function [newP] = markPeakPauses(Qd, validPeaks, validTroughs, th);
% check for same-height pts around each peak and trough found in newPT
% Qd the decimated respiration signal
% validPeaks the vector of peak indexes, on the decimated-by-5 (200Hz) signal
% validTroughs the vector of trough indexes, on the decimated-by-5 signal
% th the threshold used by newPT
m = 0; % counter for pts near each peak or trough
newP = []; % vector of pause starts & stops
thisPeak = 0; nextTrough = 0; prevTrough = 0;
numPeaks = length(validPeaks); % # of valid peaks after classifyPeaks.m
numTroughs = length(validTroughs);
for i = 1:numPeaks
thisPeak = validPeaks(i); % going to find the pause size for this peak
if validPeaks(1) < validTroughs(1) % peak-first signal
if i <= numTroughs
nextTrough = validTroughs(i); % peak-first, so next trough has same index
else
nextTrough = validTroughs(numTroughs); % if no next trough assign the last one
end;
if i > 1 & i < numTroughs
prevTrough = validTroughs(i - 1); % and previous trough has previous index
else
prevTrough = validTroughs(1); % assign to first trough
end;
else
if i < numTroughs
nextTrough = validTroughs(i + 1); % trough-first, so next trough has index + 1 number
else
nextTrough = validTroughs(numTroughs);
end;
if i <= numTroughs
prevTrough = validTroughs(i); % and previous trough has same index
else
nextTrough = validTroughs(numTroughs);
end;
end;
%%%%%%%%%%%%%% find pause to the left of the peak %%%%%%%%%%%%%%
sth = abs((Qd(prevTrough) - Qd(thisPeak)) * .30); % small threshold = 15% of slope height
mth = abs((Qd(prevTrough) - Qd(thisPeak)) * .08); % medium threshold
ssth = abs(Qd(prevTrough) - Qd(thisPeak)) * .0005;
m = -1; littles = 0; negatives = 0; stop = 0;
% loop until end of window is sth LOWER than the peak
while abs(Qd(thisPeak) - Qd(thisPeak + m)) < sth
if (thisPeak + m) == 2
m = m + 1;
break;
else
m = m - 1;
end;
end;
% now loop back until a stopping condition is met - that is the end of the peak
while stop == 0
if abs(Qd(thisPeak + m - 2) - Qd(thisPeak + m)) < ssth
littles = littles + 1; % last point has zero or not-too-steep slope
else
littles = 0; % other - medium or steep slope
end;
if (Qd(thisPeak + m) - Qd(thisPeak + m - 1) < 0)
negatives = negatives + 1; % this point lower than last
else
negatives = 0;
end;
if m == -1
m = 0; stop = 1; % back to trough point - stop
s = ['m == 1 - Lp', int2str(i)]
elseif Qd(thisPeak + m) >= Qd(thisPeak)
stop = 1; % height is same as peak point - stop
s = ['back to start level - Lp', int2str(i)]
elseif littles > 30 & ((Qd(thisPeak) - Qd(thisPeak + m)) < mth)
stop = 1; % slope not changing much anymore
m = m - 15; % move back to start of the littles
s = ['littles > 30 - Lp', int2str(i)]
elseif negatives > 10 & ((Qd(thisPeak) - Qd(thisPeak + m)) < mth)
stop = 1; % went downhill for 10 points
m = m - 10;
s = ['negatives > 10 - Lp', int2str(i)]
else
m = m + 1; % move one point closer to the trough
end;
end;
newP = [newP, (thisPeak + m)]; % add in new point
%%%%%%%%%%%%%% find pause to the right of the peak %%%%%%%%%%%%%%
sth = abs((Qd(nextTrough) - Qd(thisPeak)) * .30); % small threshold = 15% of slope height
mth = abs((Qd(nextTrough) - Qd(thisPeak)) * .08); % medium threshold
ssth = abs(Qd(nextTrough) - Qd(thisPeak)) * .0005; % super small threshold
m = 1; % set counter for checking to the right of the peak
littles = 0; negatives = 0;
stop = 0; % set marker for moving back to end of pause
% loop until end of window is sth LOWER than the peak
while (thisPeak + m + 3 < max(size(Qd))) & abs(Qd(thisPeak) - Qd(thisPeak + m)) < sth
m = m + 1;
end;
while stop == 0
thisSlope = Qd(thisPeak + m + 2) - Qd(thisPeak + m); % slope of last point
if abs(thisSlope) < ssth
littles = littles + 1; % zero or not too steep slope
else
littles = 0; % other - medium or steep slope
end;
if (Qd(thisPeak + m) - Qd(thisPeak + m + 1) < 0)
negatives = negatives + 1; % this point lower than last
else
negatives = 0;
end;
if m <= 1
m = 0; stop = 1; % back to trough point - stop
s = ['m <= 1 - Rp', int2str(i)]
elseif Qd(thisPeak + m) >= Qd(thisPeak)
stop = 1; % height is same as peak point - stop
s = ['back to start level - Rp', int2str(i)]
elseif littles > 30 & ((Qd(thisPeak) - Qd(thisPeak + m)) < mth)
stop = 1; % slope not changing much anymore
m = m + 15; % move back to the start of the 3 littles
s = ['littles > 30 - Rp', int2str(i)]
elseif negatives > 10 & ((Qd(thisPeak) - Qd(thisPeak + m)) < mth)
stop = 1; % went downhill for 10 points
m = m + 10;
s = ['negatives > 10 - Rp', int2str(i)]
else
m = m - 1; % back one point
end;
end;
newP = [newP, (thisPeak + m)]; % add in new point
end;