bex-bioacoustics 1.0.0__tar.gz

bex_bioacoustics-1.0.0/.gitignore

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+# Local config (copy bex.example.toml -> bex.toml)
+bex.toml
+
+# Hot-tier data — regenerable, never committed
+store/
+cache/
+
+# Virtual environments (app env here; runner envs under envs/*/)
+.venv/
+envs/*/.venv/
+
+# Data that must never land in the repo (PLAN.md §8 rule 4)
+data/audio
+*.flac
+*.wav
+*.mp3
+
+# Python
+__pycache__/
+*.egg-info/
+.pytest_cache/
+
+# uv lockfile: the documented install is pip; a stale lock would mislead
+uv.lock

bex_bioacoustics-1.0.0/.streamlit/config.toml

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+# BEX theme: the brand's petrol teal as the accent colour (buttons, sliders,
+# selected options, tags). The dark theme uses a slightly lighter teal, still
+# deep enough for white text on it to stay legible (4.1:1). The palette is
+# described in V1.md (HM1); ui/common.py (BRAND) holds the logo colours.
+[theme.light]
+primaryColor = "#3e6a6b"
+
+[theme.dark]
+primaryColor = "#4f868c"

bex_bioacoustics-1.0.0/LICENSE

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bex_bioacoustics-1.0.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: bex-bioacoustics
+Version: 1.0.0
+Summary: BEX, the Bioacoustics Explorer: benchmark bioacoustic ID models on your own recordings, with the geographic filter made visible
+Project-URL: Homepage, https://github.com/donora/bex
+Project-URL: Source, https://github.com/donora/bex
+Project-URL: Issues, https://github.com/donora/bex/issues
+Author-email: Mara Donora <mara.donora@gmail.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: benchmark,bioacoustics,bird song,birdnet,ecology,passive acoustic monitoring,perch
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.12
+Requires-Dist: altair>=5.0
+Requires-Dist: audioread>=3.0
+Requires-Dist: librosa>=0.10
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas>=2.0
+Requires-Dist: polars>=1.0
+Requires-Dist: pyarrow>=15.0
+Requires-Dist: soundfile>=0.12
+Requires-Dist: streamlit-image-coordinates>=0.4
+Requires-Dist: streamlit>=1.63
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# BEX — Bioacoustics Explorer
+
+**Benchmark and compare bioacoustic identification models on your own recordings.**
+
+Every bioacoustic project makes processing decisions: which model to process the data, which confidence
+threshold, whether to trust the model's location filter, etc. BEX runs your recordings
+through several models (currently BirdNET and Perch - can also add your own models), scores each against the same
+ground truth, and helps you design and quantify on a pipeline with a known precision and recall
+for every species. It also makes **the geographic filter visible**: what each model
+predicted before its location prior silenced it, and how often that filter hides a
+bird that was really there.
+
+BEX is a local app (Streamlit) plus a command line. It processes local audio.
+
+## What's in the app
+
+- **Explorer** — one recording at a time: a navigator over the whole recording
+  (where each model was right, wrong, or silent), the spectrogram with the
+  annotators' boxes, a score lane per model, an audio player on the same time axis,
+  and a window inspector.
+- **Compare models** — what each model would give you at your threshold rule: how
+  often it is right when it reports a bird, how many songs it finds, false
+  detections per hour, precision–recall, and species by species.
+- **Species scorecard** — one bird at a time: what each model found and missed,
+  on which recordings, and what it confuses the bird with.
+- **Geofilter forensics** — what a location filter hides, what that costs each
+  model in precision and recall, and which birds it suppresses most.
+- **Thresholds** — every model's threshold for every species, fitted by a rule
+  (e.g. "95% precision"), overridable by hand, and saved as named sets you can
+  apply to recordings that have no annotations.
+
+The sidebar holds the experiment's settings (dataset, models, plausibility
+profile, threshold rule) and keeps them as you move between pages.
+
+- **NB** - This app can ingest the Sierra Nevada soundscape (open-source, labelled, 33x1hr recordings with expert birdsong labels) as a demonstration set. See below ('Scoring needs annotations') for instructions.
+
+## Install
+
+Python 3.12. Developed and tested on macOS (Apple silicon).
+
+```bash
+python3.12 -m venv .venv
+.venv/bin/pip install bex-bioacoustics
+```
+
+The package is `bex-bioacoustics`; the command and the Python import are `bex`.
+
+## Quick start with your own recordings
+
+**1. Make a project folder.** BEX keeps its working data (scores, spectrograms,
+threshold sets) here, and finds it again through the `bex.toml` it writes.
+
+```bash
+mkdir my-project && cd my-project
+bex init
+```
+
+**2. Scan a folder of recordings** (WAV, FLAC, MP3 or OGG; subfolders too). Files
+stay where they are. The location is what BirdNET's filter needs; recording times
+are read from AudioMoth-style filenames.
+
+```bash
+bex scan /path/to/recordings --name my-site --site "Glen Affric" --lat 57.25 --lon -4.92
+bex melcache my-site        # the spectrograms the Explorer draws (resumable)
+bex repair my-site          # only if some files will not decode
+```
+
+**3. Run the models.** Each model runs in its own environment, because BirdNET and
+Perch cannot share dependencies with each other or with the app. The runners live
+in this repository, so clone it once:
+
+```bash
+git clone https://github.com/donora/bex bex-src
+cd bex-src/envs/birdnet
+python3.12 -m venv .venv
+.venv/bin/pip install -r requirements.txt
+.venv/bin/pip install bex-bioacoustics --no-deps
+BEX_CONFIG=/path/to/my-project/bex.toml .venv/bin/python run.py --dataset my-site
+```
+
+Perch is the same in `envs/perch` (it needs TensorFlow, so expect a larger install
+and ~80 s per hour of audio against BirdNET's ~5 s). Model weights download on
+first run. See [envs/birdnet](envs/birdnet/) and [envs/perch](envs/perch/).
+
+**4. Open the app.**
+
+```bash
+bex app
+```
+
+### Scoring needs annotations
+
+Everything above works on unlabelled audio: you can explore every model's
+detections, and apply a saved threshold set. **However, comparing models against ground
+truth needs annotations**, and in this version the only importer is for the
+annotated Sierra Nevada soundscape set that BEX was built on (`bex ingest-sne`;
+point `audio_dir` and `labels_dir` in `bex.toml` at your copy). A general importer
+for your own annotations, and a labelling mode in the Explorer, are next on the
+roadmap.
+
+## Results so far
+
+On 33 h of strongly annotated Sierra Nevada soundscapes (56 species):
+
+| model | cmAP | micro AP |
+|---|---|---|
+| BirdNET 2.4 | **0.485** | **0.817** |
+| Perch v2 (sigmoid, float32) | 0.375 | 0.646 |
+| Perch v2 (softmax) | 0.363 | 0.646 |
+
+- **BirdNET's location filter mostly hides real birds here.** Of the detections
+  it suppresses, most were annotated in that very window; one abundant resident
+  (Fox Sparrow, just under the filter's occurrence cutoff) accounts for most of it.
+- **There is no single good threshold.** Reaching 95% precision takes a threshold
+  anywhere from 0.18 to 0.98 for BirdNET depending on the species, which is why
+  BEX thresholds species by species.
+- **Perch is far "muddier"** — many more species scoring confidently in the same
+  window, much of it between close relatives — while finding more of the
+  annotated species at a matched number of detections.
+
+Every number is reproducible headlessly (`scripts/evaluate.py`,
+`scripts/compare.py`, `scripts/forensics.py`) and re-derived from the raw score
+matrices by `scripts/crosscheck.py`. [PLAN.md](PLAN.md) has the full account,
+including two representation traps (softmax readout, float16 storage) that were
+distorting the comparison and how they were resolved.
+
+## Roadmap
+
+- **Label your own data in the Explorer** — minute-by-minute labelling with the
+  models' suggestions as a guide, signed-off chunks, and versioned label sets
+  (PLAN.md, Stage 6.5).
+- An importer for your own annotations.
+- More models: region-tuned classifiers, BirdNET custom classifiers, new Perch
+  releases.
+
+[PLAN.md](PLAN.md) is the design document (architecture, metric definitions,
+staged roadmap); [V1.md](V1.md) records how version 1 of the app was designed.
+
+## Licences
+
+BEX is Apache-2.0 (see [LICENSE](LICENSE)). It ships **no model weights and no
+audio**: you download the models yourself when you set up the runners, and their
+own licences apply to your use of them.
+
+- **BirdNET**'s model weights (including its location model) are
+  **CC BY-NC-SA 4.0: non-commercial use only.** Research, conservation and
+  personal use are fine; using BirdNET for paid work needs a commercial licence
+  from the BirdNET team.
+- **Perch** is Apache-2.0.
+- Xeno-Canto recordings BEX links to are licensed per recording by their recordists.
+
+## Development
+
+```bash
+git clone https://github.com/donora/bex && cd bex
+python3.12 -m venv .venv
+.venv/bin/pip install -e ".[dev]"
+.venv/bin/pytest            # runs without audio or models; app tests skip without a store
+bex app                     # or: .venv/bin/streamlit run app.py
+```
+
+```
+app.py        the app's entry point: page setup and navigation
+ui/           the app — sidebar.py (settings), common.py (shared), pages/ (one per page)
+bex/          the library — every number the app shows is computed here
+profiles/     plausibility profiles (bring your own — PLAN.md §3c)
+envs/         one isolated runner environment per model (PLAN.md §3b)
+scripts/      the headless versions of the app's analyses
+tests/        tests, runnable without audio, models, or the store
+```