% Demonstrate the Moore_PCF

load Compact.dat; % Compact(:,1) = q; Compact(:,2) = I for compact object.
load NonCompact.dat;  % "" for noncompact object.

% Plot the raw data
figure(1); clf;
plot(Compact(:,1),2100*Compact(:,2),'b'); hold on
plot(NonCompact(:,1), 325*NonCompact(:,2),'g');
legend('Compact','NonCompact');
temp =axis; % Mark the valid q-range
q_range = [ 0.02 0.2];
plot([ q_range(1) q_range(1)], [temp(3),temp(4)],'r');
plot([ q_range(2) q_range(2)], [temp(3),temp(4)],'r');
xlabel('q (A^{-1}');ylabel('I (Pollacks)');
title('Region of Interest in I versus Q');

% Show what happens when we pick an arbitrary cut-off length
D = 200; % Assume PCF goes to zero at D = 200
[rc, pc, ec] = Moore_PCF(Compact, q_range, D);
[rnc, pnc, enc] = Moore_PCF(NonCompact, q_range,D);
figure(2); clf;
plot(rc,pc,'b'); hold on
plot(rnc,pnc,'g'); 
xlabel('r - Angstroms'); ylabel('p(r) - A^{-1}');
title('Pair Correlation Functions : D = 200 Angstroms');
legend('Compact','NonCompact');

% Now utilize error function to optimize length-scale, D
D = [130:230];
for j=1:length(D)
    [rc, pc, temp] = Moore_PCF(Compact, q_range, D(j));
    ec(j) = temp;
    [rnc, pnc, temp] = Moore_PCF(NonCompact, q_range,D(j));
    enc(j) = temp;
end

figure(3); clf;
plot(D, ec/max(ec),'b'); hold on
plot(D,enc/max(enc),'g');
xlabel('D (Angstroms)');
ylabel('Root Mean Square Fit Error - Normalized');
title('Fitting D');

% Compute the best fit of each.
[ecb idx] = min(ec); Dcb = D(idx);
[rc, pc, temp] = Moore_PCF(Compact, q_range, Dcb);
[encb idx] = min(enc); Dncb = D(idx);
[rnc, pnc,temp]= Moore_PCF(NonCompact, q_range,Dncb);
figure(4);clf;
plot(rc,pc,'b'); hold on;
plot(rnc,pnc,'g'); hold on;
xlabel('r - Angstroms'); ylabel('p(r) - A^{-1}');
title('Pair Correlation Functions');
legend('Compact','NonCompact');