sqed 0.7.0 → 0.8.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  metadata.gz: ecff3bc24d06653a25e90dd950faea277de23da61cdc7503e288d6098d8c4250
+  data.tar.gz: dd87d00a794d8edf2387c6d37d01382480ab0c161963f063764fadeee75a7f40
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+  data.tar.gz: 2594a64f5b2f575515690314176aa00db01a69dfaef925aa5a1449c7e88b67373f20060f9f4fc172b5b07198c15636d3815a95d7d518e5380d45eda82924cefe

data/lib/sqed/boundaries.rb

@@ -6,108 +6,108 @@ class Sqed
   # Layouts are Hashes defined in EXTRACTION_PATTERNS[<pattern>][<layout>]
   #
   class Boundaries
-  include Enumerable
-
-  # stores a hash
-  # References the section by integer index!
-  # In the pattern integer => [x1,y1, width, height] (ImageMagick convention rectangle descriptors)
-  # e.g.
-  #   0 => [10,10,40,40]
-  attr_reader :coordinates
-
-  # A symbol from Sqed::Config::LAYOUTS.keys
-  #   :right_t
-  attr_accessor :layout
-
-  # @return [Boolean] whether or not the last method to populate this object
-  # executed to completion
-  attr_accessor :complete
-
-  def initialize(layout = nil)
-    raise 'unrecognized layout' if layout && !SqedConfig::LAYOUTS.include?(layout)
-    @complete = false
-
-    @layout = layout
-    @coordinates = {}
-    initialize_coordinates if !@layout.nil?
-  end
+    include Enumerable
+
+    # stores a hash
+    # References the section by integer index!
+    # In the pattern integer => [x1,y1, width, height] (ImageMagick convention rectangle descriptors)
+    # e.g.
+    #   0 => [10,10,40,40]
+    attr_reader :coordinates
+
+    # A symbol from Sqed::Config::LAYOUTS.keys
+    #   :right_t
+    attr_accessor :layout
+
+    # @return [Boolean] whether or not the last method to populate this object
+    # executed to completion
+    attr_accessor :complete
+
+    def initialize(layout = nil)
+      raise Sqed::Error, 'unrecognized layout' if layout && !SqedConfig::LAYOUTS.include?(layout)
+      @complete = false
+
+      @layout = layout
+      @coordinates = {}
+      initialize_coordinates if !@layout.nil?
+    end
 
-  def initialize_coordinates
-    SqedConfig::LAYOUTS[@layout].each do |k|
-      @coordinates.merge!(k => [nil, nil, nil, nil] )
+    def initialize_coordinates
+      SqedConfig::LAYOUTS[@layout].each do |k|
+        @coordinates.merge!(k => [nil, nil, nil, nil] )
+      end
     end
-  end
 
-  # @return [Sqed::Boundaries instance]
-  #   the idea here is to create a deep copy of self, offsetting by boundary
-  #   as we go
-  def offset(boundary)
-    b = Sqed::Boundaries.new
-    (0..coordinates.length - 1).each do |i|
-      b.set(i,
-            [(x_for(i) + boundary.x_for(0)),
-             (y_for(i) + boundary.y_for(0)),
-             width_for(i),
-             height_for(i)])
+    # @return [Sqed::Boundaries instance]
+    #   the idea here is to create a deep copy of self, offsetting by boundary
+    #   as we go
+    def offset(boundary)
+      b = Sqed::Boundaries.new
+      (0..coordinates.length - 1).each do |i|
+        b.set(i,
+              [(x_for(i) + boundary.x_for(0)),
+               (y_for(i) + boundary.y_for(0)),
+               width_for(i),
+               height_for(i)])
+      end
+      b.complete = complete
+      b
     end
-    b.complete = complete
-    b
-  end
 
-  def for(section)
-    @coordinates[section]
-  end
+    def for(section)
+      @coordinates[section]
+    end
 
-  def each(&block)
-    @coordinates.each do |section_index, coords|
-      block.call([section_index, coords])
+    def each(&block)
+      @coordinates.each do |section_index, coords|
+        block.call([section_index, coords])
+      end
     end
-  end
 
-  # Overrides Enumerable
-  def count
-    @coordinates.length
-  end
+    # Overrides Enumerable
+    def count
+      @coordinates.length
+    end
 
-  def x_for(index)
-    @coordinates[index][0]
-  end
+    def x_for(index)
+      @coordinates[index][0]
+    end
 
-  def y_for(index)
-    @coordinates[index][1]
-  end
+    def y_for(index)
+      @coordinates[index][1]
+    end
 
-  def width_for(index)
-    @coordinates[index][2]
-  end
+    def width_for(index)
+      @coordinates[index][2]
+    end
 
-  def height_for(index)
-    @coordinates[index][3]
-  end
+    def height_for(index)
+      @coordinates[index][3]
+    end
 
-  def set(index, coordinates)
-    @coordinates[index] = coordinates
-  end
+    def set(index, coordinates)
+      @coordinates[index] = coordinates
+    end
 
-  def populated?
-    each do |index, coords|
-      coords.each do |c|
-        return false if c.nil?
+    def populated?
+      each do |index, coords|
+        coords.each do |c|
+          return false if c.nil?
+        end
       end
+      true
     end
-    true
-  end
 
-  def zoom(width_factor, height_factor)
-    coordinates.keys.each do |i|
-      set(i, [
+    def zoom(width_factor, height_factor)
+      coordinates.keys.each do |i|
+        set(i, [
           (x_for(i).to_f * width_factor).to_i,
           (y_for(i).to_f * height_factor).to_i,
           (width_for(i).to_f * width_factor).to_i,
           (height_for(i).to_f * height_factor).to_i
-      ])
+        ])
+      end
     end
-  end
 
   end
 end

data/lib/sqed/boundary_finder/color_line_finder.rb

@@ -15,7 +15,7 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
 
     super(image: image, layout: layout, use_thumbnail: use_thumbnail)
 
-    raise 'No layout provided.' if @layout.nil?
+    raise Sqed::Error, 'No layout provided.' if @layout.nil?
 
     # !@#? why this
     @boundary_color = boundary_color
@@ -201,6 +201,16 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
       boundaries.set(1, [ vertical.x_for(1), 0, right.width_for(0), right.height_for(0) ] )
       boundaries.set(2, [ vertical.x_for(1), right.y_for(1), right.width_for(1), right.height_for(1)] )
 
+    when :left_t
+      vertical = self.class.new(image: @image, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
+
+      ilft = image.crop(*vertical.for(0), true)
+      left = self.class.new(image: ilft, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
+
+      boundaries.set(0, vertical.for(1))
+      boundaries.set(1, [ vertical.x_for(0), 0, left.width_for(0), left.height_for(0) ] )
+      boundaries.set(2, [ vertical.x_for(0), left.y_for(1), left.width_for(1), left.height_for(1)] )
+
     when :seven_slot
       top_bottom_split = Sqed::BoundaryFinder.color_boundary_finder(image: image, scan: :columns, boundary_color: boundary_color)              # detect vertical division [array]
       left_right_split = Sqed::BoundaryFinder.color_boundary_finder(image: image, sample_subdivision_size: 1, boundary_color: boundary_color)  # detect horizontal division [array]
@@ -263,7 +273,7 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
       boundaries.set(0, [0, 0, image.columns, t[0]])  # upper section of image
       boundaries.set(1, [0, t[2], image.columns, image.rows - t[2]])  # lower section of image
 
-    else # no @layout provided !?
+    else # Hits :stage
       boundaries.set(0, [0, 0, image.columns, image.rows])   # totality of image as default
     end
 

data/lib/sqed/boundary_finder/stage_finder.rb

@@ -46,11 +46,11 @@ class Sqed::BoundaryFinder::StageFinder < Sqed::BoundaryFinder
 
   # Returns a Proc that, given a set of pixels (an edge of the image) decides
   # whether that edge is a border or not.
-  # 
-  # (img, samples = 5, threshold = 0.95, fuzz_factor = 0.5)  # initially 
+  #
+  # (img, samples = 5, threshold = 0.95, fuzz_factor = 0.5)  # initially
   # (img, samples = 50, threshold = 0.9, fuzz_factor = 0.1)   # semi-working on synthetic images 08-dec-2014 (x)
   # (img, samples = 20, threshold = 0.8, fuzz_factor = 0.2)   # WORKS with synthetic images and changes to x0, y0, width, height
-  # 
+  #
   # appears to assume sharp transition will occur in 5 pixels x/y
   #
   # how is threshold defined?

data/lib/sqed/boundary_finder.rb

@@ -33,8 +33,8 @@ class Sqed
       @layout = opts[:layout]
       @image = opts[:image]
 
-      raise 'No layout provided.' if layout.nil?
-      raise 'No image provided.' if image.nil? || image.class.name != 'Magick::Image'
+      raise Sqed::Error, 'No layout provided.' if layout.nil?
+      raise Sqed::Error, 'No image provided.' if image.nil? || image.class.name != 'Magick::Image'
 
       true
     end
@@ -166,7 +166,7 @@ class Sqed
         elsif scan == :columns
           j = image.crop(s * sample_subdivision_size, 0, 1, image.rows, true)
         else
-          raise
+          raise Sqed::Error
         end
 
         j.each_pixel do |pixel, c, r|

data/lib/sqed/extractor.rb

@@ -4,6 +4,10 @@ class Sqed
 
   # An Extractor takes Boundaries object and a metadata_map and returns a Sqed::Result
   #
+  # Extract assumes a successful preprocessing (e.g. finding boundaries, cropping images)!
+  #
+  # Only Tesseract based raises errors should be occurring at this point.
+  #
   class Extractor
 
     class Error < StandardError; end;
@@ -23,9 +27,10 @@ class Sqed
       @boundaries = opts[:boundaries]
       @image = opts[:image]
 
-      raise Error, 'boundaries not provided or provided boundary is not a Sqed::Boundaries' if boundaries.nil? || !boundaries.class.name == 'Sqed::Boundaries'
-      raise Error, 'metadata_map not provided or metadata_map not a Hash' if metadata_map.nil? || !metadata_map.class.name == 'Hash'
-      raise Error, 'image not provided' if image.nil? || !image.class.name == 'Magick::Image'
+      # TODO: `.extractable?` catches the nil? case
+      raise Sqed::Error, 'boundaries not provided or provided boundary is not a Sqed::Boundaries' if boundaries.nil? || !boundaries.kind_of?(Sqed::Boundaries)
+      raise Sqed::Error, 'metadata_map not provided or metadata_map not a Hash' if metadata_map.nil? || !metadata_map.kind_of?(Hash)
+      raise Sqed::Error, 'image not provided' if image.nil? || !image.kind_of?(Magick::Image)
     end
 
     def result

data/lib/sqed/version.rb

@@ -1,3 +1,3 @@
 class Sqed
-  VERSION = '0.7.0'.freeze
+  VERSION = '0.8.0'.freeze
 end

data/lib/sqed.rb

@@ -1,7 +1,7 @@
 # encoding: UTF-8
 
 recent_ruby = RUBY_VERSION >= '2.4.1'
-raise 'IMPORTANT: sqed gem requires ruby >= 2.4.1' unless recent_ruby
+raise Sqed::Error, 'IMPORTANT: sqed gem requires ruby >= 2.4.1' unless recent_ruby
 
 require 'rmagick'
 require 'sqed_utils'
@@ -23,9 +23,33 @@ class Sqed
   require_relative 'sqed/result'
 
 
-  # initial image which is an instance of ImageMagick::Image, containing background and stage, or just stage
+  # @return [Sqed::Boundaries instance, nil]
+  #   Contains the coordinates of the internal stage sections. Calculates when set.
+  attr_accessor :boundaries
+
+  # @return [Symbol] like `:red`, `:green`, `:blue`, defaults to `:green`
+  # describing the boundary color within the stage
+  attr_accessor :boundary_color
+
+  # @return [Sqed::BoundaryFinder::<Klass>]
+  # Provide a boundary_finder, overrides metadata taken from pattern
+  attr_accessor :boundary_finder
+
+  # @return [Boolean] defaults to `true`
+  #   when true detects border on initialization
+  attr_accessor :has_border
+
+  # initial image which is an instance of Magick::Image, containing background and stage, or just stage
   attr_accessor :image
 
+  # @return [Symbol] like `:cross`
+  # !! Provide a specific layout, passed as option :layout, overrides layout metadata taken from :pattern, defaults to `:cross`
+  attr_accessor :layout
+
+  # Provide a metadata map, overrides metadata taken from pattern.
+  # No calculations are done here.
+  attr_accessor :metadata_map
+
   # !optional! A lookup macro that if provided sets boundary_finder, layout, and metadata_map.
   # These can be individually overwritten.
   # Legal values are symbols taken from SqedConfig::EXTRACTION_PATTERNS.
@@ -39,41 +63,20 @@ class Sqed
   #   not required if layout, metadata_map, and boundary_finder are provided
   attr_accessor :pattern
 
-  # @return [Symbol] like `:cross`
-  # !! Provide a specific layout, passed as option :layout, overrides layout metadata taken from :pattern, defaults to `:cross`
-  attr_accessor :layout
-
-  # the image that is the cropped content for parsing
+  # The image that is the cropped content for parsing
+  # !! Does not require `metadata_map` or `layout`
   attr_accessor :stage_image
 
   # @return [Sqed::Boundaries instance]
   #   stores the coordinates of the stage
+  # !! Does not require `metadata_map` or `layout`
   attr_accessor :stage_boundary
 
-  # @return [Sqed::Boundaries instance]
-  #   contains the coordinates of the internal stage sections
-  attr_accessor :boundaries
-
-  # @return [Boolean] defaults to `true`
-  #   when true detects border on initialization
-  attr_accessor :has_border
-
-  # @return [Symbol] like `:red`, `:green`, `:blue`, defaults to `:green`
-  # describing the boundary color within the stage
-  attr_accessor :boundary_color
-
   # @return [Boolean] defaults to `true` (faster, less accurate)
   #  if `true` do the boundary detection (not stage detection at present)
   # against a thumbnail version of the passed image
   attr_accessor :use_thumbnail
 
-  # Provide a metadata map, overrides metadata taken from pattern
-  attr_accessor :metadata_map
-
-  # @return [Sqed::BoundaryFinder::<Klass>]
-  # Provide a boundary_finder, overrides metadata taken from pattern
-  attr_accessor :boundary_finder
-
   def initialize(**opts)
     # extraction metadata
     @image = opts[:image]
@@ -86,71 +89,102 @@ class Sqed
   #   federate extraction options
   def extraction_metadata
     {
-        boundary_finder: boundary_finder,
-        layout: layout,
-        metadata_map: metadata_map,
-        boundary_color: boundary_color,
-        has_border: has_border,
-        use_thumbnail: use_thumbnail
+      boundary_finder: boundary_finder,
+      layout: layout,
+      metadata_map: metadata_map,
+      boundary_color: boundary_color,
+      has_border: has_border,
+      use_thumbnail: use_thumbnail
     }
   end
 
-  # @return [ImageMagick::Image]
+  # @return [Magick::Image]
   #   set the image if it's not set during initialize(), not commonly used
   def image=(value)
-    @image = value
-    set_stage_boundary
-    @image
-  end
-
-  def boundaries(force = false)
-    @boundaries = get_section_boundaries if @boundaries.nil? || force
-    @boundaries
+    @image = value if value.kind_of?(::Magick::Image)
   end
 
   def stage_boundary
-    set_stage_boundary if !@stage_boundary.populated?
+    compute_stage_boundary if !@stage_boundary.populated?
     @stage_boundary
   end
 
   def stage_image
-    crop_image if @stage_image.nil?
-    @stage_image
-  end
-
-  # @return [Sqed::Boundaries instance, nil]
-  #   a boundaries instance that has the original image (prior to cropping stage) coordinates
-  def native_boundaries
-    if @boundaries.complete
-      @boundaries.offset(stage_boundary)
-    else
-      nil
-    end
+    @stage_image ||= crop_image
   end
 
   # @return [Image]
   #   crops the stage if not done, then sets/returns @stage_image
   def crop_image
-    if has_border
-      @stage_image = image.crop(*stage_boundary.for(SqedConfig.index_for_section_type(:stage, :stage)), true)
-    else
-      @stage_image = image
+
+    begin
+
+      if has_border && image
+        @stage_image = image.crop(*stage_boundary.for(SqedConfig.index_for_section_type(:stage, :stage)), true)
+      elsif image
+        @stage_image = image
+      end
+      @stage_image
+
+    rescue Sqed::Error
+      raise
+    rescue
+      raise Sqed::Error, 'error cropping image'
+    end
+
+  end
+
+  def boundaries(force = false)
+    begin
+
+      if force
+        @boundaries = get_section_boundaries
+      else
+        @boundaries ||= get_section_boundaries
+      end
+
+      @boundaries
+
+    rescue Sqed::Error
+      raise
+    rescue # XXXX
+      raise Sqed::Error, 'error processing boundaries'
     end
-    @stage_image
   end
 
+  # @return [Boolean]
+  #   `true` if all boundary detection and image processing
+  #   has been calculated with error
+  #
+  def extractable?
+    stage_image && metadata_map && boundaries
+  end
+
+  # @return [Sqed::Result, false]
   def result
-    return false if image.nil?
+    return false unless extractable?
 
     extractor = Sqed::Extractor.new(
       boundaries: boundaries,
-      metadata_map: metadata_map, #  extraction_metadata[:metadata_map],
+      metadata_map: metadata_map,
       image: stage_image
     )
 
     extractor.result
   end
 
+  private
+
+  # @return [Sqed::Boundaries instance, nil]
+  #   a boundaries instance that has the original image (prior to cropping stage) coordinates
+  def native_boundaries
+    if @boundaries.complete
+      @boundaries.offset(stage_boundary)
+    else
+      nil
+    end
+  end
+
   # @return [Hash]
   #   an overview of data/metadata, for debugging purposes only
   def attributes
@@ -160,8 +194,6 @@ class Sqed
     }.merge!(extraction_metadata)
   end
 
-  protected
-
   def configure(opts)
     configure_from_pattern(opts[:pattern])
     configure_boundary_finder(opts)
@@ -183,7 +215,7 @@ class Sqed
   def configure_from_pattern(value)
     return if value.nil?
     value = value.to_sym
-    raise "provided extraction pattern '#{value}' not defined" if !SqedConfig::EXTRACTION_PATTERNS.keys.include?(value)
+    raise Sqed::Error, "provided extraction pattern '#{value}' not defined" if !SqedConfig::EXTRACTION_PATTERNS.keys.include?(value)
     @pattern = value
     a = SqedConfig::EXTRACTION_PATTERNS[pattern]
     @boundary_finder = a[:boundary_finder]
@@ -213,31 +245,34 @@ class Sqed
   def stub_results
     @boundaries = nil
     @stage_boundary = Sqed::Boundaries.new(:internal_box)
-    set_stage_boundary if @image
+    compute_stage_boundary if @image
   end
 
+  # @return [Boundaries, nil]
   def get_section_boundaries
+
     boundary_finder.new(**section_params).boundaries
+
   end
 
   # @return [Hash]
   #   variables for the isolated stage image
   def section_params
     {
-       image: stage_image,
-       use_thumbnail: use_thumbnail,
-       layout: layout,
-       boundary_color: boundary_color
+      image: stage_image,
+      use_thumbnail: use_thumbnail,
+      layout: layout,
+      boundary_color: boundary_color
     }
   end
 
-  def set_stage_boundary
+  def compute_stage_boundary
     if has_border
       boundary = Sqed::BoundaryFinder::StageFinder.new(image: image).boundaries
-      if boundary.populated?
+      if boundary&.populated?
         @stage_boundary.set(0, boundary.for(0))
       else
-        raise 'error detecting stage'
+        raise Sqed::Error, 'error detecting stage'
       end
     else
       @stage_boundary.set(0, [0, 0, image.columns, image.rows])

data/lib/sqed_config.rb

@@ -50,12 +50,7 @@ module SqedConfig
   #      6   |---- 3
   #          | 4 |
   #
-  #
-  #       | 1
-  #    0  |----  :right_t
-  #       | 2
-  #
-  #
+  #  #
   #    0 | 1 | 2
   #   ------------
   #      | 5 | 3    :seven_slot
@@ -73,35 +68,50 @@ module SqedConfig
   #    0 | 1  :vertical_split
   #      |
   #
+  #    -------
+  #    |-----|
+  #    || 0 ||  :internal_box
+  #    |-----|
+  #    -------
+  #
+  #     0     :t
   #   -----
-  #   | 0 |   :internal_box
-  #   -----
+  #   2 | 1
+  #
   #
   #   0 | 1   :inverted_t
   #   -----
   #     2
   #
-  #     0     :t
-  #   -----
-  #   2 | 1
+  #    0 |
+  #   ---| 1   : left_t
+  #    2 |
   #
+  #      | 1
+  #    0 |---  :right_t
+  #      | 2
   #
+  #    -----
+  #    | 0 |  :stage
+  #    -----
   #
   # Hash values are used to stub out
   # the Sqed::Boundaries instance.
   LAYOUTS = {
     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],
-    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]
+    internal_box: [0],
+    stage: [0]
   }.freeze
 
   # Each element of the layout is a "section".
@@ -177,6 +187,12 @@ module SqedConfig
       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: :right_t,
+      metadata_map: { 0 => :annotated_specimen, 1 => :identifier, 2 => :image_registration }
+    },
+
     right_t: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
       layout: :right_t,

data/spec/lib/sqed_config_spec.rb

@@ -7,11 +7,11 @@ describe SqedConfig do
   end
 
   specify 'layouts' do
-    expect(SqedConfig.metadata[:layouts].keys).to contain_exactly(:t, :inverted_t, :cross, :horizontal_offset_cross, :horizontal_split, :lep_stage, :lep_stage2, :right_t, :seven_slot, :vertical_offset_cross, :vertical_split)
+    expect(SqedConfig.metadata[:layouts].keys).to contain_exactly(:stage, :t, :left_t, :inverted_t, :cross, :horizontal_offset_cross, :horizontal_split, :lep_stage, :lep_stage2, :right_t, :seven_slot, :vertical_offset_cross, :vertical_split)
   end
 
   specify 'layouts are in patterns' do
-    expect(SqedConfig.metadata[:layouts].keys + [:stage]).to contain_exactly(*SqedConfig::EXTRACTION_PATTERNS.keys)
+    expect(SqedConfig.metadata[:layouts].keys).to contain_exactly(*SqedConfig::EXTRACTION_PATTERNS.keys)
   end
 
 end

data/spec/lib/sqed_spec.rb

@@ -2,10 +2,7 @@ require 'spec_helper'
 
 describe Sqed do
 
-  let(:s) { Sqed.new(
-    pattern: :cross
-  )
-  }
+  let(:s) { Sqed.new( pattern: :cross) }
 
   context 'attributes' do
 

data/spec/lib/stage_handling/left_t_stage_spec.rb

@@ -0,0 +1,61 @@
+require 'spec_helper'
+
+describe 'handling T stage images' do
+
+  let(:image) { ImageHelpers.left_t_stage }
+  let(:sqed) do
+    Sqed.new(
+      image: image,
+      pattern: :left_t,
+      boundary_color: :red,
+      has_border: false )
+  end
+
+  let(:m) do
+    { 0 => 'annotated_specimen',
+      1 => 'identifier',
+      2 => 'image_registration'
+    }
+  end
+
+  context 'simple boundaries - without thumbnail' do
+    let(:s) { Sqed.new(
+      image: image, metadata_map: m, use_thumbnail: false,
+      layout: :left_t, 
+      boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+      boundary_color: :red,
+      has_border: false ) }
+
+    specify 'boundaries are reasonable' do
+      s.result
+      c = s.boundaries.coordinates
+      c.each do |section, values|
+        c[section].each_with_index do |v, i|
+          msg = "section #{section}, index #{i} has a bad value '#{v}'"
+          expect(v > -1).to be_truthy, msg
+        end
+      end
+    end
+  end
+
+  context 'boundaries - with_thumbnail' do
+    let(:s) { Sqed.new(
+      image: image,
+      use_thumbnail: true,
+      pattern: :left_t,
+      boundary_color: :red,
+      has_border: false ) }
+
+    specify 'boundaries are reasonable' do
+      s.result
+      c = s.boundaries.coordinates
+      c.each do |section, values|
+        c[section].each_with_index do |v, i|
+          msg = "section #{section}, index #{i} has a bad value '#{v}'"
+          expect(v > -1).to be_truthy, msg
+        end
+      end
+    end
+  end
+
+end

data/spec/lib/stage_handling/stage_spec.rb

@@ -0,0 +1,55 @@
+require 'spec_helper'
+
+describe 'handling stage images' do
+
+  let(:image) { ImageHelpers.stage }
+  let(:sqed) do
+    Sqed.new(
+      image: image,
+      pattern: :stage,
+      has_border: false )
+  end
+
+  let(:m) do
+    { 0 => 'stage' }
+  end
+
+  context 'simple boundaries - without thumbnail' do
+    let(:s) { Sqed.new(
+      image: image, metadata_map: m, use_thumbnail: false,
+      layout: :stage, 
+      boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+      has_border: false ) }
+
+    specify 'boundaries are reasonable' do
+      s.result
+      c = s.boundaries.coordinates
+      c.each do |section, values|
+        c[section].each_with_index do |v, i|
+          msg = "section #{section}, index #{i} has a bad value '#{v}'"
+          expect(v > -1).to be_truthy, msg
+        end
+      end
+    end
+  end
+
+  context 'boundaries - with_thumbnail' do
+    let(:s) { Sqed.new(
+      image: image,
+      use_thumbnail: true,
+      pattern: :stage,
+      has_border: false ) }
+
+    specify 'boundaries are reasonable' do
+      s.result
+      c = s.boundaries.coordinates
+      c.each do |section, values|
+        c[section].each_with_index do |v, i|
+          msg = "section #{section}, index #{i} has a bad value '#{v}'"
+          expect(v > -1).to be_truthy, msg
+        end
+      end
+    end
+  end
+
+end

data/spec/support/image_helpers.rb

@@ -16,6 +16,10 @@ module ImageHelpers
 
     # Stage images
 
+    def stage
+      get_image 'stage_images/stage.png'
+    end
+
     def t_stage
       get_image 'stage_images/t_stage.png'
     end
@@ -24,6 +28,10 @@ module ImageHelpers
       get_image 'stage_images/inverted_t_stage.png'
     end
 
+    def left_t_stage
+      get_image 'stage_images/left_t_stage.png'
+    end
+
     def cross_green
       get_image 'stage_images/boundary_cross_green.jpg'
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sqed
 version: !ruby/object:Gem::Version
-  version: 0.7.0
+  version: 0.8.0
 platform: ruby
 authors:
 - Matt Yoder
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-05-07 00:00:00.000000000 Z
+date: 2023-05-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -156,9 +156,11 @@ files:
 - spec/lib/sqed_utils_spec.rb
 - spec/lib/stage_handling/horizontal_offset_cross_spec.rb
 - spec/lib/stage_handling/inverted_t_stage_spec.rb
+- spec/lib/stage_handling/left_t_stage_spec.rb
 - spec/lib/stage_handling/lep_stage2_spec.rb
 - spec/lib/stage_handling/lep_stage_spec.rb
 - spec/lib/stage_handling/seven_slot_spec.rb
+- spec/lib/stage_handling/stage_spec.rb
 - spec/lib/stage_handling/t_stage_spec.rb
 - spec/spec_helper.rb
 - spec/support/files/barcode_images/code_128_barcode.png
@@ -188,9 +190,11 @@ files:
 - spec/support/files/stage_images/inhs_7_slot3.jpg
 - spec/support/files/stage_images/inhs_four_thirds.jpg
 - spec/support/files/stage_images/inverted_t_stage.png
+- spec/support/files/stage_images/left_t_stage.png
 - spec/support/files/stage_images/lep_stage.jpg
 - spec/support/files/stage_images/lep_stage2.jpg
 - spec/support/files/stage_images/lep_stage3.jpg
+- spec/support/files/stage_images/stage.png
 - spec/support/files/stage_images/t_stage.png
 - spec/support/files/test0.jpg
 - spec/support/files/test1.jpg
@@ -219,7 +223,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.22
+rubygems_version: 3.4.12
 signing_key:
 specification_version: 4
 summary: Specimens Quickly extracted and Digitized, or just "squid". A ruby gem for
@@ -240,9 +244,11 @@ test_files:
 - spec/lib/sqed_utils_spec.rb
 - spec/lib/stage_handling/horizontal_offset_cross_spec.rb
 - spec/lib/stage_handling/inverted_t_stage_spec.rb
+- spec/lib/stage_handling/left_t_stage_spec.rb
 - spec/lib/stage_handling/lep_stage2_spec.rb
 - spec/lib/stage_handling/lep_stage_spec.rb
 - spec/lib/stage_handling/seven_slot_spec.rb
+- spec/lib/stage_handling/stage_spec.rb
 - spec/lib/stage_handling/t_stage_spec.rb
 - spec/spec_helper.rb
 - spec/support/files/barcode_images/code_128_barcode.png
@@ -272,9 +278,11 @@ test_files:
 - spec/support/files/stage_images/inhs_7_slot3.jpg
 - spec/support/files/stage_images/inhs_four_thirds.jpg
 - spec/support/files/stage_images/inverted_t_stage.png
+- spec/support/files/stage_images/left_t_stage.png
 - spec/support/files/stage_images/lep_stage.jpg
 - spec/support/files/stage_images/lep_stage2.jpg
 - spec/support/files/stage_images/lep_stage3.jpg
+- spec/support/files/stage_images/stage.png
 - spec/support/files/stage_images/t_stage.png
 - spec/support/files/test0.jpg
 - spec/support/files/test1.jpg