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POLCAM-SR/lib/+Drift/testDriftCorection_RCC_interpolation.m
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| %% Test drift correction on simulated dataset | ||
| % | ||
| % Script to simulate an SMLM localization file with drift to test | ||
| % drift-correction approaches on. | ||
| % | ||
| % The 'sample' is a circle and has two fiducials in it. To be somewhat | ||
| % realistic, the fiducial is not detected in all frames. | ||
| % | ||
| % Author: Ezra Bruggeman, Lee Lab, University of Cambridge | ||
| % eb758@cam.ac.uk | ||
| % | ||
| % Last modified: 10 Jan 2021 | ||
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| clear all | ||
| close all | ||
| clc | ||
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| segmentation = 1000; | ||
| linear_drift_x = 5/segmentation; % nm/frame | ||
| linear_drift_y = -10/segmentation; % nm/frame | ||
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| numFrames = 10000; % total number of frames simulated | ||
| sigma_sample = 20; % nm, standard deviation gaussian noise on localisation error sample | ||
| sigma_fiducial = 5; % nm, standard deviation gaussian noise on localisation error fiducial | ||
| pixelsize = 57.5; % nm, pixel size (in sample space) | ||
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| rate_sample = 10; % localisations per frame from sample (should be > 1) | ||
| rate_fiducial = 1; % localisations per frame from fiducial (should be <= 1) | ||
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| radius_circle = 400; % nm, radius of sample, which is a circle | ||
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| % can be multiple | ||
| x_fiducial = [1000,1100]; | ||
| y_fiducial = [1000,600]; | ||
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| %% Simulate dataset | ||
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| [frame,x,y] = Drift.simulateDriftDataset(linear_drift_x,linear_drift_y,... | ||
| numFrames,radius_circle,x_fiducial,y_fiducial,sigma_sample,sigma_fiducial,... | ||
| rate_sample,rate_fiducial); | ||
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| figure; | ||
| scatter(x,y,20,frame,'.') | ||
| colormap jet; axis equal; grid on | ||
| xlabel('x (nm)') | ||
| ylabel('y (nm)') | ||
| title('Before drift correction') | ||
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| filter = true(size(x)); | ||
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| %% RCC | ||
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| pixelsize_hist = pixelsize/10; | ||
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| [x_corr,y_corr,dx_spline,dy_spline,dx,dy] = Drift.correctDriftRCC(frame,x,y,filter,segmentation,pixelsize_hist); | ||
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| %% | ||
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| figure('Name','RCC drift correction'); | ||
| set(0,'DefaultAxesTitleFontWeight','normal'); | ||
| subplot(2,2,1) | ||
| t = 1:numFrames; | ||
| plot(t,linear_drift_x*(t-1),'b'); hold on | ||
| plot(t,dx_spline,'--b'); | ||
| plot(t,linear_drift_y*(t-1),'r'); | ||
| plot(t,dy_spline,'--r'); | ||
| legend('dx_{true}','dx_{est}','dy_{true}','dy_{est}','Location','northwest'); | ||
| xlabel('Frame'); ylabel('Drift (nm)') | ||
| xlim([-inf inf]); | ||
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| subplot(2,2,2) | ||
| plot(dx_spline,dy_spline,'Color',0.5*[1,1,1]); hold on | ||
| scatter(dx_spline,dy_spline,10,t); axis equal | ||
| xlabel('x (nm)'); ylabel('y (nm)'); grid on | ||
| title('Drift trajectory') | ||
| xlim([-inf inf]); ylim([-inf inf]) | ||
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| subplot(2,2,3); scatter(x,y,20,frame,'.') | ||
| colormap parula; grid on; axis equal | ||
| xlabel('x (nm)') | ||
| ylabel('y (nm)') | ||
| title('Before drift correction') | ||
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| subplot(2,2,4); scatter(x_corr,y_corr,20,frame,'.') | ||
| colormap parula; grid on; axis equal | ||
| xlabel('x (nm)') | ||
| ylabel('y (nm)') | ||
| title('After drift correction') | ||
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| %% Fiducial-based drift correction | ||
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| % [x_corr,y_corr,dx,dy] = Drift.correctDriftFiducial(frame,x,y,pixelsize); | ||
| % | ||
| % figure('Name','Fiducial-based drift correction'); | ||
| % set(0,'DefaultAxesTitleFontWeight','normal'); | ||
| % | ||
| % subplot(2,2,1) | ||
| % t = linspace(0,numFrames,floor(numFrames/segmentation)); | ||
| % plot(dx,'b'); hold on | ||
| % plot(dy,'r'); | ||
| % legend('dx_{est}','dy_{est}','Location','northwest'); | ||
| % xlabel('Frame'); ylabel('Drift (nm)') | ||
| % xlim([-inf inf]); | ||
| % | ||
| % subplot(2,2,2) | ||
| % plot(dx,dy,'Color',0.5*[1,1,1]); hold on | ||
| % scatter(dx,dy,20,1:length(dx)) | ||
| % xlabel('x (nm)'); ylabel('y (nm)'); grid on | ||
| % title('Drift trajectory') | ||
| % xlim([-inf inf]); ylim([-inf inf]) | ||
| % | ||
| % subplot(2,2,3); scatter(x,y,20,frame,'.') | ||
| % colormap parula; grid on | ||
| % xlabel('x (nm)') | ||
| % ylabel('y (nm)') | ||
| % title('Before drift correction') | ||
| % subplot(2,2,4); scatter(x_corr,y_corr,20,frame,'.') | ||
| % colormap parula; grid on | ||
| % xlabel('x (nm)') | ||
| % ylabel('y (nm)') | ||
| % title('After drift correction') | ||
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