sqed 0.6.0 → 0.7.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ff31f97d4d846b9112badb1fad358118d858e028cb2835050f49ca767dbfdfba
-  data.tar.gz: 36d2dadf1291dff04b60d596b239cbbf484cf4c180182b694b103b244f8bba15
+  metadata.gz: bc1ae71edf574734410eb4f86efc79658fe01e416e6a8a2082a077107c9f982c
+  data.tar.gz: 81264b5a221c5dfdd0a2485a89dcc31962225d99de1541968a999bb10fb92e17
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-  data.tar.gz: b6f5201476f18b8ba5ad9444f6ac63f8b9d86ff1eb0a089da55521566cf3a8b57a25a5b70eb0478b8121582c5c88b34dab05cab45630b339a8649ed23855b015
+  metadata.gz: a87471a1a81d33c3c56b6e996578f0de936a78e983b8eaac5c03b68a2e806adbb11a1e846deff3a8d8b7b101c1845f04f7c42fb9cd9ba323e61e172ae5ab655e
+  data.tar.gz: 65f21307aec7b020c7c2bb27df4aeb8802724ad16e9b18fcc87afab864a102df14e0b345ca92a97a7909507f4a1e2fb6453593acf1e81f42a8731807f8b4dd98

data/.ruby-version

@@ -1 +1 @@
-2.7.1
+3.0.2

data/.travis.yml

@@ -3,7 +3,7 @@
 language: ruby
 dist: bionic
 rvm:
-  - 2.6.3
+  - 2.7.1
 #before_install:
 #  - sudo add-apt-repository -y ppa:moti-p/cc
 #  - sudo apt-get update
@@ -16,7 +16,7 @@ before_install:
   - identify -list resource | grep Disk | grep 8GiB # Check ImageMagick setting is actually working.
 branches:
   only:
-    - master
+    - main 
 notifications:
   email:
     - diapriid@gmail.com 

data/lib/sqed/boundary_finder/color_line_finder.rb

@@ -37,7 +37,7 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
     # see config/sqed_config.rb
     case layout
 
-    when :cross # 4 zones, with perfectly intersected horizontal and vertical division
+    when :cross # 4 windows, with perfectly intersected horizontal and vertical division
       v = self.class.new(image: @image, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
       h = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false).boundaries
 
@@ -171,6 +171,26 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
         bottom_right_left_top_bottom_split[0],
       ])
 
+    when :t
+      horizontal = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
+
+      bottom = image.crop(*horizontal.for(1), true)
+      btm_split = self.class.new(image: bottom, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
+
+      boundaries.set(0, horizontal.for(0))
+      boundaries.set(1, [ btm_split.x_for(1), horizontal.height_for(0), btm_split.width_for(1), btm_split.height_for(1) ] )
+      boundaries.set(2, [ 0, horizontal.height_for(0), btm_split.width_for(0), btm_split.height_for(0) ] )
+
+    when :inverted_t
+      horizontal = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
+
+      top = image.crop(*horizontal.for(0), true)
+      top_split = self.class.new(image: top, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
+
+      boundaries.set(0, [ 0,0, top_split.width_for(0), top_split.height_for(0)] )
+      boundaries.set(1, [ top_split.width_for(0), 0, top_split.width_for(1), top_split.height_for(1)] )
+      boundaries.set(2, horizontal.for(1))
+
     when :right_t
       vertical = self.class.new(image: @image, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
 

data/lib/sqed/version.rb

@@ -1,3 +1,3 @@
 class Sqed
-  VERSION = '0.6.0'.freeze
+  VERSION = '0.7.0'.freeze
 end

data/lib/sqed_config.rb

@@ -46,7 +46,7 @@ module SqedConfig
   #
   #    0 | 1 |  2
   #   --------------
-  #          | 5 |      :lep_stage2
+  #          | 5 |    :lep_stage2
   #      6   |---- 3
   #          | 4 |
   #
@@ -74,12 +74,24 @@ module SqedConfig
   #      |
   #
   #   -----
-  #   | 0 |  :internal_box
+  #   | 0 |   :internal_box
   #   -----
   #
+  #   0 | 1   :inverted_t
+  #   -----
+  #     2
+  #
+  #     0     :t
+  #   -----
+  #   2 | 1
+  #
+  #
+  #
   # Hash values are used to stub out
   # the Sqed::Boundaries instance.
   LAYOUTS = {
+    t: [0,1,2],
+    inverted_t: [0, 1, 2],
     cross: [0, 1, 2, 3],
     horizontal_offset_cross: [0, 1, 2, 3],
     horizontal_split: [0, 1],
@@ -123,6 +135,18 @@ module SqedConfig
   }.freeze
 
   EXTRACTION_PATTERNS = {
+    t: {
+      boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+      layout: :t,
+      metadata_map: { 0 => :annotated_specimen, 1 => :identifier, 2 => :image_registration }
+    },
+
+    inverted_t: {
+      boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+      layout: :inverted_t,
+      metadata_map: { 0 => :identifier, 1 => :image_registration, 2 => :annotated_specimen }
+    },
+
     cross: {
       boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
       layout: :cross,

data/spec/lib/sqed_config_spec.rb

@@ -7,13 +7,11 @@ describe SqedConfig do
   end
 
   specify 'layouts' do
-    expect(SqedConfig.metadata[:layouts].keys).to contain_exactly(:cross, :horizontal_offset_cross, :horizontal_split, :lep_stage, :lep_stage2, :right_t, :seven_slot, :vertical_offset_cross, :vertical_split)
+    expect(SqedConfig.metadata[:layouts].keys).to contain_exactly(:t, :inverted_t, :cross, :horizontal_offset_cross, :horizontal_split, :lep_stage, :lep_stage2, :right_t, :seven_slot, :vertical_offset_cross, :vertical_split)
   end
 
   specify 'layouts are in patterns' do
-    expect(SqedConfig.metadata[:layouts].keys + [:stage]).to contain_exactly(*SqedConfig::EXTRACTION_PATTERNS.keys) 
+    expect(SqedConfig.metadata[:layouts].keys + [:stage]).to contain_exactly(*SqedConfig::EXTRACTION_PATTERNS.keys)
   end
 
-
-
 end

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/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/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
@@ -51,6 +60,10 @@ module ImageHelpers
       get_image 'stage_images/lep_stage2.jpg'
     end
 
+    def lep_stage3
+      get_image 'stage_images/lep_stage3.jpg'
+    end
+
     def crossy_green_line_specimen
       get_image 'stage_images/CrossyGreenLinesSpecimen.jpg'
     end
@@ -97,7 +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
@@ -118,7 +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', '~> 4.1'
+  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 'amazing_print', '~> 1.2.1'
+  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: 0.6.0
+  version: 0.7.0
 platform: ruby
 authors:
 - Matt Yoder
 - Rich Flood
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-08-05 00:00:00.000000000 Z
+date: 2022-05-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -31,14 +31,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.1'
+        version: '4.2'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.1'
+        version: '4.2'
 - !ruby/object:Gem::Dependency
   name: rtesseract
   requirement: !ruby/object:Gem::Requirement
@@ -59,14 +59,14 @@ dependencies:
     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
@@ -101,14 +101,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.2.1
+        version: '1.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.2.1
+        version: '1.4'
 description: A utility gem to aid in the processing of images taken in the process
   of digitizing natural history collections.
 email:
@@ -155,9 +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
@@ -185,8 +187,11 @@ files:
 - 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
@@ -199,7 +204,7 @@ homepage: http://github.com/SpeciesFileGroup/sqed
 licenses:
 - NCSA
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -214,8 +219,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
-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.
@@ -234,9 +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
@@ -264,8 +271,11 @@ test_files:
 - 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