function [varargout] = zexst(varargin)
global t zeng zeng2
switch varargin{1}
case 'initial'
%FEA_Ve
%----------------------------------------------------
delete(findobj('type','figure','tag','zexst'))
zexst('DeleteFcn')
%----------------------------------------------------
%Initializing;
t=[];
zeng=[];
zeng2=[];
zeng.temperature=37;
zeng.Iinstim=[];
zeng.Iexstim=[];
zeng.re=50;
zeng.tf=10;%ms
zeng.dt=10;%us
zeng.dtmode=1; %1=fix, 2=var(coarse) 3=var(fine) 4=var(user defined)
zeng.dtmin =0.00001; %(ms).
zeng.dtmax =0.05; %(ms).
zeng.dv=[0 0; %(mv) is used when dt is variable (dtmode = 2-4)
2 10; %dtmode=2: [dvmin(mV) dvmax(mV)] - coarse
1 5; %dtmode=3: [dvmin(mV) dvmax(mV)] - fine
2 10]; %dtmode=4: [dvmin(mV) dvmax(mV)] - the GUI is not implemented yet.
zeng.dtstart=[0; %(us) used when dt is variable (dtmode = 2-4)
1;
0.2;
1];
%---------------------------------------------------
zeng2.file='Ex_03_simple_axon.m';
zeng2.method='V_backward';
zeng2.cd=cd;
zeng2.FEA=[]; %use for Finite Element Analysis
zeng2.FILESEP=filesep;
zeng2.setup=[];
zeng2.var=[];
zeng2.varlist=cell(1);
zeng2.notreadytorun=0; %set it to 0 to stop the "Calculate" when there is an error in creating dummy.
zeng2.options.vestim=1; %1) calculated or 2) imported
zeng2.backup.Iexstim=[];
zeng2.amp=1; %zeng2.amp is multiplied to the amplitude of "both Ve and Iin stimulators".
%It is convinient for threshold detection.
%For Iin(WaveForm), zeng2.amp is used at zrun
zeng2.rundisp =1; %1=show the cal-progress window and the cal time.
%0=do not show anything. Good for running analysis
zeng2.singular=0; %for detecting the singular
%---------------------------------------------------
ScreenSize=get(0,'ScreenSize');
FG_Size=[5 ScreenSize(4)-30-40 220 30];
exst.figure = figure('Color',[0.8 0.8 0.8], ...
'PaperUnits','points', ...
'DeleteFcn','zexst(''DeleteFcn'');',...
'Position',FG_Size, ...
'tag','zexst', ...
'menu','none',...
'Name','NeuroCal',...
'NumberTitle','off',...
'Resize','off',...
'ToolBar','none');
set(exst.figure,'position',FG_Size);% stupid, but I need it for WinXP
exst.text.file = uicontrol('Parent',exst.figure, ...
'Units','pixel', ...
'BackgroundColor',[0.8 0.8 0.8], ...
'HorizontalAlignment','left',...
'ListboxTop',0, ...
'Position',[5 5 200 22], ...
'String',['Model : ' zeng2.file], ...
'Style','text', ...
'Tag','StaticText1');
exst.menu.file(1)=uimenu('parent',exst.figure,'label','File');
exst.menu.file(2)=uimenu('parent',exst.menu.file(1),'label','Open model' ,'callback','zexst(''open model file'')');
exst.menu.file(3)=uimenu('parent',exst.menu.file(1),'label','Open Analysis','callback','zexst(''Open Analysis'')');
exst.menu.setting(1)=uimenu('parent',exst.figure,'label','Setting');
exst.menu.setting(2)=uimenu(exst.menu.setting(1),'label','Time' ,'callback','gui_time(''initial'',gcf)');
exst.menu.setting(3)=uimenu(exst.menu.setting(1),'label','Environment' ,'callback','gui_environment(''initial'',gcf)');
exst.menu.setting(4)=uimenu(exst.menu.setting(1),'label','Parameters' ,'callback','gui_var(''initial'',gcf)');
exst.menu.setting(5)=uimenu(exst.menu.setting(1),'label','Channels' ,'callback','gui_channel(''initial'',gcf)');
exst.menu.setting(6)=uimenu(exst.menu.setting(1),'label','Intracellular Stim','callback','gui_Iinstim(''initial'')');
exst.menu.setting(7)=uimenu(exst.menu.setting(1),'label','Extracellular Stim','callback','gui_Iexstim(''initial'')');
exst.menu.graph(1)=uimenu('parent',exst.figure,'label','Graph');
exst.menu.graph(2)=uimenu('parent',exst.menu.graph(1),'label','2D-Viewer vs time' ,'callback','zview2dt(''initial'',gcf)');
exst.menu.graph(3)=uimenu('parent',exst.menu.graph(1),'label','2D-Viewer vs space','callback','zview2ds(''initial'',gcf)');
exst.menu.graph(4)=uimenu('parent',exst.menu.graph(1),'label','3D-Viewer' ,'callback','zview3d(''initial'',gcf)');
exst.menu.opt(1)=uimenu('parent',exst.figure,'label','Options');
exst.menu.opt(2)=uimenu('parent',exst.menu.opt(1),'label','Ve-Calculated' ,'callback','zexst(''change options'')','tag','vestim','userdata',1);
exst.menu.opt(3)=uimenu('parent',exst.menu.opt(1),'label','Ve-Imported' ,'callback','zexst(''change options'')','tag','vestim','userdata',2);
set(findobj(exst.menu.opt,'tag','vestim','userdata',zeng2.options.vestim),'checked','on')
exst.menu.about=uimenu('parent',exst.figure,'label','About','callback','zexst(''about'')');
set(exst.figure,'userdata',exst);
zexst('open model file',zeng2.file)
gui_time('initial',exst.figure)
gui_var('initial',exst.figure);
zview3d('initial',exst.figure)
%----------------------------------------------------------
case 'change options'
if nargin==1
exst=get(gcbf,'userdata');
Tag=get(gcbo,'tag');
Setto=get(gcbo,'userdata');
else
Temp=findobj(0,'type','figure','Name','NeuroCal','tag','zexst');
exst=get(Temp,'userdata');
Tag=varargin{2};
Setto=varargin{3};
end
Temp=get(findobj(exst.menu.opt,'tag',Tag,'checked','on'),'userdata');
if Temp{1}==Setto
return
end
set(findobj(exst.menu.opt,'tag',Tag),'checked','off')
set(findobj(exst.menu.opt,'tag',Tag,'userdata',Setto),'checked','on')
eval(['zeng2.options.' Tag '=Setto;'])
switch Tag
case 'vestim'
temp1=findobj('type','figure','tag','gui_Iexstim');
temp2=findobj('type','figure','tag','gui_var');
switch Setto
case 1 %calculated
set(findobj(temp1,'tag','xyz'),'enable','on')
set(findobj(temp2,'tag','xyz'),'enable','on')
case 2 %imported
set(findobj(temp1,'tag','xyz'),'enable','off')
set(findobj(temp2,'tag','xyz'),'enable','off')
otherwise
zexst('err','Err in Setting Option for Ve')
end
end
case 'Open Analysis'
exst=get(gcbf,'userdata');
[Filename Path]=uigetfile([zeng2.cd zeng2.FILESEP 'Analysis' zeng2.FILESEP '*.m']);
if ~strcmp('0',num2str(Filename))
temp=find(Filename=='.');
if isempty(temp)
feval(Filename,'initial',gcbf)
else
feval(Filename(1:(temp(1)-1)),'initial',gcbf)
end
end
case 'DeleteFcn'
delete(findobj('type','figure','tag','zview2dt'))
delete(findobj('type','figure','tag','zview2ds'))
delete(findobj('type','figure','tag','zview3d'))
delete(findobj('type','figure','tag','gui_Iinstim'))
delete(findobj('type','figure','tag','gui_Iexstim'))
delete(findobj('type','figure','tag','gui_envi'))
delete(findobj('type','figure','tag','gui_time'))
delete(findobj('type','figure','tag','gui_var'))
delete(findobj('type','figure','tag','gui_channel'))
delete(findobj('type','figure','tag','ZengAnalysis'))
case 'open model file'
if nargin==1
exst=get(gcbf,'userdata');
[Filename Path]=uigetfile([zeng2.cd zeng2.FILESEP 'model' zeng2.FILESEP '*.m']);
else %=2
exst=findobj('type','figure','tag','zexst','name','NeuroCal');
exst=get(exst,'userdata');
Filename=varargin{2};
Path=[];
end
if ~strcmp('0',num2str(Filename))
tempzeng=Filename(1)+0;
if (tempzeng>=65&tempzeng<=90) | (tempzeng>=97&tempzeng<=122)
else
zexst('err',['Please rename the file name to something else beginning with a charactor a-z']);
return
end
dot=find(Filename=='.');
if ~isempty(dot)
Filename=Filename(1:(dot-1));
end
zeng2.file=Filename;
set(exst.text.file,'String',['Model : ' Filename ])
%--------------------------------
%clear varibles
if ~isempty(zeng2.var)
for temp=1:length(zeng2.varlist)
clear('global',zeng2.varlist{temp})
end
end %if ~isempty(zeng2.var)
%-------------------------------------------------------
zeng2.var=[];
zeng2.varlist=cell(1);
zeng2.dummyvar=[]; %for view2-3d
zeng2.dummymodel=[];
zeng2.dummymodelindex=[];
zeng2.setup=[];
zeng2.setup.connect=[];%Needed because [zeng.setup.connect; a b c d ] will be used in CONNECT
zeng2.setup.stimIin=[];
zeng2.setup.stimVe=[];
zeng2.setup.n_para=0; % Good for checking if you have created the neural network
zeng.Iinstim=[];
zeng.Iexstim=[];
t=[];
if isempty(Path)
eval(Filename)
else
tempzeng=length(Path);
if Path(tempzeng)=='\'
Path(tempzeng)=[];
end
addpath(Path)
eval(Filename)
end
create_dummyvar
zexst('Update GUI')
end %if ~strcmp('0',num2str(Filename))
case 'Update GUI'
%update Time----------------------------------------------------------------------------
tempzeng=findobj('type','figure','tag','gui_time');
if ~isempty(tempzeng)
settime=get(tempzeng,'userdata');
set(settime.pop.dt ,'value',zeng.dtmode)
set(settime.edit.tf,'string',num2str(zeng.tf))
set(settime.edit.dt,'string',num2str(zeng.dt))
end
%update environment----------------------------------------------------------------------------
tempzeng=findobj('type','figure','tag','gui_envi');
if ~isempty(tempzeng)
envi=get(tempzeng,'userdata');
set(envi.edit.temp,'string',num2str(zeng.temperature))
set(envi.edit.re ,'string',num2str(zeng.re))
end
%update View2d 3d----------------------------------------------------------------------------
close(findobj('type','figure','name','2D-Time : Plot'));
close(findobj('type','figure','name','2D-Space : Plot'));
close(findobj('type','figure','name','3D-Viewer : Plot'));
tempzeng=[findobj('type','figure','tag','zview2dt')];
if ~isempty(tempzeng)
for i=1:length(tempzeng)
view=get(tempzeng(i),'userdata');
view.plotvariable.var=[]; %[para var seg]
view.plotvariable.legend=cell(0);
set(tempzeng(i),'userdata',view);
%--------------------------------------------------------
%important
set(get(view.axes,'children'),'DeleteFcn','')
axes(view.axes)
legend off
delete(get(view.axes,'children'))
%--------------------------------------------------------
zview2dt('plot',tempzeng(i))
end
end
tempzeng=[findobj('type','figure','tag','zview2ds')];
if ~isempty(tempzeng)
for i=1:length(tempzeng)
view=get(tempzeng(i),'userdata');
view.plotvariable.var=[]; %[para var length]
view.plotvariable.legend=cell(0);
set(tempzeng(i),'userdata',view);
%--------------------------------------------------------
%important
set(get(view.axes,'children'),'DeleteFcn','')
axes(view.axes)
legend off
delete(get(view.axes,'children'))
%--------------------------------------------------------
zview2ds('plot',tempzeng(i))
end
end
tempzeng=findobj('type','figure','tag','zview3d');
if ~isempty(tempzeng)
for i=1:length(tempzeng)
view=get(tempzeng(i),'userdata');
view.plotvariable.var=[]; %[para var seg]
set(tempzeng(i),'userdata',view);
delete(get(view.axes,'children'))
zview3d('plot',tempzeng(i))
end
end
%update Iinstim----------------------------------------------------------------------------
tempzeng=findobj('type','figure','tag','gui_Iinstim');
if ~isempty(tempzeng)
temppo=get(tempzeng,'position');
close(tempzeng)
if ~isempty(zeng.Iinstim)
gui_Iinstim('initial',temppo)
end
end
%update Iexstim----------------------------------------------------------------------------
tempzeng=findobj('type','figure','tag','gui_Iexstim');
if ~isempty(tempzeng)
temppo=get(tempzeng,'position');
close(tempzeng)
if ~isempty(zeng.Iexstim)
gui_Iexstim('initial',temppo)
end
end
%update setting:parameters----------------------------------------------------------------------------
tempzeng=findobj('type','figure','tag','gui_var');
if ~isempty(tempzeng)
for i=1:length(tempzeng)
gui_var('update',tempzeng(i),1);
end
end
%update setting:Channel----------------------------------------------------------------------------
tempzeng=findobj('type','figure','tag','gui_channel');
if ~isempty(tempzeng)
for i=1:length(tempzeng)
gui_channel('update',tempzeng(i),1);
end
end
case 'calculate'
%To disable the buttons
%set(findobj('type','uicontrol','tag','Pushbutton'),'enable','off')
%-----------
if nargin==2 % Called by Find_Ith for detect the firing
varargout{1}=-1; % -1=Bad setting, 0=not fired, 1=fired
end
%-----------------------------------
%Before run
zeng2.notreadytorun=0;
create_initial
if zeng2.notreadytorun
set(findobj('type','uicontrol','tag','Pushbutton'),'enable','on')
return
end
create_dummyvar
if zeng2.notreadytorun
set(findobj('type','uicontrol','tag','Pushbutton'),'enable','on')
return
end
create_setting
if zeng2.notreadytorun
set(findobj('type','uicontrol','tag','Pushbutton'),'enable','on')
return
end
create_matrix
if zeng2.notreadytorun
set(findobj('type','uicontrol','tag','Pushbutton'),'enable','on')
return
end
create_dummymodel
if zeng2.notreadytorun
set(findobj('type','uicontrol','tag','Pushbutton'),'enable','on')
return
end
create_stimIin
if zeng2.notreadytorun
set(findobj('type','uicontrol','tag','Pushbutton'),'enable','on')
return
end
create_stimVe
if zeng2.notreadytorun
set(findobj('type','uicontrol','tag','Pushbutton'),'enable','on')
return
end
%ckeck dt
if isempty(zeng.dt)| zeng.dt<(zeng.dtmin*1000) | zeng.dt>(zeng.dtmax*1000) | ~isreal(zeng.dt)
zexst('err',['"dt" needs to be in between ' num2str(zeng.dtmin*1000) '-' num2str(zeng.dtmax*1000) 'us !!!, You know?']);
set(gcbo,'enable','on')
return
end
%check pulse width ----------------------------------
if zeng.dtmode==1 %fix time step
if isempty(zeng.Iinstim)
else
tempzeng=zeng.dt/1000*5;
for i=1:length(zeng.Iinstim)
if zeng.Iinstim(i).dur<tempzeng & isnumeric(zeng.Iinstim(i).amp)
zexst('err',['The time step has to be' char(13) 'at least 5 times smaller than the smallest pulse width.']);
set(gcbo,'enable','on')
return
end
end
end
if isempty(zeng.Iexstim)
else
tempzeng=zeng.dt/1000*5;
for i=1:length(zeng.Iexstim)
if zeng.Iexstim(i).dur<tempzeng & isnumeric(zeng.Iexstim(i).amp)
zexst('err',['The time step has to be' char(13) 'at least 5 times smaller than the smallest pulse width.']);
set(gcbo,'enable','on')
return
end
end
end
end
%----------------------------------
zeng2.singular=0;
if nargin==1 %normal calculationg in Neurocal
zrun
if ~isempty(find(abs(zeng2.dummyvm)>7000))
zeng2.singular=1;
disp(['---Attention-------------------------------------------------------'])
disp(['Singular detected: This can caused by a large stimulation amplitude.'])
disp(['For Iinstim, the amp should be lower than 10uA.'])
disp(['For Iexstim, make sure the coordinate of the stimulator is not right at a node.'])
disp(['-------------------------------------------------------------------'])
return
end
zdummy_return
zcal_i
elseif nargin==2 %detecting the firing
varargout{1}=zrun(varargin{2}); %varout =0(not fired), 1(fired) - varin=[Detect_Start(us) Detect_Threshold(mV)]
if ~isempty(find(abs(zeng2.dummyvm)>7000))
zeng2.singular=1;
disp(['---Attention-------------------------------------------------------'])
disp(['Singular detected: This can caused by a large stimulation amplitude.'])
disp(['For Iinstim, the amp should be lower than 10uA.'])
disp(['For Iexstim, lower the stimulation amplitude and make sure the coordinate of the stimulator is not right at a node.'])
disp(['-------------------------------------------------------------------'])
varargout{1}== -1;
return
end
end
%----------------------------------
%To enable the button
set(findobj('type','uicontrol','tag','Pushbutton'),'enable','on')
%update View after the calculation------------------------------------------------------
temp=findobj('type','figure','tag','zview2dt');
if ~isempty(temp)
for v=1:length(temp)
zview2dt('update',temp(v));
temp1=get(temp(v),'userdata');
temp2=findobj('type','figure','Tag',[num2str(temp1.figure) num2str(temp1.axes)]);
if ~isempty(temp2)
zview2dt('update-segment',temp2)
end
end
end
temp=findobj('type','figure','tag','zview2ds');
if ~isempty(temp)
for v=1:length(temp)
zview2ds('update',temp(v));
end
end
temp=[findobj('type','figure','tag','zview3d')];
if ~isempty(temp)
for v=1:length(temp)
zview3d('update',temp(v));
end
end
%----------------------------------
case 'err'
ScreenSize=max(reshape(get(0,'screensize'),2,2)');
E = dialog('name','Error',...
'tag','ZengError');
set(E,'position',[ScreenSize(1)/2-320/2 ScreenSize(2)/2-160/2 320 160]);
Temp.FG_Size=get(E,'position');
uicontrol('Parent',E, ...
'BackgroundColor',get(E,'Color'), ...
'fontsize',12,...
'fontweight','bold',...
'Position',[1 120 320 20], ... 'String','Are you nuts !!!', ...
'String','Hey man !!!', ...
'Style','text');
uicontrol('Parent',E, ...
'BackgroundColor',get(E,'Color'), ...
'HorizontalAlignment','center',...
'Position',[1 40 Temp.FG_Size(3) 60], ...
'String',varargin{2}, ...
'Style','text');
uicontrol('Parent',E, ...
'BackgroundColor',[0.85 0.8 0.75], ...
'callback','close',...
'Units','pixel', ...
'Position',[135 15 57.75 24],...
'string','OK');
case 'about'
ScreenSize=max(reshape(get(0,'screensize'),2,2)');
About = dialog('name','About Exstim');
set(About,'Position',[ScreenSize(1)/2-320/2 ScreenSize(2)/2-160/2 320 200]);
FG_Size=get(About ,'position');
uicontrol('Parent',About , ...
'BackgroundColor',get(About ,'Color'), ...
'fontsize',12,...
'fontweight','bold',...
'ForegroundColor',[0 0 1 ],...
'Position',[1 140 320 50], ...
'String',['Neural Engineering Center' char(13) 'Case Western Reserve University'], ...
'Style','text');
uicontrol('Parent',About , ...
'BackgroundColor',get(About ,'Color'), ...
'fontsize',14,...
'fontweight','normal',...
'ForegroundColor',[1 0 0 ],...
'Position',[1 120 320 20], ...
'String',['nec.cwru.edu'], ...
'Style','text');
uicontrol('Parent',About , ...
'BackgroundColor',get(About ,'Color'), ...
'fontsize',10,...
'fontweight','bold',...
'ForegroundColor',[0 0 1 ],...
'Position',[1 60 320 50], ...
'String',['Version 1.0'], ...
'Style','text');
uicontrol('Parent',About , ...
'BackgroundColor',get(About ,'Color'), ...
'fontsize',10,...
'fontweight','normal',...
'ForegroundColor',[0 00 0 ],...
'Position',[1 35 320 50], ...
'String',['Zeng Lertmanorat (Thai boy)' char(13) 'zengzeng@hotmail.com'], ...
'Style','text');
uicontrol('Parent',About , ...
'callback','close',...
'Units','pixel', ...
'Position',[135 10 57.75 24],...
'string','OK');
end %switch
