BML_NEUROOMEGA_INFO_RAW returns table with OS and header info of raw neuroomega.mat (.mpx) files.
Use as
tab = bml_neuroomega_info_raw(cfg);
'raw' files can be read by ft_read_header.
The first argument cfg is a configuration structure, which can contain
the following field:
cfg.chantype - string: channel type. Required (see table below)
cfg.path - string: path to the folder containing the .mat files. Defauts to '.'
cfg.pattern - string: file name pattern (defaults to '*.mat')
cfg.regexp - string: regular expression to filter files (defaults to '[RL]T[1-5]D[-]{0,1}\d+\.\d+([+-]M){0,1}F\d+\.mat')
cfg.time_channel - string: channel to use for TimeBegin and TimeEnd
defaults to first channel of indicated chantype in first
file detected.
cfg.rm_vars - cell of char with variables names to be removed if present
defaults to {'time_end','time_begin','filenum'}
cfg.mpx_path - string: path to the folder containing the .mpx_ files. Defauts to cfg.path
cfg.mpx_pattern - string: file name pattern (defaults to '*.mpx')
cfg.mpx_regexp - string: regular expression to filter files (defaults to '[RL]T[1-5]D[-]{0,1}\d+\.\d+([+-]M){0,1}F\d+\.mpx')
Returns a matlab 'table' with the folloing variables:
start - double: time in seconds (calculated if mpx files are found in cfg.mpx_path)
end - double: time in seconds (calculated if mpx files are found in cfg.mpx_path)
name - cell array of char: filename
folder - cell array of char: path
date - cell array of char: data of file modification
bytes - double: Size of the file in bytes
isdir - logical: 1 if name is a folder; 0 if name is a file
datenum - double: Modification date as serial date number.
chantype
Fs
nSamples
nChans
nTrials
chantype
chanunit
duration
----------------------------------------
chantype | example channel
----------------------------------------
'macro' | 'CMacro_RAW_01___Central'
'micro' | 'CRAW_01___Central'
'micro_hp' | 'CSPK_01___Central'
'analog' | 'CANALOG_IN_1'
'add_analog' | 'CADD_ANALOG_IN_1'
'micro_lfp' | 'CLFP_01___Central'
'macro_lfp' | 'CMacro_LFP_01___Central
----------------------------------------0001 function info = bml_neuroomega_info_raw(cfg) 0002 0003 % BML_NEUROOMEGA_INFO_RAW returns table with OS and header info of raw neuroomega.mat (.mpx) files. 0004 % 0005 % Use as 0006 % tab = bml_neuroomega_info_raw(cfg); 0007 % 0008 % 'raw' files can be read by ft_read_header. 0009 % 0010 % The first argument cfg is a configuration structure, which can contain 0011 % the following field: 0012 % cfg.chantype - string: channel type. Required (see table below) 0013 % cfg.path - string: path to the folder containing the .mat files. Defauts to '.' 0014 % cfg.pattern - string: file name pattern (defaults to '*.mat') 0015 % cfg.regexp - string: regular expression to filter files (defaults to '[RL]T[1-5]D[-]{0,1}\d+\.\d+([+-]M){0,1}F\d+\.mat') 0016 % cfg.time_channel - string: channel to use for TimeBegin and TimeEnd 0017 % defaults to first channel of indicated chantype in first 0018 % file detected. 0019 % cfg.rm_vars - cell of char with variables names to be removed if present 0020 % defaults to {'time_end','time_begin','filenum'} 0021 % cfg.mpx_path - string: path to the folder containing the .mpx_ files. Defauts to cfg.path 0022 % cfg.mpx_pattern - string: file name pattern (defaults to '*.mpx') 0023 % cfg.mpx_regexp - string: regular expression to filter files (defaults to '[RL]T[1-5]D[-]{0,1}\d+\.\d+([+-]M){0,1}F\d+\.mpx') 0024 % 0025 % 0026 % Returns a matlab 'table' with the folloing variables: 0027 % start - double: time in seconds (calculated if mpx files are found in cfg.mpx_path) 0028 % end - double: time in seconds (calculated if mpx files are found in cfg.mpx_path) 0029 % name - cell array of char: filename 0030 % folder - cell array of char: path 0031 % date - cell array of char: data of file modification 0032 % bytes - double: Size of the file in bytes 0033 % isdir - logical: 1 if name is a folder; 0 if name is a file 0034 % datenum - double: Modification date as serial date number. 0035 % chantype 0036 % Fs 0037 % nSamples 0038 % nChans 0039 % nTrials 0040 % chantype 0041 % chanunit 0042 % duration 0043 % 0044 % 0045 % 0046 % ---------------------------------------- 0047 % chantype | example channel 0048 % ---------------------------------------- 0049 % 'macro' | 'CMacro_RAW_01___Central' 0050 % 'micro' | 'CRAW_01___Central' 0051 % 'micro_hp' | 'CSPK_01___Central' 0052 % 'analog' | 'CANALOG_IN_1' 0053 % 'add_analog' | 'CADD_ANALOG_IN_1' 0054 % 'micro_lfp' | 'CLFP_01___Central' 0055 % 'macro_lfp' | 'CMacro_LFP_01___Central 0056 % ---------------------------------------- 0057 % 0058 0059 chantype = bml_getopt(cfg, 'chantype'); 0060 time_channel = bml_getopt_single(cfg,'time_channel'); 0061 0062 info = bml_neuroomega_info_file(cfg); 0063 0064 cfg_mpx=[]; 0065 cfg_mpx.path = bml_getopt(cfg,'mpx_path',ft_getopt(cfg,'path','.')); 0066 cfg_mpx.pattern = bml_getopt(cfg,'mpx_pattern','*.mpx'); 0067 cfg_mpx.regexp = bml_getopt(cfg,'mpx_regexp','[RL]T[1-5]D[-]{0,1}\d+\.\d+([+-]M){0,1}F\d+\.mpx'); 0068 rm_vars = bml_getopt(cfg,'rm_vars',{'time_end','time_begin','filenum'}); 0069 0070 info_mpx=bml_info_file(cfg_mpx); 0071 0072 hdr_vars={'chantype','Fs','nSamples','nChans','nTrials','chanunit','time_begin','time_end'}; 0073 hdr_table = cell2table(cell(size(info,1),length(hdr_vars))); 0074 hdr_table.Properties.VariableNames = hdr_vars; 0075 0076 assert(~isempty(chantype),'cfg.chantype required'); 0077 if isempty(time_channel) 0078 hdr1 = ft_read_header(fullfile(info.folder{1},info.name{1}),'chantype','chaninfo'); 0079 time_channel = hdr1.chaninfo(strcmp(hdr1.chaninfo.chantype,chantype),:).channel{1}; 0080 end 0081 time_begin = strcat(time_channel,'_TimeBegin'); 0082 time_end = strcat(time_channel,'_TimeEnd'); 0083 0084 for i=1:height(info) 0085 hdr = ft_read_header(fullfile(info.folder{i},info.name{i}),'chantype',chantype); 0086 hdr_table.chantype(i) = {strjoin(unique(hdr.chantype))}; 0087 hdr_table.Fs(i) = {hdr.Fs}; 0088 hdr_table.nSamples(i) = {hdr.nSamples}; 0089 hdr_table.nChans(i) = {hdr.nChans}; 0090 hdr_table.nTrials(i) = {hdr.nTrials}; 0091 hdr_table.chanunit(i) = {strjoin(unique(hdr.chanunit))}; 0092 0093 if ismember(time_begin,fields(hdr.orig)) 0094 hdr_table.time_begin(i) = {hdr.orig.(time_begin)}; 0095 hdr_table.time_end(i) = {hdr.orig.(time_end)}; 0096 else 0097 error('%s not present as mat variable in %s. \nSpecify cfg.time_channel as one of %s',... 0098 time_begin,fullfile(cfg.path,info.name{i}), strjoin(hdr.label)); 0099 end 0100 end 0101 hdr_table.Fs = cell2mat(hdr_table.Fs); 0102 hdr_table.nSamples = cell2mat(hdr_table.nSamples); 0103 hdr_table.nChans = cell2mat(hdr_table.nChans); 0104 hdr_table.nTrials = cell2mat(hdr_table.nTrials); 0105 hdr_table.time_begin = cell2mat(hdr_table.time_begin); 0106 hdr_table.time_end = cell2mat(hdr_table.time_end); 0107 0108 info = [info hdr_table]; 0109 0110 if ~isempty(info_mpx) %loading date from .mpx OS info if available 0111 info_mpx.basename = erase(info_mpx.name,'.mpx'); 0112 info_mpx=info_mpx(:,{'basename','date','datenum'}); 0113 0114 info.date=[]; 0115 info.datenum=[]; 0116 info.basename = erase(info.name,'.mat'); 0117 0118 %checking that all mat files have correspondent mpx file 0119 mat_with_no_mpx = setdiff(info.basename,info_mpx.basename); 0120 if numel(mat_with_no_mpx)>0 0121 if numel(mat_with_no_mpx)<10 0122 warning("the following files don't have correspondent .mpx file: %s", strjoin(mat_with_no_mpx)); 0123 else 0124 warning("%i .mat files don't have correspondent .mpx file", numel(mat_with_no_mpx)); 0125 end 0126 mat_with_no_mpx=table(mat_with_no_mpx); 0127 mat_with_no_mpx.Properties.VariableNames = {'basename'}; 0128 mat_with_no_mpx.date(:) = {''}; 0129 mat_with_no_mpx.datenum(:) = NaN; 0130 info_mpx = [info_mpx; mat_with_no_mpx]; 0131 end 0132 0133 info=join(info,info_mpx,'Keys','basename'); 0134 0135 %adjusting time_end to bml_date2sec origin. 0136 ends = info.time_end+nanmedian(bml_date2sec(info.date)-info.time_end); 0137 %NOTE: time_start and time_end are time coordinates of the first and 0138 %last data point. Duration is the length of the 'represented' time 0139 %therefore the correct way of calculating duration is as follows: 0140 info.duration = info.time_end - info.time_begin + 1./info.Fs; 0141 starts = ends - info.duration; 0142 info = [table(starts,ends,'VariableNames',{'starts','ends'}), info]; 0143 info.basename = []; 0144 %info=sortrows(info,'starts'); 0145 info = bml_annot_table(info); 0146 else 0147 warning('Specify cfg.mpx_path for starts/ends calculation') 0148 info=sortrows(info,'time_begin'); 0149 end 0150 0151 for i=1:numel(rm_vars) 0152 if ismember(rm_vars(i),info.Properties.VariableNames) 0153 info.(rm_vars{i}) = []; 0154 end 0155 end 0156 0157 0158 0159 0160