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more metaanalysis changes
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Ian authored and Ian committed Jul 24, 2014
1 parent 8422ad8 commit 2b8975f
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Showing 5 changed files with 117 additions and 58 deletions.
16 changes: 9 additions & 7 deletions omniplex/LFPAnalysis.m
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@
%------------------HIDDEN PROPERTIES----------%
properties (SetAccess = protected, GetAccess = public, Hidden = true)
%> bandpass frequencies
bpfreq@cell = {[1 4], [5 8], [8 14], [15 30], [30 50], [50 100], [1 250]}
bpfreq@cell = {[1 4], [4 7], [7 14], [15 30], [30 50], [50 100], [1 250]}
%> bandpass frequency names
bpnames@cell = {'\delta','\theta','\alpha','\beta','\gamma low','\gamma high','all'}
end
Expand Down Expand Up @@ -228,7 +228,6 @@ function toggleSaccadeRealign(ego)
ego.reparse;
ego.parseSpikes;
ego.doPlots = doPlots;
ego.plot('av');
if ego.p.saccadeRealign == true
disp('Saccade Realign is now ENABLED...')
else
Expand Down Expand Up @@ -393,8 +392,6 @@ function ftPreProcess(ego, cfg, removeLineNoise)
%> @return
% ===================================================================
function cfg=ftTimeLockAnalysis(ego, cfg, statcfg)
ego.results(1).av = [];
ego.results(1).avstat = [];
ft = ego.ft;
ft = rmfield(ft,'uniquetrials'); %ft_timelockanalysis > ft_selectdata generates a warning as this is an unofficial field, so remove it here
if ~exist('cfg','var') || isempty(cfg); cfg = []; end
Expand All @@ -404,6 +401,11 @@ function ftPreProcess(ego, cfg, removeLineNoise)
if ~isfield(cfg,'removemean'); cfg.removemean = 'no'; end
if ~isfield(cfg,'covariance'); cfg.covariance = 'yes'; end
cfg.channel = ft.label{ego.selectedLFP};
ego.results(1).av = [];
if strcmp(cfg.keeptrials, 'yes')
ego.results(1).avstat = [];
ego.results(1).avstatavg = [];
end
for i = 1:ego.nSelection
cfg.trials = ego.selectedTrials{i}.idx;
av{i} = ft_timelockanalysis(cfg, ft);
Expand All @@ -426,7 +428,7 @@ function ftPreProcess(ego, cfg, removeLineNoise)
if isempty(ego.stats); ego.setStats(); end
sv = ego.stats;

if isfield(av{1},'trial') %keeptrials was ON
if strcmp(cfg.keeptrials, 'yes') %keeptrials was ON
if exist('statcfg','var'); cfg = statcfg;
else cfg = []; end
cfg.channel = ft.label{ego.selectedLFP};
Expand Down Expand Up @@ -1272,7 +1274,7 @@ function select(ego)

mrange = ego.measureRange;

mtitle = ['REPARSE ' num2str(ego.LFPs(1).nVars) ' DATA VARIABLES'];
mtitle = [ego.lfpfile ': REPARSE ' num2str(ego.LFPs(1).nVars) ' VARS'];
options = {['t|' map{1}],'Choose PLX variables to merge (A, if empty parse all variables independantly):'; ...
['t|' map{2}],'Choose PLX variables to merge (B):'; ...
['t|' map{3}],'Choose PLX variables to merge (C):'; ...
Expand Down Expand Up @@ -1757,7 +1759,7 @@ function drawAverageLFPs(ego)
if isgraphics(ego.plotDestination)
h = ego.plotDestination;
else
h=figure;figpos(1,[1700 1000]);set(gcf,'Name',[ego.lfpfile ' ' av{1}.label{:}],'Color',[1 1 1]);
h=figure;figpos(1,[1700 1000]);set(gcf,'Name',[ego.lfpfile],'Color',[1 1 1]);
end
p=panel(h);
p.margin = [20 20 10 15]; %left bottom right top
Expand Down
123 changes: 84 additions & 39 deletions omniplex/LFPMeta.m
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@
end

% ===================================================================
%> @brief
%> @brief add LFPAnalysis objects to the meta list
%>
%> @param
%> @return
Expand Down Expand Up @@ -114,7 +114,7 @@ function add(me,varargin)


% ===================================================================
%> @brief
%> @brief plot individual
%>
%> @param
%> @return
Expand Down Expand Up @@ -158,8 +158,9 @@ function process(me,varargin)
me.raw{i}.plotRange = me.plotRange;

if am == 1 %timelock
cfg = [];cfg.keeptrials = 'no';
cfg = [];cfg.keeptrials = 'yes';
me.raw{i}.ftTimeLockAnalysis(cfg);

else
me.raw{i}.ftFrequencyAnalysis([],...
me.options.tw,...
Expand Down Expand Up @@ -198,7 +199,10 @@ function run(me,varargin)
end
metaA{i} = me.raw{i}.results.av{1};
metaB{i} = me.raw{i}.results.av{2};

metaA{i}.label = {'LFP'}; %force an homogeneous label name
metaB{i}.label = {'LFP'};
metaA{i}.dimord = 'chan_time';
metaB{i}.dimord = 'chan_time';
else

metaA{i} = me.raw{i}.(['fq' me.options.method]){1};
Expand All @@ -210,21 +214,32 @@ function run(me,varargin)
end

if am == 1 %timelock
cfg = [];
cfg.channel = 'all';
cfg.keepindividual = 'no';
%cfg.latency = me.measureRange;
%cfg.normalizevar = 'N' or 'N-1' (default = 'N-1')
% cfg.method = 'across' (default) or 'within', see below.
% cfg.parameter = string or cell-array indicating which
cfg = [];
cfg.channel = 'all';
cfg.keepindividual = 'no';
cfg.parameter = 'avg';
cfg.method = 'across'; %(default) or 'within', see below.
% cfg.latency = me.measureRange;
% cfg.normalizevar = 'N' or 'N-1' (default = 'N-1')
avgA = ft_timelockgrandaverage(cfg, metaA{:});
avgB = ft_timelockgrandaverage(cfg, metaB{:});
else

end



me.handles.axistabs.Selection = 2;
ho = me.handles.axisall;
delete(ho.Children);
h = uipanel('Parent',ho,'units', 'normalized', 'position', [0 0 1 1]);
ha = axes('Parent',h);
e = analysisCore.var2SE(avgA.var, avgA.dof);
areabar(avgA.time,avgA.avg, e);
hold on
e = analysisCore.var2SE(avgB.var, avgB.dof);
areabar(avgB.time, avgB.avg, e);
xlabel('Time (s)');
ylabel('Voltage (mV)');

end

end
Expand Down Expand Up @@ -286,10 +301,34 @@ function save(me, varargin)
%> @return
% ===================================================================
function spawn(me, varargin)
gh = gca;
h = figure;
figpos(1,[1000 800]);
set(h,'Color',[1 1 1]);
hh = copyobj(me.handles.axis2,h);
hh = copyobj(gh,h);
end

% ===================================================================
%> @brief
%>
%> @param
%> @return
% ===================================================================
function toggleSaccades(me, varargin)
if me.nSites > 0
firstState = false;
for i = 1 : me.nSites
if i == 1
me.raw{i}.toggleSaccadeRealign
firstState = me.raw{i}.p.saccadeRealign; %keep our first state saved
else
if firstState ~= me.raw{i}.p.saccadeRealign; %make sure all states will sync to first
me.raw{i}.toggleSaccadeRealign
end
end

end
end
end

% ===================================================================
Expand Down Expand Up @@ -464,6 +503,11 @@ function reset(me,varargin)
set(me.handles.list,'Value',1);
set(me.handles.list,'String',{''});
end
ho = me.handles.axisind;
delete(ho.Children);
ho = me.handles.axisall;
delete(ho.Children);
me.handles.axistabs.SelectedChild=1;
if isfield(me.handles,'axis1')
me.handles.axistabs.SelectedChild=2;
axes(me.handles.axis2);cla
Expand Down Expand Up @@ -554,25 +598,26 @@ function makeUI(me)
figpos(1,[1600 800])
end
me.handles(1).parent = parent;

%make context menu
hcmenu = uicontextmenu;
item1 = uimenu(hcmenu,'Label','Reparse','Callback',@me.plot);
item2 = uimenu(hcmenu,'Label','Plot','Callback',@me.plot);
item3 = uimenu(hcmenu,'Label','Remove','Callback',@me.remove);
uimenu(hcmenu,'Label','Reparse (select)','Callback',@me.reparse,'Accelerator','e');
uimenu(hcmenu,'Label','Plot (select)','Callback',@me.plot,'Accelerator','p');
uimenu(hcmenu,'Label','Remove (select)','Callback',@me.remove,'Accelerator','r');
uimenu(hcmenu,'Label','Process (all)','Callback',@me.process,'Separator','on');
uimenu(hcmenu,'Label','Run (all)','Callback',@me.run);
uimenu(hcmenu,'Label','Toggle Saccade (all)','Callback',@me.toggleSaccades);
uimenu(hcmenu,'Label','Reset (all)','Callback',@me.reset);

fs = 10;
if ismac
[s,c]=system('system_profiler SPDisplaysDataType');
if s == 0
if ~isempty(regexpi(c,'Retina LCD'))
fs = 7;
end
end
if s == 0; if ~isempty(regexpi(c,'Retina LCD')); fs = 7; end; end
end
SansFont = 'Helvetica';
MonoFont = 'Menlo';
bgcolor = [0.85 0.85 0.85];
bgcoloredit = [0.87 0.87 0.87];
MonoFont = 'Consolas';
bgcolor = [0.89 0.89 0.89];
bgcoloredit = [0.9 0.9 0.9];

handles.parent = me.handles.parent; %#ok<*PROP>
handles.root = uiextras.BoxPanel('Parent',parent,...
Expand Down Expand Up @@ -627,13 +672,13 @@ function makeUI(me)
'Tooltip','Remove a single item',...
'Callback',@me.remove,...
'String','Remove');
handles.plotbutton = uicontrol('Style','pushbutton',...
'Parent',handles.controls1,...
'Tag','LMAsavebutton',...
'FontSize', fs,...
'Tooltip','Plot data',...
'Callback',@me.plot,...
'String','Plot');
% handles.saccbutton = uicontrol('Style','pushbutton',...
% 'Parent',handles.controls1,...
% 'Tag','LMAsaccbutton',...
% 'FontSize', fs,...
% 'Tooltip','Toggle Saccade Realign',...
% 'Callback',@me.toggleSaccades,...
% 'String','Toggle Saccades');
handles.processbutton = uicontrol('Style','pushbutton',...
'Parent',handles.controls1,...
'Tag','LMArunbutton',...
Expand Down Expand Up @@ -665,13 +710,13 @@ function makeUI(me)
'FontSize', fs,...
'Callback',@me.setOptions,...
'String','Options');
handles.max = uicontrol('Style','edit',...
'Parent',handles.controls1,...
'Tag','LMAmax',...
'Tooltip','Cell Max Override',...
'FontSize', fs,...
'Callback',@me.editmax,...
'String','0');
% handles.max = uicontrol('Style','edit',...
% 'Parent',handles.controls1,...
% 'Tag','LMAmax',...
% 'Tooltip','Cell Max Override',...
% 'FontSize', fs,...
% 'Callback',@me.editmax,...
% 'String','0');
handles.weight = uicontrol('Style','edit',...
'Parent',handles.controls1,...
'Tag','LMAweight',...
Expand Down
6 changes: 3 additions & 3 deletions omniplex/analysisCore.m
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Original file line number Diff line number Diff line change
Expand Up @@ -309,9 +309,9 @@ function showInfo(ego)
function optimiseSize(ego)
if isa(ego, 'LFPAnalysis')
for i = 1: ego.nLFPs
ego.LFPs(i).sample = [];
ego.LFPs(i).data = [];
ego.LFPs(i).time = [];
%ego.LFPs(i).sample = [];
%ego.LFPs(i).data = [];
%ego.LFPs(i).time = [];
end
ego.results = struct([]);
optimiseSize(ego.p);
Expand Down
10 changes: 9 additions & 1 deletion omniplex/plxReader.m
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Original file line number Diff line number Diff line change
Expand Up @@ -435,7 +435,15 @@ function integrateEyeData(ego)
%> @return
% ===================================================================
function handles = infoBox(ego, info)
if feature('HGUsingMatlabClasses');fs = 12;else fs = 14;end
fs = 10;
if ismac
[s,c]=system('system_profiler SPDisplaysDataType');
if s == 0
if ~isempty(regexpi(c,'Retina LCD'))
fs = 7;
end
end
end
if ~exist('info','var')
ego.generateInfo();
info = ego.info;
Expand Down
20 changes: 12 additions & 8 deletions omniplex/spikeAnalysis.m
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Original file line number Diff line number Diff line change
Expand Up @@ -854,14 +854,16 @@ function selectTrials(ego)
function plotDensity(ego)
if ~isfield(ego.results,'sd'); warning('No Density parsed yet.'); return; end
disp('Plotting Density Data...')
fs = get(0,'DefaultAxesFontSize');
sd = ego.results.sd;
rate = ego.results.rate;
baseline = ego.results.baseline;
if ego.nSelection == 0; error('The selection results in no valid trials to process!'); end
h=figure;set(h,'Color',[1 1 1],'Name',[ego.file ' ' ego.names{ego.selectedUnit}]);
if length(sd) <4; figpos(1,[1000 1500]); else figpos(1,[2000 2000]); end
p=panel(h);
p.margin = [15 20 10 10]; %left bottom right top
p.fontsize = fs;
p.margin = [12 12 12 6]; %left bottom right top
p.pack('v', {3/4 []})
q = p(1);
len = ego.nSelection;
Expand Down Expand Up @@ -927,14 +929,14 @@ function plotDensity(ego)
t = [t sprintf(' R%i: %.4g ± %.3g %.3g<>%.3g', j, rate{j}.avg, e, rate{j}.CI(1), rate{j}.CI(2))];
end
disp([t sprintf(' | measureRange: %s', num2str(rate{1}.cfg.latency))]);
title(t,'FontSize',13);
title(t);
xlabel(['Time (s) [window = ' sd{1}.cfg.winfunc ' ' num2str(sd{1}.cfg.timwin) '] ']);
ylabel(yt)
set(gcf,'Renderer','OpenGL');
legend(leg);
ax=axis;
axis([ego.plotRange(1) ego.plotRange(2) ax(3) ax(4)]);
text(ego.plotRange(1),ax(3),blineText,'FontSize',10,'VerticalAlignment','baseline');
text(ego.plotRange(1),ax(3),blineText,'FontSize',fs+1,'VerticalAlignment','baseline');
set(mh,'yData',[ax(3) ax(3) ax(4) ax(4)]);
set(gca,'Layer','top');
end
Expand Down Expand Up @@ -1122,9 +1124,11 @@ function plotWaveforms(ego,timeWindow)
warning('No waveform data present, nothing to plot...')
return
end
h=figure;figpos(2,[2000 1000]);set(h,'Color',[1 1 1],'Name',[ego.file ' ' ego.names{ego.selectedUnit}]);
fs = get(0,'DefaultAxesFontSize');
h=figure;figpos(2,[1600 600]);set(h,'Color',[1 1 1],'Name',[ego.file ' ' ego.names{ego.selectedUnit}]);
p=panel(h);
p.margin = [20 20 20 20]; %left bottom right top
p.fontsize = fs-1;
p.margin = [10 8 12 8]; %left bottom right top
[row,col]=ego.optimalLayout(ego.nSelection);
p.pack(col,row);
for j = 1:length(ego.selectedTrials)
Expand Down Expand Up @@ -1157,7 +1161,7 @@ function plotWaveforms(ego,timeWindow)
waves = vertcat(waves,w);
end
end
if ~isempty(waves)
if ~isempty(waves)
nwaves = size(waves,1);
[a,e]=stderr(waves,'SD');
areabar(time,a,e,[0.7 0.7 0.7],0.75,'r-o','LineWidth',2);
Expand Down Expand Up @@ -1195,7 +1199,7 @@ function appendTrialNames(ego,hdl,idx)
mS2 = mS( mS >= 0 & mS <= ego.measureRange(2));
nMS1 = nMS1 + length(mS1);
nMS2 = nMS2 + length(mS2);
plot(mS,y(j),'yo','MarkerFaceColor',[1 1 0],'MarkerSize',4);
plot(mS, y(j), 'ro', 'MarkerFaceColor', 'none', 'MarkerSize', 4);
end
end
end
Expand All @@ -1205,7 +1209,7 @@ function appendTrialNames(ego,hdl,idx)
st = st - st;
end
yt = 1:length(st);
plot(st,yt,'go','MarkerFaceColor',[0 1 0],'MarkerSize',4);
plot(st, yt, 'go', 'MarkerFaceColor', 'none', 'MarkerSize', 4);
end
if length(idx) >= 100
fs = 9;
Expand Down

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