gps_init.m

function gps_init()
% Initializes GPS directories on a new computer
%
% Author: Alexander Conrad Nied (anied@cs.washington.edu)
%
% Changelog:
% 2013-11-22 Created
% 2013-11-24 Finished
% 2014-01-02 GPS1.9 Adds the image directory
% 2014-01-06 Removed PLV from stages and added a new stage names field
%
% GPS is a GUI-based program composed by David Gow and members of his lab
% at the Massachusetts General Hospital to automate MNE and FSL analyses
% of MR-constrained MEG/EEG data and to perform Kalman filter based Granger
% analyses of those data.
%
% Copyright (C) 2014  Alexander Conrad Nied and David Gow
% 
% 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/>.

% Confirm
files = dir();
if(sum(strcmp({files.name},'parameters')))
    answer = questdlg('This will reset GPS, are you sure?');
    if(~strcmp(answer, 'Yes'))
        return
    end
end

% Get some information
user = getenv('USER');
gpsdir = pwd;
date = datestr(now, 'YYYY-mm-DD');

% Ask the user about folders
folders = {pwd, [pwd '/parameters'], [pwd '/images'], [pwd '/logs']};
folders = inputdlg({'Main GPS folder', 'Parameters Folder', 'Images Folder', 'Logs Folder'}, 'Select where you would like to store GPS data', [1 50], folders);

% Citation tag
citation = sprintf('%%\n%% Author: Alexander Conrad Nied (anied@cs.washington.edu)\n%%\n%% Changelog:\n%% %s Automatically generated by gps_init to format GPS by user %s\n', date, user);

% Change the directory pointing program
fid = fopen([folders{1} '/functions/gps/gps_dir.m'], 'w');
fprintf(fid, 'function direc = %s\n', folders{1});
fprintf(fid, '%% Returns just the main GPS directory\n');
fprintf(fid, '%s\n', citation);
fprintf(fid, '\ndirec = ''%s/'';', folders{1});
fprintf(fid, '\n\nend\n');
fclose(fid);

% Preset Program
fid = fopen([gpsdir '/gps_presets.m'], 'w');
fprintf(fid, 'function preset = gps_presets(name)\n');
fprintf(fid, '%% Returns preset variables.\n');
fprintf(fid, '%s\n', citation);
fprintf(fid, 'switch lower(name)\n');
fprintf(fid, '    case {''gpsnum'', ''gpsfig'', ''menu figure''}\n');
fprintf(fid, '        preset = 6750000;\n');
fprintf(fid, '    case {''gpsanum'', ''gpsafig'', ''analysis figure''}\n');
fprintf(fid, '        preset = 6754000;\n');
fprintf(fid, '    case {''gpsenum'', ''gpsefig'', ''edit figure''}\n');
fprintf(fid, '        preset = 6753000;\n');
fprintf(fid, '    case {''gpsrnum'', ''gpsrfig'', ''region figure''}\n');
fprintf(fid, '        preset = 6752000;\n');
fprintf(fid, '    case {''gpspnum'', ''gpspfig'', ''plotting figure''}\n');
fprintf(fid, '        preset = 6757000;\n');
fprintf(fid, '    case {''dir'', ''directory''}\n');
fprintf(fid, '        preset = ''%s'';\n', folders{1});
fprintf(fid, '    case {''functions'', ''functiondir'', ''fdir''}\n');
fprintf(fid, '        preset = ''%s/functions'';\n', folders{1});
fprintf(fid, '    case {''parameters'', ''parameterdir'', ''pdir''}\n');
fprintf(fid, '        preset = ''%s'';\n', folders{2});
fprintf(fid, '    case {''images'', ''imagedir'', ''idir''}\n');
fprintf(fid, '        preset = ''%s'';\n', folders{3});
fprintf(fid, '    case {''logs'', ''logdir'', ''ldir''}\n');
fprintf(fid, '        preset = ''%s'';\n', folders{4});
fprintf(fid, '    case {''study''}\n');
fprintf(fid, '        preset = ''SampleStudy'';\n');
fprintf(fid, '    case {''stages''}\n');
fprintf(fid, '        preset = {''util'', ''mri'', ''meg'', ''mne'', ''granger''};\n');
fprintf(fid, '        %%preset = {''util'', ''mri'', ''meg'', ''mne'', ''plv'', ''granger''};\n');
fprintf(fid, '    case {''stage names''}\n');
fprintf(fid, '        preset = {''Utilities'', ''MRI'', ''MEG'', ''MNE'', ''Granger''};\n');
fprintf(fid, '        %%preset = {''Utilities'', ''MRI'', ''MEG'', ''MNE'', ''PLV'', ''Granger''};\n');
fprintf(fid, 'end %% switch\n');
fprintf(fid, '\nend %% function\n');
fclose(fid);

% Erase the parameters directory with everything but the sample study

answer = questdlg('Clear Parameters Folder?');
if(strcmp(answer, 'Yes'))
    parameters = dir(folders{2});
    for i = 1:length(parameters)
        folderName = parameters(i).name;
        switch folderName
            case {'.', '..'}
            case 'SampleStudy'
                % Do nothing
            case 'GPS'
                % reset userstudies.mat
                save([folders{2} '/GPS/userstudies.mat'], '');
            otherwise
                rmdir([folders{2} '/' folderName], 's')
        end % switch on the folder name
    end % for all parameter folders
end

% Clear images and logs folder
files = dir(folders{3});
for i_file = 1:length(files)
    filename = files(i_file).name;
    if(filename(1) ~= '.')
        if(files(i_file).isdir)
            rmdir([folders{3} '/' filename], 's');
        else
            delete([folders{3} '/' filename]);
        end
    end
end
if(~exist(folders{3}, 'dir'))
    mkdir(folders{3});
end

% Clear the logs folder
if(~exist(folders{4}, 'dir'))
    mkdir(folders{4});
end
delete([folders{4} '/*']);


end % function