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Add check for empty atomic structure
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@ThFriedrich
ThFriedrich committed Dec 6, 2022
1 parent bb9ce7c commit 682d16a
Showing 1 changed file with 49 additions and 46 deletions.
95 changes: 49 additions & 46 deletions matlab_functions/tfm_check_stem_setup.m
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Original file line number Diff line number Diff line change
Expand Up @@ -40,52 +40,57 @@ function fcn_check_probe(input_multem)
end

function fcn_check_slicing(input_multem)

% Slicing
[atoms, Slice] = ilc_spec_slicing(input_multem.toStruct);
[nslice, ~] = size(Slice);

figure(2); clf;
subplot(1,2,1);
plot(atoms(:, 3), atoms(:, 4), 'ok');
hold on;
for i = 1:nslice
plot([min(atoms(:, 3)) max(atoms(:, 3))], [Slice(i, 1) Slice(i, 1)], '-b', [min(atoms(:, 3)) max(atoms(:, 3))], [Slice(i, 2) Slice(i, 2)], '-b');
end
hold off;
title('Slice positions');
ylabel('z');
xlabel('x');
axis([min(atoms(:, 3)) max(atoms(:, 3)) -5 input_multem.spec_lz + 5]);
axis equal;
legend({'Atom positions','Slice boundaries'},'Location','southoutside')
set(gca,'YDir','reverse')

subplot(1,2,2);
plot3(input_multem.spec_atoms(:,2), input_multem.spec_atoms(:,3), input_multem.spec_atoms(:,4),'or');
hold on;
if input_multem.simulation_type <= 12
plot3([input_multem.scanning_x0; input_multem.scanning_xe; input_multem.scanning_xe; input_multem.scanning_x0;input_multem.scanning_x0],...
[input_multem.scanning_y0; input_multem.scanning_y0; input_multem.scanning_ye; input_multem.scanning_ye;input_multem.scanning_y0],...
[0; 0; 0; 0; 0],'-k');
legend({'Atom positions','STEM Scan Field'},'Location','southoutside')
if ~isempty(input_multem.spec_atoms)
% Slicing
[~, Slice] = ilc_spec_slicing(input_multem.toStruct);
[nslice, ~] = size(Slice);

figure(2); clf;
subplot(1,2,1);
plot(input_multem.spec_atoms(:, 2), input_multem.spec_atoms(:, 4), 'ok');
hold on;
for i = 1:nslice
plot([min(input_multem.spec_atoms(:, 2)) max(input_multem.spec_atoms(:, 2))], [Slice(i, 1) Slice(i, 1)], '-b', [min(input_multem.spec_atoms(:, 2)) max(input_multem.spec_atoms(:, 2))], [Slice(i, 2) Slice(i, 2)], '-b');
end
hold off;
title('Slice positions');
ylabel('z');
xlabel('x');
axis equal;
axis([min(input_multem.spec_atoms(:, 2))-3 max(input_multem.spec_atoms(:, 2))+3 Slice(1, 1)-3 Slice(end, 1)+3]);

legend({'Atom positions','Slice boundaries'},'Location','southoutside')
set(gca,'YDir','reverse')

subplot(1,2,2);
plot3(input_multem.spec_atoms(:,2), input_multem.spec_atoms(:,3), input_multem.spec_atoms(:,4),'or');
hold on;
if input_multem.simulation_type <= 12
plot3([input_multem.scanning_x0; input_multem.scanning_xe; input_multem.scanning_xe; input_multem.scanning_x0;input_multem.scanning_x0],...
[input_multem.scanning_y0; input_multem.scanning_y0; input_multem.scanning_ye; input_multem.scanning_ye;input_multem.scanning_y0],...
[0; 0; 0; 0; 0],'-k');
legend({'Atom positions','STEM Scan Field'},'Location','southoutside')
else
z0 = get_defocus_ref(input_multem);
[xp, yp, zp] = cylinder([0 2], 64);
surf(input_multem.iw_x+xp, input_multem.iw_y+yp, z0+(10*zp),'FaceAlpha',0.5,'EdgeColor','none','FaceColor','g')
surf(input_multem.iw_x+xp, input_multem.iw_y+yp, z0+(-10*zp),'FaceAlpha',0.5, 'EdgeColor','none','FaceColor','g')
plot3(input_multem.iw_x, input_multem.iw_y, z0,'xk');
legend({'Atom positions','Probe'},'Location','southoutside')
end

hold off;
axis equal;
title('Atom positions and Scan Field')
zlabel('z');
xlabel('x');
ylabel('y');
set(gca,'ZDir','reverse')
else
z0 = get_defocus_ref(input_multem);
[xp, yp, zp] = cylinder([0 2], 64);
surf(input_multem.iw_x+xp, input_multem.iw_y+yp, z0+(10*zp),'FaceAlpha',0.5,'EdgeColor','none','FaceColor','g')
surf(input_multem.iw_x+xp, input_multem.iw_y+yp, z0+(-10*zp),'FaceAlpha',0.5, 'EdgeColor','none','FaceColor','g')
plot3(input_multem.iw_x, input_multem.iw_y, z0,'xk');
legend({'Atom positions','Probe'},'Location','southoutside')
fprintf(2,['No atoms are specified. Check your input structure! \n']);
end

hold off;
axis equal;
title('Atom positions and Scan Field')
zlabel('z');
xlabel('x');
ylabel('y');
set(gca,'ZDir','reverse')

end

function fcn_check_detector_coverage(input_multem, detector)
Expand All @@ -97,8 +102,7 @@ function fcn_check_detector_coverage(input_multem, detector)
ly = input_multem.spec_ly;
ri_detector = input_multem.detector.cir(detector).inner_ang;
ro_detector = input_multem.detector.cir(detector).outer_ang;

clc;

gmax(1)=nx/(2*lx); gmax(2) = ny/(2*ly);
gmax_abs=min(gmax(:));
ri_detector = ilm_mrad_2_rAng(E_0,ri_detector);
Expand All @@ -111,7 +115,6 @@ function fcn_check_detector_coverage(input_multem, detector)
bwx = 2/3*(gmax_abs*cos(t));
bwy = 2/3*(gmax_abs*sin(t));


gspace=polyshape([-gmax(1) gmax(1) gmax(1) -gmax(1)],[-gmax(2) -gmax(2) gmax(2) gmax(2)]);
d=polyshape({xi,xo},{yi,yo},'Simplify',false);
figure(3); clf
Expand All @@ -131,7 +134,7 @@ function fcn_check_detector_coverage(input_multem, detector)
if tfm_pn_fact(nx,1)~=nx && tfm_pn_fact(nx,2)~=nx && tfm_pn_fact(nx,3)~=nx
fprintf(2,['Using ' num2str(nx) ' pixels in x is computationally unefficient. Consider using ' num2str(tfm_pn_fact(nx,1)) ' or ' num2str(tfm_pn_fact(nx,3)) ' instead.' '\n'])
end
if tfm_pn_fact(ny,1)~=nx && tfm_pn_fact(ny,2)~=ny && tfm_pn_fact(ny,3)~=ny
if tfm_pn_fact(ny,1)~=ny && tfm_pn_fact(ny,2)~=ny && tfm_pn_fact(ny,3)~=ny
fprintf(2,['Using ' num2str(ny) ' pixels in y is computationally unefficient. Consider using ' num2str(tfm_pn_fact(ny,1)) ' or ' num2str(tfm_pn_fact(ny,3)) ' instead.' '\n'])
end
end
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