function showBold( name, choice, curr, ave, multipanel, fig0, filename )
% showBold displays a series of bold curves of simulations all
% belonging to a simulation series.
%
% name : is either a path or a file name.
% 1. When name is a path, it is a path to the catalog which
% contains the simulations to be plotted. Those
% simulations should be located in directories found in
% a subdirectory of that path named DATA.
% 2. When name is a file name, it should be a file name
% containing the name SERIES. That file contains the
% simulations which are to be plotted
% choice: Type of bold signal. See bold.m for more
% information. Default = 5
% curr : If curr = 1, then synaptic currents are shown instead of
% BOLD signal. Default = 0
% ave : If ave = 1, then the average BOLD or current curve will
% be plotted, otherwise single curves will be
% plotted. Default = 0.
% multipanel: If multipanel = 1, then every signal will be plotted
% in its own panel. Otherwise, all signals will be
% plotted in the same panel. Default = 1.
% fig0 : The number of the figure where data should be plotted. Default = 1
%
% Change path names to suit your preferences. Places are marked % CHANGE %
if nargin < 1 | nargin > 7
disp( 'usage1: showBold( name ), ' )
disp( 'usage2: showBold( name, choice ), ' )
disp( 'usage3: showBold( name, choice, curr ), ' )
disp( 'usage4: showBold( name, choice, curr, ave ), ' )
disp( 'usage5: showBold( name, choice, curr, ave, multipanel ), ' )
disp( 'usage6: showBold( name, choice, curr, ave, multipanel, fig0), ' )
disp( 'usage7: showBold( name, choice, curr, ave, multipanel, fig0, filename ), ' )
disp( ' ' )
disp( 'CHOICES:' )
disp('1: Action Potentials from both inhibitory and excitatory populations')
disp('2: Action Potentials from excitatory population only')
disp('3: Sum of Excitatory Currents')
disp('4: Sum of Excitatory Currents onto Excitatory Cells')
disp('5: Sum of absolute values of all currents')
disp('6: Sum of all currents')
disp( ' ' )
disp( 'Do "help showBold" for further information' )
return
end
if nargin < 2
choice = 5;
end
if nargin < 3
curr = 0;
end
if nargin < 4
ave = 0;
end
if nargin < 5
multipanel = 1;
end
if nargin < 6
fig0 = 1;
end
if nargin < 7
saving = 0;
else
saving = 1;
end
fig0 = fig0-1;
smooth = 250;
rows = 4;
cols = 3;
thisdir = pwd;
% Is it a UNIX/Linux system or a Windows system
if( ispc )
pathdelimiter = '\';
rootsymbol = 'C:\'; % CHANGE %
if isempty( strmatch( rootsymbol, name ) )
name = strcat( thisdir, pathdelimiter, name );
end
home = 'C:\Documents and Settings\freedin.admin\Desktop\Neuron\STANDARDFILER'; % CHANGE %
fs = 10; %Fontsize
else
pathdelimiter = '/';
% Is name a relative path or file name?
if ~( name(1) == '~' | name(1) == pathdelimiter )
name = strcat( thisdir, pathdelimiter, name );
end
home = '/home/freedin/Neuron/STANDARDFILER/'; % CHANGE %
rootsymbol = '/'; % CHANGE %
fs = 14; %Fontsize
end
if( name(1) == '~' )
name = strcat( home, name(3:end) );
end
% Put all the directories containing simulations to be
% displayed in one long list
% alt 1: name is a path
if isempty( findstr( name, 'SERIES' ) )
name = strcat( name, pathdelimiter, 'DATA' );
d = getTree( name );
d(1) = [];
if length( d ) == 0
disp( 'No data in this catalog' )
return
end
else
% alt 2: name is a file named SERIES
fid = fopen( name );
if fid == -1
disp( 'Error: Your file name is invalid' )
return
end
d = [];
[ txt, pos ] = readUntil( fid, rootsymbol );
while pos >= 0
if( txt(end) == '~' )
txt = '~';
else
txt = '';
end
txt = strcat( txt, readUntil( fid, char(10) ) ); % char(10) = newline
d = [ d ; struct( 'name', txt ) ];
[ txt, pos ] = readUntil( fid, rootsymbol );
end
if length( d ) == 0
disp( 'No data in this catalog' )
return
end
end
pos = findstr( name, home );
if pos
titlename = strcat( '~', name( length( home ) + 1 : end ) );
else
titlename = name;
end
% printTitleName is the file name but changed into TeX format,
% so that TeX characters like _ and \ are changed inte \_ and \\
if ispc
printTitleName = [];
ind = find( titlename == '\' );
ind = [ 1 ind length( titlename ) ];
for i = 1:length( ind )-1
printTitleName = [ printTitleName titlename(ind(i):ind(i+1)) ];
end
else
printTitleName = titlename;
end
titlename = printTitleName;
ind = [ find( titlename == '_' | titlename == '^' ) length(titlename)+1 ];
printTitleName = titlename(1:ind(1)-1);
for i = 1:length( ind ) - 1
printTitleName = [ printTitleName '\' titlename(ind(i):ind(i+1)-1) ];
end
% plot the data in the catalogs in d
len = length( d );
% How many pages?
if multipanel == 1
pages = floor( (len-1) / (rows*cols) ) + 1;
for i = 1: pages
figure ( fig0+i )
clf
set( fig0+i,'Position', [ 300 * mod( ( i ), 2 ) 100 720 659 ] );
end
else
figure ( fig0+1 )
clf
set( fig0+1,'Position', [ 300 100 720 659 ] );
set( gcf, 'Name', 'BOLD' )
set( gcf, 'NumberTitle', 'off' )
end
% find number of subplots = no of modules in the nets
maxAntalModuler = 0;
for ind = 1 : len
[ t_SERIE{ind} B_SERIE{ind} ] = bold( d(ind).name, choice, curr, smooth );
maxAntalModuler = max( maxAntalModuler, length( B_SERIE{ind} ) );
end
for i = 1:maxAntalModuler
leg_SERIE{i} = [];
end
% plot bold curve for every module in every simulation
% Go through all simulations
color = 'brgky';
type = {'-','-.','--'};
zr = '000000000000';
maxlen = length( int2str( len ) );
mB = 100000;
MB = 0;
uB = 0;
if ave
aveB = zeros(length(B_SERIE{1}{i}),length(B_SERIE{1})+1);
end
for ind = 1 : len
if curr
t = t_SERIE{ind}/1000;
else
t = t_SERIE{ind};
end
B = B_SERIE{ind};
% plot bold curves for every module in a simulation
for i = 1:length( B )
indstr = int2str( ind );
indl = length( indstr );
leg = leg_SERIE{i};
leg = [ leg ; strcat( zr(1:maxlen-indl), indstr ) ];
leg_SERIE{i} = leg;
fignum = 1;
if ave
aveB(:,i+1) = aveB(:,i+1) + B{i}'/len;
aveB(:,1) = t_SERIE{1}';
else
if multipanel == 0
subplot(maxAntalModuler, 1, i);
plot( t, B{i}, strcat( color(mod(ind-1,length(color))+1), type{mod(ind-1,length(type))+1} ) )
else
fignum = floor((ind-0.5)/(rows*cols)) + 1;
figure(fig0+fignum)
subplot(rows, cols, ind-rows*cols*(fignum-1));
plot( t, B{i}, strcat( color(mod(i-1,length(color))+1), type{mod(i-1,length(type))+1} ) )
hold on
xlim([t(1) t(end)])
end
end
if curr
uB = max(uB, mean(B{i}));
mB = min(mB, min(B{i}));
else
xlim([t(1) t(end)])
mB = min(mB, min(B{i}));
MB = max(MB, max(B{i}));
end
hold on
% set( gca, 'XLim', [t(1) t(end)] )
set( gca, 'FontSize', fs )
if curr
if multipanel == 0
if i == 1
title( [ 'Bold curves in ' printTitleName ], 'FontSize', fs )
end
end
else
if multipanel == 0
if i == 1
title( [ 'Bold curves in ' printTitleName ], 'FontSize', fs )
end
end
%ylabel( ['Module ' int2str( i ) ' BOLD signal (%)'], 'FontSize', fs )
end
end
% set( gca, 'YLim', [0 N] )
% set( gca, 'XLim', Params(5:6) )
end
if ave
for i = 2:size(aveB,2)
plot(t, aveB(:,i), strcat( color(mod(i,length(color))+1), type{mod(i,length(type))+1} ) )
end
xlim([t(1) t(end)])
if curr == 0
ylim([mB MB])
else
ylim([mB 1.5*uB])
end
else
for ind = 1:len
fignum = floor((ind-0.5)/(rows*cols)) + 1;
figure(fig0+fignum)
subplot(rows, cols, ind-rows*cols*(fignum-1));
if curr == 0
ylim([mB MB])
else
ylim([mB 1.5*uB])
end
end
end
% set titles and labels
if multipanel == 0
figure( fig0+1 )
subplot( maxAntalModuler, 1, maxAntalModuler )
xlabel( 'time (s)', 'FontSize', fs )
for i = 1 : maxAntalModuler
subplot( maxAntalModuler, 1, i )
legend( leg_SERIE{i} )
set( gca, 'box', 'on' )
set( gca, 'FontSize', fs )
end
end
% adjust paper size for printing
for i = 1:fignum
figure(fig0+fignum)
set( gcf, 'PaperUnits', 'centimeters' );
set( gcf, 'PaperType', 'A4');
papersize = get( gcf, 'PaperSize' );
left = 0.02;
bottom = 0.02;
width = papersize( 1 ) - 2 * left;
height = papersize( 2 ) - 2 * left;
myfiguresize = [ left, bottom, width, height ];
set( gcf, 'PaperPosition', myfiguresize );
if saving
print( fig0+fignum, '-depsc2', [filename '_p' int2str(fignum) '.eps'] );
if ave
save( [filename '.dat'], '-ascii', 'aveB' )
end
end
end
