radiation 0.0.4 → 0.1.0

checksums.yaml

@@ -1,15 +1,7 @@
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data/.gitignore

@@ -1,17 +1,17 @@
-*.gem
-*.rbc
-.bundle
-.config
-.yardoc
-Gemfile.lock
-InstalledFiles
-_yardoc
-coverage
-doc/
-lib/bundler/man
-pkg
-rdoc
-spec/reports
-test/tmp
-test/version_tmp
-tmp
+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/.rspec

@@ -1 +1 @@
-#--color
+#--color

data/.travis.yml

@@ -1,9 +1,7 @@
-language: ruby
-rvm:
-  #- "1.8.7"
-  - "1.9.2"
-  - "1.9.3"
-  #- jruby-18mode # JRuby in 1.8 mode
-  - jruby-19mode # JRuby in 1.9 mode
-  #- rbx-18mode
-  - rbx-19mode
+language: ruby
+rvm:
+  - "1.9.2"
+  - "1.9.3"
+  - "2.0.0"
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode

data/CHANGELOG.md

@@ -1,12 +1,12 @@
-## v0.0.3
-
-* Added basic parsing for hdtv xml files
-* Changed dependency for linefit
-
-## v0.0.2
-
-* Added spectrum class with energy calibration options
-
-## v0.0.1
-
-* initial release
+## v0.0.3
+
+* Added basic parsing for hdtv xml files
+* Changed dependency for linefit
+
+## v0.0.2
+
+* Added spectrum class with energy calibration options
+
+## v0.0.1
+
+* initial release

data/Gemfile

@@ -1,5 +1,5 @@
-source 'https://rubygems.org'
-
-#gem "linefit", git: "https://github.com/janmayer/linefit.git"
-# Specify your gem's dependencies in radiation.gemspec
-gemspec
+source 'https://rubygems.org'
+
+#gem "linefit", git: "https://github.com/janmayer/linefit.git"
+# Specify your gem's dependencies in radiation.gemspec
+gemspec

data/LICENSE.txt

@@ -1,22 +1,22 @@
-Copyright (c) 2013 Jan Mayer
-
-MIT License
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+Copyright (c) 2013 Jan Mayer
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -1,45 +1,45 @@
-# Radiation
-[![Gem Version](https://badge.fury.io/rb/radiation.png)](http://badge.fury.io/rb/radiation)
-[![Build Status](https://travis-ci.org/janmayer/radiation.png?branch=master)](https://travis-ci.org/janmayer/radiation)
-[![Code Climate](https://codeclimate.com/github/janmayer/radiation.png)](https://codeclimate.com/github/janmayer/radiation)
-
-This gem provides easy access to energies and intensities from the decay of radioactive nuclei. 
-Currently two data sources are accessible: Internal (see bib files in `./data/`) and recommended values 
-by [Laboratoire National Henri Becquerel](http://www.nucleide.org/DDEP_WG/DDEPdata.htm).
-
-## Example Usage
-
-### Command line interface
-
-	$> radiation
-
-### In your ruby files:
-
-    require "radiation"
-    Radiation::Source.new(nuclide: "Ra-226").energies.collect{|e| e.value}
-
-See also files in `./samples/`.
-
-## Planned features
-
-* Efficiency calibration for given peaks or spectra
-* Better access to resources
-
-
-## Installation
-
-Requirement is a (local) ruby with rubygems. Using rvm is recommended
-    
-    $ \curl -L https://get.rvm.io | bash -s stable --ruby=1.9.3
-
-Add this line to your application's Gemfile:
-
-    gem 'radiation'
-
-And then execute:
-
-    $ bundle
-
-Or install it yourself as:
-
-    $ gem install radiation
+# Radiation
+[![Gem Version](https://badge.fury.io/rb/radiation.png)](http://badge.fury.io/rb/radiation)
+[![Build Status](https://travis-ci.org/janmayer/radiation.png?branch=master)](https://travis-ci.org/janmayer/radiation)
+[![Code Climate](https://codeclimate.com/github/janmayer/radiation.png)](https://codeclimate.com/github/janmayer/radiation)
+
+This gem provides easy access to energies and intensities from the decay of radioactive nuclei. 
+Currently two data sources are accessible: Internal (see bib files in `./data/`) and recommended values 
+by [Laboratoire National Henri Becquerel](http://www.nucleide.org/DDEP_WG/DDEPdata.htm).
+
+## Example Usage
+
+### Command line interface
+
+	$> radiation
+
+### In your ruby files:
+
+    require "radiation"
+    Radiation::Source.new(nuclide: "Ra-226").energies.collect{|e| e.value}
+
+See also files in `./samples/`.
+
+## Planned features
+
+* Efficiency calibration for given peaks or spectra
+* Better access to resources
+
+
+## Installation
+
+Requirement is a (local) ruby with rubygems. Using rvm is recommended
+    
+    $ \curl -L https://get.rvm.io | bash -s stable --ruby=1.9.3
+
+Add this line to your application's Gemfile:
+
+    gem 'radiation'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install radiation

data/Rakefile

@@ -1,6 +1,6 @@
-require "bundler/gem_tasks"
-require 'rspec/core/rake_task'
-
-RSpec::Core::RakeTask.new(:spec)
-
-task default: :spec
+require "bundler/gem_tasks"
+require 'rspec/core/rake_task'
+
+RSpec::Core::RakeTask.new(:spec)
+
+task default: :spec

data/lib/radiation/cli.rb

@@ -34,5 +34,27 @@ class CLI < Thor
 		spectrum.calibrate.calibration.each{|c| puts c}
 	end
 
+	option :resource
+	option :mini
+	desc "efficiency NUCLIDE SPECTRUM.xml", "calculate efficiencies for a spectrum"
+	long_desc <<-LONGDESC
+	Calculates relative full-peak efficiencies for a spectrum that has been analysed with HDTV. Stored peak fits in HDTV can be stored with hdtv>fit write filname.xml
+	Example: \n
+	$>radiation efficiency Ra-226 Ge00.xml
+	With --resource=nucleide.org more decay radiation sources are available.
+	With --mini=value transitions with small intensities can be supressed (default 0.3)
+	LONGDESC
+	def efficiency(nuclide, file)
+		resource = options[:resource] ? options[:resource] : "internal"
+		mini = options[:mini] ? options[:mini] : 0.3
+		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|
+			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
+
+
 end
 end

data/lib/radiation/resource/internal.rb

@@ -0,0 +1,20 @@
+# encoding: utf-8
+require 'csv'
+
+module Radiation::Resource
+	class Internal < Base
+
+		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])} }
+			rescue
+				raise "No Data for #{nuclide}"
+			end
+			self
+		end
+		
+	end
+end

data/lib/radiation/resource/nucleideorg.rb

@@ -0,0 +1,43 @@
+# encoding: utf-8
+require 'plusminus'
+require 'open-uri'
+require 'open-uri/cached'
+require 'tmpdir'
+
+
+module Radiation::Resource
+	class Nucleideorg < Base
+		
+		def fetch(nuclide)
+			@nuclide = nuclide
+			@nuclide = "Ra-226D" if @nuclide == "Ra-226" #Ra-226 in equilibrium with daughters
+			begin
+				@data[:nuclide] = @nuclide.to_s
+
+				@data[:reference] = "A. Pluquet et al. (2013). Recommended data for #{@nuclide} by the Decay Data Evaluation Project working group. Decay Data Evaluation Project, Laboratoire National Henri Becquerel, C.E. Saclay. Retrieved from http://www.nucleide.org/DDEP_WG/Nuclides/#{@nuclide}.lara.txt"
+
+				OpenURI::Cache.cache_path = "#{Dir.tmpdir}/radiation/"
+				uri = open("http://www.nucleide.org/DDEP_WG/Nuclides/#{@nuclide}.lara.txt").readlines
+				start = 0
+				uri.each_with_index do |line, lineno|
+					if line.start_with?("Half-life (s)")
+						row = line.split(' ; ')
+						@data[:halflife] = row[1].to_f.pm(row[2].to_f)
+					end
+					if line.start_with?("------")
+						start = lineno + 2
+						break
+					end
+				end
+				return @data[:transitions] = [] if start == 0 or uri.count < start
+				@data[:transitions] = uri[start...-1].collect{|line| line.split(' ; ')}.select!{|row| row[4] == "g"}.collect do |row|
+				 {:energy => row[0].to_f.pm(row[1].to_f), :intensity => row[2].to_f.pm(row[3].to_f)} 
+				end
+			rescue
+				raise "No Data for #{@nuclide}"
+			end
+			self
+		end
+
+	end
+end

data/lib/radiation/resource.rb

@@ -0,0 +1,14 @@
+# encoding: utf-8
+
+module Radiation
+	module Resource
+		class Base
+			attr_reader :data
+
+			def initialize()
+				@data = {}
+			end
+
+		end
+	end
+end

data/lib/radiation/source.rb

@@ -1,37 +1,53 @@
 # encoding: utf-8
-require 'radiation/source/resource'
 require 'combinatorics'
 
-
 module Radiation
-class Source
-	attr_reader :data
-
-	def initialize(options={})
-		@resource = options.key?(:resource) ? options[:resource].to_s : "internal"
-		fetch(options[:nuclide].to_s) if options.key?(:nuclide)
-	end
-
-	def fetch(nuclide)
-		raise "Nuclide :#{nuclide} is not valid." unless is_nuclide?(nuclide)
-		@data = Resource.new(@resource).data(nuclide)
+	class Source
+		attr_reader :resource, :nuclide, :halflife, :reference, :description, :transitions
+	
+		def initialize(options={})
+			@resource = options.key?(:resource) ? options[:resource].to_s : "internal"
+			@nuclide  = options[:nuclide].to_s if options.key?(:nuclide)
+			fetch if @resource and @nuclide
+		end
+	
+		def fetch(options={})
+			@resource = options[:resource].to_s if options.key?(:resource)
+			@nuclide  = options[:nuclide].to_s  if options.key?(:nuclide)
+			raise "Nuclide: #{@nuclide} is not valid." unless is_nuclide?(@nuclide)
+			data = case @resource
+				when "internal" then Radiation::Resource::Internal.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 read(options={})
+			@resource = "external"
+			build(options)
+			return self
+		end
+	
+		def energies
+			self.transitions.collect{|line| line[:energy]}
+		end
+	
+		def intensities
+			self.transitions.select{|line| line[:intensity] > 0}.collect{|line| {:energy => line[:energy], :intensity => line[:intensity]} }
+		end
+	
+		def is_nuclide?(nuclide)
+			!!(nuclide =~ /\A[a-zA-Z]{1,2}-\d{1,3}\z/)
+		end
+	
+	private
+		def build(data)
+			[:nuclide, :halflife, :reference, :description, :transitions].each do |key|
+				instance_variable_set("@#{key}", data[key]) if data.key?(key)
+			end
+		end
+	
 	end
-
-	def nuclide
-		@data[:nuclide]
-	end
-
-	def energies
-		@data[:lines].collect{|line| line[:energy]}
-	end
-
-	def intensities
-		@data[:lines].select{|line| line[:intensity] > 0}.collect{|line| {:energy => line[:energy], :intensity => line[:intensity]} }
-	end
-
-	def is_nuclide?(nuclide)
-		!!(nuclide =~ /\A[a-zA-Z]{1,2}-\d{1,3}\z/)
-	end
-
-end
 end

data/lib/radiation/spectrum.rb

@@ -3,76 +3,93 @@ require "linefit"
 require "plusminus"
 require "xmlsimple"
 
-module Radiation
-class Spectrum
-	attr_accessor :peaks, :source, :calibration
-
-	def initialize(options={})
-		@peaks		= options.key?(:peaks) ? options[:peaks] : []
-		@source		= options.key?(:source) ? options[:source] : nil
-		@calibration= options.key?(:calibration) ? options[:calibration] : [0, 1]
-	end
-
-	def calibrate
-		if @peaks.empty? or @peaks.select{|p| p.key?(:channel)}.empty?
-			raise "Nothing to calibrate"
+	module Radiation
+	class Spectrum
+		attr_accessor :peaks, :source, :calibration
+	
+		def initialize(options={})
+			@peaks		= options.key?(:peaks) ? options[:peaks] : []
+			@source		= options.key?(:source) ? options[:source] : nil
+			@calibration= options.key?(:calibration) ? options[:calibration] : [0, 1]
 		end
-
-		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"
-			else
-				self.guess_calibration
+	
+		def calibrate
+			if @peaks.empty? or @peaks.select{|p| p.key?(:channel)}.empty?
+				raise "Nothing to calibrate"
+			end
+	
+			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"
+				else
+					self.guess_calibration
+				end
+				self.match_channels
 			end
-			self.match_channels
+			#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
-		#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)
+	
+		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
+			return self
+		end
+	
+		def guess_calibration(energies=@source.energies, rounding=4)
+			# Build all possible combinations of known energies and peaks
+			arr = [energies, @peaks.collect{|peak| peak[:channel]}].comprehension
+			# The approximate value for b in $Energy = a + b * Channel$ will be most frequent for $a \approx 0$
+			freq = arr.collect{|a| (a.first.to_f/a.last.to_f).round(rounding) }.flatten.inject(Hash.new(0)) { |h,v| h[v] += 1; h }.sort_by{|k,v| v}
+			@calibration = [0, freq.last[0] ]
+			return self
+		end
+	
+		def channel_energy(chn)
+			@calibration[0] + @calibration[1]*chn
+		end
+	
+		def parse_hdtv(file)
+			xml = XmlSimple.xml_in(file, { 'KeyAttr' => 'name' })
+			@peaks = xml["fit"].collect{|p| p["peak"]}.flatten.collect{|p| p["uncal"]}.flatten.collect do |p|
+				{:channel => p["pos"].first["value"].first.to_f.pm(p["pos"].first["error"].first.to_f),
+		 		:counts => p["vol"].first["value"].first.to_f.pm(p["vol"].first["error"].first.to_f) } 
+			end
+			return self
+		end
+		
+		def efficiencies(rounding=4)
+			@peaks.each do |peak|
+				@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)}
 		end
-		return self
-	end
-
-	def guess_calibration(energies=@source.energies, rounding=4)
-		# Build all possible combinations of known energies and peaks
-		arr = [energies, @peaks.collect{|peak| peak[:channel]}].comprehension
-		# The approximate value for b in $Energy = a + b * Channel$ will be most frequent for $a \approx 0$
-		freq = arr.collect{|a| (a.first.to_f/a.last.to_f).round(rounding) }.flatten.inject(Hash.new(0)) { |h,v| h[v] += 1; h }.sort_by{|k,v| v}
-		@calibration = [0, freq.last[0] ]
-		return self
-	end
-
-	def channel_energy(chn)
-		@calibration[0] + @calibration[1]*chn
-	end
 
-	def parse_hdtv(file)
-		xml = XmlSimple.xml_in(file, { 'KeyAttr' => 'name' })
-		@peaks = xml["fit"].collect{|p| p["peak"]}.flatten.collect{|p| p["uncal"]}.flatten.collect do |p|
-			{:channel => p["pos"].first["value"].first.to_f.pm(p["pos"].first["error"].first.to_f),
-	 		:counts => p["vol"].first["value"].first.to_f.pm(p["vol"].first["error"].first.to_f) } 
+	private 
+		def channel_efficiency(peak)
+			peak[:counts]/peak[:intensity]
 		end
-		return self
-	end
 
+	end
 end
-end
-
-
+	
+	
 class Float
 	def approx_equal?(other,threshold=0.5)
 		if (self-other).abs < threshold    # "<" not exact either

data/lib/radiation/version.rb

@@ -1,3 +1,3 @@
-module Radiation
-  VERSION = "0.0.4"
-end
+module Radiation
+  VERSION = "0.1.0"
+end

data/lib/radiation.rb

@@ -1,7 +1,10 @@
-require "radiation/version"
-require "radiation/source"
-require "radiation/spectrum"
-
-module Radiation
-  # Your code goes here...
-end
+require "radiation/version"
+require "radiation/source"
+require "radiation/spectrum"
+require "radiation/resource"
+require 'radiation/resource/internal'
+require 'radiation/resource/nucleideorg'
+
+module Radiation
+  # Your code goes here...
+end