see CHANGELOG

ThoHiller · May 22, 2020 · 4e156b4 · 4e156b4
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diff --git a/BLOCHUS/BLOCHUS.m b/BLOCHUS/BLOCHUS.m
@@ -33,8 +33,8 @@
 %------------- BEGIN CODE --------------
 
 %% GUI 'header' info and default GUI settings
-myui.version = '0.1.2';
-myui.date = '17.05.2020';
+myui.version = '0.1.3';
+myui.date = '22.05.2020';
 myui.author = 'Thomas Hiller';
 myui.email = 'thomas.hiller[at]leibniz-liag.de';
 

diff --git a/BLOCHUS/BLOCHUS_createGUI.m b/BLOCHUS/BLOCHUS_createGUI.m
@@ -143,9 +143,9 @@ function BLOCHUS_createGUI(h,wbon)
 set(gui.main,'Visible','on');
 
 %% enable all menus
-set(gui.menu.file,'Enable','on');
-set(gui.menu.view,'Enable','on');
-set(gui.menu.help,'Enable','on');
+set(gui.menu_handles.file,'Enable','on');
+set(gui.menu_handles.view,'Enable','on');
+set(gui.menu_handles.help,'Enable','on');
 
 %% update the GUI data
 gui.myui = myui;

diff --git a/BLOCHUS/BLOCHUS_createMenus.m b/BLOCHUS/BLOCHUS_createMenus.m
@@ -30,65 +30,77 @@
 %------------- BEGIN CODE --------------
 
 %% 1. File
-gui.menu.file = uimenu(gui.figh,...
-    'Label','File','Enable','off');
+gui.menu_handles.file = uimenu(gui.figh,...
+    'Label','File',...
+    'Enable','off');
 
 % 1.1 Import
-gui.menu.file_import = uimenu(gui.menu.file,...
-    'Label','Import','Enable','on');
-
-% 1.1.1 BLOCHUS session file
-gui.menu.file_import_session = uimenu(gui.menu.file_import,...
-    'Label','Session file','Callback',@onMenuImport);
+gui.menu_handles.file_import = uimenu(gui.menu_handles.file,...
+    'Label','Import Data',...
+    'Callback',@onMenuImport);
 
 % 1.2 Export
-gui.menu.file_export = uimenu(gui.menu.file,...
-    'Label','Export');
-
-% 1.2.1 BLOCHUS session file
-gui.menu.file_export_session = uimenu(gui.menu.file_export,...
-    'Label','Session file','Callback',@onMenuExport);
+gui.menu_handles.file_export = uimenu(gui.menu_handles.file,...
+    'Label','Export Data',...
+    'Callback',@onMenuExport);
 
 % 1.3 Restart
-gui.menu.file_restart = uimenu(gui.menu.file,...
-    'Label','Restart','Separator','on','Callback',@onMenuRestartQuit);
+gui.menu_handles.file_restart = uimenu(gui.menu_handles.file,...
+    'Label','Restart',...
+    'Separator','on',...
+    'Callback',@onMenuRestartQuit);
 
 % 1.4 Quit
-gui.menu.file_quit = uimenu(gui.menu.file,...
-    'Label','Quit','Separator','on','Callback',@onMenuRestartQuit);
+gui.menu_handles.file_quit = uimenu(gui.menu_handles.file,...
+    'Label','Quit',...
+    'Callback',@onMenuRestartQuit);
 
 %% 2. Extras
-gui.menu.view = uimenu(gui.figh,...
-    'Label','View','Enable','off');
+gui.menu_handles.view = uimenu(gui.figh,...
+    'Label','View',...
+    'Enable','off');
+
 % 2.1 Tooltips (on/off)
-gui.menu.view_tooltips = uimenu(gui.menu.view,...
-    'Label','Tooltips','Checked','on','Callback',@onMenuViewShow);
+gui.menu_handles.view_tooltips = uimenu(gui.menu_handles.view,...
+    'Label','Tooltips',...
+    'Checked','on',...
+    'Callback',@onMenuView);
+
 % 2.2 Figure Toolbar
-gui.menu.view_toolbar = uimenu(gui.menu.view,...
-    'Label','Figure Toolbar','Callback',@onMenuViewShow);
-% 2.3.1 Tigures
-gui.menu.view_figures = uimenu(gui.menu.view,...
+gui.menu_handles.view_toolbar = uimenu(gui.menu_handles.view,...
+    'Label','Figure Toolbar',...
+    'Callback',@onMenuView);
+% 2.3.1 Figures
+gui.menu_handles.view_figures = uimenu(gui.menu_handles.view,...
     'Label','Figures','Separator','on');
 % 2.3.1.1 current
-gui.menu.view_figures_current = uimenu(gui.menu.view_figures,...
-    'Label','Current View','Callback',@onMenuViewFigure);
+gui.menu_handles.view_figures_current = uimenu(gui.menu_handles.view_figures,...
+    'Label','Current View',...
+    'Callback',@onMenuViewFigure);
 % 2.3.1.2 only magnetization
-gui.menu.view_figures_mag = uimenu(gui.menu.view_figures,...
-    'Label','Magnetization','Callback',@onMenuViewFigure);
+gui.menu_handles.view_figures_mag = uimenu(gui.menu_handles.view_figures,...
+    'Label','Magnetization',...
+    'Callback',@onMenuViewFigure);
 % 2.3.1.3 only ramp
-gui.menu.view_figures_ramp = uimenu(gui.menu.view_figures,...
-    'Label','Switch-off Ramp','Enable','off','Callback',@onMenuViewFigure);
+gui.menu_handles.view_figures_ramp = uimenu(gui.menu_handles.view_figures,...
+    'Label','Switch-off Ramp',...
+    'Enable','off',...
+    'Callback',@onMenuViewFigure);
 % 2.3.1.4 only pulse
-gui.menu.view_figures_pulse = uimenu(gui.menu.view_figures,...
-    'Label','Pulse','Enable','off','Callback',@onMenuViewFigure);
+gui.menu_handles.view_figures_pulse = uimenu(gui.menu_handles.view_figures,...
+    'Label','Pulse',...
+    'Enable','off',...
+    'Callback',@onMenuViewFigure);
 
 %% 3. Help
-gui.menu.help = uimenu(gui.figh,...
-    'Label','Help','Enable','off');
+gui.menu_handles.help = uimenu(gui.figh,...
+    'Label','Help',...
+    'Enable','off');
 
 % 3.1 About
-gui.menu.help_about = uimenu(gui.menu.help,...
-    'Label','About','Callback',@onMenuHelp);
+gui.menu_handles.help_about = uimenu(gui.menu_handles.help,...
+    'Label','About',...
+    'Callback',@onMenuHelp);
 
 return
 

diff --git a/BLOCHUS/BLOCHUS_createPanelPulse.m b/BLOCHUS/BLOCHUS_createPanelPulse.m
@@ -414,6 +414,8 @@
 jh.setVerticalAlignment(javax.swing.JLabel.CENTER)
 jh = findjobj(gui.text_handles.PulseAxis);
 jh.setVerticalAlignment(javax.swing.JLabel.CENTER)
+jh = findjobj(gui.text_handles.PulsePolarization);
+jh.setVerticalAlignment(javax.swing.JLabel.CENTER)
 jh = findjobj(gui.text_handles.PulseB1Factor);
 jh.setVerticalAlignment(javax.swing.JLabel.CENTER)
 jh = findjobj(gui.text_handles.PulseTtau);

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## [0.1.3] - 2020-05-22
+
+### Added
+- Two additional examples that demonstrate the creation of lookup tables (one example for pre-polarization switch-off ramps and one example for adiabatic excitation pulses).
+
+### Changed
+- Minor GUI improvements and consistency clean ups.
+
 ## [0.1.2] - 2020-05-17
 
 ### Changed
@@ -24,6 +32,7 @@
 
 Initial Version
 
+[0.1.3]: https://github.com/ThoHiller/nmr-blochus/compare/v0.1.2...v0.1.3
 [0.1.2]: https://github.com/ThoHiller/nmr-blochus/compare/v.0.1.1...v0.1.2
 [0.1.1]: https://github.com/ThoHiller/nmr-blochus/compare/v.0.1.0...v.0.1.1
 [0.1.0]: https://github.com/ThoHiller/nmr-blochus/releases/tag/v.0.1.0
diff --git a/README.md b/README.md
@@ -85,14 +85,14 @@ In no particular order and without guarantee that it will ever happen :-) :
 ### Cite as
 If you use BLOCHUS for your research, please cite it as:
 
-Thomas Hiller. (2020, May 17). ThoHiller/nmr-blochus: v0.1.2 (Version v0.1.2). Zenodo. [https://doi.org/10.5281/zenodo.3829464]
+Thomas Hiller. (2020, May 22). ThoHiller/nmr-blochus: v0.1.3 (Version v0.1.3). Zenodo. [https://doi.org/10.5281/zenodo.3829464]
 
 Note: Even though the version number might change due to updates, this DOI is permanent (represents all versions) and always links to the latest version.
 
 
 ### References
 
-1. Hiller, T., Dlugosch, R. and Müller-Petke, M., "Utilizing pre-polarization to enhance SNMR signals - effect of imperfect switch-off", Geophysical Journal International **0**(0), p.1-15, 2020, [DOI](https://doi.org/10.1093/gji/ggaa216)
+1. Hiller, T., Dlugosch, R. and Müller-Petke, M., "Utilizing pre-polarization to enhance SNMR signals - effect of imperfect switch-off", Geophysical Journal International **222**(2), p.815-826, 2020, [DOI](https://doi.org/10.1093/gji/ggaa216)
 
 - - -
 <p style="text-align: center;"> MATLAB is a registered trademark of The Mathworks, Inc. </p>
diff --git a/callbacks/checkbox/onCheckPrePolPulse.m b/callbacks/checkbox/onCheckPrePolPulse.m
@@ -47,8 +47,8 @@ function onCheckPrePolPulse(src,~)
         data.basic.type = 'std';
 
         % menu settings
-        set(gui.menu.view_figures_ramp,'Enable','off');
-        set(gui.menu.view_figures_pulse,'Enable','off');
+        set(gui.menu_handles.view_figures_ramp,'Enable','off');
+        set(gui.menu_handles.view_figures_pulse,'Enable','off');
 
         % std settings
         data.basic.Minit = [1 0 0];
@@ -111,8 +111,8 @@ function onCheckPrePolPulse(src,~)
         data.basic.type = 'prepol';
 
         % menu settings
-        set(gui.menu.view_figures_ramp,'Enable','on');
-        set(gui.menu.view_figures_pulse,'Enable','off');
+        set(gui.menu_handles.view_figures_ramp,'Enable','on');
+        set(gui.menu_handles.view_figures_pulse,'Enable','off');
 
         % std settings
         data.basic.Tsim = data.prepol.Tramp;
@@ -173,8 +173,8 @@ function onCheckPrePolPulse(src,~)
         data.basic.type = 'pulse';
 
         % menu settings
-        set(gui.menu.view_figures_ramp,'Enable','off');
-        set(gui.menu.view_figures_pulse,'Enable','on');
+        set(gui.menu_handles.view_figures_ramp,'Enable','off');
+        set(gui.menu_handles.view_figures_pulse,'Enable','on');
 
         % std settings
         data.basic.Tsim = data.pulse.Ttau;
@@ -223,8 +223,8 @@ function onCheckPrePolPulse(src,~)
         data.basic.type = 'prepolpulse';
 
         % menu settings
-        set(gui.menu.view_figures_ramp,'Enable','on');
-        set(gui.menu.view_figures_pulse,'Enable','on');
+        set(gui.menu_handles.view_figures_ramp,'Enable','on');
+        set(gui.menu_handles.view_figures_pulse,'Enable','on');
 
         % std settings
         data.basic.Minit = [1 0 0];

diff --git a/callbacks/menus/onMenuHelp.m b/callbacks/menus/onMenuHelp.m
@@ -74,7 +74,7 @@ function onMenuHelp(src,~)
     % create Figure
     hf = figure('Name','About BLOCHUS',...
         'NumberTitle','off','Tag','Help','ToolBar','none','MenuBar','none',...
-        'Resize','off','Position',[xp yp ww hh]);
+        'Resize','off','Position',[xp yp ww hh],'Visible','off');
     v1 = uix.VBox('Parent',hf,'Padding',10,'Spacing',10);
 
     % text area
@@ -116,6 +116,9 @@ function onMenuHelp(src,~)
     % text hack
     jh = findjobj(t1);
     jh.setVerticalAlignment(javax.swing.JLabel.CENTER)
+
+	% make the figure content visible
+	set(hf,'Visible','on');
 
 else
     warndlg({'onMenuHelp:','There is no figure with the BLOCHUS Tag open.'},...

diff --git a/callbacks/menus/onMenuViewShow.m → callbacks/menus/onMenuView.m b/callbacks/menus/onMenuViewShow.m → callbacks/menus/onMenuView.m
@@ -1,8 +1,8 @@
-function onMenuViewShow(src,~)
-%onMenuViewShow handles the extra menu entries
+function onMenuView(src,~)
+%onMenuView handles the extra menu entries
 %
 % Syntax:
-%       onMenuViewShow(src)
+%       onMenuView(src)
 %
 % Inputs:
 %       src - handle of the calling object
@@ -11,7 +11,7 @@ function onMenuViewShow(src,~)
 %       none
 %
 % Example:
-%       onMenuViewShow(src,~)
+%       onMenuView(src,~)
 %
 % Other m-files required:
 %       switchToolTips
@@ -39,26 +39,25 @@ function onMenuViewShow(src,~)
     data = getappdata(fig,'data');
 
     switch get(src,'Label')
-        case 'Tooltips' % switch on/off Tooltips
-            onoff = get(gui.menu.view_tooltips,'Checked');
-            switchToolTips(gui,onoff);
-            switch onoff
-                case 'on'
-                    set(gui.menu.view_tooltips,'Checked','off');
+        case 'Tooltips' % switch on/off Tooltips      
+            switch get(src,'Checked')
+                case 'on' % if it is on, switch it off
+                    switchToolTips(gui,'off');
+                    set(src,'Checked','off');
                     data.info.ToolTips = 0;
                 case 'off'
-                    set(gui.menu.view_tooltips,'Checked','on');
+                    switchToolTips(gui,'on');
+                    set(src,'Checked','on');
                     data.info.ToolTips = 1;
             end
 
         case 'Figure Toolbar' % switch on/off the default Figure Toolbar
-            onoff = get(gui.menu.view_toolbar,'Checked');
-            switch onoff
-                case 'on'
-                    set(gui.menu.view_toolbar,'Checked','off');
+            switch get(src,'Checked')
+                case 'on' % if it is on, switch it off
+                    set(src,'Checked','off');
                     viewmenufcn('FigureToolbar');
                 case 'off'
-                    set(gui.menu.view_toolbar,'Checked','on');
+                    set(src,'Checked','on');
                     viewmenufcn('FigureToolbar');
             end
     end
@@ -70,7 +69,7 @@ function onMenuViewShow(src,~)
     updateStatusInformation(fig);
 
 else
-    warndlg({'onMenuViewShow:','There is no figure with the BLOCHUS Tag open.'},...
+    warndlg({'onMenuView:','There is no figure with the BLOCHUS Tag open.'},...
         'BLOCHUS error');
 end
 

diff --git a/callbacks/push/onPushRun.m b/callbacks/push/onPushRun.m
@@ -196,9 +196,9 @@ function onPushRun(src,~)
             pulseparam.PulseType = data.pulse.Type;
             % gyromagnetic ratio [rad/s/T]
             pulseparam.gamma = odeparam.gamma;
-            % Larmor frequency [rad]
+            % Larmor frequency [rad/s]
             pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
-            % pulse amplitude [B0]
+            % pulse amplitude [T]
             pulseparam.Amp = odeparam.B0*data.pulse.B1Factor;
             % pulse frequency modulation [struct]
             pulseparam.fmod = data.results.pulse.fmod;
@@ -263,7 +263,7 @@ function onPushRun(src,~)
                 % set theta for all time steps after the pulse simply to
                 % omega0*t
                 theta(indT) = getOmega0(odeparam.gamma,odeparam.B0).*TT(indT);
-                % rotate M into rotating frame of reference
+                % get M(T) in rotating frame of reference 
                 Mrot = getMrot(MM,theta,dphi);
                 % get FFT of M in the laboratory frame of reference
                 [Xm,fmx] = getFFT(TT,MM(:,1:2));
@@ -274,7 +274,7 @@ function onPushRun(src,~)
                 set(gui.text_handles.Status,'String','Calculation of excitation pulse & relaxation ... finished.');
                 pause(0.01);
             else
-                % rotate M into rotating frame of reference
+                % get M(T) in rotating frame of reference 
                 Mrot = getMrot(MM,theta);
                 % get FFT of M in the laboratory frame of reference
                 [Xm,fmx] = getFFT(TT,MM(:,1:2));
@@ -518,9 +518,8 @@ function onPushRun(src,~)
                 % set theta for all time steps after the pulse simply to
                 % omega0*t
                 theta(indT) = getOmega0(odeparam.gamma,odeparam.B0).*TT(indT);
-                % rotate M into rotating frame of reference
-                % and account for the phase from the wait time before the
-                % pulse
+                % get M(T) in rotating frame of reference and account for
+                % the phase from the wait time before the pulse
                 MM3rot = getMrot(MM,theta,dphi+phiWait);
                 % get FFT of the pulse
                 [Xb,fbx] = getFFT(TT(TT<=Ttau),Bpulse(TT<=Ttau,1:2));
@@ -530,9 +529,8 @@ function onPushRun(src,~)
                     ' & relaxation ... finished.']);
                 pause(0.01);
             else
-                % rotate M into rotating frame of reference
-                % and account for the phase from the wait time before the
-                % pulse
+                % get M(T) in rotating frame of reference and account for
+                % the phase from the wait time before the pulse
                 MM3rot = getMrot(MM,theta,phiWait);
                 % get FFT of the pulse
                 [Xb,fbx] = getFFT(TT,Bpulse(:,1:2));
@@ -555,13 +553,16 @@ function onPushRun(src,~)
             % combine data from all stages
             TT = [TT1;TT2;TT3];
             MM = [MM1;MM2;MM3];
+
             % because there is no M in the rotating frame of reference
             % during the switch-off ramp, use the lab-frame data instead
 			%  --- IMPORTANT NOTE: ----------------------------------------
 			% The pre-polarization switch-off only "lives" in the laboratory
 			% frame of reference. However, for convenience reasons I plot
 			% the lab-frame pre-polarization data also in the rotating
-			% frame of reference! This is u-n-p-h-y-s-i-c-a-l and pure "eye candy"
+			% frame of reference! This is u-n-p-h-y-s-i-c-a-l and pure
+            % "eye candy"
+            %
 			% MM1 is lab-frame data!
 			%  -------------------------------------------------------------
             MMrot = [MM1;MM2rot;MM3rot];