BML_REREFERENCE applies re-referencing scheme to raw Use as [ref,U] = bml_rereference(cfg,raw) cfg.label - Nx1 cellstr with labels. Defaults to raw.label cfg.group - Nx1 integer array identifying groups of electrodes contacts of same group are re-referenced together values <=0 and nans are not re-referenced. If not specified, groups are defined by string before underscore '_' (i.e. ecog_*, micro_*, macro_*, audio_*, envaudio_*, etc) cfg.method - string, method to be implemented 'CAR' or 'common', common average referencing (default) 'LAR' or 'local', local average referencing 'VAR' or 'variable', variable average referencing raw - ft_datatype_raw to be re-referenced Returns ref - ft_datatype_raw with re-referenced data U - double, unmixing matrix. ref = U * raw
0001 function [ref,U] = bml_rereference(cfg,raw) 0002 0003 % BML_REREFERENCE applies re-referencing scheme to raw 0004 % 0005 % Use as 0006 % [ref,U] = bml_rereference(cfg,raw) 0007 % 0008 % cfg.label - Nx1 cellstr with labels. Defaults to raw.label 0009 % cfg.group - Nx1 integer array identifying groups of electrodes 0010 % contacts of same group are re-referenced together 0011 % values <=0 and nans are not re-referenced. 0012 % If not specified, groups are defined by string before underscore '_' 0013 % (i.e. ecog_*, micro_*, macro_*, audio_*, envaudio_*, etc) 0014 % cfg.method - string, method to be implemented 0015 % 'CAR' or 'common', common average referencing (default) 0016 % 'LAR' or 'local', local average referencing 0017 % 'VAR' or 'variable', variable average referencing 0018 % 0019 % raw - ft_datatype_raw to be re-referenced 0020 % 0021 % Returns 0022 % ref - ft_datatype_raw with re-referenced data 0023 % U - double, unmixing matrix. ref = U * raw 0024 0025 assert(isstruct(raw),"invalid raw"); 0026 assert(all(ismember({'trial','time','label'},fieldnames(raw))),"invalid raw"); 0027 0028 label = bml_getopt(cfg,'label',raw.label); 0029 group = bml_getopt(cfg,'group'); 0030 method = bml_getopt_single(cfg,'method','CAR'); 0031 0032 %inferring groups from labels 0033 if isempty(group) 0034 sl=split(label,'_'); 0035 sl=sl(:,1); 0036 usl=unique(sl); 0037 group = bml_map(sl,usl,1:length(usl)); 0038 end 0039 0040 %assigning orphan raw labels to null group 0041 in=ismember(raw.label,label); 0042 if ~all(in) 0043 label = [label;raw.label(~in)]; 0044 group = [group; zeros(sum(~in),1)]; 0045 end 0046 0047 %re-ordering group to match raw.label 0048 group = bml_map(raw.label,label,group); 0049 label = raw.label; 0050 0051 %creating null group 0052 group(ismissing(group))=0; 0053 group(group<=0)=0; 0054 g0 = sum(group<=0); 0055 0056 %keeping original order 0057 [g,g_idx]=sort(group); 0058 ug = unique(g); 0059 [N,~] = histc(g,ug); 0060 0061 %creating blocks 0062 if ismember(method,{'CAR','common'}) 0063 U_blocks=cellfun(@bml_comavgref_matrix,num2cell(N),'UniformOutput',false); 0064 elseif ismember(method,{'LAR','local'}) 0065 U_blocks=cellfun(@bml_locavgref_matrix,num2cell(N),'UniformOutput',false); 0066 elseif ismember(method,{'VAR','variable'}) 0067 warning('Using experimental method VAR, susceptible to high amplitude artifacts') 0068 0069 %calculating variance-covariance matrix 0070 cfg=[]; 0071 cfg.covariance = 'yes'; 0072 cfg.vartrllength = 2; 0073 tl_raw=ft_timelockanalysis(cfg,raw); 0074 0075 %grouping matrix into blocks 0076 COVs = cell(length(ug),1); 0077 for i=1:length(ug) 0078 COVs{i,1}=tl_raw.cov(g_idx(g==ug(i)),g_idx(g==ug(i))); 0079 end 0080 0081 %creating blocks 0082 U_blocks=cellfun(@bml_varavgref_matrix,COVs,'UniformOutput',false); 0083 0084 else 0085 error('unknown method') 0086 end 0087 0088 %replacing block by identity for null group 0089 if g0 > 0 0090 U_blocks{1} = eye(N(1)); 0091 end 0092 0093 %joining blocks 0094 U = blkdiag(U_blocks{:}); 0095 U(g_idx,g_idx) = U; 0096 %image(U,'CDataMapping','scaled') 0097 0098 %applying unmixing matrix to data 0099 ref = bml_apply(@(x) U*x, raw); 0100 0101