flex-station-data 0.3.1 → 0.3.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 021c77855ba20d73d59feec617693f9144813dd8df75bf7152e5910b725e4d96
-  data.tar.gz: 6083225e530d6237b32240da1d9d36673ee0295f7e55ff20e2d7611f9a34984f
+  metadata.gz: 8d58049eac2b497f587a9e2b467eb09ada8fe9582c3dced6985aa59f26cbe58b
+  data.tar.gz: 6154e1b4930afde05d7449df4ce0ebfce74e92d0651944d163cb4664e6c880f6
 SHA512:
-  metadata.gz: dc685111292440177fc03da73865dfdf9b70d6b9385ce23a7d622b1fbdbdd01698c7fd46beb963bb71064b58297f26ac4b0d110287eedd95f771cb859f31e20a
-  data.tar.gz: c110c96e690d26968964d7814bd3dab6347bd2bad15f9171102ac05b32a9c7dbdb6c1a23d472ddea6734062623fce8b709b964eea2eed6313ad32dddf954526b
+  metadata.gz: 0307a6c1f8cff75dba0fb93ec17b2b49ec59db99cf1d5c18d487b40d2451695bc92fcbf911f1cba2e85fe859ccc2bd107537f6422eb1a14f0a9f5c684ac735a3
+  data.tar.gz: ff7e2b5c8d363aae425010d47e7e531028ae122772be9db1098f46113f28e1d04ffd6df065000ea69c21b138342071cfc4f618638754bffb7d9353bbb172252c

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    flex-station-data (0.3.1)
+    flex-station-data (0.3.2)
       activesupport
       linefit
 

data/lib/flex_station_data/plate.rb

@@ -1,12 +1,21 @@
+require "flex_station_data/sample"
+
 module FlexStationData
   class Plate
-    attr_reader :label, :times, :temperatures, :samples
+    attr_reader :label, :times, :temperatures, :wells, :sample_map
 
-    def initialize(label, times, temperatures, samples)
+    def initialize(label, times, temperatures, wells, sample_map)
       @label = label
       @times = times
       @temperatures = temperatures
-      @samples = samples
+      @wells = wells
+      @sample_map = sample_map
+    end
+
+    def samples
+      @samples ||= sample_map.map do |label, well_labels|
+        Sample.new(label, well_labels, self)
+      end
     end
   end
 end

data/lib/flex_station_data/presenters/linear_regression/sample_hash.rb

@@ -29,13 +29,13 @@ module FlexStationData
         end
 
         def wells_hash
-          { "wells" => sample.readings.map(&:label).join(", ") }
+          { "wells" => sample.wells.join(", ") }
         end
 
         def regression_hash
           return SampleRegressionHash.headers.zip([]).to_h if errors?
 
-          SampleRegressionHash.present(times, sample.mean.values, **options).transform_values(&:first)
+          SampleRegressionHash.present(times, sample.mean, **options).transform_values(&:first)
         end
 
         def present

data/lib/flex_station_data/presenters/linear_regression/verbose_sample_csv.rb

@@ -8,7 +8,7 @@ module FlexStationData
         include Concerns::Presenter
 
         def sample_values
-          [ *sample.readings, sample.mean ].map(&:values)
+          [ *sample.values, sample.mean ]
         end
 
         def regressions_hash

data/lib/flex_station_data/presenters/plate_csv.rb

@@ -15,15 +15,20 @@ module FlexStationData
         @options = options
       end
 
+      def present
+        [
+          [ "Plate #{plate.label}" ],
+          *samples_csv
+        ]
+      end
+
+      private
+
       def samples_csv
         samples.flat_map do |sample|
           sample_presenter.present(times, sample, **options)
         end
       end
-
-      def present
-        [ ["Plate #{plate.label}"], *samples_csv ]
-      end
     end
   end
 end

data/lib/flex_station_data/presenters/plates_csv.rb

@@ -14,15 +14,20 @@ module FlexStationData
         @options = options
       end
 
+      def present
+        [
+          [ "File: #{file.basename.to_path}" ],
+          *plates_csv
+        ]
+      end
+
+      private
+
       def plates_csv
         plates.flat_map do |plate|
           plate_presenter.present(plate, **options)
         end
       end
-
-      def present
-        [ ["File: #{file.to_path}"], *plates_csv ]
-      end
     end
   end
 end

data/lib/flex_station_data/presenters/sample_csv.rb

@@ -1,5 +1,4 @@
 require "flex_station_data/concerns/presenter"
-require "flex_station_data/readings"
 require "flex_station_data/services/sample_quality"
 
 module FlexStationData
@@ -16,26 +15,24 @@ module FlexStationData
         @options = options
       end
 
-      def readings
-        @readings ||= [ Readings.new("time", times), *sample.readings, sample.mean ]
+      def errors
+        @errors ||= quality_control.call(sample, **options).reject(&:good?)
       end
 
-      def headers
-        readings.map(&:label)
+      def present
+        [
+          [ label ],
+          *body_csv,
+          [ ]
+        ]
       end
 
-      def rows
-        readings.map(&:values).transpose
-      end
+      private
 
       def label
         "Sample #{sample.label}"
       end
 
-      def errors
-        @errors ||= quality_control.call(sample, **options).reject(&:good?)
-      end
-
       def errors?
         errors.present?
       end
@@ -44,12 +41,20 @@ module FlexStationData
         errors.map(&:to_s).map(&method(:Array))
       end
 
+      def headers
+        [ "time", *sample.wells, "mean" ]
+      end
+
+      def values
+        [ times, *sample.values, sample.mean ]
+      end
+
       def values_csv
-        [ headers, *rows ]
+        [ headers, *values.transpose ]
       end
 
-      def present
-        [ [label] ] + (errors? ? errors_csv : values_csv) + [ [] ]
+      def body_csv
+        errors? ? errors_csv : values_csv
       end
     end
   end

data/lib/flex_station_data/sample.rb

@@ -1,16 +1,29 @@
-require "flex_station_data/readings"
+require "matrix"
+
+require "flex_station_data/services/compute_mean"
 
 module FlexStationData
   class Sample
-    attr_reader :label, :readings
+    attr_reader :label, :wells, :plate
+
+    delegate :wells, to: :plate, prefix: true
 
-    def initialize(label, readings)
+    def initialize(label, wells, plate)
       @label = label
-      @readings = readings
+      @wells = wells
+      @plate = plate
+    end
+
+    def values
+      wells.map(&plate_wells.method(:values))
+    end
+
+    def readings
+      @readings ||= wells.zip(values).map { |well, v| Readings.new(well, v) }
     end
 
     def mean
-      @mean ||= Readings.mean(*readings)
+      @mean ||= values.transpose.map(&ComputeMean)
     end
   end
 end

data/lib/flex_station_data/services/parse_plate.rb

@@ -1,7 +1,7 @@
 require "active_support/core_ext"
 
 require "flex_station_data/services/parse_plate_readings"
-require "flex_station_data/services/parse_plate_samples"
+require "flex_station_data/services/parse_sample_map"
 require "flex_station_data/plate"
 
 module FlexStationData
@@ -16,13 +16,13 @@ module FlexStationData
     end
 
     def data_blocks
-      plate_data.split { |row| row[0] == "~End" }
+      plate_data.split { |row| row[0] =~ /\A~End\s*\z/ }
     end
 
     def call
       times, temperatures, wells = ParsePlateReadings.call(data_blocks[0])
-      samples = ParsePlateSamples.call(data_blocks[1], wells)
-      Plate.new(label, times, temperatures, samples)
+      sample_map = ParseSampleMap.call(data_blocks[1])
+      Plate.new(label, times, temperatures, wells, sample_map)
     end
   end
 end

data/lib/flex_station_data/services/parse_plate_readings.rb

@@ -1,4 +1,5 @@
 require "active_support/core_ext"
+require "matrix"
 
 require "flex_station_data/wells"
 require "flex_station_data/concerns/service"
@@ -13,45 +14,31 @@ module FlexStationData
       @plate_readings_block = plate_readings_block
     end
 
-    def column_count
-      @column_count ||= headers.reverse.drop_while(&:blank?).size
-    end
-
-    def parsed_rows
-      @parsed_rows ||= begin
-        rows = plate_readings_data.map { |row| parse_row(row[0...column_count]) }
-        rows.select { |row| row.any?(&:present?) }
-      end
+    def headers
+      @headers ||= plate_readings_block.first.reverse.drop_while(&:blank?).reverse
     end
 
-    def parsed_columns
-      @parsed_columns ||= parsed_rows.transpose
+    def matrix
+      @matrix ||= Matrix[
+        *plate_readings_block.drop(1).map { |row| parse_row(row[0...headers.size]) }.select { |row| row.any?(&:present?) }
+      ]
     end
 
     def times
-      @times ||= parsed_columns[0].compact
+      @times ||= matrix.column(0).to_a.compact
     end
 
     def temperatures
-      @temperatures ||= parsed_columns[1].compact
-    end
-
-    def values
-      @values ||= parsed_columns.drop(2)
+      @temperatures ||= matrix.column(1).to_a.compact
     end
 
-    def wells_row_count
-      parsed_rows.size / times.size
-    end
-
-    def plate_readings_matrix
-      values.map do |values_column|
-        values_column.each_slice(wells_row_count).to_a.transpose
-      end.transpose
+    def wells_matrix
+      well_row_count = matrix.row_count / times.size
+      Matrix[*well_values.column_vectors.map { |col| col.to_a.each_slice(well_row_count).to_a.transpose }.transpose ]
     end
 
     def wells
-      Wells.new(plate_readings_matrix)
+      Wells.new(wells_matrix)
     end
 
     def call
@@ -78,12 +65,8 @@ module FlexStationData
 
     private
 
-    def headers
-      plate_readings_block.first
-    end
-
-    def plate_readings_data
-      @plate_readings_data ||= plate_readings_block.drop(1)
+    def well_values
+      matrix.minor(0..-1, 2..-1)
     end
 
     attr_reader :plate_readings_block

data/lib/flex_station_data/services/parse_sample_map.rb

@@ -0,0 +1,50 @@
+require "matrix"
+require "active_support/core_ext"
+
+require "flex_station_data/concerns/service"
+
+module FlexStationData
+  class ParseSampleMap
+    include Concerns::Service
+
+    attr_reader :sample_map_block
+
+    def initialize(sample_map_block)
+      @sample_map_block = sample_map_block
+    end
+
+    def call
+      labels.zip(matrix.column(1).to_a.each_slice(wells_per_sample).to_a).to_h
+    end
+
+    private
+
+    def parse_row(row)
+      row.take(2).map(&:presence)
+    end
+
+    def empty_row?(row)
+      row.all?(&:blank?)
+    end
+
+    def sample_map_header?(row)
+      row[0] == "Sample"
+    end
+
+    def sample_map_rows
+      sample_map_block.map(&method(:parse_row)).split(&method(:sample_map_header?)).drop(1).first.split(&method(:empty_row?)).first
+    end
+
+    def matrix
+      @matrix ||= Matrix[*sample_map_rows]
+    end
+
+    def labels
+      @labels ||= matrix.column(0).to_a.compact
+    end
+
+    def wells_per_sample
+      matrix.row_count / labels.size
+    end
+  end
+end

data/lib/flex_station_data/services/sample_quality.rb

@@ -17,7 +17,7 @@ module FlexStationData
     end
 
     def call
-      sample.readings.flat_map(&:values).map(&method(:value_quality)).uniq(&:to_s)
+      sample.values.flatten.map(&method(:value_quality)).uniq(&:to_s)
     end
   end
 end

data/lib/flex_station_data/services/value_quality.rb

@@ -1,6 +1,8 @@
 require "singleton"
 require "active_support/core_ext"
 
+require "flex_station_data/concerns/service"
+
 module FlexStationData
   class ValueQuality
     include Concerns::Service

data/lib/flex_station_data/version.rb

@@ -1,3 +1,3 @@
 module FlexStationData
-  VERSION = "0.3.1"
+  VERSION = "0.3.2"
 end

data/lib/flex_station_data/wells.rb

@@ -1,29 +1,28 @@
-require "flex_station_data/readings"
+require "matrix"
 
 module FlexStationData
   class Wells
-    def initialize(plate_readings_matrix)
-      @plate_readings_matrix = plate_readings_matrix
+    attr_reader :matrix
+
+    def initialize(matrix)
+      @matrix = matrix
     end
 
-    def readings(well_label)
-      well_index[well_label] ||= begin
-        row, column = parse_well_label(well_label)
-        Readings.new(well_label, plate_readings_matrix[row][column])
-      end
+    def values(well_label)
+      matrix[*coordinates(well_label)]
     end
 
-    def parse_well_label(well_label)
-      row, column = well_label.scan(/\A([A-Z])(\d+)\z/).first
-      [ row.ord - "A".ord, column.to_i - 1 ]
+    def coordinates(well_label)
+      coordinates_index[well_label] ||= begin
+        row, column = well_label.scan(/\A([A-Z])(\d+)\z/).first
+        [ row.ord - "A".ord, column.to_i - 1 ]
+      end
     end
 
     private
 
-    def well_index
-      @well_index ||= {}
+    def coordinates_index
+      @coordinates_index ||= {}
     end
-
-    attr_reader :plate_readings_matrix
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: flex-station-data
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.2
 platform: ruby
 authors:
 - John Carney
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-08-27 00:00:00.000000000 Z
+date: 2019-08-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -130,13 +130,12 @@ files:
 - lib/flex_station_data/presenters/plate_csv.rb
 - lib/flex_station_data/presenters/plates_csv.rb
 - lib/flex_station_data/presenters/sample_csv.rb
-- lib/flex_station_data/readings.rb
 - lib/flex_station_data/sample.rb
 - lib/flex_station_data/services/compute_mean.rb
 - lib/flex_station_data/services/load_plates.rb
 - lib/flex_station_data/services/parse_plate.rb
 - lib/flex_station_data/services/parse_plate_readings.rb
-- lib/flex_station_data/services/parse_plate_samples.rb
+- lib/flex_station_data/services/parse_sample_map.rb
 - lib/flex_station_data/services/sample_quality.rb
 - lib/flex_station_data/services/value_quality.rb
 - lib/flex_station_data/version.rb

data/lib/flex_station_data/readings.rb

@@ -1,16 +0,0 @@
-require "flex_station_data/services/compute_mean"
-
-module FlexStationData
-  class Readings
-    attr_reader :label, :values
-
-    def initialize(label, values)
-      @label = label
-      @values = values
-    end
-
-    def self.mean(*readings, label: "mean")
-      new(label, readings.map(&:values).transpose.map(&ComputeMean))
-    end
-  end
-end

data/lib/flex_station_data/services/parse_plate_samples.rb

@@ -1,49 +0,0 @@
-require "flex_station_data/readings"
-require "flex_station_data/concerns/service"
-
-require "flex_station_data/sample"
-
-module FlexStationData
-  class ParsePlateSamples
-    include Concerns::Service
-
-    def initialize(sample_map_block, wells)
-      @sample_map_block = sample_map_block
-      @wells = wells
-    end
-
-    def map_rows
-      @map_rows ||= begin
-        rows = sample_map_block.drop_while { |row| row[0] != "Sample" }.drop(1)
-        rows = rows.map { |row| row.map(&:presence) }
-        rows.take_while { |row| row.any?(&:present?) }.to_a
-      end
-    end
-
-    def map_columns
-      @map_columns ||= map_rows.transpose
-    end
-
-    def labels
-      @labels ||= map_columns[0].compact
-    end
-
-    def wells_per_sample
-      map_rows.size / labels.size
-    end
-
-    def sample_map
-      @sample_map ||= map_columns[1].each_slice(wells_per_sample).to_a
-    end
-
-    def call
-      labels.zip(sample_map).map do |label, well_labels|
-        Sample.new(label, well_labels.map(&wells.method(:readings)))
-      end
-    end
-
-    private
-
-    attr_reader :sample_map_block, :wells
-  end
-end