sqed 0.4.4 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: df36b8e8052dc45504b1a8cfb4f511b7d5af680f
-  data.tar.gz: 2557f8b06d2c521893d4bbace2c9433be420e376
+SHA256:
+  metadata.gz: d78e636e0c209d3cfd4de9f698bafd575686e1d393fd8148f3ae491d0396d140
+  data.tar.gz: 51c75913c74ccebe5a172ed64408ce176d5a04d08f788d3be46aeef1a9595e8f
 SHA512:
-  metadata.gz: a190d03073872ad472a422d96b8f62fce283c2936a18d53d6b90f7409e07acfc6f407a5125d88350a04ccecccef3709e7c4c82fa2059ba806f52685cb86948eb
-  data.tar.gz: d29c8d94a3d04c4a8461e11573fafdb7be8383d305ccb7222a05b9cb123fd4e18d135f27df551eee96970552324a91e67688e81754cad37c631472bd41dd0fb3
+  metadata.gz: 459da0e33636600618502410797123154988ce2a03f514cdf7dec9829ca6c747c5d26952ca2b247a613cd8968eb7cb5c0bcc3a6711db495e06175ec64c57da77
+  data.tar.gz: 49fc0de43216358f44e2d89089a5605ec46a5ef526b6464588ea867301719932433841fd5a071b4cc41ef7ce8013a2eb5ee7f5aaac69786d4e7b46308c0e0f1e

data/lib/sqed/boundary_finder/color_line_finder.rb

@@ -16,6 +16,8 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
     super(image: image, layout: layout, use_thumbnail: use_thumbnail)
 
     raise 'No layout provided.' if @layout.nil?
+
+    # !@#? why this
     @boundary_color = boundary_color
 
     if use_thumbnail
@@ -95,8 +97,6 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
         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]])
 

data/lib/sqed/extractor.rb

@@ -6,64 +6,64 @@ class Sqed
   #
   class Extractor
 
-  class Error < StandardError; end;
+    class Error < StandardError; end;
 
-  # a Sqed::Boundaries instance
-  attr_accessor :boundaries
+    # a Sqed::Boundaries instance
+    attr_accessor :boundaries
 
-  # @return [Hash] like `{0 => :annotated_specimen, 1 => :identifier, 2 => :image_registration }`
-  # a metadata_map hash from EXTRACTION_PATTERNS like:
-  attr_accessor :metadata_map
+    # @return [Hash] like `{0 => :annotated_specimen, 1 => :identifier, 2 => :image_registration }`
+    # a metadata_map hash from EXTRACTION_PATTERNS like:
+    attr_accessor :metadata_map
 
-  # @return [Magick::Image file]
-  attr_accessor :image
+    # @return [Magick::Image file]
+    attr_accessor :image
 
-  def initialize(**opts)
-    @metadata_map = opts[:metadata_map]
-    @boundaries = opts[:boundaries]
-    @image = opts[:image]
+    def initialize(**opts)
+      @metadata_map = opts[:metadata_map]
+      @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, 'image not provided' if image.nil? || !image.class.name == 'Magick::Image'
-  end
+      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, 'image not provided' if image.nil? || !image.class.name == 'Magick::Image'
+    end
 
-  def result
-    r = Sqed::Result.new
+    def result
+      r = Sqed::Result.new
 
-    r.sections = metadata_map.values.sort
+      r.sections = metadata_map.keys.sort.collect{|k| metadata_map[k]}
 
-    # assign the images to the result
-    boundaries.each do |section_index, coords|
-      section_type = metadata_map[section_index]
+      # assign the images to the result
+      boundaries.each do |section_index, coords|
+        section_type = metadata_map[section_index]
 
-      r.send("#{section_type}_image=", extract_image(coords))
-      r.boundary_coordinates[section_type] = coords
-    end
+        r.send("#{section_type}_image=", extract_image(coords))
+        r.boundary_coordinates[section_type] = coords
+      end
 
-    # assign the metadata to the result
-    metadata_map.each do |section_index, section_type|
-      # only extract data if a parser exists
-      if parsers = SqedConfig::SECTION_PARSERS[section_type]
-        section_image = r.send("#{section_type}_image")
-        updated = r.send(section_type)
+      # assign the metadata to the result
+      metadata_map.each do |section_index, section_type|
+        # only extract data if a parser exists
+        if parsers = SqedConfig::SECTION_PARSERS[section_type]
+          section_image = r.send("#{section_type}_image")
+          updated = r.send(section_type)
 
-        parsers.each do |p|
-          parsed_result = p.new(section_image).get_text(section_type: section_type)
-          updated[p::TYPE] = parsed_result if parsed_result && parsed_result.length > 0
-        end
+          parsers.each do |p|
+            parsed_result = p.new(section_image).get_text(section_type: section_type)
+            updated[p::TYPE] = parsed_result if parsed_result && parsed_result.length > 0
+          end
 
-        r.send("#{section_type}=", updated)
+          r.send("#{section_type}=", updated)
+        end
       end
-    end
 
-    r
-  end
+      r
+    end
 
-  # crop takes x, y, width, height
-  def extract_image(coords)
-    @image.crop(*coords, true)
-  end
+    # crop takes x, y, width, height
+    def extract_image(coords)
+      @image.crop(*coords, true)
+    end
 
   end
 end

data/lib/sqed/parser/barcode_parser.rb

@@ -18,7 +18,7 @@ class Sqed::Parser::BarcodeParser < Sqed::Parser
     @barcode
   end
 
-  # Uses the same enging as zbarimg that you can install with brew (zbarimg)
+  # Uses the same engine as zbarimg that you can install with brew (zbarimg)
   #
   def get_code_128
     nil # ZXing.decode @image.filename
@@ -29,9 +29,9 @@ class Sqed::Parser::BarcodeParser < Sqed::Parser
     [get_code_128].compact.first
   end
 
- #def get_datamatrix
- #  https://github.com/srijan/ruby-dmtx
- #end
+  #def get_datamatrix
+  #  https://github.com/srijan/ruby-dmtx
+  #end
 
   # alias to a universal method
   def get_text(section_type: :default)

data/lib/sqed/parser/ocr_parser.rb

@@ -1,5 +1,9 @@
 require 'rtesseract'
 
+# We use tempfile because Rtesseract doesn't work directly with ImageMagic::Image (any longer... apparently, maybe)
+# https://ruby-doc.org/stdlib-2.6.1/libdoc/tempfile/rdoc/Tempfile.html
+require 'tempfile'
+
 # encoding: UTF-8
 #
 # Given a single image return all text in that image.
@@ -115,19 +119,42 @@ class Sqed::Parser::OcrParser < Sqed::Parser
     params = SECTION_PARAMS[:default].dup
     params.merge!(SECTION_PARAMS[section_type])
 
-    r = RTesseract.new(img, params)
-    @extracted_text = r.to_s.strip
+    # May be able to overcome this hacky kludge messe with providing `processor:` to new
+    file = Tempfile.new('foo1')
+    begin
+      file.write(image.to_blob)
+      file.rewind
+      @extracted_text = RTesseract.new(file.path, params).to_s&.strip
+      file.close
+    ensure
+      file.close
+      file.unlink   # deletes the temp file
+    end
 
     if @extracted_text == ''
-      img = img.white_threshold(245)
-      r = RTesseract.new(img, params)
-      @extracted_text = r.to_s.strip
+      file = Tempfile.new('foo2')
+      begin
+        file.write(img.dup.white_threshold(245).to_blob)
+        file.rewind
+        @extracted_text = RTesseract.new(file.path, params).to_s&.strip
+        file.close
+      ensure
+        file.close
+        file.unlink   # deletes the temp file
+      end
     end
 
     if @extracted_text == ''
-      img = img.quantize(256,Magick::GRAYColorspace)
-      r = RTesseract.new(img, params)
-      @extracted_text = r.to_s.strip
+      file = Tempfile.new('foo3')
+      begin
+        file.write(img.dup.quantize(256,Magick::GRAYColorspace).to_blob)
+        file.rewind
+        @extracted_text = RTesseract.new(file.path, params).to_s&.strip
+        file.close
+      ensure
+        file.close
+        file.unlink   # deletes the temp file
+      end
     end
 
     @extracted_text

data/lib/sqed/version.rb

@@ -1,3 +1,3 @@
 class Sqed
-  VERSION = '0.4.4'.freeze
+  VERSION = '0.5.0'.freeze
 end

data/lib/sqed_config.rb

@@ -106,7 +106,7 @@ module SqedConfig
     collecting_event_labels: [Sqed::Parser::OcrParser],
     curator_metadata: [Sqed::Parser::OcrParser],
     determination_labels: [Sqed::Parser::OcrParser],
-    identifier: [Sqed::Parser::BarcodeParser, Sqed::Parser::OcrParser],
+    identifier: [Sqed::Parser::OcrParser, Sqed::Parser::BarcodeParser],
     image_registration: [],
     labels: [Sqed::Parser::OcrParser],
     nothing: [],
@@ -123,15 +123,15 @@ module SqedConfig
     },
 
     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 }
+      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 }
+      boundary_finder: Sqed::BoundaryFinder::CrossFinder,
+      layout: :equal_cross,
+      metadata_map: { 0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
     },
 
     cross: {
@@ -159,9 +159,23 @@ module SqedConfig
     }
   }.freeze
 
+
+  BOUNDARY_COLORS = [:red, :green, :blue, :black].freeze
+
   DEFAULT_TMP_DIR = '/tmp'.freeze
 
   def self.index_for_section_type(pattern, section_type)
     EXTRACTION_PATTERNS[pattern][:metadata_map].invert[section_type]
   end
+
+  # Format to return JSON
+  def self.metadata
+    return {
+      boundary_colors: BOUNDARY_COLORS,
+      extraction_patterns: EXTRACTION_PATTERNS,
+      section_parsers: SECTION_PARSERS,
+      layout_section_types: LAYOUT_SECTION_TYPES,
+      layouts: LAYOUTS
+    }
+  end
 end

data/spec/lib/sqed/extractor_spec.rb

@@ -4,7 +4,7 @@ describe Sqed::Extractor do
   let(:metadata_map) { 
     {0 => :specimen, 1 => :identifier, 2 => :nothing, 3 => :image_registration }
   } 
- 
+
   let(:image) { ImageHelpers.crossy_green_line_specimen }
 
   let(:boundaries) { 
@@ -29,7 +29,7 @@ describe Sqed::Extractor do
     specify '#metadata_map' do
       expect(e).to respond_to(:metadata_map)
     end
- 
+
     specify '#boundaries' do
       expect(e).to respond_to(:boundaries)
     end
@@ -37,7 +37,7 @@ describe Sqed::Extractor do
 
   context 'extracting to a #result' do
     let(:r) { e.result }
-    
+
     specify '#result retuns a Sqed::Result' do
       expect(r.class.name).to eq('Sqed::Result')
     end
@@ -52,7 +52,7 @@ describe Sqed::Extractor do
     end
 
     specify '#sections is populated with section_types' do
-      expect(r.sections).to eq( [ :identifier, :image_registration, :nothing, :specimen ] )
+      expect(r.sections).to eq( [ :specimen, :identifier, :nothing, :image_registration ] )
     end
 
     specify '#boundary_coordinates is populated with coordinates' do

data/spec/lib/sqed_config_spec.rb

@@ -0,0 +1,9 @@
+require 'spec_helper'
+
+describe SqedConfig do
+
+  specify '.metadata' do
+    expect(SqedConfig.metadata.keys).to contain_exactly(:boundary_colors, :extraction_patterns, :section_parsers, :layout_section_types, :layouts)
+  end
+
+end

data/spec/lib/sqed_spec.rb

@@ -113,7 +113,7 @@ describe Sqed do
       end
 
       specify '#text_for a :curator_metadata section' do
-        expect(rz.text_for(:curator_metadata)).to match('Frost Entomological Museum')
+        expect(rz.text_for(:curator_metadata)).to match(/Frost\s*Entomological\s*Museum/)
       end
     end
   end

data/sqed.gemspec

@@ -20,15 +20,15 @@ Gem::Specification.new do |spec|
 
   spec.add_dependency 'rake', '~> 12.3'
   spec.add_dependency 'rmagick', '~> 2.16'  
-  spec.add_dependency 'rtesseract', '~> 2.2.0'
+  spec.add_dependency 'rtesseract', '~> 3.0.2'
 
   # A qrcode reader, too many problems with compiling, dependencies
   # spec.add_dependency 'zxing_cpp', '~> 0.1.0'
 
   spec.add_development_dependency 'rspec', '~> 3.8'
-  spec.add_development_dependency 'bundler', '~> 1.5'
+  spec.add_development_dependency 'bundler', '~> 2.0'
   # spec.add_development_dependency 'did_you_mean', '~> 0.9'
-  spec.add_development_dependency 'byebug', '~> 10.0.0'
+  spec.add_development_dependency 'byebug', '~> 10.0'
   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: 0.4.4
+  version: 0.5.0
 platform: ruby
 authors:
 - Matt Yoder
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-09-17 00:00:00.000000000 Z
+date: 2019-02-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -45,14 +45,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.2.0
+        version: 3.0.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.2.0
+        version: 3.0.2
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -73,28 +73,28 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.5'
+        version: '2.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.5'
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: byebug
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 10.0.0
+        version: '10.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 10.0.0
+        version: '10.0'
 - !ruby/object:Gem::Dependency
   name: awesome_print
   requirement: !ruby/object:Gem::Requirement
@@ -150,6 +150,7 @@ files:
 - spec/lib/sqed/parser/ocr_spec.rb
 - spec/lib/sqed/parser_spec.rb
 - spec/lib/sqed/result_spec.rb
+- spec/lib/sqed_config_spec.rb
 - spec/lib/sqed_spec.rb
 - spec/lib/sqed_utils_spec.rb
 - spec/lib/stage_handling/lep_stage_spec.rb
@@ -207,8 +208,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.14
+rubygems_version: 3.0.2
 signing_key: 
 specification_version: 4
 summary: Specimens Quickly extracted and Digitized, or just "squid". A ruby gem for
@@ -224,6 +224,7 @@ test_files:
 - spec/lib/sqed/parser/ocr_spec.rb
 - spec/lib/sqed/parser_spec.rb
 - spec/lib/sqed/result_spec.rb
+- spec/lib/sqed_config_spec.rb
 - spec/lib/sqed_spec.rb
 - spec/lib/sqed_utils_spec.rb
 - spec/lib/stage_handling/lep_stage_spec.rb