function LGNcircuit
% LGN_GUI Give input vector/function to the LGN relay cell and choose
% parameters. The GUI plots the resulting LGN response including separate
% components of the response, if requested.
% including the data files and data file path
file_reg = ['dataFiles' filesep '*.dat'];
file_struct = dir(file_reg);
filenames = cell(1, length(file_struct));
for ifile = 1:length(file_struct)
filenames(1,ifile)=cellstr(file_struct(ifile).name);
end
data_path = ['dataFiles' filesep];
addpath(data_path);
% Setting default parameter values
lgn_struct=struct('eta_ffi',0.7,'tau_rg',20,'tau_rig',50,'Delta_rig',0,...
'l_rON',-1,'w_fbON',0,'w_fbOFFx',0,'tau_rc',20,'Delta_fb',10,...
'l_cON',0.1,'l_cOFF',-0.1);
in_struct=struct('form','vec',...
'interpol_method','linear',...
'data_file',' ','mode','gui');
% Set properties for the parameters table
rowname = {'eta_ffi', 'tau_rg', 'tau_rig', 'Delta_rig', 'l_rON' 'w_fbON',...
'w_fbOFFx', 'tau_rc', 'Delta_fb', 'l_cON', 'l_cOFF'};
rowname_tab = {'eta_ffi', 'tau_rg (ms)', 'tau_rig (ms)', 'Delta_rig (ms)',...
'l_rON','w_fbON','w_fbOFFx', 'tau_rc (ms)', 'Delta_fb (ms)', 'l_cON',...
'l_cOFF'};
dat = {lgn_struct.eta_ffi;...
lgn_struct.tau_rg;...
lgn_struct.tau_rig;...
lgn_struct.Delta_rig;...
lgn_struct.l_rON;...
lgn_struct.w_fbON;...
lgn_struct.w_fbOFFx;...
lgn_struct.tau_rc;...
lgn_struct.Delta_fb;...
lgn_struct.l_cON;...
lgn_struct.l_cOFF};
columnname = {'Value'};
columnformat = {'numeric'};
columneditable = true;
columnwidth = {80};
ih1 = 1;
% Initialize and hide GUI at construction.
f_width=900;
f_height=900;
f = figure('Visible','off','Tag','gui',...
'Position',[0,100,f_width,f_height]);
% 'BackgroundColor',[0.5 0.5 0.5],...
% Define an axes that covers the whole figure
%ax_root = axes('position', [0,0,1.0,1.0]);
% Construct the components
bcgp = uipanel('Parent',f,'Units','pixels',...
'BackgroundColor',[.7 .7 .7],...
'Position',[0,0,f_width,f_height]);
mp = uipanel('Parent',f,'Title','LGNcircuit','Units','pixels',...
'Position',[570,160,315,720]);
% inputform_text = uicontrol(mp,'Units','pixels','Style','text',...
% 'String','Select input format','Position',[10,730,160,20]);
% inputform_pop = uicontrol(mp,'Units','pixels','Style','popupmenu',...
% 'String',{'Data file'},...
% 'Position',[10,695,180,35],...
% 'BackgroundColor','w',...
% 'Callback',{@popup_callback});
% ipf_help = uicontrol(mp,'Units','pixels','Style','pushbutton',...
% 'String','Help',...
% 'Position',[200,704,105,30],...
% 'Tag','ipf',...
% 'Callback',{@helpbutton_callback});
inputdata_text = uicontrol(mp,'Units','pixels','Style','text',...
'String','Data file',...
'Position',[10,665,100,20]);
inputdata_pop = uicontrol(mp,'Units','pixels',...
'Style','popupmenu',...
'String',filenames,...
'BackgroundColor','w',...
'Position',[10,630,180,30],...
'Callback',{@datapop_callback});
ipd_help = uicontrol(mp,'Units','pixels','Style','pushbutton',...
'String','Help',...
'Tag','ipd',...
'Position',[200,640,105,30],...
'Callback',{@helpbutton_callback});
% interpolate_text = uicontrol(mp,'Units','pixels','Style','text',...
% 'String','Numerical interpolation method','Position',[10,295,160,40]);
% interpolate_pop = uicontrol(mp,'Style','popupmenu',...
% 'String',{'linear','spline','pchip','nearest'},...
% 'Position',[10,270,180,30],'Tag','interpop',...
% 'BackgroundColor','w',...
% 'Callback',{@interpop_callback});
% intp_help = uicontrol(mp,'Units','pixels','Style','pushbutton',...
% 'String','Help',...
% 'Tag','intp',...
% 'Position',[200,274,105,30],...
% 'Callback',{@helpbutton_callback});
im_panel = uipanel('Parent',mp,...
'Title','Model system',...
'Units','pixels',...
'BackgroundColor','w',...
'Position',[10,325,295,291]);
im_ax = axes('Parent',im_panel,...
'Units','pixels','Position',[10,10,275,251]);
im=image(imread('model6.jpg'),'Parent',im_ax);
axis off;
%set(hObject,'Color','white');
param_panel = uipanel('Parent',mp,...
'Title','Loop parameters',...
'Units','pixels',...
'Position',[10,40,240,260]);
param_table = uitable(param_panel,...
'Data',dat,...
'ColumnName',columnname,...
'ColumnFormat',columnformat,...
'ColumnEditable',columneditable,...
'ColumnWidth',columnwidth,...
'RowName',rowname_tab,...
'Units','pixels',...
'Position',[5,5,230,230],...
'CellEditCallback',{@table_callback});
ptab_help = uicontrol(mp,'Units','pixels','Style','pushbutton',...
'String','Help',...
'Tag','ptab',...
'Position',[260, 45, 45, 247],...
'Callback',{@helpbutton_callback});
hold_check = uicontrol(f,'Style','checkbox',...
'String','Keep the current plot',...
'Value',0,...%'BackgroundColor','w',...
'Position',[640,110,180,30],...
'Callback',{@holdcheck_callback});
simulate = uicontrol(f,'Units','pixels','Style','pushbutton',...
'String','Simulate',...
'Position',[675,70,90,30],...
'Callback',{@simulatebutton_callback});
mailauthor = uicontrol(f,'Units','pixels','Style','pushbutton',...
'String','Contact Authors',...
'Position',[665,30,110,30],...
'Callback',{@mailauthor_callback});
messages = uicontrol(f,'Units','pixels','Style','text',...
'String',' ',...
'Position',[570,10,315,20]);
a1 = axes('Units','pixels','Tag','a1','Position',[90,90,450,405]);
grid on
a2 = axes('Units','pixels','Tag','a2','Position',[90,585,450,270]);
grid on
%a3 = axes('Position',[0.1,0.1,0.5,0.15]);
%grid on
% Initialize the code
% Change units of the figure, so it resizes automatically
set([f, bcgp, mp, ...
inputdata_text, inputdata_pop, ipd_help, ...
param_panel, param_table, ptab_help, ...
hold_check, simulate, mailauthor, messages, ...
a1, a2, im_panel,im_ax],'Units','normalized');
% inputform_text,inputform_pop,ipf_help,...
% interpolate_text,interpolate_pop,intp_help,...
% Generate initial data
set([a1,a2],'FontSize',20)
xlabel(a1,'Time t (ms)')
ylabel(a1,'LGN response')
ylabel(a2,'Cortical response')
%ylabel(a3,'Response')
% Make the GUI visible
set(f,'Visible','on')
function popup_callback(source, eventdata)
% Determine the selected input form
str = get(source, 'String');
val = get(source, 'Value');
% Set current input to the selected input
switch str{val};
case 'Data file'
in_struct.form = 'vec';
set(inputdata_text,'String','Data file');
set(inputdata_edit,'String','Provide a data file')
case 'Function'
in_struct.form = 'fnc';
set(inputdata_text,'String','Function name/path');
set(inputdata_edit,'String','Provide a function name')
case 'In-line'
in_struct.form = 'ilfnc';
set(inputdata_text,'String','In-line function');
set(inputdata_edit,'String','Provide an in-line function (use t for time)')
end
end
function helpbutton_callback(source,eventdata)
% Opens the respective help file
str = get(source, 'Tag');
hfile = ['helpFiles/' str '_help.pdf'];
open(hfile);
end
function datapop_callback(source, eventdata)
% Set data parameters
str = get(source, 'String');
val = get(source, 'Value');
switch in_struct.form
case 'vec'
data=load(str{val});
in_struct.t_in=data(:,1);
in_struct.r_in=data(:,2);
in_struct.data_file = str{val};
clear data
plot(a1,in_struct.t_in,in_struct.r_in, 'k--',...
'LineWidth',2);
set(a1,'FontSize',20)
legend(a1,'r_g')
ylabel(a1,'LGN response')
[y1max,y1min] = find_max(a1);
axis(a1,[0,max(in_struct.t_in),1.2*y1min,1.2*y1max])
set([a1,a2],'XGrid','on','YGrid','on')
case 'fnc'
in_struct.h=user_string;
case 'ilfnc'
end
end
function interpop_callback(source, eventdata)
% Determines the selected interpolation method
str = get(source,'String');
val = get(source,'Value');
in_struct.interpol_method = str{val};
end
function table_callback(source, eventdata) %#ok<INUSL>
% Update the parameter struct
i=eventdata.Indices(1);
val=str2double(eventdata.EditData);
parname=cell2mat(rowname(i));
lgn_struct.(parname)=val;
end
function holdcheck_callback(source, eventdata)
val = get(source,'Value');
if val == 0
set([a1,a2],'NextPlot','replace')
set(messages,'String',' ')
ih1=1;
elseif val ==1
set([a1,a2],'NextPlot','add')
end
end
function simulatebutton_callback(source, eventdata) %#ok<INUSD>
% Simulate and plot
% Create the waitbar
w = waitbar(0,'Computing','Position',[300,300,288,60]);
% load the first data file if there is no other data set
if strcmp(in_struct.data_file,' ')
str = get(inputdata_pop,'String');
val = get(inputdata_pop,'Value');
defaultf=str{val};
data=load(defaultf);
in_struct.t_in=data(:,1);
in_struct.r_in=data(:,2);
in_struct.data_file = defaultf;
clear data
end
% convolution of input with feedforward kernel
[in_struct.t_g,in_struct.r_g]=filterMyInput(lgn_struct, in_struct);
% evaluate the ode/dde governing the dynamics
if (lgn_struct.Delta_fb==0)
[t_rtmp,r_rtmp] = evaluate_ode(lgn_struct, in_struct);
else
[t_rtmp,r_rtmp] = evaluate_dde(lgn_struct, in_struct);
end
% Unpacking some parameters
l_rON = lgn_struct.l_rON;
l_cON = lgn_struct.l_cON;
l_cOFF = lgn_struct.l_cOFF;
% Setting the time vector
t_r=in_struct.t_g;
% smoothing the solution by interpolation
r_rn=interp1(t_rtmp,r_rtmp,t_r,in_struct.interpol_method);
r_cON = (r_rn - l_cON) .* (r_rn - l_cON >= 0);
r_cOFF = (-r_rn + l_cOFF) .* (-r_rn + l_cOFF >= 0);
r_r = (r_rn - l_rON) .* (r_rn - l_rON >=0) + l_rON;
clear t_rtmp r_rtmp r_cONtmp r_cOFFtmp
% set the time vector for the cortical solution, no delay in
% feedforward connection at the time...
t_c = t_r; % + lgn_struct.Delta_fb;
% pack the solution and time vectors into the 'in_struct'
in_struct.t_r=t_r;
in_struct.t_c=t_c;
in_struct.r_r=r_r;
in_struct.r_cON=r_cON;
in_struct.r_cOFF=r_cOFF;
% dump parameters and in/out data to file tmp.mat
save tmp.mat lgn_struct in_struct
% unpack input vectors
t_in=in_struct.t_in;
r_in=in_struct.r_in;
% ploting the results
pl1 = plot(a1,[t_in;t_r(end)],[r_in;r_in(end)], '--',t_r,r_r,'-',...
'LineWidth',2);
set(a1,'FontSize',20)
legend(a1,'r_g','r_r')
xlabel(a1,'Time t (ms)')
ylabel(a1,'LGN response')
[y1max,y1min] = find_max(a1);
axis(a1,[0,max(t_r)-120,1.2*y1min,1.2*y1max])
pl2 = plot(a2,[0; t_c],[0; r_cON],'-',...
[0;t_c],[0; r_cOFF],'--',...
'LineWidth',2);
set(a2,'FontSize',20)
legend(a2,'r_c^{ON}','r_c^{OFF}')
ylabel(a2,'Cortical response')
[y2max,y2min] = find_max(a2);
if y2max == y2min
axis(a2,[0,max(t_r),0,0.2])
else
axis(a2,[0,max(t_r)-120,1.2*y2min,1.2*y2max])
end
% plot(a3,[0; t_c],[0; r_cOFF],'k-',...
% 'LineWidth',2)
% set(a3,'FontSize',20)
% legend(a3,'r_c^{OFF}')
% xlabel(a3,'Time t (ms)')
% ylabel(a3,'Response')
% [y3max,y3min] = find_max(a3);
% axis(a3,[0,max(t_r),1.2*y3min,1.2*y3max])
set([a1,a2],'XGrid','on','YGrid','on')
% setting colors for successive plots
%h1=get(a1,'Children');
%ih1=length(h1)/2;
linecol = ['k','b','r','c','m','y'];
if get(hold_check,'Value') == 1
if ih1<length(linecol)
ih1=ih1+1;
col = linecol(ih1);
else
set(messages,'String','All colors chosen, black will be used')
col = 'k';
end
else
col = 'k';
end
set([pl1,pl2],'Color',col)
set(pl1(1),'Color','k')
close(w)
%set(messages,'String','Done');
end
function mailauthor_callback(source, eventdata)
web mailto:gaute.einevoll@nmbu.no
end
end
function [yxmax,yxmin] = find_max(ax)
% function to find the max point of the lines in a plot
hx=get(ax,'Children');
yxraw = get(hx,'YData');
if iscell(yxraw)
m = size(yxraw);
yxmax=0;
yxmin=0;
for icell = 1:m
yxdata = cell2mat(yxraw(icell));
yxmax_tmp = max(yxdata);
yxmin_tmp = min(yxdata);
if yxmax_tmp > yxmax
yxmax=yxmax_tmp;
end
if yxmin_tmp < yxmin
yxmin = yxmin_tmp;
end
end
else
yxmax=max(max(yxraw,[],2));
yxmin=min(min(yxraw,[],2));
end
end
