ct-segmentation-toolkit 0.2.0__tar.gz

ct_segmentation_toolkit-0.2.0/LICENSE

@@ -0,0 +1,201 @@
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ct_segmentation_toolkit-0.2.0/NOTICE

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+ct-segmentation-toolkit
+Copyright 2026 Cameron B. Renteria
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this software except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+This product includes `ct_seg.denoise`, an implementation of the Noise2Inverse framework
+(Hendriksen, Pelt & Batenburg, IEEE Transactions on Computational Imaging, 2020;
+https://github.com/ahendriksen/noise2inverse). See ct_seg/denoise/ACKNOWLEDGMENTS.md.

ct_segmentation_toolkit-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ct-segmentation-toolkit
+Version: 0.2.0
+Summary: Supervised (U-Net), unsupervised (Otsu/k-means/GMM), and label-free spectral-spatial (SOM) segmentation of scientific image stacks.
+Author-email: "Cameron B. Renteria" <crentb@uw.edu>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/crentb/ct-segmentation-toolkit
+Project-URL: Issues, https://github.com/crentb/ct-segmentation-toolkit/issues
+Keywords: image segmentation,computed tomography,U-Net,self-organizing map,unsupervised,feature extraction,hyperspectral,scientific imaging
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.10
+Requires-Dist: scikit-learn>=1.3
+Requires-Dist: scikit-image>=0.21
+Requires-Dist: tifffile>=2023.1
+Requires-Dist: minisom>=2.3
+Requires-Dist: tqdm>=4.65
+Requires-Dist: Pillow>=9.0
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: torch>=2.0
+Provides-Extra: viz
+Requires-Dist: napari[all]>=0.4; extra == "viz"
+Requires-Dist: pyvista>=0.43; extra == "viz"
+Provides-Extra: mlops
+Requires-Dist: mlflow>=2.0; extra == "mlops"
+Provides-Extra: denoise
+Requires-Dist: albumentations>=1.3; extra == "denoise"
+Requires-Dist: PyYAML>=6.0; extra == "denoise"
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.1; extra == "dev"
+Requires-Dist: ruff==0.14.10; extra == "dev"
+Requires-Dist: black==26.3.1; extra == "dev"
+Requires-Dist: mypy==1.17.1; extra == "dev"
+Requires-Dist: pre-commit>=3.7; extra == "dev"
+Dynamic: license-file
+
+# ct-segmentation-toolkit
+
+[![CI](https://github.com/crentb/ct-segmentation-toolkit/actions/workflows/ci.yml/badge.svg)](https://github.com/crentb/ct-segmentation-toolkit/actions/workflows/ci.yml)
+[![License: Apache 2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+[![Python](https://img.shields.io/badge/python-3.10%E2%80%933.12-blue.svg)](pyproject.toml)
+
+Segmentation of scientific image stacks (e.g., synchrotron CT) across the full
+supervision spectrum, in one installable, tested package:
+
+- **Supervised** — a U-Net (`ct_seg.model.UNetSegmentation`) with training + inference.
+- **Unsupervised** — multi-Otsu, k-means, and GMM segmentation by intensity, with no
+  training data needed.
+- **Label-free spectral-spatial** — a Self-Organizing-Map segmenter that describes each
+  pixel by multi-scale density, structure-tensor orientation/coherence, a Gabor filter
+  bank, and local variance, then clusters the SOM nodes. The same spectral-spatial
+  feature engineering transfers directly to **hyperspectral** cubes.
+- **Self-supervised denoising** — a 2.5D **Noise2Inverse** denoiser (`ct_seg.denoise`): a
+  no-skip U-Net trained from one noisy reconstruction (no clean reference), with a Laplacian
+  Contrast Loss and edge-aware model selection. The author's own implementation of the N2I
+  framework (upstream credit in [ct_seg/denoise/ACKNOWLEDGMENTS.md](ct_seg/denoise/ACKNOWLEDGMENTS.md)).
+
+## Install
+
+```bash
+git clone https://github.com/crentb/ct-segmentation-toolkit.git
+cd ct-segmentation-toolkit
+python -m pip install -e ".[dev]"          # core + dev tools (pytest, ruff, black, mypy)
+python -m pip install -e ".[viz]"          # optional: napari labeling + pyvista viewer
+python -m pip install -e ".[mlops]"        # optional: MLflow experiment tracking
+python -m pip install -e ".[denoise]"      # optional: N2I training (albumentations, PyYAML)
+```
+
+## Python API
+
+```python
+import numpy as np
+from ct_seg import segment_kmeans, som_segment, UNetSegmentation
+
+volume = np.random.rand(16, 256, 256).astype("float32")   # (slices, H, W) in [0, 1]
+
+# Unsupervised intensity segmentation (no labels)
+labels, info = segment_kmeans(volume, num_classes=4)
+
+# Label-free spectral-spatial segmentation of a single slice
+band_map = som_segment(volume[0], n_clusters=4)
+
+# Supervised U-Net
+model = UNetSegmentation(in_channels=1, num_classes=4)
+```
+
+## Command line
+
+```bash
+# Unsupervised (otsu | kmeans | gmm)
+python -m ct_seg.segment --input /path/to/tiffs --method kmeans --num_classes 4 --save_overlay
+
+# Train a U-Net, then segment with it
+python -m ct_seg.train   --images /path/to/tiffs --masks /path/to/masks --num_classes 4
+python -m ct_seg.segment --input /path/to/tiffs --method unet --model SegOutput/best_model.pth --num_classes 4
+```
+
+(Interactive `ct_seg.labeling` (napari) and `ct_seg.viewer` (napari/pyvista) require the
+`[viz]` extra.)
+
+## Experiment tracking & profiling
+
+Training integrates optional **MLflow** logging (run parameters, per-epoch loss/mIoU,
+and the best checkpoint). Install the extra and it logs automatically; without MLflow,
+tracking is a harmless no-op and training is unaffected:
+
+```bash
+pip install -e ".[mlops]"
+python -m ct_seg.train --images ... --masks ... --num_classes 4   # logs to ./mlruns
+mlflow ui                                                          # browse runs
+```
+
+A reproducible **performance profile** (forward / train-step latency, throughput, and
+peak GPU memory) is in [docs/PERF.md](docs/PERF.md):
+
+```bash
+python scripts/profile_unet.py --device cuda --sizes 256 512
+```
+
+## Testing
+
+```bash
+pytest -m "not slow"      # fast suite (what CI runs)
+pytest                    # everything
+```
+
+## Status
+
+The supervised, unsupervised, SOM, and **Noise2Inverse denoising** paths are functional and
+tested. The denoiser (`ct_seg.denoise`) is the author's own implementation of the N2I
+framework (upstream credit in `ct_seg/denoise/ACKNOWLEDGMENTS.md`). Related published work on deep-learning
+segmentation and self-supervised denoising of synchrotron CT is available as a preprint:
+https://ssrn.com/abstract=6805001
+
+## Acknowledgments
+
+`ct_seg.denoise` implements the Noise2Inverse framework (Hendriksen, Pelt & Batenburg,
+*IEEE Transactions on Computational Imaging*, 2020; https://github.com/ahendriksen/noise2inverse).
+See [ct_seg/denoise/ACKNOWLEDGMENTS.md](ct_seg/denoise/ACKNOWLEDGMENTS.md).
+
+## License
+
+Apache-2.0 — see [LICENSE](LICENSE) and [NOTICE](NOTICE).

ct_segmentation_toolkit-0.2.0/README.md

@@ -0,0 +1,107 @@
+# ct-segmentation-toolkit
+
+[![CI](https://github.com/crentb/ct-segmentation-toolkit/actions/workflows/ci.yml/badge.svg)](https://github.com/crentb/ct-segmentation-toolkit/actions/workflows/ci.yml)
+[![License: Apache 2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+[![Python](https://img.shields.io/badge/python-3.10%E2%80%933.12-blue.svg)](pyproject.toml)
+
+Segmentation of scientific image stacks (e.g., synchrotron CT) across the full
+supervision spectrum, in one installable, tested package:
+
+- **Supervised** — a U-Net (`ct_seg.model.UNetSegmentation`) with training + inference.
+- **Unsupervised** — multi-Otsu, k-means, and GMM segmentation by intensity, with no
+  training data needed.
+- **Label-free spectral-spatial** — a Self-Organizing-Map segmenter that describes each
+  pixel by multi-scale density, structure-tensor orientation/coherence, a Gabor filter
+  bank, and local variance, then clusters the SOM nodes. The same spectral-spatial
+  feature engineering transfers directly to **hyperspectral** cubes.
+- **Self-supervised denoising** — a 2.5D **Noise2Inverse** denoiser (`ct_seg.denoise`): a
+  no-skip U-Net trained from one noisy reconstruction (no clean reference), with a Laplacian
+  Contrast Loss and edge-aware model selection. The author's own implementation of the N2I
+  framework (upstream credit in [ct_seg/denoise/ACKNOWLEDGMENTS.md](ct_seg/denoise/ACKNOWLEDGMENTS.md)).
+
+## Install
+
+```bash
+git clone https://github.com/crentb/ct-segmentation-toolkit.git
+cd ct-segmentation-toolkit
+python -m pip install -e ".[dev]"          # core + dev tools (pytest, ruff, black, mypy)
+python -m pip install -e ".[viz]"          # optional: napari labeling + pyvista viewer
+python -m pip install -e ".[mlops]"        # optional: MLflow experiment tracking
+python -m pip install -e ".[denoise]"      # optional: N2I training (albumentations, PyYAML)
+```
+
+## Python API
+
+```python
+import numpy as np
+from ct_seg import segment_kmeans, som_segment, UNetSegmentation
+
+volume = np.random.rand(16, 256, 256).astype("float32")   # (slices, H, W) in [0, 1]
+
+# Unsupervised intensity segmentation (no labels)
+labels, info = segment_kmeans(volume, num_classes=4)
+
+# Label-free spectral-spatial segmentation of a single slice
+band_map = som_segment(volume[0], n_clusters=4)
+
+# Supervised U-Net
+model = UNetSegmentation(in_channels=1, num_classes=4)
+```
+
+## Command line
+
+```bash
+# Unsupervised (otsu | kmeans | gmm)
+python -m ct_seg.segment --input /path/to/tiffs --method kmeans --num_classes 4 --save_overlay
+
+# Train a U-Net, then segment with it
+python -m ct_seg.train   --images /path/to/tiffs --masks /path/to/masks --num_classes 4
+python -m ct_seg.segment --input /path/to/tiffs --method unet --model SegOutput/best_model.pth --num_classes 4
+```
+
+(Interactive `ct_seg.labeling` (napari) and `ct_seg.viewer` (napari/pyvista) require the
+`[viz]` extra.)
+
+## Experiment tracking & profiling
+
+Training integrates optional **MLflow** logging (run parameters, per-epoch loss/mIoU,
+and the best checkpoint). Install the extra and it logs automatically; without MLflow,
+tracking is a harmless no-op and training is unaffected:
+
+```bash
+pip install -e ".[mlops]"
+python -m ct_seg.train --images ... --masks ... --num_classes 4   # logs to ./mlruns
+mlflow ui                                                          # browse runs
+```
+
+A reproducible **performance profile** (forward / train-step latency, throughput, and
+peak GPU memory) is in [docs/PERF.md](docs/PERF.md):
+
+```bash
+python scripts/profile_unet.py --device cuda --sizes 256 512
+```
+
+## Testing
+
+```bash
+pytest -m "not slow"      # fast suite (what CI runs)
+pytest                    # everything
+```
+
+## Status
+
+The supervised, unsupervised, SOM, and **Noise2Inverse denoising** paths are functional and
+tested. The denoiser (`ct_seg.denoise`) is the author's own implementation of the N2I
+framework (upstream credit in `ct_seg/denoise/ACKNOWLEDGMENTS.md`). Related published work on deep-learning
+segmentation and self-supervised denoising of synchrotron CT is available as a preprint:
+https://ssrn.com/abstract=6805001
+
+## Acknowledgments
+
+`ct_seg.denoise` implements the Noise2Inverse framework (Hendriksen, Pelt & Batenburg,
+*IEEE Transactions on Computational Imaging*, 2020; https://github.com/ahendriksen/noise2inverse).
+See [ct_seg/denoise/ACKNOWLEDGMENTS.md](ct_seg/denoise/ACKNOWLEDGMENTS.md).
+
+## License
+
+Apache-2.0 — see [LICENSE](LICENSE) and [NOTICE](NOTICE).

ct_segmentation_toolkit-0.2.0/ct_seg/__init__.py

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+"""
+ct_seg — a CT image segmentation toolkit.
+
+Supervised (U-Net), unsupervised (multi-Otsu / k-means / GMM), and label-free
+spectral-spatial (Self-Organizing Map) segmentation of scientific image stacks,
+plus self-supervised denoising (2.5D Noise2Inverse).
+
+Only the lightweight, importable APIs are exported here. The interactive tools
+(`labeling`, napari; `viewer`, pyvista) require the optional ``[viz]`` extra and
+are imported directly from their modules when needed.
+
+Import policy — torch is loaded LAZILY (PEP 562):
+    The torch-backed symbols (``UNetSegmentation``, ``count_parameters``,
+    ``unet_ns_gn``, ``LCL``) are resolved on first attribute access instead of
+    at package import. Two reasons:
+    1. Classical users (k-means / GMM / Otsu / SOM) should not pay torch's
+       import cost — or even need torch installed — to segment an image.
+    2. Robustness: on some environments (observed on anaconda + macOS ARM,
+       2026-07-15) eagerly importing torch alongside scikit-learn is FATAL —
+       torch's bundled libomp and MKL's libiomp5 both initialize OpenMP and
+       the process aborts with ``OMP: Error #179`` the moment a scikit-learn
+       thread pool spins up (e.g., KMeans inside ``som_segment``). Keeping
+       torch out of the import path unless a torch API is actually requested
+       means the classical paths can never trigger that clash.
+"""
+
+from ct_seg.segment import (
+    enhance_contrast,
+    normalize_stack,
+    segment_gmm,
+    segment_kmeans,
+    segment_otsu,
+    segment_unet,
+)
+from ct_seg.som_bands import extract_features, som_segment
+
+__version__ = "0.1.0"
+
+# torch-backed exports, resolved lazily on first access (PEP 562).
+_LAZY_TORCH_EXPORTS = {
+    "UNetSegmentation": ("ct_seg.model", "UNetSegmentation"),
+    "count_parameters": ("ct_seg.model", "count_parameters"),
+    "unet_ns_gn": ("ct_seg.denoise", "unet_ns_gn"),
+    "LCL": ("ct_seg.denoise", "LCL"),
+}
+
+__all__ = [
+    "UNetSegmentation",
+    "count_parameters",
+    "normalize_stack",
+    "enhance_contrast",
+    "segment_otsu",
+    "segment_kmeans",
+    "segment_gmm",
+    "segment_unet",
+    "extract_features",
+    "som_segment",
+    "unet_ns_gn",
+    "LCL",
+    "__version__",
+]
+
+
+def __getattr__(name):
+    """Resolve torch-backed exports on first use (see module docstring)."""
+    if name in _LAZY_TORCH_EXPORTS:
+        import importlib
+
+        module_name, attr = _LAZY_TORCH_EXPORTS[name]
+        value = getattr(importlib.import_module(module_name), attr)
+        globals()[name] = value  # cache so the import cost is paid once
+        return value
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+def __dir__():
+    """Keep tab-completion/introspection honest about the lazy exports."""
+    return sorted(list(globals().keys()) + list(_LAZY_TORCH_EXPORTS.keys()))

ct_segmentation_toolkit-0.2.0/ct_seg/denoise/__init__.py

@@ -0,0 +1,24 @@
+"""
+ct_seg.denoise — self-supervised CT denoising (2.5D Noise2Inverse).
+
+Cameron Renteria's own implementation of the Noise2Inverse (N2I) self-supervised
+tomography-denoising framework: a no-skip U-Net (Group Normalization, LeakyReLU) trained
+to map one sub-reconstruction (e.g. even-angle) to another (odd-angle), so it needs no
+clean reference image. His additions over the base method include a 2.5D adjacent-slice
+input, a Laplacian Contrast Loss (LCL) for edge preservation, edge-aware model selection,
+and automatic GPU batch-size optimization.
+
+Upstream method (credited): Noise2Inverse - Hendriksen, Pelt & Batenburg, IEEE Transactions
+on Computational Imaging 6 (2020); original code https://github.com/ahendriksen/noise2inverse
+(see ACKNOWLEDGMENTS.md). This subpackage is Copyright 2026 Cameron Renteria, Apache-2.0.
+
+Only the lightweight building blocks (model, loss, edge score) are exported here. The
+training/inference CLIs and dataset (`ct_seg.denoise.train`, `denoise_volume`,
+`denoise_slice`, `data`) require the optional ``[denoise]`` extra (albumentations, PyYAML).
+"""
+
+from ct_seg.denoise.eval import laplacian_score_batch
+from ct_seg.denoise.loss import LCL
+from ct_seg.denoise.model import unet_ns_gn
+
+__all__ = ["unet_ns_gn", "LCL", "laplacian_score_batch"]