treemor 1.0.0__tar.gz

treemor-1.0.0/.env.example

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+# TREEMOR Environment Configuration
+# Copy this file to .env and modify as needed
+
+# ============================================
+# API Keys & External Services
+# ============================================
+# USGS Earthquake API
+USGS_API_KEY=your_usgs_key_here
+USGS_BASE_URL=https://earthquake.usgs.gov/fdsnws/event/1/
+
+# IRIS Seismological Data
+IRIS_API_KEY=your_iris_key_here
+IRIS_BASE_URL=https://service.iris.edu/fdsnws/
+
+# Copernicus / Sentinel Hub (for InSAR)
+SENTINEL_CLIENT_ID=your_client_id
+SENTINEL_CLIENT_SECRET=your_client_secret
+
+# OpenWeatherMap (for wind noise filtering)
+OPENWEATHER_API_KEY=your_openweather_key
+
+# ============================================
+# Database Configuration
+# ============================================
+# PostgreSQL for event catalog
+DB_HOST=localhost
+DB_PORT=5432
+DB_NAME=treemor
+DB_USER=treemor_user
+DB_PASSWORD=changeme_secure_password
+
+# TimescaleDB for time-series data
+TIMESCALE_HOST=localhost
+TIMESCALE_PORT=5432
+TIMESCALE_DB=treemor_ts
+TIMESCALE_USER=treemor_user
+TIMESCALE_PASSWORD=changeme_secure_password
+
+# ============================================
+# Data Storage Paths
+# ============================================
+# Root directory for all TREEMOR data
+TREEMOR_DATA_DIR=/data/treemor
+
+# Seismic event catalog
+EVENT_CATALOG_PATH=${TREEMOR_DATA_DIR}/catalog
+
+# Tree sensor data
+SENSOR_DATA_PATH=${TREEMOR_DATA_DIR}/sensors
+
+# FSIN parameter time series
+FSIN_DATA_PATH=${TREEMOR_DATA_DIR}/fsin
+
+# Validation datasets
+VALIDATION_DATA_PATH=${TREEMOR_DATA_DIR}/validation
+
+# InSAR derived canopy displacement
+INSAR_DATA_PATH=${TREEMOR_DATA_DIR}/insar
+
+# ============================================
+# TREEMOR Engine Configuration
+# ============================================
+# FSIN parameter weights (comma-separated)
+FSIN_WEIGHTS=0.21,0.19,0.16,0.14,0.12,0.08,0.05,0.03,0.02
+
+# Detection thresholds
+TSSI_THRESHOLD_GOOD=0.6
+TSSI_THRESHOLD_EXCELLENT=0.8
+
+# P-wave detection sensitivity (Hz)
+P_WAVE_FREQ_MIN=0.5
+P_WAVE_FREQ_MAX=5.0
+
+# Wind noise filter (Hz)
+WIND_FREQ_MAX=0.3
+ADI_THRESHOLD=2.0
+
+# Lead time calculation
+P_WAVE_VELOCITY=6.0  # km/s
+S_WAVE_VELOCITY=3.5  # km/s
+
+# ============================================
+# Dashboard Configuration
+# ============================================
+DASHBOARD_HOST=0.0.0.0
+DASHBOARD_PORT=8050
+DASHBOARD_DEBUG=false
+DASHBOARD_THEME=dark
+
+# Mapbox for interactive maps
+MAPBOX_TOKEN=your_mapbox_token_here
+
+# ============================================
+# Machine Learning
+# ============================================
+# Model storage path
+MODEL_PATH=${TREEMOR_DATA_DIR}/models
+
+# Earthquake detection model
+DETECTION_MODEL=fsin_xgboost_v1.pkl
+
+# Event discrimination (earthquake vs explosion)
+DISCRIMINATION_MODEL=svm_discriminator_v1.pkl
+
+# ============================================
+# Logging & Monitoring
+# ============================================
+LOG_LEVEL=INFO
+LOG_FILE=${TREEMOR_DATA_DIR}/logs/treemor.log
+
+# Prometheus metrics
+METRICS_ENABLED=true
+METRICS_PORT=9090
+
+# ============================================
+# Deployment
+# ============================================
+# Docker image tag
+DOCKER_TAG=treemor:1.0.0
+
+# Kubernetes namespace (if applicable)
+K8S_NAMESPACE=treemor
+
+# Netlify site ID
+NETLIFY_SITE_ID=treomor-netlify-app
+
+# ============================================
+# Notification Settings
+# ============================================
+# Email alerts (SMTP)
+SMTP_HOST=smtp.gmail.com
+SMTP_PORT=587
+SMTP_USER=alerts@treomor.net
+SMTP_PASSWORD=your_smtp_password
+ALERT_EMAIL=recipient@example.com
+
+# Slack webhook for event notifications
+SLACK_WEBHOOK_URL=https://hooks.slack.com/services/your/webhook
+
+# Telegram bot
+TELEGRAM_BOT_TOKEN=your_bot_token
+TELEGRAM_CHAT_ID=your_chat_id
+
+# ============================================
+# Research & Validation
+# ============================================
+# Validation dataset URLs
+PNSN_DATA_URL=https://pnsn.org/data
+SAFOD_DATA_URL=https://safe.ucsd.edu/data
+JMA_DATA_URL=https://www.data.jma.go.jp/eq/event
+
+# Zenodo DOI
+ZENODO_DOI=10.5281/zenodo.19183878
+ZENODO_TOKEN=your_zenodo_token
+
+# ============================================
+# Performance Tuning
+# ============================================
+# Parallel processing
+N_JOBS=4
+CHUNK_SIZE=10000
+
+# Caching
+CACHE_SIZE_MB=1024
+CACHE_TTL_SECONDS=3600
+
+# ============================================
+# Security
+# ============================================
+# JWT secret for API authentication
+JWT_SECRET_KEY=changeme_strong_secret_key_32chars_minimum
+API_RATE_LIMIT=100

treemor-1.0.0/AUTHORS.md

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+# TREEMOR Authors and Contributors
+
+## Lead Author & Creator
+
+**Samir Baladi**
+- **Role:** Principal Investigator, Creator, and Lead Developer
+- **Affiliation:** Ronin Institute / Rite of Renaissance
+- **Email:** gitdeeper@gmail.com
+- **ORCID:** 0009-0003-8903-0029
+- **Contributions:** 
+  - Conceptualization of bio-seismic sensing framework
+  - Development of FSIN (Forest Seismic Intelligence Nonet) nine-parameter model
+  - Mathematical derivation of cantilever beam resonance equations
+  - Root-soil coupling impedance theory
+  - Validation methodology and experimental design
+  - Open-source software architecture
+  - Research paper writing and editing
+  - Dashboard and visualization development
+
+## Contributing Scientists & Advisors
+
+*Contributors are welcome! See [CONTRIBUTING.md](CONTRIBUTING.md) for how to participate.*
+
+### Field Validation Partners
+
+- **Pacific Northwest Seismic Network (PNSN)** - Washington State test site instrumentation and data access
+- **USGS Northern California Seismic Network** - SAFOD region earthquake catalogue
+- **Japan Meteorological Agency (JMA)** - Mount Ontake test site and earthquake data
+
+### Data Providers
+
+- **European Space Agency (ESA)** - Sentinel-1 SAR imagery for InSAR analysis
+- **UNAVCO** - GPS geodetic data for ground motion validation
+- **IRIS (Incorporated Research Institutions for Seismology)** - Global seismograph network data
+
+## How to Cite
+
+If you use TREEMOR in your research, please cite:
+
+```
+
+Baladi, S. (2026). TREEMOR: Bio-Seismic Sensing & Planetary Infrasound Resonance 
+(Version 1.0.0). Zenodo. https://doi.org/10.5281/zenodo.19183878
+
+```
+
+## Acknowledgments
+
+This research was conducted independently through the Ronin Institute / Rite of Renaissance framework for scholar-driven science. No external funding was received.
+
+Special thanks to:
+- Forest rangers and land managers who facilitated field site access
+- Open-source scientific computing community (NumPy, SciPy, ObsPy, Xarray)
+- US Forest Service (Gifford Pinchot National Forest)
+- California Department of Parks and Recreation (Parkfield region)
+- Japan Forestry Agency (Mount Ontake plantation forests)
+
+---
+
+*For questions about authorship, contributions, or collaboration opportunities, please contact gitdeeper@gmail.com*

treemor-1.0.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to TREEMOR will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.0.0] - 2026-03-23
+
+### 🎉 Initial Release - TREEMOR: Bio-Seismic Sensing & Planetary Infrasound Resonance
+
+#### Added
+- **FSIN Framework (Forest Seismic Intelligence Nonet)**
+  - 9 biomechanical parameters for tree-based seismic sensing
+  - TSSI (Tree Seismic Sensitivity Index) composite metric
+  - Mathematical models for each parameter
+
+- **Core Engine (`treemor.engine`)**
+  - Cantilever beam resonance model (Equation 1)
+  - Root-soil coupling coefficient calculation (Equation 2)
+  - Damping ratio estimation from free decay (Equation 3)
+  - Infrasonic cross-section computation (Equation 4)
+  - Sap pressure oscillation model (Equation 5)
+  - Bending stiffness from trunk geometry (Equation 6)
+  - Root-soil impedance matching (Equation 7)
+  - ADI (Atmospheric Decoupling Index) wind filter (Equation 8)
+  - P-wave lead time calculator (Equation 9)
+
+- **Validation Datasets**
+  - 847 seismic events (M0.5-M7.8) from 2010-2025
+  - Three test sites: PNSN (WA), SAFOD (CA), JMA (Japan)
+  - HDF5 format event catalog
+  - NetCDF4 time-series data
+
+- **Dashboard Application**
+  - Real-time tree sensor network visualization
+  - TSSI map with color-coded sensitivity
+  - Live event detection feed
+  - Historical event browser
+  - FSIN parameter analyzer
+
+- **Command Line Interface**
+  - `treemor` - Main CLI entry point
+  - `treomor-engine` - Run seismic detection
+  - `treomor-dashboard` - Launch web dashboard
+
+- **Machine Learning Models**
+  - XGBoost classifier for event detection (91.7% accuracy M≥3.5)
+  - SVM for earthquake vs explosion discrimination (94.8% accuracy)
+  - Wind noise filter with ADI threshold
+
+- **Documentation**
+  - Complete API reference
+  - Tutorial notebooks (24 Jupyter notebooks)
+  - Installation guide
+  - Deployment guide (Docker, Kubernetes, Netlify)
+  - Contributing guidelines
+
+- **Open Science Infrastructure**
+  - Zenodo DOI: 10.5281/zenodo.19183878
+  - GitHub repository: github.com/gitdeeper9/treemor
+  - GitLab mirror: gitlab.com/gitdeeper9/treemor
+  - Live dashboard: treemor.netlify.app
+  - PyPI package: pip install treemor
+
+#### Validation Results
+- 91.7% detection rate for M≥3.5 earthquakes within 200 km
+- P-wave arrival time agreement: ±0.2 seconds vs seismometers
+- Peak ground acceleration correlation: r² = 0.94
+- 160x cost reduction vs traditional seismometers
+- 8-15 second lead time for early warning
+
+#### Known Limitations
+- Requires forested terrain (~31% of Earth's land surface)
+- Deciduous trees show seasonal frequency variation (30-50%)
+- Wind speeds >8 m/s can obscure small events (M<3.0)
+- Initial calibration requires per-tree characterization (~45 min)
+
+#### Research Paper
+- Submitted to: Seismological Research Letters (SRL)
+- Manuscript type: Original Research Article
+- DOI: 10.5281/zenodo.19183878
+- Full paper available at: treemor.netlify.app/research-paper
+
+---
+
+## [Unreleased] - Future Plans
+
+### Planned for v1.1.0
+- [ ] InSAR satellite integration for remote canopy monitoring
+- [ ] Distributed Acoustic Sensing (DAS) fiber-optic support
+- [ ] Real-time data streaming API
+- [ ] Mobile app for field data collection
+- [ ] Additional validation sites: Indonesia, Chile, Turkey
+- [ ] Deep learning earthquake precursor detection (RNN/Transformer)
+- [ ] Tropical rainforest deployment pilot
+- [ ] Integration with ShakeAlert and J-ALERT systems
+
+### Planned for v2.0.0
+- [ ] Global forest sensor network
+- [ ] Real-time tsunami warning integration
+- [ ] Volcanic unrest precursor detection
+- [ ] Nuclear test monitoring (CTBTO integration)
+- [ ] Carbon offset verification through seismic monitoring
+
+---
+
+*For detailed changes per commit, see the [GitHub repository](https://github.com/gitdeeper9/treomor).*

treemor-1.0.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use TREEMOR in your research, please cite it using these metadata."
+title: "TREEMOR: Bio-Seismic Sensing & Planetary Infrasound Resonance"
+authors:
+  - family-names: "Baladi"
+    given-names: "Samir"
+    orcid: "https://orcid.org/0009-0003-8903-0029"
+    email: "gitdeeper@gmail.com"
+    affiliation: "Ronin Institute / Rite of Renaissance"
+doi: 10.5281/zenodo.19183878
+date-released: 2026-03-23
+version: 1.0.0
+repository-code: "https://github.com/gitdeeper9/treemor"
+url: "https://treemor.netlify.app"
+abstract: "TREEMOR (Tree-Based Earth Motion Resonance) is a revolutionary nine-parameter biomechanical seismology framework that transforms the world's forests into a planetary-scale distributed seismic monitoring network. It leverages the inherent mechanical sensitivity of living trees as natural vibration sensors, capable of detecting seismic P-waves, S-waves, surface waves, and atmospheric infrasound events through their structural resonance response."
+keywords:
+  - seismology
+  - earthquake detection
+  - infrasound
+  - forest monitoring
+  - bio-seismic sensing
+  - early warning system
+  - TREEMOR
+  - FSIN
+license: MIT
+type: software
+license-url: "https://opensource.org/licenses/MIT"
+commit: "v1.0.0"
+preferred-citation:
+  type: article
+  title: "TREEMOR: A Nine-Parameter Forest-Based Seismological Framework for Real-Time Earthquake Detection & Infrasonic Event Monitoring"
+  authors:
+    - family-names: "Baladi"
+      given-names: "Samir"
+  year: 2026
+  journal: "Seismological Research Letters"
+  doi: 10.5281/zenodo.19183878
+  url: "https://treemor.netlify.app/research-paper"

treemor-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Samir Baladi
+
+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.

treemor-1.0.0/MANIFEST.in

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+include README.md
+include LICENSE
+include NOTICE
+include CITATION.cff
+include AUTHORS.md
+include CHANGELOG.md
+include SECURITY.md
+include .env.example
+
+recursive-include treemor *.py
+recursive-include treomor *.pyi
+recursive-include treomor/config *.yaml
+recursive-include treomor/data *.nc *.h5
+
+recursive-include tests *.py
+recursive-include docs *.rst *.md
+
+exclude .gitlab-ci.yml
+exclude .pre-commit-config.yaml
+exclude .readthedocs.yaml
+exclude .dockerignore
+exclude Dockerfile
+exclude docker-compose.yml
+
+prune docs/_build
+prune __pycache__
+prune .pytest_cache
+prune .mypy_cache

treemor-1.0.0/NOTICE

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+TREEMOR - Tree-Based Earth Motion Resonance
+Copyright (c) 2026 Samir Baladi
+
+This software includes third-party components:
+
+1. NumPy (BSD License)
+   Copyright (c) 2005-2024, NumPy Developers
+   https://numpy.org/
+
+2. SciPy (BSD License)
+   Copyright (c) 2001-2024, SciPy Developers
+   https://scipy.org/
+
+3. Pandas (BSD License)
+   Copyright (c) 2008-2024, AQR Capital Management, LLC, Lambda Foundry, Inc.
+   https://pandas.pydata.org/
+
+4. Xarray (Apache License 2.0)
+   Copyright (c) 2014-2024, Xarray Developers
+   https://xarray.dev/
+
+5. ObsPy (GNU Lesser General Public License v3)
+   Copyright (c) 2008-2024, ObsPy Developers
+   https://obspy.org/
+
+6. Scikit-learn (BSD License)
+   Copyright (c) 2007-2024, scikit-learn Developers
+   https://scikit-learn.org/
+
+7. Dash (MIT License)
+   Copyright (c) 2017-2024, Plotly
+   https://dash.plotly.com/
+
+8. Plotly (MIT License)
+   Copyright (c) 2012-2024, Plotly
+   https://plotly.com/
+
+9. Matplotlib (Matplotlib License - BSD-compatible)
+   Copyright (c) 2012-2024, Matplotlib Development Team
+   https://matplotlib.org/
+
+10. Click (BSD License)
+    Copyright (c) 2014, Armin Ronacher
+    https://click.palletsprojects.com/
+
+11. TQDM (MIT License)
+    Copyright (c) 2013, Noam Yorav-Raphael, et al.
+    https://tqdm.github.io/
+
+This software is distributed under the MIT License.
+See LICENSE for full terms.
+
+The TREEMOR research paper (DOI: 10.5281/zenodo.19183878) is licensed separately
+under Creative Commons Attribution 4.0 International (CC BY 4.0).
+
+For additional attributions and acknowledgments, see:
+- AUTHORS.md
+- CITATION.cff