[FEATURE] - Manual manipulation of spectra inside GUI

Added a new feature to the GUI to manually manipulate spectra in the GUI. For this, you have to finish OspreyProcess. Afterwards, you have to click on the dataset you want to manipulate inside the listbox. Manipulation is done with the keyboard.

'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'

- Spectra are automatically saved if Fit button is pressed.
- Press Save MRSCont button if you want to leave without fitting.
- Final manipulations are stored inside the manual field of each FID-A MRS struct

GUI/OspreyGUI.m

@@ -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;
@@ -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',...

GUI/osp_WindowKeyDown.m

@@ -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');
@@ -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

GUI/osp_WindowKeyUp.m

@@ -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

GUI/osp_iniProcessWindow.m

@@ -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

GUI/osp_onFit.m

@@ -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);

GUI/osp_onSave.m

@@ -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