extract_all_positives.m

function [positives, edge_positives, edge_positives_zeropadded] = extract_all_positives(img,cell_indexes,radius)
% Function for extracting all positive examples from an image given a list
% of cell center indexes

    N = length(cell_indexes);
    edge_positives_idx = 1;
    positives_idx = 1;
    normal_patch_size = 2*radius+1;
    channels = size(img, 3);
    
    % for all indexes given for positive cells
    for i = 1:N
        [x, y] = extract_patch(round(cell_indexes(:,i)), radius, size(img));
        if size(x, 2) < normal_patch_size || size(y, 2) < size(x, 2)
            % Add to a special set if they are so called "edge positives
            
            if x(1) == 1 && (length(x) ~= normal_patch_size)
                ind_x_zero = 1:length(x);
                ind_x_zero = ind_x_zero + (normal_patch_size- length(x));      
            else
                ind_x_zero = 1:length(x);
            end
            if y(1) == 1 && (length(y) ~= normal_patch_size)
                ind_y_zero = 1:length(y);
                ind_y_zero = ind_y_zero + (normal_patch_size - length(y));      
            else
                ind_y_zero = 1:length(y);
            end
            zero_padded_image = zeros(normal_patch_size, normal_patch_size, channels);
            zero_padded_image(ind_y_zero,ind_x_zero,:) = img(y,x,:);
            edge_positives{edge_positives_idx} = img(y,x,:);
            edge_positives_zeropadded{edge_positives_idx} = zero_padded_image;
            
            edge_positives_idx = edge_positives_idx + 1;
        else
            % if the indexes did not go outside the image border, add the
            % patch to the positives
            positives{positives_idx} = img(y,x,:);
            positives_idx = positives_idx + 1;
        end
    end
    
    
end