sqed 0.1.3 → 0.1.4

checksums.yaml

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

@@ -47,7 +47,7 @@ class Sqed
     @stage_boundary = Sqed::Boundaries.new(:internal_box) 
     @auto_detect_border = auto_detect_border
     @pattern = pattern
-    @pattern ||= :standard_cross
+    @pattern ||= :cross
     @boundary_color = boundary_color
 
     set_stage_boundary if @auto_detect_border && @image

data/lib/sqed/version.rb

@@ -1,3 +1,3 @@
 class Sqed
-  VERSION = "0.1.3"
+  VERSION = "0.1.4"
 end

data/lib/sqed_config.rb

@@ -26,24 +26,26 @@ module SqedConfig
   #  
   #
   #    0  | 1
-  #   ----|----  :cross (height of [0, 1], [2,3] same, width of [0,1], [2,3] same, otherwise variable (i.e. height(0) != height(3))
+  #   ----|----  :cross - height of [0, 1], [2,3] same, width of [0,1], [2,3] same, otherwise variable, i.e. height(0) != height(3)
   #       | 
   #    3  | 2
   # 
+  #
   #    0  |  1
   #       |
-  #   ---------  :horizontal_offset_cross // NOT CURRENTLY IMPLEMENTED
+  #   ---------  :horizontal_offset_cross 
   #    3   | 2
   #
   #
   #    0  |  1
   #       |____
-  #   ----|      :vertical_offset_cross // matches current code !! 
+  #   ----|      :vertical_offset_cross 
   #    3  |  2
   #
   #       | 1
   #    0  |----  :right_t
   #       | 2
+  # 
   #        0
   #    --------  :horizontal_split
   #        1
@@ -98,23 +100,30 @@ module SqedConfig
       layout: :right_t,
       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 => :specimen }
-     # metadata_map: {0 => :annotated_specimen, 1 => :identifier, 2 =>:image_registration }
     },
-    standard_cross: {
+  
+   equal_cross: {
+     boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
+     layout: :equal_cross,
+     metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :specimen }
+   },
+
+    cross: {
       boundary_finder: Sqed::BoundaryFinder::CrossFinder,
       layout: :cross, 
-      metadata_map: {0 => :labels, 1 => :specimen, 2 => :identifier, 3 => :specimen_determinations }
+      metadata_map: {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :specimen }
     },
+
     stage: {
       boundary_finder: Sqed::BoundaryFinder::StageFinder,
       layout: :internal_box, 
       metadata_map: {0 => :stage}
     }
-    # etc. ...
   }
 
   DEFAULT_TMP_DIR = "/tmp"

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

@@ -1,7 +1,7 @@
 require 'spec_helper'
 
 describe Sqed::BoundaryFinder::StageFinder do 
-  let(:b) {Sqed::BoundaryFinder::StageFinder.new(image: ImageHelpers.standard_cross_green )}
+  let(:b) {Sqed::BoundaryFinder::StageFinder.new(image: ImageHelpers.cross_green )}
 
   specify '#is border contains a proc' do
     expect(b.is_border.class).to eq(Proc)

data/spec/lib/sqed/boundary_finder_spec.rb

@@ -7,7 +7,7 @@ describe Sqed::BoundaryFinder do
   end
 
   context 'when initiated with an image' do
-    let(:b) {Sqed::BoundaryFinder.new(image: ImageHelpers.standard_cross_green, layout: :vertical_offset_cross)}
+    let(:b) {Sqed::BoundaryFinder.new(image: ImageHelpers.cross_green, layout: :vertical_offset_cross)}
 
     context 'attributes' do
       specify '#img' do
@@ -23,7 +23,7 @@ describe Sqed::BoundaryFinder do
   context '.color_boundary_finder(image: image)' do
     context 'with sample_subdivision_size: 10' do
       specify 'finds the vertical dividing line in a standard cross, with border still present' do
-        center =  Sqed::BoundaryFinder.color_boundary_finder(image: ImageHelpers.standard_cross_green, sample_subdivision_size: 10 )[1]
+        center =  Sqed::BoundaryFinder.color_boundary_finder(image: ImageHelpers.cross_green, sample_subdivision_size: 10 )[1]
         expect(center).to be > 492
         expect(center).to be < 504
       end
@@ -37,7 +37,7 @@ describe Sqed::BoundaryFinder do
 
     context 'with sample_subdivision_size auto set' do
       specify 'finds the vertical dividing line in a standard cross, with border still present, when more precise' do
-        center =  Sqed::BoundaryFinder.color_boundary_finder(image: ImageHelpers.standard_cross_green, sample_cutoff_factor: 0.7)[1]
+        center =  Sqed::BoundaryFinder.color_boundary_finder(image: ImageHelpers.cross_green, sample_cutoff_factor: 0.7)[1]
         expect(center).to be > 492
         expect(center).to be < 504
       end
@@ -84,7 +84,7 @@ describe Sqed::BoundaryFinder do
       end
 
       specify 'FAILS to find the vertical dividing line in a standard cross, with border still present, when even more precise' do
-        center =  Sqed::BoundaryFinder.color_boundary_finder(image: ImageHelpers.standard_cross_green, sample_cutoff_factor: 1)
+        center =  Sqed::BoundaryFinder.color_boundary_finder(image: ImageHelpers.cross_green, sample_cutoff_factor: 1)
         expect(center).to be nil
       end
 

data/spec/lib/sqed/parser_spec.rb

@@ -2,7 +2,7 @@ require 'spec_helper'
 
 describe Sqed::Parser do
 
-  let(:image) { ImageHelpers.standard_cross_green  }
+  let(:image) { ImageHelpers.cross_green  }
   let(:p) { Sqed::Parser.new(image) }
 
   specify '#image' do

data/spec/lib/sqed_spec.rb

@@ -35,8 +35,8 @@ describe Sqed do
   end
 
   context 'initialization' do 
-    specify 'without providing a pattern assigns :standard_cross' do
-      expect(s.pattern).to eq(:standard_cross)
+    specify 'without providing a pattern assigns :cross' do
+      expect(s.pattern).to eq(:cross)
     end
   end
 
@@ -57,7 +57,7 @@ describe Sqed do
     end
 
     specify 'properly sets stage boundaries ' do
-      s.image = ImageHelpers.standard_cross_green
+      s.image = ImageHelpers.cross_green
       s.crop_image 
       # ~ (100,94, 800, 600)
       expect(s.stage_boundary.x_for(0)).to be_within(2).of 100
@@ -73,7 +73,6 @@ describe Sqed do
     let(:s) { Sqed.new(image: image, pattern: pattern) }
 
     specify '#boundaries returns a Sqed::Boundaries instance' do
-      # s.pattern = :standard_cross
       expect(s.boundaries.class.name).to eq('Sqed::Boundaries')
     end
 

data/spec/support/image_helpers.rb

@@ -15,7 +15,7 @@ module ImageHelpers
     end
 
     # Stage images 
-    def standard_cross_green
+    def cross_green
       get_image 'stage_images/boundary_cross_green.jpg'
     end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sqed
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.1.4
 platform: ruby
 authors:
 - Matt Yoder