sprout-seg 1.1.0__tar.gz

sprout_seg-1.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Yichen He
+
+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.

sprout_seg-1.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: sprout-seg
+Version: 1.1.0
+Summary: SPROUT: semi-automated parcellation of 2D and 3D greyscale images into parts, by thresholds, erosion and growing
+Author: Yichen He
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/EchanHe/SPROUT
+Project-URL: Documentation, https://github.com/EchanHe/SPROUT#readme
+Project-URL: Issues, https://github.com/EchanHe/SPROUT/issues
+Project-URL: Changelog, https://github.com/EchanHe/SPROUT/blob/main/CHANGELOG.md
+Keywords: segmentation,image analysis,micro-CT,CT,MRI,3D,multi-class,seeds,region growing
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26
+Requires-Dist: scipy>=1.15
+Requires-Dist: scikit-image>=0.22
+Requires-Dist: pandas>=2.2
+Requires-Dist: tifffile>=2024.2.12
+Requires-Dist: imagecodecs>=2025.3.30
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: psutil>=5.9
+Requires-Dist: pillow>=10
+Provides-Extra: mesh
+Requires-Dist: trimesh>=4.3; extra == "mesh"
+Requires-Dist: matplotlib>=3.8; extra == "mesh"
+Provides-Extra: ai
+Requires-Dist: nninteractive>=1.1.3; extra == "ai"
+Requires-Dist: scikit-learn; extra == "ai"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+# sprout-seg
+
+The core and command line of [SPROUT](https://github.com/EchanHe/SPROUT): multi-part segmentation of 2D and 3D greyscale images (e.g. CT, MRI) without training data. For the napari plugin, see [napari-sprout](https://pypi.org/project/napari-sprout/).
+
+- **Seeds**: thresholds and erosion split an image into parts; adaptive and sweep modes combine several settings.
+- **Grow**: seeds grow back to the full shape of each part.
+- **Prompts**: seeds as prompts for nnInteractive or SAM.
+- **Batch**: many images from one CSV. Runs on CPU.
+
+## Install
+
+```bash
+pip install sprout-seg               # command line only (e.g. on a cluster)
+pip install "napari-sprout[all]"     # with the napari plugin, napari and Qt
+```
+
+Extras: `sprout-seg[ai]` (nnInteractive; with an NVIDIA GPU, install PyTorch for your CUDA version first), `sprout-seg[mesh]` (meshes).
+
+## Use
+
+Every step is a YAML config ([templates](https://github.com/EchanHe/SPROUT/tree/main/template)):
+
+```bash
+sprout --seeds --config make_seeds.yaml
+sprout --sweep_adaptive --config sweep_adaptive_seed.yaml
+sprout --adaptive_seed --config make_adaptive_seed.yaml
+sprout --grow --config make_grow.yaml
+sprout --seeds --batch --config batch_seeds.yaml
+sprout --help
+```
+
+Docs, demo data and videos: [github.com/EchanHe/SPROUT](https://github.com/EchanHe/SPROUT).
+
+## Cite
+
+Y. He, M. Camaiti, L.E. Roberts, J.M. Mulqueeney, E. Ioannou, M. Didziokas, A. Goswami. *SPROUT: A User-friendly, Scalable Toolkit for Multi-class Segmentation of Volumetric Images.* [bioRxiv 2024](https://www.biorxiv.org/content/10.1101/2024.11.22.624847v2.abstract).
+
+MIT License.

sprout_seg-1.1.0/docs/pypi_sprout_seg.md

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+# sprout-seg
+
+The core and command line of [SPROUT](https://github.com/EchanHe/SPROUT): multi-part segmentation of 2D and 3D greyscale images (e.g. CT, MRI) without training data. For the napari plugin, see [napari-sprout](https://pypi.org/project/napari-sprout/).
+
+- **Seeds**: thresholds and erosion split an image into parts; adaptive and sweep modes combine several settings.
+- **Grow**: seeds grow back to the full shape of each part.
+- **Prompts**: seeds as prompts for nnInteractive or SAM.
+- **Batch**: many images from one CSV. Runs on CPU.
+
+## Install
+
+```bash
+pip install sprout-seg               # command line only (e.g. on a cluster)
+pip install "napari-sprout[all]"     # with the napari plugin, napari and Qt
+```
+
+Extras: `sprout-seg[ai]` (nnInteractive; with an NVIDIA GPU, install PyTorch for your CUDA version first), `sprout-seg[mesh]` (meshes).
+
+## Use
+
+Every step is a YAML config ([templates](https://github.com/EchanHe/SPROUT/tree/main/template)):
+
+```bash
+sprout --seeds --config make_seeds.yaml
+sprout --sweep_adaptive --config sweep_adaptive_seed.yaml
+sprout --adaptive_seed --config make_adaptive_seed.yaml
+sprout --grow --config make_grow.yaml
+sprout --seeds --batch --config batch_seeds.yaml
+sprout --help
+```
+
+Docs, demo data and videos: [github.com/EchanHe/SPROUT](https://github.com/EchanHe/SPROUT).
+
+## Cite
+
+Y. He, M. Camaiti, L.E. Roberts, J.M. Mulqueeney, E. Ioannou, M. Didziokas, A. Goswami. *SPROUT: A User-friendly, Scalable Toolkit for Multi-class Segmentation of Volumetric Images.* [bioRxiv 2024](https://www.biorxiv.org/content/10.1101/2024.11.22.624847v2.abstract).
+
+MIT License.

sprout_seg-1.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sprout-seg"
+dynamic = ["version"]
+description = "SPROUT: semi-automated parcellation of 2D and 3D greyscale images into parts, by thresholds, erosion and growing"
+readme = { file = "docs/pypi_sprout_seg.md", content-type = "text/markdown" }   # the PyPI page (README.MD has relative links)
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [{ name = "Yichen He" }]
+keywords = ["segmentation", "image analysis", "micro-CT", "CT", "MRI", "3D", "multi-class", "seeds", "region growing"]
+requires-python = ">=3.10"
+# Lower bounds are the versions the CI tests (requirements-ci.txt); the "latest" CI job tests the newest.
+dependencies = [
+    "numpy>=1.26",
+    "scipy>=1.15",
+    "scikit-image>=0.22",
+    "pandas>=2.2",
+    "tifffile>=2024.2.12",
+    "imagecodecs>=2025.3.30",
+    "pyyaml>=6.0",
+    "psutil>=5.9",
+    "pillow>=10",
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Image Processing",
+]
+
+[project.optional-dependencies]
+mesh = ["trimesh>=4.3", "matplotlib>=3.8"]
+ai = ["nninteractive>=1.1.3", "scikit-learn"]
+test = ["pytest"]
+
+[project.scripts]
+sprout = "sprout_core.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/EchanHe/SPROUT"
+Documentation = "https://github.com/EchanHe/SPROUT#readme"
+Issues = "https://github.com/EchanHe/SPROUT/issues"
+Changelog = "https://github.com/EchanHe/SPROUT/blob/main/CHANGELOG.md"
+
+[tool.setuptools.packages.find]
+include = ["sprout_core*"]
+
+[tool.setuptools.dynamic]
+version = { attr = "sprout_core.__version__" }

sprout_seg-1.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

sprout_seg-1.1.0/sprout_core/__init__.py

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+# sprout_core package initialization
+
+__version__ = "1.1.0"