# coherencysegpt

## PURPOSE

Multi-taper coherency computed by segmenting two univariate point processes into chunks

## SYNOPSIS

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

## DESCRIPTION

     Multi-taper coherency computed by segmenting two univariate point processes into chunks

     Usage:
     [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpt(data1,data2,win,params,segave,fscorr)
     Input:
     Note units have to be consistent. See chronux.m for more information.
           data1 (1d structure array of spike times; also accepts 1d array of spike times) -- required
           data2 (1d structure array of spike times; also accepts 1d array of spike times) -- required
           win   (length of segments) - 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 - optional 0 for don't average over segments, 1 for average - default
           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 segments 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:

- check_consistency Helper routine to check consistency of data dimensions
- getparams Helper function to convert structure params to variables used by the
- coherencypt Multi-taper coherency - point process times
- createdatamatpt Helper function to create an event triggered matrix from a single
- minmaxsptimes Find the minimum and maximum of the spike times in each channel

This function is called by:

- testscript function testscript(pname,direction,movingwin,segave,params,fscorr)

## SOURCE CODE

    0001 function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpt(data1,data2,win,params,segave,fscorr)
    0002 % Multi-taper coherency computed by segmenting two univariate point processes into chunks
    0003 %
    0004 % Usage:
    0005 % [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpt(data1,data2,win,params,segave,fscorr)
    0006 % Input:
    0007 % Note units have to be consistent. See chronux.m for more information.
    0008 %       data1 (1d structure array of spike times; also accepts 1d array of spike times) -- required
    0009 %       data2 (1d structure array of spike times; also accepts 1d array of spike times) -- required
    0010 %       win   (length of segments) - 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 - optional 0 for don't average over segments, 1 for average - default
    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 segments 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
    0062 if nargin < 3; error('Need data1 and data2 and size of segment'); end;
    0063 if nargin < 4; params=[]; end;
    0064 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
    0065 clear tapers pad fpass trialave
    0066 if nargin < 5 || isempty(segave); segave=1;end;
    0067 if nargin < 6 || isempty(fscorr); fscorr=0; end;
    0068
    0069 if nargout > 9 && err(1)~=2;
    0070     error('Cerr computed only for Jackknife. Correct inputs and run again');
    0071 end;
    0072 if nargout > 7 && err(1)==0;
    0073     error('Errors computed only if err(1) is not equal to zero');
    0074 end;
    0075
    0076 check_consistency(data1,data2);
    0077 [mintime1,maxtime1]=minmaxsptimes(data1);
    0078 [mintime2,maxtime2]=minmaxsptimes(data2);
    0079 mintime=min(mintime1,mintime2);
    0080 maxtime=max(maxtime1,maxtime2);
    0081 % dt=1/Fs;
    0082 % t=mintime:dt:maxtime+dt; % time grid for prolates
    0083 % N=length(t); % number of points in grid for dpss
    0084
    0085 E=mintime:win:maxtime; % fictitious event triggers
    0086 win=[0 win]; % use window length to define left and right limits of windows around triggers
    0087 data1=createdatamatpt(data1,E,win); % segmented data 1
    0088 data2=createdatamatpt(data2,E,win); % segmented data 2
    0089 params.trialave=segave;
    0090 if err(1)==0;
    0091    [C,phi,S12,S1,S2,f,zerosp]=coherencypt(data1,data2,params,fscorr); % compute coherency for segmented data
    0092 elseif err(1)==1;
    0093    [C,phi,S12,S1,S2,f,zerosp,confC,phistd]=coherencypt(data1,data2,params,fscorr); % compute coherency for segmented data
    0094 elseif err(1)==2;
    0095    [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypt(data1,data2,params,fscorr); % compute coherency for segmented data
    0096 end;