Minor modification.
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@ -2,22 +2,23 @@
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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"];
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folderPath = "C:/Users/Karthik/Documents/GitRepositories/Calculations/24/";
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folderPath = "C:/Users/Karthik/Documents/GitRepositories/Calculations/Data-Analyzer/20/";
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run = '0086';
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run = '0140';
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folderPath = strcat(folderPath, run);
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cam = 5;
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cam = 4;
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angle = 90;
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center = [2100, 1150];
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span = [500, 500];
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fraction = [0.1, 0.1];
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angle = 0;
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center = [95, 1042];
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span = [50, 50];
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fraction = [0.1, 0.1];
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pixel_size = 4.6e-6;
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pixel_size = 5.86e-6;
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remove_fringes = false;
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%% Compute OD image, rotate and extract ROI for analysis
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% Compute OD image, rotate and extract ROI for analysis
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% Get a list of all files in the folder with the desired file name pattern.
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filePattern = fullfile(folderPath, '*.h5');
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files = dir(filePattern);
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@ -35,36 +36,48 @@ for k = 1 : length(files)
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bkg_img = im2double(imrotate(h5read(fullFileName, append(groupList(cam), "/background")), angle));
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dark_img = im2double(imrotate(h5read(fullFileName, append(groupList(cam), "/dark")), angle));
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refimages(:,:,k) = subtract_offset(crop_image(bkg_img, center, span), fraction);
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absimages(:,:,k) = subtract_offset(crop_image(calculate_OD(atm_img, bkg_img, dark_img), center, span), fraction);
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refimages(:,:,k) = subtract_offset(crop_image(bkg_img, center, span), fraction)';
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absimages(:,:,k) = subtract_offset(crop_image(calculate_OD(atm_img, bkg_img, dark_img), center, span), fraction)';
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end
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%% Fringe removal
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optrefimages = removefringesInImage(absimages, refimages);
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absimages_fringe_removed = absimages(:, :, :) - optrefimages(:, :, :);
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nimgs = size(absimages_fringe_removed,3);
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od_imgs = cell(1, nimgs);
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for i = 1:nimgs
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od_imgs{i} = absimages_fringe_removed(:, :, i);
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% Fringe removal
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if remove_fringes
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optrefimages = removefringesInImage(absimages, refimages);
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absimages_fringe_removed = absimages(:, :, :) - optrefimages(:, :, :);
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nimgs = size(absimages_fringe_removed,3);
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od_imgs = cell(1, nimgs);
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for i = 1:nimgs
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od_imgs{i} = absimages_fringe_removed(:, :, i);
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end
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else
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nimgs = size(absimages,3);
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od_imgs = cell(1, nimgs);
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for i = 1:nimgs
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od_imgs{i} = absimages(:, :, i);
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end
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end
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%%
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figure(1)
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clf
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r = 120;
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x = 250;
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y = 250;
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set(gcf,'Position',[50 50 950 750])
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% Calculate the x and y limits for the cropped image
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y_min = center(1) - span(2) / 2;
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y_max = center(1) + span(2) / 2;
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x_min = center(2) - span(1) / 2;
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x_max = center(2) + span(1) / 2;
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% Generate x and y arrays representing the original coordinates for each pixel
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x_range = linspace(x_min, x_max, span(1));
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y_range = linspace(y_min, y_max, span(2));
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% Display the cropped image
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for k = 1 : length(od_imgs)
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imagesc(xvals, yvals, od_imgs{k})
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hold on
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th = 0:pi/50:2*pi;
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xunit = r * cos(th) + x;
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yunit = r * sin(th) + y;
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h = plot(xunit, yunit, Color='yellow');
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xlabel('µm', 'FontSize', 16)
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ylabel('µm', 'FontSize', 16)
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imagesc(x_range, y_range, od_imgs{k})
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axis equal tight;
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hcb = colorbar;
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hL = ylabel(hcb, 'Optical Density', 'FontSize', 16);
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@ -72,11 +85,42 @@ for k = 1 : length(od_imgs)
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colormap jet;
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set(gca,'CLim',[0 1.0]);
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set(gca,'YDir','normal')
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title('DMD projection: Circle of radius 200 pixels', 'FontSize', 16);
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set(gca, 'YTick', linspace(y_min, y_max, 5)); % Define y ticks
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set(gca, 'YTickLabel', flip(linspace(y_min, y_max, 5))); % Flip only the labels
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xlabel('X', 'Interpreter', 'tex','FontSize',16);
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ylabel('Y', 'Interpreter', 'tex','FontSize',16);
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drawnow;
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drawnow
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pause(0.5)
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end
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%% Overlay images
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% image_below = ;
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% image_top = ;
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% Display the first image (opaque)
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figure (2);
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clf
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set(gcf,'Position',[50 50 950 750])
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imagesc(x_range, y_range, image_below);
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hold on; % Allow overlaying of the second image
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h = imagesc(x_range, y_range, image_top); % Display the second image (translucent)
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set(h, 'AlphaData', 0.6); % Adjust transparency: 0 is fully transparent, 1 is fully opaque
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axis equal tight;
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hcb = colorbar;
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hL = ylabel(hcb, 'Optical Density', 'FontSize', 16);
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set(hL,'Rotation',-90);
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colormap jet;
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set(gca,'CLim',[0 1.0]);
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set(gca,'YDir','normal')
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set(gca, 'YTick', linspace(y_min, y_max, 5)); % Define y ticks
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set(gca, 'YTickLabel', flip(linspace(y_min, y_max, 5))); % Flip only the labels
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xlabel('X', 'Interpreter', 'tex','FontSize',16);
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ylabel('Y', 'Interpreter', 'tex','FontSize',16);
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hold off;
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%% Helper Functions
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function ret = get_offset_from_corner(img, x_fraction, y_fraction)
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