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  • Description of cohmatrixpt
    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 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 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 SOURCE CODE 0001 function C phi S12 f zerosp confC phistd Cerr cohmatrixpt data params fscorr 0002 Multi taper coherency matrix point process times 0003 0004 Usage 0005 0006 C phi S12 f zerosp confC phistd Cerr cohmatrixpt data params fscorr 0007 Input 0008 data structure array of spike times with dimension 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 bars 0040 0 p or 0 no error bars optional Default 0 0041 fscorr finite size corrections 0 don t use finite size

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/pointtimes/cohmatrixpt.html (2015-03-27)
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  • Description of getfgrid
    Outputs f frequencies findx index of the frequencies in the full frequency grid e g If Fs 1000 and nfft 1048 an fft calculation generates 512 frequencies between 0 and 500 i e Fs 2 Hz Now if fpass 0 100 findx will contain the indices in the frequency grid corresponding to frequencies 100 Hz In the case fpass 0 500 findx 1 512 CROSS REFERENCE INFORMATION This function calls This function is called by SOURCE CODE 0001 function f findx getfgrid Fs nfft fpass 0002 Helper function that gets the frequency grid associated with a given fft based computation 0003 Called by spectral estimation routines to generate the frequency axes 0004 Usage f findx getfgrid Fs nfft fpass 0005 Inputs 0006 Fs sampling frequency associated with the data required 0007 nfft number of points in fft required 0008 fpass band of frequencies at which the fft is being calculated fmin fmax in Hz required 0009 Outputs 0010 f frequencies 0011 findx index of the frequencies in the full frequency grid e g If 0012 Fs 1000 and nfft 1048 an fft calculation generates 512 frequencies 0013 between 0 and 500 i e Fs 2 Hz Now if fpass 0

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/helper/getfgrid.html (2015-03-27)
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  • Description of nex_cont
    nex file 0003 0004 adfreq n ts fn d nex cont filename varname 0005 0006 INPUT 0007 filename if empty string will use File Open dialog 0008 varname variable name 0009 0010 continuous a d data come in fragments Each fragment has a timestamp 0011 and a number of a d data points The timestamp corresponds to 0012 the time of recording of the first a d value in this fragment 0013 All the data values stored in the vector d 0014 OUTPUT 0015 n total number of data points 0016 ts array of fragment timestamps one timestamp for fragment in seconds 0017 fn number of data points in each fragment 0018 d array of a d values in millivolts 0019 0020 n 0 0021 adfreq 0 0022 ts 0 0023 fn 0 0024 d 0 0025 0026 if nargin 2 0027 disp 2 input arguments are required 0028 return 0029 end 0030 0031 if ischar filename 0 0032 disp input arguments should be character arrays 0033 return 0034 end 0035 0036 if ischar varname 0 0037 disp input arguments should be character arrays 0038 return 0039 end 0040 0041 if isempty filename 0042 fname pathname uigetfile nex Select a Nex file 0043 filename strcat pathname fname 0044 end 0045 0046 fid fopen filename r 0047 if fid 0 0048 return 0049 end 0050 0051 disp strcat file filename 0052 magic fread fid 1 int32 0053 version fread fid 1 int32 0054 comment fread fid 256 char 0055 freq fread fid 1 double 0056 tbeg fread fid 1 int32 0057 tend fread fid 1 int32 0058 nvar fread fid 1 int32 0059 fseek fid 260 cof 0060 name zeros 1 64 0061 found 0 0062 for i 1 nvar 0063 type fread fid 1 int32 0064 var version fread fid

    Original URL path: http://www.chronux.org/Documentation/chronux/dataio/HowToReadNexFilesInMatlab/nex_cont.html (2015-03-27)
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  • Description of configure_classify
    the command line 0109 function varargout configure classify OutputFcn hObject eventdata handles 0110 varargout cell array for returning output args see VARARGOUT 0111 hObject handle to figure 0112 eventdata reserved to be defined in a future version of MATLAB 0113 handles structure with handles and user data see GUIDATA 0114 0115 Get default command line output from handles structure 0116 varargout 1 handles output 0117 0118 close 0119 0120 function WinSize Callback hObject eventdata handles 0121 hObject handle to WinSize see GCBO 0122 eventdata reserved to be defined in a future version of MATLAB 0123 handles structure with handles and user data see GUIDATA 0124 0125 Hints get hObject String returns contents of WinSize as text 0126 str2double get hObject String returns contents of WinSize as a double 0127 0128 0129 Executes during object creation after setting all properties 0130 function WinSize CreateFcn hObject eventdata handles 0131 hObject handle to WinSize see GCBO 0132 eventdata reserved to be defined in a future version of MATLAB 0133 handles empty handles not created until after all CreateFcns called 0134 0135 Hint edit controls usually have a white background on Windows 0136 See ISPC and COMPUTER 0137 if ispc 0138 set hObject BackgroundColor white 0139 else 0140 set hObject BackgroundColor get 0 defaultUicontrolBackgroundColor 0141 end 0142 0143 0144 Executes on button press in OKButton 0145 function OKButton Callback hObject eventdata handles 0146 hObject handle to OKButton see GCBO 0147 eventdata reserved to be defined in a future version of MATLAB 0148 handles structure with handles and user data see GUIDATA 0149 0150 lowerfreq str2num get handles ZoomLowerFreq String Lower frequency for zooming 0151 upperfreq str2num get handles ZoomUpperFreq String Upper frequency for zooming 0152 0153 classified height str2num get handles ClassifiedHeight String the height of the image in the classified axes 0154 classified width str2num get handles ClassifiedWidth String the width of the image in the classified axes 0155 0156 Fs str2num get handles Frequency String Frequency of audio sampling per second 0157 0158 winsizeS str2num get handles WinSize String 1000 0159 stepS str2num get handles StepSize String 1000 0160 movingwin winsizeS stepS Size of the moving window in seconds the first number is the window size and the second is the step size 0161 0162 tw str2num get handles TW String 0163 0164 fpasslower str2num get handles MinFreq String Range of frequency sampling 0165 fpassupper str2num get handles MaxFreq String 0166 fpass fpasslower fpassupper 0167 0168 ierror 1 Indicates no errors encountered 0169 0170 if isempty classified height classified height 1 0171 ierror 0 0172 end 0173 0174 if isempty tw tw 0 0175 ierror 0 0176 end 0177 0178 if isempty lowerfreq lowerfreq 0 0179 ierror 0 0180 end 0181 0182 if isempty fpasslower fpasslower 0 0183 ierror 0 0184 end 0185 0186 if isempty fpassupper fpassupper fpasslower 0187 ierror 0 0188 end 0189 0190 if isempty upperfreq lowerfreq upperfreq 0191 ierror 0 0192 end 0193 0194 if isempty winsizeS winsizeS 0 0195 ierror 0 0196 end 0197 0198 if isempty stepS stepS 0 0199 ierror 0 0200 end 0201 0202 if isempty tw tw 0 0203 ierror 0 0204 else 0205 tapers tw floor 2 tw 1 Tapers for smoothing 0206 end 0207 0208 fixed get handles FixedCheckbox Value 0209 0210 if ierror 0 0211 0212 else 0213 handles output lowerfreq upperfreq classified height classified width Fs movingwin tapers fpass fixed 0214 guidata hObject handles 0215 uiresume handles figure1 0216 end 0217 0218 0219 uiresume 0220 close 0221 0222 Executes on button press in CancelButton 0223 function CancelButton Callback hObject eventdata handles 0224 hObject handle to CancelButton see GCBO 0225 eventdata reserved to be defined in a future version of MATLAB 0226 handles structure with handles and user data see GUIDATA 0227 0228 handles output 0 0229 guidata hObject handles 0230 uiresume handles figure1 0231 0232 function StepSize Callback hObject eventdata handles 0233 hObject handle to StepSize see GCBO 0234 eventdata reserved to be defined in a future version of MATLAB 0235 handles structure with handles and user data see GUIDATA 0236 0237 Hints get hObject String returns contents of StepSize as text 0238 str2double get hObject String returns contents of StepSize as a double 0239 0240 0241 Executes during object creation after setting all properties 0242 function StepSize CreateFcn hObject eventdata handles 0243 hObject handle to StepSize see GCBO 0244 eventdata reserved to be defined in a future version of MATLAB 0245 handles empty handles not created until after all CreateFcns called 0246 0247 Hint edit controls usually have a white background on Windows 0248 See ISPC and COMPUTER 0249 if ispc 0250 set hObject BackgroundColor white 0251 else 0252 set hObject BackgroundColor get 0 defaultUicontrolBackgroundColor 0253 end 0254 0255 0256 0257 function TW Callback hObject eventdata handles 0258 hObject handle to TW see GCBO 0259 eventdata reserved to be defined in a future version of MATLAB 0260 handles structure with handles and user data see GUIDATA 0261 0262 Hints get hObject String returns contents of TW as text 0263 str2double get hObject String returns contents of TW as a double 0264 0265 0266 Executes during object creation after setting all properties 0267 function TW CreateFcn hObject eventdata handles 0268 hObject handle to TW see GCBO 0269 eventdata reserved to be defined in a future version of MATLAB 0270 handles empty handles not created until after all CreateFcns called 0271 0272 Hint edit controls usually have a white background on Windows 0273 See ISPC and COMPUTER 0274 if ispc 0275 set hObject BackgroundColor white 0276 else 0277 set hObject BackgroundColor get 0 defaultUicontrolBackgroundColor 0278 end 0279 0280 0281 0282 function MinFreq Callback hObject eventdata handles 0283 hObject handle to MinFreq see GCBO 0284 eventdata reserved to be defined in a future version of MATLAB 0285 handles structure with handles and user data see GUIDATA 0286 0287 Hints get hObject String returns contents of MinFreq as text 0288 str2double get hObject String returns contents of MinFreq as a double 0289 0290 0291 Executes during object creation after setting all properties

    Original URL path: http://www.chronux.org/Documentation/chronux/wave_browser/configure_classify.html (2015-03-27)
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  • Description of getframe
    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 getnext FRAME GETNEXT VR SOURCE CODE 0001 function frame getframe vr 0002 FRAME GETFRAME VR 0003 Returns the current frame that has been read in from video VR Calling 0004 GETFRAME does not automatically advance the current frame so the user 0005 must first

    Original URL path: http://www.chronux.org/Documentation/chronux/fly_track/videoIO/videoIO_2006a/@videoReader/getframe.html (2015-03-27)
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  • Description of nex_info
    function calls This function is called by test nex SOURCE CODE 0001 function nvar names types nex info filename 0002 nex info filename read and display nex file info 0003 0004 nvar names types nex info filename 0005 0006 INPUT 0007 filename if empty string will use File Open dialog 0008 OUTPUT 0009 nvar number of variables in the file 0010 names nvar 64 array of variable names 0011 types 1 nvar array of variable types 0012 Interpretation of type values 0 neuron 1 event 2 interval 3 waveform 0013 4 population vector 5 continuous variable 6 marker 0014 0015 if nargin 1 0016 disp 1 input arguments are required 0017 return 0018 end 0019 0020 if isempty filename 0021 fname pathname uigetfile nex Select a Nex file 0022 filename strcat pathname fname 0023 end 0024 0025 fid fopen filename r 0026 if fid 1 0027 disp cannot open file 0028 return 0029 end 0030 0031 disp strcat file filename 0032 magic fread fid 1 int32 0033 version fread fid 1 int32 0034 comment fread fid 256 char 0035 freq fread fid 1 double 0036 tbeg fread fid 1 int32 0037 tend fread fid 1 int32 0038 nvar fread fid

    Original URL path: http://www.chronux.org/Documentation/chronux/dataio/HowToReadNexFilesInMatlab/nex_info.html (2015-03-27)
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  • Description of countsig
    must be sig and t If data is in 0013 samples so must sig and t The default is seconds 0014 0015 data1 structure array of spike times required 0016 data2 structure array of spike times required 0017 T1 time interval default all 0018 T2 time interval default T1 0019 parametric 0 non parametric Wilcoxon 0020 1 ttest on sqrt of counts 0021 2 Poisson assumption 0022 default 0 0023 p significance level 0 05 0024 quiet 1 no display 0 display 0025 0026 Output 0027 0028 H 1 if different 0 if not 0029 P prob of result if same 0030 M1 mean count for data1 0031 M2 mean count for data2 0032 N1 counts for data1 0033 N2 counts for data2 0034 0035 0036 if nargin 2 error I need 2 sets of spike data end 0037 data1 padNaN data1 create a zero padded data matrix from input structural array 0038 data2 padNaN data2 create a zero padded data matrix from input structural array 0039 data1 data1 data2 data2 transpose data to get it into a form acceptable to Murray s routine 0040 if nargin 3 0041 T1 min data1 1 max max data1 0042 end 0043 if nargin 4 0044 T2 T1 0045 end 0046 if nargin 5 0047 parametric 0 0048 end 0049 if nargin 6 p 0 05 end 0050 if nargin 7 quiet 0 end 0051 0052 if isempty T1 0053 T1 min data1 1 max max data1 0054 end 0055 if isempty T2 0056 T2 T1 0057 end 0058 if isempty parametric 0059 parametric 0 0060 end 0061 if isempty p 0062 p 0 05 0063 end 0064 if isempty quiet 0065 quiet 0 0066 end 0067 0068 NT1 length data1 1 0069 NT2 length data2 2 0070 0071 if NT1 4 NT2

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/pointtimes/countsig.html (2015-03-27)
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  • Description of nex_int
    n ts left ts right nex int filename varname 0002 nex int filename varname Read interval variable from a nex file 0003 0004 n ts left ts right nex int filename varname 0005 0006 INPUT 0007 filename if empty string will use File Open dialog 0008 varname variable name 0009 OUTPUT 0010 n number of intervals 0011 ts left array of left ends of the intervals in seconds 0012 ts right array of right ends of the intervals in seconds 0013 0014 n 0 0015 ts left 0 0016 ts right 0 0017 0018 if nargin 2 0019 disp 2 input arguments are required 0020 return 0021 end 0022 0023 if ischar filename 0 0024 disp input arguments should be character arrays 0025 return 0026 end 0027 0028 if ischar varname 0 0029 disp input arguments should be character arrays 0030 return 0031 end 0032 0033 if isempty filename 0034 fname pathname uigetfile nex Select a Nex file 0035 filename strcat pathname fname 0036 end 0037 0038 fid fopen filename r 0039 if fid 1 0040 disp cannot open file 0041 return 0042 end 0043 0044 disp strcat file filename 0045 magic fread fid 1 int32 0046 version fread fid 1 int32 0047 comment fread fid 256 char 0048 freq fread fid 1 double 0049 tbeg fread fid 1 int32 0050 tend fread fid 1 int32 0051 nvar fread fid 1 int32 0052 fseek fid 260 cof 0053 name zeros 1 64 0054 found 0 0055 for i 1 nvar 0056 type fread fid 1 int32 0057 var version fread fid 1 int32 0058 name fread fid 1 64 char 0059 offset fread fid 1 int32 0060 n fread fid 1 int32 0061 name char name 0062 name deblank name 0063 k strcmp name deblank varname 0064 if k 1

    Original URL path: http://www.chronux.org/Documentation/chronux/dataio/HowToReadNexFilesInMatlab/nex_int.html (2015-03-27)
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