sqed 0.2.4 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/sqed.rb

@@ -3,7 +3,7 @@
 recent_ruby = RUBY_VERSION >= '2.1.1'
 raise "IMPORTANT: sqed gem requires ruby >= 2.1.1" unless recent_ruby
 
-require "rmagick"
+require "RMagick"
 
 # Instances take the following
 # 1) A base image @image
@@ -27,6 +27,7 @@ class Sqed
   # Legal values are symbols taken from SqedConfig::EXTRACTION_PATTERNS.
   # DO NOT pass pattern outside of a sqed instance!
   # 
+  # !! Always passed as an option :target_pattern, an persisted as :pattern
   attr_accessor :pattern
 
   # Provide a specific layout, overrides layout metadata taken from pattern
@@ -50,13 +51,14 @@ class Sqed
   # Boolean, whether to do the boundary detection (not stage detection at present) against a thumbnail version of the passed image (faster, less accurate, true be default) 
   attr_accessor :use_thumbnail
 
-  # Provide a metadata map, overrides metadata taken from pattern
+  # Provide a metadata map, overrides metadata taken from pattern.  
+  # !! Always passed as an option :target_metadata_map, an persisted as :metadata_map
   attr_accessor :metadata_map
 
   # Provide a boundary_finder, overrides metadata taken from pattern
   attr_accessor :boundary_finder 
    
-  def initialize(target_image: nil, target_pattern: nil, target_layout: nil, has_border: true, boundary_color: :green, use_thumbnail: true, boundary_finder: nil, metadata_map: nil)
+  def initialize(target_image: nil, target_pattern: nil, target_layout: nil, has_border: true, boundary_color: :green, use_thumbnail: true, boundary_finder: nil, target_metadata_map: nil)
     raise 'extraction pattern not defined' if target_pattern && !SqedConfig::EXTRACTION_PATTERNS.keys.include?(target_pattern) 
 
     # data, and stubs for results
@@ -65,14 +67,14 @@ class Sqed
     @stage_boundary = Sqed::Boundaries.new(:internal_box) 
 
     # extraction metadata
-    @pattern = target_pattern  # not required if target_layout, metadata_map, and boundary_finder are provided
+    @pattern = target_pattern  # not required if target_layout, target_metadata_map, and boundary_finder are provided
 
     @has_border = has_border
     @boundary_finder = boundary_finder.constantize if boundary_finder
     @layout = target_layout 
     @layout ||= SqedConfig::EXTRACTION_PATTERNS[pattern][:layout] if pattern
 
-    @metadata_map = metadata_map
+    @metadata_map = target_metadata_map
     @boundary_color = boundary_color
     @use_thumbnail = use_thumbnail
 
@@ -147,7 +149,7 @@ class Sqed
 
     extractor = Sqed::Extractor.new(
       target_boundaries: boundaries,
-      target_metadata_map: extraction_metadata[:metadata_map],
+      target_metadata_map: extraction_metadata[:target_metadata_map],
       target_image: stage_image)
     extractor.result
   end

data/lib/sqed/extractor.rb

@@ -16,10 +16,10 @@ class Sqed::Extractor
   # a Magick::Image file
   attr_accessor :image
 
-  def initialize(target_boundaries: boundaries, target_metadata_map: metadata_map, target_image: image)
-    raise Error, 'boundaries not provided or provided boundary is not a Sqed::Boundaries' if target_boundaries.nil? || !target_boundaries.class == Sqed::Boundaries
-    raise Error, 'metadata_map not provided or metadata_map not a Hash' if target_metadata_map.nil? || !target_metadata_map.class == Hash
-    raise Error, 'image not provided' if target_image.nil? || !target_image.class.name == 'Magick::Image'
+  def initialize(target_boundaries: nil, target_metadata_map: nil, target_image: nil)
+    raise Error, 'target_boundaries not provided or provided boundary is not a Sqed::Boundaries' if target_boundaries.nil? || !target_boundaries.class == Sqed::Boundaries
+    raise Error, 'target_metadata_map not provided or target_metadata_map not a Hash' if target_metadata_map.nil? || !target_metadata_map.class == Hash
+    raise Error, 'target_image not provided' if target_image.nil? || !target_image.class.name == 'Magick::Image'
 
     @metadata_map = target_metadata_map
     @boundaries = target_boundaries

data/lib/sqed/parser/ocr_parser.rb

@@ -107,9 +107,29 @@ class Sqed::Parser::OcrParser < Sqed::Parser
   #   the ocr text 
   def text(section_type: :default)
     img = @image 
+ 
+    # resample if an image 4"x4" is less than 300dpi 
+    if img.columns * img.rows < 144000
+      img = img.resample(300)
+    end
+    
     params = SECTION_PARAMS[:default].merge(SECTION_PARAMS[section_type])
     r = RTesseract.new(img, params) 
-    @text = r.to_s.strip 
+    @text = r.to_s.strip
+
+    if @text == ""
+      img = img.white_threshold(245)
+      r = RTesseract.new(img, params) 
+      @text = r.to_s.strip
+    end
+
+    if @text == ""
+      img = img.quantize(256,Magick::GRAYColorspace)
+      r = RTesseract.new(img, params) 
+      @text = r.to_s.strip
+    end
+
+    @text
   end
 
 

data/lib/sqed/version.rb

@@ -1,3 +1,3 @@
 class Sqed
-  VERSION = "0.2.4"
+  VERSION = "0.3.0"
 end

data/lib/sqed_config.rb

@@ -115,43 +115,43 @@ module SqedConfig
     right_t: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
       layout: :right_t,
-      metadata_map: {0 => :annotated_specimen, 1 => :identifier, 2 =>:image_registration }
+      target_metadata_map: {0 => :annotated_specimen, 1 => :identifier, 2 =>:image_registration }
     },
 
     vertical_offset_cross: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
       layout: :vertical_offset_cross,
-      metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
+      target_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 }
+     target_metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
    },
 
     cross: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
       layout: :cross, 
-      metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
+      target_metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
     },
 
     stage: {
       boundary_finder: Sqed::BoundaryFinder::StageFinder,
       layout: :internal_box, 
-      metadata_map: {0 => :stage}
+      target_metadata_map: {0 => :stage}
     },
     
     seven_slot: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
       layout: :seven_slot,
-      metadata_map: {0 => :collecting_event_labels, 1 => :determination_labels, 2 => :other_labels, 3 => :image_registration, 4 => :curator_metadata, 5 => :identifier, 6 => :specimen }
+      target_metadata_map: {0 => :collecting_event_labels, 1 => :determination_labels, 2 => :other_labels, 3 => :image_registration, 4 => :curator_metadata, 5 => :identifier, 6 => :specimen }
     }
   }
 
   DEFAULT_TMP_DIR = "/tmp"
 
   def self.index_for_section_type(pattern, section_type)
-    EXTRACTION_PATTERNS[pattern][:metadata_map].invert[section_type]
+    EXTRACTION_PATTERNS[pattern][:target_metadata_map].invert[section_type]
   end
 end

data/spec/lib/sqed_spec.rb

@@ -5,6 +5,11 @@ describe Sqed do
   let(:s) {Sqed.new}
 
   context 'attributes' do
+
+    specify '#metadata_map' do
+      expect(s).to respond_to(:metadata_map)
+    end
+
     specify '#image' do
       expect(s).to respond_to(:image)
     end

data/spec/lib/stage_handling/seven_slot_spec.rb

@@ -10,7 +10,16 @@ describe 'handling 7 slot stages' do
       expect( sqed ).to be_truthy
     end
 
-    specify 'get_result without errors' do
+    specify 'get result without errors' do
+      expect( sqed.result ).to be_truthy
+    end
+  end
+
+  context 'without target_pattern' do
+    let(:m) { {"0" => "collecting_event_labels", "1" => "determination_labels", "2" => "other_labels", "3" => "image_registration", "4" => "curator_metadata", "5" => "identifier", "6" => "specimen" } }
+    let(:s) { Sqed.new(target_image: image, metadata_map: m, target_layout: :seven_slot, boundary_color: :red, has_border: false ) }
+
+    specify 'get result without errors' do
       expect( sqed.result ).to be_truthy
     end
   end

data/sqed.gemspec

@@ -19,16 +19,16 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
 
   spec.add_dependency 'rake', '~> 11.1.2'
-  spec.add_dependency 'rmagick', '~> 2.14'  
-  spec.add_dependency 'rtesseract', '~> 1.2.6'
+  spec.add_dependency 'rmagick', '~> 2.16'  
+  spec.add_dependency 'rtesseract', '~> 2.1.0'
 
   # A qrcode reader, too many problems with compiling, dependencies
   # spec.add_dependency 'zxing_cpp', '~> 0.1.0'
 
-  spec.add_development_dependency 'rspec', '~> 3.4'
+  spec.add_development_dependency 'rspec', '~> 3.6'
   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 'awesome_print', '~> 1.6'
+  spec.add_development_dependency 'byebug', '~> 9.0.6'
+  spec.add_development_dependency 'awesome_print', '~> 1.8'
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sqed
 version: !ruby/object:Gem::Version
-  version: 0.2.4
+  version: 0.3.0
 platform: ruby
 authors:
 - Matt Yoder
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-07-26 00:00:00.000000000 Z
+date: 2017-07-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -31,42 +31,42 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.14'
+        version: '2.16'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.14'
+        version: '2.16'
 - !ruby/object:Gem::Dependency
   name: rtesseract
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.2.6
+        version: 2.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.2.6
+        version: 2.1.0
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.4'
+        version: '3.6'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.4'
+        version: '3.6'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -85,30 +85,30 @@ dependencies:
   name: byebug
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 9.0.6
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 9.0.6
 - !ruby/object:Gem::Dependency
   name: awesome_print
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.8'
 description: A utility gem to aid in the processing of images taken in the process
   of digitizing natural history collections.
 email:
@@ -201,7 +201,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.4
+rubygems_version: 2.6.12
 signing_key: 
 specification_version: 4
 summary: Specimens Quickly Extracted and Digitized, or just "squid". A ruby gem for