From 235f2a63cfac60f9b2bfc0702cadefad6e0eaf50 Mon Sep 17 00:00:00 2001
From: f-nivert <florian.nivert@hotmail.fr>
Date: Fri, 8 Mar 2019 16:43:25 +0100
Subject: [PATCH] Add of the script bt-all.pl and cruise.toml
---
btl-all.pl | 541 ++++++++++++++++++++++++++++++++++++++++++++++++++++
cruise.toml | 44 +++++
2 files changed, 585 insertions(+)
create mode 100644 btl-all.pl
create mode 100644 cruise.toml
diff --git a/btl-all.pl b/btl-all.pl
new file mode 100644
index 0000000..0a9ac55
--- /dev/null
+++ b/btl-all.pl
@@ -0,0 +1,541 @@
+#!/usr/bin/perl -w
+#
+# btl-all.pl
+#
+# Genere un fichier btl avec tous les parametres a partir des fichiers
+# Seabird .btl
+#
+# $Id J Grelet avril 2014$
+#
+use strict; # necessite de declarer toutes les variables globales
+
+#use diagnostics;
+
+# use open qw(:std :utf8);
+# binmode(STDERR, ":utf8");
+use Time::Local;
+use Date::Manip;
+use Getopt::Long;
+use File::Basename;
+use Data::Dumper;
+use Oceano::Seawater;
+use Oceano::Convert;
+use Oceano::Seabird;
+use Cwd;
+use Config::Tiny;
+
+#use Tie::IxHash;
+
+#------------------------------------------------------------------------------
+# Les repertoires de sorties
+#------------------------------------------------------------------------------
+my $ascii_dir = 'ascii/';
+my $odv_dir = 'odv/';
+
+#------------------------------------------------------------------------------
+# Les variables globales
+#------------------------------------------------------------------------------
+our $VERSION = "1.0";
+my $version;
+my $help = undef;
+my $author;
+my $debug;
+my $echo;
+my $dtd;
+my $dtdLocalPath;
+my $encoding;
+
+my $hdr_file;
+my $btl_file;
+my $xml_file;
+my $odv_file;
+
+my $header_file;
+my $institute;
+my $btlType;
+my $btlSn;
+my $pi;
+my $creator;
+my $acquisitionSoftware;
+my $acquisitionVersion;
+my $processingSoftware;
+my $processingVersion;
+
+my $cycle_mesure;
+my $plateforme;
+my $contexte;
+my $timezone;
+my $format_date;
+my $processing_code;
+my $begin_date;
+my $end_date;
+my $cruisePrefix;
+my $stationPrefixLength;
+my $title_summary;
+my $comment;
+my $header;
+my @header;
+my $split;
+my %split;
+my $format;
+my @format;
+my %format;
+my %data;
+my @data;
+my %sbe35;
+
+# sbe35
+my $t90sbe35;
+
+my $code = -1; # header code
+
+# fichiers bouteille seabird .btl
+my $sbe_file;
+my ( $s_date, $e_date, $e_time, $iso_date, $t_date );
+my ( $PRFL, $BOTL );
+my ( $lat, $lat_pos, $lat_deg, $lat_min, $lat_hemi );
+my ( $long, $long_pos, $long_deg, $long_min, $long_hemi );
+my ( $julien, $date, $month, $day, $year, $heure, $min, $time );
+
+my $type_odv = 'B'; # station-type (either B, C or X for bottle, CTD or XBT data
+my $bottom_depth = 1e36;
+
+#------------------------------------------------------------------------------
+# display_version()
+# display program version
+#------------------------------------------------------------------------------
+sub display_version() {
+ print "Version: $VERSION\nAuthor: $author\n\n";
+ exit 1;
+}
+
+#------------------------------------------------------------------------------
+# usage()
+#------------------------------------------------------------------------------
+sub usage() {
+ print STDERR "\nusage: btl-all.pl [options] <files>\n\n";
+ print STDERR
+ "Options:\n --help Display this help message\n";
+ print STDERR " --version program version\n";
+ print STDERR " --debug debug info\n";
+ print STDERR " --echo display filenames processed\n";
+ print STDERR " --dtd=[local|public] define DTD\n";
+ print STDERR "examples:\n\$ perl btl-all.pl --echo data/btl/*.btl\n";
+ exit 1;
+}
+
+#------------------------------------------------------------------------------
+# get_options()
+# analyse les options
+#------------------------------------------------------------------------------
+sub get_options() {
+
+ &GetOptions(
+ "echo" => \$echo,
+ "dtd=s" => \$dtd,
+ "debug" => \$debug,
+ "version" => \$version,
+ "help" => \$help
+ ) or &usage;
+
+ &display_version if $version;
+ &usage if $help;
+}
+
+#------------------------------------------------------------------------------
+# read string key inside section in config file
+#------------------------------------------------------------------------------
+sub read_config_string() {
+ my ( $Config, $section, $key ) = @_;
+
+ my $value = $Config->{$section}->{$key};
+ if ( !defined $value ) {
+ die "Missing string '$key' in section '$section' $!";
+ }
+ return $value;
+}
+
+#------------------------------------------------------------------------------
+# read config.ini file where cruise parameter are defined
+#------------------------------------------------------------------------------
+sub read_config() {
+ my ($configFile) = @_;
+
+ # Create a config
+ my $Config = Config::Tiny->new;
+
+ $Config = Config::Tiny->read($configFile)
+ or die "Could not open '$configFile' $!";
+
+ $author = &read_config_string( $Config, 'global', 'author' );
+ $debug = &read_config_string( $Config, 'global', 'debug' );
+ $echo = &read_config_string( $Config, 'global', 'echo' );
+ $dtd = &read_config_string( $Config, 'xml', 'dtd' );
+ $dtdLocalPath = &read_config_string( $Config, 'xml', 'dtdLocalPath' );
+ $encoding = &read_config_string( $Config, 'xml', 'encoding' );
+ $cycle_mesure = &read_config_string( $Config, 'cruise', 'cycle_mesure' );
+ $plateforme = &read_config_string( $Config, 'cruise', 'plateforme' );
+ $contexte = &read_config_string( $Config, 'cruise', 'context' );
+ $timezone = &read_config_string( $Config, 'cruise', 'timezone' );
+ $format_date = &read_config_string( $Config, 'cruise', 'format_date' );
+ $processing_code =
+ &read_config_string( $Config, 'cruise', 'processing_code' );
+ $begin_date = &read_config_string( $Config, 'cruise', 'begin_date' );
+ $end_date = &read_config_string( $Config, 'cruise', 'end_date' );
+ $institute = &read_config_string( $Config, 'cruise', 'institute' );
+ $pi = &read_config_string( $Config, 'cruise', 'pi' );
+ $creator = &read_config_string( $Config, 'cruise', 'creator' );
+ $acquisitionSoftware =
+ &read_config_string( $Config, 'ctd', 'acquisitionSoftware' );
+ $acquisitionVersion =
+ &read_config_string( $Config, 'ctd', 'acquisitionVersion' );
+ $processingSoftware =
+ &read_config_string( $Config, 'ctd', 'processingSoftware' );
+ $processingVersion =
+ &read_config_string( $Config, 'ctd', 'processingVersion' );
+ $cruisePrefix = &read_config_string( $Config, 'ctd', 'cruisePrefix' );
+ $stationPrefixLength =
+ &read_config_string( $Config, 'ctd', 'stationPrefixLength' );
+ $btlType = &read_config_string( $Config, 'btl', 'type' );
+ $btlSn = &read_config_string( $Config, 'btl', 'sn' );
+ $title_summary = &read_config_string( $Config, 'btl', 'title_summary' );
+ $comment = &read_config_string( $Config, 'btl', 'comment' );
+ $header = &read_config_string( $Config, 'btl', 'header' );
+ $split = &read_config_string( $Config, 'btl', 'split' );
+ $format = &read_config_string( $Config, 'btl', 'format' );
+}
+
+#------------------------------------------------------------------------------
+# write XML header to output _ctd.xml file using oceano.dtd
+#------------------------------------------------------------------------------
+sub write_xml_header {
+ my $today = &dateFormat( undef, "%d/%m/%Y" );
+
+ print XML_BTL_FILE "<?xml version=\"1.0\" encoding=\"$encoding\"?>\n";
+
+ # les commentaires ne sont pas acceptés par XML Toolbox Matlab de Geodise
+ if ( $dtd eq 'local' ) {
+ print XML_BTL_FILE
+"<!DOCTYPE OCEANO SYSTEM \"$dtdLocalPath/$cycle_mesure/local/oceano.dtd\">\n";
+ }
+ else {
+ print XML_BTL_FILE
+'<!DOCTYPE OCEANO PUBLIC "-//US191//DTD OCEANO//FR" "http://www.brest.ird.fr/us191/database/oceano.dtd">'
+ . "\n";
+ }
+ print XML_BTL_FILE '<OCEANO TYPE="PROFIL">' . "\n";
+ print XML_BTL_FILE " <ENTETE>\n";
+ print XML_BTL_FILE " <PLATEFORME>\n";
+ print XML_BTL_FILE " <LIBELLE>$plateforme</LIBELLE>\n";
+ print XML_BTL_FILE " </PLATEFORME>\n";
+ print XML_BTL_FILE
+" <CYCLE_MESURE CONTEXTE=\"$contexte\" TIMEZONE=\"$timezone\" FORMAT=\"$format_date\">\n";
+ print XML_BTL_FILE " <LIBELLE>$cycle_mesure</LIBELLE>\n";
+ print XML_BTL_FILE " <DATE_DEBUT>$begin_date</DATE_DEBUT>\n";
+ print XML_BTL_FILE " <DATE_FIN>$end_date</DATE_FIN>\n";
+ print XML_BTL_FILE " <INSTITUT>$institute</INSTITUT>\n";
+ print XML_BTL_FILE " <RESPONSABLE>$pi</RESPONSABLE>\n";
+ print XML_BTL_FILE
+" <ACQUISITION LOGICIEL=\"$acquisitionSoftware\" version=\"$acquisitionVersion\"></ACQUISITION>\n";
+ print XML_BTL_FILE
+" <TRAITEMENT LOGICIEL=\"$processingSoftware\" version=\"$processingVersion\"></TRAITEMENT>\n";
+ print XML_BTL_FILE
+" <VALIDATION LOGICIEL=\"$0\" VERSION=\"$VERSION\" DATE=\"$today\" OPERATEUR=\"$creator\" CODIFICATION=\"OOPC\">\n";
+ print XML_BTL_FILE " <CODE>$processing_code</CODE>\n";
+ print XML_BTL_FILE " <COMMENTAIRE>$comment</COMMENTAIRE>\n";
+ print XML_BTL_FILE " <COMMENTAIRE>$title_summary</COMMENTAIRE>\n";
+ print XML_BTL_FILE " </VALIDATION>\n";
+ print XML_BTL_FILE " </CYCLE_MESURE>\n";
+ print XML_BTL_FILE
+ " <INSTRUMENT TYPE=\"$btlType\" NUMERO_SERIE=\"$btlSn\">\n";
+ print XML_BTL_FILE " </INSTRUMENT>\n";
+ print XML_BTL_FILE " </ENTETE>\n";
+ print XML_BTL_FILE " <DATA>\n";
+}
+
+#------------------------------------------------------------------------------
+# fonctions de calcul de la position/date
+#------------------------------------------------------------------------------
+sub position {
+ my ( $deg, $min, $hemi ) = @_;
+ my $sign = 1;
+ if ( $hemi eq "S" || $hemi eq "W" ) {
+ $sign = -1;
+ }
+ my $tmp = $min;
+ $min = abs $tmp;
+ my $sec = ( $tmp - $min ) * 100;
+ return ( ( $deg + ( $min + $sec / 100 ) / 60 ) * $sign );
+}
+
+#------------------------------------------------------------------------------
+#------------------------------------------------------------------------------
+#sub julian {
+# my($jj,$h,$m) = @_;
+# my $tmp = (($h * 60) + $m ) / 1440;
+# return( $jj + $tmp );
+#}
+
+#------------------------------------------------------------------------------
+# entete ODV
+#------------------------------------------------------------------------------
+sub entete_odv {
+ my $today = &dateFormat( undef, "%Y-%m-%dT%H:%M:%S" );
+ my $cwd = getcwd();
+
+ print ODV_FILE "//ODV Spreadsheet file : $odv_file\n";
+ print ODV_FILE "//Data treated : $today\n";
+ print ODV_FILE "//<DataType>Profiles</DataType>\n";
+ print ODV_FILE "//<InstrumentType>$btlType</InstrumentType>\n";
+ print ODV_FILE "//<Source>$cwd</Sources>\n";
+ print ODV_FILE "//<Creator>$creator</Creator>\n";
+ print ODV_FILE "//\n";
+ print ODV_FILE
+"Cruise\tStation\tType\tyyyy-mm-ddThh:mm:ss\tLongitude [degrees_east]\tLatitude [degrees_north]\tBot. Depth [m]\tBTL\tPres [db]\tTE01 [C]\tTE02 [C]\tPSA1 [Psu]\tPSA2 [Psu]\tDO12 [micromole/kg]\tDO22 [micromole/kg]\tFLU2 [milligram/m3]\t TUR3 [%]\tPotemp090 [C]\tCPotemp190C [C]\n";
+}
+
+#------------------------------------------------------------------------------
+# Debut du programme principal
+#------------------------------------------------------------------------------
+#&Date_Init( "TZ=UTC" );
+&Date_Init('SetDate=now,UTC');
+&read_config('../config.ini');
+&usage if ( $#ARGV == -1 );
+&get_options;
+
+# define files name
+$hdr_file = lc $ascii_dir . $cycle_mesure . '-all.btl';
+$btl_file = lc $ascii_dir . $cycle_mesure . '-all_btl';
+$xml_file = lc $ascii_dir . $cycle_mesure . '-all_btl.xml';
+$odv_file = lc $odv_dir . $cycle_mesure . '-all_btl-odv.txt';
+
+# get variables liste order from header
+@header = split /\s+/, $header;
+
+# convert variable $split from config.ini to hash, ex $split = bottle,1,month,2,...
+%split = split /,/, $split;
+
+# convert output format fron config.ini to hash
+@format = split /\s+/, $format;
+
+# build hash %format with key: PRES, value: %7.3f
+my @tmp = @format;
+foreach my $key (@header) {
+ $format{$key} = shift @tmp;
+}
+
+# test if output dirs exist and create them if not
+mkdir($odv_dir) unless ( -d $odv_dir );
+mkdir($ascii_dir) unless ( -d $ascii_dir );
+
+# ouvre les fichiers de sortie
+open( HDR_BTL_FILE, "+> $hdr_file" ) or die "Can't open file : $hdr_file\n";
+open( BTL_FILE, "+> $btl_file" ) or die "Can't open file : $btl_file\n";
+open( XML_BTL_FILE, "+> $xml_file" ) or die "Can't open file : $xml_file\n";
+open( ODV_FILE, "+> $odv_file" ) or die "Can't open file : $odv_file\n";
+
+print HDR_BTL_FILE
+" St Date_deb Heure_deb Date_fin Heure_fin Latitude Longitude Nb_btl\n\n";
+&entete_odv;
+&write_xml_header;
+print XML_BTL_FILE "$header\n";
+$header_file = "$cycle_mesure $plateforme $institute $btlType $btlSn $pi";
+print BTL_FILE "$header_file\n";
+print BTL_FILE "$header\n";
+
+# read SBE35 files
+my $dir_sbe35 = 'data/sbe35/';
+
+#my @files = grep ( -f ,<*.txt>);
+## see: https://stackoverflow.com/questions/1510305/how-can-i-get-a-list-of-all-files-with-a-certain-extension-from-a-specific-direc
+
+foreach my $file_sbe35 ( grep ( -f, <data/sbe35/*.asc> ) ) {
+
+ # recupere le numero de la station dans le nom du fichier
+ ($PRFL) = ( $file_sbe35 =~ m/$cruisePrefix(\d{$stationPrefixLength})/i );
+
+ # ouverture du fichier
+ open( SBE35_FILE, $file_sbe35 );
+ print STDERR "Lit: $file_sbe35\n" if $debug;
+ my $i = 1;
+ while (<SBE35_FILE>) {
+ if ( not( /^[*#]/ || /^\s*$/ || /^dd/ ) ) {
+
+ # print STDERR $_;
+ if (/t90\s*=\s*(\d*\.\d*)/) {
+ $t90sbe35 = ($1 >= 99.999) ? 1e+36 : $1;
+ $sbe35{"$PRFL:$i"} = $t90sbe35;
+ print STDERR $sbe35{"$PRFL:$i"} . "\n" if $debug;
+ $i++;
+ }
+ }
+ }
+ close SBE35_FILE;
+}
+
+# parcourt des fichiers .btl passes en argument sur la ligne de commande
+for ( my $i = 0 ; $i <= $#ARGV ; $i++ ) {
+ my $fileName = $ARGV[$i];
+
+ # ouverture du fichier
+ open( DATA_FILE, $fileName );
+ print STDERR "\nLit: $fileName " if $debug;
+
+ # recupere le numero de la station dans le nom du fichier
+ ($PRFL) = ( $fileName =~ m/$cruisePrefix(\d{$stationPrefixLength})/i );
+
+ $BOTL = 0;
+
+ # on lit le fichier bouteille
+ while (<DATA_FILE>) {
+
+ # decode la date et heure de debut de station
+ if (/System UpLoad Time =\s+(\.*)/) { # a modifier suivant le contexte
+ ($time) = /System UpLoad Time =\s+(\w+\s+\d+\s+\d+\s+\d+:\d+:\d+)/;
+ $date = &ParseDate($time);
+
+ # transforme le day_of_year en julian day
+ $julien = &UnixDate( $time, "%j" ) - 1;
+ $julien = &julian(
+ $julien,
+ &UnixDate( $date, "%H" ),
+ &UnixDate( $date, "%M" ),
+ &UnixDate( $date, "%S" )
+ );
+ $s_date = &UnixDate( $date, "%d/%m/%Y %H:%M:%S" );
+
+ #$t_date = &UnixDate($date,"%Y%m%d%H%M%S");
+ $t_date = &UnixDate( $date, "%q" );
+ }
+ if (/NMEA Latitude\s*=\s*(\d+\s+\d+.\d+\s+\w)/) {
+ ( $lat_deg, $lat_min, $lat_hemi ) = split " ", $1;
+ $lat_pos = &position( $lat_deg, $lat_min, $lat_hemi );
+ }
+ if (/NMEA Longitude\s*=\s*(\d+\s+\d+.\d+\s+\w)/) {
+ ( $long_deg, $long_min, $long_hemi ) = split " ", $1;
+ $long_pos = &position( $long_deg, $long_min, $long_hemi );
+
+ # print header and add 1e36 to complement columns
+ printf XML_BTL_FILE "%05d %d %7.3f %7.4f %8.4f %s", $PRFL, $code,
+ $julien, $lat_pos, $long_pos, $t_date;
+ printf XML_BTL_FILE " 1e36" x ( @header - 6 );
+ printf XML_BTL_FILE "\n";
+ printf BTL_FILE "%05d %d %7.3f %7.4f %8.4f %s", $PRFL, $code, $julien,
+ $lat_pos, $long_pos, $t_date;
+ printf BTL_FILE " 1e36" x ( @header - 6 );
+ printf BTL_FILE "\n";
+ }
+
+ # decodage du fond (sonde)
+ if (/Bottom Depth\s*:\s*(\d*)\s*\S*/i) {
+ $bottom_depth = ( $1 eq '' ) ? 1e+36 : $1;
+ }
+
+# decode la date de chaque prelevement et extrait les donnees dans la ligne correspondante
+# les parametres suivants doivent etre presents:
+# Bottle Date Sal00 Sal11 Sbeox0ML/L Sbeox0Mm/Kg Sbeox1ML/L Sbeox1Mm/Kg Sbeox0dOV/dT Sbeox1dOV/dT PrDM DepSM
+# T090C T190C C0S/m C1S/m Sbeox0V Sbeox1V (optionnels) FlECO-AFL Xmiss
+# amop
+# Bottle Date Sal00 Sal11 Sbeox0ML/L Sbeox0Mm/Kg Sbeox1ML/L Sbeox1Mm/Kg TimeJ PrDM DepSM T090C T190C
+# C0S/m C1S/m Sbeox0V Sbeox1V Upoly0 FlC CStarAt0 CStarTr0 Spar Par Cpar Sbeox0dOV/dT Sbeox1dOV/dT
+# Position Time
+# TUR3 -> CStarTr0 (transmissiometre Wetlab %)
+# TUR4 -> Upoly0 (turbidimètre)
+# LGHT;LIGHT IRRADIANCE IMMERGED PAR;micromole photon/(m2.s);0;4000;%8.3lf;9999.999;
+# LGH3;float32;light irradiance corrected par;;micromole photon/(m2.s);;TIME DEPTH LATITUDE LONGITUDE;;0;3000;%8.3f;1E+36;;0.001;;;;;;;
+# LGH4;LIGHT IRRADIANCE SURFACE PAR;micromole photon/(m2.s);0;3000;%8.3lf;9999.999;
+# LGH5 -> CPar (%)
+# #LGHT;LIGHT IRRADIANCE IMMERGED PAR;micromole photon/(m2.s);0;4000;%8.3lf;
+# FLU2 -> FlC (Chelsea Acquatracka III)
+#
+ if (/^\s+\d+\s+\w+\s+\d+\s+\d+/) {
+
+# extract values and fill hash %data with position give by hash %split from config.ini
+ @data = split /\s+/;
+ while ( my ( $key, $value ) = each(%split) ) {
+ $data{$key} = $data[$value];
+ }
+ $date =
+ &ParseDate( $data{'month'} . ' ' . $data{'day'} . ' ' . $data{'year'} );
+ $e_date = &UnixDate( $date, "%d/%m/%Y" );
+ $iso_date = &UnixDate( $date, "%Y-%m-%dT" );
+
+ # a changer eventuellement si LADCP et choix "table driven" dans seaseave
+ $BOTL += 1;
+
+ # only for profile number or station
+ $data{'PRFL'} = $PRFL;
+
+# print for each value from hash %data with format from hash %format describe in config.ini
+ foreach my $key (@header) {
+ if ( $key eq 'TE35' ) {
+ my $TE35 = defined $sbe35{"$PRFL:$BOTL"} ? $sbe35{"$PRFL:$BOTL"} : 1e36;
+ printf XML_BTL_FILE "$format{$key} ", $TE35;
+ printf BTL_FILE "$format{$key} ", $TE35;
+ }
+ else {
+ printf XML_BTL_FILE "$format{$key} ", $data{$key};
+ printf BTL_FILE "$format{$key} ", $data{$key};
+ }
+ }
+ printf XML_BTL_FILE "\n";
+ printf BTL_FILE "\n";
+ }
+
+ # decode l'heure sur la ligne suivante
+ if (/\s+(\d+:\d+:\d+)/) {
+ ($time) = /\s+(\d+:\d+:\d+)/;
+ $date = &ParseDate($time);
+ $e_time = &UnixDate( $date, "%H:%M:%S" );
+ if ( $BOTL >= 1 ) {
+ printf ODV_FILE "%s\t%05d\t%s\t%s\t%8.4f\t%7.4f",
+ $cycle_mesure, $PRFL, $type_odv,
+ $iso_date . &UnixDate( $date, "%H:%M:%S" ),
+ $long_pos, $lat_pos;
+ printf ODV_FILE ( $bottom_depth > 1e35 ) ? "\t" : "\t%6.1f",
+ $bottom_depth;
+ printf ODV_FILE "\t$format{'BOTL'}", $data{'BOTL'};
+ printf ODV_FILE "\t$format{'PRES'}", $data{'PRES'};
+ printf ODV_FILE ( $data{'TE01'} > 1e35 ) ? "\t" : "\t$format{'TE01'}",
+ $data{'TE01'};
+ printf ODV_FILE ( $data{'TE02'} > 1e35 ) ? "\t" : "\t$format{'TE02'}",
+ $data{'TE02'};
+ printf ODV_FILE ( $data{'PSA1'} > 1e35 ) ? "\t" : "\t$format{'PSA1'}",
+ $data{'PSA1'};
+ printf ODV_FILE ( $data{'PSA2'} > 1e35 ) ? "\t" : "\t$format{'PSA2'}",
+ $data{'PSA2'};
+ printf ODV_FILE "\t$format{'DO21'}", $data{'DO21'};
+ printf ODV_FILE "\t$format{'DO22'}", $data{'DO22'};
+ printf ODV_FILE "\t$format{'FLU2'}", $data{'FLU2'};
+ printf ODV_FILE "\t$format{'TUR3'}", $data{'TUR3'};
+
+ #printf ODV_FILE "\t$format{'Potemp090C'}", $data{'Potemp090C'};
+ #printf ODV_FILE "\t$format{'Potemp190C'}\n", $data{'Potemp190C'};
+ }
+ }
+ }
+
+ # pour chaque fichier, on garde la date et heure de la derniere bouteille
+ # impression a l'ecran
+ printf STDERR "%05d %s %s %s %02d%c%05.2f %s %03d\xB0%05.2f %s %2d",
+ $PRFL,
+ $s_date, $e_date, $e_time, $lat_deg, 176, $lat_min, $lat_hemi, $long_deg,
+ $long_min, $long_hemi, $BOTL
+ if $echo;
+ printf STDERR "\n" if not $debug and $echo;
+
+ # impression dans le fichier
+ printf HDR_BTL_FILE "%05d %s %s %s %02d%c%05.2f %s %03d%c%05.2f %s %2d\n",
+ $PRFL, $s_date, $e_date, $e_time, $lat_deg, 176, $lat_min, $lat_hemi,
+ $long_deg, 176, $long_min, $long_hemi, $BOTL;
+}
+
+printf STDERR "\n";
+
+print XML_BTL_FILE " </DATA>\n";
+print XML_BTL_FILE "</OCEANO>\n";
+
+close HDR_BTL_FILE;
+close XML_BTL_FILE;
+close BTL_FILE;
+close ODV_FILE;
diff --git a/cruise.toml b/cruise.toml
new file mode 100644
index 0000000..e89a637
--- /dev/null
+++ b/cruise.toml
@@ -0,0 +1,44 @@
+[global]
+author = "jgrelet IRD jmarch 2019 PIRATA-FR29 cruise"
+debug = false
+echo = true
+
+[cruise]
+cycleMesure = "PIRATA-FR29"
+plateforme = "THALASSA"
+callsign = "FNFP"
+institute = "IRD"
+timezone = "GMT"
+beginDate = "01/03/2019"
+endDate = "04/04/2019"
+pi = "BOURLES"
+creator = "Jacques.Grelet@ird.fr"
+
+[ctd]
+cruisePrefix = "fr29"
+# profile name : fr29xxx
+station = 'Station\s*:\s*\D*(\d*)'
+stationPrefixLength = 3
+titleSummary = "CTD profiles processed during PIRATA-FR29 cruise"
+typeInstrument = "SBE911+"
+instrumentNumber = "09P1263"
+isHeader = '^[*#]'
+isDevice = [ '^\*\s+(Sea-Bird)','(\*END\*)' ]
+latitude = ['Latitude\s*:\s*(\d+)\s+(\d+.\d+)\s+(\w)','NMEA Latitude\s*=\s*(\d+\s+\d+.\d+\s+\w)']
+longitude = ['Longitude\s*:\s*(\d+)\s+(\d+.\d+)\s+(\w)','NMEA Longitude\s*=\s*(\d+\s+\d+.\d+\s+\w)']
+date = 'Date\s*:\s*(\d+)/(\d+)/(\d+)'
+hour = '[Heure|Hour]\s*:\s*(\d+)[:hH](\d+):(\d+)'
+bottomDepth = 'Bottom Depth\s*:\s*(\d*\.?\d+?)\s*\S*'
+operator = 'Operator\s*:\s*(.*)'
+type = 'Type\s*:\s*(.*)'
+split = "ETDD,2,PRES,3,DEPTH,4,TEMP,5,PSAL,18,DENS,20,SVEL,22,DOX2,16,FLU2,14,FLU3,15,TUR3,13,NAVG,24"
+splitAll = "ETDD,2,PRES,3,DEPH,4,TE01,5,TE02,6,CND1,7,CND2,8,DOV1,9,DOV2,10,DVT1,11,DVT2,12,TUR3,13,FLU2,14,FLU3,15,DO12,16,DO22,17,PSA1,18,PSA2,19,DEN1,20,DEN2,21,SVEL,22,NAVG,24"
+
+[btl]
+typeInstrument = "SBE32 standard 24 Niskin bottles"
+instrumentNumber = "unknown"
+titleSummary = "Water sample during PIRATA-FR29 cruise with 20 levels"
+comment = "CTD bottles water sampling with temperature, salinity and oxygen from primary and secondary sensors"
+split = ' BOTL,1,month,2,day,3,year,4,PSA1,5,PSA2,6,DO11,7,DO12,8,DO21,9,DO22,10,Potemp090C,11,Potemp190C,12,ETDD,13,PRES,14,DEPH,15,TE01,16,TE02,17,CND1,18,CND2,19,DOV1,20,DOV2,21,DVT1,22,DVT2,23,TUR3,24,FLU2,25'
+
+
--
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