diff --git a/BLOCHUS/BLOCHUS.m b/BLOCHUS/BLOCHUS.m index 140ba1e..9564ca4 100644 --- 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 index 7c5d72c..d263292 100644 --- 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 index a11b74c..c0f58ba 100644 --- 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 index 405b09d..db5a666 100644 --- 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 index be506bd..83a8b33 100644 --- 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 index 66673f0..d012435 100644 --- 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) - - -

MATLAB is a registered trademark of The Mathworks, Inc.

\ No newline at end of file diff --git a/callbacks/checkbox/onCheckPrePolPulse.m b/callbacks/checkbox/onCheckPrePolPulse.m index 60739c8..e5435e3 100644 --- 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 index b1c0bcc..e646df8 100644 --- 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 b/callbacks/menus/onMenuView.m similarity index 71% rename from callbacks/menus/onMenuViewShow.m rename to callbacks/menus/onMenuView.m index 9bf2c98..d7857f9 100644 --- a/callbacks/menus/onMenuViewShow.m +++ b/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 index c66f4f6..a9f2c84 100644 --- 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]; diff --git a/doc/blochus/BLOCHUS/BLOCHUS.html b/doc/blochus/BLOCHUS/BLOCHUS.html index f677553..8e28ea9 100644 --- a/doc/blochus/BLOCHUS/BLOCHUS.html +++ b/doc/blochus/BLOCHUS/BLOCHUS.html @@ -105,8 +105,8 @@

SOURCE CODE ^%------------- BEGIN CODE -------------- 0034 0035 %% GUI 'header' info and default GUI settings -0036 myui.version = '0.1.2'; -0037 myui.date = '17.05.2020'; +0036 myui.version = '0.1.3'; +0037 myui.date = '22.05.2020'; 0038 myui.author = 'Thomas Hiller'; 0039 myui.email = 'thomas.hiller[at]leibniz-liag.de'; 0040 diff --git a/doc/blochus/BLOCHUS/BLOCHUS_createGUI.html b/doc/blochus/BLOCHUS/BLOCHUS_createGUI.html index afd83ba..9d67d8a 100644 --- a/doc/blochus/BLOCHUS/BLOCHUS_createGUI.html +++ b/doc/blochus/BLOCHUS/BLOCHUS_createGUI.html @@ -212,9 +212,9 @@

SOURCE CODE ^'Visible','on'); 0144 0145 %% enable all menus -0146 set(gui.menu.file,'Enable','on'); -0147 set(gui.menu.view,'Enable','on'); -0148 set(gui.menu.help,'Enable','on'); +0146 set(gui.menu_handles.file,'Enable','on'); +0147 set(gui.menu_handles.view,'Enable','on'); +0148 set(gui.menu_handles.help,'Enable','on'); 0149 0150 %% update the GUI data 0151 gui.myui = myui; diff --git a/doc/blochus/BLOCHUS/BLOCHUS_createMenus.html b/doc/blochus/BLOCHUS/BLOCHUS_createMenus.html index 8b3b816..1935e2e 100644 --- a/doc/blochus/BLOCHUS/BLOCHUS_createMenus.html +++ b/doc/blochus/BLOCHUS/BLOCHUS_createMenus.html @@ -58,7 +58,7 @@

DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

This function calls: +
  • onMenuExport handles the extra menu entries
  • onMenuHelp shows the Help Information
  • onMenuImport handles the extra menu entries
  • onMenuRestartQuit restarts or closes the GUI
  • onMenuView handles the extra menu entries
  • onMenuViewFigure shows predefined figure layouts
    • This function is called by: @@ -99,88 +99,100 @@

    SOURCE CODE ^%------------- BEGIN CODE -------------- 0031 0032 %% 1. File -0033 gui.menu.file = uimenu(gui.figh,... -0034 'Label','File','Enable','off'); -0035 -0036 % 1.1 Import -0037 gui.menu.file_import = uimenu(gui.menu.file,... -0038 'Label','Import','Enable','on'); -0039 -0040 % 1.1.1 BLOCHUS session file -0041 gui.menu.file_import_session = uimenu(gui.menu.file_import,... -0042 'Label','Session file','Callback',@onMenuImport); -0043 -0044 % 1.2 Export -0045 gui.menu.file_export = uimenu(gui.menu.file,... -0046 'Label','Export'); -0047 -0048 % 1.2.1 BLOCHUS session file -0049 gui.menu.file_export_session = uimenu(gui.menu.file_export,... -0050 'Label','Session file','Callback',@onMenuExport); -0051 -0052 % 1.3 Restart -0053 gui.menu.file_restart = uimenu(gui.menu.file,... -0054 'Label','Restart','Separator','on','Callback',@onMenuRestartQuit); -0055 -0056 % 1.4 Quit -0057 gui.menu.file_quit = uimenu(gui.menu.file,... -0058 'Label','Quit','Separator','on','Callback',@onMenuRestartQuit); -0059 -0060 %% 2. Extras -0061 gui.menu.view = uimenu(gui.figh,... -0062 'Label','View','Enable','off'); +0033 gui.menu_handles.file = uimenu(gui.figh,... +0034 'Label','File',... +0035 'Enable','off'); +0036 +0037 % 1.1 Import +0038 gui.menu_handles.file_import = uimenu(gui.menu_handles.file,... +0039 'Label','Import Data',... +0040 'Callback',@onMenuImport); +0041 +0042 % 1.2 Export +0043 gui.menu_handles.file_export = uimenu(gui.menu_handles.file,... +0044 'Label','Export Data',... +0045 'Callback',@onMenuExport); +0046 +0047 % 1.3 Restart +0048 gui.menu_handles.file_restart = uimenu(gui.menu_handles.file,... +0049 'Label','Restart',... +0050 'Separator','on',... +0051 'Callback',@onMenuRestartQuit); +0052 +0053 % 1.4 Quit +0054 gui.menu_handles.file_quit = uimenu(gui.menu_handles.file,... +0055 'Label','Quit',... +0056 'Callback',@onMenuRestartQuit); +0057 +0058 %% 2. Extras +0059 gui.menu_handles.view = uimenu(gui.figh,... +0060 'Label','View',... +0061 'Enable','off'); +0062 0063 % 2.1 Tooltips (on/off) -0064 gui.menu.view_tooltips = uimenu(gui.menu.view,... -0065 'Label','Tooltips','Checked','on','Callback',@onMenuViewShow); -0066 % 2.2 Figure Toolbar -0067 gui.menu.view_toolbar = uimenu(gui.menu.view,... -0068 'Label','Figure Toolbar','Callback',@onMenuViewShow); -0069 % 2.3.1 Tigures -0070 gui.menu.view_figures = uimenu(gui.menu.view,... -0071 'Label','Figures','Separator','on'); -0072 % 2.3.1.1 current -0073 gui.menu.view_figures_current = uimenu(gui.menu.view_figures,... -0074 'Label','Current View','Callback',@onMenuViewFigure); -0075 % 2.3.1.2 only magnetization -0076 gui.menu.view_figures_mag = uimenu(gui.menu.view_figures,... -0077 'Label','Magnetization','Callback',@onMenuViewFigure); -0078 % 2.3.1.3 only ramp -0079 gui.menu.view_figures_ramp = uimenu(gui.menu.view_figures,... -0080 'Label','Switch-off Ramp','Enable','off','Callback',@onMenuViewFigure); -0081 % 2.3.1.4 only pulse -0082 gui.menu.view_figures_pulse = uimenu(gui.menu.view_figures,... -0083 'Label','Pulse','Enable','off','Callback',@onMenuViewFigure); -0084 -0085 %% 3. Help -0086 gui.menu.help = uimenu(gui.figh,... -0087 'Label','Help','Enable','off'); -0088 -0089 % 3.1 About -0090 gui.menu.help_about = uimenu(gui.menu.help,... -0091 'Label','About','Callback',@onMenuHelp); -0092 -0093 return +0064 gui.menu_handles.view_tooltips = uimenu(gui.menu_handles.view,... +0065 'Label','Tooltips',... +0066 'Checked','on',... +0067 'Callback',@onMenuView); +0068 +0069 % 2.2 Figure Toolbar +0070 gui.menu_handles.view_toolbar = uimenu(gui.menu_handles.view,... +0071 'Label','Figure Toolbar',... +0072 'Callback',@onMenuView); +0073 % 2.3.1 Figures +0074 gui.menu_handles.view_figures = uimenu(gui.menu_handles.view,... +0075 'Label','Figures','Separator','on'); +0076 % 2.3.1.1 current +0077 gui.menu_handles.view_figures_current = uimenu(gui.menu_handles.view_figures,... +0078 'Label','Current View',... +0079 'Callback',@onMenuViewFigure); +0080 % 2.3.1.2 only magnetization +0081 gui.menu_handles.view_figures_mag = uimenu(gui.menu_handles.view_figures,... +0082 'Label','Magnetization',... +0083 'Callback',@onMenuViewFigure); +0084 % 2.3.1.3 only ramp +0085 gui.menu_handles.view_figures_ramp = uimenu(gui.menu_handles.view_figures,... +0086 'Label','Switch-off Ramp',... +0087 'Enable','off',... +0088 'Callback',@onMenuViewFigure); +0089 % 2.3.1.4 only pulse +0090 gui.menu_handles.view_figures_pulse = uimenu(gui.menu_handles.view_figures,... +0091 'Label','Pulse',... +0092 'Enable','off',... +0093 'Callback',@onMenuViewFigure); 0094 -0095 %------------- END OF CODE -------------- -0096 -0097 %% License: -0098 % GNU GPLv3 -0099 % -0100 % BLOCHUS -0101 % Copyright (C) 2019 Thomas Hiller -0102 % -0103 % This program is free software: you can redistribute it and/or modify -0104 % it under the terms of the GNU General Public License as published by -0105 % the Free Software Foundation, either version 3 of the License, or -0106 % (at your option) any later version. -0107 % -0108 % This program is distributed in the hope that it will be useful, -0109 % but WITHOUT ANY WARRANTY; without even the implied warranty of -0110 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -0111 % GNU General Public License for more details. -0112 % -0113 % You should have received a copy of the GNU General Public License -0114 % along with this program. If not, see <https://www.gnu.org/licenses/>. +0095 %% 3. Help +0096 gui.menu_handles.help = uimenu(gui.figh,... +0097 'Label','Help',... +0098 'Enable','off'); +0099 +0100 % 3.1 About +0101 gui.menu_handles.help_about = uimenu(gui.menu_handles.help,... +0102 'Label','About',... +0103 'Callback',@onMenuHelp); +0104 +0105 return +0106 +0107 %------------- END OF CODE -------------- +0108 +0109 %% License: +0110 % GNU GPLv3 +0111 % +0112 % BLOCHUS +0113 % Copyright (C) 2019 Thomas Hiller +0114 % +0115 % This program is free software: you can redistribute it and/or modify +0116 % it under the terms of the GNU General Public License as published by +0117 % the Free Software Foundation, either version 3 of the License, or +0118 % (at your option) any later version. +0119 % +0120 % This program is distributed in the hope that it will be useful, +0121 % but WITHOUT ANY WARRANTY; without even the implied warranty of +0122 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +0123 % GNU General Public License for more details. +0124 % +0125 % You should have received a copy of the GNU General Public License +0126 % along with this program. If not, see <https://www.gnu.org/licenses/>.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/blochus/BLOCHUS/BLOCHUS_createPanelPulse.html b/doc/blochus/BLOCHUS/BLOCHUS_createPanelPulse.html index 46e3eab..075ea6b 100644 --- a/doc/blochus/BLOCHUS/BLOCHUS_createPanelPulse.html +++ b/doc/blochus/BLOCHUS/BLOCHUS_createPanelPulse.html @@ -486,45 +486,47 @@

    SOURCE CODE ^return +0433 jh = findjobj(gui.text_handles.PulseTwait); +0434 jh.setVerticalAlignment(javax.swing.JLabel.CENTER) 0435 -0436 %------------- END OF CODE -------------- +0436 return 0437 -0438 %% License: -0439 % GNU GPLv3 -0440 % -0441 % BLOCHUS -0442 % Copyright (C) 2019 Thomas Hiller -0443 % -0444 % This program is free software: you can redistribute it and/or modify -0445 % it under the terms of the GNU General Public License as published by -0446 % the Free Software Foundation, either version 3 of the License, or -0447 % (at your option) any later version. -0448 % -0449 % This program is distributed in the hope that it will be useful, -0450 % but WITHOUT ANY WARRANTY; without even the implied warranty of -0451 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -0452 % GNU General Public License for more details. -0453 % -0454 % You should have received a copy of the GNU General Public License -0455 % along with this program. If not, see <https://www.gnu.org/licenses/>. +0438 %------------- END OF CODE -------------- +0439 +0440 %% License: +0441 % GNU GPLv3 +0442 % +0443 % BLOCHUS +0444 % Copyright (C) 2019 Thomas Hiller +0445 % +0446 % This program is free software: you can redistribute it and/or modify +0447 % it under the terms of the GNU General Public License as published by +0448 % the Free Software Foundation, either version 3 of the License, or +0449 % (at your option) any later version. +0450 % +0451 % This program is distributed in the hope that it will be useful, +0452 % but WITHOUT ANY WARRANTY; without even the implied warranty of +0453 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +0454 % GNU General Public License for more details. +0455 % +0456 % You should have received a copy of the GNU General Public License +0457 % along with this program. If not, see <https://www.gnu.org/licenses/>.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/blochus/callbacks/checkbox/onCheckPrePolPulse.html b/doc/blochus/callbacks/checkbox/onCheckPrePolPulse.html index 1f0d3b1..4bc963d 100644 --- a/doc/blochus/callbacks/checkbox/onCheckPrePolPulse.html +++ b/doc/blochus/callbacks/checkbox/onCheckPrePolPulse.html @@ -118,8 +118,8 @@

    SOURCE CODE ^'std'; 0048 0049 % menu settings -0050 set(gui.menu.view_figures_ramp,'Enable','off'); -0051 set(gui.menu.view_figures_pulse,'Enable','off'); +0050 set(gui.menu_handles.view_figures_ramp,'Enable','off'); +0051 set(gui.menu_handles.view_figures_pulse,'Enable','off'); 0052 0053 % std settings 0054 data.basic.Minit = [1 0 0]; @@ -182,8 +182,8 @@

    SOURCE CODE ^'prepol'; 0112 0113 % menu settings -0114 set(gui.menu.view_figures_ramp,'Enable','on'); -0115 set(gui.menu.view_figures_pulse,'Enable','off'); +0114 set(gui.menu_handles.view_figures_ramp,'Enable','on'); +0115 set(gui.menu_handles.view_figures_pulse,'Enable','off'); 0116 0117 % std settings 0118 data.basic.Tsim = data.prepol.Tramp; @@ -244,8 +244,8 @@

    SOURCE CODE ^'pulse'; 0174 0175 % menu settings -0176 set(gui.menu.view_figures_ramp,'Enable','off'); -0177 set(gui.menu.view_figures_pulse,'Enable','on'); +0176 set(gui.menu_handles.view_figures_ramp,'Enable','off'); +0177 set(gui.menu_handles.view_figures_pulse,'Enable','on'); 0178 0179 % std settings 0180 data.basic.Tsim = data.pulse.Ttau; @@ -294,8 +294,8 @@

    SOURCE CODE ^'prepolpulse'; 0224 0225 % menu settings -0226 set(gui.menu.view_figures_ramp,'Enable','on'); -0227 set(gui.menu.view_figures_pulse,'Enable','on'); +0226 set(gui.menu_handles.view_figures_ramp,'Enable','on'); +0227 set(gui.menu_handles.view_figures_pulse,'Enable','on'); 0228 0229 % std settings 0230 data.basic.Minit = [1 0 0]; diff --git a/doc/blochus/callbacks/menus/menu.html b/doc/blochus/callbacks/menus/menu.html index bea8b9b..8986e51 100644 --- a/doc/blochus/callbacks/menus/menu.html +++ b/doc/blochus/callbacks/menus/menu.html @@ -18,7 +18,7 @@

    Index for blochus\callbacks\menus

    Matlab files in this directory:

     +
  • onMenuExport
  • onMenuHelp
  • onMenuImport
  • onMenuRestartQuit
  • onMenuView
  • onMenuViewFigure
  • onMenuViewShow
    • diff --git a/doc/blochus/callbacks/menus/onMenuHelp.html b/doc/blochus/callbacks/menus/onMenuHelp.html index 01f31e6..728d19b 100644 --- a/doc/blochus/callbacks/menus/onMenuHelp.html +++ b/doc/blochus/callbacks/menus/onMenuHelp.html @@ -143,7 +143,7 @@

    SOURCE CODE ^% create Figure 0075 hf = figure('Name','About BLOCHUS',... 0076 'NumberTitle','off','Tag','Help','ToolBar','none','MenuBar','none',... -0077 'Resize','off','Position',[xp yp ww hh]); +0077 'Resize','off','Position',[xp yp ww hh],'Visible','off'); 0078 v1 = uix.VBox('Parent',hf,'Padding',10,'Spacing',10); 0079 0080 % text area @@ -186,33 +186,36 @@

    SOURCE CODE ^else -0121 warndlg({'onMenuHelp:','There is no figure with the BLOCHUS Tag open.'},... -0122 'BLOCHUS error'); -0123 end -0124 -0125 end -0126 -0127 %------------- END OF CODE -------------- -0128 -0129 %% License: -0130 % GNU GPLv3 -0131 % -0132 % BLOCHUS -0133 % Copyright (C) 2019 Thomas Hiller +0120 % make the figure content visible +0121 set(hf,'Visible','on'); +0122 +0123 else +0124 warndlg({'onMenuHelp:','There is no figure with the BLOCHUS Tag open.'},... +0125 'BLOCHUS error'); +0126 end +0127 +0128 end +0129 +0130 %------------- END OF CODE -------------- +0131 +0132 %% License: +0133 % GNU GPLv3 0134 % -0135 % This program is free software: you can redistribute it and/or modify -0136 % it under the terms of the GNU General Public License as published by -0137 % the Free Software Foundation, either version 3 of the License, or -0138 % (at your option) any later version. -0139 % -0140 % This program is distributed in the hope that it will be useful, -0141 % but WITHOUT ANY WARRANTY; without even the implied warranty of -0142 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -0143 % GNU General Public License for more details. -0144 % -0145 % You should have received a copy of the GNU General Public License -0146 % along with this program. If not, see <https://www.gnu.org/licenses/>. +0135 % BLOCHUS +0136 % Copyright (C) 2019 Thomas Hiller +0137 % +0138 % This program is free software: you can redistribute it and/or modify +0139 % it under the terms of the GNU General Public License as published by +0140 % the Free Software Foundation, either version 3 of the License, or +0141 % (at your option) any later version. +0142 % +0143 % This program is distributed in the hope that it will be useful, +0144 % but WITHOUT ANY WARRANTY; without even the implied warranty of +0145 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +0146 % GNU General Public License for more details. +0147 % +0148 % You should have received a copy of the GNU General Public License +0149 % along with this program. If not, see <https://www.gnu.org/licenses/>.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/blochus/callbacks/menus/onMenuViewShow.html b/doc/blochus/callbacks/menus/onMenuView.html similarity index 54% rename from doc/blochus/callbacks/menus/onMenuViewShow.html rename to doc/blochus/callbacks/menus/onMenuView.html index c6b99c9..2972b50 100644 --- a/doc/blochus/callbacks/menus/onMenuViewShow.html +++ b/doc/blochus/callbacks/menus/onMenuView.html @@ -2,8 +2,8 @@ "http://www.w3.org/TR/REC-html40/loose.dtd"> - Description of onMenuViewShow - + Description of onMenuView + @@ -16,20 +16,20 @@ -

    onMenuViewShow +

    onMenuView

    PURPOSE ^

    handles the extra menu entries

    SYNOPSIS ^

    -
    function onMenuViewShow(src,~)
    +
    function onMenuView(src,~)

    DESCRIPTION ^

    -
    onMenuViewShow handles the extra menu entries
+
    onMenuView handles the extra menu entries
 
  Syntax:
-       onMenuViewShow(src)
+       onMenuView(src)
 
  Inputs:
        src - handle of the calling object
@@ -38,7 +38,7 @@ 
    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • switchToolTips	 switches GUI tool tips either "on" or "off"
  • updateStatusInformation	 updates all fields inside the bottom status bar
    • 
 This function is called by:
 
@@ -68,11 +68,11 @@ 
    CROSS-REFERENCE INFORMATION ^
 
 
 <h2><a name=SOURCE CODE ^
    
-
    0001 function onMenuViewShow(src,~)
-0002 %onMenuViewShow handles the extra menu entries
+
    0001 function onMenuView(src,~)
+0002 %onMenuView handles the extra menu entries
 0003 %
 0004 % Syntax:
-0005 %       onMenuViewShow(src)
+0005 %       onMenuView(src)
 0006 %
 0007 % Inputs:
 0008 %       src - handle of the calling object
@@ -81,7 +81,7 @@ 
    SOURCE CODE ^%       none
 0012 %
 0013 % Example:
-0014 %       onMenuViewShow(src,~)
+0014 %       onMenuView(src,~)
 0015 %
 0016 % Other m-files required:
 0017 %       switchToolTips
@@ -110,62 +110,61 @@ 
    SOURCE CODE ^switch get(src,'Label')
 0042         case 'Tooltips' % switch on/off Tooltips
-0043             onoff = get(gui.menu.view_tooltips,'Checked');
-0044             switchToolTips(gui,onoff);
-0045             switch onoff
-0046                 case 'on'
-0047                     set(gui.menu.view_tooltips,'Checked','off');
-0048                     data.info.ToolTips = 0;
-0049                 case 'off'
-0050                     set(gui.menu.view_tooltips,'Checked','on');
+0043             switch get(src,'Checked')
+0044                 case 'on' % if it is on, switch it off
+0045                     switchToolTips(gui,'off');
+0046                     set(src,'Checked','off');
+0047                     data.info.ToolTips = 0;
+0048                 case 'off'
+0049                     switchToolTips(gui,'on');
+0050                     set(src,'Checked','on');
 0051                     data.info.ToolTips = 1;
 0052             end
 0053             
 0054         case 'Figure Toolbar' % switch on/off the default Figure Toolbar
-0055             onoff = get(gui.menu.view_toolbar,'Checked');
-0056             switch onoff
-0057                 case 'on'
-0058                     set(gui.menu.view_toolbar,'Checked','off');
-0059                     viewmenufcn('FigureToolbar');
-0060                 case 'off'
-0061                     set(gui.menu.view_toolbar,'Checked','on');
-0062                     viewmenufcn('FigureToolbar');
-0063             end
-0064     end
-0065     
-0066     % update GUI data
-0067     setappdata(fig,'gui',gui);
-0068     setappdata(fig,'data',data);
-0069     % update status bar
-0070     updateStatusInformation(fig);
-0071     
-0072 else
-0073     warndlg({'onMenuViewShow:','There is no figure with the BLOCHUS Tag open.'},...
-0074         'BLOCHUS error');
-0075 end
-0076 
-0077 end
-0078 
-0079 %------------- END OF CODE --------------
-0080 
-0081 %% License:
-0082 % GNU GPLv3
-0083 %
-0084 % BLOCHUS
-0085 % Copyright (C) 2019 Thomas Hiller
-0086 %
-0087 % This program is free software: you can redistribute it and/or modify
-0088 % it under the terms of the GNU General Public License as published by
-0089 % the Free Software Foundation, either version 3 of the License, or
-0090 % (at your option) any later version.
-0091 %
-0092 % This program is distributed in the hope that it will be useful,
-0093 % but WITHOUT ANY WARRANTY; without even the implied warranty of
-0094 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-0095 % GNU General Public License for more details.
-0096 %
-0097 % You should have received a copy of the GNU General Public License
-0098 % along with this program.  If not, see <https://www.gnu.org/licenses/>.
    
+0055             switch get(src,'Checked')
+0056                 case 'on' % if it is on, switch it off
+0057                     set(src,'Checked','off');
+0058                     viewmenufcn('FigureToolbar');
+0059                 case 'off'
+0060                     set(src,'Checked','on');
+0061                     viewmenufcn('FigureToolbar');
+0062             end
+0063     end
+0064     
+0065     % update GUI data
+0066     setappdata(fig,'gui',gui);
+0067     setappdata(fig,'data',data);
+0068     % update status bar
+0069     updateStatusInformation(fig);
+0070     
+0071 else
+0072     warndlg({'onMenuView:','There is no figure with the BLOCHUS Tag open.'},...
+0073         'BLOCHUS error');
+0074 end
+0075 
+0076 end
+0077 
+0078 %------------- END OF CODE --------------
+0079 
+0080 %% License:
+0081 % GNU GPLv3
+0082 %
+0083 % BLOCHUS
+0084 % Copyright (C) 2019 Thomas Hiller
+0085 %
+0086 % This program is free software: you can redistribute it and/or modify
+0087 % it under the terms of the GNU General Public License as published by
+0088 % the Free Software Foundation, either version 3 of the License, or
+0089 % (at your option) any later version.
+0090 %
+0091 % This program is distributed in the hope that it will be useful,
+0092 % but WITHOUT ANY WARRANTY; without even the implied warranty of
+0093 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+0094 % GNU General Public License for more details.
+0095 %
+0096 % You should have received a copy of the GNU General Public License
+0097 % along with this program.  If not, see <https://www.gnu.org/licenses/>.
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/blochus/callbacks/push/onPushRun.html b/doc/blochus/callbacks/push/onPushRun.html
index dae2f38..9dd577c 100644
--- a/doc/blochus/callbacks/push/onPushRun.html
+++ b/doc/blochus/callbacks/push/onPushRun.html
@@ -271,9 +271,9 @@ 
    SOURCE CODE ^% gyromagnetic ratio [rad/s/T]
 0198             pulseparam.gamma = odeparam.gamma;
-0199             % Larmor frequency [rad]
+0199             % Larmor frequency [rad/s]
 0200             pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
-0201             % pulse amplitude [B0]
+0201             % pulse amplitude [T]
 0202             pulseparam.Amp = odeparam.B0*data.pulse.B1Factor;
 0203             % pulse frequency modulation [struct]
 0204             pulseparam.fmod = data.results.pulse.fmod;
@@ -338,7 +338,7 @@ 
    SOURCE CODE ^% set theta for all time steps after the pulse simply to
 0264                 % omega0*t
 0265                 theta(indT) = getOmega0(odeparam.gamma,odeparam.B0).*TT(indT);
-0266                 % rotate M into rotating frame of reference
+0266                 % get M(T) in rotating frame of reference
 0267                 Mrot = getMrot(MM,theta,dphi);
 0268                 % get FFT of M in the laboratory frame of reference
 0269                 [Xm,fmx] = getFFT(TT,MM(:,1:2));
@@ -349,7 +349,7 @@ 
    SOURCE CODE ^'String','Calculation of excitation pulse & relaxation ... finished.');
 0275                 pause(0.01);
 0276             else
-0277                 % rotate M into rotating frame of reference
+0277                 % get M(T) in rotating frame of reference
 0278                 Mrot = getMrot(MM,theta);
 0279                 % get FFT of M in the laboratory frame of reference
 0280                 [Xm,fmx] = getFFT(TT,MM(:,1:2));
@@ -593,115 +593,116 @@ 
    SOURCE CODE ^% set theta for all time steps after the pulse simply to
 0519                 % omega0*t
 0520                 theta(indT) = getOmega0(odeparam.gamma,odeparam.B0).*TT(indT);
-0521                 % rotate M into rotating frame of reference
-0522                 % and account for the phase from the wait time before the
-0523                 % pulse
-0524                 MM3rot = getMrot(MM,theta,dphi+phiWait);
-0525                 % get FFT of the pulse
-0526                 [Xb,fbx] = getFFT(TT(TT<=Ttau),Bpulse(TT<=Ttau,1:2));
-0527                 
-0528                 % update Info field
-0529                 set(gui.text_handles.Status,'String',['Calculation of excitation pulse',...
-0530                     ' & relaxation ... finished.']);
-0531                 pause(0.01);
-0532             else
-0533                 % rotate M into rotating frame of reference
-0534                 % and account for the phase from the wait time before the
-0535                 % pulse
-0536                 MM3rot = getMrot(MM,theta,phiWait);
-0537                 % get FFT of the pulse
-0538                 [Xb,fbx] = getFFT(TT,Bpulse(:,1:2));
-0539                 
-0540                 % update Info field
-0541                 set(gui.text_handles.Status,'String','Calculation of excitation pulse ... finished.');
-0542                 pause(0.01);
-0543             end
-0544             
+0521                 % get M(T) in rotating frame of reference and account for
+0522                 % the phase from the wait time before the pulse
+0523                 MM3rot = getMrot(MM,theta,dphi+phiWait);
+0524                 % get FFT of the pulse
+0525                 [Xb,fbx] = getFFT(TT(TT<=Ttau),Bpulse(TT<=Ttau,1:2));
+0526                 
+0527                 % update Info field
+0528                 set(gui.text_handles.Status,'String',['Calculation of excitation pulse',...
+0529                     ' & relaxation ... finished.']);
+0530                 pause(0.01);
+0531             else
+0532                 % get M(T) in rotating frame of reference and account for
+0533                 % the phase from the wait time before the pulse
+0534                 MM3rot = getMrot(MM,theta,phiWait);
+0535                 % get FFT of the pulse
+0536                 [Xb,fbx] = getFFT(TT,Bpulse(:,1:2));
+0537                 
+0538                 % update Info field
+0539                 set(gui.text_handles.Status,'String','Calculation of excitation pulse ... finished.');
+0540                 pause(0.01);
+0541             end
+0542             
+0543             % -------------------------------------------------------------
+0544             %% --- 4.) final data merging ---------------------------------
 0545             % -------------------------------------------------------------
-0546             %% --- 4.) final data merging ---------------------------------
-0547             % -------------------------------------------------------------
-0548             % because the simulation was done in "local" time
-0549             % coordinates, shift the time vector to the end of the
-0550             % wait time after the switch-off
-0551             TT3 = TT + Tramp + Twait;
-0552             % save data
-0553             MM3 = MM;
-0554             
-0555             % combine data from all stages
-0556             TT = [TT1;TT2;TT3];
-0557             MM = [MM1;MM2;MM3];
-0558             % because there is no M in the rotating frame of reference
-0559             % during the switch-off ramp, use the lab-frame data instead
-0560             %  --- IMPORTANT NOTE: ----------------------------------------
-0561             % The pre-polarization switch-off only "lives" in the laboratory
-0562             % frame of reference. However, for convenience reasons I plot
-0563             % the lab-frame pre-polarization data also in the rotating
-0564             % frame of reference! This is u-n-p-h-y-s-i-c-a-l and pure "eye candy"
-0565             % MM1 is lab-frame data!
-0566             %  -------------------------------------------------------------
-0567             MMrot = [MM1;MM2rot;MM3rot];
-0568             
-0569             % remove possible duplicate points
-0570             [TT,ix] = unique(TT);
-0571             MM = MM(ix,:);
-0572             MMrot = MMrot(ix,:);
-0573             
-0574             % save combined data
-0575             data.results.basic.T = TT;
-0576             data.results.basic.M = MM;
-0577             data.results.basic.Mrot = MMrot;
-0578             
-0579             % get FFT for the combined M
-0580             [Xm,fmx] = getFFT(TT,MM(:,1:2));
-0581             data.results.basic.Mspec.fx = fmx;
-0582             data.results.basic.Mspec.X = Xm;
-0583             % save pulse FFT
-0584             data.results.pulse.Bspec.fx = fbx;
-0585             data.results.pulse.Bspec.X = Xb;
-0586 
-0587     end
-0588     % time the calculation
-0589     data.info.Timer = toc(t0);
-0590     
-0591     % update GUI data
-0592     setappdata(fig,'data',data);
-0593     % plot results
-0594     plotResults(fig);
-0595     % update status bar
-0596     updateStatusInformation(fig);
-0597     % activate animation button
-0598     set(gui.push_handles.Animate,'Enable','on');
-0599     
-0600     % change the pushbutton color back to green
-0601     set(src,'BackGroundColor','g');
-0602     
-0603 else
-0604     warndlg({'onPushRun:','There is no figure with the BLOCHUS Tag open.'},...
-0605         'BLOCHUS error');
-0606 end
-0607 
-0608 end
-0609 
-0610 %------------- END OF CODE --------------
-0611 
-0612 %% License:
-0613 % GNU GPLv3
-0614 %
-0615 % BLOCHUS
-0616 % Copyright (C) 2019 Thomas Hiller
-0617 %
-0618 % This program is free software: you can redistribute it and/or modify
-0619 % it under the terms of the GNU General Public License as published by
-0620 % the Free Software Foundation, either version 3 of the License, or
-0621 % (at your option) any later version.
-0622 %
-0623 % This program is distributed in the hope that it will be useful,
-0624 % but WITHOUT ANY WARRANTY; without even the implied warranty of
-0625 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-0626 % GNU General Public License for more details.
-0627 %
-0628 % You should have received a copy of the GNU General Public License
-0629 % along with this program.  If not, see <https://www.gnu.org/licenses/>.
    
+0546             % because the simulation was done in "local" time
+0547             % coordinates, shift the time vector to the end of the
+0548             % wait time after the switch-off
+0549             TT3 = TT + Tramp + Twait;
+0550             % save data
+0551             MM3 = MM;
+0552             
+0553             % combine data from all stages
+0554             TT = [TT1;TT2;TT3];
+0555             MM = [MM1;MM2;MM3];
+0556             
+0557             % because there is no M in the rotating frame of reference
+0558             % during the switch-off ramp, use the lab-frame data instead
+0559             %  --- IMPORTANT NOTE: ----------------------------------------
+0560             % The pre-polarization switch-off only "lives" in the laboratory
+0561             % frame of reference. However, for convenience reasons I plot
+0562             % the lab-frame pre-polarization data also in the rotating
+0563             % frame of reference! This is u-n-p-h-y-s-i-c-a-l and pure
+0564             % "eye candy"
+0565             %
+0566             % MM1 is lab-frame data!
+0567             %  -------------------------------------------------------------
+0568             MMrot = [MM1;MM2rot;MM3rot];
+0569             
+0570             % remove possible duplicate points
+0571             [TT,ix] = unique(TT);
+0572             MM = MM(ix,:);
+0573             MMrot = MMrot(ix,:);
+0574             
+0575             % save combined data
+0576             data.results.basic.T = TT;
+0577             data.results.basic.M = MM;
+0578             data.results.basic.Mrot = MMrot;
+0579             
+0580             % get FFT for the combined M
+0581             [Xm,fmx] = getFFT(TT,MM(:,1:2));
+0582             data.results.basic.Mspec.fx = fmx;
+0583             data.results.basic.Mspec.X = Xm;
+0584             % save pulse FFT
+0585             data.results.pulse.Bspec.fx = fbx;
+0586             data.results.pulse.Bspec.X = Xb;
+0587 
+0588     end
+0589     % time the calculation
+0590     data.info.Timer = toc(t0);
+0591     
+0592     % update GUI data
+0593     setappdata(fig,'data',data);
+0594     % plot results
+0595     plotResults(fig);
+0596     % update status bar
+0597     updateStatusInformation(fig);
+0598     % activate animation button
+0599     set(gui.push_handles.Animate,'Enable','on');
+0600     
+0601     % change the pushbutton color back to green
+0602     set(src,'BackGroundColor','g');
+0603     
+0604 else
+0605     warndlg({'onPushRun:','There is no figure with the BLOCHUS Tag open.'},...
+0606         'BLOCHUS error');
+0607 end
+0608 
+0609 end
+0610 
+0611 %------------- END OF CODE --------------
+0612 
+0613 %% License:
+0614 % GNU GPLv3
+0615 %
+0616 % BLOCHUS
+0617 % Copyright (C) 2019 Thomas Hiller
+0618 %
+0619 % This program is free software: you can redistribute it and/or modify
+0620 % it under the terms of the GNU General Public License as published by
+0621 % the Free Software Foundation, either version 3 of the License, or
+0622 % (at your option) any later version.
+0623 %
+0624 % This program is distributed in the hope that it will be useful,
+0625 % but WITHOUT ANY WARRANTY; without even the implied warranty of
+0626 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+0627 % GNU General Public License for more details.
+0628 %
+0629 % You should have received a copy of the GNU General Public License
+0630 % along with this program.  If not, see <https://www.gnu.org/licenses/>.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/blochus/functions/interface/plotResults.html b/doc/blochus/functions/interface/plotResults.html index 4e3cd31..2aad35d 100644 --- a/doc/blochus/functions/interface/plotResults.html +++ b/doc/blochus/functions/interface/plotResults.html @@ -236,174 +236,177 @@

    SOURCE CODE ^% adiabatic quality of switch-off ramp 0165 if strcmp(data.basic.type,'prepol') || strcmp(data.basic.type,'prepolpulse') -0166 set(get(lh,'Title'),'String',['p=',sprintf('%4.3f',data.results.prepol.p)]) -0167 end -0168 % font size -0169 set(ax,'FontSize',myui.axfontsize); -0170 -0171 end -0172 -0173 %% magnetization components on Bloch sphere -0174 function plotSphere(data,gui,frame) -0175 myui = gui.myui; -0176 -0177 % for plotting everything is in [ms] -0178 T = data.results.basic.T.*1e3; +0166 % set(get(lh,'Title'),'String',{'adiab. qual.',['p = ',sprintf('%4.3f',data.results.prepol.p)]}) +0167 set(get(ax,'Title'),'String',['adiabatic quality p = ',sprintf('%4.3f',data.results.prepol.p)]) +0168 else +0169 set(get(ax,'Title'),'String',''); +0170 end +0171 % font size +0172 set(ax,'FontSize',myui.axfontsize); +0173 +0174 end +0175 +0176 %% magnetization components on Bloch sphere +0177 function plotSphere(data,gui,frame) +0178 myui = gui.myui; 0179 -0180 % all relevant time marker -0181 Tsim = data.basic.Tsim; -0182 Ttau = data.pulse.Ttau; -0183 Tramp = data.prepol.Tramp; -0184 Twait = data.pulse.Twait; -0185 -0186 % choose reference frame to plot -0187 switch frame -0188 case 'lab' -0189 M = data.results.basic.M; -0190 ax = gui.axes_handles.SphereL; -0191 case 'rot' -0192 M = data.results.basic.Mrot; -0193 ax = gui.axes_handles.SphereR; -0194 end -0195 % norm of magnetization vector -0196 Mamp = sqrt(M(:,1).^2+M(:,2).^2+M(:,3).^2); -0197 -0198 % for visualization purposes M always gets normalized on Bloch sphere -0199 M = M./Mamp(1); +0180 % for plotting everything is in [ms] +0181 T = data.results.basic.T.*1e3; +0182 +0183 % all relevant time marker +0184 Tsim = data.basic.Tsim; +0185 Ttau = data.pulse.Ttau; +0186 Tramp = data.prepol.Tramp; +0187 Twait = data.pulse.Twait; +0188 +0189 % choose reference frame to plot +0190 switch frame +0191 case 'lab' +0192 M = data.results.basic.M; +0193 ax = gui.axes_handles.SphereL; +0194 case 'rot' +0195 M = data.results.basic.Mrot; +0196 ax = gui.axes_handles.SphereR; +0197 end +0198 % norm of magnetization vector +0199 Mamp = sqrt(M(:,1).^2+M(:,2).^2+M(:,3).^2); 0200 -0201 % chhose what to plot depending on simulation type -0202 switch data.basic.type -0203 case 'std' -0204 indS1 = 1:numel(T); % relaxation -0205 indS2 = []; % relaxation at end of "prepolpulse"-type -0206 indR = []; % switch-off ramp -0207 indB = []; % switch-off B-field -0208 indP = []; % pulse -0209 indE = numel(T); % end point -0210 Beffn = [0 0 0]; -0211 -0212 case 'prepol' -0213 indS1 = T>Tramp; -0214 indS2 = []; -0215 indR = T<=Tramp; -0216 indB = []; -0217 indP = []; -0218 indE = numel(T); -0219 % switch-off B-field trajectory -0220 Bamp = sqrt(data.results.prepol.Beff(:,1).^2+... -0221 data.results.prepol.Beff(:,2).^2+... -0222 data.results.prepol.Beff(:,3).^2); -0223 Beffn = data.results.prepol.Beff./Bamp; -0224 -0225 case 'pulse' -0226 indS1 = T>Ttau; -0227 indS2 = []; -0228 indR = []; -0229 indB = []; -0230 indP = T<=Ttau; -0231 indE = numel(T); -0232 Beffn = [0 0 0]; -0233 -0234 case 'prepolpulse' -0235 indS2 = T>Tramp & T<=Tramp+Twait; -0236 indS1 = T>Tramp+Twait+Ttau; -0237 indR = T<=Tramp; -0238 indB = []; -0239 indP = T>Tramp+Twait & T<=Tramp+Twait+Ttau; -0240 indE = numel(T); -0241 % switch-off B-field trajectory -0242 Bamp = sqrt(data.results.prepol.Beff(:,1).^2+... -0243 data.results.prepol.Beff(:,2).^2+... -0244 data.results.prepol.Beff(:,3).^2); -0245 Beffn = data.results.prepol.Beff./Bamp; -0246 end -0247 -0248 % plot data -0249 clearSingleAxis(ax); -0250 hold(ax,'on'); -0251 plot3(M(indS1,1),M(indS1,2),M(indS1,3),'LineWidth',myui.linewidth,... -0252 'Color',myui.color.basic,'Parent',ax); -0253 plot3(M(indS2,1),M(indS2,2),M(indS2,3),'LineWidth',myui.linewidth,... -0254 'Color',myui.color.wait,'Parent',ax); -0255 plot3(M(indP,1),M(indP,2),M(indP,3),'LineWidth',myui.linewidth,... -0256 'Color',myui.color.pulse,'Parent',ax); -0257 plot3(M(indR,1),M(indR,2),M(indR,3),'LineWidth',myui.linewidth,... -0258 'Color',myui.color.prepol,'Parent',ax); -0259 plot3(Beffn(:,1),Beffn(:,2),Beffn(:,3),'LineWidth',myui.linewidth,... -0260 'Color',myui.color.prepolB,'Parent',ax) -0261 plot3(M(indE,1),M(indE,2),M(indE,3),'ko','MarkerSize',8,'Parent',ax); -0262 % plot actual Bloch sphere -0263 plotBSphere(18,18,ax); -0264 % axis settings -0265 view(ax,[-35 30]); -0266 hold(ax,'off'); -0267 set(ax,'XLim',[-1.05 1.05],'YLim',[-1.05 1.05],'ZLim',[-1.05 1.05]) -0268 set(ax,'Color','w','XColor','none','YColor','none','ZColor','none'); -0269 axis(ax,'equal'); -0270 axis(ax,'tight'); -0271 -0272 end -0273 -0274 %% FFT of magnetization and pulse -0275 function plotFFT(data,gui,type) +0201 % for visualization purposes M always gets normalized on Bloch sphere +0202 M = M./Mamp(1); +0203 +0204 % chhose what to plot depending on simulation type +0205 switch data.basic.type +0206 case 'std' +0207 indS1 = 1:numel(T); % relaxation +0208 indS2 = []; % relaxation at end of "prepolpulse"-type +0209 indR = []; % switch-off ramp +0210 indB = []; % switch-off B-field +0211 indP = []; % pulse +0212 indE = numel(T); % end point +0213 Beffn = [0 0 0]; +0214 +0215 case 'prepol' +0216 indS1 = T>Tramp; +0217 indS2 = []; +0218 indR = T<=Tramp; +0219 indB = []; +0220 indP = []; +0221 indE = numel(T); +0222 % switch-off B-field trajectory +0223 Bamp = sqrt(data.results.prepol.Beff(:,1).^2+... +0224 data.results.prepol.Beff(:,2).^2+... +0225 data.results.prepol.Beff(:,3).^2); +0226 Beffn = data.results.prepol.Beff./Bamp; +0227 +0228 case 'pulse' +0229 indS1 = T>Ttau; +0230 indS2 = []; +0231 indR = []; +0232 indB = []; +0233 indP = T<=Ttau; +0234 indE = numel(T); +0235 Beffn = [0 0 0]; +0236 +0237 case 'prepolpulse' +0238 indS2 = T>Tramp & T<=Tramp+Twait; +0239 indS1 = T>Tramp+Twait+Ttau; +0240 indR = T<=Tramp; +0241 indB = []; +0242 indP = T>Tramp+Twait & T<=Tramp+Twait+Ttau; +0243 indE = numel(T); +0244 % switch-off B-field trajectory +0245 Bamp = sqrt(data.results.prepol.Beff(:,1).^2+... +0246 data.results.prepol.Beff(:,2).^2+... +0247 data.results.prepol.Beff(:,3).^2); +0248 Beffn = data.results.prepol.Beff./Bamp; +0249 end +0250 +0251 % plot data +0252 clearSingleAxis(ax); +0253 hold(ax,'on'); +0254 plot3(M(indS1,1),M(indS1,2),M(indS1,3),'LineWidth',myui.linewidth,... +0255 'Color',myui.color.basic,'Parent',ax); +0256 plot3(M(indS2,1),M(indS2,2),M(indS2,3),'LineWidth',myui.linewidth,... +0257 'Color',myui.color.wait,'Parent',ax); +0258 plot3(M(indP,1),M(indP,2),M(indP,3),'LineWidth',myui.linewidth,... +0259 'Color',myui.color.pulse,'Parent',ax); +0260 plot3(M(indR,1),M(indR,2),M(indR,3),'LineWidth',myui.linewidth,... +0261 'Color',myui.color.prepol,'Parent',ax); +0262 plot3(Beffn(:,1),Beffn(:,2),Beffn(:,3),'LineWidth',myui.linewidth,... +0263 'Color',myui.color.prepolB,'Parent',ax) +0264 plot3(M(indE,1),M(indE,2),M(indE,3),'ko','MarkerSize',8,'Parent',ax); +0265 % plot actual Bloch sphere +0266 plotBSphere(18,18,ax); +0267 % axis settings +0268 view(ax,[-35 30]); +0269 hold(ax,'off'); +0270 set(ax,'XLim',[-1.05 1.05],'YLim',[-1.05 1.05],'ZLim',[-1.05 1.05]) +0271 set(ax,'Color','w','XColor','none','YColor','none','ZColor','none'); +0272 axis(ax,'equal'); +0273 axis(ax,'tight'); +0274 +0275 end 0276 -0277 % Larmor freq. [Hz] -0278 fL = getOmega0(data.basic.gamma,data.basic.B0)/2/pi; +0277 %% FFT of magnetization and pulse +0278 function plotFFT(data,gui,type) 0279 -0280 % choose what to plot -0281 switch type -0282 case 'M' -0283 ax = gui.axes_handles.MagFFT; -0284 f = data.results.basic.Mspec.fx; -0285 X = data.results.basic.Mspec.X; -0286 lgdstr = {'Mxy','\omega_0'}; -0287 case 'B' -0288 ax = gui.axes_handles.PulseFFT; -0289 f = data.results.pulse.Bspec.fx; -0290 X = data.results.pulse.Bspec.X; -0291 lgdstr = {'B','\omega_0'}; -0292 end -0293 -0294 % plot data -0295 clearSingleAxis(ax); -0296 hold(ax,'on'); -0297 plot(f,abs(X),'r','Parent',ax); -0298 % vertical line indicating Larmor frequency -0299 line([fL fL],[0 max(abs(X))],'Color','k','LineStyle','--',... -0300 'LineWidth',0.75,'Parent',ax); -0301 hold(ax,'off'); -0302 % axis settings -0303 set(ax,'XLim',[-abs(2*fL) abs(2*fL)],'YLim',[0 max(abs(X))].*1.1); -0304 grid(ax,'on'); -0305 set(get(ax,'XLabel'),'String','F [Hz]'); -0306 set(get(ax,'YLabel'),'String','amplitude'); -0307 % legend -0308 legend(ax,lgdstr,'Location','NorthEast'); -0309 % font size -0310 set(ax,'FontSize',gui.myui.axfontsize); -0311 -0312 end -0313 -0314 %------------- END OF CODE -------------- -0315 -0316 %% License: -0317 % GNU GPLv3 -0318 % -0319 % BLOCHUS -0320 % Copyright (C) 2019 Thomas Hiller +0280 % Larmor freq. [Hz] +0281 fL = getOmega0(data.basic.gamma,data.basic.B0)/2/pi; +0282 +0283 % choose what to plot +0284 switch type +0285 case 'M' +0286 ax = gui.axes_handles.MagFFT; +0287 f = data.results.basic.Mspec.fx; +0288 X = data.results.basic.Mspec.X; +0289 lgdstr = {'Mxy','\omega_0'}; +0290 case 'B' +0291 ax = gui.axes_handles.PulseFFT; +0292 f = data.results.pulse.Bspec.fx; +0293 X = data.results.pulse.Bspec.X; +0294 lgdstr = {'B','\omega_0'}; +0295 end +0296 +0297 % plot data +0298 clearSingleAxis(ax); +0299 hold(ax,'on'); +0300 plot(f,abs(X),'r','Parent',ax); +0301 % vertical line indicating Larmor frequency +0302 line([fL fL],[0 max(abs(X))],'Color','k','LineStyle','--',... +0303 'LineWidth',0.75,'Parent',ax); +0304 hold(ax,'off'); +0305 % axis settings +0306 set(ax,'XLim',[-abs(2*fL) abs(2*fL)],'YLim',[0 max(abs(X))].*1.1); +0307 grid(ax,'on'); +0308 set(get(ax,'XLabel'),'String','F [Hz]'); +0309 set(get(ax,'YLabel'),'String','amplitude'); +0310 % legend +0311 legend(ax,lgdstr,'Location','NorthEast'); +0312 % font size +0313 set(ax,'FontSize',gui.myui.axfontsize); +0314 +0315 end +0316 +0317 %------------- END OF CODE -------------- +0318 +0319 %% License: +0320 % GNU GPLv3 0321 % -0322 % This program is free software: you can redistribute it and/or modify -0323 % it under the terms of the GNU General Public License as published by -0324 % the Free Software Foundation, either version 3 of the License, or -0325 % (at your option) any later version. -0326 % -0327 % This program is distributed in the hope that it will be useful, -0328 % but WITHOUT ANY WARRANTY; without even the implied warranty of -0329 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -0330 % GNU General Public License for more details. -0331 % -0332 % You should have received a copy of the GNU General Public License -0333 % along with this program. If not, see <https://www.gnu.org/licenses/>. +0322 % BLOCHUS +0323 % Copyright (C) 2019 Thomas Hiller +0324 % +0325 % This program is free software: you can redistribute it and/or modify +0326 % it under the terms of the GNU General Public License as published by +0327 % the Free Software Foundation, either version 3 of the License, or +0328 % (at your option) any later version. +0329 % +0330 % This program is distributed in the hope that it will be useful, +0331 % but WITHOUT ANY WARRANTY; without even the implied warranty of +0332 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +0333 % GNU General Public License for more details. +0334 % +0335 % You should have received a copy of the GNU General Public License +0336 % along with this program. If not, see <https://www.gnu.org/licenses/>.
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/blochus/functions/interface/switchToolTips.html b/doc/blochus/functions/interface/switchToolTips.html index 9176c23..ceca91b 100644 --- a/doc/blochus/functions/interface/switchToolTips.html +++ b/doc/blochus/functions/interface/switchToolTips.html @@ -23,7 +23,7 @@

    PURPOSE ^ switches GUI tool tips either "on" or "off"

    SYNOPSIS ^

    -
    function switchToolTips(gui,onoff) %#ok
    +
    function switchToolTips(gui,onoff)

    DESCRIPTION ^

    switchToolTips switches GUI tool tips either "on" or "off"
@@ -62,13 +62,13 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • onMenuViewShow	 handles the extra menu entries
    • 
+
  • onMenuView	 handles the extra menu entries
  • onMenuViewShow	 handles the extra menu entries
    • 
 
 
 
 
 
    SOURCE CODE ^
    
-
    0001 function switchToolTips(gui,onoff) %#ok<INUSL>
+
    0001 function switchToolTips(gui,onoff)
 0002 %switchToolTips switches GUI tool tips either "on" or "off"
 0003 %
 0004 % Syntax:
@@ -101,61 +101,66 @@ 
    SOURCE CODE ^%------------- BEGIN CODE --------------
 0032 
 0033 %% list of handles that have switchable tool tips
-0034 h = {'check_handles','edit_handles','popup_handles','push_handles'};
-0035 
-0036 %% process all handles
-0037 switch lower(onoff)
-0038     case 'off' % if it is off, switch it on
-0039         for i = 1:numel(h)
-0040             eval(['fnames = fieldnames(gui.',h{i},');']);
-0041             for j = 1:numel(fnames)
-0042                 eval(['ud = get(gui.',h{i},'.',fnames{j},...
-0043                     ',''UserData'');']);
-0044                 if isfield(ud,'Tooltipstr')
-0045                     tstr = ud.Tooltipstr;
-0046                     eval(['set(gui.',h{i},'.',fnames{j},...
-0047                         ',''ToolTipString'',tstr);']);
-0048                 end
-0049             end
-0050         end
-0051         
-0052     case 'on' % if it is on, switch it off
-0053         for i = 1:numel(h)
-0054             eval(['fnames = fieldnames(gui.',h{i},');']);
-0055             for j = 1:numel(fnames)
-0056                 eval(['ud = get(gui.',h{i},'.',fnames{j},...
-0057                     ',''UserData'');']);
-0058                 if isfield(ud,'Tooltipstr')
-0059                     tstr = ud.Tooltipstr;
-0060                     eval(['set(gui.',h{i},'.',fnames{j},...
-0061                         ',''ToolTipString'','''');']);
-0062                 end
-0063             end
-0064         end
-0065 end
-0066 
-0067 end
-0068 
-0069 %------------- END OF CODE --------------
-0070 
-0071 %% License:
-0072 % GNU GPLv3
-0073 %
-0074 % BLOCHUS
-0075 % Copyright (C) 2019 Thomas Hiller
-0076 %
-0077 % This program is free software: you can redistribute it and/or modify
-0078 % it under the terms of the GNU General Public License as published by
-0079 % the Free Software Foundation, either version 3 of the License, or
-0080 % (at your option) any later version.
+0034 h = {'check_handles','edit_handles','popup_handles',...
+0035     'push_handles'};
+0036 
+0037 %% process all handles
+0038 switch lower(onoff)
+0039     case 'on' % switch tool tips on
+0040         for i = 1:numel(h)
+0041             if isfield(gui,h{i})
+0042                 eval(['fnames = fieldnames(gui.',h{i},');']);
+0043                 for j = 1:numel(fnames)
+0044                     eval(['ud = get(gui.',h{i},'.',fnames{j},...
+0045                         ',''UserData'');']);
+0046                     if isfield(ud,'Tooltipstr')
+0047                         tstr = ud.Tooltipstr;
+0048                         eval(['set(gui.',h{i},'.',fnames{j},...
+0049                             ',''ToolTipString'',tstr);']);
+0050                     end
+0051                 end
+0052             end
+0053         end
+0054         
+0055     case 'off' % switch tool tips off
+0056         for i = 1:numel(h)
+0057             if isfield(gui,h{i})
+0058                 eval(['fnames = fieldnames(gui.',h{i},');']);
+0059                 for j = 1:numel(fnames)
+0060                     eval(['ud = get(gui.',h{i},'.',fnames{j},...
+0061                         ',''UserData'');']);
+0062                     if isfield(ud,'Tooltipstr')
+0063                         tstr = ud.Tooltipstr;
+0064                         eval(['set(gui.',h{i},'.',fnames{j},...
+0065                             ',''ToolTipString'','''');']);
+0066                     end
+0067                 end
+0068             end
+0069         end
+0070 end
+0071 
+0072 end
+0073 
+0074 %------------- END OF CODE --------------
+0075 
+0076 %% License:
+0077 % GNU GPLv3
+0078 %
+0079 % BLOCHUS
+0080 % Copyright (C) 2019 Thomas Hiller
 0081 %
-0082 % This program is distributed in the hope that it will be useful,
-0083 % but WITHOUT ANY WARRANTY; without even the implied warranty of
-0084 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-0085 % GNU General Public License for more details.
+0082 % This program is free software: you can redistribute it and/or modify
+0083 % it under the terms of the GNU General Public License as published by
+0084 % the Free Software Foundation, either version 3 of the License, or
+0085 % (at your option) any later version.
 0086 %
-0087 % You should have received a copy of the GNU General Public License
-0088 % along with this program.  If not, see <https://www.gnu.org/licenses/>.
    
+0087 % This program is distributed in the hope that it will be useful,
+0088 % but WITHOUT ANY WARRANTY; without even the implied warranty of
+0089 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+0090 % GNU General Public License for more details.
+0091 %
+0092 % You should have received a copy of the GNU General Public License
+0093 % along with this program.  If not, see <https://www.gnu.org/licenses/>.
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/blochus/functions/interface/updateStatusInformation.html b/doc/blochus/functions/interface/updateStatusInformation.html
index 11dbec1..fb3177a 100644
--- a/doc/blochus/functions/interface/updateStatusInformation.html
+++ b/doc/blochus/functions/interface/updateStatusInformation.html
@@ -61,7 +61,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • BLOCHUS	 is a graphical user interface (GUI) to simulate NMR spin dynamics
  • onCheckPrePolPulse	 activates / deactivates all control elements needed for
  • onMenuViewShow	 handles the extra menu entries
  • onPopupPulseType	 selects the pulse type
  • onPushRun	 starts the calculation
    • 
+
  • BLOCHUS	 is a graphical user interface (GUI) to simulate NMR spin dynamics
  • onCheckPrePolPulse	 activates / deactivates all control elements needed for
  • onMenuView	 handles the extra menu entries
  • onMenuViewShow	 handles the extra menu entries
  • onPopupPulseType	 selects the pulse type
  • onPushRun	 starts the calculation
    • 
 
 
 
diff --git a/functions/interface/plotResults.m b/functions/interface/plotResults.m
index f226b50..ee1dea8 100644
--- a/functions/interface/plotResults.m
+++ b/functions/interface/plotResults.m
@@ -163,7 +163,10 @@ function plotMag(data,gui,frame)
 
 % adiabatic quality of switch-off ramp
 if strcmp(data.basic.type,'prepol') || strcmp(data.basic.type,'prepolpulse')
-    set(get(lh,'Title'),'String',['p=',sprintf('%4.3f',data.results.prepol.p)])
+%     set(get(lh,'Title'),'String',{'adiab. qual.',['p = ',sprintf('%4.3f',data.results.prepol.p)]})
+    set(get(ax,'Title'),'String',['adiabatic quality p = ',sprintf('%4.3f',data.results.prepol.p)])
+else
+    set(get(ax,'Title'),'String','');
 end
 % font size
 set(ax,'FontSize',myui.axfontsize);
diff --git a/functions/interface/switchToolTips.m b/functions/interface/switchToolTips.m
index d74f3e4..3fedfbc 100644
--- a/functions/interface/switchToolTips.m
+++ b/functions/interface/switchToolTips.m
@@ -1,4 +1,4 @@
-function switchToolTips(gui,onoff) %#ok
+function switchToolTips(gui,onoff)
 %switchToolTips switches GUI tool tips either "on" or "off"
 %
 % Syntax:
@@ -31,34 +31,39 @@ function switchToolTips(gui,onoff) %#ok
 %------------- BEGIN CODE --------------
 
 %% list of handles that have switchable tool tips
-h = {'check_handles','edit_handles','popup_handles','push_handles'};
+h = {'check_handles','edit_handles','popup_handles',...
+    'push_handles'};
 
 %% process all handles
 switch lower(onoff)
-    case 'off' % if it is off, switch it on
+    case 'on' % switch tool tips on
         for i = 1:numel(h)
-            eval(['fnames = fieldnames(gui.',h{i},');']);
-            for j = 1:numel(fnames)
-                eval(['ud = get(gui.',h{i},'.',fnames{j},...
-                    ',''UserData'');']);
-                if isfield(ud,'Tooltipstr')
-                    tstr = ud.Tooltipstr;
-                    eval(['set(gui.',h{i},'.',fnames{j},...
-                        ',''ToolTipString'',tstr);']);
+            if isfield(gui,h{i})
+                eval(['fnames = fieldnames(gui.',h{i},');']);
+                for j = 1:numel(fnames)
+                    eval(['ud = get(gui.',h{i},'.',fnames{j},...
+                        ',''UserData'');']);
+                    if isfield(ud,'Tooltipstr')
+                        tstr = ud.Tooltipstr;
+                        eval(['set(gui.',h{i},'.',fnames{j},...
+                            ',''ToolTipString'',tstr);']);
+                    end
                 end
             end
         end
         
-    case 'on' % if it is on, switch it off
+    case 'off' % switch tool tips off
         for i = 1:numel(h)
-            eval(['fnames = fieldnames(gui.',h{i},');']);
-            for j = 1:numel(fnames)
-                eval(['ud = get(gui.',h{i},'.',fnames{j},...
-                    ',''UserData'');']);
-                if isfield(ud,'Tooltipstr')
-                    tstr = ud.Tooltipstr;
-                    eval(['set(gui.',h{i},'.',fnames{j},...
-                        ',''ToolTipString'','''');']);
+            if isfield(gui,h{i})
+                eval(['fnames = fieldnames(gui.',h{i},');']);
+                for j = 1:numel(fnames)
+                    eval(['ud = get(gui.',h{i},'.',fnames{j},...
+                        ',''UserData'');']);
+                    if isfield(ud,'Tooltipstr')
+                        tstr = ud.Tooltipstr;
+                        eval(['set(gui.',h{i},'.',fnames{j},...
+                            ',''ToolTipString'','''');']);
+                    end
                 end
             end
         end
diff --git a/scripts/example1.m b/scripts/example1.m
index 9b5f08b..ba9ec1a 100644
--- a/scripts/example1.m
+++ b/scripts/example1.m
@@ -2,8 +2,8 @@
 % This script demonstrates the basic use of the BLOCHUS ode-solver. Two
 % different protons (H & He) are used to show the effect of the sign of the
 % gyromagnetic ratio \gamma
-% 1.) Hydrogen proton (gyromagnetic ratio > 0 )
-% 2.) Helium proton (gyromagnetic ratio < 0 )
+% 1.) Hydrogen proton (gyromagnetic ratio > 0)
+% 2.) Helium proton (gyromagnetic ratio < 0)
 %
 % general settings:
 % -> magnetic field B0 is set to 50 µT
@@ -30,8 +30,6 @@
 usetest = [1 1];
 
 %% basic settings
-% get default values
-% defaults = BLOCHUS_loadDefaults('basic');
 zunit = [0 0 1]'; % z unit vector
 % ODE solver error tolerance
 tol = 1e-9;
@@ -44,22 +42,27 @@
     
     % parameter needed for the ODE
     odeparam.type = 'std';
-    odeparam.M0 = zunit; % equilibrium magnetization [A/m]
-    odeparam.B0 = 5e-5; % primary magnetic field B0 [T]
-    odeparam.T1 = 0.0010; % relaxation time T1 [s]
-    odeparam.T2 = 0.0005; % relaxation time T2 [s]
-    odeparam.gamma = getGyroRatio(nucleus); % gyromagnetic ratio [rad/s/T]
+    % equilibrium magnetization [A/m]
+    odeparam.M0 = zunit;
+    % primary magnetic field B0 [T]
+    odeparam.B0 = 5e-5;
+    % longitudinal relaxation time T1 [s]
+    odeparam.T1 = 0.0010;
+    % transversal relaxation time T2 [s]
+    odeparam.T2 = 0.0005;
+    % gyromagnetic ratio [rad/s/T]
+    odeparam.gamma = getGyroRatio(nucleus);
     
-    % initial magnetization pointing towards +x
-    Minit = [1 0 0]; % [A/m]
-    % simulation time
-    Tsim = 0.005; % [s]
+    % initial magnetization pointing towards +x  [A/m]
+    Minit = [1 0 0];
+    % simulation time [s]
+    Tsim = 0.005; 
     
     % ODE solver call
     % OUTPUT: time T and magnetization M
     [T,M] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
     
-    % rotate M(T) vector into rotating reference frame
+    % get M(T) in rotating frame of reference 
     Mrot = getMrot(M,getOmega0(odeparam.gamma,odeparam.B0).*T);
     
     f1 = figure; set(f1,'Name','example1a_ref');
@@ -99,14 +102,16 @@
     axis equal tight;
     
     % --- Helium ---
-    nucleus = '3He'; % helium proton
-    odeparam.gamma = getGyroRatio(nucleus); % gyromagnetic ratio [rad/s/T]
+    % helium proton
+    nucleus = '3He';
+    % gyromagnetic ratio [rad/s/T]
+    odeparam.gamma = getGyroRatio(nucleus); 
     
     % ODE solver call
     % OUTPUT: time T and magnetization M
     [T,M] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
     
-    % rotate M(T) vector into rotating reference frame
+    % get M(T) in rotating frame of reference
     Mrot = getMrot(M,getOmega0(odeparam.gamma,odeparam.B0).*T);
     
     f2 = figure; set(f2,'Name','example1b_ref');
@@ -156,11 +161,16 @@
     % --- T2 = T1
     % parameter needed for the ODE
     odeparam.type = 'std';
-    odeparam.M0 = zunit; % equilibrium magnetization [A/m]
-    odeparam.B0 = 5e-5; % primary magnetic field B0 [T]
-    odeparam.T1 = 0.0010; % relaxation time T1 [s]
-    odeparam.T2 = 0.0010; % relaxation time T2 [s]
-    odeparam.gamma = getGyroRatio(nucleus); % gyromagnetic ratio [rad/s/T]
+    % equilibrium magnetization [A/m]
+    odeparam.M0 = zunit;
+    % primary magnetic field B0 [T]
+    odeparam.B0 = 5e-5;
+    % longitudinal relaxation time T1 [s]
+    odeparam.T1 = 0.0010;
+    % transversal relaxation time T2 [s]
+    odeparam.T2 = 0.0010;
+     % gyromagnetic ratio [rad/s/T]
+    odeparam.gamma = getGyroRatio(nucleus);
     
     % initial magnetization pointing towards +x
     Minit = [1 0 0]; % [A/m]
@@ -171,7 +181,7 @@
     % OUTPUT: time T and magnetization M
     [T,M] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
     
-    % rotate M(T) vector into rotating reference frame
+    % get M(T) in rotating frame of reference 
     Mrot = getMrot(M,getOmega0(odeparam.gamma,odeparam.B0).*T);
     
     f3 = figure; set(f3,'Name','example1c_ref');
@@ -193,13 +203,14 @@
     set(get(ax2,'Title'),'String','T1 = T2');
     
     % --- T2 = 2*T1
-    odeparam.T2 = 0.0020; % relaxation time T2 [s]
+    % transversal relaxation time T2 [s]
+    odeparam.T2 = 0.0020; 
 
     % ODE solver call
     % OUTPUT: time T and magnetization M
     [T,M] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
     
-    % rotate M(T) vector into rotating reference frame
+    % get M(T) in rotating frame of reference 
     Mrot = getMrot(M,getOmega0(odeparam.gamma,odeparam.B0).*T);
     
     ax3 = subplot(3,2,3); hold(ax3,'on');
@@ -222,13 +233,14 @@
     set(get(ax4,'Title'),'String','T2 = 2T1');
     
     % --- T1 = 2*T2
-    odeparam.T2 = 0.0005; % relaxation time T2 [s]
+    % transversal relaxation time T2 [s]
+    odeparam.T2 = 0.0005; 
 
     % ODE solver call
     % OUTPUT: time T and magnetization M
     [T,M] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
     
-    % rotate M(T) vector into rotating reference frame
+    % get M(T) in rotating frame of reference 
     Mrot = getMrot(M,getOmega0(odeparam.gamma,odeparam.B0).*T);
     
     ax5 = subplot(3,2,5); hold(ax5,'on');
diff --git a/scripts/example2.m b/scripts/example2.m
index 39f9db5..4ca3478 100644
--- a/scripts/example2.m
+++ b/scripts/example2.m
@@ -1,6 +1,6 @@
 % script: example2.m
-% this script demonstrates how basic pulses are used with BLOCHUS
-% everything is done with a Hydrogen proton (gyromagnetic ratio > 0 )
+% This script demonstrates how basic pulses can be simulated with BLOCHUS
+% everything is done with a Hydrogen proton (gyromagnetic ratio > 0)
 %
 % settings:
 % -> magnetic field B0 is set to 50 µT
@@ -40,53 +40,93 @@
 options = odeset('RelTol',tol,'AbsTol',[tol tol tol]);
 
 %% standard parameter
-nucleus = '1H'; % hydrogen proton
+% hydrogen proton
+nucleus = '1H';
 % parameter needed for the ODE
 odeparam.type = 'pulse';
-odeparam.M0 = zunit; % equilibrium magnetization [A/m]
-odeparam.B0 = 5e-5; % primary magnetic field B0 [T]
-odeparam.T1 = 0.0010; % relaxation time T1 [s]
-odeparam.T2 = 0.0005; % relaxation time T2 [s]
-odeparam.gamma = getGyroRatio(nucleus); % gyromagnetic ratio [rad/s/T]
+% equilibrium magnetization [A/m]
+odeparam.M0 = zunit;
+% primary magnetic field B0 [T]
+odeparam.B0 = 5e-5;
+% longitudinal relaxation time T1 [s]
+odeparam.T1 = 0.0010;
+% transversal relaxation time T2 [s]
+odeparam.T2 = 0.0005;
+% gyromagnetic ratio [rad/s/T]
+odeparam.gamma = getGyroRatio(nucleus);
 
 %% pulse modulation standard values
+% pulse type [string]
 fmod.PulseType = 'pi_half';
+% shape of the modulation function [string]
 fmod.shape = 'const';
+% pulse start time [s]
 fmod.t0 = 0;
+% pulse end time [s]
 fmod.t1 = 0.005;
+% time vector [s]
 fmod.t = 0;
+% start frequency [Hz]
 fmod.v0 = 0;
+% end frequency [Hz]
 fmod.v1 = 0;
+% modulation parameter (MIDI)
 fmod.A = 1;
+% modulation parameter (MIDI)
 fmod.B = 0;
 
+% shape of the modulation function [string]
 Imod.shape = 'const';
+% check if quality factor tuning is activated [0/1]
 Imod.useQ = 0;
+% quality factor
 Imod.Q = 0;
+% quality factor off-resonance frequency [Hz]
 Imod.Qdf = 0;
+% pulse start time [s]
 Imod.t0 = 0;
+% pulse end time [s]
 Imod.t1 = 0.005;
+% time vector [s]
 Imod.t = 0;
+% start current [A]
 Imod.v0 = 1;
+% end current [A]
 Imod.v1 = 1;
+% modulation parameter (MIDI)
 Imod.A = 1;
+% modulation parameter (MIDI)
 Imod.B = 0;
 
 %% 1.) pi/2 pulse
 if usetest(1)
-    % excitation pulse parameter
+    
+    % relaxation during pulse [0/1]
     odeparam.RDP = 0;
-    odeparam.Ttau = 0.005; % [s]
+    % pulse length [s]
+    odeparam.Ttau = 0.005;
+    
+    % excitation pulse parameter
+    % pulse type [string]
     pulseparam.PulseType = fmod.PulseType;
-    pulseparam.Amp = odeparam.B0*abs((pi/2/(odeparam.gamma*odeparam.B0*odeparam.Ttau)));
+    % gyromagnetic ratio [rad/s/T]
     pulseparam.gamma = odeparam.gamma;
+    % Larmor frequency [rad/s]
     pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
+    % pulse amplitude [T]
+    pulseparam.Amp = odeparam.B0*abs((pi/2/(odeparam.gamma*odeparam.B0*odeparam.Ttau)));
+    % pulse frequency modulation [struct]
     pulseparam.fmod = fmod;
+    % pulse current modulation [struct]
     pulseparam.Imod = Imod;
+    % auxiliary pulse phase [rad]
     pulseparam.phi = 0;
+    % pulse axis [string]
     pulseparam.PulseAxis = '+x';
+    % pulse polarization [string]
     pulseparam.PulsePolarization = 'circular';
     
+    % save pulse parameter settings
     odeparam.pulseparam = pulseparam;
     
     % initial magnetization pointing towards B0 (+z)
@@ -98,7 +138,7 @@
     % OUTPUT: time T and magnetization M
     [T,M] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
     
-    % rotate M(T) vector into rotating reference frame
+    % get M(T) in rotating frame of reference
     Mrot = getMrot(M,getOmega0(odeparam.gamma,odeparam.B0).*T);
     
     f1 = figure; set(f1,'Name','example2a_ref');
@@ -141,20 +181,35 @@
 
 %% 2.) pi pulse
 if usetest(2)
+    % new pulse type
     fmod.PulseType = 'pi';
-    % excitation pulse parameter
+    
+    % relaxation during pulse [0/1]
     odeparam.RDP = 0;
-    odeparam.Ttau = 0.005; % [s]
+    % pulse length [s]
+    odeparam.Ttau = 0.005;
+    
+    % excitation pulse parameter
+    % pulse type [string]
     pulseparam.PulseType = fmod.PulseType;
-    pulseparam.Amp = odeparam.B0*abs((pi/(odeparam.gamma*odeparam.B0*odeparam.Ttau)));
+    % gyromagnetic ratio [rad/s/T]
     pulseparam.gamma = odeparam.gamma;
+    % Larmor frequency [rad/s]
     pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
+    % pulse amplitude [T]
+    pulseparam.Amp = odeparam.B0*abs((pi/(odeparam.gamma*odeparam.B0*odeparam.Ttau)));
+    % pulse frequency modulation [struct]
     pulseparam.fmod = fmod;
+    % pulse current modulation [struct]
     pulseparam.Imod = Imod;
+    % auxiliary pulse phase [rad]
     pulseparam.phi = 0;
+    % pulse axis [string]
     pulseparam.PulseAxis = '+x';
+    % pulse polarization [string]
     pulseparam.PulsePolarization = 'circular';
     
+    % save pulse parameter settings
     odeparam.pulseparam = pulseparam;
     
     % initial magnetization pointing towards B0 (+z)
@@ -166,7 +221,7 @@
     % OUTPUT: time T and magnetization M
     [T,M] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
     
-    % rotate M(T) vector into rotating reference frame
+    % get M(T) in rotating frame of reference
     Mrot = getMrot(M,getOmega0(odeparam.gamma,odeparam.B0).*T);
     
     f2 = figure; set(f2,'Name','example2b_ref');
@@ -209,20 +264,36 @@
 
 %% 3.) pi/2 pulses with different pulse axes
 if usetest(3)
+    % new pulse type
     fmod.PulseType = 'pi_half';
+    
     % excitation pulse parameter
+    % relaxation during pulse [0/1]
     odeparam.RDP = 0;
-    odeparam.Ttau = 0.005; % [s]
+    % pulse length [s]
+    odeparam.Ttau = 0.005;
+    
+    % excitation pulse parameter
+    % pulse type [string]
     pulseparam.PulseType = fmod.PulseType;
-    pulseparam.Amp = odeparam.B0*abs((pi/2/(odeparam.gamma*odeparam.B0*odeparam.Ttau)));
+    % gyromagnetic ratio [rad/s/T]
     pulseparam.gamma = odeparam.gamma;
+    % Larmor frequency [rad/s]
     pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
+    % pulse amplitude [T]
+    pulseparam.Amp = odeparam.B0*abs((pi/2/(odeparam.gamma*odeparam.B0*odeparam.Ttau)));
+    % pulse frequency modulation [struct]
     pulseparam.fmod = fmod;
+    % pulse current modulation [struct]
     pulseparam.Imod = Imod;
+    % auxiliary pulse phase [rad]
     pulseparam.phi = 0;
+    % pulse axis [string]
     pulseparam.PulseAxis = '+x';
+    % pulse polarization [string]
     pulseparam.PulsePolarization = 'circular';
     
+    % save pulse parameter settings
     odeparam.pulseparam = pulseparam;
     
     % initial magnetization pointing towards B0 (+z)
@@ -234,7 +305,7 @@
     % OUTPUT: time T and magnetization M
     [T,M] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
     
-    % rotate M(T) vector into rotating reference frame
+    % get M(T) in rotating frame of reference
     Mrot = getMrot(M,getOmega0(odeparam.gamma,odeparam.B0).*T);
     
     f3 = figure; set(f3,'Name','example2c_ref');
@@ -296,23 +367,37 @@
 % (i.e. instead of -2000 Hz it is -2100 Hz)
 % because of the negative Larmor frequency of H-protons the rotation axis
 % dips downwards for negative ratios
-if usetest(4)    
+if usetest(4)
     % df/omega_nut ratio
     ratio = -4:1:4;
-    
+    % new pulse type
     fmod.PulseType = 'pi_half';
+
     % excitation pulse parameter
+    % relaxation during pulse [0/1]
     odeparam.RDP = 0;
-    odeparam.Ttau = 0.005; % [s]
+    % pulse length [s]
+    odeparam.Ttau = 0.005;
+    
+    % excitation pulse parameter
+    % pulse type [string]
     pulseparam.PulseType = fmod.PulseType;
-    pulseparam.Amp = odeparam.B0*abs((pi/2/(odeparam.gamma*odeparam.B0*odeparam.Ttau)));
+    % gyromagnetic ratio [rad/s/T]
     pulseparam.gamma = odeparam.gamma;
+    % Larmor frequency [rad/s]
     pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
+    % pulse amplitude [T]
+    pulseparam.Amp = odeparam.B0*abs((pi/2/(odeparam.gamma*odeparam.B0*odeparam.Ttau)));
+    % pulse frequency modulation [struct]
     pulseparam.fmod = fmod;
+    % pulse current modulation [struct]
     pulseparam.Imod = Imod;
+    % auxiliary pulse phase [rad]
     pulseparam.phi = 0;
+    % pulse axis [string]
     pulseparam.PulseAxis = '+y';
-    pulseparam.PulsePolarization = 'circular';
+    % pulse polarization [string]
+    pulseparam.PulsePolarization = 'circular'; 
     
     % nutation frequency for a pi/2 pulse with 5 ms is 50 Hz
     omega_nut = (pi/2)/odeparam.Ttau/2/pi; % [Hz]
@@ -320,10 +405,12 @@
     f4 = figure; set(f4,'Name','example2d_ref');
     for i = 1:numel(ratio)
         
-        df = ratio(i)*omega_nut; % frequency offsets [Hz]
+        % frequency offsets [Hz]
+        df = ratio(i)*omega_nut; 
         pulseparam.fmod.v0 = df;
         pulseparam.fmod.v1 = df;
         
+        % save pulse parameter settings
         odeparam.pulseparam = pulseparam;
         
         % initial magnetization pointing towards B0 (+z)
@@ -342,7 +429,7 @@
         pulseparam.t = T;
         [Bpulse,~,~,theta]= getPulseTimeSeries(pulseparam);
         
-        % rotate M(T) vector into rotating reference frame
+        % get M(T) in rotating frame of reference
         Mrot = getMrot(M,theta);
         
         ax(i) = subplot(3,3,i); hold(ax(i),'on'); %#ok<*SAGROW>
@@ -375,3 +462,4 @@
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see .
+
diff --git a/scripts/example3.m b/scripts/example3.m
index 74d2ea8..f78490e 100644
--- a/scripts/example3.m
+++ b/scripts/example3.m
@@ -1,9 +1,10 @@
 % script: example3.m
-% This script demonstrates the basic use of the BLOCHUS ode-solver.
+% This script demonstrates how pre-polarization switch-off ramps are simulated
+% with BLOCHUS.
 % Both examples were also used as benchmark cases in the paper:
 %	Hiller, T., Dlugosch, R. and Müller-Petke, M., "Utilizing pre-
 %	polarization to enhance SNMR signals - effect of imperfect
-%	switch-off", Geophysical Journal International Vol. 0(0), p.1-15, 2020
+%	switch-off", Geophysical Journal International Vol. 222(2), p.815-826, 2020
 %
 % Two pre-polarization switch-off benchmarks are shown:
 %
@@ -188,13 +189,13 @@
 %% 2.) Conradi et al.(2017)
 if usetest(2)
     
-    % Fig. 4a
+    % Fig. 4a of Conradi et al.(2017)
     %     conradi_Bmax = 16/1e3; % [T]
     %     conradi_Bstar = [2000 250 120]./1e6; % [T]
     %     conradi_Tslope = 6/1e3; % [s]
     %     conradi_lgdstr = {'2000','250','120'};
     
-    % Fig. 4b
+    % Fig. 4b of Conradi et al.(2017)
     conradi_Bmax = 2.5/1e3; % [T]
     conradi_Bstar = [250 60 1]./1e6; % [T]
     conradi_Tslope = 10/1e3; % [s]
diff --git a/scripts/example4.m b/scripts/example4.m
new file mode 100644
index 0000000..fcb8d24
--- /dev/null
+++ b/scripts/example4.m
@@ -0,0 +1,230 @@
+% script: example4.m
+% This script demonstrates how to calculate lookup-tables for pre-polarization
+% switch-off ramps that can subsequently be used with MRSMatlab to forward
+% model MRS sounding curves.
+% Basically this script allows to create the data that is shown in Fig. 4
+% of the paper:
+%   Hiller, T., Dlugosch, R. and Müller-Petke, M., "Utilizing pre-
+%   polarization to enhance SNMR signals - effect of imperfect
+%   switch-off", Geophysical Journal International Vol. 222(2), p.815-826, 2020
+%
+%   general settings:
+%       - magnetic field B0 is set to 48 µT
+%       - T1, T2 - relaxation is ignored
+%
+%   lookup table parameters:
+%       - pre-polarization field Bp ranges between 4.8µT and 480mT
+%       - initial orientation between Bp and B0 varies between 0° and 180°
+%
+% See also: BLOCHUS
+% Author: Thomas Hiller
+% email: thomas.hiller[at]leibniz-liag.de
+% License: GNU GPLv3 (at end)
+
+%------------- BEGIN CODE --------------
+
+% clear data
+clear variables; clc;
+
+% because this script takes approx. 30min, ask the user before continuing
+answer = questdlg({'This script needs about 30 min. to run.',...
+    'Do you want to continue?'},'Dessert Menu','Yes','No','Yes');
+% handle response
+switch answer
+    case 'Yes'
+        % nothing to do
+    case {'No',''}
+        return
+end
+
+% output switches
+save_data = true;
+plot_data = true;
+
+% --- LOOKUP TABLE SETTINGS -----------------------------------------------
+% global lookup table settings (change as you like):
+% all four major ramp shapes
+lookup_ramps = {'exp','linexp','halfcos','lin'};
+% only three distinct switch-off times [s]
+lookup_Tramps = [0.1 1 4]/1e3;
+
+% IMPORTANT NOTE:
+% This very coarse (and basically useless) Np=10 x Nt=10 grid takes for the
+% 4x3 ramp combinations (shapes x times) roughly 30min! The resolution in
+% Fig.4 of the paper is Np=51 x Nt=360 ... so you don't want to start this
+% calculation on your normal machine.
+% local lookup table settings (careful with the discretization)
+Np = 10;
+Nt = 10;
+% pre-polarization factor [B0]
+PPfac = logspace(-1,4,Np);
+% angle between Bp and B0 [deg]
+theta = linspace(0,180,Nt);
+% -------------------------------------------------------------------------
+
+% basic settings
+zunit = [0 0 1]'; % z unit vector
+% ODE solver error tolerance
+tol = 1e-9;
+% ODE solver options
+options = odeset('RelTol',tol,'AbsTol',[tol tol tol]);
+
+% hydrogen proton
+nucleus = '1H';
+
+% parameter needed for the ODE solver
+% simulation type [string]
+odeparam.type = 'prepol';
+% equilibrium magnetization [A/m]
+odeparam.M0 = zunit;
+% primary (Earth's) magnetic field B0 [T]
+odeparam.B0 = 4.8e-5;
+% relaxation time T1 [s]
+odeparam.T1 = 2;
+% relaxation time T2 [s]
+odeparam.T2 = 1;
+% gyromagnetic ratio [rad/s/T]
+odeparam.gamma = getGyroRatio(nucleus);
+
+% pre-polarization switch-off ramp parameter
+% relaxation during switch-off [0/1]
+odeparam.RDS = 0;
+
+% because Minit is not normalized to 1, M0 needs to be adjusted
+odeparam.M0 = odeparam.B0*zunit;
+
+data = cell(numel(lookup_ramps),numel(lookup_Tramps));
+for i1 = 1:numel(lookup_ramps)
+    for i2 = 1:numel(lookup_Tramps)
+        % current switch-off ramp and time
+        ramp = lookup_ramps{i1};
+        Tramp = lookup_Tramps(i2);
+        
+        infostr1 = ['running: Ramp=',ramp,' | Tramp=',...
+            sprintf('%3.1f',Tramp*1e3),' ms'];
+        disp(infostr1);
+        
+        % create the output data matrix
+        % adiabatic quality p
+        p = zeros(numel(theta),numel(PPfac));
+        % final magnetization vector
+        Mfinal = zeros(numel(theta),numel(PPfac),3);
+        % loop over the local parameters
+        for tt = 1:numel(theta)
+            for pp = 1:numel(PPfac)
+                
+                % switch-off ramp type [string]
+                rampparam.ramp = ramp;
+                % gyromagnetic ratio [rad/s/T]
+                rampparam.gamma = odeparam.gamma;
+                % primary (Earth's) magnetic field B0 [T]
+                rampparam.B0 = odeparam.B0;
+                % amplitude of pre-polarization field [T]
+                rampparam.Bmax = PPfac(pp)*odeparam.B0;
+                % switch-off ramp time [s]
+                rampparam.Tramp = Tramp;
+                
+                % different ramps need different settings
+                switch ramp
+                    case 'exp'
+                        SwitchFactor = 1;                        
+                        % switch over ramp time [s]
+                        rampparam.Tslope = Tramp/10;
+                    case 'linexp'
+                        SwitchFactor = PPfac(pp)/10;
+                        rampparam.Tslope = Tramp/2;
+                    case {'halfcos','lin'}
+                        SwitchFactor = 1;
+                        rampparam.Tslope = Tramp;
+                end
+                % switch-over amplitude for the "linexp" ramp (factor*B0) [T]
+                rampparam.Bstar = SwitchFactor*odeparam.B0;
+
+                % initial orientation is towards y-axis
+                orient = getRotationMatrixFromAngleandAxis(deg2rad(theta(tt)),[0 1 0])*zunit;
+                % initial magnetization in the direction of B0+Bp
+                Morient = orient*rampparam.Bmax + odeparam.B0*zunit;
+                % Minit does not get normalized in this case
+                Minit = Morient;
+                % orientation of the pre-polarization pulse axis (y-axis)
+                odeparam.orient = orient;
+
+                % add the ramp parameter to the ode parameter struct
+                odeparam.rampparam = rampparam;
+                
+                % ODE solver call
+                % OUTPUT: time T and magnetization M
+                [T,M] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 rampparam.Tramp],Minit,options);
+                
+                % normalized magnetization vector at end of switch-off ramp
+                MMn = M(end,:)./norm(M(end,:));
+                % "adiabatic quality" p of the switch-off ramp
+                % -> orientation of M with respect to z_unit
+                p(tt,pp) = dot(MMn(end,:),zunit)./norm(zunit);
+                % final orientation of M
+                Mfinal(tt,pp,1:3) = M(end,:);
+                
+            end
+            infostr2 = [' | theta=',num2str(theta(tt)),'°'];
+            disp([infostr1,infostr2]);
+        end
+        disp([infostr1,' ... finished.']);
+        
+        % save the local lookup table for this particular combination of
+        % ramp shape and ramp time
+        data{i1,i2}.Tramp = Tramp;
+        data{i1,i2}.ramp = ramp;
+        data{i1,i2}.PPfac = PPfac;
+        data{i1,i2}.theta = theta;
+        data{i1,i2}.odeparam = odeparam;
+        data{i1,i2}.M = Mfinal;
+        data{i1,i2}.p = p;        
+    end
+end
+
+% save lookup table
+if save_data
+    save('example4_lookup_table.mat','data');
+end
+
+% plot data
+if plot_data
+    [xx,yy] = meshgrid(theta,PPfac);
+    figure;
+    count = 0;
+    for i1 = 1:numel(lookup_ramps)
+        for i2 = 1:numel(lookup_Tramps)
+            count = count + 1;
+            p = data{i1,i2}.p;
+            subplot(numel(lookup_ramps),numel(lookup_Tramps),count);
+            pcolor(xx,yy,p');
+            shading flat;
+            set(gca,'XTick',linspace(0,180,5),'YScale','log',...
+                'YTick',logspace(-1,4,6),'FontSize',10);
+            xlabel('\theta [deg]');
+            ylabel('Bp [B0]');
+            title([lookup_ramps{i1},' | ',sprintf('%3.1f',lookup_Tramps(i2)*1e3),'ms']);
+        end
+    end
+end
+
+%------------- END OF CODE --------------
+
+%% License:
+% GNU GPLv3
+%
+% BLOCHUS
+% Copyright (C) 2019 Thomas Hiller
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see .
diff --git a/scripts/example4_ref.png b/scripts/example4_ref.png
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diff --git a/scripts/example5.m b/scripts/example5.m
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--- /dev/null
+++ b/scripts/example5.m
@@ -0,0 +1,236 @@
+% script: example5.m
+% This script demonstrates how to calculate lookup-tables for an adiabatic
+% half passage excitation pulse that can subsequently be used with MRSMatlab
+% to forward model MRS sounding curves.
+% Basically this script allows to create the data that is shown in Fig. 4b
+% of the paper:
+%   Grunewald, E., Grombacher, D. and Walsh, D., "Adiabatic pulses enhance
+%   surface nuclear magnetic resonance measurement and survey speed for
+%   groundwater investigations", Geophysics Vol. 81(4), WB85-WB96, 2016
+%   DOI: 10.1190/GEO2015-0527.1
+%
+% NOTE: In this simulation the "My" component has a switched sign compared
+% to Grunewald et al., 2016 due to the implementation of the reference phase
+% and therewith accounting for the sign of the Larmor frequency (see e.g.
+% Levitt, 2002). In practice, this has no effect on the result.
+%
+%   general settings:
+%       - magnetic field B0 is set to 50 µT
+%       - T1, T2 - relaxation is ignored
+%
+%   lookup table parameters for SWEEP1:
+%       - B1 ranges between 0.01µT and 100µT
+%       - frequency sweeps linearly from 2100 Hz to 2300 Hz, so from -200
+%         to 0 Hz
+%       - amplitude tuning with quality factor Q=10
+%
+% See also: BLOCHUS
+% Author: Thomas Hiller
+% email: thomas.hiller[at]leibniz-liag.de
+% License: GNU GPLv3 (at end)
+
+%------------- BEGIN CODE --------------
+
+% clear data
+clear variables; clc;
+
+% because this script takes approx. 75min, ask the user before continuing
+answer = questdlg({'This script needs about 75 min. to run.',...
+    'Do you want to continue?'},'Dessert Menu','Yes','No','Yes');
+% handle response
+switch answer
+    case 'Yes'
+        % nothing to do
+    case {'No',''}
+        return
+end
+
+% output switches
+save_data = true;
+plot_data = true;
+
+% --- LOOKUP TABLE SETTINGS -----------------------------------------------
+% global lookup table settings (change as you like):
+% B1 excitation amplitude [T]
+% in the Grunewald et al., 2016 paper, there are in total 5000 points which
+% would increase the calculation time to more than 6h!
+N = 1000;
+B1 = logspace(-8,-4,N);
+% pulse length [s]
+Ttau = 0.08;
+% -------------------------------------------------------------------------
+
+% basic settings
+zunit = [0 0 1]'; % z unit vector
+% ODE solver error tolerance
+tol = 1e-9;
+% ODE solver options
+options = odeset('RelTol',tol,'AbsTol',[tol tol tol]);
+
+% hydrogen proton
+nucleus = '1H';
+
+% parameter needed for the ODE solver
+% simulation type [string]
+odeparam.type = 'pulse';
+% equilibrium magnetization [A/m]
+odeparam.M0 = zunit;
+% relaxation time T1 [s]
+odeparam.T1 = 2;
+% relaxation time T2 [s]
+odeparam.T2 = 1;
+% gyromagnetic ratio [rad/s/T]
+odeparam.gamma = getGyroRatio(nucleus);
+% primary (Earth's) magnetic field B0 [T]
+odeparam.B0 = getB0(odeparam.gamma,2300*2*pi);
+
+% pulse settings for BLOCHUS
+% dummy time vector with sampling freq 50 kHz
+tt = 0:1/50000:Ttau; % [s]
+PulseType = 'AHP';
+
+% pulse type [string]
+fmod.PulseType = PulseType;
+% shape of the modulation function [string]
+fmod.shape = 'lin';
+% time vector [s]
+fmod.t = tt;
+% pulse start time [s]
+fmod.t0 = tt(1);
+% pulse end time [s]
+fmod.t1 = tt(end);
+% start frequency [Hz]
+fmod.v0 = -200;
+% end frequency [Hz]
+fmod.v1 = 0;
+% modulation parameter (MIDI)
+fmod.A = 1;
+% modulation parameter (MIDI)
+fmod.B = 0;
+
+% pulse type [string]
+Imod.PulseType = PulseType;
+% shape of the modulation function [string]
+Imod.shape = 'lin';
+% check if quality factor tuning is activated [0/1]
+Imod.useQ = 1;
+% quality factor
+Imod.Q = 10;
+% quality factor off-resonance frequency [Hz]
+Imod.Qdf = 0;
+% time vector [s]
+Imod.t = tt;
+% pulse start time [s]
+Imod.t0 = tt(1);
+% pulse end time [s]
+Imod.t1 = tt(end);
+% start current [A]
+Imod.v0 = 1;
+% end current [A]
+Imod.v1 = 1;
+% modulation parameter (MIDI)
+Imod.A = 1;
+% modulation parameter (MIDI)
+Imod.B = 0;
+
+% output data
+Mfinal = zeros(numel(B1),6);
+for i = numel(B1):-1:1
+    
+    % relaxation during pulse [0/1]
+    odeparam.RDP = 0;
+    % pulse length [s]
+    odeparam.Ttau = tt(end);
+    
+    % excitation pulse parameter
+    % pulse type [string]
+    pulseparam.PulseType = PulseType;
+    % gyromagnetic ratio [rad/s/T]
+    pulseparam.gamma = odeparam.gamma;
+    % Larmor frequency [rad/s]
+    pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
+    % pulse amplitude [T]
+    pulseparam.Amp = B1(i);
+    % pulse frequency modulation [struct]    
+    pulseparam.fmod = fmod;
+    % pulse current modulation [struct]
+    pulseparam.Imod = Imod;
+    % auxiliary pulse phase [rad]
+    pulseparam.phi = 0;
+    % pulse axis [string]
+    pulseparam.PulseAxis = '+y';
+    % pulse polarization [string]
+    pulseparam.PulsePolarization = 'circular';
+    
+    % save pulse parameter settings
+    odeparam.pulseparam = pulseparam;
+    
+    % initial magnetization pointing towards B0 (+z) [A/m]
+    Minit = zunit;  
+    
+    % ODE solver call
+    % OUTPUT: time T and magnetization M
+    [T,M] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 odeparam.Ttau],Minit,options);
+    
+    % in order to get M in the rotating frame of reference, get the pulse
+    % phase theta for all simulation time steps
+    pulseparam.fmod.t = T;
+    pulseparam.Imod.t = T;
+    pulseparam.t = T;
+    [Bpulse,~,~,theta]= getPulseTimeSeries(pulseparam);
+    
+    % get M(T) in rotating frame of reference 
+    Mrot = getMrot(M,theta);
+    
+    % final magnetization in lab and rot fame
+    Mfinal(i,1:6) = [M(end,:) Mrot(end,:)];
+    
+    % show status
+    disp([num2str(i),' / ',num2str(numel(B1)),' done']);    
+end
+
+% save lookup table
+if save_data
+    data.odeparam = odeparam;
+    data.B1 = B1;
+    data.Mfinal = Mfinal;
+    save('example5_lookup_table.mat','data');
+end
+
+% plot data
+if plot_data
+    figure;
+    subplot(121);
+    semilogy(Mfinal(:,4),B1.*1e6);
+    xlim([-1 1]);
+    xlabel('Mx');
+    ylabel('B1 [µT]');
+    grid on;
+    
+    subplot(122);
+    semilogy(Mfinal(:,5),B1.*1e6);
+    xlim([-1 1]);
+    xlabel('My');
+    grid on;
+end
+
+%------------- END OF CODE --------------
+
+%% License:
+% GNU GPLv3
+%
+% BLOCHUS
+% Copyright (C) 2019 Thomas Hiller
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see .
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