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Corrected and updated analysis scripts.

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This commit is contained in:
Karthik 2024-09-15 17:02:06 +02:00
parent 235a436436
commit 557d84649e
2 changed files with 99 additions and 69 deletions
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43
Imaging-Response-Function-Extractor/extractIRF.m
View File

@ -2,12 +2,14 @@
groupList = ["/images/MOT_3D_Camera/in_situ_absorption", "/images/ODT_1_Axis_Camera/in_situ_absorption", "/images/ODT_2_Axis_Camera/in_situ_absorption", "/images/Horizontal_Axis_Camera/in_situ_absorption", "/images/Vertical_Axis_Camera/in_situ_absorption"]; groupList = ["/images/MOT_3D_Camera/in_situ_absorption", "/images/ODT_1_Axis_Camera/in_situ_absorption", "/images/ODT_2_Axis_Camera/in_situ_absorption", "/images/Horizontal_Axis_Camera/in_situ_absorption", "/images/Vertical_Axis_Camera/in_situ_absorption"];
folderPath = "C:/Users/Karthik/Documents/GitRepositories/Calculations/IRF/0044/"; folderPath = "C:/Users/Karthik/Documents/GitRepositories/Calculations/Imaging-Response-Function-Extractor/0127/";
cam = 5; cam = 5;
angle = 90 + 51.5; % angle = 90 + 51.5;
center = [1700, 2300]; % center = [1700, 2300];
angle = 90;
center = [2035 1250];
span = [255, 255]; span = [255, 255];
fraction = [0.1, 0.1]; fraction = [0.1, 0.1];
@ -15,17 +17,19 @@ NA = 0.6;
pixel_size = 4.6e-6; pixel_size = 4.6e-6;
lambda = 421e-9; lambda = 421e-9;
d = lambda/2/pi/NA; d = 0.61*lambda/NA;
k_cutoff = NA/lambda/1e6; k_cutoff = 2*NA/lambda/1e6; % in units of 1/µm)
removeFringe = true;
%% Compute OD image, rotate and extract ROI for analysis %% Compute OD image, rotate and extract ROI for analysis
% Get a list of all files in the folder with the desired file name pattern. % Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(folderPath, '*.h5'); filePattern = fullfile(folderPath, '*.h5');
files = dir(filePattern); files = dir(filePattern);
refimages = zeros(span(1) + 1, span(2) + 1, length(files)); refimages = zeros(span(1) + 1, span(2) + 1, length(files));
absimages = zeros(span(1) + 1, span(2) + 1, length(files)); absimages = zeros(span(1) + 1, span(2) + 1, length(files));
for k = 1 : length(files) for k = 1 : length(files)
baseFileName = files(k).name; baseFileName = files(k).name;
fullFileName = fullfile(files(k).folder, baseFileName); fullFileName = fullfile(files(k).folder, baseFileName);
@ -40,8 +44,10 @@ for k = 1 : length(files)
absimages(:,:,k) = subtract_offset(crop_image(calculate_OD(atm_img, bkg_img, dark_img), center, span), fraction); absimages(:,:,k) = subtract_offset(crop_image(calculate_OD(atm_img, bkg_img, dark_img), center, span), fraction);
end end
%% Fringe removal %% Fringe removal
if removeFringe
optrefimages = removefringesInImage(absimages, refimages); optrefimages = removefringesInImage(absimages, refimages);
absimages_fringe_removed = absimages(:, :, :) - optrefimages(:, :, :); absimages_fringe_removed = absimages(:, :, :) - optrefimages(:, :, :);
@ -50,6 +56,13 @@ od_imgs = cell(1, nimgs);
for i = 1:nimgs for i = 1:nimgs
od_imgs{i} = absimages_fringe_removed(:, :, i); od_imgs{i} = absimages_fringe_removed(:, :, i);
end end
else
nimgs = size(absimages(:, :, :),3);
od_imgs = cell(1, nimgs);
for i = 1:nimgs
od_imgs{i} = absimages(:, :, i);
end
end
%% Compute the Density Noise Spectrum %% Compute the Density Noise Spectrum
@ -106,7 +119,7 @@ for k = 1 : length(od_imgs)
ylabel('µm', 'FontSize', 16) ylabel('µm', 'FontSize', 16)
axis equal tight; axis equal tight;
colorbar colorbar
colormap (flip(jet)); colormap jet; % (flip(jet))
% set(gca,'CLim',[0 100]); % set(gca,'CLim',[0 100]);
set(gca,'YDir','normal') set(gca,'YDir','normal')
title('Single-shot image', 'FontSize', 16); title('Single-shot image', 'FontSize', 16);
@ -119,7 +132,7 @@ for k = 1 : length(od_imgs)
ylabel('µm', 'FontSize', 16) ylabel('µm', 'FontSize', 16)
axis equal tight; axis equal tight;
colorbar colorbar
colormap (flip(jet)); colormap jet; % (flip(jet))
% set(gca,'CLim',[0 100]); % set(gca,'CLim',[0 100]);
set(gca,'YDir','normal') set(gca,'YDir','normal')
title('Averaged density image', 'FontSize', 16); title('Averaged density image', 'FontSize', 16);
@ -132,7 +145,7 @@ for k = 1 : length(od_imgs)
ylabel('µm', 'FontSize', 16) ylabel('µm', 'FontSize', 16)
axis equal tight; axis equal tight;
colorbar colorbar
colormap (flip(jet)); colormap jet; % (flip(jet))
% set(gca,'CLim',[0 100]); % set(gca,'CLim',[0 100]);
set(gca,'YDir','normal') set(gca,'YDir','normal')
title('Image noise = Single-shot - Average', 'FontSize', 16); title('Image noise = Single-shot - Average', 'FontSize', 16);
@ -145,7 +158,7 @@ for k = 1 : length(od_imgs)
ylabel('µm', 'FontSize', 16) ylabel('µm', 'FontSize', 16)
axis equal tight; axis equal tight;
colorbar colorbar
colormap (flip(jet)); colormap jet; % (flip(jet))
% set(gca,'CLim',[0 100]); % set(gca,'CLim',[0 100]);
set(gca,'YDir','normal') set(gca,'YDir','normal')
title('Masked Noise', 'FontSize', 16); title('Masked Noise', 'FontSize', 16);
@ -158,7 +171,7 @@ for k = 1 : length(od_imgs)
ylabel('1/dy', 'FontSize', 16) ylabel('1/dy', 'FontSize', 16)
axis equal tight; axis equal tight;
colorbar colorbar
colormap (flip(jet)); colormap jet; % (flip(jet))
% set(gca,'CLim',[0 100]); % set(gca,'CLim',[0 100]);
set(gca,'YDir','normal') set(gca,'YDir','normal')
title('DFT', 'FontSize', 16); title('DFT', 'FontSize', 16);
@ -171,7 +184,7 @@ for k = 1 : length(od_imgs)
ylabel('1/dy', 'FontSize', 16) ylabel('1/dy', 'FontSize', 16)
axis equal tight; axis equal tight;
colorbar colorbar
colormap (flip(jet)); colormap jet; % (flip(jet))
% set(gca,'CLim',[0 100]); % set(gca,'CLim',[0 100]);
set(gca,'YDir','normal') set(gca,'YDir','normal')
title('Density Noise Spectrum = |DFT|^2', 'FontSize', 16); title('Density Noise Spectrum = |DFT|^2', 'FontSize', 16);
@ -267,7 +280,7 @@ ks = sqrt(kx.^2 + ky.^2);
profile = profile(length(profile)/2:end); profile = profile(length(profile)/2:end);
ks = ks(length(ks)/2:end); ks = ks(length(ks)/2:end);
n = 0.15; n = 0.05;
[val,slice_idx]=min(abs(ks-n)); [val,slice_idx]=min(abs(ks-n));
ks = ks(1:slice_idx); ks = ks(1:slice_idx);
profile = profile(1:slice_idx); profile = profile(1:slice_idx);
@ -275,7 +288,9 @@ plot(ks, profile, 'b*-');
% plot(profile, 'b*-'); % plot(profile, 'b*-');
grid on; grid on;
% xlim([min(ks) max(ks)]) % xlim([min(ks) max(ks)])
title('Radial average of Density Noise Spectrum', 'FontSize', 16); xlabel('k (1/µm)', 'FontSize', 16)
ylabel('Normalised amplitude', 'FontSize', 16)
title('Radial profile', 'FontSize', 16);
grid on; grid on;

65
Time-Series-Analyzer/computeRIN.m
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@ -1,5 +1,6 @@
% Script to compute the Relative Intensity Noise of a laser by recording the y-t signal % Script to compute the Relative Intensity Noise of a laser by recording the y-t signal
% by Mathias Neidig 2012_09_11 % by Mathias Neidig in 2012
% modified for DyLab use by Karthik in 2024
% The RIN is defined as % The RIN is defined as
% %
@ -12,32 +13,33 @@ close all
%% Set the directory where the data is %% Set the directory where the data is
dirDCData = ['C:\\Users\\Karthik\\Documents\\GitRepositories\\Calculations\\Time-Series-Analyzer\\Time-Series-Data\\20240807\\DC Coupling\\']; dirDCData = 'C:\\Users\\Karthik\\Documents\\GitRepositories\\Calculations\\Time-Series-Analyzer\\Time-Series-Data\\20240915\\DC_Coupling\\';
dirACData = ['C:\\Users\\Karthik\\Documents\\GitRepositories\\Calculations\\Time-Series-Analyzer\\Time-Series-Data\\20240807\\AC Coupling\\']; dirACData = 'C:\\Users\\Karthik\\Documents\\GitRepositories\\Calculations\\Time-Series-Analyzer\\Time-Series-Data\\20240915\\AC_Coupling\\';
%% Load the files which contain: - the DC coupled y-t signal to obtain the averaged power %% Load the files which contain: - the DC coupled y-t signal to obtain the averaged power
% - the AC coupled y-t signal to obtain the fluctuations % - the AC coupled y-t signal to obtain the fluctuations
% - the AC coupled y-t signal with the beam blocked to obtain the background fluctuations % - the AC coupled y-t signal with the beam blocked to obtain the background fluctuations
%-------------------------------------------------------------------------% %-------------------------------------------------------------------------%
dcsignal = readmatrix( [ dirDCData 'P7.0_M3.0_OOL.csv'] ); % dcsignal = load( [ dirDCData 'IPG1064_100W'] ); %
acsignal = readmatrix( [ dirACData 'P7.0_M3.0_OOL.csv'] ); % acsignal = load( [ dirACData 'IPG1064_100W'] ); %
bgsignal = readmatrix( [ dirACData 'Bkg_OOL.csv'] ); % bgsignal = load( [ dirACData 'Background'] ); %
picosignal = load( [ dirACData 'Picoscope_Background'] ); %
label_0 = 'Picoscope noise floor'; %
label_1 = 'Background (Picoscope + InGaAs PIN PD + Transimp amp + Buffer amp + power supply)'; %
label_2 = 'Laser output power=100 W (Incident on PD=1mW)'; %
label_3 = 'Shot-Noise limit @ 1 mW incident power'; %
%-------------------------------------------------------------------------% %-------------------------------------------------------------------------%
%% Read out the important parameters %% Read out the important parameters
time_increment = 2E-6; dcdata = dcsignal.A;
dctime = dcsignal(1:end, 1) .* time_increment; acdata = acsignal.A;
actime = acsignal(1:end, 1) .* time_increment; bgdata = bgsignal.A;
bgtime = bgsignal(1:end, 1) .* time_increment; picodata = picosignal.A;
dcdata = dcsignal(1:end, 2); N = length(dcdata); % #samples
acdata = acsignal(1:end, 2); f_s = 1/dcsignal.Tinterval; % Sample Frequency
bgdata = bgsignal(1:end, 2);
N = length(actime); % #samples
f_s = 1/time_increment; % Sample Frequency
delta_f = f_s/N; % step size in frequency domain delta_f = f_s/N; % step size in frequency domain
delta_t = 1/f_s; % time step delta_t = 1/f_s; % time step
@ -56,6 +58,7 @@ average_P = mean(dcdata.*dcdata);
% compute the power spectrum density FFT(A) x FFT*(A)/N^2 of the source & the bg % compute the power spectrum density FFT(A) x FFT*(A)/N^2 of the source & the bg
psd_src = fft(acdata) .* conj(fft(acdata))/N^2; psd_src = fft(acdata) .* conj(fft(acdata))/N^2;
psd_bg = fft(bgdata) .* conj(fft(bgdata))/N^2; psd_bg = fft(bgdata) .* conj(fft(bgdata))/N^2;
psd_pico = fft(picodata) .* conj(fft(picodata))/N^2;
% converts the psd to the single-sided psd --> psd is symmetric around zero --> omit % converts the psd to the single-sided psd --> psd is symmetric around zero --> omit
% negative frequencies and put the power into the positive ones --> spsd % negative frequencies and put the power into the positive ones --> spsd
@ -64,23 +67,28 @@ for i = 1 : N/2+1
if i>1 if i>1
spsd_src(i) = 2*psd_src(i); spsd_src(i) = 2*psd_src(i);
spsd_bg(i) = 2*psd_bg(i); spsd_bg(i) = 2*psd_bg(i);
else spsd_src(i) = psd_src(i); spsd_pico(i) = 2*psd_pico(i);
else
spsd_src(i) = psd_src(i);
spsd_bg(i) = psd_bg(i); spsd_bg(i) = psd_bg(i);
spsd_pico(i) = psd_pico(i);
end end
end end
% smooths the spsd by doing a moving average % smooths the spsd by doing a moving average
spsd_src_smooth = smooth(spsd_src,span,'moving'); spsd_src_smooth = smooth(spsd_src,span,'moving');
spsd_bg_smooth = smooth(spsd_bg, span,'moving'); spsd_bg_smooth = smooth(spsd_bg, span,'moving');
spsd_pico_smooth = smooth(spsd_pico, span,'moving');
% calculates the RIN given in dB/Hz; the factor delta_f is needed to convert from dB/bin into dB/Hz % calculates the RIN given in dB/Hz; the factor delta_f is needed to convert from dB/bin into dB/Hz
RIN_src_smooth = 10*log10(spsd_src_smooth/(average_P*delta_f)); RIN_src_smooth = 10*log10(spsd_src_smooth/(average_P*delta_f));
RIN_bg_smooth = 10*log10(spsd_bg_smooth /(average_P*delta_f)); RIN_bg_smooth = 10*log10(spsd_bg_smooth /(average_P*delta_f));
RIN_pico_smooth = 10*log10(spsd_pico_smooth /(average_P*delta_f));
% creates an array for the frequencies up to half the sampling frequency % creates an array for the frequencies up to half the sampling frequency
f = f_s/2 * linspace(0,1,N/2+1); f = f_s/2 * linspace(0,1,N/2+1);
f_smooth = smooth(f,span,'moving'); f_smooth = smooth(f,span,'moving');
%
% Calculates the shot noise limit of the used PD given the wavelength of the light source and % Calculates the shot noise limit of the used PD given the wavelength of the light source and
% incident average power % incident average power
PlanckConstant = 6.62607015E-34; PlanckConstant = 6.62607015E-34;
@ -88,21 +96,28 @@ SpeedOfLight = 299792458;
WavelengthOfLaserLight = 1064E-9; WavelengthOfLaserLight = 1064E-9;
FrequencyOfLaserLight = SpeedOfLight / WavelengthOfLaserLight; FrequencyOfLaserLight = SpeedOfLight / WavelengthOfLaserLight;
QuantumEfficiencyOfPD = 1; QuantumEfficiencyOfPD = 1;
ShotNoiseLimit = 10*log10((2 * PlanckConstant * FrequencyOfLaserLight / QuantumEfficiencyOfPD) * average_P); AverageIncidentPower = 0.001; % (in W)
ShotNoiseLimit = 10*log10((2 * PlanckConstant * FrequencyOfLaserLight) / (QuantumEfficiencyOfPD * AverageIncidentPower));
%% Plots the RIN %% Plots the RIN
% Plots the RIN vs frequency % Plots the RIN vs frequency
f_ = clf; f_ = clf;
figure(f_); figure(f_);
semilogx(f_smooth,RIN_bg_smooth,'k-') semilogx(f_smooth, RIN_pico_smooth, LineStyle = "-", Color = [.7 .7 .7])
hold on hold on
semilogx(f_smooth, RIN_bg_smooth, LineStyle = "-", Color = [.0 .0 .0])
semilogx(f_smooth,RIN_src_smooth,'r-') semilogx(f_smooth,RIN_src_smooth,'r-')
yline(ShotNoiseLimit,'--b'); yline(ShotNoiseLimit,'--b');
xlabel('Frequency [Hz]') ax = gca(f_);
ylabel('RIN [dB/Hz]') ax.XAxis.FontSize = 14;
xlim([10 max(f)]); ax.YAxis.FontSize = 14;
title('\bf Relative Intensity Noise of ODT Arm 1') xlabel('Frequency [Hz]', FontSize=16)
legend('Detector Noise', 'Power:7 V, Mod: 100%, with PID ON', 'Shot-Noise limit','Location','NorthWest'); ylabel('RIN [dBc/Hz]', FontSize=16)
xlim([10 5E6]);
ylim([-175 -55]);
title('\bf Relative Intensity Noise of IPG 1064', FontSize=16)
legend(label_0, label_1, label_2, label_3, 'Location','NorthEast', FontSize=16);
% text(1e5,-95,['\bf MovingAverage = ' num2str(span) ]); % text(1e5,-95,['\bf MovingAverage = ' num2str(span) ]);
grid on grid on