Stytra was developed and tested using Python 3.7 installed as part of the Anaconda Python distribution. Other Python versions have not been tested, although Python 3.6 will work. Python 3.5 is not supported.
The latest version of Anaconda or Miniconda is recommended. Installation without Anaconda can be achieved but dependencies issues might be difficult to resolve, especially on Windows. The following two variants of instructions have been tested:
1) Environment file¶
The provided conda environment.yml file that should install everything except the camera support (described below). The environment file should work with any recent version of Anaconda or Miniconda on all platforms.
conda env create -f environment.yml
Then, whenever you want to use Stytra, you have to activate the environment:
conda activate stytra
Many Python editors and IDEs such as PyCharm or Visual Studio Code support setting a conda environment for projects and files.
2) Manual installation¶
Stytra relies on opencv for some of its fish tracking functions. If you don’t have it installed, open the Anaconda prompt and type:
conda install opencv
Sometimes, OpenCV installation does not work properly (DLL not found error when importin cv2), this can be fixed by installing a wheel directly from https://www.lfd.uci.edu/~gohlke/pythonlibs/#opencv
If you are using Windows, git (used for tracking software versions) might not be installed. Git can also be easily installed with conda:
conda install git
Also, for some video-related operations (offline tracking and saving of stimulus videos), a version of ffmpeg with libx264 has to be installed, for this, use the conda-forge channel:
conda install -c conda-forge ffmpeg
as well as PyAV:
conda install av -c conda-forge
These are all requirements not covered by the next installation step.
PyQt5 is not listed as an explicit requirement because it should come with the Anaconda package. If you are not using Anaconda, make sure you have it installed and updated before installing Stytra!
The simplest way to install Stytra is with pip:
pip install stytra
On the other hand, if you want to modify the internals of stytra or use unreleased features, clone or download stytra from github and install it with:
pip install path_to_stytra/stytra
If you want to be able to change the stytra code and use the changed version, install using the -e argument:
pip install -e path_to_stytra/stytra
Now you can have a look at the stytra Examples gallery, or you can start Configuring a computer for Stytra experiments. In the second case, you might want to have a look at the camera APIs section below first.
Testing the installation¶
You can verify the installation by running one of the examples in stytra examples folder. To run a simple looming stimulus experiment, you can type:
python -m stytra.examples.looming_exp
If the GUI opens correctly and pressing the play button starts the stimulus: congratulations, installation was successful! If it crashes, check if you have all dependencies correctly installed. If it still does not work, open an issue on the Stytra github page.
Stytra might raise an error after quitting because of a bug in the current version of pyqtgraph (a package we are using for online plotting). If you are annoyed by the error messages when closing the program you can install the develop version of pyqtgraph from their github repository. The problem will be resolved once the next pyqtgraph version is released.
Installing camera APIs¶
Download the Ximea SDK software pacakge for your operating system, during the installation wizard make sure that you select the python API checkbox. After installation, copy the python wrapper API (in the folder where you installed XIMEA, …XIMEAAPIPythonv3ximea) into the Python site-packages folder (for anaconda, usually the folder …anaconda3Libsite-packages)
pip install git+https://github.com/morefigs/pymba.git
or, if using 64bit windows, you can grab the installation file from here. Open the terminal in the folder where you downloaded it and install:
pip install pymba-0.1-py3-none-any.whl
Spinnaker: Point Grey / FLIR¶
Go the the FLIR support website, download and install the SDK and the Python API.
Install the SDK: select the operating system, and then Latest Spinnaker Web Installer with the version appropriate for your platform (usually x64). In the installer wizard, we recommend selecting the “Camera evaluation” option, it is the smallest one and installs everything required for the Python. The other options might require installing various Visual Studio runtimes.
Download the Python package from the same link, selecting the appropriate operating system and version of Python (cp37 for Python 3.7 (recommended above) and cp36 for 3.6). Install the python module:
pip install "path_to_extracted_zip/spinnaker_python-18.104.22.168-cp37-cp37m-win_amd64.zip"
(with the file with the appropriate OS and Python versions)
National Instruments framegrabber with Mikrotron camera¶
Install the NI vision SDK. For the Mikrotron MC1362 camera, you can use this camera file. The camera file usually needs to be put into C:UsersPublicPublic DocumentsNational InstrumentsNI-IMAQData After putting the camera file there, is should be selected for the image acquisition device in NI MAX.
External hardware support¶
National Instruments Boards¶
Install the drivers and afterwards the Python package:
python -m pip install nidaqmx
To communicate with microcontroller boards usually a serial connection is used.:
pip install pyserial