Update flux_fun_to_profile_2d.m

POLOIDAL_METHOD = 'theta'; % Options: 'uniform', 'theta'

maskPFR = 1;           % If 1 then treat PFR psiN as 2 - psiN

maskPoloidalBySep = 1; % If 1 then only apply poloidal function for psiN >= 1

maskLim = 1;           % If 1 then set fun = 0 outside of g.lim

%% Settings

gfile_name = 'C:\Users\jjl\Dropbox (ORNL)\PSIscidac\WEST\g055866.47179_V2';  % efit file

nR = 200;  % Grid resolution to build surface

nZ = 300;

nR = 300;  % Grid resolution to build surface

nZ = 400;

cTanh = [1 0.04 0.3 0.1 3e-3 3e-5 0 -0.01];  % tanh coefficents, only used if RADIAL_METHOD == 'psiN'

%% Define total function

myFun = radialFun.*poloidalFun;

if maskLim

    mask = ~inpolygon(R2D,Z2D,g.lim(1,:),g.lim(2,:));

    myFun(mask) = 0;

end

%% Plot contours

figure; hold on; box on; set(gcf,'color','w');set(gca,'fontsize',14); grid on; 

axis equal;

h = pcolor(R2D,Z2D,myFun);

set(h,'edgecolor','none');

colorbar;

c = parula;

c(1,:) = [1 1 1];

colormap(c);

plot(g.lim(1,:),g.lim(2,:),'k')

plot(g.bdry(1,:),g.bdry(2,:),'k')

plot(Rtest,Ztest,'r','linew',3)