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Map_projection_pixel_map.m
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Map_projection_pixel_map.m
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function Map_projection_pixel_map()
% This function determines the pixel size in the projected map
% Pre-requisite: You must have already performed sphere fit and map projection and therefore you must have the following mat files:
% Sphere_params.mat and Map_parameters.mat
% Created by Sundar Naganathan - 2018
Folder_path = cd;
% Load the following mat files
load(strcat(Folder_path,'/binned/Sphere_fit/Sphere_params.mat'))
load(strcat(Folder_path,'/binned/Sphere_fit/Maps_eqdcylin/Map_parameters.mat'))
% if exist(strcat(Folder_path,'/Sphere_fit/Maps_eqdcylin'),'dir') ~= 7
% mkdir(strcat(Folder_path,'/Sphere_fit/Maps_eqdcylin'))
% end
Map_pixel.Downsample = 2; % By how much images were downsampled when performing fusion of multiview images
Map_pixel.Original_px_size = 0.5; % um per pixel
Map_pixel.Original_px_size_down = Map_pixel.Original_px_size * Map_pixel.Downsample; % two times downsampling
Map_pixel.Scale_factor = Map_parameters.Scale_factor;
Map_pixel.Recenter_map = Map_parameters.Recenter_map;
% Radius of sphere obtained from 'Get_embryo_surface' code
Map_pixel.Radius_sphere = Map_parameters.Radius_iterate;
% Latitude longitude limits
Map_pixel.Lat_start = 90;
Map_pixel.Lat_end = -90;
Map_pixel.Long_start = 0;
Map_pixel.Long_end = 359;
% x_map is the x-coordinate in the projected map, which is between -180 and 180 degrees.
% y_map is the y-coordinate in the projected map, which is between -90 and 90 degrees.
Start_x = Map_pixel.Long_start*Map_pixel.Scale_factor;
End_x = (Map_pixel.Long_end*Map_pixel.Scale_factor)-1;
Start_y = Map_pixel.Lat_start*Map_pixel.Scale_factor;
End_y = (Map_pixel.Lat_end*Map_pixel.Scale_factor)-1;
x_map = (Start_x:1:End_x);
y_map = (Start_y:-1:End_y);
% x_map1 = repmat(x_map,length(y_map),1);
y_map1 = repmat(y_map',1,length(x_map)); % Initialize the map
% Lambda = Map_pixel.Recenter_map+x_map1./Map_pixel.Scale_factor;
Phi = y_map1./Map_pixel.Scale_factor;
% Lambda_rad = deg2rad(Lambda);
Phi_rad = deg2rad(Phi); % Convert to radian
% Pre-initialize variables
Map_pixel.Circle_radii = nan(size(Phi_rad,1),size(Phi_rad,2),numel(Map_pixel.Radius_sphere));
Map_pixel.Pixel_size = nan(size(Phi_rad,1),size(Phi_rad,2),numel(Map_pixel.Radius_sphere));
% For each sphere radius, get the pixel size
for i = 1:numel(Map_pixel.Radius_sphere)
Map_pixel.Circle_radii(:,:,i) = Map_pixel.Radius_sphere(i) .* cos(Phi_rad);
Map_pixel.Pixel_size(:,:,i) = Map_pixel.Circle_radii(:,:,i) .* (2*pi*Map_pixel.Original_px_size_down/(360*Map_pixel.Scale_factor));
end
% Get the pixel size at the equator across maps
Pixel_size.Equator = Map_pixel.Pixel_size(round(size(Phi_rad,1)/2),1,:);
Pixel_size.Equator = Pixel_size.Equator(:);
% Save pixel size mat files
save(strcat(Folder_path,'/binned/Sphere_fit/Maps_eqdcylin/Map_pixel.mat'),'Map_pixel','-v7.3')
save(strcat(Folder_path,'/binned/Sphere_fit/Maps_eqdcylin/Pixel_size.mat'),'Pixel_size')
% Plot pixel size for full extent and mark pixel size at 45 deg
% figure,plot(Map_pixel.Pixel_size(901:end,1))
% set(gcf,'Color','w')
% set(gca,'XLim',[0 901])
% hold on
% line([450,450],[0.1 0.6],'Color','red','LineStyle','--')
% line([0,900],[0.4187 0.4187],'Color','red','LineStyle','--')
% export_fig(strcat(Folder_path,'/Sphere_fit/Maps_scalefactor10/PixelSize_variation_45deg_mark.tif'),'-q101')