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package Demeter::Plugins::SPEC; # -*- cperl -*-
use Moose;
extends 'Demeter::Plugins::FileType';
has '+is_binary' => (default => 0);
has '+description' => (default => "ESRF SPEC format");
has '+version' => (default => 0.1);
has '+output' => (default => 'list');
use Carp;
use Scalar::Util qw(looks_like_number);
use File::Path qw(remove_tree);
sub is {
my ($self) = @_;
open D, $self->file or $self->Croak("could not open " . $self->file . " as data (SPEC)\n");
my $is_spec = 0;
while (<D>) {
$is_spec += ($_ =~ m{\A\#S\s+\d+\s+zapline\s+mono});
};
close D;
return $is_spec;
};
sub fix {
my ($self) = @_;
## make a folder below the stash folder to hold the different scans in the SNBL file
## here I have chosen to use a random, six-character string for the folder name
## this MUST be a place that can be safely discarded
$self->folder(File::Spec->catfile($self->stash_folder, 'SPEC'.Demeter->randomstring(6)));
unless( mkdir $self->folder ) {
die "Unable to create $self->folder\n";
}
my $file = $self->file;
my $orig_fileline="";
my $scan_no = 0;
open D, $file or die "could not open $file as data (fix in SPEC)\n";
my $new = File::Spec->catfile($self->folder, $self->filename.'.'.1);
($new = File::Spec->catfile($self->folder, Demeter->randomstring(6).'.'.'dat')) if (length($new) > 127);
open N, ">".$new or die "could not write to $new (fix in SPEC)\n";
my @list = ();
my $header = 1;
while (<D>) {
chomp;
next if ($_ =~ m{\-+\z});
if ($_ =~ m{\A\#F\s+\/}) {
$orig_fileline = $_;
};
if ($_ =~ m{\A\#S\s+\d+\s+zapline\s+mono}) {
$scan_no=$scan_no+1;
if ($scan_no >= 2 ) {
close N;
push @list, $new;
$new = File::Spec->catfile($self->folder, $self->filename.'.'.$scan_no);
($new = File::Spec->catfile($self->folder, Demeter->randomstring(6).'.'.'dat')) if (length($new) > 127);
open N, ">".$new or die "could not write to $new (fix in SPEC)\n";
$header=1;
print N $orig_fileline, $/;
};
print N "# ", $_, $/;
next;
}
if ($_ =~ m{N\s+\d+}) {
print N "# ---------------------------------", $/;
}
elsif ($_ =~ m{\A\#L}) {
my $labels = $_;
$labels =~ s{\#L}{\#};
print N $labels, $/;
$header = 0;
}
elsif ($header == 0) {
my @nlist = split(" ", $_);
next if not looks_like_number($nlist[0]);
$nlist[0] *= 1000;
print N join(" ", @nlist), $/;
}
else {
print N $_, $/;
};
};
close N;
push @list, $new;
close D;
## set the fixed method to this array reference and return that array reference
$self->fixed(\@list);
return \@list;
};
sub suggest {
my ($self, $which) = @_;
$which ||= 'transmission';
if ($which eq 'transmission') {
return (energy => '$13',
numerator => '$8',
denominator => '$10',
ln => 1,
is_kev => 1,);
} else {
return (energy => '$13',
numerator => '$2+$3+$4+$5+$6+$7',
denominator => '$8',
ln => 0,
is_kev => 1,);
};
};
sub clean {
my ($self) = @_;
my $err = q{};
remove_tree($self->folder); #, {error=>\$err});
return $err;
};
__PACKAGE__->meta->make_immutable;
1;
__END__
=head1 NAME
Demeter::Plugin::SPEC - Import SPEC data from beamlines at ESRF
=head1 VERSION
This documentation refers to Demeter version 0.9.16.
=head1 SYNOPSIS
This plugin splits multi-scan SPEC files into separate scans that can be
loaded by athena. Orginal plugin for SPEC data from BM23 has been integrated.
=head1 Methods
=over 4
=item C<is>
Recognize the SPEC files by the zapmono command line, which contains lines
starting with the string "#S 1 zapline mono"
=item C<fix>
Split different scans into separate files. Cleanup SPEC headers that can be quite messy.
=back
=head1 USAGE NOTES
Transmission data from SNBL uses column 13 (zapenergy) for the energy
column. For transmission data, use column 10 (ion1) as the numerator
and column 8 (ion2) as the denominator.
=head1 ACKNOWLEDGMENTS
Thanks to Bruce Ravel for writing the file-array import interface and the original BM23 plugin.
=head1 BUGS AND LIMITATIONS
=over 4
=item *
This plugin is in alfa-stage and should tested against SPEC generated datafiles from additional
beamlines.
Tested: SBNL@ESRF
To be tested: BM23@ESRF
=back
=head1 AUTHOR
Eric Breynaert
Athena copyright (c) 2001-2019
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