neuro-sam 0.1.0__py3-none-any.whl → 0.1.5__py3-none-any.whl

neuro_sam/napari_utils/punet_widget.py

@@ -22,7 +22,7 @@ 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_inference import run_inference_volume
+    from neuro_sam.punet.punet_inference import run_inference_volume
 
 
 

neuro_sam/napari_utils/segmentation_module.py

@@ -7,11 +7,8 @@ from qtpy.QtWidgets import (
 )
 from qtpy.QtCore import Signal
 import torch
-import sys
-import os
-sys.path.append(os.path.dirname(os.path.abspath(__file__)))
-from contrasting_color_system import contrasting_color_manager
-from segmentation_model import DendriteSegmenter
+from .contrasting_color_system import contrasting_color_manager
+from .segmentation_model import DendriteSegmenter
 from scipy import ndimage
 from scipy.ndimage import binary_fill_holes
 from skimage.morphology import disk, binary_closing, remove_small_objects

neuro_sam/plugin.py

@@ -216,8 +216,7 @@ def load_ome_tiff_with_spacing(image_path):
     return image, (94.0, 94.0, 500.0)
 
 
-# For direct execution from command line
-if __name__ == "__main__":
+def main():
     import sys
     import argparse
     
@@ -257,4 +256,8 @@ if __name__ == "__main__":
     
     print("\nStarted NeuroSAM with anisotropic scaling support!")
     print("Configure voxel spacing in the 'Path Tracing' tab before starting analysis.")
-    napari.run()  # Start the Napari event loop
+    napari.run()  # Start the Napari event loop
+
+# For direct execution from command line
+if __name__ == "__main__":
+    main()

neuro_sam/punet/prob_unet_deepd3.py

@@ -10,9 +10,9 @@ import torch.nn.functional as F
 from torch.distributions import Normal, Independent, kl
 import numpy as np
 
-from deepd3_model import DeepD3Model
-from unet_blocks import *
-from utils import init_weights, init_weights_orthogonal_normal, l2_regularisation
+from .deepd3_model import DeepD3Model
+from .unet_blocks import *
+from .utils import init_weights, init_weights_orthogonal_normal, l2_regularisation
 
 device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
 

neuro_sam/punet/prob_unet_with_tversky.py

@@ -12,8 +12,8 @@ import torch
 import torch.nn as nn
 import torch.nn.functional as F
 from torch.distributions import kl
-from deepd3_model import DeepD3Model
-from prob_unet_deepd3 import AxisAlignedConvGaussian, Fcomb
+from .deepd3_model import DeepD3Model
+from .prob_unet_deepd3 import AxisAlignedConvGaussian, Fcomb
 
 
 class TverskyLoss(nn.Module):

neuro_sam/punet/unet_blocks.py

@@ -2,7 +2,7 @@ import torch
 import torch.nn as nn
 from torch.autograd import Variable
 import numpy as np
-from utils import init_weights
+from .utils import init_weights
 
 class DownConvBlock(nn.Module):
     """

{neuro_sam-0.1.0.dist-info → neuro_sam-0.1.5.dist-info}/METADATA

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: neuro-sam
-Version: 0.1.0
+Version: 0.1.5
 Summary: Neuro-SAM: Foundation Models for Dendrite and Dendritic Spine Segmentation
-Author-email: Nipun Arora <nipun.arora@fau.de>
+Author-email: Nipun Arora <nipunarora8@yahoo.com>
 License: MIT License
         
         Copyright (c) 2024 Nipun Arora
@@ -50,6 +50,10 @@ Requires-Dist: superqt
 Requires-Dist: magicgui
 Requires-Dist: scikit-image
 Requires-Dist: tifffile
+Requires-Dist: numba
+Requires-Dist: PyQt5
+Requires-Dist: opencv-python-headless
+Requires-Dist: matplotlib
 Dynamic: license-file
 
 <div align="center">

{neuro_sam-0.1.0.dist-info → neuro_sam-0.1.5.dist-info}/RECORD

@@ -1,5 +1,5 @@
 neuro_sam/__init__.py,sha256=0pbMqpI_nQyhP0_pfTaIg97FVEcFkS5w8gQrsMiBcG4,34
-neuro_sam/plugin.py,sha256=pL2zJtslbuinkXUOJFVbuGwSIVIf45wVGiPAJ2XUZ-I,10092
+neuro_sam/plugin.py,sha256=35z7ybZQaFTxXL78z9oNOaHghdILJ8vaAtVShyQyISo,10116
 neuro_sam/brightest_path_lib/__init__.py,sha256=vU3VvX26D2c9B26Lid09uThzKMQJYPx622SkPhxNlDI,123
 neuro_sam/brightest_path_lib/connected_componen.py,sha256=x_kjDGZ_8U2ks9kZJOOyM8_ow84UugAsPUByI-NlXFk,12734
 neuro_sam/brightest_path_lib/algorithm/__init__.py,sha256=XFYxFyx97FG7lK3_j7uA8GgunpfkOcAo2NIJU0GUn40,170
@@ -30,19 +30,19 @@ neuro_sam/napari_utils/color_utils.py,sha256=Hf5R8f0rh7b9CY1VT72o3tLGfGnnjRREkX8
 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/path_tracing_module.py,sha256=0mMAtrMmtgK_ujMzaWzIguYVDPr8nfzalaTAwgF3NaQ,44062
-neuro_sam/napari_utils/punet_widget.py,sha256=GzY8fGzx5xvitkIiD24TjWktW1ex4F7ujYjCu3Rd6xA,17058
+neuro_sam/napari_utils/punet_widget.py,sha256=_kGI4bQGbRpjSyhfZrFAqRK5RdSkdwenSrFAFv53pvs,17064
 neuro_sam/napari_utils/segmentation_model.py,sha256=uAnNvMdZVrtlaST36TpCdyoYiaNtVsQLeaPcroD-aT0,33939
-neuro_sam/napari_utils/segmentation_module.py,sha256=MKp53jn3UM5fJurC9kAV6BcHpTJWjsmbno8bbSDMhHc,28988
+neuro_sam/napari_utils/segmentation_module.py,sha256=TPn_x53uwf-WVC0vTleX2g9fCFXXWNAGtuB8Ht5vmAM,28909
 neuro_sam/napari_utils/visualization_module.py,sha256=JtZlBoKlfIwVLa2Sqg7b2KTr07fNlAcwR0M7fHsn2oM,24723
 neuro_sam/punet/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 neuro_sam/punet/deepd3_model.py,sha256=nGVEqzCPz_E4cFA6QmknW2CffDcjxH7VsdYAyTdAtY0,7509
-neuro_sam/punet/prob_unet_deepd3.py,sha256=qZcKo4dZeEemqD7PxLHZu5YB_h3Q0--W3vTRhXjYxS0,14695
-neuro_sam/punet/prob_unet_with_tversky.py,sha256=D-Ur5AfGsVl2dH35jbZL8BaHdJHzbTrHLsS-cagBzoQ,12843
+neuro_sam/punet/prob_unet_deepd3.py,sha256=syXNleUVrfYtmVveN9G461oAhumxsijsavps8in4VRw,14698
+neuro_sam/punet/prob_unet_with_tversky.py,sha256=2dBbO_BEHbhYWBXW7rXQX6s2DnqoTgBKkgk6VkgN-Ds,12845
 neuro_sam/punet/punet_inference.py,sha256=U3ne-sP1y732PISFYlV50cPbXN6eEREQue1Jf6w1Io8,8032
 neuro_sam/punet/run_inference.py,sha256=c9ATKWJvhOzNEaww_sUCI5fFS1q0bQ4GYUwNUqxWcwA,5312
-neuro_sam/punet/unet_blocks.py,sha256=xc-nZql_CSsyEeCxKIY-WIhiXG1KyRiCSIESztGJKEs,3170
+neuro_sam/punet/unet_blocks.py,sha256=ZRNKay9P3OnJ0PmtKXw_iSgUyRE1DkkGefGXwSbYZGY,3171
 neuro_sam/punet/utils.py,sha256=ibwcpkqqZ3_3Afz2VYxzplz8_8FWQ5qYQqjJiKS8hIo,1786
-neuro_sam-0.1.0.dist-info/licenses/LICENSE,sha256=akmTIN8IuZn3Y7UK_8qVQnyKDWSDcVUwB8RPGNXCojw,1068
+neuro_sam-0.1.5.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
@@ -86,8 +86,8 @@ 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-0.1.0.dist-info/METADATA,sha256=qmJWJ17j0Qlm65saFelge2KlmpYQYdU48uq0CKykyJM,9509
-neuro_sam-0.1.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-neuro_sam-0.1.0.dist-info/entry_points.txt,sha256=Mw5mxn4u8N-boA1NOR8vfbPh_JbSiKpiIuqJ-styL9M,52
-neuro_sam-0.1.0.dist-info/top_level.txt,sha256=yPbWxFcw79sErTk8zohihUHMK9LL31i3bXir2MrS4OQ,15
-neuro_sam-0.1.0.dist-info/RECORD,,
+neuro_sam-0.1.5.dist-info/METADATA,sha256=04rkWKMPdFGRctGcQgHGe69JxMENwwkzNtMHOQiGn_Y,9618
+neuro_sam-0.1.5.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+neuro_sam-0.1.5.dist-info/entry_points.txt,sha256=K0SaLior6N1REi_K0O4962Wn4DhTSos_Sx6Enx0mIm4,105
+neuro_sam-0.1.5.dist-info/top_level.txt,sha256=yPbWxFcw79sErTk8zohihUHMK9LL31i3bXir2MrS4OQ,15
+neuro_sam-0.1.5.dist-info/RECORD,,

neuro_sam-0.1.5.dist-info/entry_points.txt

@@ -0,0 +1,5 @@
+[console_scripts]
+neuro-sam = neuro_sam.plugin:main
+
+[napari.manifest]
+neuro-sam = neuro_sam:napari.yaml

neuro_sam-0.1.0.dist-info/entry_points.txt

@@ -1,2 +0,0 @@
-[napari.manifest]
-neuro-sam = neuro_sam:napari.yaml