kilosortMasterPhase3A.m

% default options are in parenthesis after the comment

addpath(genpath('[set this path]\github\KiloSort')) % path to kilosort folder
addpath(genpath('[set this path]\github\npy-matlab')) % path to npy-matlab scripts

pathToYourConfigFile = '[set this path]'; % take from Github folder and put it somewhere else (together with the master_file)
run(fullfile(pathToYourConfigFile, 'kilosortConfigPhase3A.m'))

tic; % start timer
%
if ops.GPU     
    gpuDevice(1); % initialize GPU (will erase any existing GPU arrays)
end

if strcmp(ops.datatype , 'openEphys')
   ops = convertOpenEphysToRawBInary(ops);  % convert data, only for OpenEphys
end
%
[rez, DATA, uproj] = preprocessData(ops); % preprocess data and extract spikes for initialization
rez                = fitTemplates(rez, DATA, uproj);  % fit templates iteratively
rez                = fullMPMU(rez, DATA);% extract final spike times (overlapping extraction)

% AutoMerge. rez2Phy will use for clusters the new 5th column of st3 if you run this)
%     rez = merge_posthoc2(rez);

% save matlab results file
save(fullfile(ops.root,  'rez.mat'), 'rez', '-v7.3');

% save python results file for Phy
rezToPhy(rez, ops.root);

% remove temporary file
delete(ops.fproc);
%%