time   calls  line
                  1 function flags = deglitch(d, params)
                  2 
                  3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                  4 %
                  5 %  function d = deglitch(d, params)
                  6 %
                  7 %  rough function to find and flag glitches in the data, focusing on
                  8 %  spurious points and on RFIs.  Needs a lot of improvement.  Right now
                  9 %  might flag too much data.
                 10 %
                 11 %  params = [threshld on channel 1, threshold on channel 2];
                 12 %
                 13 %  sjcm & act
                 14 %
                 15 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                 16 
                 17 % first we only want to flag on data is not the noise source.
  0.51       1   18 dnonoise = cutObs(d, 'noise', 'not'); 
                 19 
             1   20 data = dnonoise.antenna0.receiver.data; 
                 21 
                 22 % first we check to see if there spurious points.
             1   23 indSpurious = zeros(size(data,1),1); 
             1   24 stop = 0; 
             1   25 while(stop==0) 
             1   26   for m=1:size(data,2) 
  1.03       6   27     a(:,m) = smooth(data(:,m)); 
             6   28   end 
  0.02       1   29   diffVals = a-dnonoise.antenna0.receiver.data; 
  0.19       1   30   stdVals  = std(diffVals); 
  0.15       1   31   diffNorm = abs(diffVals)./repmat(stdVals, [size(diffVals,1) 1]); 
  0.03       1   32   badVals     = diffNorm>3; 
  0.01       1   33   newIndSpurious = sum(badVals,2)>1; 
                 34 
  0.01       1   35   indSpurious(newIndSpurious) = 1; 
  0.03       1   36   data(newIndSpurious,:) = a(newIndSpurious,:); 
                 37 
             1   38   l = length(find(newIndSpurious)); 
             1   39   newOnes = length(find(indSpurious)) - l; 
                 40   
             1   41   if(newOnes<1) 
             1   42     stop = 1; 
             1   43   end 
             1   44 end 
                 45 
                 46 
                 47 % next we look for values where the data spikes up over a small amount of
                 48 % time.
  0.49       1   49 da = deriv(dnonoise.antenna0.receiver.data); 
  0.03       1   50 indDeriv = abs(da(:,1))>params(1) | abs(da(:,6)>params(2)); 
                 51 
                 52 
                 53 % next we check for the boxCarRejection on the "pseudo-good" data  
                 54 % NOT DOING UNTIL WE FIND THE RIGHT PARAMETERS
                 55 %dnonoise.antenna0.receiver.data(indSpurious | indDeriv,:) = nan;
                 56 %[rfiFlag] = boxRejection(dnonoise,5,10);
                 57 %t = (dnonoise.antenna0.receiver.utc - dnonoise.antenna0.receiver.utc(1))*24*60*60;
                 58 %plot(t, log(dnonoise.antenna0.receiver.data(:,1)));
                 59 %hold on
                 60 %plot(t(rfiFlag), log(dnonoise.antenna0.receiver.data(rfiFlag,1)), '.r');
                 61 %hold off
                 62 
                 63 % combine the ones we flagged on
             1   64 indDeglitchFast = indSpurious | indDeriv; 
                 65 
                 66 % convert to size of d, (instead of dnonoise)
             1   67 indFinal = logical(zeros(size(d.flags.fast,1),1)); 
  0.01       1   68 indFinal(~d.index.noise.fast) = indDeglitchFast; 
                 69 
                 70 % convert to other timescales.
  0.08       1   71 [dnew, flags] = setNewFlag(d, indFinal, 'deglitch'); 
                 72 
             1   73 clear dnew; 
                 74 % now we have to set the proper flags in the flag field
             1   75 return; 

Other subfunctions in this file are not included in this listing.