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Merged
ftadel merged 6 commits into from
Oct 31, 2020
Merged

Enhance the LF viewer and adding more options from the keyboard #343

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4930290
Add more functionnalities to the leadfield viewer
tmedani Oct 15, 2020
028e72c
add documentation to the help panel
tmedani Oct 15, 2020
29eed5f
increase the hLabel displat window
tmedani Oct 15, 2020
2afe76c
fixe the bounding value of the threshold [0,1]
tmedani Oct 16, 2020
abe1158
revision of the function according to the PR discussion + add option …
tmedani Oct 26, 2020
0baead9
Removed extra "hold on"
ftadel Oct 31, 2020
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249 changes: 200 additions & 49 deletions toolbox/gui/view_leadfields.m
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@
% =============================================================================@
%
% Authors: John Mosher, Takfarinas Medani, Francois Tadel, 2020

% Juan Garcia-Prieto : add logarithmic scale for LF vectors

%% ===== PARSE INPUTS =====
if ischar(HeadmodelFiles)
Expand Down Expand Up @@ -149,12 +149,17 @@

%% ===== DISPLAY LEADFIELD =====
% Current sensor
useLogScale = false;
useLogScaleLegendMsg = 'Off';
iChannel = 1;
% initial value for the quiver display
quiverSize = 1;
quiverWidth = 1;
thresholdAmplitude = 1; % ratio of the amplitude
thresholdBalance = 0; % orientation of the threshold "<" or " >"
DrawArrows();
bst_progress('stop');



%% =================================================================================
% === INTERNAL CALLBACKS ==========================================================
% =================================================================================
Expand All @@ -163,34 +168,90 @@
function KeyPress_Callback(hFig, keyEvent)
switch (keyEvent.Key)
% === LEFT, RIGHT, PAGEUP, PAGEDOWN : Processed by TimeWindow ===
case {'leftarrow', 'space', 'uparrow'}
iChannel = iChannel - 1;
case 'pagedown'
iChannel = iChannel - 10;
case {'rightarrow', 'downarrow'}
iChannel = iChannel + 1;
case 'pageup'
iChannel = iChannel + 10;
case {'leftarrow',}
if ismember('shift', keyEvent.Modifier)
quiverSize = quiverSize /1.2;
elseif ismember('control', keyEvent.Modifier)
quiverWidth = quiverWidth /1.2;
elseif ismember('alt', keyEvent.Modifier)
thresholdAmplitude = thresholdAmplitude - 0.01;
else
iChannel = iChannel - 1;
end
case {'rightarrow'}
if ismember('shift', keyEvent.Modifier)
quiverSize = quiverSize * 1.2;
elseif ismember('control', keyEvent.Modifier)
quiverWidth = quiverWidth * 1.2;
elseif ismember('alt', keyEvent.Modifier)
thresholdAmplitude = thresholdAmplitude + 0.01;
else
iChannel = iChannel + 1;
end
case 'uparrow'
if ismember('shift', keyEvent.Modifier)
quiverSize = quiverSize * 1.2;
elseif ismember('control', keyEvent.Modifier)
quiverWidth = quiverWidth * 1.2;
elseif ismember('alt', keyEvent.Modifier)
thresholdAmplitude = thresholdAmplitude + 0.01;
else
if ~isempty(iRef)
iRef = iRef + 1;
end
end
case 'downarrow'
if ismember('shift', keyEvent.Modifier)
quiverSize = quiverSize / 1.2;
elseif ismember('control', keyEvent.Modifier)
quiverWidth = quiverWidth / 1.2;
elseif ismember('alt', keyEvent.Modifier)
thresholdAmplitude = thresholdAmplitude - 0.01;
else
if ~isempty(iRef)
iRef = iRef - 1;
end
end
case 'r' %% not for MEG
SelectReference();
case 't' %% not for MEG
SelectTarget();
case 's'
if ~isempty(findobj(hFig, 'Tag', 'SetVertices'))
delete(findobj(hFig, 'Tag', 'SetVertices'))
else
hold on;
plot3(HeadmodelMat{1}.GridLoc(:,1), HeadmodelMat{1}.GridLoc(:,2), HeadmodelMat{1}.GridLoc(:,3), 'r.', ...
'Parent', hAxes, ...
'Tag', 'SetVertices');
end
case 'e'
hold on;
% Plot sensors
if ~isempty(findobj(hAxes, 'Tag', 'allChannel'))
delete(findobj(hAxes, 'Tag', 'allChannel'))
if ~ismember('shift', keyEvent.Modifier)
% Plot sensors
if ~isempty(findobj(hAxes, 'Tag', 'allChannel'))
delete(findobj(hAxes, 'Tag', 'allChannel'))
else
if length(Channels) > 10
hSensors = figure_3d('PlotSensorsNet', hAxes, markersLocs, 0, 0);
set(hSensors, 'LineWidth', 1, 'MarkerSize', 5,'Tag','allChannel');
end
end
else
if length(Channels) > 10
hSensors = figure_3d('PlotSensorsNet', hAxes, markersLocs, 0, 0);
set(hSensors, 'LineWidth', 1, 'MarkerSize', 5,'Tag','allChannel');
% Plot sensors name
if ~isempty(findobj(hAxes, 'Tag', 'allChannelName'))
delete(findobj(hAxes, 'Tag', 'allChannelName'))
else
if length(Channels) > 10
%hSensors = figure_3d('PlotSensorsNet', hAxes, markersLocs, 0, 0);
%set(hSensors,'Tag','allChannelName');
channelAllName = cell(length(Channels),1);
for iChan = 1 : length(Channels)
channelAllName{iChan} = Channels(iChan).Name;
end
text(markersLocs(:,1), markersLocs(:,2), markersLocs(:,3),channelAllName,...
'color','y',...
'Parent', hAxes, ...
'Tag', 'allChannelName');
end
end
end
case 'm'
Expand All @@ -201,18 +262,54 @@ function KeyPress_Callback(hFig, keyEvent)
if ~isempty(findobj(hAxes, 'Tag', 'allChannel'))
delete(findobj(hAxes, 'Tag', 'allChannel'))
end

case 'l'
if ismember('shift', keyEvent.Modifier)
useLogScale = ~useLogScale;
if (useLogScale)
useLogScaleLegendMsg = 'On';
else
useLogScaleLegendMsg = 'Off';
end
end

case 'return'
if ismember('shift', keyEvent.Modifier)
useLogScale = ~useLogScale;
if (useLogScale)
useLogScaleLegendMsg = 'On';
else
useLogScaleLegendMsg = 'Off';
end
elseif ismember('alt', keyEvent.Modifier)
thresholdBalance = ~thresholdBalance;
else
return;
end
case 'h'
java_dialog('msgbox', ['<HTML><TABLE>' ...
'<TR><TD><B>Left arrow</B></TD><TD>Previous channel</TD></TR>' ....
'<TR><TD><B>Right arrow</B></TD><TD>Next channel</TD></TR>'....
'<TR><TD><B>Page up</B></TD><TD>Previous 10th channel</TD></TR>'....
'<TR><TD><B>Page down</B></TD><TD>Next 10th channel</TD></TR>'....
'<TR><TD><B>Left arrow</B></TD><TD>Previous target channel (red color)</TD></TR>' ....
'<TR><TD><B>Right arrow</B></TD><TD>Next target channel (red color)</TD></TR>'....
'<TR><TD><B>Up arrow</B></TD><TD>Previous ref channel (green color)</TD></TR>'....
'<TR><TD><B>Down arrow</B></TD><TD>Next ref channel (green color)</TD></TR>'....
'<TR><TD><B>Shift + uparrow</B></TD><TD>Increase the vector length</TD></TR>'...
'<TR><TD><B>Shift + downarrow</B></TD><TD>Decrease the vector length</TD></TR>'...
'<TR><TD><B>Shift + L</B></TD><TD>Toggle on/off logarithmic scale</TD></TR>'...

@ftadel ftadel Oct 24, 2020

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Looks like this is "Shift + Enter" instead

@tmedani tmedani Oct 25, 2020

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I think both are working,
"Shift + Enter" and "Shift + L"

'<TR><TD><B>Control + uparrow</B></TD><TD>Increase the vector width</TD></TR>'...
'<TR><TD><B>Control + downarrow</B></TD><TD>Decrease the vector width</TD></TR>'...
'<TR><TD><B>Alt + Enter </B></TD><TD>Toggle to superior/inferior for LF threshold</TD></TR>'...
'<TR><TD><B>Alt + uparrow </B></TD><TD>Increase Amplitude threshold</TD></TR>'...
'<TR><TD><B>Alt + downarrow </B></TD><TD>Decrease Amplitude threshold</TD></TR>'...
'<TR><TD><B>M</B></TD><TD>Change the <B>M</B>odality (MEG, EEG, SEEG, ECOG)</TD></TR>'....
'<TR><TD><B>R</B></TD><TD>Change the <B>R</B>eference electrode</TD></TR>'....
'<TR><TD><B>R</B></TD><TD>Select the <B>R</B>eference channel</TD></TR>'....
'<TR><TD><B>T</B></TD><TD>Select the <B>T</B>arget channel</TD></TR>'....
'<TR><TD><B>S</B></TD><TD>Show/hide the source grid</TR>'....
'<TR><TD><B>E</B></TD><TD>Show/hide the sensors</TD></TR></TABLE>'], 'Keyboard shortcuts');
'<TR><TD><B>E</B></TD><TD>Show/hide the sensors</TD></TR>'...
'<TR><TD><B>Shift + E</B></TD><TD>Show/hide the sensors labels</TD></TR>'...
'<TR><TD><B>0 to 9</B></TD><TD>Change view</TD></TR>'...
'</TABLE>'], 'Keyboard shortcuts');
otherwise
KeyPressFcn_bak(hQuiver, keyEvent);
KeyPressFcn_bak(hFig, keyEvent);
return;
end
% Redraw arrows
Expand All @@ -222,10 +319,24 @@ function KeyPress_Callback(hFig, keyEvent)
if (iChannel > length(Channels))
iChannel = 1;
end
% Redraw arrows
if (iRef <= 0)
iRef = length(Channels);
end
if (iRef > length(Channels))
iRef = 1;
end

if thresholdAmplitude <= 0
thresholdAmplitude = 0;
end
if thresholdAmplitude >= 1
thresholdAmplitude = 1;
end

DrawArrows();
end


%% ===== DRAW CURRENT CHANNEL =====
function DrawArrows()
% Delete previous Channels and sensors
Expand Down Expand Up @@ -255,17 +366,39 @@ function DrawArrows()
end
% Display arrows
LeadField = reshape(LeadField,3,[])'; % each column is a vector
if(useLogScale)
LeadField = LogScaleLeadfield(LeadField);
end

% thresholding
normLF = sqrt((LeadField(:,1) ).^2 +(LeadField(:,2) ).^2 + (LeadField(:,3)).^2);
[col1, ind] = sort(normLF, 'ascend');
LeadFieldReordered = LeadField(ind,:);
cdf = cumsum(col1); % Compute cdf
cdf = cdf/cdf(end); % Normalize
% Find index bellow or above the thresholding
if thresholdBalance == 0 % 0 ==> inferior and 1 is superior
index = find(cdf <= thresholdAmplitude);
iSymbole = '<=';
else
index = find(cdf > thresholdAmplitude);
iSymbole = '>';
end
dataValue = zeros(size(LeadFieldReordered));
dataValue(index,:) = LeadFieldReordered(index,:);

hQuiver(iLF) = quiver3(...
HeadmodelMat{iLF}.GridLoc(:,1), HeadmodelMat{iLF}.GridLoc(:,2), HeadmodelMat{iLF}.GridLoc(:,3), ...
LeadField(:,1), LeadField(:,2), LeadField(:,3), ...
5, ...
...HeadmodelMat{iLF}.GridLoc(:,1), HeadmodelMat{iLF}.GridLoc(:,2), HeadmodelMat{iLF}.GridLoc(:,3), ... % These two line are remaining in order to check if the thresholding display is correct
...LeadField(:,1), LeadField(:,2), LeadField(:,3), ...
HeadmodelMat{iLF}.GridLoc(ind,1), HeadmodelMat{iLF}.GridLoc(ind,2), HeadmodelMat{iLF}.GridLoc(ind,3), ...
dataValue(:,1), dataValue(:,2), dataValue(:,3), ...
quiverSize, ...
'Parent', hAxes, ...
'LineWidth', 1, ...
'LineWidth', quiverWidth, ...
'Color', ColorOrder(mod(iLF-1, length(ColorOrder)) + 1, :), ...
'Tag', 'lfArrows');
% Arrow legends
strLegend{iLF} = [SubjectName{iLF} ' : ' selectedModality ' ' HeadmodelMat{iLF}.Comment];
hold on
end

% Remove previous selected sensor
Expand Down Expand Up @@ -299,18 +432,18 @@ function DrawArrows()
end
% Title bar (channel name)
if isAvgRef
strTitle = sprintf('Channel #%d/%d (%s) | %s ref Channel = AvgRef', iChannel, length(Channels), Channels(iChannel).Name,selectedModality);
strTitle = sprintf('Target channel(red) #%d/%d (%s) | %s Ref Channel(green) = AvgRef | Amp threshold %s %s %%| Log. scale %s', iChannel, length(Channels), Channels(iChannel).Name,selectedModality, iSymbole, num2str(thresholdAmplitude*100),useLogScaleLegendMsg);
else
strTitle = sprintf('Channel #%d/%d (%s) | %s ref Channel = %s', iChannel, length(Channels), Channels(iChannel).Name,selectedModality,Channels(iRef).Name);
strTitle = sprintf('Target channel(red) #%d/%d (%s) | %s Ref Channel(green) = %s| Amp threshold %s %s %%| Log. scale %s', iChannel, length(Channels), Channels(iChannel).Name,selectedModality,Channels(iRef).Name, iSymbole, num2str(thresholdAmplitude*100),useLogScaleLegendMsg);
end
else
strTitle = sprintf('Channel #%d/%d (%s)', iChannel, length(Channels), Channels(iChannel).Name);
strTitle = sprintf('Target channel (red) #%d/%d (%s) | Amp threshold %s %s %%|Log. scale %s', iChannel, length(Channels), Channels(iChannel).Name, iSymbole,num2str(thresholdAmplitude*100),useLogScaleLegendMsg);
end

if (iChannel == 1) && (length(Channels) > 1)
strTitle = [strTitle, ' [Press arrows for next/previous channel (or H for help)]'];
end
set(hLabel, 'String', strTitle, 'Position', [10 1 1200 35]);
set(hLabel, 'String', strTitle, 'Position', [10 1 1600 35],'ForegroundColor', [1 1 1]);
% Arrows legend
legend(hQuiver, strLegend, ...
'TextColor', 'w', ...
Expand Down Expand Up @@ -351,26 +484,32 @@ function DrawArrows()
function isOk = SelectReference()
isOk = 1;
if ~strcmp(selectedModality,'MEG')
[isAvgRef, isCancel] = java_dialog('confirm', ...
['<HTML>Do you want to use the <B>average refence</B> for the ' selectedModality ' ?<BR>'...
'Otherwise you will choose one reference electrode.'], [selectedModality ' average reference'], [], ...
{'Yes, use average reference'}, 1);
if isCancel
% Ask for the reference electrode
refChan = java_dialog('combo', '<HTML>Select the reference channel (green color):<BR><BR>', [selectedModality ' reference'], [], {'Average Ref', Channels.Name});
if isempty(refChan)
isOk = 0;
return;
end
if ~isAvgRef
% Ask for the reference electrode
refChan = java_dialog('combo', '<HTML>Select the reference channel:<BR><BR>', [selectedModality ' reference'], [], {Channels.Name});
if isempty(refChan)
isOk = 0;
return;
end
iRef = find(strcmpi({Channels.Name}, refChan));
iRef = find(strcmpi({Channels.Name}, refChan));
if isempty(iRef)
isAvgRef = 1;
else
isAvgRef = 0;
end
end
end

%% ===== SET TARGET =====
function isOk = SelectTarget()
isOk = 1;
% Ask for the target electrode
trgChan = java_dialog('combo', '<HTML>Select the target channel (red color):<BR><BR>', [selectedModality ' Target'], [], {Channels.Name});
if isempty(trgChan)
isOk = 0;
return;
end
iChannel = find(strcmpi({Channels.Name}, trgChan));
end

%% ===== GET LEADFIELD =====
function GetLeadField
Expand All @@ -379,4 +518,16 @@ function DrawArrows()
LF_finale{iLF} = HeadmodelMat{iLF}.Gain(iChannels,:);
end
end

%% ===== LEADFIELD TO LOG SPACE =====
function lf_log = LogScaleLeadfield(lf)
lf_2 = lf.^2;
r = sqrt(sum(lf_2,2));
rho = sqrt(lf_2(:,1) + lf_2(:,2));
t = atan2(rho,lf(:,3));
f = atan2(lf(:,2),lf(:,1));
lf_log = [ log10(r) .* sin(t) .* cos(f) ...
log10(r) .* sin(t) .* sin(f) ...
log10(r) .* cos(t)];
end
end