stentfit 0.1.0__tar.gz

stentfit-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Vural Aktas
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

stentfit-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: stentfit
+Version: 0.1.0
+Summary: Semi-automated virtual stent implantation via contact simulation
+License: MIT
+License-File: LICENSE
+Author: Vural Aktas
+Author-email: vuralaktas6741@gmail.com
+Requires-Python: >=3.13,<3.14
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: beamme (>=0.2.0,<0.3.0)
+Requires-Dist: fourcipp (>=1.132.0)
+Requires-Dist: gmsh (>=4.15.0)
+Requires-Dist: matplotlib (>=3.11.0)
+Requires-Dist: numpy (>=2.5.1)
+Requires-Dist: pandas (>=3.0.3)
+Requires-Dist: plotly (>=6.8.0)
+Requires-Dist: scikit-image (>=0.26.0)
+Requires-Dist: scikit-learn (>=1.9.0)
+Requires-Dist: scipy (>=1.18.0)
+Requires-Dist: trimesh (>=4.12.2)
+Description-Content-Type: text/markdown
+
+# stentFIT
+
+[![Documentation Status](https://readthedocs.org/projects/stentfit/badge/?version=latest)](https://stentfit.readthedocs.io/en/latest/?badge=latest)
+
+Semi-automated virtual stent implantation with mixed-dimensional modelling
+
+Full documentation, including the API reference and workflow diagrams, is hosted at [stentfit.readthedocs.io](https://stentfit.readthedocs.io/en/latest/).
+
+`stentFIT` turns a stent surface mesh (`.stl`) into a 1D beam-element model ready for beam-to-solid contact simulation. It samples the stent surface, detects its rings, extracts a 2D skeleton per ring, wraps that skeleton back onto the 3D mid-surface, fits a B-spline to each strut curve, and meshes the result into Simo–Reissner beams with [BeamMe](https://beamme-py.github.io/beamme/). Extracting the stent's 1D wireframe is a semi-automated process: it allows manual edits of intermediate steps such as ring detection and 2D skeletonisation. It also provides a smoke test that verifies the quality of the 1D stent model inside a generated pipe-like 3D vessel.
+
+## Installation
+
+```bash
+pip install stentfit
+```
+
+Requires **Python 3.13** (pinned to match [BeamMe](https://beamme-py.github.io/beamme/)'s supported range). Core dependencies such as `beamme` (stent beam meshing and artery solid meshing), `gmsh` (artery solid meshing), and `fourcipp` are installed automatically. Running the generated simulation input files additionally requires a compiled **4C** executable, which is not included in this package. 
+
+## What it does & How to use it
+
+**1. Stent skeletonisation** ([`examples/stent_skeleton.ipynb`](examples/stent_skeleton.ipynb))
+
+- Sample a point cloud from the stent STL and align it to its centreline axis.
+- Detect rings and skeletonise each ring in 2D (optional auto-tuning + manual edits).
+- Wrap the 2D skeleton onto the local mid-surface, clean up the graph, and fit a B-spline per strut.
+- Mesh the fitted splines into a 1D Simo–Reissner beam mesh with BeamMe.
+
+Each stage writes `skeleton_points.csv`, `skeleton_splines.json`, `stent_features.json`, and interactive HTML views into the output directory.
+
+![Unrolled 2D skeleton with per-ring tuning diagnostics](docs/images/skeleton_splines_2d.png)
+
+**2. Test artery generation & simulation setup** ([`examples/test_sim_generation.ipynb`](examples/test_sim_generation.ipynb))
+
+A synthetic/parametric smoke test exercises the full mixed-dimensional chain end-to-end:
+
+- Generate a parametric test artery (straight / curved / S-bend) sized to the stent, and mesh its wall as a 3D solid with GMSH.
+- Warp the stent beam mesh onto the artery centreline.
+- Check beam-to-solid coupling compatibility (stiffness ratio, element-size ratios) and visualize the stent inside the artery via Paraview.
+- Tie the beam mesh to the artery lumen and write a schema-validated 4C simulation input file with a quasi-static radial expansion load.
+
+This confirms the stent-to-artery mapping and 4C input generation work end-to-end, using placeholder materials and tied meshtying rather than real contact such as full deployment physics (contact, HGO-C artery material, elasto-plastic beam bending) is planned but not yet implemented.
+
+![Stent beam mesh warped into a curved artery, viewed in ParaView](docs/images/paraview_stent_artery.png)
+
+## License
+
+`stentfit` was created by Vural Aktas. It is licensed under the terms of the MIT license.
+
+## Contributing
+
+Interested in contributing? Reach out at [vural.aktas@rwth-aachen.de](mailto:vural.aktas@rwth-aachen.de).
+
+## Credits
+
+`stentfit` was created with [`cookiecutter`](https://cookiecutter.readthedocs.io/en/latest/)
+and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter).
+

stentfit-0.1.0/README.md

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+# stentFIT
+
+[![Documentation Status](https://readthedocs.org/projects/stentfit/badge/?version=latest)](https://stentfit.readthedocs.io/en/latest/?badge=latest)
+
+Semi-automated virtual stent implantation with mixed-dimensional modelling
+
+Full documentation, including the API reference and workflow diagrams, is hosted at [stentfit.readthedocs.io](https://stentfit.readthedocs.io/en/latest/).
+
+`stentFIT` turns a stent surface mesh (`.stl`) into a 1D beam-element model ready for beam-to-solid contact simulation. It samples the stent surface, detects its rings, extracts a 2D skeleton per ring, wraps that skeleton back onto the 3D mid-surface, fits a B-spline to each strut curve, and meshes the result into Simo–Reissner beams with [BeamMe](https://beamme-py.github.io/beamme/). Extracting the stent's 1D wireframe is a semi-automated process: it allows manual edits of intermediate steps such as ring detection and 2D skeletonisation. It also provides a smoke test that verifies the quality of the 1D stent model inside a generated pipe-like 3D vessel.
+
+## Installation
+
+```bash
+pip install stentfit
+```
+
+Requires **Python 3.13** (pinned to match [BeamMe](https://beamme-py.github.io/beamme/)'s supported range). Core dependencies such as `beamme` (stent beam meshing and artery solid meshing), `gmsh` (artery solid meshing), and `fourcipp` are installed automatically. Running the generated simulation input files additionally requires a compiled **4C** executable, which is not included in this package. 
+
+## What it does & How to use it
+
+**1. Stent skeletonisation** ([`examples/stent_skeleton.ipynb`](examples/stent_skeleton.ipynb))
+
+- Sample a point cloud from the stent STL and align it to its centreline axis.
+- Detect rings and skeletonise each ring in 2D (optional auto-tuning + manual edits).
+- Wrap the 2D skeleton onto the local mid-surface, clean up the graph, and fit a B-spline per strut.
+- Mesh the fitted splines into a 1D Simo–Reissner beam mesh with BeamMe.
+
+Each stage writes `skeleton_points.csv`, `skeleton_splines.json`, `stent_features.json`, and interactive HTML views into the output directory.
+
+![Unrolled 2D skeleton with per-ring tuning diagnostics](docs/images/skeleton_splines_2d.png)
+
+**2. Test artery generation & simulation setup** ([`examples/test_sim_generation.ipynb`](examples/test_sim_generation.ipynb))
+
+A synthetic/parametric smoke test exercises the full mixed-dimensional chain end-to-end:
+
+- Generate a parametric test artery (straight / curved / S-bend) sized to the stent, and mesh its wall as a 3D solid with GMSH.
+- Warp the stent beam mesh onto the artery centreline.
+- Check beam-to-solid coupling compatibility (stiffness ratio, element-size ratios) and visualize the stent inside the artery via Paraview.
+- Tie the beam mesh to the artery lumen and write a schema-validated 4C simulation input file with a quasi-static radial expansion load.
+
+This confirms the stent-to-artery mapping and 4C input generation work end-to-end, using placeholder materials and tied meshtying rather than real contact such as full deployment physics (contact, HGO-C artery material, elasto-plastic beam bending) is planned but not yet implemented.
+
+![Stent beam mesh warped into a curved artery, viewed in ParaView](docs/images/paraview_stent_artery.png)
+
+## License
+
+`stentfit` was created by Vural Aktas. It is licensed under the terms of the MIT license.
+
+## Contributing
+
+Interested in contributing? Reach out at [vural.aktas@rwth-aachen.de](mailto:vural.aktas@rwth-aachen.de).
+
+## Credits
+
+`stentfit` was created with [`cookiecutter`](https://cookiecutter.readthedocs.io/en/latest/)
+and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter).

stentfit-0.1.0/pyproject.toml

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+[build-system]
+requires = ["poetry-core>=2.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "stentfit"
+version = "0.1.0"
+description = "Semi-automated virtual stent implantation via contact simulation"
+authors = ["Vural Aktas <vuralaktas6741@gmail.com>"]
+license = "MIT"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.13,<3.14" # capped to match BeamMe's supported Python range
+numpy = ">=2.5.1"
+scipy = ">=1.18.0"
+pandas = ">=3.0.3"
+matplotlib = ">=3.11.0"
+plotly = ">=6.8.0"
+trimesh = ">=4.12.2"
+scikit-image = ">=0.26.0"
+scikit-learn = ">=1.9.0"
+beamme = ">=0.2.0,<0.3.0" # 0.3.0 renamed/changed Mesh.write_vtk -> write_vtu (single-file, no beam/solid split); pin until ported
+gmsh = ">=4.15.0"    # artery solid meshing (Mac-native; replaced Cubit/CubitPy)
+# fourcipp parses & writes 4C input files (needed to import the GMSH solid mesh
+# and dump the assembled .4C.yaml). Imported unconditionally by stent_splines.py
+# (via beamme.four_c), so it must be a core dependency, not an optional group
+# (Poetry's [dependency-groups] aren't installed by plain `pip install`).
+fourcipp = ">=1.132.0"
+
+
+[dependency-groups]
+dev = [
+    "ipykernel (>=7.3.0,<8.0.0)",
+    "ipython (>=9.15.0,<10.0.0)",
+    "jupyter (>=1.1.1,<2.0.0)"
+]
+docs = [
+    "myst-nb (>=1.4.0,<2.0.0)",
+    "sphinx-autoapi (>=3.8.0,<4.0.0)",
+    "sphinx-rtd-theme (>=3.1.0,<4.0.0)",
+    "sphinxcontrib-mermaid (>=2.1.0,<3.0.0)"
+]

stentfit-0.1.0/src/stentfit/__init__.py

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+
+from importlib.metadata import version
+
+from .stent_sampling import sample_stent_points
+from .stent_rings import detect_rings
+from .stent_skeleton_2d import (skeletonize_rings_2d,
+                                save_ring_2d_checkpoint,
+                                load_ring_2d_checkpoint,
+                                edit_rings_2d_interactive,
+                                assemble_2d_skeleton)
+from .stent_skeleton_3d import (wrap_skeleton_to_3d,
+                                save_stent_features_and_views)
+from .stent_splines import (fit_skeleton_splines,
+                            mesh_skeleton_beams)
+from .stent_plotting import (plot_skeleton_splines_2d,
+                             plot_skeleton_splines_trimesh)
+from .stent_pipeline import (stent_pipeline,
+                             run_skeletonization_2d,
+                             resume_and_edit_rings,
+                             finalize_skeleton)
+
+from .artery_mesh import (mesh_artery_gmsh,
+                          import_artery_solid,
+                          assemble_beam_solid)
+from .artery_generate import generate_artery_for_stent
+from .sim_setup import (stent_feature_extraction,
+                        stent_meshing_alignment,
+                        create_assembly_mesh,
+                        paraview_mesh_files,
+                        check_coupling_assumptions,
+                        build_smoketest_input,
+                        build_smoketest_pipeline)
+
+
+
+__version__ = version("stentfit")
+
+__all__ = [
+    "sample_stent_points",
+    "detect_rings",
+    "skeletonize_rings_2d",
+    "save_ring_2d_checkpoint",
+    "load_ring_2d_checkpoint",
+    "edit_rings_2d_interactive",
+    "assemble_2d_skeleton",
+    "wrap_skeleton_to_3d",
+    "save_stent_features_and_views",
+    "fit_skeleton_splines",
+    "mesh_skeleton_beams",
+    "plot_skeleton_splines_2d",
+    "plot_skeleton_splines_trimesh",
+    "stent_pipeline",
+    "run_skeletonization_2d",
+    "resume_and_edit_rings",
+    "finalize_skeleton",
+    "mesh_artery_gmsh",
+    "import_artery_solid",
+    "assemble_beam_solid",
+    "generate_artery_for_stent",
+    "stent_feature_extraction",
+    "stent_meshing_alignment",
+    "create_assembly_mesh",
+    "paraview_mesh_files",
+    "check_coupling_assumptions",
+    "build_smoketest_input",
+    "build_smoketest_pipeline",
+]