Merge patches from branch 'objectify'

TR_EPR_script.m

@@ -4,11 +4,11 @@ close all
 %Script for calling the functions of TR-EPR toolbox
 
 %path to dataset
-% datapath = 'C:\Users\lukas\Nextcloud\Uni\Bachelorarbeit\tr-epr-simulation\example_data.mat';
+datapath = 'C:\Users\lukas\Nextcloud\Uni\Bachelorarbeit\tr-epr-simulation\example_data.mat';
-% [raw_data,params] = load_matlab(datapath);
+[raw_data,params] = load_matlab(datapath);
 
-datapath = 'C:\Users\lukas\Nextcloud\Uni\Bachelorarbeit\tr-epr-simulation\pentacene_355nm_481pt.DSC';
+% datapath = 'C:\Users\lukas\Nextcloud\Uni\Bachelorarbeit\tr-epr-simulation\pentacene_355nm_481pt.DSC';
-[raw_data,params] = load_bruker(datapath);
+% [raw_data,params] = load_bruker(datapath);
 
 [time_corr_data,params] = correct_time_baseline(raw_data,params);
 

average_maximum.m

@@ -25,11 +25,11 @@ plotpanel.Units = 'Normalized';
 plotpanel.Position = [.01 .06 .98 .92];
 %axes for plot
 ax = axes(plotpanel);
-ax.XLabel.String = 'Time';
-ax.YLabel.String = 'Intensity';
 %plot current data in figure with time as x axis
 plot(ax,dataIN)
-axis tight
+xlabel(ax,'Time Points');
+ylabel(ax,'EPR Signal / A. U.');
+axis(ax,'tight');
 
 %create push buttons
 a = uicontrol(fig,'Style','pushbutton');
@@ -91,7 +91,9 @@ uiwait(fig)
         dataOUT = dataIN / max(maxima_mean);
         %plotting result with time as x axis
         plot(ax,dataOUT)
-        axis tight
+        xlabel(ax,'Time Points');
+        ylabel(ax,'EPR Signal / A. U.');
+        axis(ax,'tight');
         %writing parameter
         params.region_of_max = [left_point right_point];
         params.max_mean = maxima_mean / max(maxima_mean);
@@ -99,7 +101,9 @@ uiwait(fig)
 
     function NormResetButtonPushed(~,~)
         plot(ax,dataIN)
-        axis tight
+        xlabel(ax,'Time Points');
+        ylabel(ax,'EPR Signal / A. U.');
+        axis(ax,'tight');
     end
 
     function NormDoneButtonPushed(~,~)

correct_magnetic_baseline.m

@@ -26,12 +26,12 @@ plotpanel.Units = 'Normalized';
 plotpanel.Position = [.01 .06 .98 .92];
 %axes for plot
 ax = axes(plotpanel);
-ax.XLabel.String = 'Magnetic field';
-ax.YLabel.String = 'Intensity';
 %plot current data in figure with field as x axis
 dataIN_transp = dataIN.';
 plot(ax,dataIN_transp)
-axis tight
+xlabel(ax,'Magnetic Field Points');
+ylabel(ax,'EPR Signal / A. U.');
+axis(ax,'tight');
 
 %create push buttons
 a = uicontrol(fig,'Style','pushbutton');
@@ -102,7 +102,9 @@ uiwait(fig)
         %plotting result with field as x axis
         dataOUT_transp = dataOUT.';
         plot(ax,dataOUT_transp)
-        axis tight
+        xlabel(ax,'Magnetic Field Points');
+        ylabel(ax,'EPR Signal / A. U.');
+        axis(ax,'tight');
         %adjusting parameter
         params.Field_Sweep = params.Field_Sweep - params.Field_Step*2*field_cut;
         params.Field_Start = params.Field_Start + params.Field_Step*field_cut;
@@ -116,7 +118,9 @@ uiwait(fig)
 
     function FieldResetButtonPushed(~,~)
         plot(ax,dataIN_transp)
-        axis tight
+        xlabel(ax,'Magnetic Field Points');
+        ylabel(ax,'EPR Signal / A. U.');
+        axis(ax,'tight');
     end
 
     function FieldDoneButtonPushed(~,~)

correct_time_baseline.m

@@ -24,11 +24,11 @@ plotpanel.Units = 'Normalized';
 plotpanel.Position = [.01 .06 .98 .92];
 %axes for plot
 ax = axes(plotpanel);
-ax.XLabel.String = 'Time';
-ax.YLabel.String = 'Intensity';
 %plot current data in figure
 plot(ax,dataIN)
-axis tight
+xlabel(ax,'Time Points');
+ylabel(ax,'EPR Signal / A. U.');
+axis(ax,'tight');
 
 %create push buttons
 a = uicontrol(fig,'Style','pushbutton');
@@ -83,14 +83,18 @@ uiwait(fig)
         end
         %plotting result
         plot(ax,dataOUT)
-        axis tight
+        xlabel(ax,'Time Points');
+        ylabel(ax,'EPR Signal / A. U.');
+        axis(ax,'tight');
         %writing parameter
         params.pretrigger = pretrigger;
     end
 
     function TimeResetButtonPushed(~,~)
         plot(ax,dataIN)
-        axis tight
+        xlabel(ax,'Time Points');
+        ylabel(ax,'EPR Signal / A. U.');
+        axis(ax,'tight');
     end
 
     function TimeDoneButtonPushed(~,~)

pre_simulation_TREPR.m

@@ -27,11 +27,11 @@ plotpanel.Units = 'Normalized';
 plotpanel.Position = [.01 .01 .7 .98];
 %axes for plot
 ax = axes(plotpanel);
-ax.XLabel.String = 'magnetic field';
-ax.YLabel.String = 'Intensity';
 %plot current data in figure with field as x axis
 plot(ax,0.1*params.Field_Vector,params.max_mean,'r')
-axis tight
+xlabel(ax,'Magnetic Field / mT');
+ylabel(ax,'EPR Signal / A. U.');
+axis(ax,'tight');
 
 %% create push buttons
 a = uicontrol(fig,'Style','pushbutton');
@@ -289,8 +289,10 @@ uiwait(fig)
         %plot result
         plot(ax,0.1*params.Field_Vector,params.max_mean,'r',...
              bfield,spec_norm,'b','LineWidth',1.2)
-        legend('experimental','simulation')
+        xlabel(ax,'Magnetic Field / mT');
-        axis tight
+        ylabel(ax,'EPR Signal / A. U.');
+        legend(ax,'experimental','simulation');
+        axis(ax,'tight');
         %write manual fit to params
         params.Manual_Sys = Sys;
         params.Triplett_pop = Exp.Temperature;

simulation_TREPR.m

@@ -24,6 +24,7 @@ eventdata.manExp.CenterSweep = 0.1*[params.Field_Center params.Field_Sweep]; % m
 eventdata.manExp.Harmonic = 0; % zeroth harmonic
 eventdata.manExp.Temperature = params.Triplett_pop;
 eventdata.simSys = params.Manual_Sys; %initialize simulation parameters
+eventdata.simSys.Temperature = params.Triplett_pop;
 eventdata.simExp = eventdata.manExp;
 eventdata.SaveStat = 0; %counter if save button was pushed
 
@@ -48,7 +49,7 @@ spec_norm = spec/max(spec); % normalize the simulation
 plot(ax,0.1*params.Field_Vector,params.max_mean,'r',...
      bfield,spec_norm,'b','LineWidth',1.2)
 xlabel 'Magnetic Field / mT'
-ylabel 'EPR signal / A. U.'
+ylabel 'EPR Signal / A. U.'
 legend('experimental','simulation')
 axis tight
 
@@ -328,15 +329,20 @@ uiwait(fig)
         %get previous simulation parameters (manual or saved)
         Sys0 = eventdata.simSys;
         Exp0 = eventdata.simExp;
+        %check if Temperature can run into negative
+        for nT = 1:3
+            if Sys0.Temperature(nT) - Vary.Temperature(nT) < 0
+                 warndlg('Triplett population boundary < 0!','Warning');
+            end
+        end
         %perform fit
-        Sys0.Temperature = [0 0 0];
         [BestSys,BestSpc] = esfit('thyme',params.max_mean,Sys0,Vary,Exp0,[],FitOpt);
         plot(ax,0.1*params.Field_Vector,params.max_mean,'r',...
-                0.1*params.Field_Vector,BestSpc,'b','LineWidth',1.2)
+                0.1*params.Field_Vector,BestSpc,'b','LineWidth',1.2);
-        xlabel 'Magnetic Field / mT'
+        xlabel(ax,'Magnetic Field / mT');
-        ylabel 'EPR signal / A. U.'
+        ylabel(ax,'EPR Signal / A. U.');
-        legend('experimental','simulation')
+        legend(ax,'experimental','simulation');
-        axis tight
+        axis(ax,'tight');
         %normalize Triplett population
         Tsum = sum(BestSys.Temperature);
         BestSys.Temperature = BestSys.Temperature ./ Tsum;