Merge branch 'objectify' trying to get rid off uncommon flows

TR_EPR_script.m

@@ -4,15 +4,17 @@ 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';
+[raw_data,params] = load_bruker(datapath);
 
 [time_corr_data,params] = correct_time_baseline(raw_data,params);
 
 [full_corr_data,params] = correct_magnetic_baseline(time_corr_data,params);
 
-[norm_data,params] = normalize_data(full_corr_data,params);
+[norm_data,params] = average_maximum(full_corr_data,params);
 
 [params] = pre_simulation_TREPR(params);
 

average_maximum.m

@@ -1,20 +1,20 @@
-function [dataOUT,params] = normalize_data(dataIN,params)
+function [dataOUT,params] = average_maximum(dataIN,params)
-%NORMALISE_DATA normalizes data by max of region
+%AVERAGE_MAXIMUM normalizes data by max of region
 %
-%   Usage: [dataOUT,params] = NORMALISE_DATA(dataIN,params), where dataIN
+%   Usage: [dataOUT,params] = AVERAGE_MAXIMUM(dataIN,params), where dataIN
 %   is a dataset loaded via the LOAD_MATLAB or LOAD_BRUKER function.
 %
 %   The function will show the input data and offer two input fields, where
 %   the left and right borders of the maximum's region should be set.
-%   By pressing "Apply" the normalization will be executed and the graph
+%   By pressing "Apply" normalization to maximum will be executed and the
-%   changes to the normalized data. The borders of the maximum region and
+%   graph changes to the normalized data. The borders of the maximum region
-%   the mean of maximums will also be appended to the params struct.
+%   and the mean of maxima will also be appended to the params struct.
 %   By pressing "Reset" the graph will return to show the original data.
 %   Exit the function by pressing "Done".
 
 %% creating UI
 fig = figure;
-fig.Name = 'Normalize Data';
+fig.Name = 'Average of Data in Maximum';
 fig.Units = 'Normalized';
 fig.Position = [.2 .2 .6 .6];
 fig.Tag = 'Normalize';
@@ -103,7 +103,7 @@ uiwait(fig)
     end
 
     function NormDoneButtonPushed(~,~)
-        close 'Normalize Data'
+        close 'Average of Data in Maximum'
     end
 
 end

correct_magnetic_baseline.m

@@ -15,7 +15,7 @@ function [dataOUT,params] = correct_magnetic_baseline(dataIN,params)
 
 %% creating UI
 fig = figure;
-fig.Name = 'Correct Magnetic Baseline';
+fig.Name = 'Correct Magnetic Field Baseline';
 fig.Units = 'Normalized';
 fig.Position = [.2 .2 .6 .6];
 fig.Tag = 'CorrMagBase';
@@ -72,7 +72,7 @@ p1.FontSize = 0.6;
 p1.Tag = 'FieldPoints';
 
 p2 = uicontrol(fig,'Style','edit');
-p2.String = 'No. points to cut';
+p2.String = 'No. points to cut before';
 p2.Units = 'Normalized';
 p2.Position = [.26 .01 .24 .05];
 p2.HorizontalAlignment = 'left';
@@ -120,7 +120,7 @@ uiwait(fig)
     end
 
     function FieldDoneButtonPushed(~,~)
-        close 'Correct Magnetic Baseline'
+        close 'Correct Magnetic Field Baseline'
     end
 
 end

example_data.xml

@@ -11744,23 +11744,11 @@
         <S>1</S>
         <g>2</g>
         <D>2150</D>
-        <D>70</D>
+        <D>75</D>
         <lw>8</lw>
         <lw>0</lw>
     </Manual_Sys>
     <Triplett_pop>0</Triplett_pop>
     <Triplett_pop>0.71429</Triplett_pop>
     <Triplett_pop>0.28571</Triplett_pop>
-    <Fitted_Simulation>
-        <S>1</S>
-        <g>1.9934</g>
-        <D>2150.3379</D>
-        <D>66.695461</D>
-        <lw>9</lw>
-        <lw>0</lw>
-        <Temperature>0</Temperature>
-        <Temperature>0.55912</Temperature>
-        <Temperature>0.44088</Temperature>
-        <weight>1</weight>
-    </Fitted_Simulation>
 </struct>

load_bruker.m

@@ -47,7 +47,7 @@ params.Accumulations = bruker_params.AVGS;
 params.laser_shotreprate = "NOT RECORDED";
 params.Field_Start = bruker_params.YMIN;
 params.Field_End = bruker_params.YMIN + bruker_params.YWID;
-params.Field_Vector = cell2mat(bruker_axes(1,2));
+params.Field_Vector = cell2mat(bruker_axes(1,2)).';
 params.mwFreq = bruker_params.MWFQ / 1e9;
 params.mwPower = bruker_params.MWPW * 1e3;
 params.QValue = "NOT RECORDED";

pre_simulation_TREPR.m

@@ -10,6 +10,9 @@ function [params] = pre_simulation_TREPR(params)
 %   different relevant paramters of TREPR simulation.
 %   By pressing "Apply" the simulation will be calculated and displayed.
 %   The simulation parameters will be saved to the params struct.
+%   Note: Triplett popluations will be processed normalized, but must not
+%   be equal.
+%   "Done" will close the window.
 
 %% creating UI
 fig = figure;
@@ -51,7 +54,7 @@ d.Callback = @PreSimDoneButtonPushed;
 
 %% create input and text fields (Triplet)
 textTrip = uicontrol(fig,'Style','text');
-textTrip.String = 'Triplett populations';
+textTrip.String = 'Triplet populations';
 textTrip.Units = 'Normalized';
 textTrip.Position = [.71 .94 .28 .05];
 textTrip.HorizontalAlignment = 'center';
@@ -70,7 +73,7 @@ textTx.FontSize = 0.6;
 textTx.Tag = 'textTx';
 
 InpTx = uicontrol(fig,'Style','edit');
-InpTx.String = '1';
+InpTx.String = '0.9';
 InpTx.Units = 'Normalized';
 InpTx.Position = [.75334 .89 .04333 .05];
 InpTx.HorizontalAlignment = 'left';
@@ -88,7 +91,7 @@ textTy.FontSize = 0.6;
 textTy.Tag = 'textTy';
 
 InpTy = uicontrol(fig,'Style','edit');
-InpTy.String = '1';
+InpTy.String = '1.0';
 InpTy.Units = 'Normalized';
 InpTy.Position = [.85001 .89 .04333 .05];
 InpTy.HorizontalAlignment = 'left';
@@ -106,7 +109,7 @@ textTz.FontSize = 0.6;
 textTz.Tag = 'textTz';
 
 InpTz = uicontrol(fig,'Style','edit');
-InpTz.String = '1';
+InpTz.String = '1.1';
 InpTz.Units = 'Normalized';
 InpTz.Position = [.94667 .89 .04333 .05];
 InpTz.HorizontalAlignment = 'left';
@@ -116,7 +119,7 @@ InpTz.Tag = 'InpTz';
 
 %% create input and text fields (D & E)
 textDE = uicontrol(fig,'Style','text');
-textDE.String = 'D tensor';
+textDE.String = 'ZFS parameters / MHz';
 textDE.Units = 'Normalized';
 textDE.Position = [.71 .77 .28 .05];
 textDE.HorizontalAlignment = 'center';
@@ -153,7 +156,7 @@ textE.FontSize = 0.6;
 textE.Tag = 'textE';
 
 InpE = uicontrol(fig,'Style','edit');
-InpE.String = '1/3 D';
+InpE.String = 'max D/3';
 InpE.Units = 'Normalized';
 InpE.Position = [.9225 .72 .0675 .05];
 InpE.HorizontalAlignment = 'left';
@@ -208,9 +211,9 @@ InpG.FontUnits = 'Normalized';
 InpG.FontSize = 0.6;
 InpG.Tag = 'InpG';
 
-%% create input and text fields (linewidth)
+%% create input and text fields (linewidths)
 textLW = uicontrol(fig,'Style','text');
-textLW.String = 'Linewidth';
+textLW.String = 'Linewidths';
 textLW.Units = 'Normalized';
 textLW.Position = [.71 .43 .28 .05];
 textLW.HorizontalAlignment = 'center';

simulation_TREPR.m

@@ -25,6 +25,7 @@ eventdata.manExp.Harmonic = 0; % zeroth harmonic
 eventdata.manExp.Temperature = params.Triplett_pop;
 eventdata.simSys = params.Manual_Sys; %initialize simulation parameters
 eventdata.simExp = eventdata.manExp;
+eventdata.SaveStat = 0; %counter if save button was pushed
 
 %% creating UI
 fig = figure;
@@ -146,7 +147,7 @@ InpTz.Tag = 'InpTz';
 
 %% create input and text fields (D & E)
 textDE = uicontrol(fig,'Style','text');
-textDE.String = 'D tensor variation';
+textDE.String = 'ZFS parameter variation / MHz';
 textDE.Units = 'Normalized';
 textDE.Position = [.71 .78 .28 .05];
 textDE.HorizontalAlignment = 'center';
@@ -191,7 +192,7 @@ InpE.FontUnits = 'Normalized';
 InpE.FontSize = 0.6;
 InpE.Tag = 'InpE';
 
-%% create input and text fields (linewidth)
+%% create input and text fields (linewidths)
 textLW = uicontrol(fig,'Style','text');
 textLW.String = 'Linewidth variations';
 textLW.Units = 'Normalized';
@@ -349,10 +350,16 @@ uiwait(fig)
         eventdata.simExp.Temperature = eventdata.BestSys.Temperature;
         %save fitted parameters to struct
         params.Fitted_Simulation = eventdata.BestSys;
+        eventdata.SaveStat = eventdata.SaveStat + 1;
     end
     
     function SimDoneButtonPushed(~,~)
-        close 'Simulation'
+        if eventdata.SaveStat == 0
+            params.Fitted_Simulation = eventdata.BestSys;
+            close 'Simulation'
+        else
+            close 'Simulation'
+        end
     end
  
 end