Perl scripts for BDMPathfinder

bdmp-properties.txt

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+# use this for commenting lines
+WORKING-PATH    = C://Users//stout//Desktop//BDMPathfinder # **CHANGE HERE** - USE MS-Windows PATH style
+#duration of the simulation (mission time)
+DURATION        = 6            # scale is 'hours'
+
+PROB-THRESHOLD  = 0.7           # probability threshold
+  # options for new plots
+PLOT-X-TICS     = 1             # xtics parameter in the plot
+PLOT-Y-TICS     = 0.01          # ytics
+TOP-PATHS       = 10             # discover top N paths ** if TOP-PATHS > 0, then only the TOP N paths are considered, otherwise, all are considered **
+VERBOSE         = 0             # shows output as they are computed

bdmp-routines.pl

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+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License version 3 as
+# published by the Free Software Foundation;
+#
+# This program 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 this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+## Perl sub-routines file
+## Active Building Center Research Programme (ABC-RP) @ Newcastle University
+## Start: 07/04/2021
+## Modified: 07/04/2021
+
+# removes spaces from beginning and end of strings
+sub  trim { my $s = shift; $s =~ s/^\s+|\s+$//g; return $s };
+
+# substitutes extra spaces in the middle of strings for single spaces
+sub strip { my $s = shift; $s =~ s/ +//g; return $s };
+
+# read the properties (file is passed by the sub-routine as parameter)
+sub read_properties {
+   my $propertyfile = shift;
+
+   my %pprop = ();
+
+   open(INFILE, "<$propertyfile") or die ($messages{"PROPERTY-FILE-NOT-FOUND"}." File: $propertyfile\n");
+   my(@proplines) = <INFILE>;
+   close(INFILE);
+
+   foreach my $line (@proplines) {
+      $line =~ s/\r\n//g;
+      $line = trim($line);
+      $line = strip($line);
+      $line = substr($line, 0, index($line, '#'));
+      next if ($line eq "" || $line =~ /^'#'/); #next if line is empty of starts with '#'
+      my($prop,$val) = split("=",$line);
+      $pprop{$prop} = $val;
+   }
+   return %pprop;
+}
+
+#print a hash
+#example of use: print_hash(\%properties); #don't forget the '\'
+sub print_hash {
+   my %hash = %{ $_[0] };
+   foreach my $key (keys %hash) {
+      print "$key -> $hash{$key}\n";
+   }
+}
+
+1;

bdmp-run-all.pl

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+#!/usr/bin/perl
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License version 3 as
+# published by the Free Software Foundation;
+#
+# This program 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 this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+## Perl script for processing a number of FIGARO template files
+## Active Building Center Research Programme (ABC-RP) @ Newcastle University
+## Start: 06/04/2021
+## Modified: 07/04/2021
+
+# BASIC INSTRUCTIONS
+#1. Create a BDMP model in RiskSpectrum ModelBuilder (RSMB)
+#   - open the properties and set option: GLOBAL_TYPE>OPTIONS>enable_detection to FALSE
+#2. For each leaf, assign a number that is unique to your analysis (e.g. 123.456)
+#   - the idea is that the script will substitute this string by a set of parameters
+#   - assign 'unique' values in the BDMP model in RSMB
+#   - for ISE leaves you will have to add values between 0 and 1, so I suggest adding 0.011010101, for instance
+#       - then generating the FIGARO0 file and replacing this string by something else more close to your original selected pattern (e.g. "123.456")
+#3. Convert the BDMP model to a FIGARO file: Open model, on tab 'Processing', click "Generate Figaro0"
+#   - change the directory to save the model to inside the BDMPathfinder is, click "save", click "instantiate"
+#4. Edit a properties file (we shipped one called 'bdmp-properties.txt')
+#   - change parameters and paths as you see fit
+#5. Edit the hash variable %parameters in the Perl script 'bdmp-scenario-builder.pl'
+#   - change the string you set in RSMB with all the variations you wish to run (e.g. '123.456' => "1;3;10;15" in hours, it will divide by 3600)
+#6. Run perl bdmp-scenario-builder.pl <MODEL>
+#   - the model must be a FIGARO model (extension .fi)
+#   - this will create a folder (with the timestamp), copy this folder and paste on the next step
+#   - this script will also create a file called 'scenarios.txt' with all scenario variations according to the model's leaaves
+#7. Run perl bdmp-run-all.pl <FOLDER> <PROPERTY-FILE>
+#   - in the end, it will create a file called 'script.R', for plotting ALL scenarios
+#8. Open RStudio, and then go to <FOLDER> and open the 'script.R', executing all commands
+
+
+use strict;
+use warnings;
+
+use Time::Local;
+use Cwd qw();
+
+use 5.010;
+use XML::LibXML;
+use List::Util qw(max);
+
+require './bdmp-routines.pl';
+
+if (@ARGV != 2) { 
+   print "missing FOLDER parameter. \nusage: perl bdmp-run-all.pl FOLDER PROPERTY-FILE\n";
+   exit;
+}
+
+# save all properties into one array variable
+my $folder = $ARGV[0];
+my $propertyfile = $ARGV[1];
+my $path = ".\\";
+
+my %properties = read_properties($propertyfile);
+
+#clean
+system("del $path$folder\\*.txt >nul 2>&1");
+system("del $path$folder\\*.R >nul 2>&1");
+system("del $path$folder\\*.mcr >nul 2>&1");
+
+#iterate through folders
+print "directory read $folder\n";
+my @files;
+opendir FILE, $path.$folder or die("Folder not found.\n");
+@files = grep !/^\.\.?$/,, readdir FILE;
+closedir FILE;
+
+my $max_prob = 0.0;
+my $tot_colours;
+
+#build new R file with MANY datasets
+
+#create a new script for RStudio
+my $R_file_contents = "".
+   "#used for the transpose function\n".
+   "library(data.table)\n".
+   "\n".
+   "#remove all objects defined earlier\n".
+   "rm(list=ls(all=TRUE))\n".
+   "#remove all plots in the environment\n".
+   "graphics.off()\n".
+   "\n".
+   "#set working directory\n";
+
+#iterate over the files and call bdmpathfinder.pl
+my $count = 0;
+my $ss_cbind = "";
+foreach my $file (sort @files) {
+   my $command = "perl bdmpathfinder.pl $path$folder/$file $propertyfile";
+   print "\tRunning $path$folder/$file ...\n";
+   system($command);
+   my $outfile = $file;
+   $outfile =~ s/.fi/.txt/g;
+   $outfile = ".//$outfile";
+
+   $count++;
+   $ss_cbind .= "t_data$count,";
+
+   $R_file_contents .= "".
+      "setwd(\"$properties{'WORKING-PATH'}//$folder\")\n".
+      "outputfile$count = \"$outfile\"\n".
+      "data$count <- read.table(outputfile$count, header=FALSE, sep=\";\")\n".
+      "maxf$count = max(count.fields(outputfile$count, sep = ';'))\n".
+      "data$count <- read.table(outputfile$count, header = FALSE, sep = \";\",  \n".
+      "           col.names = paste0(\"V\",seq_len(maxf$count)), fill = TRUE)\n".
+      "#save first column with the path names\n".
+      "pathnames$count <- data".($count)."[,1]\n".
+      "#remove first column\n".
+      "data$count\$V1 <- NULL\n".
+      "#transpose the data, because each column corresponds to a probab. over time\n".
+      "t_data$count <- transpose(data$count)\n".
+      "\n";
+}
+$ss_cbind = substr($ss_cbind, 0, length($ss_cbind)-1); #remove extra ',' in the end
+
+$tot_colours = $count;
+$max_prob = 0.3; #todo: find the maximum probability of *all* scenarios
+
+$R_file_contents .= "".
+   "#xaxs and yaxs: make the plot start at the right origin in x and y\n".
+   "#col: choose colors, if col=1 then set ONE color (black), otherwise, a set of colours (e.g. col=2:10)\n".
+   "graphics.off()\n".
+   "matplot(cbind($ss_cbind), type = c(\"l\"),main=\"Ensemble of attack paths\",cex.main=1.5,\n".
+   "        pch=1,col = 2:$tot_colours,xlim=c(1,$properties{'DURATION'}), xaxs=\"i\", yaxs=\"i\",\n".
+   "        ylim=c(0,$max_prob),ylab=\"Path probability\",xlab=\"Time (in hours)\",axes=F)\n".
+   "box()\n".
+   "axis(1, seq(0,$properties{'DURATION'},$properties{'PLOT-X-TICS'}),las=1, cex.axis=0.75, font=1)\n".
+   "axis(2, seq(0,$max_prob,$properties{'PLOT-Y-TICS'}),cex.axis=0.85, las=2)\n".
+   "par(xpd=TRUE)\n";
+#if ($properties{'TOP-PATHS'} > 0) { #commented here, because of the multiple scenarios, it gets pretty messy to draw legends inside the plotting area...
+#   $R_file_contents .= "legend(2, $max_prob, pathnames, col=2:$tot_colours, lty=1:2,pch = 1, bty = \"n\")\n";
+#}
+$R_file_contents .= "\n";
+
+my $R_file_name = "script.R";
+open(RFILE,'>', "$path$folder//".$R_file_name) or die $!;
+print RFILE $R_file_contents;
+close(RFILE);
+
+print "\nR commands (for plotting) written in file $path$folder/'$R_file_name'\n";
+
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