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Merge pull request #327 from HJZollner/develop
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lcm-integration
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@HJZollner
HJZollner authored Aug 26, 2021
2 parents f3d2829 + 126513f commit 8317ae1
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Showing 3 changed files with 68 additions and 40 deletions.
8 changes: 4 additions & 4 deletions GUI/osp_updateFitWindow.m
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Original file line number Diff line number Diff line change
Expand Up @@ -79,13 +79,13 @@ function osp_updateFitWindow(gui)
waterFitRangeString = ['Fitting range: ' num2str(MRSCont.opts.fit.rangeWater(1)) ' to ' num2str(MRSCont.opts.fit.rangeWater(2)) ' ppm'];
% Where are the metabolite names stored?
if strcmp(gui.fit.Style, 'ref') || strcmp(gui.fit.Style, 'w')
basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).water.(['np_sw_' num2str(MRSCont.processed.A{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.A{1}.spectralwidth)]).name;
basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).water.(['np_sw_' num2str(MRSCont.processed.A{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.A{gui.controls.Selected}.spectralwidth)]).name;
else if strcmp(gui.fit.Style, 'conc')
basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.A{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.A{1}.spectralwidth)]).name;
basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.A{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.A{gui.controls.Selected}.spectralwidth)]).name;
else if strcmp(gui.fit.Style, 'off')
basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.A{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.A{1}.spectralwidth)]).name;
basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.A{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.A{gui.controls.Selected}.spectralwidth)]).name;
else
basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.A{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.A{1}.spectralwidth)]).name;
basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.A{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.A{gui.controls.Selected}.spectralwidth)]).name;
end
end
end
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96 changes: 61 additions & 35 deletions plot/osp_plotModule.m
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,10 @@
colormapfig.LightAccent = [110/255 136/255 164/255];
colormapfig.Foreground = [11/255 71/255 111/255];
colormapfig.Accent = [11/255 71/255 111/255];
% Determine font accorind to os
font=osp_platform('fonts');
font = font.helvetica;


% Create main window with fixed size
screenSize = get(0,'ScreenSize');
Expand All @@ -86,19 +90,19 @@
out = figure('NumberTitle', 'off', 'Visible', 'on', 'Menu', 'none', ...
'Position', canvasSize, 'ToolBar', 'none', ...
'HandleVisibility', 'off', 'Renderer', 'painters', ...
'Color', colormapfig.Background);
'Color', colormapfig.Background, 'Tag','MainFigure');
MRSCont.flags.isGUI = 1;
Title = MRSCont.ver.Osp;

Frame = uix.Panel('Parent', out, 'Padding', 1, 'Title', Title, ...
'FontName', gui.font, 'BackgroundColor', colormapfig.Background, ...
'FontName', font, 'BackgroundColor', colormapfig.Background, ...
'ForegroundColor', colormapfig.Foreground, ...
'HighlightColor', colormapfig.Background, ...
'ShadowColor', colormapfig.Background);
input_figure = uix.VBox('Parent', Frame, 'BackgroundColor',colormapfig.Background, 'Spacing', 5);
box = uix.HBox('Parent', input_figure,'BackgroundColor',colormapfig.Background, 'Spacing',6);
Info = uix.Panel('Parent',box, 'Padding', 5, 'Title', MRSCont.files{kk},...
'FontName', gui.font, 'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground,...
'FontName', font, 'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground,...
'HighlightColor', colormapfig.Foreground, 'ShadowColor', colormapfig.Foreground);
LogoFig = figure('Visible','off');
[I, map] = imread('osprey.gif','gif');
Expand Down Expand Up @@ -143,7 +147,7 @@

% Information text panel
InfoText = uicontrol('Parent',Info,'style','text',...
'FontSize', 12, 'FontName', gui.font,'ForegroundColor', colormapfig.Foreground,...
'FontSize', 12, 'FontName', font,'ForegroundColor', colormapfig.Foreground,...
'HorizontalAlignment', 'left', 'String', '', 'BackgroundColor',colormapfig.Background);

% Get some information about the data from MRSCont to fill the info panel
Expand Down Expand Up @@ -295,7 +299,7 @@
' ppm / Hz'];
end
end
InfoText = uicontrol('Parent',Info,'style','text','FontSize', 12, 'FontName', gui.font,...
InfoText = uicontrol('Parent',Info,'style','text','FontSize', 12, 'FontName', font,...
'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);

Expand Down Expand Up @@ -354,21 +358,33 @@
resultsFontSize = 6;
case 'Osprey'
% Number of metabolites and lipid/MM basis functions
nMets = MRSCont.fit.resBasisSet.(which){1,MRSCont.info.A.unique_ndatapoint_indsort(kk)}.nMets;
nMMLip = MRSCont.fit.resBasisSet.(which){1,MRSCont.info.A.unique_ndatapoint_indsort(kk)}.nMM;
nMets = MRSCont.fit.basisSet.nMets;
nMMLip = MRSCont.fit.basisSet.nMM;
% Additional info panel string for the water fit range
waterFitRangeString = ['Fitting range: ' num2str(MRSCont.opts.fit.rangeWater(1)) ' to ' num2str(MRSCont.opts.fit.rangeWater(2)) ' ppm'];
% Where are the metabolite names stored?
basisSetNames = MRSCont.fit.resBasisSet.(which){1,MRSCont.info.A.unique_ndatapoint_indsort(kk)}.name;
if strcmp(which, 'ref') || strcmp(which, 'w')
basisSetNames = MRSCont.fit.resBasisSet.(which).water.(['np_sw_' num2str(MRSCont.processed.A{kk}.sz(1)) '_' num2str(MRSCont.processed.A{kk}.spectralwidth)]).name;
else if strcmp(which, 'conc')
basisSetNames = MRSCont.fit.resBasisSet.(which).(['np_sw_' num2str(MRSCont.processed.A{kk}.sz(1)) '_' num2str(MRSCont.processed.A{kk}.spectralwidth)]).name;
else if strcmp(which, 'off')
basisSetNames = MRSCont.fit.resBasisSet.(which).(['np_sw_' num2str(MRSCont.processed.A{kk}.sz(1)) '_' num2str(MRSCont.processed.A{kk}.spectralwidth)]).name;
else
basisSetNames = MRSCont.fit.resBasisSet.(which).(['np_sw_' num2str(MRSCont.processed.A{kk}.sz(1)) '_' num2str(MRSCont.processed.A{kk}.spectralwidth)]).name;
end
end
end
% Larger fonts for the results
resultsFontSize = 11;
end

ph0 = MRSCont.fit.results.(which).fitParams{1,gui.controls.Selected}.ph0;
ph1 = MRSCont.fit.results.(which).fitParams{1,gui.controls.Selected}.ph1;

ph0 = MRSCont.fit.results.(which).fitParams{1,kk}.ph0;
ph1 = MRSCont.fit.results.(which).fitParams{1,kk}.ph1;

if ~strcmp(which, 'ref') && ~strcmp(which, 'w')
refShift = MRSCont.fit.results.(which).fitParams{1,gui.controls.Selected}.refShift;
refFWHM = MRSCont.fit.results.(which).fitParams{1,gui.controls.Selected}.refFWHM;
refShift = MRSCont.fit.results.(which).fitParams{1,kk}.refShift;
refFWHM = MRSCont.fit.results.(which).fitParams{1,kk}.refFWHM;
end

% Build output folder filename
Expand All @@ -386,11 +402,11 @@
set(input_figure, 'Heights', [-0.12 -0.88]);
% Get parameter from file to fill the info panel
if ~strcmp (which, 'ref') && ~strcmp (which, 'w') %Metabolite data?
StatText = ['Metabolite Data -> Sequence: ' gui.load.Names.Seq '; Fitting algorithm: ' MRSCont.opts.fit.method '; Fitting Style: ' MRSCont.opts.fit.style '; Selected subspecs: ' which,...
StatText = ['Metabolite Data -> Sequence: ' Seq '; Fitting algorithm: ' MRSCont.opts.fit.method '; Fitting Style: ' MRSCont.opts.fit.style '; Selected subspecs: ' which,...
'\nFitting range: ' num2str(MRSCont.opts.fit.range(1)) ' to ' num2str(MRSCont.opts.fit.range(2)) ' ppm; Baseline knot spacing: ' num2str(MRSCont.opts.fit.bLineKnotSpace) ' ppm; ph0: ' num2str(ph0,'%1.2f'),...
'deg; ph1: ' num2str(ph1,'%1.2f') 'deg; refShift: ' num2str(refShift,'%1.2f') ' Hz; refFWHM: ' num2str(refFWHM,'%1.2f')...
' ppm\nNumber of metabolites: ' num2str(nMets) '; Number of MM/lipids: ' num2str(nMMLip) ...
' scale: ' num2str(MRSCont.fit.scale{gui.controls.Selected})];
' scale: ' num2str(MRSCont.fit.scale{kk})];
else if strcmp (which, 'ref') %Reference data?
StatText = ['Reference Data -> Sequence: ' Seq '; Fitting algorithm: ' MRSCont.opts.fit.method '; Fitting Style: ' MRSCont.opts.fit.style '; Selected subspecs: ' which,...
'\n' waterFitRangeString];
Expand All @@ -403,10 +419,10 @@
%%% 2.cc FILLING FITTED AMPLITUDE PANEL %%%
% Creates the panel on the right side with the fitted amplitudes
InfoText = uicontrol('Parent',Info,'style','text',...
'FontSize', 12, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'FontSize', 12, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
Results = uix.Panel('Parent', Plot,...
'Title', ['Raw Amplitudes'],'FontName', gui.font,'HighlightColor', colormapfig.Foreground,...
'Title', ['Raw Amplitudes'],'FontName', font,'HighlightColor', colormapfig.Foreground,...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground, 'ShadowColor', colormapfig.Foreground);
if ~strcmp (MRSCont.opts.fit.style, 'Concatenated') || strcmp(which, 'ref') || strcmp(which, 'w') %Is not concateneted or is reference/water fit
Style = which;
Expand Down Expand Up @@ -445,14 +461,14 @@
set(Results, 'Title', ['Raw Amplitudes']);
FitText = uix.HBox('Parent', Results, 'Padding', 5,'BackgroundColor',colormapfig.Background);
FitTextNames = uicontrol('Parent',FitText,'style','text',...
'FontSize', resultsFontSize, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(NameText),...
'FontSize', resultsFontSize, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(NameText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
FitTextAmpl = uicontrol('Parent',FitText,'style','text',...
'FontSize', resultsFontSize, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(RawAmplText),...
'FontSize', resultsFontSize, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(RawAmplText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
if strcmp(MRSCont.opts.fit.method, 'LCModel')
FitTextCRLB = uicontrol('Parent',FitText,'style','text',...
'FontSize', resultsFontSize, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(CRLBText),...
'FontSize', resultsFontSize, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(CRLBText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
end
else %If water/reference data is fitted Raw amplitudes are calculated with regard to water
Expand Down Expand Up @@ -480,14 +496,14 @@
set(Results, 'Title', ['Raw Water Ratio']);
FitText = uix.HBox('Parent', Results, 'Padding', 5,'BackgroundColor',colormapfig.Background);
FitTextNames = uicontrol('Parent',FitText,'style','text',...
'FontSize', resultsFontSize, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(NameText),...
'FontSize', resultsFontSize, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(NameText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
FitTextAmpl = uicontrol('Parent',FitText,'style','text',...
'FontSize', resultsFontSize, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(RawAmplText),...
'FontSize', resultsFontSize, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(RawAmplText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
if strcmp(MRSCont.opts.fit.method, 'LCModel')
FitTextCRLB = uicontrol('Parent',FitText,'style','text',...
'FontSize', resultsFontSize, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(CRLBText),...
'FontSize', resultsFontSize, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(CRLBText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
end

Expand All @@ -497,10 +513,10 @@
set(Results, 'Title', ['Raw Amplitudes']);
FitText = uix.HBox('Parent', Results, 'Padding', 5,'BackgroundColor',colormapfig.Background);
FitTextNames = uicontrol('Parent',FitText,'style','text',...
'FontSize', resultsFontSize, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(NameText),...
'FontSize', resultsFontSize, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(NameText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
FitTextAmpl = uicontrol('Parent',FitText,'style','text',...
'FontSize', resultsFontSize, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(RawAmplText),...
'FontSize', resultsFontSize, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(RawAmplText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
end
end
Expand Down Expand Up @@ -538,7 +554,7 @@
num2str(MRSCont.raw{1,kk}.geometry.size.(Geom{1}) * MRSCont.raw{1,kk}.geometry.size.(Geom{2}) * MRSCont.raw{1,kk}.geometry.size.(Geom{3})/1000) ' ml'];

InfoText = uicontrol('Parent',Info,'style','text',...
'FontSize', 12, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'FontSize', 12, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);

%%% 2.VISUALIZATION PART OF THIS TAB %%%
Expand Down Expand Up @@ -576,7 +592,7 @@
'Distribution: ' groupString '\n'];

InfoText = uicontrol('Parent',Info,'style','text',...
'FontSize', 12, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'FontSize', 12, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
Plot = uix.HBox('Parent', input_figure, 'Padding', 5,'BackgroundColor',colormapfig.Background);
set(input_figure, 'Heights', [-0.1 -0.9]);
Expand All @@ -585,13 +601,18 @@
for g = 1 : MRSCont.overview.NoGroups %Loop over groups
temp = osp_plotOverviewSpec(MRSCont, which, g, 0.1);
if g == 1
temp = get(temp,'Parent');
fig_hold = get(temp,'Parent');
fig_hold = temp;
set(fig_hold,'Tag','fig_hold');
else
ax=get(temp,'Parent');
copyobj(ax.Children, fig_hold.Children(1));
ViewAxes=get(temp,'Children');
copyobj(ViewAxes.Children, fig_hold.Children(1));
h = findall(groot,'Type','figure');
for ff = 1 : length(h)
if ~(strcmp(h(ff).Tag, 'Osprey') || strcmp(h(ff).Tag, 'TMWWaitbar') || strcmp(h(ff).Tag, 'fig_hold') || strcmp(h(ff).Tag, 'MainFigure'))
close(h(ff))
end
end
end

end
set(fig_hold.Children, 'Parent', Plot );
case 'OspreyMeanOverview' %MeanOverview
Expand All @@ -604,7 +625,7 @@
'Distribution: ' groupString '\n'];

InfoText = uicontrol('Parent',Info,'style','text',...
'FontSize', 12, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'FontSize', 12, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
Plot = uix.HBox('Parent', input_figure, 'Padding', 5,'BackgroundColor',colormapfig.Background);
set(input_figure, 'Heights', [-0.1 -0.9]);
Expand Down Expand Up @@ -640,7 +661,7 @@
'Distribution: ' groupString '\n'];

InfoText = uicontrol('Parent',Info,'style','text',...
'FontSize', 12, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'FontSize', 12, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
Plot = uix.HBox('Parent', input_figure, 'Padding', 5,'BackgroundColor',colormapfig.Background);
set(input_figure, 'Heights', [-0.1 -0.9]);
Expand All @@ -665,7 +686,7 @@
'Distribution: ' groupString '\n'];

InfoText = uicontrol('Parent',Info,'style','text',...
'FontSize', 12, 'FontName', gui.font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'FontSize', 12, 'FontName', font,'HorizontalAlignment', 'left', 'String', sprintf(StatText),...
'BackgroundColor',colormapfig.Background,'ForegroundColor', colormapfig.Foreground);
Plot = uix.HBox('Parent', input_figure, 'Padding', 5,'BackgroundColor',colormapfig.Background);
set(input_figure, 'Heights', [-0.1 -0.9]);
Expand Down Expand Up @@ -715,5 +736,10 @@

% print(out,fullfile(outputFolder,outputFile),'-dpdf') % then print it
saveas(out,fullfile(outputFolder,outputFile),'pdf');
close(out);
h = findall(groot,'Type','figure');
for ff = 1 : length(h)
if ~(strcmp(h(ff).Tag, 'Osprey') || strcmp(h(ff).Tag, 'TMWWaitbar') || strcmp(h(ff).Tag, 'MainFigure'))
close(h(ff))
end
end
end
4 changes: 3 additions & 1 deletion seg/OspreySeg.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -102,13 +102,15 @@
gunzip(niftiFile);
niftiFile = strrep(niftiFile,'.gz','');
T1ext = '.nii';
else
T1ext = T1extini;
end
if exist(fullfile(T1dir, ['c1' T1name '.nii.gz']),'file')
gunzip(fullfile(T1dir, ['c1' T1name T1ext '.gz']));
gunzip(fullfile(T1dir, ['c2' T1name T1ext '.gz']));
gunzip(fullfile(T1dir, ['c3' T1name T1ext '.gz']));
end
T1ext = strrep(T1extini,'.gz','');
T1ext = '.nii';
end


Expand Down

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