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flystim

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flystim is a software package for generating visual stimuli for neuroscience experiments. It was originally designed for fly labs, but can be used for any subject/viewer. The stimuli are perspective-corrected and can be displayed across multiple screens. Sample code, illustrating various use cases, is included in the examples directory.

Prerequisites

flystim only supports Python3, so in the commands below, the pip and python commands should refer to a Python3 install. You can either install Python3 directly or through a package manager like Conda.

On Linux, you'll also need to install a few packages via apt-get:

> sudo apt-get install build-essential libusb-1.0.0-dev libudev-dev

Installation

  1. Open a terminal, and note the current directory, since the pip commands below will clone some code from GitHub and place it in a subdirectory called src. If you prefer to place the cloned code in a different directory, you can specify that by providing the --src flag to pip.
  2. Clone and install flyrpc if you haven't already:
> git clone https://github.com/ClandininLab/flyrpc.git
> cd flyrpc
> pip install -e .
> cd ..
  1. Clone and install flystim:
> git clone https://github.com/ClandininLab/flystim.git
> cd flystim
> pip install -e .
> cd ..

If you get a permissions error when running the pip command, you can try adding the --user flag. This will cause pip to install packages in your user directory rather than to a system-wide location.

Running the Example Code

In a terminal tab, navigate to the examples directory and run one of the sample programs, such as show_all.py.

> cd flystim/examples
> python show_all.py

Each example can be exited at any time by pressing Ctrl+C.

Coordinate system

The coordinate system convention in flystim is defined as follows:

  • Yaw = rotation around the Z axis (theta)
  • Pitch = rotation around the X axis (phi)
  • Roll = rotation around the Y axis

A fly heading of (yaw=0, pitch=0, roll=0) corresponds to the fly looking down the +Y axis, the +X axis lies to the fly's right side, and +Z lies above the fly's head

Screen objects and defining subscreen geometry

A Screen object specifies a display device and a list of SubScreens, each SubScreen is defined by:

  1. Physical coordinates ( (x, y, z), in meters) that specify the screen geometry in 3D space

  2. Normalized Device Coordinates ( (x, y), [-1, +1]) ) that specify a viewport for that SubScreen. This controls where on the display device the image for this SubScreen will appear.