Renaming and spelling correction

TR_EPR_script.m

@@ -12,7 +12,7 @@ datapath = 'C:\Users\lukas\Nextcloud\Uni\Bachelorarbeit\tr-epr-simulation\exampl
 
 [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

@@ -0,0 +1,109 @@
+function [dataOUT,params] = average_maximum(dataIN,params)
+%AVERAGE_MAXIMUM normalizes data by max of region
+%
+%   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" normalization to maximum will be executed and the
+%   graph changes to the normalized data. The borders of the maximum region
+%   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 = 'Average of Data in Maximum';
+fig.Units = 'Normalized';
+fig.Position = [.2 .2 .6 .6];
+fig.Tag = 'Normalize';
+
+%panel for plot
+plotpanel = uipanel(fig);
+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
+
+%create push buttons
+a = uicontrol(fig,'Style','pushbutton');
+a.String = 'Apply';
+a.Units = 'Normalized';
+a.Position = [.52 .01 .15 .05];
+a.FontUnits = 'Normalized';
+a.FontSize = 0.6;
+a.Tag = 'Apply';
+a.Callback = @NormApplyButtonPushed;
+
+r = uicontrol(fig,'Style','pushbutton');
+r.String = 'Reset';
+r.Units = 'Normalized';
+r.Position = [.68 .01 .15 .05];
+r.FontUnits = 'Normalized';
+r.FontSize = 0.6;
+r.Tag = 'Reset';
+r.Callback = @NormResetButtonPushed;
+
+d = uicontrol(fig,'Style','pushbutton');
+d.String = 'Done';
+d.Units = 'Normalized';
+d.Position = [.84 .01 .15 .05];
+d.FontUnits = 'Normalized';
+d.FontSize = 0.6;
+d.Tag = 'Done';
+d.Callback = @NormDoneButtonPushed;
+
+%create input fields
+p1 = uicontrol(fig,'Style','edit');
+p1.String = 'Left point of max region';
+p1.Units = 'Normalized';
+p1.Position = [.01 .01 .24 .05];
+p1.HorizontalAlignment = 'left';
+p1.FontUnits = 'Normalized';
+p1.FontSize = 0.6;
+p1.Tag = 'MaxRegionLeft';
+
+p2 = uicontrol(fig,'Style','edit');
+p2.String = 'Right point of max region';
+p2.Units = 'Normalized';
+p2.Position = [.25 .01 .24 .05];
+p2.HorizontalAlignment = 'left';
+p2.FontUnits = 'Normalized';
+p2.FontSize = 0.6;
+p2.Tag = 'MaxRegionRight';
+
+uicontrol(p1); %passes focus to first input
+uiwait(fig)
+
+%% Callback functions
+    function NormApplyButtonPushed(~,~)
+        left_point = str2double(get(p1,'String'));
+        right_point = str2double(get(p2,'String'));
+        %take mean of each field line between specified min and max time
+        maxima_mean = mean(dataIN([left_point right_point],:));
+        %normalize amplitude to 1 by dividing by max of means
+        dataOUT = dataIN / max(maxima_mean);
+        %plotting result with time as x axis
+        plot(ax,dataOUT)
+        axis tight
+        %writing parameter
+        params.region_of_max = [left_point right_point];
+        params.max_mean = maxima_mean / max(maxima_mean);
+    end
+
+    function NormResetButtonPushed(~,~)
+        plot(ax,dataIN)
+        axis tight
+    end
+
+    function NormDoneButtonPushed(~,~)
+        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

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

@@ -146,7 +146,7 @@ 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 +191,7 @@ 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';