Closed-Loop Systems

In a closed-loop experiment, we want the behaviour data to generate feedback in real-time into the external world, establishing a relationship where the output of the system depends on detected sensory input. Many behavioural experiments in neuroscience require some kind of closed-loop interaction between the subject and the experimental setup. The exercises below will show you how to use the online data processing capabilities of Bonsai to create and benchmark many different kinds of closed-loop systems.

Measuring closed-loop latency

One of the most important benchmarks to evaluate the performance of a closed-loop system is the latency, or the time it takes for a change in the output to be generated in response to a change in the input.

The easiest way to measure the latency of a closed-loop system is to use a digital feedback test. In this test, we measure a binary output from the closed-loop system and feed it directly into the input sensor. We then record a series of measurements where we change the output to HIGH if the sensor detects LOW, and change it to LOW if the sensor detects HIGH. The time interval between HIGH and LOW signals will give us the total closed-loop latency of the system, also known as the round-trip time.

Exercise 1: Measuring serial port communication latency

• Connect the digital pin 8 on the Arduino to digital pin 13 using a jumper wire.
• Insert a DigitalInput source and set its Pin property to 8.
• Insert a BitwiseNot transform.
• Insert a DigitalOutput sink and configure its Pin property to pin 13.
• Insert a TimeInterval operator.
• Right-click on the TimeInterval operator and select Output > Interval > TotalMilliseconds.

Note: The TimeInterval operator measures the interval between consecutive events in an observable sequence using the high-precision event timer (HPET) in the computer. The HPET has a frequency of at least 10MHz, allowing us to accurately time intervals with sub-microsecond precision.

• Run the workflow and measure the round-trip time between digital input messages.

Exercise 2: Measuring video acquisition latency

• Connect a red LED to Arduino digital pin 13.
• Insert a CameraCapture source.
• Insert a Crop transform.
• Run the workflow and set the RegionOfInterest property to a small area around the LED.

Hint: You can use the visual editor for an easier calibration. While the workflow is running, right-click on the Crop transform and select Show Default Editor from the context menu or click in the small button with ellipsis that appears when you select the RegionOfInterest property.

• Insert a Sum (Dsp) transform and select the Val2 field from the output.

Note: The Sum (Dsp) operator adds the value of all the pixels in the image together, across all the color channels. Assuming the default BGR format, the result of summing all the pixels in the Red channel of the image will be stored in Val2. Val0 and Val1 would store the Blue and Green values, respectively. If you are using an LED with a color other than Red, please select the output field accordingly.

• Insert a GreaterThan transform.
• Insert a BitwiseNot transform.
• Insert a DigitalOutput sink and configure its Pin property to pin 13.
• Run the workflow and use the visualizer of the Sum operator to choose an appropriate threshold for GreaterThan. When connected to pin 13, the LED should flash a couple of times when the Arduino is first connected.
• Insert a DistinctUntilChanged operator after the BitwiseNot transform.

Note: The DistinctUntilChanged operator filters consecutive duplicate items from an observable sequence. In this case, we want to change the value of the LED only when the threshold output changes from LOW to HIGH, or vice-versa. This will let us measure correctly the latency between detecting a change in the input and measuring the response to that change.

• Insert the TimeInterval operator and select Output > Interval > TotalMilliseconds.
• Run the workflow and measure the round-trip time between LED triggers.

Given the measurements obtained in Exercise 2, what would you estimate is the input latency for video acquisition?

Closed-Loop Control

Exercise 3: Triggering a digital line based on region of interest activity

• Insert a CameraCapture source.
• Insert a Crop transform.
• Run the workflow and use the RegionOfInterest property to specify the desired area.
• Insert a Grayscale and a Threshold (Vision) transform (or the color segmentation operators).
• Insert a Sum (Dsp) transform, and select the Val0 field from the output.
• Insert a GreaterThan transform and configure the Value property to an appropriate threshold. Remember you can use the visualizers to see what values are coming through the Sum and what the result of the GreaterThan operator is.
• Insert the Arduino DigitalOutput sink.
• Set the Pin property of the DigitalOutput operator to 13.
• Configure the PortName property.
• Run the workflow and verify that entering the region of interest triggers the Arduino LED.
• Optional: Replace the Crop transform by a CropPolygon to allow for non-rectangular regions.

Note: The CropPolygon operator uses the Regions property to define multiple, possibly non-rectangular regions. The visual editor is similar to Crop, where you draw a rectangular box. However, in CropPolygon you can move the corners of the box by right-clicking inside the box and dragging the cursor to the new position. You can add new points by double-clicking with the left mouse button, and delete points by double-clicking with the right mouse button. You can delete regions by pressing the Del key and cycle through selected regions by pressing the Tab key.

Exercise 4: Modulating stimulus intensity based on distance to a point

• Insert a FunctionGenerator source.
• Set the Amplitude property to 500, and the Frequency property to 200.
• Insert an AudioPlayback sink.
• Externalize the Amplitude property of the FunctionGenerator using the right-click context menu.

If you run the workflow, you should hear a pure tone coming through the speakers. The FunctionGenerator periodically emits buffered waveforms with values ranging between 0 and Amplitude, the shape of which changes the properties of the tone. For example, by changing the value of Amplitude you can make the sound loud or soft. The next step is to modulate the Amplitude property dynamically based on the distance of the object to a target.

• Create a video tracking workflow using ConvertColor, HsvThreshold, and the Centroid operator to directly compute the centre of mass of a colored object.
• Insert a Subtract transform and configure the Value property to be some target coordinate in the image.

The result of the Subtract operator will be a vector pointing from the target to the centroid of the largest object. The desired distance from the centroid to the target would be the length of that vector.

• Insert an ExpressionTransform operator. This node allows you to write small mathematical and logical expressions to transform input values.
• Right-click on the ExpressionTransform operator and select Show Default Editor. Set the expression to Math.Sqrt(X*X + Y*Y).

Note: Inside the Expression editor you can access any field of the input by name. In this case X and Y represent the corresponding fields of the Point2f data type. You can check which fields are available by right-clicking the previous node. You can use all the normal arithmetical and logical operators as well as the mathematical functions available in the Math type. The default expression it means “input” and represents the input value itself.

• Connect the ExpressionTransform operator to the externalized Amplitude property.
• Run the workflow and verify that stimulus intensity is modulated by the distance of the object to the target point.
• Optional: Modulate the Frequency property instead of Amplitude.
• Optional: Use the Rescale operator to adjust the gain of the modulation by configuring the Min, Max, RangeMax and RangeMin properties. Set the RescaleType property to Clamp to restrict the output values to an allowed range.

Note: You can specify inverse relationships using Rescale if you set the maximum input value to the Min property, and the minimum input value to the Max property. In this case, a small distance will generate a large output, and a large distance will produce a small output.

Exercise 5: Triggering a digital line based on distance between objects

• Reproduce the above object tracking workflow using FindContours and BinaryRegionAnalysis.
• Insert a SortBinaryRegions transform. This operator will sort the list of objects by area, in order of largest to smallest.

To calculate the distance between the two largest objects in every frame you will need to take into account some special cases. Specifically, there is the possibility that no object is detected, or that the two objects may be touching each other and will be detected as a single object. You can develop a new operator in order to perform this specific calculation.

• Insert a PythonTransform operator. Change the Script property to the following code:

from math import sqrt

@returns(float)
def process(value):

  # no objects were detected
  if value.Count == 0:
    return float.NaN

  # only one object was detected, assume objects are touching
  elif value.Count == 1:
    return 0

  # two or more objects were detected, compute distance
  else:
    # d: displacement between two largest objects
    d = value[0].Centroid - value[1].Centroid
    return sqrt(d.X * d.X + d.Y * d.Y)

• Insert a LessThan transform and configure the Value property to an appropriate threshold.
• Connect the boolean output to Arduino pin 13 using a DigitalOutput sink.
• Run the workflow and verify that the Arduino LED is triggered when the two objects are close together.

Exercise 6: Centring the video on a tracked object

• Insert a CameraCapture source.
• Insert a WarpAffine transform. This node applies affine transformations on the input defined by the Transform matrix.
• Externalize the Transform property of the WarpAffine operator using the right-click context menu.
• Create an AffineTransform source and connect it to the externalized property.
• Run the workflow and change the values of the Translation property while visualizing the output of WarpAffine. Notice that the transformation induces a translation in the input image controlled by the values in the property.

• In a new branch, create a video tracking pipeline using ConvertColor, HsvThreshold, and the Centroid operator to directly compute the centre of mass of a colored object.
• Insert a Negate transform. This will make the X and Y coordinates of the centroid negative.

We now want to map our negative centroid to the Translation property of AffineTransform, so that we dynamically translate each frame using the negative position of the object. You can do this by using property mapping operators.

• Insert an InputMapping operator.
• Connect the InputMapping to the AffineTransform operator.
• Open the PropertyMappings editor and add a new mapping to the Translation property.
• Run the workflow. Verify the object is always placed at position (0,0). What is the problem?

Note: Generally for image coordinates, (0,0) is at the top-left corner, and the center will be at coordinates (width/2, height/2), usually (320,240) for images with 640 x 480 resolution.

• Insert an Add transform. This will add a fixed offset to the point. Configure the Value property with an offset that will place the object at the image centre, e.g. (320,240).
• Run the workflow, and verify the output of WarpAffine is now a video which is always centred on the tracked object.
• Optional: Insert a Crop transform after WarpAffine to select a bounded region around the object.
• Optional: Modify the object tracking workflow to use FindContours and BinaryRegionAnalysis.