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package Demeter::Plugins::BL8Ar; # -*- cperl -*-
use File::Basename;
use File::Copy;
use File::Spec;
use Wx qw( :everything );
use Moose;
extends 'Demeter::Plugins::FileType';
use Const::Fast;
const my $INIFILE => 'bl8ar.demeter_conf';
has '+conffile' => (default => File::Spec->catfile(Demeter->dot_folder, $INIFILE));
has '+is_binary' => (default => 0);
has '+description' => (default => 'SLRI BL8 (correct for Ar in I0)');
has '+version' => (default => 0.1);
has 'measurement_mode' => (is => 'rw', isa => 'Str', default => q{transmission});
has 'step_size' => (is => 'rw', isa => 'LaxNum', default => 0);
Demeter -> co -> read_config(File::Spec->catfile(dirname($INC{'Demeter.pm'}), 'Demeter', 'Plugins', $INIFILE));
my $ar_k = Xray::Absorption->get_energy('Ar', 'K') / Demeter->co->default('bl8ar', 'harmonic');
sub is {
my ($self) = @_;
open(my $D, '<', $self->file) or $self->Croak("could not open " . $self->file . " as data (BL8Ar)\n");
my $line = <$D>;
my $is_bl8 = ($line =~ m{BL8: X-ray Absorption Spectroscopy}) ? 1 : 0;
return 0 if not $is_bl8;
my $is_near_ar = 0;
while (<$D>) {
if ($_ =~ m{\# E0 \(eV\)\s+=\s+(\d+)}) {
$is_near_ar = 1 if (($ar_k - $1) < Demeter->co->default('bl8ar', 'margin'));
$is_near_ar = 0 if ($ar_k < $1);
last;
};
};
close $D;
return $is_near_ar;
};
sub fix {
my ($self) = @_;
my $file = $self->file;
my $new = File::Spec->catfile($self->stash_folder, $self->filename);
($new = File::Spec->catfile($self->stash_folder, "toss")) if (length($new) > 127);
open(my $D, '<', $file) or die "could not open $file as data (fix in BL8Ar)\n";
open(my $N, ">", $new) or die "could not write to $new (fix in BL8Ar)\n";
my $format = q{};
my $ncols = 0;
my $nchannels = 0;
my (@data_table, @e, @i0);
while (<$D>) {
next if ($_ =~ m{\A\s*\z});
if ($_ =~ m{\A\#}) {
print $N $_; # pass the headers through to the stash file
if ($_ =~ m{Si Drift 4-Array}) {
$self->measurement_mode('sidrift');
$ncols = 10;
$nchannels = 4;
} elsif ($_ =~ m{Transmission-mode XAS}) {
$self->measurement_mode('trans');
$ncols = 6;
$nchannels = 1;
} elsif ($_ =~ m{Ge 13-array}i) {
$self->measurement_mode('ge');
$ncols = 19;
$nchannels = 13;
};
} elsif ($_ =~ m{\AEnergy}) {
1;
} else {
$_ =~ tr{\r}{}d;
push @data_table, $_;
my @list = split(" ", $_);
push @e, $list[0];
push @i0, $list[3];
};
};
$format = "%10.5E " x $ncols . "\n";
my $ar = Demeter::Data->put(\@e, \@i0, datatype=>'xanes', bkg_e0=>$ar_k, bkg_nnorm=>2,
bkg_pre1=>Demeter->co->default('bl8ar', 'pre1'),
bkg_pre2=>Demeter->co->default('bl8ar', 'pre2'),
bkg_nor1=>Demeter->co->default('bl8ar', 'nor1'),
bkg_nor2=>Demeter->co->default('bl8ar', 'nor2'),
);
$ar->_update('background');
if (Demeter->co->default('bl8ar', 'plot')) {
$ar->po->set(e_mu=>1, e_norm=>0, e_pre=>1, e_post=>1);
$ar->po->start_plot;
$ar->plot('E');
eval 'my $message = Wx::MessageDialog->new($::app->{main}, "Plot of I0 is being displayed", "I0 plot displayed", wxOK);
$message->ShowModal;';
#print $ar->bkg_step, $/;
};
$self->step_size($ar->bkg_step);
## add a header line about the Ar step size and add a useful set of column labels
printf $N "# Ar K edge step size found in I0 = %.3f\n", $self->step_size;
print $N "# Energy BraggAngle TimeStep I0 I1 mu";
print $N " SCA0 SCA1 SCA2 SCA3" if ($self->measurement_mode eq 'sidrift');
print $N " SCA0 SCA1 SCA2 SCA3 SCA4 SCA5 SCA6 SCA7 SCA8 SCA9 SCA10 SCA11 SCA12" if ($self->measurement_mode eq 'ge');
print $N "\n";
## pass through most columns in the data table
## correct the i0 column (column 5)
## scale the mu column (column 6) by the number of channels so it is directly comparable to the corrected data
foreach my $point (@data_table) {
my @list = split(" ", $point);
my $offset = ($list[0] > $ar_k) ? $self->step_size : 0;
printf $N $format,
@list[0..2], $list[3]-$offset, $list[4], $list[5]*$nchannels, @list[6..5+$nchannels];
};
undef($ar);
close $N;
close $D;
$self->fixed($new);
return $new;
};
sub suggest {
my ($self, $which) = @_;
$which ||= 'fluorescence';
$which = 'transmission' if ($self->measurement_mode eq 'trans');
if ($which eq 'transmission') {
return (energy => '$1',
numerator => '$4',
denominator => '$5',
ln => 1,);
} else {
my $num = '$7+$8+$9+$10';
$num = '$7+$8+$9+$10+$11+$12+$13+$14+$15+$16+$17+$18+$19' if ($self->measurement_mode eq 'ge');
return (energy => '$1',
numerator => '$7+$8+$9+$10',
denominator => '$4',
ln => 0,);
};
};
1;
=head1 NAME
Demeter::Plugin::BL8Ar - filetype plugin for removing the effect of Ar in I0 at SLRI BL8
=head1 VERSION
This documentation refers to Demeter version 0.9.26.
=head1 SYNOPSIS
This plugin converts attempts to remove the effect of the edge step
visible in I0 due to Ar contamination in the I0 chamber at SLRI BL8.
This removes the edge jump visible in I0 when measuring, for instance,
the Al K edge.
The Ar step is visible due to the presence of the second harmonic in
the incident beam, which is not normally filtered in any way at BL8.
Al is probably the only K edge affected by this problem. The
fundamental or the second harmonic could impact measurement of the L3
edges of Ru, Rh, Pd, As, Se, or Br.
=head1 METHODS
=over 4
=item C<is>
This file is identified by the string "BL8: X-ray Absorption
Spectroscopy" in the first line of the file, then by an edge energy
that is within 200 volts of the Ar K edge energy divided by 2. (The
division by 2 is because the Ar signal is caused by the second
harmonic of the monochromator.)
=item C<fix>
Remove the step from I0, then suggest columns appropriate to the
measurement mode.
Note that column 6 is still the unaltered calculation of mu(E),
although it has been multiplied by the number of detector channels so
that it may be directly compared with sum of detector channels
suggested by this plugin. This allows easy comparison between the raw
and corrected measures of mu(E). Try importing column 6 as the
reference channel -- uncheck the natural log button for the reference.
=back
=head1 AUTHOR
Bruce Ravel, L<http://bruceravel.github.io/home>
http://bruceravel.github.io/demeter
=cut
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