sqed 0.5.8 → 0.6.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: b6f5201476f18b8ba5ad9444f6ac63f8b9d86ff1eb0a089da55521566cf3a8b57a25a5b70eb0478b8121582c5c88b34dab05cab45630b339a8649ed23855b015

data/.ruby-version

@@ -1 +1 @@
-2.5.1
+2.7.1

data/.travis.yml

@@ -12,6 +12,8 @@ rvm:
 before_install:
   - sudo apt-get update -qq
   - sudo apt-get install -qq tesseract-ocr tesseract-ocr-nld
+  - sudo sed -i 's/name="disk" value="1GiB"/name="disk" value="8GiB"/' /etc/ImageMagick-6/policy.xml
+  - identify -list resource | grep Disk | grep 8GiB # Check ImageMagick setting is actually working.
 branches:
   only:
     - master

data/lib/sqed.rb

@@ -17,10 +17,12 @@ require 'sqed_utils'
 #
 class Sqed
 
+  require_relative 'sqed/error'
   require_relative 'sqed_config'
   require_relative 'sqed/extractor'
   require_relative 'sqed/result'
 
+
   # initial image which is an instance of ImageMagick::Image, containing background and stage, or just stage
   attr_accessor :image
 
@@ -68,6 +70,7 @@ class Sqed
   # 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
 
@@ -165,6 +168,8 @@ class Sqed
     configure_layout(opts)
     configure_metadata_map(opts)
 
+    raise Sqed::Error, 'boundary_finder not provided' if @boundary_finder.nil?
+
     @has_border = opts[:has_border]
     @has_border = true if @has_border.nil?
 
@@ -184,12 +189,12 @@ class Sqed
     @boundary_finder = a[:boundary_finder]
     @layout = a[:layout]
     @metadata_map = a[:metadata_map]
+
     true
   end
 
   def configure_boundary_finder(opts)
-    @boundary_finder = opts[:boundary_finder].constantize if !opts[:boundary_finder].nil?
-    @boundary_finder ||= Sqed::BoundaryFinder::CrossFinder
+    @boundary_finder = opts[:boundary_finder] if !opts[:boundary_finder].nil?
   end
 
   def configure_layout(opts)
@@ -212,7 +217,7 @@ class Sqed
   end
 
   def get_section_boundaries
-    boundary_finder.new(section_params).boundaries
+    boundary_finder.new(**section_params).boundaries
   end
 
   # @return [Hash]

data/lib/sqed/boundary_finder.rb

@@ -6,6 +6,7 @@ class Sqed
   #
   class BoundaryFinder
 
+    # Problemantic (e.g. seven slot) seem to resolve at ~360
     THUMB_SIZE = 100
     COLOR_DELTA = 1.3 # color (e.g. red) must be this much be *COLOR_DELTA > than other values (e.g. blue/green)
 
@@ -18,7 +19,8 @@ class Sqed
     # A Sqed::Boundaries instance, stores the coordinates of all of the layout sections
     attr_reader :boundaries
 
-    # Whether to compress the original image to a thumbnail when finding boundaries
+    # @return Boolean
+    # Whether to compress the original image to a thumbnail when finding boundaries at certain steps of the processing
     attr_reader :use_thumbnail
 
     # when we compute using a derived thumbnail we temporarily store the full size image here
@@ -135,7 +137,7 @@ class Sqed
       while attempts < 5 do
         samples_to_take = (image_width / sample_subdivision_size).to_i - 1
         border_hits = sample_border(image, boundary_color, samples_to_take, sample_subdivision_size, scan)
-        
+
         break if border_hits.select{|k,v| v > 1}.size > 2 || sample_subdivision_size == 1
 
         sample_subdivision_size = (sample_subdivision_size.to_f / 2.0).to_i
@@ -207,7 +209,7 @@ class Sqed
     #   the start, mid, endpoint position of all (pixel) positions that have a count greater than the cutoff
     def self.frequency_stats(frequency_hash, sample_cutoff = 0)
 
-      return nil if sample_cutoff.nil? ||  sample_cutoff < 1
+      return nil if sample_cutoff.nil? || sample_cutoff < 1
       hit_ranges = []
 
       frequency_hash.each do |position, count|
@@ -236,6 +238,11 @@ class Sqed
       [hit_ranges.first, hit_ranges[(hit_ranges.length / 2).to_i], hit_ranges.last]
     end
 
+    def self.max_difference(array)
+      array.max - array.min
+    end
+
+    # Usused
 
     # Returns an Integer, the maximum of the pairwise differences of the values in the array
     # For example, given
@@ -248,10 +255,6 @@ class Sqed
       (0..array.length - 2).map{|i| (array[i] - array[i + 1]).abs }.max
     end
 
-    def self.max_difference(array)
-      array.max - array.min
-    end
-
     def self.derivative_signs(array)
       (0..array.length - 2).map { |i| (array[i + 1] - array[i]) <=> 0 }
     end

data/lib/sqed/boundary_finder/color_line_finder.rb

@@ -29,34 +29,39 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
 
   private
 
+  # boundaries.coordinates are referenced from stage image
+  #
+  # A reminder that boundaries are x1,y1, width, height
   def find_bands
-    case layout    # boundaries.coordinates are referenced from stage image
+
+    # see config/sqed_config.rb
+    case layout
 
     when :cross # 4 zones, with perfectly intersected horizontal and vertical division
       v = self.class.new(image: @image, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
-      h = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false).boundaries 
+      h = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false).boundaries
 
       return if v.nil? || h.nil?
 
-      boundaries.set(0, [0,0, v.width_for(0), h.height_for(0) ]) 
-      boundaries.set(1, [ v.x_for(1), 0, v.width_for(1), h.height_for(0) ]) 
-      boundaries.set(2, [ v.x_for(1), h.y_for(1), v.width_for(1), h.height_for(1) ]) 
-      boundaries.set(3, [0, h.y_for(1), v.width_for(0), h.height_for(1) ]) 
+      boundaries.set(0, [0,0, v.width_for(0), h.height_for(0) ])
+      boundaries.set(1, [ v.x_for(1), 0, v.width_for(1), h.height_for(0) ])
+      boundaries.set(2, [ v.x_for(1), h.y_for(1), v.width_for(1), h.height_for(1) ])
+      boundaries.set(3, [0, h.y_for(1), v.width_for(0), h.height_for(1) ])
 
     # No specs for this yet
     when :horizontal_offset_cross
       horizontal = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
 
-      itop = image.crop(*horizontal.for(0), true) 
+      itop = image.crop(*horizontal.for(0), true)
       ibottom = image.crop(*horizontal.for(1), true)
 
       top = self.class.new(image: itop, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
       bottom = self.class.new(image: ibottom, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
 
-      boundaries.set(0, [0, 0, top.width_for(0), top.height_for(0) ]) 
-      boundaries.set(1, [top.x_for(1), 0, top.width_for(1), top.height_for(1) ]) 
-      boundaries.set(2, [bottom.x_for(1), horizontal.y_for(1), bottom.width_for(1), bottom.height_for(1) ]) 
-      boundaries.set(3, [0, horizontal.y_for(1), bottom.width_for(0), bottom.height_for(0) ]) 
+      boundaries.set(0, [0, 0, top.width_for(0), top.height_for(0) ])
+      boundaries.set(1, [top.x_for(1), 0, top.width_for(1), top.height_for(1) ])
+      boundaries.set(2, [bottom.x_for(1), horizontal.y_for(1), bottom.width_for(1), bottom.height_for(1) ])
+      boundaries.set(3, [0, horizontal.y_for(1), bottom.width_for(0), bottom.height_for(0) ])
 
     when :lep_stage
       top_bottom_split = Sqed::BoundaryFinder.color_boundary_finder(image: image, scan: :columns, boundary_color: boundary_color)              # detect vertical division [array]
@@ -64,9 +69,9 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
 
       boundaries.set(6, [0, top_bottom_split[2], left_right_split[0], image.rows - top_bottom_split[2]] )
 
-      left_top_image = image.crop( 0, 0, left_right_split[0], top_bottom_split[0], true) 
+      left_top_image = image.crop( 0, 0, left_right_split[0], top_bottom_split[0], true)
 
-      left_top_split = 
+      left_top_split =
         SqedUtils.corrected_frequency(
           Sqed::BoundaryFinder.color_boundary_finder(image: left_top_image, boundary_color: boundary_color),
           max_width: left_top_image.columns,
@@ -74,8 +79,8 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
       )
 
       boundaries.set(0, [0, 0, left_top_split[1], top_bottom_split[0]] ) # keep as 1 for safety
-     
-      boundaries.set(1, [left_top_split[2], 0, left_top_image.columns - left_top_split[2], top_bottom_split[0]] ) 
+
+      boundaries.set(1, [left_top_split[2], 0, left_top_image.columns - left_top_split[2], top_bottom_split[0]] )
       boundaries.set(2, [left_right_split[2], 0, image.columns - left_right_split[0], top_bottom_split[0]] )
 
       bottom_right_image =  image.crop(left_right_split[2], top_bottom_split[2], image.columns - left_right_split[2], image.rows - top_bottom_split[2], true)
@@ -89,7 +94,7 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
 
       boundaries.set(3, [left_right_split[2] + bottom_right_split[2], top_bottom_split[2], image.columns - bottom_right_split[2], image.rows - top_bottom_split[2] ] )
 
-      bottom_right_left_image = image.crop(left_right_split[2], top_bottom_split[2], bottom_right_split[0], image.rows - top_bottom_split[2], true)  
+      bottom_right_left_image = image.crop(left_right_split[2], top_bottom_split[2], bottom_right_split[0], image.rows - top_bottom_split[2], true)
 
       bottom_right_left_split =
         SqedUtils.corrected_frequency(
@@ -101,10 +106,69 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
       boundaries.set(4, [left_right_split[2], top_bottom_split[2], bottom_right_image.columns - bottom_right_left_image.columns, bottom_right_left_split[0] ] )
 
       boundaries.set(5, [
-        left_right_split[2], 
+        left_right_split[2],
         top_bottom_split[2] + bottom_right_left_split[2],
         bottom_right_image.columns - bottom_right_left_image.columns,
-        bottom_right_left_image.rows - bottom_right_left_split[2]  
+        bottom_right_left_image.rows - bottom_right_left_split[2]
+      ])
+
+    when :lep_stage2
+      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: 2, boundary_color: boundary_color)  # detect horizontal division [array]
+
+      boundaries.set(6, [0, top_bottom_split[2], left_right_split[0], image.rows - top_bottom_split[2]] ) # OK
+
+      left_top_image = image.crop( 0, 0, left_right_split[0], top_bottom_split[0], true)
+
+      left_top_split =
+        SqedUtils.corrected_frequency(
+          Sqed::BoundaryFinder.color_boundary_finder(image: left_top_image, boundary_color: boundary_color),
+          max_width: left_top_image.columns,
+          width_factor: 1.8
+      )
+
+      boundaries.set(0, [0, 0, left_top_split[1], top_bottom_split[0]] ) # OK
+
+      boundaries.set(1, [left_top_split[2], 0, left_top_image.columns - left_top_split[2], top_bottom_split[0]] )
+      boundaries.set(2, [left_right_split[2], 0, image.columns - left_right_split[0], top_bottom_split[0]] )
+
+      bottom_right_image =  image.crop(left_right_split[2], top_bottom_split[2], image.columns - left_right_split[2], image.rows - top_bottom_split[2], true)
+
+      bottom_right_split =
+        SqedUtils.corrected_frequency(
+          Sqed::BoundaryFinder.color_boundary_finder(image: bottom_right_image, boundary_color: boundary_color, scan: :rows),
+          max_width: bottom_right_image.columns,
+          width_factor: 1.8
+      )
+
+      boundaries.set(3, [
+        left_right_split[2] + bottom_right_split[2],
+        top_bottom_split[2],
+        image.columns - bottom_right_split[2],
+        top_bottom_split[0] ])
+
+      bottom_right_left_image = image.crop(left_right_split[2], top_bottom_split[2], bottom_right_split[0], image.rows - top_bottom_split[2], true)
+
+      bottom_right_left_top_bottom_split =
+        SqedUtils.corrected_frequency(
+          Sqed::BoundaryFinder.color_boundary_finder(image: bottom_right_left_image, scan: :columns, boundary_color: boundary_color),
+          max_width: bottom_right_left_image.columns,
+          width_factor: 1.8
+      )
+
+      boundaries.set(4, [
+        left_right_split[2],
+        top_bottom_split[2] + bottom_right_left_top_bottom_split[2],
+        bottom_right_left_image.columns,
+        bottom_right_left_top_bottom_split[2]
+      ])
+
+
+      boundaries.set(5, [
+        left_right_split[2],
+        top_bottom_split[2],
+        bottom_right_left_image.columns,
+        bottom_right_left_top_bottom_split[0],
       ])
 
     when :right_t
@@ -113,13 +177,13 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
       irt = image.crop(*vertical.for(1), true)
       right = self.class.new(image: irt, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
 
-      boundaries.set(0, vertical.for(0))    
-      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)] )  
+      boundaries.set(0, vertical.for(0))
+      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 :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: 2, boundary_color: boundary_color)  # detect horizontal division [array]
+      left_right_split = Sqed::BoundaryFinder.color_boundary_finder(image: image, sample_subdivision_size: 1, boundary_color: boundary_color)  # detect horizontal division [array]
 
       boundaries.set(0, [0, 0, left_right_split[0], top_bottom_split[0]])
       boundaries.set(6, [0, top_bottom_split[2], left_right_split[0], image.rows - top_bottom_split[2]] )
@@ -128,18 +192,22 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
       right_bottom_image = image.crop(left_right_split[2], top_bottom_split[2], image.columns - left_right_split[2], image.rows - top_bottom_split[2], true)  # sections 3,4,5
 
       right_top_split = ::SqedUtils.corrected_frequency(
-        Sqed::BoundaryFinder.color_boundary_finder(image: right_top_image, boundary_color: boundary_color, scan: :rows),
-        width_factor: 1.8,
-        max_width: right_top_image.columns
+        Sqed::BoundaryFinder.color_boundary_finder(
+          image: right_top_image, boundary_color: boundary_color, scan: :rows),
+          width_factor: 1.8,
+          max_width: right_top_image.columns
       ) # vertical line b/w 1 & 2, use "corrected_frequency" to account for color bleed from previous crop
 
       boundaries.set(1, [left_right_split[2], 0, right_top_split[0], top_bottom_split[0]] )
       boundaries.set(2, [left_right_split[2] + right_top_split[2], 0, right_top_image.columns - right_top_split[2], top_bottom_split[0]])
 
       right_bottom_split = SqedUtils.corrected_frequency(
-        Sqed::BoundaryFinder.color_boundary_finder(image: right_bottom_image, scan: :columns, sample_subdivision_size: 2, boundary_color: boundary_color),
-        width_factor: 1.8,
-        max_width: right_bottom_image.rows) # horizontal line b/w (5,3) & 4, use "corrected_frequency" to account for color bleed from previous crop
+        Sqed::BoundaryFinder.color_boundary_finder(
+          image: right_bottom_image,
+          scan: :columns,
+          sample_subdivision_size: 2, boundary_color: boundary_color),
+          width_factor: 1.8,
+          max_width: right_bottom_image.rows) # horizontal line b/w (5,3) & 4, use "corrected_frequency" to account for color bleed from previous crop
 
       bottom_right_top_image = right_bottom_image.crop(0,0, image.columns - left_right_split[2], right_bottom_split[0], true) # 3,5
 
@@ -151,18 +219,18 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
     when :vertical_offset_cross   # 4 zones expected, with (varying) horizontal division in left- and right- sides of vertical division
       vertical = self.class.new(image: @image, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false).boundaries
 
-      ilt = image.crop(*vertical.for(0), true) 
+      ilt = image.crop(*vertical.for(0), true)
       irt = image.crop(*vertical.for(1), true)
 
       left = self.class.new(image: ilt, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false).boundaries   # fails
       right = self.class.new(image: irt, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries # OK
 
-      boundaries.set(0, [0, 0, left.width_for(0), left.height_for(0) ]) 
-      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) ]) 
-      boundaries.set(3, [0, left.y_for(1), left.width_for(1), left.height_for(1) ]) 
+      boundaries.set(0, [0, 0, left.width_for(0), left.height_for(0) ])
+      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) ])
+      boundaries.set(3, [0, left.y_for(1), left.width_for(1), left.height_for(1) ])
 
-    when :vertical_split 
+    when :vertical_split
       t = Sqed::BoundaryFinder.color_boundary_finder(image: image, boundary_color: boundary_color)  #detect vertical division
       return if t.nil?
       boundaries.set(0, [0, 0, t[0], image.rows])  # left section of image
@@ -175,10 +243,7 @@ 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 !?
-
       boundaries.set(0, [0, 0, image.columns, image.rows])   # totality of image as default
     end
 

data/lib/sqed/error.rb

@@ -0,0 +1,2 @@
+class Sqed::Error < StandardError
+end

data/lib/sqed/extractor.rb

@@ -23,8 +23,8 @@ 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 == Sqed::Boundaries
-      raise Error, 'metadata_map not provided or metadata_map not a Hash' if metadata_map.nil? || !metadata_map.class == Hash
+      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'
     end
 

data/lib/sqed/parser.rb

@@ -9,8 +9,9 @@ class Sqed::Parser
   attr_accessor :extracted_text
 
   def initialize(image)
+    raise Sqed::Error, 'no image passed to parser' if image.nil?
+    raise Sqed::Error, 'image is not a Magick::Image' if !(image.class.name == 'Magick::Image')
     @image = image
-    raise 'no image provided to parser' if @image && !(@image.class.name == 'Magick::Image')
   end
 
 end

data/lib/sqed/version.rb

@@ -1,3 +1,3 @@
 class Sqed
-  VERSION = '0.5.8'.freeze
+  VERSION = '0.6.0'.freeze
 end

data/lib/sqed_config.rb

@@ -17,33 +17,40 @@ require_relative 'sqed/boundary_finder/color_line_finder'
 module SqedConfig
 
   # Layouts refer to the arrangement of the divided stage.
-  # Windows are enumerated from the top left, moving around the border 
+  # 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 
+  #   ---------  :horizontal_offset_cross
   #    3    | 2
-  # 
+  #
   #
   #        0
   #    --------  :horizontal_split
   #        1
-  # 
+  #
   #
   #    0 | 1 | 2
   #   ------------
   #      | 5 |      :lep_stage
-  #    6 |---- 3  
+  #    6 |---- 3
   #      | 4 |
   #
   #
+  #    0 | 1 |  2
+  #   --------------
+  #          | 5 |      :lep_stage2
+  #      6   |---- 3
+  #          | 4 |
+  #
+  #
   #       | 1
   #    0  |----  :right_t
   #       | 2
@@ -55,21 +62,21 @@ module SqedConfig
   #    6 |--------
   #      |   4
   #
-  # 
+  #
   #    0  |  1
   #       |____
-  #   ----|      :vertical_offset_cross 
+  #   ----|      :vertical_offset_cross
   #    3  |  2
-  #  
   #
-  #        |
-  #      0 | 1  :vertical_split
-  #        |
+  #
+  #      |
+  #    0 | 1  :vertical_split
+  #      |
   #
   #   -----
   #   | 0 |  :internal_box
   #   -----
-  #  
+  #
   # Hash values are used to stub out
   # the Sqed::Boundaries instance.
   LAYOUTS = {
@@ -77,6 +84,7 @@ module SqedConfig
     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],
@@ -93,7 +101,7 @@ module SqedConfig
     :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 
+    :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
@@ -139,6 +147,12 @@ module SqedConfig
       metadata_map: { 0 => :curator_metadata, 1 => :collecting_event_labels, 2 => :image_registration, 3 => :identifier, 4 => :other_labels, 5 => :determination_labels, 6 => :specimen }
     },
 
+    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 }
+    },
+
     right_t: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
       layout: :right_t,

data/spec/lib/sqed_config_spec.rb

@@ -7,7 +7,7 @@ describe SqedConfig do
   end
 
   specify 'layouts' do
-    expect(SqedConfig.metadata[:layouts].keys).to contain_exactly(:cross, :horizontal_offset_cross, :horizontal_split, :lep_stage, :right_t, :seven_slot, :vertical_offset_cross, :vertical_split)
+    expect(SqedConfig.metadata[:layouts].keys).to contain_exactly(: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

data/spec/lib/sqed_spec.rb

@@ -2,7 +2,10 @@ require 'spec_helper'
 
 describe Sqed do
 
-  let(:s) { Sqed.new }
+  let(:s) { Sqed.new(
+    pattern: :cross
+  )
+  }
 
   context 'attributes' do
 
@@ -41,19 +44,14 @@ describe Sqed do
     specify '#use_thumbnail defaults to `true`' do
       expect(s.use_thumbnail).to eq(true)
     end
-
   end
 
-  context 'initialization' do 
-    specify 'without providing a pattern assigns nil' do
-      expect(s.pattern).to eq(nil)
-    end
+  specify 'raises without pattern or boundary_finder provided' do
+    expect{Sqed.new}.to raise_error Sqed::Error
   end
 
-  context '#result' do
-    specify 'without providing an image returns false' do
-      expect(s.result).to eq(false)
-    end
+  specify '#result without image returns false' do
+    expect(s.result).to eq(false)
   end
 
   # Intent is to just test wrapping functionality, see

data/spec/lib/stage_handling/horizontal_offset_cross_spec.rb

@@ -30,7 +30,9 @@ describe 'handling 7 slot stages' do
   end
 
   context 'simple boundaries - without thumbnail' do
-    let(:s) { Sqed.new(image: image, metadata_map: m, use_thumbnail: false, layout: :horizontal_offset_cross, boundary_color: :red, has_border: false ) }
+    let(:s) { Sqed.new(image: image, metadata_map: m, use_thumbnail: false, layout: :horizontal_offset_cross, 
+                       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+                       boundary_color: :red, has_border: false ) }
 
     specify 'boundaries are reasonable' do
       s.result

data/spec/lib/stage_handling/lep_stage2_spec.rb

@@ -0,0 +1,64 @@
+require 'spec_helper'
+
+describe 'handling lep stage images' do
+
+  let(:image) { ImageHelpers.lep_stage2 }
+  let(:sqed) do
+    Sqed.new(
+      image: image,
+      pattern: :lep_stage,
+      boundary_color: :red,
+      has_border: false )
+  end
+
+  let(:m) do
+    { 0 => :curator_metadata,
+      1 => :collecting_event_labels,
+      2 => :image_registration,
+      3 => :identifier,
+      4 => :other_labels,
+      5 => :determination_labels,
+      6 => :specimen 
+    }
+  end
+
+  context 'parses' do
+    specify 'new() without errors' do
+      expect(sqed).to be_truthy
+    end
+
+    specify 'get result without errors' do
+      expect(sqed.result).to be_truthy
+    end
+  end
+
+  context 'trickier boundaries - without thumbnail' do
+    let(:s) { Sqed.new(image: ImageHelpers.lep_stage2, use_thumbnail: false, pattern: :lep_stage2, 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 'trickier boundaries - with_thumbnail' do
+    let(:s) { Sqed.new(image: ImageHelpers.lep_stage2, use_thumbnail: true, pattern: :lep_stage2, 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/seven_slot_spec.rb

@@ -12,15 +12,65 @@ describe 'handling 7 slot stages' do
   end
 
   let(:m) do
-    { 0 => 'collecting_event_labels',
-      1 => 'determination_labels',
-      2 => 'other_labels',
-      3 => 'image_registration',
-      4 => 'curator_metadata',
-      5 => 'identifier',
-      6 => 'specimen' }
+    { 0 => :collecting_event_labels,
+      1 => :determination_labels,
+      2 => :other_labels,
+      3 => :image_registration,
+      4 => :curator_metadata,
+      5 => :identifier,
+      6 => :specimen }
   end
 
+
+  let(:w) {22.5} # 1/2 width red "tape"
+
+  let(:coords) {
+    {
+      0 => [
+        0,
+        0,
+        1674,
+        1280
+      ],
+      1 => [
+        1820,
+        0,
+        1773,
+        1280
+      ],
+      2 => [
+        3746,
+        0,
+        1726,
+        1280
+      ],
+      3 => [
+        3746,
+        1422,
+        3746,
+        836
+      ],
+      4 => [
+        1820,
+        2382,
+        3652,
+        2226
+      ],
+      5 => [
+        1820,
+        1422,
+        1773,
+        836
+      ],
+      6 => [
+        0,
+        1422,
+        1674,
+        2226
+      ]
+    }
+  }
+
   context 'parses' do
     specify 'new() without errors' do
       expect(sqed).to be_truthy
@@ -32,33 +82,58 @@ describe 'handling 7 slot stages' do
   end
 
   context 'trickier boundaries - without thumbnail' do
-    let(:s) { Sqed.new(image: ImageHelpers.inhs_stage_7_slot2, metadata_map: m, use_thumbnail: false, layout: :seven_slot, boundary_color: :red, has_border: false ) }
+    # perfect parsing currently
+    let(:s) { Sqed.new(
+      image: ImageHelpers.inhs_stage_7_slot2,
+      layout: :seven_slot, # layout + metadata map + boundary_finder signature
+      metadata_map: m,
+      boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+      use_thumbnail: false,
+      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
+          min = coords[section][i] - w
+          max = coords[section][i] + w
+          msg = "section #{section}, index #{i}, '#{v}' is out of range #{min}-#{max} "
+          expect((v > min) && (v < max)).to be_truthy, msg
         end
       end
     end
   end
 
+  # image size is a failure here
   context 'trickier boundaries - with_thumbnail' do
-    let(:s) { Sqed.new(image: ImageHelpers.inhs_stage_7_slot2, use_thumbnail: true, pattern: :seven_slot, boundary_color: :red, has_border: false ) }
+    let(:s) { Sqed.new(
+      image: ImageHelpers.inhs_stage_7_slot2,
+      use_thumbnail: true,
+      pattern: :seven_slot, # pattern signature
+      boundary_color: :red, has_border: false ) }
 
-
-    specify 'boundaries are reasonable' do
+    xspecify 'boundaries are reasonable' do
       s.result
       c = s.boundaries.coordinates
+      errors = []
+
       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
+          min = coords[section][i] - w
+          max = coords[section][i] + w
+
+          msg = "section #{section}, index #{i}, '#{v}' is #{(v - coords[section][i]).abs } out of range #{min}-#{max}"
+          if !((v > min) && (v < max))
+            errors.push msg
+          else
+            errors.push "section #{section} (#{v}) is OK"
+          end
         end
       end
+      expect(errors).to be_empty, errors.join("\n")
     end
   end
 
@@ -68,6 +143,6 @@ describe 'handling 7 slot stages' do
     specify '#result' do
       expect(s.result).to be_truthy
     end
-  end 
+  end
 
 end

data/spec/spec_helper.rb

@@ -5,7 +5,7 @@ Bundler.setup
 require 'sqed'
 require 'support/image_helpers'
 require 'byebug'
-require 'awesome_print'
+require 'amazing_print'
 require 'fileutils'
 require 'rmagick'
 

data/spec/support/image_helpers.rb

@@ -36,15 +36,19 @@ module ImageHelpers
     end
 
     def inhs_stage_7_slot
-      get_image 'stage_images/inhs_7_slot.jpg'
+      get_image 'stage_images/inhs_7_slot3.jpg'
+    end
+
+    def inhs_stage_7_slot2
+      get_image 'stage_images/inhs_7_slot2.jpg'
     end
 
     def lep_stage
       get_image 'stage_images/lep_stage.jpg'
     end
 
-    def inhs_stage_7_slot2
-      get_image 'stage_images/inhs_7_slot2.jpg'
+    def lep_stage2
+      get_image 'stage_images/lep_stage2.jpg'
     end
 
     def crossy_green_line_specimen

data/sqed.gemspec

@@ -19,8 +19,8 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
 
   spec.add_dependency 'rake', '~> 13.0'
-  spec.add_dependency 'rmagick', '~> 4.0'
-  spec.add_dependency 'rtesseract', '~> 3.0.4'
+  spec.add_dependency 'rmagick', '~> 4.1'
+  spec.add_dependency 'rtesseract', '~> 3.1'
 
   # A qrcode reader, too many problems with compiling, dependencies
   # spec.add_dependency 'zxing_cpp', '~> 0.1.0'
@@ -28,6 +28,6 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency 'rspec', '~> 3.9'
   spec.add_development_dependency 'bundler', '~> 2.0'
   spec.add_development_dependency 'byebug', '~> 11.0'
-  spec.add_development_dependency 'awesome_print', '~> 1.8'
+  spec.add_development_dependency 'amazing_print', '~> 1.2.1'
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sqed
 version: !ruby/object:Gem::Version
-  version: 0.5.8
+  version: 0.6.0
 platform: ruby
 authors:
 - Matt Yoder
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-11-18 00:00:00.000000000 Z
+date: 2020-08-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -31,28 +31,28 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '4.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '4.1'
 - !ruby/object:Gem::Dependency
   name: rtesseract
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.0.4
+        version: '3.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.0.4
+        version: '3.1'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -96,19 +96,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '11.0'
 - !ruby/object:Gem::Dependency
-  name: awesome_print
+  name: amazing_print
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: 1.2.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: 1.2.1
 description: A utility gem to aid in the processing of images taken in the process
   of digitizing natural history collections.
 email:
@@ -132,6 +132,7 @@ files:
 - lib/sqed/boundary_finder/color_line_finder.rb
 - lib/sqed/boundary_finder/cross_finder.rb
 - lib/sqed/boundary_finder/stage_finder.rb
+- lib/sqed/error.rb
 - lib/sqed/extractor.rb
 - lib/sqed/parser.rb
 - lib/sqed/parser/barcode_parser.rb
@@ -154,6 +155,7 @@ files:
 - spec/lib/sqed_spec.rb
 - spec/lib/sqed_utils_spec.rb
 - spec/lib/stage_handling/horizontal_offset_cross_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/spec_helper.rb
@@ -181,8 +183,10 @@ files:
 - spec/support/files/stage_images/horizontal_offset_cross.png
 - spec/support/files/stage_images/inhs_7_slot.jpg
 - spec/support/files/stage_images/inhs_7_slot2.jpg
+- spec/support/files/stage_images/inhs_7_slot3.jpg
 - spec/support/files/stage_images/inhs_four_thirds.jpg
 - spec/support/files/stage_images/lep_stage.jpg
+- spec/support/files/stage_images/lep_stage2.jpg
 - spec/support/files/test0.jpg
 - spec/support/files/test1.jpg
 - spec/support/files/test2.jpg
@@ -210,7 +214,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.6
+rubygems_version: 3.1.2
 signing_key: 
 specification_version: 4
 summary: Specimens Quickly extracted and Digitized, or just "squid". A ruby gem for
@@ -230,6 +234,7 @@ test_files:
 - spec/lib/sqed_spec.rb
 - spec/lib/sqed_utils_spec.rb
 - spec/lib/stage_handling/horizontal_offset_cross_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/spec_helper.rb
@@ -257,8 +262,10 @@ test_files:
 - spec/support/files/stage_images/horizontal_offset_cross.png
 - spec/support/files/stage_images/inhs_7_slot.jpg
 - spec/support/files/stage_images/inhs_7_slot2.jpg
+- spec/support/files/stage_images/inhs_7_slot3.jpg
 - spec/support/files/stage_images/inhs_four_thirds.jpg
 - spec/support/files/stage_images/lep_stage.jpg
+- spec/support/files/stage_images/lep_stage2.jpg
 - spec/support/files/test0.jpg
 - spec/support/files/test1.jpg
 - spec/support/files/test2.jpg