Module: SqedConfig

Defined in:: lib/sqed_config.rb

Overview

Sqed constants, including patterns for extraction etc.

Constant Summary collapse

LAYOUTS = Layouts refer to the arrangement of the divided stage. Windows are enumerated from the top left, moving around the border in a clockwise position. For example: 0 | 1 ----|---- :cross (any cross pattern) | 3 | 2 0 | 1 | --------- :horizontal_offset_cross 3 | 2 0 -------- :horizontal_split 1 0 | 1 | 2 ------------ | 5 | :lep_stage 6 |---- 3 | 4 | 0 | 1 | 2 -------------- | 5 | :lep_stage2 6 |---- 3 | 4 | # 0 | 1 | 2 ------------ | 5 | 3 :seven_slot 6 |-------- | 4 0 | 1 |____ ----| :vertical_offset_cross 3 | 2 | 0 | 1 :vertical_split | ------- |-----| || 0 || :internal_box |-----| ------- 0 :t ----- 2 | 1 0 | 1 :inverted_t ----- 2 0 | ---| 1 : left_t 2 | | 1 0 |--- :right_t | 2 ----- | 0 | :stage ----- Hash values are used to stub out the Sqed::Boundaries instance.

{
  t: [0,1,2],
  inverted_t: [0, 1, 2],
  right_t: [0, 1, 2],
  left_t: [0, 1, 2],
  cross: [0, 1, 2, 3],
  horizontal_offset_cross: [0, 1, 2, 3],
  horizontal_split: [0, 1],
  lep_stage: [0, 1, 2, 3, 4, 5, 6],
  lep_stage2: [0, 1, 2, 3, 4, 5, 6],
  seven_slot: [0, 1, 2, 3, 4, 5, 6],
  vertical_offset_cross: [0, 1, 2, 3],
  vertical_split: [0, 1],
  internal_box: [0],
  stage: [0]
}.freeze

LAYOUT_SECTION_TYPES = Each element of the layout is a “section”.

[
  :annotated_specimen,      # a specimen is present, and metadata is too
  :collecting_event_labels, # the section that contains collecting event labels (only)
  :curator_metadata,        # the section contains text with curator metadata
  :determination_labels,    # the section contains text that determines the specimen (only)
  :identifier,              # the section contains an identifier (e.g. barcode or unique number)
  :image_registration,      # the section contains only image registration information,
  :labels,                  # the section contains collecting event and other non-determination labels
  :nothing,                 # section is empty
  :other_labels,            # the section that contains text that misc.
  :specimen,                # the specimen only, no metadata should be present
  :stage,                   # the image contains the full stage
].freeze

SECTION_PARSERS = Links section types to data parsers

{
  annotated_specimen: [Sqed::Parser::OcrParser],
  collecting_event_labels: [Sqed::Parser::OcrParser],
  curator_metadata: [Sqed::Parser::OcrParser],
  determination_labels: [Sqed::Parser::OcrParser],
  identifier: [Sqed::Parser::OcrParser, Sqed::Parser::BarcodeParser],
  image_registration: [],
  labels: [Sqed::Parser::OcrParser],
  nothing: [],
  other_labels: [Sqed::Parser::OcrParser],
  specimen: [],
  stage: []
}.freeze

EXTRACTION_PATTERNS =

{
  t: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :t,
    metadata_map: { 0 => :annotated_specimen, 1 => :identifier, 2 => :image_registration }
  },

  inverted_t: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :inverted_t,
    metadata_map: { 0 => :identifier, 1 => :image_registration, 2 => :annotated_specimen }
  },

  cross: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :cross,
    metadata_map: { 0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
  },

  horizontal_split: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :horizontal_split,
    metadata_map: { 0 => :annotated_specimen, 1 => :identifier }
  },

  horizontal_offset_cross: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :horizontal_offset_cross,
    metadata_map: { 0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
  },

  lep_stage: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :lep_stage,
    metadata_map: { 0 => :curator_metadata, 1 => :collecting_event_labels, 2 => :image_registration, 3 => :identifier, 4 => :other_labels, 5 => :determination_labels, 6 => :specimen }
  },

  lep_stage2: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :lep_stage2,
    metadata_map: { 0 => :curator_metadata, 1 => :collecting_event_labels, 2 => :image_registration, 3 => :identifier, 4 => :other_labels, 5 => :determination_labels, 6 => :specimen }
  },

  left_t: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :left_t,
    metadata_map: { 0 => :annotated_specimen, 1 => :identifier, 2 => :image_registration }
  },

  right_t: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :right_t,
    metadata_map: { 0 => :annotated_specimen, 1 => :identifier, 2 => :image_registration }
  },

  stage: {
    boundary_finder: Sqed::BoundaryFinder::StageFinder,
    layout: :internal_box,
    metadata_map: { 0 => :stage }
  },

  seven_slot: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :seven_slot,
    metadata_map: { 0 => :collecting_event_labels, 1 => :determination_labels, 2 => :other_labels, 3 => :image_registration, 4 => :curator_metadata, 5 => :identifier, 6 => :specimen }
  },

  vertical_offset_cross: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :vertical_offset_cross,
    metadata_map: { 0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
  },

  vertical_split: {
    boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
    layout: :vertical_split,
    metadata_map: { 0 => :annotated_specimen, 1 => :identifier }
  }
}.freeze

BOUNDARY_COLORS =

[:red, :green, :blue, :black].freeze

DEFAULT_TMP_DIR =

'/tmp'.freeze

Class Method Summary collapse

.index_for_section_type(pattern, section_type) ⇒ Object
.metadata ⇒ Object

Format to return JSON that is externaly exposed.

Class Method Details

.index_for_section_type(pattern, section_type) ⇒ `Object`



231
232
233

# File 'lib/sqed_config.rb', line 231

def self.index_for_section_type(pattern, section_type)
  EXTRACTION_PATTERNS[pattern][:metadata_map].invert[section_type]
end

.metadata ⇒ `Object`

Format to return JSON that is externaly exposed

# File 'lib/sqed_config.rb', line 236

def self.metadata
  return {
    boundary_colors: BOUNDARY_COLORS,
    extraction_patterns: EXTRACTION_PATTERNS.select{|k,v| k != :stage},
    section_parsers: SECTION_PARSERS,
    layout_section_types: LAYOUT_SECTION_TYPES,
    layouts: LAYOUTS.select{|k,v| k != :internal_box }
  }
end