plot_statistics 0.3.0 → 1.0.0

data/VERSION

@@ -1 +1 @@
-0.3.0
+1.0.0

data/bin/plot_statistics

@@ -8,33 +8,25 @@ rescue LoadError
   require 'plot_statistics'
 end
 
-ARGV.each do |file_name|
-  puts "\nCommand started at: #{Time.now}\n"
-
-  file = File.new(file_name)
+ARGV.each do |filename|
+  file = File.new(filename)
+  lines = file.readlines
+  file.close
 
   puts "\n"
   puts '##########################'
-  puts "#   #{file_name}"
+  puts "#   #{filename}"
   puts '##########################'
   puts "\n"
 
-  lines = file.readlines
-
   clams = lines.map do |line|
     x, y = line.strip.split("\t")
-    PlotStatistics::Clam.new(:x => x.to_i, :y => y.to_i)
+    PlotStatistics::Clam.new(:x => x, :y => y)
   end
 
-  puts "\nActual plot started at: #{Time.now}\n"
-
   actual_plot = PlotStatistics::ClamPlot.new(clams)
-  puts actual_plot.inspect
-
-  puts "\nMonte Carlo plots started at: #{Time.now}\n"
-
   monte_carlo = PlotStatistics::MonteCarlo.new(actual_plot.number_of_clams)
-  puts monte_carlo.inspect
 
-  puts "\mCommand finished at: #{Time.now}\n"
+  output_filename = filename + '.ripleys_k.csv'
+  PlotStatistics::Output.new(:clam_plot => actual_plot, :monte_carlo => monte_carlo).write_to_file(output_filename)
 end

data/lib/plot_statistics/circle.rb

@@ -26,7 +26,7 @@ class PlotStatistics
     end
 
     def proportion_for_two_sides_out
-      if corners_outside_radius.size == 3
+      if corners_outside_circle.size == 3
         1 - ( Math.acos( distance_from_bound.pop / radius ) + Math.acos( distance_from_bound.pop / radius ) + Math::PI / 2 ) / (Math::PI * 2)
       else
         1 - ( 2 * Math.acos( distance_from_bound.pop / radius ) + 2 * Math.acos( distance_from_bound.pop / radius ) ) / (Math::PI * 2)
@@ -35,14 +35,14 @@ class PlotStatistics
 
     def find_distance_from_bounds
       [
-        (clam.y - 100).abs, # distance from top
-        (clam.x - 100).abs, # distance from right
-        clam.x,             # distance from left
-        clam.y              # distance from bottom
+        100 - clam.y, # distance from top
+        100 - clam.x, # distance from right
+        clam.x,       # distance from left
+        clam.y        # distance from bottom
       ]
     end
 
-    def corners_outside_radius
+    def corners_outside_circle
       ClamPlot::PLOT_CORNERS.map do |corner|
         distance = Math.sqrt((corner.first - clam.x) ** 2 + (corner.last - clam.y) ** 2)
         next if distance < radius

data/lib/plot_statistics/clam.rb

@@ -3,8 +3,8 @@ class PlotStatistics
     attr_accessor :x, :y, :distances
 
     def initialize(params={})
-      @x = params[:x]
-      @y = params[:y]
+      @x = params[:x].to_f
+      @y = params[:y].to_f
       @distances = params[:distances] || []
     end
 

data/lib/plot_statistics/clam_plot.rb

@@ -2,7 +2,7 @@ class PlotStatistics
   class ClamPlot
     attr_accessor :clams, :stats
 
-    AREA_OF_PLOT  = 10_000
+    AREA_OF_PLOT  = 1 # this is in meters everything else is in centimeters
     MAX_RADIUS    = 50
     PLOT_CORNERS = [[0,0], [0,100], [100,0], [100,100]]
 
@@ -18,8 +18,20 @@ class PlotStatistics
       new(clams)
     end
 
+    def self.create_regular(distance=5)
+      clams = []
+      (0..100).each do |x|
+        (0..100).each do |y|
+          mod_x = x % distance
+          mod_y = x % distance
+          clams << Clam.new(:x => x, :y => y) if mod_x == 0 && mod_y == 0
+        end
+      end
+      new(clams)
+    end
+
     def number_of_clams
-      clams.size
+      clams.size.to_f
     end
 
     def setup_clam_distances(clams)
@@ -39,18 +51,16 @@ class PlotStatistics
     def calculate_stats
       (1..MAX_RADIUS).each do |radius|
 
-        sums = clams.inject(0) do |sum, clam|
+        sums = clams.inject(0.0) do |sum, clam|
           clams_inside_circle = clam.distances.select { |distance| distance <= radius }
 
           circle_proportion = Circle.new(:clam => clam, :radius => radius).proportion_inside_plot
-          reciprocal_proportion = 1 / circle_proportion
+          reciprocal_proportion = 1.0 / circle_proportion
 
-          clams_inside_circle.inject(0) do |sum, inside_clam|
-            ( reciprocal_proportion * 1.0 ) / ( number_of_clams ** 2 )
-          end
+          reciprocal_proportion * clams_inside_circle.size
         end
 
-        k_t = AREA_OF_PLOT * sums
+        k_t = AREA_OF_PLOT * sums / (number_of_clams ** 2)
         l_t = radius - Math.sqrt( k_t / Math::PI)
 
         stats.k_ts << k_t

data/lib/plot_statistics/monte_carlo.rb

@@ -2,7 +2,7 @@ class PlotStatistics
   class MonteCarlo
     attr_accessor :plots, :stats
 
-    def initialize(number_of_clams, number_of_plots=100)
+    def initialize(number_of_clams, number_of_plots=100.0)
       @plots = (1..number_of_plots).map { ClamPlot.create_random number_of_clams }
       @stats = OpenStruct.new(:mean        => OpenStruct.new(:k_ts => [], :l_ts => []),
                               :upper_limit => OpenStruct.new(:k_ts => [], :l_ts => []),
@@ -20,8 +20,8 @@ class PlotStatistics
 
     def calculate_limits
       (0...ClamPlot::MAX_RADIUS).each do |radius|
-        threshold_k = standard_deviation_k(radius) * 2
-        threshold_l = standard_deviation_l(radius) * 2
+        threshold_k = standard_deviation_k(radius) * 2.0
+        threshold_l = standard_deviation_l(radius) * 2.0
 
         stats.upper_limit.k_ts << (stats.mean.k_ts[radius] + threshold_k)
         stats.upper_limit.l_ts << (stats.mean.l_ts[radius] + threshold_l)
@@ -31,7 +31,7 @@ class PlotStatistics
     end
 
     def standard_deviation_k(radius)
-      sum = plots.inject(0) do |sum, plot|
+      sum = plots.inject(0.0) do |sum, plot|
         (plot.stats.k_ts[radius] - stats.mean.k_ts[radius]) ** 2
       end
 
@@ -39,7 +39,7 @@ class PlotStatistics
     end
 
     def standard_deviation_l(radius)
-      sum = plots.inject(0) do |sum, plot|
+      sum = plots.inject(0.0) do |sum, plot|
         (plot.stats.l_ts[radius] - stats.mean.l_ts[radius]) ** 2
       end
 
@@ -51,7 +51,7 @@ class PlotStatistics
     end
 
     def average_k(radius)
-      sum = plots.inject(0) do |sum, plot|
+      sum = plots.inject(0.0) do |sum, plot|
         plot.stats.k_ts[radius]
       end
 
@@ -59,7 +59,7 @@ class PlotStatistics
     end
 
     def average_l(radius)
-      sum = plots.inject(0) do |sum, plot|
+      sum = plots.inject(0.0) do |sum, plot|
         plot.stats.l_ts[radius]
       end
 

data/lib/plot_statistics/output.rb

@@ -3,7 +3,25 @@ class PlotStatistics
     attr_accessor :clam_plot, :monte_carlo
 
     def initialize(params={})
+      @clam_plot = params[:clam_plot]
+      @monte_carlo = params[:monte_carlo]
+    end
+
+    def write_to_file(filename)
+      FasterCSV.open(filename, 'w') do |csv|
+        csv << ['Radius', 'K(t)', 'L(t)', 'Mean K(t)', 'Mean L(t)', 'Upper K(t)', 'Lower K(t)', 'Upper L(t)', 'Lower L(t)']
 
+        (0...ClamPlot::MAX_RADIUS).each do |position|
+          radius = position + 1
+          csv << [
+            radius,
+            clam_plot.stats.k_ts[position],               clam_plot.stats.l_ts[position],
+            monte_carlo.stats.mean.k_ts[position],        monte_carlo.stats.mean.l_ts[position],
+            monte_carlo.stats.upper_limit.k_ts[position], monte_carlo.stats.lower_limit.k_ts[position],
+            monte_carlo.stats.upper_limit.l_ts[position], monte_carlo.stats.lower_limit.l_ts[position]
+          ]
+        end
+      end
     end
   end
 end

data/lib/plot_statistics.rb

@@ -5,4 +5,5 @@ class PlotStatistics
   require File.dirname(__FILE__) + '/plot_statistics/clam'
   require File.dirname(__FILE__) + '/plot_statistics/clam_plot'
   require File.dirname(__FILE__) + '/plot_statistics/monte_carlo'
+  require File.dirname(__FILE__) + '/plot_statistics/output'
 end

data/plot_statistics.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{plot_statistics}
-  s.version = "0.3.0"
+  s.version = "1.0.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Asa Wilson"]
-  s.date = %q{2010-03-18}
+  s.date = %q{2010-03-19}
   s.default_executable = %q{plot_statistics}
   s.description = %q{This is a gem to do a Ripley's K analysis}
   s.email = %q{acvwilson@gmail.com}

metadata

@@ -3,10 +3,10 @@ name: plot_statistics
 version: !ruby/object:Gem::Version 
   prerelease: false
   segments: 
+  - 1
   - 0
-  - 3
   - 0
-  version: 0.3.0
+  version: 1.0.0
 platform: ruby
 authors: 
 - Asa Wilson
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-03-18 00:00:00 -04:00
+date: 2010-03-19 00:00:00 -04:00
 default_executable: plot_statistics
 dependencies: 
 - !ruby/object:Gem::Dependency