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iCAPs/packages/spm12/spm_check_installation.m
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spm_check_installation.m
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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) 2009-2017 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: spm_check_installation.m 7005 2017-02-03 17:32:23Z 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
%-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 '...
'will be\nautomatically 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
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. See\n'...
' http://en.wikibooks.org/wiki/SPM#Installation\n'...
' %s\n'...
'for information about how to compile MEX files for %s\n'...
'in %s %s.'],...
fullfile(d,'src','Makefile'),computer,platform,version);
end
%==========================================================================
% FUNCTION check_full
%==========================================================================
function check_full
%-Say Hello
%--------------------------------------------------------------------------
fprintf('\n');
disp( ' ___ ____ __ __ ' );
disp( '/ __)( _ \( \/ ) ' );
disp( '\__ \ )___/ ) ( Statistical Parametric Mapping ' );
disp(['(___/(__) (_/\/\_) SPM - http://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 = {'DARTEL', 'dcm_fnirs', 'dcm_meeg', 'DEM', 'FieldMap', ...
'Longitudinal', 'mci', 'MEEGtools', 'mixture', 'mlm', 'Neural_Models', ...
'OldNorm', 'OldSeg', 'Shoot', 'spectral', 'SPEM_and_DCM', 'SRender'};
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
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
%-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...');
tree = xmlread(p);
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,Inf,'*uchar');
fclose(fp);
str = char(str(:)');
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
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