fitTemplates.m

function rez = fitTemplates(rez, DATA, uproj)

nt0             = rez.ops.nt0;
rez.ops.nt0min  = ceil(20 * nt0/61);

ops = rez.ops;

rng('default');
rng(1);

Nbatch      = rez.temp.Nbatch;
Nbatch_buff = rez.temp.Nbatch_buff;

Nfilt 	= ops.Nfilt; %256+128;

ntbuff  = ops.ntbuff;
NT  	= ops.NT;

Nrank   = ops.Nrank;
Th 		= ops.Th;
maxFR 	= ops.maxFR;

Nchan 	= ops.Nchan;

batchstart = 0:NT:NT*(Nbatch-Nbatch_buff);

delta = NaN * ones(Nbatch, 1);
iperm = randperm(Nbatch);

switch ops.initialize
    case 'fromData'
        WUinit = optimizePeaks(ops,uproj);%does a scaled kmeans 
        dWU    = WUinit(:,:,1:Nfilt);
        %             dWU = alignWU(dWU);
    otherwise
        if ~isempty(getOr(ops, 'initFilePath', [])) && ~getOr(ops, 'saveInitTemps', 0)            
            load(ops.initFilePath);
            dWU = WUinit(:,:,1:Nfilt);
        else
            initialize_waves0;
            
            ipck = randperm(size(Winit,2), Nfilt);
            W = [];
            U = [];
            for i = 1:Nrank
                W = cat(3, W, Winit(:, ipck)/Nrank);
                U = cat(3, U, Uinit(:, ipck));
            end
            W = alignW(W, ops);
            
            dWU = zeros(nt0, Nchan, Nfilt, 'single');
            for k = 1:Nfilt
                wu = squeeze(W(:,k,:)) * squeeze(U(:,k,:))';
                newnorm = sum(wu(:).^2).^.5;
                W(:,k,:) = W(:,k,:)/newnorm;
                
                dWU(:,:,k) = 10 * wu;
            end
            WUinit = dWU;
        end
end
if getOr(ops, 'saveInitTemps', 0) 
    if ~isempty(getOr(ops, 'initFilePath', [])) 
        save(ops.initFilePath, 'WUinit') 
    else
       warning('cannot save initialization templates because a savepath was not specified in ops.saveInitTemps'); 
    end
end

[W, U, mu, UtU, nu] = decompose_dWU(ops, dWU, Nrank, rez.ops.kcoords);
W0 = W;
W0(NT, 1) = 0;
fW = fft(W0, [], 1);
fW = conj(fW);

nspikes = zeros(Nfilt, Nbatch);
lam =  ones(Nfilt, 1, 'single');

freqUpdate = 100 * 4;
iUpdate = 1:freqUpdate:Nbatch;


dbins = zeros(100, Nfilt);
dsum = 0;
miniorder = repmat(iperm, 1, ops.nfullpasses);
%     miniorder = repmat([1:Nbatch Nbatch:-1:1], 1, ops.nfullpasses/2);

i = 1; % first iteration

epu = ops.epu;


%%
% pmi = exp(-1./exp(linspace(log(ops.momentum(1)), log(ops.momentum(2)), Nbatch*ops.nannealpasses)));
pmi = exp(-1./linspace(1/ops.momentum(1), 1/ops.momentum(2), Nbatch*ops.nannealpasses));
% pmi = exp(-linspace(ops.momentum(1), ops.momentum(2), Nbatch*ops.nannealpasses));

% pmi  = linspace(ops.momentum(1), ops.momentum(2), Nbatch*ops.nannealpasses);
Thi  = linspace(ops.Th(1),                 ops.Th(2), Nbatch*ops.nannealpasses);
if ops.lam(1)==0
    lami = linspace(ops.lam(1), ops.lam(2), Nbatch*ops.nannealpasses);
else
    lami = exp(linspace(log(ops.lam(1)), log(ops.lam(2)), Nbatch*ops.nannealpasses));
end

if Nbatch_buff<Nbatch
    fid = fopen(ops.fproc, 'r');
end

nswitch = [0];
msg = [];
fprintf('Time %3.0fs. Optimizing templates ...\n', toc)
while (i<=Nbatch * ops.nfullpasses+1)
    % set the annealing parameters
    if i<Nbatch*ops.nannealpasses
        Th      = Thi(i);
        lam(:)  = lami(i);
        pm      = pmi(i);
    end
    
    % some of the parameters change with iteration number
    Params = double([NT Nfilt Th maxFR 10 Nchan Nrank pm epu nt0]);
    
    % update the parameters every freqUpdate iterations
    if i>1 &&  ismember(rem(i,Nbatch), iUpdate) %&& i>Nbatch
        dWU = gather_try(dWU);
        
        % break bimodal clusters and remove low variance clusters
        if  ops.shuffle_clusters &&...
                i>Nbatch && rem(rem(i,Nbatch), 4*400)==1    % i<Nbatch*ops.nannealpasses
            [dWU, dbins, nswitch, nspikes, iswitch] = ...
                replace_clusters(dWU, dbins,  Nbatch, ops.mergeT, ops.splitT, WUinit, nspikes);
        end
        
        dWU = alignWU(dWU, ops);
        
        % restrict spikes to their peak group
        %         dWU = decompose_dWU(dWU, kcoords);
        
        % parameter update
        [W, U, mu, UtU, nu] = decompose_dWU(ops, dWU, Nrank, rez.ops.kcoords);
        
        if ops.GPU
            dWU = gpuArray(dWU);
        else
            W0 = W;
            W0(NT, 1) = 0;
            fW = fft(W0, [], 1);
            fW = conj(fW);
        end
        
        NSP = sum(nspikes,2);
        if ops.showfigures
%             set(0,'DefaultFigureWindowStyle','docked')
%             figure;
            subplot(2,2,1)
            for j = 1:10:Nfilt
                if j+9>Nfilt;
                    j = Nfilt -9;
                end
                plot(log(1+NSP(j + [0:1:9])), mu(j+ [0:1:9]), 'o');
                xlabel('log of number of spikes')
                ylabel('amplitude of template')
                hold all
            end
            axis tight;
            title(sprintf('%d  ', nswitch));
            subplot(2,2,2)
            plot(W(:,:,1))
            title('timecourses of top PC')
            
            subplot(2,2,3)
            imagesc(U(:,:,1))
            title('spatial mask of top PC')
            
            drawnow
        end
        % break if last iteration reached
        if i>Nbatch * ops.nfullpasses; break; end
        
        % record the error function for this iteration
        rez.errall(ceil(i/freqUpdate))          = nanmean(delta);
        
    end
    
    % select batch and load from RAM or disk
    ibatch = miniorder(i);
    if ibatch>Nbatch_buff
        offset = 2 * ops.Nchan*batchstart(ibatch-Nbatch_buff);
        fseek(fid, offset, 'bof');
        dat = fread(fid, [NT ops.Nchan], '*int16');
    else
        dat = DATA(:,:,ibatch);
    end
    
    % move data to GPU and scale it
    if ops.GPU
        dataRAW = gpuArray(dat);
    else
        dataRAW = dat;
    end
    dataRAW = single(dataRAW);
    dataRAW = dataRAW / ops.scaleproc;
    
    % project data in low-dim space
    data = dataRAW * U(:,:);
    
    if ops.GPU
        % run GPU code to get spike times and coefficients
        [dWU, ~, id, x,Cost, nsp] = ...
            mexMPregMU(Params,dataRAW,W,data,UtU,mu, lam .* (20./mu).^2, dWU, nu);
    else
        [dWU, ~, id, x,Cost, nsp] = ...
            mexMPregMUcpu(Params,dataRAW,fW,data,UtU,mu, lam .* (20./mu).^2, dWU, nu, ops);
    end
    
    dbins = .9975 * dbins;  % this is a hard-coded forgetting factor, needs to become an option
    if ~isempty(id)
        % compute numbers of spikes
        nsp                = gather_try(nsp(:));
        nspikes(:, ibatch) = nsp;
        
        % bin the amplitudes of the spikes
        xround = min(max(1, int32(x)), 100);
        
        dbins(xround + id * size(dbins,1)) = dbins(xround + id * size(dbins,1)) + 1;
        
        % estimate cost function at this time step
        delta(ibatch) = sum(Cost)/1e3;
    end
    
    % update status
    if ops.verbose  && rem(i,20)==1
        nsort = sort(round(sum(nspikes,2)), 'descend');
        fprintf(repmat('\b', 1, numel(msg)));
        msg = sprintf('Time %2.2f, batch %d/%d, mu %2.2f, neg-err %2.6f, NTOT %d, n100 %d, n200 %d, n300 %d, n400 %d\n', ...
            toc, i,Nbatch* ops.nfullpasses,nanmean(mu(:)), nanmean(delta), round(sum(nsort)), ...
            nsort(min(size(W,2), 100)), nsort(min(size(W,2), 200)), ...
            nsort(min(size(W,2), 300)), nsort(min(size(W,2), 400)));
        fprintf(msg);
    end
    
    % increase iteration counter
    i = i+1;
end

% close the data file if it has been used
if Nbatch_buff<Nbatch
    fclose(fid);
end

if ~ops.GPU
   rez.fW = fW; % save fourier space templates if on CPU
end
rez.dWU               = gather_try(dWU);
rez.nspikes               = nspikes;
% %%