The instructions below are to install Tierpsy Tracker from the source code. I would recommend to do this only if you are using Linux or want to run the development version, otherwise use the double-click executables available for Windows (7 or latest) and OSX (Yosemite or latest) in the releases page.
- Freshly installed [miniconda] (https://conda.io/miniconda.html) or at least setup up a new enviroment.
- Optional ffmpeg: ffprobe must be accessible from the command line to calculate the video timestamps.
- C compiler compatible with cython. In Windows, you can use Visual C++ 2015 Build Tools. In OSX, if you install homebrew it will setup the C compiler without the need to download XCode from the appstore.
- Git. Here are some instructions to install it.
- Clone this repository either using the Github Desktop or from the command line as:
git clone https://github.com/ver228/tierpsy-tracker- Install the conda dependencies from the conda-forge channel:
conda config --add channels conda-forge
conda install -y numpy matplotlib pytables pandas gitpython pyqt=5 \
h5py scipy scikit-learn scikit-image seaborn xlrd cython statsmodels
conda install -y -c conda-forge keras opencv
pip install tensorflow - Install the rest of the modules: On the tierpsy-tracker root folder (the folder with the cloned repository) type:
bash installation/installation_script.sh #OSX or Linux
installation/installation_script.bat #Windows-
The most common problem in the installation is OpenCV (error in import cv2). Try a fresh miniconda installation (or a fresh enviroment) and make sure your are using the conda-forge packages. It this does not work I am afraid you would have to solve the problem by yourself (Google is your friend).
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You do not need to install manually the Open Worm Analysis Toolbox. However if you do (and I do not recommend it), be aware that there is a bug with the pip installer: it is missing some dependencies and it will create a corrupt .egg in your packages folder. Manually delete the .egg (use the error traceback to find the its location) and re-run
installation_script.sh. The script will download the Open Worm Analysis Toolbox repository and install it usingpython setup.py develop.
On Mac OSX or Linux, some test examples can be downloaded by running
installation/installation_script.sh --download_examplesThe tests can also be manually downloaded using this link. Uncompress the data and save it in the main repository folder tests/data .
You can then run the tests by running:
python tests/run_tests.py