swcgeom 0.17.2__py3-none-any.whl → 0.18.1__py3-none-any.whl

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Files changed (69) hide show
  1. swcgeom/__init__.py +14 -0
  2. swcgeom/_version.py +2 -2
  3. swcgeom/analysis/__init__.py +15 -0
  4. swcgeom/analysis/feature_extractor.py +15 -0
  5. swcgeom/analysis/features.py +15 -0
  6. swcgeom/analysis/lmeasure.py +15 -0
  7. swcgeom/analysis/sholl.py +15 -0
  8. swcgeom/analysis/trunk.py +15 -0
  9. swcgeom/analysis/visualization.py +15 -0
  10. swcgeom/analysis/visualization3d.py +15 -0
  11. swcgeom/analysis/volume.py +15 -0
  12. swcgeom/core/__init__.py +15 -0
  13. swcgeom/core/branch.py +15 -0
  14. swcgeom/core/branch_tree.py +15 -0
  15. swcgeom/core/compartment.py +15 -0
  16. swcgeom/core/node.py +15 -0
  17. swcgeom/core/path.py +15 -0
  18. swcgeom/core/population.py +15 -0
  19. swcgeom/core/swc.py +15 -0
  20. swcgeom/core/swc_utils/__init__.py +15 -1
  21. swcgeom/core/swc_utils/assembler.py +15 -0
  22. swcgeom/core/swc_utils/base.py +15 -0
  23. swcgeom/core/swc_utils/checker.py +16 -1
  24. swcgeom/core/swc_utils/io.py +17 -1
  25. swcgeom/core/swc_utils/normalizer.py +16 -1
  26. swcgeom/core/swc_utils/subtree.py +15 -0
  27. swcgeom/core/tree.py +15 -0
  28. swcgeom/core/tree_utils.py +15 -0
  29. swcgeom/core/tree_utils_impl.py +15 -0
  30. swcgeom/images/__init__.py +15 -0
  31. swcgeom/images/augmentation.py +15 -0
  32. swcgeom/images/contrast.py +15 -0
  33. swcgeom/images/folder.py +15 -0
  34. swcgeom/images/io.py +16 -1
  35. swcgeom/transforms/__init__.py +16 -0
  36. swcgeom/transforms/base.py +17 -2
  37. swcgeom/transforms/branch.py +74 -8
  38. swcgeom/transforms/branch_tree.py +82 -0
  39. swcgeom/transforms/geometry.py +22 -7
  40. swcgeom/transforms/image_preprocess.py +15 -0
  41. swcgeom/transforms/image_stack.py +16 -1
  42. swcgeom/transforms/images.py +15 -0
  43. swcgeom/transforms/mst.py +15 -0
  44. swcgeom/transforms/neurolucida_asc.py +16 -1
  45. swcgeom/transforms/path.py +15 -0
  46. swcgeom/transforms/population.py +15 -0
  47. swcgeom/transforms/tree.py +46 -5
  48. swcgeom/transforms/tree_assembler.py +19 -4
  49. swcgeom/utils/__init__.py +15 -0
  50. swcgeom/utils/debug.py +15 -0
  51. swcgeom/utils/download.py +15 -0
  52. swcgeom/utils/dsu.py +15 -0
  53. swcgeom/utils/ellipse.py +15 -0
  54. swcgeom/utils/file.py +15 -0
  55. swcgeom/utils/neuromorpho.py +18 -7
  56. swcgeom/utils/numpy_helper.py +15 -0
  57. swcgeom/utils/plotter_2d.py +15 -0
  58. swcgeom/utils/plotter_3d.py +18 -1
  59. swcgeom/utils/renderer.py +15 -0
  60. swcgeom/utils/sdf.py +15 -0
  61. swcgeom/utils/solid_geometry.py +15 -0
  62. swcgeom/utils/transforms.py +15 -0
  63. swcgeom/utils/volumetric_object.py +15 -0
  64. {swcgeom-0.17.2.dist-info → swcgeom-0.18.1.dist-info}/LICENSE +1 -1
  65. {swcgeom-0.17.2.dist-info → swcgeom-0.18.1.dist-info}/METADATA +9 -5
  66. swcgeom-0.18.1.dist-info/RECORD +68 -0
  67. swcgeom-0.17.2.dist-info/RECORD +0 -67
  68. {swcgeom-0.17.2.dist-info → swcgeom-0.18.1.dist-info}/WHEEL +0 -0
  69. {swcgeom-0.17.2.dist-info → swcgeom-0.18.1.dist-info}/top_level.txt +0 -0
swcgeom/utils/__init__.py CHANGED
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
2
+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
5
+ # You may obtain a copy of the License at
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+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
16
  """Utils."""
2
17
 
3
18
  from swcgeom.utils.debug import *
swcgeom/utils/debug.py CHANGED
@@ -1,3 +1,18 @@
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+ # Copyright 2022-2025 Zexin Yuan
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+ #
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+ # Licensed under the Apache License, Version 2.0 (the "License");
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+ # you may not use this file except in compliance with the License.
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+ # You may obtain a copy of the License at
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+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
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+ #
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+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
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+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+ # See the License for the specific language governing permissions and
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+ # limitations under the License.
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+
15
+
1
16
  """Debug helpers"""
2
17
 
3
18
  import time
swcgeom/utils/download.py CHANGED
@@ -1,3 +1,18 @@
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+ # Copyright 2022-2025 Zexin Yuan
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+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
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+ # you may not use this file except in compliance with the License.
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+ # You may obtain a copy of the License at
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+ #
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+ # http://www.apache.org/licenses/LICENSE-2.0
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+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
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+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
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+
15
+
1
16
  """Download helpers.
2
17
 
3
18
  Notes
swcgeom/utils/dsu.py CHANGED
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
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+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
5
+ # You may obtain a copy of the License at
6
+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
16
  """Disjoint Set Union Impl."""
2
17
 
3
18
  __all__ = ["DisjointSetUnion"]
swcgeom/utils/ellipse.py CHANGED
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
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+ #
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+ # Licensed under the Apache License, Version 2.0 (the "License");
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+ # you may not use this file except in compliance with the License.
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+ # You may obtain a copy of the License at
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+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
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+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
16
  """Finds the Minimum Volume Enclosing Ellipsoid."""
2
17
 
3
18
  # pylint: disable=invalid-name
swcgeom/utils/file.py CHANGED
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
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+ #
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+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
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+ # You may obtain a copy of the License at
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+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
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+ #
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+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
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+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
16
  """File related utils.
2
17
 
3
18
  Notes
@@ -1,9 +1,24 @@
1
+ # Copyright 2022-2025 Zexin Yuan
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+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
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+ # You may obtain a copy of the License at
6
+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
16
  """NeuroMorpho.org.
2
17
 
3
18
  Examples
4
19
  --------
5
20
 
6
- Metadata:
21
+ Metadata:
7
22
 
8
23
  ```json
9
24
  {
@@ -287,13 +302,9 @@ class NeuroMorpho:
287
302
  where = where or (lambda _: True)
288
303
  if isinstance(group_by, str):
289
304
  key = group_by
290
- group_by = lambda v: v[
291
- key
292
- ] # pylint: disable=unnecessary-lambda-assignment
305
+ group_by = lambda v: v[key] # pylint: disable=unnecessary-lambda-assignment
293
306
  elif group_by is None:
294
- group_by = (
295
- lambda _: None
296
- ) # pylint: disable=unnecessary-lambda-assignment
307
+ group_by = lambda _: None # pylint: disable=unnecessary-lambda-assignment
297
308
  items = []
298
309
  for k, v in tx_m.cursor():
299
310
  metadata = json.loads(v)
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
2
+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
5
+ # You may obtain a copy of the License at
6
+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
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  """Numpy related utils."""
2
17
 
3
18
  from contextlib import contextmanager
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
2
+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
5
+ # You may obtain a copy of the License at
6
+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
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  """2D Plotting utils."""
2
17
 
3
18
  from typing import Optional
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
2
+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
5
+ # You may obtain a copy of the License at
6
+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
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+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
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  """3D Plotting utils."""
2
17
 
3
18
  import numpy as np
@@ -27,5 +42,7 @@ def draw_lines_3d(
27
42
  Forwarded to `~mpl_toolkits.mplot3d.art3d.Line3DCollection`.
28
43
  """
29
44
 
30
- line_collection = Line3DCollection(lines, joinstyle=joinstyle, capstyle=capstyle, **kwargs) # type: ignore
45
+ line_collection = Line3DCollection(
46
+ lines, joinstyle=joinstyle, capstyle=capstyle, **kwargs
47
+ ) # type: ignore
31
48
  return ax.add_collection3d(line_collection)
swcgeom/utils/renderer.py CHANGED
@@ -1,3 +1,18 @@
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+ # Copyright 2022-2025 Zexin Yuan
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+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
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+ # you may not use this file except in compliance with the License.
5
+ # You may obtain a copy of the License at
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+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
16
  """Rendering related utils."""
2
17
 
3
18
  from functools import cached_property
swcgeom/utils/sdf.py CHANGED
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
2
+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
5
+ # You may obtain a copy of the License at
6
+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
16
  """Signed distance functions.
2
17
 
3
18
  Refs: https://iquilezles.org/articles/distfunctions/
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
2
+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
5
+ # You may obtain a copy of the License at
6
+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
16
  """Solid Geometry."""
2
17
 
3
18
  import numpy as np
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
2
+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
5
+ # You may obtain a copy of the License at
6
+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
16
  """3D geometry transformations."""
2
17
 
3
18
  import numpy as np
@@ -1,3 +1,18 @@
1
+ # Copyright 2022-2025 Zexin Yuan
2
+ #
3
+ # Licensed under the Apache License, Version 2.0 (the "License");
4
+ # you may not use this file except in compliance with the License.
5
+ # You may obtain a copy of the License at
6
+ #
7
+ # http://www.apache.org/licenses/LICENSE-2.0
8
+ #
9
+ # Unless required by applicable law or agreed to in writing, software
10
+ # distributed under the License is distributed on an "AS IS" BASIS,
11
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
+ # See the License for the specific language governing permissions and
13
+ # limitations under the License.
14
+
15
+
1
16
  """Volumetric object.
2
17
 
3
18
  This library implements the calculation of volumes for any shape
@@ -186,7 +186,7 @@
186
186
  same "printed page" as the copyright notice for easier
187
187
  identification within third-party archives.
188
188
 
189
- Copyright [2024] [Zexin Yuan]
189
+ Copyright [yyyy] [name of copyright owner]
190
190
 
191
191
  Licensed under the Apache License, Version 2.0 (the "License");
192
192
  you may not use this file except in compliance with the License.
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: swcgeom
3
- Version: 0.17.2
3
+ Version: 0.18.1
4
4
  Summary: Neuron geometry library for swc format
5
5
  Author-email: yzx9 <yuan.zx@outlook.com>
6
6
  License: Apache-2.0
@@ -13,7 +13,7 @@ Requires-Dist: imagecodecs>=2023.3.16
13
13
  Requires-Dist: matplotlib>=3.5.2
14
14
  Requires-Dist: numpy>=1.22.3
15
15
  Requires-Dist: pandas>=1.4.2
16
- Requires-Dist: pynrrd>=1.0.0
16
+ Requires-Dist: pynrrd>=1.1.0
17
17
  Requires-Dist: scipy>=1.9.1
18
18
  Requires-Dist: sdflit>=0.2.1
19
19
  Requires-Dist: seaborn>=0.12.0
@@ -56,16 +56,20 @@ pip install build
56
56
  pip install --editable .
57
57
  ```
58
58
 
59
- Static analysis don't support import hook used in editable install for [PEP660](https://peps.python.org/pep-0660/) since upgrade to setuptools v64+, detail infomation at [setuptools#3518](https://github.com/pypa/setuptools/issues/3518), a workaround for vscode with pylance:
59
+ Static analysis don't support import hook used in editable install for
60
+ [PEP660](https://peps.python.org/pep-0660/) since upgrade to setuptools v64+,
61
+ detail information at [setuptools#3518](https://github.com/pypa/setuptools/issues/3518),
62
+ a workaround for vscode with pylance:
60
63
 
61
64
  ```json
62
65
  {
63
- "python.analysis.extraPaths": ["/path/to/this/project"]
66
+ "python.analysis.extraPaths": ["/path/to/this/project"]
64
67
  }
65
68
  ```
66
69
 
67
70
  ## LICENSE
68
71
 
69
- This work is licensed under a <a rel="license" href="https://www.apache.org/licenses/">Apache-2.0</a>.
72
+ This work is licensed under a
73
+ <a rel="license" href="https://www.apache.org/licenses/">Apache-2.0</a>.
70
74
 
71
75
  Copyright (c) 2022-present, Zexin Yuan
@@ -0,0 +1,68 @@
1
+ swcgeom/__init__.py,sha256=i9vi8J65kOj8z_gkGkDTufHn28zNbv6panIr9AuNNoc,845
2
+ swcgeom/_version.py,sha256=WKuH__LVaZHj35m7SuPDdqOuUScbj9XEwpPI5Tns-Xw,413
3
+ swcgeom/analysis/__init__.py,sha256=ZCxLqk5aA_96C5281RristqpEp3mnKyDcPOFom2d8iU,861
4
+ swcgeom/analysis/feature_extractor.py,sha256=8hmwwWCZ8c_XcnmyY--vRygo-OAovIoMuVTHnixX8KA,14855
5
+ swcgeom/analysis/features.py,sha256=NnFRUsMO7mPoBNLQ_kwSWHSfaV1BCOYTZz6VuG2Cfi8,6905
6
+ swcgeom/analysis/lmeasure.py,sha256=RLhRIo3VOQFqisBDetP120SntWSTE2rJ-vL5l-QGT40,28688
7
+ swcgeom/analysis/sholl.py,sha256=uGElY5hXILON8uHX9phGwFeKMjWCtA1GTeoyKStkSPE,7203
8
+ swcgeom/analysis/trunk.py,sha256=f6oH2Xlpn76JjKNsC0DKFsnYGn4FP4YRucCeyUaGgjg,6147
9
+ swcgeom/analysis/visualization.py,sha256=dioNW7Y596xhUPySkr-gbcCzLFm4PPsizKAjEXgAdyI,6216
10
+ swcgeom/analysis/visualization3d.py,sha256=OIUEtxPZpwK8eDEuy8_ezh5x2oQishQ3-aj-dGselAY,3094
11
+ swcgeom/analysis/volume.py,sha256=KLEqE5OWKckdw2qsI8Ugmxi-_jePnE9N9ZN6QFC07y8,5197
12
+ swcgeom/core/__init__.py,sha256=RPx9camQEOnI1WZSxfT8Kwb3fxMtg7yPJERvyr_nDqo,1026
13
+ swcgeom/core/branch.py,sha256=xu5J12FjxXSNL3Q_Uiy5qLlMozfcdnkIDO-XyDB_CYg,4764
14
+ swcgeom/core/branch_tree.py,sha256=jFDKkBgaTCT6C4ZsGdihxBp3xC2k9v6wxE43UGW2AuY,2424
15
+ swcgeom/core/compartment.py,sha256=neoM4nyZxPnaHDnxr-T5xItrf6gqctbo8dOawlFQRlM,3850
16
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