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package Demeter::Plugins::CMC; # -*- cperl -*-
use Moose;
extends 'Demeter::Plugins::FileType';
has '+is_binary' => (default => 0);
has '+description' => (default => "APS 9BM (CMC-XOR)");
has '+version' => (default => 0.1);
sub is {
my ($self) = @_;
my $is_cmc = 0;
open D, $self->file or $self->Croak("could not open " . $self->file . " in CMC\n");
my $line;
foreach (1 .. 4) { $line = <D> };
$is_cmc = ($line =~ /^\#C.+(?:bmexafs|9bmuser)/);
close D;
return $is_cmc;
};
sub fix {
my ($self) = @_;
my $new = File::Spec->catfile($self->stash_folder, $self->filename);
($new = File::Spec->catfile($self->stash_folder, "toss")) if (length($new) > 127);
open D, $self->file or die "could not open " . $self->file . " as data (fix in MRMED)\n";
open N, ">".$new or die "could not open $new in MRMED\n";
my %keep = ();
my %dark = ();
my $col = 0;
my $header = 1;
my $column_labels = "";
while (<D>) {
next if /^\s*$/; # skip blank lines
if ($_ =~ /^#L/) { # parse column lables line
chomp;
my @labels = split(" ", $_);
shift @labels;
foreach my $l (@labels) {
if ($l =~ /^(energy|i[0-2]|iref|lytle|mca\d+)$/i) {
$keep{$col} = $l;
$column_labels .= " $l";
} elsif ($l =~ /^(i[0-2]off)$/i) { # columns with offset PVs
$dark{$col} = $l;
};
++$col;
};
print N $_,$/;
} elsif ($_ =~ /^#/) { # stream other header lines
print N $_;
} else { # data begins ...
chomp;
my @data = split(" ", $_);
if ($header) { # dig through the columns to match
# the offset-subtracted columns with
# raw signal columns
foreach my $k (sort {$a <=> $b} keys %keep) {
if ($keep{$k} =~ /i\d/i) {
foreach my $d (keys %dark) {
if ($dark{$d} =~ /$keep{$k}/) {
$dark{$keep{$k}} = ($data[$k] - $data[$d]*$data[-1]);
$dark{$keep{$k}} /= $data[-1];
};
};
};
};
print N "#C dark current: "; # make a header line with dark currents
foreach my $l (sort {$a <=> $b} keys %keep) {
if ($keep{$l} =~ /^(i[0-2])$/i) {
print N ucfirst($keep{$l}), "=", $dark{$keep{$l}}, " c/s ";
};
};
print N "$/# ---------------------------------------------$/#$column_labels$/";
$header = 0;
};
foreach my $k (sort {$a <=> $b} keys %keep) {
my $point = $data[$k];
if ($keep{$k} =~ /^i\d$/) {
$point -= $dark{$keep{$k}}*$data[-1]; # subtract dark current * integration time
};
($point = 0) if (lc($point) eq 'nan');
print N " ", $point;
};
print N $/;
};
};
close D;
close N;
$self->fixed($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 => '$7+$8+$9+$10+$11+$13',
denominator => '$2',
ln => 0,);
};
};
__PACKAGE__->meta->make_immutable;
1;
=head1 NAME
Demeter::Plugin::CMC - filetype plugin for files from APS Sector 9
=head1 VERSION
This documentation refers to Demeter version 0.9.26.
=head1 SYNOPSIS
This plugin strips the many columns not normally needed from a file
from CMC APS Sector 9 in an effort to interact with Ifeffit more
efficiently and avoid some of the pitfalls of the CMC file format.
This plugin is used with the SPEC file generated using the smaller,
upstream station and is not necessary for data files obtained from the
newer control system using the software orginally fro 20BM.
=head1 Methods
=over 4
=item C<is>
Recognize the Sector 9 BM file by the fourth line, which starts with
the Spec #C token and identifies the user as "bmexafs".
=item C<fix>
Strip out all columns except for energy, I0, I1, I2, Lytle, and mca* and write
them to a file in the stash directory. Remove dark current from the i*
channels. Also fix any instances of NaN among the data (probably only in the
ill-conceived logi0i1 column, but...) and strip out any blank lines.
=back
=head1 AUTHOR
Bruce Ravel, L<http://bruceravel.github.io/home>
http://bruceravel.github.io/demeter
=cut
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