X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2FText%2FTradition%2FAnalysis.pm;h=2de129c4ccbf0aa7aab69b6e2951e765df1292c9;hb=7f52eac8cd00b160ea9e828790cbd093dc444feb;hp=910f9947e1f368ef7f76398cf7c197b0aab28b52;hpb=9317e522bb0299ab6bdcfe2d999750719e893407;p=scpubgit%2Fstemmatology.git diff --git a/lib/Text/Tradition/Analysis.pm b/lib/Text/Tradition/Analysis.pm index 910f994..2de129c 100644 --- a/lib/Text/Tradition/Analysis.pm +++ b/lib/Text/Tradition/Analysis.pm @@ -10,146 +10,209 @@ use Text::Tradition::Stemma; use vars qw/ @EXPORT_OK /; @EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /; +=head1 NAME + +Text::Tradition::Analysis - functions for stemma analysis of a tradition + +=head1 SYNOPSIS + + use Text::Tradition; + use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; + my $t = Text::Tradition->new( + 'name' => 'this is a text', + 'input' => 'TEI', + 'file' => '/path/to/tei_parallel_seg_file.xml' ); + $t->add_stemma( 'dotfile' => $stemmafile ); + + my $variant_data = run_analysis( $tradition ); + # Recalculate rank $n treating all orthographic variants as equivalent + my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' ); + +=head1 DESCRIPTION + +Text::Tradition is a library for representation and analysis of collated +texts, particularly medieval ones. The Collation is the central feature of +a Tradition, where the text, its sequence of readings, and its relationships +between readings are actually kept. + +=head1 SUBROUTINES + +=head2 run_analysis( $tradition, $stemma_id, @merge_relationship_types ) + +Runs the analysis described in analyze_variant_location on every location +in the collation of the given tradition, against the stemma specified in +$stemma_id. If $stemma_id is not specified, it defaults to 0 (referencing +the first stemma saved for the tradition.) + +The optional @merge_relationship_types contains a list of relationship types +to treat as equivalent for the analysis. + +=begin testing + +use Text::Tradition; +use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; + +my $datafile = 't/data/florilegium_tei_ps.xml'; +my $tradition = Text::Tradition->new( 'input' => 'TEI', + 'name' => 'test0', + 'file' => $datafile ); +my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' ); +is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" ); + +my $data = run_analysis( $tradition ); +# TODO should be 21! +is( $data->{'genealogical_count'}, 42, "Got right genealogical count" ); +is( $data->{'conflict_count'}, 17, "Got right conflict count" ); +is( $data->{'variant_count'}, 58, "Got right total variant number" ); + +=end testing + +=cut + sub run_analysis { - my( $tradition ) = @_; - # What we will return - my $variants = []; - my $data = {}; + my( $tradition, $stemma_id, @collapse ) = @_; + $stemma_id = 0 unless $stemma_id; - # We need a stemma in order to run this... - unless( $tradition->stemma_count ) { - warn "Tradition '" . $tradition->name . "' has no stemma to analyze"; - return undef; - } - my $stemma = $tradition->stemma(0); # TODO allow multiple - - # We have the collation, so get the alignment table with witnesses in rows. - # Also return the reading objects in the table, rather than just the words. - my $wits = {}; - map { $wits->{$_} = 1 } $stemma->witnesses; - # For each column in the alignment table, we want to see if the existing - # groupings of witnesses match our stemma hypothesis. We also need to keep - # track of the maximum number of variants at any one location. - my $max_variants = 0; - my ( $genealogical, $conflicts ) = ( 0, 0, 0 ); + # Run the variant analysis on every rank in the graph that doesn't + # have a common reading. Return the results. + my @variants; # holds results from analyze_variant_location + my $genealogical; # counter of 'genealogical' variants + my $conflicts; # counter of conflicting readings - my $variant_groups = group_variants( $tradition->collation, $wits ); - foreach my $rank ( 0 .. $#{$variant_groups} ) { - my $groups = $variant_groups->[$rank]->{'groups'}; - my $readings = $variant_groups->[$rank]->{'readings'}; - my $lacunose = $variant_groups->[$rank]->{'lacunose'}; - - $max_variants = scalar @$groups if scalar @$groups > $max_variants; - - # We can already look up witnesses for a reading; we also want to look - # up readings for a given witness. - my $group_readings = {}; - foreach my $x ( 0 .. $#$groups ) { - $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x]; - } - - # For all the groups with more than one member, collect the list of all - # contiguous vertices needed to connect them. - my $variant_loc = analyze_variant_location( $group_readings, $groups, - $stemma->graph, $lacunose ); - $variant_loc->{'id'} = $rank; - $genealogical++ if $variant_loc->{'genealogical'}; - $conflicts += grep { $_->{'conflict'} } @{$variant_loc->{'readings'}}; - - # Now run the same analysis given the calculated distance tree(s). -# my @trees = @{$stemma->distance_trees}; -# if( @trees ) { -# foreach my $tree ( 0 .. $#trees ) { -# my $dc = analyze_variant_location( $group_readings, $groups, $tree, $lacunose, 'undirected' ); -# foreach my $rdg ( keys %$dc ) { -# my $var = $dc->{$rdg}; -# # TODO Do something with this -# } -# } -# } - - # Record that we used this variant in an analysis - push( @$variants, $variant_loc ); + # Find and mark 'common' ranks for exclusion. + my %common_rank; + foreach my $rdg ( $tradition->collation->common_readings ) { + $common_rank{$rdg->rank} = 1; } - - # Go through our variant locations, after we have seen all of them once, - # and add the number of empty columns needed by each. - foreach my $row ( @$variants ) { - my $empty = $max_variants - scalar @{$row->{'readings'}}; - $row->{'empty'} = $empty; + + foreach my $rank ( 1 .. $tradition->collation->end->rank-1 ) { + next if $common_rank{$rank}; + my $variant_row = analyze_variant_location( + $tradition, $rank, $stemma_id, @collapse ); + push( @variants, $variant_row ); + $genealogical++ if $variant_row->{'genealogical'}; + $conflicts += grep { $_->{'conflict'} } @{$variant_row->{'readings'}}; } - $data->{'variants'} = $variants; - $data->{'variant_count'} = $tradition->collation->end->rank - 1; - $data->{'conflict_count'} = $conflicts; - $data->{'genealogical_count'} = $genealogical; - return $data; + return { + 'variants' => \@variants, + 'variant_count' => scalar @variants, # TODO redundant + 'conflict_count' => $conflicts, + 'genealogical_count' => $genealogical, + }; } +=head2 group_variants( $tradition, $rank, $lacunose, @merge_relationship_types ) + +Groups the variants at the given $rank of the collation, treating any +relationships in @merge_relationship_types as equivalent. $lacunose should +be a reference to an array, to which the sigla of lacunose witnesses at this +rank will be appended. + +Returns two ordered lists $readings, $groups, where $readings->[$n] is attested +by the witnesses listed in $groups->[$n]. + +=cut + +# Return group_readings, groups, lacunose sub group_variants { - my( $c, $wits ) = @_; - my $variant_groups = []; + my( $tradition, $rank, $lacunose, $collapse ) = @_; + my $c = $tradition->collation; + # Get the alignment table readings + my %readings_at_rank; + my @gap_wits; + foreach my $tablewit ( @{$tradition->collation->alignment_table->{'alignment'}} ) { + my $rdg = $tablewit->{'tokens'}->[$rank-1]; + if( $rdg && $rdg->{'t'}->is_lacuna ) { + push( @$lacunose, $tablewit->{'witness'} ); + } elsif( $rdg ) { + $readings_at_rank{$rdg->{'t'}->text} = $rdg->{'t'}; + } else { + push( @gap_wits, $tablewit->{'witness'} ); + } + } - # We have the collation, so get the alignment table with witnesses in rows. - # Also return the reading objects in the table, rather than just the words. - my $all_wits_table = $c->make_alignment_table( 'refs', $wits ); - # Strip the list of sigla and save it for correlation to the readings. - my @table_wits = map { $_->{'witness'} } @{$all_wits_table->{'alignment'}}; - # Any witness in the stemma that has no row should be noted. - foreach ( @table_wits ) { - $wits->{$_}++; # Witnesses present in table and stemma now have value 2. - } - my @not_collated = grep { $wits->{$_} == 1 } keys %$wits; - foreach my $i ( 0 .. $all_wits_table->{'length'} - 1 ) { - # For each column in the table, group the readings by witness. - my $rdg_wits = {}; - my @col_rdgs = map { $_->{tokens}->[$i] } @{$all_wits_table->{'alignment'}}; - my $lacunose = [ @not_collated ]; - foreach my $j ( 0 .. $#col_rdgs ) { - my $rdg = $col_rdgs[$j]; - my $rdg_text = '(omitted)'; # Initialize in case of empty reading - if( $rdg ) { - if( $rdg->{'t'}->is_lacuna ) { - $rdg_text = undef; # Don't count lacunae - push( @$lacunose, $table_wits[$j] ); - } else { - $rdg_text = $rdg->{'t'}->text; - } - } - if( defined $rdg_text ) { - # Initialize the witness array if we haven't got one yet - $rdg_wits->{$rdg_text} = [] unless $rdg_wits->{$rdg_text}; - # Add the relevant witness, subject to a.c. logic - add_variant_wit( $rdg_wits->{$rdg_text}, $table_wits[$j], - $c->ac_label ); + # Group the readings, collapsing groups by relationship if needed + my %grouped_readings; + foreach my $rdg ( sort { $b->witnesses <=> $a->witnesses } values %readings_at_rank ) { + # Skip readings that have been collapsed into others. + next if exists $grouped_readings{$rdg->text} && !$grouped_readings{$rdg->text}; + my @wits = $rdg->witnesses; + if( $collapse ) { + my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; }; + foreach my $other ( $rdg->related_readings( $filter ) ) { + push( @wits, $other->witnesses ); + $grouped_readings{$other->text} = 0; } } - - # See if this column has any potentially genealogical variants. - # If not, skip to the next. - my( $groups, $readings ) = useful_variant( $rdg_wits ); - next unless $groups && $readings; - - push( @$variant_groups, - { 'groups' => $groups, 'readings' => $readings, 'lacunose' => $lacunose } ); + $grouped_readings{$rdg->text} = \@wits; + } + $grouped_readings{'(omitted)'} = \@gap_wits if @gap_wits; + # Get rid of our collapsed readings + map { delete $grouped_readings{$_} unless $grouped_readings{$_} } + keys %grouped_readings + if $collapse; + + # Return the readings and groups, sorted by size + my( @readings, @groups ); + foreach my $r ( sort { @{$grouped_readings{$b}} <=> @{$grouped_readings{$a}} } + keys %grouped_readings ) { + push( @readings, $r ); + push( @groups, $grouped_readings{$r} ); } - return $variant_groups; + return( \@readings, \@groups ); } +=head2 analyze_variant_location( $tradition, $rank, $stemma_id, @merge_relationship_types ) +Runs an analysis of the given tradition, at the location given in $rank, +against the graph of the stemma specified in $stemma_id. The argument +@merge_relationship_types is an optional list of relationship types for +which readings so related should be treated as equivalent. -# variant_row -> genealogical -# -> readings [ { text, group, conflict, missing } ] +Returns a data structure as follows: + + { 'id' => $rank, + 'genealogical' => boolean, + 'readings => [ { text => $reading_text, + group => [ witnesses ], + conflict => [ conflicting ], + missing => [ excluded ] }, ... ] + } +where 'conflicting' is the list of witnesses whose readings conflict with +this group, and 'excluded' is the list of witnesses either not present in +the stemma or lacunose at this location. + +=cut sub analyze_variant_location { - my( $group_readings, $groups, $graph, $lacunose, $undirected ) = @_; + my( $tradition, $rank, $sid, @collapse ) = @_; + $DB::single = 1 if @collapse; + # Get the readings in this tradition at this rank + my @rank_rdgs = grep { $_->rank == $rank } $tradition->collation->readings; + # Get the applicable stemma + my $undirected; # TODO Allow undirected distance tree analysis too + my $stemma = $tradition->stemma( $sid ); + my $graph = $stemma->graph; + # Figure out which witnesses we are working with + my @lacunose = _set( 'symmdiff', [ $stemma->witnesses ], + [ map { $_->sigil } $tradition->witnesses ] ); + + # Now group the readings + my( $readings, $groups ) = + group_variants( $tradition, $rank, \@lacunose, \@collapse ); + my $group_readings = {}; + # Lookup table group string -> readings + foreach my $x ( 0 .. $#$groups ) { + $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x]; + } + + # Now do the work. my $contig = {}; my $subgraph = {}; my $is_conflicted; my $conflict = {}; - my $missing = {}; - map { $missing->{$_} = 1 } @$lacunose; - my $variant_row = { 'readings' => [] }; + my $variant_row = { 'id' => $rank, 'readings' => [] }; # Mark each ms as in its own group, first. foreach my $g ( @$groups ) { my $gst = wit_stringify( $g ); @@ -190,7 +253,7 @@ sub analyze_variant_location { my $nodes_in_subtree = 0; foreach my $root ( @roots ) { # Prune the tree to get rid of extraneous hypotheticals. - $root = prune_subtree( $part, $root, $contig ); + $root = _prune_subtree( $part, $root, $contig ); # Get all the successor nodes of our root. my $tmp_reach = { $root => 1 }; map { $tmp_reach->{$_} = 1 } $part->all_successors( $root ); @@ -232,7 +295,7 @@ sub analyze_variant_location { # Write the reading. my $reading = { 'text' => $group_readings->{$gst}, - 'missing' => wit_stringify( $lacunose ), + 'missing' => wit_stringify( \@lacunose ), 'group' => $gst }; # This will change if we find no conflict if( $is_conflicted ) { $reading->{'conflict'} = $conflict->{$group_readings->{$gst}} @@ -307,10 +370,12 @@ sub analyze_variant_location { } # Now write the group and conflict information into the respective rows. + my %missing; + map { $missing{$_} = 1 } @lacunose; # quick lookup table foreach my $rdg ( @{$variant_row->{'readings'}} ) { $rdg->{'conflict'} = $conflict->{$rdg->{'text'}}; next if $rdg->{'conflict'}; - my @members = grep { $contig->{$_} eq $rdg->{'group'} && !$missing->{$_} } + my @members = grep { $contig->{$_} eq $rdg->{'group'} && !$missing{$_} } keys %$contig; $rdg->{'group'} = wit_stringify( \@members ); } @@ -319,7 +384,7 @@ sub analyze_variant_location { return $variant_row; } -sub prune_subtree { +sub _prune_subtree { my( $tree, $root, $contighash ) = @_; # First, delete hypothetical leaves / orphans until there are none left. my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } @@ -351,25 +416,12 @@ sub add_variant_wit { push( @$arr, $wit ) unless $skip; } -# Return an answer if the variant is useful, i.e. if there are at least 2 variants -# with at least 2 witnesses each. -sub useful_variant { - my( $readings ) = @_; - my $total = keys %$readings; - foreach my $var ( keys %$readings ) { - $total-- if @{$readings->{$var}} == 1; - } - return( undef, undef ) if $total <= 1; - my( $groups, $text ); - foreach my $var ( keys %$readings ) { - push( @$groups, $readings->{$var} ); - push( @$text, $var ); - } - return( $groups, $text ); -} +=head2 wit_stringify( $groups ) + +Takes an array of witness groupings and produces a string like +['A','B'] / ['C','D','E'] / ['F'] -# Take an array of witness groupings and produce a string like -# ['A','B'] / ['C','D','E'] / ['F'] +=cut sub wit_stringify { my $groups = shift; @@ -385,5 +437,32 @@ sub wit_stringify { } return join( ' / ', @gst ); } - -1; \ No newline at end of file + +sub _set { + my( $op, $lista, $listb ) = @_; + my %union; + my %scalars; + map { $union{$_} = 1; $scalars{$_} = $_ } @$lista; + map { $union{$_} += 1; $scalars{$_} = $_ } @$listb; + my @set; + if( $op eq 'intersection' ) { + @set = grep { $union{$_} == 2 } keys %union; + } elsif( $op eq 'symmdiff' ) { + @set = grep { $union{$_} == 1 } keys %union; + } elsif( $op eq 'union' ) { + @set = keys %union; + } + return map { $scalars{$_} } @set; +} + +1; + +=head1 LICENSE + +This package is free software and is provided "as is" without express +or implied warranty. You can redistribute it and/or modify it under +the same terms as Perl itself. + +=head1 AUTHOR + +Tara L Andrews Eaurum@cpan.orgE