osl_check_installation.m

function osl_check_installation(do_log,test_fslview)
	% Run diagnostic tests
	% Some tests copied from spm_check_installation (this file uses \b control characters which makes it hard to log to txt)
	% TODO - should this return an OK status?

	if nargin < 2 || isempty(test_fslview) 
		test_fslview = true;
	end
	
	if nargin < 1 || isempty(do_log) 
		do_log = true;
	end
	
	osldir = fileparts(fileparts(mfilename('fullpath')));

	% Set up printing functions
	log = @(x) fprintf(1,'%s\n',x); % Format message
	log_error = @(x,ME) fprintf(1,'%s\n%s\n%s\n',x,ME.identifier,ME.message);
	section = @(x) log(sprintf('\n------------------ %s ------------------',upper(x)));

	if do_log
		logfile = fullfile(pwd,'osl_debug_log.txt');
		if exist(logfile)
			delete(logfile);
		end
		diary(logfile)
		fprintf(1,'Writing diagnostic record to %s\n',logfile);
	end

	log('OSL DEBUG LOG');
	log(sprintf('Date: %04d-%02d-%02d %02d:%02d:%02d',fix(clock())))

	section('OSL version')
	log(sprintf('osldir = %s',osldir))
	version_file = fullfile(osldir,'version.txt');
	if exist(version_file,'file')
		type(version_file)
	else
		log('Version file missing')
	end

	% Check OS
	section('System Information');
	try
		spm_system_tests()
	catch ME
		log_error('Error getting system information',ME)
	end

	% Check Matlab version
	section('Matlab Version');
	log(sprintf('Matlab version: %s',version));
	log(sprintf('Matlab location: %s',matlabroot));

	arrayfun(@(x) log(sprintf('%s - %s',x.Name,x.Version)),ver);

	if verLessThan('matlab','8.4')
		log('FAIL - Matlab versions earlier than R2014b may have graphics errors and have limited support for OSL');
	else
		log('PASS - Matlab version is supported')
	end

	if verLessThan('matlab','7.14')
		log('FAIL - Matlab versions earlier than R2012a are not officially supported by OSL');
	end

	% Check that expected directory structure is present
	section('Directory structure');
    dirs = {'osl-core','spm12','GLEAN','HMM-MAR','layouts','MEG-ROI-nets','ohba-external','example_data','parcellations','std_masks'};
    for j = 1:length(dirs)
    	d = fullfile(osldir,dirs{j});
    	if ~exist(d)
    		log(sprintf('MISSING: %s',d));
    	else
    		log(sprintf('Located: %s',d));
    	end
    end

    input_mask = fullfile(osldir,'std_masks','MNI152_T1_8mm_brain.nii.gz');

    section('NIFTI tools');
    try
    	[a,b,c] = nii.load(input_mask);
    	log('PASS - nii.load')
    catch ME
    	log(sprintf('FAIL - nii.load\n%s',ME.message));
    end

    try
    	nii.save(a,b,c,'test.nii.gz');
    	log('PASS - nii.save')
    catch ME
    	log(sprintf('FAIL - nii.save\n%s',ME.message));
    end

	% Check that FSL is installed
	section('FSL');
	fsldir = getenv('FSLDIR');
	if isempty(fsldir)
		log('FSL environment variable not set')
		log('Attempting automatic configuration')
		try
			addpath(fullfile(osldir,'osl-core','util'));
			fsl_initialise;
		catch ME
			log_error('Error initialising FSL',ME)
		end
	else
		log(sprintf('FSLDIR: %s',fsldir));
	end

	try
		[status,res] = system('fslval');
		if status == 1
			log('PASS - fslval')
		else
			log(sprintf('FAIL - fslval. Return status = %d',status));
			log(sprintf('FAIL - fslval. Result = %s',res));
		end
	catch ME
		log(sprintf('FAIL - fslval\n%s',ME.message));
	end

	try
		runcmd('fslmaths %s -thr 100 osl_fslmaths_test.nii.gz',input_mask);
		log('PASS - fslmaths')
		delete('osl_fslmaths_test.nii.gz')
	catch ME
		log(sprintf('FAIL - fslmaths\n%s',ME.message));
	end

	if test_fslview
		try
			fslview(input_mask)
			log('PASS - fslview. Check that fslview window has appeared');
		catch ME
			log(sprintf('FAIL - fslview\n%s',ME.message));
		end
	else
		log('Skipping fslview')
	end
		
	% Check SPM 
	section('SPM')

	if exist(fullfile(osldir,'spm12'))
		try
			addpath(fullfile(osldir,'spm12'))
			spm_get_defaults('cmdline',true);
			spm('Defaults','EEG');
			spm_check()
		catch ME
			log_error('Error testing SPM',ME)
		end
	else
		log('CANNOT TEST SPM12 BECAUSE DIRECTORY IS MISSING');
	end

	section('Fieldtrip')

	try
		a = ft_getopt(struct('a',1),'a');
		log('PASS - ft_getopt()');

	catch ME
		log_error('Error testing ft_getopt',ME)
	end

	section('Folder permissions')

	try
		[~,a]=fileattrib(spm('dir'));
		if a.UserWrite == 1
			log('PASS - SPMDIR is writable');
		else
			log(sprintf('FAIL - cannot write to SPMDIR %s',spm('dir')));
		end
	catch ME
		log_error('Error testing SPMDIR write attribute',ME)
	end

	try
		[~,a]=fileattrib(fullfile(osldir,'osl.conf'));
		if a.UserWrite == 1
			log('PASS - osl.conf is writable');
		else
			log('FAIL - cannot write to osl.conf');
		end
	catch ME
		log_error('Error testing osl.conf write attribute',ME)
	end

	section('MAC OS XQUARTZ');
	if ~ismac
		log('PASS - Not required on this system');
	else
		try
			if exist('/Applications/Utilities/XQuartz.app','dir')
				log('PASS - XQuartz present');
			else
				log('FAIL - Expected /Applications/Utilities/XQuartz.app to exist');
			end
		catch ME
			log_error('Error checking XQuartz',ME)
		end
	end

	if do_log
		diary off
	end

function spm_system_tests()
	% from spm_check_installation.m

	%-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    
	   platform = system_dependent('getos');
	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
	%--------------------------------------------------------------------------
	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);

	%-Detect MEX setup
	%--------------------------------------------------------------------------
	fprintf('MEX extension: %s\n',mexext);
	try
	    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
	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

function spm_check()
	% from spm_check_installation.m

	SPMdir = which('spm.m','-ALL');
	if isempty(SPMdir)
	    fprintf('SPM is not in your MATLAB path.\n');
	    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,'-',' '));