svv 0.0.31__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (158) hide show
  1. svv-0.0.31/MANIFEST.in +21 -0
  2. svv-0.0.31/PKG-INFO +65 -0
  3. svv-0.0.31/README.md +20 -0
  4. svv-0.0.31/pyproject.toml +10 -0
  5. svv-0.0.31/setup.cfg +4 -0
  6. svv-0.0.31/setup.py +613 -0
  7. svv-0.0.31/svv/__init__.py +0 -0
  8. svv-0.0.31/svv/domain/__init__.py +0 -0
  9. svv-0.0.31/svv/domain/core/__init__.py +183 -0
  10. svv-0.0.31/svv/domain/core/a_matrix.py +180 -0
  11. svv-0.0.31/svv/domain/core/h_matrix.py +182 -0
  12. svv-0.0.31/svv/domain/core/m_matrix.py +288 -0
  13. svv-0.0.31/svv/domain/core/n_matrix.py +116 -0
  14. svv-0.0.31/svv/domain/domain.py +703 -0
  15. svv-0.0.31/svv/domain/io/__init__.py +0 -0
  16. svv-0.0.31/svv/domain/io/read.py +41 -0
  17. svv-0.0.31/svv/domain/kernel/__init__.py +0 -0
  18. svv-0.0.31/svv/domain/kernel/coordinate_system.py +233 -0
  19. svv-0.0.31/svv/domain/kernel/cost.py +163 -0
  20. svv-0.0.31/svv/domain/kernel/kernel.py +353 -0
  21. svv-0.0.31/svv/domain/patch.py +146 -0
  22. svv-0.0.31/svv/domain/routines/__init__.py +0 -0
  23. svv-0.0.31/svv/domain/routines/allocate.py +162 -0
  24. svv-0.0.31/svv/domain/routines/boolean.py +57 -0
  25. svv-0.0.31/svv/domain/routines/c_allocate.cpp +35328 -0
  26. svv-0.0.31/svv/domain/routines/c_allocate.pyx +225 -0
  27. svv-0.0.31/svv/domain/routines/c_sample.cpp +31202 -0
  28. svv-0.0.31/svv/domain/routines/c_sample.pyx +60 -0
  29. svv-0.0.31/svv/domain/routines/discretize.py +303 -0
  30. svv-0.0.31/svv/domain/routines/tetrahedralize.py +61 -0
  31. svv-0.0.31/svv/domain/solver/__init__.py +0 -0
  32. svv-0.0.31/svv/domain/solver/solver.py +108 -0
  33. svv-0.0.31/svv/domain/weingarten.py +180 -0
  34. svv-0.0.31/svv/forest/__init__.py +0 -0
  35. svv-0.0.31/svv/forest/connect/__init__.py +0 -0
  36. svv-0.0.31/svv/forest/connect/assign.py +530 -0
  37. svv-0.0.31/svv/forest/connect/base.py +152 -0
  38. svv-0.0.31/svv/forest/connect/base_connection.py +972 -0
  39. svv-0.0.31/svv/forest/connect/bezier.py +223 -0
  40. svv-0.0.31/svv/forest/connect/catmullrom.py +379 -0
  41. svv-0.0.31/svv/forest/connect/connect.py +0 -0
  42. svv-0.0.31/svv/forest/connect/curve.py +52 -0
  43. svv-0.0.31/svv/forest/connect/forest_connection.py +35 -0
  44. svv-0.0.31/svv/forest/connect/geodesic.py +96 -0
  45. svv-0.0.31/svv/forest/connect/nurbs.py +253 -0
  46. svv-0.0.31/svv/forest/connect/optimize.py +1055 -0
  47. svv-0.0.31/svv/forest/connect/tree_connection.py +417 -0
  48. svv-0.0.31/svv/forest/connect/vessel_connection.py +217 -0
  49. svv-0.0.31/svv/forest/export/__init__.py +0 -0
  50. svv-0.0.31/svv/forest/export/export_solid.py +37 -0
  51. svv-0.0.31/svv/forest/export/export_spline.py +225 -0
  52. svv-0.0.31/svv/forest/forest.py +285 -0
  53. svv-0.0.31/svv/simulation/__init__.py +0 -0
  54. svv-0.0.31/svv/simulation/boundary_conditions.py +127 -0
  55. svv-0.0.31/svv/simulation/equation.py +230 -0
  56. svv-0.0.31/svv/simulation/fluid/__init__.py +0 -0
  57. svv-0.0.31/svv/simulation/fluid/fluid_equation.py +76 -0
  58. svv-0.0.31/svv/simulation/fluid/rom/__init__.py +2 -0
  59. svv-0.0.31/svv/simulation/fluid/rom/one_d/__init__.py +10 -0
  60. svv-0.0.31/svv/simulation/fluid/rom/one_d/centerlines.py +212 -0
  61. svv-0.0.31/svv/simulation/fluid/rom/one_d/generate_1d_mesh.py +596 -0
  62. svv-0.0.31/svv/simulation/fluid/rom/one_d/io_0d.py +141 -0
  63. svv-0.0.31/svv/simulation/fluid/rom/one_d/io_1d.py +573 -0
  64. svv-0.0.31/svv/simulation/fluid/rom/one_d/io_headers.py +203 -0
  65. svv-0.0.31/svv/simulation/fluid/rom/one_d/manage.py +53 -0
  66. svv-0.0.31/svv/simulation/fluid/rom/one_d/mesh.py +834 -0
  67. svv-0.0.31/svv/simulation/fluid/rom/one_d/models.py +126 -0
  68. svv-0.0.31/svv/simulation/fluid/rom/one_d/parameters.py +134 -0
  69. svv-0.0.31/svv/simulation/fluid/rom/one_d/utils.py +163 -0
  70. svv-0.0.31/svv/simulation/fluid/rom/zero_d/__init__.py +0 -0
  71. svv-0.0.31/svv/simulation/fluid/rom/zero_d/post.py +231 -0
  72. svv-0.0.31/svv/simulation/fluid/rom/zero_d/process.py +8 -0
  73. svv-0.0.31/svv/simulation/fluid/rom/zero_d/project_solution.py +113 -0
  74. svv-0.0.31/svv/simulation/fluid/rom/zero_d/zerod_forest.py +325 -0
  75. svv-0.0.31/svv/simulation/fluid/rom/zero_d/zerod_tree.py +256 -0
  76. svv-0.0.31/svv/simulation/general_parameters.py +172 -0
  77. svv-0.0.31/svv/simulation/linear_solver.py +112 -0
  78. svv-0.0.31/svv/simulation/mesh.py +180 -0
  79. svv-0.0.31/svv/simulation/output.py +100 -0
  80. svv-0.0.31/svv/simulation/simulation.py +720 -0
  81. svv-0.0.31/svv/simulation/utils/__init__.py +0 -0
  82. svv-0.0.31/svv/simulation/utils/boundary_layer.py +697 -0
  83. svv-0.0.31/svv/simulation/utils/close_segments.cpp +31455 -0
  84. svv-0.0.31/svv/simulation/utils/extract.cpp +30220 -0
  85. svv-0.0.31/svv/simulation/utils/extract_faces.py +429 -0
  86. svv-0.0.31/svv/simulation/utils/smoothing.py +0 -0
  87. svv-0.0.31/svv/simulation/utils/test_boundary.py +321 -0
  88. svv-0.0.31/svv/tree/__init__.py +0 -0
  89. svv-0.0.31/svv/tree/branch/__init__.py +0 -0
  90. svv-0.0.31/svv/tree/branch/bifurcation.py +1938 -0
  91. svv-0.0.31/svv/tree/branch/constraints.py +135 -0
  92. svv-0.0.31/svv/tree/branch/root.py +200 -0
  93. svv-0.0.31/svv/tree/branch/triad.py +62 -0
  94. svv-0.0.31/svv/tree/collision/__init__.py +0 -0
  95. svv-0.0.31/svv/tree/collision/tree_collision.py +118 -0
  96. svv-0.0.31/svv/tree/data/__init__.py +0 -0
  97. svv-0.0.31/svv/tree/data/data.py +262 -0
  98. svv-0.0.31/svv/tree/data/units.py +228 -0
  99. svv-0.0.31/svv/tree/export/__init__.py +0 -0
  100. svv-0.0.31/svv/tree/export/export_centerlines.py +447 -0
  101. svv-0.0.31/svv/tree/export/export_solid.py +449 -0
  102. svv-0.0.31/svv/tree/tree.py +303 -0
  103. svv-0.0.31/svv/tree/utils/TreeManager.py +352 -0
  104. svv-0.0.31/svv/tree/utils/__init__.py +0 -0
  105. svv-0.0.31/svv/tree/utils/c_angle.cpp +30472 -0
  106. svv-0.0.31/svv/tree/utils/c_angle.pyx +69 -0
  107. svv-0.0.31/svv/tree/utils/c_basis.cpp +31933 -0
  108. svv-0.0.31/svv/tree/utils/c_basis.pyx +120 -0
  109. svv-0.0.31/svv/tree/utils/c_close.cpp +34756 -0
  110. svv-0.0.31/svv/tree/utils/c_close.pyx +214 -0
  111. svv-0.0.31/svv/tree/utils/c_extend.cpp +32670 -0
  112. svv-0.0.31/svv/tree/utils/c_extend.pyx +191 -0
  113. svv-0.0.31/svv/tree/utils/c_local_optimize.cpp +48443 -0
  114. svv-0.0.31/svv/tree/utils/c_local_optimize.pyx +1220 -0
  115. svv-0.0.31/svv/tree/utils/c_obb.cpp +31810 -0
  116. svv-0.0.31/svv/tree/utils/c_obb.pyx +423 -0
  117. svv-0.0.31/svv/tree/utils/c_update.cpp +32184 -0
  118. svv-0.0.31/svv/tree/utils/c_update.pyx +89 -0
  119. svv-0.0.31/svv/utils/__init__.py +0 -0
  120. svv-0.0.31/svv/utils/remeshing/Linux/__init__.py +0 -0
  121. svv-0.0.31/svv/utils/remeshing/Linux/mmg2d_O3 +0 -0
  122. svv-0.0.31/svv/utils/remeshing/Linux/mmg3d_O3 +0 -0
  123. svv-0.0.31/svv/utils/remeshing/Linux/mmgs_O3 +0 -0
  124. svv-0.0.31/svv/utils/remeshing/Mac/__init__.py +0 -0
  125. svv-0.0.31/svv/utils/remeshing/Windows/__init__.py +0 -0
  126. svv-0.0.31/svv/utils/remeshing/Windows/mmg2d_O3.exe +0 -0
  127. svv-0.0.31/svv/utils/remeshing/Windows/mmg3d_O3.exe +0 -0
  128. svv-0.0.31/svv/utils/remeshing/Windows/mmgs_O3.exe +0 -0
  129. svv-0.0.31/svv/utils/remeshing/__init__.py +13 -0
  130. svv-0.0.31/svv/utils/remeshing/remesh.py +780 -0
  131. svv-0.0.31/svv/utils/spatial/__init__.py +0 -0
  132. svv-0.0.31/svv/utils/spatial/c_distance.cpp +33713 -0
  133. svv-0.0.31/svv/utils/spatial/c_distance.pyx +476 -0
  134. svv-0.0.31/svv/visualize/__init__.py +0 -0
  135. svv-0.0.31/svv/visualize/forest/__init__.py +0 -0
  136. svv-0.0.31/svv/visualize/forest/show.py +27 -0
  137. svv-0.0.31/svv/visualize/tree/__init__.py +0 -0
  138. svv-0.0.31/svv/visualize/tree/points.py +16 -0
  139. svv-0.0.31/svv/visualize/tree/show.py +83 -0
  140. svv-0.0.31/svv.egg-info/PKG-INFO +65 -0
  141. svv-0.0.31/svv.egg-info/SOURCES.txt +156 -0
  142. svv-0.0.31/svv.egg-info/dependency_links.txt +1 -0
  143. svv-0.0.31/svv.egg-info/not-zip-safe +1 -0
  144. svv-0.0.31/svv.egg-info/requires.txt +14 -0
  145. svv-0.0.31/svv.egg-info/top_level.txt +1 -0
  146. svv-0.0.31/test/test_allocate.py +182 -0
  147. svv-0.0.31/test/test_base_curve.py +146 -0
  148. svv-0.0.31/test/test_beziercurve.py +202 -0
  149. svv-0.0.31/test/test_boolean.py +236 -0
  150. svv-0.0.31/test/test_c_allocate.py +186 -0
  151. svv-0.0.31/test/test_c_distance.py +264 -0
  152. svv-0.0.31/test/test_c_sample.py +98 -0
  153. svv-0.0.31/test/test_catmullrom_curve.py +204 -0
  154. svv-0.0.31/test/test_curve.py +132 -0
  155. svv-0.0.31/test/test_h_matrix.py +105 -0
  156. svv-0.0.31/test/test_m_matrix.py +167 -0
  157. svv-0.0.31/test/test_n_matrix.py +99 -0
  158. svv-0.0.31/test/test_nurbs_curve.py +194 -0
svv-0.0.31/MANIFEST.in ADDED
@@ -0,0 +1,21 @@
1
+ include LICENSE
2
+ include README.md
3
+
4
+ # Include all .pyx files
5
+ recursive-include svv/utils/spatial *.pyx
6
+ recursive-include svv/tree/utils *.pyx
7
+ recursive-include svv/domain/routines *.pyx
8
+
9
+ # Include all remesher executables
10
+ include svv/utils/remeshing/Linux/mmg2d_O3
11
+ include svv/utils/remeshing/Linux/mmg3d_O3
12
+ include svv/utils/remeshing/Linux/mmgs_O3
13
+
14
+ # include svv/utils/remeshing/Mac/mmg2d_O3
15
+ # include svv/utils/remeshing/Mac/mmg3d_O3
16
+ # include svv/utils/remeshing/Mac/mmgs_O3
17
+ recursive-include svv/bin *
18
+
19
+ include svv/utils/remeshing/Windows/mmg2d_O3.exe
20
+ include svv/utils/remeshing/Windows/mmg3d_O3.exe
21
+ include svv/utils/remeshing/Windows/mmgs_O3.exe
svv-0.0.31/PKG-INFO ADDED
@@ -0,0 +1,65 @@
1
+ Metadata-Version: 2.4
2
+ Name: svv
3
+ Version: 0.0.31
4
+ Summary: Synthetic vascular generation, modeling, and simulation package
5
+ Author: Zachary Sexton
6
+ Author-email: zsexton@stanford.edu
7
+ License: MIT
8
+ Classifier: Intended Audience :: Science/Research
9
+ Classifier: License :: OSI Approved :: MIT License
10
+ Classifier: Programming Language :: Python :: 3.9
11
+ Classifier: Programming Language :: Python :: 3.10
12
+ Classifier: Programming Language :: Python :: 3.11
13
+ Classifier: Programming Language :: Python :: 3.12
14
+ Classifier: Topic :: Scientific/Engineering
15
+ Classifier: Operating System :: Microsoft :: Windows
16
+ Classifier: Operating System :: POSIX :: Linux
17
+ Classifier: Operating System :: POSIX
18
+ Classifier: Operating System :: Unix
19
+ Classifier: Operating System :: MacOS
20
+ Requires-Python: >=3.9
21
+ Description-Content-Type: text/markdown
22
+ Requires-Dist: numpy<=1.24.0
23
+ Requires-Dist: scipy>=1.10.1
24
+ Requires-Dist: matplotlib>=3.7.5
25
+ Requires-Dist: Cython>=3.0.7
26
+ Requires-Dist: usearch>=2.0.0
27
+ Requires-Dist: scikit-image
28
+ Requires-Dist: tetgen
29
+ Requires-Dist: trimesh[all]
30
+ Requires-Dist: hnswlib
31
+ Requires-Dist: pyvista==0.44.2
32
+ Requires-Dist: scikit-learn
33
+ Requires-Dist: tqdm
34
+ Requires-Dist: pymeshfix==0.17.0
35
+ Requires-Dist: numexpr
36
+ Dynamic: author
37
+ Dynamic: author-email
38
+ Dynamic: classifier
39
+ Dynamic: description
40
+ Dynamic: description-content-type
41
+ Dynamic: license
42
+ Dynamic: requires-dist
43
+ Dynamic: requires-python
44
+ Dynamic: summary
45
+
46
+ # svVascularize
47
+
48
+
49
+ ![Version](https://img.shields.io/badge/version-0.0.31-blue)
50
+ ![Platform](https://img.shields.io/badge/platform-macOS%20|%20linux%20|%20windows-blue)
51
+ ![Latest Release](https://img.shields.io/github/v/release/SimVascular/svVascularize?label=latest)
52
+ [![codecov](https://codecov.io/github/SimVascular/svVascularize/graph/badge.svg)](https://codecov.io/github/SimVascular/svVascularize)
53
+ [![DOI](https://img.shields.io/badge/DOI-green)]()
54
+
55
+ <p align="left">
56
+ The svVascularize (svv) is an open-source API for automated vascular generation and multi-fidelity hemodynamic simulation
57
+ written in Python. Often small-caliber vessels are difficult or infeasible to obtain from experimental data sources
58
+ despite playing important roles in blood flow regulation and cell microenvironments. svVascularize aims to provide tissue
59
+ engineers and computational hemodynamic scientists with de novo vasculature that can easily be applied in
60
+ biomanufacturing applications or computational fluid dynamic (CFD) analysis.
61
+ </p>
62
+
63
+ * **Website:**
64
+ * **PyPi:**
65
+ * **Source code:**
svv-0.0.31/README.md ADDED
@@ -0,0 +1,20 @@
1
+ # svVascularize
2
+
3
+
4
+ ![Version](https://img.shields.io/badge/version-0.0.31-blue)
5
+ ![Platform](https://img.shields.io/badge/platform-macOS%20|%20linux%20|%20windows-blue)
6
+ ![Latest Release](https://img.shields.io/github/v/release/SimVascular/svVascularize?label=latest)
7
+ [![codecov](https://codecov.io/github/SimVascular/svVascularize/graph/badge.svg)](https://codecov.io/github/SimVascular/svVascularize)
8
+ [![DOI](https://img.shields.io/badge/DOI-green)]()
9
+
10
+ <p align="left">
11
+ The svVascularize (svv) is an open-source API for automated vascular generation and multi-fidelity hemodynamic simulation
12
+ written in Python. Often small-caliber vessels are difficult or infeasible to obtain from experimental data sources
13
+ despite playing important roles in blood flow regulation and cell microenvironments. svVascularize aims to provide tissue
14
+ engineers and computational hemodynamic scientists with de novo vasculature that can easily be applied in
15
+ biomanufacturing applications or computational fluid dynamic (CFD) analysis.
16
+ </p>
17
+
18
+ * **Website:**
19
+ * **PyPi:**
20
+ * **Source code:**
svv-0.0.31/pyproject.toml ADDED
@@ -0,0 +1,10 @@
1
+ [build-system]
2
+ requires = [
3
+ "setuptools>=45.0",
4
+ "wheel>=0.36; python_version < '3.12' ",
5
+ "cython>=3.0.7",
6
+ "numpy",
7
+ "cmake>=3.15"
8
+ ]
9
+
10
+ build-backend = "setuptools.build_meta"
svv-0.0.31/setup.cfg ADDED
@@ -0,0 +1,4 @@
1
+ [egg_info]
2
+ tag_build =
3
+ tag_date = 0
4
+