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- Description of cohmatrixc

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 Output C magnitude of coherency frequency x channels x channels phi phase of coherency frequency x channels x channels S12 cross spectral matrix frequency x channels x channels f frequencies 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 mtfftc Multi taper fourier transform continuous data This function is called by SOURCE CODE 0001 function C phi S12 f confC phistd Cerr cohmatrixc data params 0002 Multi taper coherency cross spectral matrix continuous process 0003 0004 Usage 0005 0006 C phi S12 f confC phistd Cerr cohmatrixc data params 0007 Input 0008 Note units have to be consistent See chronux m for more information 0009 data in form samples x channels required 0010 params structure with fields tapers pad Fs fpass err 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

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

Open archived version from archive - Description of gcv

REFERENCE INFORMATION This function calls locfit Smoothing noisy data using Local Regression and Likelihood rsum This function is called by gcvplot SOURCE CODE 0001 function g gcv varargin 0002 0003 fit locfit varargin 0004 rs rsum fit 0005 0006 df0 rs 1 0007 df1 rs 2 0008 llk rs 3 0009 n size fit data x 1 0010 gc 2 n llk n df0 2 0011 g llk df0 df1

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

Open archived version from archive - Description of mtspectrumtrigpt

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

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

Open archived version from archive - Description of vecr

PURPOSE SYNOPSIS function z vecr fit DESCRIPTION CROSS REFERENCE INFORMATION This function calls This function is called by SOURCE CODE 0001 function z vecr fit 0002 0003 z fit fit points kappa 0004 0005 return Generated on Fri 28 Sep

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

Open archived version from archive - Description of cohmatrixpb

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 C magnitude of coherency frequency x channels x channels phi phase of coherency frequency x channels x channels S12 cross spectral matrix frequency x channels x channels f frequencies zerosp 1 for channels where no spikes were found zero otherwise confC confidence level for C at 1 p only for err 1 1 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 err 1 2 CROSS REFERENCE INFORMATION This function calls mtfftpb Multi taper fourier transform binned point process data This function is called by SOURCE CODE 0001 function C phi S12 f zerosp confC phistd Cerr cohmatrixpb data params fscorr 0002 Multi taper coherency matrix binned point process 0003 0004 Usage 0005 0006 C phi S12 f zerosp confC phistd Cerr cohmatrixpb data params fscorr 0007 Input 0008 data in form samples x channels required 0009 params structure with fields tapers pad Fs fpass err 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 optional 0038 Default all frequencies between 0 and Fs 2 0039 err error calculation 1 p Theoretical error bars 2 p Jackknife error

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

Open archived version from archive - Description of gcvplot

INFORMATION This function calls gcv This function is called by SOURCE CODE 0001 function g gcvplot alpha varargin 0002 0003 Computes and plots the Generalized Cross Validation score GCV 0004 for local fits with different smoothing parameters 0005 0006 The first argument to gcvplot alpha should be a matrix with one 0007 or two columns first column nearest neighbor component second 0008 column constant component Each row of this matrix

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

Open archived version from archive - Description of myrandint

to Xhi use RANGE Xlow Xhi MYRANDINT M N RANGE noreplace is an M by N matrix with random integers drawn without replacement This function is based around RAND and RANDPERM and is intended as a modest imitation of Comm Toolbox s RANDINT CROSS REFERENCE INFORMATION This function calls This function is called by testAvg3 This is a calling routine to test check out the power spectrum testAvg4 This is a calling routine to test check out the power spectrum SOURCE CODE 0001 function ranInt myrandint outputRow outputCol outputRange varargin 0002 MYRANDINT M N RANGE is an M by N matrix with random integer entries 0003 drawn with replacement from elements of vector RANGE The elements in 0004 vector RANGE do not need to be contiguous or unique Actually they do 0005 not even need to be integers The function works the exact same way with 0006 noninteger elements but a warning is generated to alert the user that 0007 noninteger elements are being sampled 0008 0009 To specify a contiguous integer range from Xlow to Xhi use RANGE Xlow Xhi 0010 0011 MYRANDINT M N RANGE noreplace is an M by N matrix with random integers 0012 drawn without replacement 0013 0014 This function is based around RAND and RANDPERM and is intended as a 0015 modest imitation of Comm Toolbox s RANDINT 0016 0017 0018 if isequal size outputRange 1 2 isequal outputRange 1 outputRange 2 1 0019 warning To specify a range low high use low high 0020 end 0021 if isequal round outputRange outputRange 0022 warning Specified RANGE contains noninteger values 0023 end 0024 if isequal length outputRange length outputRange 0025 error Range must be a vector of integer values 0026 end 0027 0028 numElements outputRow outputCol 0029 0030 if isempty varargin 0031 0032 ranInt zeros

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

Open archived version from archive - Description of videoReader

we know there s a video file there chdir fileparts which videoReaderWrapper cpp Construct a videoReader object vr videoReader tests numbers uncompressed avi Do some processing on the video and display the results avgIntensity i 1 figure while next vr img getframe vr avgIntensity i mean img subplot 121 imshow img title current frame subplot 122 plot avgIntensity title avg intensity vs frame drawnow pause 0 1 i i 1 end vr close vr SEE ALSO buildVideoMex videoReader close videoReader getframe videoReader getinfo videoReader getnext videoReader next videoReader seek videoReader step videoWriter 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 SUBFUNCTIONS function n mexName plugin function plugin pluginArgs parsePlugin plugin pluginArgs SOURCE CODE 0001 function vr videoReader url varargin 0002 videoReader class constructor 0003 Creates a object that reads video streams We use a plugin 0004 architecture in the backend to do the actual reading For example 0005 on Windows DirectShow will typically be used and on Linux the 0006 ffmpeg library is often used 0007 0008 vr videoReader url 0009 Opens the given video file for reading using the default plugin 0010 On Windows DirectShow is used by default and on Linux 0011 ffmpegPopen2 is used by default For most plugins the url will 0012 really be a filename 0013 0014 vr videoReader url plugin pluginName 0015 vr videoReader url pluginName 0016 Opens the file using the manually specified plugin implementation 0017 Available plugins include 0018 0019 DirectShow preferred method on Windows 0020 Only available on Windows 0021 See INSTALL dshow txt for installation instructions 0022 Can load virtually any video file that can be played in 0023 Microsoft s Windows Media Player Note that the correct codec 0024 must be installed to read a file For example to read 0025 tests numbers 3ivx avi the user must have installed an MPEG4 0026 codec such as 3ivx www 3ivx com DivX www divx com or XviD 0027 www xvid org 0028 The URL parameter should be a filename 0029 As a convenience all forward slashes are automatically 0030 converted to backslashes 0031 0032 ffmpegPopen2 safe method on Linux 0033 Only supported on GNU Linux might work on BSD systems too like Mac 0034 OS X but this is untested 0035 See INSTALL ffmpeg txt for installation instructions 0036 Creates a separate server process to communicate with the 0037 ffmpeg libraries 0038 Works when the system s version of GCC is very different from 0039 the one that MathWorks used to compile Matlab 0040 Isolates ffmpeg errors so they typically cannot crash 0041 Matlab 0042 May allow for more flexible distribution terms for your code 0043 when it uses videoIO ffmpeg may be compiled with either 0044 the LGPL or GPL license 0045 0046 ffmpegDirect low overhead method on Linux 0047 same as ffmpegPopen2 but the ffmpeg libraries are loaded 0048 directly by the

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

Open archived version from archive