finished basic functionality for printing figures

.gitignore

@@ -1 +1,3 @@
 *.asv
+*.pdf
+*.xml

print_figure_pdf.m

@@ -1,7 +1,60 @@
-function [outputArg1,outputArg2] = print_figure_pdf(inputArg1,inputArg2)
+function [] = print_figure_pdf(data,params,type)
-%PRINT_FIGURE_PDF Summary of this function goes here
+%PRINT_FIGURE_PDF creates pdf figures of TREPR data
-%   Detailed explanation goes here
+%
-outputArg1 = inputArg1;
+%   Usage: PRINT_FIGURE_PDF(data,params,type), where data are TREPR data
-outputArg2 = inputArg2;
+%   loaded by LOAD_MATLAB or LOAD_BRUKER, params is a struct created by
+%   SIMULATION_TREPR and type a number.
+%   
+%   type = 1: 2D plot of data and simulation with magnetic field as x-axis
+%   type = 2: 3D plot of data without simulation
+
+if type == 1
+    %getting simulation values
+    Exp.mwFreq = params.mwFreq; % GHz
+    Exp.nPoints = length(params.Field_Vector);
+    Exp.CenterSweep = 0.1*[params.Field_Center params.Field_Sweep]; % mT (converted from Gauss)
+    Exp.Harmonic = 0; % zeroth harmonic
+    Exp.Temperature = params.Triplett_pop;
+    Sys = params.Fitted_Simulation;
+    %calculate simulation
+    [~,spec] = pepper(Sys,Exp);
+    spec_norm = spec/max(spec); % normalize the simulation
+    %plot invisible and print
+    figure('Visible','off')
+    plot(0.1*params.Field_Vector,params.max_mean,'r',...
+         0.1*params.Field_Vector,spec_norm,'b','LineWidth',1.2)
+    xlabel 'Magnetic Field / mT'
+    ylabel 'EPR signal / A. U.'
+    legend('experimental','simulation')
+    title(params.Name, 'Interpreter','none')
+    axis tight
+    set(gcf,'Units','Inches');
+    pos = get(gcf,'Position');
+    set(gcf,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)]);
+    figurepath = strcat(params.Path,"/",params.Name,"_Sim.pdf"); %create full filename
+    print(gcf,figurepath,'-dpdf','-r0');
+    
+elseif type == 2
+    %plot invisible and print
+    figure('Visible','off')
+    surf(0.1*params.Field_Vector, params.TimeBase*1e6, data)
+    colormap default
+    shading interp
+    view(305,10)
+    axis tight
+    xlabel 'Magnetic Field / mT'
+    ylabel 'Time / \mus'
+    zlabel 'EPR Signal / A.U.'
+    title(params.Name, 'Interpreter','none')
+    set(gcf,'Units','Inches');
+    pos = get(gcf,'Position');
+    set(gcf,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)]);
+    figurepath = strcat(params.Path,"/",params.Name,"_3D.pdf"); %create full filename
+    print(gcf,figurepath,'-dpdf','-r0');
+    
+else
+    error('Unknown plot type.');
+end
+
 end