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main.cpp
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main.cpp
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// --------------------------------------------------------------------
//
// This file is part of Luna.
//
// LUNA 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.
//
// Luna 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 Luna. If not, see <http://www.gnu.org/licenses/>.
//
// Please see LICENSE.txt for more details.
//
// --------------------------------------------------------------------
#include "luna.h"
#include "main.h"
#include "miscmath/crandom.h"
#include <fstream>
#include "utils/cgi-utils.h"
extern globals global;
extern writer_t writer;
extern logger_t logger;
extern freezer_t freezer;
void log_commands( int argc , char ** argv );
int main(int argc , char ** argv )
{
//
// initial check for display of all commands
//
log_commands( argc , argv );
//
// display version info?
//
bool show_version = argc >= 2
&& ( strcmp( argv[1] ,"-v" ) == 0 || strcmp( argv[1] ,"--version" ) == 0 );
//
// initiate global defintions
//
std::set_new_handler(NoMem);
global.init_defs();
if ( show_version )
{
global.api();
std::cerr << luna_base_version() ;
std::cerr << "Eigen library v" << EIGEN_WORLD_VERSION << "." << EIGEN_MAJOR_VERSION << "." << EIGEN_MINOR_VERSION << "\n";
std::cerr << "sqlite v" << sqlite3_libversion() << "\n";
std::exit( globals::retcode );
}
//
// usage
//
std::string usage_msg = luna_base_version() +
"url: http://zzz.bwh.harvard.edu/luna/\n"
"primary usage: luna [sample-list|EDF] [n1] [n2] [id=ID] [@param-file] \n"
" [sig=s1,s2] [var1=val1] [-o out.db] [-s COMMANDS] [< command-file]\n";
//
// Some initial options (called prior to the main banner, etc)
//
if ( argc >= 2 && strcmp( argv[1] ,"-d" ) == 0 )
{
std::string p = argc >= 3 ? argv[2] : "";
std::string p2 = argc >= 4 ? argv[3] : "";
global.api();
proc_dummy( p , p2 );
std::exit( globals::retcode );
}
//
// help mode
//
else if ( argc >= 2 && strcmp( argv[1] , "-h" ) == 0 )
{
global.api();
if ( argc == 2 ) // -h
{
std::cerr << "\n" << usage_msg << "\n\n";
std::cerr << "List of domains\n"
<< "---------------\n\n";
std::cerr << globals::cmddefs().help_domains()
<< "\n";
std::cerr << "for commands within a domain, add the domain label after -h, e.g.\n"
<< "\n luna -h annot\n\n";
std::cerr << "for options and output for a given command, add the (upper-case) command after -h, e.g.\n"
<< "\n luna -h SIGSTATS\n\n";
}
else // --h all
{
std::string p = argv[2] ;
// 'all' list all commands for all domains
if ( p == "all" )
{
std::cerr << globals::cmddefs().help_commands() << "\n";
}
// -h {domain} list all commands (non-verbose)
else if ( globals::cmddefs().is_domain(p) )
{
std::cerr << "\n" << globals::cmddefs().help_commands( p ) << "\n";
}
// -h {cmd} list all options/tables (verbose)
else if ( globals::cmddefs().is_cmd(p) )
{
std::cerr << globals::cmddefs().help( p , true , true ) << "\n";
}
// otherwise, complain
else
std::cerr << "option [" << p << "] not recognized as a domain or command\n";
}
std::exit(0);
}
//
// EVAL from the command line
//
else if ( argc == 2 && strcmp( argv[1] , "--eval" ) == 0 )
{
global.api();
proc_eval_tester( false );
exit(0);
}
//
// Verbose EVAL
//
else if ( argc == 2 && strcmp( argv[1] , "--eval-verbose" ) == 0 )
{
// as above, but w/ verbose output
global.api();
proc_eval_tester( true );
exit(0);
}
//
// PDC helper
//
else if ( argc == 2 && strcmp( argv[1] , "--pdc" ) == 0 )
{
param_t param;
build_param_from_stdin( ¶m );
//build_param_from_args( ¶m , argc , argv );
writer.nodb();
writer.begin();
writer.id( "." , "." );
pdc_t pdc;
pdc.external( param );
writer.commit();
std::exit(0);
}
//
// DUMP an XML file
//
else if ( argc == 3 && ( strcmp( argv[1] , "--xml" ) == 0 || strcmp( argv[1] , "--xml2" ) == 0 ) )
{
bool raw_format = strcmp( argv[1] , "--xml2" ) == 0 ;
global.api();
annot_t::dumpxml( argv[2] , raw_format );
std::exit(0);
}
//
// build a project list
//
if ( argc >=2 && strcmp( argv[1] , "--build" ) == 0 )
{
global.api();
std::vector<std::string> tok;
for (int i=2;i<argc;i++) tok.push_back( argv[i] );
Helper::build_sample_list( tok );
std::exit(0);
}
//
// change paths
//
if ( argc >=2 && strcmp( argv[1] , "--repath" ) == 0 )
{
global.api();
std::vector<std::string> tok;
for (int i=2;i<argc;i++) tok.push_back( argv[i] );
Helper::repath_SL( tok );
std::exit(0);
}
//
// merge EDFs (rbind)
//
if ( argc >=2 && strcmp( argv[1] , "--merge" ) == 0 )
{
//global.api();
std::vector<std::string> tok;
for (int i=2;i<argc;i++) tok.push_back( argv[i] );
Helper::merge_EDFs( tok );
std::exit(0);
}
//
// bind EDFs (cbind)
//
if ( argc >=2 && strcmp( argv[1] , "--bind" ) == 0 )
{
//global.api();
std::vector<std::string> tok;
for (int i=2;i<argc;i++) tok.push_back( argv[i] );
Helper::bind_EDFs( tok );
std::exit(0);
}
//
// map channels/ annots
//
if ( argc >=2 && strcmp( argv[1] , "--mapper" ) == 0 )
{
global.api();
// expecting form: cmap=xxx amap=xxx c=xxx a=yyy
std::vector<std::string> tok;
for (int i=2;i<argc;i++) tok.push_back( argv[i] );
Helper::channel_annot_mapper( tok , false ) ;
std::exit(0);
}
//
// map channels/ annots, HTML style output
//
if ( argc >=2 && strcmp( argv[1] , "--mapper-html" ) == 0 )
{
global.api();
// expecting form: cmap=xxx amap=xxx c=xxx a=yyy
std::vector<std::string> tok;
for (int i=2;i<argc;i++) tok.push_back( argv[i] );
Helper::channel_annot_mapper( tok , true ) ;
std::exit(0);
}
//
// special command-line driven functions that do not involve
// iterating through a sample list
//
bool cmdline_proc_fir_design = false;
bool cmdline_proc_cwt_design = false;
bool cmdline_proc_pdlib = false;
bool cmdline_proc_psc = false;
bool cmdline_proc_nmf = false;
bool cmdline_proc_ms_kmer = false;
bool cmdline_proc_ms_cmp_maps = false;
bool cmdline_proc_ms_corr_maps = false;
bool cmdline_proc_ms_label_maps = false;
bool cmdline_proc_copy_suds = false;
bool cmdline_proc_combine_suds = false;
bool cmdline_proc_cperm_test = false;
bool cmdline_proc_lgbm = false;
bool cmdline_proc_assoc = false;
bool cmdline_proc_massoc = false;
bool cmdline_proc_pops = false;
bool cmdline_proc_pops_espriors = false;
bool cmdline_proc_eval_stages = false;
bool cmdline_proc_otsu = false;
bool cmdline_proc_fft = false;
bool cmdline_proc_overlap = false;
bool cmdline_proc_gpa_prep = false;
bool cmdline_proc_gpa_run = false;
bool cmdline_proc_validate = false;
//
// use standard input versus command line for
// command-line options (e.g. --massoc, --psc, etc)
//
// e.g. default : get options from stdin: (param_from_command_line == 0)
//
// echo "load=file.dat rows" | luna --massoc -o out.db @param.txt vars=phe.txt
//
// else, if --options appears as a command line option, then take everything after that as options for --command
// i.e. to build the param_t object
//
// luna --massoc -o out.db @param.txt --options vars=phe.txt load=file.data rows
//
int param_from_command_line = 0 ;
for (int i=0; i<argc; i++)
{
if ( strcmp( argv[i] , "--options" ) == 0 ||
strcmp( argv[i] , "--opt" ) == 0 )
{
param_from_command_line = i+1;
break;
}
}
//
// parse command line
//
if ( argc == 2 && strcmp( argv[1] , "--pdlib" ) == 0 )
{
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.nodb();
writer.begin();
writer.id( "." , "." );
pdc_t::construct_pdlib( param );
writer.commit();
std::exit(0);
}
else if ( argc >= 2 )
{
// pick off any special functions here:
// i.e. the first element will not be interpreted
// as a file list, as we will run a cmdline proc and
// then quit
if ( argc >= 2 )
{
if ( strcmp( argv[1] , "--fir-design" ) == 0 ||
strcmp( argv[1] , "--fir" ) == 0 )
cmdline_proc_fir_design = true;
else if ( strcmp( argv[1] , "--cwt-design" ) == 0 ||
strcmp( argv[1] , "--cwt" ) == 0 )
cmdline_proc_cwt_design = true;
else if ( strcmp( argv[1] , "--psc" ) == 0 )
cmdline_proc_psc = true;
else if ( strcmp( argv[1] , "--gpa-prep" ) == 0 )
cmdline_proc_gpa_prep = true;
else if ( strcmp( argv[1] , "--gpa" ) == 0 )
cmdline_proc_gpa_run = true;
else if ( strcmp( argv[1] , "--nmf" ) == 0 )
cmdline_proc_nmf = true;
else if ( strcmp( argv[1] , "--cpt" ) == 0 )
cmdline_proc_cperm_test = true;
else if ( strcmp( argv[1] , "--kmer" ) == 0 )
cmdline_proc_ms_kmer = true;
else if ( strcmp( argv[1] , "--cmp-maps" ) == 0 )
cmdline_proc_ms_cmp_maps = true;
else if ( strcmp( argv[1] , "--correl-maps" ) == 0 )
cmdline_proc_ms_corr_maps = true;
else if ( strcmp( argv[1] , "--label-maps" ) == 0 )
cmdline_proc_ms_label_maps = true;
else if ( strcmp( argv[1] , "--copy-suds" ) == 0 )
cmdline_proc_copy_suds = true;
else if ( strcmp( argv[1] , "--combine-suds" ) == 0 )
cmdline_proc_combine_suds = true;
else if ( strcmp( argv[1] , "--lgbm" ) == 0 )
cmdline_proc_lgbm = true;
else if ( strcmp( argv[1] , "--assoc" ) == 0 )
cmdline_proc_assoc = true;
else if ( strcmp( argv[1] , "--massoc" ) == 0 )
cmdline_proc_massoc = true;
else if ( strcmp( argv[1] , "--pops" ) == 0 )
cmdline_proc_pops = true;
else if ( strcmp( argv[1] , "--eval-stages" ) == 0 )
cmdline_proc_eval_stages = true;
else if ( strcmp( argv[1] , "--priors" ) == 0 )
cmdline_proc_pops_espriors = true;
else if ( strcmp( argv[1] , "--otsu" ) == 0 )
cmdline_proc_otsu = true;
else if ( strcmp( argv[1] , "--fft" ) == 0 )
cmdline_proc_fft = true;
else if ( strcmp( argv[1] , "--overlap" ) == 0 )
cmdline_proc_overlap = true;
else if ( strcmp( argv[1] , "--validate" ) == 0 )
cmdline_proc_validate = true;
}
// otherwise, first element will be treated as a file list
cmd_t::input = argv[1];
// commands should be in form
// @variable-file
// key=value
// signals=S1,S2,...
// --flag ( added minus fist '-' to globals::param ), e.g. --fs, --labels
// exclude={file}
// -o output db
// -a output db { as above, except append }
// -s { rest of line is script }
// comma-separated strings (-->signals)
// a single number or range (n, n-m)
// var=value
int specified = 0;
for (int i=2;i<argc;i++)
{
// if we've had an --options command (which sets 'param_from_command_line')
// then ignore any options at or past this value, i.e. as they are specific
// for the command line tool
if ( param_from_command_line != 0 && i >= param_from_command_line )
continue;
// parse for a key=value form: if we do not have this, we assume
// it is a special variable (e.g. @include) or a numeric SL row-range
std::vector<std::string> tok =
Helper::quoted_parse( argv[i] , "=" );
// is this a special variable, e.g. path=, alias=, signal=, etc
if ( tok.size() == 2 )
{
cmd_t::parse_special( tok[0] , tok[1] );
}
// specify database for output
else if ( Helper::iequals( tok[0] , "-o" ) || Helper::iequals( tok[0] , "-a" ) )
{
// next arg will be DB
if ( i + 1 >= argc ) Helper::halt( "expecting database name after -o/a" );
cmd_t::stout_file = argv[ ++i ];
if ( Helper::iequals( tok[0] , "-a" ) ) cmd_t::append_stout_file = true;
}
// specify database for output
else if ( Helper::iequals( tok[0] , "-t" ) )
{
// next arg will be root (folder) for plain-text
if ( i + 1 >= argc ) Helper::halt( "expecting database name after -t" );
cmd_t::plaintext_root = argv[ ++i ];
cmd_t::plaintext_mode = true;
}
// luna-script from command line
else if ( Helper::iequals( tok[0] , "-s" ) )
{
// rest of args will be cmd script
for (int j=i+1;j<argc;j++) cmd_t::add_cmdline_cmd( argv[j] );
break;
}
else if ( argv[i][0] == '-' )
{
std::string f = argv[i];
globals::param.add( f.substr(1) );
}
// param file
else if ( argv[i][0] == '@' )
{
// an 'include'
std::string filename = argv[i];
bool parse_line = true;
std::string last_grp = "";
// allow missing parameter file "." i.e. to make scripting
// easier for LSF submission script that need to pass this
if ( filename.size() > 1 && filename != "@." )
{
// expand() expands out any ~/ notation to full path
filename = Helper::expand( filename.substr(1).c_str() );
if ( ! Helper::fileExists( filename ) ) Helper::halt( "could not open " + filename );
std::ifstream INC( filename.c_str() , std::ios::in );
if ( INC.bad() ) Helper::halt("could not open file: " + filename );
while ( ! INC.eof() )
{
std::string line;
//std::getline( INC , line);
Helper::safe_getline( INC , line );
if ( INC.eof() || line == "" ) continue;
// skip % comments
if ( line[0] == '%' ) continue;
// is this an include/exclude section
// +group include only if matches group, otherwise skip
// -group exclude if matches group, otherwise parse
if ( line[0] == '+' || line[0] == '-' )
{
const std::string grp = line.substr(1);
if ( grp == "" ) continue;
if ( last_grp == "" ) last_grp = line;
else if ( last_grp != line )
Helper::halt( "cannot nest +group/-group lines" );
else last_grp = "";
bool has_grp =
cmd_t::vars.find( grp ) != cmd_t::vars.end() ?
Helper::yesno( cmd_t::vars[ grp ] ) : false ;
if ( line[0] == '-' && has_grp ) parse_line = ! parse_line;
if ( line[0] == '+' && ! has_grp ) parse_line = ! parse_line;
// skip to next line now
continue;
}
else
{
// if not a control line +grp or -grp, and if we are not parsing, then skip
if ( ! parse_line ) continue;
}
// otherwise parse as a normal line: i.e. two tab-delim cols
std::vector<std::string> tok = Helper::quoted_parse( line , "\t" );
if ( tok.size() != 2 )
Helper::halt("badly formatted line ( # tabs != 2 ) in " + filename + "\n" + line );
cmd_t::parse_special( tok[0] , tok[1] );
}
INC.close();
}
}
else
{
int x;
if ( ! Helper::str2int( argv[i] , &x ) )
{
// assume this is an ID (i.e. must be a string)
globals::sample_list_ids.insert( argv[i] );
specified = 2;// i.e. done selecting
}
else if ( specified == 0 )
{
globals::sample_list_min = x;
++specified;
}
else if ( specified == 1 )
{
globals::sample_list_max = x;
++specified;
}
else
Helper::halt( "cannot parse command line: more than two sample lines specified" );
}
// only a single sample specified?
if ( specified == 1 )
{
globals::sample_list_max = globals::sample_list_min;
//logger << " restricting analysis to sample # " << globals::sample_list_max << "\n";
}
else if ( globals::sample_list_max < globals::sample_list_min )
{
int x = globals::sample_list_max;
globals::sample_list_max = globals::sample_list_min;
globals::sample_list_min = x;
}
if ( globals::sample_list_min < 0 ) globals::sample_list_min = -1;
if ( globals::sample_list_max < 0 ) globals::sample_list_max = -1;
// if ( globals::sample_list_max > globals::sample_list_min )
// logger << " restricting analysis to samples # " << globals::sample_list_min << " to " << globals::sample_list_max << "\n";
}
}
else if ( argc < 2 || ( isatty(STDIN_FILENO) || argc != 1 ) )
{
logger << usage_msg
<< "\n";
logger.off();
std::exit(1);
}
if ( std::cin.eof() || ! std::cin.good() )
Helper::halt( "no input, quitting" );
//
// -------- done parsing command args --------
//
//
// banner
//
logger.banner( globals::version , globals::date );
//
// initialize output to a STOUT db or not?
//
if ( cmd_t::stout_file.find( globals::indiv_wildcard ) != std::string::npos )
{
cmd_t::has_indiv_wildcard = true;
cmd_t::stout_template = cmd_t::stout_file;
}
// text-table mode?
if ( cmd_t::plaintext_mode )
{
writer.use_plaintext( cmd_t::plaintext_root );
}
// was an output db specified?
else if ( cmd_t::stout_file != "" )
{
// if using indiv-specific output databases, postpone this...
if ( ! cmd_t::has_indiv_wildcard )
{
// if not append-mode, first wipe it
if ( ! cmd_t::append_stout_file )
Helper::deleteFile( cmd_t::stout_file );
writer.attach( cmd_t::stout_file );
}
}
// otherwise, just send to std out
else
writer.nodb();
//
// branch off to run any cmdline driven special functions, then quit
//
//
// PSC, or NMF
//
if ( cmdline_proc_psc || cmdline_proc_nmf )
{
if ( cmdline_proc_psc && cmdline_proc_nmf )
Helper::halt( "cannot specify both --psc and --nmf" );
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
// writer.id( "." , "." );
const std::string clab = cmdline_proc_psc ? "PSC" : "NMF" ;
writer.cmd( clab , 1 , "" );
writer.level( clab, "_" + clab );
// PSC , or NMF mode:
psc_t psc;
psc.construct( param , cmdline_proc_nmf );
writer.unlevel( "_" + clab );
writer.commit();
std::exit(0);
}
//
// GPA
//
if ( cmdline_proc_gpa_prep || cmdline_proc_gpa_run )
{
if ( cmdline_proc_gpa_prep && cmdline_proc_gpa_run )
Helper::halt( "cannot specify both --prep-gpa and --gpa" );
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
const std::string clab = "GPA";
writer.cmd( clab , 1 , "" );
writer.level( clab, "_" + clab );
// run GPA (prep or run)
gpa_t gpa( param , cmdline_proc_gpa_prep );
writer.unlevel( "_" + clab );
writer.commit();
std::exit(0);
}
//
// POPS
//
if ( cmdline_proc_pops )
{
#ifdef HAS_LGBM
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "POPS" , 1 , "" );
writer.level( "POPS", "_POPS" );
pops_t pops( param );
pops.make_level2_library( param );
writer.unlevel( "_POPS" );
writer.commit();
#else
Helper::halt( "LGBM support not compiled in" );
#endif
std::exit(0);
}
//
// POPS EVAL STAGES
//
if ( cmdline_proc_eval_stages )
{
#ifdef HAS_LGBM
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "EVAL-STAGES" , 1 , "" );
writer.level( "EVAL-STAGES", "_EVAL-STAGES" );
pops_indiv_t indiv( param , param.requires( "file" ) , param.value( "file2" ) );
writer.unlevel( "_EVAL-STAGES" );
writer.commit();
#else
Helper::halt( "LGBM support not compiled in" );
#endif
std::exit(0);
}
//
// Make es-priors (as a standalone function)
//
if ( cmdline_proc_pops_espriors )
{
#ifdef HAS_LGBM
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "POPS" , 1 , "" );
writer.level( "POPS", "_POPS" );
pops_t pops( param );
pops.make_espriors( param );
writer.unlevel( "_POPS" );
writer.commit();
#else
Helper::halt( "LGBM support not compiled in" );
#endif
std::exit(0);
}
//
// Simple LGBM wrapper
//
if ( cmdline_proc_lgbm )
{
#ifdef HAS_LGBM
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "LGBM" , 1 , "" );
writer.level( "LGBM", "_LGBM" );
lgbm_cli_wrapper( param );
writer.unlevel( "_LGBM" );
writer.commit();
#else
Helper::halt( "LGBM support not compiled in" );
#endif
std::exit(0);
}
//
// LGBM-based ASSOC
//
if ( cmdline_proc_assoc )
{
#ifdef HAS_LGBM
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "ASSOC" , 1 , "" );
writer.level( "ASSOC", "_ASSOC" );
assoc_t assoc( param );
writer.unlevel( "_ASSOC" );
writer.commit();
#else
Helper::halt( "LGBM support not compiled in" );
#endif
std::exit(0);
}
//
// LGBM-based MASSOC (i.e. TLOCK-based)
//
if ( cmdline_proc_massoc )
{
#ifdef HAS_LGBM
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "MASSOC" , 1 , "" );
writer.level( "MASSOC", "_MASSOC" );
massoc_t massoc( param );
writer.unlevel( "_MASSOC" );
writer.commit();
#else
Helper::halt( "LGBM support not compiled in" );
#endif
std::exit(0);
}
//
// Basic FFT on stdin signal
//
if ( cmdline_proc_fft )
{
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "FFT" , 1 , "" );
writer.level( "FFT", "_FFT" );
dsptools::cmdline_fft( param );
writer.unlevel( "_FFT" );
writer.commit();
std::exit(0);
}
//
// --validate sample list
//
if ( cmdline_proc_validate )
{
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "VALIDATE" , 1 , "" );
writer.level( "VALIDATE", "_VALIDATE" );
Helper::validate_slist( param );
writer.unlevel( "_VALIDATE" );
writer.commit();
std::exit(0);
}
//
// OVERLAP enrichment (multi-sample case)
//
if ( cmdline_proc_overlap )
{
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "OVERLAP" , 1 , "" );
writer.level( "OVERLAP", "_OVERLAP" );
annotate_t annotate( param );
writer.unlevel( "_OVERLAP" );
writer.commit();
std::exit(0);
}
//
// Otsu thresholding
//
if ( cmdline_proc_otsu )
{
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "OTSU" , 1 , "" );
writer.level( "OTSU", "_OTSU" );
dsptools::cmdline_otsu( param );
writer.unlevel( "_OTSU" );
writer.commit();
std::exit(0);
}
//
// Cluster permitation test (CPT)
//
if ( cmdline_proc_cperm_test )
{
param_t param;
build_param( ¶m, argc, argv, param_from_command_line );
writer.begin();
writer.id( "." , "." );
writer.cmd( "CPT" , 1 , "" );