rmlinesmovingwinc

PURPOSE ^

fits significant sine waves to data (continuous data) using overlapping windows.

SYNOPSIS ^

function [datac,datafit,Amps,freqs]=rmlinesmovingwinc(data,movingwin,tau,params,p,plt,f0)

DESCRIPTION ^

 fits significant sine waves to data (continuous data) using overlapping windows.

 Usage: [datac,datafit]=rmlinesmovingwinc(data,movingwin,tau,params,p,plt)

  Inputs:  
 Note that units of Fs, fpass have to be consistent.
       data        (data in [N,C] i.e. time x channels/trials or as a single vector) - required.
       movingwin         (in the form [window winstep] i.e length of moving
                                                 window and step size)
                                                 Note that units here have
                                                 to be consistent with
                                                 units of Fs - required
       tau      parameter controlling degree of smoothing for the amplitudes - we use the
       function 1-1/(1+exp(-tau*(x-Noverlap/2)/Noverlap) in the region of overlap to smooth
       the sinewaves across the overlap region. Noverlap is the number of points 
       in the overlap region. Increasing tau leads to greater overlap smoothing, 
       typically specifying tau~10 or higher is reasonable. tau=1 gives an almost
       linear smoothing function. tau=100 gives a very steep sigmoidal. The default is tau=10.
       params      structure containing parameters - params has the
       following fields: tapers, Fs, fpass, pad
           tapers : precalculated tapers from dpss or in the one of the following
                    forms: 
                   (1) A numeric vector [TW K] where TW is the
                       time-bandwidth product and K is the number of
                       tapers to be used (less than or equal to
                       2TW-1). 
                   (2) A numeric vector [W T p] where W is the
                       bandwidth, T is the duration of the data and p 
                       is an integer such that 2TW-p tapers are used. In
                       this form there is no default i.e. to specify
                       the bandwidth, you have to specify T and p as
                       well. Note that the units of W and T have to be
                       consistent: if W is in Hz, T must be in seconds
                       and vice versa. Note that these units must also
                       be consistent with the units of params.Fs: W can
                       be in Hz if and only if params.Fs is in Hz.
                       The default is to use form 1 with TW=3 and K=5
                    Note that T has to be equal to movingwin(1).

            Fs             (sampling frequency) -- optional. Defaults to 1.
               fpass       (frequency band to be used in the calculation in the form
                                   [fmin fmax])- optional. 
                                   Default all frequencies between 0 and Fs/2
            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...). 
                    -1 corresponds to no padding, 0 corresponds to padding
                    to the next highest power of 2 etc.
                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
                       to 512 points, if pad=1, we pad to 1024 points etc.
                       Defaults to 0.
        p            (P-value to calculate error bars for) - optional.
        Defaults to 0.05/Nwin where Nwin is length of window which
        corresponds to a false detect probability of approximately 0.05.
       plt         (y/n for plot and no plot respectively) - default no
                   plot.
       f0          frequencies at which you want to remove the
                   lines - if unspecified the program uses the f statistic
                   to determine appropriate lines.

  Outputs: 
       datafit        (fitted sine waves)
       datac          (cleaned up data)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [datac,datafit,Amps,freqs]=rmlinesmovingwinc(data,movingwin,tau,params,p,plt,f0)
0002 % fits significant sine waves to data (continuous data) using overlapping windows.
0003 %
0004 % Usage: [datac,datafit]=rmlinesmovingwinc(data,movingwin,tau,params,p,plt)
0005 %
0006 %  Inputs:
0007 % Note that units of Fs, fpass have to be consistent.
0008 %       data        (data in [N,C] i.e. time x channels/trials or as a single vector) - required.
0009 %       movingwin         (in the form [window winstep] i.e length of moving
0010 %                                                 window and step size)
0011 %                                                 Note that units here have
0012 %                                                 to be consistent with
0013 %                                                 units of Fs - required
0014 %       tau      parameter controlling degree of smoothing for the amplitudes - we use the
0015 %       function 1-1/(1+exp(-tau*(x-Noverlap/2)/Noverlap) in the region of overlap to smooth
0016 %       the sinewaves across the overlap region. Noverlap is the number of points
0017 %       in the overlap region. Increasing tau leads to greater overlap smoothing,
0018 %       typically specifying tau~10 or higher is reasonable. tau=1 gives an almost
0019 %       linear smoothing function. tau=100 gives a very steep sigmoidal. The default is tau=10.
0020 %       params      structure containing parameters - params has the
0021 %       following fields: tapers, Fs, fpass, pad
0022 %           tapers : precalculated tapers from dpss or in the one of the following
0023 %                    forms:
0024 %                   (1) A numeric vector [TW K] where TW is the
0025 %                       time-bandwidth product and K is the number of
0026 %                       tapers to be used (less than or equal to
0027 %                       2TW-1).
0028 %                   (2) A numeric vector [W T p] where W is the
0029 %                       bandwidth, T is the duration of the data and p
0030 %                       is an integer such that 2TW-p tapers are used. In
0031 %                       this form there is no default i.e. to specify
0032 %                       the bandwidth, you have to specify T and p as
0033 %                       well. Note that the units of W and T have to be
0034 %                       consistent: if W is in Hz, T must be in seconds
0035 %                       and vice versa. Note that these units must also
0036 %                       be consistent with the units of params.Fs: W can
0037 %                       be in Hz if and only if params.Fs is in Hz.
0038 %                       The default is to use form 1 with TW=3 and K=5
0039 %                    Note that T has to be equal to movingwin(1).
0040 %
0041 %            Fs             (sampling frequency) -- optional. Defaults to 1.
0042 %               fpass       (frequency band to be used in the calculation in the form
0043 %                                   [fmin fmax])- optional.
0044 %                                   Default all frequencies between 0 and Fs/2
0045 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0046 %                    -1 corresponds to no padding, 0 corresponds to padding
0047 %                    to the next highest power of 2 etc.
0048 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0049 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0050 %                       Defaults to 0.
0051 %        p            (P-value to calculate error bars for) - optional.
0052 %        Defaults to 0.05/Nwin where Nwin is length of window which
0053 %        corresponds to a false detect probability of approximately 0.05.
0054 %       plt         (y/n for plot and no plot respectively) - default no
0055 %                   plot.
0056 %       f0          frequencies at which you want to remove the
0057 %                   lines - if unspecified the program uses the f statistic
0058 %                   to determine appropriate lines.
0059 %
0060 %  Outputs:
0061 %       datafit        (fitted sine waves)
0062 %       datac          (cleaned up data)
0063 if nargin < 2; error('Need data and window parameters'); end;
0064 if nargin < 4 || isempty(params); params=[]; end; 
0065 
0066 if length(params.tapers)==3 & movingwin(1)~=params.tapers(2);
0067     error('Duration of data in params.tapers is inconsistent with movingwin(1), modify params.tapers(2) to proceed')
0068 end
0069 
0070 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); % set defaults for params
0071 clear err trialave
0072 if nargin < 6; plt='n'; end;
0073 %
0074 % Window,overlap and frequency information
0075 %
0076 data=change_row_to_column(data);
0077 [N,C]=size(data);
0078 Nwin=round(Fs*movingwin(1)); % number of samples in window
0079 Nstep=round(movingwin(2)*Fs); % number of samples to step through
0080 Noverlap=Nwin-Nstep; % number of points in overlap
0081 %
0082 % Sigmoidal smoothing function
0083 %
0084 if nargin < 3 || isempty(tau); tau=10; end; % smoothing parameter for sigmoidal overlap function
0085 x=(1:Noverlap)';
0086 smooth=1./(1+exp(-tau.*(x-Noverlap/2)/Noverlap)); % sigmoidal function
0087 smooth=repmat(smooth,[1 C]);
0088 %
0089 % Start the loop
0090 %
0091 if nargin < 5 || isempty(p); p=0.05/Nwin; end % default for p value
0092 if nargin < 7 || isempty(f0); f0=[]; end; % empty set default for f0 - uses F statistics to determine the frequencies
0093 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
0094 winstart=1:Nstep:N-Nwin+1;
0095 nw=length(winstart); 
0096 datafit=zeros(winstart(nw)+Nwin-1,C);
0097 Amps=cell(1,nw);
0098 freqs=cell(1,nw);
0099 for n=1:nw;
0100    indx=winstart(n):winstart(n)+Nwin-1;
0101    datawin=data(indx,:);
0102    [datafitwin,as,fs]=fitlinesc(datawin,params,p,'n',f0);
0103    Amps{n}=as;
0104    freqs{n}=fs;
0105    datafitwin0=datafitwin;
0106    if n>1; datafitwin(1:Noverlap,:)=smooth.*datafitwin(1:Noverlap,:)+(1-smooth).*datafitwin0(Nwin-Noverlap+1:Nwin,:);end;
0107    datafit(indx,:)=datafitwin;
0108 end;
0109 datac=data(1:size(datafit,1),:)-datafit;     
0110 if strcmp(plt,'y');
0111     [S,f]=mtspectrumsegc(data,movingwin(1),params);
0112     [Sc,fc]=mtspectrumsegc(datac,movingwin(1),params);
0113     plot(f,10*log10(S),fc,10*log10(Sc));
0114 end;

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