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crosscor.m
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crosscor.m
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function crosscor(action)
%*********************************************************************
% Ian's Surface Plots for XCor Raw Data sets
%
% This reads SMR / TXT files containing spike times, computes
% the cross-correlogram for many variables, and can generate surface
% plots of a defined portion of the cross-correlogram function
%
%*********************************************************************
global TimeInterval
global PlotType CMap ShadingType
global Lighting LightAdd
global SmoothType SmoothValue
global xdata xv
global george
global loop
global corrline
global datatype
global slope
global rerun
global hw
if nargin<1;
action='Initialize';
end
switch(action)
%-------------------------------------------------------------------
case 'Initialize' %assuming we have just started
%-------------------------------------------------------------------
crosscorfig %load our GUI
xv.matlabroot=regexprep(matlabroot,'Program files','Progra~1','ignorecase');
version='Cross Correlation Analysis: V3.1a';
if exist('c:\xdata.mat','file'); delete('c:\xdata.mat'); end
if exist('c:\crosstemp','file');delete('c:\crosstemp'); end
figpos(2); %position the figure
set(gcf,'Name', version)
set(gh('RatioValue'),'String',{'Don''t Use';'25ms Ratio';'50ms Ratio';'100ms Ratio'});
set(gh('IntBox'),'String',nums2strs(0.1:0.05:1));
set(gh('IntBox'),'Value',4)
set(gh('ShuffleNumber'),'String','trials-1');
xv.StartBin=-5; xv.EndBin=5;
xv.BinWidth=4; xv.Window=200;
xv.FromTime=0; xv.ToTime=Inf;
xv.StartTrial=1; xv.EndTrial=inf;
xv.firstunit=1; xv.secondunit=2;
xv.HeldVariable=3; xv.HeldValue=1;
xv.Shuffles=0; xv.pValue=0.05;
TimeInterval=500;
george=1;
PlotType='CheckerBoard';
ShadingType='interp';
Lighting='phong';
SmoothType='none';
SmoothValue=5;
CMap='jet';
datatype='';
slope=0;
hw=0;
xdata=[];
rerun='no';
set(gcf,'DefaultLineLineWidth',1.5);
set(gcf,'DefaultAxesLineWidth',1.5);
set(gca,'Layer','top'); %ticks go over data
set(gcf,'DefaultAxesTickDir','out'); %get ticks going out
set(0,'defaultaxesfontname','Georgia');
set(0,'defaulttextfontname','Georgia');
set(0,'defaulttextfontsize',8);
%-------------------------------------------------------------------
case 'Load'
%-------------------------------------------------------------------
set(gh('RatioValue'),'Value',1);
cla;
set(gca,'Tag','XCorAxis');
if strcmp(rerun,'yes') %see if we have to reload the data or not
%--Initial Parameters
hw=0;
slope=0;
file=xdata.filename;
xdata=[];
[p,basefilename,e]=fileparts(file);
%--Reloads from temporary file
rerun='no';
xdata.filetype = 'txt';
xdata.meta=loadvstext(file);
txtcomment=textread(strcat(p,'\',basefilename,'.cmt'),'%s','delimiter','\n','whitespace','');
txtprotocol=textread(strcat(p,'\',basefilename,'.prt'),'%s','delimiter','\n','whitespace','');
else
%--Initial Parameters
xdata=[];
% xv.StartTrial=1;
% xv.EndTrial=inf;
% set(gh('StartTrial'),'String','1');
% set(gh('EndTrial'),'String','inf');
hw=0;
slope=0;
%--Get filename and run appropriate frogbit script
[fn,pn]=uigetfile({'*.smr;*.txt;*.doc','All Spikes Filetypes (*.smr *.txt *.doc)';'*.smr','VS RAW DATA File (SMR)';'*.txt','VSX Output File (TXT)';'*.doc','XCor Output File (DOC)'},'Select File Typeto Load:');
if isequal(fn,0)|isequal(pn,0);set(gh('LoadText'),'String','No Data Loaded');errordlg('No File Selected or Found!');error('File not selected');end
[p,basefilename,e]=fileparts([pn fn]);
if regexpi(e,'\.smr')
if isdir([p '\' basefilename])
cd('c:\');
disp('Deleted existing directory...');
rmdir([p '\' basefilename],'s');
cd(p);
end
s=dos([xv.matlabroot,'\user\various\vsx\vsx.exe ',pn,fn]);
pn2 = fn(1:find(fn(:)=='.')-1);
s=dos(['dir ',pn,pn2]);
if s~=0; error('Sorry VSX cannot load the data!!! Make sure files do not have the read-only attribute set...'); end
xdata.filetype = 'smr';
xdata.meta=loadvstext([pn basefilename '\' basefilename '.txt']);
txtcomment=textread(strcat(pn,basefilename,'\',basefilename,'.cmt'),'%s','delimiter','\n','whitespace','');
txtprotocol=textread(strcat(pn,basefilename,'\',basefilename,'.prt'),'%s','delimiter','\n','whitespace','');
elseif strcmpi(e,'.txt')
xdata.filetype = 'txt';
xdata.meta=loadvstext([pn,fn]);
[p,basefilename,e]=fileparts([pn fn]);
txtcomment=textread(strcat(p,'\',basefilename,'.cmt'),'%s','delimiter','\n','whitespace','');
txtprotocol=textread(strcat(p,'\',basefilename,'.prt'),'%s','delimiter','\n','whitespace','');
elseif strcmpi(e,'.doc')
errordlg('Sorry, .doc files are an old format not safe to use, please use the .SMR!');
error('Sorry, .doc files are an old format not safe to use, please use the .SMR!');
else
errordlg('Sorry, unsupported file type loaded!')
error('File selection error')
end
end
[p,basefilename,e]=fileparts(xdata.meta.filename); %seperate out the file from the path
xdata.info=['===============PROTOCOL================';txtprotocol(2:end);'===============COMMENTS================';txtcomment(2:end)];
cd(p); %change to the directory where all the spike time files live
xdata.meta.filename(xdata.meta.filename=='\')='/'; %stops annoying TeX interpertation errors
t=find(xdata.meta.filename=='/');
xdata.runname=xdata.meta.filename((t(end-2))+1:t(end)); %we make a pretty name for titles
xdata.numvars=xdata.meta.numvars;
xdata.protocol.name=xdata.meta.protocol;
xdata.protocol.desc=xdata.meta.description;
xdata.protocol.filecomm=xdata.meta.comments;
xdata.protocol.date=xdata.meta.date;
xdata.repeats=xdata.meta.repeats;
if strcmp(xdata.filetype,'smr') || strcmp(xdata.filetype,'txt')
xdata.cycles=xdata.meta.cycles;
xdata.trialtime=xdata.meta.trialtime;
xdata.modtime=xdata.meta.modtime;
if isfield(xdata.meta,'tempfreq')
xdata.tempfreq=xdata.meta.tempfreq;
else
xdata.tempfreq=[];
end
end
%-Info from GUI
xdata.cellone=xv.firstunit;
xdata.celltwo=xv.secondunit;
%-Initialise File indexes
firstnumber=0; lastnumber=1;
switch xdata.numvars
case 0 %this means we have no variables
%--This section extracts variable info and sets up the data structure
firstnumber=min(xdata.meta.matrix(:,1)); %tells us the first and last file to load
lastnumber=max(xdata.meta.matrix(:,1));
%--Set Up the Struct Matrix to hold all the cross correlograms and header data
clear slope;
xdata.filename=xdata.meta.filename;
xdata.xtitle='';
xdata.xvalues=[];
xdata.xrange=1;
xdata.ytitle='';
xdata.yvalues=[];
xdata.yrange=1;
xdata.ztitle='';
xdata.zvalues=[];
xdata.zrange=1;
xdata.matrix=[];
xdata.xcorindex=0;
xdata.xcor.values=0;
xdata.xcor.time=0;
case 1
firstnumber=min(xdata.meta.matrix(:,1)); %tells us the first and last file to load
lastnumber=max(xdata.meta.matrix(:,1));
% This section extracts variable info and sets up the data structure
xdata.filename=xdata.meta.filename;
xdata.xtitle=regexprep(xdata.meta.var{1}.title,'w\\o','with O');
xdata.xrange=xdata.meta.var{1}.range;
xdata.xvalues=xdata.meta.var{1}.values;
xdata.ytitle='';
xdata.yvalues=[];
xdata.yrange=1;
xdata.ztitle='';
xdata.zvalues=[];
xdata.zrange=1;
xdata.matrix=[xdata.xrange];
xdata.xcorindex=0;
xdata.xcor.values=0;
xdata.xcor.time=0;
case 2 %2 variables
set(gh('SmoothingMenu'),'String',{'none';'cubic';'v4';'linear';'nearest'});
firstnumber=min(xdata.meta.matrix(:,1)); %tells us the first and last file to load
lastnumber=max(xdata.meta.matrix(:,1));
%--Set Up the Struct Matrix to hold all the cross correlograms and header data
xdata.filename=xdata.meta.filename;
xdata.xtitle=regexprep(xdata.meta.var{1}.title,'w\\ o','with O');
xdata.xrange=xdata.meta.var{1}.range;
xdata.xvalues=xdata.meta.var{1}.values;
xdata.ytitle=xdata.meta.var{2}.title;
xdata.yrange=xdata.meta.var{2}.range;
xdata.yvalues=xdata.meta.var{2}.values;
xdata.ztitle='';
xdata.zvalues=[];
xdata.zrange=1;
xdata.matrix=zeros(xdata.yrange,xdata.xrange);
xdata.xcorindex=0;
xdata.xcor.values=0;
xdata.xcor.time=0;
case 3
set(gh('SmoothingMenu'),'String',{'none';'cubic';'v4';'linear';'nearest'});
% this section juggles all the variables around for selection
x=header(3,find(header(3,:) == ':')+1:end);
xv.heldvar(1).name=x(find(x(1,:)~=' ')); %this strips spaces
x=str2num(header(4,find(header(4,:) == ':')+1:end));
xv.heldvar(1).range=x;
x=str2num(header(5,find(header(5,:) == ':')+1:end));
xv.heldvar(1).values=x;
x=header(6,find(header(6,:) == ':')+1:end);
xv.heldvar(2).name=x(find(x(1,:)~=' '));
x=str2num(header(7,find(header(7,:) == ':')+1:end));
xv.heldvar(2).range=x;
x=str2num(header(8,find(header(8,:) == ':')+1:end));
xv.heldvar(2).values=x;
x=header(9,find(header(9,:) == ':')+1:end);
xv.heldvar(3).name=x(find(x(1,:)~=' '));
x=str2num(header(10,find(header(10,:) == ':')+1:end));
xv.heldvar(3).range=x;
x=str2num(header(11,find(header(11,:) == ':')+1:end));
xv.heldvar(3).values=x;
xv.vars={xv.heldvar(1).name;xv.heldvar(2).name;xv.heldvar(3).name};
xv.inuse=1;
crossvar %our little variable selector GUI
pause(0.1)
xv.inuse=0;
xyh = [2 3 1;1 3 2;1 2 3]; %lookup table of variable combinations
h=xv.HeldVariable; %index of variable held
% now we pick out which our X and Y variables actually are from text
a=find(header(1,:)=='/');
x=header(1,a(end-2):end);
xdata.filename=x(find(x(1,:)~=' ')); %this strips spaces
xdata.filename=[xdata.filename ':' num2str(xv.BinWidth) 'ms BW ' ' {' num2str(xdata.cellone) '/' num2str(xdata.celltwo) '}' ' Method=' num2str(george) ];
xdata.xtitle=xv.heldvar(xyh(h,1)).name;
xdata.xtitle=xdata.xtitle(find(xdata.xtitle(1,:)~=' '));
xdata.xrange=xv.heldvar(xyh(h,1)).range;
xdata.xvalues=xv.heldvar(xyh(h,1)).values;
xdata.ytitle=xv.heldvar(xyh(h,2)).name;
xdata.ytitle=xdata.ytitle(find(xdata.ytitle(1,:)~=' '));
xdata.yrange=xv.heldvar(xyh(h,2)).range;
xdata.yvalues=xv.heldvar(xyh(h,2)).values;
xdata.heldvar=xv.heldvar(xyh(h,3)).name;
xdata.heldvar=xdata.heldvar(find(xdata.heldvar(1,:)~=' '));
xdata.heldvalue=xv.heldvar(xyh(h,3)).values;
xdata.heldvalue=xdata.heldvalue(xv.HeldValue);
xdata.matrix=zeros(xdata.yrange,xdata.xrange);
xdata.xcorindex=0;
xdata.xcor.values=0;
xdata.xcor.time=0;
%--For filename indexing
firstnumber=1;
lastnumber=xdata.xrange*xdata.yrange;
end
%-Bar to show progress
h = waitbar(0,'Loading Raw Data and Computing Cross-Correlograms...');
%-Loads spike data for all variable values
for i=firstnumber:lastnumber
%--Filename to be loaded
filename = [basefilename '.' int2str(i)];
xdata.xcor(i).name=filename;
%--Load spike data for the 2 cells
switch xdata.filetype
case 'doc'
c1=lsd(filename,xdata.cellone,xv.StartTrial,xv.EndTrial);
c2=lsd(filename,xdata.celltwo,xv.StartTrial,xv.EndTrial);
otherwise
c1=lsd2(filename,xdata.cellone,xv.StartTrial,xv.EndTrial,xdata.trialtime,xdata.modtime);
c2=lsd2(filename,xdata.celltwo,xv.StartTrial,xv.EndTrial,xdata.trialtime,xdata.modtime);
end
xdata.raw{i}.cellone=c1;
xdata.raw{i}.celltwo=c2;
if ((xv.EndTrial==inf) && (i==1)) %i==1 so we only do this once!
xv.EndTrial=xdata.raw{i}.cellone.numtrials;
set(gh('EndTrial'),'String',num2str(xdata.raw{i}.cellone.numtrials));
set(gh('ShuffleNumber'),'String',nums2strs(1:(xdata.raw{i}.cellone.numtrials-1)));
set(gh('ShuffleNumber'),'value',xdata.raw{i}.cellone.numtrials-1);
end
if (get(gh('Shuffle'),'value')>1)
xv.shuffles=get(gh('ShuffleNumber'),'value');
else
xv.shuffles=0;
end
%--Get Crosscorrelation values and store them
[x,timebase,ci]=icorrx(xdata.raw{i},xv.BinWidth,xv.Window,xv.FromTime,xv.ToTime,xv.shuffles,get(gh('Shuffle'),'value'),xv.pValue);
xdata.xcor(i).values=round(x);
xdata.xcor(i).time=timebase;
if ~isempty(ci)
xdata.xcor(i).lcl=ci(1,:); %lower limits
xdata.xcor(i).ucl=ci(2,:); %upper limits
end
%--Update waitbar
waitbar(i/((lastnumber+1)-firstnumber),h);
end
close(h)
xdata.xcorindex=round(size(xdata.xcor(1).time,2)/2); %finds index into the 0 position
if strcmp(xdata.filetype,'txt') || strcmp(xdata.filetype,'smr')
datainfobox;
set(gh('TextDisplay'),'String',xdata.info);
axes(gh('XCorAxis'));
end
switch xdata.numvars
case 0
bar(xdata.xcor(i).time,xdata.xcor(i).values,1,'k');
title([xdata.runname ' - ' num2str(xdata.cellone) '&' num2str(xdata.celltwo) ' [' num2str(xv.BinWidth) 'ms BW|Trials:' num2str(xv.StartTrial) '-' num2str(xv.EndTrial) ']' ]);
case 1
xdata.ytitle='XCor Time (ms)';
if xdata.xcor(1).time(end)*2<=500
xdata.yvalues=xdata.xcor(1).time;
xdata.yrange=size(xdata.xcor(1).values,2);
xdata.matrix=zeros(xdata.yrange,xdata.xrange);
for i=1:xdata.xrange
xdata.matrix(:,i)=xdata.xcor(i).values;
end
else
index=round(500/xv.BinWidth);
indexnum=index*2+1;
xdata.yvalues=xdata.xcor(i).time(xdata.xcorindex-index:xdata.xcorindex+index);
xdata.yrange=length(xdata.yvalues);
xdata.matrix=zeros(indexnum,xdata.xrange);
for i=1:xdata.xrange
xdata.matrix(:,i)=xdata.xcor(i).values(xdata.xcorindex-index:xdata.xcorindex+index)';
end
end
xdata.xcorindex=round(size(xdata.xcor(1).time,2)/2); %finds index into the 0 position
set(gh('CCStartBin'),'String',cellstr(num2str(xdata.xcor(1).time')));
set(gh('CCEndBin'),'String',cellstr(num2str(xdata.xcor(1).time')));
% Set Up default Binning Parameters, assuming nearest to +-10msec
set(gh('CCStartBin'),'Value',xdata.xcorindex);
set(gh('CCEndBin'),'Value',xdata.xcorindex);
set(gh('CCHold1'),'String',cellstr(num2str(xdata.xvalues')));
set(gh('CCHold1'),'Value',1);
set(gh('CCHold2'),'String',cellstr(num2str(xdata.xvalues')));
set(gh('CCHold2'),'Value',length(xdata.xvalues));
xcormatrix;
fixfig;
case 2
%errordlg('Cross Cor had a problem loading 2 variables');
%error('Cross Cor had a problem loading 2 variables');
xdata.xcorindex=round(xdata.yrange/2);
% Set Up default Binning Parameters, assuming nearest to +-10msec
default=round(10/xv.BinWidth);
set(gh('CCStartBin'),'Value',xdata.xcorindex);
set(gh('CCEndBin'),'Value',xdata.xcorindex);
xdata.xcorindex=round(size(xdata.xcor(1).time,2)/2); %finds index into the 0 position
set(gh('CCStartBin'),'String',cellstr(num2str(xdata.xcor(1).time')));
set(gh('CCEndBin'),'String',cellstr(num2str(xdata.xcor(1).time')));
default=round(10/xv.BinWidth);
% Set Up default Binning Parameters, assuming nearest to +-10msec
set(gh('CCStartBin'),'Value',xdata.xcorindex);
set(gh('CCEndBin'),'Value',xdata.xcorindex);
xv.StartBin=xdata.xcorindex;%-default;
xv.EndBin=xdata.xcorindex;%+default;
for i=1:xdata.xrange*xdata.yrange %actually extract out our values into the matrix
xsum=sum(xdata.xcor(i).values(1,xv.StartBin:xv.EndBin));
xdata.matrix(i)=xsum;
end
xcormatrix;
otherwise
errordlg('Sorry, Cross Cor does not deal yet with 3 variables');
error('Sorry, Cross Cor does not deal yet with 3 variables');
end
%-------------------------------------------------------------------
case 'ReRun'
%-------------------------------------------------------------------
rerun='yes';
crosscor('Load');
%-------------------------------------------------------------------
case 'Load Matrix'
%-------------------------------------------------------------------
%clear xdata slope xv
origpath=pwd;
cd('c:\');
[file path]=uigetfile('*.mat','Load Processed Matrix');
if isempty(file), return, end;
filepath=[path '\' file];
cd(path);
load(filepath);
save 'c:\xdata' xdata
binvals=cellstr(num2str(xdata.yvalues'));
set(gh('CCStartBin'),'Value',1);
set(gh('CCEndBin'),'Value',1);
set(gh('CCStartBin'),'String',binvals);
set(gh('CCEndBin'),'String',binvals);
set(gh('CCBinWidth'),'String',num2str(xv.BinWidth));
set(gh('CCWindow'),'String',num2str(xv.Window));
set(gh('CCFromTime'),'String',num2str(xv.FromTime));
set(gh('CCToTime'),'String',num2str(xv.ToTime));
set(gh('CCStartTrial'),'String',num2str(xv.StartTrial));
set(gh('CCEndTrial'),'String',num2str(xv.EndTrial));
set(gh('CCFirstCell'),'Value',xv.firstunit);
set(gh('CCSecondCell'),'Value',xv.secondunit);
% Set Up default Binning Parameters, assuming nearest to +-10msec
default=round(10/xv.BinWidth);
set(gh('CCStartBin'),'Value',round(length(binvals)/2));
set(gh('CCEndBin'),'Value',round(length(binvals)/2));
%xv.StartBin=xdata.xcorindex;%-default;
%xv.EndBin=xdata.xcorindex;%+default;
% if xdata.ytitle=='XCor Time (ms)'
% xdata.numvars=1;
% end
xcormatrix;
%-------------------------------------------------------------------
case 'PlotMatrix'
%-------------------------------------------------------------------
xcormatrix;
%-------------------------------------------------------------------
case 'Save Model'
%-------------------------------------------------------------------
if exist('c:\temp.mat','file'); delete('c:\temp.mat'); end
crossmodelsave
b=xdata.xvalues';
a=cell(size(b));
for i=1:max(size(a))
a{i}=b(i)
end
set(gh('Angle'),'String',a);
loop=0;
while loop<1
pause(1)
end
loop=0;
model.sep=str2num(get(gh('Sep'),'String'));
model.size1=str2num(get(gh('Size1'),'String'));
model.size2=str2num(get(gh('Size2'),'String'));
String=get(gh('Type1'),'String');
Value=get(gh('Type1'),'Value');
model.type1=String{Value};
String=get(gh('Type2'),'String');
Value=get(gh('Type2'),'Value');
model.type2=String{Value};
model.optimum=get(gh('Angle'),'Value');
model.binwidth=xdata.xcor(1).time(2)-xdata.xcor(1).time(1);
model.window=abs(xdata.xcor(1).time(1))+abs(xdata.xcor(1).time(end));
close;
maxvalue=0;
for i=1:xdata.xrange
if max(xdata.xcor(i).values)>maxvalue
maxvalue=max(xdata.xcor(i).values);
end
end
if maxvalue==0
maxvalue=maxvalue+1;
end
model.maxvalue=maxvalue; %this is the maximum number of correlated events
data=xdata;
data.model=model;
[file path]=uiputfile('*.mat','Save Model Matrix')
if isempty(file), return, end;
cd(path)
x='data';
save(file,x);
%-------------------------------------------------------------------
case 'Save Matrix'
%-------------------------------------------------------------------
if ~isempty(xdata);
origpath=pwd;
cd('c:\');
[file path]=uiputfile('*.mat','Save Processed Matrix');
if isempty(file), return, end;
filepath=[path '\' file];
save(filepath,'xdata','xv');
cd(origpath);
else
errordlg('No Data has been Processed...');
end
%-------------------------------------------------------------------
case 'Save Text'
%-------------------------------------------------------------------
if ~isempty(xdata);
[file path]=uiputfile('*.wk1','Save Processed Matrix as WK1 file');
if isempty(file), return, end;
cd(path);
xmat=rot90(xdata.matrix);
xmat=flipud(xmat);
wk1write(file,xmat);
%dlmwrite('text.txt',xdata.matrix,'\t')
else
errordlg('No Data has been Processed...');
end
%-------------------------------------------------------------------
case 'Preview'
%-------------------------------------------------------------------
SpawnPlot(gca);
set(gca,'FontSize',6);
%-------------------------------------------------------------------
case 'Axis'
%-------------------------------------------------------------------
val=get(gh('Axeschk'), 'Value');
if val == 1
axis auto
set(findobj('UserData','AxesValues'),'Enable', 'off')
else
xmin=str2num(get(gh('CCXmintext'),'String'));
xmax=str2num(get(gh('CCXmaxtext'),'String'));
ymin=str2num(get(gh('CCYmintext'),'String'));
ymax=str2num(get(gh('CCYmaxtext'),'String'));
axis([xmin xmax ymin ymax]);
set(findobj('UserData','AxesValues'),'Enable', 'on');
end
%-------------------------------------------------------------------
case 'See Rasters' %look at Raster plots for both cells
%-------------------------------------------------------------------
xv.inuse=1;
if xdata.numvars<2
figure;
set(gcf,'Tag','ccrasterplotfig');
figpos(1,[900 700]);
set(gcf,'Color',[1 1 1]);
maxvalue=0;
firstnumber=get(gh('CCHold1'),'Value');
lastnumber=get(gh('CCHold2'),'Value');
range=lastnumber-firstnumber+1;
if xdata.numvars==0
range=1;
firstnumber=1;
lastnumber=1;
end
if range<=4
y=1;
x=range;
elseif range <=15
y=3;
x=ceil(range/3);
elseif range <=20
y=4;
x=ceil(range/4);
else
y=6;
x=ceil(range/6);
end
a=1;
for i=firstnumber:lastnumber
subaxis(y,x,a,'S',0.05,'P',0,'M',0.1);
plotraster(xdata.raw{i}.cellone, xdata.raw{i}.celltwo);
a=a+1;
box on
set(gca,'Layer','top');
set(gca,'TickDir','out'); %get ticks going out
xlabel([num2str(xdata.xvalues(i)) ' | Time (s)'],'FontSize',7)
end
suplabel([xdata.runname ' | Cells ' num2str(xdata.cellone) ' & ' num2str(xdata.celltwo)], 't');
end
%-------------------------------------------------------------------
case 'See PSTH' %look at PSTH plots for both cells
%-------------------------------------------------------------------
xv.inuse=1;
if xdata.numvars<2
figure;
set(gcf,'Tag','ccpsthplotfig');
figpos(1,[900 700]);
set(gcf,'Color',[1 1 1]);
maxvalue=0;
firstnumber=get(gh('CCHold1'),'Value');
lastnumber=get(gh('CCHold2'),'Value');
wrap=get(gh('CCWrapPSTH'),'Value');
range=lastnumber-firstnumber+1;
if xdata.numvars==0
range=1;
firstnumber=1;
lastnumber=1;
end
if range<=4
y=1;
x=range;
elseif range <=15
y=3;
x=ceil(range/3);
elseif range <=20
y=4;
x=ceil(range/4);
else
y=5;
x=ceil(range/5);
end
binwidth=10; %ms
a=1;
for i=firstnumber:lastnumber
if wrap==0
[var(a).t1,var(a).a1]=binit(xdata.raw{i}.cellone,binwidth*10,0,inf,xv.StartTrial,xv.EndTrial,0,'cor');
[var(a).t2,var(a).a2]=binit(xdata.raw{i}.celltwo,binwidth*10,0,inf,xv.StartTrial,xv.EndTrial,0,'cor');
var(a).a1= (var(a).a1/(binwidth*xdata.raw{i}.cellone.numtrials))*1000;
var(a).a2= (var(a).a2/(binwidth*xdata.raw{i}.cellone.numtrials))*1000;
else
[var(a).t1,var(a).a1]=binit(xdata.raw{i}.cellone,binwidth*10,0,inf,xv.StartTrial,xv.EndTrial,1,'cor');
[var(a).t2,var(a).a2]=binit(xdata.raw{i}.celltwo,binwidth*10,0,inf,xv.StartTrial,xv.EndTrial,1,'cor');
var(a).a1= (var(a).a1/(binwidth*xdata.raw{i}.cellone.numtrials*xdata.raw{i}.cellone.nummods))*1000;
var(a).a2= (var(a).a2/(binwidth*xdata.raw{i}.cellone.numtrials*xdata.raw{i}.cellone.nummods))*1000;
end
if max([var(a).a1 var(a).a2])>maxvalue
maxvalue=max([var(a).a1 var(a).a2]);
end
a=a+1;
end
a=1;
for i=firstnumber:lastnumber
subaxis(y,x,a,'M',0.1,'S',0.05);
h=plot(var(a).t1,var(a).a1,'k',var(a).t2,var(a).a2,'r');
set(h,'LineWidth',1.5);
xlabel(num2str(xdata.xvalues(i)),'FontSize',7)
axis tight;
set(gca,'FontSize',4);
axis([-inf inf 0 maxvalue+(maxvalue/10)]);
a=a+1;
set(gca,'Layer','top');
set(gca,'TickDir','out'); %get ticks going out
end
else
figure
maxvalue=0;
for i=1:xdata.xrange*xdata.yrange
subplot(xdata.yrange,xdata.xrange,i);
[t1,a1]=binit(xdata.raw{i}.cellone,250,0,inf,xv.StartTrial,xv.EndTrial,0);
[t2,a2]=binit(xdata.raw{i}.celltwo,250,0,inf,xv.StartTrial,xv.EndTrial,0);
if max([a1*100 a2*100])>maxvalue
maxvalue=max([a1*100 a2*100]);
end
plot(t1,a1*100,'b',t2,a2*100,'r');
%axis tight
set(gca,'FontSize',4);
%ylabel(xdata.xcor(i).name,'FontSize',5)
end
for i=1:xdata.xrange*xdata.yrange
subplot(xdata.yrange,xdata.xrange,i);
axis tight;
yaxis(0,maxvalue);
set(gca,'Layer','top');
set(gca,'TickDir','out'); %get ticks going out
end
set(gcf,'Color',[1 1 1]);
end
xv.inuse=0;
suplabel([xdata.runname ' Cells:' num2str(xdata.cellone) '&' num2str(xdata.celltwo)] ,'t');
%-------------------------------------------------------------------
case 'See XCor' %see Xcorrelograms
%-------------------------------------------------------------------
if xdata.numvars>=1
maxvalue=0;
x=ceil(xdata.xrange/3);
for i=1:xdata.xrange
if max(xdata.xcor(i).values)>maxvalue
maxvalue=max(xdata.xcor(i).values);
end
end
if maxvalue==0
maxvalue=maxvalue+1;
end
figure;
set(gcf,'Tag','cccorrplotfig');
figpos(1,[900 700]);
set(gcf,'Color',[1 1 1]);
firstnumber=get(gh('CCHold1'),'Value');
lastnumber=get(gh('CCHold2'),'Value');
range=lastnumber-firstnumber+1;
if xdata.numvars==0
range=1;
firstnumber=1;
lastnumber=1;
end
if range<=4
y=1;
x=range;
elseif range <=15
y=3;
x=ceil(range/3);
elseif range <=20
y=4;
x=ceil(range/4);
else
y=5;
x=ceil(range/5);
end
a=1;
for i=firstnumber:lastnumber
subaxis(y,x,a,'M',0.05,'S',0.05);
set(gca,'nextplot','add')
bar(xdata.xcor(i).time,xdata.xcor(i).values,1,'k')
if isfield(xdata.xcor(1),'lcl')
plot(xdata.xcor(i).time,xdata.xcor(i).lcl,'r-');
plot(xdata.xcor(i).time,xdata.xcor(i).ucl,'r-');
end
axis tight
set(gca,'FontSize',4)
xlabel(num2str(xdata.xvalues(i)),'FontSize',6)
axis([-inf inf 0 maxvalue]);
set(gca,'Layer','top');
set(gca,'TickDir','out'); %get ticks going out
a=a+1;
end
else
maxvalue=0;
for i=1:xdata.xrange*xdata.yrange
if max(xdata.xcor(i).values)>maxvalue
maxvalue=max(xdata.xcor(i).values);
end
end
if maxvalue==0
maxvalue=maxvalue+1;
end
figure
set(gcf,'Color',[1 1 1]);
for i=1:xdata.xrange*xdata.yrange
subplot(xdata.xrange,xdata.yrange,i)
bar(xdata.xcor(i).time,xdata.xcor(i).values,1,'k')
axis tight
set(gca,'FontSize',4);
set(gca,'Layer','top');
set(gca,'TickDir','out'); %get ticks going out
%ylabel(xdata.xcor(i).name,'FontSize',5)
axis([-inf inf 0 maxvalue]);
end
end
%-------------------------------------------------------------------
case 'See Tuning'
%-------------------------------------------------------------------
if xdata.numvars==1
datatype='Tune';
cla;
x=xdata.xvalues;
corrline=[];
s=get(gh('CCStartBin'),'Value');
f=get(gh('CCEndBin'),'Value');
stext=get(gh('CCStartBin'),'String');
ftext=get(gh('CCEndBin'),'String');
stext=stext{s};
ftext=ftext{f};
for i=1:xdata.xrange
xsum=sum(xdata.matrix(s:f,i));
corrline(i)=xsum;
e=xdata.matrix(s:f,i);
err(i)=std(e);
end
[e,a]=max(corrline);
angle=x(a);
set(gh('CCGauss1'),'String',num2str(max(corrline)));
set(gh('CCGauss2'),'String',num2str(5));
set(gh('CCGauss3'),'String',num2str(min(corrline)));
set(gh('CCGauss4'),'String',num2str(angle));
if max(err)==0
if size(corrline,1)>size(corrline,2)
corrline=corrline';
end
%corrline=(corrline/max(corrline))*100;
xdata.corrline=corrline;
plot(x,corrline,'k.-','MarkerSize',15);
t=[xdata.filename ' (Zero Bin)'];
title(t)
%pause(0.7);
%[file,path]=uiputfile('*.txt','Save Tuning Curve as:');
%if ~file
% h=helpdlg('No File Specified');
% pause(0.6);
% close(h);
%else
% cd(path);
% x=xdata.xvalues;
% save(file, 'x','corrline', '-ascii', '-tabs');
%end
else
err=err';
err=sqrt((err.^2/(f-s)));
xval=xdata.xvalues';
corrline=corrline';
%err=(err/max(corrline))*100;
%corrline=(corrline/max(corrline))*100;
areabar(xval,corrline,err,[.7 .7 .7],'k.-','MarkerSize',15);
xdata.corrline=corrline;
xdata.errorline=err;
t=[xdata.filename '(Bins: ' stext ' :' ftext ')'];
title(t,'FontSize',8)
%pause(0.7);
%[file,path]=uiputfile('*.txt','Save Tuning Curve as:');
%if ~file
% h=helpdlg('No File Specified');
% pause(0.7);
% close(h);
%else
% cd(path);
% x=xdata.xvalues;
% corrline=corrline';
% error=error';
% save(file, 'x','corrline', 'error', '-ascii', '-tabs');
%end
end
axis tight;
xlabel('Orientation (deg)');
ylabel('Correlated Events');
val=get(gh('Axeschk'), 'Value');
if val == 1
axis([-inf inf -inf inf]);
else
xmin=str2num(get(gh('CCXmintext'),'String'));
xmax=str2num(get(gh('CCXmaxtext'),'String'));
ymin=str2num(get(gh('CCYmintext'),'String'));
ymax=str2num(get(gh('CCYmaxtext'),'String'));
axis([xmin xmax ymin ymax]);
end
else
errordlg('Sorry, this function is for 1 variable data only')
end
%-------------------------------------------------------------------
case 'Fit Gaussian'
%-------------------------------------------------------------------
if datatype=='Tune';
cline=xdata.corrline;
x=xdata.xvalues;
s=get(gh('CCStartBin'),'Value');
f=get(gh('CCEndBin'),'Value');
stext=get(gh('CCStartBin'),'String');
ftext=get(gh('CCEndBin'),'String');
stext=stext{s};
ftext=ftext{f};
val=get(gh('Axeschk'), 'Value');
if val == 1
axis([-inf inf -inf inf]);
else
xmin=str2num(get(gh('CCXmintext'),'String'));
xmax=str2num(get(gh('CCXmaxtext'),'String'));
ymin=str2num(get(gh('CCYmintext'),'String'));
ymax=str2num(get(gh('CCYmaxtext'),'String'));
axis([xmin xmax ymin ymax]);
end
axval=axis;
a=find(x>=axval(1) & x<=axval(2));
x=x(a);
y=cline(a);
%this allows one to select interpolated or raw data to fit
%comment it out to use raw data...
xx=linspace(min(x),max(x),length(x)*20);
yy=interp1(x,y,xx,'linear');
x=xx;
y=yy;
%---------------------------------------------------------
lb=[10 1 0 -360];
ub=[1000 50 200 360];
g(1)=str2num(get(gh('CCGauss1'),'String'));
g(2)=str2num(get(gh('CCGauss2'),'String'));
if get(gh('CCGauss3Lock'),'Value')==1
g(3)=0;
else
g(3)=str2num(get(gh('CCGauss3'),'String'));
end
g(4)=str2num(get(gh('CCGauss4'),'String'));
options = optimset('Display','iter');
[g,f,exit,output]=fmincon(@fitgaussian,g,[],[],[],[],lb,ub,[],options,x,y);
gline=fitgaussian2(g,x);
if max(gline)-min(gline)<2.5
errordlg('Gaussian didn''t fit data, please try other parameters');
error('Gaussian didn''t fit data, please try other parameters');
elseif exit<=0
errordlg('Gaussian didn''t converge, please try other parameters');
error('Gaussian didn''t converge, please try other parameters');
end
hold on
plot(x,gline,'r');
axval=axis;
if axval==inf | axval==-inf
axval(1)=min(x);
axval(2)=max(x);
axval(3)=min(y);
axval(4)=max(y);
end
[n,j]=max(gline);
[nn,jj]=min(gline);
half=((n-nn)/2)+nn;
line([axval(1) axval(2)],[half half],'Color', [1 0 0],'LineStyle',':');
line([x(j) x(j)],[axval(3) axval(4)],'Color', [1 0 0],'LineStyle',':');
[o,p]=ginput(2)
[m,i]=max(gline);
n=x(j);
ap=n-o(1);
bp=o(2)-n;
hwp=(ap+bp)/2;
[o,p]=ginput(1);
t=['Gaussian HwHH = ' num2str(hwp) '|' num2str(g)];
text(o,p,t);
hold off
end
%-------------------------------------------------------------------
case 'Half Width'
%-------------------------------------------------------------------
if datatype=='Tune';
cline=[];