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  • Description of cohgramc
    Cerr cohgramc data1 data2 movingwin params 0002 Multi taper time frequency coherence cross spectrum and individual spectra continuous processes 0003 0004 Usage 0005 0006 C phi S12 S1 S2 t f confC phistd Cerr cohgramc data1 data2 movingwin params 0007 Input 0008 Note units have to be consistent Thus if movingwin is in seconds Fs 0009 has to be in Hz see chronux m for more information 0010 0011 data1 in form samples x trials required 0012 data2 in form samples x trials required 0013 movingwin in the form window winstep required 0014 params structure with fields tapers pad Fs fpass err trialave 0015 optional 0016 tapers precalculated tapers from dpss or in the one of the following 0017 forms 0018 1 A numeric vector TW K where TW is the 0019 time bandwidth product and K is the number of 0020 tapers to be used less than or equal to 0021 2TW 1 0022 2 A numeric vector W T p where W is the 0023 bandwidth T is the duration of the data and p 0024 is an integer such that 2TW p tapers are used In 0025 this form there is no default i e to specify 0026 the bandwidth you have to specify T and p as 0027 well Note that the units of W and T have to be 0028 consistent if W is in Hz T must be in seconds 0029 and vice versa Note that these units must also 0030 be consistent with the units of params Fs W can 0031 be in Hz if and only if params Fs is in Hz 0032 The default is to use form 1 with TW 3 and K 5 0033 Note that T has to be equal to movingwin 1 0034 0035 pad padding factor for the FFT optional can take values 1 0 1 2 0036 1 corresponds to no padding 0 corresponds to padding 0037 to the next highest power of 2 etc 0038 e g For N 500 if PAD 1 we do not pad if PAD 0 we pad the FFT 0039 to 512 points if pad 1 we pad to 1024 points etc 0040 Defaults to 0 0041 Fs sampling frequency optional Default 1 0042 fpass frequency band to be used in the calculation in the form 0043 fmin fmax optional 0044 Default all frequencies between 0 and Fs 2 0045 err error calculation 1 p Theoretical error bars 2 p Jackknife error bars 0046 0 p or 0 no error bars optional Default 0 0047 trialave average over trials when 1 don t average when 0 optional Default 0 0048 Output 0049 C magnitude of coherency time x frequencies x trials for trialave 0 0050 time x frequency for trialave 1 0051 phi phase of coherency time x frequencies x trials for no trial averaging 0052 time x frequency for trialave 1 0053 S12 cross spectrum time x frequencies x trials for no trial averaging 0054 time x frequency

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/continuous/cohgramc.html (2015-03-27)
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  • Description of fig9_2
    This function calls This function is called by runbook SOURCE CODE 0001 Local Regression and Likelihood Figure 9 2 0002 0003 Hardle s Motorcycle accelaration dataset 0004 Local Variance Estimation 0005 0006 Author Catherine Loader 0007 0008 NEED lfknots function to extract fit points 0009 0010 load mcyc 0011 fit locfit time y accel nn 0 1 0012 y 2 predict fit fitp what lik 0013 w predict fit fitp

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig9_2.html (2015-03-27)
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  • Description of mtspectrumpt
    finite size corrections 0 don t use finite size corrections or 1 use finite size corrections optional available only for spikes Defaults 0 t time grid over which the tapers are to be calculated this argument is useful when calling the spectrum calculation routine from a moving window spectrogram calculation routine If left empty the spike times are used to define the grid Output S spectrum with dimensions frequency x channels trials if trialave 0 dimension frequency if trialave 1 f frequencies R rate Serr error bars only if err 1 1 CROSS REFERENCE INFORMATION This function calls minmaxsptimes Find the minimum and maximum of the spike times in each channel mtfftpt Multi taper fourier transform for point process given as times This function is called by mtspecgrampt Multi taper time frequency spectrum point process times mtspectrumtrigpt Multi taper time frequency spectrum point process times SOURCE CODE 0001 function S f R Serr mtspectrumpt data params fscorr t 0002 Multi taper spectrum point process times 0003 0004 Usage 0005 0006 S f R Serr mtspectrumpt data params fscorr t 0007 Input 0008 data structure array of spike times with dimension channels trials 0009 also accepts 1d array of spike times required 0010 params structure with fields tapers pad Fs fpass err trialave 0011 optional 0012 tapers precalculated tapers from dpss or in the one of the following 0013 forms 0014 1 A numeric vector TW K where TW is the 0015 time bandwidth product and K is the number of 0016 tapers to be used less than or equal to 0017 2TW 1 0018 2 A numeric vector W T p where W is the 0019 bandwidth T is the duration of the data and p 0020 is an integer such that 2TW p tapers are used In 0021 this form there is no default i e to specify 0022 the bandwidth you have to specify T and p as 0023 well Note that the units of W and T have to be 0024 consistent if W is in Hz T must be in seconds 0025 and vice versa Note that these units must also 0026 be consistent with the units of params Fs W can 0027 be in Hz if and only if params Fs is in Hz 0028 The default is to use form 1 with TW 3 and K 5 0029 0030 pad padding factor for the FFT optional can take values 1 0 1 2 0031 1 corresponds to no padding 0 corresponds to padding 0032 to the next highest power of 2 etc 0033 e g For N 500 if PAD 1 we do not pad if PAD 0 we pad the FFT 0034 to 512 points if pad 1 we pad to 1024 points etc 0035 Defaults to 0 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 err

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/pointtimes/mtspectrumpt.html (2015-03-27)
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  • Description of test_nex
    nex file info nex marker nex marker filename varname Read a marker variable from a nex file nex ts nex ts filename varname Read timestamps from a nex file nex wf nex wf filename varname Read waveform variable from a nex file This function is called by SOURCE CODE 0001 nvar names types nex info test nex 0002 0003 n ts nex ts test nex neuron1 0004 0005 adfreq n

    Original URL path: http://www.chronux.org/Documentation/chronux/dataio/HowToReadNexFilesInMatlab/test_nex.html (2015-03-27)
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  • Description of cohgramcpb
    and binned point process 0004 0005 Usage 0006 0007 C phi S12 S1 S2 t f zerosp confC phistd Cerr cohgramcpb data1 data2 movingwin params fscorr 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 continuous data in form samples x trials required 0013 data2 binned point process data in form samples x trials required 0014 movingwin in the form window winstep required 0015 params structure with fields tapers pad Fs fpass err trialave 0016 optional 0017 tapers precalculated tapers from dpss or in the one of the following 0018 forms 0019 1 A numeric vector TW K where TW is the 0020 time bandwidth product and K is the number of 0021 tapers to be used less than or equal to 0022 2TW 1 0023 2 A numeric vector W T p where W is the 0024 bandwidth T is the duration of the data and p 0025 is an integer such that 2TW p tapers are used In 0026 this form there is no default i e to specify 0027 the bandwidth you have to specify T and p as 0028 well Note that the units of W and T have to be 0029 consistent if W is in Hz T must be in seconds 0030 and vice versa Note that these units must also 0031 be consistent with the units of params Fs W can 0032 be in Hz if and only if params Fs is in Hz 0033 The default is to use form 1 with TW 3 and K 5 0034 Note that T has to be equal to movingwin 1 0035 0036 pad padding factor for the FFT optional can take values 1 0 1 2 0037 1 corresponds to no padding 0 corresponds to padding 0038 to the next highest power of 2 etc 0039 e g For N 500 if PAD 1 we do not pad if PAD 0 we pad the FFT 0040 to 512 points if pad 1 we pad to 1024 points etc 0041 Defaults to 0 0042 Fs sampling frequency optional Default 1 0043 fpass frequency band to be used in the calculation in the form 0044 fmin fmax optional 0045 Default all frequencies between 0 and Fs 2 0046 err error calculation 1 p Theoretical error bars 2 p Jackknife error bars 0047 0 p or 0 no error bars optional Default 0 0048 trialave average over trials when 1 don t average when 0 optional Default 0 0049 fscorr finite size corrections 0 don t use finite size corrections or 0050 1 use finite size corrections optional 0051 available only for spikes Defaults 0 0052 Output 0053 C magnitude of coherency time x frequencies x trials for trialave 0 0054 time x frequency for trialave 1 0055 phi phase of coherency time x frequencies x trials for no trial averaging 0056 time x frequency

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/hybrid/cohgramcpb.html (2015-03-27)
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  • Description of findpeaks
    Output xmax locations of local maxima of data in a structure array of dimensions channels trials CROSS REFERENCE INFORMATION This function calls This function is called by fitlinesc fits significant sine waves to data continuous data SOURCE CODE 0001 function xmax findpeaks data threshold 0002 Helper function to find peaks in a given continuous valued time series x 0003 Usage xmax findpeaks data threshold 0004 Input 0005 data data in time x channels trials form or a single vector 0006 threshold if specified returns locations of peaks at which data exceeds threshold optional 0007 Output 0008 xmax locations of local maxima of data in a structure array of dimensions channels trials 0009 if nargin 1 error Need data end 0010 data change row to column data 0011 C size data 2 0012 pp1 data 1 data 1 end 1 0013 pp2 data 2 end data end 0014 xmax 1 C struct loc 0015 for ch 1 C 0016 if nargin 1 0017 xmax ch loc xmax ch loc find data ch pp1 ch 0 data ch pp2 ch 0 0018 else 0019 xmax ch loc xmax ch loc find data ch pp1 ch 0 data ch pp2 ch 0 data

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/continuous/findpeaks.html (2015-03-27)
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  • Description of mtspectrumsegc
    in form frequency x segments if segave 0 in the form frequency if segave 1 f frequencies varS variance of the log spectrum C covariance matrix of the log spectrum frequency x frequency matrix Serr error bars only for err 1 1 CROSS REFERENCE INFORMATION This function calls createdatamatc Helper function to create an event triggered matrix from univariate mtfftc Multi taper fourier transform continuous data This function is called by mtspectrum of spectrumc Multi taper segmented second spectrum spectrum of the log spectrum for a continuous process rmlinesmovingwinc fits significant sine waves to data continuous data using overlapping windows SOURCE CODE 0001 function S f varS C Serr mtspectrumsegc data win params segave 0002 Multi taper segmented spectrum for a univariate continuous process 0003 0004 Usage 0005 0006 S f varS C Serr mtspectrumsegc data win params segave 0007 Input 0008 Note units have to be consistent See chronux m for more information 0009 data single channel required 0010 win duration of the segments required 0011 params structure with fields tapers pad Fs fpass err trialave 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 trialave not used 0044 segave optional 0 for don t average

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/continuous/mtspectrumsegc.html (2015-03-27)
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  • Description of testscript
    figure subplot 211 plot f 10 log S 0113 imagesc f f C axis xy colorbar 0114 pause 0115 0116 compute segmented coherency between 1 and 2 0117 NT 10 round winseg Fs 0118 data1 dlfp 1 NT 1 data2 dlfp 1 NT 2 0119 C phi S12 S1 S2 f confC phierr Cerr coherencysegc data1 data2 winseg params 0120 figure subplot 311 plot f C subplot 312 plot f 10 log10 S1 subplot 313 plot f 10 log10 S2 0121 pause 0122 0123 compute spectrum of channel 1 triggered to events E 0124 E1 targon find targets direction 0125 data1 dlfp 1 0126 S f Serr mtspectrumtrigc data1 E1 wintrig params 0127 figure plot f 10 log10 S axis xy colorbar 0128 pause 0129 0130 compute spectrogram of channel 1 triggered to events E 0131 E1 targon find targets direction 0132 data1 dlfp 1 0133 S t f Serr mtspecgramtrigc data1 E1 wintrig movingwin params 0134 figure imagesc t f 10 log10 S axis xy colorbar 0135 pause 0136 0137 0138 Analysis point process stored as times 0139 0140 0141 dsp contains 2 channels of spikes 0142 0143 data extractdatapt dsp 20 30 extract spikes occurring between 20 and 30 seconds and compute their spectrum 0144 S f R Serr mtspectrumpt data params 0145 figure plot f 10 log10 S f 10 log10 Serr 1 f 10 log10 Serr 2 line get gca xlim 10 log10 R 10 log10 R 0146 pause 0147 0148 0149 Compute the derivative of the spectrum 0150 0151 phi 0 pi 2 0152 dS f mtdspectrumpt data phi params 0153 figure plot f dS 0154 pause 0155 0156 0157 Compute the derivative of the time frequency spectrum 0158 0159 data extractdatapt dsp 20 30 0160 data1 data 1 data2 data 2 fscorr t 0161 C phi S12 S1 S2 f zerosp confC phierr Cerr coherencypt data1 data2 params 0162 figure plot f C 0163 pause 0164 0165 0166 Compute event triggered average spectrum for one of the directions 0167 0168 E1 targon find targets direction 0169 data dsp 1 0170 S f R Serr mtspectrumtrigpt data E1 wintrig params 0171 figure plot f 10 log10 S f 10 log10 Serr 1 f 10 log10 Serr 2 line get gca xlim 10 log10 R 10 log10 R 0172 pause 0173 0174 0175 Compute the matrix of coherencies 0176 0177 data extractdatapt dsp 20 30 0178 C phi S12 f zerosp confC phierr Cerr cohmatrixpt data params fscorr 0179 0180 0181 Event triggered spectrogram first way way 0182 0183 data createdatamatpt dsp 1 E1 wintrig 0184 S t f R Serr mtspecgrampt data movingwin params 0185 figure imagesc t f 10 log10 S axis xy colorbar 0186 pause 0187 0188 0189 Derivative of the time frequency spectrum 0190 0191 data createdatamatpt dsp 1 E1 wintrig 0192 phi 0 pi 2 0193 dS t f mtdspecgrampt data movingwin phi params 0194 figure subplot 211 imagesc t f squeeze dS 1 axis xy colorbar 0195 subplot 212 imagesc

    Original URL path: http://www.chronux.org/Documentation/chronux/test/testscript.html (2015-03-27)
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