neuro-sam 0.1.5__tar.gz → 0.1.7__tar.gz

{neuro_sam-0.1.5/src/neuro_sam.egg-info → neuro_sam-0.1.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: neuro-sam
-Version: 0.1.5
+Version: 0.1.7
 Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
 Author-email: Nipun Arora <nipunarora8@yahoo.com>
 License: MIT License
@@ -54,6 +54,7 @@ Requires-Dist: numba
 Requires-Dist: PyQt5
 Requires-Dist: opencv-python-headless
 Requires-Dist: matplotlib
+Requires-Dist: requests
 Dynamic: license-file
 
 <div align="center">

{neuro_sam-0.1.5 → neuro_sam-0.1.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "neuro-sam"
-version = "0.1.5"
+version = "0.1.7"
 description = "Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation"
 readme = "README.md"
 authors = [
@@ -37,7 +37,8 @@ dependencies = [
     "numba",
     "PyQt5",
     "opencv-python-headless",
-    "matplotlib"
+    "matplotlib",
+    "requests"
 ]
 requires-python = ">=3.10"
 
@@ -55,6 +56,7 @@ include = ["neuro_sam*", "sam2*"]
 
 [project.scripts]
 neuro-sam = "neuro_sam.plugin:main"
+neuro-sam-download = "neuro_sam.utils:download_all_models"
 
 [project.entry-points."napari.manifest"]
 neuro-sam = "neuro_sam:napari.yaml"

{neuro_sam-0.1.5 → neuro_sam-0.1.7}/src/neuro_sam/napari_utils/punet_widget.py

@@ -15,14 +15,8 @@ import napari
 from napari.qt.threading import thread_worker
 
 # Import the model class
-# Assuming running from root, so punet is a package
-try:
-    from neuro_sam.punet.punet_inference import run_inference_volume
-except ImportError:
-    # Fallback if running from a different context, try to append path
-    import sys
-    sys.path.append(os.path.join(os.path.dirname(__file__), '..', 'punet'))
-    from neuro_sam.punet.punet_inference import run_inference_volume
+# Assumes installed package structure
+from neuro_sam.punet.punet_inference import run_inference_volume
 
 
 
@@ -197,13 +191,13 @@ class PunetSpineSegmentationWidget(QWidget):
     def _segmentation_worker(self, vol, params):
         import traceback
         try:
+            # Import the refactored inference function from the package
             # Import the refactored inference function from the package
             try:
                 from neuro_sam.punet.punet_inference import run_inference_volume
             except ImportError:
-                import sys
-                sys.path.append(os.path.join(os.path.dirname(__file__), '..', 'punet'))
-                from neuro_sam.punet_inference import run_inference_volume
+                # Fallback should not be needed with proper package execution
+                raise ImportError("Could not import run_inference_volume from neuro_sam.punet.punet_inference")
             
             yield "Starting inference..."
             

{neuro_sam-0.1.5 → neuro_sam-0.1.7}/src/neuro_sam/napari_utils/segmentation_model.py

@@ -8,22 +8,33 @@ from scipy.ndimage import label
 from matplotlib.path import Path
 
 
+from neuro_sam.utils import get_weights_path
+
 class DendriteSegmenter:
     """Class for segmenting dendrites from 3D image volumes using SAM2 with overlapping patches"""
     
-    def __init__(self, model_path="./Train-SAMv2/checkpoints/sam2.1_hiera_small.pt", config_path="sam2.1_hiera_s.yaml", weights_path="./Train-SAMv2/results/samv2_dendrite/dendrite_model.torch", device="cuda"):
+    def __init__(self, model_path=None, config_path="sam2.1_hiera_s.yaml", weights_path=None, device="cuda"):
         """
         Initialize the dendrite segmenter with overlapping patches.
         
         Args:
-            model_path: Path to SAM2 model checkpoint
+            model_path: Path to SAM2 model checkpoint (auto-downloaded if None)
             config_path: Path to model configuration
-            weights_path: Path to trained weights
+            weights_path: Path to trained weights (auto-downloaded if None)
             device: Device to run the model on (cpu or cuda)
         """
-        self.model_path = model_path
+        if model_path is None:
+            self.model_path = get_weights_path("sam2.1_hiera_small.pt")
+        else:
+            self.model_path = model_path
+            
         self.config_path = config_path
-        self.weights_path = weights_path
+        
+        if weights_path is None:
+            self.weights_path = get_weights_path("dendrite_model.torch")
+        else:
+            self.weights_path = weights_path
+            
         self.device = device
         self.predictor = None
 
@@ -35,8 +46,6 @@ class DendriteSegmenter:
             
             # Try importing first to catch import errors
             try:
-                import sys
-                sys.path.append('./Train-SAMv2')
                 from sam2.build_sam import build_sam2
                 from sam2.sam2_image_predictor import SAM2ImagePredictor
                 print("Successfully imported SAM2 modules")

{neuro_sam-0.1.5 → neuro_sam-0.1.7}/src/neuro_sam/napari_utils/segmentation_module.py

@@ -349,11 +349,8 @@ class SegmentationWidget(QWidget):
             # Initialize segmenter if not already done
             if self.segmenter is None:
                 self.segmenter = DendriteSegmenter(
-                    model_path="./Train-SAMv2/checkpoints/sam2.1_hiera_small.pt",
-                    config_path="sam2.1_hiera_s.yaml",
-                    weights_path="./Train-SAMv2/results/samv2_dendrite/dendrite_model.torch",
                     device=device
-                )
+                ) # Paths are now handled automatically by default args
             
             # Load the model
             success = self.segmenter.load_model()

{neuro_sam-0.1.5 → neuro_sam-0.1.7}/src/neuro_sam/plugin.py

@@ -247,11 +247,13 @@ def main():
     else:
         # Try to load a default benchmark image
         try:
-            default_path = './DeepD3_Benchmark.tif'
-            print(f"No image path provided, trying to load default: {default_path}")
+            from neuro_sam.utils import get_weights_path
+            default_path = get_weights_path('DeepD3_Benchmark.tif')
+            print(f"No image path provided, loading default: {default_path}")
             spacing_xyz = (args.x_spacing, args.y_spacing, args.z_spacing)
             viewer = run_neuro_sam(image_path=default_path, spacing_xyz=spacing_xyz)
-        except FileNotFoundError:
+        except Exception as e:
+            print(f"Failed to load default image: {e}")
             sys.exit(1)
     
     print("\nStarted NeuroSAM with anisotropic scaling support!")

{neuro_sam-0.1.5 → neuro_sam-0.1.7}/src/neuro_sam/punet/punet_inference.py

@@ -7,7 +7,7 @@ import torch
 import tifffile as tiff
 from tqdm import tqdm
 
-from prob_unet_with_tversky import ProbabilisticUnetDualLatent
+from .prob_unet_with_tversky import ProbabilisticUnetDualLatent
 
 
 def pad_to_multiple(img: np.ndarray, multiple: int = 32):

neuro_sam-0.1.7/src/neuro_sam/utils.py

@@ -0,0 +1,90 @@
+import os
+import sys
+import requests
+from pathlib import Path
+from tqdm import tqdm
+
+# Constants for Model URLs
+WEIGHTS_URLS = {
+    "DeepD3_Benchmark.tif": "https://github.com/nipunarora8/Neuro-SAM/releases/download/weights/DeepD3_Benchmark.tif",
+    "dendrite_model.torch": "https://github.com/nipunarora8/Neuro-SAM/releases/download/weights/dendrite_model.torch",
+    "sam2.1_hiera_small.pt": "https://github.com/nipunarora8/Neuro-SAM/releases/download/weights/sam2.1_hiera_small.pt",
+    "punet_best.pth": "https://github.com/nipunarora8/Neuro-SAM/releases/download/weights/punet_best.pth"
+}
+
+def get_weights_dir():
+    """Get the directory where weights are stored (~/.neuro_sam/checkpoints)."""
+    weights_dir = Path.home() / ".neuro_sam" / "checkpoints"
+    weights_dir.mkdir(parents=True, exist_ok=True)
+    return weights_dir
+
+def download_file(url, dest_path):
+    """Download a file from a URL to a destination path with a progress bar."""
+    print(f"Downloading {url} to {dest_path}...")
+    try:
+        response = requests.get(url, stream=True)
+        response.raise_for_status()
+        total_size = int(response.headers.get('content-length', 0))
+        
+        block_size = 1024 # 1 Kibibyte
+        t = tqdm(total=total_size, unit='iB', unit_scale=True)
+        
+        with open(dest_path, 'wb') as file:
+            for data in response.iter_content(block_size):
+                t.update(len(data))
+                file.write(data)
+        t.close()
+        
+        if total_size != 0 and t.n != total_size:
+            print("ERROR, something went wrong with the download")
+            return False
+        
+        print(f"Download complete: {dest_path}")
+        return True
+    except Exception as e:
+        print(f"Error downloading file: {e}")
+        if os.path.exists(dest_path):
+            os.remove(dest_path)
+        return False
+
+def get_weights_path(filename, url=None):
+    """
+    Get the path to a weights file. 
+    Checks local 'checkpoints' folder first, then ~/.neuro_sam/checkpoints.
+    If not found, downloads it.
+    """
+    # 1. Check local checkpoints folder (development mode)
+    local_path = Path("checkpoints") / filename
+    if local_path.exists():
+        return str(local_path.absolute())
+        
+    # 2. Check global cache directory
+    weights_dir = get_weights_dir()
+    cache_path = weights_dir / filename
+    
+    if cache_path.exists():
+        return str(cache_path.absolute())
+        
+    # 3. Download if not found
+    if url is None:
+        url = WEIGHTS_URLS.get(filename)
+        
+    if url:
+        print(f"Weights file {filename} not found locally. Downloading...")
+        success = download_file(url, cache_path)
+        if success:
+            return str(cache_path.absolute())
+        else:
+            raise RuntimeError(f"Failed to download {filename}")
+    else:
+        raise FileNotFoundError(f"Weights file {filename} not found and no URL provided.")
+
+def download_all_models():
+    """Download all known models to the cache directory."""
+    print("Downloading all Neuro-SAM models...")
+    for filename, url in WEIGHTS_URLS.items():
+        try:
+            get_weights_path(filename, url)
+        except Exception as e:
+            print(f"Failed to process {filename}: {e}")
+    print("All downloads processed.")

{neuro_sam-0.1.5 → neuro_sam-0.1.7/src/neuro_sam.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: neuro-sam
-Version: 0.1.5
+Version: 0.1.7
 Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
 Author-email: Nipun Arora <nipunarora8@yahoo.com>
 License: MIT License
@@ -54,6 +54,7 @@ Requires-Dist: numba
 Requires-Dist: PyQt5
 Requires-Dist: opencv-python-headless
 Requires-Dist: matplotlib
+Requires-Dist: requests
 Dynamic: license-file
 
 <div align="center">

{neuro_sam-0.1.5 → neuro_sam-0.1.7}/src/neuro_sam.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@ README.md
 pyproject.toml
 src/neuro_sam/__init__.py
 src/neuro_sam/plugin.py
+src/neuro_sam/utils.py
 src/neuro_sam.egg-info/PKG-INFO
 src/neuro_sam.egg-info/SOURCES.txt
 src/neuro_sam.egg-info/dependency_links.txt

{neuro_sam-0.1.5 → neuro_sam-0.1.7}/src/neuro_sam.egg-info/entry_points.txt

@@ -1,5 +1,6 @@
 [console_scripts]
 neuro-sam = neuro_sam.plugin:main
+neuro-sam-download = neuro_sam.utils:download_all_models
 
 [napari.manifest]
 neuro-sam = neuro_sam:napari.yaml

{neuro_sam-0.1.5 → neuro_sam-0.1.7}/src/neuro_sam.egg-info/requires.txt

@@ -18,3 +18,4 @@ numba
 PyQt5
 opencv-python-headless
 matplotlib
+requests