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NHP-pRF
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<!-- ../menu.html chronux_2_10 --><!-- menu.html test -->
<h1>testscript
</h1>

<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../../up.png"></a></h2>
<div class="box"><strong>function testscript(pname,direction,movingwin,segave,params,fscorr)</strong></div>

<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../../up.png"></a></h2>
<div class="box"><strong>This is a script file. </strong></div>

<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../../up.png"></a></h2>
<div class="fragment"><pre class="comment"> function testscript(pname,direction,movingwin,segave,params,fscorr)

 This script runs a sequence of analysis steps using the test
 data contained in data. The data consists of a single tetrode
 recording from macaque area LIP during a memory saccade experiment
 a la Pesaran et al (2002). The data is already separated into
 spikes and LFPs. LFPs are contained in variable dlfp, spikes from two
 neurons are in in a struct array dsp, and event information is in
 the following set of variables:

 trialtimes - start times of trials
 fixon - fixation light comes on
 fixacq - fixation acquired
 targon - target light on
 targoff - target light off
 fixoff - fixation off
 saccade - saccade

 Note that spikes and event times are in seconds and the sampling
 frequency for the LFP in this experiment was 1kHz.

 the script takes the following input argument - 
 pname - path name on your computer where the data file LIPdata is stored.
 direction - target direction to be analysed (0-7)

 The remaining parameters control various computations and are discussed
 in chronux.m - type Help chronux.m for more information.
 
 if nargin &lt; 4;
     error('Need 6 input parameters - see help');
 end;
 if nargin &lt; 5 | isempty(params);
    [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
 end;
 if nargin &lt; 6 | isempty(fscorr);
     fscorr=1;
 end;</pre></div>

<!-- crossreference -->
<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../../up.png"></a></h2>
This function calls:
<ul style="list-style-image:url(../../matlabicon.gif)">
<li><a href="../../chronux_2_10/spectral_analysis/continuous/coherencyc.html" class="code" title="function [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencyc(data1,data2,params)">coherencyc</a>	Multi-taper coherency,cross-spectrum and individual spectra - continuous process</li><li><a href="../../chronux_2_10/spectral_analysis/continuous/coherencysegc.html" class="code" title="function [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencysegc(data1,data2,win,params)">coherencysegc</a>	Multi-taper coherency, cross-spectrum and individual spectra with segmenting - continuous process</li><li><a href="../../chronux_2_10/spectral_analysis/continuous/cohgramc.html" class="code" title="function [C,phi,S12,S1,S2,t,f,confC,phistd,Cerr]=cohgramc(data1,data2,movingwin,params)">cohgramc</a>	Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous processes</li><li><a href="../../chronux_2_10/spectral_analysis/continuous/cohmatrixc.html" class="code" title="function [C,phi,S12,f,confC,phistd,Cerr]=cohmatrixc(data,params)">cohmatrixc</a>	Multi-taper coherency,cross-spectral matrix - continuous process</li><li><a href="../../chronux_2_10/spectral_analysis/continuous/mtdspecgramc.html" class="code" title="function [dS,t,f]=mtdspecgramc(data,movingwin,phi,params)">mtdspecgramc</a>	Multi-taper derivative of the time-frequency spectrum - continuous process</li><li><a href="../../chronux_2_10/spectral_analysis/continuous/mtdspectrumc.html" class="code" title="function [dS,f]=mtdspectrumc(data,phi,params)">mtdspectrumc</a>	Multi-taper frequency derivative of the spectrum - continuous process</li><li><a href="../../chronux_2_10/spectral_analysis/continuous/mtspecgramc.html" class="code" title="function [S,t,f,Serr]=mtspecgramc(data,movingwin,params)">mtspecgramc</a>	Multi-taper time-frequency spectrum - continuous process</li><li><a href="../../chronux_2_10/spectral_analysis/continuous/mtspecgramtrigc.html" class="code" title="function [S,t,f,Serr]=mtspecgramtrigc(data,E,win,movingwin,params)">mtspecgramtrigc</a>	Multi-taper event triggered time-frequency spectrum - continuous process</li><li><a href="../../chronux_2_10/spectral_analysis/continuous/mtspectrumc.html" class="code" title="function [S,f,Serr]=mtspectrumc(data,params)">mtspectrumc</a>	Multi-taper spectrum - continuous process</li><li><a href="../../chronux_2_10/spectral_analysis/continuous/mtspectrumsegc.html" class="code" title="function [S,f,varS,C,Serr]=mtspectrumsegc(data,win,params,segave)">mtspectrumsegc</a>	Multi-taper segmented spectrum for a univariate continuous process</li><li><a href="../../chronux_2_10/spectral_analysis/continuous/mtspectrumtrigc.html" class="code" title="function [S,f,Serr]=mtspectrumtrigc(data,E,win,params)">mtspectrumtrigc</a>	Multi-taper event triggered time-frequency spectrum - continuous process</li><li><a href="../../chronux_2_10/spectral_analysis/hybrid/coherencycpb.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpb(data1,data2,params,fscorr)">coherencycpb</a>	Multi-taper coherency,cross-spectrum and individual spectra - continuous and binned point process data</li><li><a href="../../chronux_2_10/spectral_analysis/hybrid/coherencycpt.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpt(data1,data2,params,fscorr,t)">coherencycpt</a>	Multi-taper coherency,cross-spectrum and individual spectra -continuous data and point process as times</li><li><a href="../../chronux_2_10/spectral_analysis/hybrid/coherencysegcpb.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegcpb(data1,data2,win,params,segave,fscorr)">coherencysegcpb</a>	Multi-taper coherency,cross-spectrum and individual spectra with segmenting</li><li><a href="../../chronux_2_10/spectral_analysis/hybrid/coherencysegcpt.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegcpt(data1,data2,win,params,segave,fscorr)">coherencysegcpt</a>	Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting</li><li><a href="../../chronux_2_10/spectral_analysis/hybrid/cohgramcpb.html" class="code" title="function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpb(data1,data2,movingwin,params,fscorr)">cohgramcpb</a>	Multi-taper time-frequency coherence,cross-spectrum and individual spectra</li><li><a href="../../chronux_2_10/spectral_analysis/hybrid/cohgramcpt.html" class="code" title="function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpt(data1,data2,movingwin,params,fscorr)">cohgramcpt</a>	Multi-taper time-frequency coherence,cross-spectrum and individual spectra</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/coherencypb.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypb(data1,data2,params,fscorr)">coherencypb</a>	Multi-taper coherency,cross-spectrum and individual spectra - binned point process</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/coherencysegpb.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpb(data1,data2,win,params,segave,fscorr)">coherencysegpb</a>	Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/cohgrampb.html" class="code" title="function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscorr)">cohgrampb</a>	Multi-taper time-frequency coherence,cross-spectrum and individual spectra - two binned point processes</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/cohmatrixpb.html" class="code" title="function [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpb(data,params,fscorr)">cohmatrixpb</a>	Multi-taper coherency matrix - binned point process</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/mtdspecgrampb.html" class="code" title="function [dS,t,f]=mtdspecgrampb(data,movingwin,phi,params)">mtdspecgrampb</a>	Multi-taper derivatives of time-frequency spectrum - binned point process</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/mtdspectrumpb.html" class="code" title="function [dS,f]=mtdspectrumpb(data,phi,params)">mtdspectrumpb</a>	Multi-taper spectral derivative - binned point process</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/mtspecgrampb.html" class="code" title="function [S,t,f,R,Serr]=mtspecgrampb(data,movingwin,params,fscorr)">mtspecgrampb</a>	Multi-taper time-frequency spectrum - binned point process</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/mtspecgramtrigpb.html" class="code" title="function [S,t,f,R,Serr]=mtspecgramtrigpb(data,E,win,movingwin,params,fscorr)">mtspecgramtrigpb</a>	Multi-taper event triggered time-frequency spectrum - binned point process</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/mtspectrumpb.html" class="code" title="function [S,f,R,Serr]=mtspectrumpb(data,params,fscorr)">mtspectrumpb</a>	Multi-taper spectrum - binned point process</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/mtspectrumsegpb.html" class="code" title="function [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpb(data,win,params,segave,fscorr)">mtspectrumsegpb</a>	Multi-taper segmented spectrum for a univariate binned point process</li><li><a href="../../chronux_2_10/spectral_analysis/pointbinned/mtspectrumtrigpb.html" class="code" title="function [S,f,R,Serr]=mtspectrumtrigpb(data,E,win,params,fscorr)">mtspectrumtrigpb</a>	Multi-taper event triggered time-frequency spectrum - binned point process</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>	bin spikes at a specified frequency sampling i.e. sampling rate 1/sampling</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/coherencypt.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypt(data1,data2,params,fscorr,t)">coherencypt</a>	Multi-taper coherency - point process times</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/coherencysegpt.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpt(data1,data2,win,params,segave,fscorr)">coherencysegpt</a>	Multi-taper coherency computed by segmenting two univariate point processes into chunks</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/cohgrampt.html" class="code" title="function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampt(data1,data2,movingwin,params,fscorr)">cohgrampt</a>	Multi-taper time-frequency coherence - two point processes given as times</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/cohmatrixpt.html" class="code" title="function [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpt(data,params,fscorr)">cohmatrixpt</a>	Multi-taper coherency matrix - point process times</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/createdatamatpt.html" class="code" title="function data=createdatamatpt(data,E,win)">createdatamatpt</a>	Helper function to create an event triggered matrix from a single</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/extractdatapt.html" class="code" title="function data=extractdatapt(data,t,offset)">extractdatapt</a>	Extract segements of spike times between t(1) and t(2)</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/mtdspecgrampt.html" class="code" title="function [dS,t,f]=mtdspecgrampt(data,movingwin,phi,params)">mtdspecgrampt</a>	Multi-taper derivative time-frequency spectrum - point process times</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/mtdspectrumpt.html" class="code" title="function [dS,f]=mtdspectrumpt(data,phi,params,t)">mtdspectrumpt</a>	Multi-taper spectral derivative - point process times</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/mtspecgrampt.html" class="code" title="function [S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)">mtspecgrampt</a>	Multi-taper time-frequency spectrum - point process times</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/mtspecgramtrigpt.html" class="code" title="function [S,t,f,R,Serr]=mtspecgramtrigpt(data,E,win,movingwin,params,fscorr)">mtspecgramtrigpt</a>	Multi-taper event triggered time-frequency spectrum - point process times</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/mtspectrumpt.html" class="code" title="function [S,f,R,Serr]=mtspectrumpt(data,params,fscorr,t)">mtspectrumpt</a>	Multi-taper spectrum - point process times</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/mtspectrumsegpt.html" class="code" title="function [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpt(data,win,params,segave,fscorr)">mtspectrumsegpt</a>	Multi-taper segmented spectrum for a univariate binned point process</li><li><a href="../../chronux_2_10/spectral_analysis/pointtimes/mtspectrumtrigpt.html" class="code" title="function [S,f,R,Serr]=mtspectrumtrigpt(data,E,win,params,fscorr)">mtspectrumtrigpt</a>	Multi-taper time-frequency spectrum - point process times</li></ul>
This function is called by:
<ul style="list-style-image:url(../../matlabicon.gif)">
</ul>
<!-- crossreference -->


<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../../up.png"></a></h2>
<div class="fragment"><pre>0001 <span class="comment">% function testscript(pname,direction,movingwin,segave,params,fscorr)</span>
0002 <span class="comment">%</span>
0003 <span class="comment">% This script runs a sequence of analysis steps using the test</span>
0004 <span class="comment">% data contained in data. The data consists of a single tetrode</span>
0005 <span class="comment">% recording from macaque area LIP during a memory saccade experiment</span>
0006 <span class="comment">% a la Pesaran et al (2002). The data is already separated into</span>
0007 <span class="comment">% spikes and LFPs. LFPs are contained in variable dlfp, spikes from two</span>
0008 <span class="comment">% neurons are in in a struct array dsp, and event information is in</span>
0009 <span class="comment">% the following set of variables:</span>
0010 <span class="comment">%</span>
0011 <span class="comment">% trialtimes - start times of trials</span>
0012 <span class="comment">% fixon - fixation light comes on</span>
0013 <span class="comment">% fixacq - fixation acquired</span>
0014 <span class="comment">% targon - target light on</span>
0015 <span class="comment">% targoff - target light off</span>
0016 <span class="comment">% fixoff - fixation off</span>
0017 <span class="comment">% saccade - saccade</span>
0018 <span class="comment">%</span>
0019 <span class="comment">% Note that spikes and event times are in seconds and the sampling</span>
0020 <span class="comment">% frequency for the LFP in this experiment was 1kHz.</span>
0021 <span class="comment">%</span>
0022 <span class="comment">% the script takes the following input argument -</span>
0023 <span class="comment">% pname - path name on your computer where the data file LIPdata is stored.</span>
0024 <span class="comment">% direction - target direction to be analysed (0-7)</span>
0025 <span class="comment">%</span>
0026 <span class="comment">% The remaining parameters control various computations and are discussed</span>
0027 <span class="comment">% in chronux.m - type Help chronux.m for more information.</span>
0028 <span class="comment">%</span>
0029 <span class="comment">% if nargin &lt; 4;</span>
0030 <span class="comment">%     error('Need 6 input parameters - see help');</span>
0031 <span class="comment">% end;</span>
0032 <span class="comment">% if nargin &lt; 5 | isempty(params);</span>
0033 <span class="comment">%    [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);</span>
0034 <span class="comment">% end;</span>
0035 <span class="comment">% if nargin &lt; 6 | isempty(fscorr);</span>
0036 <span class="comment">%     fscorr=1;</span>
0037 <span class="comment">% end;</span>
0038 pname=<span class="string">'data'</span>;
0039 params.Fs=1000; <span class="comment">% sampling frequency</span>
0040 params.fpass=[10 100]; <span class="comment">% band of frequencies to be kept</span>
0041 params. tapers=[3 5]; <span class="comment">% taper parameters</span>
0042 params.pad=2; <span class="comment">% pad factor for fft</span>
0043 params.err=[2 0.05];
0044 params.trialave=1;
0045 movingwin=[0.5 0.05];
0046 segave=1;
0047 direction=5;
0048 
0049 wintrig=[5*movingwin(1) 5*movingwin(1)];
0050 winseg=2*movingwin(1);
0051 <span class="comment">%</span>
0052 <span class="comment">% Load data</span>
0053 <span class="comment">%</span>
0054 eval([<span class="string">'load LIPdata.mat'</span>]);
0055 <span class="comment">% %</span>
0056 <span class="comment">% % Create rearranged data blocks for further analysis: We are going to</span>
0057 <span class="comment">% % extract segments of data centered on the target off times from the first channel of LFP data and the from one of the two spike trains</span>
0058 <span class="comment">% %</span>
0059 <span class="comment">% %</span>
0060 <span class="comment">% indx1=find(targets==5);indx2=find(targets==1); % trials to preferred and antipreferred direction</span>
0061 <span class="comment">% E1=targon(indx1); E2=targon(indx2); % target on times trials to preferred adn anti-preferred directions</span>
0062 <span class="comment">% dlfp1=createdatamatc(dlfp(:,1),E1,Fs,wintrig);dlfp2=createdatamatc(dlfp(:,1),E2,Fs,wintrig); % extract event triggered segments of the first LFP channel</span>
0063 <span class="comment">% dsp1=createdatamatpt(dsp(1),E1,wintrig); dsp2=createdatamatpt(dsp(1),E2,wintrig); % the same for one of the spike trains</span>
0064 
0065 <span class="comment">% compute spectrum of the first few seconds of LFP channels 1-2</span>
0066 NT=round(params.Fs*10*movingwin(1));
0067 data=dlfp(1:NT,:); data1=data(:,1:2);
0068 [S,f,Serr]=<a href="../../chronux_2_10/spectral_analysis/continuous/mtspectrumc.html" class="code" title="function [S,f,Serr]=mtspectrumc(data,params)">mtspectrumc</a>(data1,params);
0069 figure;
0070 plot(f,10*log10(S),f,10*log10(Serr(1,:)),f,10*log10(Serr(2,:))); xlabel(<span class="string">'Frequency Hz'</span>); ylabel(<span class="string">'Spectrum'</span>);
0071 <span class="comment">%%% pause</span>
0072 
0073 <span class="comment">% compute derivative of the spectrum for the same data</span>
0074 phi=[0 pi/2];
0075 [dS,f]=<a href="../../chronux_2_10/spectral_analysis/continuous/mtdspectrumc.html" class="code" title="function [dS,f]=mtdspectrumc(data,phi,params)">mtdspectrumc</a>(data1,phi,params);
0076 figure;
0077 plot(f,dS(1,:),f,dS(2,:)); xlabel(<span class="string">'frequency Hz'</span>); ylabel(<span class="string">'Derivatives'</span>); legend(<span class="string">'Time'</span>,<span class="string">'Frequency'</span>);
0078 <span class="comment">%%% pause</span>
0079 
0080 <span class="comment">% compute coherency between  channels 1-2 and  3-4</span>
0081 data1=data(:,1:2);data2=data(:,3:4);
0082 [C,phi,S12,S1,S2,f,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/continuous/coherencyc.html" class="code" title="function [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencyc(data1,data2,params)">coherencyc</a>(data1,data2,params); 
0083 figure;plot(f,C,f,Cerr(1,:),f,Cerr(2,:));xlabel(<span class="string">'frequency'</span>); ylabel(<span class="string">'Coherency'</span>);
0084 <span class="comment">%%% pause</span>
0085 
0086 <span class="comment">% coherency matrix of data1</span>
0087 [C,phi,S12,f,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/continuous/cohmatrixc.html" class="code" title="function [C,phi,S12,f,confC,phistd,Cerr]=cohmatrixc(data,params)">cohmatrixc</a>(data1,params);
0088 
0089 <span class="comment">% compute spectrogram for 1-2</span>
0090 [S,t,f,Serr]=<a href="../../chronux_2_10/spectral_analysis/continuous/mtspecgramc.html" class="code" title="function [S,t,f,Serr]=mtspecgramc(data,movingwin,params)">mtspecgramc</a>(data1,movingwin,params);
0091 figure;imagesc(t,f,10*log10(S)'); axis xy; colorbar
0092 <span class="comment">%%% pause</span>
0093 
0094 <span class="comment">% compute time-frequency derivative of the spectrogram for 1-2</span>
0095 phi=[0 pi/2];
0096 [dS,t,f]=<a href="../../chronux_2_10/spectral_analysis/continuous/mtdspecgramc.html" class="code" title="function [dS,t,f]=mtdspecgramc(data,movingwin,phi,params)">mtdspecgramc</a>(data1,movingwin,phi,params);
0097 <span class="comment">% pause</span>
0098 <span class="comment">% figure;subplot(211);imagesc(t,f,squeeze(dS(1,:,:))'); axis xy; colorbar;</span>
0099 <span class="comment">% subplot(212);imagesc(t,f,squeeze(dS(2,:,:))'); axis xy; colorbar;</span>
0100 <span class="comment">% %%% pause</span>
0101 
0102 <span class="comment">% compute coherogram between 1-2 and 3-4</span>
0103 NT=round(movingwin(1)*Fs);
0104 [C,phi,S12,S1,S2,t,f,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/continuous/cohgramc.html" class="code" title="function [C,phi,S12,S1,S2,t,f,confC,phistd,Cerr]=cohgramc(data1,data2,movingwin,params)">cohgramc</a>(data1,data2,movingwin,params);
0105 figure;imagesc(t,f,C'); axis xy; colorbar;
0106 <span class="comment">%%% pause</span>
0107 
0108 <span class="comment">% compute segmented spectrum of 1</span>
0109 NT=10*round(winseg*Fs);
0110 data1=dlfp(1:NT,1);
0111 [S,f,varS,C,Serr]=<a href="../../chronux_2_10/spectral_analysis/continuous/mtspectrumsegc.html" class="code" title="function [S,f,varS,C,Serr]=mtspectrumsegc(data,win,params,segave)">mtspectrumsegc</a>(data1,winseg,params,segave);
0112 figure; subplot(211);plot(f,10*log(S));
0113 imagesc(f,f,C); axis xy;colorbar;
0114 <span class="comment">%%% pause</span>
0115 
0116 <span class="comment">% compute segmented coherency between 1 and 2</span>
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]=<a href="../../chronux_2_10/spectral_analysis/continuous/coherencysegc.html" class="code" title="function [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencysegc(data1,data2,win,params)">coherencysegc</a>(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 <span class="comment">%%% pause</span>
0122 
0123 <span class="comment">% compute spectrum of channel 1 triggered to events E</span>
0124 E1=targon(find(targets==direction)); 
0125 data1=dlfp(:,1); 
0126 [S,f,Serr]=<a href="../../chronux_2_10/spectral_analysis/continuous/mtspectrumtrigc.html" class="code" title="function [S,f,Serr]=mtspectrumtrigc(data,E,win,params)">mtspectrumtrigc</a>(data1,E1,wintrig,params);
0127 figure;plot(f,10*log10(S)'); axis xy; colorbar;
0128 <span class="comment">%%% pause</span>
0129 
0130 <span class="comment">% compute spectrogram of channel 1 triggered to events E</span>
0131 E1=targon(find(targets==direction)); 
0132 data1=dlfp(:,1); 
0133 [S,t,f,Serr]=<a href="../../chronux_2_10/spectral_analysis/continuous/mtspecgramtrigc.html" class="code" title="function [S,t,f,Serr]=mtspecgramtrigc(data,E,win,movingwin,params)">mtspecgramtrigc</a>(data1,E1,wintrig,movingwin,params);
0134 figure; imagesc(t,f,10*log10(S)'); axis xy; colorbar;
0135 <span class="comment">%%% pause</span>
0136 
0137 <span class="comment">%</span>
0138 <span class="comment">% Analysis - point process stored as times</span>
0139 <span class="comment">%</span>
0140 
0141 <span class="comment">% dsp contains 2 channels of spikes</span>
0142 
0143 data=<a href="../../chronux_2_10/spectral_analysis/pointtimes/extractdatapt.html" class="code" title="function data=extractdatapt(data,t,offset)">extractdatapt</a>(dsp,[20 30]); <span class="comment">% extract spikes occurring between 20 and 30 seconds and compute their spectrum</span>
0144 [S,f,R,Serr]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/mtspectrumpt.html" class="code" title="function [S,f,R,Serr]=mtspectrumpt(data,params,fscorr,t)">mtspectrumpt</a>(data,params);
0145 figure; plot(f,10*log10(S),f,10*log10(Serr(1,:)),f,10*log10(Serr(2,:)));line(get(gca,<span class="string">'xlim'</span>),[10*log10(R) 10*log10(R)]);
0146 <span class="comment">%%% pause</span>
0147 
0148 <span class="comment">%</span>
0149 <span class="comment">% Compute the derivative of the spectrum</span>
0150 <span class="comment">%</span>
0151 phi=[0 pi/2];
0152 [dS,f]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/mtdspectrumpt.html" class="code" title="function [dS,f]=mtdspectrumpt(data,phi,params,t)">mtdspectrumpt</a>(data,phi,params);
0153 figure; plot(f,dS);
0154 <span class="comment">%%% pause</span>
0155 
0156 <span class="comment">%</span>
0157 <span class="comment">% Compute the derivative of the time-frequency spectrum</span>
0158 <span class="comment">%</span>
0159 data=<a href="../../chronux_2_10/spectral_analysis/pointtimes/extractdatapt.html" class="code" title="function data=extractdatapt(data,t,offset)">extractdatapt</a>(dsp,[20 30]);
0160 data1=data(1); data2=data(2);fscorr=[];t=[];
0161 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/coherencypt.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypt(data1,data2,params,fscorr,t)">coherencypt</a>(data1,data2,params);
0162 figure; plot(f,C);
0163 <span class="comment">%%% pause</span>
0164 
0165 <span class="comment">%</span>
0166 <span class="comment">% Compute event triggered average spectrum for one of the directions</span>
0167 <span class="comment">%</span>
0168 E1=targon(find(targets==direction));
0169 data=dsp(1); 
0170 [S,f,R,Serr]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/mtspectrumtrigpt.html" class="code" title="function [S,f,R,Serr]=mtspectrumtrigpt(data,E,win,params,fscorr)">mtspectrumtrigpt</a>(data,E1,wintrig,params);
0171 figure;plot(f,10*log10(S),f,10*log10(Serr(1,:)),f,10*log10(Serr(2,:))); line(get(gca,<span class="string">'xlim'</span>),[10*log10(R) 10*log10(R)]); 
0172 <span class="comment">%%% pause</span>
0173 
0174 <span class="comment">%</span>
0175 <span class="comment">% Compute the matrix of coherencies</span>
0176 <span class="comment">%</span>
0177 data=<a href="../../chronux_2_10/spectral_analysis/pointtimes/extractdatapt.html" class="code" title="function data=extractdatapt(data,t,offset)">extractdatapt</a>(dsp,[20 30]);
0178 [C,phi,S12,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/cohmatrixpt.html" class="code" title="function [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpt(data,params,fscorr)">cohmatrixpt</a>(data,params,fscorr);
0179 
0180 <span class="comment">%</span>
0181 <span class="comment">% Event triggered spectrogram - first way way</span>
0182 <span class="comment">%</span>
0183 data=<a href="../../chronux_2_10/spectral_analysis/pointtimes/createdatamatpt.html" class="code" title="function data=createdatamatpt(data,E,win)">createdatamatpt</a>(dsp(1),E1,wintrig);
0184 [S,t,f,R,Serr]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/mtspecgrampt.html" class="code" title="function [S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)">mtspecgrampt</a>(data,movingwin,params);
0185 figure;imagesc(t,f,10*log10(S)'); axis xy; colorbar;
0186 <span class="comment">%%% pause</span>
0187 
0188 <span class="comment">%</span>
0189 <span class="comment">% Derivative of the time-frequency spectrum</span>
0190 <span class="comment">%</span>
0191 data=<a href="../../chronux_2_10/spectral_analysis/pointtimes/createdatamatpt.html" class="code" title="function data=createdatamatpt(data,E,win)">createdatamatpt</a>(dsp(1),E1,wintrig);
0192 phi=[0 pi/2];
0193 [dS,t,f]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/mtdspecgrampt.html" class="code" title="function [dS,t,f]=mtdspecgrampt(data,movingwin,phi,params)">mtdspecgrampt</a>(data,movingwin,phi,params);
0194 figure; subplot(211); imagesc(t,f,squeeze(dS(1,:,:))'); axis xy; colorbar;
0195 subplot(212); imagesc(t,f,squeeze(dS(2,:,:))'); axis xy; colorbar;
0196 
0197 <span class="comment">%</span>
0198 <span class="comment">% Coherogram between the two spike trains</span>
0199 <span class="comment">%</span>
0200 data1=<a href="../../chronux_2_10/spectral_analysis/pointtimes/createdatamatpt.html" class="code" title="function data=createdatamatpt(data,E,win)">createdatamatpt</a>(dsp(1),E1,wintrig);
0201 data2=<a href="../../chronux_2_10/spectral_analysis/pointtimes/createdatamatpt.html" class="code" title="function data=createdatamatpt(data,E,win)">createdatamatpt</a>(dsp(2),E1,wintrig);
0202 [C,phi,S12,S1,S2,t,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/cohgrampt.html" class="code" title="function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampt(data1,data2,movingwin,params,fscorr)">cohgrampt</a>(data1,data2,movingwin,params,fscorr);
0203 figure;imagesc(t,f,C');axis xy; colorbar
0204 <span class="comment">% %%% pause</span>
0205 
0206 <span class="comment">%</span>
0207 <span class="comment">% Event Triggered spectrogram another way</span>
0208 <span class="comment">%</span>
0209 data=dsp(1);
0210 [S,t,f,R,Serr]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/mtspecgramtrigpt.html" class="code" title="function [S,t,f,R,Serr]=mtspecgramtrigpt(data,E,win,movingwin,params,fscorr)">mtspecgramtrigpt</a>(data,E1,wintrig,movingwin,params);
0211 imagesc(t,f,10*log10(S)'); axis xy; colorbar
0212 <span class="comment">%</span>
0213 <span class="comment">% Segmented spectrum</span>
0214 <span class="comment">%</span>
0215 data=<a href="../../chronux_2_10/spectral_analysis/pointtimes/extractdatapt.html" class="code" title="function data=extractdatapt(data,t,offset)">extractdatapt</a>(dsp,[20 30]);
0216 data=data(1);
0217 [S,f,R,varS]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/mtspectrumsegpt.html" class="code" title="function [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpt(data,win,params,segave,fscorr)">mtspectrumsegpt</a>(data,winseg,params);
0218 plot(f,10*log10(S)); line(get(gca,<span class="string">'xlim'</span>),[10*log10(R) 10*log10(R)]);
0219 <span class="comment">%</span>
0220 <span class="comment">% Segmented coherency</span>
0221 <span class="comment">%</span>
0222 data=<a href="../../chronux_2_10/spectral_analysis/pointtimes/extractdatapt.html" class="code" title="function data=extractdatapt(data,t,offset)">extractdatapt</a>(dsp,[20 30]);
0223 data1=data(1);data2=data(2);
0224 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/coherencysegpt.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpt(data1,data2,win,params,segave,fscorr)">coherencysegpt</a>(data1,data2,winseg,params);
0225 figure; subplot(311); plot(f,C);subplot(312); plot(f,10*log10(S1));subplot(313); plot(f,10*log10(S2))
0226 <span class="comment">%</span>
0227 <span class="comment">% Analysis - hybrid: one continous and one point process stored as times</span>
0228 <span class="comment">%</span>
0229 offset=1;
0230 data1=dlfp(20000:30000,1); data2=<a href="../../chronux_2_10/spectral_analysis/pointtimes/extractdatapt.html" class="code" title="function data=extractdatapt(data,t,offset)">extractdatapt</a>(dsp,[20 30],offset);data2=data2(1).times;
0231 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/hybrid/coherencycpt.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpt(data1,data2,params,fscorr,t)">coherencycpt</a>(data1,data2,params);
0232 figure; subplot(311); plot(f,C);subplot(312); plot(f,10*log10(S1));subplot(313); plot(f,10*log10(S2))
0233 
0234 
0235 data1=dlfp(20000:30000,1); data2=<a href="../../chronux_2_10/spectral_analysis/pointtimes/extractdatapt.html" class="code" title="function data=extractdatapt(data,t,offset)">extractdatapt</a>(dsp,[20 30],offset);data2=data2(1).times;
0236 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/hybrid/coherencysegcpt.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegcpt(data1,data2,win,params,segave,fscorr)">coherencysegcpt</a>(data1,data2,winseg,params,segave,fscorr);
0237 figure; subplot(311); plot(f,C);subplot(312); plot(f,10*log10(S1));subplot(313); plot(f,10*log10(S2))
0238 
0239 
0240 data1=dlfp(20000:30000,1); data2=<a href="../../chronux_2_10/spectral_analysis/pointtimes/extractdatapt.html" class="code" title="function data=extractdatapt(data,t,offset)">extractdatapt</a>(dsp,[20 30],offset);data2=data2(1).times;
0241 [C,phi,S12,S1,S2,t,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/hybrid/cohgramcpt.html" class="code" title="function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpt(data1,data2,movingwin,params,fscorr)">cohgramcpt</a>(data1,data2,movingwin,params,fscorr);
0242 figure; subplot(311); imagesc(t,f,C');axis xy; colorbar; subplot(312);imagesc(t,f,10*log10(S1)');axis xy; colorbar; subplot(313); imagesc(t,f,10*log10(S2)');axis xy; colorbar
0243 
0244 
0245 <span class="comment">%  Analysis: Binned spike counts</span>
0246 
0247 [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs,[20 30]); <span class="comment">% extract spikes occurring between 20 and 30 seconds</span>
0248 
0249 data=dN;
0250 [S,f,R,Serr]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/mtspectrumpb.html" class="code" title="function [S,f,R,Serr]=mtspectrumpb(data,params,fscorr)">mtspectrumpb</a>(data,params);
0251 plot(f,10*log10(S),f,10*log10(Serr(1,:)), f,10*log10(Serr(2,:))); <span class="comment">%line(get(gca,'xlim'),[10*log10(R) 10*log10(R)]);</span>
0252 
0253 data=dN;
0254 phi=[0 pi/2];
0255 [dS,f]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/mtdspectrumpb.html" class="code" title="function [dS,f]=mtdspectrumpb(data,phi,params)">mtdspectrumpb</a>(data,phi,params);
0256 figure; plot(f,dS); 
0257 
0258 data=dN;
0259 data1=data(:,1); data2=data(:,2);fscorr=[];t=[];
0260 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/coherencypb.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypb(data1,data2,params,fscorr)">coherencypb</a>(data1,data2,params);
0261 figure; subplot(311); plot(f,C);subplot(312); plot(f,10*log10(S1)); subplot(313); plot(f,10*log10(S2));
0262 
0263 E=targon(find(targets==direction)); E=E(find(E&gt;20 &amp; E&lt;450)); [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs,[20 500]);data=dN(:,1);
0264 [S,f,R,Serr]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/mtspectrumtrigpb.html" class="code" title="function [S,f,R,Serr]=mtspectrumtrigpb(data,E,win,params,fscorr)">mtspectrumtrigpb</a>(data,E,wintrig,params);
0265 figure;plot(f,10*log10(S),f,10*log10(Serr(1,:)),f,10*log10(Serr(2,:)));
0266 
0267 [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs,[20 30]); <span class="comment">% extract spikes occurring between 20 and 30 seconds</span>
0268 data=dN;
0269 [C,phi,S12,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/cohmatrixpb.html" class="code" title="function [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpb(data,params,fscorr)">cohmatrixpb</a>(data,params,fscorr);
0270 
0271 [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs,[20 30]); <span class="comment">% extract spikes occurring between 20 and 30 seconds</span>
0272 data=dN;
0273 [S,t,f,R,Serr]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/mtspecgrampb.html" class="code" title="function [S,t,f,R,Serr]=mtspecgrampb(data,movingwin,params,fscorr)">mtspecgrampb</a>(data,movingwin,params);
0274 figure;imagesc(t,f,10*log10(S)'); axis xy; colorbar
0275 
0276 clear R Serr Cerr S C phierr dN dS data1 data2
0277 
0278 [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs,[20 30]); <span class="comment">% extract spikes occurring between 20 and 30 seconds</span>
0279 data=dN;
0280 phi=[0 pi/2];
0281 [dS,t,f]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/mtdspecgrampb.html" class="code" title="function [dS,t,f]=mtdspecgrampb(data,movingwin,phi,params)">mtdspecgrampb</a>(data,movingwin,phi,params);
0282 
0283 [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs,[20 30]); <span class="comment">% extract spikes occurring between 20 and 30 seconds</span>
0284 data=dN;
0285 data1=data(:,1); data2=data(:,2);
0286 [C,phi,S12,S1,S2,t,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/cohgrampb.html" class="code" title="function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscorr)">cohgrampb</a>(data1,data2,movingwin,params,fscorr);
0287 
0288 [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs); <span class="comment">% extract spikes</span>
0289 dN=dN(:,1);
0290 E=E(1:6);
0291 data=dN;
0292 [S,t,f,R,Serr]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/mtspecgramtrigpb.html" class="code" title="function [S,t,f,R,Serr]=mtspecgramtrigpb(data,E,win,movingwin,params,fscorr)">mtspecgramtrigpb</a>(data,E,wintrig,movingwin,params);
0293 
0294 [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs,[20 30]); <span class="comment">% extract spikes occurring between 20 and 30 seconds</span>
0295 data=dN;
0296 data=data(:,1);
0297 [S,f,R,varS]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/mtspectrumsegpb.html" class="code" title="function [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpb(data,win,params,segave,fscorr)">mtspectrumsegpb</a>(data,winseg,params,segave,fscorr);
0298 figure; plot(f,10*log10(S)); line(get(gca,<span class="string">'xlim'</span>),10*log10([R R])); 
0299 
0300 [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs,[20 30]); <span class="comment">% extract spikes occurring between 20 and 30 seconds</span>
0301 data=dN;
0302 data1=data(:,1);data2=data(:,2);
0303 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/pointbinned/coherencysegpb.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpb(data1,data2,win,params,segave,fscorr)">coherencysegpb</a>(data1,data2,winseg,params);
0304 
0305 <span class="comment">%</span>
0306 <span class="comment">% Analysis - hybrid: one continous and one point process stored as counts</span>
0307 <span class="comment">%</span>
0308 data1=dlfp(20000:30000,:);data1=data1(:,1:2); [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs,[20 30]); <span class="comment">% extract spikes occurring between 20 and 30 seconds</span>
0309 data2=dN; data2=data2(1:<span class="keyword">end</span>,:);
0310 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/hybrid/coherencycpb.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpb(data1,data2,params,fscorr)">coherencycpb</a>(data1,data2,params);
0311 
0312 data1=data1(:,1); data2=data2(:,1);
0313 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/hybrid/coherencysegcpb.html" class="code" title="function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegcpb(data1,data2,win,params,segave,fscorr)">coherencysegcpb</a>(data1,data2,winseg,params,segave,fscorr);
0314 
0315 
0316 data1=dlfp(20000:30000,:); data1=data1(:,1:2);
0317 [dN,t]=<a href="../../chronux_2_10/spectral_analysis/pointtimes/binspikes.html" class="code" title="function [dN,t]=binspikes(data,Fs,t)">binspikes</a>(dsp,params.Fs,[20 30]); <span class="comment">% extract spikes occurring between 20 and 30 seconds</span>
0318 data2=dN; data2=data2(1:<span class="keyword">end</span>,:);
0319 [C,phi,S12,S1,S2,t,f,zerosp,confC,phierr,Cerr]=<a href="../../chronux_2_10/spectral_analysis/hybrid/cohgramcpb.html" class="code" title="function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpb(data1,data2,movingwin,params,fscorr)">cohgramcpb</a>(data1,data2,movingwin,params,fscorr);
0320</pre></div>
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