Module: SqedConfig

Defined in:

lib/sqed_config.rb

Overview

Sqed constants, including patterns for extraction etc.

Constant Summary

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 |

    | 1
 0  |----  :right_t
    | 2

 0 | 1 | 2
------------
   | 5 | 3    :seven_slot
 6 |--------
   |   4

 0  |  1
    |____
----|      :vertical_offset_cross 
 3  |  2

     |
   0 | 1  :vertical_split
     |

-----
| 0 |  :internal_box
-----

Hash values are used to stub out the Sqed::Boundaries instance.

{
  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],
  right_t: [0, 1, 2],
  seven_slot: [0, 1, 2, 3, 4, 5, 6],
  vertical_offset_cross: [0, 1, 2, 3],
  vertical_split: [0, 1],
  internal_box: [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 =

{
  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 }
  },

  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

• .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

# File 'lib/sqed_config.rb', line 177

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 182

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