# Build & run test setup
cargo run --release -- --config distribution/test.jsonTo setup SLEAP tracking, look at distribution/sleap.
To build BioTracker v4, a rust toolchain and OpenCV must be installed.
The build requires the Rust toolchain, version >= 1.68. It can be installed by following the official guide.
OpenCV can be installed using your system package manager.
# Ubuntu / Debian
sudo apt install libopencv-dev
# Arch
sudo pacman -S opencv
# macOS
brew install opencvBioTracker v4 is built and executed with cargo. It is recommended to use the
--release flag to optimize the build.
cargo run --releaseAs a modular application, BioTracker v4 requires further configuration
specifying which components should be used for tracking. This is done by
supplying a JSON configuration file at startup, using the --config flag. When
using cargo, arguments to the BioTracker are passed after a separating
double-dash (--).
The test configuration may be used to quickly run the application. It can can be executed by calling:
cargo run --release -- --config distribution/test.jsonWhile this configuration is useful for testing basic features, it does not do any tracking. Please refer to distribution/sleap for a guide on how to setup a real tracking pipeline.
The CLI may be used to automate some settings at startup. It is documented behind the --help argument:
biotracker4 --help
Distributed framework for animal tracking
Usage: biotracker4 [OPTIONS] --config <CONFIG>
Options:
-v, --video <VIDEO>
Open video file on startup
--entity-count <ENTITY_COUNT>
Start experiment with <count> entities
--realtime <REALTIME>
Skip frames if tracking is too slow [possible values: true, false]
--config <CONFIG>
Path to configuration json
--port <PORT>
Port for biotracker core [default: 27342]
--seek <SEEK>
Seek to frame
--cv-worker-threads <CV_WORKER_THREADS>
Number of OpenCV worker threads [default: 4]
--track <TRACK>
Path to robofish track file
--force-camera-config <FORCE_CAMERA_CONFIG>
Force loading of camera settings, this makes it possible to apply undistortion to videos
--port-range-start <PORT_RANGE_START>
Start of range of ports which are assigned to components [default: 28000]
-h, --help
Print help
-V, --version
Print versionYou need to install llvm with homebrew:
brew install llvmor, if it is installed already, you may have to add it to your environment manually:
# 1. Locate libclang.dylib, then copy the result into a variable.
# (e.g. /opt/homebrew/Cellar/llvm/16.0.6/lib/)
find / -name libclang.dylib 2>/dev/null
LIBCLANG=$YOUR_FIND_RESULT
# 2. Set environment variable
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$LIBCLANG
# 3. (optional) To set the environment variable permanently, edit your shell config file, or run
echo "export DYLD_LIBRARY_PATH=$LIBCLANG:$DYLD_LIBRARY_PATH" >> ~/.zshrc`This happens during setup of the python virtualenv, e.g. while running
distribution/sleap/setup.sh. Uninstall grpcio and grpcio-tools and reinstall
them with the --no-binary flag. Make sure you have activated the biotracker
venv:
# From the root of the git repository
source distribution/sleap/biotracker-venv/bin/activate
pip install grpcio --no-binary :all:
pip install --no-binary :all: grpcio-tools --ignore-installedThis work is licensed under GPL 3.0 (or any later version). Individual files contain the following tag instead of the full license text:
SPDX-License-Identifier: GPL-3.0-or-later
This enables machine processing of license information based on the SPDX License Identifiers available here: https://spdx.org/licenses/
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