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maximpavlivMMathisLabsneakers-the-ratarturoptophys
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[WIP] Continue work on Integration with DeepLabCut 3.0 (DeepLabCut#127)
* Update benchmark.py - changed benchmarking link; needs testing * fix DeepLabCut#112 - don't subset cpuinfo (DeepLabCut#114) * Introduce CI/CD for TensorFLow version (DeepLabCut#122) * Update .gitignore * CI/CD update python version * CI/CD update actions versions * CI/CD update trigger events * CI/CD update MacOS version * dlclibrary set version to >=0.0.6 * Poetry lock * Poetry lock * Pyproject.toml update tensorflow installation * Poetry lock * Install specific tensorflow-io-gcs-filesystem for windows * Poetry lock * Update deprecated section name * Poetry lock * CI/CD test on python 3.11, 3.12, 3.13 as well * Update testing.yml - rename to main - add tables installation --------- Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> * master --> main * Update testing.yml * Update benchmark.py * Update README & benchmarking script (DeepLabCut#126) * Update README.md fix test instructions * Update check_install.py * Update check_install.py * Update check_install.py * Update pyproject.toml (DeepLabCut#125) * Update pyproject.toml - adding support for python 3.11, 3.12, 3.13 * Update testing.yml * Update testing.yml * Update pyproject.toml * Update testing.yml * Update pyproject.toml * Update poetry.lock * Update poetry.lock * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update testing.yml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update testing.yml * Update pyproject.toml * Update pyproject.toml * Update poetry.lock * Update testing.yml * Update testing.yml * Update testing.yml - remove poetry (for now) * Update testing.yml * Update testing.yml * Update testing.yml * Update testing.yml * Update testing.yml * updated poetry.lock * updated * Update testing.yml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update testing.yml testing 3.11 * Update testing.yml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update testing.yml * updated test for win32 * Update testing.yml * Update testing.yml * Update testing.yml * Update testing.yml * Fix download_benchmarking_data() * Ignore __MACOSX directories * Run tests on all PRs * tensorflow-io-gcs-filesystem - python=3.9 * Pin python to 3.10 version * WIP refactor benchmarking: __init__.py * WIP refactor benchmarking: remove dupplicates * WIP refactor benchmarking: warning * WIP refactor benchmarking: close live * WIP refactor benchmarking: resize and pixels * WIP refactor benchmarking: get_sys_info * Update benchmark.py (DeepLabCut#123) * WIP refactor benchmarking: Delete dupplicate scripts * WIP refactor benchmarking: Introduce Engine * WIP refactor benchmarking: benchmark() method * WIP refactor benchmarking: benchmark_videos() * CI/CD: add torch installation * WIP refactor benchmarking: extract Engine * Refactor benchmarking: model_type in benchmark_videos() * Delete poetry lock * Fix frame_batch initialization in runner.py when low detection confidence (DeepLabCut#138) --------- Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> Co-authored-by: Jonny Saunders <sneakers-the-rat@protonmail.com> Co-authored-by: Artur <35294812+arturoptophys@users.noreply.github.com>
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‎.github/workflows/testing.yml‎

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push:
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branches: [main]
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pull_request:
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branches: [main]
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jobs:
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build:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Set up Python
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uses: conda-incubator/setup-miniconda@v3
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with:
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channels: conda-forge,defaults
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channel-priority: strict
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python-version: ${{ matrix.python-version }}
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- name: Install ffmpeg
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run: |
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if [ "$RUNNER_OS" == "Linux" ]; then
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choco install ffmpeg
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fi
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shell: bash
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- name: Install PyTables through Conda
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- name: Install and test
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shell: bash -el {0} # Important: activates the conda environment
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run: |
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conda install pytables==3.8.0 "numpy<2"
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run: poetry lock --no-cache
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- name: Install project dependencies
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run: poetry install --with dev
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run: poetry install --with dev --extras "tf" --extras "pytorch"
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- name: Run DLC Live Tests
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run: poetry run dlc-live-test --nodisplay
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- name: Run Functional Benchmark Test
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run: poetry run pytest tests/test_benchmark_script.py
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‎README.md‎

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Note, you can then test your installation by installing poetry (`pip install poetry`), then running:
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```python
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poetry run dlc-live-test
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```

‎benchmarking/run_dlclive_benchmark.py‎

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import glob
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from dlclive import benchmark_videos, download_benchmarking_data
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from dlclive.engine import Engine
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datafolder = os.path.join(
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pathlib.Path(__file__).parent.absolute(), "Data-DLC-live-benchmark"
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if not os.path.isdir(out_dir):
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os.mkdir(out_dir)
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for m in dog_models:
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benchmark_videos(m, dog_video, output=out_dir, n_frames=n_frames, pixels=pixels)
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for m in mouse_models:
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benchmark_videos(m, mouse_video, output=out_dir, n_frames=n_frames, pixels=pixels)
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for model_path in dog_models:
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benchmark_videos(
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model_path=model_path,
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model_type="base" if Engine.from_model_path(model_path) == Engine.TENSORFLOW else "pytorch",
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video_path=dog_video,
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output=out_dir,
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n_frames=n_frames,
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pixels=pixels
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)
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for model_path in mouse_models:
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benchmark_videos(
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model_path=model_path,
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model_type="base" if Engine.from_model_path(model_path) == Engine.TENSORFLOW else "pytorch",
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video_path=mouse_video,
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output=out_dir,
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n_frames=n_frames,
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pixels=pixels
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)

‎dlclive/__init__.py‎

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from dlclive.dlclive import DLCLive
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from dlclive.processor.processor import Processor
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from dlclive.version import VERSION, __version__
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from dlclive.benchmark import benchmark_videos, download_benchmarking_data

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