Counting number of bursts

How can I count the number of periods of activity above a certain threshold?

I have an EMG signal with some bursts of activity above baseline. I have used the following code to identify those periods of activity (at least 200 points) above a predetermined threshold value that I have chosen:

above_threshold = (EMG_signal > threshold);
spanLocs = bwlabel(above_threshold);
spanLength = regionprops(spanLocs, 'area');
spanLength = [spanLength.Area];
goodSpans = find(spanLength>=200); 
allInSpans = find(ismember(spanLocs, goodSpans));

Now I would like to count the number of bursts that have been identified above (i.e. see image attached. In this example, in red are shown the bursts identified).

Any help is much appreciated. Thanks a lot. Antonio

Answer 1

[Image Analyst]

Simply call bwareafilt and bwlabel. So get rid of all that and just simply have this:

EMG_signal = [1 2 4 2 0 0 2 2 0 2 0 2 2 2] % Sample signal with 2 bursts
threshold = 1.5
above_threshold = (EMG_signal > threshold)
minAcceptableLength = 3; % or 200 or whatever.
% Find spans that are long enough.
isLongEnough = bwareafilt(above_threshold, [minAcceptableLength, inf])
% Count the number of spans (bursts) that are long enough.
[labeledSpans, numberOfBursts] = bwlabel(isLongEnough)

[Antonio Morales]

How could I add the following condition to the example above?:

I want the number of spans (bursts) that are long enough counted only when there are a minimum of samples between two spans, otherwise it would be counted as only one span.

Any feedback on this is much appreciated.

[Image Analyst]

You can call bwareaopen() to get rid of "holes" of short zeros between valid spans. What if a span is not long enough, like it's only 2 long instead of 3, but if you get rid of a span of zeros in between two such spans then it now becomes long enough. Do you want that consolidated span or not?

[Antonio Morales]

No, if a span is not long enough at first, it should not be counted as span even if after getting rid of zeros between spans it becomes long enough. How could that be worked around?

Thank you.

[Image Analyst]

Try this:

EMG_signal = [1 1 2 4 2 0 0 2 2 0 2 0 2 2 2 0 4 4 4 4 1] % Sample signal with 2 bursts
threshold = 1.5
above_threshold = (EMG_signal > threshold)
minAcceptableLength = 3; % or 200 or whatever.
% Find spans that are long enough.
isLongEnough = bwareafilt(above_threshold, [minAcceptableLength, inf])
% Specify the max number of zeros 0's there are that should be filled in.
maxHoleSize = 4;
holes = bwareafilt(~isLongEnough, [0, maxHoleSize])
% Don't take any holes if they are on the front or end of the vector
% because they are not bounded by spans on each side.
firstZero = find(holes, 1, 'first')
lastZero = find(holes, 1, 'last')
holes(1:firstZero) = 0;
holes(lastZero:end) = 0
% Now fill in the hoels by ORing:
isLongEnough = isLongEnough | holes;
% Count the number of spans (bursts) that are long enough.
[labeledSpans, numberOfBursts] = bwlabel(isLongEnough)
% Find the lengths of all the spans
props = regionprops(labeledSpans, 'Area');
allLengths = [props.Area]