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  • Description of getparams
    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 trialave average over trials when 1 don t average when 0 optional Default 0 Outputs The fields listed above as well as the struct params The fields are used by some routines and the struct is used by others Though returning both involves overhead it is a safer simpler thing to do CROSS REFERENCE INFORMATION This function calls This function is called by SOURCE CODE 0001 function tapers pad Fs fpass err trialave params getparams params 0002 Helper function to convert structure params to variables used by the 0003 various routines also performs checks to ensure that parameters are 0004 defined returns default values if they are not defined 0005 0006 Usage tapers pad Fs fpass err trialave params getparams params 0007 0008 Inputs 0009 params structure with fields tapers pad Fs fpass err trialave 0010 optional 0011 tapers precalculated tapers from dpss or in the one of the following 0012 forms 0013 1 A numeric vector TW K where TW is the 0014 time bandwidth product and K is the number of 0015 tapers to be used less than or equal to 0016 2TW 1 0017 2 A numeric vector W T p where W is the 0018 bandwidth T is the duration of the data and p 0019 is an integer such that 2TW p tapers are used In 0020 this form there is no default i e to specify 0021 the bandwidth you have to specify T and p as 0022 well Note that the units of W and T have to be 0023 consistent if W is in Hz T must be in seconds 0024 and vice versa Note that these units must also 0025 be consistent with the units of params Fs W can 0026 be in Hz if and only if params Fs is in Hz 0027 The default is to use form 1 with TW 3 and K 5 0028 0029 pad padding factor for the FFT optional can take values 1 0 1 2 0030 1 corresponds to no padding 0 corresponds to padding 0031 to the next highest power of 2 etc 0032 e g For N 500 if PAD 1 we do not pad if PAD 0 we pad the FFT 0033 to 512 points if pad 1 we pad to 1024 points etc 0034 Defaults to 0 0035 Fs sampling frequency optional Default 1 0036 fpass frequency band to be used in the calculation in the form 0037 fmin fmax

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/helper/getparams.html (2015-03-27)
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  • Description of plot_vector
    lower and upper confidence intervals for X1 lower upper x f Or simply a single number specifying an f independent confidence level c controls the color of the plot input b g r etc Default b w controls the width of the lines input 1 1 5 2 etc CROSS REFERENCE INFORMATION This function calls This function is called by SOURCE CODE 0001 function plot vector X f plt Xerr c w 0002 Function to plot a frequency dependent vector X If error bars are specified in Xerr 0003 it also plots them Xerr can either contain upper and lower confidence intervals 0004 on X or simply a theoretical confidence level for the coherence Used 0005 to plot the spectrum and coherency 0006 Usage plot vector X f plt Xerr c 0007 Inputs 0008 X input vector as a function of frequency f see third argument 0009 f f axis grid for plot Default 1 length X 0010 plt l for log n for no log 0011 Xerr lower and upper confidence intervals for X1 lower upper x f Or 0012 simply a single number specifying an f independent confidence 0013 level 0014 c controls the color of the plot input b g r etc Default b 0015 w controls the width of the lines input 1 1 5 2 etc 0016 0017 if nargin 1 error Need data end 0018 N length X 0019 if nargin 2 isempty f 0020 f 1 N 0021 end 0022 if length f N error frequencies and data have incompatible lengths end 0023 if nargin 3 isempty plt 0024 plt l 0025 end 0026 if nargin 4 isempty Xerr 0027 Xerr 0028 end 0029 if nargin 5 isempty c 0030 c b 0031 end 0032 if nargin 6 isempty w 0033 w 1

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/plots/plot_vector.html (2015-03-27)
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  • Description of CrossSpecMat
    averages over trials continuous process 0006 0007 Usage 0008 0009 Sc Cmat Ctot Cvec Cent f CrossSpecMat data win params 0010 Input 0011 Note units have to be consistent See chronux m for more information 0012 data in form samples x channels x trials 0013 win duration of non overlapping window 0014 params structure with fields tapers pad Fs fpass 0015 optional 0016 tapers precalculated tapers from dpss or in the form NW K e g 3 5 optional 0017 If not specified use NW K 3 5 0018 pad padding factor for the FFT optional Defaults to 0 0019 e g For N 500 if PAD 0 we pad the FFT 0020 to 512 points if PAD 2 we pad the FFT 0021 to 2048 points etc 0022 Fs sampling frequency optional Default 1 0023 fpass frequency band to be used in the calculation in the form 0024 fmin fmax optional 0025 Default all frequencies between 0 and Fs 2 0026 Output 0027 Sc cross spectral matrix frequency x channels x channels 0028 Cmat Coherence matrix frequency x channels x channels 0029 Ctot Total coherence SV 1 2 sum SV 2 frequency 0030 Cvec leading Eigenvector frequency x channels 0031 Cent A different measure of total coherence GM AM of SV 2s 0032 f frequencies 0033 d ndims data 0034 if d 2 error Need multidimensional array end 0035 if d 2 N C size data end 0036 if d 3 N C Ntr size data end 0037 if nargin 3 params end 0038 tapers pad Fs fpass err trialave params getparams params 0039 clear err trialave params 0040 nwin round win Fs nfft 2 nextpow2 nwin pad 0041 f findx getfgrid Fs nfft fpass 0042 tapers dpsschk tapers nwin Fs check tapers 0043 Sc zeros length findx C

    Original URL path: http://www.chronux.org/Documentation/chronux/old/CrossSpecMat.html (2015-03-27)
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  • Description of extractdatapb
    function is called by SOURCE CODE 0001 function data extractdatapb data Fs t 0002 Extract segements of binned point process data between t 1 and t 2 0003 Usage data extractdatapb data Fs t 0004 0005 Input 0006 data binned point process data in the form samples x channels or single 0007 vector 0008 Fs sampling frequency 0009 t time as a 2d vector t 1 t 2 0010 Note

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/pointbinned/extractdatapb.html (2015-03-27)
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  • Description of hatmatrix
    CROSS REFERENCE INFORMATION This function calls lfknots locfit Smoothing noisy data using Local Regression and Likelihood This function is called by SOURCE CODE 0001 function z hatmatrix varargin 0002 0003 fit locfit varargin module hatm 0004 z lfknots fit 0005

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/m/hatmatrix.html (2015-03-27)
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  • Description of plotbyfactor
    function calls This function is called by lfplot Plot for one or two dimensions a locfit fit SOURCE CODE 0001 function plotbyfactor x y f 0002 0003 very simplistic version of plotbyfactor 0004 no symbols will crash if more than 8 levels 0005 0006 0007 z unique f 0008 cols b r g m c y k w 0009 0010 for i 1 length z 0011 u find f z

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/m/plotbyfactor.html (2015-03-27)
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  • Description of CrossSpecMatc
    spectral matrix frequency x channels x channels Cmat Coherence matrix frequency x channels x channels Ctot Total coherence SV 1 2 sum SV 2 frequency Cvec leading Eigenvector frequency x channels Cent A different measure of total coherence GM AM of SV 2s f frequencies CROSS REFERENCE INFORMATION This function calls mtfftc Multi taper fourier transform continuous data This function is called by SOURCE CODE 0001 function Sc Cmat Ctot Cvec Cent f CrossSpecMatc data win params 0002 Multi taper cross spectral matrix another routine allows for multiple trials and channels 0003 Does not do confidence intervals Also this routine always averages over trials continuous process 0004 0005 Usage 0006 0007 Sc Cmat Ctot Cvec Cent f CrossSpecMatc data win params 0008 Input 0009 Note units have to be consistent See chronux m for more information 0010 data in form samples x channels x trials 0011 win duration of non overlapping window 0012 params structure with fields tapers pad Fs fpass 0013 optional 0014 tapers precalculated tapers from dpss or in the one of the following 0015 forms 0016 1 A numeric vector TW K where TW is the 0017 time bandwidth product and K is the number of 0018 tapers to be used less than or equal to 0019 2TW 1 0020 2 A numeric vector W T p where W is the 0021 bandwidth T is the duration of the data and p 0022 is an integer such that 2TW p tapers are used In 0023 this form there is no default i e to specify 0024 the bandwidth you have to specify T and p as 0025 well Note that the units of W and T have to be 0026 consistent if W is in Hz T must be in seconds 0027 and vice versa Note that these units must also 0028 be consistent with the units of params Fs W can 0029 be in Hz if and only if params Fs is in Hz 0030 The default is to use form 1 with TW 3 and K 5 0031 0032 pad padding factor for the FFT optional Defaults to 0 0033 e g For N 500 if PAD 0 we pad the FFT 0034 to 512 points if PAD 2 we pad the FFT 0035 to 2048 points etc 0036 Fs sampling frequency optional Default 1 0037 fpass frequency band to be used in the calculation in the form 0038 fmin fmax optional 0039 Default all frequencies between 0 and Fs 2 0040 Output 0041 Sc cross spectral matrix frequency x channels x channels 0042 Cmat Coherence matrix frequency x channels x channels 0043 Ctot Total coherence SV 1 2 sum SV 2 frequency 0044 Cvec leading Eigenvector frequency x channels 0045 Cent A different measure of total coherence GM AM of SV 2s 0046 f frequencies 0047 d ndims data 0048 if d 2 error Need multidimensional array end 0049 if d 2 N C size data end 0050 if d 3 N C Ntr

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/continuous/CrossSpecMatc.html (2015-03-27)
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  • Description of extractdatapt
    be Hz If E is in samples so are win and t and Fs 1 In case of spike times the units have to be consistent with the units of data as well Output data spike times between t 1 and t 2 CROSS REFERENCE INFORMATION This function calls This function is called by CrossSpecMatpt cohgrampt Multi taper time frequency coherence two point processes given as times mtdspecgrampt Multi taper derivative time frequency spectrum point process times mtspecgrampt Multi taper time frequency spectrum point process times SOURCE CODE 0001 function data extractdatapt data t offset 0002 Extract segements of spike times between t 1 and t 2 0003 Usage data extractdatapt data t offset 0004 0005 Input 0006 data structural array of spike times for each channel trial or a single 0007 array of spike times 0008 t time as a 2d vector t 1 t 2 0009 offset 0 1 if 1 store the spike times relative to start of window i e t 1 0010 if 0 don t reset the times Default 0 0011 Note that all times can be in arbitrary units But the units have to be 0012 consistent So if E is in secs win t have to be in secs and Fs has to 0013 be Hz If E is in samples so are win and t and Fs 1 In case of spike 0014 times the units have to be consistent with the units of data as well 0015 0016 Output 0017 data spike times between t 1 and t 2 0018 if nargin 2 error Need data and times end 0019 if t 1 0 t 2 t 1 0020 error times cannot be negative and t 2 has to greater than t 1 0021 end 0022 if nargin 3 isempty

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/pointtimes/extractdatapt.html (2015-03-27)
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