INSTALLATION.md

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.

System Requirements

• Python 3.6 (I would recommend to use miniconda).
• 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.

Installation

1. Install dependencies:

Using pip:

pip install numpy matplotlib tables pandas pyqt5 h5py scipy scikit-learn scikit-image seaborn xlrd cython statsmodels numba keras==2.1.5 tensorflow opencv-python-headless

Using anaconda:

conda install --channel conda-forge numpy matplotlib pytables pandas gitpython pyqt h5py \
scipy scikit-learn scikit-image seaborn xlrd cython statsmodels numba keras=2.1.5 opencv tensorflow 

2. Clone this repository either using the Github Desktop or from the command line as:

git clone https://github.com/ver228/tierpsy-tracker

3. Install the rest of the modules. Firts move to the tierpsy-tracker root folder (the folder with the cloned repository) as:

cd tierpsy-tracker

Then install the rest of the modules using the following command according to your operative system.

bash installation/installation_script.sh #OSX or Linux

installation/installation_script.bat #Windows

Possible Issues

• 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).

• 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 using python setup.py develop.

Test Data

On Mac OSX or Linux, some test data can be downloaded by running

installation/installation_script.sh --download_examples

The 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