wave_clus.m

function varargout = wave_clus(varargin)
% WAVE_CLUS M-file for wave_clus.fig
%      WAVE_CLUS, by itself, creates a new WAVE_CLUS or raises the existing
%      singleton*.
%
%      H = WAVE_CLUS returns the handle to a new WAVE_CLUS or the handle to
%      the existing singleton*.
%
%      WAVE_CLUS('Property','Value',...) creates a new WAVE_CLUS using the
%      given property value pairs. Unrecognized properties are passed via
%      varargin to wave_clus_OpeningFcn.  This calling syntax produces a
%      warning when there is an existing singleton*.
%
%      WAVE_CLUS('CALLBACK') and WAVE_CLUS('CALLBACK',hObject,...) call the
%      local function named CALLBACK in WAVE_CLUS.M with the given input
%      arguments.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help wave_clus

% Last Modified by GUIDE v2.5 14-Jan-2009 10:01:11

% JMG101208
% USER_DATA DEFINITIONS
% USER_DATA{1} = par;
% USER_DATA{2} = spikes;
% USER_DATA{3} = index;
% USER_DATA{4} = clu;
% USER_DATA{5} = tree;
% USER_DATA{7} = inspk;
% USER_DATA{6} = classes(:)'
% USER_DATA{8} = temp
% USER_DATA{9} = classes(:)', backup for non-forced classes
% USER_DATA{10} = clustering_results
% USER_DATA{11} = clustering_results_bk
% USER_DATA{12} = ipermut, indexes of the previously permuted spikes for clustering taking random number of points 
% USER_DATA{13} = forced, boolean vector for forced spikes,  
% USER_DATA{14} = forced_bk, backup boolean vector for forced spikes,  
% USER_DATA{15} = rejected, boolean vector for rejected spikes. Vector only used in develop mode.
% USER_DATA{16} = rejected_bk,  backup boolean vector for rejected spikes. Vector only used in develop mode.
% USER_DATA{17} - USER_DATA{19}, for future changes
% USER_DATA{20} - USER_DATA{42}, fix clusters

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @wave_clus_OpeningFcn, ...
                   'gui_OutputFcn',  @wave_clus_OutputFcn, ...
                   'gui_LayoutFcn',  [], ...
                   'gui_Callback',   []);
if nargin && isstr(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 wave_clus is made visible.
function wave_clus_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   unrecognized PropertyName/PropertyValue pairs from the
%            command line (see VARARGIN)

% Choose default command line output for wave_clus
handles.output = hObject;
set(handles.isi1_accept_button,'value',1);
set(handles.isi2_accept_button,'value',1);
set(handles.isi3_accept_button,'value',1);
set(handles.spike_shapes_button,'value',1);
set(handles.plot_all_button,'value',1);
set(handles.plot_average_button,'value',0);
set(handles.fix1_button,'value',0);
set(handles.fix2_button,'value',0);
set(handles.fix3_button,'value',0);


% Update handles structure
guidata(hObject, handles);

% UIWAIT makes wave_clus wait for user response (see UIRESUME)
% uiwait(handles.figure1);


% --- Outputs from this function are returned to the command line.
function varargout = wave_clus_OutputFcn(hObject, eventdata, handles)
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;

clus_colors = [0 0 1; 1 0 0; 0 0.5 0; 0 0.75 0.75; 0.75 0 0.75; 0.75 0.75 0; 0.25 0.25 0.25];
set(0,'DefaultAxesColorOrder',clus_colors)


% --- Executes on button press in load_data_button.
function load_data_button_Callback(hObject, eventdata, handles)
% select file
[filename, pathname] = uigetfile('*.*','Select file'); % Use only the supported extensions can bring case-sensitive related problems.

% if any file was selected, cancel the loading
if ~ischar(pathname)
    return
end

set(handles.file_name,'string',['Loading:    ' pathname filename]); drawnow

cla(handles.cont_data);
clear functions % reset functions, force to reload set_parameters next
handles.par = set_parameters();

cd(pathname);

handles.par.filename = filename;

for i = 1:3
    si = num2str(i);
    set(eval(['handles.isi' si '_accept_button']),'value',1);
    set(eval(['handles.isi' si '_reject_button']),'value',0);
    set(eval(['handles.fix' si '_button']),'value',0);
    
   
    eval(['set(handles.isi' si '_nbins,''string'',handles.par.nbins);']);
    eval(['set(handles.isi' si '_bin_step,''string'',handles.par.bin_step);']);
end

set(handles.isi0_nbins,'string',handles.par.nbins);
set(handles.isi0_bin_step,'string',handles.par.bin_step);

% Sets to zero fix buttons from aux figures
for i=4:handles.par.max_clus
    eval(['handles.par.fix' num2str(i) '=0;'])
end

for i =0:handles.par.max_clus
    si = num2str(i);
    eval(['handles.par.nbins' si ' = handles.par.nbins;']);  % # of bins for the ISI histograms
    eval(['handles.par.bin_step' si ' = handles.par.bin_step;']);  % percentage number of bins to plot
end

data_handler = readInData(handles.par);
handles.par = data_handler.par;

handles.par.fname_in = 'tmp_data_wc';                       % temporary filename used as input for SPC
handles.par.fname = ['data_' data_handler.nick_name];
handles.par.nick_name = data_handler.nick_name;
handles.par.fnamesave = handles.par.fname;                  %filename if "save clusters" button is pressed
handles.par.fnamespc = 'data_wc';

handles.par = data_handler.update_par(handles.par);
handles.par.file_name_to_show = [pathname filename];

if data_handler.with_results %data have _times files
    [clu, tree, spikes, index, inspk, ipermut, classes, forced,temp] = data_handler.load_results();
    rejected = data_handler.load_rejected();
    handles.setclus = 1;
else
    if data_handler.with_spikes  %data have some time of _spikes files
        [spikes, index] = data_handler.load_spikes(); 
        if ~data_handler.with_wc_spikes
            [spikes] = spike_alignment(spikes,handles.par);
        elseif isfield(handles.par,'channels')
        	handles.par.inputs = handles.par.inputs * handles.par.channels;
        end
    else    
        set(handles.file_name,'string','Detecting spikes ...'); drawnow
        index = [];
        spikes = [];
        for n = 1:data_handler.max_segments
            x = data_handler.get_segment();
            [new_spikes, temp_aux_th, new_index]  = amp_detect(x, handles.par);
            index = [index data_handler.index2ts(new_index)]; %new_index to ms
            spikes = [spikes; new_spikes];
        end
    end
    
    if size(spikes,1) < 15
        	ME = MException('MyComponent:notEnoughSpikes', 'Less than 15 spikes detected');
            throw(ME)
    end
    
    set(handles.file_name,'string','Calculating spike features ...'); drawnow
    [inspk] = wave_features(spikes,handles.par);                 %Extract spike features.
    
    if handles.par.permut == 'y'
        if handles.par.match == 'y';
            naux = min(handles.par.max_spk,size(inspk,1));
            ipermut = randperm(length(inspk));
            ipermut(naux+1:end) = [];
        else
            ipermut = randperm(length(inspk));
        end
        inspk_aux = inspk(ipermut,:);
    else
        if handles.par.match == 'y';
            naux = min(handles.par.max_spk,size(inspk,1));
            inspk_aux = inspk(1:naux,:);
        else
            inspk_aux = inspk;
        end
    end

    %Interaction with SPC
    set(handles.file_name,'string','Running SPC ...'); drawnow
    fname_in = handles.par.fname_in;
    save(fname_in,'inspk_aux','-ascii');                      %Input file for SPC
    
    [clu,tree] = run_cluster(handles.par);
    forced = false(size(spikes,1) ,1);
    rejected = false(1, size(spikes,1));
    handles.setclus = 2; %uses min cluster size but doesn't reset force
end

if (data_handler.with_raw || data_handler.with_psegment) && handles.par.cont_segment         %raw exists
    [xd_sub, sr_sub] = data_handler.get_signal_sample();
    Plot_continuous_data(xd_sub, sr_sub, handles); drawnow
    clear xd_sub
end

%Fixing lost elements of clu . Skiped elements will be  class -1 because in
%all the uses of clu are like: clu(temp,3:end)+1
if handles.par.permut == 'y' && ~isempty(clu)
    if isempty(ipermut) %load from old result without ipermut or par, but par.permut=='y'
       ipermut = 1:length(inspk);
    end
    clu_aux = zeros(size(clu,1),2 + size(spikes,1)) -1;%when update classes from clu, not selected go to cluster 1001
    clu_aux(:,ipermut+2) = clu(:,(1:length(ipermut))+2);
    clu_aux(:,1:2) = clu(:,1:2);
    clu = clu_aux;
    clear clu_aux
end


USER_DATA = get(handles.wave_clus_figure,'userdata');
USER_DATA{1} = handles.par;
USER_DATA{2} = spikes;
USER_DATA{3} = index;
USER_DATA{4} = clu;
USER_DATA{5} = tree;
USER_DATA{7} = inspk;
if exist('ipermut','var') && ~isempty(ipermut)
    USER_DATA{12} = ipermut;
end
USER_DATA{13} = forced;
USER_DATA{14} = forced;
USER_DATA{15} = rejected;  %the clusters numbers are sorted
USER_DATA{16} = rejected;  %the clusters numbers are sorted

set(handles.min_clus_edit,'string',num2str(handles.par.min_clus));

if  data_handler.with_gui_status
    [saved_gui_status, current_temp] = data_handler.get_gui_status();
    clustering_results = zeros(length(classes),4);
    clustering_results(:,1) = repmat(current_temp,length(classes),1);
    for i=1:max(classes)
      clustering_results(classes==i,3)  = temp(i);
    end
    
    clustering_results(:,2) = classes'; % GUI classes 
    clustering_results(:,4) = saved_gui_status;
    handles.undo = 1;
    
elseif data_handler.with_results
    clustering_results(:,1) = repmat(temp(1),length(classes),1); % GUI temperatures
    clustering_results(:,2) = classes'; % GUI classes 
    for i=1:max(classes)
    	clustering_results(classes==i,3)  = temp(i);
    end 
    clustering_results(:,4) = classes'; % original classes 
    handles.undo = 1;
    
else
    %Selects temperature.
    temp = find_temp(tree, handles.par); 
    classes = clu(temp,3:end)+1;
    if handles.par.permut == 'n'
        classes = [classes zeros(1,max(size(spikes,1)-handles.par.max_spk,0))];
    end

    % definition of clustering_results
    clustering_results = [];
    clustering_results(:,1) = repmat(temp,length(classes),1); % GUI temperatures
    clustering_results(:,2) = classes'; % GUI classes 
    clustering_results(:,3) = repmat(temp,length(classes),1); % original temperatures 
    clustering_results(:,4) = classes'; % original classes 
    handles.undo = 0;
end

if data_handler.with_results && ~ data_handler.with_spc
    temp = -1;                              % This will work as a flag for not drawing the temperature diagram
    cla(handles.temperature_plot,'reset');
end

clustering_results(:,5) = repmat(handles.par.min_clus,length(classes),1); % minimum number of clusters
USER_DATA{6} = classes(:)';
if exist('current_temp','var')
    USER_DATA{8} = current_temp;
else
    USER_DATA{8} = temp(1);
end
USER_DATA{10} = clustering_results;
USER_DATA{11} = clustering_results;
handles.force = 0;
handles.merge = 0;

handles.minclus = handles.par.min_clus;

USER_DATA{13} = forced;
USER_DATA{14} = forced;
set(handles.wave_clus_figure,'userdata',USER_DATA);

clear clustering_results classes rejected spikes
% mark clusters when new data is loaded
guidata(hObject, handles); %this is need for plot the isi histograms

plot_spikes(handles); %This function edits userdata
USER_DATA = get(handles.wave_clus_figure,'userdata');
set(handles.wave_clus_figure,'userdata',USER_DATA);


if isfield(handles,'force_unforce_button') && (nnz(forced)>0)
	set(handles.force_unforce_button,'Value',1)
    set(handles.force_unforce_button,'String','FORCED')
    %set(handles.change_temperature_button,'enable','off');
end
if isfield(handles,'edit_max_force_dist')
    set(handles.edit_max_force_dist,'string',num2str(handles.par.template_sdnum));
end


set(handles.file_name,'string',handles.par.file_name_to_show);

% --- Executes on button press in change_temperature_button.
function change_temperature_button_Callback(hObject, eventdata, handles)
[temp,aux,button] = ginput(1);                                          %gets the mouse input
if button == 3
	return
end
if temp < handles.par.mintemp
    temp = 1;
elseif temp>handles.par.maxtemp
    temp = floor((handles.par.maxtemp-handles.par.mintemp)/handles.par.tempstep);
else
    temp = round((temp-handles.par.mintemp)/handles.par.tempstep); %temp from value to index
end

min_clus = round(aux);
set(handles.min_clus_edit,'string',num2str(min_clus));

USER_DATA = get(handles.wave_clus_figure,'userdata');
rejected = USER_DATA{15};
USER_DATA{16} = rejected;
par = USER_DATA{1};
par.min_clus = min_clus;
clu = USER_DATA{4};
classes = clu(temp, 3:end) + 1;
classes(rejected) = 0;
USER_DATA{1} = par;
USER_DATA{6} = classes(:)';
USER_DATA{8} = temp;

handles.minclus = min_clus;
set(handles.wave_clus_figure,'userdata',USER_DATA);
handles.setclus = 0;
handles.force = 0;
handles.merge = 0;

handles.undo = 0;
plot_spikes(handles);
if isfield(handles,'force_unforce_button')
	set(handles.force_unforce_button,'Value',0)
    set(handles.force_unforce_button,'String','Force')
end

% --- Change min_clus_edit     
function min_clus_edit_Callback(hObject, eventdata, handles)
USER_DATA = get(handles.wave_clus_figure,'userdata');
par = USER_DATA{1};  
par.min_clus = str2num(get(hObject, 'String'));
clu = USER_DATA{4};
temp = USER_DATA{8};
classes = clu(temp,3:end)+1;
USER_DATA{1} = par;
USER_DATA{6} = classes(:)';
USER_DATA{16} = USER_DATA{15};
clustering_results = USER_DATA{10};
clustering_results(:,5) = par.min_clus;
set(handles.wave_clus_figure,'userdata',USER_DATA);
handles.setclus = 0;
handles.force = 0;
handles.merge = 0;
handles.undo = 0;

handles.minclus = par.min_clus;
plot_spikes(handles);


% --- Executes on button press in save_clusters_button.
function save_clusters_button_Callback(hObject, eventdata, handles, developer_mode)
USER_DATA = get(handles.wave_clus_figure,'userdata');
classes = USER_DATA{6};
clustering_results = USER_DATA{10};
rejected = USER_DATA{15};

USER_DATA{16} =  rejected;     %update bk of rejected spikes
USER_DATA{15} = false(size(rejected));
set(handles.wave_clus_figure,'userdata',USER_DATA);
handles.setclus = 1;
handles.force = 0;
handles.merge = 0;

handles.undo = 0;
plot_spikes(handles)

USER_DATA = get(handles.wave_clus_figure,'userdata');
spikes = USER_DATA{2};
used_par = USER_DATA{1};
index = USER_DATA{3};
classes = USER_DATA{6};
gui_classes_data = USER_DATA{10};

% Classes should be consecutive numbers
classes_names = nonzeros(sort(unique(classes)));
for i= 1:length(classes_names)
   c = classes_names(i);
   if c~= i
       classes(classes == c) = i;
   end
end

%Saves clusters
cluster_class = zeros(size(spikes,1),2);
cluster_class(:,1) = classes(:);
cluster_class(:,2) = USER_DATA{3}';

outfile=['times_' used_par.nick_name];

par = struct;
par = update_parameters(par,used_par,'relevant');

gui_status = struct();
gui_status.current_temp =  gui_classes_data(1,1);
gui_status.original_classes = gui_classes_data(1:end,4);

Temp = zeros(length(classes_names));
for i = 1:length(classes_names)
    Temp(i) = gui_classes_data(find(classes==i,1,'first'),3);
end
forced = USER_DATA{13};

var_list = ' cluster_class par spikes gui_status forced index Temp';

if ~isempty(USER_DATA{7})
    inspk = USER_DATA{7};
    var_list = strcat(var_list , ' inspk');
end

if ~isempty(USER_DATA{12})
    ipermut = USER_DATA{12};
    var_list = strcat(var_list , ' ipermut');
end
       
if developer_mode
	var_list = strcat(var_list , ' rejected');
end

currentver = version;
if currentver(1) >= 7
    var_list = strcat(var_list , ' -v6;');
else
    var_list = strcat(var_list , ';');
end

eval(['save ' outfile var_list]);
if exist([handles.par.fnamespc '.dg_01.lab'],'file')
    copyfile([handles.par.fnamespc '.dg_01.lab'], [handles.par.fnamesave '.dg_01.lab']);
    copyfile([handles.par.fnamespc '.dg_01'], [handles.par.fnamesave '.dg_01']);
end

%Save figures
h_figs = get(0,'children');
h_fig = findobj(h_figs,'tag','wave_clus_figure');
h_fig1 = findobj(h_figs,'tag','wave_clus_aux');
h_fig2 = findobj(h_figs,'tag','wave_clus_aux1');
h_fig3 = findobj(h_figs,'tag','wave_clus_aux2');
h_fig4 = findobj(h_figs,'tag','wave_clus_aux3');
h_fig5 = findobj(h_figs,'tag','wave_clus_aux4');
h_fig6 = findobj(h_figs,'tag','wave_clus_aux5');

if ~isempty(h_fig)
    figure(h_fig); set(gcf, 'PaperUnits', 'inches', 'PaperType', 'A4', 'PaperPositionMode', 'auto','PaperOrientation','portrait');
    eval(['print(h_fig,''-dpng'',''fig2print_' outfile(7:end)  ''',''-r300'')' ]);
end
if ~isempty(h_fig1)
    figure(h_fig1); set(gcf,'PaperUnits', 'inches', 'PaperType', 'A4', 'PaperPositionMode', 'auto','PaperOrientation','portrait');
    eval(['print(h_fig1,''-dpng'',''fig2print_' outfile(7:end) 'a' ''',''-r300'')' ]);
end
if ~isempty(h_fig2)
    figure(h_fig2); set(gcf, 'PaperUnits', 'inches', 'PaperType', 'A4', 'PaperPositionMode', 'auto','PaperOrientation','portrait');
    eval(['print(h_fig2,''-dpng'',''fig2print_' outfile(7:end) 'b' ''',''-r300'')' ]);
end
if ~isempty(h_fig3)
    figure(h_fig3); set(gcf, 'PaperUnits', 'inches', 'PaperType', 'A4', 'PaperPositionMode', 'auto','PaperOrientation','portrait');
    eval(['print(h_fig3,''-dpng'',''fig2print_' outfile(7:end) 'c' ''',''-r300'')' ]);
end
if ~isempty(h_fig4)
    figure(h_fig4); set(gcf, 'PaperUnits', 'inches', 'PaperType', 'A4', 'PaperPositionMode', 'auto','PaperOrientation','portrait');
    eval(['print(h_fig4,''-dpng'',''fig2print_' outfile(7:end) 'd' ''',''-r300'')' ]);
end
if ~isempty(h_fig5)
    figure(h_fig5); set(gcf,'PaperUnits', 'inches', 'PaperType', 'A4', 'PaperPositionMode', 'auto','PaperOrientation','portrait');
    eval(['print(h_fig5,''-dpng'',''fig2print_' outfile(7:end) 'e' ''',''-r300'')' ]);
end
if ~isempty(h_fig6)
    figure(h_fig6); set(gcf, 'PaperUnits', 'inches', 'PaperType', 'A4', 'PaperPositionMode', 'auto','PaperOrientation','portrait');
    eval(['print(h_fig6,''-dpng'',''fig2print_' outfile(7:end) 'f' ''',''-r300'')' ]);
end
set(hObject,'value',0);


% --- Executes on button press in set_parameters_button.
function set_parameters_button_Callback(hObject, eventdata, handles)
    %helpdlg('Check the set_parameters files in the subdirectory
    %Wave_clus\Parameters_files');
    set_parameters_ui()

    
%SETTING OF FORCE MEMBERSHIP
% --------------------------------------------------------------------
    
function force_unforce_button_Callback(hObject, eventdata, handles)    
    
    USER_DATA = get(handles.wave_clus_figure,'userdata');
    par = USER_DATA{1};
    classes = USER_DATA{6};
    forced = USER_DATA{13};
    USER_DATA{14} = forced;     %save forced in forced_bk
    rejected = USER_DATA{15};
    USER_DATA{16} = USER_DATA{15}; %update bk of rejected spikes
    button_state = get(hObject,'Value');
    if button_state == get(hObject,'Max')
        spikes = USER_DATA{2};
        inspk = USER_DATA{7};
        USER_DATA{16} = rejected;
        
        if get(handles.fix1_button,'value') ==1     
            fix_class = USER_DATA{20}';
            classes(fix_class) = -1;
        end
        if get(handles.fix2_button,'value') ==1     
            fix_class = USER_DATA{21}';
            classes(fix_class) = -1;
        end
        if get(handles.fix3_button,'value') ==1     
            fix_class = USER_DATA{22}';
            classes(fix_class )= -1;
        end
        % Get fixed clusters from aux figures
        for i=4:par.max_clus
            eval(['fixx = par.fix' num2str(i) ';']);
            if fixx == 1
                fix_class = USER_DATA{22+i-3}';
                classes(fix_class) = -1;
            end
        end

        to_force = (~rejected)' & (classes==0);
        switch par.force_feature
            case 'spk'
                f_in  = spikes(classes>0,:);
                f_out = spikes(to_force,:);
            case 'wav'
                if isempty(inspk)
                    set(handles.file_name,'string','Calculating spike features ...');
                    [inspk] = wave_features(spikes,par);        % Extract spike features.
                    USER_DATA{7} = inspk;
                end
                f_in  = inspk(classes>0,:);
                f_out = inspk(to_force,:);
        end

        class_in = classes(classes>0);
        class_out = force_membership_wc(f_in, class_in, f_out, par);
        forced = forced(:) | to_force(:);
        classes(to_force) = class_out;
        USER_DATA{13} = forced;
        
        clustering_results = USER_DATA{10};
        handles.minclus = clustering_results(1,5);
        handles.force = 1;
        handles.setclus = 1;
        set(hObject,'String','FORCED')
        %set(handles.change_temperature_button,'enable','off');
    else
%         clu = USER_DATA{4};
%         temp = USER_DATA{8};
%         classes = clu(temp,3:end)+1;       
        
        new_forced = zeros(size(forced));
        % Fixed clusters are not considered for forcing
%         if get(handles.fix1_button,'value') ==1     
%             fix_class = USER_DATA{20}';
%             new_forced(fix_class) =forced(fix_class);
%         end
%         if get(handles.fix2_button,'value') ==1     
%             fix_class = USER_DATA{21}';
%             new_forced(fix_class) =forced(fix_class);
%         end
%         if get(handles.fix3_button,'value') ==1     
%             fix_class = USER_DATA{22}';
%             new_forced(fix_class) =forced(fix_class);
%         end
%         % Get fixed clusters from aux figures
%         for i=4:par.max_clus
%             eval(['fixx = par.fix' num2str(i) ';']);
%             if fixx == 1
%                 fix_class = USER_DATA{22+i-3}';
%                 new_forced(fix_class) =forced(fix_class);
%             end
%         end
        set(handles.fix1_button,'value',0);
        set(handles.fix2_button,'value',0);
        set(handles.fix3_button,'value',0);
        for i=4:par.max_clus
            eval(['par.fix' num2str(i) '=0;']);
        end
        classes(forced(:) & (~new_forced(:)) & (~rejected(:))) = 0;  %the elements that before were forced but it isn't force any more, pass to class 0
        USER_DATA{13} = new_forced; 
        handles.force = 0;
        handles.setclus = 1;
        set(hObject,'String','Force')
        %set(handles.change_temperature_button,'enable','on');
    end
    USER_DATA{6} = classes(:)';
    
    handles.merge = 0;
    
    handles.undo = 0;
    set(handles.wave_clus_figure,'userdata',USER_DATA)
    plot_spikes(handles);



    
function manual_clus_button_Callback(hObject, eventdata,handles_local, cl)
    
    if isfield(handles_local,'wave_clus_figure')
        USER_DATA = get(handles_local.wave_clus_figure,'userdata');
        handles = handles_local;
    else
        h_figs = get(0,'children');
        h_fig = findobj(h_figs,'tag','wave_clus_figure');
        USER_DATA = get(h_fig,'UserData');
        handles = guidata(h_fig);
    end

    spikes = USER_DATA{2};
    classes = USER_DATA{6};
    forced = USER_DATA{13};   
    
    if cl == -1
        rect = getrect(handles_local.projections);
        valids = ~USER_DATA{15}(:); %First, I don't select the rejected
    else
        eval(['rect = getrect(handles_local.spikes' num2str(cl) ');']);
        valids = ~USER_DATA{15}(:) & (classes(:)==cl); %First, I don't select the rejected
    end
    xind = max(1, ceil(rect(1)));
    xend = min(size(spikes,2),floor(rect(1) + rect(3)));
    xD = xend-xind;
    ymin = rect(2);
    ymax = rect(2) + rect(4);
    yD = ymin - ymax;
    if xD==0 || yD == 0; return; end
    [Mh, Mpos] = max(spikes(valids,xind:xend)');
    [mh ,mpos] = min(spikes(valids,xind:xend)');
    if ceil(rect(1)) < 1 %if rect is out the axis, extreme in border count like inside the rectangle
        xiborder=0;
    else
        xiborder=1;
    end
    if floor(rect(1) + rect(3)) > size(spikes,2) %if rect is out the axis, extreme in border count like inside the rectangle
        xeborder = xD+2; 
    else
        xeborder = xD;   
    end    
    sp_selected = (Mh >= ymin & Mh <= ymax) & (Mpos > xiborder & Mpos < xeborder);
    sp_selected = sp_selected |((mh >= ymin & mh <= ymax) & (mpos > xiborder & mpos < xeborder));
    valids(valids==1) = sp_selected;
    
    clus_n = max(classes) + 1;
    USER_DATA{14} = forced;
    
    forced(valids) = 0;
    classes(valids)= clus_n;
    handles.new_manual = valids;
    handles.setclus = 1;
    handles.force = 0;
    handles.merge = 0;
    
    handles.undo = 0;
    USER_DATA{6} = classes(:)';
    USER_DATA{13} = forced;
    USER_DATA{16} = USER_DATA{15}; %update bk of rejected spikes
    
    if isfield(handles,'wave_clus_figure')
        set(handles.wave_clus_figure,'userdata',USER_DATA)
    else
        set(h_fig,'userdata',USER_DATA)
    end

    plot_spikes(handles);

    
    
% PLOT ALL PROJECTIONS BUTTON
% --------------------------------------------------------------------
function Plot_all_projections_button_Callback(hObject, eventdata, handles)
USER_DATA = get(handles.wave_clus_figure,'userdata');
par = USER_DATA{1};
if par.channels > 1
    Plot_amplitudes(handles)
else
    Plot_all_features(handles)
end
% --------------------------------------------------------------------

% fix buttons --------------------------------------------------------------------
function fix_button_Callback(hObject, eventdata, handles)
b_name = get(gcbo,'Tag');
cn = regexp(b_name, '\d+', 'match');

USER_DATA = get(handles.wave_clus_figure,'userdata');
classes = USER_DATA{6};
fix_class = find(classes== str2double(cn{1}));

if get(eval(['handles.fix' cn{1} '_button']),'value') ==1
    USER_DATA{19+str2double(cn{1})} = fix_class;  %20 for class 1, etc
else
    USER_DATA{19+str2double(cn{1})} = [];
end
set(handles.wave_clus_figure,'userdata',USER_DATA)
h_figs=get(0,'children');
h_fig4 = findobj(h_figs,'tag','wave_clus_aux');
h_fig3 = findobj(h_figs,'tag','wave_clus_aux1');
h_fig2 = findobj(h_figs,'tag','wave_clus_aux2');
h_fig1 = findobj(h_figs,'tag','wave_clus_aux3');
set(h_fig4,'userdata',USER_DATA)
set(h_fig3,'userdata',USER_DATA)
set(h_fig2,'userdata',USER_DATA)
set(h_fig1,'userdata',USER_DATA)

%SETTING OF SPIKE FEATURES OR PROJECTIONS
% --------------------------------------------------------------------
function spike_shapes_button_Callback(hObject, eventdata, handles)
set(gcbo,'value',1);
set(handles.spike_features_button,'value',0);
USER_DATA = get(handles.wave_clus_figure,'userdata');
cluster_results = USER_DATA{10};
handles.setclus = 1;
handles.force = 0;
handles.merge = 0;

handles.undo = 0;
handles.minclus = cluster_results(1,5);
plot_spikes(handles);
% -------------------------------------------------------------------
function spike_features_button_Callback(hObject, eventdata, handles)
set(gcbo,'value',1);
set(handles.spike_shapes_button,'value',0);
USER_DATA = get(handles.wave_clus_figure,'userdata');
cluster_results = USER_DATA{10};
handles.setclus = 1;
handles.force = 0;
handles.merge = 0;

handles.undo = 0;
handles.minclus = cluster_results(1,5);
plot_spikes(handles);


%SETTING OF SPIKE PLOTS
% --------------------------------------------------------------------
function plot_all_button_Callback(hObject, eventdata, handles)
set(hObject,'value',1);
set(handles.plot_average_button,'value',0);
USER_DATA = get(handles.wave_clus_figure,'userdata');
cluster_results = USER_DATA{10};
handles.setclus = 1;
handles.force = 0;
handles.merge = 0;

handles.undo = 0;
handles.minclus = cluster_results(1,5);
plot_spikes(handles);
% --------------------------------------------------------------------
function plot_average_button_Callback(hObject, eventdata, handles)
set(hObject,'value',1);
set(handles.plot_all_button,'value',0);
USER_DATA = get(handles.wave_clus_figure,'userdata');
cluster_results = USER_DATA{10};
handles.setclus = 1;
handles.force = 0;
handles.merge = 0;

handles.undo = 0;
handles.minclus = cluster_results(1,5);
plot_spikes(handles);


%SETTING OF ISI HISTOGRAMS
function isi_nbins_Callback(hObject, eventdata, handles)
b_name = get(hObject,'Tag');
cn = regexp(b_name, '\d+', 'match');
USER_DATA = get(handles.wave_clus_figure,'userdata');
par = USER_DATA{1};
%cluster_results = USER_DATA{10};
eval(['par.nbins' cn{1}  '= str2num(get(hObject, ''String''));']);

USER_DATA{1} = par;
set(handles.wave_clus_figure,'userdata',USER_DATA);
draw_histograms(handles,  str2double(cn{1}),USER_DATA);

% --------------------------------------------------------------------
function isi_bin_step_Callback(hObject, eventdata, handles)
b_name = get(hObject,'Tag');
cn = regexp(b_name, '\d+', 'match');
USER_DATA = get(handles.wave_clus_figure,'userdata');
par = USER_DATA{1};
%cluster_results = USER_DATA{10};
eval(['par.bin_step' cn{1}  '= str2num(get(hObject, ''String''));']);

USER_DATA{1} = par;
set(handles.wave_clus_figure,'userdata',USER_DATA);
draw_histograms(handles, str2double(cn{1}),USER_DATA);
            

%SETTING OF ISI BUTTONS
% --------------------------------------------------------------------
function isi_accept_button_Callback(hObject, eventdata, handles)
set(hObject,'value',1);
b_name = get(gcbo,'Tag');
cn = regexp(b_name, '\d+', 'match');
eval(['set(handles.isi' cn{1} '_reject_button,''value'',0);']);

function isi_reject_button_Callback(hObject, eventdata, handles,developer_mode)
set(hObject,'value',1);
b_name = get(gcbo,'Tag');
cn = str2double(regexp(b_name, '\d+', 'match'));

eval(['set(handles.isi' int2str(cn) '_accept_button,''value'',0);'])
USER_DATA = get(handles.wave_clus_figure,'userdata');
classes = USER_DATA{6};
if cn == 3
    if nnz(classes==3)==0
        nlab = imread('filelist_wc.xlj','jpg'); 
        figure('color','k'); image(nlab); axis off; set(gcf,'NumberTitle','off');
    end
end

if developer_mode
    if get(handles.pumenu_reject,'Value')==1
        rejected = USER_DATA{15};
        USER_DATA{16} = rejected; %update bk of rejected spikes
        rejected(classes==cn) = true;
        USER_DATA{15} = rejected;
   else
        USER_DATA{16} = USER_DATA{15};
   end
end
forced = USER_DATA{13};
USER_DATA{14} = forced;
forced(classes==cn) = 0;
USER_DATA{13} = forced;

classes(classes==cn) = 0;
USER_DATA{6} = classes;

clustering_results = USER_DATA{10};
USER_DATA{11} = clustering_results; % Save backup
clustering_results(:,2) = classes;
USER_DATA{10} = clustering_results; 


h_figs = get(0,'children');
h_fig{1} = findobj(h_figs,'tag','wave_clus_aux');
h_fig{2} = findobj(h_figs,'tag','wave_clus_aux1');
h_fig{3} = findobj(h_figs,'tag','wave_clus_aux2');
h_fig{4} = findobj(h_figs,'tag','wave_clus_aux3');
h_fig{5} = findobj(h_figs,'tag','wave_clus_aux4');
h_fig{6} = findobj(h_figs,'tag','wave_clus_aux5');
set(handles.wave_clus_figure,'userdata',USER_DATA);

for h = h_fig
    set(h{1},'userdata',USER_DATA)
end

set(hObject,'value',0);
eval(['cla(handles.spikes' int2str(cn) ',''reset'');']);
eval(['cla(handles.isi' int2str(cn) ',''reset'');']);
eval(['set(handles.isi' int2str(cn) '_accept_button,''value'',1);']);


% --- Executes on button press in undo_button.
function undo_button_Callback(hObject, eventdata, handles)
handles.force = 0;
handles.merge = 0;
handles.undo = 1;
handles.setclus = 1;

USER_DATA = get(handles.wave_clus_figure,'userdata');
par = USER_DATA{1};
clustering_results_bk = USER_DATA{11};
forced_bk =  USER_DATA{14};

USER_DATA{13} = forced_bk;

USER_DATA{15} = USER_DATA{16}; %use bk of rejected spikes

USER_DATA{6} = clustering_results_bk(:,2); % old gui classes
USER_DATA{10} = clustering_results_bk;
handles.minclus = clustering_results_bk(1,5);
USER_DATA{8} = clustering_results_bk(1,1); % old gui temperatures
set(handles.wave_clus_figure,'userdata',USER_DATA)
plot_spikes(handles) % plot_spikes updates USER_DATA{11}
set(handles.min_clus_edit,'string',num2str(handles.minclus));

if isfield(handles,'force_unforce_button')
    if any(forced_bk)
        set(handles.force_unforce_button,'Value',1)
        set(handles.force_unforce_button,'String','FORCED')
    %set(handles.change_temperature_button,'enable','off');
    else
        set(handles.force_unforce_button,'Value',0)
        set(handles.force_unforce_button,'String','Force')
    end
end


% --- Executes on button press in merge_button.
function merge_button_Callback(hObject, eventdata, handles)
handles.force = 0;
handles.merge = 1;
handles.undo = 0;
handles.setclus = 1;

USER_DATA = get(handles.wave_clus_figure,'userdata');
clustering_results = USER_DATA{10};
handles.minclus = clustering_results(1,5);
USER_DATA{16} = USER_DATA{15}; %use bk of rejected spikes
set(handles.wave_clus_figure,'userdata',USER_DATA);
plot_spikes(handles)


% --- Change min_clus_edit     
function max_force_dist_edit_Callback(hObject, eventdata, handles)
    USER_DATA = get(handles.wave_clus_figure,'userdata');
    par = USER_DATA{1};  
    par.template_sdnum = str2num(get(hObject, 'String'));
    USER_DATA{1} = par;
    set(handles.wave_clus_figure,'userdata',USER_DATA);

%SETTING OF FORCE MEMBERSHIP
% --------------------------------------------------------------------
function force_button_Callback(hObject, eventdata, handles)
USER_DATA = get(handles.wave_clus_figure,'userdata');
par = USER_DATA{1};
spikes = USER_DATA{2};
classes = USER_DATA{6};
inspk = USER_DATA{7};
forced = USER_DATA{13};
rejected = USER_DATA{15};
USER_DATA{16} = rejected;

if get(handles.fix1_button,'value') ==1     
    fix_class = USER_DATA{20}';
    classes(fix_class) = -1;
end
if get(handles.fix2_button,'value') ==1     
    fix_class = USER_DATA{21}';
    classes(fix_class) = -1;
end
if get(handles.fix3_button,'value') ==1     
    fix_class = USER_DATA{22}';
    classes(fix_class )= -1;
end
% Get fixed clusters from aux figures
for i=4:par.max_clus
    eval(['fixx = par.fix' num2str(i) ';']);
    if fixx == 1
        fix_class = USER_DATA{22+i-3}';
        classes(fix_class) = -1;
    end
end

to_force = (~rejected)' & (classes==0);
switch par.force_feature
    case 'spk'
        f_in  = spikes(classes>0,:);
        f_out = spikes(to_force,:);
    case 'wav'
        if isempty(inspk)
            set(handles.file_name,'string','Calculating spike features ...');
            [inspk] = wave_features(spikes,par);        % Extract spike features.
            USER_DATA{7} = inspk;
        end
        f_in  = inspk(classes>0,:);
        f_out = inspk(to_force,:);
end

class_in = classes(classes>0);
class_out = force_membership_wc(f_in, class_in, f_out, par);
USER_DATA{14} = forced;                     % Save force in force_bk.
forced = forced(:) | to_force(:);

classes(to_force) = class_out;
USER_DATA{13} = forced;
USER_DATA{6} = classes(:)';
USER_DATA{16} = USER_DATA{15}; %update bk of rejected spikes
set(handles.wave_clus_figure,'userdata',USER_DATA)
clustering_results = USER_DATA{10};
handles.minclus = clustering_results(1,5);
handles.setclus = 1;
handles.force = 1;
handles.merge = 0;

handles.undo = 0;
plot_spikes(handles);

function unforce_button_Callback(hObject, eventdata, handles)
    USER_DATA = get(handles.wave_clus_figure,'userdata');
    forced = USER_DATA{13};
    classes = USER_DATA{6};
    par = USER_DATA{1};
    USER_DATA{14} = forced;     %save forced in forced_bk
    new_forced = zeros(size(forced));
    % Fixed clusters are not considered for forcing
    if get(handles.fix1_button,'value') ==1     
        fix_class = USER_DATA{20}';
        new_forced(fix_class) =forced(fix_class);
    end
    if get(handles.fix2_button,'value') ==1     
        fix_class = USER_DATA{21}';
        new_forced(fix_class) =forced(fix_class);
    end
    if get(handles.fix3_button,'value') ==1     
        fix_class = USER_DATA{22}';
        new_forced(fix_class) =forced(fix_class);
    end
    % Get fixed clusters from aux figures
    for i=4:par.max_clus
        eval(['fixx = par.fix' num2str(i) ';']);
        if fixx == 1
            fix_class = USER_DATA{22+i-3}';
            new_forced(fix_class) =forced(fix_class);
        end
    end
    rejected = USER_DATA{15};
    USER_DATA{16} = rejected; %update bk of rejected spikes
    classes(forced(:) & (~new_forced(:)) & (~rejected(:))) = 0;  %the elements that before were forced but it isn't force any more, pass to class 0
    handles.setclus = 1;
    handles.force = 0;
    handles.merge = 0;
    
    handles.undo = 0;
    USER_DATA{6} = classes(:)';
    USER_DATA{13} = new_forced;
    
    set(handles.wave_clus_figure,'userdata',USER_DATA)
    plot_spikes(handles);
    
    
function reject2clus_Callback(hObject, eventdata, handles)
    USER_DATA = get(handles.wave_clus_figure,'userdata');

    classes = USER_DATA{6};
    
    rejected = USER_DATA{15};
    USER_DATA{16} =  rejected;     %update bk of rejected spikes
    clus_n = max(classes) + 1;
    classes(rejected)= clus_n;
    USER_DATA{15} = false(size(rejected));
    
    handles.setclus = 1;
    handles.force = 0;
    handles.merge = 0;
    
    handles.undo = 0;
    USER_DATA{6} = classes(:)';
    USER_DATA{14} = USER_DATA{13};
    set(handles.wave_clus_figure,'userdata',USER_DATA)
    plot_spikes(handles);

       
function force_type_cb_Callback(hObject, handles)
%str = get(hObject, 'String');
val = get(hObject,'Value');
force_list{1}=[];
force_list{2}='center';
force_list{3}='nn';
force_list{4}='mahal';
force_list{5}='ml';
if val ~= 1
    USER_DATA = get(handles.wave_clus_figure,'userdata');
    par = USER_DATA{1};
    par.template_type = force_list{val};
    USER_DATA{1} = par ;
    set(handles.wave_clus_figure,'userdata',USER_DATA);
end


% --- Executes on button press in Plot_polytrode_channels_button.
function Plot_polytrode_button_Callback(hObject, eventdata, handles)
USER_DATA = get(handles.wave_clus_figure,'userdata');
par = USER_DATA{1};
if par.channels > 1
    Plot_polytrode(handles)
end


function  logo_axes_CreateFcn(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.

matlabImage = imread('logo.png');
image(matlabImage,'Parent',hObject);
axis(hObject, 'off');
axis(hObject, 'image');

% --- Executes during object creation, after setting all properties.
function isi_line_CreateFcn(hObject, eventdata, handles)
% hObject    handle to isi0_bin_step (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc
    set(hObject,'BackgroundColor','white');
else
    set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end


% --- Executes during object creation, after setting all properties.
function min_clus_edit_CreateFcn(hObject, eventdata, handles)
% hObject    handle to min_clus_edit (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end