├── .gitignore ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── LICENSE.txt ├── README.md ├── bin ├── OceanOptics_example.py ├── PupilCore_get_properties.py ├── PupilCore_lightstamper_minimal.py ├── PupilCore_notifications.py ├── STLAB_OceanOptics_sample.py ├── STLAB_PupilCore_PLR.py ├── STLAB_PupilCore_pupillometer_v1.py ├── STLAB_Scene_example.py ├── STLAB_minimal.py ├── STLAB_video_file_example.py ├── external_info.csv ├── external_spectra.csv ├── ocean_optics_temperature_darkcal_data_script.py ├── oo_info.csv ├── oo_spectra.csv ├── pipr_analysis_script.py ├── pipr_experiment_script.py ├── pipr_group_analysis_script.py ├── pupil_analysis_minimal.py ├── sinusoid_analysis_script.py ├── sinusoid_video_experiment_script.py ├── ss_generateFinalReport.py ├── stlab_info.csv └── stlab_spectra.csv ├── docs ├── 01_includeme.rst ├── 02_purpose.rst ├── 03_installation.rst ├── 04_overview.rst ├── 04a_pyplr_and_pupil_core.ipynb ├── 04b_stlab_light_source.ipynb ├── 04c_integrating_sphere.ipynb ├── 04d_analysis.ipynb ├── 04e_silent_substitution.ipynb ├── 05_example_protocols.rst ├── 05a_plr_simple.ipynb ├── 05b_plr_psychopy.ipynb ├── 05c_plr_stlab.ipynb ├── 05d_pipr_stlab.ipynb ├── 05f_pupil_core_camera_sync.ipynb ├── 06_example_analyses.rst ├── 06a_pipr_analysis_pipeline.ipynb ├── 06b_pupil_core_timing_analysis.ipynb ├── 06c_finding_stlab_settings.ipynb ├── 06d_silent_substitution_STLAB.ipynb ├── 07_api.rst ├── 08_developers.rst ├── 09_acknowledgements.rst ├── 10_funding.rst ├── 11_citation.rst ├── Makefile ├── README.rst ├── conf.py ├── dev_notes.ipynb ├── index.rst ├── make.bat └── refs.bib ├── examples ├── PFR │ ├── pupillometer_v1.py │ └── stimuli │ │ ├── PLR-3000-10-mw.dsf │ │ ├── PLR-3000-121-mw.dsf │ │ ├── PLR-3000-180-mw.dsf │ │ └── PLR-3000-50-mw.dsf ├── PIPR │ ├── pipr_stlab.py │ └── stimuli │ │ ├── 1s_blue.dsf │ │ ├── 1s_red.dsf │ │ ├── make_pipr_stimuli.py │ │ └── pipr_stims.png └── psychopy_pyplr_example.py ├── logo └── orange_eye.png ├── matlab ├── legacy │ ├── bv_getWithDefault.m │ ├── bv_primariesToSettings.m │ ├── bv_proceedDialogue.m │ ├── bv_runExperiment.m │ ├── bv_runPupilProtocol.m │ ├── bv_setSettings.m │ ├── bv_setupDevice.m │ ├── bv_turnAllOff.m │ ├── jsonlab │ │ ├── AUTHORS.txt │ │ ├── ChangeLog.txt │ │ ├── LICENSE_BSD.txt │ │ ├── LICENSE_GPLv3.txt │ │ ├── README.rst │ │ ├── README.txt │ │ ├── examples │ │ │ ├── demo_jsonlab_basic.m │ │ │ ├── demo_ubjson_basic.m │ │ │ ├── example1.json │ │ │ ├── example2.json │ │ │ ├── example3.json │ │ │ ├── example4.json │ │ │ ├── jsonlab_basictest.matlab │ │ │ ├── jsonlab_selftest.m │ │ │ ├── jsonlab_selftest.matlab │ │ │ └── jsonlab_speedtest.m │ │ ├── jsonopt.m │ │ ├── loadjson.m │ │ ├── loadubjson.m │ │ ├── mergestruct.m │ │ ├── package.json │ │ ├── savejson.m │ │ ├── saveubjson.m │ │ ├── struct2jdata.m │ │ └── varargin2struct.m │ ├── stimuli20190610.mat │ └── urlread2 │ │ ├── http_createHeader.m │ │ ├── http_paramsToString.m │ │ ├── license.txt │ │ ├── urlread2.m │ │ ├── urlread_notes.txt │ │ ├── urlread_todos.txt │ │ └── urlread_versionInfo.txt ├── lightsafety │ ├── spd_source1_100Pct.csv │ ├── spd_source1_5Pct.csv │ ├── spd_source2_100Pct.csv │ └── spd_source2_5Pct.csv └── silent_substitution │ ├── colorimetry │ └── lin2012xyz10e_1_7sf.csv │ ├── contrast_calc.m │ ├── data │ ├── corrected_oo_spectra.csv │ └── stlab_alphaopic.csv │ ├── make_stimuli.m │ ├── nlconstraint_ss.m │ └── predict_lmsri.m ├── notebooks ├── CIE_plots.ipynb ├── PIPR_analysis.ipynb ├── PLR-3000-STLAB-settings.ipynb ├── PLR-3000-analysis.ipynb ├── PLR-3000_spectrometer_validation.ipynb ├── chirps.ipynb ├── making_video_files_for_STLAB.ipynb ├── manuscript_figures.ipynb ├── ocean_optics_temperature_darkcal.ipynb ├── old_STLAB_introduction.ipynb ├── pfr_timing_pupil_core_mac_windows.ipynb ├── plr_pipr_example_experiment.ipynb ├── plr_with_pupil_core.ipynb ├── pyplr_analysis_pipeline.ipynb └── stlab_oo_spectrometer_regression.ipynb ├── paper ├── 2021.06.02.446731v1.full.pdf └── pyplr -a-versatile,-integrated-system-of-hardware-and-software-for-researching-the-human-pupillary-light-reflex.bib ├── pyplr ├── CIE.py ├── __init__.py ├── calibrate.py ├── graphing.py ├── jeti.py ├── leduino.py ├── oceanops.py ├── plr.py ├── preproc.py ├── protocol.py ├── pupil.py ├── spectools.py ├── stlab.py ├── stlabhelp.py ├── stlabsampler.py ├── stlabscene.py └── utils.py ├── pyproject.toml ├── requirements.txt └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PyPlr/cvd_pupillometry/HEAD/.gitignore -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PyPlr/cvd_pupillometry/HEAD/CITATION.cff -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: 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