Daniel@0: function varargout = mirsum(orig,varargin)
Daniel@0: %   s = mirsum(f) sums the envelope of the multi-channel object f.
Daniel@0: %
Daniel@0: %   Optional arguments:
Daniel@0: %       mirsum(f,'Centered') centers the resulting envelope.
Daniel@0: %       mirsum(f,'Mean') divides the summation by the number of channels.
Daniel@0: 
Daniel@0: %       mirsum(f,'Weights')...
Daniel@0: 
Daniel@0:         c.key = 'Centered';
Daniel@0:         c.type = 'Boolean';
Daniel@0:         c.default = 0;
Daniel@0:         c.when = 'After';
Daniel@0:     option.c = c;
Daniel@0: 
Daniel@0:         m.key = 'Mean';
Daniel@0:         m.type = 'Boolean';
Daniel@0:         m.default = 0;
Daniel@0:         m.when = 'After';
Daniel@0:     option.m = m;
Daniel@0: 
Daniel@0:         adj.key = 'Adjacent';
Daniel@0:         adj.type = 'Integer';
Daniel@0:         adj.default = 1;
Daniel@0:     option.adj = adj;
Daniel@0: 
Daniel@0:         weights.key = 'Weights';
Daniel@0:         weights.type = 'Integer';
Daniel@0:         weights.default = [];
Daniel@0:     option.weights = weights;    
Daniel@0:     
Daniel@0: specif.option = option;
Daniel@0: 
Daniel@0: if isamir(orig,'mirtemporal')
Daniel@0:     specif.eachchunk = @eachtemporalchunk;
Daniel@0:     specif.combinechunk = 'Concat'; %@combinetemporalchunk;
Daniel@0: else
Daniel@0:     specif.combinechunk = @combinechunk;
Daniel@0: end
Daniel@0: varargout = mirfunction(@mirsum,orig,varargin,nargout,specif,@init,@main);
Daniel@0: 
Daniel@0: 
Daniel@0: function [x type] = init(x,option)
Daniel@0: type = mirtype(x);
Daniel@0: 
Daniel@0: 
Daniel@0: function s = main(x,option,postoption)
Daniel@0: x = purgedata(x);
Daniel@0: if iscell(x)
Daniel@0:     x = x{1};
Daniel@0: end
Daniel@0: d = get(x,'Data');
Daniel@0: pp = get(x,'PeakPos');
Daniel@0: pv = get(x,'PeakVal');
Daniel@0: pm = get(x,'PeakMode');
Daniel@0: p = get(x,'Pos');
Daniel@0: sc = cell(1,length(d));
Daniel@0: spp = cell(1,length(d));
Daniel@0: spv = cell(1,length(d));
Daniel@0: spm = cell(1,length(d));
Daniel@0: for h = 1:length(d)
Daniel@0:     dh = d{h};
Daniel@0:     sch = cell(1,length(dh));
Daniel@0:     spph = cell(1,length(dh));
Daniel@0:     spvh = cell(1,length(dh));
Daniel@0:     spmh = cell(1,length(dh));
Daniel@0:     for i = 1:length(dh)
Daniel@0:         % Summation of signal
Daniel@0:         s3 = size(dh{i},3);
Daniel@0:         if not(isempty(option.weights))
Daniel@0:             weights = reshape(option.weights,1,1,length(option.weights));
Daniel@0:             if length(weights)~=s3
Daniel@0:                 %warning('WARNING in MIRSUM..');
Daniel@0:                 weights = weights(1,1,1:s3);
Daniel@0:             end
Daniel@0:             dh{i} = dh{i}.*repmat(weights,[size(dh{i},1),size(dh{i},2),1]);
Daniel@0:         end
Daniel@0:         if option.adj < 2
Daniel@0:             sch{i} = sum(dh{i},3);
Daniel@0:         else
Daniel@0:             m0 = option.adj;
Daniel@0:             nc1 = size(dh{i},3);
Daniel@0:             nc2 = ceil(nc1/m0);
Daniel@0:             sch{i} = zeros(size(dh{i},1),size(dh{i},2),nc2);
Daniel@0:             for j = 1:nc2
Daniel@0:                 sch{i}(:,:,j) = sum(dh{i}(:,:,(j-1)*m0+1:min(j*m0,nc1))...
Daniel@0:                                         ,3);
Daniel@0:             end
Daniel@0:         end
Daniel@0:         % Summation of peaks
Daniel@0:         if not(isempty(pp)) && not(isempty(pp{1}))
Daniel@0:             ppi = pp{h}{i};
Daniel@0:             pvi = pv{h}{i};
Daniel@0:             pmi = pm{h}{i};
Daniel@0:             nfr = size(ppi,2);
Daniel@0:             nbd = size(ppi,3);
Daniel@0:             sppi = cell(1,nfr,1);
Daniel@0:             spvi = cell(1,nfr,1);
Daniel@0:             spmi = cell(1,nfr,1);
Daniel@0:             for j = 1:nfr
Daniel@0:                 sppj = [];
Daniel@0:                 spvj = [];
Daniel@0:                 spmj = [];
Daniel@0:                 for k = 1:nbd
Daniel@0:                     ppk = ppi{1,j,k};
Daniel@0:                     pvk = pvi{1,j,k};
Daniel@0:                     pmk = pmi{1,j,k};
Daniel@0:                     for l = 1:length(ppk)
Daniel@0:                         fp = find(ppk(l) == sppj);
Daniel@0:                         if fp
Daniel@0:                             spvj(fp) = spvj(fp) + pvk(l);
Daniel@0:                         else
Daniel@0:                             sppj(end+1) = ppk(l);
Daniel@0:                             spvj(end+1) = pvk(l);
Daniel@0:                             spmj(end+1) = pmk(l);
Daniel@0:                         end
Daniel@0:                     end
Daniel@0:                 end
Daniel@0:                 sppi{1,j,1} = sppj;
Daniel@0:                 spvi{1,j,1} = spvj;
Daniel@0:                 spmi{1,j,1} = spmj;
Daniel@0:             end
Daniel@0:             spph{i} = sppi;
Daniel@0:             spvh{i} = spvi;
Daniel@0:             spmh{i} = spmi;
Daniel@0:         else
Daniel@0:             spph{i} = [];
Daniel@0:             spvh{i} = [];
Daniel@0:             spmh{i} = [];
Daniel@0:         end
Daniel@0:         if not(isempty(p)) && not(isempty(p{h}))
Daniel@0:             p{h}{i} = p{h}{i}(:,:,1);
Daniel@0:         end
Daniel@0:     end
Daniel@0:     sc{h} = sch;
Daniel@0:     spp{h} = spph;
Daniel@0:     spv{h} = spvh;
Daniel@0:     spm{h} = spmh;
Daniel@0: end
Daniel@0: s = set(x,'Data',sc,'Pos',p,'PeakPos',spp,'PeakVal',spv,'PeakMode',spm);
Daniel@0: if not(isempty(postoption))
Daniel@0:     s = post(s,postoption);
Daniel@0: end
Daniel@0: 
Daniel@0: 
Daniel@0: function s = post(s,option)
Daniel@0: if option.c
Daniel@0:     d = get(s,'Data');
Daniel@0:     for k = 1:length(d)
Daniel@0:         for i = 1:length(d{k})
Daniel@0:             d{k}{i} = center(d{k}{i});
Daniel@0:         end
Daniel@0:     end
Daniel@0:     s = set(s,'Data',d);
Daniel@0: end
Daniel@0: if option.m
Daniel@0:     d = get(s,'Data');
Daniel@0:     ch = get(s,'Channels');
Daniel@0:     if not(isempty(ch))
Daniel@0:         for k = 1:length(d)
Daniel@0:             for i = 1:length(d{k})
Daniel@0:                 d{k}{i} = d{k}{i}/length(ch{k});
Daniel@0:             end
Daniel@0:             ch{k} = [1];
Daniel@0:         end
Daniel@0:         s = set(s,'Data',d,'Channels',ch);
Daniel@0:     end
Daniel@0: end
Daniel@0: 
Daniel@0: 
Daniel@0: function [y orig] = eachtemporalchunk(orig,option,missing)
Daniel@0: [y orig] = mirsum(orig,option);
Daniel@0: 
Daniel@0: 
Daniel@0: %function y = combinetemporalchunk(old,new)
Daniel@0: %do = get(old,'Data');
Daniel@0: %to = get(old,'Time');
Daniel@0: %dn = get(new,'Data');
Daniel@0: %tn = get(new,'Time');
Daniel@0: %y = set(old,'Data',{{[do{1}{1};dn{1}{1}]}},...
Daniel@0: %            'Time',{{[to{1}{1};tn{1}{1}]}});
Daniel@0: %        
Daniel@0:         
Daniel@0: function y = combinechunk(old,new)
Daniel@0: if isa(old,'mirspectrum')
Daniel@0:     warning('WARNING IN MIRSUM: not yet fully generalized to mirspectrum')
Daniel@0: end
Daniel@0: do = get(old,'Data');
Daniel@0: do = do{1}{1};
Daniel@0: dn = get(new,'Data');
Daniel@0: dn = dn{1}{1};
Daniel@0: if length(dn) < length(do)
Daniel@0:     dn(length(do),:,:) = 0; % Zero-padding
Daniel@0: end
Daniel@0: y = set(old,'ChunkData',do+dn);