TestBench_Microlith_BrightFieldThroughFocus.m

%% Simulated image of the Siemens star from the MBL/NNF amplitude target under bright-field microscope.
%
%  The image is simulated in-focus and at defocus of 0.5 and 1um.
% 
% Written by Shalin Mehta, www.mshalin.com 
% License: GPL v3 or later.

% This file is part of microlith package.
% 
%     microlith is free software: you can redistribute it and/or modify
%     it under the terms of the GNU General Public License as published by
%     the Free Software Foundation, either version 3 of the License, or
%     (at your option) any later version.
% 
%     microlith is distributed in the hope that it will be useful,
%     but WITHOUT ANY WARRANTY; without even the implied warranty of
%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%     GNU General Public License for more details.
% 
%     You should have received a copy of the GNU General Public License
%     along with microlith.  If not, see <http://www.gnu.org/licenses/>.

%% Set parameters of the microscope and the object.

clear all; clc;

wavelength=0.577; NAo=1.3;
RISiO2=1.55;
ThickSiO2=0.09;
zsim=[0 0.5 1];
Rsim=7; % Radius over which simulation is performed.
xsim=-Rsim:0.02:Rsim;

%% Choose small simulation region for reasonable runtime.

SimensPattern=mblnnfSiemens(xsim,xsim,0);
%  Open the matlabpool if parallel computing toolbox is installed.
% matlabpool 3;

%% Parameters of dark-field microscope and the image.
BFparams.NAo=NAo;
BFparams.wavelength=wavelength;
BFparams.NAc=NAo;
BFparams.nImm=1.515;
BFparams.nEmbb=1.33;

BFsys=microlith(xsim,zsim);
BFsys.computesys('Brightfield',BFparams);
BFThroughFocus=BFsys.computeimage(SimensPattern,'multiCPU');

%% Computation takes time, so results of computation may be saved.
%save([savedir 'MBLNNF_SiemensStar_BFimg.mat'],'BFsys');
%load([savedir 'MBLNNF_SiemensStar_BFimg.mat'],'BFsys');

%% Compare images and the pattern.
% Notice the artifacts very close to the edge. This example illustrates the
% need for the simulation grid to be slightly larger than the feature of
% interest. At defocus of 0.5 um, the resolution is slightly degraded. At
% defocus of 1 um, we start seeing contrast reversals.

figure(1); set(1,'Color','white','defaultaxesfontsize',16);
colormap gray;

h(1)=subplot(221);
imagesc(xsim,xsim,SimensPattern); axis equal; axis tight; colorbar;
title('Mask');

h(2)=subplot(222);
imagesc(xsim,xsim,BFsys.img(:,:,1)); axis equal; axis tight; colorbar;
title('In focus image');

h(3)=subplot(223);
imagesc(xsim,xsim,BFsys.img(:,:,2)); axis equal; axis tight; colorbar;
title('Defocused image, 0.5 \mum');


h(4)=subplot(224);
imagesc(xsim,xsim,BFsys.img(:,:,3)); axis equal; axis tight; colorbar;
title('Defocused image, 1 \mum');

linkaxes(h);