neuro-sam 0.1.8__py3-none-any.whl → 0.1.10__py3-none-any.whl

neuro_sam/napari_utils/segmentation_module.py

@@ -172,18 +172,6 @@ class SegmentationWidget(QWidget):
         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)
-        
-        # Dendrite structure enhancement
-        self.enhance_dendrite_cb = QCheckBox("Enhance Tubular Dendrite Structure")
-        self.enhance_dendrite_cb.setChecked(True)
-        self.enhance_dendrite_cb.setToolTip("Apply morphological operations to connect dendrite segments and make tubular structure")
-        params_layout.addWidget(self.enhance_dendrite_cb)
-        
         # # Minimum dendrite size for noise removal
         # min_size_layout = QHBoxLayout()
         # min_size_layout.addWidget(QLabel("Min Dendrite Size (pixels):"))
@@ -404,20 +392,9 @@ class SegmentationWidget(QWidget):
             
             # Get segmentation parameters
             patch_size = self.patch_size_spin.value()
-            enable_boundary_smoothing = self.enable_boundary_smoothing_cb.isChecked()
-            enhance_dendrite = self.enhance_dendrite_cb.isChecked()
             use_full_volume = False
             
-            # Update UI
-            enhancement_info = [f"{patch_size}x{patch_size} overlapping patches (50%)"]
-            if enable_boundary_smoothing:
-                enhancement_info.append("light cleanup")
-            if enhance_dendrite:
-                enhancement_info.append("tubular structure enhancement")
-            
-            enhancement_str = " + ".join(enhancement_info)
-            
-            self.status_label.setText(f"Status: Running dendrite segmentation on {path_name} with {enhancement_str}...")
+            self.status_label.setText(f"Status: Running dendrite segmentation on {path_name}...")
             self.segmentation_progress.setValue(0)
             self.run_segmentation_btn.setEnabled(False)
             
@@ -434,15 +411,11 @@ class SegmentationWidget(QWidget):
             print(f"Segmenting dendrite path '{path_name}' from frame {start_frame} to {end_frame}")
             print(f"Path has {len(brightest_path)} points")
             print(f"Parameters: patch_size={patch_size}x{patch_size}, overlap=50% (stride={patch_size//2})")
-            print(f"Light boundary cleanup: {enable_boundary_smoothing}")
             # print(f"Dendrite enhancement: {enhance_dendrite}, Min dendrite size: {min_dendrite_size} pixels")
             
             # 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
@@ -542,11 +515,6 @@ class SegmentationWidget(QWidget):
                 total_pixels = np.sum(binary_masks)
                 
                 result_text = f"Results: Dendrite segmentation completed - {total_pixels} pixels segmented"
-                result_text += f"\nMethod: {enhancement_str}"
-                result_text += f"\nOverlap: 50% (stride={patch_size//2})"
-                # result_text += f"\nMin dendrite size: {min_dendrite_size} pixels"
-                if enable_boundary_smoothing:
-                    result_text += f"\nLight boundary cleanup applied"
                 
                 self.status_label.setText(result_text)
                 

{neuro_sam-0.1.8.dist-info → neuro_sam-0.1.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: neuro-sam
-Version: 0.1.8
+Version: 0.1.10
 Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
 Author-email: Nipun Arora <nipunarora8@yahoo.com>
 License: MIT License

{neuro_sam-0.1.8.dist-info → neuro_sam-0.1.10.dist-info}/RECORD

@@ -33,7 +33,7 @@ neuro_sam/napari_utils/main_widget.py,sha256=yahfPLwmhBt_hImpRykIObzfMwbVZvVJTEK
 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=iObM5k8VkARtB_rcqAQGzKJ-PmaAKLeFJD14_Jy6xhs,28732
+neuro_sam/napari_utils/segmentation_module.py,sha256=pp2WoWO6mfYQ4CLduiEC-_o3oQhqs7Vcz4i2B6ATnIc,26796
 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-0.1.8.dist-info/licenses/LICENSE,sha256=akmTIN8IuZn3Y7UK_8qVQnyKDWSDcVUwB8RPGNXCojw,1068
+neuro_sam-0.1.10.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-0.1.8.dist-info/METADATA,sha256=1vHp2trqfoQL7eP7aia_Xqa8H9f2b6JjsPECvGpsqrk,9746
-neuro_sam-0.1.8.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-neuro_sam-0.1.8.dist-info/entry_points.txt,sha256=EQg0SmFbnbGGcchHq5ROmhO9pkgby72Y5G5w90WyLZI,220
-neuro_sam-0.1.8.dist-info/top_level.txt,sha256=yPbWxFcw79sErTk8zohihUHMK9LL31i3bXir2MrS4OQ,15
-neuro_sam-0.1.8.dist-info/RECORD,,
+neuro_sam-0.1.10.dist-info/METADATA,sha256=Hrn823PdxJxnip5w28nz7ZXZhwpzwznikmQ2eqops7M,9747
+neuro_sam-0.1.10.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+neuro_sam-0.1.10.dist-info/entry_points.txt,sha256=EQg0SmFbnbGGcchHq5ROmhO9pkgby72Y5G5w90WyLZI,220
+neuro_sam-0.1.10.dist-info/top_level.txt,sha256=yPbWxFcw79sErTk8zohihUHMK9LL31i3bXir2MrS4OQ,15
+neuro_sam-0.1.10.dist-info/RECORD,,