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Kilosort2Neurosuite.m
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Kilosort2Neurosuite.m
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function Kilosort2Neurosuite(rez)
% Converts KiloSort output (.rez structure) to Neurosuite files: fet,res,clu,spk files.
% Based on the GPU enable filter from Kilosort and fractions from Brendon
% Watson's code for saving Neurosuite files.
% The script has a high memory usage as all waveforms are loaded into
% memory at the same time. If you experience a memory error, increase
% your swap/cashe file, and increase the amount of memory MATLAB can use.
%
% 1) Waveforms are extracted from the dat file via GPU enabled filters.
% 2) Features are calculated in parfor loops.
%
% Inputs:
% rez - rez structure from Kilosort
%
% By Peter Petersen 2018
% petersen.peter@gmail.com
t1 = tic;
spikeTimes = uint64(rez.st3(:,1)); % uint64
spikeTemplates = uint32(rez.st3(:,2)); % uint32 % template id for each spike
kcoords = rez.ops.kcoords;
basename = rez.ops.basename;
Nchan = rez.ops.Nchan;
samples = rez.ops.nt0;
templates = zeros(Nchan, size(rez.W,1), rez.ops.Nfilt, 'single');
for iNN = 1:rez.ops.Nfilt
templates(:,:,iNN) = squeeze(rez.U(:,iNN,:)) * squeeze(rez.W(:,iNN,:))';
end
amplitude_max_channel = [];
for i = 1:size(templates,3)
[~,amplitude_max_channel(i)] = max(range(templates(:,:,i)'));
end
template_kcoords = kcoords(amplitude_max_channel);
kcoords2 = unique(template_kcoords);
ia = [];
for i = 1:length(kcoords2)
kcoords3 = kcoords2(i);
if mod(i,4)==1; fprintf('\n'); end
fprintf(['Loading data for spike group ', num2str(kcoords3),'. '])
template_index = find(template_kcoords == kcoords3);
ia{i} = find(ismember(spikeTemplates,template_index));
end
rez.ia = ia;
fprintf('\n'); toc(t1)
fprintf('\nSaving .clu files to disk (cluster indexes)')
for i = 1:length(kcoords2)
kcoords3 = kcoords2(i);
if mod(i,4)==1; fprintf('\n'); end
fprintf(['Saving .clu file for group ', num2str(kcoords3),'. '])
tclu = spikeTemplates(ia{i});
tclu = cat(1,length(unique(tclu)),double(tclu));
cluname = fullfile([basename '.clu.' num2str(kcoords3)]);
fid=fopen(cluname,'w');
fprintf(fid,'%.0f\n',tclu);
fclose(fid);
clear fid
end
fprintf('\n'); toc(t1)
fprintf('\nSaving .res files to disk (spike times)')
for i = 1:length(kcoords2)
kcoords3 = kcoords2(i);
tspktimes = spikeTimes(ia{i});
if mod(i,4)==1; fprintf('\n'); end
fprintf(['Saving .res file for group ', num2str(kcoords3),'. '])
resname = fullfile([basename '.res.' num2str(kcoords3)]);
fid=fopen(resname,'w');
fprintf(fid,'%.0f\n',tspktimes);
fclose(fid);
clear fid
end
fprintf('\n'); toc(t1)
fprintf('\nExtracting waveforms\n')
waveforms_all = Kilosort_ExtractWaveforms(rez);
fprintf('\n'); toc(t1)
fprintf('\nSaving .spk files to disk (waveforms)')
for i = 1:length(kcoords2)
if mod(i,4)==1; fprintf('\n'); end
fprintf(['Saving .spk for group ', num2str(kcoords2(i)),'. '])
fid=fopen([basename,'.spk.',num2str(kcoords2(i))],'w');
fwrite(fid,waveforms_all{i}(:),'int16');
fclose(fid);
end
fprintf('\n'); toc(t1)
fprintf('\nComputing PCAs')
% Starting parpool if stated in the Kilosort settings
if (rez.ops.parfor & isempty(gcp('nocreate'))); parpool; end
for i = 1:length(kcoords2)
kcoords3 = kcoords2(i);
if mod(i,2)==1; fprintf('\n'); end
fprintf(['Computing PCAs for group ', num2str(kcoords3),'. '])
PCAs_global = zeros(3,sum(kcoords==kcoords3),length(ia{i}));
waveforms = waveforms_all{i};
waveforms2 = reshape(waveforms,[size(waveforms,1)*size(waveforms,2),size(waveforms,3)]);
wranges = int64(range(waveforms2,1));
wpowers = int64(sum(waveforms2.^2,1)/size(waveforms2,1)/100);
% Calculating PCAs in parallel if stated in ops.parfor
if isempty(gcp('nocreate'))
for k = 1:size(waveforms,1)
PCAs_global(:,k,:) = pca(zscore(permute(waveforms(k,:,:),[2,3,1]),[],2),'NumComponents',3)';
end
else
parfor k = 1:size(waveforms,1)
PCAs_global(:,k,:) = pca(zscore(permute(waveforms(k,:,:),[2,3,1]),[],2),'NumComponents',3)';
end
end
fprintf(['Saving .fet files for group ', num2str(kcoords3),'. '])
PCAs_global2 = reshape(PCAs_global,size(PCAs_global,1)*size(PCAs_global,2),size(PCAs_global,3));
factor = (2^15)./max(abs(PCAs_global2'));
PCAs_global2 = int64(PCAs_global2 .* factor');
fid=fopen([basename,'.fet.',num2str(kcoords3)],'w');
Fet = double([PCAs_global2; wranges; wpowers; spikeTimes(ia{i})']);
nFeatures = size(Fet, 1);
formatstring = '%d';
for ii=2:nFeatures
formatstring = [formatstring,'\t%d'];
end
formatstring = [formatstring,'\n'];
fprintf(fid, '%d\n', nFeatures);
fprintf(fid,formatstring,Fet);
fclose(fid);
end
fprintf('\n'); toc(t1)
fprintf('\nComplete!')
function waveforms_all = Kilosort_ExtractWaveforms(rez)
% Extracts waveforms from a dat file using GPU enable filters.
% Based on the GPU enable filter from Kilosort.
% All settings and content are extracted from the rez input structure
%
% Inputs:
% rez - rez structure from Kilosort
%
% Outputs:
% waveforms_all - structure with extracted waveforms
% Extracting content from the .rez file
ops = rez.ops;
NT = ops.NT;
if exist('ops.fbinary') == 0
warning(['Binary file does not exist: ', ops.fbinary])
end
d = dir(ops.fbinary);
NchanTOT = ops.NchanTOT;
chanMap = ops.chanMap;
chanMapConn = chanMap(rez.connected>1e-6);
kcoords = ops.kcoords;
ia = rez.ia;
spikeTimes = rez.st3(:,1);
if ispc
dmem = memory;
memfree = dmem.MemAvailableAllArrays/8;
memallocated = min(ops.ForceMaxRAMforDat, dmem.MemAvailableAllArrays) - memfree;
memallocated = max(0, memallocated);
else
memallocated = ops.ForceMaxRAMforDat;
end
ops.ForceMaxRAMforDat = 10000000000;
memallocated = ops.ForceMaxRAMforDat;
nint16s = memallocated/2;
NTbuff = NT + 4*ops.ntbuff;
Nbatch = ceil(d.bytes/2/NchanTOT /(NT-ops.ntbuff));
Nbatch_buff = floor(4/5 * nint16s/ops.Nchan /(NT-ops.ntbuff)); % factor of 4/5 for storing PCs of spikes
Nbatch_buff = min(Nbatch_buff, Nbatch);
DATA =zeros(NT, NchanTOT,Nbatch_buff,'int16');
if isfield(ops,'fslow')&&ops.fslow<ops.fs/2
[b1, a1] = butter(3, [ops.fshigh/ops.fs,ops.fslow/ops.fs]*2, 'bandpass');
else
[b1, a1] = butter(3, ops.fshigh/ops.fs*2, 'high');
end
if isfield(ops,'xml')
disp('Loading xml from rez for probe layout')
xml = ops.xml;
elseif exist(fullfile(ops.root,[ops.basename,'.xml']))==2
disp('Loading xml for probe layout from root folder')
xml = LoadXml(fullfile(ops.root,[ops.basename,'.xml']));
ops.xml = xml;
end
fid = fopen(ops.fbinary, 'r');
waveforms_all = [];
% kcoords2 = unique(ops.kcoords);
template_kcoords = kcoords(amplitude_max_channel);
kcoords2 = unique(template_kcoords);
channel_order = {};
indicesTokeep = {};
% connected_index = zeros(size(rez.connected));
% connected_index(rez.connected)=1:length(chanMapConn);
for i = 1:length(kcoords2)
kcoords3 = kcoords2(i);
waveforms_all{i} = zeros(sum(kcoords==kcoords3),ops.nt0,size(rez.ia{i},1));
if exist('xml')
[channel_order,channel_index] = sort(xml.AnatGrps(kcoords2(i)).Channels+1);
[~,indicesTokeep{i},~] = intersect(chanMapConn,channel_order);
%indicesTokeep{i} = connected_index(indicesTokeep{i});
end
end
fprintf('Extraction of waveforms begun \n')
for ibatch = 1:Nbatch
if mod(ibatch,10)==0
if ibatch~=10
fprintf(repmat('\b',[1 length([num2str(round(100*(ibatch-10)/Nbatch)), ' percent complete'])]))
end
fprintf('%d percent complete', round(100*ibatch/Nbatch));
end
offset = max(0, 2*NchanTOT*((NT - ops.ntbuff) * (ibatch-1) - 2*ops.ntbuff));
if ibatch==1
ioffset = 0;
else
ioffset = ops.ntbuff;
end
fseek(fid, offset, 'bof');
buff = fread(fid, [NchanTOT NTbuff], '*int16');
% keyboard;
if isempty(buff)
break;
end
nsampcurr = size(buff,2);
if nsampcurr<NTbuff
buff(:, nsampcurr+1:NTbuff) = repmat(buff(:,nsampcurr), 1, NTbuff-nsampcurr);
end
if ops.GPU
dataRAW = gpuArray(buff);
else
dataRAW = buff;
end
dataRAW = dataRAW';
dataRAW = single(dataRAW);
dataRAW = dataRAW(:, chanMapConn);
dataRAW = dataRAW-median(dataRAW,2);
datr = filter(b1, a1, dataRAW);
datr = flipud(datr);
datr = filter(b1, a1, datr);
datr = flipud(datr);
DATA = gather_try(int16( datr(ioffset + (1:NT),:)));
dat_offset = offset/NchanTOT/2+ioffset;
% Saves the waveforms occuring within each batch
for i = 1:length(kcoords2)
kcoords3 = kcoords2(i);
% ch_subset = 1:length(chanMapConn);
temp = find(ismember(spikeTimes(ia{i}), [ops.nt0/2+1:size(DATA,1)-ops.nt0/2] + dat_offset));
temp2 = spikeTimes(ia{i}(temp))-dat_offset;
startIndicies = temp2-ops.nt0/2+1;
stopIndicies = temp2+ops.nt0/2;
X = cumsum(accumarray(cumsum([1;stopIndicies(:)-startIndicies(:)+1]),[startIndicies(:);0]-[0;stopIndicies(:)]-1)+1);
X = X(1:end-1);
waveforms_all{i}(:,:,temp) = reshape(DATA(X,indicesTokeep{i})',size(indicesTokeep{i},1),ops.nt0,[]);
end
end
end
end