coherence_lines

status =coherence_lines(freqs,obs,array,lines,coherencefname);

freqs = frequencies to plot, e.g. [3 30] limits the plot to  3 and 30 Hz  
obs = observations in the power file to plot (defaults to all)
array = either an array name,e.g., 'all','hemisphere','quadrant','frontback',
    or 'oned' or a list of channels
 Restrictions nobs <= 3. If nobs == 1 and multiple frequencies 
 are listed then freqs < = 3. If nobs > 1 obs go on same plot one for
 each freq.  if nobs == 1 all the freqs go on the same plot
lines = 'black' or 'color'
coherencefname = coherencefilename (can be gui by skipping this param)

note also draws in solid black coherence due to uncorrelated sources
in the four spheres model.  If 'laplacian' is a reference the curve
for laplacians is drawn as well.

0001 function status =coherence_lines(freqs,obs,array,lines,coherencefname);
0002 %status =coherence_lines(freqs,obs,array,lines,coherencefname);
0003 %
0004 %freqs = frequencies to plot, e.g. [3 30] limits the plot to  3 and 30 Hz
0005 %obs = observations in the power file to plot (defaults to all)
0006 %array = either an array name,e.g., 'all','hemisphere','quadrant','frontback',
0007 %    or 'oned' or a list of channels
0008 % Restrictions nobs <= 3. If nobs == 1 and multiple frequencies
0009 % are listed then freqs < = 3. If nobs > 1 obs go on same plot one for
0010 % each freq.  if nobs == 1 all the freqs go on the same plot
0011 %lines = 'black' or 'color'
0012 %coherencefname = coherencefilename (can be gui by skipping this param)
0013 %
0014 %note also draws in solid black coherence due to uncorrelated sources
0015 %in the four spheres model.  If 'laplacian' is a reference the curve
0016 %for laplacians is drawn as well.
0017 if nargin < 5
0018     [fid] = get_fid('rb');
0019 else
0020     fid = fopen(coherencefname,'rb');
0021 end;
0022 version = fread(fid,1,'int16');
0023 if version ~= -2
0024     error('this is not a coherence file');
0025 end;
0026  [nfiles,obs_labels,Epoch,Window_Length,NEpoch,Nbad_chan,bad_chan,ref_flag,reference,NChan,NFreq] = rd_anal_hdr(fid);
0027 if nargin == 0
0028     freqs = [0:40];
0029     obs = [1:nfiles];
0030     array = 'all';
0031     lines = 'black';
0032 end;
0033 if nargin == 1
0034     obs = [1:nfiles];
0035     array = 'all';
0036     lines = 'black';
0037 end;        
0038 if nargin == 2
0039     array = 'all';
0040     lines = 'black';
0041 end;    
0042 if nargin == 3
0043     lines = 'black';
0044 end;
0045 if isempty(lines)
0046     lines = 'black';
0047 end
0048 if isempty(array)
0049     array = 'all';
0050 end
0051 if isempty(obs)
0052     obs = [1:nfiles];
0053 end;
0054 if isempty(freqs)
0055     freqs = [0:40];
0056 end;
0057 if size(obs,2) > 3
0058     fclose('all')
0059     error('too many observations > 3 to be plotted in a single plot')
0060 end;
0061 if size(obs,2) == 1
0062     if size(freqs,2) > 3 
0063         error('too many frequencies for a single plot')
0064     end;
0065 end;
0066 ch_pair_indices;
0067 if strcmp(lines,'black')
0068 line_type = ['k- ';'k--';'k-.'];
0069 scat_type = ['kx';'ko';'k.'];
0070 else    
0071 line_type = ['b-';'r-';'k-'];
0072 scat_type = ['kx';'ko';'k.'];
0073 end;
0074 coherencemax = 1;
0075 iline = 1;
0076 [xelec,yelec,zelec] = electrodes(129);
0077 twod_dist = twod_pos(xelec,yelec,zelec,9.2);
0078 coherence_array = real(get_eeg_coherence(fid,freqs,obs,nfiles,NChan,NFreq,Epoch));
0079 [dist,bcohpotential,bcohlaplacian] = baseline_coherence(0.2,80,8,8.2,8.7,9.2,7.8);
0080 if isstr(array)
0081     [arrayg,gnames] = arrays(array,[]);
0082 else
0083     arrayg = array;
0084 end
0085 if size(obs,2) > 1
0086     for g = 1:size(arrayg,1)
0087             for i= 1:size(freqs,2)
0088                 figure
0089                 hold on
0090                 for io = 1:size(obs,2)
0091                     if  ~(ref_flag(obs(io)) == 5|ref_flag(obs(io)) == 7)
0092                         hold on,bar(dist,bcohpotential,'w-');
0093                     elseif ref_flag(obs(io)) == 5 
0094                         hold on,bar(dist,bcohlaplacian,'w-');
0095                     end;
0096                 end
0097                 iline = 1;
0098                 
0099                 for j = 1:size(obs,2)
0100                 
0101                     if isstr(array)
0102                         [arrayh,hnames] = arrays(array,bad_chan(obs(j),find(bad_chan(obs(j),:))));
0103                     else
0104                         arrayh = array;
0105                     end
0106                 pairels = arrayh(g,find(arrayh(g,:)));
0107                 npairs = size(pairels,2)*(size(pairels,2)+1)/2;
0108                 pairs = zeros(1,npairs);
0109                 ipairs = 1;
0110                 for ip = 1:size(pairels,2)
0111                     for jp=ip:size(pairels,2)
0112                         pairs(ipairs) = chpair(pairels(ip),pairels(jp));
0113                         ipairs = ipairs + 1;
0114                     end;
0115                 end;
0116                 pairnames = hnames(g,:);
0117 %                hold on, plot(real(twod_dist(pairs)),coherence_array((j-1)*size(freqs,2)+i,pairs),scat_type(iline,:))
0118                 p_coh = polyfit(twod_dist(pairs),coherence_array((j-1)*size(freqs,2)+i,pairs),4);
0119                 coh_fit = real(polyval(p_coh,[0:1:fix(max(twod_dist(pairs)))]));
0120                 hold on, plot([0:1:max(twod_dist(pairs))],coh_fit,line_type(iline,:)), axis([0 max(twod_dist(pairs))+1 0 1])
0121                 title(['Coherence versus Distance:  @' int2str(freqs(i)) ' Hz ' hnames(g,:)]);
0122                 hold on, plot([9 10 ],[1-0.1*j 1-0.1*j],line_type(iline,:))
0123                 text([11],[1-0.1*j],[deblank(setstr(obs_labels(obs(j),:)))])
0124                 xlabel('Interelectrode Distance (cm)')
0125                 ylabel('Coherence')
0126                  iline = iline+ 1;
0127             end
0128         end
0129     end
0130 else
0131     if isstr(array)
0132         [arrayh,hnames] = arrays(array,bad_chan(obs,find(bad_chan(obs,:))));
0133     else
0134         arrayh = array;
0135     end
0136     for g = 1:size(arrayh,1)
0137         iline = 1;
0138         figure
0139         hold on
0140         for io = 1:size(obs,2)
0141             if  ~(ref_flag(obs(io)) == 5|ref_flag(obs(io)) == 7)
0142                 hold on,bar(dist,bcohpotential,'w-');
0143             elseif ref_flag(obs(io)) == 5
0144                 hold on,bar(dist,bcohlaplacian,'w-');
0145             end;
0146         end
0147         for j = 1:size(freqs,2)
0148             pairels = arrayh(g,find(arrayh(g,:)));
0149             
0150             npairs = size(pairels,2)*(size(pairels,2)+1)/2;
0151             pairs = zeros(1,npairs);
0152             ipairs = 1;
0153             for ip = 1:size(pairels,2)
0154                 for jp=ip:size(pairels,2)
0155                     pairs(ipairs) = chpair(pairels(ip),pairels(jp));
0156                     ipairs = ipairs + 1;
0157                 end;
0158             end;
0159             chpair(pairels(1),pairels(2))
0160             pairnames = hnames(g,:);
0161             
0162 %            hold on, plot(real(twod_dist(pairs)),coherence_array(j,pairs),scat_type(iline,:))
0163             p_coh = polyfit(real(twod_dist(pairs)),coherence_array(j,pairs),4);
0164             coh_fit = real(polyval(p_coh,[0:1:fix(max(twod_dist(pairs)))]));
0165             hold on, plot([0:1:max(twod_dist(pairs))],coh_fit,line_type(iline,:)), axis([0 max(twod_dist(pairs))+1 0 1])
0166             title(['Coherence versus Distance: ' deblank(setstr(obs_labels(obs(1),:))) ' ' hnames(g,:)]);
0167             hold on, plot([9 10],[1-0.1*j 1-0.1*j],linetype(iline,:))
0168             text([11],[1-0.1*j],[int2str(freqs(j)) ' Hz'])
0169             xlabel('Interelectrode Distance (cm)')
0170             ylabel('Coherence')
0171             iline = iline+ 1;
0172         end
0173     end
0174 end
0175 status = 1;
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