accusleepy 0.6.0__py3-none-any.whl

accusleepy-0.6.0.dist-info/METADATA

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+Metadata-Version: 2.3
+Name: accusleepy
+Version: 0.6.0
+Summary: Python implementation of AccuSleep
+License: GPL-3.0-only
+Author: Zeke Barger
+Author-email: zekebarger@gmail.com
+Requires-Python: >=3.11,<3.14
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: fastparquet (>=2024.11.0,<2025.0.0)
+Requires-Dist: joblib (>=1.4.2,<2.0.0)
+Requires-Dist: matplotlib (>=3.10.1,<4.0.0)
+Requires-Dist: numpy (>=2.2.4,<3.0.0)
+Requires-Dist: pandas (>=2.2.3,<3.0.0)
+Requires-Dist: pillow (>=11.1.0,<12.0.0)
+Requires-Dist: pre-commit (>=4.2.0,<5.0.0)
+Requires-Dist: pyside6 (>=6.9.0,<7.0.0)
+Requires-Dist: scipy (>=1.15.2,<2.0.0)
+Requires-Dist: toml (>=0.10.2,<0.11.0)
+Requires-Dist: torch (>=2.6.0,<3.0.0)
+Requires-Dist: torchvision (>=0.21.0,<0.22.0)
+Requires-Dist: tqdm (>=4.67.1,<5.0.0)
+Description-Content-Type: text/markdown
+
+# AccuSleePy
+
+## Description
+
+AccuSleePy is set of graphical user  interfaces for scoring rodent sleep
+using EEG and EMG recordings.
+It offers the following improvements over the MATLAB version (AccuSleep):
+
+- Up to 10 brain states can be configured through the user interface
+- Classification models can be trained through the user interface
+    - Model files contain useful metadata (brain state configuration,
+      epoch length, number of epochs)
+    - Models optimized for real-time scoring can be trained
+- Lists of recordings can be imported and exported for repeatable batch processing
+- Undo/redo functionality in the manual scoring interface
+
+If you use AccuSleep in your research, please cite our
+[publication](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224642):
+
+Barger, Z., Frye, C. G., Liu, D., Dan, Y., & Bouchard, K. E. (2019). Robust, automated sleep scoring by a compact neural network with distributional shift correction. *PLOS ONE, 14*(12), 1–18.
+
+The data and models associated with AccuSleep are available at https://osf.io/py5eb/
+
+Please contact zekebarger (at) gmail (dot) com with any questions or comments about the software.
+
+
+## Installation
+
+- (recommended) create a new virtual environment (using
+[venv](https://docs.python.org/3/library/venv.html),
+[conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html),
+etc.) with python >=3.11,<3.14
+- (optional) if you have a CUDA device and want to speed up model training, [install PyTorch](https://pytorch.org/)
+- `pip install accusleepy`
+- (optional) download a classification model from https://osf.io/py5eb/ under /python_format/models/
+
+Note that upgrading or reinstalling the package will overwrite any changes
+to the [config file](accusleepy/config.json).
+
+## Usage
+
+`python -m accusleepy` will open the primary interface.
+
+[Guide to the primary interface](accusleepy/gui/text/main_guide.md)
+
+[Guide to the manual scoring interface](accusleepy/gui/text/manual_scoring_guide.md)
+
+## Changelog
+
+- 0.6.0: Confidence scores can now be displayed and saved. Retraining your models is recommended
+    since the new calibration feature will make the confidence scores more accurate.
+- 0.5.0: Performance improvements
+- 0.4.5: Added support for python 3.13, **removed support for python 3.10.**
+- 0.4.4: Performance improvements
+- 0.4.3: Improved unit tests and user manuals
+- 0.4.0: Improved visuals and user manuals
+- 0.1.0-0.3.1: Early development versions
+
+## Screenshots
+
+Primary interface
+![AccuSleePy primary interface](accusleepy/gui/images/primary_window.png)
+
+Manual scoring interface
+![AccuSleePy manual scoring interface](accusleepy/gui/images/viewer_window.png)
+
+## Acknowledgements
+
+We would like to thank [Franz Weber](https://www.med.upenn.edu/weberlab/) for creating an
+early version of the manual labeling interface. The code that
+creates spectrograms comes from the
+[Prerau lab](https://github.com/preraulab/multitaper_toolbox/blob/master/python/multitaper_spectrogram_python.py)
+with only minor modifications.
+Jim Bohnslav's [deepethogram](https://github.com/jbohnslav/deepethogram) served as an
+incredibly useful reference when reimplementing this project in python.
+The model calibration code added in version 0.6.0 comes from Geoff Pleiss'
+[temperature scaling repo](https://github.com/gpleiss/temperature_scaling).
+

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accusleepy-0.6.0.dist-info/WHEEL

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