function Skuld(varargin)
% Make the entire GUI for Skuld
% ----------------------------------------------------
% Optional argument can be a preset filename, which would be directly
% loaded into the GUI upon start-up.
% Make figure:
f=figure('Units','pixels',...
'Position',[350 100 900 650],...
'Resize','off',...
'Renderer','zbuffer',...
'NumberTitle','off',...
'Menubar','none',...
'Toolbar','none',...
'Name','Skuld',...
'DeleteFcn',@Skuld_DeleteFcn);
% Define axes
handles.axsMain = axes('Units','pixels',...
'Position',[100 150 400 400]);
% Define panels
% Panel Network information
handles.pnlNwkInf = uipanel('Units','pixels',...
'Position',[600 520 275 100],...
'BackgroundColor',get(gcf,'Color'),...
'Title','Network information');
handles.lblCllTtl_fixed = uicontrol('Parent',handles.pnlNwkInf,...
'Style','text',...
'Units','pixels',...
'Position',[10 50 165 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','Number of cells:',...
'HorizontalAlignment','right');
handles.lblCllTtl = uicontrol('Parent',handles.pnlNwkInf,...
'Style','text',...
'Units','pixels',...
'Position',[180 50 50 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','--',...
'HorizontalAlignment','left');
handles.lblTypTtl_fixed = uicontrol('Parent',handles.pnlNwkInf,...
'Style','text',...
'Units','pixels',...
'Position',[10 30 165 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','Number of celltypes:',...
'HorizontalAlignment','right');
handles.lblTypTtl = uicontrol('Parent',handles.pnlNwkInf,...
'Style','text',...
'Units','pixels',...
'Position',[180 30 50 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','--',...
'HorizontalAlignment','left');
handles.lblConTtl_fixed = uicontrol('Parent',handles.pnlNwkInf,...
'Style','text',...
'Units','pixels',...
'Position',[10 10 165 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','Number of connections:',...
'HorizontalAlignment','right');
handles.lblConTtl = uicontrol('Parent',handles.pnlNwkInf,...
'Style','text',...
'Units','pixels',...
'Position',[180 10 50 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','--',...
'HorizontalAlignment','left');
% Panel Cell information
handles.pnlCllInf = uipanel('Units','pixels',...
'Position',[600 50 275 450],...
'BackgroundColor',get(gcf,'Color'),...
'Title','Cell information');
handles.lblCllId_fixed = uicontrol('Parent',handles.pnlCllInf,...
'Style','text',...
'Units','pixels',...
'Position',[10 410 165 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','Cell ID:',...
'HorizontalAlignment','right');
handles.lblCllId = uicontrol('Parent',handles.pnlCllInf,...
'Style','text',...
'Units','pixels',...
'Position',[180 410 50 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','--',...
'HorizontalAlignment','left');
handles.lblCllTyp_fixed = uicontrol('Parent',handles.pnlCllInf,...
'Style','text',...
'Units','pixels',...
'Position',[10 390 165 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','Type:',...
'HorizontalAlignment','right');
handles.lblCllTyp = uicontrol('Parent',handles.pnlCllInf,...
'Style','text',...
'Units','pixels',...
'Position',[180 390 50 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','--',...
'HorizontalAlignment','left');
handles.lblIncCon_fixed = uicontrol('Parent',handles.pnlCllInf,...
'Style','text',...
'Units','pixels',...
'Position',[10 370 165 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','Connections in:',...
'HorizontalAlignment','right');
handles.lblIncCon = uicontrol('Parent',handles.pnlCllInf,...
'Style','text',...
'Units','pixels',...
'Position',[180 370 50 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','--',...
'HorizontalAlignment','left');
handles.axsIncCon = axes('Parent',handles.pnlCllInf,...
'Units','pixels',...
'Position',[10 205 255 160],...
'Visible','off');
handles.lblOutCon_fixed = uicontrol('Parent',handles.pnlCllInf,...
'Style','text',...
'Units','pixels',...
'Position',[10 180 165 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','Connections out:',...
'HorizontalAlignment','right');
handles.lblOutCon = uicontrol('Parent',handles.pnlCllInf,...
'Style','text',...
'Units','pixels',...
'Position',[180 180 50 20],...
'BackgroundColor',get(gcf,'Color'),...
'String','--',...
'HorizontalAlignment','left');
handles.axsOutCon = axes('Parent',handles.pnlCllInf,...
'Units','pixels',...
'Position',[10 10 255 160],...
'Visible','off');
% Menubar (in Depth-First-Search order)
% File menu
handles.mnFile = uimenu('Parent',gcf,...
'Label','File');
handles.mnLoadData = uimenu('Parent',handles.mnFile,...
'Label','Load data',...
'Callback',@mnLoadData_Callback);
handles.mnClose = uimenu('Parent',handles.mnFile,...
'Label','Close',...
'Callback',@mnClose_Callback);
% Cell menu
handles.mnCell = uimenu('Parent',gcf,...
'Label','Cell');
handles.mnSltCll = uimenu('Parent',handles.mnCell,...
'Label','Select cell',...
'Callback',@mnSltCll_Callback);
handles.mnShwVm = uimenu('Parent',handles.mnCell,...
'Separator','on',...
'Label','Vm trace',...
'Callback',@mnShwVm_Callback);
handles.mnCllISI = uimenu('Parent',handles.mnCell,...
'Label','ISI distribution',...
'Callback',@mnCllISI_Callback);
handles.mnAtSpec = uimenu('Parent',handles.mnCell,...
'Label','Auto spectrum',...
'Callback',@mnAtSpec_Callback);
handles.mnCllRst = uimenu('Parent',handles.mnCell,...
'Label','Raster plot',...
'Callback',@mnCllRst_Callback);
handles.mnIncCon = uimenu('Parent',handles.mnCell,...
'Separator','On',...
'Label','Incoming connections',...
'Callback',@mnIncCon_Callback);
handles.mnIncCll = uimenu('Parent',handles.mnCell,...
'Label','Incoming cells',...
'Callback',@mnIncCll_Callback);
handles.mnOutCon = uimenu('Parent',handles.mnCell,...
'Label','Outgoing connections',...
'Callback',@mnOutCon_Callback);
handles.mnOutCll = uimenu('Parent',handles.mnCell,...
'Label','Outgoing cells',...
'Callback',@mnOutCll_Callback);
% Population menu
handles.mnPopInf = uimenu('Parent',gcf,...
'Label','Population');
handles.mnMnVm = uimenu('Parent',handles.mnPopInf,...
'Label','Mean Vm',...
'Callback',@mnMnVm_Callback);
handles.mnSpkBns = uimenu('Parent',handles.mnPopInf,...
'Label','Firing rates',...
'Callback',@mnSpkBns_Callback);
handles.mnPopRst = uimenu('Parent',handles.mnPopInf,...
'Label','Raster plot',...
'Callback',@mnPopRst_Callback);
% Network menu
handles.mnNetwork= uimenu('Parent',gcf,...
'Label','Network');
handles.mnShwEEG = uimenu('Parent',handles.mnNetwork,...
'Label','Show EEG/LFP',...
'Callback',@mnShwEEG_Callback);
% Window menu
handles.mnWindow = uimenu('Parent',gcf,...
'Label','Window');
handles.mnCloseAll = uimenu('Parent',handles.mnWindow,...
'Label','Close all plots',...
'Callback',@mnCloseAll_Callback);
% Help menu
handles.mnHelp = uimenu('Parent',gcf,...
'Label','Help');
handles.mnDoc = uimenu('Parent',handles.mnHelp,...
'Label','Documentation',...
'Callback',@mnDoc_Callback);
handles.mnAbt = uimenu('Parent',handles.mnHelp,...
'Label','About Skuld',...
'Callback',@mnAbt_Callback);
% Toolbar
% read icons first
iconDir = fullfile(matlabroot,'toolbox','matlab','icons');
iconOpen = load(fullfile(iconDir,'opendoc.mat'));
iconRot = load(fullfile(iconDir,'rotate.mat'));
% Make objects
handles.tbrToolbar = uitoolbar('Parent',gcf);
handles.tbrLoadData = uipushtool('Parent',handles.tbrToolbar,...
'CData',iconOpen.cdata,...
'TooltipString','Load Data',...
'ClickedCallback',@tbrLoadData_ClickedCallback);
handles.tbrRotate = uitoggletool('Parent',handles.tbrToolbar,...
'CData',iconRot.cdata,...
'TooltipString','Rotate 3D',...
'OnCallback','rotate3d on',...
'OffCallback','rotate3d off');
% ----------------------------------------------------
% Choose default command line output for Skuld
% handles.FilePaths = {};
% handles.Network = {};
% handles.Data = {};
% handles.CellTypesRaw = {};
handles.ChangedNetwork = 0;
handles.ChangedData = 0;
handles.NeuronSelected = NaN;
handles.SecondaryPlots.LinkViewHandles = [];
handles.SecondaryPlots.FigureHandles = [];
handles.MenuOptions.CellSelected = [handles.mnShwVm, handles.mnCllISI, handles.mnAtSpec, handles.mnCllRst];
handles.MenuOptions.SpikeData = [handles.mnCllISI, handles.mnAtSpec, handles.mnCllRst, ...
handles.mnSpkBns, handles.mnPopRst];
handles.MenuOptions.VmData = [handles.mnShwVm, handles.mnMnVm];
handles = InitializeMenu(handles);
% Update handles structure
guidata(gcf, handles);
% Check if preset file should be loaded:
if(~isempty(varargin))
LoadData(gcf, varargin{1})
end
% --- Executes during object deletion, before destroying properties.
function Skuld_DeleteFcn(hObject, eventdata, handles)
% hObject handle to Skuld (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
close(handles.SecondaryPlots.FigureHandles);
% --------------------------------------------------------- FILE MENU ---
function mnLoadData_Callback(hObject, eventdata, handles)
% hObject handle to mnLoadData (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
LoadData(gcbf);
function mnClose_Callback(hObject, eventdata, handles)
% hObject handle to mnClose (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDAT A)
close(gcf);
% --------------------------------------------------------- CELL MENU ---
function mnSltCll_Callback(hObject, eventdata, handles)
% hObject handle to mnSltCll (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcbo);
% Popup a dialog to enter the cell number
RequestedID = str2double(inputdlg('Enter a cell ID','Select cell'));
% Check if a number has been entered
if(~isempty(RequestedID) && ~isnan(RequestedID))
% Make an integer of the number
ID = floor(RequestedID);
% Determine if the value is within range
if(ID>0 && ID<=handles.Data.nCells)
% Deselect previous cell (if necessary)
if(~isnan(handles.NeuronSelected))
handles = DeselectNeuron(handles.NeuronSelected,handles);
end
% Select new cell
handles.NeuronSelected = ID;
handles = SelectNeuron(ID,handles);
guidata(hObject,handles);
end
end
function mnShwVm_Callback(hObject, eventdata, handles)
% hObject handle to mnShwVm (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
% Prepare data
time = (1:(handles.Data.Vm.Duration*handles.Data.Vm.SamplingRate))/handles.Data.Vm.SamplingRate;
Vm = handles.Data.Vm.Data(:,handles.NeuronSelected);
% Call window and plot
[Fig, Ax] = MakeSecondaryFigure(gcbf);
AddFilterMenu(Fig); % Adds filter optionality to this figure
AddPlaySoundToolbar(Fig); % Adds button to play recording
plot(time,Vm);
title(['Membrane potential of cell ' num2str(handles.NeuronSelected)]);
xlabel('time (s)');
ylabel('Vm (V)');
set(Ax,'YLimMode','manual');
% Obtain handles of the new figure to store data in the figure
FigHandles = guidata(Fig);
% Store data
FigHandles.Data.T = time;
FigHandles.Data.Y = Vm;
FigHandles.Data.SamplingRate = handles.Data.Vm.SamplingRate;
% Store filters
FigHandles.Filter.Low = [];
FigHandles.Filter.High = [];
guidata(Fig,FigHandles);
% Process new handles
handles.SecondaryPlots.LinkViewHandles = [handles.SecondaryPlots.LinkViewHandles Ax];
handles.SecondaryPlots.FigureHandles = [handles.SecondaryPlots.FigureHandles Fig];
guidata(hObject,handles);
function mnCllISI_Callback(hObject, eventdata, handles)
% hObject handle to mnShwVm (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
[t, pd, mean, cv, tot_sp] = ISIdist(handles.Data.NeuronSpikes.Data{handles.NeuronSelected},2,200);
if(~isempty(pd))
Fig=figure;
Ax=axes;
bar(Ax,t,pd);
title(Ax,'ISI-distribution');
xlabel(Ax,'interspike interval [msec]');
ylabel(Ax,'probability per bin');
meant = sprintf('mean = %.3g [msec]',mean);
cvt = sprintf('cv = %.2g ',cv);
totspkt = sprintf('number of spikes = %g',tot_sp);
text(0.4,0.97,totspkt,'Units','normalized','Parent',Ax);
text(0.4,0.90,meant,'Units','normalized','Parent',Ax);
text(0.4,0.83,cvt,'Units','normalized','Parent',Ax);
handles.SecondaryPlots.FigureHandles = [handles.SecondaryPlots.FigureHandles Fig];
end
guidata(hObject,handles);
function mnAtSpec_Callback(hObject, eventdata, handles)
% hObject handle to mnShwVm (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
[Pxx,f,Fig] = AutoSpectrum_SpikeTrain(handles.Data.NeuronSpikes.Data{handles.NeuronSelected},180,1);
if(~isempty(Fig))
handles.SecondaryPlots.FigureHandles = [handles.SecondaryPlots.FigureHandles Fig];
end
guidata(hObject,handles);
function mnCllRst_Callback(hObject, eventdata, handles)
% hObject handle to mnShwRst (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
if(handles.Options.Network)
% Prepare data
% Identify cell IDs first
IDsIn = find(handles.Data.Network.ConnectionMatrix(:,handles.NeuronSelected));
IDsOut = find(handles.Data.Network.ConnectionMatrix(handles.NeuronSelected,:));
IDs = [IDsIn(:); handles.NeuronSelected; IDsOut(:)];
% Determine corresponding delays next
ConnectionsIn = nonzeros(handles.Data.Network.ConnectionMatrix(IDsIn,handles.NeuronSelected));
ConnectionsOut = nonzeros(handles.Data.Network.ConnectionMatrix(handles.NeuronSelected,IDsOut));
if(handles.Options.NeuroSimNetwork)
Delays = [handles.Data.Network.ConnectionDetails.Delay(ConnectionsIn); 0; -handles.Data.Network.ConnectionDetails.Delay(ConnectionsOut)];
else
% No delays are present, set them all to zero:
Delays = zeros(length(IDs),1);
end
% Values along Y-axis for each ID
PlotLevel = 1+length(IDsIn)-(1:length(IDs));
else
IDs = 1:handles.Data.nCells;
PlotLevel = IDs;
Delays = zeros(size(IDs));
end
PlotHandles = zeros(size(IDs));
CumCell = cumsum(handles.Data.CellTypes.Number);
[Fig,Ax] = MakeSecondaryFigure(gcbf);
AddAlignRasterMenu(Fig);
% Make contextmenu that is required for cell information
cmnRasterCellInfo = uicontextmenu('Callback',@cmnRasterRequestInfo);
mnRasterCellID = uimenu('Parent',cmnRasterCellInfo,'Enable','Off');
hold on
for iID = 1:length(IDs)
SP = handles.Data.NeuronSpikes.Data{IDs(iID)};
if(~isempty(SP))
Type = find(CumCell>=IDs(iID),1); % Identify type of neuron
% PlotHandles(iID) = plot(SP,ones(size(SP))*(1+length(IDsIn)-iID),handles.Data.CellTypes.Symbol{Type}, ...
PlotHandles(iID) = plot(SP,ones(size(SP))*PlotLevel(iID),handles.Data.CellTypes.Symbol{Type}, ...
'MarkerFaceColor',handles.Data.CellTypes.Color(Type,:),...
'MarkerSize',4,...
'MarkerEdgeColor','none',...
'UIContextMenu',cmnRasterCellInfo);
end
end
title(['Rasterplot of cell ' num2str(handles.NeuronSelected) ' and connecting cells']);
xlabel('time (s)');
set(Ax,'YLimMode','manual');
% Process new handles for main struct
handles.SecondaryPlots.LinkViewHandles = [handles.SecondaryPlots.LinkViewHandles Ax];
handles.SecondaryPlots.FigureHandles = [handles.SecondaryPlots.FigureHandles Fig];
guidata(hObject,handles);
% Process handles for this figure only
FigureHandles = guidata(Fig);
FigureHandles.Data.PlotCellIDs = IDs;
FigureHandles.Data.PlotHandles = PlotHandles;
FigureHandles.Data.Delays = Delays;
guidata(Fig,FigureHandles);
function mnIncCon_Callback(hObject, eventdata, handles)
% hObject handle to mnIncCon (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
handles.View.IncomingConnections = 1 - handles.View.IncomingConnections;
if(handles.View.IncomingConnections == 1)
set(handles.mnIncCon,'Checked','on');
if(~isnan(handles.NeuronSelected))
handles.PlotHandles.IncomingConnections = PlotIncomingConnections(handles.NeuronSelected);
end
else
set(handles.mnIncCon,'Checked','off');
try,
delete(handles.PlotHandles.IncomingConnections);
handles.PlotHandles.IncomingConnections = [];
end
end
guidata(hObject,handles);
function mnIncCll_Callback(hObject, eventdata, handles)
% hObject handle to mnIncCll (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
handles.View.IncomingCells = 1 - handles.View.IncomingCells;
if(handles.View.IncomingCells == 1)
set(handles.mnIncCll,'Checked','on');
if(~isnan(handles.NeuronSelected))
handles.PlotHandles.IncomingCells = PlotIncomingCells(handles.NeuronSelected);
end
else
set(handles.mnIncCll,'Checked','off');
try,
set(handles.PlotHandles.IncomingCells,'MarkerEdgeColor','none');
handles.PlotHandles.IncomingCells = [];
end
end
guidata(hObject,handles);
function mnOutCon_Callback(hObject, eventdata, handles)
% hObject handle to mnOutCon (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
handles.View.OutgoingConnections = 1 - handles.View.OutgoingConnections;
if(handles.View.OutgoingConnections == 1)
set(handles.mnOutCon,'Checked','on');
if(~isnan(handles.NeuronSelected))
handles.PlotHandles.OutgoingConnections = PlotOutgoingConnections(handles.NeuronSelected);
end
else
set(handles.mnOutCon,'Checked','off');
try,
delete(handles.PlotHandles.OutgoingConnections);
handles.PlotHandles.OutgoingConnections = [];
end
end
guidata(hObject,handles);
function mnOutCll_Callback(hObject, eventdata, handles)
% hObject handle to mnOutCll (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
handles.View.OutgoingCells = 1 - handles.View.OutgoingCells;
if(handles.View.OutgoingCells == 1)
set(handles.mnOutCll,'Checked','on');
if(~isnan(handles.NeuronSelected))
handles.PlotHandles.OutgoingCells = PlotOutgoingCells(handles.NeuronSelected);
end
else
set(handles.mnOutCll,'Checked','off');
try,
set(handles.PlotHandles.OutgoingCells,'MarkerEdgeColor','none');
handles.PlotHandles.OutgoingCells = [];
end
end
guidata(hObject,handles);
% --------------------------------------------------- POPULATION MENU ---
function mnMnVm_Callback(hObject, eventdata, handles)
% hObject handle to mnMnVm (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
% Request data to plot
if(length(handles.Data.CellTypes.Name)>1)
[PlotTypes,Ok] = listdlg('ListString',handles.Data.CellTypes.Name,...
'InitialValue',[1 2],'Name','Mean Vm',...
'PromptString','Select populations to plot','ListSize',[200 180]);
else
PlotTypes = [1];
Ok = 1;
end
if(Ok)
% Request data
CumCell = cumsum([0 handles.Data.CellTypes.Number]);
for iType = 1:length(PlotTypes)
PlotData(:,iType) = mean(handles.Data.Vm.Data(:,[CumCell(PlotTypes(iType))+(1:handles.Data.CellTypes.Number(PlotTypes(iType)))]),2);
end
time = (1:(handles.Data.Vm.Duration*handles.Data.Vm.SamplingRate))/handles.Data.Vm.SamplingRate;
% Call window and plot
[Fig, Ax] = MakeSecondaryFigure(gcbf);
AddFilterMenu(Fig); % Adds filter optionality to this figure
plot(time,PlotData);
title('Mean membrane potential of populations');
xlabel('time (s)');
ylabel('Mean Vm (V)');
set(Ax,'YLimMode','manual');
legend({handles.Data.CellTypes.Name{PlotTypes}});
% Obtain handles of the new figure to store data in the figure
FigHandles = guidata(Fig);
% Store data
FigHandles.Data.T = time;
FigHandles.Data.Y = PlotData;
FigHandles.Data.SamplingRate = handles.Data.Vm.SamplingRate;
% Store filters
FigHandles.Filter.Low = [];
FigHandles.Filter.High = [];
guidata(Fig,FigHandles);
% Process new handles
handles.SecondaryPlots.LinkViewHandles = [handles.SecondaryPlots.LinkViewHandles Ax];
handles.SecondaryPlots.FigureHandles = [handles.SecondaryPlots.FigureHandles Fig];
guidata(hObject,handles);
end
function mnSpkBns_Callback(hObject, eventdata, handles)
% hObject handle to mnSpkBns (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
if(length(handles.Data.CellTypes.Name)>1)
[PlotTypes,Ok] = listdlg('ListString',handles.Data.CellTypes.Name,...
'InitialValue',[1 2],'Name','Mean Vm',...
'PromptString','Select populations to plot','ListSize',[200 180]);
else
PlotTypes = [1];
Ok = 1;
end
% Cancel execution if 'cancel' is pressed
if(Ok==0)
return;
end
% Ask for time resulution of the bins
BinTime = str2double(inputdlg('Enter a bin size in ms','Spike bins',1,{'1'}));
if(Ok && ~isempty(BinTime) && ~isnan(BinTime))
% Determine binsize in datapoints
BinSize = BinTime/1000; % Conversion from ms
% Make empty array
Bins = zeros(ceil(handles.Data.NeuronSpikes.Duration/BinSize),length(PlotTypes));
BinCenters = (0.5:size(Bins,1))*BinSize;
% Request data
CumCell = cumsum([0 handles.Data.CellTypes.Number]);
for iType = 1:length(PlotTypes)
% for iCell = [CumCell(PlotTypes(iType))+(1:handles.Data.CellTypes.Number(PlotTypes(iType)))]
% BinIDs = ceil(handles.Data.NeuronSpikes.Data{iCell}/BinSize);
% Bins(BinIDs,iType) = Bins(BinIDs,iType)+1;
% end
% Bins(:,iType) = Bins(:,iType)/(handles.Data.CellTypes.Number(iType)*BinTime/1000);
CellIDs = CumCell(PlotTypes(iType))+(1:handles.Data.CellTypes.Number(PlotTypes(iType)));
SpikeTimes = cell2mat({handles.Data.NeuronSpikes.Data{CellIDs}}');
Bins(:,iType) = hist(SpikeTimes,BinCenters)/(handles.Data.CellTypes.Number(iType)*BinTime/1000);
end
time = BinSize*(1:ceil(handles.Data.NeuronSpikes.Duration/BinSize));
% Call window and plot
[Fig, Ax] = MakeSecondaryFigure(gcbf);
% plot(time',Bins);
plot(BinCenters(:),Bins);
title('Acitivity of populations');
xlabel('time (s)');
ylabel('Population firing rate');
set(Ax,'YLimMode','manual');
legend({handles.Data.CellTypes.Name{PlotTypes}});
% Process new handles
handles.SecondaryPlots.LinkViewHandles = [handles.SecondaryPlots.LinkViewHandles Ax];
handles.SecondaryPlots.FigureHandles = [handles.SecondaryPlots.FigureHandles Fig];
guidata(hObject,handles);
end
function mnPopRst_Callback(hObject, eventdata, handles)
% hObject handle to mnShwRst (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
% Request data to plot
if(length(handles.Data.CellTypes.Name)>1)
[PlotTypes,Ok] = listdlg('ListString',handles.Data.CellTypes.Name,...
'InitialValue',[1 2],'Name','Mean Vm',...
'PromptString','Select populations to plot','ListSize',[200 180]);
else
PlotTypes = [1];
Ok = 1;
end
if(Ok)
PlotHandles = zeros(sum(handles.Data.CellTypes.Number(PlotTypes)),1);
IDs = zeros(size(PlotHandles));
CumCell = [0 cumsum(handles.Data.CellTypes.Number)];
[Fig,Ax] = MakeSecondaryFigure(gcbf);
hold on
% Make contextmenu that is required for cell information
cmnRasterCellInfo = uicontextmenu('Callback',@cmnRasterRequestInfo);
mnRasterCellID = uimenu('Parent',cmnRasterCellInfo,'Enable','Off');
PlotID = 1;
for Type = PlotTypes
for iCell = (1:handles.Data.CellTypes.Number(Type))+CumCell(Type)
SP = handles.Data.NeuronSpikes.Data{iCell};
if(~isempty(SP))
PlotHandles(PlotID) = plot(SP,ones(size(SP))*PlotID,handles.Data.CellTypes.Symbol{Type}, ...
'MarkerFaceColor',handles.Data.CellTypes.Color(Type,:),...
'MarkerSize',4,...
'MarkerEdgeColor','none',...
'UIContextMenu',cmnRasterCellInfo);
end
IDs(PlotID) = iCell;
PlotID = PlotID+1;
end
end
title('Rasterplot of selected populations');
xlabel('time (s)');
set(Ax,'YLimMode','manual','YDir','reverse','YTickLabel',{});
% Process new handles for main struct
handles.SecondaryPlots.LinkViewHandles = [handles.SecondaryPlots.LinkViewHandles Ax];
handles.SecondaryPlots.FigureHandles = [handles.SecondaryPlots.FigureHandles Fig];
guidata(hObject,handles);
% Process handles for this figure only
FigureHandles = guidata(Fig);
FigureHandles.Data.PlotCellIDs = IDs;
FigureHandles.Data.PlotHandles = PlotHandles;
guidata(Fig,FigureHandles);
end
% ------------------------------------------------------ NETWORK MENU ---
function mnShwEEG_Callback(hObject, eventdata, handles)
% hObject handle to mnShwEEG (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
time = (1:(handles.Data.EEG.Duration*handles.Data.EEG.SamplingRate))/handles.Data.EEG.SamplingRate;
% Make axes and plot
[Fig,Ax] = MakeSecondaryFigure(gcbf);
AddFilterMenu(Fig); % Adds filter optionality to this figure
plot(time,handles.Data.EEG.Data);
title('Artificial EEG');
xlabel('time (s)');
ylabel('Electrode (V)');
set(Ax,'YLimMode','manual');
% Obtain handles of the new figure to store data in the figure
FigHandles = guidata(Fig);
% Store data
FigHandles.Data.T = time;
FigHandles.Data.Y = handles.Data.EEG.Data(:);
FigHandles.Data.SamplingRate = handles.Data.EEG.SamplingRate;
% Store filters
FigHandles.Filter.Low = [];
FigHandles.Filter.High = [];
guidata(Fig,FigHandles);
% Process new handles
handles.SecondaryPlots.LinkViewHandles = [handles.SecondaryPlots.LinkViewHandles Ax];
handles.SecondaryPlots.FigureHandles = [handles.SecondaryPlots.FigureHandles Fig];
guidata(hObject,handles);
% ------------------------------------------------------- WINDOW MENU ---
function mnCloseAll_Callback(hObject, eventdata, handles)
% hObject handle to mnCloseAll (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(gcf);
% This function closes all secondary plot windows
close(handles.SecondaryPlots.FigureHandles);
handles.SecondaryPlots.FigureHandles = [];
handles.SecondaryPlots.LinkViewHandles = [];
guidata(hObject,handles);
% --------------------------------------------------------- HELP MENU ---
function mnDoc_Callback(hObject, eventdata, handles)
% hObject handle to mnDoc (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
open Documentation.pdf
function mnAbt_Callback(hObject, eventdata, handles)
% hObject handle to mnAbt (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
figAbt = figure('Units','pixels',...
'Position',[700 700 300 450],...
'WindowStyle','modal',...
'NumberTitle','off',...
'Name','About',...
'Resize','off');
button = uicontrol('Style','pushbutton',...
'Units','pixels',...
'Position',[0 0 300 450],...
'CData',imread('About.png'),...
'Callback','close(gcf)');
% ----------------------------------------------------------- TOOLBAR ---
function tbrLoadData_ClickedCallback(hObject, eventdata, handles)
% hObject handle to tbrLoadData (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
LoadData(gcbf);
% ------------------------------------------------- GENERAL FUNCTIONS ---
function handles = InitializeMenu(handles)
% This function sets all checkmarks in the menu and adjusts the internal
% variables accordingly
set(handles.mnIncCon,'Checked','on');
handles.View.IncomingConnections = 1;
set(handles.mnOutCon,'Checked','on');
handles.View.OutgoingConnections = 1;
set(handles.mnIncCll,'Checked','off');
handles.View.IncomingCells = 0;
set(handles.mnOutCll,'Checked','off');
handles.View.OutgoingCells = 0;
% Some items are only available when data is loaded
set([handles.mnSltCll,handles.mnShwEEG],'Enable','Off');
set([handles.MenuOptions.CellSelected, handles.MenuOptions.SpikeData, handles.MenuOptions.VmData],'Enable','off');
function LoadData(MainFig,varargin)
handles = guidata(MainFig);
if(isempty(varargin))
handles.Load = LoadDataFig(MainFig);
else
handles.Load = LoadDataFig(MainFig,varargin{1});
end
uiwait(handles.Load);
handles = guidata(MainFig);
if(handles.DataLoaded == 0)
return
end
set([handles.MenuOptions.CellSelected,handles.MenuOptions.SpikeData, handles.MenuOptions.VmData],'Enable','Off');
% if handles.ChangedNetwork
% A new network is available
% Simplify the information of the network
handles.Data.CellTypes = InterpretCellTypes(handles.Data.CellTypesRaw);
% Update network info panel
set(handles.lblCllTtl,'String',num2str(handles.Data.nCells));
set(handles.lblTypTtl,'String',num2str(length(handles.Data.CellTypes.Name)));
handles.Options.Network = 0;
handles.Options.NeuroSimNetwork = 0;
if(isfield(handles.Data,'Network')) % A network is given
% Update network info panel
set(handles.lblCllTtl,'String',num2str(handles.Data.nCells));
set(handles.lblTypTtl,'String',num2str(length(handles.Data.CellTypes.Name)));
if(isfield(handles.Data.Network,'ConnectionDetails')) % NeuroSim network
handles.Options.NeuroSimNetwork = 1;
set(handles.lblConTtl,'String',num2str(sum(handles.Data.Network.ConnectionCount)));
else
% handles.Data.Network.ConnectionMatrix = (handles.Data.Network.ConnectionMatrix ~= 0);
set(handles.lblConTtl,'String',num2str(nnz(handles.Data.Network.ConnectionMatrix)));
end
handles.Options.Network = 1;
end
set(handles.mnSltCll,'Enable','On');
% Deselect current cell
if(~isnan(handles.NeuronSelected))
handles = DeselectNeuron(handles.NeuronSelected,handles);
end
% Plot the new network
handles.NeuronSelected = NaN; % No neuron can be selected in the new plot
handles.PlotHandles.Cells = PlotNewCells(handles.axsMain,handles.Data.CellPositions,handles.Data.CellTypes);
handles.ChangedNetwork = 0;
% end
% if handles.ChangedData
% A new dataset is available
% Close all secondary plots, because the data is not valid anymore
close(handles.SecondaryPlots.FigureHandles);
handles.SecondaryPlots.FigureHandles = [];
handles.SecondaryPlots.LinkViewHandles = [];
% Look at spike data
handles.Options.Vm = 0;
handles.Options.NeuronSpikes = 0;
if(isfield(handles.Data,'Vm'))
% Vm is given
% Determine the SpikeTimes of the System
handles.Data.NeuronSpikes.Data = Vm2NeuronSpikes(handles.Data.Vm.Data,handles.Data.Vm.Threshold,handles.Data.Vm.SamplingRate);
handles.Data.NeuronSpikes.Duration = handles.Data.Vm.Duration;
handles.Options.Vm = 1;
handles.Options.NeuronSpikes = 1;
set([handles.MenuOptions.SpikeData, handles.MenuOptions.VmData],'Enable','On');
elseif(isfield(handles.Data,'SpikeTimes'))
% Spike times are given
handles.Data.NeuronSpikes.Data = SpikeTimes2NeuronSpikes(handles.Data.SpikeTimes,handles.Data.nCells);
handles.Data.NeuronSpikes.Duration = max(handles.Data.SpikeTimes(:,1));
handles.Options.NeuronSpikes = 1;
set(handles.MenuOptions.SpikeData,'Enable','On');
else
% No spike data
try
handles.Data = rmfield(handles.Data,'NeuronSpikes');
end
end
handles.Options.EEG = 0;
if(isfield(handles.Data,'EEG'))
handles.Options.EEG = 1;
set(handles.mnShwEEG,'Enable','On');
end
handles.ChangedData = 0;
% end
set(handles.MenuOptions.CellSelected,'Enable','Off');
guidata(MainFig,handles);
function CellTypes = InterpretCellTypes(Raw)
% This functions returns a struct containing the information of the Raw
% CellTypes, which is formated in a Nx6 cell array
nType = size(Raw,1);
CellTypes.Show = [Raw{:,1}];
CellTypes.Name = {Raw{:,2}};
CellTypes.Number = [Raw{:,3}];
CellTypes.EIType = {Raw{:,4}};
CellTypes.Symbol = {Raw{:,5}};
for iType = 1:nType
CellTypes.Color(iType,:) = sscanf(Raw{iType,6},'[%f %f %f]',3);
end
% -------------------------------------------- NETWORK PLOT FUNCTIONS ---
function PlotHandles = PlotNewCells(axeshandle,CellPositions,CellTypes)
% This function plots all cells when a new network has to be plotted
axes(axeshandle);
reset(axeshandle);
cla
set(axeshandle,'ZDir','reverse');
hold on
box on
% daspect([1,1,15]);
PlotHandles = zeros(1,sum(CellTypes.Number));
nType = length(CellTypes.Show);
CumCell = cumsum([0 CellTypes.Number]);
for iType = 1:nType
for iCell = CumCell(iType)+(1:CellTypes.Number(iType))
PlotHandles(iCell) = plot3(CellPositions(iCell,1),CellPositions(iCell,2),CellPositions(iCell,3), ...
CellTypes.Symbol{iType},'MarkerFaceColor',CellTypes.Color(iType,:), 'MarkerEdgeColor','none',...
'ButtonDownFcn',@ClickCell);
end
end
axis vis3d
function PlotHandles = PlotOutgoingConnections(CellId)
% This function plots the lines for the outgoing synaptic connections from
% a single neuron given by CellId
% The handles to all the plotted lines are returned in an array
handles = guidata(gcbo);
ConnectIds = find(handles.Data.Network.ConnectionMatrix(CellId,:));
nConnect = length(ConnectIds);
PlotHandles = zeros(length(ConnectIds));
for iConnection = 1:nConnect
Cells = [CellId ConnectIds(iConnection)];
PlotHandles(iConnection) = plot3(handles.Data.CellPositions(Cells,1),handles.Data.CellPositions(Cells,2), ...
handles.Data.CellPositions(Cells,3),'k');
end
% Order the children of the axes such that the lines will be behind the
% other plots
Children = get(handles.axsMain,'Children');
Children = Children([(nConnect+1):end, 1:nConnect]);
set(handles.axsMain,'Children',Children);
function PlotHandles = PlotOutgoingCells(CellId)
% This function highlights the cells for the outgoing synaptic connections from
% a single neuron given by CellId
% The handles to all the plotted lines are returned in an array
handles = guidata(gcbo);
ConnectIds = find(handles.Data.Network.ConnectionMatrix(CellId,:));
PlotHandles = handles.PlotHandles.Cells(ConnectIds);
set(PlotHandles,'MarkerEdgeColor',[0 0 0]);
function PlotHandles = PlotIncomingConnections(CellId)
% This function plots the lines for the incoming synaptic connections from
% a single neuron given by CellId
% The handles to all the plotted lines are returned in an array
handles = guidata(gcbo);
ConnectIds = find(handles.Data.Network.ConnectionMatrix(:,CellId));
nConnect = length(ConnectIds);
PlotHandles = zeros(length(ConnectIds));
for iConnection = 1:nConnect
Cells = [CellId ConnectIds(iConnection)];
PlotHandles(iConnection) = plot3(handles.Data.CellPositions(Cells,1),handles.Data.CellPositions(Cells,2), ...
handles.Data.CellPositions(Cells,3),'c');
end
% Order the children of the axes such that the lines will be behind the
% other plots
Children = get(handles.axsMain,'Children');
Children = Children([(nConnect+1):end, 1:nConnect]);
set(handles.axsMain,'Children',Children);
function PlotHandles = PlotIncomingCells(CellId)
% This function highlights the cells for the outgoing synaptic connections from
% a single neuron given by CellId
% The handles to all the plotted lines are returned in an array
handles = guidata(gcbo);
ConnectIds = find(handles.Data.Network.ConnectionMatrix(:,CellId));
PlotHandles = handles.PlotHandles.Cells(ConnectIds);
set(PlotHandles,'MarkerEdgeColor',[0 1 1]);
function ClickCell(src,eventdata)
handles = guidata(gcbo);
% Check if a neuron was already selected
if isnan(handles.NeuronSelected)
% No neuron was selected before
handles.NeuronSelected = find(handles.PlotHandles.Cells == src);
handles = SelectNeuron(handles.NeuronSelected,handles);
else
% A neuron was selected already
% Check if it was the same or another
if handles.PlotHandles.Cells(handles.NeuronSelected) == src
% Same neuron has been clicked, deselect is
handles = DeselectNeuron(handles.NeuronSelected,handles);
handles.NeuronSelected = NaN;
else
% A different neuron has been clicked: select this and deselect old
handles = DeselectNeuron(handles.NeuronSelected,handles);
handles.NeuronSelected = find(handles.PlotHandles.Cells == src);
handles = SelectNeuron(handles.NeuronSelected,handles);
end
end
guidata(gcbo,handles);
function handles = SelectNeuron(CellId,handles)
% This function performs all actions to select a neuron
% Update the info panel
set(handles.lblCllId,'String',num2str(CellId));
CumCell = cumsum(handles.Data.CellTypes.Number);
Type = find(CumCell>=CellId,1); % Identify type of neuron
set(handles.lblCllTyp,'String',handles.Data.CellTypes.Name{Type});
if(handles.Options.Network)
% Find connections and count them:
ConIn = find(handles.Data.Network.ConnectionMatrix(:,CellId));
set(handles.lblIncCon,'String',num2str(length(ConIn)));
ConOut = find(handles.Data.Network.ConnectionMatrix(CellId,:));
set(handles.lblOutCon,'String',num2str(length(ConOut)));
% Make histograms of the connections, categorize by cell type:
Borders = 1+[0 CumCell];
CountIn = histc(ConIn,Borders);
CountOut = histc(ConOut,Borders);
TypeIn = find(CountIn);
TypeOut = find(CountOut);
if(length(ConIn)>0)
H = pie(handles.axsIncCon,CountIn(TypeIn),{handles.Data.CellTypes.Name{TypeIn}});
% The ColorMap option seems to be buggy, use for-loop instead:
for iFace=1:length(TypeIn)
set(H(2*iFace-1),'FaceColor',handles.Data.CellTypes.Color(TypeIn(iFace),:));
end
end
if(length(ConOut)>0)
H = pie(handles.axsOutCon,CountOut(TypeOut),{handles.Data.CellTypes.Name{TypeOut}});
for iFace=1:length(TypeOut)
set(H(2*iFace-1),'FaceColor',handles.Data.CellTypes.Color(TypeOut(iFace),:));
end
end
end
% Change appearance of neuron
ColorSelect = [1 0 1];
set(handles.PlotHandles.Cells(handles.NeuronSelected),'MarkerEdgeColor',ColorSelect);
% See if other stuff has to be plotted:
if(handles.Options.Network)
if(handles.View.OutgoingConnections == 1)
handles.PlotHandles.OutgoingConnections = PlotOutgoingConnections(handles.NeuronSelected);
end
if handles.View.OutgoingCells
handles.PlotHandles.OutgoingCells = PlotOutgoingCells(handles.NeuronSelected);
end
if(handles.View.IncomingConnections == 1)
handles.PlotHandles.IncomingConnections = PlotIncomingConnections(handles.NeuronSelected);
end
if handles.View.IncomingCells
handles.PlotHandles.IncomingCells = PlotIncomingCells(handles.NeuronSelected);
end
end
% Update items in the menu
if(handles.Options.Vm)
set(intersect(handles.MenuOptions.CellSelected,handles.MenuOptions.VmData),'Enable','On');
end
if(handles.Options.NeuronSpikes)
set(intersect(handles.MenuOptions.CellSelected,handles.MenuOptions.SpikeData),'Enable','On');
end
function handles = DeselectNeuron(CellId,handles)
% This function performs all actions to deselect a neuron
% Update the info panel
set(handles.lblCllId,'String','--');
set(handles.lblCllTyp,'String','--');
set(handles.lblIncCon,'String','--');
set(handles.lblOutCon,'String','--');
cla(handles.axsIncCon);
cla(handles.axsOutCon);
% Change appearance of neuron
set(handles.PlotHandles.Cells(CellId),'MarkerEdgeColor','none');
% See if stuff has to be cleaned up:
try,
delete(handles.PlotHandles.OutgoingConnections);
handles.PlotHandles.OutgoingConnections = [];
end
try,
set(handles.PlotHandles.OutgoingCells,'MarkerEdgeColor','none');
handles.PlotHandles.OutgoingCells = [];
end
try,
delete(handles.PlotHandles.IncomingConnections);
handles.PlotHandles.IncomingConnections = [];
end
try,
set(handles.PlotHandles.IncomingCells,'MarkerEdgeColor','none');
handles.PlotHandles.IncomingCells = [];
end
% Update items in the menu
set(handles.MenuOptions.CellSelected,'Enable','Off');
% ------------------------------------------ SECONDARY PLOT FUNCTIONS ---
function [FigHandle, AxesHandle] = MakeSecondaryFigure(ParentHandle)
% This functions generates a modified secondary plot window for details of
% the network
% Make figure and axes
FigHandle = figure;
AxesHandle = axes;
set(FigHandle,'DeleteFcn',@DeleteSecondaryPlot)
handles = guidata(FigHandle);
% Add some stuff to the menu
handles.mnSkuld = uimenu(FigHandle,'Label','Skuld');
handles.mnLinkView = uimenu(handles.mnSkuld,'Label','Link view',...
'Checked','On',...
'Callback',@secplotmnLinkView);
% Modify the view tools
ZoomFunc = zoom(FigHandle);
PanFunc = pan(FigHandle);
set([ZoomFunc PanFunc],'ActionPostCallback',@secplotLinkView);
% Set variables
handles.Handles.Parent = ParentHandle;
handles.Handles.Axes = AxesHandle;
handles.LinkView = 1;
%handles.Handles.mnLinkView = mnLinkView;
guidata(FigHandle,handles);
function secplotmnLinkView(src,eventdata)
% This function toggles the LinkView option of the figure
handles = guidata(gcbf);
handles.LinkView = 1 - handles.LinkView;
if(handles.LinkView == 1)
% Update menu
set(handles.mnLinkView,'Checked','On');
% Obtain handles from main figure and add this axes handle
MainHandles = guidata(handles.Handles.Parent);
MainHandles.SecondaryPlots.LinkViewHandles = [MainHandles.SecondaryPlots.LinkViewHandles handles.Handles.Axes];
% Store new MainHandles
guidata(handles.Handles.Parent,MainHandles);
else
% Update menu
set(handles.mnLinkView,'Checked','Off');
% Obtain data from main figure and delete this axes handle
MainHandles = guidata(handles.Handles.Parent);
ID = find(MainHandles.SecondaryPlots.LinkViewHandles == handles.Handles.Axes);
MainHandles.SecondaryPlots.LinkViewHandles(ID) = [];
% Store new data
guidata(handles.Handles.Parent,MainHandles);
end
guidata(gcbf,handles);
function secplotLinkView(src, eventdata)
% This function sets the X-limits of all linked windows similar to this one
fighandle = get(eventdata.Axes,'Parent');
handles = guidata(fighandle);
% If figure set to LinkView, zoom others as well
if(handles.LinkView == 1)
% Obtain handle of main figure and retrieve the list of linked windows
MainHandles = guidata(handles.Handles.Parent);
HandleList = MainHandles.SecondaryPlots.LinkViewHandles;
% Obtain XLim from this window (hence new view range) and apply to other
rng = get(eventdata.Axes,'XLim');
set(HandleList,'XLim',rng);
end
function DeleteSecondaryPlot(src,eventdata)
% This functions is called when a secondary plot window is closed. It
% removes the related handles from all lists
handles = guidata(src);
MainHandles = guidata(handles.Handles.Parent); % handles from main figure
IDax = find(MainHandles.SecondaryPlots.LinkViewHandles == handles.Handles.Axes);
MainHandles.SecondaryPlots.LinkViewHandles(IDax) = [];
IDfig = find(MainHandles.SecondaryPlots.FigureHandles == src);
MainHandles.SecondaryPlots.FigureHandles(IDfig) = [];
% Updata MainHandles
guidata(handles.Handles.Parent,MainHandles);
% ---------------------------------------------- BUTTERWORTH FILTERS ----
function AddFilterMenu(FigHandle)
% This function adds the filter options to the plot window
% Obtain handles:
handles = guidata(FigHandle);
% Add menu items
handles.mnHighPassSwitch = uimenu(handles.mnSkuld,'Label','High pass filter',...
'Separator','on',...
'Checked','off',...
'Callback',@secplotmnHighPassSwitch_Callback);
handles.mnHighPassEdit = uimenu(handles.mnSkuld,'Label',' Modify',...
'Callback',@secplotmnHighPassEdit_Callback);
handles.mnLowPassSwitch = uimenu(handles.mnSkuld,'Label','Low pass filter',...
'Separator','on',...
'Checked','off',...
'Callback',@secplotmnLowPassSwitch_Callback);
handles.mnLowPassEdit = uimenu(handles.mnSkuld,'Label',' Modify',...
'Callback',@secplotmnLowPassEdit_Callback);
% Set both modify buttons to idle
set([handles.mnHighPassEdit handles.mnLowPassEdit],'Enable','off');
handles.Filter.HighPassOn = 0;
handles.Filter.LowPassOn = 0;
guidata(FigHandle,handles);
function secplotmnLowPassSwitch_Callback(src,eventdata)
% This function turns the low pass filter on the data on/off
handles = guidata(gcf);
handles.Filter.LowPassOn = 1 - handles.Filter.LowPassOn;
if(handles.Filter.LowPassOn == 1)
set(handles.mnLowPassSwitch,'Checked','on');
set(handles.mnLowPassEdit,'Enable','on');
% If no filter has been set previously, new settings are prompted
if(numel(handles.Filter.Low) == 0)
% Give dialog box for settings
Prefs=inputdlg({'Order','Cut-off (Hz)'},'Low-pass Butterworth',1,{'2','80'});
% Check whether OK has been pressed
if(~isempty(Prefs))
% Design filter
[b,a] = butter(str2num(Prefs{1}),2*str2num(Prefs{2})/handles.Data.SamplingRate,'low');
handles.Filter.Low = [a;b];
handles.Filter.LowSettings = Prefs;
else
% Filter activation has been cancelled, restore everything
handles.Filter.LowPassOn = 0;
set(handles.mnLowPassSwitch,'Checked','off');
set(handles.mnLowPassEdit,'Enable','off');
handles.Filter.Low = [];
end
end
% Store filter 'locally'
Low = handles.Filter.Low;
else
set(handles.mnLowPassSwitch,'Checked','off');
set(handles.mnLowPassEdit,'Enable','off');
Low = [];
end
% Determine whether the High-pass filter is activated
if(handles.Filter.HighPassOn == 1)
High = handles.Filter.High;
else
High = [];
end
% Apply filters to data and plot
FilterAndPlot(handles.Handles.Axes,...
handles.Data.T, handles.Data.Y,...
High, Low);
% Store handles
guidata(gcf,handles);
function secplotmnLowPassEdit_Callback(src,eventdata)
% This function turns the low pass filter on the data on/off
handles = guidata(gcf);
Prefs=inputdlg({'Order','Cut-off (Hz)'},'Low-pass Butterworth',1,handles.Filter.LowSettings);
if(~isempty(Prefs))
% OK has been clicked, store new filter
handles.Filter.LowSettings = Prefs;
else
% Don't change filter when cancel has been hit
Prefs = handles.Filter.LowSettings;
end
% Design filter
[b,a] = butter(str2num(Prefs{1}),2*str2num(Prefs{2})/handles.Data.SamplingRate,'low');
handles.Filter.Low = [a;b];
% Store filter 'locally'
Low = handles.Filter.Low;
% Determine whether the High-pass filter is activated
if(handles.Filter.HighPassOn == 1)
High = handles.Filter.High;
else
High = [];
end
% Apply filters to data and plot
FilterAndPlot(handles.Handles.Axes,...
handles.Data.T, handles.Data.Y,...
High, Low);
% Store handles
guidata(gcf,handles);
function secplotmnHighPassSwitch_Callback(src,eventdata)
% This function turns the low pass filter on the data on/off
handles = guidata(gcf);
handles.Filter.HighPassOn = 1 - handles.Filter.HighPassOn;
if(handles.Filter.HighPassOn == 1)
set(handles.mnHighPassSwitch,'Checked','on');
set(handles.mnHighPassEdit,'Enable','on');
% If no filter has been set previously, new settings are prompted
if(numel(handles.Filter.High) == 0)
% Give dialog box for settings
Prefs=inputdlg({'Order','Cut-off (Hz)'},'High-pass Butterworth',1,{'1','2'});
% Check whether OK has been pressed
if(~isempty(Prefs))
% Design filter
[b,a] = butter(str2num(Prefs{1}),2*str2num(Prefs{2})/handles.Data.SamplingRate,'high');
handles.Filter.High = [a;b];
handles.Filter.HighSettings = Prefs;
else
% Filter activation has been cancelled, restore everything
handles.Filter.HighPassOn = 0;
set(handles.mnHighPassSwitch,'Checked','off');
set(handles.mnHighPassEdit,'Enable','off');
handles.Filter.High = [];
end
end
% Store filter 'locally'
High = handles.Filter.High;
else
set(handles.mnHighPassSwitch,'Checked','off');
set(handles.mnHighPassEdit,'Enable','off');
High = [];
end
% Determine whether the High-pass filter is activated
if(handles.Filter.LowPassOn == 1)
Low = handles.Filter.Low;
else
Low = [];
end
% Apply filters to data and plot
FilterAndPlot(handles.Handles.Axes,...
handles.Data.T, handles.Data.Y,...
High, Low);
% Store handles
guidata(gcf,handles);
function secplotmnHighPassEdit_Callback(src,eventdata)
% This function turns the low pass filter on the data on/off
handles = guidata(gcf);
Prefs=inputdlg({'Order','Cut-off (Hz)'},'High-pass Butterworth',1,handles.Filter.HighSettings);
if(~isempty(Prefs))
% OK has been clicked, store new filter
handles.Filter.HighSettings = Prefs;
else
% Don't change filter when cancel has been hit
Prefs = handles.Filter.HighSettings;
end
% Design filter
[b,a] = butter(str2num(Prefs{1}),2*str2num(Prefs{2})/handles.Data.SamplingRate,'high');
handles.Filter.High = [a;b];
% Store filter 'locally'
High = handles.Filter.High;
% Determine whether the High-pass filter is activated
if(handles.Filter.LowPassOn == 1)
Low = handles.Filter.Low;
else
Low = [];
end
% Apply filters to data and plot
FilterAndPlot(handles.Handles.Axes,...
handles.Data.T, handles.Data.Y,...
High, Low);
% Store handles
guidata(gcf,handles);
function FilterAndPlot(AxesHandle,T,Y,High,Low)
% This function applies the specified filters to the given data set and
% plots the result in the axes indicated by AxesHandle.
% First store the current figure settings:
Lims = get(AxesHandle,{'XLim','YLim'});
% A high pass filter is defined:
if(~isempty(High))
Y = filter(High(2,:),High(1,:),Y,[],1);
end
% A low pass filter is defined:
if(~isempty(Low))
Y = filter(Low(2,:),Low(1,:),Y,[],1);
end
% Plot and set axes limits to original values.
plot(AxesHandle,T,Y);
axis(AxesHandle,[Lims{:}]);
% ------------------------------------------- RASTER PLOT EXTENSIONS ----
function AddAlignRasterMenu(FigHandle)
% Obtain handles:
handles = guidata(FigHandle);
% Add menu item
handles.mnAlignRaster = uimenu(handles.mnSkuld,'Label','Delay correction',...
'Separator','on',...
'Checked','off',...
'Callback',@secplotmnAlignRaster_Callback);
% Currently not aligned
handles.AlignRaster = 0;
guidata(FigHandle,handles);
function cmnRasterRequestInfo(src,eventdata)
% This function is called when the UIContextMenu is requested to show the
% cell ID of a slected cell
% Get handles of this figure
handles = guidata(gcf);
% Find cell ID
plotID = find(handles.Data.PlotHandles == gco); % find the ID of the plot
ID = handles.Data.PlotCellIDs(plotID);
mnName = get(src,'Children'); % Get the menu item that actually displays the name
set(mnName,'Label',num2str(ID));
function secplotmnAlignRaster_Callback(src,eventdata)
% This function aligns the APs in the rasterplot such that the dots
% represent PSPs
handles = guidata(gcf);
% First store the current figure settings:
Lims = get(handles.Handles.Axes,{'XLim','YLim'});
% Change state:
handles.AlignRaster = 1 - handles.AlignRaster;
if(handles.AlignRaster == 1)
set(handles.mnAlignRaster,'Checked','on');
% Re-align spikes by adding Delays
for iCell = 1:length(handles.Data.Delays)
% Access XData of plot and shift it
if(handles.Data.PlotHandles(iCell) ~= 0)
X = get(handles.Data.PlotHandles(iCell),'XData');
set(handles.Data.PlotHandles(iCell),'XData',X + handles.Data.Delays(iCell));
end
end
else
set(handles.mnAlignRaster,'Checked','off');
% Align spikes by subtracting Delays
for iCell = 1:length(handles.Data.Delays)
% Access XData of plot and shift it
if(handles.Data.PlotHandles(iCell) ~= 0)
X = get(handles.Data.PlotHandles(iCell),'XData');
set(handles.Data.PlotHandles(iCell),'XData',X - handles.Data.Delays(iCell));
end
end
end
% Restore axis limits
axis(handles.Handles.Axes,[Lims{:}]);
guidata(gcf,handles);
% ----------------------------------------------- VM PLOT EXTENSIONS ----
function AddPlaySoundToolbar(FigHandle)
% Fetch handles
handles = guidata(FigHandle);
% Get picture:
iconDir = fullfile(matlabroot,'toolbox','matlab','icons');
[Temp,map] = imread(fullfile(iconDir,'greenarrowicon.gif'));
iconPlay = ind2rgb(Temp,map);
% Find handle of current toolbar:
ht = findall(FigHandle,'Tag','FigureToolBar');
% Make objects
if(~isempty(ht))
handles.tbrLoadData = uipushtool('Parent',ht,...
'CData',iconPlay,...
'TooltipString','Play as sound',...
'ClickedCallback',@secplottbrPlaySound_ClickedCallback);
else
handles.tbrLoadData = uipushtool('CData',iconPlay,...
'TooltipString','Play as sound',...
'ClickedCallback',@secplottbrPlaySound_ClickedCallback);
end
guidata(FigHandle,handles);
function secplottbrPlaySound_ClickedCallback(hObject, eventdata)
handles = guidata(hObject);
soundsc(handles.Data.Y,handles.Data.SamplingRate);