mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-18 00:49:09 +09:00
103 lines
3.7 KiB
Matlab
103 lines
3.7 KiB
Matlab
function [probe, mask] = make_tem_probe(dx, N, param)
|
|
%MAKE_TEM_PROBE Generate probe functions produced by object lens in
|
|
% transmission electron microscope.
|
|
% Written by Yi Jiang based on Eq.(2.10) in Advanced Computing in Electron
|
|
% Microscopy (2nd edition) by Dr.Kirkland
|
|
%
|
|
% Outputs:
|
|
% probe: complex probe functions
|
|
% mask: 2D Fourier mask function determined by alpha_max
|
|
%
|
|
% Inputs:
|
|
% dx: pixel size in angstrom
|
|
% N: number of pixels in each side of the 2D probe
|
|
% param: probe parameters and other settings
|
|
|
|
% parse inputs
|
|
parse_param = inputParser;
|
|
parse_param.KeepUnmatched = true;
|
|
parse_param.addParameter('df', 0, @isnumeric) %first-order aberration (defocus) in angstrom
|
|
parse_param.addParameter('C3', 0, @isnumeric) %third-order spherical aberration in angstrom
|
|
parse_param.addParameter('C5', 0, @isnumeric) %fifth-order spherical aberration in angstrom
|
|
parse_param.addParameter('C7', 0, @isnumeric) %seventh-order spherical aberration in angstrom
|
|
parse_param.addParameter('f_a2', 0, @isnumeric) %twofold astigmatism in angstrom
|
|
parse_param.addParameter('theta_a2', 0, @isnumeric) %azimuthal orientation in radian
|
|
parse_param.addParameter('f_a3', 0, @isnumeric) %threefold astigmatism in angstrom
|
|
parse_param.addParameter('theta_a3', 0, @isnumeric) %azimuthal orientation in radian
|
|
parse_param.addParameter('f_c3', 0, @isnumeric) %coma in angstrom
|
|
parse_param.addParameter('theta_c3', 0, @isnumeric) %azimuthal orientation in radian
|
|
|
|
parse_param.addParameter('shifts', [0,0], @isnumeric) %shift probe center in angstrom
|
|
parse_param.addParameter('N_z', 1, @isnumeric) %number of focal planes
|
|
parse_param.addParameter('voltage', 300, @isnumeric) %beam voltage
|
|
parse_param.addParameter('alpha_max', 30, @isnumeric) %semi-convergence angle
|
|
parse_param.addParameter('plotting', 0, @islogical) %plot probes
|
|
|
|
parse_param.parse(param)
|
|
p = parse_param.Results;
|
|
|
|
lambda = 12.398/sqrt((2*511.0+p.voltage).*p.voltage); %angstrom
|
|
|
|
amax = p.alpha_max*1e-3; %in rad
|
|
amin = 0;
|
|
|
|
klimitmax = amax/lambda;
|
|
klimitmin = amin/lambda;
|
|
dk = 1/(dx*N);
|
|
|
|
if p.N_z==1
|
|
dff = p.df;
|
|
else
|
|
dff = linspace(-floor(p.N_z/2),ceil(p.N_z/2)-1,p.N_z)*p.df; %angstrom
|
|
end
|
|
|
|
kx = linspace(-floor(N/2),ceil(N/2)-1,N);
|
|
[kX,kY] = meshgrid(kx,kx);
|
|
|
|
kX = kX.*dk;
|
|
kY = kY.*dk;
|
|
kR = sqrt(kX.^2+kY.^2);
|
|
theta = atan2(kY,kX);
|
|
chi = zeros(N,N,p.N_z);
|
|
probe = zeros(N,N,p.N_z);
|
|
|
|
mask = single(kR<=klimitmax).*single(kR>=klimitmin);
|
|
for i= 1:p.N_z
|
|
chi(:,:,i) = -pi*lambda*kR.^2*dff(i);
|
|
if p.C3~=0; chi(:,:,i) = chi(:,:,i) + pi/2*p.C3*lambda^3*kR.^4; end
|
|
if p.C5~=0; chi(:,:,i) = chi(:,:,i) + pi/3*p.C5*lambda^5*kR.^6; end
|
|
if p.C7~=0; chi(:,:,i) = chi(:,:,i) + pi/4*p.C7*lambda^7*kR.^8; end
|
|
if p.f_a2~=0; chi(:,:,i) = chi(:,:,i) + pi*p.f_a2*lambda*kR.^2*sin(2*(theta-p.theta_a2)); end
|
|
if p.f_a3~=0; chi(:,:,i) = chi(:,:,i) + 2*pi/3*p.f_a3*lambda^2*kR.^3*sin(3*(theta-p.theta_a3)); end
|
|
if p.f_c3~=0; chi(:,:,i) = chi(:,:,i) + 2*pi/3*p.f_c3*lambda^2*kR.^3*sin(theta-p.theta_c3); end
|
|
|
|
phase = exp(-1i.*chi(:,:,i)).*exp(-2*pi*1i*p.shifts(1).*kX).*exp(-2*pi*1i*p.shifts(2).*kY);
|
|
probe(:,:,i) = mask.*phase;
|
|
probe(:,:,i) = fftshift(ifft2(ifftshift(probe(:,:,i))));
|
|
probe(:,:,i) = probe(:,:,i)/sum(sum(abs(probe(:,:,i))));
|
|
end
|
|
|
|
if p.plotting
|
|
figure
|
|
subplot(1,2,1)
|
|
imagesc(abs(mask))
|
|
axis image
|
|
title('Fourier mask magnitude')
|
|
|
|
subplot(1,2,2)
|
|
colormap parula
|
|
iaxis{1} = ([1 N]-floor(N/2)+1)*dx/10;
|
|
iaxis{2} = ([1 N]-floor(N/2)+1)*dx/10;
|
|
imagesc3D(iaxis{1},iaxis{2},abs(probe))
|
|
xlabel('nm')
|
|
ylabel('nm')
|
|
axis image
|
|
|
|
title('Probe magnitude')
|
|
end
|
|
|
|
%probe = probe/(L/N)^2; %normalize the probe. Because in reciprocal space
|
|
%the zero frequency amplitute is 1, so, the summation is also one.
|
|
end
|
|
|