MAJOR corrections to scripts to extract densities
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@ -5,7 +5,15 @@ function [AveragePCD] = extractAveragePeakColumnDensity(folder_path, run_index,
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format long
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% Load data
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Data = load(sprintf(horzcat(folder_path, '/Run_%03i/psi_gs.mat'),run_index),'psi','Params','Transf','Observ');
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filePath = sprintf(horzcat(folder_path, '/Run_%03i/psi_gs.mat'), run_index);
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try
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Data = load(filePath, 'psi', 'Params', 'Transf', 'Observ');
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catch ME
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warning('Failed to load file: %s\n%s', filePath, ME.message);
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AveragePCD = NaN;
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return;
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end
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Params = Data.Params;
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Transf = Data.Transf;
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@ -1,96 +1,177 @@
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function [UCD] = extractAverageUnitCellDensity(folder_path, run_index, radius, minPeakHeight, SuppressPlotFlag)
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function [UCD] = extractAverageUnitCellDensity(folder_path, run_index, radius, minPeakHeight, SuppressPlotFlag)
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set(0,'defaulttextInterpreter','latex')
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set(groot, 'defaultAxesTickLabelInterpreter','latex'); set(groot, 'defaultLegendInterpreter','latex');
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format long
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set(groot, 'defaultAxesTickLabelInterpreter','latex');
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set(groot, 'defaultLegendInterpreter','latex');
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% Load data
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Data = load(sprintf(horzcat(folder_path, '/Run_%03i/psi_gs.mat'),run_index),'psi','Params','Transf','Observ');
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filePath = sprintf(horzcat(folder_path, '/Run_%03i/psi_gs.mat'), run_index);
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try
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Data = load(filePath, 'psi', 'Params', 'Transf', 'Observ');
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catch ME
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warning('Failed to load file: %s\n%s', filePath, ME.message);
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UCD = NaN;
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return;
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end
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Params = Data.Params;
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Transf = Data.Transf;
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Observ = Data.Observ;
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if isgpuarray(Data.psi)
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psi = gather(Data.psi);
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else
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psi = Data.psi;
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end
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if isgpuarray(Data.Observ.residual)
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Observ.residual = gather(Data.Observ.residual);
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else
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Observ.residual = Data.Observ.residual;
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end
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% Axes scaling and coordinates in micrometers
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x = Transf.x * Params.l0 * 1e6;
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y = Transf.y * Params.l0 * 1e6;
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z = Transf.z * Params.l0 * 1e6;
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dz = z(2)-z(1);
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% Compute probability density |psi|^2
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n = abs(psi).^2;
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nxy = squeeze(trapz(n*dz,3));
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state = nxy';
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peaks = extractPeaks(state, radius, minPeakHeight);
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peakHeights = state(peaks);
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[row, col] = find(peaks);
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[~, maxIdx] = max(peakHeights);
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MaxPeakLocation = [row(maxIdx), col(maxIdx)];
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% Voronoi diagram of peak positions
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points = [col, row]; % Voronoi uses [x, y]
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[V, C] = voronoin(points);
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psi = gather(Data.psi);
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% Voronoi cell of the max peak
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Vcell_indices = C{maxIdx};
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% Plot the Voronoi cell
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if all(Vcell_indices > 0) && all(Vcell_indices <= size(V, 1)) && ~any(isinf(V(Vcell_indices, 1)))
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vx = interp1(1:numel(x), x, V(Vcell_indices,1), 'linear', 'extrap');
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vy = interp1(1:numel(y), y, V(Vcell_indices,2), 'linear', 'extrap');
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% Close the polygon by repeating the first vertex
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vx(end+1) = vx(1);
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vy(end+1) = vy(1);
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% Compute area of the Voronoi cell polygon using the shoelace formula
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AreaOfVoronoiCell = polyarea(vx, vy); % Area of Voronoi cell around max peak in um^2
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else
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warning('Voronoi cell for max peak is unbounded or invalid.');
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% Axes in micrometers
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x = Transf.x * Params.l0 * 1e6;
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y = Transf.y * Params.l0 * 1e6;
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z = Transf.z * Params.l0 * 1e6;
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dz = z(2) - z(1);
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% Compute integrated density
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n = abs(psi).^2;
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nxy = squeeze(trapz(n * dz, 3));
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state = nxy';
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% Fourier spectrum for orientation detection
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F = fftshift(abs(fft2(state - mean(state(:)))));
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[nx, ny] = size(state);
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kx = linspace(-pi / (x(2) - x(1)), pi / (x(2) - x(1)), nx);
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ky = linspace(-pi / (y(2) - y(1)), pi / (y(2) - y(1)), ny);
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[KX, KY] = meshgrid(kx, ky);
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theta = atan2(KY, KX);
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% Remove center/DC
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R = sqrt(KX.^2 + KY.^2);
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F(R < 0.1 * max(kx(:))) = 0;
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% Angular histogram of power spectrum
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nbins = 180;
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angles = linspace(-pi, pi, nbins);
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powerAngular = zeros(1, nbins);
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for k = 1:nbins-1
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mask = theta >= angles(k) & theta < angles(k+1);
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powerAngular(k) = sum(F(mask), 'all');
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end
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% Create grid points mesh
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[X, Y] = meshgrid(x, y); % Note: size(X) and size(Y) match size(state)
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% Determine points inside Voronoi polygon
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inCellMask = inpolygon(X, Y, vx, vy);
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% Sum all state values inside the Voronoi cell polygon
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NumberOfParticlesInVoronoiCell = sum(state(inCellMask));
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powerAngular(end) = powerAngular(1); % wrap around
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UCD = NumberOfParticlesInVoronoiCell / AreaOfVoronoiCell;
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% Anisotropy measure
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peakRatio = max(powerAngular) / mean(powerAngular);
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% Threshold to distinguish stripe vs droplet
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isStripe = peakRatio > 20;
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if ~isStripe
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% === DROPLET MODE: Voronoi cell ===
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peaks = extractPeaks(state, radius, minPeakHeight);
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[row, col] = find(peaks);
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peakHeights = state(peaks);
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[~, maxIdx] = max(peakHeights);
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MaxPeakLocation = [row(maxIdx), col(maxIdx)];
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points = [col, row];
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[V, C] = voronoin(points);
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Vcell_indices = C{maxIdx};
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if all(Vcell_indices > 0) && all(Vcell_indices <= size(V,1)) && ~any(isinf(V(Vcell_indices, 1)))
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vx = interp1(1:numel(x), x, V(Vcell_indices,1), 'linear', 'extrap');
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vy = interp1(1:numel(y), y, V(Vcell_indices,2), 'linear', 'extrap');
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vx(end+1) = vx(1);
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vy(end+1) = vy(1);
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AreaOfVoronoiCell = polyarea(vx, vy);
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[X, Y] = meshgrid(x, y);
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inCellMask = inpolygon(X, Y, vx, vy);
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NumberOfParticles = sum(state(inCellMask));
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UCD = NumberOfParticles / AreaOfVoronoiCell;
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else
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warning('Voronoi cell for max peak is invalid.');
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UCD = NaN;
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end
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else
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% === STRIPE MODE: Use rectangular unit cell aligned with stripe direction ===
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[~, idxMax] = max(F(:));
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stripeAngle = theta(idxMax); % radians
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% Rotate image to align stripes horizontally
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rotatedState = imrotate(state, -rad2deg(stripeAngle), 'bilinear', 'crop');
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% Estimate vertical stripe spacing (stripe-normal direction)
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stripeProfileY = mean(rotatedState, 2) - mean(rotatedState(:));
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fftY = abs(fft(stripeProfileY));
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fftY(1:3) = 0;
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[~, fyIdx] = max(fftY(1:floor(end/2)));
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spacingY = round(numel(stripeProfileY) / fyIdx);
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% Estimate horizontal spacing (along-stripe periodicity)
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stripeProfileX = mean(rotatedState, 1) - mean(rotatedState(:));
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fftX = abs(fft(stripeProfileX));
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fftX(1:3) = 0;
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[~, fxIdx] = max(fftX(1:floor(end/2)));
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spacingX = round(numel(stripeProfileX) / fxIdx);
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% Find stripe center (vertical)
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[~, centerY] = max(stripeProfileY);
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rowRange = max(1, centerY - round(0.5 * spacingY)) : ...
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min(size(rotatedState,1), centerY + round(0.5 * spacingY));
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% Find repeat center along stripe direction (horizontal)
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[~, centerX] = max(stripeProfileX);
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colRange = max(1, centerX - round(0.5 * spacingX)) : ...
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min(size(rotatedState,2), centerX + round(0.5 * spacingX));
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% Extract unit cell region
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unitCellRegion = rotatedState(rowRange, colRange);
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NumberOfParticles = sum(unitCellRegion(:));
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AreaOfUnitCell = numel(unitCellRegion) * abs(x(2)-x(1)) * abs(y(2)-y(1));
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UCD = NumberOfParticles / AreaOfUnitCell;
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end
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% Optional plot
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if ~SuppressPlotFlag
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figure(1);
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clf
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set(gcf,'Position', [100, 100, 900, 900])
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plotxy = pcolor(x,y,state);
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set(plotxy, 'EdgeColor', 'none');
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hold on;
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plot(x(MaxPeakLocation(2)), y(MaxPeakLocation(1)), 'w+', 'MarkerSize', 8, 'LineWidth', 1.5);
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plot(vx, vy, 'w-', 'LineWidth', 1.5);
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cbar1 = colorbar;
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cbar1.Label.Interpreter = 'latex';
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% cbar1.Ticks = []; % Disable the ticks
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colormap(gca, Helper.Colormaps.plasma())
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xlabel('$x$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16)
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ylabel('$y$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16)
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title(['UCD = ' num2str(UCD) ' \mum^{-2}'], ...
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'Interpreter', 'tex', 'FontSize', 16)
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set(gca, 'FontSize', 16); % For tick labels only
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if ~isStripe
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plotxy = pcolor(x,y,state);
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set(plotxy, 'EdgeColor', 'none');
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hold on;
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plot(vx, vy, 'w-', 'LineWidth', 2);
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cbar1 = colorbar;
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cbar1.Label.Interpreter = 'latex';
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% cbar1.Ticks = []; % Disable the ticks
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colormap(gca, Helper.Colormaps.plasma())
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xlabel('$x$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16)
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ylabel('$y$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16)
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title(['UCD = ' num2str(UCD) ' \mum^{-2}'], ...
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'Interpreter', 'tex', 'FontSize', 16)
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set(gca, 'FontSize', 16); % For tick labels only
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else
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imagesc(rotatedState);
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axis image;
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cbar1 = colorbar;
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cbar1.Label.Interpreter = 'latex';
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colormap(gca, Helper.Colormaps.plasma())
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xlabel('$y$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16)
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ylabel('$x$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16)
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% Title with UCD
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title(['UCD = ' num2str(UCD, '%.3f') ' $\mu$m$^{-2}$'], ...
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'Interpreter', 'latex', 'FontSize', 16)
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% Highlight unit cell region
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rectX = colRange(1) - 0.5;
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rectY = rowRange(1) - 0.5;
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rectW = length(colRange);
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rectH = length(rowRange);
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rectangle('Position', [rectX, rectY, rectW, rectH], ...
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'EdgeColor', 'w', 'LineWidth', 2);
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title(sprintf('UCD = %.4f $\\mu$m$^{-2}$', UCD), ...
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'Interpreter', 'latex', 'FontSize', 16);
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end
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end
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end
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end
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function [peaks_mask] = extractPeaks(image, radius, minPeakHeight)
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peaks = imregionalmax(image);
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@ -593,7 +593,7 @@ JobNumber = 0;
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SuppressPlotFlag = false;
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AveragePCD = Scripts.extractAveragePeakColumnDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
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%% Extract average unit cell density
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%% Extract average unit cell density - Droplets
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Radius = 2; % The radius within which peaks will be considered duplicates
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PeakThreshold = 3E3;
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SaveDirectory = 'D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/HighN/aS_9.562000e+01_theta_000_phi_000_N_712500';
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@ -601,6 +601,19 @@ JobNumber = 0;
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SuppressPlotFlag = false;
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UCD = Scripts.extractAverageUnitCellDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
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%% Extract average unit cell density - Stripes
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Radius = 2; % The radius within which peaks will be considered duplicates
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PeakThreshold = 3E3;
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SaveDirectory = 'D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/HighN/aS_9.562000e+01_theta_000_phi_000_N_1529167';
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JobNumber = 0;
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SuppressPlotFlag = false;
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UCD = Scripts.extractAverageUnitCellDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
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NUM_ATOMS_LIST = [100000 304167 508333 712500 916667 1120833 1325000 ...
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1529167 1733333 1937500 2141667 2345833 2550000 2754167 ...
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2958333 3162500 3366667 3570833 3775000 3979167 4183333 ...
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4387500 4591667 4795833 5000000];
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%% Plot number of droplets
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% Parameters
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Radius = 2;
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@ -676,60 +689,140 @@ SuppressPlotFlag = true;
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SCATTERING_LENGTH_RANGE = [95.62];
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NUM_ATOMS_LIST = [50000 54545 59091 63636 68182 72727 77273 81818 86364 90909 95455 100000 304167 508333 712500 916667 1120833 1325000 ...
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1529167 1733333 1937500 2141667 2345833 2550000 2754167 2958333 3162500 3366667 3570833 3775000 3979167 4183333 4387500 ...
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4591667 4795833 5000000];
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NUM_ATOMS_LIST_FULL = [100000 304167 508333 712500 916667 1120833 1325000 1529167 1733333 1937500 2141667 2345833 2550000 2754167 2958333 3162500 3366667 3570833 3775000 3979167 4183333 4387500 4591667 4795833 5000000];
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NUM_ATOMS_LIST_INSET = [50000 54545 59091 63636 68182 72727 77273 81818 86364 90909 95455];
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% Prepare figure
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figure(1);
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clf;
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set(gcf,'Position', [100, 100, 1000, 700]);
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hold on;
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% Color order for better visibility
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% Color order
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colors = lines(length(SCATTERING_LENGTH_RANGE));
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% Store legend labels
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legendEntries = cell(1, length(SCATTERING_LENGTH_RANGE));
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% Store data for both sets
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AverageCDs_full = zeros(length(SCATTERING_LENGTH_RANGE), length(NUM_ATOMS_LIST_FULL));
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AverageCDs_inset = zeros(length(SCATTERING_LENGTH_RANGE), length(NUM_ATOMS_LIST_INSET));
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% Main plot
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main_ax = axes;
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hold(main_ax, 'on');
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% Loop over scattering lengths
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for j = 1:length(SCATTERING_LENGTH_RANGE)
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aS = SCATTERING_LENGTH_RANGE(j);
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% Format scattering length in scientific notation with 6 decimal places
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aS_string = sprintf('%.6e', aS);
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% Construct base directory for this aS
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baseDir = ['D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/aS_' ...
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baseDir = ['D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/HighN/aS_' ...
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aS_string '_theta_000_phi_000_N_'];
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% Preallocate results for this curve
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AverageCDs = zeros(size(NUM_ATOMS_LIST));
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% Loop over all atom numbers
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for i = 1:length(NUM_ATOMS_LIST)
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N = NUM_ATOMS_LIST(i);
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% Full list
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for i = 1:length(NUM_ATOMS_LIST_FULL)
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N = NUM_ATOMS_LIST_FULL(i);
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SaveDirectory = [baseDir num2str(N)];
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% Call your droplet counting function
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AverageCDs(i) = Scripts.extractAveragePeakColumnDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
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AverageCDs_full(j,i) = Scripts.extractAveragePeakColumnDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
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end
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% Plot curve
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plot(NUM_ATOMS_LIST, AverageCDs, 'o-', ...
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'Color', colors(j, :), 'LineWidth', 1.5);
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baseDir = ['D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/LowN/aS_' ...
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aS_string '_theta_000_phi_000_N_'];
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% Inset list
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for i = 1:length(NUM_ATOMS_LIST_INSET)
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N = NUM_ATOMS_LIST_INSET(i);
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SaveDirectory = [baseDir num2str(N)];
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AverageCDs_inset(j,i) = Scripts.extractAveragePeakColumnDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
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end
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% Store legend entry
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legendEntries{j} = ['a_s = ' num2str(aS) 'a_o'];
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% Plot main curve
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x = NUM_ATOMS_LIST_FULL;
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y = AverageCDs_full(j,:);
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valid = ~isnan(y); % logical index of valid points
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plot(main_ax,x(valid), y(valid), 'o-', ...
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'Color', colors(j,:), 'LineWidth', 1.5);
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end
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% Finalize plot
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xlabel('Number of Atoms', 'Interpreter', 'tex', 'FontSize', 16);
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ylabel('Average Peak Column Density', 'Interpreter', 'tex', 'FontSize', 16);
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title(TitleString, 'Interpreter', 'tex', 'FontSize', 18);
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legend(legendEntries, 'Interpreter', 'tex', 'FontSize', 12, 'Location', 'bestoutside');
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legend(arrayfun(@(aS) sprintf('a_s = %.2f a_0', aS), SCATTERING_LENGTH_RANGE, ...
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'UniformOutput', false), ...
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'Interpreter', 'tex', 'FontSize', 12, 'Location', 'bestoutside');
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grid(main_ax, 'on');
|
||||
|
||||
% Inset plot
|
||||
inset_ax = axes('Position', [0.45 0.18 0.28 0.28]); % Normalized position [x y w h]
|
||||
box(inset_ax, 'on');
|
||||
hold(inset_ax, 'on');
|
||||
|
||||
for j = 1:length(SCATTERING_LENGTH_RANGE)
|
||||
plot(inset_ax, NUM_ATOMS_LIST_INSET, AverageCDs_inset(j,:), 'o-', ...
|
||||
'Color', colors(j,:), 'LineWidth', 1.2);
|
||||
end
|
||||
|
||||
set(inset_ax, 'FontSize', 8);
|
||||
title(inset_ax, 'Low-N', 'FontSize', 9);
|
||||
grid(inset_ax, 'on');
|
||||
xlabel(inset_ax, 'N', 'FontSize', 9);
|
||||
ylabel(inset_ax, 'CD', 'FontSize', 9);
|
||||
|
||||
%% Plot average unit cell density
|
||||
Radius = 2;
|
||||
PeakThreshold = 3E3;
|
||||
JobNumber = 0;
|
||||
SuppressPlotFlag = true; % Suppress plots during batch processing
|
||||
TitleString = "[ \omega_x, \omega_y, \omega_z ] = 2 \pi \times [ 50, 20, 150 ] Hz; \theta = 0^\circ";
|
||||
|
||||
|
||||
SCATTERING_LENGTH_RANGE = [95.62];
|
||||
|
||||
NUM_ATOMS_LIST = [712500 916667 1120833 1325000 1529167 1733333 1937500 2141667 2345833 2550000 2754167 2958333 3162500 3366667 3570833];
|
||||
|
||||
UCD_values = zeros(length(SCATTERING_LENGTH_RANGE), length(NUM_ATOMS_LIST));
|
||||
|
||||
% Prepare figure
|
||||
figure(1);
|
||||
clf;
|
||||
set(gcf,'Position', [100, 100, 1000, 700]);
|
||||
hold on
|
||||
|
||||
% Color order
|
||||
colors = lines(length(SCATTERING_LENGTH_RANGE));
|
||||
|
||||
for j = 1:length(SCATTERING_LENGTH_RANGE)
|
||||
aS = SCATTERING_LENGTH_RANGE(j);
|
||||
aS_string = sprintf('%.6e', aS);
|
||||
|
||||
baseDir = ['D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/HighN/aS_' ...
|
||||
aS_string '_theta_000_phi_000_N_'];
|
||||
|
||||
for i = 1:length(NUM_ATOMS_LIST)
|
||||
N = NUM_ATOMS_LIST(i);
|
||||
% Construct folder path for this N
|
||||
SaveDirectory = sprintf('%s%d', baseDir, N);
|
||||
try
|
||||
UCD_values(j,i) = Scripts.extractAverageUnitCellDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
|
||||
catch ME
|
||||
warning('Error processing N=%d: %s', N, ME.message);
|
||||
UCD_values(j,i) = NaN; % mark as NaN on error
|
||||
end
|
||||
end
|
||||
|
||||
x = NUM_ATOMS_LIST;
|
||||
y = UCD_values(j,:);
|
||||
|
||||
valid = ~isnan(y); % logical index of valid points
|
||||
plot(x(valid), y(valid), 'o-', 'Color', colors(j,:), 'LineWidth', 1.5);
|
||||
|
||||
end
|
||||
|
||||
xlabel('Number of Atoms', 'Interpreter', 'latex', 'FontSize', 16);
|
||||
ylabel('Unit Cell Density (UCD) [$\mu m^{-2}$]', 'Interpreter', 'latex', 'FontSize', 16);
|
||||
title(TitleString, 'Interpreter', 'tex', 'FontSize', 18);
|
||||
legend(arrayfun(@(aS) sprintf('a_s = %.2f a_0', aS), SCATTERING_LENGTH_RANGE, ...
|
||||
'UniformOutput', false), ...
|
||||
'Interpreter', 'tex', 'FontSize', 12, 'Location', 'bestoutside');
|
||||
set(gca, 'FontSize', 14);
|
||||
grid on;
|
||||
hold off;
|
||||
|
||||
%% Plot TF radii of unmodulated states
|
||||
% Parameters
|
||||
|
||||
Loading…
Reference in New Issue
Block a user