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<!-- ../menu.html chronux_2_10 --><!-- menu.html test -->
<h1>testAvg3
</h1>

<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../../up.png"></a></h2>
<div class="box"><strong>This is a calling routine to test &amp; check out the power spectrum &amp;</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">
 This is a calling routine to test &amp; check out the power spectrum &amp;
 spectrogram routines for unequal segment lengths. In addition, use it 
 to compare with Chronux routines when segments are of equal length.</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/chronux.html" class="code" title="function chronux">chronux</a>	This library performs time-frequency analysis (mostly using the</li><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/mtspectrumc.html" class="code" title="function [S,f,Serr]=mtspectrumc(data,params)">mtspectrumc</a>	Multi-taper spectrum - continuous process</li><li><a href="myrandint.html" class="code" title="function ranInt = myrandint(outputRow,outputCol,outputRange,varargin)">myrandint</a>	MYRANDINT(M,N,RANGE) is an M-by-N matrix with random integer entries</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">%</span>
0002 <span class="comment">% This is a calling routine to test &amp; check out the power spectrum &amp;</span>
0003 <span class="comment">% spectrogram routines for unequal segment lengths. In addition, use it</span>
0004 <span class="comment">% to compare with Chronux routines when segments are of equal length.</span>
0005 <span class="comment">%</span>
0006 clear all;
0007 
0008 gram = 0 ; <span class="comment">% 0=spectra, 1=coherence</span>
0009 <a href="../../chronux_2_10/spectral_analysis/chronux.html" class="code" title="function chronux">chronux</a> = 0; <span class="comment">% 1=compare, 0=don't</span>
0010 line = 0;
0011 
0012 nSamples = 4210; 
0013 nChannels = 1; 
0014 nSegments = 1;
0015 movingwin = [50, 50];
0016 
0017 <span class="comment">%</span>
0018 <span class="comment">% Spectral Parameters</span>
0019 <span class="comment">%</span>
0020 params.fpass = [ 0 0.5 ];
0021 params.pad = 2;
0022 params.err = [1 0.85];  <span class="comment">% err(1)=0 is no err estimates; err(1)=1 is asymptotic estimates; err(1)=2 is Jacknife</span>
0023 params.trialave = 1;
0024 params.Fs = 1;
0025 
0026 <span class="comment">%</span>
0027 <span class="comment">% Tapers issues</span>
0028 <span class="comment">%</span>
0029 halfBandWidth = 2.5; 
0030 kCap = 2*halfBandWidth - 1;
0031 <span class="comment">%params.tapers = [ halfBandWidth, kCap ];</span>
0032 params.tapers = [ halfBandWidth, 1 ];
0033 
0034 <span class="comment">%</span>
0035 <span class="comment">% Basic checks on inputs</span>
0036 <span class="comment">%</span>
0037 <span class="keyword">if</span> (gram==1) &amp;&amp; (nChannels &lt; 2), error( <span class="string">'Coherence requires at least 2 channels...'</span> ); <span class="keyword">end</span> 
0038 <span class="keyword">if</span> (nSegments==1) &amp;&amp; (params.err(1)==2), error( <span class="string">'Jacknife requires more than 1 segment'</span>); <span class="keyword">end</span>
0039 
0040 <span class="comment">%</span>
0041 <span class="comment">% Generate segments endpoints randomly</span>
0042 <span class="comment">% myrandint is a 3rd party routine (from matlab site)</span>
0043 <span class="comment">%</span>
0044 <span class="keyword">if</span> ~<a href="../../chronux_2_10/spectral_analysis/chronux.html" class="code" title="function chronux">chronux</a>
0045     <span class="comment">% Randomly generated segment end points</span>
0046     sMarkers = reshape( sort( <a href="myrandint.html" class="code" title="function ranInt = myrandint(outputRow,outputCol,outputRange,varargin)">myrandint</a>( 2*nSegments, 1, [ 1 : nSamples ], <span class="string">'noreplace'</span> ) )', 2, nSegments )';
0047 <span class="keyword">else</span>
0048     <span class="comment">% Equal length segments (to compare with Chronux)</span>
0049     sMarkers = ones( nSegments, 2 ); 
0050     sMarkers( :, 2 ) = round( nSamples/2 ); 
0051 <span class="keyword">end</span>
0052 
0053 <span class="comment">%</span>
0054 <span class="comment">% Randomly generate the time series</span>
0055 <span class="comment">%</span>
0056 fulldata = randn( nSamples, nChannels );  
0057 <span class="keyword">if</span> line <span class="comment">% add line harmonic for testing purposes</span>
0058     f1 = 0.45; a1 = 0.20;
0059     f2 = 0.25; a2 = 0.15;
0060     <span class="keyword">for</span> c=1:size(fulldata,2)
0061         mx = max(fulldata(:,c));
0062         fulldata(:,c) = fulldata(:,c) + a1*mx*sin( f1*2*pi*[1:size(fulldata,1)]') + a2*mx*sin( f2*2*pi*[1:size(fulldata,1)]') ;
0063     <span class="keyword">end</span>
0064 <span class="keyword">end</span>
0065 
0066 <span class="comment">%</span>
0067 <span class="comment">% Randomly select a few channels</span>
0068 <span class="comment">%</span>
0069 chIndices = sort( <a href="myrandint.html" class="code" title="function ranInt = myrandint(outputRow,outputCol,outputRange,varargin)">myrandint</a>( ceil(nChannels/1.5), 1, [ 1 : nChannels ], <span class="string">'noreplace'</span> ) );
0070 <span class="comment">%chIndices = [ 1 : nChannels ];</span>
0071 
0072 <span class="comment">%</span>
0073 <span class="comment">% Create a data matrix with all the segments aligned one after another</span>
0074 <span class="comment">%</span>
0075 totalSegmentLength = sum( sMarkers(:,2) - sMarkers(:,1) + 1 );
0076 data = zeros( totalSegmentLength, length(chIndices) ); <span class="comment">% preallocate to ensure contiguous memory</span>
0077 newMarkers(1,1) = 1; 
0078 newMarkers(1,2) = sMarkers(1,2) - sMarkers(1,1) + 1;
0079 data( newMarkers(1,1):newMarkers(1,2), : ) = fulldata( sMarkers(1,1):sMarkers(1,2), chIndices(:));
0080 <span class="keyword">for</span> sg = 2:size( sMarkers, 1 )
0081     newMarkers(sg,1) = newMarkers(sg-1,2) + 1; 
0082     newMarkers(sg,2) = newMarkers(sg,1) + sMarkers(sg,2) - sMarkers(sg,1);
0083     data( newMarkers(sg,1):newMarkers(sg,2), : ) = fulldata( sMarkers(sg,1):sMarkers(sg,2), chIndices(:));
0084 <span class="keyword">end</span>
0085 
0086 <span class="comment">% To ensure that we check results from array indices beyond 1</span>
0087 <span class="keyword">if</span> nChannels &gt; 1
0088     ix = sort( <a href="myrandint.html" class="code" title="function ranInt = myrandint(outputRow,outputCol,outputRange,varargin)">myrandint</a>( 1, 2, [1:length(chIndices)], <span class="string">'noreplace'</span> ) ); <span class="comment">% Arbitrarily pick two indices from selected channels for testing results</span>
0089     i1=ix(1); i2=ix(2);
0090     <span class="comment">% iC = m + (n-1)*(n-2)/2, for elements of the the coherence matrix, Cmn</span>
0091     iC = ix(1) + (ix(2)-1)*(ix(2)-2)/2;
0092 <span class="keyword">else</span>
0093     ix = sort( <a href="myrandint.html" class="code" title="function ranInt = myrandint(outputRow,outputCol,outputRange,varargin)">myrandint</a>( 1, 1, [1:length(chIndices)], <span class="string">'noreplace'</span> ) ); <span class="comment">% Arbitrarily pick 1 indices from selected channels for testing results</span>
0094     i1=ix(1);
0095 <span class="keyword">end</span>
0096 
0097 <span class="comment">%</span>
0098 <span class="comment">% Power spectrum/spectrogram/coherence/coherogram</span>
0099 <span class="comment">%</span>
0100 <span class="keyword">if</span> gram==0
0101     [ S, f, Serr ] = ueSpectrogram( data, movingwin, params, newMarkers );
0102     figure; plotvector( S(:,i1), f, <span class="string">'l'</span>, squeeze(Serr(:,:,i1)) );
0103     <span class="comment">%figure; plot( f, 10*log10( S(:,i1) )); title('Avg. Routine:: Spectrum');</span>
0104 <span class="keyword">elseif</span> gram==1
0105     [Cmn,Phimn,Smn,Smm,f,I,ConfC,PhiStd,Cerr] = ueCoherence( data, params, newMarkers );
0106     <span class="comment">%  C(i,j) = Cmn(:,k) where k = j + (1/2)*(i-1)*(i-2)</span>
0107     figure; plot( f, 10*log10( Cmn(:,iC) ) ); title(<span class="string">'Avg. Routine:: Coherence-Magnitude'</span>);
0108     <span class="comment">%figure; plot( f, phimn(:,iC) ); title('Avg. Routine:: Coherence-Phase');</span>
0109     disp( [<span class="string">'Confidence levelfor C (confC) at (1-p) level: '</span> num2str( ConfC(iC)) ] );
0110 <span class="keyword">end</span>
0111 
0112 <span class="comment">%</span>
0113 <span class="comment">% Use to check against Chronux: only for equal length segments</span>
0114 <span class="comment">%</span>
0115 <span class="keyword">if</span> <a href="../../chronux_2_10/spectral_analysis/chronux.html" class="code" title="function chronux">chronux</a>
0116     cdata = repmat( fulldata( sMarkers(1,1):sMarkers(1,2), chIndices(i1) ), 1, nSegments ); <span class="comment">% round(nSamples/2) x nSegments</span>
0117     params.trialave = 1;
0118     <span class="keyword">if</span> gram==0
0119         [ cS, cf, cSerr ] = <a href="../../chronux_2_10/spectral_analysis/continuous/mtspectrumc.html" class="code" title="function [S,f,Serr]=mtspectrumc(data,params)">mtspectrumc</a>( cdata, params );
0120         figure; plot( cf, 10*log10( cS )); title(<span class="string">'Chronux:: Spectrum'</span>);
0121         figure; plot( cf, 10*log10(cSerr(1,:)), cf, 10*log10(cSerr(2,:)) ); title(<span class="string">'Chronux Error-Bar Computations'</span>);
0122         figure; plot( cf, 10*log10( cS ) - 10*log10( S(:,i1) )); title(<span class="string">'Error in Spectrum = |New Routines - Chronux|'</span>);
0123         figure; plot( cf, 10*log10(cSerr(1,:)) - 10*log10(Serr(1,:,i1)), cf, 10*log10(cSerr(2,:)) - 10*log10(Serr(2,:,i1)) );title(<span class="string">'Error in Error-Bar Computations = |New Routines - Chronux| '</span>);
0124     <span class="keyword">elseif</span> gram==1
0125         cdata2 = repmat( fulldata( sMarkers(1,1):sMarkers(1,2), chIndices(i2) ), 1, nSegments ); <span class="comment">% round(nSamples/2) x nSegments</span>
0126         params.trialave = 1;
0127         
0128         [cC,cphi,cS12,cS1,cS2,cf,cconfC,cphistd,cCerr]=<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>( cdata, cdata2, params );
0129         
0130         figure; plot( cf, 10*log10( cC(:,1) ) ); title(<span class="string">'Chronux:: Coherence-Magnitude'</span>);
0131         figure; plot( cf, 10*log10( cC(:,1) ) - 10*log10( Cmn(:,iC) ) ); title(<span class="string">'Error in Coherence = |New Routines - Chronux|'</span>);
0132         <span class="comment">% Phase may give a problem of 2pi difference... look into it.</span>
0133         figure; plot( cf, cphi(:,1) -  Phimn(:,iC) ); title(<span class="string">'Error in Phase = |New Routines - Chronux|'</span>);
0134         <span class="comment">%</span>
0135         <span class="comment">% Note the remaining quantities do not really need to checked since</span>
0136         <span class="comment">% coherence = cross-spectrum/power spectra* power spectra, ie C = S12/(S1*S2)</span>
0137         <span class="comment">% so unlikely that S12, S1, S2 are incorrect if C is correct.</span>
0138         <span class="keyword">if</span> 1
0139             figure; plot( cf, 10*log10( cS1(:,1) ) - 10*log10( Smm(:,ix(1)) ) ); title(<span class="string">'Error in Power Spectrogram-1 = |New Routines - Chronux|'</span>);
0140             figure; plot( cf, 10*log10( cS2(:,1) ) - 10*log10( Smm(:,ix(2)) ) ); title(<span class="string">'Error in Power Spectrogram-2 = |New Routines - Chronux|'</span>);
0141         <span class="keyword">end</span>
0142         <span class="comment">%</span>
0143         <span class="comment">% Error-Bars &amp; Confidence Levels</span>
0144         disp( [<span class="string">'Confidence levelfor C (confC) at (1-p) level: '</span> num2str( cconfC) <span class="string">' (Chronux)'</span> ] );
0145         disp( [<span class="string">'Error in confidence level, confC: '</span> num2str( ConfC(iC) - cconfC ) ] );     
0146         <span class="comment">%figure; plot( cf, cphistd(:,1), f, phistd(:,iC) ); title('Phase-Error-Bar Computations');</span>
0147         figure; plot( cf, cphistd(1,:,1) -  PhiStd(1,:,iC) ); title(<span class="string">'Error in PhiStd-1'</span>);
0148         figure; plot( cf, cphistd(2,:,1) -  PhiStd(2,:,iC) ); title(<span class="string">'Error in PhiStd-2'</span>);
0149         figure; plot( cf, abs(cCerr(1,:,1) -  Cerr(1,:,iC)), cf, abs(cCerr(2,:,1) -  Cerr(2,:,iC))  ); title(<span class="string">'Error in Abs(Coherence)-Error-Bar Computations = |New Routines - Chronux|'</span>);
0150     <span class="keyword">end</span>
0151 <span class="keyword">end</span>
0152 
0153     
0154 
0155 
0156</pre></div>
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