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Thresholding of isosurface without creating a new one #31

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Thresholding of isosurface without creating a new one #31

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b01c08e
better way to find files
chinmaychinara91 Aug 8, 2024
77b048d
for SEEG implantation, prevent loading multiple instances of the same…
chinmaychinara91 Aug 8, 2024
a4e7fb4
update isosurface patch with new values rather than deleting and relo…
chinmaychinara91 Aug 9, 2024
5f0b71d
added comments to commit a4e7fb4
chinmaychinara91 Aug 9, 2024
966fbeb
remove isosurface threshold slider from Surface tab; add option to po…
chinmaychinara91 Aug 9, 2024
1b09efb
set the min and max limits of CT thresholding to the popup menu option
chinmaychinara91 Aug 9, 2024
8aaf10a
fix isoValue value display update on the menu pop up
chinmaychinara91 Aug 10, 2024
d9d65bb
move the `isovalue` menu to the top
chinmaychinara91 Aug 12, 2024
1b99a59
keyboard shortcut for larger threshold; menu option for fine tuning
chinmaychinara91 Aug 12, 2024
3a1a9f7
refactor code and update comments
chinmaychinara91 Aug 12, 2024
b347f1f
use `regexp` instead of `strfind`
chinmaychinara91 Aug 14, 2024
ccb301d
updated history text and mesh fields
chinmaychinara91 Aug 14, 2024
dc3ccce
bug fix: if isosurface is present in database but not open ; open in …
chinmaychinara91 Aug 21, 2024
a5878bf
coarse tuning +/- 300; fine tuning +/- 50
chinmaychinara91 Aug 23, 2024
1459c25
refactor code with comments
chinmaychinara91 Aug 23, 2024
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58 changes: 38 additions & 20 deletions toolbox/anatomy/tess_isosurface.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@
MeshFile = [];
iSurface = [];
isSave = true;
global GlobalData;

% Parse inputs
if (nargin < 3) || isempty(Comment)
Expand Down Expand Up @@ -128,6 +129,7 @@

%% ===== CREATE SURFACE =====
% Compute isosurface
sMesh = db_template('LoadedSurface');
bst_progress('start', 'Generate thresholded isosurface from CT', 'Creating isosurface...');
[sMesh.Faces, sMesh.Vertices] = mri_isosurface(sMri.Cube, isoValue);
bst_progress('inc', 10);
Expand All @@ -145,6 +147,8 @@
sMesh.Vertices = bst_bsxfun(@times, sMesh.Vertices, sMri.Voxsize);
% Convert to SCS
sMesh.Vertices = cs_convert(sMri, 'mri', 'scs', sMesh.Vertices ./ 1000);
sMesh.Comment = sprintf('isoSurface (ISO_%d)', isoValue);
sMesh.VertConn = tess_vertconn(sMesh.Vertices, sMesh.Faces);

%% ===== SAVE FILES =====
if isSave
Expand All @@ -154,28 +158,42 @@
SurfaceDir = bst_fullfile(ProtocolInfo.SUBJECTS, bst_fileparts(CtFile));
% Get the mesh file
MeshFile = bst_fullfile(SurfaceDir, 'tess_isosurface.mat');

% Replace existing isoSurface surface (tess_isosurface.mat)
[sSubjectTmp, iSubjectTmp, iSurfaceTmp] = bst_get('SurfaceFile', MeshFile);
if ~isempty(iSurfaceTmp)
file_delete(file_fullpath(MeshFile), 1);
sSubjectTmp.Surface(iSurfaceTmp) = [];
bst_set('Subject', iSubjectTmp, sSubjectTmp);
end
% Get isoSurface (tess_isosurface.mat)
[~, ~, iSurface] = bst_get('SurfaceFile', MeshFile);

% Save isosurface
sMesh.Comment = sprintf('isoSurface (ISO_%d)', isoValue);
sMesh = bst_history('add', sMesh, 'threshold_ct', 'CT thresholded isosurface generated with Brainstorm');
bst_save(MeshFile, sMesh, 'v7');
iSurface = db_add_surface(iSubject, MeshFile, sMesh.Comment);
% Display mesh with 3D orthogonal slices of the default MRI
MriFile = sSubject.Anatomy(1).FileName;
hFig = bst_figures('GetFiguresByType', '3DViz');
if isempty(hFig)
hFig = view_mri_3d(MriFile, [], 0.3, []);
sMesh.FileName = file_short(MeshFile);
sMesh.Name = 'Other';
% if isosurface not created create it
if isempty(iSurface)
sMesh = bst_history('add', sMesh, 'threshold_ct', 'CT thresholded isosurface generated with Brainstorm');
bst_save(MeshFile, sMesh, 'v7');
iSurface = db_add_surface(iSubject, MeshFile, sMesh.Comment);
MriFile = sSubject.Anatomy(1).FileName;
hFig = bst_figures('GetFiguresByType', '3DViz');
if isempty(hFig)
hFig = view_mri_3d(MriFile, [], 0.3, []);
end
view_surface(MeshFile, [], [], hFig, []);
else % else just update the isosurface surface patch with new computed values
% update the surface displayed in figure
hFig = bst_figures('GetFiguresByType', '3DViz');
TessInfo = getappdata(hFig, 'Surface');
iSurfPatch = find(cellfun(@(c)(~isempty(strfind(char(c), 'tess_isosurface'))), {TessInfo.SurfaceFile}));
set(TessInfo(iSurfPatch).hPatch, 'Vertices', sMesh.Vertices);
set(TessInfo(iSurfPatch).hPatch, 'Faces', sMesh.Faces);
set(TessInfo(iSurfPatch).hPatch, 'FaceVertexCData', ones(size(sMesh.Vertices)));
TessInfo(iSurfPatch).nVertices = size(sMesh.Vertices, 1);
TessInfo(iSurfPatch).nFaces = size(sMesh.Faces, 1);
setappdata(hFig, 'Surface', TessInfo);
% update the GlobalData with new surface
iSurfGlobal = find(file_compare({GlobalData.Surface.FileName}, sMesh.FileName));
GlobalData.Surface(iSurfGlobal) = sMesh;
% update the surface in tess_isosurface.mat
sMesh = bst_history('add', sMesh, 'threshold_ct', 'CT thresholded isosurface updated');
bst_save(MeshFile, sMesh, 'v7');
% reload the subject to reflect updated values
db_reload_subjects(iSubject);
end
view_surface(MeshFile, 0.6, [], hFig, []);
panel_surface('SetIsoValue', isoValue);
else
% Return surface
MeshFile = sMesh.Vertices;
Expand Down
55 changes: 54 additions & 1 deletion toolbox/gui/figure_3d.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1071,8 +1071,28 @@ function FigureKeyPressedCallback(hFig, keyEvent)
case {'uparrow', 'downarrow'}
% If there are tensors displayed: update display
Handles = bst_figures('GetFigureHandles', hFig);
TessInfo = getappdata(hFig, 'Surface');
iSurf = find(cellfun(@(c)(~isempty(strfind(char(c), 'tess_isosurface'))), {TessInfo.SurfaceFile}));
if isfield(Handles, 'TensorDisplay') && ~isempty(Handles.TensorDisplay)
PlotTensorCut(hFig, [], [], [], keyEvent.Key, []);
% isovalue
elseif ismember('shift', keyEvent.Modifier) && ~isempty(iSurf)
SubjectFile = getappdata(hFig, 'SubjectFile');
sSubject = bst_get('Subject', SubjectFile);
iCt = find(cellfun(@(c)(~isempty(strfind(char(c), '_volct'))), {sSubject.Anatomy.FileName}));
CtFile = sSubject.Anatomy(iCt(1)).FileName;
sCt = bst_memory('LoadMri', CtFile);
sSurface = bst_memory('LoadSurface', TessInfo(iSurf(1)).SurfaceFile);
val = regexp(sSurface.Comment, '\d+', 'match');
if strcmpi(keyEvent.Key, 'uparrow')
if (str2double(val(1))+100 >= double(sCt.Histogram.whiteLevel)) && (str2double(val(1))+100 <= double(sCt.Histogram.intensityMax))
tess_isosurface(CtFile, str2double(val(1))+100);
end
else
if (str2double(val(1))-100 >= double(sCt.Histogram.whiteLevel)) && (str2double(val(1))-100 <= double(sCt.Histogram.intensityMax))
tess_isosurface(CtFile, str2double(val(1))-100);
end
end
% Up/Down: Process by Freq panel
else
panel_freq('FreqKeyCallback', keyEvent);
Expand Down Expand Up @@ -1556,6 +1576,8 @@ function ApplyViewToAllFigures(hSrcFig, isView, isSurfProp)
%% ===== POPUP MENU =====
% Show a popup dialog about the target 3DViz figure
function DisplayFigurePopup(hFig)
import java.awt.*;
import javax.swing.*;
import java.awt.event.KeyEvent;
import javax.swing.KeyStroke;
import org.brainstorm.icon.*;
Expand Down Expand Up @@ -1662,6 +1684,37 @@ function DisplayFigurePopup(hFig)
end
jPopup.addSeparator();
end

% ==== MENU: ISOSURFACE ====
% Create isosurface
iSurf = find(cellfun(@(c)(~isempty(strfind(char(c), 'tess_isosurface'))), {TessInfo.SurfaceFile}));
if ~isempty(iSurf)
% get the CT file details
SubjectFile = getappdata(hFig, 'SubjectFile');
sSubject = bst_get('Subject', SubjectFile);
iCt = find(cellfun(@(c)(~isempty(strfind(char(c), '_volct'))), {sSubject.Anatomy.FileName}));
CtFile = sSubject.Anatomy(iCt(1)).FileName;
sCt = bst_memory('LoadMri', CtFile);
% panel operations
jPanel = gui_component('Panel');
jPanel.setOpaque(0);
jPopup.add(jPanel);
% Title
jLabel = gui_component('label', [], '', '<HTML><B>isoValue threshold </B>', IconLoader.ICON_SURFACE);
jPanel.add(jLabel, BorderLayout.WEST);
% Spin button
sSurface = bst_memory('LoadSurface', TessInfo(iSurf).SurfaceFile);
val = regexp(sSurface.Comment, '\d+', 'match');
spinmodel = SpinnerNumberModel(str2double(val(1)), double(sCt.Histogram.whiteLevel), double(sCt.Histogram.intensityMax), 50);
jSpinner = JSpinner(spinmodel);
jSpinner.setPreferredSize(Dimension(55,25));
% jSpinner.setToolTipText(strTooltip);
java_setcb(spinmodel, 'StateChangedCallback', @(h,ev)tess_isosurface(CtFile, jSpinner.getValue()));
jPanel.add(jSpinner, BorderLayout.EAST);
% jButtonSet = gui_component('button', [], '', 'Set', [], [], @(h,ev)tess_isosurface(CtFile, jSpinner.getValue()));
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@chinmaychinara91 chinmaychinara91 Aug 12, 2024 •
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for commit 1b99a59 also removed the need to another button click

% jButtonSet.setPreferredSize(Dimension(55,25));
% jPanel.add(jButtonSet, BorderLayout.EAST);
end

% ==== MENU: 2DLAYOUT ====
if strcmpi(FigureType, 'Topography') && strcmpi(GlobalData.DataSet(iDS).Figure(iFig).Id.SubType, '2DLayout')
Expand Down Expand Up @@ -1853,7 +1906,7 @@ function DisplayFigurePopup(hFig)
jMenuMontage = gui_component('Menu', jPopup, [], 'Montage', IconLoader.ICON_TS_DISPLAY_MODE);
panel_montage('CreateFigurePopupMenu', jMenuMontage, hFig);
end

% ==== MENU: COLORMAPS ====
% Create the colormaps menus
bst_colormaps('CreateAllMenus', jPopup, hFig, 0);
Expand Down
105 changes: 0 additions & 105 deletions toolbox/gui/panel_surface.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -107,20 +107,6 @@
% Quick preview
java_setcb(jSliderSurfSmoothValue, 'StateChangedCallback', @(h,ev)SliderQuickPreview(jSliderSurfSmoothValue, jLabelSurfSmoothValue, 1));

% Threshold title
jLabelSurfIsoValueTitle = gui_component('label', jPanelSurfaceOptions, 'br', 'Thresh.:');
% Min size slider
jSliderSurfIsoValue = JSlider(1, GetIsoValueMaxRange(), 1);
jSliderSurfIsoValue.setPreferredSize(Dimension(SLIDER_WIDTH, DEFAULT_HEIGHT));
jSliderSurfIsoValue.setToolTipText('isoSurface Threshold');
java_setcb(jSliderSurfIsoValue, 'MouseReleasedCallback', @(h,ev)SliderCallback(h, ev, 'SurfIsoValue'), ...
'KeyPressedCallback', @(h,ev)SliderCallback(h, ev, 'SurfIsoValue'));
jPanelSurfaceOptions.add('tab hfill', jSliderSurfIsoValue);
% IsoValue label
jLabelSurfIsoValue = gui_component('label', jPanelSurfaceOptions, [], ' 1', {JLabel.RIGHT, Dimension(LABEL_WIDTH, DEFAULT_HEIGHT)});
% Quick preview
java_setcb(jSliderSurfIsoValue, 'StateChangedCallback', @(h,ev)SliderQuickPreview(jSliderSurfIsoValue, jLabelSurfIsoValue, 0));

% Buttons
jButtonSurfColor = gui_component('button', jPanelSurfaceOptions, 'br center', 'Color', {Dimension(BUTTON_WIDTH, DEFAULT_HEIGHT), Insets(0,0,0,0)}, 'Set surface color', @ButtonSurfColorCallback);
jButtonSurfSulci = gui_component('toggle', jPanelSurfaceOptions, '', 'Sulci', {Dimension(BUTTON_WIDTH, DEFAULT_HEIGHT), Insets(0,0,0,0)}, 'Show/hide sulci map', @ButtonShowSulciCallback);
Expand Down Expand Up @@ -228,9 +214,6 @@
'jButtonSurfColor', jButtonSurfColor, ...
'jLabelSurfSmoothValue', jLabelSurfSmoothValue, ...
'jSliderSurfSmoothValue', jSliderSurfSmoothValue, ...
'jLabelSurfIsoValueTitle',jLabelSurfIsoValueTitle, ...
'jLabelSurfIsoValue', jLabelSurfIsoValue, ...
'jSliderSurfIsoValue', jSliderSurfIsoValue, ...
'jButtonSurfSulci', jButtonSurfSulci, ...
'jButtonSurfEdge', jButtonSurfEdge, ...
'jSliderResectX', jSliderResectX, ...
Expand Down Expand Up @@ -258,8 +241,6 @@ function SliderQuickPreview(jSlider, jText, isPercent)
nVertices = str2num(char(jLabelNbVertices.getText()));
sliderSizeVector = GetSliderSizeVector(nVertices);
jText.setText(sprintf('%d', sliderSizeVector(double(jSlider.getValue()))));
elseif (jSlider == jSliderSurfIsoValue)
jText.setText(sprintf('%d', double(jSlider.getValue())));
elseif isPercent
jText.setText(sprintf('%d%%', double(jSlider.getValue())));
else
Expand Down Expand Up @@ -410,42 +391,6 @@ function SliderCallback(hObject, event, target)
case 'SurfSmoothValue'
SurfSmoothValue = jSlider.getValue() / 100;
SetSurfaceSmooth(hFig, iSurface, SurfSmoothValue, 1);

case 'SurfIsoValue'
% get the handles
hFig = bst_figures('GetFiguresByType', '3DViz');
SubjectFile = getappdata(hFig, 'SubjectFile');
if ~isempty(SubjectFile)
sSubject = bst_get('Subject', SubjectFile);
CtFile = [];
MeshFile = [];
for i=1:length(sSubject.Anatomy)
if ~isempty(regexp(sSubject.Anatomy(i).FileName, 'CT', 'match'))
CtFile = sSubject.Anatomy(i).FileName;
end
end
for i=1:length(sSubject.Surface)
if ~isempty(regexp(sSubject.Surface(i).FileName, 'tess_isosurface', 'match'))
MeshFile = sSubject.Surface(i).FileName;
end
end
end

% ask user if they want to proceed
isProceed = java_dialog('confirm', 'Do you want to proceed generating mesh with new isoValue ?', 'Changing threshold');
if ~isProceed
[sSubjectTmp, iSubjectTmp, iSurfaceTmp] = bst_get('SurfaceFile', MeshFile);
isoValue = regexp(sSubjectTmp.Surface(iSurfaceTmp).Comment, '\d*', 'match');
SetIsoValue(str2double(isoValue{1}));
return;
end

% get the iso value from slider
isoValue = jSlider.getValue();

% remove the old isosurface and generate and load the new one
ButtonRemoveSurfaceCallback();
tess_isosurface(CtFile, isoValue);

case 'DataAlpha'
% Update value in Surface array
Expand Down Expand Up @@ -528,42 +473,6 @@ function SliderCallback(hObject, event, target)
end
end

%% ===== GET SLIDER ISOVALUE =====
function isoValue = GetIsoValueMaxRange()
% get the handles
hFig = bst_figures('GetFiguresByType', '3DViz');
if ~isempty(hFig)
SubjectFile = getappdata(hFig, 'SubjectFile');
if ~isempty(SubjectFile)
sSubject = bst_get('Subject', SubjectFile);
CtFile = [];
for i=1:length(sSubject.Anatomy)
if ~isempty(regexp(sSubject.Anatomy(i).FileName, 'CT', 'match'))
CtFile = sSubject.Anatomy(i).FileName;
end
end
end

if ~isempty(CtFile)
sMri = bst_memory('LoadMri', CtFile);
isoValue = double(sMri.Histogram.intensityMax);
end
else
isoValue = 4500.0;
end
end

%% ===== SET SLIDER ISOVALUE =====
function SetIsoValue(isoValue)
% get panel controls
ctrl = bst_get('PanelControls', 'Surface');
if isempty(ctrl)
return;
end
ctrl.jLabelSurfIsoValue.setText(sprintf('%d', isoValue));
ctrl.jSliderSurfIsoValue.setValue(isoValue);
end

%% ===== SCROLL MRI CUTS =====
function ScrollMriCuts(hFig, direction, value) %#ok<DEFNU>
% Get Mri and figure Handles
Expand Down Expand Up @@ -1132,11 +1041,6 @@ function UpdateSurfaceProperties()
end
% If surface is sliced MRI
isAnatomy = strcmpi(TessInfo(iSurface).Name, 'Anatomy');
if ~isempty(regexp(TessInfo(iSurface).SurfaceFile, 'isosurface', 'match'))
isIsoSurface = 1;
else
isIsoSurface = 0;
end

% ==== Surface properties ====
% Number of vertices
Expand All @@ -1152,15 +1056,6 @@ function UpdateSurfaceProperties()
% Surface smoothing ALPHA
ctrl.jSliderSurfSmoothValue.setValue(100 * TessInfo(iSurface).SurfSmoothValue);
ctrl.jLabelSurfSmoothValue.setText(sprintf('%d%%', round(100 * TessInfo(iSurface).SurfSmoothValue)));
% Show/hide isoSurface thresholding
ctrl.jSliderSurfIsoValue.setVisible(isIsoSurface);
ctrl.jLabelSurfIsoValueTitle.setVisible(isIsoSurface);
ctrl.jLabelSurfIsoValue.setVisible(isIsoSurface);
if isIsoSurface
[sSubjectTmp, iSubjectTmp, iSurfaceTmp] = bst_get('SurfaceFile', TessInfo(iSurface).SurfaceFile);
isoValue = regexp(sSubjectTmp.Surface(iSurfaceTmp).Comment, '\d*', 'match');
SetIsoValue(str2double(isoValue{1}));
end
% Show sulci button
ctrl.jButtonSurfSulci.setSelected(TessInfo(iSurface).SurfShowSulci);
% Show surface edges button
Expand Down
6 changes: 4 additions & 2 deletions toolbox/tree/tree_callbacks.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -226,12 +226,13 @@
% Get displayable modalities for this file
[tmp, DisplayMod] = bst_get('ChannelModalities', filenameRelative);
DisplayMod = intersect(DisplayMod, {'EEG','MEG','MEG GRAD','MEG MAG','ECOG','SEEG','ECOG+SEEG','NIRS'});
hFig = bst_figures('GetFiguresByType','3DViz');
% If only one modality
if ~isempty(DisplayMod)
if strcmpi(DisplayMod{1}, 'ECOG+SEEG') || (length(DisplayMod) >= 2) && all(ismember({'SEEG','ECOG'}, DisplayMod))
DisplayChannels(bstNodes, 'ECOG+SEEG', 'cortex', 1);
elseif strcmpi(DisplayMod{1}, 'SEEG')
DisplayChannels(bstNodes, DisplayMod{1}, 'anatomy', 1, 0);
DisplayChannels(bstNodes, DisplayMod{1}, 'anatomy', 1, 0, hFig);
elseif strcmpi(DisplayMod{1}, 'ECOG')
DisplayChannels(bstNodes, DisplayMod{1}, 'cortex', 1);
elseif ismember(DisplayMod{1}, {'MEG','MEG GRAD','MEG MAG'})
Expand Down Expand Up @@ -835,6 +836,7 @@
% Get avaible modalities for this data file
[AllMod, DisplayMod] = bst_get('ChannelModalities', filenameRelative);
Device = bst_get('ChannelDevice', filenameRelative);
hFig = bst_figures('GetFiguresByType','3DViz');
% Replace SEEG+ECOG with iEEG
if ~isempty(AllMod) && all(ismember({'SEEG','ECOG'}, AllMod))
AllMod = cat(2, {'ECOG+SEEG'}, setdiff(AllMod, {'SEEG','ECOG'}));
Expand Down Expand Up @@ -923,7 +925,7 @@
end
% === SEEG IMPLANTATION ===
if (length(bstNodes) == 1) && ((isempty(AllMod) && strcmpi(sStudy.Name, 'implantation')) || any(ismember({'SEEG','ECOG','ECOG+SEEG'}, AllMod)))
gui_component('MenuItem', jPopup, [], 'SEEG/ECOG implantation', IconLoader.ICON_SEEG_DEPTH, [], @(h,ev)DisplayChannels(bstNodes, 'SEEG', 'anatomy', 1, 0));
gui_component('MenuItem', jPopup, [], 'SEEG/ECOG implantation', IconLoader.ICON_SEEG_DEPTH, [], @(h,ev)DisplayChannels(bstNodes, 'SEEG', 'anatomy', 1, 0, hFig));
end
% === SEEG CONTACT LABELLING ===
if (length(bstNodes) == 1) && ~isempty(AllMod) && any(ismember({'SEEG','ECOG','ECOG+SEEG'}, AllMod))
Expand Down