Please note that Charlie has been superseded by Charlie 2 (https://github.com/sammosummo/Charlie2). I'm no longer developing or supporting Charlie 1.
- Author
Samuel R. Mathias
- Contact
- Web site
- Github
- Version
0.2.0
Charlie is a free, open-source, cross-platform neurocognitive test battery written in Python. It is currently being used to collect data for a project from our laboratory, but may be used freely by all. Although all of the tests are functional and there are some nice features (see below), Charlie is still under development. I'm continually adding more features and fixing bugs as they arise.
- Charlie currently contains 22 neuocognitive tests, with more planned. Each test has a docstring with citations; have a look in the charlie/tests folder to see what's available.
- Data are recorded after each trial. This means that you have access to trial-specific data rather than just the summary data. It also means that the tests are resumable; that is, the progress of each subject is retained. This prevents a subject from performing a test twice, and allows them to pick up where they left off, if a test gets interrupted.
- Summary statistics are automatically computed after a subject completes a test. All of the data (summary and trial-specific) are stored within various formats, including within human-readable CSVs, "pickled" Python objects, and within an SQLite database.
- Tests can be run individually or in batches.
- Because Charlie is written in Python, it is easy to modify or add new tests.
- Charlie is cross-platform. So long as your system can run Python 2.7 (most can), you can use Charlie.
- Charlie can administer self-report questionnaires prior to a test or battery of tests. This feature is functional, but has not been debugged as extensively tested as the cognitive tests.
- At the end of a test or batch, the data stored locally can be automatically backed up to a remote server via sftp. This feature is currently very crude. I plan to refine it and add more backup options in the future.
- Charlie is written in Python and uses various third-party packages. In the future, I plan to create a stand-alone version.
- Charlie is a command-line program. It has a GUI, but I haven't figured out how to make it work with tests run in batch mode. (This has proven to be a great source of frustration for me.)
- Charlie isn't currently a regular Python package, so isn't installable via pip. I haven't yet decided whether to do this.
Charlie uses Python as a number of its third-party pacakges: numpy, scipy, pandas, pygame, web.py, paramiko, and pyside/pyqt. If you are an experienced Python user, simply install all of these in whatever way you prefer. If you are not a Python user and are on Windows, do the following:
- Download and install Miniconda from here: https://repo.continuum.io/miniconda/Miniconda-latest-Windows-x86.exe
- Open a command prompt, and type the following commands, one by one: :: conda update conda conda install pip numpy scipy pandas pyside paramiko pip install web.py
- Download and install Pygame: http://pygame.org/ftp/pygame-1.9.2a0.win32-py2.7.msi
- Download Charlie: https://github.com/sammosummo/Charlie/archive/master.zip
If you are on Mac, do the following instead:
- Download the Miniconda bash script: https://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh
- Execute the script by opening a terminal window, setting the current directory to your downloads folder using the cd command, and typing the line: :: sudo bash Miniconda-latest-MacOSX-x86_64.sh
- Restart your terminal and type these commands: :: conda update conda conda install pip numpy scipy pandas pyside paramiko binstar pip install web.py ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" brew install sdl sdl_ttf sdl_image sdl_mixer portmidi conda install -c https://conda.binstar.org/quasiben pygame
- Download Charlie: https://github.com/sammosummo/Charlie/archive/master.zip
If you downloaded the zip file (step 4 above), unzip it somewhere on your computer, it shouldn't matter where. Then open a command window/terminal, and cd to the Charlie-master/charlie directory. There should be a file called run.py in that directory.
Tests and batches are run from the command line by executing the run.py script. Options are supplied Unix-style. To get a list of all available options, type: :: python run.py -h The help string should be clear, but if you have any difficulties, feel free to drop me an email.