neuro-sam 0.1.11__py3-none-any.whl → 0.1.13__py3-none-any.whl

neuro_sam/brightest_path_lib/visualization/tube_data.py

@@ -7,13 +7,13 @@ from concurrent.futures import ThreadPoolExecutor
 from neuro_sam.brightest_path_lib.algorithm.waypointastar_speedup import quick_accurate_optimized_search
 
 # Numba-optimized core functions
-@nb.njit(cache=True, parallel=True)
+@nb.njit(cache=True)
 def compute_tangent_vectors_fast(path_array):
     """Fast computation of tangent vectors using numba"""
     n_points = path_array.shape[0]
     tangents = np.zeros_like(path_array, dtype=np.float64)
     
-    for i in nb.prange(n_points):
+    for i in range(n_points):
         if i == 0:
             if n_points > 1:
                 tangent = path_array[1] - path_array[0]
@@ -84,13 +84,13 @@ def create_orthogonal_basis_fast(forward):
 
     return up, right
 
-@nb.njit(cache=True, parallel=True)
+@nb.njit(cache=True)
 def sample_viewing_plane_fast(image, current_point, up, right, plane_size):
     """Fast viewing plane sampling with bounds checking"""
     plane_shape = (plane_size * 2 + 1, plane_size * 2 + 1)
     normal_plane = np.zeros(plane_shape, dtype=np.float64)
     
-    for i in nb.prange(plane_shape[0]):
+    for i in range(plane_shape[0]):
         for j in range(plane_shape[1]):
             # Calculate 3D point
             point_3d = (current_point + 

neuro_sam/napari_utils/main_widget.py

@@ -971,10 +971,13 @@ class NeuroSAMWidget(QWidget):
                 layer = self.viewer.add_image(
                     final_stack, 
                     name=layer_name, 
-                    colormap='gray',
-                    interpolation='nearest'
+                    colormap='gray'
                 )
                 
+                # Set interpolation
+                layer.interpolation2d = 'nearest'
+                layer.interpolation3d = 'nearest'
+                
                 # Force 2D view
                 self.viewer.dims.ndisplay = 2
                 

neuro_sam/napari_utils/segmentation_module.py

@@ -13,61 +13,6 @@ from scipy import ndimage
 from scipy.ndimage import binary_fill_holes
 from skimage.morphology import disk, binary_closing, remove_small_objects
 
-
-def fast_refine_dendrite_boundaries(image, dendrite_mask):
-    """
-    Fast, lightweight boundary refinement for dendrites
-    Only basic morphological operations - no gradients
-    """
-    if not np.any(dendrite_mask):
-        return dendrite_mask
-    
-    # Simple morphological cleanup only
-    # Fill holes in dendrites (should be solid tubes)
-    filled_mask = binary_fill_holes(dendrite_mask)
-    
-    # Light closing to connect nearby segments
-    closed_mask = binary_closing(filled_mask, disk(2))
-    
-    # Remove very small objects
-    labeled_mask, num_labels = ndimage.label(closed_mask)
-    cleaned_mask = closed_mask.copy()
-    
-    for label_id in range(1, num_labels + 1):
-        component = (labeled_mask == label_id)
-        if np.sum(component) < 20:  # Small threshold for dendrites
-            cleaned_mask[component] = 0
-    
-    return cleaned_mask.astype(np.uint8)
-
-
-def fast_refine_dendrite_volume_boundaries(image_volume, mask_volume, brightest_path):
-    """
-    Fast dendrite boundary refinement - only process frames that have dendrite path
-    """
-    refined_volume = mask_volume.copy()
-    
-    # Only process frames that have dendrite path
-    path_frames = set()
-    for point in brightest_path:
-        path_frames.add(int(point[0]))
-    
-    print(f"Fast dendrite light cleanup on {len(path_frames)} frames with dendrite...")
-    
-    for z in path_frames:
-        if 0 <= z < image_volume.shape[0] and np.any(mask_volume[z]):
-            refined_volume[z] = fast_refine_dendrite_boundaries(image_volume[z], mask_volume[z])
-    
-    # Report changes
-    original_pixels = np.sum(mask_volume > 0)
-    refined_pixels = np.sum(refined_volume > 0)
-    change = refined_pixels - original_pixels
-    
-    print(f"Dendrite light cleanup: {original_pixels} -> {refined_pixels} pixels ({change:+d}, {change/original_pixels*100:+.1f}%)")
-    
-    return refined_volume.astype(np.uint8)
-
-
 class SegmentationWidget(QWidget):
     """Widget for performing dendrite segmentation with boundary smoothing"""
     
@@ -171,34 +116,6 @@ class SegmentationWidget(QWidget):
         self.patch_size_spin.setToolTip("Size of overlapping patches (128x128 recommended)")
         patch_size_layout.addWidget(self.patch_size_spin)
         params_layout.addLayout(patch_size_layout)
-
-        # Enable boundary cleanup for dendrites
-        self.enable_boundary_smoothing_cb = QCheckBox("Enable Light Boundary Cleanup")
-        self.enable_boundary_smoothing_cb.setChecked(False)  # Disabled by default for speed
-        self.enable_boundary_smoothing_cb.setToolTip("Apply light morphological cleanup (hole filling, small object removal)")
-        params_layout.addWidget(self.enable_boundary_smoothing_cb)
-        
-        # # Minimum dendrite size for noise removal
-        # min_size_layout = QHBoxLayout()
-        # min_size_layout.addWidget(QLabel("Min Dendrite Size (pixels):"))
-        # self.min_dendrite_size_spin = QSpinBox()
-        # self.min_dendrite_size_spin.setRange(50, 500)
-        # self.min_dendrite_size_spin.setValue(100)
-        # self.min_dendrite_size_spin.setToolTip("Minimum size of dendrite objects to keep (removes noise)")
-        # min_size_layout.addWidget(self.min_dendrite_size_spin)
-        # params_layout.addLayout(min_size_layout)
-        
-        # Frame range
-        # self.use_full_volume_cb = QCheckBox("Process Full Volume")
-        # self.use_full_volume_cb.setChecked(False)
-        # self.use_full_volume_cb.setToolTip("Process entire volume instead of just path range")
-        # params_layout.addWidget(self.use_full_volume_cb)
-        
-        # Processing method info
-        # method_info = QLabel("Method: 50% overlapping patches + optional light cleanup")
-        # method_info.setWordWrap(True)
-        # method_info.setStyleSheet("color: #0066cc; font-style: italic;")
-        # params_layout.addWidget(method_info)
         
         params_section.setLayout(params_layout)
         layout.addWidget(params_section)
@@ -395,8 +312,6 @@ class SegmentationWidget(QWidget):
             path_data = self.state['paths'][path_id]
             path_name = path_data['name']
             brightest_path = path_data['data']
-
-            enable_boundary_smoothing = self.enable_boundary_smoothing_cb.isChecked()
             
             # Get segmentation parameters
             patch_size = self.patch_size_spin.value()
@@ -423,10 +338,7 @@ class SegmentationWidget(QWidget):
             
             # Progress callback function
             def update_progress(current, total):
-                if enable_boundary_smoothing:
-                    progress = int((current / total) * 80)  # 0-80%
-                else:
-                    progress = int((current / total) * 90)  # 0-90%
+                progress = int((current / total) * 90)  # 0-90%
                 self.segmentation_progress.setValue(progress)
             
             # Try to run the segmentation with overlapping patches
@@ -439,16 +351,6 @@ class SegmentationWidget(QWidget):
                 progress_callback=update_progress
             )
             
-            # Apply light boundary cleanup if requested
-            if enable_boundary_smoothing and result_masks is not None:
-                self.segmentation_progress.setValue(80)
-                print("Applying light dendrite boundary cleanup...")
-                napari.utils.notifications.show_info("Light dendrite cleanup...")
-                
-                refined_masks = fast_refine_dendrite_volume_boundaries(self.image, result_masks, brightest_path)
-                result_masks = refined_masks
-                self.segmentation_progress.setValue(90)
-            
             # Process the results
             if result_masks is not None:
                 # Ensure masks are binary (0 or 1)

{neuro_sam-0.1.11.dist-info → neuro_sam-0.1.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: neuro-sam
-Version: 0.1.11
+Version: 0.1.13
 Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
 Author-email: Nipun Arora <nipunarora8@yahoo.com>
 License: MIT License

{neuro_sam-0.1.11.dist-info → neuro_sam-0.1.13.dist-info}/RECORD

@@ -24,16 +24,16 @@ neuro_sam/brightest_path_lib/node/node.py,sha256=Pfq8Swm3XWu6gErJlXzN7JyJ9J4bFsv
 neuro_sam/brightest_path_lib/visualization/__init__.py,sha256=WZ1QT3JqhHquh3dxwXKeQ5vmfuBj70sNI0_JBzrNKNY,195
 neuro_sam/brightest_path_lib/visualization/flythrough.py,sha256=bs-rqgwEXUZOYUkN6FOZAl2FkcRus7Ma1jWtZ1VRA1Q,5087
 neuro_sam/brightest_path_lib/visualization/flythrough_all.py,sha256=3MIYTl2q3oVszuaLOl-QS4zQISsCk1JlVcURCtc-pw0,17886
-neuro_sam/brightest_path_lib/visualization/tube_data.py,sha256=b0YfKUWzk4FT6_mUdLexIp-s4ipLsiGDt20diweA4BM,15570
+neuro_sam/brightest_path_lib/visualization/tube_data.py,sha256=Ual2g2mzHwGI8GStp2AsrEtiP9MdB8zdYwYFortulV8,15532
 neuro_sam/brightest_path_lib/visualization/tube_flythrough.py,sha256=Lt5sLqvj20AiiXl8SXlt6vQlHXQXtB91-FNFGl-YmU8,9160
 neuro_sam/napari_utils/anisotropic_scaling.py,sha256=VA6Sd9zEhIAhzjAGto2cOjE9mocNx9NFWXec2TQpvew,19266
 neuro_sam/napari_utils/color_utils.py,sha256=Hf5R8f0rh7b9CY1VT72o3tLGfGnnjRREkX8iWsiiu7k,4243
 neuro_sam/napari_utils/contrasting_color_system.py,sha256=a-lt_3zJLDL9YyIdWJhFDGMYzBb6yH85cV7BNCabbdI,6771
-neuro_sam/napari_utils/main_widget.py,sha256=yahfPLwmhBt_hImpRykIObzfMwbVZvVJTEKKzMZ11bw,48588
+neuro_sam/napari_utils/main_widget.py,sha256=VIsVkJ28NXyFoc97xI7d3Ykiy61nyBaMbyKHO0z3mx4,48696
 neuro_sam/napari_utils/path_tracing_module.py,sha256=bDhSawWNMfY-Vs-Zdt8XTb90pLkD9jUBRqpbC2_6li0,44070
 neuro_sam/napari_utils/punet_widget.py,sha256=WCAND8YLn4CA_20YW4quwcuJ_xEqPAc7GHrSBk4Anw0,16928
 neuro_sam/napari_utils/segmentation_model.py,sha256=mHXVjksqEcxHRH5KWp5-hXLEnRHgGhwPUxyUkV8eJGM,34141
-neuro_sam/napari_utils/segmentation_module.py,sha256=g3Fs9Jqe4Vtdz96-S-I_ajs1mjv4Nev0HdEGlmH8-18,27446
+neuro_sam/napari_utils/segmentation_module.py,sha256=t5BjuYnvSHHkt4zaUDQvkiCOnaYEFi6pDgtCIeMdGY0,23136
 neuro_sam/napari_utils/visualization_module.py,sha256=JtZlBoKlfIwVLa2Sqg7b2KTr07fNlAcwR0M7fHsn2oM,24723
 neuro_sam/punet/deepd3_model.py,sha256=nGVEqzCPz_E4cFA6QmknW2CffDcjxH7VsdYAyTdAtY0,7509
 neuro_sam/punet/prob_unet_deepd3.py,sha256=syXNleUVrfYtmVveN9G461oAhumxsijsavps8in4VRw,14698
@@ -47,7 +47,7 @@ neuro_sam/training/train_dendrites.py,sha256=TMG4YrrQV0Q784omMziXsB71tNICEmGLYSH
 neuro_sam/training/utils/__init__.py,sha256=4hbcx57NtRu8nryvXQYqmXK4hyUgUYNDz97kCw3Efs8,31
 neuro_sam/training/utils/prompt_generation_dendrites.py,sha256=_ntzXNV1lXPrpInRKaZ5CPpq3akF2IuD1naOXbTC8TU,3201
 neuro_sam/training/utils/stream_dendrites.py,sha256=qS_ZWrhJdW1Sg3RBjoRUJFlCV0u5X1Ns_tjYgJUjWJw,11024
-neuro_sam-0.1.11.dist-info/licenses/LICENSE,sha256=akmTIN8IuZn3Y7UK_8qVQnyKDWSDcVUwB8RPGNXCojw,1068
+neuro_sam-0.1.13.dist-info/licenses/LICENSE,sha256=akmTIN8IuZn3Y7UK_8qVQnyKDWSDcVUwB8RPGNXCojw,1068
 sam2/__init__.py,sha256=uHyh6VzVS4F2box0rPDpN5UmOVKeQNK0CIaTKG9JQZ4,395
 sam2/automatic_mask_generator.py,sha256=Zt8mbb4UQSMFrjOY8OwbshswOpMhaxAtdn5sTuXUw9c,18461
 sam2/benchmark.py,sha256=m3o1BriIQuwJAx-3zQ_B0_7YLhN84G28oQSV5sGA3ak,2811
@@ -91,8 +91,8 @@ sam2/utils/__init__.py,sha256=NL2AacVHZOe41zp4kF2-ZGcUCi9zFwh1Eo9spNjN0Ko,197
 sam2/utils/amg.py,sha256=t7MwkOKvcuBNu4FcjzKv9BpO0av5Zo9itZ8b3WQMpdg,12842
 sam2/utils/misc.py,sha256=AWAMAcFhzQedcQb7HU2oRc-RqjGrK87K-MsVG21tIKI,13090
 sam2/utils/transforms.py,sha256=ujpk9GAMYvIJIGpt87QOP88TPtrjL61liDG7DCptEUY,4885
-neuro_sam-0.1.11.dist-info/METADATA,sha256=IClHWfaA9ApPwCyM4lK6smvFP8B9UGtiG0y_y2l0Ejk,9747
-neuro_sam-0.1.11.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-neuro_sam-0.1.11.dist-info/entry_points.txt,sha256=EQg0SmFbnbGGcchHq5ROmhO9pkgby72Y5G5w90WyLZI,220
-neuro_sam-0.1.11.dist-info/top_level.txt,sha256=yPbWxFcw79sErTk8zohihUHMK9LL31i3bXir2MrS4OQ,15
-neuro_sam-0.1.11.dist-info/RECORD,,
+neuro_sam-0.1.13.dist-info/METADATA,sha256=eMqJUJUL6Kur_2m4wQfR8fUiED-JIGVh18tgE57APb8,9747
+neuro_sam-0.1.13.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+neuro_sam-0.1.13.dist-info/entry_points.txt,sha256=EQg0SmFbnbGGcchHq5ROmhO9pkgby72Y5G5w90WyLZI,220
+neuro_sam-0.1.13.dist-info/top_level.txt,sha256=yPbWxFcw79sErTk8zohihUHMK9LL31i3bXir2MrS4OQ,15
+neuro_sam-0.1.13.dist-info/RECORD,,