initial commit

ptycho/diagnosis/view_scan_positions.m

@@ -0,0 +1,81 @@
+close all
+addpath(fullfile(pwd,'utils'))
+%%
+figure1 = figure('Color',[1 1 1],'OuterPosition',[100 100 1800 600]);
+%set(gcf,'Outerposition',[100 100 1800 600])
+clf()
+%set(gca,'color','white')
+scale = p.dx_spec; 
+%object_roi = object(p.object_ROI{:},:);
+aobject = angle(object);
+range = sp_quantile(angle(object_roi), [1e-3, 1-1e-3],10);
+aobject = (aobject  - range(1)) / (range(2) - range(1));
+Np_o = size(object);
+grids = {(-ceil(Np_o(2)/2):ceil(Np_o(2)/2)-1)*scale(2), ...
+         (-ceil(Np_o(1)/2):ceil(Np_o(1)/2)-1)*scale(1)}; 
+imagesc(grids{:}, aobject, [-2, 1]); % reduce contrast 
+colormap bone 
+axis xy
+hold on 
+pos = outputs.probe_positions;
+pos_0 = outputs.probe_positions_0;
+
+%pos = pos + Np_o([2,1])/2;
+%pos_scales = (pos-Np_o([2,1])/2) .* scale([2,1]); 
+pos_scales = pos .* scale([2,1]); 
+pos_scales_0 = pos_0 .* scale([2,1]); 
+%mean_err = mean(std(pos_err)); 
+%range = max(pos) - min(pos); 
+%up = 0.02 * min(range) / mean_err; 
+%rounding_order = 10^floor(log10(up)); 
+%up = ceil(up / rounding_order)*rounding_order;
+scatter( pos_scales(:,1),  pos_scales(:,2),'.r')
+scatter( pos_scales_0(:,1),  pos_scales_0(:,2),10, '.','MarkerEdgeColor','b')
+
+%hold off 
+axis equal xy tight 
+range =  [min(pos_scales(:,1)), max(pos_scales(:,1)), min(pos_scales(:,2)), max(pos_scales(:,2))];
+axis(range)
+title(['\fontsize{16}{\color{blue}initial positions, '...
+'\color{red}refined positions}'])
+%title('Initial positions: blue. Refined positions: red. Current probe position: Black')
+%ylabel('Position [\mum]') %for x-ray
+%xlabel('Position [\mum]')
+ylabel('Position [A]') %for electron
+xlabel('Position [A]')
+
+%%
+close all
+figure
+subplot(2,2,1)
+plot(outputs.relative_pixel_scale,'.','MarkerSize',4)
+axis tight 
+ylabel('Relative pixel scaling correction [-]')
+xlabel('Iteration')
+title('Scales')
+hold off 
+grid on 
+
+subplot(2,2,2)
+plot(outputs.asymmetry*100,'.','MarkerSize',4)
+axis tight 
+ylabel('Asymmetry [%]')
+xlabel('Iteration')
+title('Asymmetry')
+grid on 
+
+subplot(2,2,3)
+plot(outputs.rotation,'.','MarkerSize',4)
+axis tight 
+ylabel('Rotation  [deg]')
+xlabel('Iteration')
+title('Rotation')
+grid on 
+
+subplot(2,2,4)
+plot(outputs.shear,'.','MarkerSize',4)
+axis tight 
+ylabel('Shear  [deg]')
+xlabel('Iteration')
+title('Shear')
+grid on