sqed 0.5.0 → 0.5.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/.ruby-version

@@ -1 +1 @@
-2.4.3
+2.5.1

data/lib/sqed/boundary_finder/color_line_finder.rb

@@ -32,6 +32,32 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
   def find_bands
     case layout    # boundaries.coordinates are referenced from stage image
 
+    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 
+
+      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) ]) 
+
+    # 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) 
+      ibottom = image.crop(*horizontal.for(1), true)
+
+      top = self.class.new(image: ilt, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
+      bottom = self.class.new(image: irt, 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) ]) 
+
     when :lep_stage
       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]
@@ -81,6 +107,16 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
         bottom_right_left_image.rows - bottom_right_left_split[2]  
       ])
 
+    when :right_t
+      vertical = self.class.new(image: @image, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
+
+      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)] )  
+
     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]
@@ -112,29 +148,6 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
 
       boundaries.set(4, [left_right_split[2], top_bottom_split[2] + right_bottom_split[2], image.columns - left_right_split[2], right_bottom_image.rows ])
 
-    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
-      boundaries.set(1, [t[2], 0, image.columns - t[2], image.rows])  # right section of image
-
-    when :horizontal_split
-      t = Sqed::BoundaryFinder.color_boundary_finder(image: image, scan: :columns, boundary_color: boundary_color)  # set to detect horizontal division
-      return if t.nil?
-
-      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
-
-    when :right_t # only 3 zones expected, with horizontal division in right-side of vertical division
-      vertical = self.class.new(image: @image, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
-
-      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)] )  
-
     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
 
@@ -149,31 +162,20 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
       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) ]) 
 
-      # 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) 
-      ibottom = image.crop(*horizontal.for(1), true)
-
-      top = self.class.new(image: ilt, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
-      bottom = self.class.new(image: irt, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
+    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
+      boundaries.set(1, [t[2], 0, image.columns - t[2], image.rows])  # right section of image
 
-      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 :horizontal_split
+      t = Sqed::BoundaryFinder.color_boundary_finder(image: image, scan: :columns, boundary_color: boundary_color)  # set to detect horizontal division
+      return if t.nil?
 
-    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 
+      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
 
-      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) ]) 
 
     else # no @layout provided !?
 

data/lib/sqed/version.rb

@@ -1,3 +1,3 @@
 class Sqed
-  VERSION = '0.5.0'.freeze
+  VERSION = '0.5.1'.freeze
 end

data/lib/sqed_config.rb

@@ -21,42 +21,33 @@ module SqedConfig
   # in a clockwise position.  For example:
   #
   #    0  | 1
-  #   ----|----  :equal_cross (always perfectly divided through the center)
-  #    3  | 2
-  #
-  #
-  #    0  | 1
-  #   ----|----  :cross - height of [0, 1], [2,3] same, width of [0,1], [2,3] same, otherwise variable, i.e. height(0) != height(3)
+  #   ----|----  :cross (any cross pattern)
   #       |
   #    3  | 2
-  #
+  # 
   #
   #    0  |  1
   #       |
   #   ---------  :horizontal_offset_cross 
-  #    3   | 2
+  #    3    | 2
+  # 
   #
+  #        0
+  #    --------  :horizontal_split
+  #        1
+  # 
+  #
+  #    0 | 1 | 2
+  #   ------------
+  #      | 5 |      :lep_stage
+  #    6 |---- 3  
+  #      | 4 |
   #
-  #    0  |  1
-  #       |____
-  #   ----|      :vertical_offset_cross 
-  #    3  |  2
   #
   #       | 1
   #    0  |----  :right_t
   #       | 2
   #
-  #        0
-  #    --------  :horizontal_split
-  #        1
-  #
-  #        |
-  #      0 | 1  :vertical_split
-  #        |
-  #
-  #   -----
-  #   | 0 |  :internal_box
-  #   -----
   #
   #    0 | 1 | 2
   #   ------------
@@ -64,25 +55,33 @@ module SqedConfig
   #    6 |--------
   #      |   4
   #
-  #    0 | 1 | 2
-  #   ------------
-  #      | 5 |      :lep_stage
-  #    6 |---- 3  
-  #      | 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.
-  # TODO: deprecate for simpler breakdown (cross, split, t)
   LAYOUTS = {
     cross: [0, 1, 2, 3],
-    vertical_offset_cross: [0, 1, 2, 3],
+    horizontal_offset_cross: [0, 1, 2, 3],
     horizontal_split: [0, 1],
-    vertical_split: [0, 1],
+    lep_stage: [0, 1, 2, 3, 4, 5, 6],
     right_t: [0, 1, 2],
-    left_t: [0, 1, 2],
-    internal_box: [0],
     seven_slot: [0, 1, 2, 3, 4, 5, 6],
-    lep_stage: [0, 1, 2, 3, 4, 5, 6]
+    vertical_offset_cross: [0, 1, 2, 3],
+    vertical_split: [0, 1],
+    internal_box: [0]
   }.freeze
 
   # Each element of the layout is a "section".
@@ -116,34 +115,40 @@ module SqedConfig
   }.freeze
 
   EXTRACTION_PATTERNS = {
-    right_t: {
+    cross: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
-      layout: :right_t,
-      metadata_map: { 0 => :annotated_specimen, 1 => :identifier, 2 => :image_registration }
+      layout: :cross,
+      metadata_map: { 0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
     },
 
-    vertical_offset_cross: {
+    horizontal_split: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
-      layout: :vertical_offset_cross,
-      metadata_map: { 0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
+      layout: :horizontal_split,
+      metadata_map: { 0 => :annotated_specimen, 1 => :identifier }
     },
 
-    equal_cross: {
-      boundary_finder: Sqed::BoundaryFinder::CrossFinder,
-      layout: :equal_cross,
+    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 }
     },
 
-    cross: {
+    lep_stage: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
-      layout: :cross,
-      metadata_map: { 0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
+      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}
+      metadata_map: { 0 => :stage }
     },
 
     seven_slot: {
@@ -152,14 +157,19 @@ module SqedConfig
       metadata_map: { 0 => :collecting_event_labels, 1 => :determination_labels, 2 => :other_labels, 3 => :image_registration, 4 => :curator_metadata, 5 => :identifier, 6 => :specimen }
     },
 
-    lep_stage: {
+    vertical_offset_cross: {
       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 }
+      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
@@ -168,14 +178,14 @@ module SqedConfig
     EXTRACTION_PATTERNS[pattern][:metadata_map].invert[section_type]
   end
 
-  # Format to return JSON
+  # Format to return JSON that is externaly exposed
   def self.metadata
     return {
       boundary_colors: BOUNDARY_COLORS,
-      extraction_patterns: EXTRACTION_PATTERNS,
+      extraction_patterns: EXTRACTION_PATTERNS.select{|k,v| k != :stage},
       section_parsers: SECTION_PARSERS,
       layout_section_types: LAYOUT_SECTION_TYPES,
-      layouts: LAYOUTS
+      layouts: LAYOUTS.select{|k,v| k != :internal_box }
     }
   end
 end

data/spec/lib/sqed_config_spec.rb

@@ -6,4 +6,14 @@ describe SqedConfig do
     expect(SqedConfig.metadata.keys).to contain_exactly(:boundary_colors, :extraction_patterns, :section_parsers, :layout_section_types, :layouts)
   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)
+  end
+
+  specify 'layouts are in patterns' do
+    expect(SqedConfig.metadata[:layouts].keys + [:stage]).to contain_exactly(*SqedConfig::EXTRACTION_PATTERNS.keys) 
+  end
+
+
+
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sqed
 version: !ruby/object:Gem::Version
-  version: 0.5.0
+  version: 0.5.1
 platform: ruby
 authors:
 - Matt Yoder
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-02-06 00:00:00.000000000 Z
+date: 2019-02-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -208,7 +208,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.2
+rubyforge_project: 
+rubygems_version: 2.7.8
 signing_key: 
 specification_version: 4
 summary: Specimens Quickly extracted and Digitized, or just "squid". A ruby gem for