How do I eliminate points outside the contour lines? - matlab

Question

I have the code that generate a plot which has points plotted both inside and outside the contour line. I want to eliminate the points outside the outermost contour line. I'm using gaussian copula function.
plot(givenData(:,1),givenData(:,2),'b.','MarkerSize',3);
givenData is a 5000x2 matrix and I want only those values that lie inside the outer contour line to be plotted.
plot i'm getting
plot i want to generate
i want to eliminate the points lying outside the red contour which are shown as geen dots.
function [xgrid,ygrid,Z] = biVariateContourPlotsGMMCopula(givenData,gmmObject,~,numMeshPoints,x_dim,y_dim)
d = 2;
if nargin < 5
x_dim = 1;
y_dim = 2;
end
if x_dim == y_dim
hist(givenData(:,x_dim),10);
return;
end
numMeshPoints = min(numMeshPoints,256);
givenData = givenData(:,[x_dim y_dim]);
alpha = gmmObject.alpha;
mu = gmmObject.mu(:,[x_dim y_dim]);
sigma = gmmObject.sigma([x_dim y_dim],[x_dim y_dim],:) + 0.005*repmat(eye(d),[1 1 numel(alpha)]);
gmmObject = gmdistribution(mu,sigma,alpha);
bin_num = 256;
for j = 1:2
l_limit = min(gmmObject.mu(:,j))-3*(max(gmmObject.Sigma(j,j,:))^0.5);
u_limit = max(gmmObject.mu(:,j))+3*(max(gmmObject.Sigma(j,j,:))^0.5);
xmesh_inverse_space{j} = (l_limit:(u_limit-l_limit)/(bin_num-1):u_limit);
end
[~,pdensity{i},xmesh{i}]=kde(currentVar,numMeshPoints);
pdensity{i}(pdensity{i}<0) = 0;
cdensity{i} = cumsum(pdensity{i});
cdensity{i} = (cdensity{i}-min(cdensity{i}))/(max(cdensity{i})-min(cdensity{i})); % scaling the cdensity value to be between [0 1]
end
[xgrid,ygrid] = meshgrid(xmesh{1}(2:end-1),xmesh{2}(2:end-1));
for k = 1:d
marginalLogLikelihood_grid{k} = log(pdensity{k}(2:end-1)+eps);
marginalCDFValues_grid{k} = cdensity{k}(2:end-1);
end
[marg1,marg2] = meshgrid(marginalLogLikelihood_grid{1},marginalLogLikelihood_grid{2});
[xg,yg] = meshgrid(marginalCDFValues_grid{1},marginalCDFValues_grid{2});
inputMatrix = [reshape(xg,numel(xg),1) reshape(yg,numel(yg),1)];
copulaLogLikelihoodVals = gmmCopulaPDF(inputMatrix,gmmObject,xmesh_inverse_space);
Z = reshape(copulaLogLikelihoodVals,size(marg1,1),size(marg1,2));
Z = Z+marg1+marg2;
Z = exp(Z);
plot(givenData(:,1),givenData(:,2),'b.','MarkerSize',3);hold
contour(xgrid,ygrid,Z,40,'EdgeColor',[1 0 0]);
axis tight;