fiff_read_evoked_all

 [data] = fiff_read_evoked_all(fname)

 Read all evoked data set (averages only)

0001 function [data] = fiff_read_evoked_all(fname)
0002 %
0003 % [data] = fiff_read_evoked_all(fname)
0004 %
0005 % Read all evoked data set (averages only)
0006 %
0007 
0008 
0009 %
0010 %   Author : Matti Hamalainen, MGH Martinos Center
0011 %   License : BSD 3-clause
0012 %
0013 %
0014 %   Revision 1.6  2009/03/30 11:37:37  msh
0015 %   Added copying of measurement info blocks from the original like in mne_browse_raw
0016 %
0017 %   Revision 1.5  2008/03/28 13:35:51  msh
0018 %   Accommodate evoked files from xplotter, which may have channel information
0019 %   local to the evoked block
0020 %
0021 %   Revision 1.4  2007/11/13 10:55:32  msh
0022 %   Specify the second argument to all calls to the exist function
0023 %
0024 %   Revision 1.3  2006/10/14 11:47:32  msh
0025 %   Omitted listing of nepoch from the diagnostic output
0026 %
0027 %   Revision 1.2  2006/10/14 11:39:58  msh
0028 %   Fixed errors in fiff_read_evoked_all
0029 %
0030 %   Revision 1.1  2006/10/04 20:12:37  msh
0031 %   Added fiff_read_evoked_all
0032 %   Modified fiff_pick_channels_evoked to handle multiple data sets
0033 %   Added bad channel writing to fiff_write_evoked
0034 %
0035 %
0036 
0037 global FIFF;
0038 if isempty(FIFF)
0039     FIFF = fiff_define_constants();
0040 end
0041 
0042 me='MNE:fiff_read_evoked_all';
0043 
0044 if nargin ~= 1
0045     error(me,'Incorrect number of arguments');
0046 end
0047 %
0048 %   Open the file
0049 %
0050 fprintf(1,'Reading %s ...\n',fname);
0051 [ fid, tree ] = fiff_open(fname);
0052 %
0053 %   Read the measurement info
0054 %
0055 [ info, meas ] = fiff_read_meas_info(fid,tree);
0056 info.filename = fname;
0057 %
0058 %   Locate the data of interest
0059 %
0060 processed = fiff_dir_tree_find(meas,FIFF.FIFFB_PROCESSED_DATA);
0061 if length(processed) == 0
0062     fclose(fid);
0063     error(me,'Could not find processed data');
0064 end
0065 %
0066 evoked = fiff_dir_tree_find(meas,FIFF.FIFFB_EVOKED);
0067 if length(evoked) == 0
0068     fclose(fid);
0069     error(me,'Could not find evoked data');
0070 end
0071 %
0072 %   Identify the aspects
0073 %
0074 naspect = 0;
0075 is_smsh = [];
0076 for k = 1:length(evoked)
0077     sets(k).aspects = fiff_dir_tree_find(evoked(k),FIFF.FIFFB_ASPECT);
0078     sets(k).naspect = length(sets(k).aspects);
0079     if sets(k).naspect > 0
0080         is_smsh = [ is_smsh zeros(1,sets(k).naspect) ];
0081         naspect = naspect + sets(k).naspect;
0082     end
0083     saspects  = fiff_dir_tree_find(evoked(k), FIFF.FIFFB_SMSH_ASPECT);
0084     nsaspects = length(saspects);
0085     if nsaspects > 0
0086         sets(k).naspect = sets(k).naspect + nsaspects;
0087         sets(k).aspects = [ sets(k).aspects saspects ];
0088         is_smsh = [ is_smsh ones(1,sets(k).naspect) ];
0089         naspect = naspect + nsaspects;
0090     end
0091 end
0092 if naspect == 0
0093     fclose(fid);
0094     error(me,'No evoked data aspects found');
0095 end
0096 fprintf(1,'\t%d evoked data sets containing a total of %d data aspects in %s\n',length(evoked),naspect,fname);
0097 if ~isempty(info.comps)
0098     fprintf(1,'\t\t%d CTF compensation matrices available\n',length(info.comps));
0099 end
0100 %
0101 %   Next locate the evoked data set
0102 %
0103 p = 1;
0104 for e = 1:length(evoked)
0105     if e == 1
0106         %
0107         %   Find local channel information
0108         %
0109         my_evoked = evoked(e);
0110         nchan = 0;
0111         sfreq = -1;
0112         q = 0;
0113         for k = 1:my_evoked.nent
0114             kind = my_evoked.dir(k).kind;
0115             pos  = my_evoked.dir(k).pos;
0116             switch kind
0117                 case FIFF.FIFF_NCHAN
0118                     tag = fiff_read_tag(fid,pos);
0119                     nchan = tag.data;
0120                 case FIFF.FIFF_SFREQ
0121                     tag = fiff_read_tag(fid,pos);
0122                     sfreq = tag.data;
0123                 case FIFF.FIFF_CH_INFO
0124                     q = q+1;
0125                     tag = fiff_read_tag(fid,pos);
0126                     chs(q) = tag.data;
0127             end
0128         end
0129         if nchan > 0
0130             if ~exist('chs','var')
0131                 fclose(fid);
0132                 error(me, ...
0133                     'Local channel information was not found when it was expected.');
0134             end
0135             if length(chs) ~= nchan
0136                 fclose(fid);
0137                 error(me, ...
0138                     'Number of channels and number of channel definitions are different');
0139             end
0140             info.chs   = chs;
0141             info.nchan = nchan;
0142             fprintf(1, ...
0143                 '\tFound channel information in evoked data. nchan = %d\n',nchan);
0144             if sfreq > 0
0145                 info.sfreq = sfreq;
0146             end
0147         end
0148     end
0149     for a = 1:sets(e).naspect
0150         my_evoked = evoked(e);
0151         my_aspect = sets(e).aspects(a);
0152         %
0153         %   Now find the data in the evoked block
0154         %
0155         for k = 1:my_evoked.nent
0156             kind = my_evoked.dir(k).kind;
0157             pos  = my_evoked.dir(k).pos;
0158             switch kind
0159                 case FIFF.FIFF_COMMENT
0160                     tag = fiff_read_tag(fid,pos);
0161                     comment = tag.data;
0162                 case FIFF.FIFF_FIRST_SAMPLE
0163                     tag = fiff_read_tag(fid,pos);
0164                     first = tag.data;
0165                 case FIFF.FIFF_LAST_SAMPLE
0166                     tag = fiff_read_tag(fid,pos);
0167                     last = tag.data;
0168             end
0169         end
0170         if ~exist('comment','var')
0171             comment = 'No comment';
0172         end
0173         nsamp = last-first+1;
0174         %
0175         % Read the data in the aspect block
0176         %
0177         nepoch = 0;
0178         for k = 1:my_aspect.nent
0179             kind = my_aspect.dir(k).kind;
0180             pos  = my_aspect.dir(k).pos;
0181             switch kind
0182                 case FIFF.FIFF_COMMENT
0183                     tag = fiff_read_tag(fid,pos);
0184                     comment = tag.data;
0185                 case FIFF.FIFF_ASPECT_KIND
0186                     tag = fiff_read_tag(fid,pos);
0187                     aspect_kind = tag.data;
0188                 case FIFF.FIFF_NAVE
0189                     tag = fiff_read_tag(fid,pos);
0190                     nave = tag.data;
0191                 case FIFF.FIFF_EPOCH
0192                     nepoch = nepoch + 1;
0193                     tag = fiff_read_tag(fid,pos);
0194                     epoch(nepoch) = tag;
0195             end
0196         end
0197         if ~exist('nave','var')
0198             nave = 1;
0199         end
0200         if aspect_kind == FIFF.FIFFV_ASPECT_AVERAGE
0201             fprintf(1,'\tFound the data of interest:\n');
0202             fprintf(1,'\t\tt = %10.2f ... %10.2f ms (%s)\n',1000*first/info.sfreq,1000*last/info.sfreq,comment);
0203             fprintf(1,'\t\tnave = %d aspect type = %d\n',...
0204                 nave,aspect_kind);
0205             if nepoch ~= 1 && nepoch ~= info.nchan
0206                 fclose(fid);
0207                 error(me,'Number of epoch tags is unreasonable (nepoch = %d nchan = %d)',nepoch,info.nchan);
0208             end
0209             %
0210             %       Put the old style epochs together
0211             %
0212             if nepoch == 1
0213                 all = epoch(1).data;
0214             else
0215                 all = epoch(1).data';
0216                 for k = 2:nepoch
0217                     all = [ all ; epoch(k).data' ];
0218                 end
0219             end
0220             if size(all,2) ~= nsamp
0221                 fclose(fid);
0222                 error(me,'Incorrect number of samples (%d instead of %d)',size(all,2),nsamp);
0223             end
0224             %
0225             %   Calibrate
0226             %
0227             for k = 1:info.nchan
0228                 cals(k) = info.chs(k).cal;
0229             end
0230             all = diag(cals)*all;
0231             %
0232             %   Put it all together
0233             %
0234             one.aspect_kind = aspect_kind;
0235             one.is_smsh = is_smsh(p);
0236             if exist('nave','var')
0237                 one.nave = nave;
0238             else
0239                 one.nave  = 1;
0240             end
0241             one.first = first;
0242             one.last  = last;
0243             if exist('comment','var')
0244                 one.comment = comment;
0245             end
0246             %
0247             %       Times for convenience and the actual epoch data
0248             %
0249             one.times = double(one.first:1:one.last)/info.sfreq;
0250             one.epochs = all;
0251             if p == 1
0252                 data.info      = info;
0253                 data.evoked(1) = one;
0254             else
0255                 data.evoked(p) = one;
0256             end
0257             clear('one');
0258             p = p + 1;
0259         end
0260         clear('comment');
0261         clear('nave');
0262     end
0263 end
0264 
0265 fclose(fid);
0266 
0267 return;
0268 
0269     function [tag] = find_tag(node,findkind)
0270         
0271         for p = 1:node.nent
0272             kind = node.dir(p).kind;
0273             pos  = node.dir(p).pos;
0274             if kind == findkind
0275                 tag = fiff_read_tag(fid,pos);
0276                 return;
0277             end
0278         end
0279         tag = [];
0280         return
0281     end
0282 
0283 end
0284 
0285