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package Demeter::Plugins::Lytle;
use Const::Fast;
const my $INIFILE => 'lytle.demeter_conf';
use Moose;
extends 'Demeter::Plugins::FileType';
has '+conffile' => (default => File::Spec->catfile(Demeter->dot_folder, $INIFILE));
has '+is_binary' => (default => 0);
has '+description' => (default => "the Lytle database file stored by encoder value");
has '+version' => (default => 0.2);
use Demeter::Constants qw($R2D $HC);
use File::Basename;
use File::Copy;
use File::Spec;
use Scalar::Util qw(looks_like_number);
use List::MoreUtils qw(all);
Demeter -> co -> read_config(File::Spec->catfile(dirname($INC{'Demeter.pm'}), 'Demeter', 'Plugins', $INIFILE));
sub is {
my ($self) = @_;
open D, $self->file or $self->Croak("could not open " . $self->file . " as data (Lytle)\n");
my $first = <D>;
close D;
return 1 if ($first =~ m{\A\s*NPTS\s+NS\s+CUEDGE\s+CUHITE});
#return 1 if ($first =~ m{\A\s*CUEDGE\s+START\s+STOP\s+BEG\s+FSCTS});
return 0;
};
sub fix {
my ($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 D, $file or die "could not open $file as data (fix in Lytle)\n";
open N, ">".$new or die "could not write to $new (fix in Lytle)\n";
my ($stpdeg, $dspacing) = (Demeter->co->default('lytle', 'stpdeg'), Demeter->co->default('lytle', 'dspace'));
while (<D>) {
chomp;
next if (m{\A\s*\z});
$_ =~ s{(E(-|\+)\d+)-}{$1 }g; # fix what appears to be a Fortran formatting overrun
my @list = split(" ", $_);
if ($_ =~ m{\A\s*NPTS}) { # first two lines, snarf mono parameters
print N "# ", $_, $/;
my $line = <D>;
print N "# ", $line;
my @fields = split(" ", $line);
($dspacing, $stpdeg) = @fields[4,5];
} elsif ($_ =~ m{\A\s*(?:DELTA|DELEND|SEC|OFFSETS?)}) { # various headers
print N "# ", $_, $/;
} elsif (all {looks_like_number($_)} @list) {
#my $line = <D>;
#$line =~ s{(E[-+]\d+)-}{$1 -}gi;
#my @fields = split(" ", $line);
my $steps = shift @list;
my $energy = $HC / (2 * $dspacing) / sin( $steps / ($R2D * $stpdeg));
print N join(" ", sprintf("%12.5E", $energy), @list) . $/;
} else { #($_ =~ m{\d{1,2}-\d{1,2}\-\d{1,2}\s*\z}) { # comment line with date at end
#print "found it!\n";
print N "# ", $_, $/;
print N "# -----------------------", $/;
print N "# energy i0 it if ir", $/;
};
};
close N;
close D;
$self->fixed($new);
return $new;
};
sub suggest {
my ($self, $which) = @_;
$which ||= 'transmission';
if ($which eq 'transmission') {
return (energy => '$1',
numerator => '$2',
denominator => '$3',
ln => 1,);
} else {
return (energy => '$1',
numerator => '$4',
denominator => '$2',
ln => 0,);
};
};
__PACKAGE__->meta->make_immutable;
1;
=head1 NAME
Demeter::Plugin::Lytle - Import Lytle database files stored by encoder value.
=head1 VERSION
This documentation refers to Demeter version 0.9.26.
=head1 SYNOPSIS
Import Lytle data of the sort that stores encoder value and requires a
transformation to energy. See question 3 at
L<http://cars9.uchicago.edu/ifeffit/FAQ/Data_Handling>.
=head1 DESCRIPTION
This parses the header to obtain the monochromator d-spacing and the
steps per degree, then uses those values to convert the first column
-- which contains encoder values -- into energy values. All headers
are simply commented and no attempt is made to write column labels,
The Lytle files that are processed by this plugin have headers that
look like this:
NPTS NS CUEDGE CUHITE DSPACE STPDEG STEPMM START STOP SCALE
480 4 84294. 200000. 1.92017 4000. 3150. 85290. 74500. 2.000
DELTA: 50. 8. 16. 32. 46.
DELEND: 84788. 83804. 81216. 76752. 71076.
SEC: 2.000 2.000 2.000 2.000 2.000
OFFSET: 1830. 1937. 366. 851. 4. 6. 137. 4. 6. 18. 641. 3. 2. 5. 61. 20. 93. 232. 0. 0. 0. 0. 0. 0.
5% CU/CAB IN H2 AT 40C 7 9 6-10-83
=head1 BUGS AND LIMITATIONS
=over 4
=item *
Given that the Lytle database stores the files as unix compressed (.Z)
files, directly read compressed files using Archive::Zip
=back
=head1 AUTHOR
Bruce Ravel, L<http://bruceravel.github.io/home>
http://bruceravel.github.io/demeter
=cut
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