run_csdm_2eeg

status=run_csdm_2eeg(noffset,nsamp,avg_cells,bad_chans,ses_fname,reference)
version 1    1/8/96

parameters

    noffset = offset in samples from beginning of trial to begin analysis
    nsamp = number of samples, must be even (converted into Npoints)
    avg_cells = arrays of cells to use (optional)
        supports cell collapsing, e.g. [1 2; 3 6] means 1 and 2 are
        collapsed toproduce output cell 1 and 3 and 6 collapsed 
        to produce output cell 2.  If no cell collapsing is wanted 
        you must still separate output cells by semicolons
        e.g. [ 1; 2; 3; 6];
    bad_chans = additional bad_channels not to use (optionals)
     ses_fname = filename including path containing data
    reference = reference to usein calculation (optional) defualts to 
        the average reference 

Modification History
     Created by Ramesh Srinivasan 1/8/96

0001 function status=run_csdm_2eeg(noffset,nsamp,avg_cells,bad_chans,ses_fname,reference)
0002 %status=run_csdm_2eeg(noffset,nsamp,avg_cells,bad_chans,ses_fname,reference)
0003 %version 1    1/8/96
0004 %
0005 %parameters
0006 %
0007 %    noffset = offset in samples from beginning of trial to begin analysis
0008 %    nsamp = number of samples, must be even (converted into Npoints)
0009 %    avg_cells = arrays of cells to use (optional)
0010 %        supports cell collapsing, e.g. [1 2; 3 6] means 1 and 2 are
0011 %        collapsed toproduce output cell 1 and 3 and 6 collapsed
0012 %        to produce output cell 2.  If no cell collapsing is wanted
0013 %        you must still separate output cells by semicolons
0014 %        e.g. [ 1; 2; 3; 6];
0015 %    bad_chans = additional bad_channels not to use (optionals)
0016 %     ses_fname = filename including path containing data
0017 %    reference = reference to usein calculation (optional) defualts to
0018 %        the average reference
0019 %
0020 %Modification History
0021 %     Created by Ramesh Srinivasan 1/8/96
0022 
0023 %Initialize return argument
0024 status = -1;
0025 
0026 %Define constants
0027 ses_hdr_offsets_v;
0028 TRUE = 1; FALSE = 0;
0029 
0030 %Check number of input arguments
0031 if ~((nargin == 6))
0032     error('Number of input arguments must be 6.');
0033 end
0034 if rem(nsamp,2) ~= 0
0035     error ('nsamp must be a multiple of two')
0036 end;
0037 if  isempty(reference)
0038     reference = 'average';
0039 end; 
0040 %Initialize input and output fids
0041 ses_fid = -1;
0042 ave_fid = -1;
0043 %First try batch mode
0044 ses_fid = fopen(ses_fname, 'r');
0045 if ses_fid == -1
0046     error(['Could not open input file' ses_fname '.']);
0047 end
0048 %Read the session file EGIS header
0049 [ses_fhdr,ses_chdr,ses_ename,ses_czeros,ses_cgains,ses_cnames,ses_fcom,ses_ftext,ses_coff]=rd_egis_hdr_v(ses_fid);
0050 if isempty(avg_cells)
0051     avg_cells = [1:ses_fhdr(NCells)]';
0052 end;
0053 if isempty(noffset)
0054     noffset = 0;
0055 end;
0056 if isempty(nsamp)
0057     nsamp = fix(ses_chdr(1,NSamp)/2)*2;
0058 end;
0059     
0060 %Bullshit cell number?
0061 if any(avg_cells > ses_fhdr(NCells))
0062     error('A specified cell number is greater than the number of cells in file.');
0063 end
0064 %Too many bad_chans?
0065 if length(bad_chans) > ses_fhdr(NChan)
0066      error(['Too many bad channels specified for this data file.']);
0067 end
0068 %Check bad_chans argument
0069 if any(bad_chans > ses_fhdr(NChan))
0070     error('A specified bad channel is greater than the number of channels in file.');
0071 end
0072 
0073 %Read the MacAverager .edc edit codes file
0074 ses_mask = artifact_edit(ses_fname, ses_fhdr, ses_chdr,0);
0075 %add the bad channels mask argument to the .edc information
0076 ses_mask(:, bad_chans) = zeros(size(ses_mask,1),length(bad_chans));
0077 
0078 if strcmp(reference,'laplacian')
0079     [xelec,yelec,zelec] = electrodes(NChan+1);
0080 end;
0081 if strcmp(reference(1:2),'co')
0082     [xelec,yelec,zelec] = electrodes(NChan+1);
0083     sources = xyz2tp(xelec,yelec,zelec);
0084     A = transfer_matrix(500,0.2,80,8,8.2,8.7,9.2,7.8,sources,sources);
0085 end;
0086 num_cells_avg = size(avg_cells,1);
0087 %Begin csdm calculation
0088 for c=1:num_cells_avg
0089     accessed_cell = 0;
0090     ncol = size(find(avg_cells(c,:)),2);
0091     disp(['Processing output cell ' int2str(c)]);
0092     accessed_cell = FALSE;
0093     start_samp = noffset +1;
0094     stop_samp = noffset +nsamp;
0095     ncsdm = (ses_fhdr(NChan)+2)*(ses_fhdr(NChan)+1)/2;
0096     avgdata = zeros(nsamp/2,ncsdm);
0097     for icol = 1:ncol
0098         thecell = avg_cells(c,icol);
0099         for t=1:ses_chdr(thecell, NTrials)
0100             ses_mask_cell_offset = sum(ses_chdr(1:thecell, NTrials)) - ses_chdr(thecell,NTrials);
0101             if sum(ses_mask(ses_mask_cell_offset + t,:)) > 0    
0102                 if accessed_cell == FALSE
0103                     trialdata = rd_onetr_allch(ses_fid, ses_coff(thecell), t, ses_fhdr(NChan), ses_chdr(thecell, NPoints), 'bof');
0104                     accessed_cell = TRUE;
0105                 else
0106                     trialdata = rd_onetr_allch(ses_fid, ses_coff(thecell), t, ses_fhdr(NChan), ses_chdr(thecell, NPoints), 'cof');
0107                 end
0108                 %Convert matrix to microvolts
0109                 trialdata2 = cal_gain(trialdata,ses_cgains,ses_czeros);
0110                 %Reference Matrix
0111                 if ~(strcmp(reference,'laplacian')|strcmp(reference(1:2),'co'))
0112                     [ref_trialdata,masknew] = new_reference(trialdata2,ses_mask(ses_mask_cell_offset + t,:),reference);
0113                     ref_trialdata = ref_trialdata.*(ones(size(ref_trialdata,1),1)*masknew);
0114                     ses_mask(ses_mask_cell_offset+t,:) = masknew;
0115                 elseif strcmp(reference,'laplacian')
0116                     good_chan = find(ses_mask(ses_mask_cell_offset + t,:));    
0117                     ref_trialdata = laplacian_trial([trialdata2 zeros(size(trialdata2,1),1)],good_chan,xelec,yelec,zelec);
0118                     masknew = ses_mask(ses_mask_cell_offset + t,:);
0119                 elseif strcmp(reference(1:8),'cortical')
0120                     good_chan = find(ses_mask(ses_mask_cell_offset + t,:));
0121                     good_trial = zeros(size(trialdata2,1),size(good_chan,2));
0122                     trialdata3 = average_reference(trialdata2(:,1:NChan),ses_mask(ses_mask_cell_offset + t,:));
0123                     good_trial = trialdata3(:,good_chan);
0124                     good_A = zeros(size(good_chan,2),size(good_chan,2));
0125                     good_A = A(good_chan,good_chan);
0126                     ref_trialdata = zeros(size(trialdata3,1),size(trialdata3,2));
0127                     sigma_m = 1;
0128                     sigma_v = str2num(reference(9:10));
0129             
0130                     [m,deviations] = bayes_dipole_trial(good_A,good_trial',sigma_v,sigma_m);
0131                     ref_trialdata(:,good_chan) = m';
0132                     masknew = ses_mask(ses_mask_cell_offset + t,:);
0133                 end
0134                     
0135                 %zero average epoch
0136                 ref_trialdata = zeromean(ref_trialdata,start_samp,stop_samp);                    
0137                 %add to average stack
0138                     
0139                 avgdata = avgdata + csdm(ref_trialdata(start_samp:stop_samp,:));
0140                 %else
0141                 %disp(['Skipping trial ' int2str(t)]);
0142             end
0143         end
0144     end;
0145     num_good_trials = zeros(1,ses_fhdr(NChan)+1);
0146     for icol = 1:ncol
0147         thecell = avg_cells(c,icol);
0148         ses_mask_cell_offset = sum(ses_chdr(1:thecell,NTrials)) - ses_chdr(thecell,NTrials);
0149         start_offset = ses_mask_cell_offset + 1;
0150         stop_offset = start_offset + ses_chdr(thecell,NTrials) - 1;
0151         num_good_trials = num_good_trials+ sum(ses_mask(start_offset:stop_offset,:));
0152     end;
0153     %divides are different for amplitude and phase
0154     icount = 1;
0155     good_cross = zeros(1,size(avgdata,2));
0156     for ichan = 1:ses_fhdr(NChan)+1
0157         for jchan = ichan:ses_fhdr(NChan)+1
0158             good_cross(icount) = min([num_good_trials(ichan) num_good_trials(jchan)]);
0159             if good_cross(icount) == 0
0160                 good_cross(icount) = 1;
0161             end;
0162             icount = icount+1;
0163         end;
0164     end;
0165     avgdata = avgdata./(ones(nsamp/2,1)*good_cross);
0166     disp(['Writing csdm data file output cell:' int2str(c)]);
0167     ave_fname = [ses_fname(5:12) 'tc' int2str(c) '.' reference(1:4) '.csdm'];
0168     ave_fid = fopen(ave_fname,'wb'); 
0169     version = -1;
0170     fwrite(ave_fid,version,'int16');
0171     SampRate
0172     ses_chdr(c,SampRate)
0173     Epoch = nsamp/ses_chdr(c,SampRate);
0174     fwrite(ave_fid,Epoch,'int16');
0175     fwrite(ave_fid,ses_chdr(c,NTrials),'int16')
0176     fwrite(ave_fid,max(good_cross),'int16');
0177     Nbad_chan = size(bad_chans,2);
0178     fwrite(ave_fid,Nbad_chan,'int16');
0179     fwrite(ave_fid,bad_chans,'int16');
0180     if strcmp(reference,'average')
0181         ref_flag = 1;
0182     elseif strcmp(reference,'avgmast')
0183         ref_flag = 2;
0184     elseif strcmp(reference,'perimeter');
0185         ref_flag = 3;
0186     elseif strcmp(reference,'vertex');
0187         ref_flag = 4;
0188     elseif strcmp(reference,'laplacian');
0189         ref_flag = 5;
0190     elseif strcmp(reference(1:8),'cortical');
0191         ref_flag = 7;
0192     else
0193         ref_flag = 6;
0194     end;
0195     fwrite(ave_fid,ref_flag,'int16');
0196     if ref_flag == 6
0197         fwrite(ave_fid,size(reference,2),'int16');
0198         fwrite(ave_fid,reference,'int16');
0199     end
0200     if ref_flag == 7
0201         sigma_v = str2num(reference(9:10));
0202         fwrite(ave_fid,sigma_v,'int16');
0203     end;
0204     max_freq = 50*Epoch + 1;
0205     fwrite(ave_fid,max_freq,'int16');
0206     fwrite(ave_fid,size(avgdata,2),'int16');
0207     num_written = fwrite(ave_fid, (real(avgdata(1:max_freq,:)))', 'float');
0208     num_written = fwrite(ave_fid, (imag(avgdata(1:max_freq,:)))', 'float');
0209     fclose(ave_fid);
0210 end
0211 
0212 fclose('all');
0213 disp('Finished CSDM Calculation.');
0214 status = 1;
0215 
0216 
0217 
0218 
0219 
0220