seperate each package and add them if unzip and add them if needed

Author: amibahreini

.gitignore

@@ -1,12 +1,6 @@
 ./~/
-matlab_scripts/eeglab*
-matlab_scripts/inexact*
-matlab_scripts/VisLab-EEG-Clean-Tools*
-matlab_scripts/EEG-Clean-Tools-master*
-matlab_scripts/__MACOSX/
-matlab_scripts/asr*
-matlab_scripts/artifact_subspace_reconstruction*
-matlab_scripts/MARA-master/
+matlab_scripts/*
+!matlab_scripts/*.zip
 state.mat
 *_state.mat
 *.m~

RunAutomagic.m

@@ -1,17 +1,3 @@
-%% This script starts automagic and unzips required libraries
-
-% unzip EEGLAB once
-eeglabdir = dir('./matlab_scripts/eeglab13_6_5b/');
-if isempty(eeglabdir)
-    unzip('./matlab_scripts/eeglab13_6_5b.zip','./matlab_scripts/');
-end
-
-% Unzip inexact ALM once
-eeglabdir = dir('./matlab_scripts/inexact_alm_rpca/');
-if isempty(eeglabdir)
-    unzip('./matlab_scripts/inexact_alm_rpca.zip','./matlab_scripts/');
-end
-
-addpath(genpath('.'))
-mainGUI
+%% This script starts Automagic
+run gui/mainGUI
 

gui/mainGUI.m

@@ -89,12 +89,12 @@ function mainGUI_OpeningFcn(hObject, eventdata, handles, varargin)
 % Add project paths
 % Checks 'project.m' as an example of a file in /src. Could be any other file
 % in /src
-if( ~exist('Subject.m', 'file')) 
+addpath(genpath(('./')));
+if( ~exist('Subject.m', 'file'))
     addpath('../src/');
     addpath('../preprocessing/');
 end
 
-
 % Set Constant Values
 handles.CGV = ConstantGlobalValues;
 

matlab_scripts/MARA-master.zip

@@ -22,19 +22,22 @@
                             'NOTCH_OTHER',   [], ...
                             'RUN_MESSAGE', 'Perform Filtering...')
 
+        EEGLabCsts = struct('ZIP', 'eeglab14_1_2b.zip')
+                     
         CRDCsts = struct('URL', 'http://sccn.ucsd.edu/eeglab/plugins/clean_rawdata0.32.zip', ...
-                         'ZIP', 'clean_rawdata.zip', ...
+                         'ZIP', 'clean_rawdata0.32.zip', ...
                          'RUN_MESSAGE', 'Finding bad channels...');
 
         PrepCsts = struct('URL', 'https://github.com/VisLab/EEG-Clean-Tools/archive/master.zip', ...
-                          'ZIP', 'EEG-Clean-Tools.zip')
+                          'ZIP', 'VisLab-EEG-Clean-Tools.zip')
 
         RPCACsts = struct(...
             'URL', 'http://perception.csl.illinois.edu/matrix-rank/Files/inexact_alm_rpca.zip', ...
             'ZIP', 'inexact_alm_rpca.zip', ...
             'RUN_MESSAGE', 'Performing Robust PCA  (this may take a while...)');
 
         MARACsts = struct(...
+            'ZIP', 'MARA-master.zip', ...
             'REQ_CHAN_LABELS', {{'C3','C4','Cz','F3','F4','F7','F8',...
             'Fp1','Fp2','Fz','LM','NAS','O1','O2','Oz','P3','P4','P7'...
             ,'P8','Pz','RM','T7','T8'}}, ...
@@ -54,4 +57,25 @@
         Settings = struct('pathToSteps', '/allSteps');
 
     end
+    
+    methods(Static)
+        function path = LIBRARY_PATH()
+            if ispc
+                slash = '\';
+                home = [getenv('HOMEDRIVE') getenv('HOMEPATH')];
+            else
+                slash = '/';
+                home = getenv('HOME');
+            end
+            
+            name = 'matlab_scripts';
+            if exist(name, 'dir')
+                path = ['matlab_scripts' slash];
+            elseif exist('preprocessing', 'dir')
+                path = ['..' slash 'matlab_scripts' slash];
+            else
+                path = [home slash 'matlab_scripts' slash];
+            end
+        end
+    end
 end

matlab_scripts/VisLab-EEG-Clean-Tools.zip

@@ -0,0 +1,34 @@
+function addCRD()
+% addCRD  Unzip and add the CRD package
+%
+% Copyright (C) 2017  Amirreza Bahreini, [email protected]
+% 
+% 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/>
+CSTS = PreprocessingConstants;
+ZIPName = CSTS.CRDCsts.ZIP;
+libraryPath = CSTS.LIBRARY_PATH;
+
+parts = strsplit(ZIPName, '.zip');
+folderName = parts{1};
+
+folderName = [libraryPath folderName];
+ZIPName = [libraryPath ZIPName];
+
+if ~ exist(folderName, 'dir')
+    unzip(ZIPName, folderName);
+end
+addpath(genpath(folderName));
+fprintf('clean_rawdata() package successfully unzipped. Continuing preprocessing....\n');
+    
+end

matlab_scripts/clean_rawdata0.32.zip

@@ -22,20 +22,25 @@
 % 
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
+CSTS = PreprocessingConstants;
+ZIPName = CSTS.EEGLabCsts.ZIP;
+libraryPath = CSTS.LIBRARY_PATH;
 
+parts = strsplit(ZIPName, '.zip');
+folderName = parts{1};
 
-% System dependence:
-if(ispc)
-    slash = '\';
-else
-    slash = '/';
+folderName = [libraryPath folderName];
+ZIPName = [libraryPath ZIPName];
+
+if ~ exist(folderName, 'dir')
+    unzip(ZIPName, libraryPath);
 end
+eeglab_paths = genpath(folderName);
 
-matlab_paths = genpath(['..' slash 'matlab_scripts' slash]);
 if(ispc)
-    parts = strsplit(matlab_paths, ';');
+    parts = strsplit(eeglab_paths, ';');
 else
-    parts = strsplit(matlab_paths, ':');
+    parts = strsplit(eeglab_paths, ':');
 end
 
 % Exclude paths which create conflicts
@@ -46,10 +51,10 @@
 Index = not(~contains(parts, 'dpss'));
 parts(Index) = [];
 if(ispc)
-    matlab_paths = strjoin(parts, ';');
+    eeglab_paths = strjoin(parts, ';');
 else
-    matlab_paths = strjoin(parts, ':');
+    eeglab_paths = strjoin(parts, ':');
 end
-addpath(matlab_paths);
+addpath(eeglab_paths);
 
 end

matlab_scripts/eeglab13_6_5b.zip

@@ -0,0 +1,34 @@
+function addMARA()
+% addMARA  Unzip and add the MARA package
+%
+% Copyright (C) 2017  Amirreza Bahreini, [email protected]
+% 
+% 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/>
+CSTS = PreprocessingConstants;
+ZIPName = CSTS.MARACsts.ZIP;
+libraryPath = CSTS.LIBRARY_PATH;
+
+parts = strsplit(ZIPName, '.zip');
+folderName = parts{1};
+
+folderName = [libraryPath folderName];
+ZIPName = [libraryPath ZIPName];
+
+if ~ exist(folderName, 'dir')
+    unzip(ZIPName, libraryPath);
+end
+addpath(genpath(folderName));
+fprintf('MARA package successfully unzipped. Continuing preprocessing....\n');
+    
+end

matlab_scripts/eeglab14_1_2b.zip

@@ -0,0 +1,34 @@
+function addPREP()
+% addPREP  Unzip and add the PREP package
+%
+% Copyright (C) 2017  Amirreza Bahreini, [email protected]
+% 
+% 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/>
+CSTS = PreprocessingConstants;
+ZIPName = CSTS.PrepCsts.ZIP;
+libraryPath = CSTS.LIBRARY_PATH;
+
+parts = strsplit(ZIPName, '.zip');
+folderName = parts{1};
+
+folderName = [libraryPath folderName];
+ZIPName = [libraryPath ZIPName];
+
+if ~ exist(folderName, 'dir')
+    unzip(ZIPName, libraryPath);
+end
+addpath(genpath(folderName));
+fprintf('PREP package successfully unzipped. Continuing preprocessing....\n');
+    
+end

preprocessing/PreprocessingConstants.m

@@ -1,14 +1,14 @@
-function parts = downloadAndAddPaths(varargin)
-% downloadAndAddPaths  Add path and download required packages
-%   If a required package is not in the path, it adds or downloads them to
-%   the path.
+function parts = addPaths(varargin)
+% addPaths  Unzip and add required paths
+%   If a required package is not in the path, it adds them to the path.
 %   A very naive approach is taken to see if the library is in path or not: 
 %   simply check if one of their files exists or not.
 %   
-%   parts = downloadAndAddPaths(varargin)
+%   parts = addPaths(varargin)
 %   Where varargin is an optional parameter. When given, it should be a
-%   struct with optional fields PrepParams and CRDParams corresponding to
-%   PREP parameters and cleanrawdatA() parameters.
+%   struct with optional fields PrepParams, CRDParams, RPCAParams and 
+%   MARAParams corresponding to PREP parameters, cleanrawdata() parameters, 
+%   RPCA parameters and MARA parameters.
 %   
 %   If varargin is ommited, default values are used. If any fields of
 %   varargin is ommited, corresponsing default value is used. Please see
@@ -30,14 +30,21 @@
 % 
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
+CSTS = PreprocessingConstants;
 defaults = DefaultParameters;
 p = inputParser;
 addParameter(p,'PrepParams', defaults.PrepParams, @isstruct);
 addParameter(p,'CRDParams', defaults.CRDParams, @isstruct);
+addParameter(p,'RPCAParams', defaults.RPCAParams, @isstruct);
+addParameter(p,'MARAParams', defaults.MARAParams, @isstruct);
 parse(p, varargin{:});
 PrepParams = p.Results.PrepParams;
 CRDParams = p.Results.CRDParams;
+RPCAParams = p.Results.RPCAParams;
+MARAParams = p.Results.MARAParams;
+libraryPath = CSTS.LIBRARY_PATH;
+
+addpath(libraryPath);
 
 parts = [];
 if(~exist('pop_fileio', 'file'))
@@ -46,12 +53,22 @@
 
 % Check and download if PREP does not exist
 if( ~isempty(PrepParams) && ~ exist('performReference.m', 'file'))
-    downloadPREP();
+    addPREP();
 end
 
 % Check and download if cleanrawdata() does not exist
 if( ~isempty(CRDParams) && ~ exist('clean_artifacts.m', 'file'))
-    downloadCRD();
+    addCRD();
+end
+
+% Check and download if cleanrawdata() does not exist
+if( ~isempty(RPCAParams) && ~ exist('inexact_alm_rpca.m', 'file'))
+    addRPCA();
+end
+
+% Check and download if cleanrawdata() does not exist
+if( ~isempty(MARAParams) && ~ exist('MARA.m', 'file'))
+    addMARA();
 end
 
 end

preprocessing/addCRD.m

@@ -0,0 +1,34 @@
+function addRPCA()
+% addRPCA  Unzip and add the RPCA package
+%
+% Copyright (C) 2017  Amirreza Bahreini, [email protected]
+% 
+% 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/>
+CSTS = PreprocessingConstants;
+ZIPName = CSTS.RPCACsts.ZIP;
+libraryPath = CSTS.LIBRARY_PATH;
+
+parts = strsplit(ZIPName, '.zip');
+folderName = parts{1};
+
+folderName = [libraryPath folderName];
+ZIPName = [libraryPath ZIPName];
+
+if ~ exist(folderName, 'dir')
+    unzip(ZIPName, libraryPath);
+end
+addpath(genpath(folderName));
+fprintf('RPCA package successfully unzipped. Continuing preprocessing....\n');
+    
+end