ThresholdDetection.m

function [cutdata, start1, end1] = ThresholdDetection( Vector, threshold, Fs )
%ThresholdDetection( Vector, threshold ) Takes Vector parts above threshold
%   [ parts, starts, ends ] = ThresholdDetection( Vector, threshold )

%Turn Fs into a time. We want about 60 ms (for now) before the ap crossed the threshold and 60 ms
%at the end %%note%% put this to 180ms 05/15/2017 for analysis of extended
%aps. Seems of at the front, but might consider splitting into 2 variables
%if the end of previous APs becomes included.
apExtendEnd = (300*(Fs/1000));
apExtendFront = (60*(Fs/1000));

%% find start and end points
a=Vector>=threshold;
a=a(:);
a=[0;a;0];
a=diff(a);
starts=find(a==1);
ends=find(a==-1)-1;

%move the start and end point of each event to capture whole event
start1=(starts - apExtendFront);
end1=(ends + apExtendEnd);

%check for out of range events
firstEvent = 1;
lastEvent = length(starts);
if isempty(end1) == 0
    if (start1(1) < 0)
        firstEvent = firstEvent + 1; %if the trace starts in the middle of an event, that event is thrown out
    end
    if (length(ends)<length(starts))
        lastEvent = length(starts) - 1; %if there is an event that doesn't "end", at the end of a trace, it is thrown out
    end
    while (end1(lastEvent)>length(Vector))
        lastEvent = lastEvent - 1; %if the end point for cutting is moved past the end of the original trace, the last event is thrown out
    end
    eventsInRange = lastEvent - firstEvent + 1;
    
    %Want to add element that causes exit of threshold detection if no events
    %are detected aka there is nothing in the trace
    %% cutting
    %Need to do some cleanup here
    cutdata={};
    winlen = floor(50*(Fs/1000)); %length of window equals 50 ms time sampling rate (Fs)
    disp(winlen);
    
    for i=1:eventsInRange
        try
            ap = Vector(start1(i+firstEvent-1):end1(i+firstEvent-1));
            apTrue = 0;
            for j = winlen:winlen:floor(length(ap)/winlen)*winlen-winlen
                if (min(ap(j:(j+winlen),1))>threshold)
                    apTrue = 1;
                end
            end
            if apTrue>0
                cutdata{length(cutdata)+1,1}=Vector(start1(i+firstEvent-1):end1(i+firstEvent-1));
            end
        catch ME
            disp('Error occured in batch');
        end
    end
else if isempty(end1) == 1
        cutdata = [] ;
        start1 = [] ;
        end1 = [] ;
    
end
end