sqed 0.3.2 → 0.4.0

data/lib/sqed/result.rb

@@ -1,71 +1,74 @@
-# A Sqed::Result is a container for the results of the
-# the data extraction for the full stage 
-#
-class Sqed::Result
+class Sqed
 
-  SqedConfig::LAYOUT_SECTION_TYPES.each do |k|
-    attr_accessor "#{k}_image".to_sym
-    attr_accessor k
-  end
- 
-  # a hash with section_type => [ ] 
-  attr_accessor :boundary_coordinates
-
-  # an array of section type
-  attr_accessor :sections
-
-  def initialize
-    @boundary_coordinates = {}
+  # A Sqed::Result is a container for the results of the
+  # the data extraction for the full stage
+  #
+  class Result
     SqedConfig::LAYOUT_SECTION_TYPES.each do |k|
-      send("#{k}=", {}) 
-      @boundary_coordinates[k] = [nil, nil, nil, nil]
+      attr_accessor "#{k}_image".to_sym
+
+      # @return [Hash] `barcode: '', text: ''`
+      attr_accessor k
     end
-  end
 
-  # return [String, nil]
-  #   the text derived from the OCR parsing of the section
-  def text_for(section)
-    send(section)[:text] 
-  end
+    # @return [Hash] of `section_type: [ ]`
+    attr_accessor :boundary_coordinates
 
-  # return [String, nil]
-  #   the text derived from the barcode parsing of the section
-  def barcode_text_for(section)
-    send(section)[:barcode]
-  end
+    # @return [Array]
+    #   of section type
+    attr_accessor :sections
 
-  # return [Hash]
-  #   a map of layout_section_type => value (if there is a value), 
-  #   i.e. all possible parsed text values returned from the parser
-  def text
-    result = {} 
-    SqedConfig::LAYOUT_SECTION_TYPES.each do |k|
-      v = self.send(k)
-      result.merge!(k => v) if v[:barcode] || v[:text] 
+    def initialize
+      @boundary_coordinates = {}
+      SqedConfig::LAYOUT_SECTION_TYPES.each do |k|
+        send("#{k}=", {})
+        @boundary_coordinates[k] = [nil, nil, nil, nil]
+      end
     end
-    result
-  end
 
-  # return [Hash]
-  #   a map of layout_section_type => Rmagick::Image
-  def images
-    result = {} 
-    SqedConfig::LAYOUT_SECTION_TYPES.each do |k|
-      image = self.send("#{k}_image")
-      result.merge!(k => image) if image
+    # return [String, nil]
+    #   the text derived from the OCR parsing of the section
+    def text_for(section)
+      send(section)[:text]
     end
-    result
-  end
 
-  # return [True]
-  #   write the images in #images to tmp/ 
-  def write_images
-    images.each do |k, img|
-      img.write("tmp/#{k}.jpg")
+    # return [String, nil]
+    #   the text derived from the barcode parsing of the section
+    def barcode_text_for(section)
+      send(section)[:barcode]
     end
-    true
-  end
 
-end
+    # return [Hash]
+    #   a map of layout_section_type => value (if there is a value),
+    #   i.e. all possible parsed text values returned from the parser
+    def text
+      result = {}
+      SqedConfig::LAYOUT_SECTION_TYPES.each do |k|
+        v = send(k)
+        result[k] = v if v[:barcode] || v[:text]
+      end
+      result
+    end
 
+    # return [Hash]
+    #   a map of layout_section_type => Rmagick::Image
+    def images
+      result = {}
+      SqedConfig::LAYOUT_SECTION_TYPES.each do |k|
+        image = send("#{k}_image")
+        result[k] = image if image
+      end
+      result
+    end
 
+    # return [True]
+    #   write the images in #images to tmp/
+    def write_images
+      images.each do |k, img|
+        img.write("tmp/#{k}.jpg")
+      end
+      true
+    end
+
+  end
+end

data/lib/sqed/version.rb

@@ -1,3 +1,3 @@
 class Sqed
-  VERSION = "0.3.2"
+  VERSION = '0.4.0'.freeze
 end

data/lib/sqed_config.rb

@@ -1,16 +1,14 @@
-# encoding: UTF-8
-
 # require 'zxing'
 
-require_relative "sqed/parser"
-require_relative "sqed/parser/ocr_parser"
-require_relative "sqed/parser/barcode_parser"
+require_relative 'sqed/parser'
+require_relative 'sqed/parser/ocr_parser'
+require_relative 'sqed/parser/barcode_parser'
 
-require_relative "sqed/boundaries"
-require_relative "sqed/boundary_finder"
-require_relative "sqed/boundary_finder/cross_finder"
-require_relative "sqed/boundary_finder/stage_finder"
-require_relative "sqed/boundary_finder/color_line_finder"
+require_relative 'sqed/boundaries'
+require_relative 'sqed/boundary_finder'
+require_relative 'sqed/boundary_finder/cross_finder'
+require_relative 'sqed/boundary_finder/stage_finder'
+require_relative 'sqed/boundary_finder/color_line_finder'
 
 # Sqed constants, including patterns for extraction etc.
 #
@@ -23,13 +21,13 @@ module SqedConfig
   #    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)
-  #       | 
+  #       |
   #    3  | 2
-  # 
+  #
   #
   #    0  |  1
   #       |
@@ -45,7 +43,7 @@ module SqedConfig
   #       | 1
   #    0  |----  :right_t
   #       | 2
-  # 
+  #
   #        0
   #    --------  :horizontal_split
   #        1
@@ -58,30 +56,28 @@ module SqedConfig
   #   | 0 |  :internal_box
   #   -----
   #
-  #    0 | 1 | 2  
+  #    0 | 1 | 2
   #   ------------
   #      | 5 | 3    :seven_slot
   #    6 |--------
   #      |   4
   #
   #
-  #
-
   # 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_split: [0,1],
-    vertical_split: [0,1],
-    right_t: [0,1,2],
-    left_t: [0,1,2],
+    cross: [0, 1, 2, 3],
+    vertical_offset_cross: [0, 1, 2, 3],
+    horizontal_split: [0, 1],
+    vertical_split: [0, 1],
+    right_t: [0, 1, 2],
+    left_t: [0, 1, 2],
     internal_box: [0],
-    seven_slot: [0,1,2,3,4,5,6]
-  }
+    seven_slot: [0, 1, 2, 3, 4, 5, 6]
+  }.freeze
 
-  # Each element of the layout is a "section".  
+  # Each element of the layout is a "section".
   LAYOUT_SECTION_TYPES = [
     :annotated_specimen,      # a specimen is present, and metadata is too
     :collecting_event_labels, # the section that contains collecting event labels (only)
@@ -91,67 +87,67 @@ module SqedConfig
     :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. 
+    :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 
-  ] 
+    :stage,                   # the image contains the full stage
+  ].freeze
 
   # Links section types to data parsers
   SECTION_PARSERS = {
-    annotated_specimen: [ Sqed::Parser::OcrParser],
-    collecting_event_labels: [ Sqed::Parser::OcrParser],
-    curator_metadata: [  Sqed::Parser::OcrParser ],
-    deterimination_labels: [ Sqed::Parser::OcrParser ],
-    identifier: [ Sqed::Parser::BarcodeParser, Sqed::Parser::OcrParser ],
+    annotated_specimen: [Sqed::Parser::OcrParser],
+    collecting_event_labels: [Sqed::Parser::OcrParser],
+    curator_metadata: [Sqed::Parser::OcrParser],
+    determination_labels: [Sqed::Parser::OcrParser],
+    identifier: [Sqed::Parser::BarcodeParser, Sqed::Parser::OcrParser],
     image_registration: [],
-    labels: [ Sqed::Parser::OcrParser ],
+    labels: [Sqed::Parser::OcrParser],
     nothing: [],
-    other_labels: [ Sqed::Parser::OcrParser ],
+    other_labels: [Sqed::Parser::OcrParser],
     specimen: [],
     stage: []
-  }
+  }.freeze
 
   EXTRACTION_PATTERNS = {
     right_t: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
       layout: :right_t,
-      target_metadata_map: {0 => :annotated_specimen, 1 => :identifier, 2 =>:image_registration }
+      metadata_map: { 0 => :annotated_specimen, 1 => :identifier, 2 => :image_registration }
     },
 
     vertical_offset_cross: {
-      boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
-      layout: :vertical_offset_cross,
-      target_metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
+        boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+        layout: :vertical_offset_cross,
+        metadata_map: { 0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
+    },
+
+    equal_cross: {
+        boundary_finder: Sqed::BoundaryFinder::CrossFinder,
+        layout: :equal_cross,
+        metadata_map: { 0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
     },
-  
-   equal_cross: {
-     boundary_finder: Sqed::BoundaryFinder::CrossFinder,
-     layout: :equal_cross,
-     target_metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
-   },
 
     cross: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
-      layout: :cross, 
-      target_metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
+      layout: :cross,
+      metadata_map: { 0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
     },
 
     stage: {
       boundary_finder: Sqed::BoundaryFinder::StageFinder,
-      layout: :internal_box, 
-      target_metadata_map: {0 => :stage}
+      layout: :internal_box,
+      metadata_map: { 0 => :stage}
     },
-    
+
     seven_slot: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
       layout: :seven_slot,
-      target_metadata_map: {0 => :collecting_event_labels, 1 => :determination_labels, 2 => :other_labels, 3 => :image_registration, 4 => :curator_metadata, 5 => :identifier, 6 => :specimen }
+      metadata_map: { 0 => :collecting_event_labels, 1 => :determination_labels, 2 => :other_labels, 3 => :image_registration, 4 => :curator_metadata, 5 => :identifier, 6 => :specimen }
     }
-  }
+  }.freeze
 
-  DEFAULT_TMP_DIR = "/tmp"
+  DEFAULT_TMP_DIR = '/tmp'.freeze
 
   def self.index_for_section_type(pattern, section_type)
-    EXTRACTION_PATTERNS[pattern][:target_metadata_map].invert[section_type]
+    EXTRACTION_PATTERNS[pattern][:metadata_map].invert[section_type]
   end
 end

data/spec/lib/sqed/boundaries_spec.rb

@@ -33,7 +33,7 @@ describe Sqed::Boundaries do
   end
 
   context '#offset' do
-    let(:s) { Sqed.new(target_image: ImageHelpers.crossy_green_line_specimen, target_pattern: :vertical_offset_cross) }
+    let(:s) { Sqed.new(image: ImageHelpers.crossy_green_line_specimen, pattern: :vertical_offset_cross) }
     let(:offset_boundaries) { 
       s.crop_image
       s.boundaries.offset(s.stage_boundary) 

data/spec/lib/sqed/boundary_finder/color_line_finder_spec.rb

@@ -1,32 +1,32 @@
 require 'spec_helper'
 
-describe Sqed::BoundaryFinder::ColorLineFinder do 
+describe Sqed::BoundaryFinder::ColorLineFinder do
 
   let(:image) { ImageHelpers.crossy_green_line_specimen }
 
-  let(:b) { Sqed::BoundaryFinder::StageFinder.new(target_image: image) }
-  let(:c) {b.boundaries}
+  let(:b) { Sqed::BoundaryFinder::StageFinder.new(image: image) }
+  let(:c) { b.boundaries }
   let(:d) { image.crop(*c.for(0), true) }
-  
-  let(:e) { Sqed::BoundaryFinder::ColorLineFinder.new(target_image: d, target_layout: :right_t, use_thumbnail: false) }
+
+  let(:e) { Sqed::BoundaryFinder::ColorLineFinder.new(image: d, layout: :right_t, use_thumbnail: false) }
   let(:f) { e.boundaries }
-  let(:g) { Sqed::BoundaryFinder::ColorLineFinder.new(target_image: d, target_layout: :vertical_offset_cross, use_thumbnail: false)}
+  let(:g) { Sqed::BoundaryFinder::ColorLineFinder.new(image: d, layout: :vertical_offset_cross, use_thumbnail: false)}
   let(:h) { g.boundaries }
-  let(:gv) { Sqed::BoundaryFinder::ColorLineFinder.new(target_image: d, target_layout: :vertical_split, use_thumbnail: false) }
+  let(:gv) { Sqed::BoundaryFinder::ColorLineFinder.new(image: d, layout: :vertical_split, use_thumbnail: false) }
   let(:hv) { gv.boundaries }
- 
+
   let(:ah) { ImageHelpers.vertical_offset_cross_red }
-  let(:bh) { Sqed::BoundaryFinder::StageFinder.new(target_image: ah) }
+  let(:bh) { Sqed::BoundaryFinder::StageFinder.new(image: ah) }
   let(:ch) { bh.boundaries }
   let(:dh) { ah.crop(*ch.for(0), true) }
-  let(:gh) { Sqed::BoundaryFinder::ColorLineFinder.new(target_image: dh, target_layout: :horizontal_split, boundary_color: :red, use_thumbnail: false) } # was :horizontal_split
+  let(:gh) { Sqed::BoundaryFinder::ColorLineFinder.new(image: dh, layout: :horizontal_split, boundary_color: :red, use_thumbnail: false) } # was :horizontal_split
   let(:hh) { gh.boundaries }
 
-  let(:ibs) { ImageHelpers.black_stage_green_line_specimen } 
-  let(:bbs) { Sqed::BoundaryFinder::StageFinder.new(target_image: ibs) } 
+  let(:ibs) { ImageHelpers.black_stage_green_line_specimen }
+  let(:bbs) { Sqed::BoundaryFinder::StageFinder.new(image: ibs) }
   let(:cbs) { bbs.boundaries }
   let(:dbs) { ibs.crop(*cbs.for(0), true) }
-  let(:gbs) { Sqed::BoundaryFinder::ColorLineFinder.new(target_image: dbs, target_layout: :vertical_offset_cross, use_thumbnail: false) }
+  let(:gbs) { Sqed::BoundaryFinder::ColorLineFinder.new(image: dbs, layout: :vertical_offset_cross, use_thumbnail: false) }
   let(:hbs) { gbs.boundaries }
 
   specify 'initial image columns are as expected for :image above' do
@@ -49,7 +49,7 @@ describe Sqed::BoundaryFinder::ColorLineFinder do
     end
   end
 
-  specify "CrossGreenLinesSpecimen using right_t layout should yield 3 rectangular boundaries" do
+  specify 'CrossGreenLinesSpecimen using right_t layout should yield 3 rectangular boundaries' do
     # use the f object for right_t
     f.each do |i, coord|
       q = d.crop(*coord, true)
@@ -58,7 +58,7 @@ describe Sqed::BoundaryFinder::ColorLineFinder do
 
     expect(f.count).to eq(3)
     pct = 0.02
-    
+
     expect(f.x_for(0)).to be_within(1).of(1)
     expect(f.y_for(0)).to be_within(1).of(1)
     expect(f.width_for(0)).to be_within(pct*2051).of(2051)
@@ -75,7 +75,7 @@ describe Sqed::BoundaryFinder::ColorLineFinder do
     expect(f.height_for(2)).to be_within(pct*964).of(964)
   end
 
-  specify "CrossGreenLinesSpecimen using vertical_offset_cross layout should yield 4 rectangular boundaries" do
+  specify 'CrossGreenLinesSpecimen using vertical_offset_cross layout should yield 4 rectangular boundaries' do
     h.each do |i, coord|
       q = d.crop(*coord, true)
       q.write("tmp/q1#{i}.jpg")
@@ -106,7 +106,7 @@ describe Sqed::BoundaryFinder::ColorLineFinder do
     expect(h.height_for(3)).to be_within(pct*897).of(897)
   end
 
-  specify "CrossGreenLinesSpecimen using vertical_split layout should yield 2 rectangular boundaries" do
+  specify 'CrossGreenLinesSpecimen using vertical_split layout should yield 2 rectangular boundaries' do
     hv.each do |k, v|
       q = d.crop(*v, true)
       q.write("tmp/q2#{k}.jpg")
@@ -124,7 +124,7 @@ describe Sqed::BoundaryFinder::ColorLineFinder do
     expect(hv.height_for(1)).to be_within(0.02*1990).of(1990)
   end
 
-  specify "boundary_vertical_offset_cross_red using horizontal_split layout should yield 2 rectangular boundaries" do
+  specify 'boundary_vertical_offset_cross_red using horizontal_split layout should yield 2 rectangular boundaries' do
     hh.each do |k, v|
       q = dh.crop(*v, true)
       q.write("tmp/q3#{k}.jpg")
@@ -136,7 +136,7 @@ describe Sqed::BoundaryFinder::ColorLineFinder do
     expect(hh.coordinates[1]).to eq([0, 154, 799, 445])                            # for quadrant 1
   end
 
-  specify "offset cross method on black stage specimen should yield 4 rectangular boundaries for 0" do
+  specify 'offset cross method on black stage specimen should yield 4 rectangular boundaries for 0' do
     (hbs.first[0]..hbs.count - 1).each do |j|
       q = dbs.crop(*hbs.for(j), true)
       q.write("tmp/qb#{j}.jpg")
@@ -149,17 +149,17 @@ describe Sqed::BoundaryFinder::ColorLineFinder do
     expect(hbs.height_for(0)).to be_within(pct*506).of(506)
   end
 
-  specify "offset cross method on black stage specimen should yield 4 rectangular boundaries for 1" do
+  specify 'offset cross method on black stage specimen should yield 4 rectangular boundaries for 1' do
     expect(hbs.width_for(1)).to be_within(0.02*447).of(447)
     expect(hbs.height_for(1)).to be_within(0.02*487).of(487)
   end
 
-  specify "offset cross method on black stage specimen should yield 4 rectangular boundaries for 2" do
+  specify 'offset cross method on black stage specimen should yield 4 rectangular boundaries for 2' do
     expect(hbs.width_for(2)).to be_within(0.02*447).of(447)
     expect(hbs.height_for(2)).to be_within(0.02*1680).of(1680)
   end
 
-  specify "offset cross method on black stage specimen should yield 4 rectangular boundaries for 3" do
+  specify 'offset cross method on black stage specimen should yield 4 rectangular boundaries for 3' do
     expect(hbs.width_for(3)).to be_within(0.02*2999).of(2999)
     expect(hbs.height_for(3)).to be_within(0.02*1677).of(1677)
   end
@@ -167,7 +167,7 @@ describe Sqed::BoundaryFinder::ColorLineFinder do
   context 'thumbnail processing finds reasonable boundaries' do
 
     let(:thumb) { ImageHelpers.frost_stage_thumb  }
-    let(:finder) { Sqed::BoundaryFinder::ColorLineFinder.new(target_image: thumb, target_layout: :cross, use_thumbnail: false)}
+    let(:finder) { Sqed::BoundaryFinder::ColorLineFinder.new(image: thumb, layout: :cross, use_thumbnail: false)}
     let(:finder_boundaries) { finder.boundaries }
 
     let(:pct)  { 0.08 }
@@ -179,7 +179,7 @@ describe Sqed::BoundaryFinder::ColorLineFinder do
   #   end
   # }
 
-    specify "for section 0" do
+    specify 'for section 0' do
       expect(finder_boundaries.x_for(0)).to be_within(pct*thumb.columns).of(0)
       expect(finder_boundaries.y_for(0)).to be_within(pct*0).of(0)
       expect(finder_boundaries.width_for(0)).to be_within(pct*66).of(66)