brainfc 0.3.0__tar.gz

brainfc-0.3.0/.gitattributes

@@ -0,0 +1,16 @@
+* text=auto
+*.py text eol=lf
+*.md text eol=lf
+*.json text eol=lf
+*.yml text eol=lf
+*.yaml text eol=lf
+*.ts text eol=lf
+*.tsx text eol=lf
+*.js text eol=lf
+*.cjs text eol=lf
+*.html text eol=lf
+*.svg text eol=lf
+*.txt text eol=lf
+docs/assets/ARCHIFY-LICENSE text eol=lf
+*.png binary
+*.cmd text eol=crlf

brainfc-0.3.0/.github/ISSUE_TEMPLATE/bug.yml

@@ -0,0 +1,22 @@
+name: Bug report
+description: Report a reproducible problem without uploading participant data.
+body:
+  - type: input
+    id: version
+    attributes:
+      label: Package version and Python / OS
+    validations:
+      required: true
+  - type: textarea
+    id: steps
+    attributes:
+      label: Minimal reproduction
+      description: Use synthetic data or a small non-sensitive example.
+    validations:
+      required: true
+  - type: textarea
+    id: behavior
+    attributes:
+      label: Expected behavior, actual behavior, and error
+    validations:
+      required: true

brainfc-0.3.0/.github/pull_request_template.md

@@ -0,0 +1,7 @@
+## Change
+
+Describe the problem and resulting behavior.
+
+## Validation
+
+Report relevant numerical, API, documentation or browser checks. Note any changed defaults, ordering, units or provenance.

brainfc-0.3.0/.github/workflows/ci.yml

@@ -0,0 +1,65 @@
+name: CI
+on:
+  push:
+  pull_request:
+  workflow_call:
+
+permissions:
+  contents: read
+
+jobs:
+  python:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python: ['3.11', '3.12']
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+      - run: python -m pip install ".[dev]"
+      - run: python -m pytest -q
+      - run: python -m ruff check src tests examples scripts
+
+  distribution:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - uses: actions/setup-node@v4
+        with:
+          node-version: '22'
+          cache: npm
+          cache-dependency-path: frontend/package-lock.json
+      - run: python -m pip install -e ".[dev]"
+      - run: npm ci
+        working-directory: frontend
+      - run: npm run check && npm run build
+        working-directory: frontend
+      - run: python scripts/generate_reference.py --check
+      - run: python scripts/check_release.py
+      - run: python -m build
+      - run: python -m twine check dist/*.whl dist/*.tar.gz
+      - run: python scripts/check_release.py --dist dist
+      - run: python scripts/smoke_wheel.py --wheel-dir dist
+      - run: npx playwright install --with-deps chromium
+        working-directory: frontend
+      - run: npm run test:ui
+        working-directory: frontend
+      - uses: actions/upload-artifact@v4
+        with:
+          name: python-distributions
+          path: |
+            dist/*.whl
+            dist/*.tar.gz
+      - uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: browser-evidence
+          path: .work/release-browser
+

brainfc-0.3.0/.github/workflows/publish.yml

@@ -0,0 +1,51 @@
+name: Publish Python distributions
+on:
+  workflow_dispatch:
+    inputs:
+      target:
+        description: Package index (run from the exact version tag)
+        required: true
+        default: testpypi
+        type: choice
+        options: [testpypi, pypi]
+
+permissions:
+  contents: read
+
+jobs:
+  verify:
+    uses: ./.github/workflows/ci.yml
+  publish:
+    needs: verify
+    runs-on: ubuntu-latest
+    environment:
+      name: ${{ inputs.target }}
+    permissions:
+      contents: read
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Require the exact version tag
+        env:
+          RELEASE_REF: ${{ github.ref }}
+        run: |
+          python - <<'PY'
+          import os, runpy
+          version = runpy.run_path('src/brainfc/_version.py')['__version__']
+          assert os.environ['RELEASE_REF'] == f'refs/tags/v{version}', 'Run this workflow from the exact vVERSION tag.'
+          PY
+      - uses: actions/download-artifact@v4
+        with:
+          name: python-distributions
+          path: dist
+      - name: Publish to TestPyPI
+        if: inputs.target == 'testpypi'
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+      - name: Publish to PyPI
+        if: inputs.target == 'pypi'
+        uses: pypa/gh-action-pypi-publish@release/v1

brainfc-0.3.0/.gitignore

@@ -0,0 +1,23 @@
+.venv/
+.work/
+outputs/
+dist/
+build/
+*.egg-info/
+__pycache__/
+.pytest_cache/
+.ruff_cache/
+frontend/node_modules/
+*.log
+.venv*/
+.env
+.env.*
+.pypirc
+license.txt
+*.nii
+*.nii.gz
+*.dcm
+*.npy
+*.npz
+*.mat
+*.gii

brainfc-0.3.0/CHANGELOG.md

@@ -0,0 +1,34 @@
+# 更新记录
+
+## 0.3.0 — 2026-09-12
+
+- 正式采用分发名 `brainfc`、Python 导入名 `brainfc`、命令行 `brainfc`。
+- 默认安装包含科学计算和本地网页，无需额外选择 `[web]`。
+- 原有函数、处理顺序与结果契约保持不变；完整 API 和示例同步新名称。
+- 源码单独存放于新的 `brainfc` 目录，旧发行包及结果保留。
+- 本地构建验证，尚未上传 PyPI。
+
+## 0.2.1 — 2026-09-12
+
+原名 fMRI Connect 的本地开源发布准备版本。
+
+- 补全 Python 处理函数、Config 参数、Connectome 方法的源码 docstring 与自动生成参考。
+- 增加中文使用指南、格式/方法/输出契约、命令行全参数、本地 HTTP 指南、离线手册和可运行示例。
+- HTTP 请求增加明确的字段模型，缺失/未知字段返回 422；OpenAPI 提供实际参数定义。
+- 补齐 `fisher_z.npy`、`timeseries.npy`、`manifest.json` 的直接下载入口。
+- 包版本、命令行、HTTP 和结果 provenance 使用同一版本来源，修复旧版本硬编码。
+- 修复预检查对 MGZ 头信息的 NIfTI 假设，并允许沿用文件名已明确的空间；未知预检查阶段会报错。
+- 准备独立源码发布包、许可证/第三方说明、贡献说明、引用信息与 GitHub CI/手动 PyPI 发布流程。
+
+数值估计与去噪算法未作更改。现有完整输出目录保留原来的数据和来源记录。
+
+## 0.2.0 — 2026-09-12
+
+- 三步引导、自动读取元数据/配套文件、来源明确的 ABIDE/ADNI/ADHD-200/MDD/PPMI 方案提示。
+- 平滑脑壳、前方 ROI 悬停名称和与 3D 同步的八视图筛选。
+- 44 项 Python 测试和本地浏览器交互验证；原始 fMRIPrep 全流程未实跑。
+
+## 0.1.0 — 2026-09-12
+
+- 单 run 体积/CIFTI/GIFTI/表格读取、ROI 均值、混杂回归、删帧、Pearson/Spearman/偏相关与 Fisher-z。
+- Python API、CLI、本地网页、矩阵/八视图/离线报告、来源指纹与外部预处理适配器。

brainfc-0.3.0/CITATION.cff

@@ -0,0 +1,16 @@
+cff-version: 1.2.0
+message: "If you use this software, cite this software version and the original methods and atlases used in your analysis."
+type: software
+title: "BrainFC"
+repository-code: "https://github.com/hanxiangmin/brainfc"
+abstract: "Local single-run fMRI to ROI time series and signed functional connectivity, with a Python API, command line, and local graphical interface."
+authors:
+  - name: "BrainFC contributors"
+version: 0.3.0
+date-released: 2026-09-12
+license: Apache-2.0
+keywords:
+  - fMRI
+  - functional connectivity
+  - neuroimaging
+  - connectome

brainfc-0.3.0/CONTRIBUTING.md

@@ -0,0 +1,38 @@
+# 贡献与开发
+
+本目录可作为独立仓库根目录，不依赖父级 Hyper-Brain 源码。普通用户不需要开发工具。
+
+## 环境
+
+```shell
+python -m venv .venv
+# 激活虚拟环境后：
+python -m pip install -e ".[dev]"
+cd frontend
+npm ci
+cd ..
+```
+
+## 提交前验证
+
+```shell
+python -m ruff check src tests examples scripts
+python -m pytest -q
+python scripts/generate_reference.py
+python scripts/check_release.py
+python scripts/generate_reference.py --check
+python -m build
+python -m twine check dist/*.whl dist/*.tar.gz
+```
+
+前端改动运行 `npm run check`、`npm run build`；构建后的 JS/CSS 与第三方许可证随包分发，需要一起更新。`npm run test:ui` 会启动临时本地服务并使用 Playwright，首次需要 `npx playwright install chromium`，也可通过 `FMRI_TEST_CHROMIUM` 指定已有浏览器。
+
+函数 docstring 采用 NumPy 风格；更改函数/默认值后重新生成参考和 OpenAPI。`Config` 是科学参数的唯一默认来源。版本改 `src/brainfc/_version.py`，并同步 frontend/package.json 与 package-lock.json；Vite 从该文件读显示版本。
+
+## 数值与数据约定
+
+新增方法要检查 ROI 排序、signed 权重、原始帧索引、空间/单位、混杂处理及输入不覆盖。使用合成数据构造可验证的期望值；真实数据验证写明取得范围、预处理版本和图谱来源。
+
+不提交原始影像、个人数据、下载缓存、许可证文件、账号令牌或结果目录。用于说明的截图必须说明是合成信号还是实际数据。已有发布结果应保留，新的实验输出到新目录。
+
+报告缺陷时提供版本、文件类型、脱敏后的最小示例、期望行为和实际错误。不要在公开 issue 上传受限影像或包含本地个人信息的完整 provenance。

brainfc-0.3.0/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
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+
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+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
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+      meet the following conditions:
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+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
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+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
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+
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+      may provide additional or different license terms and conditions
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+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
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+      whether in tort (including negligence), contract, or otherwise,
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brainfc-0.3.0/NOTICE

@@ -0,0 +1,19 @@
+BrainFC
+Copyright 2026 BrainFC contributors
+
+The 3D viewer in frontend/src/vendor is derived from Hyper-Brain 0.3.0
+https://github.com/hanxiangmin/Hyper-Brain (Apache License 2.0).
+Adapted 2026-09-12. Changes include eight camera directions, coordinate bounds,
+smoothed display surfaces, translucent materials, foreground hover labels,
+and synchronized edge selection and eight-view export.
+Analysis is independent of Hyper-Brain.
+React and Three.js are distributed under their MIT licenses. Their complete
+license texts are included with the bundled frontend in THIRD_PARTY_NOTICES.txt.
+Atlas and participant datasets are not included in the distribution; their
+licenses and citations are determined by the original providers.
+
+The standalone diagram viewer in docs/assets/processing.html is generated with
+archify skill 2.16 (MIT), https://github.com/tt-a1i/archify.
+The accompanying license is in docs/assets/ARCHIFY-LICENSE.
+The README hero is AI-generated conceptual product artwork; the separately
+identified application previews use synthetic signals and are actual renders.

brainfc-0.3.0/PKG-INFO

@@ -0,0 +1,97 @@
+Metadata-Version: 2.5
+Name: brainfc
+Version: 0.3.0
+Summary: Local fMRI to functional connectivity: Python API, offline GUI and eight-view brain networks
+Project-URL: Homepage, https://github.com/hanxiangmin/brainfc
+Project-URL: Source, https://github.com/hanxiangmin/brainfc
+Project-URL: Issues, https://github.com/hanxiangmin/brainfc/issues
+Project-URL: Documentation, https://github.com/hanxiangmin/brainfc/tree/main/docs
+Author: BrainFC contributors
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+License-File: src/brainfc/web/static/THIRD_PARTY_NOTICES.txt
+Keywords: bids,connectome,fmri,functional-connectivity,neuroimaging
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.11
+Requires-Dist: fastapi>=0.115
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: nibabel>=5.2
+Requires-Dist: nilearn<0.15,>=0.14
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas>=2.1
+Requires-Dist: python-multipart>=0.0.20
+Requires-Dist: scikit-image>=0.23
+Requires-Dist: scikit-learn>=1.4
+Requires-Dist: scipy>=1.12
+Requires-Dist: uvicorn>=0.30
+Provides-Extra: dev
+Requires-Dist: build>=1.2; extra == 'dev'
+Requires-Dist: hatchling>=1.27; extra == 'dev'
+Requires-Dist: httpx>=0.27; extra == 'dev'
+Requires-Dist: markdown>=3.6; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Requires-Dist: pyyaml>=6; extra == 'dev'
+Requires-Dist: ruff>=0.9; extra == 'dev'
+Requires-Dist: twine>=6; extra == 'dev'
+Description-Content-Type: text/markdown
+
+![BrainFC: functional connectivity, made visible](https://raw.githubusercontent.com/hanxiangmin/brainfc/main/docs/assets/brainfc-hero.png)
+
+# BrainFC
+
+**fMRI → ROI time series → functional connectivity → matrix, eight-view and interactive 3D reports.**
+
+BrainFC is a Python library with a command-line interface and a local graphical interface. Both interfaces use the same processing core. The default installation includes the GUI and an offline API manual. Python 3.11 or newer is required; ordinary users do not need Node.js.
+
+## Install and launch
+
+```shell
+pip install brainfc
+brainfc serve
+```
+
+The interface opens at `http://127.0.0.1:8766`. Choose the built-in demo to generate synthetic NIfTI inputs and a complete report without downloading participant data. The offline manual is available at `/reference/` and the HTTP API schema at `/docs`.
+
+## Python API
+
+```python
+from brainfc import Config, extract_connectome
+
+# A TSV with a header: rows are time points, columns are ROI signals.
+result = extract_connectome(
+    "signals.tsv",
+    config=Config(detrend=False, standardize=False),
+)
+matrix = result.connectivity
+result.save("results/run-001")
+```
+
+The destination must be new. For volume images, supply an integer-label atlas in the same explicitly named space and confirm that spatial preprocessing is complete. Filtering, confound regression and censoring must match the provenance of the input signals; the example above does not add temporal denoising.
+
+## Capabilities
+
+- Read supported NiBabel volume containers, CIFTI time series, paired GIFTI data/labels, and CSV/TSV/TXT/1D/NPY/NPZ/MAT tables (excluding MAT v7.3).
+- Extract ROI means; apply confound regression, temporal cleaning and censoring while retaining original frame indices.
+- Compute Pearson, Spearman or Ledoit-Wolf partial correlations, with a separate Fisher-z matrix.
+- Export arrays, tables, quality records, input fingerprints, figures and an offline interactive report.
+- Synchronize selected connections and display thresholds between the 3D viewer and eight anatomical views. Display filtering does not modify the complete signed matrix.
+
+Raw DICOM/BIDS spatial preprocessing requires external dcm2niix/fMRIPrep. BrainFC provides command adapters; it does not implement that preprocessing itself. The complete external raw-data chain has not been validated in this release. This package does not provide disease diagnosis or cohort-level inference.
+
+## Documentation and source
+
+- [Quickstart](https://github.com/hanxiangmin/brainfc/blob/main/docs/quickstart.md)
+- [Complete Python API](https://github.com/hanxiangmin/brainfc/blob/main/docs/api-reference.md)
+- [Python usage guide](https://github.com/hanxiangmin/brainfc/blob/main/docs/python-api.md)
+- [Input formats and processing contract](https://github.com/hanxiangmin/brainfc/blob/main/docs/formats.md)
+- [Source code and issues](https://github.com/hanxiangmin/brainfc)
+
+Licensed under Apache-2.0. The 3D viewer is adapted from Hyper-Brain; BrainFC runs independently. Dataset and atlas licenses remain with their original providers.

brainfc-0.3.0/PYPI.md

@@ -0,0 +1,52 @@
+![BrainFC: functional connectivity, made visible](https://raw.githubusercontent.com/hanxiangmin/brainfc/main/docs/assets/brainfc-hero.png)
+
+# BrainFC
+
+**fMRI → ROI time series → functional connectivity → matrix, eight-view and interactive 3D reports.**
+
+BrainFC is a Python library with a command-line interface and a local graphical interface. Both interfaces use the same processing core. The default installation includes the GUI and an offline API manual. Python 3.11 or newer is required; ordinary users do not need Node.js.
+
+## Install and launch
+
+```shell
+pip install brainfc
+brainfc serve
+```
+
+The interface opens at `http://127.0.0.1:8766`. Choose the built-in demo to generate synthetic NIfTI inputs and a complete report without downloading participant data. The offline manual is available at `/reference/` and the HTTP API schema at `/docs`.
+
+## Python API
+
+```python
+from brainfc import Config, extract_connectome
+
+# A TSV with a header: rows are time points, columns are ROI signals.
+result = extract_connectome(
+    "signals.tsv",
+    config=Config(detrend=False, standardize=False),
+)
+matrix = result.connectivity
+result.save("results/run-001")
+```
+
+The destination must be new. For volume images, supply an integer-label atlas in the same explicitly named space and confirm that spatial preprocessing is complete. Filtering, confound regression and censoring must match the provenance of the input signals; the example above does not add temporal denoising.
+
+## Capabilities
+
+- Read supported NiBabel volume containers, CIFTI time series, paired GIFTI data/labels, and CSV/TSV/TXT/1D/NPY/NPZ/MAT tables (excluding MAT v7.3).
+- Extract ROI means; apply confound regression, temporal cleaning and censoring while retaining original frame indices.
+- Compute Pearson, Spearman or Ledoit-Wolf partial correlations, with a separate Fisher-z matrix.
+- Export arrays, tables, quality records, input fingerprints, figures and an offline interactive report.
+- Synchronize selected connections and display thresholds between the 3D viewer and eight anatomical views. Display filtering does not modify the complete signed matrix.
+
+Raw DICOM/BIDS spatial preprocessing requires external dcm2niix/fMRIPrep. BrainFC provides command adapters; it does not implement that preprocessing itself. The complete external raw-data chain has not been validated in this release. This package does not provide disease diagnosis or cohort-level inference.
+
+## Documentation and source
+
+- [Quickstart](https://github.com/hanxiangmin/brainfc/blob/main/docs/quickstart.md)
+- [Complete Python API](https://github.com/hanxiangmin/brainfc/blob/main/docs/api-reference.md)
+- [Python usage guide](https://github.com/hanxiangmin/brainfc/blob/main/docs/python-api.md)
+- [Input formats and processing contract](https://github.com/hanxiangmin/brainfc/blob/main/docs/formats.md)
+- [Source code and issues](https://github.com/hanxiangmin/brainfc)
+
+Licensed under Apache-2.0. The 3D viewer is adapted from Hyper-Brain; BrainFC runs independently. Dataset and atlas licenses remain with their original providers.