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)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;