Scripting

Lets start with this, it should have everything we need to use:

/**
 * Intermediate Scripting 2 - wait_until
 *
 * Demonstrates more advanced wait commands, specifically wait_until, which
 *   make it easier to write and mantain scripts.
 *
 * made: 2017-03-17
 * by:   William A. Norman
 */

// Takes a single image with red lights.
var protocol = new CameraProtocol("example_protocol")
    protocol.setAnalysisID       ("example")
    protocol.setNumberLoops      ( 1 )
    protocol.setFramesPerLoop    ([ 1 ])
    protocol.setMeasuringLight   ([ 1 ])
    protocol.setSaturationFlash  ([ 0 ])
    protocol.setExposure         ([ "50us" ])
    protocol.setFrameInterval    ([ "70ms" ])

// Set starting conditions
set_intensity(0)

// Take a sample imageset
run_protocol(protocol)

We're going to use the protocol to demonstrate how wait_until can effect the day.

Say we want to start this experiment at 06:00, tomorrow. But we don't want to be there that early, and we don't want to have to use any math with the wait command. The answer is wait_until:

// Events after this will not happen until 06:00 (real time!)
wait_until("06:00")

set_intensity(100)
run_protocol(protocol)

Go ahead and run the script now, and you'll see that it executes at the time you specified.

Lets take a look at the data from the run you just did.

• root
  • Timeline.xml
  • cam_0
    • day_-1
    • day_0
  • cam_1
    • day_-1
    • day_0
  • cam_2
    • day_-1
    • day_0

Wait, where did day_0 come from? We didn't have an EOD in that script!

It turns out the chamber cannot have events before and after the first wait_until in the same day. Because scripts frequently have starting conditions, a wait_until, another condition, THEN the first EOD, it will implicitly switch to day 0 after the first wait_until if no EODs have been give, or if only EOD(-1) was given. It will NOT do this unless it is on day -1.

So what does this mean for you, as you write a script? If you're not using wait_until, you don't have to worry about anything. If you are, don't call EOD until AFTER the first wait_until, or if you need EOD's before that, make sure you call it directly after the first wait_until.

Well, we don't want our data on day_-1 OR day_0.. we want it to start on day_1. So lets make it! Put this snippet directly after that wait_until:

// Start of real data capture
EOD(1)

Reguardless of if you're using wait_until or not, you want to declare your first EOD before your first day of real data. Days at or under 0 are generally reserved for system/debug use, and experiment setup. Don't use them on real data!

Lets add another light change, 30 seconds after hte last one:

// This will happen 30 seconds after 06:00
wait("30s")

set_intensity(200)
run_protocol(protocol)

If you run that, it will wait_until 06:00, set the intensity to 100, run the protocol, then wait 30 more seconds before setting the intensity to 200 and running the protocol again.

In effect, a wait(30min) after a wait_until(06:00) is exactly the same as a wait_until(06:30).

Try adding this to your script (but remember to delete it afterwords!)

wait("30min")
wait_until("06:28")

set_intensity(300)
run_protocol(protocol)

Compile that and lets take a look at the graph...

Oh my! That doesn't look like a 28 minute wait at all. That's because when the last wait_until(06:28) hit, wait(30min) command had already pushed it past 06:28- so the wait_until waited until the NEXT 06:28, almost 24 hours later!

Anyway, you can delete that part of the code now.

Okay, the complete script should now look like this:

/**
 * Intermediate Scripting 2 - wait_until
 *
 * Demonstrates more advanced wait commands, specifically wait_until, which
 *   make it easier to write and mantain scripts.
 *
 * made: 2017-03-17
 * by:   William A. Norman
 */

// Takes a single image with red lights.
var protocol = new CameraProtocol("example_protocol")
    protocol.setAnalysisID       ("example")
    protocol.setNumberLoops      ( 1 )
    protocol.setFramesPerLoop    ([ 1 ])
    protocol.setMeasuringLight   ([ 1 ])
    protocol.setSaturationFlash  ([ 0 ])
    protocol.setExposure         ([ "50us" ])
    protocol.setFrameInterval    ([ "70ms" ])

// Set starting conditions
set_intensity(0)

// Take a sample imageset
run_protocol(protocol)

// Events after this will not happen until 06:00 (real time!)
wait_until("06:00")

// Start of real data capture
EOD(1)

set_intensity(100)
run_protocol(protocol)

// This will happen 30 seconds after 06:00
wait("30s")

set_intensity(200)
run_protocol(protocol)