niftimesh 0.1.0__tar.gz

niftimesh-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Justin
+
+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.

niftimesh-0.1.0/MANIFEST.in

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+include LICENSE
+include README.md
+include pyproject.toml
+recursive-include examples *.py *.md
+include examples/data/lung_lobe_seg.nii.gz
+graft assets
+global-exclude __pycache__ *.py[cod]

niftimesh-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: niftimesh
+Version: 0.1.0
+Summary: Watertight, smooth STL reconstruction from NIfTI segmentations (boolean-CSG peel or independent organs).
+Author: Justin
+License: MIT
+Project-URL: Homepage, https://github.com/77even/NiftiMesh
+Project-URL: Repository, https://github.com/77even/NiftiMesh
+Project-URL: Issues, https://github.com/77even/NiftiMesh/issues
+Keywords: nifti,stl,segmentation,marching-cubes,mesh,medical-imaging,csg,vtk,meshlib,3d-reconstruction,surface
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Topic :: Multimedia :: Graphics :: 3D Modeling
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.21
+Requires-Dist: scipy>=1.7
+Requires-Dist: vtk>=9.1
+Requires-Dist: nibabel>=3.2
+Provides-Extra: csg
+Requires-Dist: meshlib>=3.0; extra == "csg"
+Provides-Extra: sitk
+Requires-Dist: SimpleITK>=2.0; extra == "sitk"
+Provides-Extra: all
+Requires-Dist: meshlib>=3.0; extra == "all"
+Requires-Dist: SimpleITK>=2.0; extra == "all"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: meshlib>=3.0; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Dynamic: license-file
+
+<div align="center">
+
+# NiftiMesh
+
+**Watertight, smooth STL reconstruction from NIfTI segmentations.**
+
+[![PyPI](https://img.shields.io/pypi/v/niftimesh.svg)](https://pypi.org/project/niftimesh/)
+[![Python](https://img.shields.io/pypi/pyversions/niftimesh.svg)](https://pypi.org/project/niftimesh/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+
+</div>
+
+Turn a multi-label `.nii.gz` segmentation into one clean, closed STL surface per
+label — **solid, watertight, manifold, self-intersection-free**. In `csg` mode,
+adjacent regions share their interface seam *bit-identically*, so the parts
+assemble seamlessly in 3D Slicer / Mimics.
+
+<img src="https://raw.githubusercontent.com/77even/NiftiMesh/main/assets/comparison.png" width="100%">
+<img src="https://raw.githubusercontent.com/77even/NiftiMesh/main/assets/closeup.png" width="100%">
+
+*Left → right: naive marching cubes (voxel staircase) · a typical 3D Slicer
+default export · NiftiMesh (smooth, watertight, seamless).*
+
+## What it's for
+
+A multi-label segmentation volume → per-label STL meshes. Two modes:
+
+- **`csg`** — for **one structure split by internal interfaces**: lung lobes /
+  segments, Couinaud liver segments. Neighbouring labels share their cut seam
+  exactly (no crack, no black line).
+- **`independent`** — for **disjoint organs** (liver + spleen + kidneys, vessels):
+  each label becomes its own closed, smoothed surface.
+
+You define the output names — nothing is hard-coded to any anatomy.
+
+## Install
+
+```bash
+pip install "niftimesh[csg]"   # csg mode (needs meshlib)
+pip install niftimesh          # independent + naive modes only
+```
+
+Python ≥ 3.9. NIfTI is read via `nibabel` (bundled) or `SimpleITK` if installed.
+
+## Usage
+
+```bash
+# names from a JSON file: {"1": "left_lower_lobe", "2": "left_upper_lobe", ...}
+niftimesh seg.nii.gz out/ --mode csg --label-names names.json --suffix _3d
+
+# omit --label-names to get label_1.stl, label_2.stl, ...
+niftimesh organs.nii.gz out/ --mode independent
+```
+
+```python
+from niftimesh import nifti_to_stl
+
+nifti_to_stl("seg.nii.gz", "out/", mode="csg",
+             label_names={1: "left_lower_lobe", 2: "left_upper_lobe"})
+
+# in-memory: numpy (z, y, x) label volume -> {label: vtkPolyData}
+from niftimesh import reconstruct
+meshes = reconstruct(seg, spacing=(0.84, 0.84, 1.0), mode="independent")
+```
+
+## License
+
+[MIT](LICENSE) © 2026 Justin

niftimesh-0.1.0/README.md

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+<div align="center">
+
+# NiftiMesh
+
+**Watertight, smooth STL reconstruction from NIfTI segmentations.**
+
+[![PyPI](https://img.shields.io/pypi/v/niftimesh.svg)](https://pypi.org/project/niftimesh/)
+[![Python](https://img.shields.io/pypi/pyversions/niftimesh.svg)](https://pypi.org/project/niftimesh/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+
+</div>
+
+Turn a multi-label `.nii.gz` segmentation into one clean, closed STL surface per
+label — **solid, watertight, manifold, self-intersection-free**. In `csg` mode,
+adjacent regions share their interface seam *bit-identically*, so the parts
+assemble seamlessly in 3D Slicer / Mimics.
+
+<img src="https://raw.githubusercontent.com/77even/NiftiMesh/main/assets/comparison.png" width="100%">
+<img src="https://raw.githubusercontent.com/77even/NiftiMesh/main/assets/closeup.png" width="100%">
+
+*Left → right: naive marching cubes (voxel staircase) · a typical 3D Slicer
+default export · NiftiMesh (smooth, watertight, seamless).*
+
+## What it's for
+
+A multi-label segmentation volume → per-label STL meshes. Two modes:
+
+- **`csg`** — for **one structure split by internal interfaces**: lung lobes /
+  segments, Couinaud liver segments. Neighbouring labels share their cut seam
+  exactly (no crack, no black line).
+- **`independent`** — for **disjoint organs** (liver + spleen + kidneys, vessels):
+  each label becomes its own closed, smoothed surface.
+
+You define the output names — nothing is hard-coded to any anatomy.
+
+## Install
+
+```bash
+pip install "niftimesh[csg]"   # csg mode (needs meshlib)
+pip install niftimesh          # independent + naive modes only
+```
+
+Python ≥ 3.9. NIfTI is read via `nibabel` (bundled) or `SimpleITK` if installed.
+
+## Usage
+
+```bash
+# names from a JSON file: {"1": "left_lower_lobe", "2": "left_upper_lobe", ...}
+niftimesh seg.nii.gz out/ --mode csg --label-names names.json --suffix _3d
+
+# omit --label-names to get label_1.stl, label_2.stl, ...
+niftimesh organs.nii.gz out/ --mode independent
+```
+
+```python
+from niftimesh import nifti_to_stl
+
+nifti_to_stl("seg.nii.gz", "out/", mode="csg",
+             label_names={1: "left_lower_lobe", 2: "left_upper_lobe"})
+
+# in-memory: numpy (z, y, x) label volume -> {label: vtkPolyData}
+from niftimesh import reconstruct
+meshes = reconstruct(seg, spacing=(0.84, 0.84, 1.0), mode="independent")
+```
+
+## License
+
+[MIT](LICENSE) © 2026 Justin

niftimesh-0.1.0/examples/README.md

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+# Examples
+
+`data/lung_lobe_seg.nii.gz` is a 5-label pulmonary-lobe segmentation
+(238×512×512, ~211 KB) used as a sample.
+
+```bash
+pip install "niftimesh[csg]"
+
+# Python: you define the label names (see convert.py)
+python examples/convert.py
+
+# CLI: names from a JSON file ({"1": "left_lower_lobe", ...}), or omit for label_<n>
+niftimesh data/lung_lobe_seg.nii.gz out/ --mode csg --label-names names.json --suffix _3d
+```

niftimesh-0.1.0/examples/convert.py

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+#!/usr/bin/env python3
+"""Minimal end-to-end example: a NIfTI segmentation -> per-label STL files.
+
+    python examples/convert.py            # uses the bundled lung-lobe sample
+    python examples/convert.py my_seg.nii.gz out_dir csg
+"""
+
+import sys
+from pathlib import Path
+
+from niftimesh import nifti_to_stl
+
+HERE = Path(__file__).resolve().parent
+
+# You define the names. Here: the bundled 5-label lung-lobe sample.
+LABEL_NAMES = {
+    1: "left_lower_lobe",
+    2: "left_upper_lobe",
+    3: "right_lower_lobe",
+    4: "right_middle_lobe",
+    5: "right_upper_lobe",
+}
+
+
+def main():
+    inp = sys.argv[1] if len(sys.argv) > 1 else str(HERE / "data" / "lung_lobe_seg.nii.gz")
+    out = sys.argv[2] if len(sys.argv) > 2 else "out"
+    mode = sys.argv[3] if len(sys.argv) > 3 else "csg"
+
+    written = nifti_to_stl(inp, out, mode=mode, label_names=LABEL_NAMES, suffix="_3d")
+    print(f"Wrote {len(written)} STL file(s) to {out}/:")
+    for p in written:
+        print("  ", Path(p).name)
+
+
+if __name__ == "__main__":
+    main()

niftimesh-0.1.0/niftimesh/__init__.py

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+"""NiftiMesh -- watertight, smooth STL reconstruction from NIfTI segmentations.
+
+Two reconstruction modes:
+
+* ``csg``         -- boolean-CSG peel. Splits ONE connected structure by its
+                     internal interfaces into per-label solids that share each
+                     fissure seam bit-identically (lung lobes / segments,
+                     Couinaud liver segments). No cracks, no black seam lines.
+* ``independent`` -- each label built as its own closed, smoothed, watertight
+                     surface (disjoint multi-organ scenes).
+
+Quick start::
+
+    from niftimesh import nifti_to_stl
+
+    # one structure split by internal interfaces (lobes, segments) -> csg
+    nifti_to_stl("lobe_seg.nii.gz", "out/", mode="csg",
+                 label_names={1: "left_lower", 2: "left_upper"})
+
+    # disjoint organs -> independent
+    nifti_to_stl("organs.nii.gz", "out/", mode="independent")
+"""
+
+from ._version import __version__
+from .builder import CSGMeshBuilder
+from .convert import nifti_to_stl, reconstruct, save_meshes
+from .naive import build_naive
+
+__all__ = [
+    "__version__",
+    "CSGMeshBuilder",
+    "nifti_to_stl",
+    "reconstruct",
+    "save_meshes",
+    "build_naive",
+]

niftimesh-0.1.0/niftimesh/__main__.py

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+import sys
+
+from .cli import main
+
+if __name__ == "__main__":
+    sys.exit(main())

niftimesh-0.1.0/niftimesh/_version.py

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+__version__ = "0.1.0"