How can I calculate daylight autonomy from energy plus -Illuminance output (that is point in time)?

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If you have the daylight illuminance, all you need is the illuminance target (setpoint) -- which you can get from the daylighting control point in the EnergyPlus model -- and then it's just a simple calculation for DA:

if daylightIlluminance >= illuminanceSetpoint DA=1 else DA=0 end

Typically, DA is calculated spatially (i.e. for all the points in the illuminance map), for the entire year, and then is plotted with respect to the percentage of the year (usually occupied hours) that DA is met. If you have the values in a .csv file already, you could whip up something in Excel or the plotting tool of your choice to visualize this data easily.

For what it's worth, OpenStudio exports DA (as well as cDA and UDI) to a csv file for you automatically, if you use Radiance for your daylighting simulation engine (in lieu of EnergyPlus' built-in engine). If you look in the project directory, locate the file /run/1-Ruby-0/DaylightingMetrics.csv. This has a space-by-space summary of DA, cDA, and UDI. You get the total-hours and percentage-of-analysis-period each metric's standard is met, for daylit hours, occupied hours, and daylit+occupied hours -- all based on the setpoint found in the space's primary daylighting control point.