Module: Transformed

Defined in:
lib/rbbt/ner/segment/transformed.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#transformation_stack ⇒ Object

Returns the value of attribute transformation_stack.



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# File 'lib/rbbt/ner/segment/transformed.rb', line 26

def transformation_stack
  @transformation_stack
end

#transformed_segments ⇒ Object

Returns the value of attribute transformed_segments.



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# File 'lib/rbbt/ner/segment/transformed.rb', line 26

def transformed_segments
  @transformed_segments
end

Class Method Details

.ansi(text, entities, colors = nil) ⇒ Object 



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# File 'lib/rbbt/ner/segment/transformed.rb', line 180

def self.ansi(text, entities, colors = nil)


end

.transform(text, segments, replacement = nil, &block) ⇒ Object 



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# File 'lib/rbbt/ner/segment/transformed.rb', line 6

def self.transform(text, segments, replacement = nil, &block)

  text.extend Transformed
  text.replace_segments(segments, replacement, &block)

  text
end

.with_transform(text, segments, replacement = nil) ⇒ Object 



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# File 'lib/rbbt/ner/segment/transformed.rb', line 14

def self.with_transform(text, segments, replacement = nil)

  text.extend Transformed
  text.replace_segments(segments, replacement)

  segments = yield text

  segments = nil unless Array === segments && Segment === segments.first

  text.restore(segments, true)
end

Instance Method Details

#fix_segment(segment, range, diff) ⇒ Object 



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# File 'lib/rbbt/ner/segment/transformed.rb', line 140

def fix_segment(segment, range, diff)
  case
    # Before
  when segment.end < range.begin
    # After
  when segment.offset.to_i > range.end + diff
    segment.offset = segment.offset.to_i - diff
    # Includes
  when (segment.offset.to_i <= range.begin and segment.end >= range.end + diff)
    segment.replace self[segment.offset.to_i..segment.end - diff]
  else
    raise "Segment Overlaps"
  end
end

#replace_segments(segments, replacement = nil, &block) ⇒ Object

def self.sort(segments)

segments.compact.sort do |a,b|
  case
  when ((a.nil? && b.nil?) || (a.offset.nil? && b.offset.nil?))
    0
  when (a.nil? || a.offset.nil?)
    -1
  when (b.nil? || b.offset.nil?)
    +1
    # Non-overlap
  when (a.end < b.offset.to_i || b.end < a.offset.to_i)
    b.offset <=> a.offset
    # b includes a
  when (a.offset.to_i >= b.offset.to_i && a.end <= b.end)
    -1
    # b includes a
  when (b.offset.to_i >= a.offset.to_i && b.end <= a.end)
    +1
    # Overlap
  when (a.offset.to_i > b.offset.to_i && a.end > b.end || b.offset.to_i > a.offset.to_i && b.end > a.end)
    b.length <=> a.length
  else
    raise "Unexpected case in sort: #{a.range} - #{b.range}"
  end
end

end



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# File 'lib/rbbt/ner/segment/transformed.rb', line 89

def replace_segments(segments, replacement = nil, &block)
  @transformed_segments ||= {}
  @transformation_stack ||= []
  stack = []

  segments = [segments] unless Array === segments 
  orig_length = self.length
  Segment.sort(segments).each do |segment|
    next if segment.offset.nil?
    shift = shift segment.range

    next if shift.nil?

    shift_begin, shift_end = shift

    text_offset = self.respond_to?(:offset)? self.offset.to_i : 0
    updated_begin = segment.offset.to_i + shift_begin - text_offset
    updated_end   = segment.range.last + shift_end - text_offset

    updated_range = (updated_begin..updated_end)

    updated_text = self[updated_begin..updated_end]
    if updated_text.nil?
      Log.warn "Range outside of segment: #{self.length} #{segment.locus} (#{updated_range})"
      next
    end

    original_text = segment.dup
    segment.replace updated_text

    case
    when block_given?
      new =  block.call(segment)
    when String === replacement
      new = replacement
    when Proc === replacement
      new = replacement.call(segment)
    end

    diff = new.length - segment.segment_length

    self[updated_begin..updated_end] = new

    @transformed_segments[segment.object_id] = [segment.range, diff, updated_text, updated_range, @transformed_segments.size]

    segment.replace original_text
    stack << segment.object_id
  end
  @transformation_stack << stack
end

#restore(segments = [], first_only = false) ⇒ Object

Restore the sentence from all transformation. Segments that are passed as parameters are restored from transformed space to original space



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# File 'lib/rbbt/ner/segment/transformed.rb', line 157

def restore(segments = [], first_only = false)
  return segments if @transformation_stack.empty?

  if first_only
    @transformation_stack.pop.reverse.each do |id|
      orig_range, diff, text, range = @transformed_segments.delete id

      new_range = (range.begin..range.last + diff)
      self[new_range] = text
      segments.each do |segment|
        next unless Segment === segment
        fix_segment(segment, range, diff)
      end if Array === segments
    end
    segments
  else
    while @transformation_stack.any?
      restore(segments, true)
    end
    segments
  end
end

#shift(segment_o) ⇒ Object 



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# File 'lib/rbbt/ner/segment/transformed.rb', line 28

def shift(segment_o)
  begin_shift = 0
  end_shift = 0

  @transformed_segments.sort_by{|id, info| info.last}.each{|id,info| 
    pseg_o, diff = info

    case
      # Before
    when segment_o.last + end_shift < pseg_o.begin
      # After
    when (segment_o.begin + begin_shift > pseg_o.last)
      begin_shift += diff
      end_shift += diff
      # Includes
    when (segment_o.begin + begin_shift <= pseg_o.begin and segment_o.last + end_shift >= pseg_o.last)
      end_shift += diff
      # Inside
    when (segment_o.begin + begin_shift >= pseg_o.begin and segment_o.last + end_shift <= pseg_o.last)
      return nil
      # Overlaps start
    when (segment_o.begin + begin_shift <= pseg_o.begin and segment_o.last + end_shift <= pseg_o.last)
      return nil
      # Overlaps end
    when (segment_o.begin + begin_shift >= pseg_o.begin and segment_o.last + end_shift >= pseg_o.last)
      return nil
   else
      raise "Unknown overlaps: #{segment_o.inspect} - #{pseg_o.inspect}"
    end
  }

  [begin_shift, end_shift]
end