mne-rt 1.0.0__tar.gz

mne_rt-1.0.0/.gitattributes

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mne_rt-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 payamsash
+
+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.

mne_rt-1.0.0/MANIFEST.in

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+include LICENSE
+include README.md
+include pyproject.toml
+include src/mne_rt/config_methods.yml
+
+# Docs, examples and build artefacts are not needed to install the package
+prune docs
+prune build
+prune tests
+prune examples
+prune paper
+prune material
+prune data

mne_rt-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: mne-rt
+Version: 1.0.0
+Summary: MNE-RT — real-time M/EEG signal processing and analysis
+Author-email: "Payam S. Shabestari" <payam.sadeghi74@gmail.com>
+Maintainer-email: "Payam S. Shabestari" <payam.sadeghi74@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/payamsash/mne-rt
+Project-URL: Documentation, https://payamsash.github.io/mne-rt/
+Project-URL: Repository, https://github.com/payamsash/mne-rt
+Project-URL: Bug Tracker, https://github.com/payamsash/mne-rt/issues
+Keywords: neurofeedback,EEG,MEG,brain-computer interface,real-time,LSL,source localisation,signal processing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Human Machine Interfaces
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mne>=1.8
+Requires-Dist: mne-lsl>=1.7
+Requires-Dist: mne-connectivity>=0.7
+Requires-Dist: mne-features>=0.3
+Requires-Dist: mne-icalabel>=0.5
+Requires-Dist: numpy<3,>=2.0
+Requires-Dist: scipy>=1.13
+Requires-Dist: matplotlib>=3.9
+Requires-Dist: nibabel>=5.0
+Requires-Dist: PyQt6>=6.7
+Requires-Dist: pyqtgraph>=0.13
+Requires-Dist: qtpy>=2.4
+Requires-Dist: pyserial>=3.0
+Requires-Dist: fooof>=1.0
+Requires-Dist: pyunlocbox>=0.5.2
+Requires-Dist: pactools>=0.3
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: python-osc>=1.8
+Requires-Dist: imageio[ffmpeg]>=2.28
+Provides-Extra: viz
+Requires-Dist: pyvista>=0.44; extra == "viz"
+Requires-Dist: pyvistaqt>=0.11.1; extra == "viz"
+Requires-Dist: vtk>=9.3; extra == "viz"
+Provides-Extra: riemann
+Requires-Dist: pyriemann>=0.7; extra == "riemann"
+Provides-Extra: bids
+Requires-Dist: mne-bids>=0.14; extra == "bids"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Provides-Extra: lint
+Requires-Dist: ruff; extra == "lint"
+Requires-Dist: mypy; extra == "lint"
+Requires-Dist: pre-commit; extra == "lint"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7; extra == "docs"
+Requires-Dist: pydata-sphinx-theme>=0.14; extra == "docs"
+Requires-Dist: sphinx-gallery>=0.15; extra == "docs"
+Requires-Dist: numpydoc>=1.6; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=1.25; extra == "docs"
+Requires-Dist: sphinx-tabs>=3.4; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex>=2.6; extra == "docs"
+Requires-Dist: seaborn>=0.12; extra == "docs"
+Provides-Extra: full
+Requires-Dist: pyvista>=0.44; extra == "full"
+Requires-Dist: pyvistaqt>=0.11.1; extra == "full"
+Requires-Dist: vtk>=9.3; extra == "full"
+Requires-Dist: pyriemann>=0.7; extra == "full"
+Requires-Dist: mne-bids>=0.14; extra == "full"
+Requires-Dist: pytest; extra == "full"
+Requires-Dist: pytest-cov; extra == "full"
+Requires-Dist: ruff; extra == "full"
+Requires-Dist: mypy; extra == "full"
+Requires-Dist: pre-commit; extra == "full"
+Requires-Dist: sphinx>=7; extra == "full"
+Requires-Dist: pydata-sphinx-theme>=0.14; extra == "full"
+Requires-Dist: sphinx-gallery>=0.15; extra == "full"
+Requires-Dist: numpydoc>=1.6; extra == "full"
+Requires-Dist: sphinx-autodoc-typehints>=1.25; extra == "full"
+Requires-Dist: sphinx-tabs>=3.4; extra == "full"
+Requires-Dist: sphinxcontrib-bibtex>=2.6; extra == "full"
+Requires-Dist: seaborn>=0.12; extra == "full"
+Dynamic: license-file
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/payamsash/mne-rt/main/docs/source/_static/mne_rt_logo.svg" alt="MNE-RT Logo" width="480"/>
+</p>
+
+<p align="center">
+  <strong>MNE-RT — Real-time M/EEG Signal Processing</strong><br>
+  From amplifier to 3-D brain display in a single, researcher-friendly API
+</p>
+
+<p align="center">
+  <a href="https://github.com/payamsash/mne-rt/blob/main/LICENSE"><img alt="License: MIT" src="https://img.shields.io/github/license/payamsash/mne-rt?color=green"></a>
+  <a href="https://pypi.org/project/mne-rt/"><img alt="PyPI" src="https://img.shields.io/pypi/v/mne-rt?color=blue"></a>
+  <a href="https://pypi.org/project/mne-rt/"><img alt="Python" src="https://img.shields.io/pypi/pyversions/mne-rt"></a>
+  <a href="https://payamsash.github.io/mne-rt/"><img alt="Docs" src="https://img.shields.io/badge/docs-online-brightgreen?logo=readthedocs&logoColor=white"></a>
+</p>
+
+---
+
+**MNE-RT** is an open-source Python library for **real-time M/EEG signal
+processing**, built on [MNE-Python](https://mne.tools) and
+[MNE-LSL](https://mne.tools/mne-lsl). It covers the full closed-loop pipeline —
+from amplifier to 3-D brain display — in a single API designed for neurofeedback,
+BCI, and clinical or basic-science monitoring.
+
+## Highlights
+
+| Feature | Details |
+|---|---|
+| **20 NF modalities** | Band power, ERD/ERS, laterality, Hjorth, spectral centroid, CFC, connectivity, graph Laplacian — sensor and source space |
+| **10 adaptive protocols** | Z-score, threshold, percentile, staircase, operant, RL, sham, multi-band, and cross-session transfer |
+| **5 artifact correction methods** | ASR, adaptive LMS, GEDAI, ORICA, real-time Maxwell/SSS (MEG) |
+| **9 live visualisation windows** | Scrolling raw · NF signal · epoch overlays · scalp topo · 3-D brain · butterfly · ERP comparison · TFR heatmaps |
+| **Feature combiners** | Weighted sum, geometric mean, z-scored norm, or any sklearn estimator |
+| **External feedback output** | OSC (Max/MSP, SuperCollider) and LSL outlet (PsychoPy, OpenViBE, BCI2000) |
+| **BIDS-compatible saving** | Session JSON + TSV with full metadata, artifact rate, and SNR |
+| **CLI** | `mne-rt info` · `mne-rt demo` · `mne-rt baseline` · `mne-rt run` |
+| **Mock mode** | Full pipeline without hardware via built-in LSL replay |
+
+## Installation
+
+```bash
+pip install mne-rt                 # core package
+pip install "mne-rt[full]"         # + 3-D viz, dev tools, docs
+```
+
+<details>
+<summary>Other installation methods</summary>
+
+**uv (fast Rust-based installer):**
+```bash
+uv pip install mne-rt
+uv pip install "mne-rt[full]"
+```
+
+**Development install from source:**
+```bash
+git clone https://github.com/payamsash/mne-rt.git
+cd mne-rt
+pip install -e ".[dev]"
+```
+
+</details>
+
+Verify:
+```bash
+mne-rt info     # prints MNE-RT and dependency versions
+mne-rt demo     # runs a 60-second mock neurofeedback session
+```
+
+## Quick start
+
+```python
+from mne_rt import RTStream
+from mne_rt.protocols import ZScoreProtocol
+
+# 1 — Create a session object
+nf = RTStream(
+    subject_id="sub01",
+    session="01",
+    subjects_dir="/data/subjects",
+    montage="easycap-M1",
+)
+
+# 2 — Connect to a live LSL stream (or replay a file without hardware)
+nf.connect_to_lsl(mock_lsl=True)
+
+# 3 — Record a resting-state baseline (bad channels, ICA, noise cov)
+nf.record_baseline(duration=120)
+
+# 4 — Run a closed-loop NF session
+nf.record_main(
+    duration=300,
+    modality=["sensor_power", "erd_ers"],
+    protocol=ZScoreProtocol(direction="up", zscore_threshold=0.5),
+    show_nf_signal=True,
+    show_topo=True,
+)
+
+# 5 — Save results (BIDS-compatible JSON + TSV)
+nf.save()
+```
+
+## CLI
+
+```bash
+# Print version and all dependency versions
+mne-rt info
+
+# Quick demo — no amplifier needed
+mne-rt demo --duration 60 --modality sensor_power erd_ers
+
+# Record a resting-state baseline
+mne-rt baseline --subject sub01 --subjects-dir /data --session 01
+
+# Run a full session with artifact correction and live displays
+mne-rt run --subject sub01 --subjects-dir /data --duration 600 \
+           --modality sensor_power erd_ers \
+           --artifact-correction asr \
+           --topo --brain
+```
+
+## Documentation
+
+Full documentation (API reference, tutorials, visualization gallery) is available at
+**[payamsash.github.io/mne-rt](https://payamsash.github.io/mne-rt/)**.
+
+## Cite
+
+If you use MNE-RT in your research, please cite:
+
+```bibtex
+@inproceedings{shabestari2025advances,
+  title        = {Advances on Real Time {M/EEG} Neural Feature Extraction},
+  author       = {Shabestari, Payam S and Ribes, Delphine and D{\'e}fayes, Lara
+                  and Cai, Danpeng and Groves, Emily and Behjat, Harry H
+                  and Van de Ville, Dimitri and Kleinjung, Tobias
+                  and Naas, Adrian and Henchoz, Nicolas and others},
+  booktitle    = {2025 IEEE 38th International Symposium on Computer-Based
+                  Medical Systems (CBMS)},
+  pages        = {337--338},
+  year         = {2025},
+  organization = {IEEE}
+}
+```
+
+## Acknowledgements
+
+Development was supported by the
+[Swiss National Science Foundation](https://www.snf.ch/en) (grant 208164 —
+*Advancing Neurofeedback in Tinnitus*).
+
+## License
+
+[MIT License](LICENSE) — © 2025 Payam S. Shabestari