coherencysegcpt

PURPOSE ^

Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting

SYNOPSIS ^

function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegcpt(data1,data2,win,params,segave,fscorr)

DESCRIPTION ^

 Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting 
   two univariate time series into chunks - continuous and point process stored as times

 Usage:
 [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegcpt(data1,data2,win,params,segave,fscorr)
 Input: 
 Note units have to be consistent. See chronux.m for more information.
       data1 (column vector, continuous data) -- required
       data2 (1d structure array of spike times; also accepts 1d array of spike times) -- required
       params: structure with fields tapers, pad, Fs, fpass, err
       - optional
           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

            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.
           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.
       segave (average over segments for 1, don't average for 0)- optional. Default 1
       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 (magnitude of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1)
       phi (phase of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1)
       S12 (cross spectrum -  frequencies x segments if segave=0; dimension frequencies if segave=1)
       S1 (spectrum 1 - frequencies x segments if segave=0; dimension frequencies if segave=1)
       S2 (spectrum 2 - frequencies x segments if segave=0; dimension frequencies if segave=1)
       f (frequencies)
       zerosp (1 for trials where no spikes were found, 0 otherwise)
       confC (confidence level for C at 1-p %) - only for err(1)>=1
       phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi
                Note that phi + 2 phistd and phi - 2 phistd will give 95% confidence
                bands for phi - only for err(1)>=1 
       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegcpt(data1,data2,win,params,segave,fscorr)
0002 % Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting
0003 %   two univariate time series into chunks - continuous and point process stored as times
0004 %
0005 % Usage:
0006 % [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegcpt(data1,data2,win,params,segave,fscorr)
0007 % Input:
0008 % Note units have to be consistent. See chronux.m for more information.
0009 %       data1 (column vector, continuous data) -- required
0010 %       data2 (1d structure array of spike times; also accepts 1d array of spike times) -- required
0011 %       params: structure with fields tapers, pad, Fs, fpass, err
0012 %       - optional
0013 %           tapers : precalculated tapers from dpss or in the one of the following
0014 %                    forms:
0015 %                   (1) A numeric vector [TW K] where TW is the
0016 %                       time-bandwidth product and K is the number of
0017 %                       tapers to be used (less than or equal to
0018 %                       2TW-1).
0019 %                   (2) A numeric vector [W T p] where W is the
0020 %                       bandwidth, T is the duration of the data and p
0021 %                       is an integer such that 2TW-p tapers are used. In
0022 %                       this form there is no default i.e. to specify
0023 %                       the bandwidth, you have to specify T and p as
0024 %                       well. Note that the units of W and T have to be
0025 %                       consistent: if W is in Hz, T must be in seconds
0026 %                       and vice versa. Note that these units must also
0027 %                       be consistent with the units of params.Fs: W can
0028 %                       be in Hz if and only if params.Fs is in Hz.
0029 %                       The default is to use form 1 with TW=3 and K=5
0030 %
0031 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0032 %                    -1 corresponds to no padding, 0 corresponds to padding
0033 %                    to the next highest power of 2 etc.
0034 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0035 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0036 %                       Defaults to 0.
0037 %           Fs   (sampling frequency) - optional. Default 1.
0038 %           fpass    (frequency band to be used in the calculation in the form
0039 %                                   [fmin fmax])- optional.
0040 %                                   Default all frequencies between 0 and Fs/2
0041 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0042 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0043 %       segave (average over segments for 1, don't average for 0)- optional. Default 1
0044 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or
0045 %                1 (use finite size corrections) - optional
0046 %                (available only for spikes). Defaults 0.
0047 % Output:
0048 %       C (magnitude of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1)
0049 %       phi (phase of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1)
0050 %       S12 (cross spectrum -  frequencies x segments if segave=0; dimension frequencies if segave=1)
0051 %       S1 (spectrum 1 - frequencies x segments if segave=0; dimension frequencies if segave=1)
0052 %       S2 (spectrum 2 - frequencies x segments if segave=0; dimension frequencies if segave=1)
0053 %       f (frequencies)
0054 %       zerosp (1 for trials where no spikes were found, 0 otherwise)
0055 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0056 %       phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi
0057 %                Note that phi + 2 phistd and phi - 2 phistd will give 95% confidence
0058 %                bands for phi - only for err(1)>=1
0059 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0060 
0061 if nargin < 3; error('Need data1 and data2 and size of segment'); end;
0062 if nargin < 4; params=[]; end;
0063 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0064 if nargin < 5 || isempty(segave); segave=1;end;
0065 if nargin < 6 || isempty(fscorr); fscorr=0; end;
0066 if nargout > 7 && err(1)==0;
0067 %   Errors computed only if err(1) is non-zero. Need to change params and run again.
0068     error('When errors are desired, err(1) has to be non-zero.');
0069 end;
0070 if nargout > 9 && err(1)~=2; 
0071     error('Cerr computed only for Jackknife. Correct inputs and run again');
0072 end;
0073 
0074 
0075 N=check_consistency(data1,data2,1);
0076 dt=1/Fs; % sampling interval
0077 T=N*dt; % length of data in seconds
0078 E=0:win:T-win; % fictitious event triggers
0079 win=[0 win]; % use window length to define left and right limits of windows around triggers
0080 data1=createdatamatc(data1,E,Fs,win); % segmented data 1
0081 data2=createdatamatpt(data2,E,win); % segmented data 2
0082 params.trialave=segave;
0083 if nargout==7;
0084   [C,phi,S12,S1,S2,f,zerosp]=coherencycpt(data1,data2,params,fscorr); % compute coherency for segmented data
0085 elseif nargout==9; 
0086   [C,phi,S12,S1,S2,f,zerosp,confC,phistd]=coherencycpt(data1,data2,params,fscorr); % compute coherency for segmented data
0087 elseif nargout==10;
0088   [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpt(data1,data2,params,fscorr); % compute coherency for segmented data
0089 end;

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