karthik/Calculations
1
0
Fork 0
Code Issues Pull Requests repo.project_board Releases Wiki Activity

Latest Analysis scripts.

Browse Source
This commit is contained in:
Karthik 2025-04-10 23:19:23 +02:00
parent c5ebb76b9d
commit 50722c5140
2 changed files with 319 additions and 160 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

371
Data-Analyzer/fourierAnalysis.m
View File

@ -61,40 +61,6 @@ else
od_imgs{i} = absimages(:, :, i); od_imgs{i} = absimages(:, :, i);
end end
end end
%% Display Images
figure(1)
clf
set(gcf,'Position',[50 50 950 750])
% Calculate the x and y limits for the cropped image
y_min = center(1) - span(2) / 2;
y_max = center(1) + span(2) / 2;
x_min = center(2) - span(1) / 2;
x_max = center(2) + span(1) / 2;
% Generate x and y arrays representing the original coordinates for each pixel
x_range = linspace(x_min, x_max, span(1));
y_range = linspace(y_min, y_max, span(2));
% Display the cropped image
for k = 1 : length(od_imgs)
imagesc(x_range, y_range, od_imgs{k})
axis equal tight;
hcb = colorbar;
hL = ylabel(hcb, 'Optical Density', 'FontSize', 16);
set(hL,'Rotation',-90);
colormap jet;
set(gca,'CLim',[0 3.0]);
set(gca,'YDir','normal')
set(gca, 'YTick', linspace(y_min, y_max, 5)); % Define y ticks
set(gca, 'YTickLabel', flip(linspace(y_min, y_max, 5))); % Flip only the labels
xlabel('Horizontal', 'Interpreter', 'tex','FontSize',16);
ylabel('Vertical', 'Interpreter', 'tex','FontSize',16);
drawnow
pause(0.5)
end
%% Get rotation angles %% Get rotation angles
theta_values = zeros(1, length(files)); theta_values = zeros(1, length(files));
@ -116,7 +82,8 @@ end
fft_imgs = cell(1, nimgs); fft_imgs = cell(1, nimgs);
% Create VideoWriter object for movie % Create VideoWriter object for movie
videoFile = VideoWriter('Single_Shot_FFT.avi', 'Motion JPEG AVI'); videoFile = VideoWriter('Single_Shot_FFT.mp4', 'MPEG-4');
videoFile.Quality = 100; % Set quality to maximum (0–100)
videoFile.FrameRate = 2; % Set the frame rate (frames per second) videoFile.FrameRate = 2; % Set the frame rate (frames per second)
open(videoFile); % Open the video file to write open(videoFile); % Open the video file to write
@ -127,9 +94,9 @@ for k = 1 : length(od_imgs)
figure(2); figure(2);
clf clf
set(gcf,'Position',[50 50 1500 550]) set(gcf,'Position',[500 100 1000 800])
set(gca,'FontSize',16,'Box','On','Linewidth',2); t = tiledlayout(2, 2, 'TileSpacing', 'compact', 'Padding', 'compact'); % 1x4 grid
t = tiledlayout(1, 3, 'TileSpacing', 'compact', 'Padding', 'compact'); % 1x2 grid font = 'Bahnschrift';
% Calculate the x and y limits for the cropped image % Calculate the x and y limits for the cropped image
y_min = center(1) - span(2) / 2; y_min = center(1) - span(2) / 2;
@ -142,37 +109,48 @@ for k = 1 : length(od_imgs)
y_range = linspace(y_min, y_max, span(2)); y_range = linspace(y_min, y_max, span(2));
% Display the cropped image % Display the cropped image
nexttile ax1 = nexttile;
imagesc(x_range, y_range, IMG) imagesc(x_range, y_range, IMG)
% Define normalized positions (relative to axis limits) % Define normalized positions (relative to axis limits)
x_offset = 0.025; % 5% offset from the edges x_offset = 0.025; % 5% offset from the edges
y_offset = 0.025; % 5% offset from the edges y_offset = 0.025; % 5% offset from the edges
% Top-right corner (normalized axis coordinates) % Top-right corner (normalized axis coordinates)
text(1 - x_offset, 1 - y_offset, ['Angle: ', num2str(theta_values(k), '%.1f')], ... hText = text(1 - x_offset, 1 - y_offset, ['Angle: ', num2str(theta_values(k), '%.1f')], ...
'Color', 'white', 'FontWeight', 'bold', 'Interpreter', 'tex', 'FontSize', 20, 'Units', 'normalized', 'HorizontalAlignment', 'right', 'VerticalAlignment', 'top'); 'Color', 'white', 'FontWeight', 'bold', 'Interpreter', 'tex', 'FontSize', 20, 'Units', 'normalized', 'HorizontalAlignment', 'right', 'VerticalAlignment', 'top');
axis equal tight; axis equal tight;
hcb = colorbar; hcb = colorbar;
hL = ylabel(hcb, 'Optical Density', 'FontSize', 16); colormap(ax1, 'jet');
set(gca, 'FontSize', 14); % For tick labels only
hL = ylabel(hcb, 'Optical Density');
set(hL,'Rotation',-90); set(hL,'Rotation',-90);
set(gca,'YDir','normal') set(gca,'YDir','normal')
set(gca, 'YTick', linspace(y_min, y_max, 5)); % Define y ticks set(gca, 'YTick', linspace(y_min, y_max, 5)); % Define y ticks
set(gca, 'YTickLabel', flip(linspace(y_min, y_max, 5))); % Flip only the labels set(gca, 'YTickLabel', flip(linspace(y_min, y_max, 5))); % Flip only the labels
xlabel('X', 'Interpreter', 'tex','FontSize',16); hXLabel = xlabel('X (pixels)', 'Interpreter', 'tex');
ylabel('Y', 'Interpreter', 'tex','FontSize',16); hYLabel = ylabel('Y (pixels)', 'Interpreter', 'tex');
hTitle = title('OD Image', 'Interpreter', 'tex');
set([hXLabel, hYLabel, hL, hText], 'FontName', font)
set([hXLabel, hYLabel, hL], 'FontSize', 14)
set(hTitle, 'FontName', font, 'FontSize', 16, 'FontWeight', 'bold'); % Set font and size for title
nexttile ax2 = nexttile;
imagesc(x_range, y_range, IMGBIN) imagesc(x_range, y_range, IMGBIN)
axis equal tight; axis equal tight;
hcb = colorbar; hcb = colorbar;
colormap(ax2, 'parula');
set(gca, 'FontSize', 14); % For tick labels only
set(gca,'YDir','normal') set(gca,'YDir','normal')
set(gca, 'YTick', linspace(y_min, y_max, 5)); % Define y ticks set(gca, 'YTick', linspace(y_min, y_max, 5)); % Define y ticks
set(gca, 'YTickLabel', flip(linspace(y_min, y_max, 5))); % Flip only the labels set(gca, 'YTickLabel', flip(linspace(y_min, y_max, 5))); % Flip only the labels
xlabel('X', 'Interpreter', 'tex','FontSize',16); hXLabel = xlabel('X (pixels)', 'Interpreter', 'tex');
ylabel('Y', 'Interpreter', 'tex','FontSize',16); hYLabel = ylabel('Y (pixels)', 'Interpreter', 'tex');
title('Denoised - Masked - Binarized','FontSize',16); hTitle = title('Denoised - Masked - Binarized', 'Interpreter', 'tex');
nexttile set([hXLabel, hYLabel, hL], 'FontName', font)
set([hXLabel, hYLabel, hL], 'FontSize', 14)
set(hTitle, 'FontName', font, 'FontSize', 16, 'FontWeight', 'bold'); % Set font and size for title
ax3 = nexttile;
[rows, cols] = size(IMGFFT); [rows, cols] = size(IMGFFT);
zoom_size = 50; % Zoomed-in region around center zoom_size = 50; % Zoomed-in region around center
mid_x = floor(cols/2); mid_x = floor(cols/2);
@ -184,69 +162,46 @@ for k = 1 : length(od_imgs)
x_offset = 0.025; % 5% offset from the edges x_offset = 0.025; % 5% offset from the edges
y_offset = 0.025; % 5% offset from the edges y_offset = 0.025; % 5% offset from the edges
% Top-right corner (normalized axis coordinates) % Top-right corner (normalized axis coordinates)
text(1 - x_offset, 1 - y_offset, ['Angle: ', num2str(theta_values(k), '%.1f')], ... % hText = text(1 - x_offset, 1 - y_offset, ['Angle: ', num2str(theta_values(k), '%.1f')], ...
'Color', 'white', 'FontWeight', 'bold', 'Interpreter', 'tex', 'FontSize', 20, 'Units', 'normalized', 'HorizontalAlignment', 'right', 'VerticalAlignment', 'top'); % 'Color', 'white', 'FontWeight', 'bold', 'Interpreter', 'tex', 'FontSize', 20, 'Units', 'normalized', 'HorizontalAlignment', 'right', 'VerticalAlignment', 'top');
axis equal tight; axis equal tight;
hcb = colorbar; hcb = colorbar;
colormap(ax3, 'jet');
set(gca, 'FontSize', 14); % For tick labels only
set(gca,'YDir','normal') set(gca,'YDir','normal')
xlabel('X', 'Interpreter', 'tex','FontSize',16); hXLabel = xlabel('X (pixels)', 'Interpreter', 'tex');
ylabel('Y', 'Interpreter', 'tex','FontSize',16); hYLabel = ylabel('Y (pixels)', 'Interpreter', 'tex');
title('Fourier Power Spectrum','FontSize',16); hTitle = title('Fourier Power Spectrum', 'Interpreter', 'tex');
set([hXLabel, hYLabel, hL, hText], 'FontName', font)
set([hXLabel, hYLabel, hL], 'FontSize', 14)
set(hTitle, 'FontName', font, 'FontSize', 16, 'FontWeight', 'bold'); % Set font and size for title
drawnow % Plot the angular structure factor
pause(0.5) %{
nexttile
[theta_vals, angular_intensity] = computeAngularDistribution(zoomedIMGFFT, 10, 20, 100, 75);
polarhistogram('BinEdges', theta_vals, 'BinCounts', angular_intensity, ...
'FaceColor', [0.2 0.6 0.9], 'EdgeColor', 'k');
set(gca, 'FontSize', 14); % For tick labels only
hTitle = title('Angular Distribution', 'Interpreter', 'tex');
set(hTitle, 'FontName', font)
set(hTitle, 'FontName', font, 'FontSize', 16, 'FontWeight', 'bold'); % Set font and size for title
%}
% Plot the angular structure factor
nexttile
[theta_vals, S_theta] = computeAngularStructureFactor(zoomedIMGFFT, 10, 20, 180, 75, 2);
% Capture the current frame and write it to the video plot(theta_vals/pi, S_theta,'Linewidth',2);
frame = getframe(gcf); % Capture the current figure as a frame set(gca, 'FontSize', 14); % For tick labels only
writeVideo(videoFile, frame); % Write the frame to the video hXLabel = xlabel('\theta (\pi)', 'Interpreter', 'tex');
end hYLabel = ylabel('S(\theta)', 'Interpreter', 'tex');
hTitle = title('Angular Structure Factor', 'Interpreter', 'tex');
set([hXLabel, hYLabel, hL, hText], 'FontName', font)
set([hXLabel, hYLabel, hL], 'FontSize', 14)
set(hTitle, 'FontName', font, 'FontSize', 16, 'FontWeight', 'bold'); % Set font and size for title
grid on
% Close the video file
close(videoFile);
%% Averaged FFT
% Assuming od_imgs is a cell array of size 4*n
n = length(fft_imgs) / 4; % Calculate n
fft_imgs_avg = cell(1, n); % Initialize the new cell array to hold the averaged images
for i = 1:n
% Take the 4 corresponding images from od_imgs
img1 = fft_imgs{4*i-3}; % 1st image in the group
img2 = fft_imgs{4*i-2}; % 2nd image in the group
img3 = fft_imgs{4*i-1}; % 3rd image in the group
img4 = fft_imgs{4*i}; % 4th image in the group
% Compute the average of these 4 images
avg_img = (img1 + img2 + img3 + img4) / 4;
% Store the averaged image in the new cell array
fft_imgs_avg{i} = avg_img;
end
% Create VideoWriter object for movie
videoFile = VideoWriter('Averaged_FFT.avi', 'Motion JPEG AVI');
videoFile.FrameRate = 2; % Set the frame rate (frames per second)
open(videoFile); % Open the video file to write
figure(3)
clf
set(gcf,'Position',[50 50 950 750])
% Display the cropped image
for k = 1 : length(fft_imgs_avg)
imagesc(log(1 + fft_imgs_avg{k}));
% Define normalized positions (relative to axis limits)
x_offset = 0.025; % 5% offset from the edges
y_offset = 0.025; % 5% offset from the edges
% Top-right corner (normalized axis coordinates)
text(1 - x_offset, 1 - y_offset, ['Angle: ', num2str(theta_values(k), '%.1f')], ...
'Color', 'white', 'FontWeight', 'bold', 'Interpreter', 'tex', 'FontSize', 20, 'Units', 'normalized', 'HorizontalAlignment', 'right', 'VerticalAlignment', 'top');
axis equal tight;
hcb = colorbar;
set(gca,'YDir','normal')
xlabel('X', 'Interpreter', 'tex','FontSize',16);
ylabel('Y', 'Interpreter', 'tex','FontSize',16);
title('Averaged Fourier Power Spectrum','FontSize',16);
drawnow drawnow
pause(0.5) pause(0.5)
@ -271,7 +226,8 @@ function [IMGFFT, IMGBIN] = computeFourierTransform(I)
% F_mag - 2D Fourier power spectrum (shifted) % F_mag - 2D Fourier power spectrum (shifted)
% Preprocessing: Denoise % Preprocessing: Denoise
I_filt = imgaussfilt(I, 1); % adjust sigma as needed filtered = imgaussfilt(I, 10);
I_filt = I - filtered; % adjust sigma as needed
% Elliptical mask parameters % Elliptical mask parameters
[rows, cols] = size(I_filt); [rows, cols] = size(I_filt);
@ -304,12 +260,15 @@ function [IMGFFT, IMGBIN] = computeFourierTransform(I)
I_masked = I_filt .* ellipseMask; I_masked = I_filt .* ellipseMask;
% Apply global intensity threshold mask % Apply global intensity threshold mask
intensity_thresh = 0.8; intensity_thresh = 0.20;
intensity_mask = I_masked > intensity_thresh; intensity_mask = I_masked > intensity_thresh;
I_masked = I_masked .* intensity_mask; I_masked = I_masked .* intensity_mask;
% Adaptive binarization % Adaptive binarization and cleanup
IMGBIN = imbinarize(I_masked, 'adaptive', 'Sensitivity', 0.0); IMGBIN = imbinarize(I_masked, 'adaptive', 'Sensitivity', 0.0);
IMGBIN = imdilate(IMGBIN, strel('disk', 2));
IMGBIN = imerode(IMGBIN, strel('disk', 1));
IMGBIN = imfill(IMGBIN, 'holes');
% Compute 2D Fourier Transform % Compute 2D Fourier Transform
F = fft2(double(I)); F = fft2(double(I));
@ -333,6 +292,58 @@ function [IMGFFT, IMGBIN] = computeFourierTransform(I)
end end
function [theta_vals, S_theta] = computeAngularStructureFactor(IMGFFT, r_min, r_max, num_bins, threshold, sigma)
% Apply threshold to isolate strong peaks
IMGFFT(IMGFFT < threshold) = 0;
% Prepare polar coordinates
[ny, nx] = size(IMGFFT);
[X, Y] = meshgrid(1:nx, 1:ny);
cx = ceil(nx/2);
cy = ceil(ny/2);
R = sqrt((X - cx).^2 + (Y - cy).^2);
Theta = atan2(Y - cy, X - cx); % range [-pi, pi]
% Choose radial band
radial_mask = (R >= r_min) & (R <= r_max);
% Initialize the angular structure factor array
S_theta = zeros(1, num_bins); % Pre-allocate for 180 angle bins
% Define the angle values for the x-axis
theta_vals = linspace(0, pi, num_bins);
% Loop through each angle bin
for i = 1:180
angle_start = (i-1) * pi / num_bins;
angle_end = i * pi / num_bins;
% Define a mask for the given angle range
angle_mask = (Theta >= angle_start & Theta < angle_end);
bin_mask = radial_mask & angle_mask;
% Extract the Fourier components for the given angle
fft_angle = IMGFFT .* bin_mask;
% Integrate the Fourier components over the radius at the angle
S_theta(i) = sum(sum(abs(fft_angle).^2)); % Compute structure factor (sum of squared magnitudes)
end
% Create a 1D Gaussian kernel
half_width = ceil(3 * sigma);
x = -half_width:half_width;
gauss_kernel = exp(-x.^2 / (2 * sigma^2));
gauss_kernel = gauss_kernel / sum(gauss_kernel); % normalize
% Apply convolution (circular padding to preserve periodicity)
S_theta = conv([S_theta(end-half_width+1:end), S_theta, S_theta(1:half_width)], gauss_kernel, 'same');
S_theta = S_theta(half_width+1:end-half_width); % crop back to original size
% Normalize to maximum value of 1
S_theta = S_theta / max(S_theta);
end
function ret = getBkgOffsetFromCorners(img, x_fraction, y_fraction) function ret = getBkgOffsetFromCorners(img, x_fraction, y_fraction)
% image must be a 2D numerical array % image must be a 2D numerical array
[dim1, dim2] = size(img); [dim1, dim2] = size(img);
@ -475,3 +486,147 @@ function [optrefimages] = removefringesInImage(absimages, refimages, bgmask)
optrefimages(:,:,j)=reshape(R*c,[ydim xdim]); optrefimages(:,:,j)=reshape(R*c,[ydim xdim]);
end end
end end
% Deprecated
%% Display Images
%{
figure(1)
clf
set(gcf,'Position',[50 50 950 750])
% Calculate the x and y limits for the cropped image
y_min = center(1) - span(2) / 2;
y_max = center(1) + span(2) / 2;
x_min = center(2) - span(1) / 2;
x_max = center(2) + span(1) / 2;
% Generate x and y arrays representing the original coordinates for each pixel
x_range = linspace(x_min, x_max, span(1));
y_range = linspace(y_min, y_max, span(2));
% Display the cropped image
for k = 1 : length(od_imgs)
imagesc(x_range, y_range, od_imgs{k})
axis equal tight;
hcb = colorbar;
hL = ylabel(hcb, 'Optical Density');
set(hL,'Rotation',-90);
colormap jet;
set(gca,'CLim',[0 3.0]);
set(gca,'YDir','normal')
set(gca, 'YTick', linspace(y_min, y_max, 5)); % Define y ticks
set(gca, 'YTickLabel', flip(linspace(y_min, y_max, 5))); % Flip only the labels
xlabel('X', 'Interpreter', 'tex');
ylabel('Y', 'Interpreter', 'tex');
drawnow
pause(0.5)
end
%}
%% Averaged FFT
%{
% Assuming od_imgs is a cell array of size 4*n
n = length(fft_imgs) / 4; % Calculate n
fft_imgs_avg = cell(1, n); % Initialize the new cell array to hold the averaged images
for i = 1:n
% Take the 4 corresponding images from od_imgs
img1 = fft_imgs{4*i-3}; % 1st image in the group
img2 = fft_imgs{4*i-2}; % 2nd image in the group
img3 = fft_imgs{4*i-1}; % 3rd image in the group
img4 = fft_imgs{4*i}; % 4th image in the group
% Compute the average of these 4 images
avg_img = (img1 + img2 + img3 + img4) / 4;
% Store the averaged image in the new cell array
fft_imgs_avg{i} = avg_img;
end
% Create VideoWriter object for movie
videoFile = VideoWriter('Averaged_FFT.mp4', 'MPEG-4');
videoFile.Quality = 100; % Set quality to maximum (0–100)
videoFile.FrameRate = 2; % Set the frame rate (frames per second)
open(videoFile); % Open the video file to write
% Display the cropped image
for k = 1 : length(fft_imgs_avg)
figure(3)
clf
set(gcf,'Position',[50 50 1500 550])
set(gca,'FontSize',16,'Box','On','Linewidth',2);
t = tiledlayout(1, 2, 'TileSpacing', 'compact', 'Padding', 'compact'); % 1x2 grid
nexttile
imagesc(log(1 + fft_imgs_avg{k}));
% Define normalized positions (relative to axis limits)
x_offset = 0.025; % 5% offset from the edges
y_offset = 0.025; % 5% offset from the edges
% Top-right corner (normalized axis coordinates)
text(1 - x_offset, 1 - y_offset, ['Angle: ', num2str(theta_values(k), '%.1f')], ...
'Color', 'white', 'FontWeight', 'bold', 'Interpreter', 'tex', 'FontSize', 20, 'Units', 'normalized', 'HorizontalAlignment', 'right', 'VerticalAlignment', 'top');
axis equal tight;
hcb = colorbar;
set(gca,'YDir','normal')
xlabel('X', 'Interpreter', 'tex','FontSize',16);
ylabel('Y', 'Interpreter', 'tex','FontSize',16);
title('Averaged Fourier Power Spectrum','FontSize',16);
% Plot the angular structure factor
nexttile
[theta_vals, angular_intensity] = computeAngularDistribution(fft_imgs_avg{k}, 10, 20, 100, 75);
polarhistogram('BinEdges', theta_vals, 'BinCounts', angular_intensity, ...
'FaceColor', [0.2 0.6 0.9], 'EdgeColor', 'k');
title('Angular Distribution');
drawnow
pause(0.5)
% Capture the current frame and write it to the video
frame = getframe(gcf); % Capture the current figure as a frame
writeVideo(videoFile, frame); % Write the frame to the video
end
% Close the video file
close(videoFile);
%}
%% Angular Distribution
%{
function [theta_vals, angular_intensity] = computeAngularDistribution(IMGFFT, r_min, r_max, num_bins, threshold)
% Apply threshold to isolate strong peaks
IMGFFT(IMGFFT < threshold) = 0;
% Prepare polar coordinates
[ny, nx] = size(IMGFFT);
[X, Y] = meshgrid(1:nx, 1:ny);
cx = ceil(nx/2);
cy = ceil(ny/2);
R = sqrt((X - cx).^2 + (Y - cy).^2);
Theta = atan2(Y - cy, X - cx); % range [-pi, pi]
% Choose radial band
mask = (R >= r_min) & (R <= r_max);
% Bin intensities by angle
theta_vals = linspace(-pi, pi, num_bins+1);
angular_intensity = zeros(1, num_bins);
for i = 1:num_bins
t0 = theta_vals(i);
t1 = theta_vals(i+1);
bin_mask = mask & (Theta >= t0) & (Theta < t1);
tmp = mean(IMGFFT(bin_mask), 'all');
if tmp > 50
angular_intensity(i) = tmp;
else
angular_intensity(i) = 0;
end
end
end
%}

30
Data-Analyzer/plotImages.m
View File

@ -2,24 +2,26 @@
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/Data-Analyzer/"; folderPath = "C:/Users/Karthik/Documents/GitRepositories/Calculations/Data-Analyzer/";
run = '0140'; run = '0013';
cam = 4; folderPath = strcat(folderPath, run);
cam = 5;
angle = 0; angle = 0;
center = [95, 1042]; center = [1285, 2105];
span = [50, 50]; span = [200, 200];
fraction = [0.1, 0.1]; fraction = [0.1, 0.1];
pixel_size = 5.86e-6; pixel_size = 5.86e-6;
removeFringes = false; removeFringes = false;
%}
%{
folderPath = "C:/Users/Karthik/Documents/GitRepositories/Calculations/Imaging-Response-Function-Extractor/"; folderPath = "C:/Users/Karthik/Documents/GitRepositories/Calculations/Imaging-Response-Function-Extractor/";
run = '0096'; run = '0096';
@ -35,15 +37,16 @@ fraction = [0.1, 0.1];
pixel_size = 5.86e-6; pixel_size = 5.86e-6;
removeFringes = false; removeFringes = false;
%}
% 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);
@ -60,6 +63,7 @@ for k = 1 : length(files)
end end
% Fringe removal % Fringe removal
if removeFringes if removeFringes
optrefimages = removefringesInImage(absimages, refimages); optrefimages = removefringesInImage(absimages, refimages);
absimages_fringe_removed = absimages(:, :, :) - optrefimages(:, :, :); absimages_fringe_removed = absimages(:, :, :) - optrefimages(:, :, :);
@ -70,14 +74,13 @@ if removeFringes
od_imgs{i} = absimages_fringe_removed(:, :, i); od_imgs{i} = absimages_fringe_removed(:, :, i);
end end
else else
nimgs = size(absimages,3); nimgs = size(absimages(:, :, :),3);
od_imgs = cell(1, nimgs); od_imgs = cell(1, nimgs);
for i = 1:nimgs for i = 1:nimgs
od_imgs{i} = absimages(:, :, i); od_imgs{i} = absimages(:, :, i);
end end
end end
%% Display Images
%%
figure(1) figure(1)
clf clf
@ -98,10 +101,10 @@ for k = 1 : length(od_imgs)
imagesc(x_range, y_range, od_imgs{k}) imagesc(x_range, y_range, od_imgs{k})
axis equal tight; axis equal tight;
hcb = colorbar; hcb = colorbar;
hL = ylabel(hcb, 'Normalised Optical Density', 'FontSize', 16); hL = ylabel(hcb, 'Optical Density', 'FontSize', 16);
set(hL,'Rotation',-90); set(hL,'Rotation',-90);
colormap jet; colormap jet;
set(gca,'CLim',[0 1.0]); set(gca,'CLim',[0 3.0]);
set(gca,'YDir','normal') set(gca,'YDir','normal')
set(gca, 'YTick', linspace(y_min, y_max, 5)); % Define y ticks set(gca, 'YTick', linspace(y_min, y_max, 5)); % Define y ticks
set(gca, 'YTickLabel', flip(linspace(y_min, y_max, 5))); % Flip only the labels set(gca, 'YTickLabel', flip(linspace(y_min, y_max, 5))); % Flip only the labels
@ -112,6 +115,7 @@ for k = 1 : length(od_imgs)
pause(0.5) pause(0.5)
end end
%% Overlay images %% Overlay images
% image_below = ; % image_below = ;