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`
ThoHiller · May 16, 2020 · e74ecb4 · e74ecb4
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diff --git a/BLOCHUS/BLOCHUS.m b/BLOCHUS/BLOCHUS.m
@@ -33,8 +33,8 @@
 %------------- BEGIN CODE --------------
 
 %% GUI 'header' info and default GUI settings
-myui.version = '0.1.0';
-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
@@ -83,7 +83,7 @@
     'FontSize',myui.fontsize,...
     'UserData',struct('Tooltipstr',tstr,'defaults',data.init.B0),...    
     'Callback',@onEditValue);
-tstr = '<HTML><b>Omega</b><sub>0</sub> frequency in [Hz].<br>';
+tstr = ['<HTML>Larmor frequency <b>',char(hex2dec('3C9')),'</b><sub>0</sub> in [Hz].<br>'];
 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
@@ -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
@@ -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
@@ -11,9 +11,9 @@
 **BLOCHUS** is a set of MATLAB<sup>TM</sup> 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
@@ -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
@@ -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
@@ -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
@@ -42,29 +42,70 @@ 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
             ax1 = subplot(3,2,1,'Parent',expfig);
             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');