function [newT] = markTroughPauses(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 (only valid), on the decimated-by-5 (200Hz) signal
% validTroughs the vector of trough indexes (only valid), on the decimated-by-5 signal
% th the threshold used by newPT
m = 0; % counter for pts near each peak or trough
newT = []; % matrix of new trough elements
thisTrough = 0; nextPeak = 0; prevPeak = 0;
numPeaks = max(size(validPeaks)); % # of valid peaks after classifyPeaks.m
numTroughs = max(size(validTroughs));
for i = 1:numTroughs
thisTrough = validTroughs(i); % going to find the pause size for this trough
if validPeaks(1) < validTroughs(1) % peak-first signal
prevPeak = validPeaks(i); % peak-first, so prev peak has same index as this trough
%s = 'peak-first'
if i < numPeaks
nextPeak = validPeaks(i + 1); % next peak has index + 1 number
else
nextPeak = validPeaks(numPeaks); % if no end peak, assign to last one
end;
else % trough-first signal
%s = 'trough-first'
if i > 1
prevPeak = validPeaks(i - 1); % trough-first, so prev peak has index i - 1
else
prevPeak = validPeaks(1); % if the first trough, can't use peak i - 1, so use peak 2
end;
if i < numPeaks
nextPeak = validPeaks(i); % trough-first, so next peak has index i
else
nextPeak = validPeaks(numPeaks); % don't want to fall off the end if there is one peak too few
end;
end;
%%%%%%%%%%%%%%%%%%%%%%% find the pause to the LEFT of this trough %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
sth = abs((Qd(prevPeak) - Qd(thisTrough)) * .30); % small threshold = 15% of slope height
mth = abs((Qd(prevPeak) - Qd(thisTrough)) * .08); % medium threshold
ssth = abs(Qd(prevPeak) - Qd(thisTrough)) * .0005; % super-small threshold
m = -1; littles = 0; negatives = 0; stop = 0; % set markers
% loop until end of window is sth HIGHER than the trough
while (Qd(thisTrough + m) - Qd(thisTrough)) < sth
if (thisTrough + m) == 2
m = m + 1
break;
else
m = m - 1; % back up one more step
end;
end;
if thisTrough == 11499
s = ['m = ', int2str(m), ' before looping back']
end;
while stop == 0 % now loop back towards the trough until a stopping condition is met
if abs(Qd(thisTrough + m) - Qd(thisTrough + m - 1)) < ssth % slope of last point less than ssth
littles = littles + 1; % zero or not too steep slope
else
littles = 0; % other - medium or steep slope
end;
if (Qd(thisTrough + m - 2) - Qd(thisTrough + m) < 0)
negatives = negatives + 1; % this point lower than last - should be higher
else
negatives = 0;
end;
if thisTrough == 11499
s = ['m = ', int2str(m), ' looping back']
end;
if m == -1
m = 0;
stop = 1; % back to trough point - stop
s = ['m == -1 - LT', int2str(i), ' thisTrough=', int2str(thisTrough), ' mark=', int2str(thisTrough + m)]
elseif Qd(thisTrough + m) <= Qd(thisTrough)
stop = 1; % height is lower or equal to the trough - stop
s = ['back to start level - LT', int2str(i), ' thisTrough=', int2str(thisTrough), ' mark=', int2str(thisTrough + m)]
elseif littles > 30 & ((Qd(thisTrough + m) - Qd(thisTrough)) < mth)
stop = 1; % slope not changing much anymore
m = m - 15; % move back to middle of the 3 littles
s = ['littles > 30 - LT', int2str(i), ' thisTrough=', int2str(thisTrough), ' mark=', int2str(thisTrough + m)]
elseif negatives > 10 & ((Qd(thisTrough + m) - Qd(thisTrough)) < mth)
stop = 1; % went the wrong direction for 10 points in a row
m = m - 10;
s = ['negatives > 10 - LT', int2str(i), ' thisTrough=', int2str(thisTrough), ' mark=', int2str(thisTrough + m)]
else
m = m + 1; % move one point more towards the trough
end;
end;
newT = [newT, (thisTrough + m)]; % add in new point
%%%%%%%%%%%%%%%%%%%%%%% find the pause to the RIGHT of this trough %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
sth = abs((Qd(nextPeak) - Qd(thisTrough)) * .30); % small threshold = 15% of slope height
mth = abs((Qd(prevPeak) - Qd(thisTrough)) * .08); % medium threshold
ssth = abs(Qd(nextPeak) - Qd(thisTrough)) * .0005;
m = 1; % set counter for checking to the right of the trough
littles = 0; negatives = 0; stop = 0; % set marker for moving back to end of pause
% loop until end of window is sth HIGHER than the trough
while (thisTrough + m + 3 < max(size(Qd))) & (Qd(thisTrough + m) - Qd(thisTrough)) < sth
m = m + 1;
end;
while stop == 0 % now loop back towards the trough until a stopping condition is met
thisSlope = Qd(thisTrough + m + 2) - Qd(thisTrough + 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(thisTrough + m + 1) - Qd(thisTrough + m) < 0)
negatives = negatives + 1; % this point lower than last - should be higher
else
negatives = 0;
end;
if m <= 1
m = 0; stop = 1; % back to trough point - stop
s = ['m <= 1 - RT', int2str(i), ' thisTrough=', int2str(thisTrough), ' mark=', int2str(thisTrough + m)]
elseif Qd(thisTrough + m) <= Qd(thisTrough)
stop = 1; % height is lower or equal to the trough - stop
s = ['back to start level - RT', int2str(i), ' thisTrough=', int2str(thisTrough), ' mark=', int2str(thisTrough + m)]
elseif littles > 30 & ((Qd(thisTrough + m) - Qd(thisTrough)) < mth)
stop = 1; % slope not changing much anymore
m = m + 15; % move back to the start of the 3 littles
s = ['littles > 30 - RT', int2str(i), ' thisTrough=', int2str(thisTrough), ' mark=', int2str(thisTrough + m)]
elseif negatives > 10 & ((Qd(thisTrough + m) - Qd(thisTrough)) < mth)
stop = 1; % went the wrong direction for 10 points in a row
m = m + 10;
s = ['negatives > 10 - RT', int2str(i), ' thisTrough=', int2str(thisTrough), ' mark=', int2str(thisTrough + m)]
else
m = m - 1; % back one point
end;
end;
newT = [newT, (thisTrough + m)]; % add in new point
end;