3.0.dist-info/entry_points.txt,sha256=o8PzJR8kFnXlKZufoYGBIHpiosM-P4PZeKZXJjtPS6Y,61
-lattice_sub-1.3.0.dist-info/top_level.txt,sha256=BOuW-sm4G-fQtsWPRdeLzWn0WS8sDYVNKIMj5I3JXew,20
-lattice_sub-1.3.0.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_subtraction/__init__.py

@@ -19,7 +19,7 @@ Example:
     >>> result.save("output.mrc")
 """
 
-__version__ = "1.3.0"
+__version__ = "1.3.1"
 __author__ = "George Stephenson & Vignesh Kasinath"
 
 from .config import Config

lattice_subtraction/visualization.py

@@ -139,13 +139,15 @@ def create_comparison_figure_with_threshold(
     optimal_threshold: float,
     optimal_quality: float,
     title: str = "Lattice Subtraction Comparison",
-    figsize: Tuple[int, int] = (24, 6),
+    figsize: Tuple[int, int] = (14, 12),
     dpi: int = 150,
 ):
     """
     Create a 4-panel comparison figure with threshold optimization curve.
     
-    Layout: [Original] [Subtracted] [Difference] [Threshold vs Quality]
+    Layout (2x2 grid):
+        [Original]        [Subtracted]
+        [Difference]      [Threshold Curve]
     
     Args:
         original: Original image array
@@ -166,44 +168,44 @@ def create_comparison_figure_with_threshold(
     # Compute difference
     difference = original - processed
     
-    # Create figure with 4 panels (1 row, 4 columns)
-    fig, axes = plt.subplots(1, 4, figsize=figsize)
+    # 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: Original
-    axes[0].imshow(original, cmap='gray', vmin=vmin, vmax=vmax)
-    axes[0].set_title(f'Original\n{original.shape}')
-    axes[0].axis('off')
+    # 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: 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')
+    # 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: Difference (removed lattice)
+    # Panel 3 (bottom-left): Difference (removed lattice)
     diff_std = np.std(difference)
-    axes[2].imshow(
+    axes[1, 0].imshow(
         difference, 
         cmap='RdBu_r',
         vmin=-diff_std * 3, 
         vmax=diff_std * 3
     )
-    axes[2].set_title('Difference (Removed Lattice)')
-    axes[2].axis('off')
+    axes[1, 0].set_title('Difference (Removed Lattice)')
+    axes[1, 0].axis('off')
     
-    # Panel 4: Threshold vs Quality Score curve
-    axes[3].plot(thresholds, quality_scores, 'b-', linewidth=2, label='Quality Score')
-    axes[3].axvline(x=optimal_threshold, color='r', linestyle='--', linewidth=2, 
+    # 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[3].scatter([optimal_threshold], [optimal_quality], color='r', s=100, zorder=5)
-    axes[3].set_xlabel('Threshold', fontsize=11)
-    axes[3].set_ylabel('Lattice Removal Efficacy', fontsize=11)
-    axes[3].set_title(f'Threshold Optimization\nOptimal = {optimal_threshold:.3f}')
-    axes[3].legend(loc='best', fontsize=9)
-    axes[3].grid(True, alpha=0.3)
-    axes[3].set_xlim(thresholds.min(), thresholds.max())
+    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)