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- Description of mtspecgramtrigpt

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 events when 1 don t average when 0 optional Default 0 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 S Spectrogram with dimensions time x frequency x events if trialave 0 dimensions time x frequency if trialave 1 t times f frequencies R spike rate Serr error bars only if err 1 1 CROSS REFERENCE INFORMATION This function calls createdatamatpt Helper function to create an event triggered matrix from a single mtspecgrampt Multi taper time frequency spectrum point process times This function is called by SOURCE CODE 0001 function S t f R Serr mtspecgramtrigpt data E win movingwin params fscorr 0002 Multi taper event triggered time frequency spectrum point process times 0003 0004 Usage 0005 0006 S t f R Serr mtspecgramtrigpt data E win movingwin params fscorr 0007 Input 0008 data univariate spike data 1d structure array of spike times 0009 also accepts 1d array of spike times required 0010 E event times required 0011 win in the form winl winr i e window around each event 0012 required 0013 movingwin in the form window winstep i e length of moving 0014 window and step size 0015 required 0016 params structure with fields tapers pad Fs fpass err trialave 0017 optional 0018 tapers precalculated tapers from dpss or in the one of the following 0019 forms 0020 1 A numeric vector TW K where TW is the 0021 time bandwidth product and K is the number of 0022 tapers to be used less than or equal to 0023 2TW 1 0024 2 A numeric vector W T p where W is the 0025 bandwidth T is the duration of the data and p 0026 is an integer such that 2TW p tapers are used In 0027 this form there is no default i e to specify 0028 the bandwidth you have to specify T and p as 0029 well Note that the units of W and T have to be 0030 consistent if W is in Hz T must be in seconds 0031 and vice versa Note that these units must also 0032 be consistent with the units of params Fs W can 0033 be in Hz if and only if params Fs is in Hz 0034 The default is to use form 1 with TW 3 and K 5 0035 Note that T has to be equal to movingwin 1 0036 0037 pad padding factor for the FFT optional can take

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

Open archived version from archive - Description of step

0 are not the same end vr close vr FNUM should be an integer After the videoReader constructor is called NEXT SEEK or STEP should be called at least once before GETFRAME is called See videoReader getinfo for more details on how many frames can be read from a video SEE ALSO videoReader Copyright c 2006 Gerald Dalley See MIT txt in the installation directory for licensing details especially when using this library on GNU Linux CROSS REFERENCE INFORMATION This function calls This function is called by SOURCE CODE 0001 function fn step vr delta 0002 WORKED STEP VR DELTA 0003 Moves the frame counter by DELTA frames for video VR This is a 0004 generalization of NEXT Returns 0 on an unsuccessful STEP Note that 0005 not all plugins support stepping especially with negative numbers In 0006 the following example both IM1 and IM2 should be the same for most 0007 plugins 0008 vr videoReader myurl 0009 if next vr error couldn t read first frame end 0010 im1 getframe vr 0011 if step vr 1 error could not step back to frame 0 end 0012 im2 getframe vr 0013 if any im1 im2 0014 error first frame and

Original URL path: http://www.chronux.org/Documentation/chronux/fly_track/videoIO/videoIO_2006a/@videoReader/step.html (2015-03-27)

Open archived version from archive - Description of coherencysegcpt

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 coherencycpt Multi taper coherency cross spectrum and individual spectra continuous data and point process as times 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

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

Open archived version from archive - Description of fig8_1

Likelihood Figure 8 1 0002 0003 Discrimination Classification simple example using 0004 logistic regression 0005 0006 Author Catherine Loader 0007 0008 NEED level 0 5 for contour plot 0009 0010 load cltrain 0011 fit locfit x1 x2 y family binomial scale 0 0012 figure Name fig8 1 logistic regression 0013 lfplot fit contour 0014 hold on 0015 u find y 0 0016 plot x1 u x2 u 0017 u find

Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig8_1.html (2015-03-27)

Open archived version from archive - Description of mtspectrum_of_spectrumc

frequency band to be used in the calculation in the form fmin fmax optional Default all frequencies between 0 and Fs 2 Output SS second spectrum in form frequency x segments x trials x channels if segave 0 in the form frequency x trials x channels if segave 1 tau frequencies CROSS REFERENCE INFORMATION This function calls createdatamatc Helper function to create an event triggered matrix from univariate mtspectrumc Multi taper spectrum continuous process mtspectrumsegc Multi taper segmented spectrum for a univariate continuous process This function is called by SOURCE CODE 0001 function SS tau mtspectrum of spectrumc data win tapers2spec params 0002 Multi taper segmented second spectrum spectrum of the log spectrum for a continuous process 0003 This routine computes the second spectrum by explicitly evaluating the 0004 Fourier transform since the spectrum is symmetric in frequency it uses 0005 a cosine transform 0006 0007 Usage 0008 0009 SS tau mtspectrum of spectrumc data win tapers2spec params 0010 Input 0011 Note units have to be consistent See chronux m for more information 0012 data single channel required 0013 win duration of the segments required 0014 tapers2spec tapers used for the spectrum of spectrum computation 0015 required in the form use TW K Note that spectrum of the 0016 spectrum involves computing two Fourier transforms While the first 0017 transform of the original data is always computed using the 0018 multi taper method the current routine allows the user to specify 0019 whether or not to use this method for the second transform use 1 0020 means use tapers use anything other than 1 means do not use the 0021 multitaper method If use 1 then tapers2spec controls the 0022 smoothing for the second Fourier transform Otherwise a direct 0023 Fourier transform is computed 0024 params structure with fields tapers pad Fs fpass err trialave 0025 optional 0026 tapers precalculated tapers from dpss or in the one of the following 0027 forms 0028 1 A numeric vector TW K where TW is the 0029 time bandwidth product and K is the number of 0030 tapers to be used less than or equal to 0031 2TW 1 0032 2 A numeric vector W T p where W is the 0033 bandwidth T is the duration of the data and p 0034 is an integer such that 2TW p tapers are used In 0035 this form there is no default i e to specify 0036 the bandwidth you have to specify T and p as 0037 well Note that the units of W and T have to be 0038 consistent if W is in Hz T must be in seconds 0039 and vice versa Note that these units must also 0040 be consistent with the units of params Fs W can 0041 be in Hz if and only if params Fs is in Hz 0042 The default is to use form 1 with TW 3 and K 5 0043 0044 pad padding factor for the FFT optional can take values 1 0

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

Open archived version from archive - Description of coherencysegpb

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 phistd jackknife theoretical 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 CROSS REFERENCE INFORMATION This function calls coherencypb Multi taper coherency cross spectrum and individual spectra binned point process createdatamatpb This function is called by SOURCE CODE 0001 function C phi S12 S1 S2 f zerosp confC phistd Cerr coherencysegpb data1 data2 win params segave fscorr 0002 Multi taper coherency cross spectrum and individual spectra computed by segmenting 0003 two univariate binned point processes into chunks 0004 0005 Usage 0006 C phi S12 S1 S2 f zerosp confC phistd Cerr coherencysegpb 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 binned point process data required 0010 data2 column vector binned point process data required 0011 win length of segments required 0012 params structure with fields tapers pad Fs fpass err 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 can take values 1 0 1 2 0033 1 corresponds to no padding 0 corresponds to padding 0034 to the next highest power of 2 etc 0035 e g For N 500 if PAD 1 we do not pad if PAD 0 we pad the FFT 0036 to 512 points if pad 1 we pad to 1024 points etc 0037 Defaults to 0 0038 Fs sampling frequency optional Default 1 0039 fpass frequency band to be used in the calculation in the form 0040 fmin fmax optional

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

Open archived version from archive - Description of fig8_2

contour plot Author Catherine Loader CROSS REFERENCE INFORMATION This function calls This function is called by runbook SOURCE CODE 0001 Local Regression and Likelihood Figure 8 2 0002 0003 Discrimination Classification simple example using 0004 density estimation 0005 0006 First compute density estimates fit0 fit1 family rate 0007 output is in events per unit area for each class in the 0008 training sample The ratio fit1 fit1 fit0 estimates the 0009 posterior probability that an observation comes from population 1 0010 0011 plotting the classification boundary is slightly tricky it depends 0012 on both fits so lfplot can t be used Instead both fits must be 0013 evaluated on the same grid of values which is then used to make a 0014 contour plot 0015 0016 Author Catherine Loader 0017 0018 load cltrain 0019 u0 find y 0 0020 u1 find y 1 0021 fit0 locfit x1 u0 x2 u0 y u0 family rate scale 0 0022 fit1 locfit x1 u1 x2 u1 y u1 family rate scale 0 0023 0024 v0 3 6 0 50 50 0025 v1 2 2 4 2 0 49 49 0026 predict returns log rate 0027 z predict fit0 v0 v1 predict fit1 v0

Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig8_2.html (2015-03-27)

Open archived version from archive - Description of mtspectrumc

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 channels when 1 don t average when 0 optional Default 0 Output S spectrum in form frequency x channels trials if trialave 0 in the form frequency if trialave 1 f frequencies Serr error bars only for err 1 1 CROSS REFERENCE INFORMATION This function calls mtfftc Multi taper fourier transform continuous data This function is called by ftestc computes the F statistic for sine wave in locally white noise continuous data mtspecgramc Multi taper time frequency spectrum continuous process mtspectrum of spectrumc Multi taper segmented second spectrum spectrum of the log spectrum for a continuous process mtspectrumtrigc Multi taper event triggered time frequency spectrum continuous process rmlinesc removes significant sine waves from data continuous data SOURCE CODE 0001 function S f Serr mtspectrumc data params 0002 Multi taper spectrum continuous process 0003 0004 Usage 0005 0006 S f Serr mtspectrumc data params 0007 Input 0008 Note units have to be consistent See chronux m for more information 0009 data in form samples x channels trials 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

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

Open archived version from archive