setup_image_registration_repository.m

function setup_image_registration_repository()
% SETUP_IMAGE_REGISTRATION_REPOSITORY Call this function to setup and compile necessary files
%
% setup_image_registration_repository
%
% INPUT ARGUEMNTS
% N/A
%
% OPTIONAL INPUT ARGUEMNTS
% N/A
%
% OUTPUT ARGUEMNTS
% N/A


% Copyright (c) 2014 Daniel Forsberg
% danne.forsberg@outlook.com
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program.  If not, see <http://www.gnu.org/licenses/>.

% Get folder of current file and go to folder
folder = fileparts(mfilename('fullpath'));
currentFolder = pwd;
cd(folder)

addpath(genpath(folder))

%% Download external dependencies if needed

% Load external dependencies and check which are missing
load externalDependenciesImageRegistration
missingExternalDependencies = [];
for k = 1 : length(fileNames)
    if ~exist(fileNames{k},'file')
        missingExternalDependencies(end + 1) = k;
    end
end

% Ask missing files should be downloaded
if ~isempty(missingExternalDependencies)
    disp('The following files, which are necessary for the image registration repository are missing:')
    for k = 1 : length(missingExternalDependencies)
        disp(fileNames{k})
    end
    answer = input('Would you like to download them? [y]/[n] ','s');
    
    % If yes, download missing files
    if strcmp(lower(answer),'y') || strcmp(lower(answer),'yes')
        if ~exist([folder,filesep,'external-dependencies'],'dir')
            mkdir('external-dependencies')
        end
        cd('external-dependencies')
        for k = 1 : length(missingExternalDependencies)
            disp(['Downloading: ',fileNames{missingExternalDependencies(k)}])
            urlwrite(urls{missingExternalDependencies(k)},...
                fileNames{missingExternalDependencies(k)});
        end
        addpath(pwd)
    end
end

%% Add external dependencies path
if exist([folder,filesep,'external-dependencies'],'dir')
    addpath([folder,filesep,'external-dependencies'])
end

% Go back to original folder
cd(currentFolder)

%% Compile mex files
[folder,~,~] = fileparts(mfilename('fullpath'));

compile_mex_files([folder,filesep,'external',filesep,'misc']);

compile_mex_files([folder,filesep,'external',filesep,'spatial_domain_toolbox'],...
    'filesToExclude',{'antigradient.c'});

compile_mex_files([folder,filesep,'registration',filesep,'polynomial-expansion'],...
    'fileExtension','cpp');

%% Create various filters

% Quadrature filters for linear phase-difference registration
if ~exist('quadratureFiltersLinearRegistration2D.mat')
    disp('Missing quadrature filters needed for phase-based linear registration in 2D.')
    disp('Attempting to create them.')
    create_quadrature_filters_for_phase_difference_registration2d();
end
if ~exist('quadratureFiltersLinearRegistration3D.mat')
    disp('Missing quadrature filters needed for phase-based linear registration in 3D.')
    disp('Attempting to create them.')
    create_quadrature_filters_for_phase_difference_registration3d();
end

% quadrature filter for morphon registration
if ~exist('quadratureFiltersForMorphonRegistration2D.mat')
    disp('Missing quadrature filters needed for phase-based non-linear registration in 2D.')
    disp('Attempting to create them.')
    create_quadrature_filters_for_morphon_registration2d();
end
if ~exist('quadratureFiltersForMorphonRegistration3D.mat')
    disp('Missing quadrature filters needed for phase-based non-linear registration in 3D.')
    disp('Attempting to create them.')
    create_quadrature_filters_for_morphon_registration3d();
end