Home > vbmeg > functions > common > utility > vb_combine_eeg_files.m

vb_combine_eeg_files

PURPOSE ^

combine plural .eeg.mat files and create a single .eeg.mat file

SYNOPSIS ^

function [eeg_data] = vb_combine_eeg_files(in_files, out_file, ext_spec)

DESCRIPTION ^

 combine plural .eeg.mat files and create a single .eeg.mat file

 [usage]
   [eeg_data] = vb_combine_eeg_files(in_files, out_file, ext_spec)

 [input]
   in_files : <required> <<cell array>> .eeg.mat files to be combined
   out_file : <required> <<string>> combined file
   ext_spec : <optional> <<struct>> 
            :  .bin_data_dir : <optional> relative path from new_file
            :    This field is valid only when #3 argument newfile is 
            :  specified.
            :  if this field is not given or is empty, sampling data
            :  will be stored internally (eeg_data).

 [output]
   eeg_data : combined data 

 [note]
   See also :
     vb_combine_meg_files

 [history]
   2012-11-20 (Sako) initial version

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SUBFUNCTIONS ^

SOURCE CODE ^

0001 function [eeg_data] = vb_combine_eeg_files(in_files, out_file, ext_spec)
0002 % combine plural .eeg.mat files and create a single .eeg.mat file
0003 %
0004 % [usage]
0005 %   [eeg_data] = vb_combine_eeg_files(in_files, out_file, ext_spec)
0006 %
0007 % [input]
0008 %   in_files : <required> <<cell array>> .eeg.mat files to be combined
0009 %   out_file : <required> <<string>> combined file
0010 %   ext_spec : <optional> <<struct>>
0011 %            :  .bin_data_dir : <optional> relative path from new_file
0012 %            :    This field is valid only when #3 argument newfile is
0013 %            :  specified.
0014 %            :  if this field is not given or is empty, sampling data
0015 %            :  will be stored internally (eeg_data).
0016 %
0017 % [output]
0018 %   eeg_data : combined data
0019 %
0020 % [note]
0021 %   See also :
0022 %     vb_combine_meg_files
0023 %
0024 % [history]
0025 %   2012-11-20 (Sako) initial version
0026 
0027 % --- CHECK ARGUMENTS --- %
0028 if ~exist('in_files', 'var'), in_files = []; end
0029 if ~exist('out_file', 'var'), out_file = ''; end
0030 if ~exist('ext_spec', 'var'), ext_spec = []; end
0031 [in_files, out_file, ext_spec] = ...
0032   inner_check_arguments(in_files, out_file, ext_spec);
0033 
0034 % --- MAIN PROCEDURE --------------------------------------------------------- %
0035 %
0036 n_eeg = length(in_files);
0037 if n_eeg == 0
0038   eeg_data = [];
0039   fprintf('(%s) in_files is empty\n', mfilename);
0040   return;
0041 end
0042 
0043 if n_eeg == 1
0044   eeg_data = vb_load_meg_data(in_files{1});
0045   fprintf('(%s) there is nothing to do\n', mfilename);
0046   return;
0047 end
0048 
0049 % --- check contents of in_files
0050 chk_result = inner_is_combinable(in_files);
0051 
0052 if ~chk_result
0053   eeg_data = [];
0054   return;
0055 end
0056 
0057 last_trial = 0;
0058 n_repeat = 0;
0059 
0060 % --- EEGinfo - basically adopt the first data
0061 EEGinfo = vb_load_measurement_info(in_files{1});
0062 
0063 active_trial = [];
0064 trial = [];
0065 base_file = [];
0066 
0067 
0068 % --- concatenate data
0069 load_spec.ChannelType = 'ALL';
0070 
0071 for i_eeg = 1:n_eeg
0072   % --- eeg_data
0073   cur_eeg = vb_load_meg_data(in_files{i_eeg}, load_spec);
0074   cur_channel = size(cur_eeg, 1);
0075   cur_sample  = size(cur_eeg, 2);
0076   cur_trial   = size(cur_eeg, 3);
0077 
0078   start_tr = last_trial + 1;
0079   end_tr   = last_trial + cur_trial;
0080   eeg_data(:,:,start_tr:end_tr) = cur_eeg;
0081   last_trial = end_tr;
0082 
0083   cur_info = vb_load_measurement_info(in_files{i_eeg});
0084   n_repeat = n_repeat + cur_info.Nrepeat;
0085   
0086   if isfield(cur_info, 'Trial')
0087     trial_idx_new = start_tr : end_tr;
0088     for i = 1:cur_trial
0089       cur_info.Trial(i).number = trial_idx_new(i);
0090     end
0091     trial = [trial; cur_info.Trial];
0092   end
0093   
0094   if isfield(cur_info, 'ActiveTrial')
0095     active_trial = [active_trial; cur_info.ActiveTrial];
0096   end
0097   
0098   if isfield(cur_info, 'File')
0099     base_file = [base_file; cur_info.File.BaseFile];
0100   end
0101   
0102 end
0103 
0104 % --- re-arrange EEGinfo
0105 EEGinfo.Nrepeat = n_repeat;
0106 EEGinfo.Trial = trial;
0107 EEGinfo.ActiveTrial = active_trial;
0108 
0109 Measurement = EEGinfo.Measurement;
0110 
0111 [ch_name, data_type, bin_data_dir, bin_data_dir_rel] = ...
0112   inner_solve_external_data(out_file, ext_spec, EEGinfo);
0113 
0114 % ----- EEGinfo.File
0115 EEGinfo.File.BaseFile = base_file;
0116 
0117 [out_path, out_name] = vb_get_file_parts(out_file);
0118 EEGinfo.File.OutputDir = out_path;
0119 EEGinfo.File.EEGFile = out_name;
0120 EEGinfo.File.DataDir = bin_data_dir_rel;
0121 
0122 if isempty(bin_data_dir)
0123   
0124   save(out_file, 'eeg_data', 'Measurement', 'EEGinfo');
0125 else
0126   save(out_file, 'Measurement', 'EEGinfo');
0127 
0128   vb_define_device;
0129   file_ext = FILE_EXT_BIN_CH_EEG;
0130   
0131   n_channel = EEGinfo.Nchannel;
0132   ch_name = EEGinfo.ChannelName;
0133   
0134   for i_ch = 1:n_channel
0135 
0136     datafile = sprintf('%s/%s.%s', bin_data_dir, ch_name{i_ch}, file_ext);
0137     cur_fid = fopen(datafile, 'wb');
0138     if cur_fid == -1
0139       error('(%s)cannot open file (%s)', mfilename, datafile);
0140     end
0141 
0142     fwrite(cur_fid, eeg_data(i_ch,:,:), data_type{i_ch});
0143     fclose(cur_fid);
0144     fprintf('--- %s\n', datafile);
0145   end
0146   
0147   % ----- Status channel
0148   n_data_type = length(data_type);
0149   if (n_data_type == size(eeg_data, 1)) && (n_data_type > n_channel)
0150     i_ch = i_ch + 1;
0151     datafile = sprintf('%s/%s.%s', bin_data_dir, STATUS_CH_LABEL, file_ext);
0152     cur_fid = fopen(datafile, 'wb');
0153     if cur_fid == -1
0154       error('(%s)cannot open file (%s)', mfilename, datafile);
0155     end
0156 
0157     fwrite(cur_fid, eeg_data(i_ch,:,:), data_type{i_ch});
0158     fclose(cur_fid);
0159     fprintf('--- %s\n', datafile);
0160   end
0161 end
0162 return;
0163 %
0164 % --- END OF MAIN PROCEDURE -------------------------------------------------- %
0165 
0166 
0167 % --- INNER FUNCTIONS -------------------------------------------------------- %
0168 %
0169 % --- inner_check_arguments()
0170 %
0171 function [in_files, out_file, ext_spec] = ...
0172   inner_check_arguments(in_files, out_file, ext_spec)
0173 func_ = mfilename;
0174 
0175 if isempty(in_files)
0176   error('(%s) in_fiels is a required parameter', func_);
0177 end
0178 
0179 if isempty(out_file)
0180   error('(%s) out_file is a required parameter', func_);
0181 end
0182 
0183 return;
0184 %
0185 % --- end of inner_check_arguments()
0186 
0187 % --- inner_is_combinable()
0188 %
0189 function [chk_result] = inner_is_combinable(in_files)
0190 func_ = mfilename;
0191 chk_result = true;
0192 n_file = length(in_files);
0193 
0194 % --- read data
0195 for i_file = 1:n_file
0196   cur_eeg = load(in_files{i_file}, 'Measurement', 'EEGinfo');
0197   
0198   % --- check variables of minimum format
0199   if ~isfield(cur_eeg, 'Measurement')
0200     fprintf('(%s) =FALSE= cannot find ''Measurement'' parameter\n', func_);
0201     chk_result = false;
0202     return;
0203   end
0204   measure{i_file} = cur_eeg.Measurement;
0205   
0206   if ~isfield(cur_eeg, 'EEGinfo')
0207     fprintf('(%s) =FALSE= cannot find ''EEGinfo'' parameter\n', func_);
0208     chk_result = false;
0209     return;
0210   end
0211   eeg_info(i_file) = cur_eeg.EEGinfo;
0212   
0213 end  
0214 
0215 % --- Measurement
0216 for i_eeg = 1:n_file
0217   if ~isfield(eeg_info(i_eeg), 'Measurement')
0218     fprintf('(%s) EEGinfo(%d) does not have ''Measurement'' field\n', ...
0219       func_, i_eeg);
0220     chk_result = false;
0221     return;
0222   end
0223 end
0224 for i_eeg = 1:n_file
0225   if ~strcmpi(measure{i_eeg}, eeg_info(i_eeg).Measurement)
0226     fprintf('(%s) Measurement is different\n', func_);
0227     chk_result = false;
0228     return;
0229   end
0230 end
0231 
0232 for i_eeg = 2:n_file
0233   if ~strcmpi(measure{i_eeg-1}, measure{i_eeg})
0234     fprintf('(%s) Measurement is different\n', func_);
0235     chk_result = false;
0236     return;
0237   end
0238 end
0239 
0240 % --- EEGinfo - Promary variables - there or not there
0241 for i_eeg = 1:n_file
0242   if ~isfield(eeg_info(i_eeg), 'Measurement')
0243     fprintf('(%s) EEGinfo(%d) does not have ''Measurement'' field\n', ...
0244       func_, i_eeg);
0245     chk_result = false;
0246     return;
0247   end
0248   if ~isfield(eeg_info(i_eeg), 'Device')
0249     fprintf('(%s) EEGinfo(%d) does not have ''Device'' field\n', ...
0250       func_, i_eeg);
0251     chk_result = false;
0252     return;
0253   end
0254   if ~isfield(eeg_info(i_eeg), 'Nchannel')
0255     fprintf('(%s) EEGinfo(%d) does not have ''Nchannel'' field\n', ...
0256       func_, i_eeg);
0257     chk_result = false;
0258     return;
0259   end
0260   if ~isfield(eeg_info(i_eeg), 'Nsample')
0261     fprintf('(%s) EEGinfo(%d) does not have ''Nsample'' field\n', ...
0262       func_, i_eeg);
0263     chk_result = false;
0264     return;
0265   end
0266   if ~isfield(eeg_info(i_eeg), 'Nrepeat')
0267     fprintf('(%s) EEGinfo(%d) does not have ''Nrepeat'' field\n', ...
0268       func_, i_eeg);
0269     chk_result = false;
0270     return;
0271   end
0272   if ~isfield(eeg_info(i_eeg), 'Pretrigger')
0273     fprintf('(%s) EEGinfo(%d) does not have ''Pretrigger'' field\n', ...
0274       func_, i_eeg);
0275     chk_result = false;
0276     return;
0277   end
0278   if ~isfield(eeg_info(i_eeg), 'SampleFrequency')
0279     fprintf('(%s) EEGinfo(%d) does not have ''SampleFrequency'' field\n', ...
0280       func_, i_eeg);
0281     chk_result = false;
0282     return;
0283   end
0284   if ~isfield(eeg_info(i_eeg), 'Coord')
0285     fprintf('(%s) EEGinfo(%d) does not have ''Coord'' field\n', ...
0286       func_, i_eeg);
0287     chk_result = false;
0288     return;
0289   end
0290 end
0291 
0292 % --- EEGinfo - each field of minimum format
0293 % ----- EEGinfo.Measurement
0294 for i_eeg = 2:n_file
0295   if ~strcmpi(eeg_info(i_eeg-1).Measurement, eeg_info(i_eeg).Measurement)
0296     fprintf('(%s) EEGinfo(%d).Measurement is different from EEGinfo(%d)\n', ...
0297       func_, i_eeg-1, i_eeg);
0298     chk_result = false;
0299     return;
0300   end
0301 end
0302 
0303 % ----- EEGinfo.Device
0304 for i_eeg = 2:n_file
0305   if ~strcmpi(eeg_info(i_eeg-1).Device, eeg_info(i_eeg).Device)
0306     fprintf('(%s) EEGinfo(%d).Device is different from EEGinfo(%d)\n', ...
0307       func_, i_eeg-1, i_eeg);
0308     chk_result = false;
0309     return;
0310   end
0311 end
0312 
0313 % ----- EEGinfo.Nchannel
0314 for i_eeg = 2:n_file
0315   if eeg_info(i_eeg-1).Nchannel ~= eeg_info(i_eeg).Nchannel
0316     fprintf('(%s) EEGinfo(%d).Nchannel is different from EEGinfo(%d)\n', ...
0317       func_, i_eeg-1, i_eeg);
0318     chk_result = false;
0319     return;
0320   end
0321 end
0322 
0323 % ----- EEGinfo.Nsample
0324 for i_eeg = 2:n_file
0325   if eeg_info(i_eeg-1).Nsample ~= eeg_info(i_eeg).Nsample
0326     fprintf('(%s) EEGinfo(%d).Nsample is different from EEGinfo(%d)\n', ...
0327       func_, i_eeg-1, i_eeg);
0328     chk_result = false;
0329     return;
0330   end
0331 end
0332 
0333 % ----- EEGinfo.Pretrigger
0334 for i_eeg = 2:n_file
0335   if eeg_info(i_eeg-1).Pretrigger ~= eeg_info(i_eeg).Pretrigger
0336     fprintf('(%s) EEGinfo(%d).Pretrigger is different from EEGinfo(%d)\n', ...
0337       func_, i_eeg-1, i_eeg);
0338     chk_result = false;
0339     return;
0340   end
0341 end
0342 
0343 % ----- EEGinfo.SampleFrequency
0344 for i_eeg = 2:n_file
0345   if eeg_info(i_eeg-1).SampleFrequency ~= eeg_info(i_eeg).SampleFrequency
0346     fprintf( ...
0347       '(%s) EEGinfo(%d).SampleFrequency is different from EEGinfo(%d)\n', ...
0348       func_, i_eeg-1, i_eeg);
0349     chk_result = false;
0350     return;
0351   end
0352 end
0353 
0354 % ----- EEGinfo.Coord
0355 for i_eeg = 2:n_file
0356   if ~isequal(eeg_info(i_eeg-1).Coord, eeg_info(i_eeg).Coord)
0357     fprintf('(%s) EEGinfo(%d).Coord is different from EEGinfo(%d)\n', ...
0358       func_, i_eeg-1, i_eeg);
0359     chk_result = false;
0360     return;
0361   end
0362 end
0363 
0364 return;
0365 %
0366 % --- end of inner_is_combinable()
0367 
0368 
0369 % --- inner_solve_external_data()
0370 %
0371 function [ch_name, data_type, bin_data_dir, bin_data_dir_rel] = ...
0372   inner_solve_external_data(out_file, ext_spec, EEGinfo)
0373 
0374 bin_data_dir = '';
0375 bin_data_dir_rel = '';
0376 
0377 ch_name = '';
0378 data_type = '';
0379 
0380 if isempty(out_file) || isempty(ext_spec)
0381   return;
0382 end
0383 
0384 if ~isfield(ext_spec, 'bin_data_dir') || isempty(ext_spec.bin_data_dir)
0385   return;
0386 end
0387 
0388 [out_path_base] = vb_get_file_parts(out_file);
0389 if isempty(out_path_base)
0390   out_path_base = '.';
0391 end
0392 
0393 bin_data_dir = [out_path_base '/' ext_spec.bin_data_dir];
0394 
0395 if ~isfield(EEGinfo, 'ChannelName') || isempty(EEGinfo.ChannelName)
0396   % --- EEGinfo.ChannelName is required if you store data externally
0397   bin_data_dir = [];
0398   return;
0399 end
0400 ch_name = EEGinfo.ChannelName;
0401 
0402 if ~isfield(EEGinfo, 'DataType') || isempty(EEGinfo.DataType)
0403   bin_data_dir = [];
0404   return;
0405 end
0406 data_type = EEGinfo.DataType;
0407 
0408 if exist(bin_data_dir, 'dir') ~= 7
0409   vb_mkdir(bin_data_dir);
0410 end
0411 
0412 bin_data_dir_rel = ext_spec.bin_data_dir;
0413 return;
0414 %
0415 % --- end of inner_solve_external_data()
0416 
0417 %
0418 % --- END OF INNER FUNCTIONS ------------------------------------------------- %
0419 
0420 % --- END OF FILE --- %
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