Getting Started

Our code is hosted here: https://github.com/U8NWXD/scorevideo_lib

Getting the Code and Dependencies

1. Choose where you want to download the code, and navigate to that directory. Then download the code.

   $ cd path/to/desired/directory
   $ git clone https://github.com/U8NWXD/scorevideo_lib
   

2. Install python 3 from https://python.org or via your favorite package manager

3. Install virtualenv

   $ pip3 install virtualenv
   

4. If you get a note from pip about virtualenv not being in your PATH, you need to perform this step. PATH is a variable accessible from any bash terminal you run, and it tells bash where to look for the commands you enter. It is a list of directories separated by :. You can see yours by running echo $PATH. To run virtualenv commands, you need to add python’s packages to your PATH by editing or creating the file ~/.bash_profile on MacOS. To that file add the following lines:

   PATH="<Path from pip message>:$PATH"
   export PATH
   

5. Then you can install dependencies into a virtual environment

   $ cd scorevideo_lib
   $ virtualenv -p python3 venv
   $ source venv/bin/activate
   $ pip install -r requirements.txt
   

Now you’re ready to use the library! You can check out the API reference here.

Note

If your data is from dyad assays and structured accordingly, you can transfer lights-on marks my running the transfer_lights_on_marks.py tool in the directory of log files like so: python transfer_lights_on_marks.py. If you aren’t sure if these requirements are met, they probably aren’t. This is only useful for a few researchers.