make new external channel data files after filtering
[usage]
result = vb_megfile_filter_ch_data(meg_file, proc_spec, new_meg_file)
[input]
meg_file : <required> <<file>> MEG-MAT file (.meg.mat)
proc_spec : <required> <<struct>> struct defined process specifications
: .parm : <required> <<struct>>
: : .filt_suffix
: : .bias_flg
: : .highpass
: : .lowpass
: : .highpass_online
: : .lowpass_online
: : .common_flg
: : .fsamp
: .ch_type : channel type ['MEG'] - case-insensitive
: .ch_name : channel name {Nchannel x 1}
: : if this is given, it is applied ahead of ch_type
new_meg_file : <required> <<file>> filtered MEG-MAT file(.meg.mat)
: This parameter must include the full extension.
: ".meg.mat"
--- Meaning of preprocess parameter
.bias_flg : Bias correction flag (=0/1/2 : OFF/Bias/Linear)
= N > 5: Bias correction by first N sample
--- Filter parameters
.highpass : Highpass filter cutoff frequency [Hz]
.lowpass : Lowpass filter cutoff frequency [Hz]
--- Type of filter specification
.highpass_online : filter order of IIR highpass filter
= 0: FIR highpass filter (eegfilt)
= 1: online highpass filter (exponential)
> 1: Butterworth highpass filter (filtfilt)
< 0: Butterworth highpass filter (online)
.lowpass_online : filter order of IIR lowpass filter
= 0: FIR lowpass filter (eegfilt)
= 1: online lowpass filter (exponential)
> 1: Butterworth lowpass filter (filtfilt)
< 0: Butterworth lowpass filter (online)
.fsamp : Down sampling frequency [Hz]
.common_flg : Common reference flag (=1/0 : ON/OFF)
if these fields are empty, corresponding process is not done
[output]
result : <<struct>> depends on current process
[note]
@see vb_filter_raw_data.m
@see vb_megfile_import_extra_data.m
[history]
2009-06-19 (Sako) initial version
2009-08-20 (Sako) modified to complain if plural trial data
2010-06-25 (Sako) added ch_name and modified help
2010-07-02 (Sako) modified progress indicator
2016-11-25 (rhayashi) modified specification(new_meg_file)
2018-08-23 (rhayashi) Filtering is done by referring to ch_name.
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function result = vb_megfile_filter_ch_data(meg_file, proc_spec, new_meg_file) 0002 % make new external channel data files after filtering 0003 % [usage] 0004 % result = vb_megfile_filter_ch_data(meg_file, proc_spec, new_meg_file) 0005 % [input] 0006 % meg_file : <required> <<file>> MEG-MAT file (.meg.mat) 0007 % proc_spec : <required> <<struct>> struct defined process specifications 0008 % : .parm : <required> <<struct>> 0009 % : : .filt_suffix 0010 % : : .bias_flg 0011 % : : .highpass 0012 % : : .lowpass 0013 % : : .highpass_online 0014 % : : .lowpass_online 0015 % : : .common_flg 0016 % : : .fsamp 0017 % : .ch_type : channel type ['MEG'] - case-insensitive 0018 % : .ch_name : channel name {Nchannel x 1} 0019 % : : if this is given, it is applied ahead of ch_type 0020 % new_meg_file : <required> <<file>> filtered MEG-MAT file(.meg.mat) 0021 % : This parameter must include the full extension. 0022 % : ".meg.mat" 0023 % 0024 % --- Meaning of preprocess parameter 0025 % .bias_flg : Bias correction flag (=0/1/2 : OFF/Bias/Linear) 0026 % = N > 5: Bias correction by first N sample 0027 % 0028 % --- Filter parameters 0029 % .highpass : Highpass filter cutoff frequency [Hz] 0030 % .lowpass : Lowpass filter cutoff frequency [Hz] 0031 % 0032 % --- Type of filter specification 0033 % .highpass_online : filter order of IIR highpass filter 0034 % = 0: FIR highpass filter (eegfilt) 0035 % = 1: online highpass filter (exponential) 0036 % > 1: Butterworth highpass filter (filtfilt) 0037 % < 0: Butterworth highpass filter (online) 0038 % 0039 % .lowpass_online : filter order of IIR lowpass filter 0040 % = 0: FIR lowpass filter (eegfilt) 0041 % = 1: online lowpass filter (exponential) 0042 % > 1: Butterworth lowpass filter (filtfilt) 0043 % < 0: Butterworth lowpass filter (online) 0044 % 0045 % .fsamp : Down sampling frequency [Hz] 0046 % .common_flg : Common reference flag (=1/0 : ON/OFF) 0047 % if these fields are empty, corresponding process is not done 0048 % [output] 0049 % result : <<struct>> depends on current process 0050 % [note] 0051 % @see vb_filter_raw_data.m 0052 % @see vb_megfile_import_extra_data.m 0053 % [history] 0054 % 2009-06-19 (Sako) initial version 0055 % 2009-08-20 (Sako) modified to complain if plural trial data 0056 % 2010-06-25 (Sako) added ch_name and modified help 0057 % 2010-07-02 (Sako) modified progress indicator 0058 % 2016-11-25 (rhayashi) modified specification(new_meg_file) 0059 % 2018-08-23 (rhayashi) Filtering is done by referring to ch_name. 0060 % Copyright (C) 2011, ATR All Rights Reserved. 0061 % License : New BSD License(see VBMEG_LICENSE.txt) 0062 0063 % --- CHECK ARGUMENTS --- % 0064 if ~exist('meg_file', 'var'), meg_file = ''; end 0065 if ~exist('proc_spec', 'var'), proc_spec = []; end 0066 if ~exist('new_meg_file', 'var'), new_meg_file = ''; end 0067 [meg_file, proc_spec, new_meg_file] = inner_check_arguments(meg_file, proc_spec, new_meg_file); 0068 0069 meg_info = vb_load_measurement_info(meg_file); 0070 0071 % --- this function is for only single trial data 0072 if vb_info_get_Nrepeat(meg_info) > 1 0073 err_msg = ['this filtering function should be applied to ' ... 0074 'continuously measured data file without trial extraction.']; 0075 error('%s', err_msg); 0076 end 0077 0078 0079 % --- MAIN PROCEDURE --------------------------------------------------------- % 0080 % 0081 result = []; 0082 0083 % Preparation for creating new_meg_file 0084 [p_, f_, e_] = vb_get_file_parts(new_meg_file); 0085 new_meg_dir = p_; 0086 new_meg_filename = [f_, e_]; 0087 bin_dir_name = new_meg_filename(1:strfind(new_meg_filename, '.meg.mat')-1); 0088 proc_spec.new_bin_dir = ['./' bin_dir_name]; 0089 0090 % Create binary directory for new_meg_file 0091 new_bin_dir = fullfile(new_meg_dir, proc_spec.new_bin_dir); 0092 if exist(new_bin_dir, 'dir') ~= 7 0093 vb_mkdir(new_bin_dir); 0094 end 0095 0096 % set Default: ch_type = 'MEG' 0097 if ~isfield(proc_spec, 'ch_name') 0098 ch_info = vb_load_channel_info(meg_file); 0099 proc_spec.ch_name = ch_info.Name; 0100 end 0101 0102 % Filtering 0103 inner_filter_ch_data(meg_file, proc_spec, new_meg_file); 0104 0105 fprintf('save: %s\n',new_meg_file); 0106 0107 return; 0108 % 0109 % --- END OF MAIN PROCEDURE -------------------------------------------------- % 0110 0111 % --- INNER FUNCTIONS -------------------------------------------------------- % 0112 % 0113 % --- inner_check_arguments() 0114 % 0115 function [meg_file, proc_spec, new_meg_file] = inner_check_arguments(meg_file, proc_spec, new_meg_file) 0116 func_ = mfilename; 0117 0118 % --- check meg_file 0119 if isempty(meg_file) 0120 error('(%s) meg_file is a required parameter', func_); 0121 end 0122 0123 if exist(meg_file, 'file') ~= 2 0124 error('(%s) cannot find meg_file : %s', func_, meg_file); 0125 end 0126 0127 if isempty(proc_spec) 0128 error('(%s) proc_spec is a required parameter', func_); 0129 end 0130 0131 if ~isfield(proc_spec, 'parm') 0132 error('(%s) parm is a required field of proc_spec', func_); 0133 end 0134 if isempty(new_meg_file) 0135 error('(%s) new_meg_file is a required parameter', func_); 0136 end 0137 if ~strcmp(new_meg_file(end-7:end), '.meg.mat') 0138 error('(%s) specified new_meg_file should have ''.meg.mat''', func_); 0139 end 0140 0141 if ~isfield(proc_spec, 'ch_type') 0142 proc_spec.ch_type = 'MEG'; 0143 end 0144 proc_spec.ch_type = upper(proc_spec.ch_type); 0145 return; 0146 % 0147 % --- end of inner_check_arguments() 0148 0149 0150 % --- inner_filter_ch_data() 0151 % 0152 function inner_filter_ch_data(meg_file, proc_spec, new_file) 0153 0154 ch_info = vb_load_channel_info(meg_file, 'ALL'); 0155 0156 % filterling channel 0157 filtering_ch_list = proc_spec.ch_name; 0158 if ~iscell(filtering_ch_list) 0159 filtering_ch_list = {filtering_ch_list}; 0160 end 0161 0162 % Original information 0163 meg_info = vb_load_measurement_info(meg_file); 0164 proc_spec.parm.freq = vb_meginfo_get_sampling_frequency(meg_info); 0165 0166 % Check weather do downsampling or not 0167 do_downsample = false; 0168 if isfield(proc_spec.parm, 'fsamp') && ~isempty(proc_spec.parm.fsamp) 0169 % Downsampling causes format change. 0170 do_downsample = true; 0171 dsamp_parm.freq = vb_meginfo_get_sampling_frequency(meg_info); % old 0172 dsamp_parm.fsamp = proc_spec.parm.fsamp; % new 0173 end 0174 0175 % Load data 0176 load_spec.ChannelName = ch_info.Name; 0177 load_spec.ChannelType = 'ALL'; 0178 load_spec.ActiveChannel = 0; % all channels 0179 Nall_ch = length(ch_info.Name); 0180 0181 data = vb_load_meg_data(meg_file, load_spec); 0182 0183 % Search filtering target 0184 filter_ch_ix = []; 0185 for n=1:length(filtering_ch_list) 0186 ix = strmatch(filtering_ch_list{n}, ch_info.Name, 'exact'); 0187 if isempty(ix) 0188 error('Unknown channel specified : %s', filtering_ch_list{n}); 0189 else 0190 filter_ch_ix = [filter_ch_ix; ix]; 0191 end 0192 end 0193 0194 % test filter to get new sampling number. 0195 p_data = vb_filter_raw_data(data(1, :), proc_spec.parm); 0196 p_data = zeros(Nall_ch, size(p_data, 2)); 0197 0198 % Filtering 0199 if do_downsample 0200 % filtering and downsampling to specified channel 0201 p_data(filter_ch_ix, :) = vb_filter_raw_data(data(filter_ch_ix, :), proc_spec.parm); 0202 0203 % apply only downsampling to other channel 0204 dsamp_ch_ix = setdiff([1:Nall_ch]', filter_ch_ix); 0205 if ~isempty(dsamp_ch_ix) 0206 p_data(dsamp_ch_ix, :) = vb_filter_raw_data(data(dsamp_ch_ix, :), dsamp_parm); 0207 end 0208 else 0209 % filtering 0210 0211 % copy from original 0212 p_data = data; 0213 0214 % filtering to specified channel 0215 p_data(filter_ch_ix, :) = vb_filter_raw_data(data(filter_ch_ix, :), proc_spec.parm); 0216 end 0217 0218 % Create new_file 0219 base_meg = load(meg_file); 0220 base_meg.MEGinfo.saveman.data_dir = proc_spec.new_bin_dir; 0221 base_meg.MEGinfo.Nsample = size(p_data,2); 0222 base_meg.MEGinfo.SampleFreq = proc_spec.parm.fsamp; 0223 vb_save_struct(new_file, base_meg); 0224 0225 vb_megfile_import_extra_data(new_file, p_data, ch_info, 1); 0226 return; 0227 % 0228 % --- end of inner_filter_ch_data()