Class: SledImage

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::IsData, Shared::Notes, Shared::Tags
Defined in:
app/models/sled_image.rb

Overview

A SledImage contains the metadata to parse one image into many depictions.

  • if ‘metadata` is provided without a `collection_object` stub then Specimen is assumed

A section is verbatim from sled

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Shared::IsData

#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_destroyable?, #is_editable?, #is_in_use?, #is_in_users_projects?, #metamorphosize, #similar

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Tags

#reject_tags, #tag_with, #tagged?, #tagged_with?

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#_column_total ⇒ Object (private)

Internal processing



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# File 'app/models/sled_image.rb', line 36

def _column_total
  @_column_total
end

#_first_identifier ⇒ Object (private)

Internal processing



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# File 'app/models/sled_image.rb', line 36

def _first_identifier
  @_first_identifier
end

#_identifier_matrix ⇒ Array of Arrays (private)

Returns:

  • (Array of Arrays) 


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# File 'app/models/sled_image.rb', line 39

def _identifier_matrix
  @_identifier_matrix
end

#_row_total ⇒ Object (private)

Internal processing



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# File 'app/models/sled_image.rb', line 36

def _row_total
  @_row_total
end

#collection_object_params ⇒ Object

Stubs coming from UI



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# File 'app/models/sled_image.rb', line 22

def collection_object_params
  @collection_object_params
end

#depiction_params ⇒ Object

Stubs coming from UI



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# File 'app/models/sled_image.rb', line 25

def depiction_params
  @depiction_params
end

#metadata ⇒ JSON

Returns position coordinates.

Returns:

  • (JSON) —

    position coordinates



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# File 'app/models/sled_image.rb', line 15

class SledImage < ApplicationRecord
  include Housekeeping
  include Shared::Tags
  include Shared::Notes
  include Shared::IsData

  # Stubs coming from UI
  attr_accessor :collection_object_params # note, tag, deterimination

  # Stubs coming from UI
  attr_accessor :depiction_params # for is_metadata_depiction

  # @param step_identifier [String]
  #  defaults to 'column', used only to compute object identifiers
  attr_accessor :step_identifier_on #row, column

  # If assigned to 'nuke', and .destroy, then will
  # additionall destroy all related collection objects
  attr_accessor :nuke

  # Internal processing
  attr_accessor :_first_identifier, :_row_total, :_column_total

  # A nil value occurs when `!section.metadata.nil?`
  attr_accessor :_identifier_matrix

  belongs_to :image, inverse_of: :sled_image
  has_many :depictions, through: :image
  has_many :collection_objects, through: :depictions, source: :depiction_object, source_type: 'CollectionObject'

  before_destroy :destroy_related

  validates_presence_of :image
  validates_uniqueness_of :image_id

  after_save :set_cached, unless: Proc.new {|n| n.metadata&.empty? || errors.any? } # must be before process
  after_save :process, unless: Proc.new { |n| n.metadata&.empty? }

  # zero beers
  def total(direction = 'row')
    i = nil
    metadata.each do |o|
      i = o[direction] if i.nil? || (!i.nil? && o[direction] > i)
    end
    i
  end

  def metadata=(value)
    if value.kind_of? Array
      write_attribute(:metadata, value)
    elsif value.kind_of? String
      write_attribute(:metadata, JSON.parse(value))
    elsif value.nil?
      write_attribute(:metadata, [])
    else
      raise
    end
  end

  def summary
    m = []
    metadata.each do |s|
      c = s['column'].to_i
      r = s['row'].to_i
      m[r] ||= []
      d = depiction_for(s)
      m[r][c] = {
        depiction_id: d&.id,
        collection_object_id: d&.depiction_object_id,
        identifier: d&.depiction_object&.identifiers&.first&.cached
      }
    end
    m
  end

  def depiction_for(section)
    x,y = section['column'], section['row']
    depictions.where(sled_image_x_position: x, sled_image_y_position: y).first
  end

  def step_identifier_on
    @step_identifier_on ||= 'column'
  end

  private

  def destroy_related
    if nuke == 'nuke'
      collection_objects.reload.each do |d|
        d.destroy
      end
    end

    depictions.each do |d|
      d.destroy
    end
    true
  end

  def new_collection_object
    CollectionObject.new(collection_object_params)
  end

  def _first_identifier
    @_first_identifier ||= new_collection_object.identifiers&.first&.identifier&.to_i
  end

  def _row_total
    @_row_total ||= total('row')
  end

  def _column_total
    @_column_total ||= total('column')
  end

  # @return [Array of Arrays]
  def _identifier_matrix
    @_identifier_matrix ||= get_identifier_matrix
  end

  def identity_matrix
    i = []
    metadata.each do |s|
      r = s['row'].to_i
      c = s['column'].to_i
      i[r] ||= []
      i[r][c] = s['metadata'].blank? ? 0 : 1
    end
    i
  end

  def increment_matrix
    i = []
    j = identity_matrix
    k = 0
    case step_identifier_on
    when 'row'
      (0.._row_total).each do |r|
        (0.._column_total).each do |c|
          k += j[r][c]
          i[r] ||= []
          i[r][c] = (j[r][c] == 1 ? 0 : k)
        end
      end

    when 'column'
      (0.._column_total).each do |c|
        (0.._row_total).each do |r|
          k += j[r][c]
          i[r] ||= []
          i[r][c] = (j[r][c] == 1 ? 0 : k)
        end
      end
    end
    i
  end

  def get_identifier_matrix
    i = increment_matrix

    m = []

    metadata.each do |s|
      r = s['row'].to_i
      c = s['column'].to_i
      m[r] ||= []
      m[r][c] = nil if !s['metadata'].blank?
      next if !s['metadata'].blank? || _first_identifier.nil?

      inc = r + c - i[r][c] + _first_identifier
      v = nil
      case step_identifier_on
      when 'row'
        v = (r * _column_total) + inc
      when 'column'
        v = (c * _row_total) + inc
      end

      m[r][c] = v
    end
    @_identifier_matrix = m
  end

  def identifier_for(section)
    _identifier_matrix[section['row'].to_i][section['column'].to_i]
  end

  def process
    depictions.any? ?  syncronize : create_objects
    true
  end

  def create_objects
    return true unless !collection_object_params.nil?
    begin
      metadata.each do |i|
        next unless i['metadata'].blank?
        p = collection_object_params.merge(
          depictions_attributes: [
            {
              sled_image_id: id,
              image_id: image_id,
              svg_clip: svg_clip(i),
              svg_view_box: svg_view_box(i),
              sled_image_x_position: i['column'],
              sled_image_y_position: i['row'],
              is_metadata_depiction: is_metadata_depiction?
            }
          ]
        )

        j = identifier_for(i)

        # Check to see if object exists
        if j && k = Identifier::Local::CatalogNumber.find_by(p[:identifiers_attributes].first.merge(identifier: j, identifier_object_type: 'CollectionObject'))
          # Remove the identifier attributes, identifier exists
          p.delete :identifiers_attributes
          p.delete :tags_attributes
          p.delete :notes_attributes
          p.delete :taxon_determinations_attributes
          p.delete :data_attributes_attributes
          p.delete :total

          k.identifier_object.update!(p)
        else
          c = CollectionObject.new(p)

          if c.identifiers.first
            c.identifiers.first.identifier = identifier_for(i)
          end
          c.save!
        end

      end
    rescue ActiveRecord::RecordInvalid => e
      errors.add(:base, e.message)
      raise
    end
    true
  end

  def syncronize
    if metadata_was == []
      process if !metadata&.empty?
    else
      # At this point we only allow coordinate updates
      metadata.each do |i|
        next if !i['metadata'].nil?
        if d = depiction_for(i)
          d.update_columns(
            svg_clip: svg_clip(i),
            svg_view_box: svg_view_box(i),
          )
        end
      end
    end
    true
  end

  def set_cached
    update_columns(
      cached_total_collection_objects: total_metadata_objects,
      cached_total_rows: _row_total,
      cached_total_columns: _column_total
    )
  end

  def total_metadata_objects
    metadata.count
  end

  # x1, y1, x2, y2
  def coordinates(section)
    [
      section['upperCorner']['x'].to_f, section['upperCorner']['y'].to_f,
      section['lowerCorner']['x'].to_f, section['lowerCorner']['y'].to_f]
  end


  def svg_view_box(section)
    view_box_values(section).join(' ')
  end

  # @return top left x, top left y, height, width
  def view_box_values(section)
    x1, y1, x2, y2 = coordinates(section)
    [x1, y1, x2 - x1, y2 - y1]
  end

  def svg_clip(section)
    x, y, h, w = view_box_values(section)
    "<rect x=\"#{x}\" y=\"#{y}\" width=\"#{h}\" height=\"#{w}\" />"
  end

  private

  def is_metadata_depiction?
    if depiction_params && !depiction_params.empty?
      a = depiction_params[:is_metadata_depiction]
      ((a == 'true') || (a == true)) ? true : false
    else
      false
    end
  end

end

#nuke ⇒ Object

If assigned to ‘nuke’, and .destroy, then will additionall destroy all related collection objects



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# File 'app/models/sled_image.rb', line 33

def nuke
  @nuke
end

#object_layout ⇒ JSON

Returns ROI metadata per metadata type, expandable to all sled sections.

Returns:

  • (JSON) —

    ROI metadata per metadata type, expandable to all sled sections



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# File 'app/models/sled_image.rb', line 15

class SledImage < ApplicationRecord
  include Housekeeping
  include Shared::Tags
  include Shared::Notes
  include Shared::IsData

  # Stubs coming from UI
  attr_accessor :collection_object_params # note, tag, deterimination

  # Stubs coming from UI
  attr_accessor :depiction_params # for is_metadata_depiction

  # @param step_identifier [String]
  #  defaults to 'column', used only to compute object identifiers
  attr_accessor :step_identifier_on #row, column

  # If assigned to 'nuke', and .destroy, then will
  # additionall destroy all related collection objects
  attr_accessor :nuke

  # Internal processing
  attr_accessor :_first_identifier, :_row_total, :_column_total

  # A nil value occurs when `!section.metadata.nil?`
  attr_accessor :_identifier_matrix

  belongs_to :image, inverse_of: :sled_image
  has_many :depictions, through: :image
  has_many :collection_objects, through: :depictions, source: :depiction_object, source_type: 'CollectionObject'

  before_destroy :destroy_related

  validates_presence_of :image
  validates_uniqueness_of :image_id

  after_save :set_cached, unless: Proc.new {|n| n.metadata&.empty? || errors.any? } # must be before process
  after_save :process, unless: Proc.new { |n| n.metadata&.empty? }

  # zero beers
  def total(direction = 'row')
    i = nil
    metadata.each do |o|
      i = o[direction] if i.nil? || (!i.nil? && o[direction] > i)
    end
    i
  end

  def metadata=(value)
    if value.kind_of? Array
      write_attribute(:metadata, value)
    elsif value.kind_of? String
      write_attribute(:metadata, JSON.parse(value))
    elsif value.nil?
      write_attribute(:metadata, [])
    else
      raise
    end
  end

  def summary
    m = []
    metadata.each do |s|
      c = s['column'].to_i
      r = s['row'].to_i
      m[r] ||= []
      d = depiction_for(s)
      m[r][c] = {
        depiction_id: d&.id,
        collection_object_id: d&.depiction_object_id,
        identifier: d&.depiction_object&.identifiers&.first&.cached
      }
    end
    m
  end

  def depiction_for(section)
    x,y = section['column'], section['row']
    depictions.where(sled_image_x_position: x, sled_image_y_position: y).first
  end

  def step_identifier_on
    @step_identifier_on ||= 'column'
  end

  private

  def destroy_related
    if nuke == 'nuke'
      collection_objects.reload.each do |d|
        d.destroy
      end
    end

    depictions.each do |d|
      d.destroy
    end
    true
  end

  def new_collection_object
    CollectionObject.new(collection_object_params)
  end

  def _first_identifier
    @_first_identifier ||= new_collection_object.identifiers&.first&.identifier&.to_i
  end

  def _row_total
    @_row_total ||= total('row')
  end

  def _column_total
    @_column_total ||= total('column')
  end

  # @return [Array of Arrays]
  def _identifier_matrix
    @_identifier_matrix ||= get_identifier_matrix
  end

  def identity_matrix
    i = []
    metadata.each do |s|
      r = s['row'].to_i
      c = s['column'].to_i
      i[r] ||= []
      i[r][c] = s['metadata'].blank? ? 0 : 1
    end
    i
  end

  def increment_matrix
    i = []
    j = identity_matrix
    k = 0
    case step_identifier_on
    when 'row'
      (0.._row_total).each do |r|
        (0.._column_total).each do |c|
          k += j[r][c]
          i[r] ||= []
          i[r][c] = (j[r][c] == 1 ? 0 : k)
        end
      end

    when 'column'
      (0.._column_total).each do |c|
        (0.._row_total).each do |r|
          k += j[r][c]
          i[r] ||= []
          i[r][c] = (j[r][c] == 1 ? 0 : k)
        end
      end
    end
    i
  end

  def get_identifier_matrix
    i = increment_matrix

    m = []

    metadata.each do |s|
      r = s['row'].to_i
      c = s['column'].to_i
      m[r] ||= []
      m[r][c] = nil if !s['metadata'].blank?
      next if !s['metadata'].blank? || _first_identifier.nil?

      inc = r + c - i[r][c] + _first_identifier
      v = nil
      case step_identifier_on
      when 'row'
        v = (r * _column_total) + inc
      when 'column'
        v = (c * _row_total) + inc
      end

      m[r][c] = v
    end
    @_identifier_matrix = m
  end

  def identifier_for(section)
    _identifier_matrix[section['row'].to_i][section['column'].to_i]
  end

  def process
    depictions.any? ?  syncronize : create_objects
    true
  end

  def create_objects
    return true unless !collection_object_params.nil?
    begin
      metadata.each do |i|
        next unless i['metadata'].blank?
        p = collection_object_params.merge(
          depictions_attributes: [
            {
              sled_image_id: id,
              image_id: image_id,
              svg_clip: svg_clip(i),
              svg_view_box: svg_view_box(i),
              sled_image_x_position: i['column'],
              sled_image_y_position: i['row'],
              is_metadata_depiction: is_metadata_depiction?
            }
          ]
        )

        j = identifier_for(i)

        # Check to see if object exists
        if j && k = Identifier::Local::CatalogNumber.find_by(p[:identifiers_attributes].first.merge(identifier: j, identifier_object_type: 'CollectionObject'))
          # Remove the identifier attributes, identifier exists
          p.delete :identifiers_attributes
          p.delete :tags_attributes
          p.delete :notes_attributes
          p.delete :taxon_determinations_attributes
          p.delete :data_attributes_attributes
          p.delete :total

          k.identifier_object.update!(p)
        else
          c = CollectionObject.new(p)

          if c.identifiers.first
            c.identifiers.first.identifier = identifier_for(i)
          end
          c.save!
        end

      end
    rescue ActiveRecord::RecordInvalid => e
      errors.add(:base, e.message)
      raise
    end
    true
  end

  def syncronize
    if metadata_was == []
      process if !metadata&.empty?
    else
      # At this point we only allow coordinate updates
      metadata.each do |i|
        next if !i['metadata'].nil?
        if d = depiction_for(i)
          d.update_columns(
            svg_clip: svg_clip(i),
            svg_view_box: svg_view_box(i),
          )
        end
      end
    end
    true
  end

  def set_cached
    update_columns(
      cached_total_collection_objects: total_metadata_objects,
      cached_total_rows: _row_total,
      cached_total_columns: _column_total
    )
  end

  def total_metadata_objects
    metadata.count
  end

  # x1, y1, x2, y2
  def coordinates(section)
    [
      section['upperCorner']['x'].to_f, section['upperCorner']['y'].to_f,
      section['lowerCorner']['x'].to_f, section['lowerCorner']['y'].to_f]
  end


  def svg_view_box(section)
    view_box_values(section).join(' ')
  end

  # @return top left x, top left y, height, width
  def view_box_values(section)
    x1, y1, x2, y2 = coordinates(section)
    [x1, y1, x2 - x1, y2 - y1]
  end

  def svg_clip(section)
    x, y, h, w = view_box_values(section)
    "<rect x=\"#{x}\" y=\"#{y}\" width=\"#{h}\" height=\"#{w}\" />"
  end

  private

  def is_metadata_depiction?
    if depiction_params && !depiction_params.empty?
      a = depiction_params[:is_metadata_depiction]
      ((a == 'true') || (a == true)) ? true : false
    else
      false
    end
  end

end

#step_identifier_on ⇒ Object

Parameters:

  • step_identifier (String) —

    defaults to ‘column’, used only to compute object identifiers



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# File 'app/models/sled_image.rb', line 29

def step_identifier_on
  @step_identifier_on
end

Instance Method Details

#coordinates(section) ⇒ Object (private)

x1, y1, x2, y2



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# File 'app/models/sled_image.rb', line 287

def coordinates(section)
  [
    section['upperCorner']['x'].to_f, section['upperCorner']['y'].to_f,
    section['lowerCorner']['x'].to_f, section['lowerCorner']['y'].to_f]
end

#create_objects ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 207

def create_objects
  return true unless !collection_object_params.nil?
  begin
    metadata.each do |i|
      next unless i['metadata'].blank?
      p = collection_object_params.merge(
        depictions_attributes: [
          {
            sled_image_id: id,
            image_id: image_id,
            svg_clip: svg_clip(i),
            svg_view_box: svg_view_box(i),
            sled_image_x_position: i['column'],
            sled_image_y_position: i['row'],
            is_metadata_depiction: is_metadata_depiction?
          }
        ]
      )

      j = identifier_for(i)

      # Check to see if object exists
      if j && k = Identifier::Local::CatalogNumber.find_by(p[:identifiers_attributes].first.merge(identifier: j, identifier_object_type: 'CollectionObject'))
        # Remove the identifier attributes, identifier exists
        p.delete :identifiers_attributes
        p.delete :tags_attributes
        p.delete :notes_attributes
        p.delete :taxon_determinations_attributes
        p.delete :data_attributes_attributes
        p.delete :total

        k.identifier_object.update!(p)
      else
        c = CollectionObject.new(p)

        if c.identifiers.first
          c.identifiers.first.identifier = identifier_for(i)
        end
        c.save!
      end

    end
  rescue ActiveRecord::RecordInvalid => e
    errors.add(:base, e.message)
    raise
  end
  true
end

#depiction_for(section) ⇒ Object 



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# File 'app/models/sled_image.rb', line 90

def depiction_for(section)
  x,y = section['column'], section['row']
  depictions.where(sled_image_x_position: x, sled_image_y_position: y).first
end

#destroy_related ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 101

def destroy_related
  if nuke == 'nuke'
    collection_objects.reload.each do |d|
      d.destroy
    end
  end

  depictions.each do |d|
    d.destroy
  end
  true
end

#get_identifier_matrix ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 172

def get_identifier_matrix
  i = increment_matrix

  m = []

  metadata.each do |s|
    r = s['row'].to_i
    c = s['column'].to_i
    m[r] ||= []
    m[r][c] = nil if !s['metadata'].blank?
    next if !s['metadata'].blank? || _first_identifier.nil?

    inc = r + c - i[r][c] + _first_identifier
    v = nil
    case step_identifier_on
    when 'row'
      v = (r * _column_total) + inc
    when 'column'
      v = (c * _row_total) + inc
    end

    m[r][c] = v
  end
  @_identifier_matrix = m
end

#identifier_for(section) ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 198

def identifier_for(section)
  _identifier_matrix[section['row'].to_i][section['column'].to_i]
end

#identity_matrix ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 135

def identity_matrix
  i = []
  metadata.each do |s|
    r = s['row'].to_i
    c = s['column'].to_i
    i[r] ||= []
    i[r][c] = s['metadata'].blank? ? 0 : 1
  end
  i
end

#increment_matrix ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 146

def increment_matrix
  i = []
  j = identity_matrix
  k = 0
  case step_identifier_on
  when 'row'
    (0.._row_total).each do |r|
      (0.._column_total).each do |c|
        k += j[r][c]
        i[r] ||= []
        i[r][c] = (j[r][c] == 1 ? 0 : k)
      end
    end

  when 'column'
    (0.._column_total).each do |c|
      (0.._row_total).each do |r|
        k += j[r][c]
        i[r] ||= []
        i[r][c] = (j[r][c] == 1 ? 0 : k)
      end
    end
  end
  i
end

#is_metadata_depiction? ⇒ Boolean (private)

Returns:

  • (Boolean) 


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# File 'app/models/sled_image.rb', line 311

def is_metadata_depiction?
  if depiction_params && !depiction_params.empty?
    a = depiction_params[:is_metadata_depiction]
    ((a == 'true') || (a == true)) ? true : false
  else
    false
  end
end

#new_collection_object ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 114

def new_collection_object
  CollectionObject.new(collection_object_params)
end

#process ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 202

def process
  depictions.any? ?  syncronize : create_objects
  true
end

#set_cached ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 274

def set_cached
  update_columns(
    cached_total_collection_objects: total_metadata_objects,
    cached_total_rows: _row_total,
    cached_total_columns: _column_total
  )
end

#summary ⇒ Object 



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# File 'app/models/sled_image.rb', line 74

def summary
  m = []
  metadata.each do |s|
    c = s['column'].to_i
    r = s['row'].to_i
    m[r] ||= []
    d = depiction_for(s)
    m[r][c] = {
      depiction_id: d&.id,
      collection_object_id: d&.depiction_object_id,
      identifier: d&.depiction_object&.identifiers&.first&.cached
    }
  end
  m
end

#svg_clip(section) ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 304

def svg_clip(section)
  x, y, h, w = view_box_values(section)
  "<rect x=\"#{x}\" y=\"#{y}\" width=\"#{h}\" height=\"#{w}\" />"
end

#svg_view_box(section) ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 294

def svg_view_box(section)
  view_box_values(section).join(' ')
end

#syncronize ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 256

def syncronize
  if metadata_was == []
    process if !metadata&.empty?
  else
    # At this point we only allow coordinate updates
    metadata.each do |i|
      next if !i['metadata'].nil?
      if d = depiction_for(i)
        d.update_columns(
          svg_clip: svg_clip(i),
          svg_view_box: svg_view_box(i),
        )
      end
    end
  end
  true
end

#total(direction = 'row') ⇒ Object

zero beers



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# File 'app/models/sled_image.rb', line 54

def total(direction = 'row')
  i = nil
  metadata.each do |o|
    i = o[direction] if i.nil? || (!i.nil? && o[direction] > i)
  end
  i
end

#total_metadata_objects ⇒ Object (private) 



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# File 'app/models/sled_image.rb', line 282

def total_metadata_objects
  metadata.count
end

#view_box_values(section) ⇒ Object (private)

Returns top left x, top left y, height, width.

Returns:

  • top left x, top left y, height, width



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# File 'app/models/sled_image.rb', line 299

def view_box_values(section)
  x1, y1, x2, y2 = coordinates(section)
  [x1, y1, x2 - x1, y2 - y1]
end