spm_check_installation.m

function varargout = spm_check_installation(action)
% Check SPM installation
% FORMAT spm_check_installation('basic')
% Perform a superficial check of SPM installation [default].
%
% FORMAT spm_check_installation('full')
% Perform an in-depth diagnostic of SPM installation.
%
% FORMAT rev = spm_check_installation('rev')
% Return a lower bound of SPM SVN Revision number.
% 
% FORMAT spm_check_installation('build')
% Build signature of SPM distribution as used by 'full' option.
% (for developers)
%__________________________________________________________________________
% Copyright (C) 2009-2019 Wellcome Trust Centre for Neuroimaging

% Guillaume Flandin
% $Id: spm_check_installation.m 7752 2019-12-13 12:58:59Z guillaume $

if isdeployed, return; end

%-Select action
%--------------------------------------------------------------------------
if ~nargin, action = 'basic'; end
switch lower(action)
    case 'basic'
        check_basic;
    case 'full'
        check_full;
    case 'rev'
        varargout = { get_rev };
    case 'build'
        build_signature;
    otherwise
        error('Unknown action to perform.');
end

%==========================================================================
% FUNCTION check_basic
%==========================================================================
function check_basic

%-Platform: MATLAB, GNU Octave
%--------------------------------------------------------------------------
if exist('OCTAVE_VERSION','builtin')
    platform = 'Octave';
else
    platform = 'MATLAB';
end

%-Initial check of the MATLAB path (for functions in fieldtrip/compat)
%--------------------------------------------------------------------------
if exist('ft_check_path') % this should not exist
    p = mfilename('fullpath'); p = p(1:end-22); % cannot use fileparts
    sw = warning('off','backtrace');
    warning(sprintf([...
        'You appear to have added all SPM subfolders to the function\n'...
        'search path. This is NOT recommended.\n'...
        'You only need to add SPM main directory; relevant subfolders\n'...
        'will be automatically added by SPM when needed.\n'...
        'You can clear the function search path by typing the following:\n'...
        '    spm_rmpath\n'...
        '    addpath(''%s'')\n'...
        'For more information, type the following:\n'...
        '    help pathtool'],p));
    warning(sw);
end

%-Minimal MATLAB version required
%--------------------------------------------------------------------------
minVer = '7.4';
try
    v = spm_check_version('matlab',minVer);
catch
    error('A problem occurred with spm_check_version.m.');
end
if v < 0
    error([...
        'SPM12 requires MATLAB %s onwards in order to run.\n'...
        'This MATLAB version is %s.'], minVer, version);
end

%-Check installation
%--------------------------------------------------------------------------
spm('Ver','',1);
d = spm('Dir');

%-Check the MATLAB search path
%--------------------------------------------------------------------------
p = textscan(path,'%s','delimiter',pathsep); p = p{1};
if ~ismember(lower(d),lower(p))
    error(sprintf([...
        'You do not appear to have the function search path set up\n'...
        'to include your SPM12 distribution. This means that you\n'...
        'can start SPM in this directory, but if your change to\n'...
        'another directory then %s will be unable to find the\n'...
        'SPM functions. You can use the addpath command in %s\n'...
        'to set it up:\n'...
        '    addpath(''%s'')\n'...
        'For more information, type the following:\n'...
        '    help path\n' ...
        '    help pathtool'],platform,platform,d));
end
if ismember(lower(fullfile(d,'src')),lower(p))
    warning(sprintf([...
        'You appear to have added all SPM subfolders to the function\n'...
        'search path. This is NOT recommended.\n'...
        'You only need to add SPM main directory; relevant subfolders\n'...
        'will be automatically added by SPM when needed.\n'...
        'You can clear the function search path by typing the following:\n'...
        '    spm_rmpath\n'...
        '    addpath(''%s'')\n'...
        'For more information, type the following:\n'...
        '    help pathtool'],d));
end

%-Ensure that the original release - as well as the updates - was installed
%--------------------------------------------------------------------------
if ~exist(fullfile(d,'@nifti','fieldnames.m'),'file') % File that should not have changed
    if isunix
        error(sprintf([...
            'There appears to be some problem with the installation.\n'...
            'The original spm12.zip distribution should be installed\n'...
            'and the updates installed on top of this. Unix commands\n'...
            'to do this are:\n'...
            '   unzip spm12.zip\n'...
            '   unzip -o spm12_updates_r????.zip -d spm12\n'...
            'For more information, type the following:\n'...
            '    help spm_update']));
    else
        error(sprintf([...
            'There appears to be some problem with the installation.\n'...
            'The original spm12.zip distribution should be installed\n'...
            'and the updates installed on top of this.\n'...
            'For more information, type the following:\n'...
            '    help spm_update']));
    end
end

%-Ensure that the files were unpacked correctly
%--------------------------------------------------------------------------
if ispc
    try
        t = load(fullfile(d,'MIP.mat'));
    catch
        error(sprintf([...
            'There appears to be some problem reading the MATLAB .mat\n'...
            'files from the SPM distribution. This is probably\n'...
            'something to do with the way that the distribution was\n'...
            'unpacked. If you used WinZip, then ensure that\n'...
            'TAR file smart CR/LF conversion is disabled\n'...
            '(under the Miscellaneous Configuration Options).']));
    end
    if ~exist(fullfile(d,'toolbox','dcm_meeg','spm_dcm_erp.m'),'file')
        error(sprintf([...
            'There appears to be some problem with the installation.\n'...
            'This is probably something to do with the way that the\n'...
            'distribution was unbundled from the original .zip files.\n'...
            'Please ensure that the files are unpacked so that the\n'...
            'directory structure is retained.']));
    end
end

%-Check the MEX files
%--------------------------------------------------------------------------
try
    feval(@spm_bsplinc,1,ones(1,6));
catch
    if ismac
        url = 'https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)';
    elseif isunix
        url = 'https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux';
    elseif ispc
        url = 'https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Windows';
    else
        url = 'https://www.wikibooks.org/wiki/SPM#Installation';
    end
    if strcmpi(platform,'octave')
        url = 'https://en.wikibooks.org/wiki/SPM/Octave#Compilation';
    end
    error([...
        'SPM uses a number of MEX files, which are compiled functions.\n'...
        'These need to be compiled for the various platforms on which SPM\n'...
        'is run. It seems that the compiled files for your computer platform\n'...
        'are missing or not compatible. See\n'...
        '   %s\n'...
        'for information about how to compile MEX files for %s\n'...
        'in %s %s.'],...
        url,computer,platform,version);
end

%==========================================================================
% FUNCTION check_full
%==========================================================================
function check_full

%-Say Hello
%--------------------------------------------------------------------------
fprintf('\n');
disp( ' ___  ____  __  __                                           ' );
disp( '/ __)(  _ \(  \/  )                                          ' );
disp( '\__ \ )___/ )    (   Statistical Parametric Mapping          ' );
disp(['(___/(__)  (_/\/\_)  SPM - https://www.fil.ion.ucl.ac.uk/spm/']);
fprintf('\n');

%-
%-------------------------------------------------------------------------------
if exist('OCTAVE_VERSION','builtin')
    software = 'Octave';
else
    software = 'MATLAB';
end

%-Detect SPM directory
%--------------------------------------------------------------------------
SPMdir = cellstr(which('spm.m','-ALL'));
if isempty(SPMdir)
    fprintf('SPM is not in your %s path.\n',software);
    return;
elseif numel(SPMdir) > 1
    fprintf('SPM seems to appear in several different folders:\n');
    for i=1:numel(SPMdir)
        fprintf('  * %s\n',SPMdir{i});
    end
    fprintf('Remove all but one with ''pathtool'' or ''spm_rmpath''.\n');
    return;
else
    fprintf('SPM is installed in: %s\n',fileparts(SPMdir{1}));
end
SPMdir = fileparts(SPMdir{1});

%-Detect SPM version and revision number
%--------------------------------------------------------------------------
v = struct('Name','','Version','','Release','','Date','');
try
    fid = fopen(fullfile(SPMdir,'Contents.m'),'rt');
    if fid == -1
        fprintf('Cannot open ''%s'' for reading.\n',fullfile(SPMdir,'Contents.m'));
        return;
    end
    l1 = fgetl(fid); l2 = fgetl(fid);
    fclose(fid);
    l1 = strtrim(l1(2:end)); l2 = strtrim(l2(2:end));
    t  = textscan(l2,'%s','delimiter',' '); t = t{1};
    v.Name = l1; v.Date = t{4};
    v.Version = t{2}; v.Release = t{3}(2:end-1);
catch
    fprintf('Cannot obtain SPM version & revision number.\n');
    return;
end
fprintf('SPM version is %s (%s, %s)\n', ...
    v.Release,v.Version,strrep(v.Date,'-',' '));

%-Detect SPM toolboxes
%--------------------------------------------------------------------------
officials = {'DAiSS', 'DARTEL', 'dcm_fnirs', 'dcm_meeg', 'DEM', 'FieldMap', ...
    'Longitudinal', 'mci', 'MEEGtools', 'mixture', 'mlm', 'Neural_Models', ...
    'NVC', 'OldNorm', 'OldSeg', 'Shoot', 'spectral', 'SPEM_and_DCM', ...
    'SRender', 'TSSS'};
dd = dir(fullfile(SPMdir,'toolbox'));
dd = {dd([dd.isdir]).name};
dd(strncmp('.',dd,1)) = [];
dd = setdiff(dd,officials);
fprintf('SPM toolboxes:');
for i=1:length(dd)
    fprintf(' %s',dd{i});
end
if isempty(dd), fprintf(' none'); end
fprintf('\n');

%-Detect MATLAB & toolboxes
%--------------------------------------------------------------------------
fprintf('%s is installed in: %s\n',software,matlabroot);
fprintf('%s version is %s\n',software,version);
fprintf('%s toolboxes: ',software); hastbx = false;
if license('test','signal_toolbox') && ~isempty(ver('signal'))
    vtbx = ver('signal'); hastbx = true;
    fprintf('signal (v%s) ',vtbx.Version);
end
if license('test','image_toolbox') && ~isempty(ver('images'))
    vtbx = ver('images'); hastbx = true;
    fprintf('images (v%s) ',vtbx.Version);
end
if license('test','statistics_toolbox') && ~isempty(ver('stats'))
    vtbx = ver('stats'); hastbx = true;
    fprintf('stats (v%s)',vtbx.Version);
end
if ~hastbx, fprintf('none.'); end
fprintf('\n');

%-Detect Platform and Operating System
%--------------------------------------------------------------------------
[C, maxsize] = computer;
fprintf('Platform: %s (maxsize=%d)\n', C, maxsize);
if ispc
   platform = [system_dependent('getos'),' ',system_dependent('getwinsys')];
elseif ismac
    [fail, input] = unix('sw_vers');
    if ~fail
    platform = strrep(input, 'ProductName:', '');
    platform = strrep(platform, sprintf('\t'), '');
    platform = strrep(platform, sprintf('\n'), ' ');
    platform = strrep(platform, 'ProductVersion:', ' Version: ');
    platform = strrep(platform, 'BuildVersion:', 'Build: ');
    else
        platform = system_dependent('getos');
    end
else
   try
       platform = system_dependent('getos');
   catch
       [dummy, platform] = system('uname -sr');
       platform = deblank(platform);
   end
end
fprintf('OS: %s\n', platform);

%-Detect Java
%--------------------------------------------------------------------------
fprintf('%s\n', version('-java'));
fprintf('Java support: ');
level = {'jvm', 'awt', 'swing', 'desktop'};
for i=1:numel(level)
    if isempty(javachk(level{i})), fprintf('%s ',level{i}); end
end
fprintf('\n');

%-Detect Monitor(s)
%--------------------------------------------------------------------------
M = get(0,'MonitorPositions');
fprintf('Monitor(s):');
for i=1:size(M,1)
    fprintf(' [%d %d %d %d]',M(i,:));
end
fprintf(' (%dbit)\n', get(0,'ScreenDepth'));

%-Detect OpenGL rendering
%--------------------------------------------------------------------------
if strcmpi(software,'matlab')
    S =  opengl('data');
    fprintf('OpenGL version: %s',S.Version);
    if S.Software, fprintf('(Software)\n'); else fprintf('(Hardware)\n'); end
    fprintf('OpenGL renderer: %s (%s)\n',S.Vendor,S.Renderer);
end

%-Detect MEX setup
%--------------------------------------------------------------------------
fprintf('MEX extension: %s\n',mexext);
try
    if ~exist('OCTAVE_VERSION','builtin')
        cc = mex.getCompilerConfigurations('C','Selected');
        if ~isempty(cc)
            cc = cc(1); % can be C or C++
            fprintf('C Compiler: %s (%s).\n', cc.Name, cc.Version);
            fprintf('C Compiler settings: %s (''%s'')\n', ...
                cc.Details.CompilerExecutable, cc.Details.OptimizationFlags);
        else
            fprintf('No C compiler is selected (see mex -setup)\n');
        end
    else
        mkoctfile('--version');
        fprintf('C Compiler: %s.\n', deblank(mkoctfile('--print','CC')));
        fprintf('ALL_CFLAGS: %s.\n', deblank(mkoctfile('--print','ALL_CFLAGS')));
        fprintf('ALL_LDFLAGS: %s.\n', deblank(mkoctfile('--print','ALL_LDFLAGS')));
    end
end
try
    [sts, m] = fileattrib(fullfile(SPMdir,'src'));
    m = [m.UserRead m.UserWrite m.UserExecute ...
         m.GroupRead m.GroupWrite m.GroupExecute ...
         m.OtherRead m.OtherWrite m.OtherExecute];
    r = 'rwxrwxrwx'; r(~m) = '-';
    fprintf('C Source code permissions: dir %s, ', r);
    [sts, m] = fileattrib(fullfile(SPMdir,'src','spm_resels_vol.c'));
    m = [m.UserRead m.UserWrite m.UserExecute ...
         m.GroupRead m.GroupWrite m.GroupExecute ...
         m.OtherRead m.OtherWrite m.OtherExecute];
    r = 'rwxrwxrwx'; r(~m) = '-';
    fprintf('file %s\n',r);
end

%-Get file details for local SPM installation
%--------------------------------------------------------------------------
fprintf('%s\n',repmat('-',1,70));
l = generate_listing(SPMdir);
fprintf('%s %40s\n','Parsing local installation...','...done');

%-Get file details for most recent public version
%--------------------------------------------------------------------------
fprintf('Downloading SPM information...');
url = sprintf('http://www.fil.ion.ucl.ac.uk/spm/software/%s/%s.xml',...
    lower(v.Release),lower(v.Release));
try
    p = [tempname '.xml'];
    urlwrite(url,p);
catch
    fprintf('\nCannot access URL %s\n',url);
    return;
end
fprintf('%40s\n','...done');

%-Parse it into a MATLAB structure
%--------------------------------------------------------------------------
fprintf('Parsing SPM information...');
try
    tree = xmlread(p);
catch
    fprintf('\nParsing failed\n');
    delete(p);
    return;
end
delete(p);
r    = struct([]); ind = 1;
if tree.hasChildNodes
    for i=0:tree.getChildNodes.getLength-1
        m = tree.getChildNodes.item(i);
        if strcmp(m.getNodeName,'signature')
            m = m.getChildNodes;
            for j=0:m.getLength-1
                if strcmp(m.item(j).getNodeName,'file')
                    n = m.item(j).getChildNodes;
                    for k=0:n.getLength-1
                        o = n.item(k);
                        if ~strcmp(o.getNodeName,'#text')
                            try
                                s = char(o.getChildNodes.item(0).getData);
                            catch
                                s = '';
                            end
                            switch char(o.getNodeName)
                                case 'name'
                                    r(ind).file = s;
                                case 'id'
                                    r(ind).id = str2num(s);
                                otherwise
                                    r(ind).(char(o.getNodeName)) = s;
                            end
                        end
                    end
                    ind = ind + 1;
                end
            end
        end
    end
end
fprintf('%44s\n','...done');

%-Compare local and public versions
%--------------------------------------------------------------------------
fprintf('%s\n',repmat('-',1,70));
compare_versions(l,r);
fprintf('%s\n',repmat('-',1,70));

%==========================================================================
% FUNCTION compare_versions
%==========================================================================
function compare_versions(l,r)

%-Uniformise file names
%--------------------------------------------------------------------------
a = {r.file}; a = strrep(a,'\','/'); [r.file] = a{:};
a = {l.file}; a = strrep(a,'\','/'); [l.file] = a{:};

%-Look for missing or unknown files
%--------------------------------------------------------------------------
[x,ir,il] = setxor({r.file},{l.file});
if isempty(ir) && isempty(il)
    fprintf('No missing or unknown files\n');
else
    if ~isempty(ir)
        fprintf('File(s) missing in your installation:\n');
    end
    for i=1:length(ir)
        fprintf(' * %s\n', r(ir(i)).file);
    end
    if ~isempty(ir) && ~isempty(il), fprintf('%s\n',repmat('-',1,70)); end
    if ~isempty(il)
        fprintf('File(s) not part of the current version of SPM:\n');
    end
    for i=1:length(il)
        fprintf(' * %s\n', l(il(i)).file);
    end
end

fprintf('%s\n',repmat('-',1,70));

%-Look for local changes or out-of-date files
%--------------------------------------------------------------------------
[tf, ir] = ismember({r.file},{l.file});
dispc = true;
for i=1:numel(r)
    if tf(i)
        if ~isempty(r(i).id) && (isempty(l(ir(i)).id) || (r(i).id ~= l(ir(i)).id))
            dispc = false;
            fprintf('File %s is not up to date (r%d vs r%d)\n', ...
                r(i).file, r(i).id, l(ir(i)).id);
        end
        if ~isempty(r(i).md5) && ~isempty(l(ir(i)).md5) && ~strcmp(r(i).md5,l(ir(i)).md5)
            dispc = false;
            fprintf('File %s has been edited (checksum mismatch)\n', r(i).file);
        end
    end
end
if dispc
    fprintf('No local change or out-of-date files\n');
end

%==========================================================================
% FUNCTION get_rev
%==========================================================================
function rev = get_rev

spm('Ver','',1);
d   = spm('Dir');
l   = generate_listing(d);
l(strncmp('external', {l.file}, 8)) = [];
rev = max([l.id]);

%==========================================================================
% FUNCTION build_signature
%==========================================================================
function build_signature

[v,r] = spm('Ver','',1);
d     = spm('Dir');
l     = generate_listing(d);

fprintf('Saving %s signature in %s\n',...
    v, fullfile(pwd,sprintf('%s_signature.xml',v)));
fid = fopen(fullfile(pwd,sprintf('%s_signature.xml',v)),'wt');
fprintf(fid,'<?xml version="1.0"?>\n');
fprintf(fid,'<!-- Signature for %s r%s -->\n',v,r);
fprintf(fid,'<signature>\n');
for i=1:numel(l)
    fprintf(fid,'  <file>\n');
    fprintf(fid,'    <name>%s</name>\n',l(i).file);
    fprintf(fid,'    <id>%d</id>\n',l(i).id);
    fprintf(fid,'    <date>%s</date>\n',l(i).date);
    fprintf(fid,'    <md5>%s</md5>\n',l(i).md5);
    fprintf(fid,'  </file>\n');
end
fprintf(fid,'</signature>\n');
fclose(fid);

%==========================================================================
% FUNCTION generate_listing
%==========================================================================
function l = generate_listing(d,r,l)

if nargin < 2
    r = '';
end
if nargin < 3
    l = struct([]);
end

%-List content of folder
%--------------------------------------------------------------------------
ccd = fullfile(d,r);
fprintf('%-10s: %58s','Directory',ccd(max(1,length(ccd)-57):end));
dd  = dir(ccd);
f   = {dd(~[dd.isdir]).name};
dispw = false;

for i=1:length(f)
    [p,name,ext] = fileparts(f{i});
    info = struct('file','', 'id',[], 'date','', 'md5','');
    if ismember(ext,{'.m','.man','.txt','.xml','.c','.h',''})
        [info, sts] = extract_info(fullfile(ccd,f{i}));
        if ~sts, dispw = true; end
    end
    info.file = fullfile(r,f{i});
    try
        try
            info.md5 = md5sum(fullfile(ccd,f{i}));
        catch
            %[s, info.md5] = system(['md5sum "' fullfile(ccd,f{i}) '"']);
            %info.md5 = strtok(info.md5);
        end
    end
    if isempty(l), l = info;
    else l(end+1) = info;
    end
    if isempty(r) && strcmp(ext,'.m')
        w = cellstr(which(f{i},'-ALL'));
        if numel(w) > 1 && ~strcmpi(f{i},'Contents.m')
            if ~dispw, fprintf('\n'); end
            dispw = true;
            fprintf('File %s appears %d times in your MATLAB path:\n',f{i},numel(w));
            for j=1:numel(w)
                if j==1 && ~strncmp(d,w{1},length(d))
                    fprintf('  %s (SHADOWING)\n',w{1});
                else
                    fprintf('  %s\n',w{j});
                end
            end
        end
    end
end
if ~dispw, fprintf('%s',repmat(sprintf('\b'),1,70)); end

%-Recursively extract subdirectories
%--------------------------------------------------------------------------
dd = {dd([dd.isdir]).name};
dd(strncmp('.',dd,1)) = [];
for i=1:length(dd)
    l = generate_listing(d,fullfile(r,dd{i}),l);
end

%==========================================================================
% FUNCTION extract_info
%==========================================================================
function [svnprops, sts] = extract_info(f)
%Extract Subversion properties (Id tag)

sts = true;
svnprops = struct('file',f, 'id',[], 'date','', 'md5','');

fp  = fopen(f,'rt');
str = fread(fp,'*uint8');
fclose(fp);
str = native2unicode(str(:)','iso-8859-1');

r = regexp(str,['\$Id: (?<file>\S+) (?<id>[0-9]+) (?<date>\S+) ' ...
                '(\S+Z) (?<author>\S+) \$'],'names');
                
if isempty(r) || isempty(r(1).file)
    %sts = false;
    %fprintf('\n%s has no SVN Id.\n',f);
else
    svnprops.file = r(1).file;
    svnprops.id   = str2num(r(1).id);
    svnprops.date = r(1).date;
    [p,name,ext]  = fileparts(f);
    if ~strcmp(svnprops.file,[name ext])
        sts = false;
        fprintf('\nSVN Id does not match filename for file:\n  %s\n',f);
    end
end
if numel(r) > 1
    %sts = false;
    %fprintf('\n%s has several SVN Ids.\n',f);
end