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batch_run_ks.old
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batch_run_ks.old
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function batch_run_ks(varargin)
%==========================================================================
p = inputParser();
p.addParameter('mcdatapath', [], @(x) ischar(x));
p.addParameter('MEAtype', [], @(x) ischar(x));
p.addParameter('Experimenttype', [], @(x) ischar(x));
p.addParameter('AnalyzeMultipleExp', true, @(x) islogical(x));
p.addParameter('verbose', true, @(x) islogical(x));
p.parse(varargin{:});
verbose = p.Results.verbose;
multiexpflag = p.Results.AnalyzeMultipleExp;
rootpaths = p.Results.mcdatapath;
meatypes = p.Results.MEAtype;
exptypes = p.Results.Experimenttype; % option to change initial ops for cell culture, MHK Nov 2019
if isempty(rootpaths) || ~exist(rootpaths,'dir')
if multiexpflag
[rootpaths, meatypes, exptypes] = getmultiplepaths(rootpaths);
else
rootpaths = uigetdir([],'Select mcd data folder');
rootpaths = {rootpaths}; % convert to cell to run it seemlessly with batch files
end
end
%==========================================================================
up = userpath; [pp, ~] = fileparts(up);
KilosortPath = fullfile(pp, 'GitHub\KiloSortMEA');
NpyMatlabPath = fullfile(pp, 'GitHub\npy-matlab');
addpath(genpath(KilosortPath)); addpath(genpath(NpyMatlabPath));
%================================================================
for iexp = 1:numel(rootpaths)
%----------------------------------------------------------------------
kssortedpath = fullfile(rootpaths{iexp},'ks_sorted');
% make ks sorted folder
if ~exist(kssortedpath,'dir'), mkdir(kssortedpath); end
%----------------------------------------------------------------------
% make diary
diarypath = fullfile(kssortedpath, 'ks_output_logger.txt');
if exist(diarypath, 'file'); delete(diarypath); end
diary(diarypath); diary on;
%----------------------------------------------------------------------
binname = 'alldata.dat';
binpath = fullfile(kssortedpath, binname);
%----------------------------------------------------------------------
metadata = [];
metadata.root = rootpaths{iexp};
metadata.meatype = meatypes{iexp};
metadata.exptypes = exptypes{iexp};
%----------------------------------------------------------------------
% search for ks binary in the root folder or do conversion
if exist(binpath,'file')
disp('Kilosort binary found!')
% load bininfo
bininfopath = fullfile(metadata.root,'ks_sorted','bininfo.mat');
if ~exist(bininfopath,'file')
error("Can't find bininfo.mat, exiting");
end
ifile = load(bininfopath); bininfo = ifile.bininfo;
else
%----------------------------------------------------------------------
%read frametimes
if ~exist(fullfile(rootpaths{iexp}, 'frametimes'),'dir')
fprintf('Extracting frametimings...\n');
readFrametimes('mcdatapath', rootpaths{iexp});
end
%----------------------------------------------------------------------
disp('Kilosort binary missing, starting conversion...')
metadata = getmcdmetadata(metadata,verbose);
% do conversion
convpath = fullfile('G:\DATA_sorted', binname);
bininfo = convertToKsRawBinary(metadata, convpath);
disp('Conversion completed!');
%move file to the root
disp('Moving the file back to root...'); tic;
save(fullfile(kssortedpath, 'bininfo.mat'),'bininfo', '-v7.3');
movefile(convpath, fullfile(metadata.root,'ks_sorted'));
% write text file for eventmarkers used in Phy amplitude view
ksEventMarkers(kssortedpath, metadata.root);
fprintf('Done! Took %.2f min\n', toc/60);
end
%----------------------------------------------------------------------
metadata.bininfo = bininfo;
metadata.binpath = binpath;
metadata.whpath = fullfile('G:\DATA_sorted', 'temp_wh.dat');
%----------------------------------------------------------------------
% get options and make channel map
ops = getKsOptionsMEA(metadata);
%----------------------------------------------------------------------
% sort data
gpuDevice(1); %initialize GPU (erases any existing GPU arrays)
rez = preprocessData(ops); % preprocess data and extract spikes for initialization
rez = fitTemplates(rez); % fit templates iteratively
gpuDevice(1); %initialize GPU (erases any existing GPU arrays)
rez = fullMPMUNew2(rez);% extract final spike times (overlapping extraction)
delete(ops.fproc); % remove temporary file
%----------------------------------------------------------------------
% save sorted data to the original folder
fprintf('Saving results to Phy \n')
rezToPhy(rez, kssortedpath); %rezToPhy
rez.cProj = []; rez.cProjPC = [];
% save matlab results file
fprintf('Saving final results in rez \n')
save(fullfile(ops.root, 'ks_sorted','rez.mat'),'rez', '-v7.3');
clear ops metadata;
%----------------------------------------------------------------------
diary off;
%----------------------------------------------------------------------
end
%==========================================================================
end
function mtdat = getmcdmetadata(mtdat, verbose)
stimfiles = dir([mtdat.root,filesep,'*.mcd']);
mtdat.recording_type = 'mcd';
if numel(stimfiles) == 0
stimfiles = dir([mtdat.root,filesep,'*.h5']);
mtdat.recording_type = 'h5';
end
[~, expname]= fileparts(mtdat.root);
if isempty(stimfiles)
error('Hey yo!, there aint no recoreded MCD/H5 data in this folder! good luck with analysis');
end
if verbose
disp([repmat('-',1,20),' Experiment : ',expname,' ', repmat('-',1,20)]);
end
%sort filenames
namelist = {stimfiles.name}';
filenum = cellfun(@(x)sscanf(x,'%d_yy.txt'),namelist);
[~,Sidx] = sort(filenum);
stimfiles = stimfiles(Sidx);
mtdat.mcdfilenames = {stimfiles.name}';
mtdat.mcdfilesize = [stimfiles.bytes]'/(2^10^3);
mtdat.totalexpsize = sum(mtdat.mcdfilesize);
mtdat.exptime = {stimfiles.date}';
[str,dt] = deal(cell(size(stimfiles,1),1));
for jj = 1:size(stimfiles,1)
str{jj} = [num2str(jj,'%02d'),':',repmat(' ',1,5),mtdat.mcdfilenames{jj}(1:15),' ... ',...
mtdat.mcdfilenames{jj}(end-3:end), repmat(' ',1,5),'size: ',num2str(mtdat.mcdfilesize(jj),'%.3g'),...
' GB', repmat(' ',1,5),'recorded at: ', mtdat.exptime{jj}];
gp = strfind(mtdat.exptime{jj},':');
dt{jj} = mtdat.exptime{jj}(1:gp(1)-4);
end
mtdat.expdate = cell2mat(unique(dt));
mtdat.label = str;
if verbose
disp(str);
disp([repmat('-',1,40),'> Total size: ', num2str(mtdat.totalexpsize,'%.3g')]);
disp([repmat('-',1,40),'> Experiment date: ', mtdat.expdate(1,:)]);
disp(repmat(' ',2,1))
end
end
function [pathlist, meatypelist, exptypelist] = getmultiplepaths(batchtxtpath)
if isempty(batchtxtpath) || ~exist(batchtxtpath,'file')
[batchpathfile,batchfilepath] = uigetfile('*.txt','Select the text file for all the data folders');
else
[batchfilepath,batchpathfile,batchfileformat] = fileparts(batchtxtpath);
batchpathfile = [batchpathfile,batchfileformat];
end
fid = fopen(fullfile(batchfilepath,batchpathfile),'r');
C = textscan(fid,'%s %s %s','whitespace','','Delimiter',',');
fclose(fid);
pathlist = C{1};
meatypelist = strrep(C{2},' ','');
if size(C{1},1) > 1 && size(C{1},1) > size(C{3},1) % this to fill up last empty text
C{3}{size(C{1},1)} = '';
end
if isempty(C{3})
exptypelist = {''};
else
exptypelist = C{3};
end
end