cohgrampt

PURPOSE ^

Multi-taper time-frequency coherence - two point processes given as times

SYNOPSIS ^

function [C,phi,t,f,confC,phierr,Cerr]=cohgrampt(data1,data2,movingwin,tapers,pad,Fs,fpass,err,trialave,fscorr)

DESCRIPTION ^

 Multi-taper time-frequency coherence - two point processes given as times
 process 

 Usage:

 [C,phi,t,f,confC,phierr,Cerr]=cohgramcpb(data1,data2,movingwin,tapers,nfft,Fs,fpass,err,trialave)
 Input: 
 Note units have to be consistent. Thus, if movingwin is in seconds, Fs
 has to be in Hz. see chronux.m for more information.

       data1 (structure array of spike times) -- required
       data2 (structure array of spike times) -- required
       movingwin (in the form [window winstep] -- required
       tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not 
                                                 specified, use [NW K]=[3 5]
        pad            (padding factor for the FFT) - optional. Defaults to 0.  
                       e.g. For N = 500, if PAD = 0, we pad the FFT 
                       to 512 points; if PAD = 2, we pad the FFT
                       to 2048 points, etc.
       Fs   (sampling frequency) - optional. Default 1.
       fpass    (frequency band to be used in the calculation in the form
                                   [fmin fmax])- optional. 
                                   Default all frequencies between 0 and Fs/2
       err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
                                   [0 p] or 0 - no error bars) - optional. Default 0.
       trialave (average over trials when 1, don't average when 0) - optional. Default 0
       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
                (available only for spikes). Defaults 0.
 Output:
       C (abs of coherency frequency index x channels/trials)
       phi (phase of coherency frequency x channels/trials)
       t (time)
       f (frequencies)
       confC (confidence level for c at 1-p %)
       phierr (error bars for phi)
       Cerr  (Jackknife error bars for C - use only for Jackknife)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [C,phi,t,f,confC,phierr,Cerr]=cohgrampt(data1,data2,movingwin,tapers,pad,Fs,fpass,err,trialave,fscorr)
0002 % Multi-taper time-frequency coherence - two point processes given as times
0003 % process
0004 %
0005 % Usage:
0006 %
0007 % [C,phi,t,f,confC,phierr,Cerr]=cohgramcpb(data1,data2,movingwin,tapers,nfft,Fs,fpass,err,trialave)
0008 % Input:
0009 % Note units have to be consistent. Thus, if movingwin is in seconds, Fs
0010 % has to be in Hz. see chronux.m for more information.
0011 %
0012 %       data1 (structure array of spike times) -- required
0013 %       data2 (structure array of spike times) -- required
0014 %       movingwin (in the form [window winstep] -- required
0015 %       tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not
0016 %                                                 specified, use [NW K]=[3 5]
0017 %        pad            (padding factor for the FFT) - optional. Defaults to 0.
0018 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0019 %                       to 512 points; if PAD = 2, we pad the FFT
0020 %                       to 2048 points, etc.
0021 %       Fs   (sampling frequency) - optional. Default 1.
0022 %       fpass    (frequency band to be used in the calculation in the form
0023 %                                   [fmin fmax])- optional.
0024 %                                   Default all frequencies between 0 and Fs/2
0025 %       err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0026 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0027 %       trialave (average over trials when 1, don't average when 0) - optional. Default 0
0028 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
0029 %                (available only for spikes). Defaults 0.
0030 % Output:
0031 %       C (abs of coherency frequency index x channels/trials)
0032 %       phi (phase of coherency frequency x channels/trials)
0033 %       t (time)
0034 %       f (frequencies)
0035 %       confC (confidence level for c at 1-p %)
0036 %       phierr (error bars for phi)
0037 %       Cerr  (Jackknife error bars for C - use only for Jackknife)
0038 
0039 if nargin < 3; error('Need data1 and data2 and window parameters'); end;
0040 C1]=length(data1);C2=length(data2);
0041 if C1~=C2; error('data incompatible'); end;
0042 [mintime,maxtime]=minmaxsptimes(data1);
0043 tn=[mintime+movingwin(1)/2:movingwin(2):maxtime-movingwin(1)/2];
0044 if nargin < 4; tapers=[3 5]; end;
0045 if nargin < 5;pad=0;end;
0046 if nargin < 6; Fs=1; end;
0047 if nargin < 7; fpass=[0 Fs/2]; end;
0048 if nargin < 8; err=0; end;
0049 if nargin < 9 trialave=0;end;
0050 if nargin < 10; fscorr=0; end;
0051 if nargout > 6 & err(1)~=2; 
0052     error('Cerr computed only for Jackknife. Correct inputs and run again');
0053 end;
0054 
0055 if isempty(tapers); tapers=[3 5]; end;
0056 if isempty(pad);pad=0;end;
0057 if isempty(Fs); Fs=1; end;
0058 if isempty(fpass); fpass=[0 Fs/2]; end;
0059 if isempty(err); err=0; end;
0060 if isempty(trialave); trialave=0;end;
0061 if isempty(fscorr);fscorr=0;end
0062 
0063 Nwin=round(Fs*movingwin(1)); % number of samples in window
0064 Nstep=round(movingwin(2)*Fs); % number of samples to step through
0065 nfft=2^(nextpow2(Nwin)+pad);
0066 [f,findx]=getfgrid(Fs,nfft,fpass); 
0067 tapers=dpsschk(tapers,Nwin)/sqrt(Fs); % check tapers
0068 nw=length(tn);
0069 for n=1:nw;
0070    t=linspace(tn(n)-movingwin(1)/2,tn(n)+movingwin(1)/2,Nwin);
0071    datawin1=extractspdata(data1,[t(1) t(end)]);datawin2=extractspdata(data1,[t(1) t(end)]);
0072    if nargout==7;
0073      [c,ph,f,confc,phie,cerr]=coherencypt(datawin1,datawin2,tapers,pad,Fs,fpass,err,trialave,fscorr);
0074      confC=confc;
0075      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0076      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0077      Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
0078      Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
0079    elseif nargout==6;
0080      [c,ph,f,confc,phie]=coherencypt(datawin1,datawin2,tapers,pad,Fs,fpass,err,trialave,fscorr);
0081      confC=confc;
0082      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0083      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0084    else
0085      [c,ph,f]=coherencycpt(datawin1,datawin2,tapers,pad,Fs,fpass,err,trialave,fscorr);
0086    end;
0087    C(n,:,:)=c;
0088    phi(n,:,:)=ph;
0089 end;
0090 t=tn;
0091 C=squeeze(C); phi=squeeze(phi);if nargout==7;Cerr=squeeze(Cerr);end;
0092 if nargout==6; phierr=squeeze(phierr);end

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