sqed 0.1.4 → 0.1.5

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: f38950c622a96cda352855e494e97ce3bdb8bf8e
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data/lib/sqed.rb

@@ -36,30 +36,30 @@ class Sqed
   attr_accessor :boundaries
  
   # Boolean, whether to detect the border on initialization, i.e. new()
-  attr_accessor :auto_detect_border 
+  attr_accessor :has_border 
  
   # a symbol, :red, :green, :blue, describing the boundary color within the stage 
   attr_accessor :boundary_color
 
-  def initialize(image: image, pattern: pattern, auto_detect_border: true, boundary_color: :green)
+  def initialize(image: image, pattern: pattern, has_border: true, boundary_color: :green)
+    raise 'extraction pattern not defined' if pattern && !SqedConfig::EXTRACTION_PATTERNS.keys.include?(pattern) 
+ 
     @image = image
     @boundaries = nil
     @stage_boundary = Sqed::Boundaries.new(:internal_box) 
-    @auto_detect_border = auto_detect_border
+    @has_border = has_border
     @pattern = pattern
     @pattern ||= :cross
     @boundary_color = boundary_color
 
-    set_stage_boundary if @auto_detect_border && @image
+    set_stage_boundary if @image
   end
 
-  # This handles the case of
-  #   s = Sqed.new()  # no image: @some_image on init
-  #   s.image = @some_image
-  #
+  # Attributes accessor overides
   def image=(value)
     @image = value
-    set_stage_boundary if @auto_detect_border 
+    set_stage_boundary 
+    @image
   end
 
   def boundaries(force = false)
@@ -67,32 +67,36 @@ class Sqed
     @boundaries
   end
 
+  def stage_boundary
+    set_stage_boundary if !@stage_boundary.populated?
+    @stage_boundary
+  end
+
+  def stage_image
+   crop_image if @stage_image.nil?
+   @stage_image 
+  end
+
   # Return [Sqed::Boundaries instance]
   #   a boundaries instance that has the original image (prior to cropping stage) coordinates
   def native_boundaries
     # check for @boundaries.complete first? OR handle partial detections  ?!
     if @boundaries.complete
-      @boundaries.offset(@stage_boundary)
+      @boundaries.offset(stage_boundary)
     else
       nil
     end 
   end
 
-  # return [Image]
-  #   crops the image if not already done
-  def stage_image
-    crop_image if @stage_boundary.complete && @stage_image.nil?
-    @stage_image 
-  end
-
   # return [Image]
   #   crops the stage if not done, then sets/returns @stage_image
   def crop_image
-    if @stage_boundary.complete
-      @stage_image = @image.crop(*@stage_boundary.for(SqedConfig.index_for_section_type(:stage, :stage)), true)
+    if @has_border 
+      @stage_image = @image.crop(*stage_boundary.for(SqedConfig.index_for_section_type(:stage, :stage)), true)
     else
       @stage_image = @image 
     end
+    @stage_image
   end
 
   def result
@@ -108,8 +112,8 @@ class Sqed
     {
       image: @image,
       boundaries: @boundaries,
-      stage_boundary: @stage_boundary,
-      auto_detect_border: @auto_detect_border,
+      stage_boundary: stage_boundary,
+      has_border: @has_border,
       pattern: @pattern,
       boundary_color: @boundary_color
     }
@@ -118,12 +122,19 @@ class Sqed
   protected
 
   def set_stage_boundary
-    @stage_boundary = Sqed::BoundaryFinder::StageFinder.new(image: @image).boundaries
-    if !@stage_boundary.complete
-      @stage_boundary.coordinates[0] = [0, 0, @image.columns, @image.rows] 
+    if @has_border
+      boundary = Sqed::BoundaryFinder::StageFinder.new(image: @image).boundaries
+      if boundary.populated? 
+        @stage_boundary.set(0, boundary.for(0)) #  = boundary
+      else
+        raise 'error detecting stage'
+      end
+    else
+      @stage_boundary.set(0, [0, 0, @image.columns, @image.rows])
     end
   end
 
+  # TODO make this a setter
   def get_section_boundaries
     boundary_finder_class = SqedConfig::EXTRACTION_PATTERNS[@pattern][:boundary_finder]
 

data/lib/sqed/boundaries.rb

@@ -84,11 +84,11 @@ class Sqed::Boundaries
   end
 
   def populated?
-      @coordinates.each do |c|
-        return false if c[0].nil?
+    self.each do |index, coords|
+      coords.each do |c|
+        return false if c.nil?
       end
+    end
     true 
   end
-
-
 end

data/lib/sqed/version.rb

@@ -1,3 +1,3 @@
 class Sqed
-  VERSION = "0.1.4"
+  VERSION = "0.1.5"
 end

data/lib/sqed_config.rb

@@ -91,7 +91,7 @@ module SqedConfig
     identifier: [ Sqed::Parser::BarcodeParser, Sqed::Parser::OcrParser ],
     deterimination_labels: [ Sqed::Parser::OcrParser ],
     curator_metadata: [  Sqed::Parser::OcrParser ],
-    specimen: [ Sqed::Parser::OcrParser ],
+    annotated_specimen: [ Sqed::Parser::OcrParser] 
   }
 
   EXTRACTION_PATTERNS = {
@@ -104,19 +104,19 @@ 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 => :specimen }
+      metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
     },
   
    equal_cross: {
-     boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+     boundary_finder: Sqed::BoundaryFinder::CrossFinder,
      layout: :equal_cross,
-     metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :specimen }
+     metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
    },
 
     cross: {
-      boundary_finder: Sqed::BoundaryFinder::CrossFinder,
+      boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
       layout: :cross, 
-      metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :specimen }
+      metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }
     },
 
     stage: {

data/spec/lib/sqed/boundary_finder/color_line_finder_spec.rb

@@ -172,12 +172,12 @@ describe Sqed::BoundaryFinder::ColorLineFinder do
 
     let(:pct)  { 0.08 }
 
-    before {
-      finder.boundaries.each do |i, coord|
-     #  q = thumb.crop(*coord, true)
-     #  q.write("tmp/thumb#{i}.jpg")
-      end
-    }
+  # before {
+  #    finder.boundaries.each do |i, coord|
+  #    q = thumb.crop(*coord, true)
+  #    q.write("tmp/thumb#{i}.jpg")
+  #   end
+  # }
 
     specify "for section 0" do
       expect(finder_boundaries.x_for(0)).to be_within(pct*thumb.columns).of(0)

data/spec/lib/sqed/boundary_finder_spec.rb

@@ -94,7 +94,6 @@ describe Sqed::BoundaryFinder do
         expect(center).to be < 1332 
       end
     end
-
   end
 
   context '.frequency_stats(frequency_hash, samples_taken)' do

data/spec/lib/sqed/result_spec.rb

@@ -22,7 +22,7 @@ describe Sqed::Result do
 
   context 'with a new() result' do
     specify '#text_for(section)' do
-      expect(r.text_for(:specimen)).to eq(nil)
+      expect(r.text_for(:annotated_specimen)).to eq(nil)
     end
 
     specify '#barcode_text_for(section)' do

data/spec/lib/sqed_spec.rb

@@ -25,8 +25,8 @@ describe Sqed do
       expect(s).to respond_to(:boundaries)
     end
 
-    specify '#auto_detect_border' do
-      expect(s).to respond_to(:auto_detect_border)
+    specify '#has_border' do
+      expect(s).to respond_to(:has_border)
     end
 
     specify '#boundary_color' do
@@ -67,10 +67,10 @@ describe Sqed do
     end
   end
 
-  context 'all together' do
+  context 'all together, without border' do
     let(:image) { ImageHelpers.frost_stage }
     let(:pattern) { :vertical_offset_cross }
-    let(:s) { Sqed.new(image: image, pattern: pattern) }
+    let(:s) { Sqed.new(image: image, pattern: pattern, has_border: false)  }
 
     specify '#boundaries returns a Sqed::Boundaries instance' do
       expect(s.boundaries.class.name).to eq('Sqed::Boundaries')
@@ -99,8 +99,8 @@ describe Sqed do
           expect(r.text_for(:identifier)).to match('000041196')
         end
 
-        specify 'for a specimen section' do
-          expect(r.text_for(:specimen)).to match('Saucier Creek')
+        specify 'for an annotated_specimen section' do
+          expect(r.text_for(:annotated_specimen)).to match('Saucier Creek')
         end
 
         specify 'for a curator_metadata section' do
@@ -110,4 +110,44 @@ describe Sqed do
     end
   end
 
+  context 'all together, with border' do
+    let(:image) { ImageHelpers.greenline_image }
+    let(:pattern) { :right_t }
+    let(:s) { Sqed.new(image: image, pattern: pattern, has_border: false)  }
+
+    specify '#boundaries returns a Sqed::Boundaries instance' do
+      expect(s.boundaries.class.name).to eq('Sqed::Boundaries')
+    end
+
+    specify '#stage_image returns an Magick::Image' do
+      expect(s.stage_image.class.name).to eq('Magick::Image')
+    end
+
+    specify '#crop_image returns an Magick::Image' do
+      expect(s.crop_image.class.name).to eq('Magick::Image')
+    end
+
+    specify '#crop_image returns #stage_image' do
+      expect(s.crop_image).to eq(s.stage_image)
+    end
+
+    context '#result' do
+      let(:r) { s.result }
+      specify 'returns a Sqed::Result' do
+        expect(r.class.name).to eq('Sqed::Result')
+      end
+
+      context 'extracted data' do
+        specify 'for an :identifier section' do
+          expect(r.text_for(:identifier)).to match('000085067')
+        end
+
+        specify 'for a specimen section' do
+          expect(r.text_for(:annotated_specimen)).to match('Aeshna')
+        end
+      end
+    end
+  end
+
+
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sqed
 version: !ruby/object:Gem::Version
-  version: 0.1.4
+  version: 0.1.5
 platform: ruby
 authors:
 - Matt Yoder