load specified data from MEG-MAT file which has data internally
[usage]
[data, channel_info] = vb_megfile_load_data_internal(megfile, ...
loadspec, new_file, return_swt, verbose_swt, cmplmnt_swt)
[input]
megfile : <required> <<file>> MEG-MAT file
loadspec : <required> <<struct>> loading instruction
.ChannelName : <optional> channel name list [Nch x 1] []
: name(string) list of target channel
: The way to be used this depends on the
: "ChannelSwitch" field
: e.g.
: {'1';'2';'3';'4'}
: If this is empty, all the channels are
: specified
.ChannelSwitch : <optiolal> <<boolean>> [true] | false
: Which is "ChannelName", to read, or not?
: [true] : to read
: false : to omit
.ChannelType : <optional> <<string>> channel type
: [(depend on vb_loadspec_check.m)]
: 'MEG' : MEG channel data
: 'EXTRA' : extra channel data
: 'REFERENCE' : reference channel data
: 'AXIAL' : AxialGradioMeter
: 'PLANAR' : PlanarGradioMeter
: 'ALL' : 'MEG'+'EXTRA'+'REFERENCE'
: - case insensitive
.Trigger : <optional> trigger sample number list []
: [Ntrigger(Ntrial) x 1]
: e.g. [1000;2000;3000]
: if plural triggers are specified to trial data,
: make from sample and to sample by applying the
: first trigger
.Pretrigger : <optional> sample number of pretrigger []
.Posttrigger : <optional> sample number of posttrigger []
.TrialNumber : <optional> trial number list [] [Ntrial x 1]
: "1" start
: e.g. [1;2;3]
: empty means that all the trials are specified
.ActiveChannel : <optional> <<boolean>> [false]
: active channel filter switch
: true) active channels
: false) all the channels
.ActiveTrial : <optional> <<boolean>> [false]
: active trial filter switch
: valid only when data type is Evoked_Raw
: true) active trials
: false) all the trials
.saveman : <optional> <<struct>>
: if you want to store data externally, this field is
: necessary.
: if this field is not given or is empty, sampling data
: will store internally.
: .data_dir : directory (relative path) for external file
: .precision : usually 'float64'
new_file : <optional> new MEG-MAT file name which is stored picked up
: data and changed information []
: if this is empty, new file will not be created
return_swt : <optional> <<boolean>>
: switch whether return loaded data or not
: [true] | false
verbose_swt : <optional> <<boolean>>
: switch whether output verbose message or not
: [true] | false
cmplmnt_swt : <optional> <<boolean>> [false]
: NOT BE SUPPORTED NOW
: switch to complement to load data from external data
: if you do not get data from internal data
: true : try to get from external data
: false : do not try
[output]
data : read data [Nchannel x Nsample x Ntrial]
channel_info : <<struct>> channel information of loaded data
: .Active [Nchannel x 1]
: .Name [Nchannel x 1]
: .Type [Nchannel x 1]
: .ID [Nchannel x 1]
[note]
devided vb_megfile_load_data into external type and this internal one
See also
vb_megfile_load_data, vb_megfile_load_data_external
vb_megfile_make_new_megfile
[history]
2008-04-24 (Sako) initial version
2008-06-05 (Sako) modified interface spec - ChannelType, channel_info
2009-07-03 (Sako) modified channel_info
2010-06-30 (Sako) supported storing data externally
2010-07-01 (Sako) modified how to pick up trial data
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [data, channel_info] = vb_megfile_load_data_internal( ... 0002 megfile, loadspec, new_file, return_swt, verbose_swt, cmplmnt_swt) 0003 % load specified data from MEG-MAT file which has data internally 0004 % 0005 % [usage] 0006 % [data, channel_info] = vb_megfile_load_data_internal(megfile, ... 0007 % loadspec, new_file, return_swt, verbose_swt, cmplmnt_swt) 0008 % 0009 % [input] 0010 % megfile : <required> <<file>> MEG-MAT file 0011 % 0012 % loadspec : <required> <<struct>> loading instruction 0013 % .ChannelName : <optional> channel name list [Nch x 1] [] 0014 % : name(string) list of target channel 0015 % : The way to be used this depends on the 0016 % : "ChannelSwitch" field 0017 % : e.g. 0018 % : {'1';'2';'3';'4'} 0019 % : If this is empty, all the channels are 0020 % : specified 0021 % .ChannelSwitch : <optiolal> <<boolean>> [true] | false 0022 % : Which is "ChannelName", to read, or not? 0023 % : [true] : to read 0024 % : false : to omit 0025 % .ChannelType : <optional> <<string>> channel type 0026 % : [(depend on vb_loadspec_check.m)] 0027 % : 'MEG' : MEG channel data 0028 % : 'EXTRA' : extra channel data 0029 % : 'REFERENCE' : reference channel data 0030 % : 'AXIAL' : AxialGradioMeter 0031 % : 'PLANAR' : PlanarGradioMeter 0032 % : 'ALL' : 'MEG'+'EXTRA'+'REFERENCE' 0033 % : - case insensitive 0034 % .Trigger : <optional> trigger sample number list [] 0035 % : [Ntrigger(Ntrial) x 1] 0036 % : e.g. [1000;2000;3000] 0037 % : if plural triggers are specified to trial data, 0038 % : make from sample and to sample by applying the 0039 % : first trigger 0040 % .Pretrigger : <optional> sample number of pretrigger [] 0041 % .Posttrigger : <optional> sample number of posttrigger [] 0042 % .TrialNumber : <optional> trial number list [] [Ntrial x 1] 0043 % : "1" start 0044 % : e.g. [1;2;3] 0045 % : empty means that all the trials are specified 0046 % .ActiveChannel : <optional> <<boolean>> [false] 0047 % : active channel filter switch 0048 % : true) active channels 0049 % : false) all the channels 0050 % .ActiveTrial : <optional> <<boolean>> [false] 0051 % : active trial filter switch 0052 % : valid only when data type is Evoked_Raw 0053 % : true) active trials 0054 % : false) all the trials 0055 % .saveman : <optional> <<struct>> 0056 % : if you want to store data externally, this field is 0057 % : necessary. 0058 % : if this field is not given or is empty, sampling data 0059 % : will store internally. 0060 % : .data_dir : directory (relative path) for external file 0061 % : .precision : usually 'float64' 0062 % 0063 % new_file : <optional> new MEG-MAT file name which is stored picked up 0064 % : data and changed information [] 0065 % : if this is empty, new file will not be created 0066 % return_swt : <optional> <<boolean>> 0067 % : switch whether return loaded data or not 0068 % : [true] | false 0069 % verbose_swt : <optional> <<boolean>> 0070 % : switch whether output verbose message or not 0071 % : [true] | false 0072 % cmplmnt_swt : <optional> <<boolean>> [false] 0073 % : NOT BE SUPPORTED NOW 0074 % : switch to complement to load data from external data 0075 % : if you do not get data from internal data 0076 % : true : try to get from external data 0077 % : false : do not try 0078 % [output] 0079 % data : read data [Nchannel x Nsample x Ntrial] 0080 % channel_info : <<struct>> channel information of loaded data 0081 % : .Active [Nchannel x 1] 0082 % : .Name [Nchannel x 1] 0083 % : .Type [Nchannel x 1] 0084 % : .ID [Nchannel x 1] 0085 % [note] 0086 % devided vb_megfile_load_data into external type and this internal one 0087 % See also 0088 % vb_megfile_load_data, vb_megfile_load_data_external 0089 % vb_megfile_make_new_megfile 0090 % 0091 % [history] 0092 % 2008-04-24 (Sako) initial version 0093 % 2008-06-05 (Sako) modified interface spec - ChannelType, channel_info 0094 % 2009-07-03 (Sako) modified channel_info 0095 % 2010-06-30 (Sako) supported storing data externally 0096 % 2010-07-01 (Sako) modified how to pick up trial data 0097 % 0098 % Copyright (C) 2011, ATR All Rights Reserved. 0099 % License : New BSD License(see VBMEG_LICENSE.txt) 0100 0101 % --- CHECK ARGUMENTS --- % 0102 if ~exist('megfile', 'var'), megfile = []; end 0103 if ~exist('loadspec', 'var'), loadspec = []; end 0104 if ~exist('new_file', 'var'), new_file = []; end 0105 if ~exist('return_swt', 'var'), return_swt = []; end 0106 if ~exist('verbose_swt', 'var'), verbose_swt = []; end 0107 if ~exist('cmplmnt_swt', 'var'), cmplmnt_swt = []; end 0108 [meginfo, bexp_src, exdata_src, refdata_src, ... 0109 ch_list, target_sample, tr_list, ... 0110 new_file, return_swt, root_dir, loadspec, VERBOSE, DO_COMPLEMENT] = ... 0111 inner_check_arguments(megfile, loadspec, new_file, return_swt, ... 0112 verbose_swt, cmplmnt_swt); 0113 0114 % --- MAIN PROCEDURE --------------------------------------------------------- % 0115 % 0116 if VERBOSE >= 5 % temporarily upper than <notice> level 0117 fprintf(' --- now loading ...\n'); 0118 end 0119 0120 n_trial = vb_info_get_Nrepeat(meginfo); 0121 if n_trial == 1 0122 n_trial_new = size(target_sample,1); 0123 else 0124 n_trial_new = length(tr_list); 0125 end 0126 n_sample_new = target_sample(1,2)-target_sample(1,1)+1; 0127 0128 % 0129 % --- get channel labels 0130 % 0131 meg_labels = vb_meginfo_get_channel_label_meg(meginfo); 0132 ext_labels = vb_meginfo_get_channel_label_extra(meginfo); 0133 ref_labels = vb_meginfo_get_channel_label_refmg(meginfo); 0134 0135 bexp = []; 0136 exdata = []; 0137 refdata = []; 0138 0139 % 0140 % --- EXTRA CHANNEL DATA 0141 % 0142 if ~isempty(ext_labels) 0143 [ext_ch_idx] = vb_util_get_index(ext_labels, ch_list); 0144 if ~isempty(ext_ch_idx) 0145 ext_ch_idx = vb_util_arrange_list(ext_ch_idx, 0); 0146 end 0147 else 0148 ext_ch_idx = []; 0149 end 0150 0151 % if MEGfile has 'bexp_ext' data, pick up from it 0152 if ~isempty(exdata_src) && ~isempty(ext_ch_idx) 0153 n_channel_new = length(ext_ch_idx); 0154 exdata = zeros(n_channel_new, n_sample_new, n_trial_new); 0155 0156 if n_trial == 1 0157 for i_trial = 1:n_trial_new 0158 exdata(:,:,i_trial) = exdata_src(ext_ch_idx, ... 0159 target_sample(i_trial,1):target_sample(i_trial,2)); 0160 end 0161 else 0162 exdata = exdata_src(ext_ch_idx, ... 0163 target_sample(1,1):target_sample(1,2), tr_list); 0164 end 0165 end 0166 0167 % 0168 % --- MEG CHANNEL DATA 0169 % 0170 if ~isempty(meg_labels) 0171 [meg_ch_idx] = vb_util_get_index(meg_labels, ch_list); 0172 if ~isempty(meg_ch_idx) 0173 meg_ch_idx = vb_util_arrange_list(meg_ch_idx, 0); 0174 end 0175 else 0176 meg_ch_idx = []; 0177 end 0178 0179 % if MEGfile has 'bexp' data, pick up from it 0180 if ~isempty(bexp_src) && ~isempty(meg_ch_idx) 0181 n_channel_new = length(meg_ch_idx); 0182 bexp = zeros(n_channel_new, n_sample_new, n_trial_new); 0183 0184 if n_trial == 1 0185 for i_trial = 1:n_trial_new 0186 bexp(:,:,i_trial) = bexp_src(meg_ch_idx, ... 0187 target_sample(i_trial,1):target_sample(i_trial,2)); 0188 end 0189 else 0190 bexp = bexp_src(meg_ch_idx, ... 0191 target_sample(1,1):target_sample(1,2), tr_list); 0192 end 0193 end 0194 0195 0196 % 0197 % --- REFERENCE MAGNETOMETER CHANNEL DATA 0198 % 0199 if ~isempty(ref_labels) 0200 [ref_ch_idx] = vb_util_get_index(ref_labels, ch_list); 0201 if ~isempty(ref_ch_idx) 0202 ref_ch_idx = vb_util_arrange_list(ref_ch_idx, 0); 0203 end 0204 else 0205 ref_ch_idx = []; 0206 end 0207 0208 % if MEGfile has 'eeg' data, pick up from it 0209 if ~isempty(refdata_src) && ~isempty(ref_ch_idx) 0210 n_channel_new = length(ref_ch_idx); 0211 refdata = zeros(n_channel_new, n_sample_new, n_trial_new); 0212 0213 if n_trial == 1 0214 for i_trial = 1:n_trial_new 0215 refdata(:,:,i_trial) = refdata_src(ref_ch_idx, ... 0216 target_sample(i_trial,1):target_sample(i_trial,2)); 0217 end 0218 else 0219 refdata = refdata_src(ref_ch_idx, ... 0220 target_sample(1,1):target_sample(1,2), tr_list); 0221 end 0222 end 0223 0224 % 0225 % --- get read channels' label 0226 % 0227 read_meg_ch = meg_labels(meg_ch_idx); 0228 read_ext_ch = ext_labels(ext_ch_idx); 0229 read_ref_ch = ref_labels(ref_ch_idx); 0230 0231 0232 % if DO_COMPLEMENT 0233 % % if MEGfile does not have 'bexp' nor 'eeg' 0234 % if isempty(bexp) && isempty(exdata) && isempty(refdata) 0235 % if ~isempty(read_meg_ch) 0236 % bexp = vb_meginfo_read_data_file( ... 0237 % meginfo, read_meg_ch, target_sample, 1, tr_label_list, root_dir); 0238 % else 0239 % bexp = []; 0240 % end 0241 % 0242 % if ~isempty(read_ext_ch) 0243 % exdata = vb_meginfo_read_data_file( ... 0244 % meginfo, read_ext_ch, target_sample, 1, tr_label_list, root_dir); 0245 % else 0246 % exdata = []; 0247 % end 0248 % 0249 % if ~isempty(read_ref_ch) 0250 % refdata = vb_meginfo_read_data_file( ... 0251 % meginfo, read_ref_ch, target_sample, 1, tr_label_list, root_dir); 0252 % else 0253 % refdata = []; 0254 % end 0255 % 0256 % elseif isempty(bexp) && ~isempty(meg_ch_idx) 0257 % 0258 % bexp = vb_meginfo_read_data_file(meginfo, ... 0259 % ch_list(meg_ch_idx), target_sample, [], tr_label_list, root_dir); 0260 % 0261 % elseif isempty(exdata) && ~isempty(ext_ch_idx) 0262 % 0263 % exdata = vb_meginfo_read_data_file(meginfo, ... 0264 % ch_list(ext_ch_idx), target_sample, [], tr_label_list, root_dir); 0265 % 0266 % elseif isempty(refdata) && ~isempty(ref_ch_idx) 0267 % 0268 % refdata = vb_meginfo_read_data_file(meginfo, ... 0269 % ch_list(ref_ch_idx), target_sample, [], tr_label_list, root_dir); 0270 % 0271 % else 0272 % % --- do nothing 0273 % end 0274 % end 0275 0276 % --- actions after loading 0277 0278 % ----- save new meg-mat file 0279 if ~isempty(new_file) 0280 new_acqtype = vb_meginfo_get_next_acq_type(meginfo); 0281 0282 vb_megfile_make_new_megfile(megfile, new_file, loadspec, ... 0283 read_meg_ch, read_ext_ch, read_ref_ch, ... 0284 bexp, exdata, refdata, new_acqtype, target_sample); 0285 end 0286 0287 0288 % 0289 % --- return values 0290 % 0291 % ----- arrange data 0292 data = [bexp;exdata;refdata]; 0293 0294 % ------- ChannelInfo 0295 % .Active 0296 % .Name 0297 % .Type 0298 % .ID 0299 channel_info = vb_megfile_make_channel_info(megfile, ... 0300 read_meg_ch, read_ext_ch, read_ref_ch); 0301 0302 0303 % ----- decide return value 0304 if ~return_swt 0305 data = []; 0306 end 0307 return; 0308 % 0309 % --- END OF MAIN PROCEDURE -------------------------------------------------- % 0310 0311 % --- INNER FUNCTIONS -------------------------------------------------------- % 0312 % 0313 % --- inner_check_arguments() 0314 % 0315 function [meginfo, meg_data, ext_data, ref_data, ... 0316 read_ch_list, target_samples, trial_idx, ... 0317 new_file, return_swt, root_dir, loadspec, verbose_level, cmplmnt_swt] = ... 0318 inner_check_arguments(megfile, loadspec, new_file, return_swt, ... 0319 verbose_level, cmplmnt_swt) 0320 func_ = mfilename; 0321 0322 if isempty(megfile) 0323 error('(%s)megfile is a required parameter', func_); 0324 end 0325 0326 if exist(megfile, 'file') ~= 2 0327 error('(%s)cannot find megfile : %s', func_, megfile); 0328 end 0329 0330 meginfo = vb_megfile_load_meginfo(megfile); 0331 0332 % ----- megfile directory 0333 root_dir = vb_get_file_parts(megfile); 0334 0335 0336 % ----- load stored data on megfile 0337 meg_data = vb_megfile_get_internal_data_meg(megfile); 0338 ext_data = vb_megfile_get_internal_data_ext(megfile); 0339 ref_data = vb_megfile_get_internal_data_ref(megfile); 0340 0341 % ----- complement LoadSpec 0342 loadspec = vb_loadspec_check(loadspec, megfile); 0343 0344 % ----- match channels to read [Nch x 1] 0345 read_ch_list = loadspec.ChannelName; 0346 0347 0348 target_samples = vb_loadspec_make_trial_sample(loadspec); 0349 if isempty(target_samples) 0350 n_sample = vb_info_get_sample_number(meginfo); 0351 target_samples = [1 n_sample]; 0352 end 0353 0354 0355 % ----- trial list 0356 % ----- target samples [Ntrial x 2] 0357 N_trial = vb_info_get_Nrepeat(meginfo); 0358 if N_trial == 1 0359 % trial_list = []; 0360 trial_idx = []; 0361 0362 else 0363 org_info = vb_load_measurement_info(megfile); 0364 org_trial = org_info.Trial; 0365 org_trial_idx = [org_trial.number]; 0366 0367 if size(target_samples, 1) > 1 0368 fprintf('(%s) loadspec.Trigger may be wrong\n', mfilename); 0369 target_samples = target_samples(1,:); 0370 end 0371 0372 if isempty(loadspec.TrialNumber) 0373 cur_trial = vb_info_get_trial_data(meginfo); 0374 trial_idx = 1:length(cur_trial); 0375 else 0376 cur_trial = vb_info_get_trial_data(meginfo, loadspec.TrialNumber); 0377 dst_trial_idx = [cur_trial.number]; 0378 [result, trial_idx] = ... 0379 vb_util_check_numerical_lists(org_trial_idx, dst_trial_idx); 0380 end % if ~isempty(loadspec.TrialNumber) 0381 0382 if length(trial_idx) ~= length(cur_trial) 0383 error('(%s) bad trial_idx', func_); 0384 end 0385 0386 if loadspec.ActiveTrial && isequal(org_trial_idx(:), loadspec.TrialNumber(:)); 0387 % if loadspec.TrialNumber not specified, 0388 % load only active trial data. 0389 active_list = vb_info_get_active_trial(meginfo); 0390 if isempty(active_list) 0391 active_list = [cur_trial.Active]; 0392 end 0393 trial_idx = trial_idx(active_list==true); 0394 end 0395 end 0396 loadspec.TrialNumber = trial_idx; 0397 0398 if isempty(new_file) 0399 % require no action 0400 end 0401 0402 if isempty(return_swt) 0403 return_swt = true; 0404 end 0405 0406 if isempty(new_file) && ~return_swt 0407 error('(%s)wrong combination - empty output file and no return', func_); 0408 end 0409 0410 if isempty(verbose_level) 0411 verbose_level = 1; 0412 end 0413 0414 % if isempty(cmplmnt_swt) 0415 % cmplmnt_swt = false; 0416 % end 0417 cmplmnt_swt = false; 0418 return; 0419 % 0420 % --- end of inner_check_arguments() 0421 % 0422 % --- END OF INNER FUNCTIONS ------------------------------------------------- % 0423 0424 % --- END OF FILE --- %