sqed 0.0.1

data/spec/lib/sqed_spec.rb

@@ -0,0 +1,200 @@
+require 'spec_helper'
+require 'RMagick'
+describe Sqed do
+
+  let(:s) {Sqed.new}
+
+  context 'attributes' do
+    specify '#image' do
+      expect(s).to respond_to(:image)
+    end
+
+    specify '#pattern' do
+      expect(s).to respond_to(:pattern)
+    end
+
+    specify '#stage_image' do
+      expect(s).to respond_to(:image)
+    end
+  end
+
+  context 'initialization' do 
+    specify 'without providing a pattern assigns :standard_cross' do
+      expect(s.pattern).to eq(:standard_cross)
+    end
+  end
+
+  context 'asking for a result' do
+    specify 'without providing an image returns false' do
+      expect(s.result).to eq(false)
+    end
+  end
+
+  context 'with a test image' do
+    let(:a) { ImageHelpers.test0_image }
+    before {
+      s.image = a
+    }
+
+    specify '#crop_image' do        #should expand to multiple cases of image border types
+      expect(s.crop_image).to be_truthy
+      expect(s.stage_image.columns < a.columns).to be(true)
+      expect(s.stage_image.rows < a.rows).to be(true)
+    end
+
+    specify '#boundaries returns a Sqed::Boundaries instance' do
+      s.pattern = :standard_cross
+      expect(s.boundaries.class).to eq(Sqed::Boundaries)
+    end
+  end
+
+  context 'stage image with a border' do
+    let(:a) { ImageHelpers.standard_cross_green }
+    before {
+      s.image = a
+      s.crop_image
+    }
+    specify 'stage boundary is created for standard_ cross_green ~ (100,94, 800, 600)' do
+      expect(s.stage_boundary.x_for(0)).to be_within(2).of 100
+      expect(s.stage_boundary.y_for(0)).to be_within(2).of 94
+      expect(s.stage_boundary.width_for(0)).to be_within(2).of 800
+      expect(s.stage_boundary.height_for(0)).to be_within(2).of 600
+    end
+  end
+
+  context 'offset boundaries from original crossy_green_line_specimen image ' do
+    before(:all) {
+      @s = Sqed.new(image: ImageHelpers.crossy_green_line_specimen, pattern: :offset_cross)
+      @s.crop_image
+      @offset_boundaries = @s.boundaries.offset(@s.stage_boundary)
+      wtf = 0
+    }
+
+    specify "offset and size should match internal found areas " do
+      sbx = @s.stage_boundary.x_for(0)
+      sby = @s.stage_boundary.y_for(0)
+
+      sl =  @s.boundaries.coordinates.length  # may be convenient to clone this model for other than 4 boundaries found
+      expect(sl).to eq(4)    #for offset cross pattern and valid image
+      expect(@s.boundaries.complete).to be(true)
+      expect(@offset_boundaries.complete).to be(true)
+      (0..sl - 1).each do |i|
+        # check all the x/y      
+        expect(@offset_boundaries.x_for(i)).to eq(@s.boundaries.x_for(i) + sbx)
+        expect(@offset_boundaries.y_for(i)).to eq(@s.boundaries.y_for(i) + sby)
+
+        # check all width/heights
+        expect(@offset_boundaries.width_for(i)).to eq(@s.boundaries.width_for(i))
+        expect(@offset_boundaries.height_for(i)).to eq(@s.boundaries.height_for(i))
+      end
+    end
+
+    specify "find image, barcode, and text content" do
+      bc = Sqed::Extractor.new(boundaries: [0, 0, @s.image.columns, @s.image.rows], image: @s.image, layout: :offset_cross)
+      poc = Sqed::Parser::OcrParser.new(bc.extract_image(@offset_boundaries.coordinates[1]))
+      expect(poc.text).to eq('000085067')
+    end
+
+  end
+
+  context 'offset boundaries from crossy_black_line_specimen image ' do
+    before(:all) {
+      @s = Sqed.new(image: ImageHelpers.crossy_black_line_specimen, pattern: :offset_cross, boundary_color: :black)
+      @s.crop_image
+      @offset_boundaries = @s.boundaries.offset(@s.stage_boundary)
+      wtf = 0
+    }
+
+    specify "offset and size should match internal found areas " do        ##**** actually fails
+
+      sbx = @s.stage_boundary.x_for(0)
+      sby = @s.stage_boundary.y_for(0)
+
+      sl =  @s.boundaries.coordinates.length  # may be convenient to clone this model for other than 4 boundaries found
+      expect(sl).to eq(4)    #for offset cross pattern and valid image
+      expect(@s.boundaries.complete).to be(true)
+      expect(@offset_boundaries.complete).to be(true)
+      (0..sl - 1).each do |i|
+        # check all the x/y
+        expect(@offset_boundaries.x_for(i)).to eq(@s.boundaries.x_for(i) + sbx)
+        expect(@offset_boundaries.y_for(i)).to eq(@s.boundaries.y_for(i) + sby)
+
+        # check all width/heights
+        expect(@offset_boundaries.width_for(i)).to eq(@s.boundaries.width_for(i))
+        expect(@offset_boundaries.height_for(i)).to eq(@s.boundaries.height_for(i))
+      end
+    end
+  end
+
+  context 'offset boundaries from  black_green_line_specimen image ' do
+    before(:all) {
+      @s = Sqed.new(image: ImageHelpers.black_stage_green_line_specimen, pattern: :offset_cross)
+      @s.crop_image
+      @offset_boundaries = @s.boundaries.offset(@s.stage_boundary)
+      wtf = 0
+    }
+
+    specify "offset and size should match internal found areas " do
+      sbx = @s.stage_boundary.x_for(0)
+      sby = @s.stage_boundary.y_for(0)
+
+      sl =  @s.boundaries.coordinates.length  # may be convenient to clone this model for other than 4 boundaries found
+      expect(sl).to eq(4)    #for offset cross pattern and valid image
+      expect(@s.boundaries.complete).to be(true)
+      expect(@offset_boundaries.complete).to be(true)
+      (0..sl - 1).each do |i|
+        # check all the x/y
+        expect(@offset_boundaries.x_for(i)).to eq(@s.boundaries.x_for(i) + sbx)
+        expect(@offset_boundaries.y_for(i)).to eq(@s.boundaries.y_for(i) + sby)
+
+        # check all width/heights
+        expect(@offset_boundaries.width_for(i)).to eq(@s.boundaries.width_for(i))
+        expect(@offset_boundaries.height_for(i)).to eq(@s.boundaries.height_for(i))
+      end
+    end
+
+    specify "find image, barcode, and text content" do
+      bc = Sqed::Extractor.new(boundaries: [0, 0, @s.image.columns, @s.image.rows], image: @s.image, layout: :offset_cross)
+      # ioc = bc.extract_image(@offset_boundaries.coordinates[3])
+      # iioc = ioc.crop(384, 140, 1420, 572, true)
+      poc = Sqed::Parser::OcrParser.new(bc.extract_image(@offset_boundaries.coordinates[3]).crop(400, 140, 1420, 600, true))
+      # expect(poc.text).to eq('000085067')
+      ppc = Sqed::Parser::OcrParser.new(ImageHelpers.black_stage_green_line_specimen_label)
+      poc.image.write('tmp/poc.jpg')
+      ppc.image.write('tmp/ppc.jpg')
+      expect(ppc.text).to eq(poc.text)
+    end
+
+  end
+
+  context 'offset boundaries from original red_line image ' do
+    before(:all) {
+      @s = Sqed.new(image: ImageHelpers.offset_cross_red, pattern: :right_t, boundary_color: :red)
+      @s.crop_image
+      @offset_boundaries = @s.boundaries.offset(@s.stage_boundary)
+      wtf = 0
+    }
+
+    specify "offset and size should match internal found areas " do
+      sbx = @s.stage_boundary.x_for(0)  # only a single boundary
+      sby = @s.stage_boundary.y_for(0)
+      pct = 0.02
+
+      sl =  @s.boundaries.coordinates.length  # may be convenient to clone this model for other than 4 boundaries found
+      expect(sl).to eq(3)    #for offset cross pattern and valid image
+      expect(@s.boundaries.complete).to be(true)
+      expect(@offset_boundaries.complete).to be(true)
+      expect(@s.stage_boundary.width_for(0)).to be_within(pct*800).of(800)
+      expect(@s.stage_boundary.height_for(0)).to be_within(pct*600).of(600)
+      (0..sl - 1).each do |i|
+        # check all the x/y
+        expect(@offset_boundaries.x_for(i)).to eq(@s.boundaries.x_for(i) + sbx)
+        expect(@offset_boundaries.y_for(i)).to eq(@s.boundaries.y_for(i) + sby)
+
+        # check all width/heights
+        expect(@offset_boundaries.width_for(i)).to eq(@s.boundaries.width_for(i))
+        expect(@offset_boundaries.height_for(i)).to eq(@s.boundaries.height_for(i))
+      end
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,34 @@
+require 'rubygems'
+require 'bundler/setup'
+Bundler.setup
+
+require 'sqed'
+require 'support/image_helpers'
+require 'byebug'
+require 'awesome_print'
+require 'fileutils'
+require 'RMagick'
+
+FileUtils::mkdir_p 'tmp'
+
+RSpec.configure do |config|
+
+  config.raise_errors_for_deprecations!
+
+   config.run_all_when_everything_filtered = false 
+   # config.filter_run :focus
+
+  # Run specs in random order to surface order dependencies. If you find an
+  # order dependency and want to debug it, you can fix the order by providing
+  # the seed, which is printed after each run.
+  #     --seed 1234
+  # config.order = 'random'
+
+end
+
+def in_range(value, percentage, midpoint)  #order of second and third params to be consistent with be_within
+  # value is a scalar for testing against the range, percentage is a float less than 1, midpoint is the nominal center of the range
+  return (value <= midpoint*(1.0 + percentage)) & (value >= midpoint*(1.0 - percentage))
+end
+
+

data/spec/support/image_helpers.rb

@@ -0,0 +1,78 @@
+module ImageHelpers
+
+  BASE_PATH = '../files/'
+
+  class << self
+
+    def get_image(file_name)
+      Image.read(File.expand_path(BASE_PATH + file_name, __FILE__)).first
+    end
+
+    # Images
+
+    def test0_image
+      get_image('test3.jpg')
+    end
+
+    def greenline_image
+      get_image 'greenlineimage.jpg'
+    end
+
+    def ocr_image
+      get_image 'test4.jpg'
+    end
+
+    def barcode_image
+      get_image 'test_barcode.jpg'
+    end
+
+    def labels_image
+      get_image 'types_8.jpg'
+    end
+
+    def foo3_image
+      get_image 'foo3.jpg'
+    end
+
+    # Images for boundary tests (otherwise empty)
+
+    def standard_cross_green
+      get_image 'boundary_cross_green.jpg'
+    end
+
+    def crossy_green_line_specimen
+      get_image 'CrossyGreenLinesSpecimen.jpg'
+    end
+    def crossy_black_line_specimen
+      get_image 'CrossyBlackLinesSpecimen.jpg'
+    end
+
+    def black_stage_green_line_specimen
+      get_image 'black_stage_green_line_specimen.jpg'
+    end
+
+    def black_stage_green_line_specimen_label
+      get_image 'label_images/black_stage_green_line_specimen_label.jpg'
+    end
+
+    def offset_cross_red
+      get_image 'boundary_offset_cross_red.jpg'
+    end
+
+    def right_t_green
+      get_image 'boundary_right_t_green.jpg'
+    end
+
+    def left_t_yellow
+      get_image 'boundary_left_t_yellow.jpg'
+    end
+
+    def of_size(width = 1024, height = 768)
+       Image.new(width, height) {
+        self.background_color = 'white'
+      }
+    end
+
+  end 
+
+end

data/sqed.gemspec

@@ -0,0 +1,31 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'sqed/version'
+
+Gem::Specification.new do |spec|
+  spec.name        = "sqed"
+  spec.version     = Sqed::VERSION
+  spec.authors     = ["Matt Yoder", "Rich Flood"]
+  spec.email       = ["diapriid@gmail.com"]
+  spec.summary     = %q{Specimens Quickly Extracted and Digitized, or just "squid". A ruby gem for image related specimen accessioning.}
+  spec.description = %q{A utility gem to aid in the processing of images taken in the process of digitizing natural history collections.}
+  spec.homepage    = "http://github.com/SpeciesFileGroup/sqed"
+  spec.license     = "NCSA"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency 'rake'
+  spec.add_dependency 'rmagick', '~> 2.13.2'
+  spec.add_dependency 'rtesseract'
+
+  spec.add_development_dependency 'bundler', '~> 1.5'
+  spec.add_development_dependency 'did_you_mean', '~> 0.9'
+  spec.add_development_dependency 'byebug'
+  spec.add_development_dependency 'rspec'
+  spec.add_development_dependency 'awesome_print', '~> 1.6'
+end
+

metadata

@@ -0,0 +1,244 @@
+--- !ruby/object:Gem::Specification
+name: sqed
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Matt Yoder
+- Rich Flood
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-06-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rmagick
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.13.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.13.2
+- !ruby/object:Gem::Dependency
+  name: rtesseract
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+- !ruby/object:Gem::Dependency
+  name: did_you_mean
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: awesome_print
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+description: A utility gem to aid in the processing of images taken in the process
+  of digitizing natural history collections.
+email:
+- diapriid@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/sqed.rb
+- lib/sqed/boundaries.rb
+- lib/sqed/boundary_finder.rb
+- lib/sqed/boundary_finder/color_line_finder.rb
+- lib/sqed/boundary_finder/cross_finder.rb
+- lib/sqed/boundary_finder/stage_finder.rb
+- lib/sqed/extractor.rb
+- lib/sqed/parser.rb
+- lib/sqed/parser/barcode_parser.rb
+- lib/sqed/parser/ocr_parser.rb
+- lib/sqed/result.rb
+- lib/sqed/version.rb
+- lib/sqed_config.rb
+- spec/lib/sqed/boundaries_spec.rb
+- spec/lib/sqed/boundary_finder/color_line_finder_spec.rb
+- spec/lib/sqed/boundary_finder/cross_finder_spec.rb
+- spec/lib/sqed/boundary_finder/stage_finder_spec.rb
+- spec/lib/sqed/boundary_finder_spec.rb
+- spec/lib/sqed/extractor_spec.rb
+- spec/lib/sqed/parser_spec.rb
+- spec/lib/sqed/result_spec.rb
+- spec/lib/sqed_spec.rb
+- spec/spec_helper.rb
+- spec/support/files/2Dbarcode.png
+- spec/support/files/CrossyBlackLinesSpecimen.jpg
+- spec/support/files/CrossyGreenLinesSpecimen.jpg
+- spec/support/files/Quadrant_2_3.jpg
+- spec/support/files/black_stage_green_line_specimen.jpg
+- spec/support/files/boundary_cross_green.jpg
+- spec/support/files/boundary_left_t_yellow.jpg
+- spec/support/files/boundary_offset_cross_red.jpg
+- spec/support/files/boundary_right_t_green.jpg
+- spec/support/files/greenlineimage.jpg
+- spec/support/files/label_images/black_stage_green_line_specimen_label.jpg
+- spec/support/files/test0.jpg
+- spec/support/files/test1.jpg
+- spec/support/files/test2.jpg
+- spec/support/files/test3.jpg
+- spec/support/files/test4.jpg
+- spec/support/files/test4OLD.jpg
+- spec/support/files/test_barcode.JPG
+- spec/support/files/test_ocr0.jpg
+- spec/support/files/types_21.jpg
+- spec/support/files/types_8.jpg
+- spec/support/image_helpers.rb
+- sqed.gemspec
+homepage: http://github.com/SpeciesFileGroup/sqed
+licenses:
+- NCSA
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.5
+signing_key: 
+specification_version: 4
+summary: Specimens Quickly Extracted and Digitized, or just "squid". A ruby gem for
+  image related specimen accessioning.
+test_files:
+- spec/lib/sqed/boundaries_spec.rb
+- spec/lib/sqed/boundary_finder/color_line_finder_spec.rb
+- spec/lib/sqed/boundary_finder/cross_finder_spec.rb
+- spec/lib/sqed/boundary_finder/stage_finder_spec.rb
+- spec/lib/sqed/boundary_finder_spec.rb
+- spec/lib/sqed/extractor_spec.rb
+- spec/lib/sqed/parser_spec.rb
+- spec/lib/sqed/result_spec.rb
+- spec/lib/sqed_spec.rb
+- spec/spec_helper.rb
+- spec/support/files/2Dbarcode.png
+- spec/support/files/CrossyBlackLinesSpecimen.jpg
+- spec/support/files/CrossyGreenLinesSpecimen.jpg
+- spec/support/files/Quadrant_2_3.jpg
+- spec/support/files/black_stage_green_line_specimen.jpg
+- spec/support/files/boundary_cross_green.jpg
+- spec/support/files/boundary_left_t_yellow.jpg
+- spec/support/files/boundary_offset_cross_red.jpg
+- spec/support/files/boundary_right_t_green.jpg
+- spec/support/files/greenlineimage.jpg
+- spec/support/files/label_images/black_stage_green_line_specimen_label.jpg
+- spec/support/files/test0.jpg
+- spec/support/files/test1.jpg
+- spec/support/files/test2.jpg
+- spec/support/files/test3.jpg
+- spec/support/files/test4.jpg
+- spec/support/files/test4OLD.jpg
+- spec/support/files/test_barcode.JPG
+- spec/support/files/test_ocr0.jpg
+- spec/support/files/types_21.jpg
+- spec/support/files/types_8.jpg
+- spec/support/image_helpers.rb