X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2FText%2FTradition%2FAnalysis.pm;h=2de129c4ccbf0aa7aab69b6e2951e765df1292c9;hb=c12bb87843b49eee09f588126ac7d375046b29fd;hp=f4605ed8d230756ba067dc260b5a6dadc3097af2;hpb=94a077d641e8c906d7131a059b009f335781337a;p=scpubgit%2Fstemmatology.git diff --git a/lib/Text/Tradition/Analysis.pm b/lib/Text/Tradition/Analysis.pm index f4605ed..2de129c 100644 --- a/lib/Text/Tradition/Analysis.pm +++ b/lib/Text/Tradition/Analysis.pm @@ -2,191 +2,408 @@ package Text::Tradition::Analysis; use strict; use warnings; +use Benchmark; +use Exporter 'import'; use Text::Tradition; use Text::Tradition::Stemma; -sub new { - my( $class, $args ) = @_; - my $self = {}; - bless( $self, $class ); - $self->{'data'} = []; - foreach my $t ( @{$args->{'traditions'}} ) { - $self->run_analysis( $t->{'file'}, $t->{'stemmadot'} ); - } - return $self; -} +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( $self, $file, $stemmadot ) = @_; - # What we will return - my $svg; - my $variants = []; - my $data = {}; + my( $tradition, $stemma_id, @collapse ) = @_; + $stemma_id = 0 unless $stemma_id; - # Read in the file and stemma - my $tradition = Text::Tradition->new( - 'input' => 'Self', - 'file' => $file, - 'linear' => 1, - ); - $data->{'title'} = $tradition->name; + # 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 $stemma = Text::Tradition::Stemma->new( - 'collation' => $tradition->collation, - 'dot' => $stemmadot, - ); - # We will return the stemma picture - $svg = $stemma->as_svg( { size => "8,7.5" } );; - $data->{'svg'} = $svg; - - # 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 = $tradition->collation->make_alignment_table( 'refs' ); - - # For each column in the alignment table, we want to see if the existing - # groupings of witnesses match our stemma hypothesis. We also want, at the - # end, to produce an HTML table with all the variants. - my $html_columns = 0; - my ( $total, $genealogical, $conflicts ) = ( 0, 0, 0 ); - - # Strip the list of sigla and save it for correlation to the readings. - my $col_wits = shift @$all_wits_table; + # Find and mark 'common' ranks for exclusion. + my %common_rank; + foreach my $rdg ( $tradition->collation->common_readings ) { + $common_rank{$rdg->rank} = 1; + } - # We will return a data structure, an array for each row that looks like: - # { id = X, genealogical = Y, readings = [ text = X, group = Y], empty = N } - foreach my $i ( 0 .. $#$all_wits_table ) { - # For each column in the table, group the readings by witness. - my $rdg_wits = {}; - my $col_rdgs = shift @$all_wits_table; - my $rank; - my $lacunose = []; - 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->is_lacuna ) { - $rdg_text = undef; # Don't count lacunae - push( @$lacunose, $col_wits->[$j] ); - } else { - $rdg_text = $rdg->text; - # Get the rank from any real reading; they should be identical. - $rank = $rdg->rank; - } - } - 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}, $col_wits->[$j], - $tradition->collation->ac_label ); - } - } - - # See if this column has any potentially genealogical variants. - # If not, skip to the next. - $total++ unless scalar keys %$rdg_wits == 1; - my( $groups, $readings ) = useful_variant( $rdg_wits ); - next unless $groups && $readings; - - # Keep track of our widest row - $html_columns = scalar @$groups if scalar @$groups > $html_columns; - - # 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. - # TODO: deal with a.c. reading logic - $DB::single = 1 if $rank == 25; - my $variant_row = analyze_variant_location( $group_readings, $groups, - $stemma->apsp, $lacunose ); - $variant_row->{'id'} = $rank; + 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'}}; + } + + 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]. - # 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, -# $stemma->distance_apsps->[$tree] ); -# 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_row ); +=cut + +# Return group_readings, groups, lacunose +sub group_variants { + 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'} ); + } } - # Go through our variant rows, after we have seen all of them once, - # and add the number of empty columns needed by each. - foreach my $row ( @$variants ) { - my $empty = $html_columns - scalar @{$row->{'readings'}}; - $row->{'empty'} = $empty; + # 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; + } + } + $grouped_readings{$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; - # Populate self with our analysis data. - $data->{'variants'} = $variants; - $data->{'variant_count'} = $total; - $data->{'conflict_count'} = $conflicts; - $data->{'genealogical_count'} = $genealogical; - push( @{$self->{'data'}}, $data ); + # 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( \@readings, \@groups ); } -# variant_row -> genealogical -# -> readings [ { text, group, conflict, missing } ] +=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. + +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, $apsp, $lacunose ) = @_; - my %contig; + 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 ); - map { $contig{$_} = $gst } @$g; + map { $contig->{$_} = $gst } @$g; } + # Now for each unmarked node in the graph, initialize an array + # for possible group memberships. We will use this later to + # resolve potential conflicts. + map { $contig->{$_} = [] unless $contig->{$_} } $graph->vertices; foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) { - my @members = @$g; - my $gst = wit_stringify( $g ); # $gst is now the name of this group. - while( @members ) { - # Gather the list of vertices that are needed to join all members. - my $curr = pop @members; - foreach my $m ( @members ) { - foreach my $v ( $apsp->path_vertices( $curr, $m ) ) { - $contig{$v} = $gst unless exists $contig{$v}; - next if $contig{$v} eq $gst; - # Record what is conflicting. TODO do we use this? - $conflict->{$group_readings->{$gst}} = $group_readings->{$contig{$v}}; + my $gst = wit_stringify( $g ); # This is the group name + my $reachable = { $g->[0] => 1 }; + # Copy the graph, and delete all non-members from the new graph. + my $part = $graph->copy; + my $group_root; + $part->delete_vertices( + grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices ); + + # Now look to see if our group is connected. + if( $undirected ) { # For use with distance trees etc. + # Find all vertices reachable from the first (arbitrary) group + # member. If we are genealogical this should include them all. + map { $reachable->{$_} = 1 } $part->all_reachable( $g->[0] ); + # TODO This is a terrible way to do distance trees, since all + # non-leaf nodes are included in every graph part now. We may + # have to go back to SPDP. + } else { + if( @$g > 1 ) { + # Dispense with the trivial case of one reading. + # We have to take directionality into account. + # How many root nodes do we have? + my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst } + $part->source_vertices; + # Assuming that @$g > 1, find the first root node that has at + # least one successor belonging to our group. If this reading + # is genealogical, there should be only one, but we will check + # that implicitly later. + my $nodes_in_subtree = 0; + foreach my $root ( @roots ) { + # Prune the tree to get rid of extraneous hypotheticals. + $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 ); + # Skip this root if none of our successors are in our group + # (e.g. isolated 'hypothetical' witnesses with no group) + next unless grep { $contig->{$_} } keys %$tmp_reach; + if( keys %$tmp_reach > $nodes_in_subtree ) { + $nodes_in_subtree = keys %$tmp_reach; + $reachable = $tmp_reach; + $group_root = $root; + } } + } # else it is a single-node group, nothing to calculate. + } + + # None of the 'reachable' nodes should be marked as being in another + # group. Paint the 'hypotheticals' with our group while we are at it, + # unless there is a conflict present. + foreach ( keys %$reachable ) { + if( ref $contig->{$_} ) { + push( @{$contig->{$_}}, $gst ); + } elsif( $contig->{$_} ne $gst ) { + $conflict->{$group_readings->{$gst}} = $group_readings->{$contig->{$_}}; + } # else it is an 'extant' node marked with our group already. + } + # None of the unreachable nodes should be in our group either. + foreach ( $part->vertices ) { + next if $reachable->{$_}; + if( $contig->{$_} eq $gst ) { + $conflict->{$group_readings->{$gst}} = $group_readings->{$gst}; + last; } } + + # Now, if we have a conflict, we can write the reading in full. If not, + # we have to save the subgraph so that we can resolve possible conflicts + # on hypothetical nodes. + $is_conflicted = 1 if exists $conflict->{$group_readings->{$gst}}; + # Write the reading. my $reading = { 'text' => $group_readings->{$gst}, - 'missing' => wit_stringify( $lacunose ), - 'conflict' => exists( $conflict->{$group_readings->{$gst}} ) }; - if( $reading->{'conflict'} ) { - $reading->{'group'} = $gst; + 'missing' => wit_stringify( \@lacunose ), + 'group' => $gst }; # This will change if we find no conflict + if( $is_conflicted ) { + $reading->{'conflict'} = $conflict->{$group_readings->{$gst}} } else { - my @all_vertices = grep { $contig{$_} eq $gst && !$missing{$_} } keys %contig; - $reading->{'group'} = wit_stringify( \@all_vertices ); + # Save the relevant subgraph. + $subgraph->{$gst} = { 'graph' => $part, + 'root' => $group_root, + 'reachable' => $reachable }; } push( @{$variant_row->{'readings'}}, $reading ); } - $variant_row->{'genealogical'} = keys %$conflict ? undef : 1; + + # Now that we have gone through all the rows, check the hypothetical + # readings for conflict if we haven't found one yet. + if( keys %$subgraph && !keys %$conflict ) { + my @resolve; + foreach ( keys %$contig ) { + next unless ref $contig->{$_}; + if( scalar @{$contig->{$_}} > 1 ) { + push( @resolve, $_ ); + } else { + $contig->{$_} = scalar @{$contig->{$_}} ? $contig->{$_}->[0] : ''; + } + } + # Do we still have a possible conflict? + my $still_contig = {}; + foreach my $h ( @resolve ) { + # For each of the hypothetical readings with more than one possibility, + # try deleting it from each of its member subgraphs in turn, and see + # if that breaks the contiguous grouping. + # TODO This can still break in a corner case where group A can use + # either vertex 1 or 2, and group B can use either vertex 2 or 1. + # Revisit this if necessary; it could get brute-force nasty. + foreach my $gst ( @{$contig->{$h}} ) { + my $gpart = $subgraph->{$gst}->{'graph'}->copy; + my $reachable = $subgraph->{$gst}->{'reachable'}; + $gpart->delete_vertex( $h ); + # Is everything else still reachable from the root? + # TODO If $h was the root, see if we still have a single root. + my %still_reachable = ( $subgraph->{$gst}->{'root'} => 1 ); + map { $still_reachable{$_} = 1 } + $gpart->all_successors( $subgraph->{$gst}->{'root'} ); + foreach my $v ( keys %$reachable ) { + next if $v eq $h; + if( !$still_reachable{$v} + && ( $contig->{$v} eq $gst + || ( exists $still_contig->{$v} + && $still_contig->{$v} eq $gst ) ) ) { + # We need $h. + if( exists $still_contig->{$h} ) { + # Conflict! + $conflict->{$group_readings->{$gst}} = + $group_readings->{$still_contig->{$h}}; + } else { + $still_contig->{$h} = $gst; + } + last; + } # else we don't need $h in this group. + } + } + } + + # Now, assuming no conflict, we have some hypothetical vertices in + # $still_contig that are the "real" group memberships. Replace these + # in $contig. + unless ( keys %$conflict ) { + foreach my $v ( keys %$contig ) { + next unless ref $contig->{$v}; + $contig->{$v} = $still_contig->{$v}; + } + } + } + + # 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{$_} } + keys %$contig; + $rdg->{'group'} = wit_stringify( \@members ); + } + + $variant_row->{'genealogical'} = !( keys %$conflict ); return $variant_row; } +sub _prune_subtree { + my( $tree, $root, $contighash ) = @_; + # First, delete hypothetical leaves / orphans until there are none left. + my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } + $tree->successorless_vertices; + while( @orphan_hypotheticals ) { + $tree->delete_vertices( @orphan_hypotheticals ); + @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } + $tree->successorless_vertices; + } + # Then delete a hypothetical root with only one successor, moving the + # root to the child. + while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) { + my @nextroot = $tree->successors( $root ); + $tree->delete_vertex( $root ); + $root = $nextroot[0]; + } + # The tree has been modified in place, but we need to know the new root. + return $root; +} # Add the variant, subject to a.c. representation logic. # This assumes that we will see the 'main' version before the a.c. version. sub add_variant_wit { @@ -199,25 +416,12 @@ sub add_variant_wit { push( @$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; @@ -233,5 +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