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various updates on visualization functions
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Matthias Schultze-Kraft committed Feb 20, 2014
1 parent e5175c8 commit 7547251
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Showing 32 changed files with 145 additions and 196 deletions.
2 changes: 1 addition & 1 deletion online/demos/demo_bbcionline_calibrate_and_apply_CSP_for_motor_imagery.m
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Expand Up @@ -48,7 +48,7 @@
cnt_cfy= struct('fs',1/mean(diff(time)), 'x',cfy, ...
'clab', {{sprintf('cfy %s vs %s', calib.result.classes{:})}});
epo_cfy= proc_segmentation(cnt_cfy, calib.mrk, [0 5000]);
fig_set(1, 'Name','classifier output', 'clf',1);
fig_set(1, 'Name','classifier output', 'Clf',1);
plot_channel(epo_cfy);

BTB= BTB_memo;
4 changes: 2 additions & 2 deletions online/demos/demo_bbcionline_calibrate_and_apply_EEG_and_NIRS.m
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Expand Up @@ -84,13 +84,13 @@
cnt_cfy_EEG= struct('fs', 1/mean(diff(time(idx_EEG))), ...
'x', cfy(idx_EEG), 'clab',{{'cfy-EEG'}});
epo_cfy_EEG= proc_segmentation(cnt_cfy_EEG, mrk_cfy, [-5000 15000]);
fig_set(1, 'Name','EEG classifier output', 'clf',1);
fig_set(1, 'Name','EEG classifier output', 'Clf',1);
plot_channel(epo_cfy_EEG);

cnt_cfy_NIRS= struct('fs', 1/mean(diff(time(idx_NIRS))), ...
'x', cfy(idx_NIRS), 'clab',{{'cfy-NIRS'}});
epo_cfy_NIRS= proc_segmentation(cnt_cfy_NIRS, mrk_cfy, [-5000 15000]);
fig_set(2, 'Name','NIRS classifier output', 'clf',1);
fig_set(2, 'Name','NIRS classifier output', 'Clf',1);
plot_channel(epo_cfy_NIRS);

BTB= BTB_memo;
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4 changes: 2 additions & 2 deletions online/demos/demo_bbcionline_calibrate_and_apply_NIRS.m
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Expand Up @@ -43,11 +43,11 @@
cnt_cfy= struct('fs', 1/mean(diff(time)), 'x',cfy, ...
'clab', {{sprintf('cfy %s vs %s', calib.result.classes{:})}});
epo_cfy= proc_segmentation(cnt_cfy, calib.mrk, [-10000 20000]);
fig_set(1, 'Name','classifier output', 'clf',1);
fig_set(1, 'Name','classifier output', 'Clf',1);
plot_channel(epo_cfy);

epo_auc= proc_aucValues(epo_cfy);
fig_set(2, 'clf',1, 'Name','AUC of classifier outputs');
fig_set(2, 'Clf',1, 'Name','AUC of classifier outputs');
plot_channel(epo_auc);

% The
3 changes: 3 additions & 0 deletions visualization/Contents.m
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Expand Up @@ -17,6 +17,8 @@
%
%MNT_ADAPTMONTAGE - Adapts an electrode montage to another electrode set
%MNT_RESTRICTMONTAGE - Restrict an electrode montage to a subset of channels
%MNT_RESTRICTNIRSMONTAGE - restrict a NIRS montage to a subset of channels
%MNT_GETNIRSMONTAGE - Get montage with NIRS channel positions
%MNT_SCALPTOGRID - Montage for grid plot with boxes at scalp locations
%MNT_SETELECTRODEPOSITIONS - Electrode positions of standard named channels
%MNT_SETGRID - Define a new eletrode grid layout for an electrode montage
Expand All @@ -31,6 +33,7 @@
%PLOT_SCALPLOADING - Visualize single channel loadings of a weight vector
%PLOT_SCALPOUTLINE - Schematic sketch of the scalp
%PLOT_SCALPPATTERN - Display average trials as scalp topography
%PLOT_CSPANALYSIS - Show CSP filters and patterns as topographies
%PLOT_SCOREMATRIX - Visualizes score matrix of e.g. r-values


19 changes: 1 addition & 18 deletions visualization/grid_addBars.m
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Expand Up @@ -68,12 +68,6 @@
[opt, isdefault]= opt_setDefaults(opt, props);
opt_checkProplist(opt, props);

% If figure is already inVisible jvm_* functions should not be called
fig_Visible = strcmp(get(gcf,'Visible'),'on');
if fig_Visible
jvm= jvm_hideFig;
end

if ~ismatrix(fv.x),
error('only one Class allowed');
end
Expand Down Expand Up @@ -124,10 +118,6 @@
opt.Colormap(iswhite,:)= 0.9999*[1 1 1];
end
H.image= 'sorry: fakeimage - no handle';
% if ~isempty(opt.HScale),
% warning('sorry, no Colorbar in local colormap mode (so far)');
% opt.HScale= [];
% end
else
set(gcf, 'colormap',opt.Colormap);
end
Expand Down Expand Up @@ -218,15 +208,14 @@
fv.x(fv.x < opt.CLim(1)) = opt.CLim(1);
image_localColormap(fv.x(:,ci)', opt.Colormap, 'CLim',opt.CLim);
else
% H.image(jj)= image(fv.t, 1, fv.x(:,ci)', 'cDataMapping','scaled');
H.image(jj)= image(fv.x(:,ci)', 'cDataMapping','scaled');
end
set(H.ax(jj), AxesStyle{:});
ud= struct('type','ERP plus: bar', 'chan', str_vec2str(fv.clab(ci)));
set(H.ax(jj), 'userData',ud);
hold off;
if strcmp(get(H.ax(jj), 'box'), 'on'),
h= axis_redrawFrame(H.ax(jj), 'LineWidth',0.3);
h= axis_redrawFrame(H.ax(jj), 0.3);
if jj==1,
H.frame= h;
else
Expand All @@ -235,7 +224,6 @@
end
end
if diff(opt.CLim)==0, opt.CLim(2)= opt.CLim(2)+eps; end
%set(H.ax, 'xLim',fv.t([1 end]), 'xTick',[], 'yTick',[], 'CLim',opt.CLim);
set(H.ax, 'xLim',[0.5 size(fv.x,1)+0.5], 'xTick',[], 'yTick',[], ...
'CLim',opt.CLim);

Expand Down Expand Up @@ -279,11 +267,6 @@
end
end


if nargout==0,
clear H;
end

if fig_Visible
jvm_restoreFig(jvm, opt);
end
4 changes: 2 additions & 2 deletions visualization/grid_markInterval.m
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Expand Up @@ -36,7 +36,7 @@
k= 0;
for ih= hsp,
k= k+1;
axis_getQuitely(ih); %% this lets the legend vanish behind the axis
axis_getQuietly(ih); %% this lets the legend vanish behind the axis
yPatch= get(ih, 'yLim');
H.line(:,k)= line(ival([1 2; 1 2]), yPatch([1 1; 2 2]), ...
'Color',0.5*markCol, 'LineWidth',0.3);
Expand All @@ -51,7 +51,7 @@
end
set(H.line, 'UserData','ival line');
set(H.patch, 'EdgeColor','none', 'UserData','ival patch');
axis_getQuitely(old_ax);
axis_getQuietly(old_ax);
if isfield(get(old_ax,'UserData'),'hleg') & ...
~isnan(getfield(get(old_ax,'UserData'), 'hleg')),
legend;
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12 changes: 9 additions & 3 deletions visualization/grid_markTimePoint.m
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Expand Up @@ -2,11 +2,17 @@
%GRID_MARKTIMEPOINT - Draw a time point inside grid plots as a vertical
%line
%
%grid_markTimePoint(tp, <chans, Linespec>)
%Synposis:
% H= grid_markTimePoint(TP, <CHANS, LINESPEC>)
%
%Input:
% TP: time point [msec]
% CHANS: channels which should be marked, default [] meaning all
% TP: time point [msec]
% CHANS: channels which should be marked, default [] meaning all
% LINESPEC: property/value list defining specifications for drawing the
% line
%
%Output:
% H: handle to line object

if ~exist('chans','var'), chans=[]; end

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26 changes: 3 additions & 23 deletions visualization/grid_plot.m
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Expand Up @@ -107,11 +107,6 @@
[opt, isdefault]= opt_setDefaults(opt, props);
opt_checkProplist(opt, props, props_channel, props_addScale);

% fig_Visible = strcmp(get(gcf,'Visible'),'on'); % If figure is already inVisible jvm_* functions should not be called
% if fig_Visible
% jvm= jvm_hideFig;
% end

if nargin<2 || isempty(mnt),
mnt= struct('clab',{epo.clab});
else
Expand Down Expand Up @@ -240,25 +235,19 @@
DisplayChannels= intersect(DisplayChannels, find(~isnan(mnt.box(1,1:end-1))),'legacy');
end
nDisps= length(DisplayChannels);
% mnt.clab{DisplayChannels(ii)} may differ from epo.clab{ii}, e.g. the former
% may be 'C3' while the latter is 'C3 lap'
idx= util_chanind(epo, mnt.clab(DisplayChannels));
axestitle= epo.clab(idx);

%w_cm= warning('query', 'bci:missing_channels');
%warning('off', 'bci:missing_channels');
%all_idx= 1:length(mnt.clab);
yLim= zeros(length(opt.ScaleGroup), 2);
for ig= 1:length(opt.ScaleGroup),
ax_idx= util_chanind(mnt.clab(DisplayChannels), opt.ScaleGroup{ig});
if isempty(ax_idx), continue; end
% ch_idx= find(ismember(all_idx, ax_idx));
ch_idx= util_chanind(epo, mnt.clab(DisplayChannels(ax_idx)));
if isnumeric(opt.ScalePolicy{ig}),
yLim(ig,:)= opt.ScalePolicy{ig};
else
dd= epo.x(:,ch_idx,:);
% idx= find(~isinf(dd(:)));
idx= find(abs(dd(:))<opt.ScaleUpperLimit & ...
abs(dd(:))>=opt.ScaleLowerLimit);
yl= [nanmin(dd(idx)) nanmax(dd(idx))];
Expand All @@ -283,12 +272,8 @@
yLim(ig,:)= [-1 1];
end
if ig==1 && length(ax_idx)>1,
% scale_with_group1= setdiff(1:nDisps, util_chanind(mnt.clab(DisplayChannels), ...
% [opt.ScaleGroup{2:end}]));
% set(H.ax(scale_with_group1), 'yLim',yLim(ig,:));
ch2group= ones(1,nDisps);
else
% set(H.ax(ax_idx), 'yLim',yLim(ig,:));
ch2group(ax_idx)= ig;
for ia= ax_idx,
if max(abs(yLim(ig,:)))>=100,
Expand Down Expand Up @@ -321,7 +306,6 @@
end
end
end
%warning(w_cm);

H.ax= zeros(1, nDisps);
opt_plot= {'Legend',1, 'Title','', 'UnitDispPolicy','none', ...
Expand All @@ -335,9 +319,9 @@
ic= DisplayChannels(ia);
if ~isempty(opt.Axes),
H.ax(ia)= opt.Axes(ic);
axis_getQuitely(H.ax(ia));
axis_getQuietly(H.ax(ia));
else
H.ax(ia)= axis_getQuitely('position', gridutil_getAxisPos(mnt, ic));
H.ax(ia)= axis_getQuietly('position', gridutil_getAxisPos(mnt, ic));
end
cchan = plot_channel(epo, mnt.clab{ic}, opt_channel, opt_plot{:}, ...
'YLim', yLim(ch2group(ia),:), ...
Expand Down Expand Up @@ -413,7 +397,7 @@
end

if ~isempty(opt.ShiftAxesUp) && opt.ShiftAxesUp~=0,
axis_shiftUp(opt.ShiftAxesUp);
gridutil_shiftAxesUp(opt.ShiftAxesUp);
end

if opt.HeadMode,
Expand All @@ -430,7 +414,3 @@
if nargout==0,
clear H;
end

% if fig_Visible
% jvm_restoreFig(jvm);
% end
2 changes: 1 addition & 1 deletion visualization/image_localColormap.m
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Expand Up @@ -45,7 +45,7 @@ function image_localColormap(C, cmap, varargin)
opt_checkProplist(opt, props);

[sy,sx]= size(C);
if isdefault.Optimize & sx==1,
if isdefault.Optimize && sx==1,
opt.Optimize= 'columns';
end

Expand Down
30 changes: 15 additions & 15 deletions visualization/mnt_getNIRSMontage.m
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@@ -1,19 +1,22 @@
function mnt = mnt_getNIRSMontage(varargin)
%MNT_GETNIRSMONTAGE - get montage with NIRS channel positions for a given set
% of sources and detectors. NIRS channels are placed half-way
% between a source and a detector on a spherical head model.
%MNT_GETNIRSMONTAGE - Get montage with NIRS channel positions
%
%Description:
% get montage with NIRS channel positions for a given set of sources and
% detectors. NIRS channels are placed half-way between a source and a
% detector on a spherical head model.
%
%Synopsis:
% MNT = nirs_getMontage(CLABSOURCE,CLABDETECTOR,<OPT>)
% If you give channels labels of the source and detectors (should
% correspond to EEG channel labels), montages for source and
% detectors are produced, as well as montages for the
% source-detector combinations.
% MNT = nirs_getMontage(CLABSOURCE,CLABDETECTOR,<OPT>)
% If you give channels labels of the source and detectors (should
% correspond to EEG channel labels), montages for source and
% detectors are produced, as well as montages for the
% source-detector combinations.
%
% MNT = nirs_getMontage(MNT,<OPT>)
% You can provide a montage struct wherein source and detector
% montages are already given in .source and .detector fields.
% In this case, only the source-detector combinations are determined.
% MNT = nirs_getMontage(MNT,<OPT>)
% You can provide a montage struct wherein source and detector
% montages are already given in .source and .detector fields.
% In this case, only the source-detector combinations are determined.
%
%Input
% OPT: struct or property/value list of optional properties:
Expand All @@ -40,13 +43,11 @@
% .detector - struct with montage for the detectors
%
%See also: setElectrodeMontage, nirs_reduceMontage
%

% [email protected] 2011
% Markus Wenzel 2013 (adapted it to the new toolbox)
% Jan Mehnert February 2014 (ready for public BBCI toolbox) ([email protected])


props= {'ClabPolicy' 'label' 'CHAR'
'Projection' 'euclidean' 'CHAR'
'PositionFcn' @mntutil_posExt55 'FUNC'
Expand Down Expand Up @@ -78,7 +79,6 @@
mnt.source = mnt_setElectrodePositions(clabSource, 'PositionFcn', opt.PositionFcn);
mnt.detector = mnt_setElectrodePositions(clabDetector, 'PositionFcn', opt.PositionFcn);
end


if any(isnan(mnt.source.pos_3d(:))) || any(isnan(mnt.detector.pos_3d(:)))
warning(['Some source/detector positions are NaN. Note that the NIRS channels '...
Expand Down
20 changes: 10 additions & 10 deletions visualization/mnt_restrictMontage.m
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Expand Up @@ -2,22 +2,22 @@
%MNT_RESTRICTMONTAGE - Restrict an electrode montage to a subset of channels.
%
%Synposis:
% mnt= mnt_restrictMontage(MNT, CHANS);
% mnt= mnt_restrictMontage(MNT, DAT);
% mnt= mnt_restrictMontage(MNT, CHANS);
% mnt= mnt_restrictMontage(MNT, DAT);
%
%Input:
% MNT: display montage, see setElectrodeMontage, setDisplayMontage
% CHANS: channels, format as accepted by util_chanind
% DAT: structure which has a field 'clab', such as cnt, epo, ...
% MNT: display montage, see setElectrodeMontage, setDisplayMontage
% CHANS: channels, format as accepted by util_chanind
% DAT: structure which has a field 'clab', such as cnt, epo, ...
%
%Output:
% MNT: updated display montage
% MNT: updated display montage
%
%Example:
% [cnt, mrk, mnt]= loadProcessedEEG('Gabriel_00_09_05/selfpaced2sGabriel');
% cnt_lap= proc_laplace(cnt);
% mnt= mnt_restrictMontage(mnt, cnt_lap);
% plotScalpPattern(mnt, cnt_lap.x(10000,:));
% [cnt, mrk, mnt]= loadProcessedEEG('Gabriel_00_09_05/selfpaced2sGabriel');
% cnt_lap= proc_laplace(cnt);
% mnt= mnt_restrictMontage(mnt, cnt_lap);
% plotScalpPattern(mnt, cnt_lap.x(10000,:));

if nargin==2 && isstruct(varargin{1}),
if isfield(varargin{1}, 'clab'),
Expand Down
20 changes: 11 additions & 9 deletions visualization/mnt_restrictNIRSMontage.m
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Original file line number Diff line number Diff line change
@@ -1,9 +1,11 @@
function mnt = mnt_restrictNIRSMontage(mnt,varargin)
%MNT_RESTRICTNIRSMONTAGE - restricts the NIRS montage by selecting (a)
% specified NIRS channels and/or (b) sources or detectors and
% keeping only the corresponding NIRS channels AND/OR (c) keeping only
% informative NIRS channels (ie channels corresponding to a relatively
% small source-detector distance).
%MNT_RESTRICTNIRSMONTAGE - restrict a NIRS montage to a subset of channels
%
%Descpription:
% Restricts the NIRS montage by selecting (a) specified NIRS channels
% and/or (b) sources or detectors and keeping only the corresponding NIRS
% channels and/or (c) keeping only informative NIRS channels (i.e. channels
% corresponding to a relatively small source-detector distance).
%
%Synopsis:
% MNT = mnt_restrictNIRSMontage(MNT, CHANS, <OPT>)
Expand Down Expand Up @@ -36,8 +38,8 @@
%Output:
% MNT: updated montage
%
%Note: Use proc_selectChannels to reduce the NIRS data (cnt,dat,epo)
% according to the new montage.
%Note: Use proc_selectChannels to reduce the NIRS data (cnt, dat, epo)
% according to the new montage.
%
%See also: mnt_restrictMontage

Expand All @@ -50,7 +52,8 @@
'Detector' {} 'CHAR|CELL{CHAR}'
'RemoveOptodes' 1 'BOOL'
'HeadRadius' 10 'DOUBLE'
'Dist' 3.5 'DOUBLE'};
'Dist' 3.5 'DOUBLE'
};

if nargin==0,
mnt= props; return
Expand All @@ -74,7 +77,6 @@
opt_checkProplist(opt, props);
misc_checkType(mnt, 'STRUCT');


if ischar(opt.Source)
opt.Source = {opt.Source};
end
Expand Down
2 changes: 1 addition & 1 deletion visualization/plot_barWithAntenna.m
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@
};

if nargin==0,
dat= props; return
H= props; return
end

misc_checkType(y,'!DOUBLE[- -]');
Expand Down
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