batbot 0.1.2__tar.gz

batbot-0.1.2/CHANGELOG.rst

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+=========
+Changelog
+=========
+
+TODO
+----
+
+* Make PyPI
+* Make Readthedocs
+* Make Huggingface
+* Reset git history
+* Fix CI/CD
+* Add example Colab notebooks
+* Port over spectrogram and model inference code from BatAI
+* Update tests
+* Update documentation
+
+Version 0.0.1
+-------------
+
+New Version

batbot-0.1.2/ISSUES.rst

@@ -0,0 +1,10 @@
+============
+Known Issues
+============
+
+TODO:
+- Fix CI/CD docker build
+- Add API documentation, tutorials, and examples
+- Create example notebooks with Google colab
+- Crate discord / discourse community board
+- [BatAI] Upload training scripts with MLFlow support, database export with celery

batbot-0.1.2/LICENSE

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batbot-0.1.2/MANIFEST.in

@@ -0,0 +1,8 @@
+# Include the README and SECURITY documents
+include *.rst
+
+# Include the license file
+include LICENSE
+
+# Include examples files for testing
+include examples/example1.wav

batbot-0.1.2/PKG-INFO

@@ -0,0 +1,352 @@
+Metadata-Version: 2.4
+Name: batbot
+Version: 0.1.2
+Summary: Machine Learning app for the Kitware BatAI Project
+Home-page: https://github.com/Kitware
+Author: Kitware
+Author-email: vision@kitware.com
+License: MIT
+Project-URL: Documentation, https://batbot.readthedocs.io
+Project-URL: Source, https://github.com/Kitware
+Requires-Python: >=3.7
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: cryptography
+Requires-Dist: cython
+Requires-Dist: librosa
+Requires-Dist: line_profiler
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: opencv-python-headless
+Requires-Dist: Pillow
+Requires-Dist: pooch
+Requires-Dist: pyastar2d>=1.1.1
+Requires-Dist: rich
+Requires-Dist: scikit-image
+Requires-Dist: shapely
+Requires-Dist: sphinx-click
+Requires-Dist: tqdm
+Provides-Extra: test
+Requires-Dist: pytest>=6.2.2; extra == "test"
+Requires-Dist: pycodestyle; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: all
+Requires-Dist: pytest>=6.2.2; extra == "all"
+Requires-Dist: pycodestyle; extra == "all"
+Requires-Dist: pytest-cov; extra == "all"
+Dynamic: license-file
+
+Kitware BatBot
+==============
+
+|Tests| |Codecov| |Wheel| |Docker| |ReadTheDocs|
+
+.. image:: https://github.com/Kitware/batbot/raw/main/assets/logo.png
+   :alt: Batbot
+   :align: center
+
+.. contents:: Quick Links
+    :backlinks: none
+
+.. sectnum::
+
+Development Environment
+-----------------------
+
+.. code-block:: bash
+
+    # Find repo on host machine
+    cd ~/code/batbot
+
+    # Build Docker image
+    docker build -t kitware/batbot:latest .
+
+    # Start Docker container using image
+    docker run \
+       -it \
+       --rm \
+       --entrypoint bash \
+       --name batbot \
+       -v $(pwd):/code \
+       kitware/batbot:latest
+
+    ########################
+    # Inside the container #
+    ########################
+
+    # Activate Python environment
+    source /venv/bin/activate
+
+    # Install local version
+    pip install -e .
+
+    # Run batbot
+    batbot --help
+
+Spectrogram Extraction
+----------------------
+
+Here are the steps for extracting the compressed spectrogram:
+
+* Create the STFT
+
+  * Load the original waveform at the original sample rate
+  * Resample waveform to 250kHz
+  * Convert to a STFT spectrogram (fft=512, method=blackmanharris, window=256, hop=16)
+  * Convert complex power STFT to amplitude STFT (dB)
+
+* Normalize the STFT
+
+  * Trim STFT to minimum and maximum frequencies (5kHz to 120kHz)
+  * Subtract the per-freqency median dB (reduce any spectral bias / shift)
+  * Set global dynamic range to -80 dB from the global maximum amplitude
+  * Calculate the global median non-minimum dB (greater than -80dB)
+  * Calculate the median absolute deviation (MAD)
+  * Autogain the dynamic range to (5 * MAD) below the global amplitude median, if necessary
+
+* Quantize the STFT
+
+  * Quantize the floating-point amplitude STFT to a 16-bit integer representation spanning the full dynamic range (65,536 bins)
+  * Vertically flip the spectrogram (low frequencies on bottom) and convert to a C-contiguous array
+
+* Find Candidate Chirps
+
+  * Create a 12ms sliding window with a 3ms stride
+  * Keep the time windows that show a substantial right-skew across 10% of the frequency range
+  * Add any user-provided time windows (annotations) to the found candidates windows
+  * Merge any overlapping time windows into a set of contiguous time ranges
+  * Tighten the candidate time ranges (and separate as needed) by repeating the same skew-based filter with a smaller sliding window and stride
+
+* Extract Chirp Metrics
+
+  * *for each candidate chirp*
+  * *Start*: First, find the peak amplitude location.
+  * Step 1 - Normalize the chirp to the full 16-bit range.  Calculate a histogram and identify the most common dB and standard deviation.  Scale the amplitude values using an inverted PDF, weighting each value by its inverse probability of being noise (values below the most common dB are set to zero)
+  * Step 2 - Apply a median filter and re-normalize
+  * Step 3 - Apply a morphological open operation
+  * Step 4 - Blur the chirp (k=5) and re-normalize
+  * Step 5 - Find contours using the "marching squares" algorithm and select the one that contains the peak amplitude.  Extract the convex hull of the contour and smooth the resulting outline
+  * Step 6 - Extract a segmentation mask for the contour
+  * Step 7 - Locate the harmonic (doubling the frequency) and echo (right edge of the contour to the end of the chirp time range) regions.  Remove any overlapping noise from the chirp contour.
+  * Step 8 - Locate the start, end, and characteristic frequency points (peak amplitude) and calculate an optimization cost grid for the contour using the masked amplitudes.
+  * Step 9 - Solve a minimum distance optimization using A* that also maximizes the amplutide values from start to end points.
+  * Step 10 - Smooth the contour path, extract the contour's slope, then identify the knee, heel, and other defining attributes.
+  * *End*: Finally, if any of the above steps fails, or the chirp's attributes do not make semantic sense, then skip the candidate chirp.
+
+* Create Output
+
+  * Collect all valid chirps regions and metadata, create a compressed spectrogram
+  * Write the 16-bit spectrogram as a series of 8-bit JPEGs image chunks (max width per chunk 50k pixels)
+  * Write the file and chirp metadata to a JSON file.
+
+How to Install
+--------------
+
+.. code-block:: bash
+
+    pip install batbot
+
+or, from source:
+
+.. code-block:: bash
+
+   git clone https://github.com/Kitware/batbot
+   cd batbot
+   pip install -e .
+
+To then add GPU acceleration, you need to replace `onnxruntime` with `onnxruntime-gpu`:
+
+.. code-block:: bash
+
+   pip uninstall -y onnxruntime
+   pip install onnxruntime-gpu
+
+How to Run
+----------
+
+You can run the Gradio demo with:
+
+.. code-block:: bash
+
+   python app.py
+
+To run with Docker:
+
+.. code-block:: bash
+
+   cd batbot
+   docker run \
+     -it \
+     --entrypoint bash \
+     --rm \
+     --name batbot \
+     -v $(pwd):/code \
+     kitware/batbot:latest
+
+or to run the Gradio app:
+
+.. code-block:: bash
+
+   docker run \
+     -it \
+     --rm \
+     -p 7860:7860 \
+     --gpus all \
+     --name batbot \
+     kitware/batbot:latest \
+     python3 app.py
+
+To run with Docker Compose:
+
+.. code-block:: yaml
+
+    version: "3"
+
+    services:
+      batbot:
+        image: kitware/batbot:latest
+        command: python3 app.py
+        ports:
+          - "7860:7860"
+        environment:
+          CLASSIFIER_BATCH_SIZE: 512
+        restart: unless-stopped
+        deploy:
+          resources:
+            reservations:
+              devices:
+                - driver: nvidia
+                  device_ids: ["all"]
+                  capabilities: [gpu]
+
+and run ``docker compose up -d``.
+
+How to Build and Deploy
+-----------------------
+
+Docker Hub
+==========
+
+The application can also be built into a Docker image and is hosted on Docker Hub as ``kitware/batbot:latest``.  Any time the ``main`` branch is updated or a tagged release is made (see the PyPI instructions below), an automated GitHub CD action will build and deploy the newest image to Docker Hub automatically.
+
+To do this manually, use the code below:
+
+.. code-block:: bash
+
+    docker login
+
+    export DOCKER_BUILDKIT=1
+    export DOCKER_CLI_EXPERIMENTAL=enabled
+    docker buildx create --name multi-arch-builder --use
+
+    docker buildx build \
+        -t kitware/batbot:latest \
+        --platform linux/amd64 \
+        --push \
+        .
+
+PyPI
+====
+
+To upload the latest BatBot version to the Python Package Index (PyPI), follow the steps below:
+
+#. Edit ``batbot/__init__.py:65`` and set ``VERSION`` to the desired version
+
+    .. code-block:: python
+
+        VERSION = 'X.Y.Z'
+
+
+#. Push any changes and version update to the ``main`` branch on GitHub and wait for CI tests to pass
+
+    .. code-block:: bash
+
+        git pull origin main
+        git commit -am "Release for Version X.Y.Z"
+        git push origin main
+
+
+#. Tag the ``main`` branch as a new release using the `SemVer pattern <https://semver.org/>`_ (e.g., ``vX.Y.Z``)
+
+    .. code-block:: bash
+
+        git pull origin main
+        git tag vX.Y.Z
+        git push origin vX.Y.Z
+
+
+#. Wait for the automated GitHub CD actions to build and push to `PyPI <https://pypi.org/project/batbot/>`_ and `Docker Hub <https://hub.docker.com/r/kitware/batbot>`_.
+
+Tests and Coverage
+------------------
+
+You can run the automated tests in the ``tests/`` folder by running:
+
+.. code-block:: bash
+
+    pip install -r requirements/optional.txt
+    pytest
+
+You may also get a coverage percentage by running:
+
+.. code-block:: bash
+
+    coverage html
+
+and open the `coverage/html/index.html` file in your browser.
+
+Building Documentation
+----------------------
+
+There is Sphinx documentation in the ``docs/`` folder, which can be built by running:
+
+.. code-block:: bash
+
+    cd docs/
+    pip install -r requirements/optional.txt
+    sphinx-build -M html . build/
+
+Logging
+-------
+
+The script uses Python's built-in logging functionality called ``logging``.  All print functions are replaced with ``log.info()``, which sends the output to two places:
+
+#. the terminal window, and
+#. the file `batbot.log`
+
+Code Formatting
+---------------
+
+It's recommended that you use ``pre-commit`` to ensure linting procedures are run
+on any code you write.  See `pre-commit.com <https://pre-commit.com/>`_ for more information.
+
+Reference `pre-commit's installation instructions <https://pre-commit.com/#install>`_ for software installation on your OS/platform. After you have the software installed, run ``pre-commit install`` on the command line. Now every time you commit to this project's code base the linter procedures will automatically run over the changed files.  To run pre-commit on files preemtively from the command line use:
+
+.. code-block:: bash
+
+    pip install -r requirements/optional.txt
+    pre-commit run --all-files
+
+The code base has been formatted by `Black <https://black.readthedocs.io/en/stable/>`_.  Furthermore, try to conform to ``PEP8``.  You should set up your preferred editor to use ``flake8`` as its Python linter, but pre-commit will ensure compliance before a git commit is completed.  This will use the ``flake8`` configuration within ``setup.cfg``, which ignores several errors and stylistic considerations.  See the ``setup.cfg`` file for a full and accurate listing of stylistic codes to ignore.
+
+
+.. |Tests| image:: https://github.com/Kitware/batbot/actions/workflows/testing.yaml/badge.svg?branch=main
+    :target: https://github.com/Kitware/batbot/actions/workflows/testing.yaml
+    :alt: GitHub CI
+
+.. |Codecov| image:: https://codecov.io/gh/Kitware/batbot/branch/main/graph/badge.svg?token=FR6ITMWQNI
+    :target: https://app.codecov.io/gh/Kitware/batbot
+    :alt: Codecov
+
+.. |Wheel| image:: https://github.com/Kitware/batbot/actions/workflows/python-publish.yaml/badge.svg
+    :target: https://github.com/Kitware/batbot/actions/workflows/python-publish.yaml
+    :alt: Python Wheel
+
+.. |Docker| image:: https://img.shields.io/docker/image-size/kitware/batbot/latest
+    :target: https://hub.docker.com/r/kitware/batbot
+    :alt: Docker
+
+.. |ReadTheDocs| image:: https://readthedocs.org/projects/batbot/badge/?version=latest
+    :target: https://kitware-batbot.readthedocs.io/en/latest/?badge=latest
+    :alt: ReadTheDocs