habitat-analysis 1.0.1__tar.gz

habitat_analysis-1.0.1/CITATION.cff

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+cff-version: 1.2.0
+message: >-
+  If you use HABIT in scientific work, please cite it using the metadata below.
+title: "HABIT: Habitat Analysis - Biomedical Imaging Toolkit"
+abstract: >-
+  HABIT is an open-source toolkit for tumour habitat analysis and intratumoral
+  heterogeneity quantification. It covers image preprocessing, voxel-level
+  feature construction, supervoxel and population-level habitat clustering,
+  habitat-level feature extraction (including multiregional spatial interaction
+  and intratumoral heterogeneity scores), and downstream machine-learning
+  modelling and evaluation.
+type: software
+authors:
+  - family-names: Li
+    given-names: Chao
+    email: lichao19870617@163.com
+  - family-names: Dong
+    given-names: Mengshi
+  - name: HABIT Contributors
+version: 0.1.0
+license: Apache-2.0
+repository-code: "https://github.com/lichao312214129/HABIT"
+url: "https://lichao312214129.github.io/HABIT"
+keywords:
+  - radiomics
+  - tumour habitat
+  - intratumoral heterogeneity
+  - medical imaging
+  - machine learning

habitat_analysis-1.0.1/LICENSE

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habitat_analysis-1.0.1/MANIFEST.in

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+# Apache-2.0 requires the license and the NOTICE attributions to travel with
+# every redistribution, so they must be present in source distributions too.
+include LICENSE
+include NOTICE
+include CITATION.cff
+include README.md
+include README_en.md
+include pyproject.toml
+include setup.py
+
+# Include C sources for supervoxel texture matrix extension in sdists.
+recursive-include habit/kernels/radiomics/cext/src *.c
+recursive-include habit/kernels/radiomics/cext/src *.h
+
+# Bundled PyRadiomics parameter presets (default params_file fallbacks).
+recursive-include habit/resources/radiomics *.yaml
+
+# PEP 561 marker for users of static type checkers.
+include habit/py.typed
+
+# Keep published sdists lean: never ship the developer test suite or local
+# build / demo artefacts (they are not part of the installable package).
+prune tests
+prune demo_data
+prune docs
+prune developer
+prune .github
+prune build
+prune dist
+
+# Next-generation web GUI (API bridge, presets, built frontend).
+recursive-include habit-gui/bridge *.py
+recursive-include habit-gui/api *.py
+recursive-include habit-gui/presets *.yaml
+recursive-include habit-gui/web/dist *
+prune habit-gui/web/node_modules

habitat_analysis-1.0.1/NOTICE

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+HABIT (Habitat Analysis: Biomedical Imaging Toolkit)
+Copyright (c) 2024-2026 Li Chao, Dong Mengshi and HABIT Contributors.
+
+This product is licensed under the Apache License, Version 2.0. A copy of the
+license is included in the LICENSE file at the root of this distribution.
+
+If you redistribute HABIT or a derivative work, Apache-2.0 section 4(d)
+requires that you also carry a readable copy of the attribution notices below.
+
+When HABIT is used in scientific work, the authors additionally request -- but
+do not require as a condition of this license -- that you cite the project. See
+CITATION.cff for citation metadata.
+
+---------------------------------------------------------------------------
+Third-party components incorporated into HABIT
+---------------------------------------------------------------------------
+
+1. VMAF
+   https://github.com/Netflix/vmaf
+   Copyright (c) 2020 Netflix, Inc.
+   Licensed under BSD-2-Clause-Patent
+
+   The DeLong AUC comparison routines in
+   habit/core/machine_learning/statistics/delong_test.py are adapted from this
+   project.
+
+2. PyTorchRadiomics
+   https://github.com/lyhyl/pytorchradiomics
+   Copyright (c) lyhyl and PyTorchRadiomics contributors
+   Licensed under the MIT License
+
+   The GPU feature classes in habit/kernels/radiomics/torchradiomics/ are
+   vendored from this project and adapted for HABIT.
+
+---------------------------------------------------------------------------
+Runtime dependencies
+---------------------------------------------------------------------------
+
+HABIT depends on third-party packages that are installed separately and remain
+governed by their own licenses, including PyRadiomics, SimpleITK, ANTsPy,
+scikit-learn, scikit-image, pandas, NumPy, SciPy, XGBoost, and pydicom. Those
+licenses are not reproduced here; consult each package's own distribution.

habitat_analysis-1.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: habitat-analysis
+Version: 1.0.1
+Summary: Habitat Analysis: Biomedical Imaging Toolkit (HABIT)
+Author: lichao19870617@163.com
+Author-email: Li Chao <lichao19870617@163.com>
+License: Apache-2.0
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10,<3.13
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: numpy<2,>=1.26
+Requires-Dist: SimpleITK<3,>=2.2
+Requires-Dist: matplotlib<4,>=3.8
+Requires-Dist: scipy<2,>=1.11
+Requires-Dist: openpyxl<4,>=3.1
+Requires-Dist: pandas<3,>=2.1
+Requires-Dist: tqdm<5,>=4.66
+Requires-Dist: scikit-learn<2,>=1.4
+Requires-Dist: joblib<2,>=1.3
+Requires-Dist: scikit-image<0.27,>=0.23
+Requires-Dist: seaborn<1,>=0.13
+Requires-Dist: PyYAML<7,>=6.0
+Requires-Dist: click<9,>=8.1
+Requires-Dist: chardet<8,>=5.0
+Requires-Dist: pydicom<4,>=3.0
+Requires-Dist: pydantic<3,>=2.7
+Requires-Dist: kneed<1,>=0.8
+Requires-Dist: pyarrow<22,>=15
+Provides-Extra: radiomics
+Requires-Dist: pyradiomics<3.1,>=3.0.1; extra == "radiomics"
+Provides-Extra: gui
+Requires-Dist: fastapi>=0.100; extra == "gui"
+Requires-Dist: uvicorn[standard]>=0.22; extra == "gui"
+Provides-Extra: ml
+Requires-Dist: xgboost<4,>=2.1; extra == "ml"
+Requires-Dist: imbalanced-learn<1,>=0.12; extra == "ml"
+Requires-Dist: mrmr-selection<1,>=0.2.8; extra == "ml"
+Requires-Dist: statsmodels<1,>=0.14; extra == "ml"
+Provides-Extra: registration
+Requires-Dist: antspyx<1,>=0.4.2; extra == "registration"
+Provides-Extra: analysis
+Requires-Dist: krippendorff<1,>=0.8; extra == "analysis"
+Requires-Dist: shap<1,>=0.45; extra == "analysis"
+Requires-Dist: plotly<7,>=5.20; extra == "analysis"
+Requires-Dist: pingouin<1,>=0.5.4; extra == "analysis"
+Requires-Dist: lifelines<1,>=0.28; extra == "analysis"
+Requires-Dist: scikit-survival<1,>=0.23; extra == "analysis"
+Provides-Extra: automl
+Requires-Dist: autogluon.tabular[catboost,lightgbm]<2,>=1.2; extra == "automl"
+Provides-Extra: all
+Requires-Dist: pyradiomics<3.1,>=3.0.1; extra == "all"
+Requires-Dist: xgboost<4,>=2.1; extra == "all"
+Requires-Dist: imbalanced-learn<1,>=0.12; extra == "all"
+Requires-Dist: mrmr-selection<1,>=0.2.8; extra == "all"
+Requires-Dist: statsmodels<1,>=0.14; extra == "all"
+Requires-Dist: antspyx<1,>=0.4.2; extra == "all"
+Requires-Dist: krippendorff<1,>=0.8; extra == "all"
+Requires-Dist: shap<1,>=0.45; extra == "all"
+Requires-Dist: plotly<7,>=5.20; extra == "all"
+Requires-Dist: pingouin<1,>=0.5.4; extra == "all"
+Requires-Dist: lifelines<1,>=0.28; extra == "all"
+Requires-Dist: scikit-survival<1,>=0.23; extra == "all"
+Requires-Dist: autogluon.tabular[catboost,lightgbm]<2,>=1.2; extra == "all"
+Requires-Dist: fastapi>=0.100; extra == "all"
+Requires-Dist: uvicorn[standard]>=0.22; extra == "all"
+Provides-Extra: torch
+Requires-Dist: torch<3,>=2.4; extra == "torch"
+Dynamic: author
+Dynamic: license-file
+Dynamic: requires-python
+
+# Habitat Analysis: Biomedical Imaging Toolkit (HABIT)
+
+**Tumor habitat analysis and intratumoral heterogeneity quantification** for clinical and radiomics research. Workflows are driven by YAML configs: preprocessing, habitat segmentation, feature extraction, and optional machine learning.
+
+**Language / 语言**：[English](https://github.com/lichao312214129/HABIT/blob/main/README_en.md) | [简体中文](https://github.com/lichao312214129/HABIT/blob/main/README.md)
+
+---
+
+## Documentation
+
+**Online docs**: [https://lichao312214129.github.io/HABIT](https://lichao312214129.github.io/HABIT)
+
+Local build: `cd docs && make html` → `docs/build/html/index.html`
+
+### Suggested learning path
+
+| Step | Topic | Link |
+|------|--------|------|
+| 1 | Install HABIT | [Installation](https://lichao312214129.github.io/HABIT/tutorial/installation.html) |
+| 2 | Demo workflow | [Quickstart](https://lichao312214129.github.io/HABIT/tutorial/quickstart.html) |
+| 3 | Web GUI (under development) | [Web GUI](https://lichao312214129.github.io/HABIT/gui/index.html) |
+| 4 | Step-by-step how-to | [How-to index](https://lichao312214129.github.io/HABIT/how_to/index.html) |
+| 5 | YAML parameters | [Configuration](https://lichao312214129.github.io/HABIT/configuration/index.html) |
+
+### Workflow chapters
+
+| Step | Link |
+|------|------|
+| Prepare data | [Prepare data](https://lichao312214129.github.io/HABIT/how_to/prepare_data.html) |
+| Preprocessing | [Preprocess](https://lichao312214129.github.io/HABIT/how_to/preprocess.html) |
+| Habitat segmentation | [Segment habitat](https://lichao312214129.github.io/HABIT/how_to/segment_habitat.html) |
+| Feature extraction | [Extract features](https://lichao312214129.github.io/HABIT/how_to/extract_features.html) |
+| Machine learning | [Train model](https://lichao312214129.github.io/HABIT/how_to/train_model.html) |
+| Model comparison | [Compare models](https://lichao312214129.github.io/HABIT/how_to/compare_models.html) |
+| FAQ | [FAQ](https://lichao312214129.github.io/HABIT/troubleshooting/faq.html) |
+
+### Tools & more
+
+| Topic | Link |
+|--------|------|
+| CLI overview | [CLI reference](https://lichao312214129.github.io/HABIT/reference/cli.html) |
+| Contributing | [Contributing](https://lichao312214129.github.io/HABIT/development/contributing.html) |
+
+---
+
+## Bundled config templates
+
+After cloning or unpacking the repo, use the **`config/`** folder at the **project root** (sibling to the `habit/` Python package). See [`config/README_CONFIG.md`](https://github.com/lichao312214129/HABIT/blob/main/config/README_CONFIG.md) and [Configuration reference](https://lichao312214129.github.io/HABIT/configuration/index.html).
+
+---
+
+## Source & demo data
+
+- **Windows lightweight one-click installer (recommended)**: [Installation](https://lichao312214129.github.io/HABIT/tutorial/installation.html)
+  - Extract to a short ASCII-only path, open `launchers/`, run `一键安装HABIT.bat`, then use `启动HABIT命令行.bat`
+  - The default environment contains imaging, habitat, and standard ML dependencies only; run `一键启用HABIT-AutoML.bat` or `一键启用HABIT-进阶分析.bat` from `launchers/` only when those features are needed
+  - Optional NVIDIA acceleration is installed separately with `launchers/一键启用HABIT-GPU.bat`, after the CPU environment passes verification
+- **Source**: [GitHub](https://github.com/lichao312214129/HABIT)
+- **Demo data**: [Quickstart](https://lichao312214129.github.io/HABIT/tutorial/quickstart.html)
+
+---
+
+## Support & citation
+
+- **Issues**: [GitHub Issues](https://github.com/lichao312214129/HABIT/issues)
+- **Citation**: see [CITATION.cff](https://github.com/lichao312214129/HABIT/blob/main/CITATION.cff)
+- **License**: [Apache License 2.0](https://github.com/lichao312214129/HABIT/blob/main/LICENSE). Free for academic and commercial use; the only obligation is to retain the copyright and license notices and to ship [NOTICE](https://github.com/lichao312214129/HABIT/blob/main/NOTICE) with redistributions. When HABIT supports scientific work, the authors request -- but do not require as a license condition -- that you cite it

habitat_analysis-1.0.1/README.md

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+# Habitat Analysis: Biomedical Imaging Toolkit (HABIT)
+
+**肿瘤生境（Habitat）分析与瘤内异质性评估工具箱** — 面向临床与影像组学研究，通过 YAML 配置驱动预处理、生境分割、特征提取与机器学习。
+
+**语言 / Language**：[简体中文](https://github.com/lichao312214129/HABIT/blob/main/README.md) | [English](https://github.com/lichao312214129/HABIT/blob/main/README_en.md)
+
+---
+
+## 文档（主要内容请在此阅读）
+
+**在线文档（推荐，英文）**：[https://lichao312214129.github.io/HABIT](https://lichao312214129.github.io/HABIT)
+
+本地构建：进入 `docs/` 目录执行 `make html`，在 `docs/build/html/index.html` 打开。
+
+### 推荐学习路径
+
+| 顺序 | 说明 | 链接 |
+|------|------|------|
+| 1 | **安装** HABIT（Windows 推荐便携包） | [安装](https://lichao312214129.github.io/HABIT/tutorial/installation.html) |
+| 2 | 跑通 Demo | [Demo 教程](https://lichao312214129.github.io/HABIT/tutorial/quickstart.html) |
+| 3 | 图形界面（开发中，暂不建议日常使用） | [Web GUI](https://lichao312214129.github.io/HABIT/gui/index.html) |
+| 4 | 用自己的数据逐步操作 | [操作指南](https://lichao312214129.github.io/HABIT/how_to/index.html) |
+| 5 | 修改 YAML 参数 | [配置参考](https://lichao312214129.github.io/HABIT/configuration/index.html) |
+| 6 | 查特征公式（写论文） | [特征参考](https://lichao312214129.github.io/HABIT/reference/features/index.html) |
+
+### 按流程查阅
+
+| 步骤 | 文档 |
+|------|------|
+| 准备数据 | [准备数据](https://lichao312214129.github.io/HABIT/how_to/prepare_data.html) |
+| 影像预处理 | [预处理](https://lichao312214129.github.io/HABIT/how_to/preprocess.html) |
+| 生境分割 | [生境分割](https://lichao312214129.github.io/HABIT/how_to/segment_habitat.html) |
+| 特征提取 | [特征提取](https://lichao312214129.github.io/HABIT/how_to/extract_features.html) |
+| 机器学习 | [机器学习](https://lichao312214129.github.io/HABIT/how_to/train_model.html) |
+| 模型对比 | [模型对比](https://lichao312214129.github.io/HABIT/how_to/compare_models.html) |
+| 遇到问题 | [常见问题](https://lichao312214129.github.io/HABIT/troubleshooting/faq.html) |
+
+### 其它
+
+| 主题 | 文档 |
+|------|------|
+| 命令索引 | [命令参考](https://lichao312214129.github.io/HABIT/reference/cli.html) |
+| 参与开发 | [贡献指南](https://lichao312214129.github.io/HABIT/development/contributing.html) |
+
+---
+
+## 内置配置模板
+
+获取源码后，在**项目根目录**（与 Python 包 `habit/` 同级，而非 `habit/` 包内部）提供 [`config/`](config/) 目录，内含预处理、生境分割、特征提取、机器学习等**可参考的示例 YAML**。建议先阅读 [`config/README_CONFIG.md`](config/README_CONFIG.md) 中的场景索引，再复制对应文件并按 `#%%====` 块修改路径；各字段含义见 [配置参考](https://lichao312214129.github.io/HABIT/configuration/index.html)。
+
+---
+
+## 源码与演示数据
+
+- **pip 安装（开发者 / 嵌入其它环境）**：需要 Python **3.10–3.12**
+  ```bash
+  pip install habitat-analysis
+  # 或从源码：
+  pip install .
+  habit --version
+  # 代码中仍然：import habit
+  ```
+  PyRadiomics **不是**默认依赖。需要组学特征时（已本地验证的可靠写法）：
+  ```bash
+  conda install -c conda-forge pyradiomics
+  # 或 pip（务必钉死 3.0.1；不要裸装最新 3.1.0，源码包会失败）：
+  pip install "pyradiomics==3.0.1"
+  ```
+  其它可选能力：`pip install "habitat-analysis[ml,analysis,registration]"`。详见[安装指南](https://lichao312214129.github.io/HABIT/tutorial/installation.html)。
+- **Windows 轻量一键安装（推荐）**：[安装指南](https://lichao312214129.github.io/HABIT/tutorial/installation.html)
+  - 解压轻量 ZIP 到纯英文、无空格的短路径（例如 `D:\HABIT`）
+  - 打开 `launchers/`，双击 `一键安装HABIT.bat`；安装器会在项目内创建锁定的 Python 3.10 环境，不要求预装 Python 或 Conda，也不会修改用户 PATH
+  - 安装完成后，在 `launchers/` 中双击 `启动HABIT命令行.bat`
+  - 默认环境只包含基础影像、habitat 与常规模型依赖；仅在确实使用对应功能时，在 `launchers/` 中运行 `一键启用HABIT-AutoML.bat` 或 `一键启用HABIT-进阶分析.bat`
+  - NVIDIA GPU 为可选增强：先保证 CPU 环境通过自检，再在 `launchers/` 中双击 `一键启用HABIT-GPU.bat`；失败时基础 CPU 环境仍可用
+  - 轻量 ZIP 已包含 `config/`；跑 Demo 时仅需从网盘下载 [`demo_data.rar`](https://pan.baidu.com/s/1K1m8U47wUWV9CCUNahNZuw?pwd=9ws9)（提取码 **9ws9**）— 见 [Demo 教程](https://lichao312214129.github.io/HABIT/tutorial/quickstart.html)
+- **源码**：[GitHub 仓库](https://github.com/lichao312214129/HABIT) · [下载 ZIP](https://github.com/lichao312214129/HABIT/archive/refs/heads/main.zip)（安装见 [安装指南](https://lichao312214129.github.io/HABIT/tutorial/installation.html)）
+- **演示数据 / 测试**：[`demo_data.rar`](https://pan.baidu.com/s/1K1m8U47wUWV9CCUNahNZuw?pwd=9ws9)（**9ws9**）；可选 [`tests.zip` 打包目录](https://pan.baidu.com/s/1EAcC2s4qIKGp1h08UtbApA?pwd=vv2c)（**vv2c**）。`config/` 已内置于源码和轻量 ZIP — 见 [Demo 教程](https://lichao312214129.github.io/HABIT/tutorial/quickstart.html)
+
+---
+
+## 支持与引用
+
+- **问题反馈**：[GitHub Issues](https://github.com/lichao312214129/HABIT/issues) · [lichao19870617@163.com](mailto:lichao19870617@163.com)
+- **引用**：见 [CITATION.cff](CITATION.cff) 与文档 [致谢](https://lichao312214129.github.io/HABIT/acknowledgments.html)
+- **许可**：[Apache License 2.0](LICENSE)。可自由用于学术与商业用途，唯一义务是保留版权与许可声明，并在再分发时附带 [NOTICE](NOTICE)。用于科研工作时，作者恳请（但不作为许可条件）引用 HABIT
+
+**开发团队**：HABIT 开发团队（详见 [致谢](https://lichao312214129.github.io/HABIT/acknowledgments.html)）

habitat_analysis-1.0.1/README_en.md

@@ -0,0 +1,67 @@
+# Habitat Analysis: Biomedical Imaging Toolkit (HABIT)
+
+**Tumor habitat analysis and intratumoral heterogeneity quantification** for clinical and radiomics research. Workflows are driven by YAML configs: preprocessing, habitat segmentation, feature extraction, and optional machine learning.
+
+**Language / 语言**：[English](https://github.com/lichao312214129/HABIT/blob/main/README_en.md) | [简体中文](https://github.com/lichao312214129/HABIT/blob/main/README.md)
+
+---
+
+## Documentation
+
+**Online docs**: [https://lichao312214129.github.io/HABIT](https://lichao312214129.github.io/HABIT)
+
+Local build: `cd docs && make html` → `docs/build/html/index.html`
+
+### Suggested learning path
+
+| Step | Topic | Link |
+|------|--------|------|
+| 1 | Install HABIT | [Installation](https://lichao312214129.github.io/HABIT/tutorial/installation.html) |
+| 2 | Demo workflow | [Quickstart](https://lichao312214129.github.io/HABIT/tutorial/quickstart.html) |
+| 3 | Web GUI (under development) | [Web GUI](https://lichao312214129.github.io/HABIT/gui/index.html) |
+| 4 | Step-by-step how-to | [How-to index](https://lichao312214129.github.io/HABIT/how_to/index.html) |
+| 5 | YAML parameters | [Configuration](https://lichao312214129.github.io/HABIT/configuration/index.html) |
+
+### Workflow chapters
+
+| Step | Link |
+|------|------|
+| Prepare data | [Prepare data](https://lichao312214129.github.io/HABIT/how_to/prepare_data.html) |
+| Preprocessing | [Preprocess](https://lichao312214129.github.io/HABIT/how_to/preprocess.html) |
+| Habitat segmentation | [Segment habitat](https://lichao312214129.github.io/HABIT/how_to/segment_habitat.html) |
+| Feature extraction | [Extract features](https://lichao312214129.github.io/HABIT/how_to/extract_features.html) |
+| Machine learning | [Train model](https://lichao312214129.github.io/HABIT/how_to/train_model.html) |
+| Model comparison | [Compare models](https://lichao312214129.github.io/HABIT/how_to/compare_models.html) |
+| FAQ | [FAQ](https://lichao312214129.github.io/HABIT/troubleshooting/faq.html) |
+
+### Tools & more
+
+| Topic | Link |
+|--------|------|
+| CLI overview | [CLI reference](https://lichao312214129.github.io/HABIT/reference/cli.html) |
+| Contributing | [Contributing](https://lichao312214129.github.io/HABIT/development/contributing.html) |
+
+---
+
+## Bundled config templates
+
+After cloning or unpacking the repo, use the **`config/`** folder at the **project root** (sibling to the `habit/` Python package). See [`config/README_CONFIG.md`](https://github.com/lichao312214129/HABIT/blob/main/config/README_CONFIG.md) and [Configuration reference](https://lichao312214129.github.io/HABIT/configuration/index.html).
+
+---
+
+## Source & demo data
+
+- **Windows lightweight one-click installer (recommended)**: [Installation](https://lichao312214129.github.io/HABIT/tutorial/installation.html)
+  - Extract to a short ASCII-only path, open `launchers/`, run `一键安装HABIT.bat`, then use `启动HABIT命令行.bat`
+  - The default environment contains imaging, habitat, and standard ML dependencies only; run `一键启用HABIT-AutoML.bat` or `一键启用HABIT-进阶分析.bat` from `launchers/` only when those features are needed
+  - Optional NVIDIA acceleration is installed separately with `launchers/一键启用HABIT-GPU.bat`, after the CPU environment passes verification
+- **Source**: [GitHub](https://github.com/lichao312214129/HABIT)
+- **Demo data**: [Quickstart](https://lichao312214129.github.io/HABIT/tutorial/quickstart.html)
+
+---
+
+## Support & citation
+
+- **Issues**: [GitHub Issues](https://github.com/lichao312214129/HABIT/issues)
+- **Citation**: see [CITATION.cff](https://github.com/lichao312214129/HABIT/blob/main/CITATION.cff)
+- **License**: [Apache License 2.0](https://github.com/lichao312214129/HABIT/blob/main/LICENSE). Free for academic and commercial use; the only obligation is to retain the copyright and license notices and to ship [NOTICE](https://github.com/lichao312214129/HABIT/blob/main/NOTICE) with redistributions. When HABIT supports scientific work, the authors request -- but do not require as a license condition -- that you cite it