├── .coveragerc ├── .coveralls.yml ├── .gitattributes ├── .github └── workflows │ └── tests.yml ├── .gitignore ├── .readthedocs.yml ├── CITATION.cff ├── CNAME ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── autopilot ├── __init__.py ├── agents │ ├── __init__.py │ ├── base.py │ ├── pilot.py │ └── terminal.py ├── data │ ├── __init__.py │ ├── interfaces │ │ ├── __init__.py │ │ ├── base.py │ │ ├── datajoint.py │ │ ├── nwb.py │ │ └── tables.py │ ├── modeling │ │ ├── __init__.py │ │ ├── base.py │ │ └── links.py │ ├── models │ │ ├── __init__.py │ │ ├── biography.py │ │ ├── protocol.py │ │ ├── researcher.py │ │ └── subject.py │ ├── subject.py │ └── units │ │ ├── __init__.py │ │ ├── base.py │ │ └── derived.py ├── exceptions.py ├── external │ └── __init__.py ├── gui │ ├── __init__.py │ ├── dialog.py │ ├── gui.py │ ├── menus │ │ ├── __init__.py │ │ ├── file.py │ │ ├── plots.py │ │ ├── plugins.py │ │ ├── swarm.py │ │ ├── tests.py │ │ └── tools.py │ ├── plots │ │ ├── __init__.py │ │ ├── geom.py │ │ ├── info.py │ │ ├── plot.py │ │ └── video.py │ ├── styles.py │ └── widgets │ │ ├── __init__.py │ │ ├── input.py │ │ ├── list.py │ │ ├── model.py │ │ ├── protocol.py │ │ ├── subject.py │ │ └── terminal.py ├── hardware │ ├── __init__.py │ ├── cameras.py │ ├── gpio.py │ ├── i2c.py │ └── usb.py ├── networking │ ├── __init__.py │ ├── message.py │ ├── node.py │ └── station.py ├── prefs.py ├── root.py ├── setup │ ├── __init__.py │ ├── __main__.py │ ├── forms.py │ ├── install_pyspin.sh │ ├── request_helpers.py │ ├── run_script.py │ ├── scripts.py │ ├── setup_autopilot.py │ ├── setup_mlx90640.sh │ └── welcome_msg.txt ├── stim │ ├── __init__.py │ ├── managers.py │ ├── sound │ │ ├── __init__.py │ │ ├── base.py │ │ ├── jackclient.py │ │ ├── pyoserver.py │ │ └── sounds.py │ ├── stim.py │ └── visual │ │ ├── __init__.py │ │ ├── visuals.py │ │ └── xclient.py ├── tasks │ ├── __init__.py │ ├── children.py │ ├── free_water.py │ ├── gonogo.py │ ├── graduation.py │ ├── nafc.py │ ├── protocol_scripts.py │ ├── task.py │ └── test.py ├── transform │ ├── __init__.py │ ├── coercion.py │ ├── geometry.py │ ├── image.py │ ├── logical.py │ ├── math.py │ ├── selection.py │ ├── timeseries.py │ ├── transforms.py │ └── units.py ├── utils │ ├── __init__.py │ ├── common.py │ ├── decorators.py │ ├── hydration.py │ ├── invoker.py │ ├── log_parsers.py │ ├── loggers.py │ ├── plugins.py │ ├── registry.py │ ├── requires.py │ ├── types.py │ └── wiki.py └── viz │ ├── __init__.py │ ├── psychometric.py │ └── trial_viewer.py ├── conftest.py ├── docs ├── .buildinfo ├── .nojekyll ├── Makefile ├── __CNAME ├── _images │ ├── Screenshot from 2019-09-24 09-51-04.png │ ├── Screenshot from 2019-09-24 09-53-47.png │ ├── autopilot_logo.svg │ ├── autopilot_logo_banner.png │ ├── classes_zmq.png │ ├── discussion_link.png │ ├── docs_link.png │ ├── favicon.svg │ ├── figure_protocol.png │ ├── gonogo.png │ ├── hardware_link.png │ ├── hardware_link_construction.png │ ├── icon_agent.png │ ├── icon_cameras.svg │ ├── icon_data.png │ ├── icon_data.svg │ ├── icon_gpio.svg │ ├── icon_gui.png │ ├── icon_gui.svg │ ├── icon_hardware.png │ ├── icon_i2c.svg │ ├── icon_networking.svg │ ├── icon_pilot.svg │ ├── icon_plots.svg │ ├── icon_sound.svg │ ├── icon_stim.png │ ├── icon_task.png │ ├── icon_tasks.svg │ ├── icon_terminal.svg │ ├── icon_transform.png │ ├── icon_usb.svg │ ├── icon_viz.png │ ├── inheritance-0019c9f54272224b96ca705e78dddfe2663572b3.png │ ├── inheritance-0019c9f54272224b96ca705e78dddfe2663572b3.png.map │ ├── inheritance-05fbd8f01292c1cebec49e0d28ad3892eee2ae74.png │ ├── inheritance-05fbd8f01292c1cebec49e0d28ad3892eee2ae74.png.map │ ├── inheritance-0b798ad60c309e0ce4fb358c2012ad425d8a1060.png │ ├── inheritance-0b798ad60c309e0ce4fb358c2012ad425d8a1060.png.map │ ├── inheritance-0ed1bfeeb06777de7bbb7314d1c2106e288f883b.png │ ├── inheritance-0ed1bfeeb06777de7bbb7314d1c2106e288f883b.png.map │ ├── inheritance-12555714348a5eb2a46f51f9a1eb6f44188f9a54.png │ ├── 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subject_4.png │ ├── terminal.png │ ├── whole_system_black.png │ └── whole_system_black.svg ├── _static │ ├── ajax-loader.gif │ ├── autopilot_logo.png │ ├── autopilot_logo.svg │ ├── autopilot_logo_half.png │ ├── autopilot_logo_med.png │ ├── autopilot_logo_white.svg │ ├── comment-bright.png │ ├── comment-close.png │ ├── comment.png │ ├── css │ │ ├── autopilot_sass.css │ │ ├── autopilot_theme.css │ │ ├── badge_only.css │ │ ├── theme.css │ │ └── theme_pretty.css │ ├── down-pressed.png │ ├── down.png │ ├── file.png │ ├── grid-dark.png │ ├── grid.png │ ├── grid_dark.png │ ├── minus.png │ ├── plus.png │ ├── restyle.css │ ├── up-pressed.png │ └── up.png ├── _templates │ ├── autosummary │ │ └── class.rst │ ├── class.rst │ ├── class_old.rst │ ├── layout.html │ ├── rtd_layout.html │ └── theme.conf ├── agents │ ├── base.rst │ ├── index.rst │ ├── pilot.rst │ └── terminal.rst ├── autopilot_docs.bib ├── changelog │ ├── index.rst │ ├── v0.2.0.rst │ ├── v0.3.0.rst │ ├── v0.4.0.rst │ └── v0.5.0.md ├── conf.py ├── data │ ├── index.md │ ├── interfaces │ │ ├── base.rst │ │ ├── datajoint.rst │ │ ├── index.md │ │ ├── nwb.rst │ │ └── tables.rst │ ├── modeling │ │ └── index.md │ ├── models │ │ ├── biography.rst │ │ ├── index.md │ │ ├── protocol.rst │ │ ├── researcher.rst │ │ └── subject.rst │ ├── subject.rst │ └── units │ │ └── index.rst ├── examples │ ├── blink.rst │ ├── gonogo.rst │ └── index.md ├── external.rst ├── graphics │ ├── autopilot_logo_small.svg │ └── logo.png ├── gui │ ├── dialog.rst │ ├── index.rst │ ├── menus.rst │ ├── plots │ │ ├── geom.md │ │ ├── index.md │ │ ├── info.md │ │ ├── plot.md │ │ └── video.md │ └── widgets │ │ ├── index.rst │ │ ├── input.rst │ │ ├── list.rst │ │ ├── model.rst │ │ ├── protocol.rst │ │ ├── subject.rst │ │ └── terminal.rst ├── guide │ ├── configuration.md │ ├── faq.md │ ├── hardware.rst │ ├── installation.pilot.rst.bak │ ├── installation.rst │ ├── installation.terminal.rst.bak │ ├── overview.rst │ ├── plugins.rst │ ├── quickstart.rst │ ├── task.rst │ └── training.rst ├── hardware │ ├── cameras.rst │ ├── gpio.rst │ ├── i2c.rst │ ├── index.rst │ └── usb.rst ├── includes │ ├── autopilot_logo_banner.html │ ├── autopilot_logo_banner.svg │ ├── autopilot_logo_small.svg │ ├── logo.html │ └── module_map.html ├── index.rst ├── local_directives.py ├── localext │ ├── __init__.py │ └── fulltoc.py ├── networking │ ├── index.rst │ ├── message.rst │ ├── node.rst │ └── station.rst ├── notes │ ├── building.txt │ ├── c_extensions.txt │ ├── ci_on_pi.txt │ ├── mac_pyside_install_issues.txt │ ├── multiproccessing_probs.txt │ ├── picapture_notes.txt │ ├── scarps │ │ └── param_widget.txt │ ├── setup_changes.txt │ ├── spinnaker_notes.txt │ └── visual_stim.txt ├── objects.inv ├── prefs.rst ├── references.rst ├── root │ └── index.md ├── searchindex.js ├── setup │ ├── index.rst │ ├── run_script.rst │ └── scripts.rst ├── stim │ ├── index.rst │ ├── managers.rst │ └── sound │ │ ├── base.rst │ │ ├── index.rst │ │ ├── jackclient.rst │ │ ├── pyoserver.rst │ │ └── sounds.rst ├── styles │ ├── _components.scss │ ├── _overrides.scss │ └── main.scss ├── tasks │ ├── children.rst │ ├── free_water.rst │ ├── graduation.rst │ ├── index.rst │ ├── nafc.rst │ └── task.rst ├── tests │ ├── index.rst │ ├── test_networking.rst │ ├── test_plugins.rst │ ├── test_prefs.rst │ ├── test_registry.rst │ ├── test_setup.rst │ ├── test_sounds.rst │ ├── test_terminal.rst │ ├── test_transforms.rst │ └── test_utils.rst ├── todo.rst ├── transform │ ├── coercion.rst │ ├── geometry.rst │ ├── image.rst │ ├── index.rst │ ├── logical.rst │ ├── selection.rst │ ├── timeseries.rst │ └── units.rst ├── utils │ ├── common.rst │ ├── decorators.rst │ ├── hydration.rst │ ├── index.rst │ ├── invoker.rst │ ├── log_parsers.rst │ ├── loggers.rst │ ├── plugins.rst │ ├── registry.rst │ ├── requires.rst │ ├── types.rst │ └── wiki.rst └── viz │ ├── index.rst │ ├── psychometric.rst │ └── trial_viewer.rst ├── examples ├── __init__.py ├── prefs │ ├── pilot_prefs.json │ └── terminal_prefs.json ├── 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