New additions, minor modifications to existing files

.gitignore

@@ -9,5 +9,6 @@ Time-Series-Analyzer/Time-Series-Data
 *.gif
 *.mp4
 *.bat
+*.json
 .ipynb_checkpoints/
 .vscode/

Data-Analyzer/compareSpectralWeights.m

@@ -0,0 +1,75 @@
+%% Track spectral weight across the transition
+
+set(0,'defaulttextInterpreter','latex')
+set(groot, 'defaultAxesTickLabelInterpreter','latex'); set(groot, 'defaultLegendInterpreter','latex');
+
+format long
+
+% Load data
+Data   = load('C:/Users/Karthik/Documents/GitRepositories/Calculations/Data-Analyzer/B2.3G/WithoutProcessing/DropletsToStripes.mat', 'unique_theta', 'mean_sf', 'stderr_sf');
+
+down_scan_parameter_values = Data.unique_theta;
+dts_mean_sf      = Data.mean_sf;
+down_stderr_sf    = Data.stderr_sf;
+
+Data   = load('C:/Users/Karthik/Documents/GitRepositories/Calculations/Data-Analyzer/B2.3G/WithoutProcessing/StripesToDroplets.mat', 'unique_theta', 'mean_sf', 'stderr_sf');
+
+std_theta_values = Data.unique_theta;
+std_mean_sf      = Data.mean_sf;
+std_stderr_sf    = Data.stderr_sf;
+
+figure(1);
+set(gcf,'Position',[100 100 950 750])
+errorbar(down_scan_parameter_values, dts_mean_sf, down_stderr_sf, 'o--', ...
+    'LineWidth', 1.5, 'MarkerSize', 6, 'CapSize', 5, 'DisplayName' , 'Droplets to Stripes');
+hold on
+errorbar(std_theta_values, std_mean_sf, std_stderr_sf, 'o--', ...
+    'LineWidth', 1.5, 'MarkerSize', 6, 'CapSize', 5, 'DisplayName', 'Stripes to Droplets');
+set(gca, 'FontSize', 14);   % For tick labels only
+hXLabel = xlabel('\alpha (degrees)', 'Interpreter', 'tex');
+hYLabel = ylabel('Spectral Weight', 'Interpreter', 'tex');
+hTitle = title('B = 2.3 G', 'Interpreter', 'tex');
+legend
+set([hXLabel, hYLabel], 'FontName', font)
+set([hXLabel, hYLabel], 'FontSize', 14)
+set(hTitle, 'FontName', font, 'FontSize', 16, 'FontWeight', 'bold');  % Set font and size for title
+grid on
+
+%%
+
+%% Track spectral weight across the transition
+
+set(0,'defaulttextInterpreter','latex')
+set(groot, 'defaultAxesTickLabelInterpreter','latex'); set(groot, 'defaultLegendInterpreter','latex');
+
+format long
+
+% Load data
+Data   = load('C:/Users/Karthik/Documents/GitRepositories/Calculations/Data-Analyzer/RampDownSL.mat', 'unique_scan_parameter_values', 'mean_sf', 'stderr_sf');
+
+down_scan_parameter_values = Data.unique_scan_parameter_values;
+down_mean_sf      = Data.mean_sf;
+down_stderr_sf    = Data.stderr_sf;
+
+Data   = load('C:/Users/Karthik/Documents/GitRepositories/Calculations/Data-Analyzer/RampUpSL.mat', 'unique_scan_parameter_values', 'mean_sf', 'stderr_sf');
+
+up_scan_parameter_values = Data.unique_scan_parameter_values;
+up_mean_sf               = Data.mean_sf;
+up_stderr_sf             = Data.stderr_sf;
+
+figure(1);
+set(gcf,'Position',[100 100 950 750])
+errorbar(down_scan_parameter_values, down_mean_sf, down_stderr_sf, 'o--', ...
+    'LineWidth', 1.5, 'MarkerSize', 6, 'CapSize', 5, 'DisplayName' , 'BEC to Droplets');
+hold on
+errorbar(up_scan_parameter_values, up_mean_sf, up_stderr_sf, 'o--', ...
+    'LineWidth', 1.5, 'MarkerSize', 6, 'CapSize', 5, 'DisplayName', 'Droplets to BEC');
+set(gca, 'FontSize', 14);   % For tick labels only
+hXLabel = xlabel('B_z (G)', 'Interpreter', 'tex');
+hYLabel = ylabel('Spectral Weight', 'Interpreter', 'tex');
+hTitle = title('\alpha = 0', 'Interpreter', 'tex');
+legend
+set([hXLabel, hYLabel], 'FontName', font)
+set([hXLabel, hYLabel], 'FontSize', 14)
+set(hTitle, 'FontName', font, 'FontSize', 16, 'FontWeight', 'bold');  % Set font and size for title
+grid on

Dipolar-Gas-Simulator/+Scripts/run_locally_compare_numerical_methods.m

@@ -0,0 +1,127 @@
+% Compare numerical methods
+
+%% - Polyak's heavy-ball GD
+
+OptionsStruct = struct;
+
+OptionsStruct.NumberOfAtoms           = 40000;
+OptionsStruct.DipolarPolarAngle       = deg2rad(0);
+OptionsStruct.DipolarAzimuthAngle     = 0;
+OptionsStruct.ScatteringLength        = 95;
+
+OptionsStruct.TrapFrequencies         = [30, 60, 90];
+OptionsStruct.TrapPotentialType       = 'Harmonic';
+
+OptionsStruct.NumberOfGridPoints      = [128, 64, 64];
+OptionsStruct.Dimensions              = [30, 20, 20];
+OptionsStruct.UseApproximationForLHY  = true;
+OptionsStruct.IncludeDDICutOff        = true;
+OptionsStruct.CutoffType              = 'Cylindrical';
+OptionsStruct.SimulationMode          = 'EnergyMinimization';  % 'ImaginaryTimeEvolution' | 'RealTimeEvolution' | 'EnergyMinimization'
+OptionsStruct.GradientDescentMethod   = 'HeavyBall';           % 'HeavyBall' | 'NonLinearCGD' 
+OptionsStruct.MaxIterationsForGD      = 1000;
+OptionsStruct.NoiseScaleFactor        = 0.010;
+
+OptionsStruct.PlotLive                = true;
+OptionsStruct.JobNumber               = 0;
+OptionsStruct.RunOnGPU                = false;
+OptionsStruct.SaveData                = true;
+OptionsStruct.SaveDirectory           = './Results/Data_3D/GradientDescent';
+options                               = Helper.convertstruct2cell(OptionsStruct);
+
+sim                                   = Simulator.DipolarGas(options{:});
+pot                                   = Simulator.Potentials(options{:});
+sim.Potential                         = pot.trap();
+
+%-% Run Simulation %-%
+NumberOfOutputs                       = 5;
+[Params, Transf, psi, V, VDk, stats]  = Helper.runWithProfiling(@() sim.run(), NumberOfOutputs, OptionsStruct.SaveDirectory);
+fprintf('Runtime: %.3f seconds\n', stats.runtime);
+fprintf('Memory used: %.2f MB\n', stats.workspaceMemoryMB);
+
+clear all
+
+%% - Non-linear CGD
+
+OptionsStruct = struct;
+
+OptionsStruct.NumberOfAtoms           = 40000;
+OptionsStruct.DipolarPolarAngle       = deg2rad(0);
+OptionsStruct.DipolarAzimuthAngle     = 0;
+OptionsStruct.ScatteringLength        = 95;
+
+OptionsStruct.TrapFrequencies         = [30, 60, 90];
+OptionsStruct.TrapPotentialType       = 'Harmonic';
+
+OptionsStruct.NumberOfGridPoints      = [128, 64, 64];
+OptionsStruct.Dimensions              = [30, 20, 20];
+OptionsStruct.UseApproximationForLHY  = true;
+OptionsStruct.IncludeDDICutOff        = true;
+OptionsStruct.CutoffType              = 'Cylindrical';
+OptionsStruct.SimulationMode          = 'EnergyMinimization';  % 'ImaginaryTimeEvolution' | 'RealTimeEvolution' | 'EnergyMinimization'
+OptionsStruct.GradientDescentMethod   = 'NonLinearCGD';           % 'HeavyBall' | 'NonLinearCGD' 
+OptionsStruct.MaxIterationsForGD      = 1000;
+OptionsStruct.NoiseScaleFactor        = 0.010;
+
+OptionsStruct.PlotLive                = true;
+OptionsStruct.JobNumber               = 1;
+OptionsStruct.RunOnGPU                = false;
+OptionsStruct.SaveData                = true;
+OptionsStruct.SaveDirectory           = './Results/Data_3D/GradientDescent';
+options                               = Helper.convertstruct2cell(OptionsStruct);
+
+sim                                   = Simulator.DipolarGas(options{:});
+pot                                   = Simulator.Potentials(options{:});
+sim.Potential                         = pot.trap();
+
+%-% Run Simulation %-%
+NumberOfOutputs                       = 5;
+[Params, Transf, psi, V, VDk, stats]  = Helper.runWithProfiling(@() sim.run(), NumberOfOutputs, OptionsStruct.SaveDirectory);
+fprintf('Runtime: %.3f seconds\n', stats.runtime);
+fprintf('Memory used: %.2f MB\n', stats.workspaceMemoryMB);
+
+clear all
+
+%% - Imaginary time propagation
+
+OptionsStruct = struct;
+
+OptionsStruct.NumberOfAtoms           = 40000;
+OptionsStruct.DipolarPolarAngle       = deg2rad(0);
+OptionsStruct.DipolarAzimuthAngle     = 0;
+OptionsStruct.ScatteringLength        = 95;
+
+OptionsStruct.TrapFrequencies         = [30, 60, 90];
+OptionsStruct.TrapPotentialType       = 'Harmonic';
+
+OptionsStruct.NumberOfGridPoints      = [128, 64, 64];
+OptionsStruct.Dimensions              = [30, 20, 20];
+OptionsStruct.UseApproximationForLHY  = true;
+OptionsStruct.IncludeDDICutOff        = true;
+OptionsStruct.CutoffType              = 'Cylindrical';
+OptionsStruct.SimulationMode          = 'ImaginaryTimeEvolution';     % 'ImaginaryTimeEvolution' | 'RealTimeEvolution' | 'EnergyMinimization'
+OptionsStruct.TimeStepSize            = 1E-3;            % in s
+OptionsStruct.MinimumTimeStepSize     = 1E-6;            % in s
+OptionsStruct.TimeCutOff              = 1E5;             % in s
+OptionsStruct.EnergyTolerance         = 5E-10;
+OptionsStruct.ResidualTolerance       = 1E-08;
+OptionsStruct.NoiseScaleFactor        = 0.010;
+
+OptionsStruct.PlotLive                = true;
+OptionsStruct.JobNumber               = 0;
+OptionsStruct.RunOnGPU                = false;
+OptionsStruct.SaveData                = true;
+OptionsStruct.SaveDirectory           = './Results/Data_3D/AnisotropicTrap/Tilted0';
+options                               = Helper.convertstruct2cell(OptionsStruct);
+
+sim                                   = Simulator.DipolarGas(options{:});
+pot                                   = Simulator.Potentials(options{:});
+sim.Potential                         = pot.trap();
+
+%-% Run Simulation %-%
+NumberOfOutputs                       = 5;
+[Params, Transf, psi, V, VDk, stats]  = Helper.runWithProfiling(@() sim.run(), NumberOfOutputs, OptionsStruct.SaveDirectory);
+fprintf('Runtime: %.3f seconds\n', stats.runtime);
+fprintf('Memory used: %.2f MB\n', stats.workspaceMemoryMB);
+
+clear all

Estimations/2DQHOHeavyBallGradientDescent.m

@@ -104,3 +104,7 @@ subplot(2,3,3); imagesc(x, y, abs(psi).^2 - abs(psi_analytic).^2); title('Differ
 subplot(2,3,[4 5 6]); plot(1:idx, energy, 'b-', 'LineWidth', 1.5); hold on;
 yline(1, 'r--', 'Analytical E=1'); xlabel('Iteration'); ylabel('Energy');
 title('Energy Convergence'); grid on; legend('Numerical', 'Analytical');
+
+%%
+
+

Imaging-Response-Function-Extractor/extractIRF.m

@@ -11,9 +11,7 @@ folderPath    = strcat(folderPath, run);
 cam           = 5; 
 
 angle         = 0;
-% center        = [1137, 2023];
 center        = [1141, 2049];
-% center        = [1166, 2055];
 span          = [255, 255];
 fraction      = [0.1, 0.1];
 
@@ -29,7 +27,7 @@ d             = 1.22 * (lambda / NA);
 AbbeLimit     = lambda / (2 * NA); 
 
 % Maximum resolvable spatial frequency for the coherent case
-k_cutoff      = (NA/lambda) * 1e-6; % (in units of 1/µm)
+k_cutoff      = 2 * pi * (NA/lambda) * 1e-6; % (in units of 1/µm)
 
 removeFringes = false;
 
@@ -38,8 +36,8 @@ removeFringes = false;
 
 filePattern = fullfile(folderPath, '*.h5');
 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)
     baseFileName = files(k).name;
@@ -103,14 +101,14 @@ ky       = 2*pi*vy;  % Wavenumber axis in Y
 
 % Create Circular Mask
 n        = 2^8;                    % size of mask
-mask     = zeros(n);
+fftmask  = zeros(n);
 I        = 1:n; 
 x        = I-n/2;                  % mask x-coordinates 
 y        = n/2-I;                  % mask y-coordinates
 [X,Y]    = meshgrid(x,y);          % create 2-D mask grid
 R        = 32;                     % aperture radius
-A        = (X.^2 + Y.^2 <= R^2);   % circular aperture of radius R
+A          = (X.^2 + Y.^2 <= R^2);   % circular aperture of radius R
-mask(A)  = 1;                      % set mask elements inside aperture to 1
+fftmask(A) = 1;                      % set mask elements inside aperture to 1
 
 % Calculate Power Spectrum and plot
 figure(1)
@@ -122,7 +120,7 @@ t = tiledlayout(2, 3, 'TileSpacing', 'compact', 'Padding', 'compact');
 
 for k = 1 : length(od_imgs)
     mean_subtracted_od_imgs{k} = od_imgs{k} - mean_od_img;
-    masked_img                 = mean_subtracted_od_imgs{k} .* mask;
+    masked_img                 = mean_subtracted_od_imgs{k} .* fftmask;
     density_fft{k}             = (1/numel(masked_img)) * abs(fftshift(fft2(masked_img)));
     density_noise_spectrum{k}  = density_fft{k}.^2;
     
@@ -161,7 +159,7 @@ for k = 1 : length(od_imgs)
     
     % Tile 4: Masked Noise
     nexttile(4);
-    imagesc(xvals, yvals, mean_subtracted_od_imgs{k} .* mask)
+    imagesc(xvals, yvals, mean_subtracted_od_imgs{k} .* fftmask)
     xlabel('\mum', 'Interpreter', 'tex', 'FontSize', 16)
     ylabel('\mum', 'Interpreter', 'tex', 'FontSize', 16)
     axis equal tight;
@@ -216,27 +214,27 @@ colormap(flip(jet));
 title('Average Density Noise Spectrum', 'FontSize', 16);
 grid on;
 
-centers = ginput;
+centers      = ginput;
-radius = 3;
+radius       = 3;
-% Plot where clicked.
+% Plot where clicked
-hVC  = viscircles(centers, radius, 'Color', 'r', 'LineWidth', 2);
+hVC          = viscircles(centers, radius, 'Color', 'r', 'LineWidth', 2);
-xc = centers(:,1);
+xc           = centers(:,1);
-yc = centers(:,2);
+yc           = centers(:,2);
 [yDim, xDim] = size(averagePowerSpectrum);
-[xx,yy] = meshgrid(1:yDim,1:xDim);
+[xx,yy]      = meshgrid(1:yDim,1:xDim);
-mask = false(xDim,yDim);
+MaskToRemoveUnwantedPeaks         = false(xDim,yDim);
 for ii = 1:size(centers, 1)
-	mask = mask | hypot(xx - xc(ii), yy - yc(ii)) <= radius;
+	MaskToRemoveUnwantedPeaks     = MaskToRemoveUnwantedPeaks | hypot(xx - xc(ii), yy - yc(ii)) <= radius;
 end
-mask = not(mask);
+MaskToRemoveUnwantedPeaks         = not(MaskToRemoveUnwantedPeaks);
 
 % Ask user if the circle is acceptable.
 message = sprintf('Is this acceptable?');
 button = questdlg(message, message, 'Accept', 'Reject and Quit', 'Accept');
 if contains(button, 'Accept','IgnoreCase',true)
-    image = mask.*averagePowerSpectrum;
+    image = MaskToRemoveUnwantedPeaks.*averagePowerSpectrum;
     image(image==0) = NaN;
-    imagesc(kx*1E-6, ky*1E-6, mask.*abs(10*log10(averagePowerSpectrum)))
+    imagesc(kx*1E-6, ky*1E-6, MaskToRemoveUnwantedPeaks.*abs(10*log10(averagePowerSpectrum)))
     hold on
     xlabel('k_x (\mum^{-1})', 'Interpreter', 'tex', 'FontSize', 16)
     ylabel('k_y (\mum^{-1})', 'Interpreter', 'tex', 'FontSize', 16)
@@ -386,101 +384,6 @@ xlim([1, xSize]);
 ylim([1, ySize]);
 zlim([min(10 * log10(averagePowerSpectrum(:))), max(10 * log10(averagePowerSpectrum(:)))]);  % Optional for Z-axis limits
 
-
-%% Decompose in Zernike Polynomial basis
-
-N          = size(averagePowerSpectrum, 1);
-[X, Y]     = meshgrid(linspace(-1, 1, N));
-
-max_n      = 6; % Adjust based on your needs
-basis      = [];
-orders     = [];
-
-for n = 0:max_n
-    for m = -n:2:n
-        % Generate Zernike polynomial for (n, m)
-        Z = zernike_polynomial(n, m, X, Y);
-        % Flatten and store valid points
-        basis = [basis, Z(mask)];
-        orders = [orders; [n, m]];
-    end
-end
-
-data       = 10 * log10(averagePowerSpectrum);
-valid_data = data(mask);
-
-% Solve Ax = b (A = basis matrix, b = data)
-coeffs     = basis \ valid_data(:);
-
-% Reconstruct the surface using the coefficients
-reconstructed               = basis * coeffs;
-reconstructed_surface       = zeros(size(X));
-reconstructed_surface(mask) = reconstructed;
-
-figure(5)
-clf
-set(gcf,'Position',[100, 100, 1500, 700])
-
-% Create tiled layout with 2 rows and 3 columns
-t = tiledlayout(1, 3, 'TileSpacing', 'compact', 'Padding', 'compact');
-
-nexttile(1);
-imagesc(data); title('Imaging Response Function', 'FontSize', 16);
-axis square;
-colorbar
-colormap(jet);
-grid on;
-
-nexttile(2);
-imagesc(reconstructed_surface); title('Reconstructed with Zernike', 'FontSize', 16);
-axis square;
-colorbar
-colormap(jet);
-grid on;
-
-nexttile(3);
-imagesc(data - reconstructed_surface); title('Residuals', 'FontSize', 16);
-axis square;
-colorbar
-colormap(jet);
-grid on;
-
-disp('Zernike Coefficients:');
-disp('---------------------');
-for i = 1:length(coeffs)
-    fprintf('Order (n=%d, m=%d): Coefficient = %.4f\n', orders(i,1), orders(i,2), coeffs(i));
-end
-
-% Plot Zernike Coeffecients
-
-% Find the index of the (n=0, m=0) term
-idx_remove = find(orders(:,1) == 0 & orders(:,2) == 0);
-
-% Remove the Z_0^0 term from coefficients and orders
-coeffs_filtered = coeffs;
-coeffs_filtered(idx_remove) = [];
-orders_filtered = orders;
-orders_filtered(idx_remove, :) = [];
-
-% Generate labels for filtered modes (n, m)
-labels_filtered = cell(length(coeffs_filtered), 1);
-for i = 1:length(coeffs_filtered)
-    labels_filtered{i} = sprintf('(%d, %d)', orders_filtered(i,1), orders_filtered(i,2));
-end
-
-figure(6)
-clf
-set(gcf,'Position',[100, 100, 1500, 700])
-bar(coeffs_filtered, 'FaceColor', [0.2, 0.6, 0.8]); % Customize bar color
-ylim([-2.0, 2.0])
-title('Zernike Coefficients', 'FontSize', 16);
-xlabel('Zernike Mode (n, m)', 'FontSize', 16);
-ylabel('Coefficient Value', 'FontSize', 16);
-xticks(1:length(coeffs_filtered)); % Set x-ticks for all coefficients
-xticklabels(labels_filtered); % Assign (n, m) labels
-xtickangle(45); % Rotate labels for readability
-grid on;
-
 %% Helper Functions
 
 function ret = getBkgOffsetFromCorners(img, x_fraction, y_fraction)