From e74ecb40d4b07603e355a27a4ea920b063abdf23 Mon Sep 17 00:00:00 2001 From: Thomas Hiller Date: Sat, 16 May 2020 23:00:03 +0200 Subject: [PATCH] 1. bug fix: in `onPushRun.m` the adiabatic quality p was incorrectly calculated when the total simulation time exceeded the actual switch-off ramp time 2. bug fix: both axes for the pulse frequency and current modulation are now show correctly when exporting the *Current View* figure from the menu 3. new feature: an animation of the latest result can be played for all parameter combinations (e.g. *Pulse + Relaxation* or *Pre-polarization switch-off + Pulse + Relaxation*, etc.) 4. typo fixing within comments and `README.md` --- BLOCHUS/BLOCHUS.m | 4 +- BLOCHUS/BLOCHUS_createPanelBasic.m | 2 +- BLOCHUS/BLOCHUS_createPanelControl.m | 2 +- CHANGELOG.md | 13 + README.md | 4 +- callbacks/checkbox/onCheckPrePolPulse.m | 2 + callbacks/checkbox/onCheckPulseQ.m | 2 +- callbacks/edits/onEditValue.m | 82 +- callbacks/menus/onMenuViewFigure.m | 92 +- callbacks/popup/onPopupPulseAxis.m | 4 +- callbacks/popup/onPopupPulseDFmode.m | 2 +- callbacks/popup/onPopupPulseImode.m | 2 +- callbacks/popup/onPopupPulsePolarization.m | 2 +- callbacks/popup/onPopupPulseType.m | 2 +- callbacks/push/onPushAnimate.m | 1051 +++++++++++---- callbacks/push/onPushRun.m | 38 +- doc/blochus/BLOCHUS/BLOCHUS.html | 4 +- .../BLOCHUS/BLOCHUS_createPanelBasic.html | 2 +- .../BLOCHUS/BLOCHUS_createPanelControl.html | 4 +- .../checkbox/onCheckPrePolPulse.html | 58 +- .../callbacks/checkbox/onCheckPulseQ.html | 4 +- doc/blochus/callbacks/edits/onEditValue.html | 726 ++++++----- .../callbacks/menus/onMenuViewFigure.html | 358 +++--- .../callbacks/popup/onPopupPulseAxis.html | 8 +- .../callbacks/popup/onPopupPulseDFmode.html | 4 +- .../callbacks/popup/onPopupPulseImode.html | 4 +- .../popup/onPopupPulsePolarization.html | 4 +- .../callbacks/popup/onPopupPulseType.html | 4 +- doc/blochus/callbacks/push/menu.html | 2 +- doc/blochus/callbacks/push/onPushAnimate.html | 1129 ++++++++++++---- doc/blochus/callbacks/push/onPushRun.html | 1138 +++++++++-------- doc/blochus/functions/blochsim/getFFT.html | 2 +- doc/blochus/functions/blochsim/getOmega0.html | 2 +- .../functions/interface/clearSingleAxis.html | 2 +- .../interface/getPulseParameters.html | 70 +- .../interface/getRampParameters.html | 50 +- doc/blochus/functions/interface/menu.html | 2 +- .../functions/interface/plotBSphere.html | 2 +- .../{plotBpulse.html => plotPulse.html} | 93 +- doc/blochus/functions/interface/plotRamp.html | 2 +- .../functions/interface/plotResults.html | 461 +++---- functions/interface/getPulseParameters.m | 8 + functions/interface/getRampParameters.m | 2 + .../interface/{plotBpulse.m => plotPulse.m} | 33 +- functions/interface/plotResults.m | 41 +- 45 files changed, 3462 insertions(+), 2061 deletions(-) create mode 100644 CHANGELOG.md rename doc/blochus/functions/interface/{plotBpulse.html => plotPulse.html} (69%) rename functions/interface/{plotBpulse.m => plotPulse.m} (78%) diff --git a/BLOCHUS/BLOCHUS.m b/BLOCHUS/BLOCHUS.m index 8dac6e1..4aee16d 100644 --- a/BLOCHUS/BLOCHUS.m +++ b/BLOCHUS/BLOCHUS.m @@ -33,8 +33,8 @@ %------------- BEGIN CODE -------------- %% GUI 'header' info and default GUI settings -myui.version = '0.1.0'; -myui.date = '15.05.2020'; +myui.version = '0.1.1'; +myui.date = '16.05.2020'; myui.author = 'Thomas Hiller'; myui.email = 'thomas.hiller[at]leibniz-liag.de'; diff --git a/BLOCHUS/BLOCHUS_createPanelBasic.m b/BLOCHUS/BLOCHUS_createPanelBasic.m index 08994be..778e17b 100644 --- a/BLOCHUS/BLOCHUS_createPanelBasic.m +++ b/BLOCHUS/BLOCHUS_createPanelBasic.m @@ -83,7 +83,7 @@ 'FontSize',myui.fontsize,... 'UserData',struct('Tooltipstr',tstr,'defaults',data.init.B0),... 'Callback',@onEditValue); -tstr = 'Omega0 frequency in [Hz].
'; +tstr = ['Larmor frequency ',char(hex2dec('3C9')),'0 in [Hz].
']; gui.edit_handles.Omega0 = uicontrol('Style','Edit',... 'Parent',setB0,... 'String',sprintf('%7.2f',data.init.Omega0(1)),... diff --git a/BLOCHUS/BLOCHUS_createPanelControl.m b/BLOCHUS/BLOCHUS_createPanelControl.m index 746b224..48fbca3 100644 --- a/BLOCHUS/BLOCHUS_createPanelControl.m +++ b/BLOCHUS/BLOCHUS_createPanelControl.m @@ -45,7 +45,7 @@ 'UserData',struct('Tooltipstr',tstr),... 'Callback',@onPushRun); -tstr = 'Show animation of the last result.'; +tstr = 'Show animation of the latest result.'; gui.push_handles.Animate = uicontrol('Style','pushbutton',... 'Parent',gui.panels.Control.HBox,... 'String','ANIMATE',... diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..f930f9b --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,13 @@ +#### Changelog + +##### Version v.0.1.1 + +1. bug fix: in `onPushRun.m` the adiabatic quality p was incorrectly calculated when the total simulation time exceeded the actual switch-off ramp time +2. bug fix: both axes for the pulse frequency and current modulation are now show correctly when exporting the *Current View* figure from the menu +3. new feature: an animation of the latest result can be played for all parameter combinations (e.g. *Pulse + Relaxation* or *Pre-polarization switch-off + Pulse + Relaxation*, etc.) +4. typo fixing within comments and `README.md` + + +##### Version v.0.1.0 + +Initial Version diff --git a/README.md b/README.md index cbdf39f..8e3a367 100644 --- a/README.md +++ b/README.md @@ -11,9 +11,9 @@ **BLOCHUS** is a set of MATLABTM tools, that allow some basic simulations of (S)NMR spin dynamics based on the Bloch equations. The Bloch equations are solved in the laboratory frame of reference with MATLABs built-in `ode45` solver. Because it was developed within the scope of a near surface SNMR project, its main features are the simulation of (1) pre-polarization switch-off ramps and (2) excitation pulses. The main front-end to the underlying simulation tools is a graphical user interface (GUI) that allows playing around with the different features and helps to understand the basic concepts of (S)NMR spin dynamics. #### Basic features: -1. Choose between different protons (e.g. *Hydrogen*, *Helium*, *Flourine*, etc.) +1. Choose between different protons (e.g. *Hydrogen*, *Helium*, *Fluorine*, etc.) 2. Choose between different pre-polarization switch-off ramp shapes (e.g. *exponential*, *linear*, *half cosine*, etc.) with arbitrary ramp time -3. Choose between different excitation pulses (*pi/2*, *pi*, *adiabatic half passage*, etc.) with arbitrary off-resonant frequency, or in case of the adiabatic pulses, arbitrary frequency and current modulation. +3. Choose between different excitation pulses (*pi/2*, *pi*, *adiabatic half passage*, etc.) with arbitrary off-resonance frequency, or in case of the adiabatic pulses, arbitrary frequency and current modulation. - - - diff --git a/callbacks/checkbox/onCheckPrePolPulse.m b/callbacks/checkbox/onCheckPrePolPulse.m index 0463f2d..bee76f5 100644 --- a/callbacks/checkbox/onCheckPrePolPulse.m +++ b/callbacks/checkbox/onCheckPrePolPulse.m @@ -262,6 +262,8 @@ function onCheckPrePolPulse(src,~) data = getappdata(fig,'data'); end + % because the settings changed, deactivate the "Animate" button + set(gui.push_handles.Animate,'Enable','off'); % update all data inside the GUI setappdata(fig,'data',data); % update status bar diff --git a/callbacks/checkbox/onCheckPulseQ.m b/callbacks/checkbox/onCheckPulseQ.m index 9840913..0590785 100644 --- a/callbacks/checkbox/onCheckPulseQ.m +++ b/callbacks/checkbox/onCheckPulseQ.m @@ -53,7 +53,7 @@ function onCheckPulseQ(src,~) % get GUI data data = getappdata(fig,'data'); % plot pulse - plotBpulse(gui.figh); + plotPulse(gui.figh); else warndlg({'onCheckPulseQ:','There is no figure with the BLOCHUS Tag open.'},... diff --git a/callbacks/edits/onEditValue.m b/callbacks/edits/onEditValue.m index 73b2b25..35d06ef 100644 --- a/callbacks/edits/onEditValue.m +++ b/callbacks/edits/onEditValue.m @@ -19,7 +19,7 @@ function onEditValue(src,~) % getOmega0 % getPulseParameters % getRampParameters -% plotBpulse +% plotPulse % plotRamp % % Subfunctions: @@ -50,37 +50,20 @@ function onEditValue(src,~) % get the user data of the field ud = get(src,'UserData'); - if isstruct(ud) % for new fields - % get the default values [default min max] - defaults = ud.defaults; - - % check if the value is numeric - % if not reset to defaults stored in user data - if isnan(val) - set(src,'String',num2str(defaults(1))); - val = str2double(get(src,'String')); - end - % check if the value is out of bounds - % if yes reset to default - if val < defaults(2) || val > defaults(3) - set(src,'String',num2str(defaults(1))); - val = str2double(get(src,'String')); %#ok<*NASGU> - end - - else % old style (Needs to be removed after the refactoring) - % check if the value is numeric - % if not reset to defaults stored in user data - if isnan(val) - set(src,'String',num2str(ud(3))); - val = str2double(get(src,'String')); - end - % check if the value is out of bounds - % if yes reset to default - if val < ud(1) || val > ud(2) - set(src,'String',num2str(ud(3))); - val = str2double(get(src,'String')); %#ok<*NASGU> - end - disp(['there is still an old style edit field:',tag]) + % get the default values [default min max] + defaults = ud.defaults; + + % check if the value is numeric + % if not reset to defaults stored in user data + if isnan(val) + set(src,'String',num2str(defaults(1))); + val = str2double(get(src,'String')); + end + % check if the value is out of bounds + % if yes reset to default + if val < defaults(2) || val > defaults(3) + set(src,'String',num2str(defaults(1))); + val = str2double(get(src,'String')); %#ok<*NASGU> end % get the data field to update from the field tag @@ -175,6 +158,7 @@ function onEditValue(src,~) % ------------------------------------------------------------- % --- PRE-POLARIZATION ---------------------------------------- % ------------------------------------------------------------- + case {'prepol_Factor','prepol_SwitchFactor'} % check if the ramp type is "melton1995", if yes update the % switch-off time to maintain the same switch-off rate @@ -231,6 +215,7 @@ function onEditValue(src,~) % ------------------------------------------------------------- % --- PULSE --------------------------------------------------- % ------------------------------------------------------------- + case 'pulse_B1Factor' % if the pulse amplitude changes some settings have to be % adjusted, depending on the chosen pulse type @@ -239,10 +224,12 @@ function onEditValue(src,~) switch data.pulse.Type case 'pi_half' % in case of "pi_half" the pulse length gets updated - data.pulse.Ttau = abs(1e3*(pi/2/(data.basic.gamma*data.basic.B0*data.pulse.B1Factor))); + data.pulse.Ttau = abs(1e3*(pi/2/(data.basic.gamma*... + data.basic.B0*data.pulse.B1Factor))); case 'pi' % in case of "pi" the pulse length gets updated - data.pulse.Ttau = abs(1e3*(pi/(data.basic.gamma*data.basic.B0*data.pulse.B1Factor))); + data.pulse.Ttau = abs(1e3*(pi/(data.basic.gamma*... + data.basic.B0*data.pulse.B1Factor))); end set(gui.edit_handles.PulseTtau,'String',num2str(data.pulse.Ttau)); % in case of pure "Pulse" update the total simulation time @@ -257,13 +244,13 @@ function onEditValue(src,~) % update pulse settings getPulseParameters(fig); data = getappdata(fig,'data'); - plotBpulse(fig); + plotPulse(fig); otherwise % update pulse settings getPulseParameters(fig); data = getappdata(fig,'data'); - plotBpulse(fig); + plotPulse(fig); end case 'pulse_Ttau' @@ -274,10 +261,12 @@ function onEditValue(src,~) switch data.pulse.Type case 'pi_half' % in case of "pi_half" the pulse amplitude gets updated - data.pulse.B1Factor = abs(1e3*(pi/2/(data.basic.gamma*data.basic.B0*data.pulse.Ttau))); + data.pulse.B1Factor = abs(1e3*(pi/2/(data.basic.gamma*... + data.basic.B0*data.pulse.Ttau))); case 'pi' % in case of "pi" the pulse amplitude gets updated - data.pulse.B1Factor = abs(1e3*(pi/(data.basic.gamma*data.basic.B0*data.pulse.Ttau))); + data.pulse.B1Factor = abs(1e3*(pi/(data.basic.gamma*... + data.basic.B0*data.pulse.Ttau))); end set(gui.edit_handles.PulseB1Factor,'String',num2str(data.pulse.B1Factor)); % in case of pure "Pulse" update the total simulation time @@ -292,7 +281,7 @@ function onEditValue(src,~) % update pulse settings getPulseParameters(fig); data = getappdata(fig,'data'); - plotBpulse(fig); + plotPulse(fig); case 'MIDI_OR' % in case of "MIDI_OR" the PulseTtau-field holds the @@ -301,7 +290,8 @@ function onEditValue(src,~) % update pulse length data.pulse.Ttau = abs(data.pulse.MIDINP/data.basic.Omega0)*1e3; % update pulse amplitude to pi/2 value - data.pulse.B1Factor = abs(1e3*(pi/2/(data.basic.gamma*data.basic.B0*data.pulse.Ttau))); + data.pulse.B1Factor = abs(1e3*(pi/2/(data.basic.gamma*... + data.basic.B0*data.pulse.Ttau))); set(gui.edit_handles.PulseB1Factor,'String',num2str(data.pulse.B1Factor)); % in case of pure "Pulse" update the total simulation time switch data.basic.type @@ -315,7 +305,7 @@ function onEditValue(src,~) % update pulse settings getPulseParameters(fig); data = getappdata(fig,'data'); - plotBpulse(fig); + plotPulse(fig); case 'MIDI_AP' % in case of "MIDI_AP" the PulseTtau-field holds the @@ -339,7 +329,7 @@ function onEditValue(src,~) end setappdata(fig,'data',data); % update pulse plot - plotBpulse(fig); + plotPulse(fig); otherwise % for all other pulse types ("free" & "AHP") @@ -356,7 +346,7 @@ function onEditValue(src,~) % update pulse settings getPulseParameters(fig); data = getappdata(fig,'data'); - plotBpulse(fig); + plotPulse(fig); end otherwise @@ -366,10 +356,12 @@ function onEditValue(src,~) setappdata(fig,'data',data); getPulseParameters(fig); data = getappdata(fig,'data'); - plotBpulse(fig); + plotPulse(fig); otherwise - % nothing to do for all other fields e.g. T1, T2, Tsim + % because the pulse data changed, deactivate the + % "Animate" button + set(gui.push_handles.Animate,'Enable','off'); end end diff --git a/callbacks/menus/onMenuViewFigure.m b/callbacks/menus/onMenuViewFigure.m index 2635c61..0d7fab3 100644 --- a/callbacks/menus/onMenuViewFigure.m +++ b/callbacks/menus/onMenuViewFigure.m @@ -42,14 +42,54 @@ function onMenuViewFigure(src,~) % opening the export figure expfig = figure; - % create the axes layout on the export figure + % due to the two axes on the pulse modulation panel, we need to know + % before creating the new figure if this panel is active + isdual = false; + if get(gui.panels.Plot.Pulse,'Selection') == 1 + isdual = true; + end + + % create the axes layout on the export figure and get the axes + % positions switch get(src,'Label') - case {'Current View','Magnetization','Switch-off Ramp'} + case 'Current View' + % we copy all visible axes in a 2x2 grid + ax1 = subplot(2,2,1,'Parent',expfig); + ax2 = subplot(2,2,2,'Parent',expfig); + ax3 = subplot(2,2,3,'Parent',expfig); + pos1 = get(ax1,'Position'); + pos2 = get(ax2,'Position'); + pos3 = get(ax3,'Position'); + delete(ax1); + delete(ax2); + delete(ax3); + if isdual + ax4a = subplot(2,4,7,'Parent',expfig); + ax4b = subplot(2,4,8,'Parent',expfig); + pos4a = get(ax4a,'Position'); + pos4b = get(ax4b,'Position'); + delete(ax4a); + delete(ax4b); + else + ax4 = subplot(2,2,4,'Parent',expfig); + pos4 = get(ax4,'Position'); + delete(ax4); + end + + case {'Magnetization','Switch-off Ramp'} % we copy all visible axes in a 2x2 grid ax1 = subplot(2,2,1,'Parent',expfig); ax2 = subplot(2,2,2,'Parent',expfig); ax3 = subplot(2,2,3,'Parent',expfig); ax4 = subplot(2,2,4,'Parent',expfig); + pos1 = get(ax1,'Position'); + pos2 = get(ax2,'Position'); + pos3 = get(ax3,'Position'); + pos4 = get(ax4,'Position'); + delete(ax1); + delete(ax2); + delete(ax3); + delete(ax4); case 'Pulse' % we copy pulse parameter in a 3x2 grid @@ -57,14 +97,15 @@ function onMenuViewFigure(src,~) ax2 = subplot(3,2,2,'Parent',expfig); ax3 = subplot(3,2,[3 4],'Parent',expfig); ax4 = subplot(3,2,[5 6],'Parent',expfig); + pos1 = get(ax1,'Position'); + pos2 = get(ax2,'Position'); + pos3 = get(ax3,'Position'); + pos4 = get(ax4,'Position'); + delete(ax1); + delete(ax2); + delete(ax3); + delete(ax4); end - % get the default positions - pos1 = get(ax1,'Position'); - pos2 = get(ax2,'Position'); - pos3 = get(ax3,'Position'); - pos4 = get(ax4,'Position'); - % delete axes - delete(ax1);delete(ax2);delete(ax3);delete(ax4); % copy the GUI axes to the export figure switch get(src,'Label') @@ -99,7 +140,8 @@ function onMenuViewFigure(src,~) end switch pul case 1 - ax4 = copyobj(gui.axes_handles.PulseSetupF,expfig); + ax4a = copyobj(gui.axes_handles.PulseSetupF,expfig); + ax4b = copyobj(gui.axes_handles.PulseSetupI,expfig); case 2 ax4 = copyobj(gui.axes_handles.PulseB,expfig); case 3 @@ -132,11 +174,26 @@ function onMenuViewFigure(src,~) set(expfig,'Name','BLOCHUS: Pulse'); end + % adjust the axes positions - set(ax1,'Position',pos1); - set(ax2,'Position',pos2); - set(ax3,'Position',pos3); - set(ax4,'Position',pos4); + switch get(src,'Label') + case 'Current View' + set(ax1,'Position',pos1); + set(ax2,'Position',pos2); + set(ax3,'Position',pos3); + if isdual + set(ax4a,'Position',pos4a); + set(ax4b,'Position',pos4b); + else + set(ax4,'Position',pos4); + end + + otherwise + set(ax1,'Position',pos1); + set(ax2,'Position',pos2); + set(ax3,'Position',pos3); + set(ax4,'Position',pos4); + end % adjust the position of the export figure set(expfig,'Position',[posf(1)+300 posf(2) (posf(3)-300)*0.8 posf(4)*0.8]); @@ -146,7 +203,12 @@ function onMenuViewFigure(src,~) case 'Current View' lgh1 = legend(ax1,'show'); lgh3 = legend(ax3,'show'); - lgh4 = legend(ax4,'show'); + if isdual + lgh4a = legend(ax4a,'show'); + lgh4b = legend(ax4b,'show'); + else + lgh4 = legend(ax4,'show'); + end case 'Magnetization' lgh1 = legend(ax1,'show'); diff --git a/callbacks/popup/onPopupPulseAxis.m b/callbacks/popup/onPopupPulseAxis.m index 2dfaed7..e8ec384 100644 --- a/callbacks/popup/onPopupPulseAxis.m +++ b/callbacks/popup/onPopupPulseAxis.m @@ -15,7 +15,7 @@ function onPopupPulseAxis(src,~) % % Other m-files required: % getPulseParameters -% plotBpulse +% plotPulse % % Subfunctions: % none @@ -60,7 +60,7 @@ function onPopupPulseAxis(src,~) % get GUI data data = getappdata(fig,'data'); % plot pulse - plotBpulse(gui.figh); + plotPulse(gui.figh); else warndlg({'onPopupPulseAxis:','There is no figure with the BLOCHUS Tag open.'},... diff --git a/callbacks/popup/onPopupPulseDFmode.m b/callbacks/popup/onPopupPulseDFmode.m index 556e929..14d1ef1 100644 --- a/callbacks/popup/onPopupPulseDFmode.m +++ b/callbacks/popup/onPopupPulseDFmode.m @@ -83,7 +83,7 @@ function onPopupPulseDFmode(src,~) % update GUI data setappdata(fig,'data',data); % plot pulse - plotBpulse(gui.figh); + plotPulse(gui.figh); else warndlg({'onPopupPulseDFmode:','There is no figure with the BLOCHUS Tag open.'},... diff --git a/callbacks/popup/onPopupPulseImode.m b/callbacks/popup/onPopupPulseImode.m index a44732d..5806b9c 100644 --- a/callbacks/popup/onPopupPulseImode.m +++ b/callbacks/popup/onPopupPulseImode.m @@ -85,7 +85,7 @@ function onPopupPulseImode(src,~) % update GUI data setappdata(fig,'data',data); % plot pulse - plotBpulse(gui.figh); + plotPulse(gui.figh); else warndlg({'onPopupPulseDFmode:','There is no figure with the BLOCHUS Tag open.'},... diff --git a/callbacks/popup/onPopupPulsePolarization.m b/callbacks/popup/onPopupPulsePolarization.m index d531903..2b8ec8d 100644 --- a/callbacks/popup/onPopupPulsePolarization.m +++ b/callbacks/popup/onPopupPulsePolarization.m @@ -58,7 +58,7 @@ function onPopupPulsePolarization(src,~) % update GUI data setappdata(fig,'data',data); % plot pulse - plotBpulse(gui.figh); + plotPulse(gui.figh); else warndlg({'onPopupPulsePolarization:','There is no figure with the BLOCHUS Tag open.'},... diff --git a/callbacks/popup/onPopupPulseType.m b/callbacks/popup/onPopupPulseType.m index a73468d..7b26288 100644 --- a/callbacks/popup/onPopupPulseType.m +++ b/callbacks/popup/onPopupPulseType.m @@ -226,7 +226,7 @@ function onPopupPulseType(src,~) % update GUI data setappdata(fig,'data',data); % plot pulse - plotBpulse(fig); + plotPulse(fig); % update status bar updateStatusInformation(fig); else diff --git a/callbacks/push/onPushAnimate.m b/callbacks/push/onPushAnimate.m index 80bf0d4..271eaf5 100644 --- a/callbacks/push/onPushAnimate.m +++ b/callbacks/push/onPushAnimate.m @@ -1,264 +1,829 @@ function onPushAnimate(src,~) -fig = findobj('Tag','BLOCHUS'); -gui = getappdata(fig,'gui'); -data = getappdata(fig,'data'); +%onPushAnimate animates the results of the latest simulation +% +% Syntax: +% onPushAnimate(src) +% +% Inputs: +% src - handle of the calling object +% +% Outputs: +% none +% +% Example: +% onPushAnimate(src) +% +% Other m-files required: +% clearSingleAxis +% plotBSphere +% plotPulse +% plotRamp +% plotResults +% +% Subfunctions: +% none +% +% MAT-files required: +% none +% +% See also: BLOCHUS +% Author: Thomas Hiller +% email: thomas.hiller[at]leibniz-liag.de +% License: GNU GPLv3 (at end) -% change the pushbutton color to indicate that an animation is running -set(src,'BackGroundColor','r'); -pause(0.01); +%------------- BEGIN CODE -------------- -NoFrames = 100; -FPS = 24; +% get GUI handle +fig = ancestor(src,'figure','toplevel'); -newblue = [0 0.4470 0.7410]; -neworange = [0.8500 0.3250 0.0980]; - -switch data.basic.type +if ~isempty(fig) && strcmp(get(fig,'Tag'),'BLOCHUS') + % get GUI data + gui = getappdata(fig,'gui'); + data = getappdata(fig,'data'); + myui = gui.myui; - case 'std' - set(gui.text_handles.Status,'String','Animation running ...'); - pause(0.01); - Mamp = zeros(numel(data.TT),1); - for i=1:numel(data.TT) - Mamp(i,1) = norm(data.MM(i,:)); % amplitude of M - end - - dt = data.TT(end)/NoFrames; - time = 0:dt:data.TT(end); - - axes(gui.axes_handles.MagL); - cla(gui.axes_handles.MagL); - h1 = animatedline('Color','r','LineWidth',2,'Parent',gui.axXYZL); - h2 = animatedline('Color','g','LineWidth',2,'Parent',gui.axXYZL); - h3 = animatedline('Color','b','LineWidth',2,'Parent',gui.axXYZL); - h4 = animatedline('Color','k','LineWidth',2,'LineStyle','--','Parent',gui.axXYZL); - - axes(gui.axes_handles.MagR); - cla(gui.axes_handles.MagR); - h7 = animatedline('Color','r','LineWidth',2,'Parent',gui.axXYZR); - h8 = animatedline('Color','g','LineWidth',2,'Parent',gui.axXYZR); - h9 = animatedline('Color','b','LineWidth',2,'Parent',gui.axXYZR); - h10 = animatedline('Color','k','LineWidth',2,'LineStyle','--','Parent',gui.axXYZR); - - axes(gui.axSphereL); - cla(gui.axSphereL); - hold(gui.axSphereL,'on'); - plotBSphere(18,18,gui.axSphereL); - h5 = animatedline('Color',myui.color.basic,'LineWidth',2,'Parent',gui.axSphereL); - - axes(gui.axSphereR); - cla(gui.axSphereR); - hold(gui.axSphereR,'on'); - plotBSphere(18,18,gui.axSphereR); - h6 = animatedline('Color',myui.color.basic,'LineWidth',2,'Parent',gui.axSphereR); - - for nf = 1:NoFrames-1 - - x1 = data.TT(data.TT>=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=t(nf) & T=t(nf) & T1=t(nf) & T2=time(nf) & data.TT=time(nf) & data.TT=time(nf) & data.TT=t(nf) & T1=t(nf) & T2=time(nf) & data.TT=time(nf) & data.results.prepol.t./1e3=time(nf) & data.results.prepol.t./1e3=time(nf) & data.results.prepol.t./1e3= time(nf) - x2 = data.results.prepol.t(data.results.prepol.t./1e3>=time(nf) & data.results.prepol.t./1e3=time(nf) & tt./1e3=t(nf) & T1t(nf) & T2<=t(nf+1); % t2? + yBx = Beffn(indt2,1); + yBy = Beffn(indt2,2); + yBz = Beffn(indt2,3); + yBramp = Bval(indt2,1); + + % add the M data to the sphere (prepol color) + addpoints(h3dMa,yMxx,yMyy,yMzz); + % add the B-field trace to the sphere + addpoints(h3dB,yBx,yBy,yBz); + elseif t(nf)>Tramp && t(nf) <= Tramp+Twait + % add the M data to the sphere (wait color) + addpoints(h3dMb,yMxx,yMyy,yMzz); + elseif t(nf)>Tramp+Twait && t(nf) <= Tsim-Trelax + % add the M data to the sphere (pulse color) + addpoints(h3dMc,yMxx,yMyy,yMzz); + elseif t(nf) > Tsim-Trelax + % after the pulse is over + % add the M data to the sphere (basic color) + addpoints(h3dMd,yMxx,yMyy,yMzz); + end + % sphere axis settings + view(ax2,Mview); + set(ax2,'XLim',[-1.05 1.05],'YLim',[-1.05 1.05],'ZLim',[-1.05 1.05]) + set(ax2,'Color','w','XColor','none','YColor','none','ZColor','none'); + axis(ax2,'equal'); + axis(ax2,'tight'); - y10 = y10a(data.results.prepol.t./1e3>=time(nf) & data.results.prepol.t./1e3=time(nf) & data.results.prepol.t./1e3=Tramp+Twait && t(nf) < Tsim-Trelax + indt3 = T3+Tramp+Twait>=t(nf) & T3+Tramp+Twait=time(nf) & tt./1e3=time(nf) & tt./1e3. diff --git a/callbacks/push/onPushRun.m b/callbacks/push/onPushRun.m index 889fdf9..c66f4f6 100644 --- a/callbacks/push/onPushRun.m +++ b/callbacks/push/onPushRun.m @@ -45,6 +45,8 @@ function onPushRun(src,~) % change the pushbutton color to indicate that a calculation is running set(src,'BackGroundColor','r'); + % reset the color of the animate button + set(gui.push_handles.Animate,'BackGroundColor',[.94 .94 .94]); % basic parameter that are always needed % z unit vector @@ -151,10 +153,13 @@ function onPushRun(src,~) [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options); % normalized magnetization vector at end of switch-off ramp - MMn = MM(end,:)./norm(MM(end,:)); + % because the simulation can be longer than the ramp, find the + % last point of the ramp to calculate the adiabatic quality p + indt = find(TT<=rampparam.Tramp,1,'last'); + MMn = MM(indt,:)./norm(MM(indt,:)); % "adiabatic quality" p of the switch-off ramp - % -> orientation of M with respect to z_unit - p = dot(MMn(end,:),zunit)./norm(zunit); + % -> orientation of M with respect to z_unit + p = dot(MMn,zunit)./norm(zunit); % save data data.results.basic.T = TT; @@ -260,9 +265,9 @@ function onPushRun(src,~) theta(indT) = getOmega0(odeparam.gamma,odeparam.B0).*TT(indT); % rotate M into rotating frame of reference Mrot = getMrot(MM,theta,dphi); - % get FFTof M in the laboratory frame of reference + % get FFT of M in the laboratory frame of reference [Xm,fmx] = getFFT(TT,MM(:,1:2)); - % get FFT for the pulse + % get FFT of the pulse [Xb,fbx] = getFFT(TT(TT<=Ttau),Bpulse(TT<=Ttau,1:2)); % update Info field @@ -271,9 +276,9 @@ function onPushRun(src,~) else % rotate M into rotating frame of reference Mrot = getMrot(MM,theta); - % get FFTof M in the laboratory frame of reference + % get FFT of M in the laboratory frame of reference [Xm,fmx] = getFFT(TT,MM(:,1:2)); - % get FFT for the pulse + % get FFT of the pulse [Xb,fbx] = getFFT(TT,Bpulse(:,1:2)); % update Info field @@ -292,6 +297,12 @@ function onPushRun(src,~) % this is basically the combination of all of the above % simulation types + % --- 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" + % ------------------------------------------------------------- % these times we will later on, so init them already here % total simulation time [s] @@ -511,7 +522,7 @@ function onPushRun(src,~) % and account for the phase from the wait time before the % pulse MM3rot = getMrot(MM,theta,dphi+phiWait); - % get FFT pulse B-field + % get FFT of the pulse [Xb,fbx] = getFFT(TT(TT<=Ttau),Bpulse(TT<=Ttau,1:2)); % update Info field @@ -523,7 +534,7 @@ function onPushRun(src,~) % and account for the phase from the wait time before the % pulse MM3rot = getMrot(MM,theta,phiWait); - % get FFT pulse B-field + % get FFT of the pulse [Xb,fbx] = getFFT(TT,Bpulse(:,1:2)); % update Info field @@ -546,6 +557,13 @@ function onPushRun(src,~) 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" + % MM1 is lab-frame data! + % ------------------------------------------------------------- MMrot = [MM1;MM2rot;MM3rot]; % remove possible duplicate points @@ -608,4 +626,4 @@ function onPushRun(src,~) % 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 . \ No newline at end of file +% along with this program. If not, see . diff --git a/doc/blochus/BLOCHUS/BLOCHUS.html b/doc/blochus/BLOCHUS/BLOCHUS.html index 0a6e019..cc1f0b7 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 = '0.1.0'; -0037 myui.date = '15.05.2020'; +0036 myui.version = '0.1.1'; +0037 myui.date = '16.05.2020'; 0038 myui.author = 'Thomas Hiller'; 0039 myui.email = 'thomas.hiller[at]leibniz-liag.de'; 0040 diff --git a/doc/blochus/BLOCHUS/BLOCHUS_createPanelBasic.html b/doc/blochus/BLOCHUS/BLOCHUS_createPanelBasic.html index 35a3501..8bdfb8c 100644 --- a/doc/blochus/BLOCHUS/BLOCHUS_createPanelBasic.html +++ b/doc/blochus/BLOCHUS/BLOCHUS_createPanelBasic.html @@ -155,7 +155,7 @@

SOURCE CODE ^'FontSize',myui.fontsize,... 0084 'UserData',struct('Tooltipstr',tstr,'defaults',data.init.B0),... 0085 'Callback',@onEditValue); -0086 tstr = '<HTML><b>Omega</b><sub>0</sub> frequency in [Hz].<br>'; +0086 tstr = ['<HTML>Larmor frequency <b>',char(hex2dec('3C9')),'</b><sub>0</sub> in [Hz].<br>']; 0087 gui.edit_handles.Omega0 = uicontrol('Style','Edit',... 0088 'Parent',setB0,... 0089 'String',sprintf('%7.2f',data.init.Omega0(1)),... diff --git a/doc/blochus/BLOCHUS/BLOCHUS_createPanelControl.html b/doc/blochus/BLOCHUS/BLOCHUS_createPanelControl.html index 198806a..ed0698c 100644 --- a/doc/blochus/BLOCHUS/BLOCHUS_createPanelControl.html +++ b/doc/blochus/BLOCHUS/BLOCHUS_createPanelControl.html @@ -60,7 +60,7 @@

DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

This function calls: +
  • onPushAnimate animates the results of the latest simulation
  • onPushGrid resets the axes grid to equal size
  • onPushRun starts the calculation
    • This function is called by: @@ -116,7 +116,7 @@

    SOURCE CODE ^'UserData',struct('Tooltipstr',tstr),... 0046 'Callback',@onPushRun); 0047 -0048 tstr = 'Show animation of the last result.'; +0048 tstr = 'Show animation of the latest result.'; 0049 gui.push_handles.Animate = uicontrol('Style','pushbutton',... 0050 'Parent',gui.panels.Control.HBox,... 0051 'String','ANIMATE',... diff --git a/doc/blochus/callbacks/checkbox/onCheckPrePolPulse.html b/doc/blochus/callbacks/checkbox/onCheckPrePolPulse.html index cea12a6..dbc219c 100644 --- a/doc/blochus/callbacks/checkbox/onCheckPrePolPulse.html +++ b/doc/blochus/callbacks/checkbox/onCheckPrePolPulse.html @@ -333,37 +333,39 @@

    SOURCE CODE ^'data'); 0263 end 0264 -0265 % update all data inside the GUI -0266 setappdata(fig,'data',data); -0267 % update status bar -0268 updateStatusInformation(fig); -0269 else -0270 warndlg({'onCheckPrePolPulse:','There is no figure with the BLOCHUS Tag open.'},... -0271 'BLOCHUS error'); -0272 end -0273 +0265 % because the settings changed, deactivate the "Animate" button +0266 set(gui.push_handles.Animate,'Enable','off'); +0267 % update all data inside the GUI +0268 setappdata(fig,'data',data); +0269 % update status bar +0270 updateStatusInformation(fig); +0271 else +0272 warndlg({'onCheckPrePolPulse:','There is no figure with the BLOCHUS Tag open.'},... +0273 'BLOCHUS error'); 0274 end 0275 -0276 %------------- END OF CODE -------------- +0276 end 0277 -0278 %% License: -0279 % GNU GPLv3 -0280 % -0281 % BLOCHUS -0282 % Copyright (C) 2019 Thomas Hiller -0283 % -0284 % This program is free software: you can redistribute it and/or modify -0285 % it under the terms of the GNU General Public License as published by -0286 % the Free Software Foundation, either version 3 of the License, or -0287 % (at your option) any later version. -0288 % -0289 % This program is distributed in the hope that it will be useful, -0290 % but WITHOUT ANY WARRANTY; without even the implied warranty of -0291 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -0292 % GNU General Public License for more details. -0293 % -0294 % You should have received a copy of the GNU General Public License -0295 % along with this program. If not, see <https://www.gnu.org/licenses/>. +0278 %------------- END OF CODE -------------- +0279 +0280 %% License: +0281 % GNU GPLv3 +0282 % +0283 % BLOCHUS +0284 % Copyright (C) 2019 Thomas Hiller +0285 % +0286 % This program is free software: you can redistribute it and/or modify +0287 % it under the terms of the GNU General Public License as published by +0288 % the Free Software Foundation, either version 3 of the License, or +0289 % (at your option) any later version. +0290 % +0291 % This program is distributed in the hope that it will be useful, +0292 % but WITHOUT ANY WARRANTY; without even the implied warranty of +0293 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +0294 % GNU General Public License for more details. +0295 % +0296 % You should have received a copy of the GNU General Public License +0297 % 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/onCheckPulseQ.html b/doc/blochus/callbacks/checkbox/onCheckPulseQ.html index 9d5acac..c8af8c8 100644 --- a/doc/blochus/callbacks/checkbox/onCheckPulseQ.html +++ b/doc/blochus/callbacks/checkbox/onCheckPulseQ.html @@ -58,7 +58,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • getPulseParameters updates all relevant pulse settings
  • plotPulse plots different pulse parameter
    • This function is called by: @@ -122,7 +122,7 @@

    SOURCE CODE ^% get GUI data 0054 data = getappdata(fig,'data'); 0055 % plot pulse -0056 plotBpulse(gui.figh); +0056 plotPulse(gui.figh); 0057 0058 else 0059 warndlg({'onCheckPulseQ:','There is no figure with the BLOCHUS Tag open.'},... diff --git a/doc/blochus/callbacks/edits/onEditValue.html b/doc/blochus/callbacks/edits/onEditValue.html index 90b47c7..867530e 100644 --- a/doc/blochus/callbacks/edits/onEditValue.html +++ b/doc/blochus/callbacks/edits/onEditValue.html @@ -46,7 +46,7 @@

    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls:
      -
    • onEditValue updates all edit field values, checks for wrong inputs and
    • onPopupPrePolRamp selects the pre-polarization switch-off ramp
    • getB0 calculates the magnetic field from a given angular frequency and
    • getOmega0 calculates the angular frequency from a given B-field and
    • getPulseParameters updates all relevant pulse settings
    • getRampParameters updates all relevant switch-off ramp settings
    • plotBpulse plots different pulse parameter
    • plotRamp plots different pre-polarization switch-off ramp parameter
    +
  • onEditValue updates all edit field values, checks for wrong inputs and
  • onPopupPrePolRamp selects the pre-polarization switch-off ramp
  • getB0 calculates the magnetic field from a given angular frequency and
  • getOmega0 calculates the angular frequency from a given B-field and
  • getPulseParameters updates all relevant pulse settings
  • getRampParameters updates all relevant switch-off ramp settings
  • plotPulse plots different pulse parameter
  • plotRamp plots different pre-polarization switch-off ramp parameter
    • This function is called by: @@ -96,7 +96,7 @@

    SOURCE CODE ^% getOmega0 0020 % getPulseParameters 0021 % getRampParameters -0022 % plotBpulse +0022 % plotPulse 0023 % plotRamp 0024 % 0025 % Subfunctions: @@ -127,373 +127,365 @@

    SOURCE CODE ^% get the user data of the field 0051 ud = get(src,'UserData'); 0052 -0053 if isstruct(ud) % for new fields -0054 % get the default values [default min max] -0055 defaults = ud.defaults; -0056 -0057 % check if the value is numeric -0058 % if not reset to defaults stored in user data -0059 if isnan(val) -0060 set(src,'String',num2str(defaults(1))); -0061 val = str2double(get(src,'String')); -0062 end -0063 % check if the value is out of bounds -0064 % if yes reset to default -0065 if val < defaults(2) || val > defaults(3) -0066 set(src,'String',num2str(defaults(1))); -0067 val = str2double(get(src,'String')); %#ok<*NASGU> -0068 end -0069 -0070 else % old style (Needs to be removed after the refactoring) -0071 % check if the value is numeric -0072 % if not reset to defaults stored in user data -0073 if isnan(val) -0074 set(src,'String',num2str(ud(3))); -0075 val = str2double(get(src,'String')); -0076 end -0077 % check if the value is out of bounds -0078 % if yes reset to default -0079 if val < ud(1) || val > ud(2) -0080 set(src,'String',num2str(ud(3))); -0081 val = str2double(get(src,'String')); %#ok<*NASGU> -0082 end -0083 disp(['there is still an old style edit field:',tag]) -0084 end -0085 -0086 % get the data field to update from the field tag -0087 out = createDataString(tag); -0088 % update the corresponding data field -0089 updstr = [out.updstr,'=val;']; -0090 eval(updstr); -0091 -0092 % update the data inside the GUI -0093 setappdata(fig,'data',data); -0094 -0095 % depending on the particular edit field, further actions are -0096 % necessary -0097 switch tag -0098 % ----------------------------------------------------------------- -0099 % --- BASICS ------------------------------------------------------ -0100 % ----------------------------------------------------------------- -0101 case 'basic_B0' -0102 % new Larmor frequency due to changed B0 -0103 data.basic.Omega0 = getOmega0(data.basic.gamma,data.basic.B0)/2/pi; -0104 % update the GUI fields -0105 set(gui.edit_handles.Omega0,'String',sprintf('%7.2f',data.basic.Omega0)); -0106 setappdata(fig,'data',data); -0107 % if "Pulse" is activated, update the pulse as if the -0108 % pulse length (or number of periods) would have been changed -0109 % manually -0110 if get(gui.check_handles.Pulse,'Value') == 1 -0111 onEditValue(gui.edit_handles.PulseTtau); -0112 data = getappdata(fig,'data'); -0113 end -0114 % if "PrePol" is activated and the active ramp is "melton1995" -0115 % update the switch-off ramp settings due to the changed Larmor -0116 % frequency -0117 if get(gui.check_handles.PrePol,'Value') == 1 && ... -0118 get(gui.popup_handles.PrePolRamp,'Value') == 5 -0119 setappdata(fig,'data',data); -0120 onPopupPrePolRamp(gui.popup_handles.PrePolRamp); -0121 data = getappdata(fig,'data'); -0122 end -0123 if get(gui.check_handles.PrePol,'Value') == 1 -0124 setappdata(fig,'data',data); -0125 getRampParameters(fig); -0126 data = getappdata(fig,'data'); -0127 end -0128 -0129 case 'basic_Omega0' -0130 % fix sign if it is wrong -0131 if (data.basic.gamma > 0 && data.basic.Omega0 > 0) || ... -0132 (data.basic.gamma < 0 && data.basic.Omega0 < 0) -0133 data.basic.Omega0 = -data.basic.Omega0; -0134 end -0135 % new B0 due to changed Larmor frequency -0136 data.basic.B0 = getB0(data.basic.gamma,data.basic.Omega0*2*pi); -0137 % update the GUI fields -0138 set(gui.edit_handles.Omega0,'String',sprintf('%7.2f',data.basic.Omega0)); -0139 set(gui.edit_handles.B0,'String',sprintf('%5.4e',data.basic.B0)); -0140 setappdata(fig,'data',data); -0141 % if "Pulse" is activated, update the pulse as if the -0142 % pulse length (or number of periods) would have been changed -0143 % manually -0144 if get(gui.check_handles.Pulse,'Value') == 1 -0145 onEditValue(gui.edit_handles.PulseTtau); -0146 data = getappdata(fig,'data'); -0147 end -0148 % if "PrePol" is activated and the active ramp is "melton1995" -0149 % update the switch-off ramp settings due to the changed Larmor -0150 % frequency -0151 if get(gui.check_handles.PrePol,'Value') == 1 && ... -0152 get(gui.popup_handles.PrePolRamp,'Value') == 5 -0153 setappdata(fig,'data',data); -0154 onPopupPrePolRamp(gui.popup_handles.PrePolRamp); -0155 data = getappdata(fig,'data'); -0156 end -0157 if get(gui.check_handles.PrePol,'Value') == 1 -0158 setappdata(fig,'data',data); -0159 getRampParameters(fig); -0160 data = getappdata(fig,'data'); -0161 end -0162 -0163 case 'basic_Minitx' -0164 % x-component of init magnetization -0165 data.basic.Minit(1) = val; -0166 -0167 case 'basic_Minity' -0168 % y-component of init magnetization -0169 data.basic.Minit(2) = val; -0170 -0171 case 'basic_Minitz' -0172 % z-component of init magnetization -0173 data.basic.Minit(3) = val; -0174 -0175 % ------------------------------------------------------------- -0176 % --- PRE-POLARIZATION ---------------------------------------- -0177 % ------------------------------------------------------------- -0178 case {'prepol_Factor','prepol_SwitchFactor'} -0179 % check if the ramp type is "melton1995", if yes update the -0180 % switch-off time to maintain the same switch-off rate -0181 if get(gui.popup_handles.PrePolRamp,'Value') == 5 -0182 % k / rate -0183 GAMMA = data.prepol.Factor/data.prepol.SwitchFactor; -0184 % corresponding ramp time -0185 Tramp = GAMMA/(data.basic.B0*data.basic.gamma)*1e3; % [ms] -0186 data.prepol.Tramp = Tramp; -0187 data.prepol.Tslope = Tramp; -0188 switch data.basic.type -0189 case 'prepol' -0190 data.basic.Tsim = Tramp; -0191 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); -0192 otherwise -0193 % nothing to do -0194 end -0195 setappdata(fig,'data',data); -0196 set(gui.edit_handles.PrePolTramp,'String',num2str(data.prepol.Tramp)); -0197 set(gui.edit_handles.PrePolTslope,'String',num2str(data.prepol.Tslope)); -0198 end -0199 % update switch-off ramp settings -0200 getRampParameters(fig); -0201 data = getappdata(fig,'data'); -0202 plotRamp(fig); -0203 -0204 case {'prepol_Theta','prepol_Phi','prepol_Tslope'} -0205 % update switch-off ramp settings -0206 getRampParameters(fig); -0207 data = getappdata(fig,'data'); -0208 plotRamp(fig); -0209 -0210 case 'prepol_Tramp' -0211 % for "linear" and "half cosine" ramp set the Tslope value, -0212 % which is not need here equal to Tramp -0213 if strcmp(data.prepol.Ramp,'lin') || strcmp(data.prepol.Ramp,'halfcos') -0214 data.prepol.Tslope = data.prepol.Tramp; -0215 set(gui.edit_handles.PrePolTslope,'String',num2str(data.prepol.Tslope)); -0216 end -0217 % in case of pure "PrePol" update the total simulation time -0218 switch data.basic.type -0219 case 'prepol' -0220 data.basic.Tsim = data.prepol.Tramp; -0221 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); -0222 otherwise -0223 % nothing to do -0224 end -0225 setappdata(fig,'data',data); -0226 % update switch-off ramp settings -0227 getRampParameters(fig); -0228 data = getappdata(fig,'data'); -0229 plotRamp(fig); -0230 -0231 % ------------------------------------------------------------- -0232 % --- PULSE --------------------------------------------------- -0233 % ------------------------------------------------------------- -0234 case 'pulse_B1Factor' -0235 % if the pulse amplitude changes some settings have to be -0236 % adjusted, depending on the chosen pulse type -0237 switch data.pulse.Type -0238 case {'pi_half','pi'} -0239 switch data.pulse.Type -0240 case 'pi_half' -0241 % in case of "pi_half" the pulse length gets updated -0242 data.pulse.Ttau = abs(1e3*(pi/2/(data.basic.gamma*data.basic.B0*data.pulse.B1Factor))); -0243 case 'pi' -0244 % in case of "pi" the pulse length gets updated -0245 data.pulse.Ttau = abs(1e3*(pi/(data.basic.gamma*data.basic.B0*data.pulse.B1Factor))); -0246 end -0247 set(gui.edit_handles.PulseTtau,'String',num2str(data.pulse.Ttau)); -0248 % in case of pure "Pulse" update the total simulation time -0249 switch data.basic.type -0250 case 'pulse' -0251 data.basic.Tsim = data.pulse.Ttau; -0252 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); -0253 otherwise -0254 % nothing to do -0255 end -0256 setappdata(fig,'data',data); -0257 % update pulse settings -0258 getPulseParameters(fig); -0259 data = getappdata(fig,'data'); -0260 plotBpulse(fig); -0261 -0262 otherwise -0263 % update pulse settings -0264 getPulseParameters(fig); -0265 data = getappdata(fig,'data'); -0266 plotBpulse(fig); -0267 end -0268 -0269 case 'pulse_Ttau' -0270 % if the pulse length changes some settings have to be -0271 % adjusted, depending on the chosen pulse type -0272 switch data.pulse.Type -0273 case {'pi_half','pi'} -0274 switch data.pulse.Type -0275 case 'pi_half' -0276 % in case of "pi_half" the pulse amplitude gets updated -0277 data.pulse.B1Factor = abs(1e3*(pi/2/(data.basic.gamma*data.basic.B0*data.pulse.Ttau))); -0278 case 'pi' -0279 % in case of "pi" the pulse amplitude gets updated -0280 data.pulse.B1Factor = abs(1e3*(pi/(data.basic.gamma*data.basic.B0*data.pulse.Ttau))); -0281 end -0282 set(gui.edit_handles.PulseB1Factor,'String',num2str(data.pulse.B1Factor)); -0283 % in case of pure "Pulse" update the total simulation time -0284 switch data.basic.type -0285 case 'pulse' -0286 data.basic.Tsim = data.pulse.Ttau; -0287 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); -0288 otherwise -0289 % nothing to do -0290 end -0291 setappdata(fig,'data',data); -0292 % update pulse settings -0293 getPulseParameters(fig); -0294 data = getappdata(fig,'data'); -0295 plotBpulse(fig); -0296 -0297 case 'MIDI_OR' -0298 % in case of "MIDI_OR" the PulseTtau-field holds the -0299 % number of periods -0300 data.pulse.MIDINP = val; -0301 % update pulse length -0302 data.pulse.Ttau = abs(data.pulse.MIDINP/data.basic.Omega0)*1e3; -0303 % update pulse amplitude to pi/2 value -0304 data.pulse.B1Factor = abs(1e3*(pi/2/(data.basic.gamma*data.basic.B0*data.pulse.Ttau))); -0305 set(gui.edit_handles.PulseB1Factor,'String',num2str(data.pulse.B1Factor)); -0306 % in case of pure "Pulse" update the total simulation time -0307 switch data.basic.type -0308 case 'pulse' -0309 data.basic.Tsim = data.pulse.Ttau; -0310 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); -0311 otherwise -0312 % nothing to do -0313 end -0314 setappdata(fig,'data',data); -0315 % update pulse settings -0316 getPulseParameters(fig); -0317 data = getappdata(fig,'data'); -0318 plotBpulse(fig); -0319 -0320 case 'MIDI_AP' -0321 % in case of "MIDI_AP" the PulseTtau-field holds the -0322 % number of periods -0323 data.pulse.MIDINP = val; -0324 % update pulse length assuming a constant frequency -0325 data.pulse.Ttau = abs(data.pulse.MIDINP/data.basic.Omega0)*1e3; -0326 % now calculate the actual pulse settings -0327 setappdata(fig,'data',data); -0328 getPulseParameters(fig); -0329 data = getappdata(fig,'data'); -0330 % adjust the pulse length to the actual value -0331 data.pulse.Ttau = data.pulse_MIDI.t(end)*1e3; -0332 % in case of pure "Pulse" update the total simulation time -0333 switch data.basic.type -0334 case 'pulse' -0335 data.basic.Tsim = data.pulse.Ttau; -0336 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); -0337 otherwise -0338 % nothing to do -0339 end -0340 setappdata(fig,'data',data); -0341 % update pulse plot -0342 plotBpulse(fig); -0343 -0344 otherwise -0345 % for all other pulse types ("free" & "AHP") -0346 % in case of pure "Pulse" update the total simulation time -0347 switch data.basic.type -0348 case 'pulse' -0349 data.basic.Tsim = data.pulse.Ttau; -0350 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); -0351 otherwise -0352 % nothing to do -0353 end -0354 % update GUI data -0355 setappdata(fig,'data',data); -0356 % update pulse settings +0053 % get the default values [default min max] +0054 defaults = ud.defaults; +0055 +0056 % check if the value is numeric +0057 % if not reset to defaults stored in user data +0058 if isnan(val) +0059 set(src,'String',num2str(defaults(1))); +0060 val = str2double(get(src,'String')); +0061 end +0062 % check if the value is out of bounds +0063 % if yes reset to default +0064 if val < defaults(2) || val > defaults(3) +0065 set(src,'String',num2str(defaults(1))); +0066 val = str2double(get(src,'String')); %#ok<*NASGU> +0067 end +0068 +0069 % get the data field to update from the field tag +0070 out = createDataString(tag); +0071 % update the corresponding data field +0072 updstr = [out.updstr,'=val;']; +0073 eval(updstr); +0074 +0075 % update the data inside the GUI +0076 setappdata(fig,'data',data); +0077 +0078 % depending on the particular edit field, further actions are +0079 % necessary +0080 switch tag +0081 % ----------------------------------------------------------------- +0082 % --- BASICS ------------------------------------------------------ +0083 % ----------------------------------------------------------------- +0084 case 'basic_B0' +0085 % new Larmor frequency due to changed B0 +0086 data.basic.Omega0 = getOmega0(data.basic.gamma,data.basic.B0)/2/pi; +0087 % update the GUI fields +0088 set(gui.edit_handles.Omega0,'String',sprintf('%7.2f',data.basic.Omega0)); +0089 setappdata(fig,'data',data); +0090 % if "Pulse" is activated, update the pulse as if the +0091 % pulse length (or number of periods) would have been changed +0092 % manually +0093 if get(gui.check_handles.Pulse,'Value') == 1 +0094 onEditValue(gui.edit_handles.PulseTtau); +0095 data = getappdata(fig,'data'); +0096 end +0097 % if "PrePol" is activated and the active ramp is "melton1995" +0098 % update the switch-off ramp settings due to the changed Larmor +0099 % frequency +0100 if get(gui.check_handles.PrePol,'Value') == 1 && ... +0101 get(gui.popup_handles.PrePolRamp,'Value') == 5 +0102 setappdata(fig,'data',data); +0103 onPopupPrePolRamp(gui.popup_handles.PrePolRamp); +0104 data = getappdata(fig,'data'); +0105 end +0106 if get(gui.check_handles.PrePol,'Value') == 1 +0107 setappdata(fig,'data',data); +0108 getRampParameters(fig); +0109 data = getappdata(fig,'data'); +0110 end +0111 +0112 case 'basic_Omega0' +0113 % fix sign if it is wrong +0114 if (data.basic.gamma > 0 && data.basic.Omega0 > 0) || ... +0115 (data.basic.gamma < 0 && data.basic.Omega0 < 0) +0116 data.basic.Omega0 = -data.basic.Omega0; +0117 end +0118 % new B0 due to changed Larmor frequency +0119 data.basic.B0 = getB0(data.basic.gamma,data.basic.Omega0*2*pi); +0120 % update the GUI fields +0121 set(gui.edit_handles.Omega0,'String',sprintf('%7.2f',data.basic.Omega0)); +0122 set(gui.edit_handles.B0,'String',sprintf('%5.4e',data.basic.B0)); +0123 setappdata(fig,'data',data); +0124 % if "Pulse" is activated, update the pulse as if the +0125 % pulse length (or number of periods) would have been changed +0126 % manually +0127 if get(gui.check_handles.Pulse,'Value') == 1 +0128 onEditValue(gui.edit_handles.PulseTtau); +0129 data = getappdata(fig,'data'); +0130 end +0131 % if "PrePol" is activated and the active ramp is "melton1995" +0132 % update the switch-off ramp settings due to the changed Larmor +0133 % frequency +0134 if get(gui.check_handles.PrePol,'Value') == 1 && ... +0135 get(gui.popup_handles.PrePolRamp,'Value') == 5 +0136 setappdata(fig,'data',data); +0137 onPopupPrePolRamp(gui.popup_handles.PrePolRamp); +0138 data = getappdata(fig,'data'); +0139 end +0140 if get(gui.check_handles.PrePol,'Value') == 1 +0141 setappdata(fig,'data',data); +0142 getRampParameters(fig); +0143 data = getappdata(fig,'data'); +0144 end +0145 +0146 case 'basic_Minitx' +0147 % x-component of init magnetization +0148 data.basic.Minit(1) = val; +0149 +0150 case 'basic_Minity' +0151 % y-component of init magnetization +0152 data.basic.Minit(2) = val; +0153 +0154 case 'basic_Minitz' +0155 % z-component of init magnetization +0156 data.basic.Minit(3) = val; +0157 +0158 % ------------------------------------------------------------- +0159 % --- PRE-POLARIZATION ---------------------------------------- +0160 % ------------------------------------------------------------- +0161 +0162 case {'prepol_Factor','prepol_SwitchFactor'} +0163 % check if the ramp type is "melton1995", if yes update the +0164 % switch-off time to maintain the same switch-off rate +0165 if get(gui.popup_handles.PrePolRamp,'Value') == 5 +0166 % k / rate +0167 GAMMA = data.prepol.Factor/data.prepol.SwitchFactor; +0168 % corresponding ramp time +0169 Tramp = GAMMA/(data.basic.B0*data.basic.gamma)*1e3; % [ms] +0170 data.prepol.Tramp = Tramp; +0171 data.prepol.Tslope = Tramp; +0172 switch data.basic.type +0173 case 'prepol' +0174 data.basic.Tsim = Tramp; +0175 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); +0176 otherwise +0177 % nothing to do +0178 end +0179 setappdata(fig,'data',data); +0180 set(gui.edit_handles.PrePolTramp,'String',num2str(data.prepol.Tramp)); +0181 set(gui.edit_handles.PrePolTslope,'String',num2str(data.prepol.Tslope)); +0182 end +0183 % update switch-off ramp settings +0184 getRampParameters(fig); +0185 data = getappdata(fig,'data'); +0186 plotRamp(fig); +0187 +0188 case {'prepol_Theta','prepol_Phi','prepol_Tslope'} +0189 % update switch-off ramp settings +0190 getRampParameters(fig); +0191 data = getappdata(fig,'data'); +0192 plotRamp(fig); +0193 +0194 case 'prepol_Tramp' +0195 % for "linear" and "half cosine" ramp set the Tslope value, +0196 % which is not need here equal to Tramp +0197 if strcmp(data.prepol.Ramp,'lin') || strcmp(data.prepol.Ramp,'halfcos') +0198 data.prepol.Tslope = data.prepol.Tramp; +0199 set(gui.edit_handles.PrePolTslope,'String',num2str(data.prepol.Tslope)); +0200 end +0201 % in case of pure "PrePol" update the total simulation time +0202 switch data.basic.type +0203 case 'prepol' +0204 data.basic.Tsim = data.prepol.Tramp; +0205 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); +0206 otherwise +0207 % nothing to do +0208 end +0209 setappdata(fig,'data',data); +0210 % update switch-off ramp settings +0211 getRampParameters(fig); +0212 data = getappdata(fig,'data'); +0213 plotRamp(fig); +0214 +0215 % ------------------------------------------------------------- +0216 % --- PULSE --------------------------------------------------- +0217 % ------------------------------------------------------------- +0218 +0219 case 'pulse_B1Factor' +0220 % if the pulse amplitude changes some settings have to be +0221 % adjusted, depending on the chosen pulse type +0222 switch data.pulse.Type +0223 case {'pi_half','pi'} +0224 switch data.pulse.Type +0225 case 'pi_half' +0226 % in case of "pi_half" the pulse length gets updated +0227 data.pulse.Ttau = abs(1e3*(pi/2/(data.basic.gamma*... +0228 data.basic.B0*data.pulse.B1Factor))); +0229 case 'pi' +0230 % in case of "pi" the pulse length gets updated +0231 data.pulse.Ttau = abs(1e3*(pi/(data.basic.gamma*... +0232 data.basic.B0*data.pulse.B1Factor))); +0233 end +0234 set(gui.edit_handles.PulseTtau,'String',num2str(data.pulse.Ttau)); +0235 % in case of pure "Pulse" update the total simulation time +0236 switch data.basic.type +0237 case 'pulse' +0238 data.basic.Tsim = data.pulse.Ttau; +0239 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); +0240 otherwise +0241 % nothing to do +0242 end +0243 setappdata(fig,'data',data); +0244 % update pulse settings +0245 getPulseParameters(fig); +0246 data = getappdata(fig,'data'); +0247 plotPulse(fig); +0248 +0249 otherwise +0250 % update pulse settings +0251 getPulseParameters(fig); +0252 data = getappdata(fig,'data'); +0253 plotPulse(fig); +0254 end +0255 +0256 case 'pulse_Ttau' +0257 % if the pulse length changes some settings have to be +0258 % adjusted, depending on the chosen pulse type +0259 switch data.pulse.Type +0260 case {'pi_half','pi'} +0261 switch data.pulse.Type +0262 case 'pi_half' +0263 % in case of "pi_half" the pulse amplitude gets updated +0264 data.pulse.B1Factor = abs(1e3*(pi/2/(data.basic.gamma*... +0265 data.basic.B0*data.pulse.Ttau))); +0266 case 'pi' +0267 % in case of "pi" the pulse amplitude gets updated +0268 data.pulse.B1Factor = abs(1e3*(pi/(data.basic.gamma*... +0269 data.basic.B0*data.pulse.Ttau))); +0270 end +0271 set(gui.edit_handles.PulseB1Factor,'String',num2str(data.pulse.B1Factor)); +0272 % in case of pure "Pulse" update the total simulation time +0273 switch data.basic.type +0274 case 'pulse' +0275 data.basic.Tsim = data.pulse.Ttau; +0276 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); +0277 otherwise +0278 % nothing to do +0279 end +0280 setappdata(fig,'data',data); +0281 % update pulse settings +0282 getPulseParameters(fig); +0283 data = getappdata(fig,'data'); +0284 plotPulse(fig); +0285 +0286 case 'MIDI_OR' +0287 % in case of "MIDI_OR" the PulseTtau-field holds the +0288 % number of periods +0289 data.pulse.MIDINP = val; +0290 % update pulse length +0291 data.pulse.Ttau = abs(data.pulse.MIDINP/data.basic.Omega0)*1e3; +0292 % update pulse amplitude to pi/2 value +0293 data.pulse.B1Factor = abs(1e3*(pi/2/(data.basic.gamma*... +0294 data.basic.B0*data.pulse.Ttau))); +0295 set(gui.edit_handles.PulseB1Factor,'String',num2str(data.pulse.B1Factor)); +0296 % in case of pure "Pulse" update the total simulation time +0297 switch data.basic.type +0298 case 'pulse' +0299 data.basic.Tsim = data.pulse.Ttau; +0300 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); +0301 otherwise +0302 % nothing to do +0303 end +0304 setappdata(fig,'data',data); +0305 % update pulse settings +0306 getPulseParameters(fig); +0307 data = getappdata(fig,'data'); +0308 plotPulse(fig); +0309 +0310 case 'MIDI_AP' +0311 % in case of "MIDI_AP" the PulseTtau-field holds the +0312 % number of periods +0313 data.pulse.MIDINP = val; +0314 % update pulse length assuming a constant frequency +0315 data.pulse.Ttau = abs(data.pulse.MIDINP/data.basic.Omega0)*1e3; +0316 % now calculate the actual pulse settings +0317 setappdata(fig,'data',data); +0318 getPulseParameters(fig); +0319 data = getappdata(fig,'data'); +0320 % adjust the pulse length to the actual value +0321 data.pulse.Ttau = data.pulse_MIDI.t(end)*1e3; +0322 % in case of pure "Pulse" update the total simulation time +0323 switch data.basic.type +0324 case 'pulse' +0325 data.basic.Tsim = data.pulse.Ttau; +0326 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); +0327 otherwise +0328 % nothing to do +0329 end +0330 setappdata(fig,'data',data); +0331 % update pulse plot +0332 plotPulse(fig); +0333 +0334 otherwise +0335 % for all other pulse types ("free" & "AHP") +0336 % in case of pure "Pulse" update the total simulation time +0337 switch data.basic.type +0338 case 'pulse' +0339 data.basic.Tsim = data.pulse.Ttau; +0340 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim)); +0341 otherwise +0342 % nothing to do +0343 end +0344 % update GUI data +0345 setappdata(fig,'data',data); +0346 % update pulse settings +0347 getPulseParameters(fig); +0348 data = getappdata(fig,'data'); +0349 plotPulse(fig); +0350 end +0351 +0352 otherwise +0353 switch data.basic.type +0354 % update all changes related to the pulse modulation +0355 case {'pulse','prepolpulse'} +0356 setappdata(fig,'data',data); 0357 getPulseParameters(fig); 0358 data = getappdata(fig,'data'); -0359 plotBpulse(fig); -0360 end -0361 -0362 otherwise -0363 switch data.basic.type -0364 % update all changes related to the pulse modulation -0365 case {'pulse','prepolpulse'} -0366 setappdata(fig,'data',data); -0367 getPulseParameters(fig); -0368 data = getappdata(fig,'data'); -0369 plotBpulse(fig); -0370 -0371 otherwise -0372 % nothing to do for all other fields e.g. T1, T2, Tsim -0373 end -0374 end -0375 -0376 % update GUI data -0377 setappdata(fig,'data',data); -0378 else -0379 warndlg({'onEditValue:','There is no figure with the BLOCHUS Tag open.'},... -0380 'BLOCHUS error'); -0381 end -0382 -0383 end -0384 -0385 %% helper function to create the update string -0386 function out = createDataString(tag) -0387 % find the underscore -0388 ind = strfind(tag,'_'); -0389 % the panel name is before the underscore -0390 out.panel = tag(1:ind(1)-1); -0391 % the field name afterwards -0392 out.field = tag(ind(1)+1:end); -0393 % replace the underscore with a dot -0394 tag(ind) = '.'; -0395 % create the update string -0396 out.updstr = ['data.',tag]; -0397 -0398 end -0399 -0400 %------------- END OF CODE -------------- -0401 -0402 %% License: -0403 % GNU GPLv3 +0359 plotPulse(fig); +0360 +0361 otherwise +0362 % because the pulse data changed, deactivate the +0363 % "Animate" button +0364 set(gui.push_handles.Animate,'Enable','off'); +0365 end +0366 end +0367 +0368 % update GUI data +0369 setappdata(fig,'data',data); +0370 else +0371 warndlg({'onEditValue:','There is no figure with the BLOCHUS Tag open.'},... +0372 'BLOCHUS error'); +0373 end +0374 +0375 end +0376 +0377 %% helper function to create the update string +0378 function out = createDataString(tag) +0379 % find the underscore +0380 ind = strfind(tag,'_'); +0381 % the panel name is before the underscore +0382 out.panel = tag(1:ind(1)-1); +0383 % the field name afterwards +0384 out.field = tag(ind(1)+1:end); +0385 % replace the underscore with a dot +0386 tag(ind) = '.'; +0387 % create the update string +0388 out.updstr = ['data.',tag]; +0389 +0390 end +0391 +0392 %------------- END OF CODE -------------- +0393 +0394 %% License: +0395 % GNU GPLv3 +0396 % +0397 % BLOCHUS +0398 % Copyright (C) 2019 Thomas Hiller +0399 % +0400 % This program is free software: you can redistribute it and/or modify +0401 % it under the terms of the GNU General Public License as published by +0402 % the Free Software Foundation, either version 3 of the License, or +0403 % (at your option) any later version. 0404 % -0405 % BLOCHUS -0406 % Copyright (C) 2019 Thomas Hiller -0407 % -0408 % This program is free software: you can redistribute it and/or modify -0409 % it under the terms of the GNU General Public License as published by -0410 % the Free Software Foundation, either version 3 of the License, or -0411 % (at your option) any later version. -0412 % -0413 % This program is distributed in the hope that it will be useful, -0414 % but WITHOUT ANY WARRANTY; without even the implied warranty of -0415 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -0416 % GNU General Public License for more details. -0417 % -0418 % You should have received a copy of the GNU General Public License -0419 % along with this program. If not, see <https://www.gnu.org/licenses/>. +0405 % This program is distributed in the hope that it will be useful, +0406 % but WITHOUT ANY WARRANTY; without even the implied warranty of +0407 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +0408 % GNU General Public License for more details. +0409 % +0410 % You should have received a copy of the GNU General Public License +0411 % along with this program. If not, see <https://www.gnu.org/licenses/>.
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    \ No newline at end of file diff --git a/doc/blochus/callbacks/menus/onMenuViewFigure.html b/doc/blochus/callbacks/menus/onMenuViewFigure.html index 1a16a7b..f6b3ed8 100644 --- a/doc/blochus/callbacks/menus/onMenuViewFigure.html +++ b/doc/blochus/callbacks/menus/onMenuViewFigure.html @@ -111,156 +111,218 @@

    SOURCE CODE ^% opening the export figure 0043 expfig = figure; 0044 -0045 % create the axes layout on the export figure -0046 switch get(src,'Label') -0047 case {'Current View','Magnetization','Switch-off Ramp'} -0048 % we copy all visible axes in a 2x2 grid -0049 ax1 = subplot(2,2,1,'Parent',expfig); -0050 ax2 = subplot(2,2,2,'Parent',expfig); -0051 ax3 = subplot(2,2,3,'Parent',expfig); -0052 ax4 = subplot(2,2,4,'Parent',expfig); -0053 -0054 case 'Pulse' -0055 % we copy pulse parameter in a 3x2 grid -0056 ax1 = subplot(3,2,1,'Parent',expfig); -0057 ax2 = subplot(3,2,2,'Parent',expfig); -0058 ax3 = subplot(3,2,[3 4],'Parent',expfig); -0059 ax4 = subplot(3,2,[5 6],'Parent',expfig); -0060 end -0061 % get the default positions -0062 pos1 = get(ax1,'Position'); -0063 pos2 = get(ax2,'Position'); -0064 pos3 = get(ax3,'Position'); -0065 pos4 = get(ax4,'Position'); -0066 % delete axes -0067 delete(ax1);delete(ax2);delete(ax3);delete(ax4); -0068 -0069 % copy the GUI axes to the export figure -0070 switch get(src,'Label') -0071 case 'Current View' -0072 mag = get(gui.panels.Plot.Mag,'Selection'); -0073 sph = get(gui.panels.Plot.Sphere,'Selection'); -0074 pre = get(gui.panels.Plot.PrePol,'Selection'); -0075 pul = get(gui.panels.Plot.Pulse,'Selection'); -0076 switch mag -0077 case 1 -0078 ax1 = copyobj(gui.axes_handles.MagL,expfig); -0079 case 2 -0080 ax1 = copyobj(gui.axes_handles.MagR,expfig); -0081 case 3 -0082 ax1 = copyobj(gui.axes_handles.MagFFT,expfig); -0083 end -0084 switch sph -0085 case 1 -0086 ax2 = copyobj(gui.axes_handles.SphereL,expfig); -0087 case 2 -0088 ax2 = copyobj(gui.axes_handles.SphereR,expfig); -0089 end -0090 switch pre -0091 case 1 -0092 ax3 = copyobj(gui.axes_handles.Bpre,expfig); -0093 case 2 -0094 ax3 = copyobj(gui.axes_handles.alpha,expfig); -0095 case 3 -0096 ax3 = copyobj(gui.axes_handles.dadt,expfig); -0097 case 4 -0098 ax3 = copyobj(gui.axes_handles.wda,expfig); -0099 end -0100 switch pul -0101 case 1 -0102 ax4 = copyobj(gui.axes_handles.PulseSetupF,expfig); -0103 case 2 -0104 ax4 = copyobj(gui.axes_handles.PulseB,expfig); -0105 case 3 -0106 ax4 = copyobj(gui.axes_handles.PulseFFT,expfig); -0107 end -0108 -0109 set(expfig,'Name','BLOCHUS: Current View'); -0110 -0111 case 'Magnetization' -0112 ax1 = copyobj(gui.axes_handles.MagL,expfig); -0113 ax2 = copyobj(gui.axes_handles.SphereL,expfig); -0114 ax3 = copyobj(gui.axes_handles.MagR,expfig); -0115 ax4 = copyobj(gui.axes_handles.SphereR,expfig); -0116 -0117 set(expfig,'Name','BLOCHUS: Magnetization'); -0118 -0119 case 'Switch-off Ramp' -0120 ax1 = copyobj(gui.axes_handles.Bpre,expfig); -0121 ax2 = copyobj(gui.axes_handles.alpha,expfig); -0122 ax3 = copyobj(gui.axes_handles.dadt,expfig); -0123 ax4 = copyobj(gui.axes_handles.wda,expfig); -0124 -0125 set(expfig,'Name','BLOCHUS: Switch-off Ramp'); -0126 -0127 case 'Pulse' -0128 ax1 = copyobj(gui.axes_handles.PulseSetupF,expfig); -0129 ax2 = copyobj(gui.axes_handles.PulseSetupI,expfig); -0130 ax3 = copyobj(gui.axes_handles.PulseB,expfig); -0131 ax4 = copyobj(gui.axes_handles.PulseFFT,expfig); -0132 -0133 set(expfig,'Name','BLOCHUS: Pulse'); -0134 end -0135 % adjust the axes positions -0136 set(ax1,'Position',pos1); -0137 set(ax2,'Position',pos2); -0138 set(ax3,'Position',pos3); -0139 set(ax4,'Position',pos4); -0140 -0141 % adjust the position of the export figure -0142 set(expfig,'Position',[posf(1)+300 posf(2) (posf(3)-300)*0.8 posf(4)*0.8]); -0143 -0144 % show legends -0145 switch get(src,'Label') -0146 case 'Current View' -0147 lgh1 = legend(ax1,'show'); -0148 lgh3 = legend(ax3,'show'); -0149 lgh4 = legend(ax4,'show'); +0045 % due to the two axes on the pulse modulation panel, we need to know +0046 % before creating the new figure if this panel is active +0047 isdual = false; +0048 if get(gui.panels.Plot.Pulse,'Selection') == 1 +0049 isdual = true; +0050 end +0051 +0052 % create the axes layout on the export figure and get the axes +0053 % positions +0054 switch get(src,'Label') +0055 case 'Current View' +0056 % we copy all visible axes in a 2x2 grid +0057 ax1 = subplot(2,2,1,'Parent',expfig); +0058 ax2 = subplot(2,2,2,'Parent',expfig); +0059 ax3 = subplot(2,2,3,'Parent',expfig); +0060 pos1 = get(ax1,'Position'); +0061 pos2 = get(ax2,'Position'); +0062 pos3 = get(ax3,'Position'); +0063 delete(ax1); +0064 delete(ax2); +0065 delete(ax3); +0066 if isdual +0067 ax4a = subplot(2,4,7,'Parent',expfig); +0068 ax4b = subplot(2,4,8,'Parent',expfig); +0069 pos4a = get(ax4a,'Position'); +0070 pos4b = get(ax4b,'Position'); +0071 delete(ax4a); +0072 delete(ax4b); +0073 else +0074 ax4 = subplot(2,2,4,'Parent',expfig); +0075 pos4 = get(ax4,'Position'); +0076 delete(ax4); +0077 end +0078 +0079 case {'Magnetization','Switch-off Ramp'} +0080 % we copy all visible axes in a 2x2 grid +0081 ax1 = subplot(2,2,1,'Parent',expfig); +0082 ax2 = subplot(2,2,2,'Parent',expfig); +0083 ax3 = subplot(2,2,3,'Parent',expfig); +0084 ax4 = subplot(2,2,4,'Parent',expfig); +0085 pos1 = get(ax1,'Position'); +0086 pos2 = get(ax2,'Position'); +0087 pos3 = get(ax3,'Position'); +0088 pos4 = get(ax4,'Position'); +0089 delete(ax1); +0090 delete(ax2); +0091 delete(ax3); +0092 delete(ax4); +0093 +0094 case 'Pulse' +0095 % we copy pulse parameter in a 3x2 grid +0096 ax1 = subplot(3,2,1,'Parent',expfig); +0097 ax2 = subplot(3,2,2,'Parent',expfig); +0098 ax3 = subplot(3,2,[3 4],'Parent',expfig); +0099 ax4 = subplot(3,2,[5 6],'Parent',expfig); +0100 pos1 = get(ax1,'Position'); +0101 pos2 = get(ax2,'Position'); +0102 pos3 = get(ax3,'Position'); +0103 pos4 = get(ax4,'Position'); +0104 delete(ax1); +0105 delete(ax2); +0106 delete(ax3); +0107 delete(ax4); +0108 end +0109 +0110 % copy the GUI axes to the export figure +0111 switch get(src,'Label') +0112 case 'Current View' +0113 mag = get(gui.panels.Plot.Mag,'Selection'); +0114 sph = get(gui.panels.Plot.Sphere,'Selection'); +0115 pre = get(gui.panels.Plot.PrePol,'Selection'); +0116 pul = get(gui.panels.Plot.Pulse,'Selection'); +0117 switch mag +0118 case 1 +0119 ax1 = copyobj(gui.axes_handles.MagL,expfig); +0120 case 2 +0121 ax1 = copyobj(gui.axes_handles.MagR,expfig); +0122 case 3 +0123 ax1 = copyobj(gui.axes_handles.MagFFT,expfig); +0124 end +0125 switch sph +0126 case 1 +0127 ax2 = copyobj(gui.axes_handles.SphereL,expfig); +0128 case 2 +0129 ax2 = copyobj(gui.axes_handles.SphereR,expfig); +0130 end +0131 switch pre +0132 case 1 +0133 ax3 = copyobj(gui.axes_handles.Bpre,expfig); +0134 case 2 +0135 ax3 = copyobj(gui.axes_handles.alpha,expfig); +0136 case 3 +0137 ax3 = copyobj(gui.axes_handles.dadt,expfig); +0138 case 4 +0139 ax3 = copyobj(gui.axes_handles.wda,expfig); +0140 end +0141 switch pul +0142 case 1 +0143 ax4a = copyobj(gui.axes_handles.PulseSetupF,expfig); +0144 ax4b = copyobj(gui.axes_handles.PulseSetupI,expfig); +0145 case 2 +0146 ax4 = copyobj(gui.axes_handles.PulseB,expfig); +0147 case 3 +0148 ax4 = copyobj(gui.axes_handles.PulseFFT,expfig); +0149 end 0150 -0151 case 'Magnetization' -0152 lgh1 = legend(ax1,'show'); -0153 lgh3 = legend(ax3,'show'); -0154 -0155 case 'Switch-off Ramp' -0156 lgh1 = legend(ax1,'show'); -0157 lgh2 = legend(ax2,'show'); -0158 lgh4 = legend(ax4,'show'); -0159 set(lgh4,'Interpreter','latex','Location','best'); +0151 set(expfig,'Name','BLOCHUS: Current View'); +0152 +0153 case 'Magnetization' +0154 ax1 = copyobj(gui.axes_handles.MagL,expfig); +0155 ax2 = copyobj(gui.axes_handles.SphereL,expfig); +0156 ax3 = copyobj(gui.axes_handles.MagR,expfig); +0157 ax4 = copyobj(gui.axes_handles.SphereR,expfig); +0158 +0159 set(expfig,'Name','BLOCHUS: Magnetization'); 0160 -0161 case 'Pulse' -0162 lgh1 = legend(ax1,'show'); -0163 lgh2 = legend(ax2,'show'); -0164 lgh3 = legend(ax3,'show'); -0165 lgh4 = legend(ax4,'show'); -0166 end -0167 -0168 else -0169 warndlg({'onMenuViewFigure:','There is no figure with the BLOCHUS Tag open.'},... -0170 'BLOCHUS error'); -0171 end -0172 -0173 end -0174 -0175 %------------- END OF CODE -------------- -0176 -0177 %% License: -0178 % GNU GPLv3 -0179 % -0180 % BLOCHUS -0181 % Copyright (C) 2019 Thomas Hiller -0182 % -0183 % This program is free software: you can redistribute it and/or modify -0184 % it under the terms of the GNU General Public License as published by -0185 % the Free Software Foundation, either version 3 of the License, or -0186 % (at your option) any later version. -0187 % -0188 % This program is distributed in the hope that it will be useful, -0189 % but WITHOUT ANY WARRANTY; without even the implied warranty of -0190 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -0191 % GNU General Public License for more details. -0192 % -0193 % You should have received a copy of the GNU General Public License -0194 % along with this program. If not, see <https://www.gnu.org/licenses/>. +0161 case 'Switch-off Ramp' +0162 ax1 = copyobj(gui.axes_handles.Bpre,expfig); +0163 ax2 = copyobj(gui.axes_handles.alpha,expfig); +0164 ax3 = copyobj(gui.axes_handles.dadt,expfig); +0165 ax4 = copyobj(gui.axes_handles.wda,expfig); +0166 +0167 set(expfig,'Name','BLOCHUS: Switch-off Ramp'); +0168 +0169 case 'Pulse' +0170 ax1 = copyobj(gui.axes_handles.PulseSetupF,expfig); +0171 ax2 = copyobj(gui.axes_handles.PulseSetupI,expfig); +0172 ax3 = copyobj(gui.axes_handles.PulseB,expfig); +0173 ax4 = copyobj(gui.axes_handles.PulseFFT,expfig); +0174 +0175 set(expfig,'Name','BLOCHUS: Pulse'); +0176 end +0177 +0178 % adjust the axes positions +0179 switch get(src,'Label') +0180 case 'Current View' +0181 set(ax1,'Position',pos1); +0182 set(ax2,'Position',pos2); +0183 set(ax3,'Position',pos3); +0184 if isdual +0185 set(ax4a,'Position',pos4a); +0186 set(ax4b,'Position',pos4b); +0187 else +0188 set(ax4,'Position',pos4); +0189 end +0190 +0191 otherwise +0192 set(ax1,'Position',pos1); +0193 set(ax2,'Position',pos2); +0194 set(ax3,'Position',pos3); +0195 set(ax4,'Position',pos4); +0196 end +0197 +0198 % adjust the position of the export figure +0199 set(expfig,'Position',[posf(1)+300 posf(2) (posf(3)-300)*0.8 posf(4)*0.8]); +0200 +0201 % show legends +0202 switch get(src,'Label') +0203 case 'Current View' +0204 lgh1 = legend(ax1,'show'); +0205 lgh3 = legend(ax3,'show'); +0206 if isdual +0207 lgh4a = legend(ax4a,'show'); +0208 lgh4b = legend(ax4b,'show'); +0209 else +0210 lgh4 = legend(ax4,'show'); +0211 end +0212 +0213 case 'Magnetization' +0214 lgh1 = legend(ax1,'show'); +0215 lgh3 = legend(ax3,'show'); +0216 +0217 case 'Switch-off Ramp' +0218 lgh1 = legend(ax1,'show'); +0219 lgh2 = legend(ax2,'show'); +0220 lgh4 = legend(ax4,'show'); +0221 set(lgh4,'Interpreter','latex','Location','best'); +0222 +0223 case 'Pulse' +0224 lgh1 = legend(ax1,'show'); +0225 lgh2 = legend(ax2,'show'); +0226 lgh3 = legend(ax3,'show'); +0227 lgh4 = legend(ax4,'show'); +0228 end +0229 +0230 else +0231 warndlg({'onMenuViewFigure:','There is no figure with the BLOCHUS Tag open.'},... +0232 'BLOCHUS error'); +0233 end +0234 +0235 end +0236 +0237 %------------- END OF CODE -------------- +0238 +0239 %% License: +0240 % GNU GPLv3 +0241 % +0242 % BLOCHUS +0243 % Copyright (C) 2019 Thomas Hiller +0244 % +0245 % This program is free software: you can redistribute it and/or modify +0246 % it under the terms of the GNU General Public License as published by +0247 % the Free Software Foundation, either version 3 of the License, or +0248 % (at your option) any later version. +0249 % +0250 % This program is distributed in the hope that it will be useful, +0251 % but WITHOUT ANY WARRANTY; without even the implied warranty of +0252 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +0253 % GNU General Public License for more details. +0254 % +0255 % You should have received a copy of the GNU General Public License +0256 % 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/popup/onPopupPulseAxis.html b/doc/blochus/callbacks/popup/onPopupPulseAxis.html index 73f3d1b..4a28444 100644 --- a/doc/blochus/callbacks/popup/onPopupPulseAxis.html +++ b/doc/blochus/callbacks/popup/onPopupPulseAxis.html @@ -42,7 +42,7 @@

    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • getPulseParameters updates all relevant pulse settings
  • plotPulse plots different pulse parameter
    • This function is called by: @@ -85,7 +85,7 @@

    SOURCE CODE ^% 0016 % Other m-files required: 0017 % getPulseParameters -0018 % plotBpulse +0018 % plotPulse 0019 % 0020 % Subfunctions: 0021 % none @@ -130,7 +130,7 @@

    SOURCE CODE ^% get GUI data 0061 data = getappdata(fig,'data'); 0062 % plot pulse -0063 plotBpulse(gui.figh); +0063 plotPulse(gui.figh); 0064 0065 else 0066 warndlg({'onPopupPulseAxis:','There is no figure with the BLOCHUS Tag open.'},... diff --git a/doc/blochus/callbacks/popup/onPopupPulseDFmode.html b/doc/blochus/callbacks/popup/onPopupPulseDFmode.html index 91e46e2..dd31982 100644 --- a/doc/blochus/callbacks/popup/onPopupPulseDFmode.html +++ b/doc/blochus/callbacks/popup/onPopupPulseDFmode.html @@ -59,7 +59,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • getPulseParameters updates all relevant pulse settings
  • plotPulse plots different pulse parameter
    • This function is called by: @@ -153,7 +153,7 @@

    SOURCE CODE ^% update GUI data 0084 setappdata(fig,'data',data); 0085 % plot pulse -0086 plotBpulse(gui.figh); +0086 plotPulse(gui.figh); 0087 0088 else 0089 warndlg({'onPopupPulseDFmode:','There is no figure with the BLOCHUS Tag open.'},... diff --git a/doc/blochus/callbacks/popup/onPopupPulseImode.html b/doc/blochus/callbacks/popup/onPopupPulseImode.html index 22a29ee..99e93de 100644 --- a/doc/blochus/callbacks/popup/onPopupPulseImode.html +++ b/doc/blochus/callbacks/popup/onPopupPulseImode.html @@ -59,7 +59,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • getPulseParameters updates all relevant pulse settings
  • plotPulse plots different pulse parameter
    • This function is called by: @@ -155,7 +155,7 @@

    SOURCE CODE ^% update GUI data 0086 setappdata(fig,'data',data); 0087 % plot pulse -0088 plotBpulse(gui.figh); +0088 plotPulse(gui.figh); 0089 0090 else 0091 warndlg({'onPopupPulseDFmode:','There is no figure with the BLOCHUS Tag open.'},... diff --git a/doc/blochus/callbacks/popup/onPopupPulsePolarization.html b/doc/blochus/callbacks/popup/onPopupPulsePolarization.html index a1b5e12..75219be 100644 --- a/doc/blochus/callbacks/popup/onPopupPulsePolarization.html +++ b/doc/blochus/callbacks/popup/onPopupPulsePolarization.html @@ -59,7 +59,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • getPulseParameters updates all relevant pulse settings
  • plotPulse plots different pulse parameter
    • This function is called by: @@ -128,7 +128,7 @@

    SOURCE CODE ^% update GUI data 0059 setappdata(fig,'data',data); 0060 % plot pulse -0061 plotBpulse(gui.figh); +0061 plotPulse(gui.figh); 0062 0063 else 0064 warndlg({'onPopupPulsePolarization:','There is no figure with the BLOCHUS Tag open.'},... diff --git a/doc/blochus/callbacks/popup/onPopupPulseType.html b/doc/blochus/callbacks/popup/onPopupPulseType.html index 480e5be..d39daaf 100644 --- a/doc/blochus/callbacks/popup/onPopupPulseType.html +++ b/doc/blochus/callbacks/popup/onPopupPulseType.html @@ -59,7 +59,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • onEditValue updates all edit field values, checks for wrong inputs and
  • onPopupPulseDFmode selects the frequency modulation for an adiabatic pulse
  • onPopupPulseImode selects the current modulation for an adiabatic pulse
  • getPulseParameters updates all relevant pulse settings
  • plotPulse plots different pulse parameter
  • updateStatusInformation updates all fields inside the bottom status bar
    • This function is called by: @@ -296,7 +296,7 @@

    SOURCE CODE ^% update GUI data 0227 setappdata(fig,'data',data); 0228 % plot pulse -0229 plotBpulse(fig); +0229 plotPulse(fig); 0230 % update status bar 0231 updateStatusInformation(fig); 0232 else diff --git a/doc/blochus/callbacks/push/menu.html b/doc/blochus/callbacks/push/menu.html index 561abd1..a9987d0 100644 --- a/doc/blochus/callbacks/push/menu.html +++ b/doc/blochus/callbacks/push/menu.html @@ -18,7 +18,7 @@

    Index for blochus\callbacks\push

    Matlab files in this directory:

    +
  • onPushAnimate
  • onPushAxView
  • onPushGrid
  • onPushRun
    • diff --git a/doc/blochus/callbacks/push/onPushAnimate.html b/doc/blochus/callbacks/push/onPushAnimate.html index 3e10666..3a5c9d0 100644 --- a/doc/blochus/callbacks/push/onPushAnimate.html +++ b/doc/blochus/callbacks/push/onPushAnimate.html @@ -4,7 +4,7 @@ Description of onPushAnimate - + @@ -20,19 +20,49 @@

    onPushAnimate

    PURPOSE ^

    -
    +
    animates the results of the latest simulation

    SYNOPSIS ^

    function onPushAnimate(src,~)

    DESCRIPTION ^

    -
    
+
    onPushAnimate animates the results of the latest simulation
+
+ Syntax:
+       onPushAnimate(src)
+
+ Inputs:
+       src - handle of the calling object
+
+ Outputs:
+       none
+
+ Example:
+       onPushAnimate(src)
+
+ Other m-files required:
+       clearSingleAxis
+       plotBSphere
+       plotPulse
+       plotRamp
+       plotResults
+
+ Subfunctions:
+       none
+
+ MAT-files required:
+       none
+
+ See also: BLOCHUS
+ Author: Thomas Hiller
+ email: thomas.hiller[at]leibniz-liag.de
+ License: GNU GPLv3 (at end)
    
 
 
 
    CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
      
-
    • plotBSphere	 plots a (Bloch)-Sphere (basically a unit sphere) with
    • plotResults	 plots results depending on the chosen settings
    
+
  • clearSingleAxis	 clears an individual axis
  • plotBSphere	 plots a (Bloch)-Sphere (basically a unit sphere) with
  • plotPulse	 plots different pulse parameter
  • plotRamp	 plots different pre-polarization switch-off ramp parameter
  • plotResults	 plots results depending on the chosen settings
    • 
 This function is called by:
 
@@ -42,269 +72,834 @@ 
    CROSS-REFERENCE INFORMATION ^
 
 <h2><a name=SOURCE CODE ^
    
 
    0001 function onPushAnimate(src,~)
-0002 fig  = findobj('Tag','BLOCHUS');
-0003 gui  = getappdata(fig,'gui');
-0004 data = getappdata(fig,'data');
-0005 
-0006 % change the pushbutton color to indicate that an animation is running
-0007 set(src,'BackGroundColor','r');
-0008 pause(0.01);
-0009 
-0010 NoFrames = 100;
-0011 FPS = 24;
-0012 
-0013 newblue = [0 0.4470 0.7410];
-0014 neworange = [0.8500 0.3250 0.0980];
-0015 
-0016 switch data.basic.type
-0017     
-0018     case 'std'
-0019         set(gui.text_handles.Status,'String','Animation running ...');
-0020         pause(0.01);
-0021         Mamp = zeros(numel(data.TT),1);
-0022         for i=1:numel(data.TT)
-0023             Mamp(i,1) = norm(data.MM(i,:)); % amplitude of M
-0024         end
-0025         
-0026         dt = data.TT(end)/NoFrames;
-0027         time = 0:dt:data.TT(end);
-0028         
-0029         axes(gui.axes_handles.MagL);
-0030         cla(gui.axes_handles.MagL);
-0031         h1 = animatedline('Color','r','LineWidth',2,'Parent',gui.axXYZL);
-0032         h2 = animatedline('Color','g','LineWidth',2,'Parent',gui.axXYZL);
-0033         h3 = animatedline('Color','b','LineWidth',2,'Parent',gui.axXYZL);
-0034         h4 = animatedline('Color','k','LineWidth',2,'LineStyle','--','Parent',gui.axXYZL);
-0035         
-0036         axes(gui.axes_handles.MagR);
-0037         cla(gui.axes_handles.MagR);
-0038         h7 = animatedline('Color','r','LineWidth',2,'Parent',gui.axXYZR);
-0039         h8 = animatedline('Color','g','LineWidth',2,'Parent',gui.axXYZR);
-0040         h9 = animatedline('Color','b','LineWidth',2,'Parent',gui.axXYZR);
-0041         h10 = animatedline('Color','k','LineWidth',2,'LineStyle','--','Parent',gui.axXYZR);
-0042         
-0043         axes(gui.axSphereL);
-0044         cla(gui.axSphereL);
-0045         hold(gui.axSphereL,'on');
-0046         plotBSphere(18,18,gui.axSphereL);
-0047         h5 = animatedline('Color',myui.color.basic,'LineWidth',2,'Parent',gui.axSphereL);
-0048         
-0049         axes(gui.axSphereR);
-0050         cla(gui.axSphereR);
-0051         hold(gui.axSphereR,'on');
-0052         plotBSphere(18,18,gui.axSphereR); 
-0053         h6 = animatedline('Color',myui.color.basic,'LineWidth',2,'Parent',gui.axSphereR);
-0054         
-0055         for nf = 1:NoFrames-1
-0056             
-0057             x1 = data.TT(data.TT>=time(nf) & data.TT<time(nf+1)).*1e3;
-0058             y1 = data.MM(data.TT>=time(nf) & data.TT<time(nf+1),1);
-0059             y2 = data.MM(data.TT>=time(nf) & data.TT<time(nf+1),2);
-0060             y3 = data.MM(data.TT>=time(nf) & data.TT<time(nf+1),3);
-0061             y1R = data.MMrot(data.TT>=time(nf) & data.TT<time(nf+1),1);
-0062             y2R = data.MMrot(data.TT>=time(nf) & data.TT<time(nf+1),2);
-0063             y3R = data.MMrot(data.TT>=time(nf) & data.TT<time(nf+1),3);
-0064             y4 = Mamp(data.TT>=time(nf) & data.TT<time(nf+1))./Mamp(1);
-0065             addpoints(h1,x1,y1);
-0066             addpoints(h2,x1,y2);
-0067             addpoints(h3,x1,y3);
-0068             addpoints(h4,x1,y4);
-0069             
-0070             legend(gui.axes_handles.MagL,'M_x','M_y','M_z','Location','SouthEast');
-0071             set(gui.axes_handles.MagL,'XLim',[min(data.TT.*1e3) max(data.TT.*1e3)],...
-0072                 'XTick',linspace(min(data.TT.*1e3),max(data.TT.*1e3),5))
-0073             set(get(gui.axes_handles.MagL,'XLabel'),'String','t [ms]');
-0074             set(get(gui.axes_handles.MagL,'YLabel'),'String','M');
-0075             set(get(gui.axes_handles.MagL,'Title'),'String','magnetization components - lab frame');
-0076             
-0077             
-0078             addpoints(h7,x1,y1R);
-0079             addpoints(h8,x1,y2R);
-0080             addpoints(h9,x1,y3R);
-0081             addpoints(h10,x1,y4);
-0082             
-0083             legend(gui.axes_handles.MagR,'M_x','M_y','M_z','Location','SouthEast');
-0084             set(gui.axXYZR,'XLim',[min(data.TT.*1e3) max(data.TT.*1e3)],...
-0085                 'XTick',linspace(min(data.TT.*1e3),max(data.TT.*1e3),5))
-0086             set(get(gui.axes_handles.MagR,'XLabel'),'String','t [ms]');
-0087             set(get(gui.axes_handles.MagR,'YLabel'),'String','M');
-0088             set(get(gui.axes_handles.MagR,'Title'),'String','magnetization components - rot frame');
-0089             
-0090             addpoints(h5,y1,y2,y3);
-0091             view([134 30]);
-0092             set(gui.axSphereL,'Color','w','XColor','none','YColor','none','ZColor','none');
-0093             axis equal tight
-0094             
-0095             addpoints(h6,y1R,y2R,y3R);
-0096             set(gui.axSphereR,'Color','w','XColor','none','YColor','none','ZColor','none');
-0097             axis equal tight
-0098             
-0099             pause(1/FPS);
-0100         end
-0101         hold(gui.axes_handles.MagL,'off');
-0102         hold(gui.axes_handles.MagR,'off');
-0103         hold(gui.axSphereL,'off');
-0104         hold(gui.axSphereR,'off');
-0105         set(gui.text_handles.Status,'String','Animation running ... done.');
-0106         pause(0.01);
-0107         
-0108     case 'prepol'
-0109         set(gui.text_handles.Status,'String','Animation running ...');
-0110         pause(0.01);
-0111         Mamp = zeros(numel(data.TT),1);
-0112         MM = zeros(numel(data.TT),3);
-0113         for i=1:numel(data.TT)
-0114             Mamp(i,1) = norm(data.MM(i,:)); % amplitude of M
-0115             MM(i,:) = data.MM(i,:)./Mamp(1); % normalize to initial M
-0116         end
-0117         Beffn = zeros(numel(data.results.prepol.t),3);
-0118         for i=1:numel(data.results.prepol.t)
-0119             Beffn(i,:) = data.results.prepol.Beff(i,:)./norm(data.results.prepol.Beff(i,:));
-0120         end
-0121         
-0122         dt = data.TT(end)/NoFrames;
-0123         time = 0:dt:data.TT(end);
-0124         
-0125         cla(gui.axXYZL);
-0126         axes(gui.axXYZL);
-0127         h1 = animatedline('Color','r','LineWidth',2,'Parent',gui.axXYZL);
-0128         h2 = animatedline('Color','g','LineWidth',2,'Parent',gui.axXYZL);
-0129         h3 = animatedline('Color','b','LineWidth',2,'Parent',gui.axXYZL);
-0130         h4 = animatedline('Color','k','LineWidth',2,'LineStyle','--','Parent',gui.axXYZL);
-0131         if data.prepol.Tramp < data.basic.Tsim
-0132             h11 = animatedline('Color',[0.8 0.8 0.8],'LineWidth',1,'Parent',gui.axXYZL);
-0133         end
-0134         
-0135         cla(gui.axSphereL);
-0136         axes(gui.axSphereL);
-0137         plotBlochSphere(30,30); hold on;
-0138         h5a = animatedline('Color',myui.color.prepol,'LineWidth',2,'Parent',gui.axSphereL);
-0139         h5b = animatedline('Color',myui.color.basic,'LineWidth',2,'Parent',gui.axSphereL);
-0140         h6 = animatedline('Color',myui.color.prepolB,'LineWidth',2,'Parent',gui.axSphereL);
-0141         
-0142         cla(gui.axBpre);
-0143         axes(gui.axBpre);
-0144         h10 = animatedline('Color',myui.color.prepolB,'LineWidth',2,'Parent',gui.axBpre);
-0145         y10a = data.results.prepol.Bp./data.basic.B0;
-0146         
-0147         cla(gui.axalpha);
-0148         axes(gui.axalpha);
-0149         h7 = animatedline('Color',myui.color.prepolB,'LineWidth',2,'Parent',gui.axalpha);
-0150         
-0151         cla(gui.axes_handles.dadt);
-0152         axes(gui.axes_handles.dadt);
-0153         h8 = animatedline('Color',myui.color.prepolB,'LineWidth',2,'Parent',gui.axes_handles.dadt);
-0154         y8a = data.results.prepol.dadt;
-0155         tt = data.results.prepol.t(1:end-1);
-0156         
-0157         cla(gui.axes_handles.wda);
-0158         axes(gui.axes_handles.wda);
-0159         h9 = animatedline('Color',myui.color.prepolB,'LineWidth',2,'Parent',gui.axes_handles.wda);
-0160         y9a = data.results.prepol.omega(1:numel(data.results.prepol.dadt))./data.results.prepol.dadt;
-0161         
-0162         for nf = 1:NoFrames-1
-0163             
-0164             x1 = data.TT(data.TT>=time(nf) & data.TT<time(nf+1)).*1e3;
-0165             y1 = MM(data.TT>=time(nf) & data.TT<time(nf+1),1);
-0166             y2 = MM(data.TT>=time(nf) & data.TT<time(nf+1),2);
-0167             y3 = MM(data.TT>=time(nf) & data.TT<time(nf+1),3);
-0168             
-0169             if time(nf)<data.prepol.Tramp/1e3
-0170                 y1a = MM(data.TT>=time(nf) & data.TT<time(nf+1),1);
-0171                 y2a = MM(data.TT>=time(nf) & data.TT<time(nf+1),2);
-0172                 y3a = MM(data.TT>=time(nf) & data.TT<time(nf+1),3);
-0173             else
-0174                 y1b = MM(data.TT>=time(nf) & data.TT<time(nf+1),1);
-0175                 y2b = MM(data.TT>=time(nf) & data.TT<time(nf+1),2);
-0176                 y3b = MM(data.TT>=time(nf) & data.TT<time(nf+1),3);
-0177             end
-0178             
-0179             y4 = Mamp(data.TT>=time(nf) & data.TT<time(nf+1))./Mamp(1);
-0180             addpoints(h1,x1,y1);
-0181             addpoints(h2,x1,y2);
-0182             addpoints(h3,x1,y3);
-0183             addpoints(h4,x1,y4);
-0184             if data.prepol.Tramp < data.basic.Tsim
-0185                 addpoints(h11,[data.prepol.Tramp data.prepol.Tramp],[min(min(MM)) max(max(MM))]);
-0186             end
-0187             
-0188             legend(gui.axXYZL,'M_x','M_y','M_z','Location','SouthEast');
-0189             set(gui.axXYZL,'XLim',[min(data.TT.*1e3) max(data.TT.*1e3)],...
-0190                 'XTick',linspace(min(data.TT.*1e3),max(data.TT.*1e3),5),...
-0191                 'YLim',[min(min(MM)) max(max(MM))])
-0192             set(get(gui.axXYZL,'XLabel'),'String','t [ms]');
-0193             set(get(gui.axXYZL,'YLabel'),'String','M');
-0194             set(get(gui.axXYZL,'Title'),'String',['projection M \rightarrow B_0 p = ',sprintf('%4.3f',data.results.prepol.p)]);
-0195             
-0196             y6(:,1) = Beffn(data.results.prepol.t./1e3>=time(nf) & data.results.prepol.t./1e3<time(nf+1),1);
-0197             y6(:,2) = Beffn(data.results.prepol.t./1e3>=time(nf) & data.results.prepol.t./1e3<time(nf+1),2);
-0198             y6(:,3) = Beffn(data.results.prepol.t./1e3>=time(nf) & data.results.prepol.t./1e3<time(nf+1),3);
-0199             if time(nf)<data.prepol.Tramp/1e3
-0200                 addpoints(h5a,y1a,y2a,y3a);
-0201             else
-0202                 addpoints(h5b,y1b,y2b,y3b);
-0203             end
-0204             addpoints(h6,y6(:,1),y6(:,2),y6(:,3));
-0205             set(gui.axSphereL,'XGrid','on','YGrid','on','ZGrid','on','Box','on');
-0206             axis(gui.axSphereL,'equal','tight'); view(3);
-0207             set(get(gui.axSphereL,'XLabel'),'String','X');
-0208             set(get(gui.axSphereL,'YLabel'),'String','Y');
-0209             set(get(gui.axSphereL,'ZLabel'),'String','Z');
-0210             set(get(gui.axSphereL,'Title'),'String','"Bloch sphere"');
-0211             
-0212             if data.results.prepol.t(end)/1e3 >= time(nf)
-0213                 x2 = data.results.prepol.t(data.results.prepol.t./1e3>=time(nf) & data.results.prepol.t./1e3<time(nf+1));
-0214                 x3 = tt(tt./1e3>=time(nf) & tt./1e3<time(nf+1));
-0215                 
-0216                 y10 = y10a(data.results.prepol.t./1e3>=time(nf) & data.results.prepol.t./1e3<time(nf+1));
-0217                 addpoints(h10,x2,y10);
-0218                 set(gui.axBpre,'XLim',[min(data.results.prepol.t) max(data.results.prepol.t)],'YLim',[0 data.prepol.Factor]);
-0219                 set(get(gui.axBpre,'XLabel'),'String','t [ms]');
-0220                 set(get(gui.axBpre,'YLabel'),'String','B_{pre} [B_0]');
-0221                 set(get(gui.axBpre,'Title'),'String','B_{pre} switch-off ramp');
-0222                 
-0223                 y7 = data.results.prepol.alpha(data.results.prepol.t./1e3>=time(nf) & data.results.prepol.t./1e3<time(nf+1));
-0224                 addpoints(h7,x2,y7);
-0225                 set(gui.axalpha,'XLim',[min(data.results.prepol.t) max(data.results.prepol.t)],'YLim',[min(data.results.prepol.alpha) max(data.results.prepol.alpha)]);
-0226                 set(get(gui.axalpha,'XLabel'),'String','t [ms]');
-0227                 set(get(gui.axalpha,'YLabel'),'String','\alpha [deg]');
-0228                 set(get(gui.axalpha,'Title'),'String','angle \alpha between B_0 and B_{eff}');
-0229                 
-0230                 y8 = y8a(tt./1e3>=time(nf) & tt./1e3<time(nf+1));
-0231                 addpoints(h8,x3,y8);
-0232                 set(gui.axes_handles.dadt,'XLim',[min(data.results.prepol.t) max(data.results.prepol.t)],'YLim',[min(data.results.prepol.dadt) max(data.results.prepol.dadt)]);
-0233                 set(get(gui.axes_handles.dadt,'XLabel'),'String','t [ms]');
-0234                 set(get(gui.axes_handles.dadt,'YLabel'),'String','d\alpha / dt');
-0235                 set(get(gui.axes_handles.dadt,'Title'),'String','time derivative of \alpha');
-0236                 
-0237                 y9 = y9a(tt./1e3>=time(nf) & tt./1e3<time(nf+1));
-0238                 addpoints(h9,x3,y9);
-0239                 set(gui.axes_handles.wda,'XLim',[min(data.results.prepol.t) max(data.results.prepol.t)],'YScale','log','YLim',[min(y9a) max(y9a)]);
-0240                 set(get(gui.axes_handles.wda,'XLabel'),'String','t [ms]');
-0241                 set(get(gui.axes_handles.wda,'YLabel'),'String','\omega / d\alpha');
-0242                 set(get(gui.axes_handles.wda,'Title'),'String','adiabatic criterion(?)');
-0243             end
-0244             clear y1 y2 y3 y4 y6 y7 y8 y9
-0245             pause(1/FPS);
-0246         end
-0247         hold(gui.axXYZL,'off');
-0248         hold(gui.axSphereL,'off');
-0249         set(gui.text_handles.Status,'String','Animation running ... done.');
-0250         pause(0.01);
-0251         
-0252     case 'pulse'
-0253         mgh = msgbox('Not yet implemented.','BLOCHUS info');
-0254         
-0255     case 'prepolpulse'
-0256         mgh = msgbox('Not yet implemented.','BLOCHUS info');
-0257 end
-0258 
-0259 
-0260 % change the pushbutton color back to green
-0261 % set(src,'BackGroundColor','g');
-0262 set(src,'BackGroundColor',[.94 .94 .94]);
-0263 plotResults(fig);
-0264 end % onPushAnimate
    
+0002 %onPushAnimate animates the results of the latest simulation
+0003 %
+0004 % Syntax:
+0005 %       onPushAnimate(src)
+0006 %
+0007 % Inputs:
+0008 %       src - handle of the calling object
+0009 %
+0010 % Outputs:
+0011 %       none
+0012 %
+0013 % Example:
+0014 %       onPushAnimate(src)
+0015 %
+0016 % Other m-files required:
+0017 %       clearSingleAxis
+0018 %       plotBSphere
+0019 %       plotPulse
+0020 %       plotRamp
+0021 %       plotResults
+0022 %
+0023 % Subfunctions:
+0024 %       none
+0025 %
+0026 % MAT-files required:
+0027 %       none
+0028 %
+0029 % See also: BLOCHUS
+0030 % Author: Thomas Hiller
+0031 % email: thomas.hiller[at]leibniz-liag.de
+0032 % License: GNU GPLv3 (at end)
+0033 
+0034 %------------- BEGIN CODE --------------
+0035 
+0036 % get GUI handle
+0037 fig = ancestor(src,'figure','toplevel');
+0038 
+0039 if ~isempty(fig) && strcmp(get(fig,'Tag'),'BLOCHUS')
+0040     % get GUI data
+0041     gui = getappdata(fig,'gui');
+0042     data = getappdata(fig,'data');
+0043     myui = gui.myui;
+0044     
+0045     % change the pushbutton color to indicate that an animation is running
+0046     set(src,'BackGroundColor','r');
+0047     % update the status info
+0048     set(gui.text_handles.Status,'String','Animation running ...');
+0049     pause(0.01);
+0050     
+0051     % ask the user for the number of frames to show
+0052     % default is 100
+0053     prompt = {'\fontsize{9} Number of frames (default is 100):'};
+0054     title = 'Number of Frames';
+0055     dims = [1 50];
+0056     definput = {'100'};
+0057     opts.Interpreter = 'tex';
+0058     answer = inputdlg(prompt,title,dims,definput);
+0059     if ~isempty(answer)
+0060         NoFrames = str2double(answer{1});
+0061         if isnan(NoFrames) || NoFrames<1
+0062             NoFrames = 100;
+0063         end
+0064     else
+0065          NoFrames = 100;
+0066     end    
+0067     
+0068     switch data.basic.type        
+0069         case 'std'
+0070             % the two important timings
+0071             Tsim = data.basic.Tsim;
+0072             
+0073             % get the data to animate
+0074             T = data.results.basic.T.*1e3;
+0075             M = data.results.basic.M;
+0076             Mrot = data.results.basic.Mrot;
+0077             Mxy = sqrt(M(:,1).^2+M(:,2).^2);
+0078             Mamp = sqrt(M(:,1).^2+M(:,2).^2+M(:,3).^2);
+0079             
+0080             % get the visible magnetization axis and data
+0081             switch get(gui.panels.Plot.Mag,'Selection')
+0082                 case 1
+0083                     ax1 = gui.axes_handles.MagL;
+0084                     M1 = M;
+0085                 case 2
+0086                     ax1 = gui.axes_handles.MagR;
+0087                     M1 = Mrot;
+0088                 case 3
+0089                     ax1 = gui.axes_handles.MagL;
+0090                     % auto set FFT to lab frame
+0091                     set(gui.panels.Plot.Mag,'Selection',1)
+0092             end
+0093             Mylim = get(ax1,'YLim');
+0094             % get the visible Bloch sphere axis and data
+0095             switch get(gui.panels.Plot.Sphere,'Selection')
+0096                 case 1
+0097                     ax2 = gui.axes_handles.SphereL;
+0098                     M2 = M;
+0099                 case 2
+0100                     ax2 = gui.axes_handles.SphereR;
+0101                     M2 = Mrot;
+0102             end            
+0103             Mview = get(ax2,'View');
+0104             
+0105             % time vector
+0106             t = linspace(0,Tsim,NoFrames);
+0107             
+0108             % initialize all axes and animation lines
+0109             axes(ax1);
+0110             cla(ax1);
+0111             hMx = animatedline('Color','r','LineWidth',2,'Parent',ax1);
+0112             hMy = animatedline('Color','g','LineWidth',2,'Parent',ax1);
+0113             hMz = animatedline('Color','b','LineWidth',2,'Parent',ax1);
+0114             hMxy = animatedline('Color','m','LineWidth',2,'Parent',ax1);
+0115             hMn = animatedline('Color','k','LineWidth',2,'LineStyle','--','Parent',ax1);
+0116             set(get(ax1,'XLabel'),'String','t [ms]');
+0117             set(get(ax1,'YLabel'),'String','magnetization M');
+0118             grid(ax1,'on');
+0119             set(ax1,'FontSize',myui.axfontsize);
+0120             
+0121             axes(ax2);
+0122             cla(ax2);
+0123             hold(ax2,'on');
+0124             plotBSphere(18,18,ax2);
+0125             h3dM = animatedline('Color',myui.color.basic,'LineWidth',2,'Parent',ax2);
+0126             
+0127             % loop over the data
+0128             for nf = 1:NoFrames-1
+0129                 
+0130                 % get the index vector of the current data to plot
+0131                 indt = T>=t(nf) & T<t(nf+1);
+0132                 % current time vector
+0133                 x = T(indt);
+0134                 
+0135                 % get data to plot for M
+0136                 % left panel
+0137                 yMx = M1(indt,1);
+0138                 yMy = M1(indt,2);
+0139                 yMz = M1(indt,3);
+0140                 yMxy = Mxy(indt,1);
+0141                 yMn = Mamp(indt,1);
+0142 
+0143                 % plot data into axes
+0144                 addpoints(hMx,x,yMx);
+0145                 addpoints(hMy,x,yMy);
+0146                 addpoints(hMz,x,yMz);
+0147                 addpoints(hMxy,x,yMxy);
+0148                 addpoints(hMn,x,yMn);
+0149                 
+0150                 legend(ax1,'x','M','z','Location','SouthWest');
+0151                 set(ax1,'XLim',[min(T) max(T)],'YLim',Mylim);
+0152                 lh = legend(ax1,'x','y','z','|xy|','|M|','Location','SouthWest');
+0153                 
+0154                 % Bloch sphere
+0155                 yMxx = M2(indt,1);
+0156                 yMyy = M2(indt,2);
+0157                 yMzz = M2(indt,3);
+0158                 
+0159                 addpoints(h3dM,yMxx,yMyy,yMzz);
+0160                 view(ax2,Mview);
+0161                 set(ax2,'Color','w','XColor','none','YColor','none','ZColor','none');
+0162                 axis(ax2,'equal');
+0163                 axis(ax2,'tight');
+0164                 
+0165                 % pause a bit to show the animation
+0166                 % drawnow limitrate works also but is a bit too fast
+0167                 pause(1/24);
+0168                 % drawnow limitrate;
+0169             end
+0170             hold(ax1,'off');
+0171             hold(ax2,'off');
+0172             
+0173         case 'prepol'
+0174             % get the results data
+0175             basic = data.results.basic;
+0176             prepol = data.results.prepol;
+0177             
+0178             % the two important timings
+0179             Tsim = data.basic.Tsim;
+0180             Tramp = data.prepol.Tramp;
+0181             
+0182             % get the data to animate
+0183             T1 = basic.T.*1e3;
+0184             M = basic.M;
+0185             Mxy = sqrt(M(:,1).^2+M(:,2).^2);
+0186             Mamp = sqrt(M(:,1).^2+M(:,2).^2+M(:,3).^2);
+0187             M = M./data.basic.B0;
+0188             Mxy = Mxy./data.basic.B0;
+0189             Mamp = Mamp./data.basic.B0;
+0190             % switch-off B-field trajectory
+0191             Bamp = sqrt(prepol.Beff(:,1).^2+prepol.Beff(:,2).^2+prepol.Beff(:,3).^2);
+0192             Beffn = prepol.Beff./Bamp;
+0193             
+0194             % set the M axes handles
+0195             set(gui.panels.Plot.Mag,'Selection',1);
+0196             set(gui.panels.Plot.Sphere,'Selection',1);
+0197             ax1 = gui.axes_handles.MagL;
+0198             ax2 = gui.axes_handles.SphereL;
+0199             Mylim = get(ax1,'YLim');
+0200             Mview = get(ax2,'View');
+0201             
+0202             % get the visible PrePol Ramp parameter axes and data
+0203             % only this needs to be shown
+0204             T2 = prepol.t.*1e3;
+0205             switch get(gui.panels.Plot.PrePol,'Selection')
+0206                 case 1
+0207                     ax3 = gui.axes_handles.Bpre;
+0208                     Bval = prepol.Bp./data.basic.B0;
+0209                     ylab = 'Bp [B0]';
+0210                 case 2
+0211                     ax3 = gui.axes_handles.alpha;
+0212                     Bval = rad2deg(prepol.alpha);
+0213                     ylab = '\alpha [deg]';
+0214                 case 3
+0215                     ax3 = gui.axes_handles.dadt;
+0216                     Bval = prepol.dadt;
+0217                     ylab = 'd\alpha / dt';
+0218                 case 4
+0219                     ax3 = gui.axes_handles.wda;
+0220                     Bval = prepol.dadt./prepol.omega(1:numel(prepol.dadt));
+0221                     ylab = '(d\alpha/dt) / \gammaB';
+0222             end
+0223             Bylim = get(ax3,'YLim');
+0224 
+0225             % time vector
+0226             dt = Tsim(end)/NoFrames;
+0227             % including all relevant time markers
+0228             t = unique([0:dt:Tsim Tramp]);
+0229             % adapt the number frames
+0230             NoFrames = numel(t);
+0231             
+0232             % initialize all axes and animation lines
+0233             axes(ax1);
+0234             cla(ax1);
+0235             hMx = animatedline('Color','r','LineWidth',2,'Parent',ax1);
+0236             hMy = animatedline('Color','g','LineWidth',2,'Parent',ax1);
+0237             hMz = animatedline('Color','b','LineWidth',2,'Parent',ax1);
+0238             hMxy = animatedline('Color','m','LineWidth',2,'Parent',ax1);
+0239             hMn = animatedline('Color','k','LineWidth',2,'LineStyle','--','Parent',ax1);
+0240             set(get(ax1,'XLabel'),'String','t [ms]');
+0241             set(get(ax1,'YLabel'),'String','magnetization M');
+0242             grid(ax1,'on');
+0243             set(ax1,'FontSize',myui.axfontsize);
+0244             
+0245             axes(ax2);
+0246             cla(ax2);
+0247             hold(ax2,'on');
+0248             plotBSphere(18,18,ax2);
+0249             h3dMa = animatedline('Color',myui.color.prepol,'LineWidth',2,'Parent',ax2);
+0250             h3dMb = animatedline('Color',myui.color.basic,'LineWidth',2,'Parent',ax2);
+0251             h3dB = animatedline('Color',myui.color.prepolB,'LineWidth',2,'Parent',ax2);
+0252             
+0253             axes(ax3);
+0254             clearSingleAxis(ax3);
+0255             hB = animatedline('Color',myui.color.prepolB,'LineWidth',2,'Parent',ax3);
+0256             set(get(ax3,'XLabel'),'String','t [ms]');
+0257             set(get(ax3,'YLabel'),'String',ylab);
+0258             grid(ax3,'on');
+0259             set(ax3,'FontSize',myui.axfontsize);
+0260             
+0261             % loop over the data
+0262             for nf = 1:NoFrames-1
+0263                 % get the index vector of the current data to plot
+0264                 indt = T1>=t(nf) & T1<t(nf+1);
+0265                 % get the current time vector for M
+0266                 x1 = T1(indt);
+0267                 % get data to plot for M
+0268                 yMx = M(indt,1);
+0269                 yMy = M(indt,2);
+0270                 yMz = M(indt,3);
+0271                 yMxy = Mxy(indt,1);
+0272                 yMn = Mamp(indt,1);
+0273                 
+0274                 % plot M into lab frame axes
+0275                 addpoints(hMx,x1,yMx);
+0276                 addpoints(hMy,x1,yMy);
+0277                 addpoints(hMz,x1,yMz);
+0278                 addpoints(hMxy,x1,yMxy);
+0279                 addpoints(hMn,x1,yMn);
+0280                 % M axis settings
+0281                 set(ax1,'XLim',[min(T1) max(T1)],'YLim',Mylim);
+0282                 lh = legend(ax1,'x','y','z','|xy|','|M|','Location','SouthWest');
+0283                 
+0284                 % as long as we are in the "ramp" phase gather the data of
+0285                 % the effective B-field to plot as a trace on the Bloch
+0286                 % sphere and the ramp parameter that is plotted into the
+0287                 % prepol-panel
+0288                 if t(nf) < Tramp
+0289                     indt2 = T2>=t(nf) & T2<t(nf+1);
+0290                     yBx = Beffn(indt2,1);
+0291                     yBy = Beffn(indt2,2);
+0292                     yBz = Beffn(indt2,3);
+0293                     yBramp = Bval(indt2,1);
+0294                     
+0295                     % add the M data to the sphere (prepol color)
+0296                     addpoints(h3dMa,yMx./Mamp(1),yMy./Mamp(1),yMz./Mamp(1));
+0297                     % add the B-field trace to the sphere
+0298                     addpoints(h3dB,yBx,yBy,yBz);
+0299                 else
+0300                     % after the ramp is over
+0301                     % add the M data to the sphere (basic color)
+0302                     addpoints(h3dMb,yMx./Mamp(1),yMy./Mamp(1),yMz./Mamp(1));
+0303                 end
+0304                 % sphere axis settings
+0305                 view(ax2,Mview);
+0306                 set(ax2,'XLim',[-1.05 1.05],'YLim',[-1.05 1.05],'ZLim',[-1.05 1.05])
+0307                 set(ax2,'Color','w','XColor','none','YColor','none','ZColor','none');
+0308                 axis(ax2,'equal');
+0309                 axis(ax2,'tight');
+0310                 
+0311                 % plot the ramp parameter
+0312                 if t(nf) < Tramp
+0313                     x2 = T2(indt2);
+0314                     addpoints(hB,x2,yBramp);
+0315                     set(ax3,'XLim',[min(T2) max(T2)],'YLim',Bylim);
+0316                 end
+0317                 
+0318                 % pause a bit to show the animation
+0319                 % drawnow limitrate works also but is a bit too fast
+0320                 pause(1/24);
+0321                 % drawnow limitrate;
+0322                 
+0323             end
+0324             hold(ax1,'off');
+0325             hold(ax2,'off');
+0326             hold(ax3,'off');
+0327             
+0328             % show the Ramp parameter again
+0329             plotRamp(fig);
+0330             
+0331         case 'pulse'
+0332             % get the results data
+0333             basic = data.results.basic;
+0334             pulse = data.results.pulse;
+0335             
+0336             % the two important timings
+0337             Tsim = data.basic.Tsim;
+0338             Ttau = data.pulse.Ttau;
+0339             
+0340             % get the data to animate
+0341             T1 = basic.T.*1e3;
+0342             M = basic.M;
+0343             Mrot = basic.Mrot;
+0344             Mxy = sqrt(M(:,1).^2+M(:,2).^2);
+0345             Mamp = sqrt(M(:,1).^2+M(:,2).^2+M(:,3).^2);
+0346             
+0347             % get the visible magnetization axis and data
+0348             switch get(gui.panels.Plot.Mag,'Selection')
+0349                 case 1
+0350                     ax1 = gui.axes_handles.MagL;
+0351                     M1 = M;
+0352                 case 2
+0353                     ax1 = gui.axes_handles.MagR;
+0354                     M1 = Mrot;
+0355                 case 3
+0356                     ax1 = gui.axes_handles.MagL;
+0357                     % auto set FFT to lab frame
+0358                     set(gui.panels.Plot.Mag,'Selection',1)
+0359             end
+0360             Mylim = get(ax1,'YLim');
+0361             % get the visible Bloch sphere axis and data
+0362             switch get(gui.panels.Plot.Sphere,'Selection')
+0363                 case 1
+0364                     ax2 = gui.axes_handles.SphereL;
+0365                     M2 = M;
+0366                 case 2
+0367                     ax2 = gui.axes_handles.SphereR;
+0368                     M2 = Mrot;
+0369             end
+0370             Mview = get(ax2,'View');
+0371             
+0372             % get the visible Pulse parameter axes and data
+0373             % only this needs to be shown
+0374             T2 = pulse.t;
+0375             % switch for df/I modulation axes
+0376             showdual = false;
+0377             switch get(gui.panels.Plot.Pulse,'Selection')
+0378                 case 1
+0379                     ax3a = gui.axes_handles.PulseSetupF;
+0380                     ax3b = gui.axes_handles.PulseSetupI;
+0381                     P1 = [pulse.df pulse.I];
+0382                     ylaba = 'df [Hz]';
+0383                     ylabb = 'I [A]';
+0384                     Pylima = get(ax3a,'YLim');
+0385                     Pylimb = get(ax3b,'YLim');
+0386                     showdual = true;
+0387                 case {2,3}
+0388                     ax3 = gui.axes_handles.PulseB;
+0389                     P1 = pulse.Bxy./data.basic.B0;
+0390                     ylab = 'B_1 [B_0]';
+0391                     % if FFT is visible, set axes to pulse amplitude
+0392                     set(gui.panels.Plot.Pulse,'Selection',2)
+0393                     Pylim = get(ax3,'YLim');
+0394             end
+0395             
+0396             % time vector
+0397             dt = Tsim(end)/NoFrames;
+0398             % including all relevant time markers
+0399             t = unique([0:dt:Tsim Ttau]);
+0400             % adapt the number frames
+0401             NoFrames = numel(t);
+0402             
+0403             % initialize all axes and animation lines
+0404             axes(ax1);
+0405             cla(ax1);
+0406             hMx = animatedline('Color','r','LineWidth',2,'Parent',ax1);
+0407             hMy = animatedline('Color','g','LineWidth',2,'Parent',ax1);
+0408             hMz = animatedline('Color','b','LineWidth',2,'Parent',ax1);
+0409             hMxy = animatedline('Color','m','LineWidth',2,'Parent',ax1);
+0410             hMn = animatedline('Color','k','LineWidth',2,'LineStyle','--','Parent',ax1);
+0411             set(get(ax1,'XLabel'),'String','t [ms]');
+0412             set(get(ax1,'YLabel'),'String','magnetization M');
+0413             grid(ax1,'on');
+0414             set(ax1,'FontSize',myui.axfontsize);
+0415             
+0416             axes(ax2);
+0417             cla(ax2);
+0418             hold(ax2,'on');
+0419             plotBSphere(18,18,ax2);
+0420             h3dMa = animatedline('Color',myui.color.pulse,'LineWidth',2,'Parent',ax2);
+0421             h3dMb = animatedline('Color',myui.color.basic,'LineWidth',2,'Parent',ax2);
+0422             
+0423             if showdual
+0424                 clearSingleAxis(ax3a);
+0425                 hPx = animatedline('Color',myui.color.pulse,'LineWidth',2,'Parent',ax3a);
+0426                 set(get(ax3a,'XLabel'),'String','t [ms]');
+0427                 set(get(ax3a,'YLabel'),'String',ylaba);
+0428                 grid(ax3a,'on');
+0429                 set(ax3a,'FontSize',myui.axfontsize);
+0430                 
+0431                 clearSingleAxis(ax3b);
+0432                 hPy = animatedline('Color',myui.color.pulse,'LineWidth',2,'Parent',ax3b);
+0433                 set(get(ax3b,'XLabel'),'String','t [ms]');
+0434                 set(get(ax3b,'YLabel'),'String',ylabb);
+0435                 grid(ax3b,'on');
+0436                 set(ax3b,'FontSize',myui.axfontsize);
+0437             else
+0438                 clearSingleAxis(ax3);
+0439                 hPx = animatedline('Color','r','LineWidth',2,'Parent',ax3);
+0440                 hPy = animatedline('Color','g','LineWidth',2,'Parent',ax3);
+0441                 set(get(ax3,'XLabel'),'String','t [ms]');
+0442                 set(get(ax3,'YLabel'),'String',ylab);
+0443                 grid(ax3,'on');
+0444                 set(ax3,'FontSize',myui.axfontsize);
+0445             end
+0446             
+0447             % loop over the data
+0448             for nf = 1:NoFrames-1
+0449                 % get the index vector of the current data to plot
+0450                 indt = T1>=t(nf) & T1<t(nf+1);
+0451                 % get the current time vector for M
+0452                 x1 = T1(indt);
+0453                 % get data to plot for M
+0454                 yMx = M1(indt,1);
+0455                 yMy = M1(indt,2);
+0456                 yMz = M1(indt,3);
+0457                 yMxx = M2(indt,1);
+0458                 yMyy = M2(indt,2);
+0459                 yMzz = M2(indt,3);
+0460                 yMxy = Mxy(indt,1);
+0461                 yMn = Mamp(indt,1);
+0462                 
+0463                 % plot M into lab frame axes
+0464                 addpoints(hMx,x1,yMx);
+0465                 addpoints(hMy,x1,yMy);
+0466                 addpoints(hMz,x1,yMz);
+0467                 addpoints(hMxy,x1,yMxy);
+0468                 addpoints(hMn,x1,yMn);
+0469                 % M axis settings
+0470                 set(ax1,'XLim',[min(T1) max(T1)],'YLim',Mylim);
+0471                 lh = legend(ax1,'x','y','z','|xy|','|M|','Location','SouthWest');
+0472                 
+0473                 % as long as we are in the "pulse" phase
+0474                 if t(nf) < Ttau
+0475                     % add the M data to the sphere (pulse color)
+0476                     addpoints(h3dMa,yMxx,yMyy,yMzz);
+0477                 else
+0478                     % after the ramp is over
+0479                     % add the M data to the sphere (basic color)
+0480                     addpoints(h3dMb,yMxx,yMyy,yMzz);
+0481                 end
+0482                 % sphere axis settings
+0483                 view(ax2,Mview);
+0484                 set(ax2,'XLim',[-1.05 1.05],'YLim',[-1.05 1.05],'ZLim',[-1.05 1.05])
+0485                 set(ax2,'Color','w','XColor','none','YColor','none','ZColor','none');
+0486                 axis(ax2,'equal');
+0487                 axis(ax2,'tight');
+0488                 
+0489                 % plot the Pulse parameter
+0490                 if t(nf) < Ttau
+0491                     indt2 = T2>=t(nf) & T2<t(nf+1); % t2?
+0492                     x2 = T2(indt2);
+0493                     yBx = P1(indt2,1);
+0494                     yBy = P1(indt2,2);
+0495                     
+0496                     addpoints(hPx,x2,yBx);
+0497                     addpoints(hPy,x2,yBy);
+0498                     if showdual
+0499                         set(ax3a,'XLim',[min(T2) max(T2)],'YLim',Pylima);
+0500                         lh = legend(ax3a,'df mod.','Location','SouthEast');
+0501                         
+0502                         set(ax3b,'XLim',[min(T2) max(T2)],'YLim',Pylimb);
+0503                         lh = legend(ax3b,'I mod.','Location','SouthEast');
+0504                     else
+0505                         set(ax3,'XLim',[min(T2) max(T2)],'YLim',Pylim);
+0506                         lh = legend(ax3,'x','y','Location','SouthWest');
+0507                     end
+0508                 end
+0509                 
+0510                 % pause a bit to show the animation
+0511                 % drawnow limitrate works also but is a bit too fast
+0512                 pause(1/24);
+0513                 % drawnow limitrate;
+0514                 
+0515             end
+0516             hold(ax1,'off');
+0517             hold(ax2,'off');
+0518             if showdual
+0519                 hold(ax3a,'off');
+0520                 hold(ax3b,'off');
+0521             else
+0522                 hold(ax3,'off');
+0523             end
+0524             % show the Pulse parameter again
+0525             plotPulse(fig);
+0526             
+0527         case 'prepolpulse'
+0528             % get the results data
+0529             basic = data.results.basic;
+0530             prepol = data.results.prepol;
+0531             pulse = data.results.pulse;
+0532             
+0533             % the important timings
+0534             Tsim = data.basic.Tsim;
+0535             Tramp = data.prepol.Tramp;
+0536             Ttau = data.pulse.Ttau;
+0537             Twait = data.pulse.Twait;
+0538             Trelax = Tsim-Tramp-Twait-Ttau;
+0539             
+0540             % get the data to animate
+0541             T1 = basic.T.*1e3;
+0542             M = basic.M;
+0543             Mrot = basic.Mrot;
+0544             Mxy = sqrt(M(:,1).^2+M(:,2).^2);
+0545             Mamp = sqrt(M(:,1).^2+M(:,2).^2+M(:,3).^2);
+0546             % normalize the magnetization
+0547             M = M./data.basic.B0;
+0548             Mrot = Mrot./data.basic.B0;
+0549             Mxy = Mxy./data.basic.B0;
+0550             Mamp = Mamp./data.basic.B0;
+0551             % switch-off B-field trajectory
+0552             Bamp = sqrt(prepol.Beff(:,1).^2+prepol.Beff(:,2).^2+prepol.Beff(:,3).^2);
+0553             Beffn = prepol.Beff./Bamp;
+0554             
+0555             % get the visible magnetization axis and data
+0556             switch get(gui.panels.Plot.Mag,'Selection')
+0557                 case 1
+0558                     ax1 = gui.axes_handles.MagL;
+0559                     M1 = M;
+0560                 case 2
+0561                     ax1 = gui.axes_handles.MagR;
+0562                     M1 = Mrot;
+0563                 case 3
+0564                     ax1 = gui.axes_handles.MagL;
+0565                     % auto set FFT to lab frame
+0566                     set(gui.panels.Plot.Mag,'Selection',1)
+0567             end
+0568             Mylim = get(ax1,'YLim');            
+0569             % get the visible Bloch sphere axis and data
+0570             switch get(gui.panels.Plot.Sphere,'Selection')
+0571                 case 1
+0572                     ax2 = gui.axes_handles.SphereL;
+0573                     M2 = M;
+0574                 case 2
+0575                     ax2 = gui.axes_handles.SphereR;
+0576                     M2 = Mrot;
+0577             end
+0578             Mview = get(ax2,'View');
+0579             
+0580             % get the visible PrePol Ramp parameter axis and data
+0581             T2 = prepol.t.*1e3;
+0582             switch get(gui.panels.Plot.PrePol,'Selection')
+0583                 case 1
+0584                     ax3 = gui.axes_handles.Bpre;
+0585                     Bval = prepol.Bp./data.basic.B0;
+0586                     ylab = 'Bp [B0]';
+0587                 case 2
+0588                     ax3 = gui.axes_handles.alpha;
+0589                     Bval = rad2deg(prepol.alpha);
+0590                     ylab = '\alpha [deg]';
+0591                 case 3
+0592                     ax3 = gui.axes_handles.dadt;
+0593                     Bval = prepol.dadt;
+0594                     ylab = 'd\alpha / dt';
+0595                 case 4
+0596                     ax3 = gui.axes_handles.wda;
+0597                     Bval = prepol.dadt./prepol.omega(1:numel(prepol.dadt));
+0598                     Bval = [Bval;Bval(end)];
+0599                     ylab = '(d\alpha/dt) / \gammaB';
+0600             end
+0601             Bylim = get(ax3,'YLim');
+0602             
+0603             % get the visible Pulse parameter axes and data
+0604             T3 = pulse.t;
+0605             % switch for df/I modulation axes
+0606             showdual = false;
+0607             switch get(gui.panels.Plot.Pulse,'Selection')
+0608                 case 1
+0609                     ax4a = gui.axes_handles.PulseSetupF;
+0610                     ax4b = gui.axes_handles.PulseSetupI;
+0611                     P1 = [pulse.df pulse.I];
+0612                     ylaba = 'df [Hz]';
+0613                     ylabb = 'I [A]';
+0614                     Pylima = get(ax4a,'YLim');
+0615                     Pylimb = get(ax4b,'YLim');
+0616                     showdual = true;
+0617                 case {2,3}
+0618                     ax4 = gui.axes_handles.PulseB;
+0619                     P1 = pulse.Bxy./data.basic.B0;
+0620                     ylab = 'B_1 [B_0]';
+0621                     % if FFT is visible, set axes to pulse amplitude
+0622                     set(gui.panels.Plot.Pulse,'Selection',2)
+0623                     Pylim = get(ax4,'YLim');
+0624             end
+0625 
+0626             % time vector
+0627             dt = Tsim(end)/NoFrames;
+0628             % including all relevant time markers
+0629             t = unique([0:dt:Tsim Tramp Tramp+Twait Tramp+Twait+Ttau]);
+0630             % adapt the number frames
+0631             NoFrames = numel(t);
+0632 
+0633             % initialize all axes and animation lines
+0634             axes(ax1);
+0635             cla(ax1);
+0636             hMx = animatedline('Color','r','LineWidth',2,'Parent',ax1);
+0637             hMy = animatedline('Color','g','LineWidth',2,'Parent',ax1);
+0638             hMz = animatedline('Color','b','LineWidth',2,'Parent',ax1);
+0639             hMxy = animatedline('Color','m','LineWidth',2,'Parent',ax1);
+0640             hMn = animatedline('Color','k','LineWidth',2,'LineStyle','--','Parent',ax1);
+0641             set(get(ax1,'XLabel'),'String','t [ms]');
+0642             set(get(ax1,'YLabel'),'String','magnetization M');
+0643             grid(ax1,'on');
+0644             set(ax1,'FontSize',myui.axfontsize);
+0645             
+0646             axes(ax2);
+0647             cla(ax2);
+0648             hold(ax2,'on');
+0649             plotBSphere(18,18,ax2);
+0650             h3dMa = animatedline('Color',myui.color.prepol,'LineWidth',2,'Parent',ax2);
+0651             h3dMb = animatedline('Color',myui.color.wait,'LineWidth',2,'Parent',ax2);
+0652             h3dMc = animatedline('Color',myui.color.pulse,'LineWidth',2,'Parent',ax2);
+0653             h3dMd = animatedline('Color',myui.color.basic,'LineWidth',2,'Parent',ax2);
+0654             h3dB = animatedline('Color',myui.color.prepolB,'LineWidth',2,'Parent',ax2);
+0655             
+0656             axes(ax3);
+0657             clearSingleAxis(ax3);
+0658             hB = animatedline('Color',myui.color.prepolB,'LineWidth',2,'Parent',ax3);
+0659             set(get(ax3,'XLabel'),'String','t [ms]');
+0660             set(get(ax3,'YLabel'),'String',ylab);
+0661             grid(ax3,'on');
+0662             set(ax3,'FontSize',myui.axfontsize);
+0663             
+0664             if showdual
+0665                 clearSingleAxis(ax4a);
+0666                 hPx = animatedline('Color',myui.color.pulse,'LineWidth',2,'Parent',ax4a);
+0667                 set(get(ax4a,'XLabel'),'String','t [ms]');
+0668                 set(get(ax4a,'YLabel'),'String',ylaba);
+0669                 grid(ax4a,'on');
+0670                 set(ax4a,'FontSize',myui.axfontsize);
+0671                 
+0672                 clearSingleAxis(ax4b);
+0673                 hPy = animatedline('Color',myui.color.pulse,'LineWidth',2,'Parent',ax4b);
+0674                 set(get(ax4b,'XLabel'),'String','t [ms]');
+0675                 set(get(ax4b,'YLabel'),'String',ylabb);
+0676                 grid(ax4b,'on');
+0677                 set(ax4b,'FontSize',myui.axfontsize);
+0678             else
+0679                 clearSingleAxis(ax4);
+0680                 hPx = animatedline('Color','r','LineWidth',2,'Parent',ax4);
+0681                 hPy = animatedline('Color','g','LineWidth',2,'Parent',ax4);
+0682                 set(get(ax4,'XLabel'),'String','t [ms]');
+0683                 set(get(ax4,'YLabel'),'String',ylab);
+0684                 grid(ax4,'on');
+0685                 set(ax4,'FontSize',myui.axfontsize);
+0686             end
+0687             
+0688             % loop over the data
+0689             for nf = 1:NoFrames-1
+0690                 % get the index vector of the current M data to plot
+0691                 indt = T1>=t(nf) & T1<t(nf+1);
+0692                 % get the current time vector for M
+0693                 x1 = T1(indt);
+0694                 % get data to plot for M
+0695                 yMx = M1(indt,1);
+0696                 yMy = M1(indt,2);
+0697                 yMz = M1(indt,3);
+0698                 yMxx = M2(indt,1)./Mamp(1);
+0699                 yMyy = M2(indt,2)./Mamp(1);
+0700                 yMzz = M2(indt,3)./Mamp(1);
+0701                 yMxy = Mxy(indt,1);
+0702                 yMn = Mamp(indt,1);
+0703                 
+0704                 % plot M into the left panel
+0705                 addpoints(hMx,x1,yMx);
+0706                 addpoints(hMy,x1,yMy);
+0707                 addpoints(hMz,x1,yMz);
+0708                 addpoints(hMxy,x1,yMxy);
+0709                 addpoints(hMn,x1,yMn);
+0710                 % M axis settings
+0711                 set(ax1,'XLim',[min(T1) max(T1)],'YLim',Mylim);
+0712                 lh = legend(ax1,'x','y','z','|xy|','|M|','Location','SouthWest');
+0713                 
+0714                 % plot into the Bloch sphere
+0715                 % as long as we are in the "pulse" phase
+0716                 if t(nf) < Tramp
+0717                     indt2 = T2>t(nf) & T2<=t(nf+1); % t2?
+0718                     yBx = Beffn(indt2,1);
+0719                     yBy = Beffn(indt2,2);
+0720                     yBz = Beffn(indt2,3);
+0721                     yBramp = Bval(indt2,1);
+0722                     
+0723                     % add the M data to the sphere (prepol color)
+0724                     addpoints(h3dMa,yMxx,yMyy,yMzz);
+0725                     % add the B-field trace to the sphere
+0726                     addpoints(h3dB,yBx,yBy,yBz);
+0727                 elseif t(nf)>Tramp && t(nf) <= Tramp+Twait
+0728                     % add the M data to the sphere (wait color)
+0729                     addpoints(h3dMb,yMxx,yMyy,yMzz);
+0730                 elseif t(nf)>Tramp+Twait && t(nf) <= Tsim-Trelax
+0731                     % add the M data to the sphere (pulse color)
+0732                     addpoints(h3dMc,yMxx,yMyy,yMzz);
+0733                 elseif t(nf) > Tsim-Trelax
+0734                     % after the pulse is over
+0735                     % add the M data to the sphere (basic color)
+0736                     addpoints(h3dMd,yMxx,yMyy,yMzz);
+0737                 end
+0738                 % sphere axis settings
+0739                 view(ax2,Mview);
+0740                 set(ax2,'XLim',[-1.05 1.05],'YLim',[-1.05 1.05],'ZLim',[-1.05 1.05])
+0741                 set(ax2,'Color','w','XColor','none','YColor','none','ZColor','none');
+0742                 axis(ax2,'equal');
+0743                 axis(ax2,'tight');
+0744                 
+0745                 % plot the ramp parameter
+0746                 if t(nf) < Tramp
+0747                     x2 = T2(indt2);
+0748                     addpoints(hB,x2,yBramp);
+0749                     set(ax3,'XLim',[min(T2) max(T2)],'YLim',Bylim);
+0750                 end
+0751                 
+0752                 % plot the Pulse parameter
+0753                 if t(nf)>=Tramp+Twait && t(nf) < Tsim-Trelax
+0754                     indt3 = T3+Tramp+Twait>=t(nf) & T3+Tramp+Twait<t(nf+1);
+0755                     x3 = T3(indt3);
+0756                     yBx = P1(indt3,1);
+0757                     yBy = P1(indt3,2);
+0758                     
+0759                     addpoints(hPx,x3,yBx);
+0760                     addpoints(hPy,x3,yBy);
+0761                     if showdual
+0762                         set(ax4a,'XLim',[min(T3) max(T3)],'YLim',Pylima);
+0763                         lh = legend(ax4a,'df mod.','Location','SouthEast');
+0764                         
+0765                         set(ax4b,'XLim',[min(T3) max(T3)],'YLim',Pylimb);
+0766                         lh = legend(ax4b,'I mod.','Location','SouthEast');
+0767                     else
+0768                         set(ax4,'XLim',[min(T3) max(T3)],'YLim',Pylim);
+0769                         lh = legend(ax4,'x','y','Location','SouthWest');
+0770                     end
+0771                 end
+0772                 
+0773                 % pause a bit to show the animation
+0774                 % drawnow limitrate works also but is a bit too fast
+0775                 pause(1/24);
+0776                 % drawnow limitrate;
+0777                 
+0778             end
+0779             hold(ax1,'off');
+0780             hold(ax2,'off');
+0781             hold(ax3,'off');
+0782             if showdual
+0783                 hold(ax4a,'off');
+0784                 hold(ax4b,'off');
+0785             else
+0786                 hold(ax4,'off');
+0787             end
+0788             % show the Ramp parameter again
+0789             plotRamp(fig);
+0790             % show the Pulse parameter again
+0791             plotPulse(fig);    
+0792     end
+0793     
+0794     % reset the pushbutton color
+0795     set(src,'BackGroundColor',[.94 .94 .94]);
+0796     % update the status info
+0797     set(gui.text_handles.Status,'String','Animation running ... finished.');
+0798     % done
+0799     pause(0.01);
+0800     % show the results parameter again
+0801     plotResults(fig);
+0802     
+0803 else
+0804     warndlg({'onPushAnimate:','There is no figure with the BLOCHUS Tag open.'},...
+0805         'BLOCHUS error');
+0806 end
+0807 
+0808 end
+0809 
+0810 %------------- END OF CODE --------------
+0811 
+0812 %% License:
+0813 % GNU GPLv3
+0814 %
+0815 % BLOCHUS
+0816 % Copyright (C) 2019 Thomas Hiller
+0817 %
+0818 % This program is free software: you can redistribute it and/or modify
+0819 % it under the terms of the GNU General Public License as published by
+0820 % the Free Software Foundation, either version 3 of the License, or
+0821 % (at your option) any later version.
+0822 %
+0823 % This program is distributed in the hope that it will be useful,
+0824 % but WITHOUT ANY WARRANTY; without even the implied warranty of
+0825 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+0826 % GNU General Public License for more details.
+0827 %
+0828 % You should have received a copy of the GNU General Public License
+0829 % 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 79ef27d..dae2f38 100644
--- a/doc/blochus/callbacks/push/onPushRun.html
+++ b/doc/blochus/callbacks/push/onPushRun.html
@@ -120,570 +120,588 @@ 
    SOURCE CODE ^% change the pushbutton color to indicate that a calculation is running
 0047     set(src,'BackGroundColor','r');
-0048     
-0049     % basic parameter that are always needed
-0050     % z unit vector
-0051     zunit = [0 0 1]';
-0052     % initial magnetization [A/m]
-0053     Minit = data.basic.Minit(:);
-0054     % total simulation time Tsim [s]
-0055     Tsim = data.basic.Tsim/1e3; 
-0056     
-0057     % parameter needed for the ODE solver
-0058     % simulation type [string]
-0059     odeparam.type = data.basic.type;
-0060     % equilibrium magnetization [A/m]
-0061     odeparam.M0 = data.basic.M0(:);
-0062     % primary (Earth's) magnetic field B0 [T]
-0063     odeparam.B0 = data.basic.B0;
-0064     % longitudinal relaxation time T1 [s]
-0065     odeparam.T1 = data.basic.T1relax/1e3;
-0066     % transversal relaxation time T2 [s]
-0067     odeparam.T2 = data.basic.T2relax/1e3;
-0068     % gyromagnetic ratio [rad/s/T]
-0069     odeparam.gamma = data.basic.gamma; 
-0070     
-0071     % ODE solver error tolerance
-0072     tol = 1e-9;
-0073     % ODE solver options
-0074     options = odeset('RelTol',tol,'AbsTol',[tol tol tol]);
-0075     
-0076     % time the calculation
-0077     t0 = tic;
-0078     switch data.basic.type
-0079         case 'std'
-0080             % update Info field
-0081             set(gui.text_handles.Status,'String','Calculation of relaxation ...');
-0082             pause(0.01);
-0083             
-0084             % normalized initial magnetization
-0085             Minit = Minit./norm(Minit);
-0086             % update the corresponding GUI fields
-0087             data.basic.Minit = Minit;
-0088             set(gui.edit_handles.Minitx,'String',sprintf('%4.3f',Minit(1)));
-0089             set(gui.edit_handles.Minity,'String',sprintf('%4.3f',Minit(2)));
-0090             set(gui.edit_handles.Minitz,'String',sprintf('%4.3f',Minit(3)));
-0091             
-0092             % ODE solver call
-0093             % OUTPUT: time T and magnetization M
-0094             [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
-0095             
-0096             % save data
-0097             data.results.basic.T = TT;
-0098             data.results.basic.M = MM;
-0099             
-0100             % rotate M into rotating frame of reference
-0101             Mrot = getMrot(MM,getOmega0(odeparam.gamma,odeparam.B0).*TT);
-0102             data.results.basic.Mrot = Mrot;
-0103             
-0104             % get FFTof M in the laboratory frame of reference
-0105             [Xm,fx] = getFFT(TT,MM(:,1:2));
-0106             data.results.basic.Mspec.fx = fx;
-0107             data.results.basic.Mspec.X = Xm;
-0108             
-0109             % update Info field
-0110             set(gui.text_handles.Status,'String','Calculation of relaxation ... finished.');
-0111             pause(0.01);
-0112             
-0113         case 'prepol'
-0114             % update Info field
-0115             set(gui.text_handles.Status,'String','Calculation of pre-polarization switch-off ...');
-0116             pause(0.01);
-0117             
-0118             % initial magnetization in the direction of B0+Bp
-0119             Morient = data.results.prepol.orient*data.results.prepol.Bmax + odeparam.B0*zunit;
-0120             % Minit does not get normalized in this case
-0121             Minit = Morient;%./norm(Morient);
-0122             % because Minit is not normalized to 1, M0 needs to be adjusted
-0123             odeparam.M0 = odeparam.B0*zunit;
-0124             % update the corresponding GUI fields
-0125             set(gui.edit_handles.Minitx,'String',sprintf('%4.3f',Minit(1)/norm(Minit)));
-0126             set(gui.edit_handles.Minity,'String',sprintf('%4.3f',Minit(2)/norm(Minit)));
-0127             set(gui.edit_handles.Minitz,'String',sprintf('%4.3f',Minit(3)/norm(Minit)));
-0128             
-0129             % orientation of the pre-polarization pulse axis
-0130             odeparam.orient = data.results.prepol.orient;
-0131             
-0132             % pre-polarization switch-off ramp parameter
-0133             % relaxation during switch-off [0/1]
-0134             odeparam.RDS = data.prepol.RDS;
-0135             % switch-off ramp type [string]
-0136             rampparam.ramp = data.prepol.Ramp;            
-0137             % amplitude of pre-polarization field
-0138             rampparam.Bmax = data.results.prepol.Bmax;
-0139             % switch over magnetization (for linexp case)
-0140             rampparam.Bstar = data.results.prepol.Bstar;
-0141             % switch-off ramp time [s]
-0142             rampparam.Tramp = data.prepol.Tramp/1e3;
-0143             % switch over ramp time [s] (for linexp case)
-0144             rampparam.Tslope = data.prepol.Tslope/1e3;
-0145             
-0146             % add the ramp parameter to the ode parameter struct
-0147             odeparam.rampparam = rampparam;
-0148             
-0149             % ODE solver call
-0150             % OUTPUT: time T and magnetization M
-0151             [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
-0152             
-0153             % normalized magnetization vector at end of switch-off ramp
-0154             MMn = MM(end,:)./norm(MM(end,:));
-0155             % "adiabatic quality" p of the switch-off ramp
-0156             % -> orientation of M with respect to z_unit
-0157             p = dot(MMn(end,:),zunit)./norm(zunit);
-0158             
-0159             % save data
-0160             data.results.basic.T = TT;
-0161             data.results.basic.M = MM;
-0162             data.results.prepol.p = p;
+0048     % reset the color of the animate button
+0049     set(gui.push_handles.Animate,'BackGroundColor',[.94 .94 .94]);
+0050     
+0051     % basic parameter that are always needed
+0052     % z unit vector
+0053     zunit = [0 0 1]';
+0054     % initial magnetization [A/m]
+0055     Minit = data.basic.Minit(:);
+0056     % total simulation time Tsim [s]
+0057     Tsim = data.basic.Tsim/1e3; 
+0058     
+0059     % parameter needed for the ODE solver
+0060     % simulation type [string]
+0061     odeparam.type = data.basic.type;
+0062     % equilibrium magnetization [A/m]
+0063     odeparam.M0 = data.basic.M0(:);
+0064     % primary (Earth's) magnetic field B0 [T]
+0065     odeparam.B0 = data.basic.B0;
+0066     % longitudinal relaxation time T1 [s]
+0067     odeparam.T1 = data.basic.T1relax/1e3;
+0068     % transversal relaxation time T2 [s]
+0069     odeparam.T2 = data.basic.T2relax/1e3;
+0070     % gyromagnetic ratio [rad/s/T]
+0071     odeparam.gamma = data.basic.gamma; 
+0072     
+0073     % ODE solver error tolerance
+0074     tol = 1e-9;
+0075     % ODE solver options
+0076     options = odeset('RelTol',tol,'AbsTol',[tol tol tol]);
+0077     
+0078     % time the calculation
+0079     t0 = tic;
+0080     switch data.basic.type
+0081         case 'std'
+0082             % update Info field
+0083             set(gui.text_handles.Status,'String','Calculation of relaxation ...');
+0084             pause(0.01);
+0085             
+0086             % normalized initial magnetization
+0087             Minit = Minit./norm(Minit);
+0088             % update the corresponding GUI fields
+0089             data.basic.Minit = Minit;
+0090             set(gui.edit_handles.Minitx,'String',sprintf('%4.3f',Minit(1)));
+0091             set(gui.edit_handles.Minity,'String',sprintf('%4.3f',Minit(2)));
+0092             set(gui.edit_handles.Minitz,'String',sprintf('%4.3f',Minit(3)));
+0093             
+0094             % ODE solver call
+0095             % OUTPUT: time T and magnetization M
+0096             [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
+0097             
+0098             % save data
+0099             data.results.basic.T = TT;
+0100             data.results.basic.M = MM;
+0101             
+0102             % rotate M into rotating frame of reference
+0103             Mrot = getMrot(MM,getOmega0(odeparam.gamma,odeparam.B0).*TT);
+0104             data.results.basic.Mrot = Mrot;
+0105             
+0106             % get FFTof M in the laboratory frame of reference
+0107             [Xm,fx] = getFFT(TT,MM(:,1:2));
+0108             data.results.basic.Mspec.fx = fx;
+0109             data.results.basic.Mspec.X = Xm;
+0110             
+0111             % update Info field
+0112             set(gui.text_handles.Status,'String','Calculation of relaxation ... finished.');
+0113             pause(0.01);
+0114             
+0115         case 'prepol'
+0116             % update Info field
+0117             set(gui.text_handles.Status,'String','Calculation of pre-polarization switch-off ...');
+0118             pause(0.01);
+0119             
+0120             % initial magnetization in the direction of B0+Bp
+0121             Morient = data.results.prepol.orient*data.results.prepol.Bmax + odeparam.B0*zunit;
+0122             % Minit does not get normalized in this case
+0123             Minit = Morient;%./norm(Morient);
+0124             % because Minit is not normalized to 1, M0 needs to be adjusted
+0125             odeparam.M0 = odeparam.B0*zunit;
+0126             % update the corresponding GUI fields
+0127             set(gui.edit_handles.Minitx,'String',sprintf('%4.3f',Minit(1)/norm(Minit)));
+0128             set(gui.edit_handles.Minity,'String',sprintf('%4.3f',Minit(2)/norm(Minit)));
+0129             set(gui.edit_handles.Minitz,'String',sprintf('%4.3f',Minit(3)/norm(Minit)));
+0130             
+0131             % orientation of the pre-polarization pulse axis
+0132             odeparam.orient = data.results.prepol.orient;
+0133             
+0134             % pre-polarization switch-off ramp parameter
+0135             % relaxation during switch-off [0/1]
+0136             odeparam.RDS = data.prepol.RDS;
+0137             % switch-off ramp type [string]
+0138             rampparam.ramp = data.prepol.Ramp;            
+0139             % amplitude of pre-polarization field
+0140             rampparam.Bmax = data.results.prepol.Bmax;
+0141             % switch over magnetization (for linexp case)
+0142             rampparam.Bstar = data.results.prepol.Bstar;
+0143             % switch-off ramp time [s]
+0144             rampparam.Tramp = data.prepol.Tramp/1e3;
+0145             % switch over ramp time [s] (for linexp case)
+0146             rampparam.Tslope = data.prepol.Tslope/1e3;
+0147             
+0148             % add the ramp parameter to the ode parameter struct
+0149             odeparam.rampparam = rampparam;
+0150             
+0151             % ODE solver call
+0152             % OUTPUT: time T and magnetization M
+0153             [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
+0154             
+0155             % normalized magnetization vector at end of switch-off ramp
+0156             % because the simulation can be longer than the ramp, find the
+0157             % last point of the ramp to calculate the adiabatic quality p
+0158             indt = find(TT<=rampparam.Tramp,1,'last');
+0159             MMn = MM(indt,:)./norm(MM(indt,:));
+0160             % "adiabatic quality" p of the switch-off ramp
+0161             % -> orientation of M with respect to z_unit
+0162             p = dot(MMn,zunit)./norm(zunit);
 0163             
-0164             % update Info field
-0165             set(gui.text_handles.Status,'String','Calculation of pre-polarization switch-off ... finished.');
-0166             pause(0.01);
-0167             
-0168             % activate the lab-frame panels to show the results
-0169             set(gui.panels.Plot.Mag,'Selection',1);
-0170             set(gui.panels.Plot.Sphere,'Selection',1);
-0171             
-0172         case 'pulse'
-0173             % update Info field
-0174             set(gui.text_handles.Status,'String','Calculation of excitation pulse ...');
-0175             pause(0.01);
+0164             % save data
+0165             data.results.basic.T = TT;
+0166             data.results.basic.M = MM;
+0167             data.results.prepol.p = p;
+0168             
+0169             % update Info field
+0170             set(gui.text_handles.Status,'String','Calculation of pre-polarization switch-off ... finished.');
+0171             pause(0.01);
+0172             
+0173             % activate the lab-frame panels to show the results
+0174             set(gui.panels.Plot.Mag,'Selection',1);
+0175             set(gui.panels.Plot.Sphere,'Selection',1);
 0176             
-0177             % normalized initial magnetization
-0178             Minit = Minit./norm(Minit);
-0179             % update the corresponding GUI fields
-0180             data.basic.Minit = Minit;
-0181             set(gui.edit_handles.Minitx,'String',sprintf('%4.3f',Minit(1)));
-0182             set(gui.edit_handles.Minity,'String',sprintf('%4.3f',Minit(2)));
-0183             set(gui.edit_handles.Minitz,'String',sprintf('%4.3f',Minit(3)));
-0184             
-0185             % excitation pulse parameter
-0186             % relaxation during pulse [0/1]
-0187             odeparam.RDP = data.pulse.RDP;
-0188             % pulse length [s]
-0189             odeparam.Ttau = data.pulse.Ttau/1e3;
-0190             % pulse type [string]
-0191             pulseparam.PulseType = data.pulse.Type;
-0192             % gyromagnetic ratio [rad/s/T]
-0193             pulseparam.gamma = odeparam.gamma;
-0194             % Larmor frequency [rad]
-0195             pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
-0196             % pulse amplitude [B0]
-0197             pulseparam.Amp = odeparam.B0*data.pulse.B1Factor;
-0198             % pulse frequency modulation [struct]
-0199             pulseparam.fmod = data.results.pulse.fmod;
-0200             % pulse current modulation [struct]
-0201             pulseparam.Imod = data.results.pulse.Imod;
-0202             % auxiliary pulse phase [rad]
-0203             pulseparam.phi = 0;
-0204             % pulse axis [string]
-0205             pulseparam.PulseAxis = data.pulse.Axis;
-0206             % pulse polarization [string]
-0207             pulseparam.PulsePolarization = data.pulse.Polarization;
-0208             % if the discrete MIDI pulses are used add the corresponding
-0209             % data
-0210             if isfield(data,'pulse_MIDI')
-0211                 % MIDI pulse data [struct]
-0212                 pulseparam.MIDI = data.pulse_MIDI;
-0213             end
-0214             
-0215             % add the pulse parameter to the ode parameter struct
-0216             odeparam.pulseparam = pulseparam;
-0217             
-0218             % ODE solver call
-0219             % OUTPUT: time T and magnetization M
-0220             switch data.pulse.Type
-0221                 case {'MIDI_OR','MIDI_AP'}
-0222                     % if Tsim > Ttau extend the discrete time steps
-0223                     % this is needed because for the discrete pulses
-0224                     % specific time steps are fed into the solver
-0225                     Tsim = unique([data.pulse_MIDI.t;(0:1/50e3:Tsim)']);
-0226                     [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),Tsim,Minit,options);
-0227                 otherwise
-0228                     [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
-0229             end
-0230             
-0231             % save data
-0232             data.results.basic.T = TT;
-0233             data.results.basic.M = MM;
-0234             
-0235             % in order to transform M in the rotating frame of reference
-0236             % get the pulse phase theta for all simulated time steps
-0237             pulseparam.fmod.t = TT;
-0238             pulseparam.Imod.t = TT;
-0239             pulseparam.t = TT;
-0240             % get also the pulse amplitudes at these time steps
-0241             [Bpulse,~,~,theta] = getPulseTimeSeries(pulseparam);
-0242             
-0243             % if the simulation is longer then the pulse (additional
-0244             % relaxation afterwards), correct for the pulse phase for
-0245             % points AFTER the pulse by simply calculating the phase at
-0246             % the end of the pulse
-0247             if data.basic.Tsim>data.pulse.Ttau
-0248                 % correction phase
-0249                 dphi = zeros(size(theta));
-0250                 % pulse length
-0251                 Ttau = odeparam.Ttau;
-0252                 % get pulse phase at the end of the pulse
-0253                 dphival = getPulsePhase(Ttau,0,pulseparam,1);
-0254                 % and add it to the correction phase for all time steps after
-0255                 % the pulse
-0256                 indT = TT>Ttau;
-0257                 dphi(indT) = dphival;
-0258                 % set theta for all time steps after the pulse simply to
-0259                 % omega0*t
-0260                 theta(indT) = getOmega0(odeparam.gamma,odeparam.B0).*TT(indT);
-0261                 % rotate M into rotating frame of reference
-0262                 Mrot = getMrot(MM,theta,dphi);
-0263                 % get FFTof M in the laboratory frame of reference
-0264                 [Xm,fmx] = getFFT(TT,MM(:,1:2));
-0265                 % get FFT for the pulse
-0266                 [Xb,fbx] = getFFT(TT(TT<=Ttau),Bpulse(TT<=Ttau,1:2));
-0267                 
-0268                 % update Info field
-0269                 set(gui.text_handles.Status,'String','Calculation of excitation pulse & relaxation ... finished.');
-0270                 pause(0.01);
-0271             else
-0272                 % rotate M into rotating frame of reference
-0273                 Mrot = getMrot(MM,theta);
-0274                 % get FFTof M in the laboratory frame of reference
-0275                 [Xm,fmx] = getFFT(TT,MM(:,1:2));
-0276                 % get FFT for the pulse
-0277                 [Xb,fbx] = getFFT(TT,Bpulse(:,1:2));
-0278                 
-0279                 % update Info field
-0280                 set(gui.text_handles.Status,'String','Calculation of excitation pulse ... finished.');
-0281                 pause(0.01);
-0282             end
-0283             
-0284             % save data
-0285             data.results.basic.Mrot = Mrot;
-0286             data.results.basic.Mspec.fx = fmx;
-0287             data.results.basic.Mspec.X = Xm;
-0288             data.results.pulse.Bspec.fx = fbx;
-0289             data.results.pulse.Bspec.X = Xb;
-0290             
-0291         case 'prepolpulse'
-0292             
-0293             % this is basically the combination of all of the above
-0294             % simulation types
+0177         case 'pulse'
+0178             % update Info field
+0179             set(gui.text_handles.Status,'String','Calculation of excitation pulse ...');
+0180             pause(0.01);
+0181             
+0182             % normalized initial magnetization
+0183             Minit = Minit./norm(Minit);
+0184             % update the corresponding GUI fields
+0185             data.basic.Minit = Minit;
+0186             set(gui.edit_handles.Minitx,'String',sprintf('%4.3f',Minit(1)));
+0187             set(gui.edit_handles.Minity,'String',sprintf('%4.3f',Minit(2)));
+0188             set(gui.edit_handles.Minitz,'String',sprintf('%4.3f',Minit(3)));
+0189             
+0190             % excitation pulse parameter
+0191             % relaxation during pulse [0/1]
+0192             odeparam.RDP = data.pulse.RDP;
+0193             % pulse length [s]
+0194             odeparam.Ttau = data.pulse.Ttau/1e3;
+0195             % pulse type [string]
+0196             pulseparam.PulseType = data.pulse.Type;
+0197             % gyromagnetic ratio [rad/s/T]
+0198             pulseparam.gamma = odeparam.gamma;
+0199             % Larmor frequency [rad]
+0200             pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
+0201             % pulse amplitude [B0]
+0202             pulseparam.Amp = odeparam.B0*data.pulse.B1Factor;
+0203             % pulse frequency modulation [struct]
+0204             pulseparam.fmod = data.results.pulse.fmod;
+0205             % pulse current modulation [struct]
+0206             pulseparam.Imod = data.results.pulse.Imod;
+0207             % auxiliary pulse phase [rad]
+0208             pulseparam.phi = 0;
+0209             % pulse axis [string]
+0210             pulseparam.PulseAxis = data.pulse.Axis;
+0211             % pulse polarization [string]
+0212             pulseparam.PulsePolarization = data.pulse.Polarization;
+0213             % if the discrete MIDI pulses are used add the corresponding
+0214             % data
+0215             if isfield(data,'pulse_MIDI')
+0216                 % MIDI pulse data [struct]
+0217                 pulseparam.MIDI = data.pulse_MIDI;
+0218             end
+0219             
+0220             % add the pulse parameter to the ode parameter struct
+0221             odeparam.pulseparam = pulseparam;
+0222             
+0223             % ODE solver call
+0224             % OUTPUT: time T and magnetization M
+0225             switch data.pulse.Type
+0226                 case {'MIDI_OR','MIDI_AP'}
+0227                     % if Tsim > Ttau extend the discrete time steps
+0228                     % this is needed because for the discrete pulses
+0229                     % specific time steps are fed into the solver
+0230                     Tsim = unique([data.pulse_MIDI.t;(0:1/50e3:Tsim)']);
+0231                     [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),Tsim,Minit,options);
+0232                 otherwise
+0233                     [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim],Minit,options);
+0234             end
+0235             
+0236             % save data
+0237             data.results.basic.T = TT;
+0238             data.results.basic.M = MM;
+0239             
+0240             % in order to transform M in the rotating frame of reference
+0241             % get the pulse phase theta for all simulated time steps
+0242             pulseparam.fmod.t = TT;
+0243             pulseparam.Imod.t = TT;
+0244             pulseparam.t = TT;
+0245             % get also the pulse amplitudes at these time steps
+0246             [Bpulse,~,~,theta] = getPulseTimeSeries(pulseparam);
+0247             
+0248             % if the simulation is longer then the pulse (additional
+0249             % relaxation afterwards), correct for the pulse phase for
+0250             % points AFTER the pulse by simply calculating the phase at
+0251             % the end of the pulse
+0252             if data.basic.Tsim>data.pulse.Ttau
+0253                 % correction phase
+0254                 dphi = zeros(size(theta));
+0255                 % pulse length
+0256                 Ttau = odeparam.Ttau;
+0257                 % get pulse phase at the end of the pulse
+0258                 dphival = getPulsePhase(Ttau,0,pulseparam,1);
+0259                 % and add it to the correction phase for all time steps after
+0260                 % the pulse
+0261                 indT = TT>Ttau;
+0262                 dphi(indT) = dphival;
+0263                 % 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
+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));
+0270                 % get FFT of the pulse
+0271                 [Xb,fbx] = getFFT(TT(TT<=Ttau),Bpulse(TT<=Ttau,1:2));
+0272                 
+0273                 % update Info field
+0274                 set(gui.text_handles.Status,'String','Calculation of excitation pulse & relaxation ... finished.');
+0275                 pause(0.01);
+0276             else
+0277                 % rotate M into 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));
+0281                 % get FFT of the pulse
+0282                 [Xb,fbx] = getFFT(TT,Bpulse(:,1:2));
+0283                 
+0284                 % update Info field
+0285                 set(gui.text_handles.Status,'String','Calculation of excitation pulse ... finished.');
+0286                 pause(0.01);
+0287             end
+0288             
+0289             % save data
+0290             data.results.basic.Mrot = Mrot;
+0291             data.results.basic.Mspec.fx = fmx;
+0292             data.results.basic.Mspec.X = Xm;
+0293             data.results.pulse.Bspec.fx = fbx;
+0294             data.results.pulse.Bspec.X = Xb;
 0295             
-0296             % these times we will later on, so init them already here
-0297             % total simulation time [s]
-0298             Tsim = data.basic.Tsim/1e3;
-0299             % switch-off ramp time [s]
-0300             Tramp = data.prepol.Tramp/1e3;
-0301             % wait time between switch-off ramp and pulse [s]
-0302             Twait = data.pulse.Twait/1e3;
-0303             % pulse length [s]
-0304             Ttau = data.pulse.Ttau/1e3;
-0305             
-0306             % check if the simulation time is long enough to process all
-0307             % different stages, if not fix it
-0308             % NOTE: of course the simulation time can be longer (relaxation)
-0309             % after the pulse
-0310             if Tsim-(Tramp+Twait+Ttau) < 0
-0311                 Tsim = Tramp+Twait+Ttau;
-0312                 % update the corresponding GUI data and field
-0313                 data.basic.Tsim = Tsim*1e3; % [ms]
-0314                 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim));
-0315                 % no relaxation after excitation pulse
-0316                 Trelax = 0;
-0317             else
-0318                 % relaxation after excitation pulse [s]
-0319                 Trelax = Tsim-(Tramp+Twait+Ttau);
-0320             end
-0321             
-0322             % -------------------------------------------------------------
-0323             %% --- 1.) pre-polarization switch-off ------------------------
-0324             % -------------------------------------------------------------
-0325             % update Info field
-0326             set(gui.text_handles.Status,'String','Calculation of pre-polarization switch-off ...');
-0327             pause(0.01);
-0328             
-0329             % initial magnetization in the direction of B0+Bp
-0330             Morient = data.results.prepol.orient*data.results.prepol.Bmax + odeparam.B0*zunit;
-0331              % Minit does not get normalized in this case
-0332             Minit = Morient;%./norm(Morient);
-0333             % because Minit is not normalized to 1, M0 needs to be adjusted
-0334             odeparam.M0 = odeparam.B0*zunit;
-0335             % update the corresponding GUI fields
-0336             set(gui.edit_handles.Minitx,'String',sprintf('%4.3f',Minit(1)/norm(Minit)));
-0337             set(gui.edit_handles.Minity,'String',sprintf('%4.3f',Minit(2)/norm(Minit)));
-0338             set(gui.edit_handles.Minitz,'String',sprintf('%4.3f',Minit(3)/norm(Minit)));
-0339 
-0340             % update the simulation type
-0341             odeparam.type = 'prepol';
-0342             
-0343             % orientation of the pre-polarization pulse axis
-0344             odeparam.orient = data.results.prepol.orient;
-0345             
-0346             % pre-polarization switch-off ramp parameter
-0347             % relaxation during switch-off [0/1]
-0348             odeparam.RDS = data.prepol.RDS;
-0349             % switch-off ramp type [string]
-0350             rampparam.ramp = data.prepol.Ramp;            
-0351             % amplitude of pre-polarization field
-0352             rampparam.Bmax = data.results.prepol.Bmax;
-0353             % switch over magnetization (for linexp case)
-0354             rampparam.Bstar = data.results.prepol.Bstar;
-0355             % switch-off ramp time [s]
-0356             rampparam.Tramp = Tramp;
-0357             % switch over ramp time [s] (for linexp case)
-0358             rampparam.Tslope = data.prepol.Tslope/1e3;
-0359             
-0360             % add the ramp parameter to the ode parameter struct
-0361             odeparam.rampparam = rampparam;
-0362             
-0363             % ODE solver call
-0364             % OUTPUT: time T and magnetization M
-0365             [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tramp],Minit,options);
-0366             
-0367             % data of the first stage
-0368             TT1 = TT;
-0369             MM1 = MM;
-0370 
-0371             % normalized magnetization vector at end of switch-off ramp
-0372             MMn = MM(end,:)./norm(MM(end,:));
-0373             % "adiabatic quality" p of the switch-off ramp
-0374             % -> orientation of M with respect to z_unit
-0375             data.results.prepol.p = dot(MMn(end,:),zunit)./norm(zunit);
-0376             
-0377             % -------------------------------------------------------------
-0378             %% --- 2.) wait time (if any) ---------------------------------
-0379             % -------------------------------------------------------------
-0380             if Twait > 0
-0381                 % update Info field
-0382                 set(gui.text_handles.Status,'String','Calculation of wait time ...');
-0383                 pause(0.01);
-0384                 % initial magnetization is the end of the switch-off ramp
-0385                 Minit2 = MM1(end,:)';
-0386                 % update the simulation type
-0387                 odeparam.type = 'std';
-0388                 
-0389                 % ODE solver call
-0390                 % OUTPUT: time T and magnetization M
-0391                 [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Twait],Minit2,options);
-0392                 
-0393                 % rotate M into rotating frame of reference
-0394                 MM2rot = getMrot(MM,getOmega0(odeparam.gamma,odeparam.B0).*TT);
-0395                 % get the additional phase at the end of the wait time
-0396                 phiWait = getOmega0(odeparam.gamma,odeparam.B0).*TT(end);
-0397                 
-0398                 % because the simulation was done in "local" time
-0399                 % coordinates, shift the time vector to the end of the
-0400                 % switch-off ramp
-0401                 TT2 = TT + Tramp;
-0402                 % save data
-0403                 MM2 = MM;
-0404                 % initial magnetization for the pulse is the end of the
-0405                 % wait time period
-0406                 Minit3 = MM2(end,:)';
-0407             else
-0408                 % if wait time is 0, use dummy values
-0409                 TT2 = [];
-0410                 MM2 = [];
-0411                 MM2rot = [];
-0412                 phiWait = 0;
-0413                 % initial magnetization for the pulse is the end of the
-0414                 % switch-off ramp
-0415                 Minit3 = MM1(end,:)';
-0416             end
-0417             
-0418             % -------------------------------------------------------------
-0419             %% --- 3.) excitation pulse -----------------------------------
-0420             % -------------------------------------------------------------
-0421             
-0422             % update the simulation type
-0423             odeparam.type = 'pulse';
-0424 
-0425             % excitation pulse parameter
-0426             % relaxation during pulse [0/1]
-0427             odeparam.RDP = data.pulse.RDP;
-0428             % pulse length [s]
-0429             odeparam.Ttau = Ttau;
-0430             
-0431             % pulse type [string]
-0432             pulseparam.PulseType = data.pulse.Type;
-0433             % gyromagnetic ratio [rad/s/T]
-0434             pulseparam.gamma = odeparam.gamma;
-0435             % Larmor frequency [rad]
-0436             pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
-0437             % pulse amplitude [B0]
-0438             pulseparam.Amp = odeparam.B0*data.pulse.B1Factor;
-0439             % pulse frequency modulation [struct]
-0440             pulseparam.fmod = data.results.pulse.fmod;
-0441             % pulse current modulation [struct]
-0442             pulseparam.Imod = data.results.pulse.Imod;
-0443             % auxiliary pulse phase [rad]
-0444             pulseparam.phi = 0;
-0445             % pulse axis [string]
-0446             pulseparam.PulseAxis = data.pulse.Axis;
-0447             % pulse polarization [string]
-0448             pulseparam.PulsePolarization = data.pulse.Polarization;
-0449             % if the discrete MIDI pulses are used add the corresponding
-0450             % data
-0451             if isfield(data,'pulse_MIDI')
-0452                 % MIDI pulse data [struct]
-0453                 pulseparam.MIDI = data.pulse_MIDI;
-0454             end
-0455 
-0456             % add the pulse parameter to the ode parameter struct
-0457             odeparam.pulseparam = pulseparam;
-0458             
-0459             % update Info field
-0460             set(gui.text_handles.Status,'String','Calculation of excitation pulse ...');
-0461             pause(0.01);
-0462             
-0463             % if there is a time span after the pulse
-0464             if abs(Trelax) > eps
-0465                 % the "local" simulation time is prolonged
-0466                 Tsim1 = Ttau+Trelax;
-0467             else
-0468                 % otherwise the "local" simulation time is simply the pulse
-0469                 % length
-0470                 Tsim1 = Ttau;
-0471             end
-0472             
-0473             % ODE solver call
-0474             % OUTPUT: time T and magnetization M
-0475             switch data.pulse.Type
-0476                 case {'MIDI_OR','MIDI_AP'}
-0477                     % if Tsim1 > Ttau extend the discrete time steps
-0478                     % this is needed because for the discrete pulses
-0479                     % specific time steps are fed into the solver
-0480                     Tsim1 = unique([data.pulse_MIDI.t;(0:1/50e3:Tsim1)']);
-0481                     [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),Tsim1,Minit3,options);
-0482                 otherwise
-0483                     [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim1],Minit3,options);
-0484             end
-0485             
-0486             % in order to transform M in the rotating frame of reference
-0487             % get the pulse phase theta for all simulated time steps
-0488             pulseparam.fmod.t = TT;
-0489             pulseparam.Imod.t = TT;
-0490             pulseparam.t = TT;
-0491             % get also the pulse amplitudes at these time steps
-0492             [Bpulse,~,~,theta] = getPulseTimeSeries(pulseparam);
-0493             
-0494             % if the simulation is longer then the pulse (additional
-0495             % relaxation afterwards), correct for the pulse phase for
-0496             % points AFTER the pulse by simply calculating the phase at
-0497             % the end of the pulse
-0498             if abs(Trelax) > eps%max(Tsim1)>Ttau
-0499                 % correction phase
-0500                 dphi = zeros(size(theta));
-0501                 % get pulse phase at the end of the pulse
-0502                 dphival = getPulsePhase(Ttau,0,pulseparam,1);
-0503                 % and add it to the correction phase for all time steps after
-0504                 % the pulse
-0505                 indT = TT>Ttau;
-0506                 dphi(indT) = dphival;
-0507                 % set theta for all time steps after the pulse simply to
-0508                 % omega0*t
-0509                 theta(indT) = getOmega0(odeparam.gamma,odeparam.B0).*TT(indT);
-0510                 % rotate M into rotating frame of reference
-0511                 % and account for the phase from the wait time before the
-0512                 % pulse
-0513                 MM3rot = getMrot(MM,theta,dphi+phiWait);
-0514                 % get FFT pulse B-field
-0515                 [Xb,fbx] = getFFT(TT(TT<=Ttau),Bpulse(TT<=Ttau,1:2));
-0516                 
-0517                 % update Info field
-0518                 set(gui.text_handles.Status,'String',['Calculation of excitation pulse',...
-0519                     ' & relaxation ... finished.']);
-0520                 pause(0.01);
-0521             else
-0522                 % rotate M into rotating frame of reference
-0523                 % and account for the phase from the wait time before the
-0524                 % pulse
-0525                 MM3rot = getMrot(MM,theta,phiWait);
-0526                 % get FFT pulse B-field
-0527                 [Xb,fbx] = getFFT(TT,Bpulse(:,1:2));
-0528                 
-0529                 % update Info field
-0530                 set(gui.text_handles.Status,'String','Calculation of excitation pulse ... finished.');
+0296         case 'prepolpulse'
+0297             
+0298             % this is basically the combination of all of the above
+0299             % simulation types
+0300             %  --- IMPORTANT NOTE: ----------------------------------------
+0301             % The pre-polarization switch-off only "lives" in the laboratory
+0302             % frame of reference. However, for convenience reasons I plot
+0303             % the lab-frame pre-polarization data also in the rotating
+0304             % frame of reference! This is u-n-p-h-y-s-i-c-a-l and pure "eye candy"
+0305             %  -------------------------------------------------------------
+0306             
+0307             % these times we will later on, so init them already here
+0308             % total simulation time [s]
+0309             Tsim = data.basic.Tsim/1e3;
+0310             % switch-off ramp time [s]
+0311             Tramp = data.prepol.Tramp/1e3;
+0312             % wait time between switch-off ramp and pulse [s]
+0313             Twait = data.pulse.Twait/1e3;
+0314             % pulse length [s]
+0315             Ttau = data.pulse.Ttau/1e3;
+0316             
+0317             % check if the simulation time is long enough to process all
+0318             % different stages, if not fix it
+0319             % NOTE: of course the simulation time can be longer (relaxation)
+0320             % after the pulse
+0321             if Tsim-(Tramp+Twait+Ttau) < 0
+0322                 Tsim = Tramp+Twait+Ttau;
+0323                 % update the corresponding GUI data and field
+0324                 data.basic.Tsim = Tsim*1e3; % [ms]
+0325                 set(gui.edit_handles.Tsim,'String',num2str(data.basic.Tsim));
+0326                 % no relaxation after excitation pulse
+0327                 Trelax = 0;
+0328             else
+0329                 % relaxation after excitation pulse [s]
+0330                 Trelax = Tsim-(Tramp+Twait+Ttau);
+0331             end
+0332             
+0333             % -------------------------------------------------------------
+0334             %% --- 1.) pre-polarization switch-off ------------------------
+0335             % -------------------------------------------------------------
+0336             % update Info field
+0337             set(gui.text_handles.Status,'String','Calculation of pre-polarization switch-off ...');
+0338             pause(0.01);
+0339             
+0340             % initial magnetization in the direction of B0+Bp
+0341             Morient = data.results.prepol.orient*data.results.prepol.Bmax + odeparam.B0*zunit;
+0342              % Minit does not get normalized in this case
+0343             Minit = Morient;%./norm(Morient);
+0344             % because Minit is not normalized to 1, M0 needs to be adjusted
+0345             odeparam.M0 = odeparam.B0*zunit;
+0346             % update the corresponding GUI fields
+0347             set(gui.edit_handles.Minitx,'String',sprintf('%4.3f',Minit(1)/norm(Minit)));
+0348             set(gui.edit_handles.Minity,'String',sprintf('%4.3f',Minit(2)/norm(Minit)));
+0349             set(gui.edit_handles.Minitz,'String',sprintf('%4.3f',Minit(3)/norm(Minit)));
+0350 
+0351             % update the simulation type
+0352             odeparam.type = 'prepol';
+0353             
+0354             % orientation of the pre-polarization pulse axis
+0355             odeparam.orient = data.results.prepol.orient;
+0356             
+0357             % pre-polarization switch-off ramp parameter
+0358             % relaxation during switch-off [0/1]
+0359             odeparam.RDS = data.prepol.RDS;
+0360             % switch-off ramp type [string]
+0361             rampparam.ramp = data.prepol.Ramp;            
+0362             % amplitude of pre-polarization field
+0363             rampparam.Bmax = data.results.prepol.Bmax;
+0364             % switch over magnetization (for linexp case)
+0365             rampparam.Bstar = data.results.prepol.Bstar;
+0366             % switch-off ramp time [s]
+0367             rampparam.Tramp = Tramp;
+0368             % switch over ramp time [s] (for linexp case)
+0369             rampparam.Tslope = data.prepol.Tslope/1e3;
+0370             
+0371             % add the ramp parameter to the ode parameter struct
+0372             odeparam.rampparam = rampparam;
+0373             
+0374             % ODE solver call
+0375             % OUTPUT: time T and magnetization M
+0376             [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tramp],Minit,options);
+0377             
+0378             % data of the first stage
+0379             TT1 = TT;
+0380             MM1 = MM;
+0381 
+0382             % normalized magnetization vector at end of switch-off ramp
+0383             MMn = MM(end,:)./norm(MM(end,:));
+0384             % "adiabatic quality" p of the switch-off ramp
+0385             % -> orientation of M with respect to z_unit
+0386             data.results.prepol.p = dot(MMn(end,:),zunit)./norm(zunit);
+0387             
+0388             % -------------------------------------------------------------
+0389             %% --- 2.) wait time (if any) ---------------------------------
+0390             % -------------------------------------------------------------
+0391             if Twait > 0
+0392                 % update Info field
+0393                 set(gui.text_handles.Status,'String','Calculation of wait time ...');
+0394                 pause(0.01);
+0395                 % initial magnetization is the end of the switch-off ramp
+0396                 Minit2 = MM1(end,:)';
+0397                 % update the simulation type
+0398                 odeparam.type = 'std';
+0399                 
+0400                 % ODE solver call
+0401                 % OUTPUT: time T and magnetization M
+0402                 [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Twait],Minit2,options);
+0403                 
+0404                 % rotate M into rotating frame of reference
+0405                 MM2rot = getMrot(MM,getOmega0(odeparam.gamma,odeparam.B0).*TT);
+0406                 % get the additional phase at the end of the wait time
+0407                 phiWait = getOmega0(odeparam.gamma,odeparam.B0).*TT(end);
+0408                 
+0409                 % because the simulation was done in "local" time
+0410                 % coordinates, shift the time vector to the end of the
+0411                 % switch-off ramp
+0412                 TT2 = TT + Tramp;
+0413                 % save data
+0414                 MM2 = MM;
+0415                 % initial magnetization for the pulse is the end of the
+0416                 % wait time period
+0417                 Minit3 = MM2(end,:)';
+0418             else
+0419                 % if wait time is 0, use dummy values
+0420                 TT2 = [];
+0421                 MM2 = [];
+0422                 MM2rot = [];
+0423                 phiWait = 0;
+0424                 % initial magnetization for the pulse is the end of the
+0425                 % switch-off ramp
+0426                 Minit3 = MM1(end,:)';
+0427             end
+0428             
+0429             % -------------------------------------------------------------
+0430             %% --- 3.) excitation pulse -----------------------------------
+0431             % -------------------------------------------------------------
+0432             
+0433             % update the simulation type
+0434             odeparam.type = 'pulse';
+0435 
+0436             % excitation pulse parameter
+0437             % relaxation during pulse [0/1]
+0438             odeparam.RDP = data.pulse.RDP;
+0439             % pulse length [s]
+0440             odeparam.Ttau = Ttau;
+0441             
+0442             % pulse type [string]
+0443             pulseparam.PulseType = data.pulse.Type;
+0444             % gyromagnetic ratio [rad/s/T]
+0445             pulseparam.gamma = odeparam.gamma;
+0446             % Larmor frequency [rad]
+0447             pulseparam.omega0 = getOmega0(odeparam.gamma,odeparam.B0);
+0448             % pulse amplitude [B0]
+0449             pulseparam.Amp = odeparam.B0*data.pulse.B1Factor;
+0450             % pulse frequency modulation [struct]
+0451             pulseparam.fmod = data.results.pulse.fmod;
+0452             % pulse current modulation [struct]
+0453             pulseparam.Imod = data.results.pulse.Imod;
+0454             % auxiliary pulse phase [rad]
+0455             pulseparam.phi = 0;
+0456             % pulse axis [string]
+0457             pulseparam.PulseAxis = data.pulse.Axis;
+0458             % pulse polarization [string]
+0459             pulseparam.PulsePolarization = data.pulse.Polarization;
+0460             % if the discrete MIDI pulses are used add the corresponding
+0461             % data
+0462             if isfield(data,'pulse_MIDI')
+0463                 % MIDI pulse data [struct]
+0464                 pulseparam.MIDI = data.pulse_MIDI;
+0465             end
+0466 
+0467             % add the pulse parameter to the ode parameter struct
+0468             odeparam.pulseparam = pulseparam;
+0469             
+0470             % update Info field
+0471             set(gui.text_handles.Status,'String','Calculation of excitation pulse ...');
+0472             pause(0.01);
+0473             
+0474             % if there is a time span after the pulse
+0475             if abs(Trelax) > eps
+0476                 % the "local" simulation time is prolonged
+0477                 Tsim1 = Ttau+Trelax;
+0478             else
+0479                 % otherwise the "local" simulation time is simply the pulse
+0480                 % length
+0481                 Tsim1 = Ttau;
+0482             end
+0483             
+0484             % ODE solver call
+0485             % OUTPUT: time T and magnetization M
+0486             switch data.pulse.Type
+0487                 case {'MIDI_OR','MIDI_AP'}
+0488                     % if Tsim1 > Ttau extend the discrete time steps
+0489                     % this is needed because for the discrete pulses
+0490                     % specific time steps are fed into the solver
+0491                     Tsim1 = unique([data.pulse_MIDI.t;(0:1/50e3:Tsim1)']);
+0492                     [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),Tsim1,Minit3,options);
+0493                 otherwise
+0494                     [TT,MM] = ode45(@(t,m) fcn_BLOCHUS_ode(t,m,odeparam),[0 Tsim1],Minit3,options);
+0495             end
+0496             
+0497             % in order to transform M in the rotating frame of reference
+0498             % get the pulse phase theta for all simulated time steps
+0499             pulseparam.fmod.t = TT;
+0500             pulseparam.Imod.t = TT;
+0501             pulseparam.t = TT;
+0502             % get also the pulse amplitudes at these time steps
+0503             [Bpulse,~,~,theta] = getPulseTimeSeries(pulseparam);
+0504             
+0505             % if the simulation is longer then the pulse (additional
+0506             % relaxation afterwards), correct for the pulse phase for
+0507             % points AFTER the pulse by simply calculating the phase at
+0508             % the end of the pulse
+0509             if abs(Trelax) > eps%max(Tsim1)>Ttau
+0510                 % correction phase
+0511                 dphi = zeros(size(theta));
+0512                 % get pulse phase at the end of the pulse
+0513                 dphival = getPulsePhase(Ttau,0,pulseparam,1);
+0514                 % and add it to the correction phase for all time steps after
+0515                 % the pulse
+0516                 indT = TT>Ttau;
+0517                 dphi(indT) = dphival;
+0518                 % 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             end
-0533             
-0534             % -------------------------------------------------------------
-0535             %% --- 4.) final data merging ---------------------------------
-0536             % -------------------------------------------------------------
-0537             % because the simulation was done in "local" time
-0538             % coordinates, shift the time vector to the end of the
-0539             % wait time after the switch-off
-0540             TT3 = TT + Tramp + Twait;
-0541             % save data
-0542             MM3 = MM;
-0543             
-0544             % combine data from all stages
-0545             TT = [TT1;TT2;TT3];
-0546             MM = [MM1;MM2;MM3];
-0547             % because there is no M in the rotating frame of reference
-0548             % during the switch-off ramp, use the lab-frame data instead
-0549             MMrot = [MM1;MM2rot;MM3rot];
-0550             
-0551             % remove possible duplicate points
-0552             [TT,ix] = unique(TT);
-0553             MM = MM(ix,:);
-0554             MMrot = MMrot(ix,:);
-0555             
-0556             % save combined data
-0557             data.results.basic.T = TT;
-0558             data.results.basic.M = MM;
-0559             data.results.basic.Mrot = MMrot;
-0560             
-0561             % get FFT for the combined M
-0562             [Xm,fmx] = getFFT(TT,MM(:,1:2));
-0563             data.results.basic.Mspec.fx = fmx;
-0564             data.results.basic.Mspec.X = Xm;
-0565             % save pulse FFT
-0566             data.results.pulse.Bspec.fx = fbx;
-0567             data.results.pulse.Bspec.X = Xb;
-0568 
-0569     end
-0570     % time the calculation
-0571     data.info.Timer = toc(t0);
-0572     
-0573     % update GUI data
-0574     setappdata(fig,'data',data);
-0575     % plot results
-0576     plotResults(fig);
-0577     % update status bar
-0578     updateStatusInformation(fig);
-0579     % activate animation button
-0580     set(gui.push_handles.Animate,'Enable','on');
-0581     
-0582     % change the pushbutton color back to green
-0583     set(src,'BackGroundColor','g');
-0584     
-0585 else
-0586     warndlg({'onPushRun:','There is no figure with the BLOCHUS Tag open.'},...
-0587         'BLOCHUS error');
-0588 end
-0589 
-0590 end
-0591 
-0592 %------------- END OF CODE --------------
-0593 
-0594 %% License:
-0595 % GNU GPLv3
-0596 %
-0597 % BLOCHUS
-0598 % Copyright (C) 2019 Thomas Hiller
-0599 %
-0600 % This program is free software: you can redistribute it and/or modify
-0601 % it under the terms of the GNU General Public License as published by
-0602 % the Free Software Foundation, either version 3 of the License, or
-0603 % (at your option) any later version.
-0604 %
-0605 % This program is distributed in the hope that it will be useful,
-0606 % but WITHOUT ANY WARRANTY; without even the implied warranty of
-0607 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-0608 % GNU General Public License for more details.
-0609 %
-0610 % You should have received a copy of the GNU General Public License
-0611 % along with this program.  If not, see <https://www.gnu.org/licenses/>.
+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             
+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/>.
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/blochus/functions/blochsim/getFFT.html b/doc/blochus/functions/blochsim/getFFT.html
index a22018e..9fca5cc 100644
--- a/doc/blochus/functions/blochsim/getFFT.html
+++ b/doc/blochus/functions/blochsim/getFFT.html
@@ -63,7 +63,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • onPushRun	 starts the calculation
    • 
+
  • onPushRun	 starts the calculation
  • getPulseParameters	 updates all relevant pulse settings
    • 
 
 
 
diff --git a/doc/blochus/functions/blochsim/getOmega0.html b/doc/blochus/functions/blochsim/getOmega0.html
index 13807c7..8b46092 100644
--- a/doc/blochus/functions/blochsim/getOmega0.html
+++ b/doc/blochus/functions/blochsim/getOmega0.html
@@ -63,7 +63,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • BLOCHUS_loadDefaults	 loads default GUI data values
  • onEditValue	 updates all edit field values, checks for wrong inputs and
  • onPopupNucleus	 selects the nucleus (proton) to use for the simulation
  • onPushRun	 starts the calculation
  • getPulseParameters	 updates all relevant pulse settings
  • plotResults	 plots results depending on the chosen settings
    • 
+
  • BLOCHUS_loadDefaults	 loads default GUI data values
  • onEditValue	 updates all edit field values, checks for wrong inputs and
  • onPopupNucleus	 selects the nucleus (proton) to use for the simulation
  • onPushRun	 starts the calculation
  • getPulseParameters	 updates all relevant pulse settings
  • plotPulse	 plots different pulse parameter
  • plotResults	 plots results depending on the chosen settings
    • 
 
 
 
diff --git a/doc/blochus/functions/interface/clearSingleAxis.html b/doc/blochus/functions/interface/clearSingleAxis.html
index 35215db..21bae86 100644
--- a/doc/blochus/functions/interface/clearSingleAxis.html
+++ b/doc/blochus/functions/interface/clearSingleAxis.html
@@ -61,7 +61,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • BLOCHUS_createGridPlots	 creates the "Plots" grid panel
  • onCheckPrePolPulse	 activates / deactivates all control elements needed for
  • plotResults	 plots results depending on the chosen settings
    • 
+
  • BLOCHUS_createGridPlots	 creates the "Plots" grid panel
  • onCheckPrePolPulse	 activates / deactivates all control elements needed for
  • onPushAnimate	 animates the results of the latest simulation
  • plotPulse	 plots different pulse parameter
  • plotResults	 plots results depending on the chosen settings
    • 
 
 
 
diff --git a/doc/blochus/functions/interface/getPulseParameters.html b/doc/blochus/functions/interface/getPulseParameters.html
index 93b6807..a6ac509 100644
--- a/doc/blochus/functions/interface/getPulseParameters.html
+++ b/doc/blochus/functions/interface/getPulseParameters.html
@@ -60,7 +60,7 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
      
-
    • getMIDI_Tx	 creates discrete on-resonant or adiabatic pulses
    • getOmega0	 calculates the angular frequency from a given B-field and
    • getPulseTimeSeries	 returns the B-field amplitudes of the pulse either for a
    
+
  • getFFT	 calculates the FFT for a given time and signal pair
  • getMIDI_Tx	 creates discrete on-resonant or adiabatic pulses
  • getOmega0	 calculates the angular frequency from a given B-field and
  • getPulseTimeSeries	 returns the B-field amplitudes of the pulse either for a
    • 
 This function is called by:
 
@@ -310,38 +310,46 @@ 
    SOURCE CODE ^% dummy time vector [ms]
 0240 data.results.pulse.t = pulse_t'.*1e3;
 0241 
-0242 % update data
-0243 data.results.pulse.fmod = fmod;
-0244 data.results.pulse.Imod = Imod;
-0245 data.results.pulse.df = df;
-0246 data.results.pulse.I = I;
-0247 data.results.pulse.Bxy = pulse_Bxy;
-0248 
-0249 % update GUI data
-0250 setappdata(fig,'data',data);
-0251 
-0252 end
+0242 % get FFT of the pulse
+0243 [Xb,fbx] = getFFT(pulse_t(:),pulse_Bxy(:,1:2));
+0244                 
+0245 % update data
+0246 data.results.pulse.fmod = fmod;
+0247 data.results.pulse.Imod = Imod;
+0248 data.results.pulse.df = df;
+0249 data.results.pulse.I = I;
+0250 data.results.pulse.Bxy = pulse_Bxy;
+0251 data.results.pulse.Bspec.fx = fbx;
+0252 data.results.pulse.Bspec.X = Xb;
 0253 
-0254 %------------- END OF CODE --------------
-0255 
-0256 %% License:
-0257 % GNU GPLv3
-0258 %
-0259 % BLOCHUS
-0260 % Copyright (C) 2019 Thomas Hiller
-0261 %
-0262 % This program is free software: you can redistribute it and/or modify
-0263 % it under the terms of the GNU General Public License as published by
-0264 % the Free Software Foundation, either version 3 of the License, or
-0265 % (at your option) any later version.
+0254 % because the pulse data changed, deactivate the "Animate" button
+0255 set(gui.push_handles.Animate,'Enable','off');
+0256 
+0257 % update GUI data
+0258 setappdata(fig,'data',data);
+0259 
+0260 end
+0261 
+0262 %------------- END OF CODE --------------
+0263 
+0264 %% License:
+0265 % GNU GPLv3
 0266 %
-0267 % This program is distributed in the hope that it will be useful,
-0268 % but WITHOUT ANY WARRANTY; without even the implied warranty of
-0269 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-0270 % GNU General Public License for more details.
-0271 %
-0272 % You should have received a copy of the GNU General Public License
-0273 % along with this program.  If not, see <https://www.gnu.org/licenses/>.
+0267 % BLOCHUS
+0268 % Copyright (C) 2019 Thomas Hiller
+0269 %
+0270 % This program is free software: you can redistribute it and/or modify
+0271 % it under the terms of the GNU General Public License as published by
+0272 % the Free Software Foundation, either version 3 of the License, or
+0273 % (at your option) any later version.
+0274 %
+0275 % This program is distributed in the hope that it will be useful,
+0276 % but WITHOUT ANY WARRANTY; without even the implied warranty of
+0277 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+0278 % GNU General Public License for more details.
+0279 %
+0280 % You should have received a copy of the GNU General Public License
+0281 % 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/getRampParameters.html b/doc/blochus/functions/interface/getRampParameters.html
index 6637438..45e3f83 100644
--- a/doc/blochus/functions/interface/getRampParameters.html
+++ b/doc/blochus/functions/interface/getRampParameters.html
@@ -172,31 +172,33 @@ 
    SOURCE CODE ^% update GUI data
-0106 setappdata(fig,'data',data);
-0107 end
-0108 
-0109 %------------- END OF CODE --------------
+0104 % because the ramp data changed, deactivate the "Animate" button
+0105 set(gui.push_handles.Animate,'Enable','off');
+0106 
+0107 % update GUI data
+0108 setappdata(fig,'data',data);
+0109 end
 0110 
-0111 %% License:
-0112 % GNU GPLv3
-0113 %
-0114 % BLOCHUS
-0115 % Copyright (C) 2019 Thomas Hiller
-0116 %
-0117 % This program is free software: you can redistribute it and/or modify
-0118 % it under the terms of the GNU General Public License as published by
-0119 % the Free Software Foundation, either version 3 of the License, or
-0120 % (at your option) any later version.
-0121 %
-0122 % This program is distributed in the hope that it will be useful,
-0123 % but WITHOUT ANY WARRANTY; without even the implied warranty of
-0124 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-0125 % GNU General Public License for more details.
-0126 %
-0127 % You should have received a copy of the GNU General Public License
-0128 % along with this program.  If not, see <https://www.gnu.org/licenses/>.
+0111 %------------- END OF CODE --------------
+0112 
+0113 %% License:
+0114 % GNU GPLv3
+0115 %
+0116 % BLOCHUS
+0117 % Copyright (C) 2019 Thomas Hiller
+0118 %
+0119 % This program is free software: you can redistribute it and/or modify
+0120 % it under the terms of the GNU General Public License as published by
+0121 % the Free Software Foundation, either version 3 of the License, or
+0122 % (at your option) any later version.
+0123 %
+0124 % This program is distributed in the hope that it will be useful,
+0125 % but WITHOUT ANY WARRANTY; without even the implied warranty of
+0126 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+0127 % GNU General Public License for more details.
+0128 %
+0129 % You should have received a copy of the GNU General Public License
+0130 % 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/menu.html b/doc/blochus/functions/interface/menu.html
index d421ef2..53c5991 100644
--- a/doc/blochus/functions/interface/menu.html
+++ b/doc/blochus/functions/interface/menu.html
@@ -18,7 +18,7 @@ 
    Index for blochus\functions\interface
    
 
 
    Matlab files in this directory:
    
 
+
  • clearSingleAxis 
  • findParentOfType 
  • getAngleBetweenVectors 
  • getPulseParameters 
  • getRampParameters 
  • minimizePanel 
  • onFigureSizeChange 
  • plotBSphere 
  • plotBpulse 
  • plotPulse 
  • plotRamp 
  • plotResults 
  • switchToolTips 
  • updateStatusInformation 
    • 
 
 
    Other Matlab-specific files in this directory:
    
 
      
diff --git a/doc/blochus/functions/interface/plotBSphere.html b/doc/blochus/functions/interface/plotBSphere.html
index 95545c7..e98f26a 100644
--- a/doc/blochus/functions/interface/plotBSphere.html
+++ b/doc/blochus/functions/interface/plotBSphere.html
@@ -66,7 +66,7 @@ 
      CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
    • onPushAnimate	
    • plotResults	 plots results depending on the chosen settings
    
+
  • onPushAnimate	 animates the results of the latest simulation
  • plotResults	 plots results depending on the chosen settings
    • 
 
 
 
diff --git a/doc/blochus/functions/interface/plotBpulse.html b/doc/blochus/functions/interface/plotPulse.html
similarity index 69%
rename from doc/blochus/functions/interface/plotBpulse.html
rename to doc/blochus/functions/interface/plotPulse.html
index d2a938a..d3088a0 100644
--- a/doc/blochus/functions/interface/plotBpulse.html
+++ b/doc/blochus/functions/interface/plotPulse.html
@@ -2,8 +2,8 @@
                 "http://www.w3.org/TR/REC-html40/loose.dtd">
 
 
-  Description of plotBpulse
-  
+  Description of plotPulse
+  
   
   
   
@@ -16,20 +16,20 @@
 
 
 
-
    plotBpulse
+
    plotPulse
 
    
 
 
    PURPOSE ^
    
 
     plots different pulse parameter
    
 
 
    SYNOPSIS ^
    
-
    function plotBpulse(fig) 
    
+
    function plotPulse(fig) 
    
 
 
    DESCRIPTION ^
    
-
    plotBpulse plots different pulse parameter
+
    plotPulse plots different pulse parameter
 
  Syntax:
-       plotBpulse(fig)
+       plotPulse(fig)
 
  Inputs:
        fig - figure handle
@@ -38,7 +38,7 @@ 
    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
      
-
    
+
  • getOmega0	 calculates the angular frequency from a given B-field and
  • clearSingleAxis	 clears an individual axis
    • 
 This function is called by:
 
+
  • onCheckPulseQ	 updates the checkbox that activates quality factor tuning
  • onEditValue	 updates all edit field values, checks for wrong inputs and
  • onPopupPulseAxis	 sets the orientation of the pulse axis
  • onPopupPulseDFmode	 selects the frequency modulation for an adiabatic pulse
  • onPopupPulseImode	 selects the current modulation for an adiabatic pulse
  • onPopupPulsePolarization	 selects the pulse polarization
  • onPopupPulseType	 selects the pulse type
  • onPushAnimate	 animates the results of the latest simulation
    • 
 
 
 
 
 
    SOURCE CODE ^
    
-
    0001 function plotBpulse(fig)
-0002 %plotBpulse plots different pulse parameter
+
    0001 function plotPulse(fig)
+0002 %plotPulse plots different pulse parameter
 0003 %
 0004 % Syntax:
-0005 %       plotBpulse(fig)
+0005 %       plotPulse(fig)
 0006 %
 0007 % Inputs:
 0008 %       fig - figure handle
@@ -80,7 +80,7 @@ 
    SOURCE CODE ^%       none
 0012 %
 0013 % Example:
-0014 %       plotBpulse(gui.figh)
+0014 %       plotPulse(gui.figh)
 0015 %
 0016 % Other m-files required:
 0017 %       none
@@ -159,28 +159,53 @@ 
    SOURCE CODE ^'x','y','Location','SouthWest');
 0091 set(ax,'FontSize',myui.axfontsize);
 0092 
-0093 end
-0094 
-0095 %------------- END OF CODE --------------
+0093 %% FFT
+0094 % Larmor freq. [Hz]
+0095 fL = getOmega0(data.basic.gamma,data.basic.B0)/2/pi;
 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/>.
    
+0097 ax = gui.axes_handles.PulseFFT;
+0098 f = data.results.pulse.Bspec.fx;
+0099 X = data.results.pulse.Bspec.X;
+0100 % plot data
+0101 clearSingleAxis(ax);
+0102 hold(ax,'on');
+0103 plot(f,abs(X),'r','Parent',ax);
+0104 % vertical line indicating Larmor frequency
+0105 line([fL fL],[0 max(abs(X))],'Color','k','LineStyle','--',...
+0106     'LineWidth',0.75,'Parent',ax);
+0107 hold(ax,'off');
+0108 % axis settings
+0109 set(ax,'XLim',[-abs(2*fL) abs(2*fL)],'YLim',[0 max(abs(X))].*1.1);
+0110 grid(ax,'on');
+0111 set(get(ax,'XLabel'),'String','F [Hz]');
+0112 set(get(ax,'YLabel'),'String','amplitude');
+0113 % legend
+0114 legend(ax,'B','\omega_0','Location','NorthEast');
+0115 % font size
+0116 set(ax,'FontSize',myui.axfontsize);
+0117 
+0118 end
+0119 
+0120 %------------- END OF CODE --------------
+0121 
+0122 %% License:
+0123 % GNU GPLv3
+0124 %
+0125 % BLOCHUS
+0126 % Copyright (C) 2019 Thomas Hiller
+0127 %
+0128 % This program is free software: you can redistribute it and/or modify
+0129 % it under the terms of the GNU General Public License as published by
+0130 % the Free Software Foundation, either version 3 of the License, or
+0131 % (at your option) any later version.
+0132 %
+0133 % This program is distributed in the hope that it will be useful,
+0134 % but WITHOUT ANY WARRANTY; without even the implied warranty of
+0135 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+0136 % GNU General Public License for more details.
+0137 %
+0138 % You should have received a copy of the GNU General Public License
+0139 % 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/plotRamp.html b/doc/blochus/functions/interface/plotRamp.html
index 840d1a9..aefd2fa 100644
--- a/doc/blochus/functions/interface/plotRamp.html
+++ b/doc/blochus/functions/interface/plotRamp.html
@@ -61,7 +61,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • onEditValue	 updates all edit field values, checks for wrong inputs and
  • onPopupPrePolRamp	 selects the pre-polarization switch-off ramp
    • 
+
  • onEditValue	 updates all edit field values, checks for wrong inputs and
  • onPopupPrePolRamp	 selects the pre-polarization switch-off ramp
  • onPushAnimate	 animates the results of the latest simulation
    • 
 
 
 
diff --git a/doc/blochus/functions/interface/plotResults.html b/doc/blochus/functions/interface/plotResults.html
index d0b9010..4e3cd31 100644
--- a/doc/blochus/functions/interface/plotResults.html
+++ b/doc/blochus/functions/interface/plotResults.html
@@ -63,7 +63,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 <li><a href=getOmega0	 calculates the angular frequency from a given B-field and
  • clearSingleAxis	 clears an individual axis
  • plotBSphere	 plots a (Bloch)-Sphere (basically a unit sphere) with
    • 
 This function is called by:
 
+
  • onMenuImport	 handles the extra menu entries
  • onPushAnimate	 animates the results of the latest simulation
  • onPushRun	 starts the calculation
    • 
 
 
 
    SUBFUNCTIONS ^
    
@@ -168,237 +168,242 @@ 
    SOURCE CODE ^end
-0098 % norm of magnetization vector
-0099 Mamp = sqrt(M(:,1).^2+M(:,2).^2+M(:,3).^2);
-0100 
-0101 % normalize M in case of pre-polarization
-0102 % and adjust axis limits
-0103 switch data.basic.type
-0104     case {'prepol','prepolpulse'}
-0105         M = M./data.basic.B0;
-0106         Mamp = Mamp./data.basic.B0;
-0107         d = max(M(:))-min(M(:));
-0108         ymin = min(M(:))-d/20;
-0109         ymax = max(M(:))+d/20;
-0110     otherwise
-0111         ymin = -1.05;
-0112         ymax = 1.05;
-0113 end
-0114 
-0115 % plot the data
-0116 clearSingleAxis(ax);
-0117 hold(ax,'on');
-0118 plot(T,M(:,1),'LineWidth',gui.myui.linewidth,'Color','r','Parent',ax);
-0119 plot(T,M(:,2),'LineWidth',gui.myui.linewidth,'Color','g','Parent',ax);
-0120 plot(T,M(:,3),'LineWidth',gui.myui.linewidth,'Color','b','Parent',ax);
-0121 plot(T,sqrt(M(:,1).^2+M(:,2).^2),'LineWidth',gui.myui.linewidth,...
-0122     'Color','m','Parent',ax);
-0123 plot(T,Mamp,'LineWidth',gui.myui.linewidth,'Color','k',...
-0124     'LineStyle','--','Parent',ax);
-0125 set(ax,'XLim',[min(T) max(T)],'YLim',[ymin ymax]);
-0126 
-0127 % -------------------------------------------------------------------------
-0128 % plot vertical line at end of switch-off ramp
-0129 if (strcmp(data.basic.type,'prepol') || strcmp(data.basic.type,'prepolpulse'))...
-0130         && Tramp < Tsim
-0131     plot([Tramp Tramp],get(ax,'YLim'),'LineStyle','--',...
-0132         'Color',myui.color.prepol,'LineWidth',1,'Tag','MarkerLines',...
-0133         'HandleVisibility','off','Parent',ax);
-0134 end
-0135 % plot vertical line at end of pulse
-0136 if strcmp(data.basic.type,'pulse') && Ttau < Tsim
-0137     plot([Ttau Ttau],get(ax,'YLim'),'LineStyle','--',...
-0138         'Color',myui.color.pulse,'LineWidth',1,'Tag','MarkerLines',...
-0139         'HandleVisibility','off','Parent',ax);
-0140 end
-0141 % plot vertical line at end of pulse
-0142 if strcmp(data.basic.type,'prepolpulse')
-0143     plot([Ttau+Tramp+Twait Ttau+Tramp+Twait],get(ax,'YLim'),'LineStyle','--',...
-0144         'Color',myui.color.pulse,'LineWidth',1,'Tag','MarkerLines',...
-0145         'HandleVisibility','off','Parent',ax);
-0146     if Twait > 0
-0147          plot([Tramp+Twait Tramp+Twait],get(ax,'YLim'),'LineStyle','--',...
-0148              'Color',myui.color.wait,'LineWidth',1,'Tag','MarkerLines',...
-0149              'HandleVisibility','off','Parent',ax);
-0150     end
-0151 end
-0152 % -------------------------------------------------------------------------
-0153 hold(ax,'off');
-0154 
-0155 % axis settings
-0156 grid(ax,'on');
-0157 set(get(ax,'XLabel'),'String','t [ms]');
-0158 set(get(ax,'YLabel'),'String','magnetization M');
-0159 % legend
-0160 lh = legend(ax,'x','y','z','|xy|','|M|','Location','SouthWest');
-0161 
-0162 % adiabatic quality of switch-off ramp
-0163 if strcmp(data.basic.type,'prepol') || strcmp(data.basic.type,'prepolpulse')
-0164     set(get(lh,'Title'),'String',['p=',sprintf('%4.3f',data.results.prepol.p)])
-0165 end
-0166 % font size
-0167 set(ax,'FontSize',gui.myui.axfontsize);
-0168 
-0169 end
+0098 % xy-component of magnetization vector
+0099 Mxy = sqrt(M(:,1).^2+M(:,2).^2);
+0100 % norm of magnetization vector
+0101 Mamp = sqrt(M(:,1).^2+M(:,2).^2+M(:,3).^2);
+0102 
+0103 % normalize M in case of pre-polarization
+0104 % and adjust axis limits
+0105 switch data.basic.type
+0106     case {'prepol','prepolpulse'}
+0107         M = M./data.basic.B0;
+0108         Mxy = Mxy./data.basic.B0;
+0109         Mamp = Mamp./data.basic.B0;
+0110         d = max([M(:);Mxy(:)])-min([M(:);Mxy(:)]);
+0111         ymin = min([M(:);Mxy(:)])-d/20;
+0112         ymax = max([M(:);Mxy(:)])+d/20;
+0113     otherwise
+0114         ymin = -1.05;
+0115         ymax = 1.05;
+0116 end
+0117 
+0118 % plot the data
+0119 clearSingleAxis(ax);
+0120 hold(ax,'on');
+0121 plot(T,M(:,1),'LineWidth',myui.linewidth,'Color','r','Parent',ax);
+0122 plot(T,M(:,2),'LineWidth',myui.linewidth,'Color','g','Parent',ax);
+0123 plot(T,M(:,3),'LineWidth',myui.linewidth,'Color','b','Parent',ax);
+0124 plot(T,Mxy,'LineWidth',myui.linewidth,'Color','m','Parent',ax);
+0125 plot(T,Mamp,'LineWidth',myui.linewidth,'Color','k',...
+0126     'LineStyle','--','Parent',ax);
+0127 set(ax,'XLim',[min(T) max(T)],'YLim',[ymin ymax]);
+0128 
+0129 % -------------------------------------------------------------------------
+0130 % plot vertical line at end of switch-off ramp
+0131 if (strcmp(data.basic.type,'prepol') || strcmp(data.basic.type,'prepolpulse'))...
+0132         && Tramp < Tsim
+0133     plot([Tramp Tramp],get(ax,'YLim'),'LineStyle','--',...
+0134         'Color',myui.color.prepol,'LineWidth',1,'Tag','MarkerLines',...
+0135         'HandleVisibility','off','Parent',ax);
+0136 end
+0137 % plot vertical line at end of pulse
+0138 if strcmp(data.basic.type,'pulse') && Ttau < Tsim
+0139     plot([Ttau Ttau],get(ax,'YLim'),'LineStyle','--',...
+0140         'Color',myui.color.pulse,'LineWidth',1,'Tag','MarkerLines',...
+0141         'HandleVisibility','off','Parent',ax);
+0142 end
+0143 % plot vertical line at end of pulse
+0144 if strcmp(data.basic.type,'prepolpulse')
+0145     plot([Ttau+Tramp+Twait Ttau+Tramp+Twait],get(ax,'YLim'),'LineStyle','--',...
+0146         'Color',myui.color.pulse,'LineWidth',1,'Tag','MarkerLines',...
+0147         'HandleVisibility','off','Parent',ax);
+0148     if Twait > 0
+0149          plot([Tramp+Twait Tramp+Twait],get(ax,'YLim'),'LineStyle','--',...
+0150              'Color',myui.color.wait,'LineWidth',1,'Tag','MarkerLines',...
+0151              'HandleVisibility','off','Parent',ax);
+0152     end
+0153 end
+0154 % -------------------------------------------------------------------------
+0155 hold(ax,'off');
+0156 
+0157 % axis settings
+0158 grid(ax,'on');
+0159 set(get(ax,'XLabel'),'String','t [ms]');
+0160 set(get(ax,'YLabel'),'String','magnetization M');
+0161 % legend
+0162 lh = legend(ax,'x','y','z','|xy|','|M|','Location','SouthWest');
+0163 
+0164 % 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 %% magnetization components on Bloch sphere
-0172 function plotSphere(data,gui,frame)
-0173 myui = gui.myui;
-0174 
-0175 % for plotting everything is in [ms]
-0176 T = data.results.basic.T.*1e3;
-0177 
-0178 % all relevant time marker
-0179 Tsim = data.basic.Tsim;
-0180 Ttau = data.pulse.Ttau;
-0181 Tramp = data.prepol.Tramp;
-0182 Twait = data.pulse.Twait;
-0183 
-0184 % choose reference frame to plot
-0185 switch frame
-0186     case 'lab'
-0187         M = data.results.basic.M;
-0188         ax = gui.axes_handles.SphereL;
-0189     case 'rot'
-0190         M = data.results.basic.Mrot;
-0191         ax = gui.axes_handles.SphereR;
-0192 end
-0193 % norm of magnetization vector
-0194 Mamp = sqrt(M(:,1).^2+M(:,2).^2+M(:,3).^2);
-0195 
-0196 % for visualization purposes M always gets normalized on Bloch sphere
-0197 M = M./Mamp(1);
-0198 
-0199 % chhose what to plot depending on simulation type
-0200 switch data.basic.type
-0201     case 'std'
-0202         indS1 = 1:numel(T); % relaxation
-0203         indS2 = []; % relaxation at end of "prepolpulse"-type
-0204         indR = []; % switch-off ramp
-0205         indB = []; % switch-off B-field
-0206         indP = []; % pulse
-0207         indE = numel(T); % end point
-0208         Beffn = [0 0 0];
-0209         
-0210     case 'prepol'
-0211         indS1 = T>Tramp;
-0212         indS2 = [];
-0213         indR = T<=Tramp;
-0214         indB = [];
-0215         indP = [];
-0216         indE = numel(T);
-0217         % switch-off B-field trajectory
-0218         Bamp = sqrt(data.results.prepol.Beff(:,1).^2+data.results.prepol.Beff(:,2).^2+data.results.prepol.Beff(:,3).^2);
-0219         Beffn = data.results.prepol.Beff./Bamp;
-0220         
-0221     case 'pulse'
-0222         indS1 = T>Ttau;
-0223         indS2 = [];
-0224         indR = [];
-0225         indB = [];
-0226         indP = T<=Ttau;
-0227         indE = numel(T);
-0228         Beffn = [0 0 0];
-0229         
-0230     case 'prepolpulse'
-0231         indS2 = T>Tramp & T<=Tramp+Twait;
-0232         indS1 = T>Tramp+Twait+Ttau;
-0233         indR = T<=Tramp;
-0234         indB = [];
-0235         indP = T>Tramp+Twait & T<=Tramp+Twait+Ttau;
-0236         indE = numel(T);
-0237         % switch-off B-field trajectory
-0238         Bamp = sqrt(data.results.prepol.Beff(:,1).^2+data.results.prepol.Beff(:,2).^2+data.results.prepol.Beff(:,3).^2);
-0239         Beffn = data.results.prepol.Beff./Bamp;
-0240 end
-0241 
-0242 % plot data
-0243 clearSingleAxis(ax);
-0244 hold(ax,'on');
-0245 plot3(M(indS1,1),M(indS1,2),M(indS1,3),'LineWidth',gui.myui.linewidth,...
-0246     'Color',myui.color.basic,'Parent',ax);
-0247 plot3(M(indS2,1),M(indS2,2),M(indS2,3),'LineWidth',gui.myui.linewidth,...
-0248     'Color',myui.color.wait,'Parent',ax);
-0249 plot3(M(indP,1),M(indP,2),M(indP,3),'LineWidth',gui.myui.linewidth,...
-0250     'Color',myui.color.pulse,'Parent',ax);
-0251 plot3(M(indR,1),M(indR,2),M(indR,3),'LineWidth',gui.myui.linewidth,...
-0252     'Color',myui.color.prepol,'Parent',ax);
-0253 plot3(Beffn(:,1),Beffn(:,2),Beffn(:,3),'LineWidth',gui.myui.linewidth,...
-0254     'Color',myui.color.prepolB,'Parent',ax)
-0255 plot3(M(indE,1),M(indE,2),M(indE,3),'ko','MarkerSize',8,'Parent',ax);
-0256 % plot actual Bloch sphere
-0257 plotBSphere(18,18,ax);
-0258 % axis settings
-0259 view(ax,[-35 30]);
-0260 hold(ax,'off');
-0261 set(ax,'XLim',[-1.05 1.05],'YLim',[-1.05 1.05],'ZLim',[-1.05 1.05])
-0262 set(ax,'Color','w','XColor','none','YColor','none','ZColor','none');
-0263 axis(ax,'equal');
-0264 axis(ax,'tight');
-0265 
-0266 end
-0267 
-0268 %% FFT of magnetization and pulse
-0269 function plotFFT(data,gui,type)
-0270 myui = gui.myui;
+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;
+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);
+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 % Larmor freq. [Hz]
-0273 fL = getOmega0(data.basic.gamma,data.basic.B0)/2/pi;
-0274 
-0275 % choose what to plot
-0276 switch type
-0277     case 'M'
-0278         ax = gui.axes_handles.MagFFT;
-0279         f = data.results.basic.Mspec.fx;
-0280         X = data.results.basic.Mspec.X;
-0281         lgdstr = {'Mxy','\omega_0'};
-0282     case 'B'
-0283         ax = gui.axes_handles.PulseFFT;
-0284         f = data.results.pulse.Bspec.fx;
-0285         X = data.results.pulse.Bspec.X;
-0286         lgdstr = {'B','\omega_0'};
-0287 end
-0288 
-0289 % plot data
-0290 clearSingleAxis(ax);
-0291 hold(ax,'on');
-0292 plot(f,abs(X),'r','Parent',ax);
-0293 % vertical line indicating Larmor frequency
-0294 line([fL fL],[0 max(abs(X))],'Color','k','LineStyle','--',...
-0295     'LineWidth',0.75,'Parent',ax);
-0296 hold(ax,'off');
-0297 % axis settings
-0298 set(ax,'XLim',[-abs(2*fL) abs(2*fL)],'YLim',[0 max(abs(X))].*1.1);
-0299 grid(ax,'on');
-0300 set(get(ax,'XLabel'),'String','F [Hz]');
-0301 set(get(ax,'YLabel'),'String','amplitude');
-0302 % legend
-0303 legend(ax,lgdstr,'Location','NorthEast');
-0304 % font size
-0305 set(ax,'FontSize',gui.myui.axfontsize);
-0306 
-0307 end
-0308 
-0309 %------------- END OF CODE --------------
-0310 
-0311 %% License:
-0312 % GNU GPLv3
-0313 %
-0314 % BLOCHUS
-0315 % Copyright (C) 2019 Thomas Hiller
-0316 %
-0317 % This program is free software: you can redistribute it and/or modify
-0318 % it under the terms of the GNU General Public License as published by
-0319 % the Free Software Foundation, either version 3 of the License, or
-0320 % (at your option) any later version.
+0272 end
+0273 
+0274 %% FFT of magnetization and pulse
+0275 function plotFFT(data,gui,type)
+0276 
+0277 % Larmor freq. [Hz]
+0278 fL = getOmega0(data.basic.gamma,data.basic.B0)/2/pi;
+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
 0321 %
-0322 % This program is distributed in the hope that it will be useful,
-0323 % but WITHOUT ANY WARRANTY; without even the implied warranty of
-0324 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-0325 % GNU General Public License for more details.
+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 % You should have received a copy of the GNU General Public License
-0328 % along with this program.  If not, see <https://www.gnu.org/licenses/>.
    
+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/>.
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/functions/interface/getPulseParameters.m b/functions/interface/getPulseParameters.m
index cf389ae..43c730c 100644
--- a/functions/interface/getPulseParameters.m
+++ b/functions/interface/getPulseParameters.m
@@ -239,12 +239,20 @@ function getPulseParameters(fig)
 % dummy time vector [ms]
 data.results.pulse.t = pulse_t'.*1e3;
 
+% get FFT of the pulse
+[Xb,fbx] = getFFT(pulse_t(:),pulse_Bxy(:,1:2));
+                
 % update data
 data.results.pulse.fmod = fmod;
 data.results.pulse.Imod = Imod;
 data.results.pulse.df = df;
 data.results.pulse.I = I;
 data.results.pulse.Bxy = pulse_Bxy;
+data.results.pulse.Bspec.fx = fbx;
+data.results.pulse.Bspec.X = Xb;
+
+% because the pulse data changed, deactivate the "Animate" button
+set(gui.push_handles.Animate,'Enable','off');
 
 % update GUI data
 setappdata(fig,'data',data);
diff --git a/functions/interface/getRampParameters.m b/functions/interface/getRampParameters.m
index 14ea588..56553f5 100644
--- a/functions/interface/getRampParameters.m
+++ b/functions/interface/getRampParameters.m
@@ -101,6 +101,8 @@ function getRampParameters(fig)
 data.results.prepol.omega = omega;
 data.results.prepol.dadt = dadt;
 
+% because the ramp data changed, deactivate the "Animate" button
+set(gui.push_handles.Animate,'Enable','off');
 
 % update GUI data
 setappdata(fig,'data',data);
diff --git a/functions/interface/plotBpulse.m b/functions/interface/plotPulse.m
similarity index 78%
rename from functions/interface/plotBpulse.m
rename to functions/interface/plotPulse.m
index 1fb3983..74c969c 100644
--- a/functions/interface/plotBpulse.m
+++ b/functions/interface/plotPulse.m
@@ -1,8 +1,8 @@
-function plotBpulse(fig)
-%plotBpulse plots different pulse parameter
+function plotPulse(fig)
+%plotPulse plots different pulse parameter
 %
 % Syntax:
-%       plotBpulse(fig)
+%       plotPulse(fig)
 %
 % Inputs:
 %       fig - figure handle
@@ -11,7 +11,7 @@ function plotBpulse(fig)
 %       none
 %
 % Example:
-%       plotBpulse(gui.figh)
+%       plotPulse(gui.figh)
 %
 % Other m-files required:
 %       none
@@ -90,6 +90,31 @@ function plotBpulse(fig)
 legend(ax,'x','y','Location','SouthWest');
 set(ax,'FontSize',myui.axfontsize);
 
+%% FFT
+% Larmor freq. [Hz]
+fL = getOmega0(data.basic.gamma,data.basic.B0)/2/pi;
+
+ax = gui.axes_handles.PulseFFT;
+f = data.results.pulse.Bspec.fx;
+X = data.results.pulse.Bspec.X;
+% plot data
+clearSingleAxis(ax);
+hold(ax,'on');
+plot(f,abs(X),'r','Parent',ax);
+% vertical line indicating Larmor frequency
+line([fL fL],[0 max(abs(X))],'Color','k','LineStyle','--',...
+    'LineWidth',0.75,'Parent',ax);
+hold(ax,'off');
+% axis settings
+set(ax,'XLim',[-abs(2*fL) abs(2*fL)],'YLim',[0 max(abs(X))].*1.1);
+grid(ax,'on');
+set(get(ax,'XLabel'),'String','F [Hz]');
+set(get(ax,'YLabel'),'String','amplitude');
+% legend
+legend(ax,'B','\omega_0','Location','NorthEast');
+% font size
+set(ax,'FontSize',myui.axfontsize);
+
 end
 
 %------------- END OF CODE --------------
diff --git a/functions/interface/plotResults.m b/functions/interface/plotResults.m
index 1017835..f226b50 100644
--- a/functions/interface/plotResults.m
+++ b/functions/interface/plotResults.m
@@ -95,6 +95,8 @@ function plotMag(data,gui,frame)
         M = data.results.basic.Mrot;
         ax = gui.axes_handles.MagR;
 end
+% xy-component of magnetization vector
+Mxy = sqrt(M(:,1).^2+M(:,2).^2);
 % norm of magnetization vector
 Mamp = sqrt(M(:,1).^2+M(:,2).^2+M(:,3).^2);
 
@@ -103,10 +105,11 @@ function plotMag(data,gui,frame)
 switch data.basic.type
     case {'prepol','prepolpulse'}
         M = M./data.basic.B0;
+        Mxy = Mxy./data.basic.B0;
         Mamp = Mamp./data.basic.B0;
-        d = max(M(:))-min(M(:));
-        ymin = min(M(:))-d/20;
-        ymax = max(M(:))+d/20;
+        d = max([M(:);Mxy(:)])-min([M(:);Mxy(:)]);
+        ymin = min([M(:);Mxy(:)])-d/20;
+        ymax = max([M(:);Mxy(:)])+d/20;
     otherwise
         ymin = -1.05;
         ymax = 1.05;
@@ -115,12 +118,11 @@ function plotMag(data,gui,frame)
 % plot the data
 clearSingleAxis(ax);
 hold(ax,'on');
-plot(T,M(:,1),'LineWidth',gui.myui.linewidth,'Color','r','Parent',ax);
-plot(T,M(:,2),'LineWidth',gui.myui.linewidth,'Color','g','Parent',ax);
-plot(T,M(:,3),'LineWidth',gui.myui.linewidth,'Color','b','Parent',ax);
-plot(T,sqrt(M(:,1).^2+M(:,2).^2),'LineWidth',gui.myui.linewidth,...
-    'Color','m','Parent',ax);
-plot(T,Mamp,'LineWidth',gui.myui.linewidth,'Color','k',...
+plot(T,M(:,1),'LineWidth',myui.linewidth,'Color','r','Parent',ax);
+plot(T,M(:,2),'LineWidth',myui.linewidth,'Color','g','Parent',ax);
+plot(T,M(:,3),'LineWidth',myui.linewidth,'Color','b','Parent',ax);
+plot(T,Mxy,'LineWidth',myui.linewidth,'Color','m','Parent',ax);
+plot(T,Mamp,'LineWidth',myui.linewidth,'Color','k',...
     'LineStyle','--','Parent',ax);
 set(ax,'XLim',[min(T) max(T)],'YLim',[ymin ymax]);
 
@@ -164,7 +166,7 @@ function plotMag(data,gui,frame)
     set(get(lh,'Title'),'String',['p=',sprintf('%4.3f',data.results.prepol.p)])
 end
 % font size
-set(ax,'FontSize',gui.myui.axfontsize);
+set(ax,'FontSize',myui.axfontsize);
 
 end
 
@@ -215,7 +217,9 @@ function plotSphere(data,gui,frame)
         indP = [];
         indE = numel(T);
         % switch-off B-field trajectory
-        Bamp = sqrt(data.results.prepol.Beff(:,1).^2+data.results.prepol.Beff(:,2).^2+data.results.prepol.Beff(:,3).^2);
+        Bamp = sqrt(data.results.prepol.Beff(:,1).^2+...
+            data.results.prepol.Beff(:,2).^2+...
+            data.results.prepol.Beff(:,3).^2);
         Beffn = data.results.prepol.Beff./Bamp;
         
     case 'pulse'
@@ -235,22 +239,24 @@ function plotSphere(data,gui,frame)
         indP = T>Tramp+Twait & T<=Tramp+Twait+Ttau;
         indE = numel(T);
         % switch-off B-field trajectory
-        Bamp = sqrt(data.results.prepol.Beff(:,1).^2+data.results.prepol.Beff(:,2).^2+data.results.prepol.Beff(:,3).^2);
+        Bamp = sqrt(data.results.prepol.Beff(:,1).^2+...
+            data.results.prepol.Beff(:,2).^2+...
+            data.results.prepol.Beff(:,3).^2);
         Beffn = data.results.prepol.Beff./Bamp;
 end
 
 % plot data
 clearSingleAxis(ax);
 hold(ax,'on');
-plot3(M(indS1,1),M(indS1,2),M(indS1,3),'LineWidth',gui.myui.linewidth,...
+plot3(M(indS1,1),M(indS1,2),M(indS1,3),'LineWidth',myui.linewidth,...
     'Color',myui.color.basic,'Parent',ax);
-plot3(M(indS2,1),M(indS2,2),M(indS2,3),'LineWidth',gui.myui.linewidth,...
+plot3(M(indS2,1),M(indS2,2),M(indS2,3),'LineWidth',myui.linewidth,...
     'Color',myui.color.wait,'Parent',ax);
-plot3(M(indP,1),M(indP,2),M(indP,3),'LineWidth',gui.myui.linewidth,...
+plot3(M(indP,1),M(indP,2),M(indP,3),'LineWidth',myui.linewidth,...
     'Color',myui.color.pulse,'Parent',ax);
-plot3(M(indR,1),M(indR,2),M(indR,3),'LineWidth',gui.myui.linewidth,...
+plot3(M(indR,1),M(indR,2),M(indR,3),'LineWidth',myui.linewidth,...
     'Color',myui.color.prepol,'Parent',ax);
-plot3(Beffn(:,1),Beffn(:,2),Beffn(:,3),'LineWidth',gui.myui.linewidth,...
+plot3(Beffn(:,1),Beffn(:,2),Beffn(:,3),'LineWidth',myui.linewidth,...
     'Color',myui.color.prepolB,'Parent',ax)
 plot3(M(indE,1),M(indE,2),M(indE,3),'ko','MarkerSize',8,'Parent',ax);
 % plot actual Bloch sphere
@@ -267,7 +273,6 @@ function plotSphere(data,gui,frame)
 
 %% FFT of magnetization and pulse
 function plotFFT(data,gui,type)
-myui = gui.myui;
 
 % Larmor freq. [Hz]
 fL = getOmega0(data.basic.gamma,data.basic.B0)/2/pi;