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Randomisations: Refactor and cache constant labels #952

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merged 3 commits into from
Nov 12, 2024
Merged

Randomisations: Refactor and cache constant labels #952

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a8911aa
Rand: refactor constant label parsing
shawnlaffan Nov 12, 2024
e1b51b9
Rand: Cache constant labels parsed from string
shawnlaffan Nov 12, 2024
80f2659
Rand: Cache constant labels basedatas
shawnlaffan Nov 12, 2024
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104 changes: 68 additions & 36 deletions lib/Biodiverse/Randomise.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -776,29 +776,26 @@ sub verify_cwd_is_writeable_for_checkpoints {
return 1;
}

sub get_randomised_basedata {
my $self = shift;
my %args = @_;

# no need to generate a separate set if no labels to hold constant
return $self->_get_randomised_basedata (%args)
if !$args{labels_not_to_randomise};
sub _parse_labels_not_to_randomise {
my ($self, %args) = @_;

my $bd = $args{basedata_ref} || $self->get_param ('BASEDATA_REF');
my $constant_labels = $args{labels_not_to_randomise};

my $const_bd = Biodiverse::BaseData->new($bd->get_params_hash);
my $non_const_bd = Biodiverse::BaseData->new($bd->get_params_hash);
$const_bd->rename (new_name => $const_bd->get_name . ' constant label subset');
$non_const_bd->rename (new_name => $non_const_bd->get_name . ' random label subset');
return if !$constant_labels;

if (!ref $constant_labels) {
state $cache_key = 'CONSTANT_LABELS_ARRAY';
if (my $cache = $self->get_cached_value ($cache_key)) {
$constant_labels = $cache;
}
elsif (!is_ref $constant_labels) {
$constant_labels = [split /[\r\n]+/, $constant_labels];
# Maybe we were passed a list of key value pairs
# This can happen with pasting from GUI popups
my $label1 = $constant_labels->[0];
# copy-pasted from a GUI cell popup
if (!$bd->exists_label(label => $label1) && $label1 =~ /(.+)\t+\d+$/) {
if ($bd->exists_label(label => $1)) {
if ($bd->exists_label(label => $1)) {
for my $label (@$constant_labels) {
$label =~ s/\s+\d+$//;
}
Expand All @@ -808,34 +805,69 @@ sub get_randomised_basedata {
say "[Randomise] Constant labels, first 0..$n are "
. join ' ', @$constant_labels[0 .. $n];
}

my $csv_object = $bd->get_csv_object (
sep_char => $bd->get_param('JOIN_CHAR'),
quote_char => $bd->get_param('QUOTES'),
);

my %const_label_hash;
@const_label_hash{@$constant_labels} = undef;
for my $label ($bd->get_labels) {
my $groups = $bd->get_groups_with_label_as_hash_aa ($label);
$self->set_cached_value ($cache_key => $constant_labels);

# we should cache the constant BD
my $target_bd = exists $const_label_hash{$label} ? $const_bd : $non_const_bd;
$target_bd->add_elements_collated_by_label (
data => {$label => $groups},
csv_object => $csv_object,
);
}
foreach my $empty_gp ($bd->get_empty_groups) {
$const_bd->add_element (
group => $empty_gp,
count => 0,
allow_empty_groups => 1,
return wantarray ? @$constant_labels : $constant_labels;
}

sub get_randomised_basedata {
my $self = shift;
my %args = @_;

# no need to generate a separate set if no labels to hold constant
return $self->_get_randomised_basedata (%args)
if !$args{labels_not_to_randomise};

my $bd = $args{basedata_ref} || $self->get_param ('BASEDATA_REF');
my $constant_labels = $self->_parse_labels_not_to_randomise(%args);

state $cache_key_const_bd = 'CONSTANT_LABELS_CONST_BASEDATA';
state $cache_key_rand_bd = 'CONSTANT_LABELS_RAND_BASEDATA';

my $const_bd = $self->get_cached_value ($cache_key_const_bd);
my $non_const_bd = $self->get_cached_value ($cache_key_rand_bd);

if (!$const_bd && !$non_const_bd) {
$const_bd = Biodiverse::BaseData->new($bd->get_params_hash);
$non_const_bd = Biodiverse::BaseData->new($bd->get_params_hash);

$const_bd->rename(new_name => $const_bd->get_name . ' constant label subset');
$non_const_bd->rename(new_name => $non_const_bd->get_name . ' random label subset');

my $csv_object = $bd->get_csv_object(
sep_char => $bd->get_param('JOIN_CHAR'),
quote_char => $bd->get_param('QUOTES'),
);

my %const_label_hash;
@const_label_hash{@$constant_labels} = undef;
for my $label ($bd->get_labels) {
my $groups = $bd->get_groups_with_label_as_hash_aa($label);

# we should cache the constant BD
my $target_bd = exists $const_label_hash{$label} ? $const_bd : $non_const_bd;
$target_bd->add_elements_collated_by_label(
data => { $label => $groups },
csv_object => $csv_object,
);
}
foreach my $empty_gp ($bd->get_empty_groups) {
$const_bd->add_element(
group => $empty_gp,
count => 0,
allow_empty_groups => 1,
);
}

$const_bd->rebuild_spatial_index;
$non_const_bd->rebuild_spatial_index; # sometimes the non_const basedata is "missing" groups

$self->set_cached_value ($cache_key_const_bd => $const_bd);
$self->set_cached_value ($cache_key_rand_bd => $non_const_bd);
}

$const_bd->rebuild_spatial_index;
$non_const_bd->rebuild_spatial_index; # sometimes the non_const basedata is "missing" groups
# randomise the "randomisable" one
my $new_rand_bd = $self->_get_randomised_basedata (%args, basedata_ref => $non_const_bd);

# add the constant labels
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