sqed 0.5.8 → 0.7.1

data/spec/lib/sqed_spec.rb

@@ -2,7 +2,10 @@ require 'spec_helper'
 
 describe Sqed do
 
-  let(:s) { Sqed.new }
+  let(:s) { Sqed.new(
+    pattern: :cross
+  )
+  }
 
   context 'attributes' do
 
@@ -41,19 +44,14 @@ describe Sqed do
     specify '#use_thumbnail defaults to `true`' do
       expect(s.use_thumbnail).to eq(true)
     end
-
   end
 
-  context 'initialization' do 
-    specify 'without providing a pattern assigns nil' do
-      expect(s.pattern).to eq(nil)
-    end
+  specify 'raises without pattern or boundary_finder provided' do
+    expect{Sqed.new}.to raise_error Sqed::Error
   end
 
-  context '#result' do
-    specify 'without providing an image returns false' do
-      expect(s.result).to eq(false)
-    end
+  specify '#result without image returns false' do
+    expect(s.result).to eq(false)
   end
 
   # Intent is to just test wrapping functionality, see

data/spec/lib/stage_handling/horizontal_offset_cross_spec.rb

@@ -30,7 +30,9 @@ describe 'handling 7 slot stages' do
   end
 
   context 'simple boundaries - without thumbnail' do
-    let(:s) { Sqed.new(image: image, metadata_map: m, use_thumbnail: false, layout: :horizontal_offset_cross, boundary_color: :red, has_border: false ) }
+    let(:s) { Sqed.new(image: image, metadata_map: m, use_thumbnail: false, layout: :horizontal_offset_cross, 
+                       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+                       boundary_color: :red, has_border: false ) }
 
     specify 'boundaries are reasonable' do
       s.result

data/spec/lib/stage_handling/inverted_t_stage_spec.rb

@@ -0,0 +1,61 @@
+require 'spec_helper'
+
+describe 'handling inverted T stage images' do
+
+  let(:image) { ImageHelpers.inverted_t_stage }
+  let(:sqed) do
+    Sqed.new(
+      image: image,
+      pattern: :inverted_t,
+      boundary_color: :red,
+      has_border: false )
+  end
+
+  let(:m) do
+    { 0 => 'identifier',
+      1 => 'image_registration',
+      2 => 'annotated_specimen',
+    }
+  end
+
+  context 'simple boundaries - without thumbnail' do
+    let(:s) { Sqed.new(
+      image: image, metadata_map: m, use_thumbnail: false,
+      layout: :inverted_t,
+      boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+      boundary_color: :red,
+      has_border: false ) }
+
+    specify 'boundaries are reasonable' do
+      s.result
+      c = s.boundaries.coordinates
+      c.each do |section, values|
+        c[section].each_with_index do |v, i|
+          msg = "section #{section}, index #{i} has a bad value '#{v}'"
+          expect(v > -1).to be_truthy, msg
+        end
+      end
+    end
+  end
+
+  context 'boundaries - with_thumbnail' do
+    let(:s) { Sqed.new(
+      image: image,
+      use_thumbnail: true,
+      pattern: :inverted_t,
+      boundary_color: :red,
+      has_border: false ) }
+
+    specify 'boundaries are reasonable' do
+      s.result
+      # s.result.write_images
+      c = s.boundaries.coordinates
+      c.each do |section, values|
+        c[section].each_with_index do |v, i|
+          msg = "section #{section}, index #{i} has a bad value '#{v}'"
+          expect(v > -1).to be_truthy, msg
+        end
+      end
+    end
+  end
+end

data/spec/lib/stage_handling/lep_stage2_spec.rb

@@ -0,0 +1,64 @@
+require 'spec_helper'
+
+describe 'handling lep stage images' do
+
+  let(:image) { ImageHelpers.lep_stage2 }
+  let(:sqed) do
+    Sqed.new(
+      image: image,
+      pattern: :lep_stage,
+      boundary_color: :red,
+      has_border: false )
+  end
+
+  let(:m) do
+    { 0 => :curator_metadata,
+      1 => :collecting_event_labels,
+      2 => :image_registration,
+      3 => :identifier,
+      4 => :other_labels,
+      5 => :determination_labels,
+      6 => :specimen 
+    }
+  end
+
+  context 'parses' do
+    specify 'new() without errors' do
+      expect(sqed).to be_truthy
+    end
+
+    specify 'get result without errors' do
+      expect(sqed.result).to be_truthy
+    end
+  end
+
+  context 'trickier boundaries - without thumbnail' do
+    let(:s) { Sqed.new(image: ImageHelpers.lep_stage2, use_thumbnail: false, pattern: :lep_stage2, boundary_color: :red, has_border: false ) }
+
+    specify 'boundaries are reasonable' do
+      s.result
+      c = s.boundaries.coordinates
+      c.each do |section, values|
+        c[section].each_with_index do |v, i|
+          msg = "section #{section}, index #{i} has a bad value '#{v}'"
+          expect(v > -1).to be_truthy, msg
+        end
+      end
+    end
+  end
+
+  context 'trickier boundaries - with_thumbnail' do
+    let(:s) { Sqed.new(image: ImageHelpers.lep_stage2, use_thumbnail: true, pattern: :lep_stage2, boundary_color: :red, has_border: false ) }
+
+    specify 'boundaries are reasonable' do
+      s.result
+      c = s.boundaries.coordinates
+      c.each do |section, values|
+        c[section].each_with_index do |v, i|
+          msg = "section #{section}, index #{i} has a bad value '#{v}'"
+          expect(v > -1).to be_truthy, msg
+        end
+      end
+    end
+  end 
+end

data/spec/lib/stage_handling/seven_slot_spec.rb

@@ -12,15 +12,65 @@ describe 'handling 7 slot stages' do
   end
 
   let(:m) do
-    { 0 => 'collecting_event_labels',
-      1 => 'determination_labels',
-      2 => 'other_labels',
-      3 => 'image_registration',
-      4 => 'curator_metadata',
-      5 => 'identifier',
-      6 => 'specimen' }
+    { 0 => :collecting_event_labels,
+      1 => :determination_labels,
+      2 => :other_labels,
+      3 => :image_registration,
+      4 => :curator_metadata,
+      5 => :identifier,
+      6 => :specimen }
   end
 
+
+  let(:w) {22.5} # 1/2 width red "tape"
+
+  let(:coords) {
+    {
+      0 => [
+        0,
+        0,
+        1674,
+        1280
+      ],
+      1 => [
+        1820,
+        0,
+        1773,
+        1280
+      ],
+      2 => [
+        3746,
+        0,
+        1726,
+        1280
+      ],
+      3 => [
+        3746,
+        1422,
+        3746,
+        836
+      ],
+      4 => [
+        1820,
+        2382,
+        3652,
+        2226
+      ],
+      5 => [
+        1820,
+        1422,
+        1773,
+        836
+      ],
+      6 => [
+        0,
+        1422,
+        1674,
+        2226
+      ]
+    }
+  }
+
   context 'parses' do
     specify 'new() without errors' do
       expect(sqed).to be_truthy
@@ -32,33 +82,58 @@ describe 'handling 7 slot stages' do
   end
 
   context 'trickier boundaries - without thumbnail' do
-    let(:s) { Sqed.new(image: ImageHelpers.inhs_stage_7_slot2, metadata_map: m, use_thumbnail: false, layout: :seven_slot, boundary_color: :red, has_border: false ) }
+    # perfect parsing currently
+    let(:s) { Sqed.new(
+      image: ImageHelpers.inhs_stage_7_slot2,
+      layout: :seven_slot, # layout + metadata map + boundary_finder signature
+      metadata_map: m,
+      boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+      use_thumbnail: false,
+      boundary_color: :red,
+      has_border: false ) }
 
     specify 'boundaries are reasonable' do
       s.result
       c = s.boundaries.coordinates
+
       c.each do |section, values|
         c[section].each_with_index do |v, i|
-          msg = "section #{section}, index #{i} has a bad value '#{v}'"
-          expect(v > -1).to be_truthy, msg
+          min = coords[section][i] - w
+          max = coords[section][i] + w
+          msg = "section #{section}, index #{i}, '#{v}' is out of range #{min}-#{max} "
+          expect((v > min) && (v < max)).to be_truthy, msg
         end
       end
     end
   end
 
+  # image size is a failure here
   context 'trickier boundaries - with_thumbnail' do
-    let(:s) { Sqed.new(image: ImageHelpers.inhs_stage_7_slot2, use_thumbnail: true, pattern: :seven_slot, boundary_color: :red, has_border: false ) }
+    let(:s) { Sqed.new(
+      image: ImageHelpers.inhs_stage_7_slot2,
+      use_thumbnail: true,
+      pattern: :seven_slot, # pattern signature
+      boundary_color: :red, has_border: false ) }
 
-
-    specify 'boundaries are reasonable' do
+    xspecify 'boundaries are reasonable' do
       s.result
       c = s.boundaries.coordinates
+      errors = []
+
       c.each do |section, values|
         c[section].each_with_index do |v, i|
-          msg = "section #{section}, index #{i} has a bad value '#{v}'"
-          expect(v > -1).to be_truthy, msg
+          min = coords[section][i] - w
+          max = coords[section][i] + w
+
+          msg = "section #{section}, index #{i}, '#{v}' is #{(v - coords[section][i]).abs } out of range #{min}-#{max}"
+          if !((v > min) && (v < max))
+            errors.push msg
+          else
+            errors.push "section #{section} (#{v}) is OK"
+          end
         end
       end
+      expect(errors).to be_empty, errors.join("\n")
     end
   end
 
@@ -68,6 +143,6 @@ describe 'handling 7 slot stages' do
     specify '#result' do
       expect(s.result).to be_truthy
     end
-  end 
+  end
 
 end

data/spec/lib/stage_handling/t_stage_spec.rb

@@ -0,0 +1,61 @@
+require 'spec_helper'
+
+describe 'handling T stage images' do
+
+  let(:image) { ImageHelpers.t_stage }
+  let(:sqed) do
+    Sqed.new(
+      image: image,
+      pattern: :t,
+      boundary_color: :red,
+      has_border: false )
+  end
+
+  let(:m) do
+    { 0 => 'annotated_specimen',
+      1 => 'identifier',
+      2 => 'image_registration'
+    }
+  end
+
+  context 'simple boundaries - without thumbnail' do
+    let(:s) { Sqed.new(
+      image: image, metadata_map: m, use_thumbnail: false,
+      layout: :t, 
+      boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+      boundary_color: :red,
+      has_border: false ) }
+
+    specify 'boundaries are reasonable' do
+      s.result
+      c = s.boundaries.coordinates
+      c.each do |section, values|
+        c[section].each_with_index do |v, i|
+          msg = "section #{section}, index #{i} has a bad value '#{v}'"
+          expect(v > -1).to be_truthy, msg
+        end
+      end
+    end
+  end
+
+  context 'boundaries - with_thumbnail' do
+    let(:s) { Sqed.new(
+      image: image,
+      use_thumbnail: true,
+      pattern: :t,
+      boundary_color: :red,
+      has_border: false ) }
+
+    specify 'boundaries are reasonable' do
+      s.result
+      c = s.boundaries.coordinates
+      c.each do |section, values|
+        c[section].each_with_index do |v, i|
+          msg = "section #{section}, index #{i} has a bad value '#{v}'"
+          expect(v > -1).to be_truthy, msg
+        end
+      end
+    end
+  end
+
+end

data/spec/spec_helper.rb

@@ -5,7 +5,7 @@ Bundler.setup
 require 'sqed'
 require 'support/image_helpers'
 require 'byebug'
-require 'awesome_print'
+require 'amazing_print'
 require 'fileutils'
 require 'rmagick'
 

data/spec/support/image_helpers.rb

@@ -9,12 +9,21 @@ module ImageHelpers
     end
 
     def of_size(width = 1024, height = 768)
-      Magick::Image.new(width, height) {
-        self.background_color = 'white'
+      Magick::Image.new(width, height) { |i|
+        i.background_color = 'white'
       }
     end
 
-    # Stage images 
+    # Stage images
+
+    def t_stage
+      get_image 'stage_images/t_stage.png'
+    end
+
+    def inverted_t_stage
+      get_image 'stage_images/inverted_t_stage.png'
+    end
+
     def cross_green
       get_image 'stage_images/boundary_cross_green.jpg'
     end
@@ -36,15 +45,23 @@ module ImageHelpers
     end
 
     def inhs_stage_7_slot
-      get_image 'stage_images/inhs_7_slot.jpg'
+      get_image 'stage_images/inhs_7_slot3.jpg'
+    end
+
+    def inhs_stage_7_slot2
+      get_image 'stage_images/inhs_7_slot2.jpg'
     end
 
     def lep_stage
       get_image 'stage_images/lep_stage.jpg'
     end
 
-    def inhs_stage_7_slot2
-      get_image 'stage_images/inhs_7_slot2.jpg'
+    def lep_stage2
+      get_image 'stage_images/lep_stage2.jpg'
+    end
+
+    def lep_stage3
+      get_image 'stage_images/lep_stage3.jpg'
     end
 
     def crossy_green_line_specimen
@@ -93,7 +110,7 @@ module ImageHelpers
       get_image 'barcode_images/osuc_datamatric_barcode.png'
     end
 
-    # label (text) images 
+    # label (text) images
 
     # NOT USED
     def black_stage_green_line_specimen_label
@@ -114,7 +131,7 @@ module ImageHelpers
 
     # Real life, black border, no internal boundaries
     def test3_image
-      get_image 'test3.jpg' 
+      get_image 'test3.jpg'
     end
 
     def foo3_image

data/sqed.gemspec

@@ -19,15 +19,15 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
 
   spec.add_dependency 'rake', '~> 13.0'
-  spec.add_dependency 'rmagick', '~> 4.0'
-  spec.add_dependency 'rtesseract', '~> 3.0.4'
+  spec.add_dependency 'rmagick', '~> 4.2'
+  spec.add_dependency 'rtesseract', '~> 3.1'
 
   # A qrcode reader, too many problems with compiling, dependencies
   # spec.add_dependency 'zxing_cpp', '~> 0.1.0'
 
-  spec.add_development_dependency 'rspec', '~> 3.9'
+  spec.add_development_dependency 'rspec', '~> 3.11'
   spec.add_development_dependency 'bundler', '~> 2.0'
   spec.add_development_dependency 'byebug', '~> 11.0'
-  spec.add_development_dependency 'awesome_print', '~> 1.8'
+  spec.add_development_dependency 'amazing_print', '~> 1.4'
 end
 

metadata

@@ -1,15 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: sqed
 version: !ruby/object:Gem::Version
-  version: 0.5.8
+  version: 0.7.1
 platform: ruby
 authors:
 - Matt Yoder
 - Rich Flood
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2019-11-18 00:00:00.000000000 Z
+date: 2022-06-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -31,42 +31,42 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '4.2'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '4.2'
 - !ruby/object:Gem::Dependency
   name: rtesseract
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.0.4
+        version: '3.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.0.4
+        version: '3.1'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.9'
+        version: '3.11'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.9'
+        version: '3.11'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -96,19 +96,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '11.0'
 - !ruby/object:Gem::Dependency
-  name: awesome_print
+  name: amazing_print
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: '1.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: '1.4'
 description: A utility gem to aid in the processing of images taken in the process
   of digitizing natural history collections.
 email:
@@ -132,6 +132,7 @@ files:
 - lib/sqed/boundary_finder/color_line_finder.rb
 - lib/sqed/boundary_finder/cross_finder.rb
 - lib/sqed/boundary_finder/stage_finder.rb
+- lib/sqed/error.rb
 - lib/sqed/extractor.rb
 - lib/sqed/parser.rb
 - lib/sqed/parser/barcode_parser.rb
@@ -154,8 +155,11 @@ files:
 - spec/lib/sqed_spec.rb
 - spec/lib/sqed_utils_spec.rb
 - spec/lib/stage_handling/horizontal_offset_cross_spec.rb
+- spec/lib/stage_handling/inverted_t_stage_spec.rb
+- spec/lib/stage_handling/lep_stage2_spec.rb
 - spec/lib/stage_handling/lep_stage_spec.rb
 - spec/lib/stage_handling/seven_slot_spec.rb
+- spec/lib/stage_handling/t_stage_spec.rb
 - spec/spec_helper.rb
 - spec/support/files/barcode_images/code_128_barcode.png
 - spec/support/files/barcode_images/datamatrix_barcode.png
@@ -181,8 +185,13 @@ files:
 - spec/support/files/stage_images/horizontal_offset_cross.png
 - spec/support/files/stage_images/inhs_7_slot.jpg
 - spec/support/files/stage_images/inhs_7_slot2.jpg
+- spec/support/files/stage_images/inhs_7_slot3.jpg
 - spec/support/files/stage_images/inhs_four_thirds.jpg
+- spec/support/files/stage_images/inverted_t_stage.png
 - spec/support/files/stage_images/lep_stage.jpg
+- spec/support/files/stage_images/lep_stage2.jpg
+- spec/support/files/stage_images/lep_stage3.jpg
+- spec/support/files/stage_images/t_stage.png
 - spec/support/files/test0.jpg
 - spec/support/files/test1.jpg
 - spec/support/files/test2.jpg
@@ -195,7 +204,7 @@ homepage: http://github.com/SpeciesFileGroup/sqed
 licenses:
 - NCSA
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -210,8 +219,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.6
-signing_key: 
+rubygems_version: 3.2.22
+signing_key:
 specification_version: 4
 summary: Specimens Quickly extracted and Digitized, or just "squid". A ruby gem for
   image based specimen accessioning.
@@ -230,8 +239,11 @@ test_files:
 - spec/lib/sqed_spec.rb
 - spec/lib/sqed_utils_spec.rb
 - spec/lib/stage_handling/horizontal_offset_cross_spec.rb
+- spec/lib/stage_handling/inverted_t_stage_spec.rb
+- spec/lib/stage_handling/lep_stage2_spec.rb
 - spec/lib/stage_handling/lep_stage_spec.rb
 - spec/lib/stage_handling/seven_slot_spec.rb
+- spec/lib/stage_handling/t_stage_spec.rb
 - spec/spec_helper.rb
 - spec/support/files/barcode_images/code_128_barcode.png
 - spec/support/files/barcode_images/datamatrix_barcode.png
@@ -257,8 +269,13 @@ test_files:
 - spec/support/files/stage_images/horizontal_offset_cross.png
 - spec/support/files/stage_images/inhs_7_slot.jpg
 - spec/support/files/stage_images/inhs_7_slot2.jpg
+- spec/support/files/stage_images/inhs_7_slot3.jpg
 - spec/support/files/stage_images/inhs_four_thirds.jpg
+- spec/support/files/stage_images/inverted_t_stage.png
 - spec/support/files/stage_images/lep_stage.jpg
+- spec/support/files/stage_images/lep_stage2.jpg
+- spec/support/files/stage_images/lep_stage3.jpg
+- spec/support/files/stage_images/t_stage.png
 - spec/support/files/test0.jpg
 - spec/support/files/test1.jpg
 - spec/support/files/test2.jpg