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InstallECGkit.m
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%% Installation script of ecg-kit
% Script to install this toolbox.
%
% ****************************************************************
% ** Check the pretty printed help documentation in help folder **
% ****************************************************************
%
% Example
%
% Installecg-kit()
%
% or
%
% Installecg-kit(false)
%
% to avoid checking online for updates.
%
% See also UnInstallecg-kit
%
% Author: Mariano Llamedo Soria
% <matlab:web('mailto:[email protected]','-browser') (email)>
% Version: 0.1 beta
% Birthdate: 01/09/2012
% Last update: 18/10/2014
% Copyright 2008-2015
%
function InstallECGkit(bIgnoreUpdate)
backup_string = 'ecg-kit_backup';
if( nargin < 1 || ~islogical(bIgnoreUpdate) )
bIgnoreUpdate = false;
end
fprintf(1, 'Adding paths\n' );
%path related constants.
root_path = [fileparts(mfilename('fullpath')) filesep ];
%path related constants.
default_paths = { ...
[ root_path ';' ]; ...
[ root_path 'help' filesep ';' ]; ...
[ root_path 'common' filesep ';' ]; ...
[ root_path 'common' filesep 'a2hbc' filesep ';' ]; ...
[ root_path 'common' filesep 'a2hbc' filesep 'scripts' filesep ';' ]; ...
[ root_path 'common' filesep 'export_fig' filesep ';' ]; ...
[ root_path 'common' filesep 'wavedet' filesep ';' ]; ...
[ root_path 'common' filesep 'plot2svg' filesep ';' ]; ...
[ root_path 'common' filesep 'ppg' filesep ';' ]; ...
[ root_path 'common' filesep 'prtools' filesep ';' ]; ...
[ root_path 'common' filesep 'prtools_addins' filesep ';' ]; ...
[ root_path 'common' filesep 'bin' filesep ';' ]; ...
[ root_path 'common' filesep 'kur' filesep ';' ]; ...
[ root_path 'common' filesep 'LIBRA' filesep ';' ]; ...
};
cellfun(@(a)(addpath(a)), default_paths);
% get the correct command names in this architecture.
sys_cmds = sys_command_strings();
% ECGkit_URL_str = 'http://ecg-kit.readthedocs.org/en/master/';
ECGkit_URL_str = 'https://github.com/marianux/ecg-kit/releases';
% Version info.
fid = fopen([ root_path 'LatestVersion' ]);
if fid < 0
% version check not possible - force update message
this_release_str = 'v0.1.1 beta - 05/05/2015';
else
try
this_release_str = fgetl(fid);
fclose(fid);
catch MException
fclose(fid);
throw(MException);
end
end
% URL check for updates
% Check admin privileges
bAdminPrivs = HasAdminPrivs(false);
if( ~bAdminPrivs )
disp_string_framed('*red', 'No admin/root privileges');
cprintf('SystemCommands', 'To install tab-completion feature with the ecg-kit, it is suggested to run this script with administrator/root privileges.\nRun Matlab as administrator or ' );
cprintf('*red', 'answer "YES"' );
cprintf('SystemCommands', ' when the system asks for permission. Otherwise, tab completion will not be available.\n\n' );
end
% Check if the GUI is up and working
bUseDesktop = usejava('desktop');
bMatlab = isMatlab();
bOctave = isOctave();
if( bMatlab )
matlab_ver = ver('Matlab');
if( str2double(matlab_ver.Version) < 8 )
cprintf('Red', 'Check updates manually since the Matlab version is too old to do it automatically.\n' );
bIgnoreUpdate = true;
end
elseif( bOctave )
disp_string_framed('[1,0.5,0]', 'Octave is not fully supported');
cprintf('Red', 'Although you can find problems using the toolbox in Octave, I am trying to make it fully compatible. Please report any problem that you could find.\n\n' );
% Special functions not compatible with Matlab
octave_files = { ...
'octave -ECGt.m' 'ECGtask.m' ...
};
for ii = 1:size(octave_files,1)
octave_file_src = fullfile(root_path,'common', octave_files{ii,1});
octave_file_dst = fullfile(root_path,'common', octave_files{ii,2});
status = copyfile(octave_file_src, octave_file_dst, 'f');
if( status == 0 )
disp_string_framed('*Red', 'Installation Error' );
fprintf(1, 'Failed copying "%s" -->> "%s".\n', octave_file_src, octave_file_dst );
cellfun(@(a)(rmpath(a)), default_paths);
return
end
end
end
if ~bIgnoreUpdate
fprintf(1, 'Checking for updates\n' );
if( bMatlab )
[strResponse, URLstatus] = urlread( ECGkit_URL_str,'TimeOut',5);
elseif( bOctave )
[strResponse, URLstatus] = urlread( ECGkit_URL_str);
end
if( URLstatus == 1 )
aux_pattern_pre = '/marianux/ecg-kit/tree/';
aux_idx = strfind(strResponse, aux_pattern_pre);
if( ~isempty(aux_idx) )
aux_pattern_pos = '" ';
aux_idx2 = strfind(strResponse(aux_idx(1):end), aux_pattern_pos);
if( ~isempty(aux_idx2) )
online_latest_release_str = strResponse(aux_idx(1)+(length(aux_pattern_pre):(aux_idx2(1)-2)) );
if( islater(online_latest_release_str, this_release_str) )
disp_string_framed('*Red', sprintf('ecg-kit %s version available', online_latest_release_str) );
fprintf(1, 'Consider updating %s.\n', '<a href = "matlab: web(''http://marianux.github.io/ecg-kit/'', ''-browser'' )">here</a>' );
cellfun(@(a)(rmpath(a)), default_paths);
return
end
end
end
end
end
fprintf(1, 'Compiling sources\n' );
%Check compilation of source MEX files
common_path = [ root_path 'common' filesep];
source_files = dir([ common_path '*.c'] );
lsource_files = length(source_files);
if(bOctave)
prev_folder = cd(common_path);
end
try
for ii = 1:lsource_files
[~, source_file_name] = fileparts( source_files(ii).name);
mex_file = dir([common_path source_file_name '.' mexext ]);
if( isempty(mex_file) || mex_file.datenum <= source_files(ii).datenum )
if( bMatlab )
eval(['mex -outdir ''' common_path ''' ''' [common_path source_files(ii).name] '''']);
elseif(bOctave)
eval(['mkoctfile --mex ''' [common_path source_files(ii).name] '''']);
end
end
end
catch MException
if( ismac() )
disp_string_framed(2, 'Mex files compilation failed' );
fprintf(2, '\nAs we don''t include binaries for MAC, you will have to ask for help in order tu debug this error, here is the cause:\n');
rethrow(MException);
else
if( bUseDesktop )
disp_string_framed('[1,0.5,0]', 'Mex files compilation failed' );
cprintf('[1,0.5,0]', '\nBut don''t worry, the kit includes several precompiled binaries for most architectures.\nTry the examples to check if yours is included. Down is the report error, use in case you want to ask for help in the forum:\n');
% report just in case
else
disp_string_framed(2, 'Mex files compilation failed' );
end
report = getReport(MException);
fprintf(2, '\n%s\n', report);
end
end
if(bOctave)
cd(prev_folder);
end
if( bUseDesktop || bOctave )
if( bMatlab )
% Tab completion of selected functions
% Modify the TC.xml and TC.xsd
fprintf(1, 'Installing tab-completion feature.\n' );
bTabInstallError = false;
fid = 0;
tcxml_filename = fullfile(matlabroot,'toolbox', 'local', 'TC.xml');
tcxsd_filename = fullfile(matlabroot,'toolbox', 'local', 'TC.xsd');
tmp_path = tempdir();
my_tcxml_filename = [tmp_path 'TC.xml' ];
my_tcxsd_filename = [tmp_path 'TC.xsd' ];
if( exist(tcxml_filename, 'file') && exist(tcxsd_filename, 'file'))
status = copyfile(tcxml_filename, my_tcxml_filename, 'f');
status = status & copyfile(tcxsd_filename, my_tcxsd_filename, 'f');
else
status = false;
end
if( status )
if( exist([tcxml_filename backup_string ], 'file') )
str_command = [];
else
str_command = [ sys_cmds.copy_command ' "' tcxml_filename '" "' tcxml_filename backup_string '"' sys_cmds.command_sep_str ];
end
if( ~exist([tcxsd_filename backup_string ], 'file') )
str_command = [ str_command sys_cmds.copy_command ' "' tcxsd_filename '" "' tcxsd_filename backup_string '"' sys_cmds.command_sep_str ];
end
try
last_binding = [];
bStartFound = false;
bFinishFound = false;
fid = fopen(my_tcxml_filename, 'r+');
if( fid > 0 )
while( ~feof(fid) && ~bFinishFound )
str_aux = fgetl(fid);
if( ~bStartFound && ~isempty(strfind( str_aux, '<!-- ecg-kit start -->')) )
bStartFound = true;
break
elseif( ~isempty(strfind( str_aux, '</TC>')) )
bFinishFound = true;
break
elseif( ~isempty(strfind( str_aux, '</binding>')) )
last_binding = ftell(fid);
end
end
if( ~bStartFound && bFinishFound && ~isempty(last_binding) )
fseek(fid, last_binding, 'bof');
our_fid = fopen( [ root_path 'common' filesep 'TC.xml_additions.xml' ] , 'r');
if( our_fid > 0 )
fwrite(fid, fread(our_fid, inf, '*uint8') );
fclose(our_fid);
end
end
fclose(fid);
else
bTabInstallError = true;
end
catch
if( fid > 0 )
fclose(fid);
end
bTabInstallError = true;
end
try
start_idx = [];
bStartFound = false;
fid = fopen(my_tcxsd_filename, 'r+');
if( fid > 0 )
while( ~feof(fid) )
last_binding = ftell(fid);
str_aux = fgetl(fid);
if( ~bStartFound && ~isempty(strfind( str_aux, '<!-- ecg-kit start')) )
bStartFound = true;
break
elseif( isempty(start_idx) && ~isempty(strfind( str_aux, '<xsd:pattern value="-[A-Za-z0-9]+" />')) )
fseek(fid, 0, 'bof');
str_aux_pre = rowvec(fread(fid, last_binding, '*char'));
str_aux = rowvec(fgetl(fid));
str_aux_post = rowvec(fread(fid, inf, '*char'));
fseek(fid, 0, 'bof');
fwrite(fid, [str_aux_pre sprintf('<!-- ecg-kit start\n') str_aux sprintf('\necg-kit end -->\n <xsd:pattern value="[-_A-Za-z0-9]+" />\n') str_aux_post], 'char' );
end
end
fclose(fid);
else
bTabInstallError = true;
end
catch
if( fid > 0 )
fclose(fid);
end
bTabInstallError = true;
end
if( bTabInstallError)
disp_string_framed('[1,0.5,0]', 'Could not setup tab completion');
cprintf('[1,0.5,0]', 'Some error happened during the tab completion installation, but don''t worry, this will not diminish the ecg-kit functionality.\nDo it manually or ask for help in the forum.\n' );
else
% apply changes
str_command = [ str_command ...
sys_cmds.copy_command ' "' my_tcxml_filename '" "' tcxml_filename '"' sys_cmds.command_sep_str ...
sys_cmds.copy_command ' "' my_tcxsd_filename '" "' tcxsd_filename '"'...
];
[status, ~] = system( str_command, '-runAsAdmin' );
if( status == 0 )
cprintf('*blue', 'Remember to restart Matlab for function''s "tab completion" changes to take effect.\n' );
else
disp_string_framed('[1,0.5,0]', 'Could not setup tab completion');
cprintf('[1,0.5,0]', 'Some error happened during the tab completion installation, but don''t worry, this will not diminish the ecg-kit functionality.\nDo it manually or ask for help in the forum.\n' );
end
end
end
end
bOk = savepath();
if( bOk == 0 )
fprintf(1, 'done !\n' );
disp_string_framed('*Blue', sprintf('ecg-kit for Matlab %s', this_release_str) );
str_aux = [ 'examples' filesep 'examples.m'];
if( bMatlab )
fprintf(1, '%s was correctly installed.\n\nYou can start reading the %s, or if you prefer, trying these %s.\nGo to the %s if you need help.\n', ...
'<a href = "matlab: web(''http://marianux.github.io/ecg-kit/'', ''-browser'' )">ecg-kit</a>', ...
'<a href = "matlab: web(''http://ecg-kit.readthedocs.org/en/master/'', ''-browser'' )">documentation</a>', ...
[ '<a href = "matlab: opentoline(' str_aux ',1)">examples</a>' ], ...
'<a href = "matlab: web(''https://groups.google.com/forum/#!forum/ecg-kit-users'', ''-browser'' )">forum</a>');
elseif( bOctave )
fprintf(1, [ 'ecg-kit was correctly installed.\n\nYou can start reading the documentation, or if you prefer, trying these examples.\nGo to the forum if you need help.\n\n' ...
'web-page: http://marianux.github.io/ecg-kit/\n', ...
'documentation: http://ecg-kit.readthedocs.org/en/master/\n', ...
'examples: .\' filesep 'examples\' filesep 'examples.m\n', ...
'forum: https://groups.google.com/forum/#!forum/ecg-kit-users\n' ]);
end
else
if( ispc() )
home_path = [getenv('HOMEDRIVE') getenv('HOMEPATH') ];
elseif( isunix() )
home_path = getenv('HOME');
elseif( ismac() )
home_path = getenv('HOME');
end
if( home_path(end) ~= filesep )
home_path = [home_path filesep];
end
bOk = savepath([home_path 'pathdef.m'] );
if( bOk ~= 0 )
disp_string_framed(2, 'Path Not Saved');
fprintf(2, 'Save path manually to install the ecg-kit permanently for future sessions.\n');
end
end
end
end