bin/sse

   1 #!/usr/bin/perl
   2
   3 use FindBin qw($Bin);
   4 use lib "$Bin/../lib";
   5
   6 # Don't edit the line below, it must look exactly like this.
   7 # Everything above this line will be replaced #
   8
   9 use PsN;
  10 use model;
  11 use tool::sse;
  12 use strict;
  13 use debug;
  14 use Getopt::Long;
  15 use common_options;
  16
  17 my $cmd_line = $0 . " " . join( " ", @ARGV );
  18
  19 ## Configure the command line parsing
  20 Getopt::Long::config("auto_abbrev");
  21
  22 my %options;
  23 ## Declare the options
  24
  25 my %required_options = ( 'samples:i' => '100');
  26 my %optional_options = ( 'alternative_models:s' => 'alt1.mod,alt2.mod,...',
  27                          'ref_ofv:i' => '500',
  28                          'parallel_simulations:i' => '1',
  29                          'estimate_simulation!' => '1' );
  30                          #"bins:i" => '',
  31                          #"selection_method:s" => '\'random\'|\'consecutive\'' );
  32
  33 my $res = GetOptions( \%options,
  34                       @common_options::get_opt_strings,
  35                       keys(%required_options),
  36                       keys(%optional_options) );
  37 exit unless $res;
  38
  39 common_options::set_globals( \%options, 'sse' );
  40 common_options::get_defaults( \%options, 'sse' );
  41 common_options::sanity_checks( \%options, 'sse' );
  42
  43 my %help_text;
  44
  45 $help_text{Pre_help_message} = <<'EOF';
  46   sse
  47
  48     Perl script for Stochastic Simulation and Estimation of NONMEM models.
  49
  50   Usage:
  51 EOF
  52
  53 $help_text{Options} = <<'EOF';
  54     Options:
  55
  56       The options are given here in their long form. Any option may be
  57       abbreviated to any nonconflicting prefix. The -threads option
  58       may be abbreviated to -t(or even -thr) but -debug may not be
  59       abbreviated to -d because it conflicts with -debug_packages and
  60       -debug_subroutines.
  61
  62       The following options are valid:
  63 EOF
  64
  65 $help_text{-h} = <<'EOF';
  66       -h | -?
  67
  68       With -h or -? sse will print a list of options and exit.
  69 EOF
  70
  71 $help_text{-help} = <<'EOF';
  72       -help
  73
  74       With -help sse will print this, longer, help message.
  75 EOF
  76
  77 $help_text{-alternative_models} = <<'EOF';
  78       -alternative_models=alt1.mod,alt2.mod,...
  79
  80       List of one or more alternative models to use for estimation
  81       with simulated datasets. The filenames must be comma-separated,
  82       no spaces.
  83 EOF
  84
  85 $help_text{-samples} = <<'EOF';
  86       -samples=N
  87
  88       The number of simulated datasets to generate.
  89 EOF
  90
  91 $help_text{-estimate_simulation} = <<'EOF';
  92       -estimate_simulation
  93
  94       By default, the simulation model is also used for estimation with
  95       the simulated datasets. The resulting OFV values are used as reference
  96       when evaluating the estimation results of alternative models. By setting
  97       -no-estimate_simulation the estimation of the simulation model is turned
  98       off, and the first alternative model is used as reference instead. See
  99       also -ref_ofv.
 100 EOF
 101
 102 $help_text{-ref_ofv} = <<'EOF';
 103       -ref_ofv=500
 104
 105       Instead of using the OFV values from the estimation of a model as
 106       reference when evaluating the other estimation results,
 107       it is possible to set a fixed reference OFV value. If using ref_ofv,
 108       it is not allowed to also estimate the simulation model.
 109 EOF
 110 $help_text{-parallel_simulations} = <<'EOF';
 111       -parallel_simulations=1
 112
 113       parallel_simulations govern the number of simulations that will
 114       be done in parallel. Normally simulations are quite fast and
 115       need only be run one at a time. See the threads option for
 116       controll over the number of estimations to do in parallel.
 117 EOF
 118
 119 $help_text{Post_help_message} = <<'EOF';
 120       Also see 'execute -help' for a description of common options.
 121 EOF
 122
 123 common_options::online_help( 'sse', \%options, \%help_text, \%required_options, \%optional_options);
 124
 125 ## Check that we do have a model file
 126 if ( scalar(@ARGV) < 1 ) {
 127   print "A simulation model file must be specified. Use 'sse -h' for help.\n";
 128   exit;
 129 }
 130
 131 if( scalar(@ARGV) > 1 ){
 132   print "SSE can only handle one modelfile, you listed: ",join(',',@ARGV),". Use 'sse -h' for help.\n";die;
 133   exit;
 134 }
 135
 136 unless ( defined $options{'samples'} ){
 137   print "samples must be given\n" ;
 138   exit;
 139 }
 140
 141 unless ( defined $options{'clean'} ){
 142   # Clean is by default much stricter in sse
 143   $options{'clean'} = 3;
 144 }
 145
 146 my $eval_string = common_options::model_parameters(\%options);
 147
 148 my $model = model -> new ( eval( $eval_string ),
 149                            filename                    => $ARGV[0],
 150                            ignore_missing_output_files => 1 );
 151
 152
 153 my @alternatives=();
 154
 155 if ( defined $options{'alternative_models'} ){
 156   #split string, assume comma separated
 157   foreach my $altfile (split(/,/,$options{'alternative_models'})){
 158     if (length($altfile)>0){
 159       my $alternative_model = model ->
 160           new ( eval( $eval_string ),filename => $altfile,ignore_missing_output_files => 1 );
 161       push(@alternatives,$alternative_model);
 162     }
 163   }
 164   if (scalar(@alternatives)<1){
 165     die "Error: Option alternative_models used, but list of filenames could not be parsed.\n";
 166   }
 167 }else{
 168   print "No alternative model given, will only estimate simulation model.\n" ;
 169
 170 }
 171
 172 my $sse = tool::sse ->
 173     new ( eval( $common_options::parameters ),
 174           estimate_simulation => $options{'estimate_simulation'},
 175           ref_ofv            => $options{'ref_ofv'},
 176           parallel_simulations => $options{'parallel_simulations'},
 177           models             => [ $model ],
 178           top_tool           => 1,
 179           alternative_models => \@alternatives,
 180           samples            => $options{'samples'} );
 181 open(CMD, ">", $sse -> directory . "/command.txt");
 182 print CMD $cmd_line, "\n";
 183 close(CMD);
 184
 185 $sse -> run;
 186 $sse -> prepare_results;
 187 $sse -> print_results;
 188