radiation 0.1.0 → 0.1.1

data/lib/radiation/cli.rb

@@ -19,6 +19,11 @@ class CLI < Thor
 		puts Radiation::Source.new(nuclide: nuclide, resource: resource).intensities.collect{|l| [l[:energy].value, l[:energy].delta, l[:intensity].value, l[:intensity].delta].join("\t") }
 	end
 
+	desc "resources", "List available data resources"
+	def resources
+		puts Radiation::Source.new.resources
+	end
+
 	option :resource
 	desc "calibrate NUCLIDE SPECTRUM.xml", "calibrate a spectrum"
 	long_desc <<-LONGDESC
@@ -50,7 +55,7 @@ class CLI < Thor
 		source   = Radiation::Source.new(nuclide: nuclide, resource: resource)
 		spectrum = Radiation::Spectrum.new(source: source ).parse_hdtv(file)
 		puts ["E_ɣ", "I_ɣ", "ΔI_ɣ", "e", "Δe"].join("\t")
-		spectrum.calibrate.efficiencies.select{|p| p[:intensity] > mini}.sort_by{|k| k[:energy]}.each do |p|
+		spectrum.calibrate.efficiencies.peaks.select{|p| p[:intensity] > mini}.sort_by{|k| k[:energy]}.each do |p|
 			puts [ p[:energy].to_f.round(1), p[:intensity].value, p[:intensity].delta, p[:efficiency].value.round(1), p[:efficiency].delta.round(1) ].join("\t")
 		end
 	end

data/lib/radiation/resource/iaea.rb

@@ -0,0 +1,28 @@
+# encoding: utf-8
+require 'json'
+
+module Radiation::Resource
+	class IAEA < Base
+		# FIXME: Better path creation
+		PATH = File.join(File.dirname(__FILE__), "../../../data")
+		FILENAME = "iaea-xgamma.json"
+
+		def fetch(nuclide)
+			@nuclide = nuclide
+			begin
+				@data = load_data(@nuclide)
+				# FIXME: Better conversion from x, x_uncertainty to pm
+				@data[:transitions].collect!{|t| { :energy => t[:energy].to_f.pm(t[:energy_uncertainty].to_f), :intensity => t[:intensity].to_f.pm(t[:intensity_uncertainty].to_f)} }
+			rescue
+				raise "No Data for #{@nuclide}"
+			end
+			self
+		end
+
+		private
+		def load_data(nuclide)
+			JSON.parse( IO.read("#{PATH}/#{FILENAME}"), {:symbolize_names => true} ).select{|n| n[:nuclide] == nuclide}.first
+		end
+
+	end
+end

data/lib/radiation/resource/internal.rb

@@ -3,18 +3,24 @@ require 'csv'
 
 module Radiation::Resource
 	class Internal < Base
-
+		# FIXME: Better path creation
+		PATH = File.join(File.dirname(__FILE__), "../../../data")
+		
 		def fetch(nuclide)
 			@nuclide = nuclide
 			begin
-				path = File.join(File.dirname(__FILE__), "../../../data")
 				@data[:nuclide] = @nuclide.to_s
-				@data[:transitions] = CSV.read("#{path}/#{@nuclide}.csv",  {col_sep: ';', converters: :numeric}).collect{|row| {:energy => row[0].pm(0), :intensity => row[1].pm(row[2])} }
+				@data[:transitions] = load_data(@nuclide).collect{|row| {:energy => row[0].pm(0), :intensity => row[1].pm(row[2])} }
 			rescue
 				raise "No Data for #{nuclide}"
 			end
 			self
 		end
-		
+
+		private
+		def load_data(nuclide)
+			CSV.read("#{PATH}/#{nuclide}.csv",  {col_sep: ';', converters: :numeric})
+		end
+	
 	end
 end

data/lib/radiation/source.rb

@@ -1,6 +1,4 @@
 # encoding: utf-8
-require 'combinatorics'
-
 module Radiation
 	class Source
 		attr_reader :resource, :nuclide, :halflife, :reference, :description, :transitions
@@ -17,12 +15,17 @@ module Radiation
 			raise "Nuclide: #{@nuclide} is not valid." unless is_nuclide?(@nuclide)
 			data = case @resource
 				when "internal" then Radiation::Resource::Internal.new.fetch(@nuclide).data
+				when "iaea" then Radiation::Resource::IAEA.new.fetch(@nuclide).data
 				when "nucleide.org" then Radiation::Resource::Nucleideorg.new.fetch(@nuclide).data
 				else raise "Unknown Datasource"
 			end
 			build(data)
 			return self
 		end
+
+		def resources
+			["internal", "iaea", "nucleide.org"]
+		end
 	
 		def read(options={})
 			@resource = "external"

data/lib/radiation/spectrum.rb

@@ -1,9 +1,10 @@
 # encoding: utf-8
+require 'combinatorics'
 require "linefit"
 require "plusminus"
 require "xmlsimple"
 
-	module Radiation
+module Radiation
 	class Spectrum
 		attr_accessor :peaks, :source, :calibration
 	
@@ -20,30 +21,14 @@ require "xmlsimple"
 	
 			if @peaks.select{|p| p.key?(:channel) and p.key?(:energy)}.empty?
 				if @calibration == [0,1] and @source.nil?
-					raise "No channel <-> energy associations. Specify a Source or a preleminary calibration to improve"
+					raise "No channel <-> energy associations. Specify a Source or a preliminary calibration to improve"
 				else
 					self.guess_calibration
 				end
 				self.match_channels
 			end
-			#calibrate using linefit
-			mpeaks = @peaks.delete_if{|p| p[:energy] == nil}
-			x = mpeaks.collect{|p| p[:channel]}
-			y = mpeaks.collect{|p| p[:energy]}
-			lineFit = LineFit.new
-			lineFit.setData(x,y)
-			intercept, slope = lineFit.coefficients
-			varianceIntercept, varianceSlope = lineFit.varianceOfEstimates
-			@calibration = [intercept.pm(Math.sqrt(varianceIntercept)), slope.pm(Math.sqrt(varianceSlope))]
-			return self
-		end
-	
-		def match_channels(energies=@source.energies, rounding=4)
-			@peaks.each do |peak|
-				energies.each do |energy|
-					peak[:energy] = energy if channel_energy(peak[:channel]).to_f.approx_equal?(energy, rounding)
-				end
-			end
+
+			@calibration = apply_linefit(@peaks)
 			return self
 		end
 	
@@ -70,22 +55,49 @@ require "xmlsimple"
 		end
 		
 		def efficiencies(rounding=4)
+			self.match_channels
+			@peaks.select{|p| p.key?(:intensity) and p.key?(:counts)}.each{|p| p[:efficiency] = channel_efficiency(p)}
+			return self
+		end
+
+		def match_channels(source=@source, rounding=4)
 			@peaks.each do |peak|
-				@source.transitions.each do |transition|
+				source.transitions.each do |transition|
 					if channel_energy(peak[:channel]).to_f.approx_equal?(transition[:energy], rounding)
 						peak[:energy] = transition[:energy]
 						peak[:intensity] = transition[:intensity] if transition[:intensity] > 0
 					end
 				end
 			end
-			@peaks.select{|p| p.key?(:intensity) and p.key?(:counts)}.each{|p| p[:efficiency] = channel_efficiency(p)}
+			return self
 		end
 
-	private 
+
 		def channel_efficiency(peak)
 			peak[:counts]/peak[:intensity]
 		end
 
+	private
+		def apply_linefit(peaks)
+			#calibrate using linefit
+			mpeaks = peaks.delete_if{|p| p[:energy] == nil}
+			x = mpeaks.collect{|p| p[:channel]}
+			y = mpeaks.collect{|p| p[:energy]}
+			lineFit = LineFit.new
+
+			# Use weighted calibration when possible
+			if mpeaks.count{|p| p[:intensity] and p[:intensity] > 0} == mpeaks.count
+				weights = mpeaks.collect{|p| p[:intensity].nil? ? 0 : p[:intensity]}
+				lineFit.setData(x,y,weights)
+			else
+				lineFit.setData(x,y)
+			end
+			
+			intercept, slope = lineFit.coefficients
+			varianceIntercept, varianceSlope = lineFit.varianceOfEstimates
+			return [intercept.pm(Math.sqrt(varianceIntercept.abs)), slope.pm(Math.sqrt(varianceSlope.abs))]
+		end
+
 	end
 end
 	

data/lib/radiation/version.rb

@@ -1,3 +1,3 @@
 module Radiation
-  VERSION = "0.1.0"
+  VERSION = "0.1.1"
 end

data/lib/radiation.rb

@@ -4,6 +4,7 @@ require "radiation/spectrum"
 require "radiation/resource"
 require 'radiation/resource/internal'
 require 'radiation/resource/nucleideorg'
+require 'radiation/resource/iaea'
 
 module Radiation
   # Your code goes here...

data/radiation.gemspec

@@ -1,32 +1,32 @@
-# coding: utf-8
-lib = File.expand_path('../lib', __FILE__)
-$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
-require 'radiation/version'
-
-Gem::Specification.new do |spec|
-  spec.name          = "radiation"
-  spec.version       = Radiation::VERSION
-  spec.authors       = ["Jan Mayer"]
-  spec.email         = ["jan.mayer@ikp.uni-koeln.de"]
-  spec.description   = %q{Decay Radiation}
-  spec.summary       = %q{This gem provides easy access to energies and intensities from the decay of radioactive nuclei}
-  spec.homepage      = "https://github.com/janmayer/radiation"
-  spec.license       = "MIT"
-
-  spec.files         = `git ls-files`.split($/)
-  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
-  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
-  spec.require_paths = ["lib"]
-
-  spec.add_dependency "plusminus"
-  spec.add_dependency "open-uri-cached"
-  spec.add_dependency "combinatorics"
-  spec.add_dependency "linefit"
-  spec.add_dependency "xml-simple"
-  spec.add_dependency "thor"
-
-  
-  spec.add_development_dependency "bundler", "~> 1.3"
-  spec.add_development_dependency "rake"
-  spec.add_development_dependency "rspec"
-end
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'radiation/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "radiation"
+  spec.version       = Radiation::VERSION
+  spec.authors       = ["Jan Mayer"]
+  spec.email         = ["jan.mayer@ikp.uni-koeln.de"]
+  spec.description   = %q{Decay Radiation}
+  spec.summary       = %q{This gem provides easy access to energies and intensities from the decay of radioactive nuclei}
+  spec.homepage      = "https://github.com/janmayer/radiation"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency "plusminus"
+  spec.add_dependency "open-uri-cached"
+  spec.add_dependency "combinatorics"
+  spec.add_dependency "linefit"
+  spec.add_dependency "xml-simple"
+  spec.add_dependency "thor"
+
+  
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "rspec"
+end