imageCropping.m

function [crop_nw_loc,folder_out,fmt] = imageCropping(folder_in,ext_in,numImages,max_def_idx,crop)
%This function crops the input images to include only the region of
%interest
%
% INPUTS
% -------------------------------------------------------------------------
%   folder_in: folder containing orginal images
%   ext_in: image formate extention
%   folder_in: folder containing orginal images
%   sSize: interrogation window (subset) size
%   max_def_index: string specifying where the max deformation occurs
%                   use 'center' or 'c' for the center image,
%                   'end' or 'e' for the last image,
%                   'beginning' or 'b' for the first,
%                   or specific with an integer
%   crop: string to specify whether to crop images, set to 'y' or 'yes' to crop
% OUTPUTS
% -------------------------------------------------------------------------
%   crop_nw_loc: location of the northwest corner of the cropped region
%   folder_out: the location where the images were placed
%
%NOTES
% -------------------------------------------------------------------------
%

%% Setup

%Output variables
fmt = 'tif';
ext_out = strcat('.',fmt);

prefixes = cell(1,26^3);
alphab = {'a','b','c','d','e','f','g','h','i','j','k','l','m','n','o',...
    'p','q','r','s','t','u','v','w','x','y','z'};

kk = 0;
for hh = 1:length(alphab)
    for ii = 1:length(alphab)
        for jj = 1:length(alphab)
            kk = kk + 1;
            prefixes{kk} = strcat(alphab{hh},alphab{ii},alphab{jj});
        end
    end
end

%% Read in image filenames
files = dir(strcat(folder_in,filesep,'*',ext_in));
loc = strcat(folder_in,filesep,'*',ext_in);
if isempty(files)
    fprintf('NO IMAGE FILES FOUND UNDER: %s \n',loc)
end
if strcmp(numImages,'all'), numImages = inf; end
l = min(length(files),numImages);

%% Get Cropping Region
if strcmp(crop, 'yes')||strcmp(crop, 'y')
    
    
    folder_out = strcat(folder_in,filesep,'cropped_images',filesep);
    %Make a new output folder if none exists
    if exist(folder_out,'dir') ~= 7
        mkdir(folder_out);
    end
    
    if strcmp(max_def_idx,'center')||strcmp(max_def_idx,'c')
        im_loc = ceil(l/2);
    elseif strcmp(max_def_idx,'end')||strcmp(max_def_idx,'e')
        im_loc = l;
    elseif strcmp(max_def_idx,'beginning')||strcmp(max_def_idx,'b')
        im_loc = 1;
    else
        im_loc = max_def_idx;
    end
    
    figure
    try
        imagesc(rgb2gray(imread(strcat(folder_in,filesep,files(im_loc).name))))
    catch
        imagesc(imread(strcat(folder_in,filesep,files(im_loc).name)))
    end
    title('Click to select cropping region. Define two points: top left and bottom right')
    axis('image'); colormap gray
    [X,Y] = ginput(2);
    X = ceil(X);
    Y = ceil(Y);
    X_ss(1) = X(1); %- mod(X(1),max(sSize))+max(sSize); %place the point such that an
    %interger number of subsets is used
    %Crop agressively.
    X_ss(2) = X(2);% - mod(X(2),max(sSize));
    Y_ss(1) = Y(1);% - mod(Y(1),max(sSize))+max(sSize);
    Y_ss(2) = Y(2);% - mod(Y(2),max(sSize));
    close
    
    crop_nw_loc = [X_ss(1),Y_ss(1)];
    
    %% Crop and write out files
    
    image_idx = 1:l;
    % Loop through files
    for ii = 1:length(image_idx)
        READ = imread(strcat(folder_in,filesep,files(image_idx(ii)).name));
        try
            READ = rgb2gray(READ);
        catch
        end
        IMG = double(READ(Y_ss(1):Y_ss(2),X_ss(1):X_ss(2),1)); %Cropped size from ginput
        IMG = IMG/(max(IMG(:))); %normalize due to weird behavior of 12 bit images
        
        dir_filename = strcat(folder_out,prefixes{image_idx(ii)},'_image_number_',...
            num2str(image_idx(ii)),ext_out); %use prefix to ensure proper ordering
        imwrite(IMG,dir_filename,fmt); %Write the file with the specified settings
    end
    
elseif length(crop) == 4
    folder_out = strcat(folder_in,filesep,'cropped_images',filesep);
    %Make a new output folder if none exists
    if exist(folder_out,'dir') ~= 7
        mkdir(folder_out);
    end
    
    %crop to the user-entered size
    crop_nw_loc = [crop(1),crop(2)];
    X_ss(1) = crop(1);
    X_ss(2) = crop(3);
    Y_ss(1) = crop(2);
    Y_ss(2) = crop(4);
    
    image_idx = 1:l;
    % Loop through files
    for ii = 1:length(image_idx)
        READ = imread(strcat(folder_in,filesep,files(image_idx(ii)).name));
        try
            READ = rgb2gray(READ);
        catch
        end
        IMG = double(READ(Y_ss(1):Y_ss(2),X_ss(1):X_ss(2),1)); %Cropped size from ginput
        IMG = IMG/(max(IMG(:))); %normalize due to weird behavior of 12 bit images
        
        dir_filename = strcat(folder_out,prefixes{image_idx(ii)},'_image_number_',...
            num2str(image_idx(ii)),ext_out); %use prefix to ensure proper ordering
        imwrite(IMG,dir_filename,fmt); %Write the file with the specified settings
    end
    
else
    
    folder_out = folder_in;
    fmt = ext_in;
    crop_nw_loc = [1,1];
    
end