deepextractor 0.1.0__tar.gz

deepextractor-0.1.0/.gitattributes

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+# Pretrained model weights are hosted on Hugging Face Hub (tomdooney/deepextractor).
+# They are downloaded automatically on first use and cached locally in pretrained/.
+# Do NOT track pretrained/ in git — add it to .gitignore instead.
+
+# Track bundled data assets with git-lfs
+assets/*.pkl            filter=lfs diff=lfs merge=lfs -text
+assets/cdvgan/**        filter=lfs diff=lfs merge=lfs -text
+
+# Strip notebook outputs automatically on commit
+*.ipynb filter=nbstripout

deepextractor-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # needed for setuptools-scm to read git tags
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Build distributions
+        run: |
+          pip install build
+          python -m build
+
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write  # required for Trusted Publisher (OIDC)
+    steps:
+      - name: Download build artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

deepextractor-0.1.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.pyo
+*.pyd
+.Python
+*.egg-info/
+dist/
+build/
+.eggs/
+*.egg
+*.whl
+
+# Virtual environments
+.venv/
+venv/
+env/
+.env
+
+# Setuptools-scm generated version file
+src/deepextractor/_version.py
+
+# Testing
+.coverage
+.pytest_cache/
+htmlcov/
+coverage.xml
+
+# Type checking
+.mypy_cache/
+
+# Linting
+.ruff_cache/
+
+# Jupyter
+notebooks/.ipynb_checkpoints/
+.ipynb_checkpoints/
+
+# Large generated data files — regenerate with the CLI scripts
+data/
+*.npy
+losses/
+evaluation/
+saved_predictions/
+
+# pretrained/ is a local cache for HuggingFace weights — do not commit
+pretrained/
+
+# Track bundled assets (scalers, cdvgan weights) via git-lfs (see .gitattributes)
+!assets/**
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+.DS_Store
+
+# Docs build
+docs/_build/
+docs/api/_autosummary/
+docs/notebooks/

deepextractor-0.1.0/.readthedocs.yaml

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+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  apt_packages:
+    - pandoc
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements: [docs]
+
+sphinx:
+  configuration: docs/conf.py

deepextractor-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0] - 2026-04-01
+
+### Added
+- Initial pip-installable package structure
+- `deepextractor.models` — U-Net 1D/2D, DnCNN 1D, Autoencoder 1D/2D architectures
+- `deepextractor.data` — PyTorch Dataset classes for time-series and spectrogram data
+- `deepextractor.training` — training loop and trainer CLI entry point
+- `deepextractor.generation` — synthetic glitch signal generators and data generation scripts
+- `deepextractor.evaluation` — simulated evaluation metrics
+- `deepextractor.utils` — checkpoints, signal processing, metrics, I/O, visualization
+- Sphinx documentation with Furo dark theme
+- CLI entry points: `deepextractor-train`, `deepextractor-generate`, `deepextractor-specgen`, `deepextractor-evaluate`
+- Pretrained checkpoint weights hosted on Hugging Face Hub, downloaded automatically on first use
+- Bundled GravitySpy O3a sample dataset (`assets/data_o3a_sample.csv`) — 170 high-confidence glitch examples across 17 classes
+- Jupyter notebook tutorials: minimal example, glitch reconstruction, training from scratch

deepextractor-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Tom Dooney
+
+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.

deepextractor-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: deepextractor
+Version: 0.1.0
+Summary: Deep learning framework for reconstructing gravitational wave signals and glitches from LIGO detector data
+Author: Tom Dooney
+License: MIT License
+        
+        Copyright (c) 2026 Tom Dooney
+        
+        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.
+        
+Project-URL: Repository, https://github.com/tomdooney95/deepextractor
+Project-URL: Documentation, https://deepextractor.readthedocs.io/
+Project-URL: Paper, https://link.aps.org/doi/10.1103/s91m-c2jw
+Keywords: gravitational-waves,LIGO,deep-learning,glitch,signal-processing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+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
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<2.0,>=1.26
+Requires-Dist: torch>=2.1
+Requires-Dist: matplotlib>=3.9
+Requires-Dist: scienceplots>=2.1
+Requires-Dist: pandas>=2.2
+Requires-Dist: tqdm>=4.67
+Requires-Dist: scikit-learn>=1.5
+Requires-Dist: gwpy>=3.0
+Requires-Dist: pycbc>=2.7
+Requires-Dist: scipy>=1.11
+Requires-Dist: huggingface_hub>=0.20
+Requires-Dist: bilby>=2.0
+Provides-Extra: generative
+Requires-Dist: tensorflow>=2.14; extra == "generative"
+Requires-Dist: gengli>=0.2; extra == "generative"
+Provides-Extra: dev
+Requires-Dist: pytest>=8; extra == "dev"
+Requires-Dist: pytest-cov>=5; extra == "dev"
+Requires-Dist: ruff>=0.4; extra == "dev"
+Requires-Dist: mypy>=1.10; extra == "dev"
+Requires-Dist: nbstripout>=0.7; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7; extra == "docs"
+Requires-Dist: sphinx-autoapi>=3; extra == "docs"
+Requires-Dist: furo>=2024.1.29; extra == "docs"
+Requires-Dist: myst-parser>=3; extra == "docs"
+Requires-Dist: nbsphinx>=0.9; extra == "docs"
+Requires-Dist: ipykernel; extra == "docs"
+Provides-Extra: all
+Requires-Dist: deepextractor[dev,docs,generative]; extra == "all"
+Dynamic: license-file
+
+# DeepExtractor
+
+Deep learning framework for reconstructing gravitational-wave signals and glitches from LIGO detector data.
+
+Built for LIGO's O3 observing run (Hanford and Livingston detectors). Described in the paper:
+
+> **Time-domain reconstruction of signals and glitches in gravitational wave data with deep learning**
+> Dooney, Narola, Bromuri, Curier, Van Den Broeck, Caudill, Tan — *Phys. Rev. D* 112, 044022 (2025)
+> [10.1103/s91m-c2jw](https://link.aps.org/doi/10.1103/s91m-c2jw)
+
+**[Documentation](https://deepextractor.readthedocs.io/)** | **[GitHub](https://github.com/tomdooney95/deepextractor)** | **[PyPI](https://pypi.org/project/deepextractor/)**
+
+---
+
+## How it works
+
+LIGO strain data contains both astrophysical signals and instrumental glitches — short-duration noise transients that can mimic or obscure gravitational-wave events. DeepExtractor frames glitch reconstruction as a supervised denoising problem:
+
+```
+Input:  h(t)  = background noise  +  glitch/signal
+Output: n̂(t)  = predicted background
+Result: ĝ(t)  = h(t) − n̂(t)   ← reconstructed glitch or signal
+```
+
+The model is a **U-Net** operating on STFT spectrograms (magnitude + phase). The default model, `DeepExtractor_257`, uses a 4-level U-Net with feature maps `[64, 128, 256, 512]`.
+
+---
+
+## Installation
+
+```bash
+pip install deepextractor
+```
+
+Requires Python ≥ 3.10 and PyTorch ≥ 2.1. Pretrained weights are downloaded automatically from Hugging Face Hub on first use — no manual step required.
+
+**Install from source:**
+
+```bash
+git clone https://github.com/tomdooney95/deepextractor.git
+cd deepextractor
+pip install -e ".[dev]"
+```
+
+---
+
+## Quickstart
+
+```python
+import numpy as np
+import deepextractor
+
+# Load model (bilby noise variant by default)
+model = deepextractor.DeepExtractorModel()
+
+# Reconstruct — extract the transient from noisy strain
+noisy_strain = np.random.randn(8192)             # replace with real data
+reconstructed = model.reconstruct(noisy_strain)  # extracted signal
+background    = model.background(noisy_strain)   # noise estimate
+
+# One-liner convenience function
+reconstructed = deepextractor.reconstruct(noisy_strain)
+```
+
+Two pretrained variants are available:
+
+| Variant | Use case |
+|---|---|
+| `bilby_noise` (default) | Simulated LIGO/Virgo noise, injection studies |
+| `real_noise` | Real LIGO O3 detector data |
+
+---
+
+## Bundled dataset
+
+The package ships a sample of the [GravitySpy LIGO O3a high-confidence catalogue](https://doi.org/10.5281/zenodo.1476551) at `assets/data_o3a_sample.csv` — 10 H1 examples per glitch class (17 classes, 170 rows total), SNR > 15.
+
+```python
+import pandas as pd
+import importlib.resources as resources
+
+with resources.path("deepextractor", "assets") as assets:
+    df = pd.read_csv(assets / "data_o3a_sample.csv")
+
+print(df["label"].value_counts())
+```
+
+---
+
+## CLI tools
+
+```bash
+# Train a model
+deepextractor-train --model DeepExtractor_257 --data-dir data/spectrogram_domain/
+
+# Generate training data
+deepextractor-generate --output-dir data/ --num-train 250000
+
+# Convert time-domain data to spectrograms
+deepextractor-specgen --input-dir data/time_domain/ --output-dir data/spectrogram_domain/
+
+# Evaluate a trained model
+deepextractor-evaluate --model DeepExtractor_257 --checkpoint-dir checkpoints/ --data-dir data/
+```
+
+---
+
+## Citation
+
+```bibtex
+@article{s91m-c2jw,
+  title     = {Time-domain reconstruction of signals and glitches in gravitational wave data with deep learning},
+  author    = {Dooney, Tom and Narola, Harsh and Bromuri, Stefano and Curier, R. Lyana and Van Den Broeck, Chris and Caudill, Sarah and Tan, Daniel Stanley},
+  journal   = {Phys. Rev. D},
+  volume    = {112},
+  issue     = {4},
+  pages     = {044022},
+  numpages  = {24},
+  year      = {2025},
+  month     = {Aug},
+  publisher = {American Physical Society},
+  doi       = {10.1103/s91m-c2jw},
+  url       = {https://link.aps.org/doi/10.1103/s91m-c2jw}
+}
+```

deepextractor-0.1.0/README.md

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+# DeepExtractor
+
+Deep learning framework for reconstructing gravitational-wave signals and glitches from LIGO detector data.
+
+Built for LIGO's O3 observing run (Hanford and Livingston detectors). Described in the paper:
+
+> **Time-domain reconstruction of signals and glitches in gravitational wave data with deep learning**
+> Dooney, Narola, Bromuri, Curier, Van Den Broeck, Caudill, Tan — *Phys. Rev. D* 112, 044022 (2025)
+> [10.1103/s91m-c2jw](https://link.aps.org/doi/10.1103/s91m-c2jw)
+
+**[Documentation](https://deepextractor.readthedocs.io/)** | **[GitHub](https://github.com/tomdooney95/deepextractor)** | **[PyPI](https://pypi.org/project/deepextractor/)**
+
+---
+
+## How it works
+
+LIGO strain data contains both astrophysical signals and instrumental glitches — short-duration noise transients that can mimic or obscure gravitational-wave events. DeepExtractor frames glitch reconstruction as a supervised denoising problem:
+
+```
+Input:  h(t)  = background noise  +  glitch/signal
+Output: n̂(t)  = predicted background
+Result: ĝ(t)  = h(t) − n̂(t)   ← reconstructed glitch or signal
+```
+
+The model is a **U-Net** operating on STFT spectrograms (magnitude + phase). The default model, `DeepExtractor_257`, uses a 4-level U-Net with feature maps `[64, 128, 256, 512]`.
+
+---
+
+## Installation
+
+```bash
+pip install deepextractor
+```
+
+Requires Python ≥ 3.10 and PyTorch ≥ 2.1. Pretrained weights are downloaded automatically from Hugging Face Hub on first use — no manual step required.
+
+**Install from source:**
+
+```bash
+git clone https://github.com/tomdooney95/deepextractor.git
+cd deepextractor
+pip install -e ".[dev]"
+```
+
+---
+
+## Quickstart
+
+```python
+import numpy as np
+import deepextractor
+
+# Load model (bilby noise variant by default)
+model = deepextractor.DeepExtractorModel()
+
+# Reconstruct — extract the transient from noisy strain
+noisy_strain = np.random.randn(8192)             # replace with real data
+reconstructed = model.reconstruct(noisy_strain)  # extracted signal
+background    = model.background(noisy_strain)   # noise estimate
+
+# One-liner convenience function
+reconstructed = deepextractor.reconstruct(noisy_strain)
+```
+
+Two pretrained variants are available:
+
+| Variant | Use case |
+|---|---|
+| `bilby_noise` (default) | Simulated LIGO/Virgo noise, injection studies |
+| `real_noise` | Real LIGO O3 detector data |
+
+---
+
+## Bundled dataset
+
+The package ships a sample of the [GravitySpy LIGO O3a high-confidence catalogue](https://doi.org/10.5281/zenodo.1476551) at `assets/data_o3a_sample.csv` — 10 H1 examples per glitch class (17 classes, 170 rows total), SNR > 15.
+
+```python
+import pandas as pd
+import importlib.resources as resources
+
+with resources.path("deepextractor", "assets") as assets:
+    df = pd.read_csv(assets / "data_o3a_sample.csv")
+
+print(df["label"].value_counts())
+```
+
+---
+
+## CLI tools
+
+```bash
+# Train a model
+deepextractor-train --model DeepExtractor_257 --data-dir data/spectrogram_domain/
+
+# Generate training data
+deepextractor-generate --output-dir data/ --num-train 250000
+
+# Convert time-domain data to spectrograms
+deepextractor-specgen --input-dir data/time_domain/ --output-dir data/spectrogram_domain/
+
+# Evaluate a trained model
+deepextractor-evaluate --model DeepExtractor_257 --checkpoint-dir checkpoints/ --data-dir data/
+```
+
+---
+
+## Citation
+
+```bibtex
+@article{s91m-c2jw,
+  title     = {Time-domain reconstruction of signals and glitches in gravitational wave data with deep learning},
+  author    = {Dooney, Tom and Narola, Harsh and Bromuri, Stefano and Curier, R. Lyana and Van Den Broeck, Chris and Caudill, Sarah and Tan, Daniel Stanley},
+  journal   = {Phys. Rev. D},
+  volume    = {112},
+  issue     = {4},
+  pages     = {044022},
+  numpages  = {24},
+  year      = {2025},
+  month     = {Aug},
+  publisher = {American Physical Society},
+  doi       = {10.1103/s91m-c2jw},
+  url       = {https://link.aps.org/doi/10.1103/s91m-c2jw}
+}
+```

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