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SpikeVisualizationGUI_byElectrode.m
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function varargout = SpikeVisualizationGUI_byElectrode(varargin)
% MATLAB code for SpikeVisualizationGUI_byElectrode.fig
% Last Modified by GUIDE v2.5 27-Oct-2018 16:32:28
% version 0.7 (nov 2017), tested in R2017b
% version 0.5 (sept 2016), tested in R2014b
% Vincent Prevosto
% email: vp35 at duke.edu
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @SpikeVisualizationGUI_byElectrode_OpeningFcn, ...
'gui_OutputFcn', @SpikeVisualizationGUI_byElectrode_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
%% --- Executes just before SpikeVisualizationGUI_byElectrode is made visible.
function SpikeVisualizationGUI_byElectrode_OpeningFcn(hObject, ~, handles, varargin)
% Choose default command line output for SpikeVisualizationGUI_byElectrode
handles.output = hObject;
if ~isempty(varargin)
handles=CatStruct(handles,varargin{:}); % CatStruct available here:
% http://www.mathworks.com/matlabcentral/fileexchange/7842-CatStruct
if isfield(handles,'fname')
set(handles.TB_FileName,'string',handles.fname(1:end-4));
else
set(handles.TB_FileName,'string','');
end
if isempty(handles.spikeFile)
% check if spike sorting results are present in export folder
cd(handles.exportDir);
listExportDir=dir;
listExportDir=listExportDir(cellfun('isempty',cellfun(@(x) strfind('.',x(end)),{listExportDir.name},'UniformOutput',false)));
spikeFileIdx=cellfun(@(x) contains(x,'_spikes.mat'),{listExportDir.name});
if logical(sum(spikeFileIdx))
handles.spikeFile=listExportDir(spikeFileIdx).name;
else %maybe spike sorting results are sub folder
spikeSortingFolderIdx=[listExportDir.isdir];
spikeSortingFolder=[handles.exportDir filesep listExportDir(spikeSortingFolderIdx).name];
listSpikeSortingFolder=dir(spikeSortingFolder);
spikeFileIdx=cellfun(@(x) contains(x,'result'),{listSpikeSortingFolder.name});
if logical(sum(spikeFileIdx))
handles.exportDir=spikeSortingFolder;
handles.spikeFile=listSpikeSortingFolder(spikeFileIdx).name;
else
% ask user to select file to load
[handles.spikeFile,handles.exportDir] = uigetfile({'*.mat;*.hdf5;*.csv','Export Formats';...
'*.dat','Raw data';'*.*','All Files' },'Select data to load',cd);
if handles.spikeFile==0
handles=rmfield(handles,'spikeFile');
handles.exportDir=cd;
end
end
end
end
else
try
handles.userinfo=UserDirInfo;
catch
handles.userinfo=[];
handles.userinfo.user=getenv('username');
end
%% get most recently changed data folder (looks for a folder named "export")
if isfield(handles.userinfo,'directory')
exportDir=regexprep(handles.userinfo.directory,'\\\w+$','\\export');
else
[exportDir,handles.userinfo.directory]=deal(cd);
end
dataDirListing=dir(exportDir);
if ~isempty(dataDirListing)
%removing dots
dataDirListing=dataDirListing(cellfun('isempty',cellfun(@(x) strfind(x,'.'),...
{dataDirListing.name},'UniformOutput',false)));
%removing other folders
dataDirListing=dataDirListing(cellfun('isempty',cellfun(@(x)...
regexp('Behav | Video | Impedance',x),... % list | all | unwanted | folders | here
{dataDirListing.name},'UniformOutput',false)));
[~,fDateIdx]=sort([dataDirListing.datenum],'descend');
recentDataFolder=[exportDir filesep dataDirListing(fDateIdx(1)).name filesep];
else
recentDataFolder=cd;
end
% ask user to select file to load
[handles.spikeFile,handles.exportDir] = uigetfile({'*.mat;*.hdf5;*.csv','Export Formats';...
'*.dat','Raw data';'*.*','All Files' },'Select data to load',recentDataFolder);
if handles.spikeFile==0
handles.spikeFile='';
handles.exportDir=recentDataFolder;
end
end
%define figure colormap
colormapSeed=lines;
handles.cmap=[colormapSeed(1:7,:);(colormapSeed+flipud(colormap(copper)))/2;autumn];
if isfield(handles,'spikeFile') && ~isempty(handles.spikeFile) && sum(strfind(handles.spikeFile,'.dat'))
GetSortedSpikes_PB_Callback(hObject, handles);
end
handles.fileLoaded=0;
%create classification table
handles.classification = table([],[],[],categorical(),{},'VariableNames',{'SortID','Channel','UnitNumber','Classification','Comment'});
if isfield(handles,'spikeFile')
handles=LoadSpikes(handles);
handles=LoadRawData(handles);
end
% Update handles structure
guidata(hObject, handles);
%% --- Executes (conditional) at startup and on button press in GetSortedSpikes_PB.
function GetSortedSpikes_PB_Callback(hObject, ~, handles)
if ~isfield(handles,'datFile')
handles.datFile=[cell2mat(regexp(handles.spikeFile,'.+(?=\_\w+\_\w+\.)','match')) '_nopp'];
end
[status,cmdout]=RunSpykingCircus(cd,handles.datFile,{'runspkc,exportspikes'});
if handles.GetSortedSpikes_PB.ForegroundColor(1)==0.3490
handles.GetSortedSpikes_PB.ForegroundColor=[0.2 0.5 0.7];
else
handles.GetSortedSpikes_PB.ForegroundColor=[0.3490 0.2000 0.3294];
end
%% Load data function
function handles=LoadSpikes(handles)
if isfield(handles,'subset')
handles = rmfield(handles,'subset');
end
% if isfield(handles,'spikeFile')
% handles = rmfield(handles,'spikeFile');
% end
if isfield(handles,'offlineSort_SpikeFile')
handles = rmfield(handles,'offlineSort_SpikeFile');
end
% function declaration
axis_name= @(x) sprintf('Chan %.0f',x);
if isfield(handles,'fname') && strcmp(handles.fname,'')
set(handles.TB_FileName,'string','')
else
if ~isfield(handles,'fname') && isfield(handles,'rec_info')
try
handles.fname=handles.rec_info.exportname;
catch
handles.fname=handles.datFile;
end
end
if handles.fileLoaded==0 & strfind(handles.spikeFile,'Resorted.mat')
cd(handles.exportDir);
spikeData=load(handles.spikeFile);
handles.loadingDir=handles.exportDir;
handles.loadingFile=handles.spikeFile;
handles = rmfield(handles,{'spikeFile','exportDir'});
if isfield(handles,'rec_info')
handles = rmfield(handles,'rec_info');
end
if isfield(handles,'Spikes')
handles = rmfield(handles,'Spikes');
end
if isfield(spikeData,'classification')
handles = rmfield(handles,'classification');
end
if isfield(handles,'userinfo') & isfield(spikeData,'userinfo')
handles = rmfield(handles,'userinfo');
end
handles=CatStruct(handles,spikeData);
clear spikeData;
elseif handles.fileLoaded==0
%% load spike data from matlab export, if exists
cd(handles.exportDir);
exportDirListing=dir;
if isempty({exportDirListing(~cellfun('isempty',cellfun(@(x) strfind(x,'_spikes.'),...
{exportDirListing.name},'UniformOutput',false))).name})
handles.offlineSort_SpikeDir=handles.exportDir;
handles.offlineSort_SpikeFile=handles.spikeFile;
%go one folder up
exportDirUp=handles.exportDir(1:regexp(handles.exportDir,'\\\w+\\$'));
exportDirListing=dir(exportDirUp);
handles.spikeFile={exportDirListing(~cellfun('isempty',cellfun(@(x) strfind(x,'_spikes.'),...
{exportDirListing.name},'UniformOutput',false))).name};
if ~isempty(handles.spikeFile)
handles.exportDir=exportDirUp;
cd(handles.exportDir);
end
end
% if ~isfield(handles,'fname') && isfield(handles,'offlineSort_SpikeFile')
% handles.fname=regexp(handles.offlineSort_SpikeFile,'.+?(?=\.)','match');
% handles.fname=handles.fname{1};
% end
if iscell(handles.spikeFile) && size(handles.spikeFile,2)>1
% ask which export file is the good one
[whichOne,status] = listdlg('PromptString','Select correct spike file:',...
'SelectionMode','single',...
'ListString',handles.spikeFile);
if status==1
handles.spikeFile=handles.spikeFile{whichOne};
else
handles.spikeFile=[];
end
% nameComp=cellfun(@(name) sum(ismember(handles.fname(1:end-4),...
% name(1:size(handles.fname(1:end-4),2)))) ,handles.spikeFile);
% if abs(diff(nameComp))<2 %that can be tricky for some files
% %select the most recent
% fileDates=datenum({exportDirListing(~cellfun('isempty',cellfun(@(x) strfind(x,'_spikes.'),...
% {exportDirListing.name},'UniformOutput',false))).date});
% handles.spikeFile=handles.spikeFile{fileDates==max(fileDates)};
% else
% handles.spikeFile=handles.spikeFile{nameComp==max(nameComp)};
% end
else
if iscell(handles.spikeFile)
try
handles.spikeFile=handles.spikeFile{:};
catch
handles.spikeFile=[];
end
end
end
% end
% handles.exportDir='C:\Data\export\PrV75_61_optostim2_BR_6Ch_SyncCh_CAR';
% cd(handles.exportDir);
% handles.spikeFile='PrV75_61_optostim2_BR_6Ch_SyncCh_CAR_Ch3.mat';
set(handles.TB_FileName,'string',[handles.exportDir handles.spikeFile])
%% Load spike data
if ~isempty(handles.spikeFile) && ~strcmp(get(handles.Spikes_PrevSorted_Menu,'Checked'),'on')
spikeData=load(handles.spikeFile);
if isfield(handles,'Spikes')
% This will delete all Spikes data including any changes to HandSort
% Might want to change that in future version
handles = rmfield(handles,'Spikes');
end
handles=CatStruct(handles,spikeData);
%clear
clear spikeData;
end
% check if we need to load recording info
if ~isfield(handles,'rec_info')
try
if ~isempty(handles.spikeFile)
fileName=regexp(handles.spikeFile,'.+(?=_\w+.mat$)','match');
recInfo=load([fileName{:} '_info.mat']);
elseif ~isempty(handles.offlineSort_SpikeFile)
exportDirListing=dir(cd);
if sum(cellfun(@(x) contains(x,{'_info.';'recInfo'}),...
{exportDirListing.name}))
fileName=exportDirListing(cellfun(@(x) contains(x,{'_info.';'recInfo.'}),...
{exportDirListing.name})).name;
recInfo=load(fileName);
else %might be in folder above
exportDirListing=dir('..');
fileName=exportDirListing(~cellfun('isempty',cellfun(@(x) strfind(x,'_info.'),...
{exportDirListing.name},'UniformOutput',false))).name;
currDir=cd; cd('..');
recInfo=load(fileName); cd(currDir);
end
end
catch
[fileInfoName,fileInfoDir,FilterIndex] = uigetfile({'*.mat;*.txt','File Info Formats';...
'*.*','All Files' },'Select file providing basic recording info, or cancel and enter info');
if FilterIndex==0 % display prompt
prompt={'Sampling rate',...
'Number of channels in spike-sorted file',...
'uV/bit'};
name='Data file information';
numlines=1;
defaultanswer={'30000','32','0.25'};
options.Resize='on';
options.WindowStyle='normal';
info=inputdlg(prompt,name,numlines,defaultanswer,options);
info=cellfun(@(field) str2double(field),info,'UniformOutput',false);
info{2}=1:info{2};
recInfo.rec_info=cell2struct(info, {'samplingRate','exportedChan','bitResolution'}, 1);
else
recInfo=load(fullfile(fileInfoDir,fileInfoName));
end
end
% just in case the field is named differently
field = fieldnames(recInfo);
if ~strcmp(field{:},'rec_info')
[recInfo.('rec_info')] = recInfo.(field{:});
recInfo = rmfield(recInfo,field);
end
%concatenate
if isfield(handles,'rec_info')
handles = rmfield(handles,'rec_info');
end
handles=CatStruct(handles,recInfo);
%clear
clear recInfo;
end
if isfield(handles,'offlineSort_SpikeFile')
% cd(handles.exportDir);
if logical(regexp(handles.offlineSort_SpikeFile,'Ch\d+.')) % Spike2
cd(handles.offlineSort_SpikeDir);
handles.Spikes.Offline_Sorting=LoadSpikeData_byElectrode(handles.offlineSort_SpikeFile,...
handles.rec_info.numRecChan,handles.rec_info.samplingRate);
elseif contains(handles.offlineSort_SpikeFile,'.hdf5') % Spyking-Circus
% first load raw traces in memory
fileName=regexp(handles.offlineSort_SpikeFile,'.+(?=\.\w+\.\w+$)','match');
% tb_filename=[tb_filename{1} '.dat'];
if ~exist([fileName{:} '.dat'],'file') && ~exist([fileName{:} '.mat'],'file')
% try one folder up
cd ..
end
if ~exist([fileName{:} '.dat'],'file') && ~exist([fileName{:} '.mat'],'file')
% then ask where it is
[handles.datFile,handles.datDir] = uigetfile({'*.dat;*.mat','Data Formats';...
'*.*','All Files' },'Select data file for spike waveform extraction');
else
if exist([fileName{1} '.dat'],'file')
handles.datFile=[fileName{1} '.dat'];
elseif exist([fileName{1} '.mat'],'file')
handles.datFile=[fileName{1} '.mat'];
end
handles.datDir=cd;
end
if strfind(handles.datFile,'.mat') % .mat file contain rawData
load(handles.datFile);
elseif strfind(handles.datFile,'.dat')
rawData = memmapfile(fullfile(handles.datDir,handles.datFile),'Format','int16');
end
%% then import spike Data
cd(handles.offlineSort_SpikeDir);
if ~isfield(handles.rec_info,'bitResolution') || isempty(handles.rec_info.bitResolution)
handles.rec_info.bitResolution=0.25; %default 0.25 bit per uV
end
handles.Spikes.Offline_Sorting=LoadSpikeData_byElectrode(handles.offlineSort_SpikeFile,rawData,...
numel(handles.rec_info.exportedChan),handles.rec_info.samplingRate,handles.rec_info.bitResolution); %handles.tracesInfo.size(1)
clear rawData;
elseif contains(handles.offlineSort_SpikeFile,'rez.mat') % KiloSort
fileName={exportDirListing(~cellfun('isempty',cellfun(@(x) strfind(x,'.dat'),...
{exportDirListing.name},'UniformOutput',false))).name};
if length(fileName)>1 %iscell(fileName) &&
fileName=fileName{~cellfun('isempty',cellfun(@(x)...
strfind(x,handles.rec_info.exportname),...
fileName,'UniformOutput',false))};
else
fileName=fileName{:};
end
% tb_filename=[tb_filename{1} '.dat'];
if ~exist(fileName,'file') % then ask where it is
[handles.datFile,handles.datDir] = uigetfile({'*.dat;*.mat','Data Formats';...
'*.*','All Files' },'Select data file for spike waveform extraction');
else
handles.datFile=fileName;
handles.datDir=cd;
end
if strfind(handles.datFile,'.mat') % .mat file contain rawData
load(handles.datFile);
elseif strfind(handles.datFile,'.dat')
rawData = memmapfile(fullfile(handles.datDir,handles.datFile),'Format','int16');
end
%then import
cd(handles.offlineSort_SpikeDir);
if ~isfield(handles.rec_info,'bitResolution') || isempty(handles.rec_info.bitResolution)
handles.rec_info.bitResolution=0.25; %default 0.25 uV/bit
end
handles.Spikes.Offline_Sorting=LoadSpikeData_byElectrode(handles.offlineSort_SpikeFile,rawData,...
numel(handles.rec_info.exportedChan),handles.rec_info.samplingRate,handles.rec_info.bitResolution); %handles.tracesInfo.size(1)
clear rawData;
elseif contains(handles.offlineSort_SpikeFile,'.csv') || ...
contains(handles.offlineSort_SpikeFile,'_jrc.mat') % assuming JRClust
fileName=exportDirListing(~cellfun('isempty',cellfun(@(x) strfind(x,'.dat'),...
{exportDirListing.name},'UniformOutput',false))).name;
if iscell(fileName) && length(fileName)>1
fileName=exportDirListing(~cellfun('isempty',cellfun(@(x) strfind(x,rec_info.exportname),...
fileName,'UniformOutput',false))).name;
end
% tb_filename=[tb_filename{1} '.dat'];
if ~exist(fileName,'file') % then ask where it is
[handles.datFile,handles.datDir] = uigetfile({'*.dat;*.mat','Data Formats';...
'*.*','All Files' },'Select data file for spike waveform extraction');
else
handles.datFile=fileName;
handles.datDir=cd;
end
if strfind(handles.datFile,'.mat') % .mat file contain rawData
load(handles.datFile);
elseif strfind(handles.datFile,'.dat')
rawData = memmapfile(fullfile(handles.datDir,handles.datFile),'Format','int16');
end
%then import
cd(handles.offlineSort_SpikeDir);
if ~isfield(handles.rec_info,'bitResolution') || isempty(handles.rec_info.bitResolution)
handles.rec_info.bitResolution=0.25; %default 0.25 uV/bit
end
handles.Spikes.Offline_Sorting=LoadSpikeData_byElectrode(handles.offlineSort_SpikeFile,...
rawData,numel(handles.rec_info.exportedChan),handles.rec_info.samplingRate,...
handles.rec_info.bitResolution); %handles.tracesInfo.size(1)
clear rawData;
end
cd(handles.exportDir);
end
if strcmp(get(handles.Spikes_Th_Menu,'Checked'),'on')
%extract waveforms if needed
if ~isfield(handles.Spikes.Offline_Threshold,'Waveforms')
% first load raw traces
fileName=regexp(handles.spikeFile,'.+(?=_\w+.\w+$)','match');
load([fileName{:} '_raw.mat']);
%then import
handles.Spikes=LoadSpikeData_byElectrode(handles.spikeFile,...
handles.Spikes.Offline_Threshold.electrode,...
handles.Spikes.Offline_Threshold.samplingRate(:,1),rawData);
clear rawData
end
end
if isfield(handles.Spikes,'HandSort')
% all good
elseif isfield(handles.Spikes,'Online_Sorting') || isfield(handles.Spikes,'Offline_Sorting') ...
|| isfield(handles.Spikes,'Offline_Threshold')
if isfield(handles.Spikes,'Offline_Threshold') && strcmp(get(handles.Spikes_Th_Menu,'Checked'),'on')
set(handles.Spikes_SortOff_Menu,'Checked','off');
set(handles.Spikes_SortOn_Menu,'Checked','off');
handles.Spikes.HandSort.Units=handles.Spikes.Offline_Threshold.Units;
handles.Spikes.HandSort.SpikeTimes=handles.Spikes.Offline_Threshold.SpikeTimes;
handles.Spikes.HandSort.Waveforms=handles.Spikes.Offline_Threshold.Waveforms;
handles.Spikes.HandSort.samplingRate=handles.Spikes.Offline_Threshold.samplingRate;
elseif isfield(handles.Spikes,'Offline_Sorting') || strcmp(get(handles.Spikes_SortOff_Menu,'Checked'),'on')
set(handles.Spikes_SortOff_Menu,'Checked','on');
set(handles.Spikes_SortOn_Menu,'Checked','off');
handles.Spikes.HandSort.Units=handles.Spikes.Offline_Sorting.Units;
handles.Spikes.HandSort.SpikeTimes=handles.Spikes.Offline_Sorting.SpikeTimes;
handles.Spikes.HandSort.Waveforms=handles.Spikes.Offline_Sorting.Waveforms;
handles.Spikes.HandSort.samplingRate=handles.Spikes.Offline_Sorting.samplingRate;
elseif isfield(handles.Spikes,'Online_Sorting') || strcmp(get(handles.Spikes_SortOn_Menu,'Checked'),'on')
set(handles.Spikes_SortOff_Menu,'Checked','off');
set(handles.Spikes_SortOn_Menu,'Checked','on');
handles.Spikes.HandSort.Units=handles.Spikes.Online_Sorting.Units;
handles.Spikes.HandSort.SpikeTimes=handles.Spikes.Online_Sorting.SpikeTimes;
handles.Spikes.HandSort.Waveforms=handles.Spikes.Online_Sorting.Waveforms;
handles.Spikes.HandSort.samplingRate=handles.Spikes.Online_Sorting.samplingRate;
end
% set data classes
handles.Spikes.HandSort.SpikeTimes=...
cellfun(@(spktimes) uint32(spktimes), handles.Spikes.HandSort.SpikeTimes,'UniformOutput',false); %safe for about 40 hours of recording
handles.Spikes.HandSort.Units=...
cellfun(@(units) int8(units), handles.Spikes.HandSort.Units,'UniformOutput',false); %256 units per channel max
handles.Spikes.HandSort.Waveforms=...
cellfun(@(wfs) int16(wfs), handles.Spikes.HandSort.Waveforms,'UniformOutput',false); %256 units per channel max
handles.Spikes.HandSort.samplingRate=uint32(handles.Spikes.HandSort.samplingRate); %uint16 should be enough, but just to be on the safe side
%squeeze in case of ND array
squeezeIt=cellfun(@(x) numel(size(x))>2, handles.Spikes.HandSort.Waveforms,'UniformOutput',true);
if sum(squeezeIt)
handles.Spikes.HandSort.Waveforms=...
cellfun(@(x) squeeze(x), handles.Spikes.HandSort.Waveforms,'UniformOutput',false);
handles.Spikes.HandSort.Waveforms(~squeezeIt)=...
cellfun(@(x) transpose(x), handles.Spikes.HandSort.Waveforms(~squeezeIt),'UniformOutput',false);
end
% re-order along time scale if needed
timeOrder=cellfun(@(times) sum(diff(times)<0),...
handles.Spikes.HandSort.SpikeTimes,'UniformOutput',true);
if sum(timeOrder)
[~,timeIndices]=cellfun(@(times) sort(times),...
handles.Spikes.HandSort.SpikeTimes,'UniformOutput',false);
handles.Spikes.HandSort.Units=cellfun(@(units,times) units(times),...
handles.Spikes.HandSort.Units,timeIndices,'UniformOutput',false);
handles.Spikes.HandSort.SpikeTimes=cellfun(@(spktimes,times) spktimes(times),...
handles.Spikes.HandSort.SpikeTimes,timeIndices,'UniformOutput',false);
handles.Spikes.HandSort.Waveforms=cellfun(@(wf,times) wf(times,:),...
handles.Spikes.HandSort.Waveforms,timeIndices,'UniformOutput',false);
end
% check if empty cells
nonEmpty=~cellfun('isempty',handles.Spikes.HandSort.Units);
% if negative unit IDs (-1), shift all to get 0 as lowest ID
negUnits=cellfun(@(units) sum(units<0), handles.Spikes.HandSort.Units(nonEmpty),...
'UniformOutput',true);
if sum(negUnits)
handles.Spikes.HandSort.Units(nonEmpty)=...
cellfun(@(units) units+abs(min(units)),...
handles.Spikes.HandSort.Units(nonEmpty),'UniformOutput',false);
end
% permute dimensions if not the right orientation
permuteIt=cellfun(@(x,y) find(size(x)==length(y))==1,...
handles.Spikes.HandSort.Waveforms(nonEmpty),...
handles.Spikes.HandSort.Units(nonEmpty),'UniformOutput',true);
if sum(permuteIt)
handles.Spikes.HandSort.Waveforms(nonEmpty)=...
cellfun(@(x) transpose(x), handles.Spikes.HandSort.Waveforms(nonEmpty),...
'UniformOutput',false);
end
permuteIt=cellfun(@(x) size(x,1)<numel(x), handles.Spikes.HandSort.Units(nonEmpty),...
'UniformOutput',true);
if sum(permuteIt) % check units are not right as well
handles.Spikes.HandSort.Units(nonEmpty)=...
cellfun(@(x) transpose(x), handles.Spikes.HandSort.Units(nonEmpty),'UniformOutput',false);
end
% downsample spike times to 1 millisecond bins
% spikeTimes=handles.Spikes.HandSort.SpikeTimes;
for chNum=1:size(handles.Spikes.HandSort.samplingRate,1)
handles.Spikes.HandSort.samplingRate(chNum,2)=1000;
if ~isempty(handles.Spikes.HandSort.SpikeTimes{chNum,1})
handles.Spikes.HandSort.SpikeTimes{chNum,2}=...
uint32(handles.Spikes.HandSort.SpikeTimes{chNum,1})/...
(handles.Spikes.HandSort.samplingRate(chNum,1)/...
handles.Spikes.HandSort.samplingRate(chNum,2));
else
handles.Spikes.HandSort.SpikeTimes{chNum,2}=[];
end
% spikeTimeIdx=zeros(1,size(Spikes.Offline_Threshold.data{ChExN,1},2));
% spikeTimeIdx(Spikes.Offline_Threshold.data{ChExN,1})=1;
%
% binSize=1;
% numBin=ceil(max(spikeTimes{chNum})/...
% (handles.Spikes.HandSort.samplingRate(chNum,1)/...
% handles.Spikes.HandSort.samplingRate(chNum,2))/binSize);
% % binspikeTime = histogram(double(spikeTimes), numBin); %plots directly histogram
% [data,binEdges] = histcounts(double(spikeTimes{chNum}),...
% linspace(0,max(double(spikeTimes{chNum})),numBin));
% data(data>1)=1; %no more than 1 spike per ms
end
end
end
%% Set number of electrodes and units,
% when opening GUI, selects cluster with most spikes and
% electrode with most spikes from that cluster
if strcmp(get(handles.SelectElectrode_LB,'string'),'none')
if diff(size(handles.rec_info.exportedChan))>0
handles.rec_info.exportedChan=handles.rec_info.exportedChan';
end
set(handles.SelectElectrode_LB,'string',num2str(handles.rec_info.exportedChan));
if isfield(handles.Spikes,'Online_Sorting') || isfield(handles.Spikes,'Offline_Sorting')
% numUnits=cellfun(@(x) sum(length(x)*unique(x)), handles.Spikes.HandSort.Units);
allUnits=cellfun(@(units) units, handles.Spikes.HandSort.Units,'UniformOutput',false);
unitID=mode(cell2mat(allUnits));
unitDispersion=cellfun(@(units) sum(units==unitID), handles.Spikes.HandSort.Units);
% electrodeNum=find(numUnits==max(numUnits),1);
electrodeNum=find(unitDispersion==max(unitDispersion));
set(handles.SelectElectrode_LB,'value',electrodeNum);
else
set(handles.SelectElectrode_LB,'value',1)
end
else
electrodeNum=get(handles.SelectElectrode_LB,'value');
end
%% color electrode by shanks
if isfield(handles.rec_info,'probeID')
try
handles.userinfo=UserDirInfo;
catch
handles.userinfo=[];
end
if ~isfield(handles.userinfo,'probemap')
if ~exist('probemaps', 'dir')
handles.userinfo.probemap = uigetdir(cd,'select probe maps location');
path(handles.userinfo.probemap,path)
else
allPathDirs=strsplit(path,pathsep);
handles.userinfo.probemap=allPathDirs{find(cellfun(@(pathdir) contains(pathdir,'probemaps'),allPathDirs),1)};
end
mapping=load([handles.userinfo.probemap filesep handles.rec_info.probeID '.mat']);
handles.rec_info.differentShanks=logical(bwlabel(mod([mapping.(handles.rec_info.probeID).Shank]+1,2)));
else
handles.rec_info.differentShanks=logical(bwlabel(mod([handles.rec_info.probeLayout.Shank]+1,2)));
end
electrodeList= cellstr(get(handles.SelectElectrode_LB,'String'))';
colorChannels=cell(length(electrodeList),1);
for elNum=1:length(electrodeList) % ASSUMING ALL EXPORTED CHANNELS ARE SORTED !
if handles.rec_info.differentShanks(elNum)>0
colorChannels(elNum)=cellfun(@(thatChannel) sprintf(['<HTML><BODY bgcolor="%s">'...
'<FONT color="%s">%s</FONT></BODY></HTML>'],... %size="+1"
'black','white', thatChannel),electrodeList(elNum),'UniformOutput',false);
else
colorChannels(elNum)=cellfun(@(thatChannel) sprintf(['<HTML><BODY bgcolor="%s">'...
'<FONT color="%s">%s</FONT></BODY></HTML>'],... %size="+1"
'white','black', thatChannel),electrodeList(elNum),'UniformOutput',false);
end
end
set(handles.SelectElectrode_LB, 'String', colorChannels);
set(handles.SelectElectrode_LB ,'ListboxTop',max([1 electrodeNum-3]));
end
% namestr = cellstr(get(hObject, 'String'));
% validx = get(hObject, 'Value');
% newstr = regexprep(namestr{validx}, '"red"','"green"');
% namestr{validx} = newstr;
% set(hObject, 'String', namestr);
%% initialize variables
unitsIdx=handles.Spikes.HandSort.Units{electrodeNum};
waveForms=handles.Spikes.HandSort.Waveforms{electrodeNum};
% if numel(size(waveForms))>2
% waveForms=squeeze(waveForms);
% end
if ~isempty(unitsIdx)
% how many units on that electrode?
unitsID=unique(unitsIdx); %number of clustered units
set(handles.SelectUnit_LB,'string',num2str(unitsID));
handles=ClassificationColor(handles);
set(handles.SelectUnit_LB,'value',find(unitsID>0));
%% take out big ouliers
% if find(size(waveForms)==length(unitsIdx))==1
% waveForms=waveForms';
% end
WFmeanZ=mean(abs(zscore(single(waveForms))),2);
% if more than one, plot it and keep
if sum(WFmeanZ>6)>1
figure('name', 'Artifacts','position',[30 500 500 400]);
plot(waveForms(:,WFmeanZ>6)','linewidth',2.5); hold on;
plot(mean(waveForms,2),'linewidth',2.5);
legend({'Artifact','Mean waveforms'});
title('Potential artifacts removed, mean sigma > 6');
else
handles.Spikes.HandSort.Units{electrodeNum}(WFmeanZ>6)=-9;%artifacts
end
% here's how this can work:
% Spikes detected from threshold are the benchmark (unit code = 0).
% May want to extract waveforms, but most important is the time.
% Sorted units (whatever the source) "color" those units. One spike per ms max.
handles=Plot_Unsorted_WF(handles);
if get(handles.ShowWF_CB,'value')
handles=Plot_Sorted_WF(handles);
else
cla(handles.SortedUnits_Axes);
end
Plot_Mean_WF(handles);
Plot_ISI(handles);
Plot_ACG(handles);
Plot_XCG(handles);
else
% unitsID=[];
cla(handles.SortedUnits_Axes);
cla(handles.MeanSortedUnits_Axes);
cla(handles.ISI_Axes);
cla(handles.ACG_Axes);
cla(handles.XCorr_Axes);
set(handles.SelectUnit_LB,'string',num2str(0));
set(handles.SelectUnit_LB,'value',1);
end
handles.fileLoaded=1;
end
%% Load raw traces function
function handles=LoadRawData(handles)
try
if ~(isfield(handles,'datFile') && ~isempty(strfind(handles.datFile,'.mat')))
handles.datFile=regexp(handles.spikeFile,'.+(?=_\w+.\w+$)','match');
handles.datFile=[handles.datFile{:} '_raw.mat'];
handles.datDir=cd;
end
handles.tracesInfo=whos('-file',fullfile(handles.datDir,handles.datFile));
handles.tracesInfo=rmfield(handles.tracesInfo,...
{'bytes','global','sparse','complex','nesting','persistent'});
if strfind(fullfile(handles.datDir,handles.datFile),'nopp')
handles.tracesInfo.preproc=0;
else
% if "raw" data has been pre-processed already, do
% not process later
handles.tracesInfo.preproc=1;
end
handles.traces = matfile(fullfile(handles.datDir,handles.datFile));
catch % try to load from .dat file
if ~(isfield(handles,'datFile') && contains(fullfile(handles.datDir,handles.datFile),'.dat'))
if isfield(handles,'offlineSort_SpikeFile')
handles.datFile=regexp(handles.offlineSort_SpikeFile,'.+?(?=\.)','match');
handles.datFile=[handles.datFile{1} '.dat'];
handles.datDir=cd;
else
% ask user for raw data file
end
end
if ~exist(fullfile(handles.datDir,handles.datFile),'file')
if isfield(handles,'loadingDir') & exist(fullfile(handles.loadingDir,...
handles.datFile),'file') % might have been moved
handles.datDir=handles.loadingDir;
end
end
handles.traces = memmapfile(fullfile(handles.datDir,handles.datFile),'Format','int16');
handles.tracesInfo= struct('name','rawData',...
'size',size(handles.traces.Data),...
'numChan',numel(handles.rec_info.exportedChan),...
'source','dat');
try
%check in params file if data was filtered, and find threshold value
fid = fopen([fullfile(handles.datDir,handles.datFile(1:end-4)) '.params'],'r');
catch
fid=-1;
end
if fid~=-1
params=fread(fid,'*char')';
if contains(regexp(params,'(?<=filter_done\s+=\s)\w+(?=\s)','match','once'), 'True')
handles.tracesInfo.preproc=1;
else
handles.tracesInfo.preproc=0;
end
handles.rec_info.threshold=regexp(params,'(?<=spike_thresh\s+=\s)\w+(?=\s)','match','once');
fclose(fid);
else
handles.tracesInfo.preproc=0;
end
end
handles.tracesInfo.excerptSize=handles.rec_info.samplingRate/2; %1 second as default (-:+ around loc)
if isa(handles.traces,'memmapfile')
handles.tracesInfo.excerptLocation=round(max(handles.tracesInfo.size)/2/numel(handles.rec_info.exportedChan)); %mid-recording as default
set(handles.TW_slider,'max',max(handles.tracesInfo.size)/numel(handles.rec_info.exportedChan));
else
handles.tracesInfo.excerptLocation=round(max(handles.tracesInfo.size)/2);
set(handles.TW_slider,'max',max(handles.tracesInfo.size));
end
% set(handles.TW_slider,'sliderstep',[0.01 max([0.01,...
% handles.tracesInfo.excerptSize/max(handles.tracesInfo.size)])]);
% plot "raw" (filtered) trace
DisplayTraces(handles);
% plot spike rasters
DisplayRasters(handles);
%% Plot unsorted spikes
function handles=Plot_Unsorted_WF(handles)
electrodeNum=get(handles.SelectElectrode_LB,'value');
waveForms=handles.Spikes.HandSort.Waveforms{electrodeNum};
unitsIdx=handles.Spikes.HandSort.Units{electrodeNum};
samplingRate=handles.Spikes.HandSort.samplingRate(electrodeNum,1);
%% Plot unsorted spikes
numWFtoPlot=str2double(get(handles.ShowHowManyUWF_ET,'string'));
if sum(unitsIdx==0)>numWFtoPlot %then only plot subset of waveforms
subset=find(unitsIdx==0);
handles.subset{1}=subset(1:ceil(sum(unitsIdx==0)/numWFtoPlot):end);
else
handles.subset{1}=find(unitsIdx==0);
end
axes(handles.UnsortedUnits_Axes); hold on;
cla(handles.UnsortedUnits_Axes);
set(handles.UnsortedUnits_Axes,'Visible','on');
if find(size(waveForms)==length(unitsIdx))==1
waveForms=waveForms';
end
plot(waveForms(:,handles.subset{1}),'linewidth',1,'Color',[0 0 0 0.2]);
lineH=flipud(findobj(gca,'Type', 'line'));
% childH=flipud(get(gca,'Children'));
for lineTag=1:size(lineH,1)
lineH(lineTag).Tag=num2str(handles.subset{1}(lineTag)); %Tag the unit ID
end
% foo=reshape([lineH.YData],size([lineH.YData],2)/size(lineH,1),size(lineH,1));
% faa=reshape([childH.YData],size([childH.YData],2)/size(childH,1),size(childH,1));
% lineH(80).Tag
% figure; hold on;
% plot(foo(:,80));
% plot(waveForms(:,handles.subset{1}(80)));
% [lineH.Tag]=deal(num2str(handles.subset{1}));
set(gca,'XTick',linspace(0,size(waveForms(:,handles.subset{1}),1),5),...
'XTickLabel',round(linspace(-round(size(waveForms(:,handles.subset{1}),1)/2),...
round(size(waveForms(:,handles.subset{1}),1)/2),5)/(double(samplingRate)/1000),2),'TickDir','out');
% ordinateLabels=str2num(get(gca,'YTickLabel'))/4;
% set(gca,'YTickLabel',num2str(ordinateLabels));
% legend('Unclustered waveforms','location','southeast')
axis('tight');box off;
xlabel('Time (ms)');
ylabelh=ylabel('Voltage (\muV)');
set(ylabelh,'interpreter','tex');
set(gca,'Color','white','FontSize',10,'FontName','Calibri');
%% Plot clusters
function handles=Plot_Sorted_WF(handles)
electrodeNum=get(handles.SelectElectrode_LB,'value');
waveForms=handles.Spikes.HandSort.Waveforms{electrodeNum};
unitsIdx=handles.Spikes.HandSort.Units{electrodeNum};
samplingRate=handles.Spikes.HandSort.samplingRate(electrodeNum,1);
% selected unit ids
axes(handles.SortedUnits_Axes); hold on;%colormap lines; cmap=colormap;
cla(handles.SortedUnits_Axes);
set(handles.SortedUnits_Axes,'Visible','on');
if get(handles.ShowAllUnits_RB,'value') %all units
unitID=ReturnUnits(handles.SelectUnit_LB);
selectedUnitsListIdx=find(unitID>0);
selectedUnits=unitID(selectedUnitsListIdx);
else %or selected units
unitID=ReturnUnits(handles.SelectUnit_LB);
if unitID==0
return;
end
selectedUnitsListIdx=get(handles.SelectUnit_LB,'value');
if isempty(selectedUnitsListIdx) & ~isempty(unitID)
set(handles.SelectUnit_LB,'value',1);
selectedUnitsListIdx=1;
end
if sum(~ismember(unique(unitsIdx(unitsIdx>=0)),unitID))>0
unitID=unique(unitsIdx);
end
if isempty(selectedUnitsListIdx) || selectedUnitsListIdx(end)>length(unitID)
selectedUnitsListIdx=length(unitID);
end
selectedUnits=unitID(selectedUnitsListIdx);
selectedUnitsListIdx=selectedUnitsListIdx(selectedUnits>0);
selectedUnits=selectedUnits(selectedUnits>0);
end
numWFtoPlot=str2double(get(handles.ShowHowManyWF_ET,'string'));
numUnits=nan(1,length(selectedUnits));
for unitP=1:length(selectedUnits)
numUnits(unitP)=sum(unitsIdx==selectedUnits(unitP));
%if there are too many waveforms to plot
if sum(unitsIdx==selectedUnits(unitP))>numWFtoPlot %then only plot subset of waveforms
subset=find(unitsIdx==selectedUnits(unitP));
handles.subset{selectedUnitsListIdx(unitP)}=subset(1:round(numUnits(unitP)/numWFtoPlot):end);
else
handles.subset{selectedUnitsListIdx(unitP)}=find(unitsIdx==selectedUnits(unitP));
end
%make sure waveforms can be plotted
if find(size(waveForms)==length(unitsIdx))==1
waveForms=waveForms'; %figure; hold on; plot(waveForms(:,1:10))
end
plot(waveForms(:,handles.subset{selectedUnitsListIdx(unitP)}),...
'linewidth',1,'Color',[handles.cmap(unitID(selectedUnitsListIdx(unitP)),:),0.4],...
'Tag',num2str(selectedUnits(unitP)));
%Change waveform tags from cluster number to unit ID
lineH=flipud(findobj(gca,'Type', 'line'));
skippedTags=0;
if unitP==1 %define keepTags
keepTags=cell(size(lineH,1),1);
end
for lineTag=1:size(lineH,1)
% check if it's the right cluster
if strcmp(lineH(lineTag).Tag,num2str(selectedUnits(unitP)))
%record Tags
keepTags{lineTag,1}=num2str(handles.subset{selectedUnitsListIdx(unitP)}(lineTag-skippedTags)); %Tag the unit ID
else
skippedTags=skippedTags+1;
end
end
% figure;hold on
% plot(lineH(lineTag).YData);
% plot(waveForms(:,handles.subset{selectedUnitsListIdx(unitP)}(lineTag-passedTags)))
end
%apply Tags
if exist('lineH','var')
for lineTag=1:size(lineH,1)
lineH(lineTag).Tag=keepTags{lineTag};
end
firstOfClus=[1, find(diff(cellfun(@(col) sum(col), {lineH.Color})))+1];
legH=legend(lineH(firstOfClus),{num2str(numUnits')},'location','southeast');
set(legH,'Box','Off','FontSize',7,'LineWidth',0.2,'Position',...
[0.54 legH.Position(2)+legH.Position(3)-0.01 0 0]);
end
set(gca,'Ylim',[min(min(waveForms)) max(max(waveForms))],'XTick',linspace(0,size(waveForms(:,handles.subset{selectedUnitsListIdx(unitP)}),1),5),...
'XTickLabel',round(linspace(-round(size(waveForms(:,handles.subset{selectedUnitsListIdx(unitP)}),1)/2),...
round(size(waveForms(:,handles.subset{selectedUnitsListIdx(unitP)}),1)/2),5)/(double(samplingRate)/1000),2),...
'TickDir','out');
axis('tight');box off;
xlabel('Time (ms)');
ylabel('Voltage (\muV)');
set(gca,'Color','white','FontSize',10,'FontName','Calibri');
hold off
%% Plot mean waveforms
function Plot_Mean_WF(handles)
electrodeNum=get(handles.SelectElectrode_LB,'value');
waveForms=handles.Spikes.HandSort.Waveforms{electrodeNum};
unitsIdx=handles.Spikes.HandSort.Units{electrodeNum};
samplingRate=handles.Spikes.HandSort.samplingRate(electrodeNum,1);
axes(handles.MeanSortedUnits_Axes); hold on;%colormap lines;
cla(handles.MeanSortedUnits_Axes);
set(handles.MeanSortedUnits_Axes,'Visible','on');
if get(handles.ShowAllUnits_RB,'value')
unitID=ReturnUnits(handles.SelectUnit_LB);
selectedUnitsListIdx=find(unitID>0);
selectedUnits=unitID(selectedUnitsListIdx);
else
unitID=ReturnUnits(handles.SelectUnit_LB);
if unitID==0
return;
end
selectedUnitsListIdx=get(handles.SelectUnit_LB,'value');
if isempty(selectedUnitsListIdx) || selectedUnitsListIdx(end)>length(unitID)
selectedUnitsListIdx=length(unitID);
end
selectedUnits=unitID(selectedUnitsListIdx);
end
numWFtoPlot=str2double(get(handles.ShowHowManyWF_ET,'string'));
for unitP=1:length(selectedUnits)
if selectedUnits(unitP)==0
continue
end
%if subset is not defined
if size(handles.subset,2)<selectedUnitsListIdx(unitP) || isempty(handles.subset{selectedUnitsListIdx(unitP)})
if sum(unitsIdx==selectedUnits(unitP))>numWFtoPlot %then only plot subset of waveforms
subset=find(unitsIdx==selectedUnits(unitP));
handles.subset{selectedUnitsListIdx(unitP)}=subset(1:round(sum(unitsIdx==selectedUnits(unitP))/numWFtoPlot):end);
else
handles.subset{selectedUnitsListIdx(unitP)}=find(unitsIdx==selectedUnits(unitP));
end
end
selectWF=single(waveForms(:,unitsIdx==selectedUnits(unitP))');
if ~isnan(mean(selectWF))
lineh(unitP)=plot(mean(selectWF),'linewidth',2,'Color',[handles.cmap(unitID(selectedUnitsListIdx(unitP)),:),0.7]);
wfSEM=std(selectWF)/ sqrt(size(selectWF,2)); %standard error of the mean
wfSEM = wfSEM * 1.96; % 95% of the data will fall within 1.96 standard deviations of a normal distribution
patch([1:length(wfSEM),fliplr(1:length(wfSEM))],...
[mean(selectWF)-wfSEM,fliplr(mean(selectWF)+wfSEM)],...
handles.cmap(unitID(selectedUnitsListIdx(unitP)),:),'EdgeColor','none','FaceAlpha',0.2);
%duplicate mean unit waveform over unsorted plot
% plot(handles.UnsortedUnits_Axes,mean(selectWF),'linewidth',2,'Color',handles.cmap(unitP,:));
if unitP==1
delete(findobj(handles.UnsortedUnits_Axes,'Type', 'patch'));
end
patch([1:length(wfSEM),fliplr(1:length(wfSEM))],...
[mean(selectWF)-wfSEM,fliplr(mean(selectWF)+wfSEM)],...
handles.cmap(unitID(selectedUnitsListIdx(unitP)),:),'EdgeColor','none','FaceAlpha',0.5,'Parent', handles.UnsortedUnits_Axes);
set(handles.UnsortedUnits_Axes,'Color','white','FontSize',10,'FontName','Calibri');
end
end
set(gca,'XTick',linspace(0,size(waveForms(:,handles.subset{selectedUnitsListIdx(unitP)}),1),5),...
'XTickLabel',round(linspace(-round(size(waveForms(:,handles.subset{selectedUnitsListIdx(unitP)}),1)/2),...
round(size(waveForms(:,handles.subset{selectedUnitsListIdx(unitP)}),1)/2),5)/(double(samplingRate)/1000),2),'TickDir','out');
% ordinateLabels=str2num(get(gca,'YTickLabel'))/4;
% set(gca,'YTickLabel',num2str(ordinateLabels));
if exist('selectWF','var')
legH=legend(lineh,{num2str(selectedUnits)},'location','southeast');
set(legH,'Box','Off');
end
axis('tight');box off;
xlabel('Time (ms)');
ylabel('Voltage (\muV)');
set(gca,'Color','white','FontSize',10,'FontName','Calibri');
hold off
%% Plot traces
function dataExcerpt=DisplayTraces(handles)
electrodeNum=get(handles.SelectElectrode_LB,'value');
if isa(handles.traces,'memmapfile')
% exwdw=[((30000*106)-15000)*28:((30000*106)+15000)*28-1];
% % dataExcerpt=rawData.Data(exwdw);
% dataExcerpt=handles.traces.Data(exwdw);
% dataExcerpt=reshape(dataExcerpt,[28 30000]);
% figure;
% plot(dataExcerpt(10,:))
% title('el10 106')
winIdxStart=((handles.tracesInfo.excerptLocation-...
double(handles.tracesInfo.excerptSize))*numel(handles.rec_info.exportedChan))+1;
if mod(winIdxStart,numel(handles.rec_info.exportedChan))~=1 %set window index to correct point in data vector
winIdxStart=winIdxStart-...
mod(winIdxStart,numel(handles.rec_info.exportedChan))-...
numel(handles.rec_info.exportedChan)+1; % set index loc to first electrode
% (numel(handles.rec_info.exportedChan) - electrodeNum); % set index loc to selected electrode
end
winIdxEnd=winIdxStart+...
(2*handles.tracesInfo.excerptSize*numel(handles.rec_info.exportedChan));
excerptWindow=winIdxStart:winIdxEnd-1;
if size(excerptWindow,2)>(2*handles.tracesInfo.excerptSize*...
numel(handles.rec_info.exportedChan)) %for some reason
excerptWindow=excerptWindow(1:end-(size(excerptWindow,2)-...
(2*handles.tracesInfo.excerptSize*numel(handles.rec_info.exportedChan))));
end
dataExcerpt=handles.traces.Data(excerptWindow);
dataExcerpt=reshape(dataExcerpt,[numel(handles.rec_info.exportedChan)...
handles.tracesInfo.excerptSize*2]);
% foo=handles.traces.Data;
% foo=reshape(foo,[numel(handles.rec_info.exportedChan)...
% size(foo,1)/numel(handles.rec_info.exportedChan)]);
else
excerptWindow=handles.tracesInfo.excerptLocation-...
handles.tracesInfo.excerptSize:handles.tracesInfo.excerptLocation+handles.tracesInfo.excerptSize-1;
dataExcerpt=handles.traces.(handles.tracesInfo.name)(:,excerptWindow);
end
if handles.tracesInfo.preproc==0 % raw data is presumed bandpassed filtered at this point
preprocOption={'CAR','all'};
dataExcerpt=PreProcData(dataExcerpt,handles.rec_info.samplingRate,preprocOption);
end
dataExcerpt=int32(dataExcerpt(electrodeNum,:));
axes(handles.TimeRaster_Axes);
cla(handles.TimeRaster_Axes);
set(handles.TimeRaster_Axes,'Visible','on');
plot(handles.TimeRaster_Axes,dataExcerpt,'k','linewidth',0.1); hold on;
% threshold
if isfield(handles.rec_info,'threshold')
threshold=str2double(handles.rec_info.threshold);
plot(ones(1,size(dataExcerpt,2))*threshold*mad(single(dataExcerpt)),'--','Color',[0 0 0 0.3]);
plot(ones(1,size(dataExcerpt,2))*-threshold*mad(single(dataExcerpt)),'--','Color',[0 0 0 0.3]);
else
% threshold=8;
end
hold off;
timeLabels=round(linspace(round(handles.tracesInfo.excerptLocation-...
handles.tracesInfo.excerptSize)/(handles.rec_info.samplingRate/1000),...
round(handles.tracesInfo.excerptLocation+handles.tracesInfo.excerptSize)/...
(handles.rec_info.samplingRate/1000),4)./1000,3); % duration(X,'Format','h')
set(handles.TimeRaster_Axes,'xtick',round(linspace(0,max(get(handles.TimeRaster_Axes,'xtick')),4)),...
'xticklabel',timeLabels); %,'TickDir','out');
set(handles.TimeRaster_Axes,'ytick',[],'yticklabel',[]); %'ylim'
axis('tight');box off;
set(handles.TimeRaster_Axes,'Color','white','FontSize',12,'FontName','calibri');
% if isa(handles.traces,'memmapfile')