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Merge pull request #719 from HJZollner/develop
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[FEATURE] - Manual manipulation of spectra inside GUI
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@HJZollner
HJZollner authored Apr 15, 2024
2 parents 8527cb4 + 39c6788 commit 95cbe5d
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Showing 15 changed files with 742 additions and 34 deletions.
22 changes: 21 additions & 1 deletion GUI/OspreyGUI.m
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,8 @@
gui.controls.Tab = 1;
gui.controls.Number = 1;
gui.controls.KeyPress = 0;
%Manual manipulation like phasing performed
gui.process.ManualManipulation = 0;
%File selections for each sub function
gui.load.Selected = 1;
gui.process.Selected = 1;
Expand Down Expand Up @@ -440,7 +442,25 @@
gui.layout.ListBox = uicontrol('Style', 'list','BackgroundColor', 'w','FontName', gui.font,'BackgroundColor',gui.colormap.Background, ...
'Parent', gui.layout.controlPanel, 'String',gui.layout.RedFileList(:) , ...
'Value', gui.controls.Selected, 'Interruptible', 'on', 'BusyAction', 'cancel', ...
'ForegroundColor',gui.colormap.Foreground, 'TooltipString', 'Select a file you want to inspect.','Tag','SubjectListBox');
'ForegroundColor',gui.colormap.Foreground, 'TooltipString', sprintf(['Select a file you want to inspect.\n\r\n' ...
'Other intersting key presses after clicking are:\n' ...
'left arrow - remove data\n' ...
'right arrow - add data\n\r\n' ...
'In the Processed Tab you can manipulate the averaged spectrum as follows:\n' ...
'a - Subtract 5 degree from ph0\n' ...
'd - Add 5 degree to ph0\n' ...
'q - Subtract 0.00001 s from ph1\n' ...
'e - Add 0.00001 s to ph1\n' ...
's - Subtract 1 Hz from f\n' ...
'w - Add 1 Hz to f\n' ...
'f - Add 180 degree to ph0\n\r\n' ...
'You can change the axis of the processed plot as follows:\n' ...
'r - Reset y-axis limits\n' ...
'z - Zoom out y-axis\n' ...
'x - Zoom in y-axis\n' ...
'c - Move y-axis center down\n' ...
'v - Move y-axis center up' ...
]),'Tag','SubjectListBox');
if MRSCont.flags.isMRSI
gui.layout.MRSILocPanel = uix.Panel('Parent', gui.layout.leftMenu, 'Title', 'Voxel Location','BackgroundColor',gui.colormap.Background);
set(gui.layout.MRSILocPanel,'Units','Normalized','Position',[0.5 0 0.66 0.1], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold',...
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200 changes: 200 additions & 0 deletions GUI/osp_WindowKeyDown.m
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ function osp_WindowKeyDown(~,EventData,gui)
% 31 downarrow
% Get MRSCont from hidden class container
MRSCont = getappdata(gui.figure,'MRSCont');
gui.controls.PhasePress = 0;
MRSCont.flags.exclude = 1;
if strcmp(EventData.Key, 'uparrow') % scrolling up
OldValue = get( gui.layout.ListBox,'value');
Expand Down Expand Up @@ -129,5 +130,204 @@ function osp_WindowKeyDown(~,EventData,gui)
end
end
end
if strcmp(EventData.Key, 'f') % 180 degree flip
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 1;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 0;
gui.process.ManualManipulation = 1;
end
if strcmp(EventData.Key, 'd') % positive phase
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 1;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 0;
gui.process.ManualManipulation = 1;
end
if strcmp(EventData.Key, 'a') % negative phase
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 1;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 0;
gui.process.ManualManipulation = 1;
end
if strcmp(EventData.Key, 'e') % positive phase1
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 1;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 0;
gui.process.ManualManipulation = 1;
end
if strcmp(EventData.Key, 'q') % negative phase1
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 1;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 0;
gui.process.ManualManipulation = 1;
end
if strcmp(EventData.Key, 'w') % positive freq
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 1;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 0;
gui.process.ManualManipulation = 1;
end
if strcmp(EventData.Key, 's') % negative freq
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 1;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 0;
gui.process.ManualManipulation = 1;
end
if strcmp(EventData.Key, 'r') % reset axis
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 1;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 0;
end
if strcmp(EventData.Key, 'z') % zoom out
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 1;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 0;
end
if strcmp(EventData.Key, 'x') % zoom in
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 1;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 0;
end
if strcmp(EventData.Key, 'c') % move up
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 1;
gui.controls.MoveDown = 0;
end
if strcmp(EventData.Key, 'v') % move down
gui.controls.KeyPress = 1;
gui.controls.PhasePress = 1;
gui.controls.posPhase0Shift = 0;
gui.controls.negPhase0Shift = 0;
gui.controls.posPhase1Shift = 0;
gui.controls.negPhase1Shift = 0;
gui.controls.flipPhase = 0;
gui.controls.posFreqShift = 0;
gui.controls.negFreqShift = 0;
gui.controls.resetAxis = 0;
gui.controls.zoomOut = 0;
gui.controls.zoomIn = 0;
gui.controls.MoveUp = 0;
gui.controls.MoveDown = 1;
end
setappdata(gui.figure,'MRSCont',MRSCont); % Write MRSCont into hidden container in gui class
end
7 changes: 6 additions & 1 deletion GUI/osp_WindowKeyUp.m
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Original file line number Diff line number Diff line change
Expand Up @@ -25,5 +25,10 @@ function osp_WindowKeyUp(~,~,gui)
% 2020-01-16: First version of the code.
%%% 1. GET HANDLES %%%
gui.controls.KeyPress = 0;
osp_updateListBox(gui);
if gui.controls.PhasePress == 0
osp_updateListBox(gui);
else
gui.controls.PhasePress = 0;
osp_phaseProWindow(gui)
end
end
1 change: 1 addition & 0 deletions GUI/osp_iniProcessWindow.m
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Original file line number Diff line number Diff line change
Expand Up @@ -270,6 +270,7 @@ function osp_iniProcessWindow(gui)
close(h(ff))
end
end
gui.controls.YLimits = [];
gui.info.nYvoxels = MRSCont.processed.metab{1, 1}.subspecs;
setappdata(gui.figure,'MRSCont',MRSCont); % Write MRSCont into hidden container in gui class
end
24 changes: 24 additions & 0 deletions GUI/osp_onFit.m
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,30 @@ function osp_onFit( ~, ~ ,gui)
set(gui.layout.fitTab, 'SelectionChangedFcn','');
gui.layout.b_fit.Enable = 'off';
gui.layout.tabs.Selection = 3;
if gui.process.ManualManipulation
% Optional: write edited files to LCModel .RAW files
if MRSCont.opts.saveLCM && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
[MRSCont] = osp_saveLCM(MRSCont);
end

% Optional: write edited files to jMRUI .txt files
if MRSCont.opts.savejMRUI && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
[MRSCont] = osp_saveJMRUI(MRSCont);
end

% Optional: write edited files to vendor specific format files readable to
% LCModel and jMRUI
% SPAR/SDAT if Philips
% RDA if Siemens
if MRSCont.opts.saveVendor && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
[MRSCont] = osp_saveVendor(MRSCont);
end

% Optional: write edited files to NIfTI-MRS format
if MRSCont.opts.saveNII && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
[MRSCont] = osp_saveNII(MRSCont);
end
end
[gui,MRSCont] = osp_processingWindow(gui,MRSCont);
%%% 2. CALL OSPREYFIT %%%
MRSCont = OspreyFit(MRSCont);
Expand Down
28 changes: 28 additions & 0 deletions GUI/osp_onSave.m
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Original file line number Diff line number Diff line change
Expand Up @@ -43,4 +43,32 @@ function osp_onSave( ~, ~,gui)
setappdata(gui.figure,'MRSCont',MRSCont); % Write MRSCont into hidden container in gui class
set(gui.figure,'HandleVisibility','on');
toc(refProcessTime);

if gui.process.ManualManipulation
fprintf('Rewriting MRS data after manual manipulation...\n');
% Optional: write edited files to LCModel .RAW files
if MRSCont.opts.saveLCM && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
[MRSCont] = osp_saveLCM(MRSCont);
end

% Optional: write edited files to jMRUI .txt files
if MRSCont.opts.savejMRUI && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
[MRSCont] = osp_saveJMRUI(MRSCont);
end

% Optional: write edited files to vendor specific format files readable to
% LCModel and jMRUI
% SPAR/SDAT if Philips
% RDA if Siemens
if MRSCont.opts.saveVendor && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
[MRSCont] = osp_saveVendor(MRSCont);
end

% Optional: write edited files to NIfTI-MRS format
if MRSCont.opts.saveNII && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
[MRSCont] = osp_saveNII(MRSCont);
end
fprintf('... done.\n');
end

end % onExit
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