radiation 0.1.3 → 0.1.4

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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/CHANGELOG.md

@@ -1,12 +1,42 @@
-## 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
+## v0.1.4
+
+* Added list to resources and CLI
+* Example for 30 seconds en
+* Changed number formatting in CLI, see plusminus nio_write
+
+## v0.1.3
+
+* Removed internal resource in favor of IAEA Data
+
+## v0.1.2
+
+* Fixing bug with percentage based intensities
+* Gnuplot fitting experiments
+
+## v0.1.1
+
+* Weighted fits
+* Added IAEA recommended data
+
+## v0.1.0
+
+* Added initial efficiency calculations
+* Modified class structure of resources.
+* Fixed rspec: Replaced round() with be_within
+
+## v0.0.4
+
+* Added CLI
+
+## 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 +1,6 @@
-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 'coveralls', require: false
+#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 +1,52 @@
-# 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:
+
+* IAEA [xgamma](http://www-nds.iaea.org/xgamma_standards/) recommended values (default)
+* Laboratoire National Henri Becquerel [DDEP](http://www.nucleide.org/DDEP_WG/DDEPdata.htm) recommended data
+
+Note that IAEA data is compiled and filtered with energy and efficiency calibration in mind, while DDEP data ist focused on completeness.
+
+
+## Example Usage
+
+The radiation gem can be use in two ways:
+
+### Command line interface
+
+	$ radiation
+	$ radiation source Na-22
+	=> E_ɣ      ΔE_ɣ    I_ɣ     ΔI_ɣ
+	=> 511.0    0.0     1.798   2E-03
+	=> 1274.537 0.003   0.9994  1E-04
+
+Refer to the CLI for more options.
+
+### In your ruby files:
+
+    require "radiation"
+    Radiation::Source.new(nuclide: "Ra-226").energies.collect{|e| e.value}
+
+See files in `./samples/`.
+
+
+## Installation
+
+Requirement is a (local) ruby with rubygems. Using rvm is recommended
+
+### Installing ruby locally on a debian based system
+    
+    $ \curl -L https://get.rvm.io | bash -s stable
+    $ source ~/.bashrc
+    $ rvm mount -r http://rvm.io/binaries/debian/7.0/x86_64/ruby-2.0.0-p247.tar.bz2 --verify-downloads 1
+    $ rvm use --default 2.0.0
+
+### Installing the gem
+
+    $ gem install radiation
+
+Or use bundler.

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

@@ -15,8 +15,19 @@ class CLI < Thor
 	desc "source NUCLIDE", "decay radiation data"
 	def source(nuclide)
 		resource = options[:resource] ? options[:resource] : "iaea"
-		puts ["E_ɣ", "ΔE_ɣ", "I_ɣ", "ΔI_ɣ"].join("\t")
-		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") }
+		puts ["#E_ɣ", "ΔE_ɣ", "I_ɣ", "ΔI_ɣ"].join("\t")
+		puts Radiation::Source.new(nuclide: nuclide, resource: resource).intensities.collect{|l| [l[:energy].nio_write, l[:energy].delta, l[:intensity].nio_write, "%.0E" % l[:intensity].delta].join("\t") }
+	end
+
+	option :resource
+	desc "list", "List available nuclei"
+	def list
+		resource = options[:resource] ? options[:resource] : "iaea"
+		puts case resource
+			when "iaea" then Radiation::Resource::IAEA.new.list
+			when "nucleide.org" then Radiation::Resource::Nucleideorg.new.list
+			else raise "Unknown Datasource"
+		end
 	end
 
 	desc "resources", "List available data resources"
@@ -54,9 +65,9 @@ class CLI < Thor
 		mini = options[:mini] ? options[:mini].to_f : 0.003
 		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")
+		puts ["#E_ɣ", "ΔE_ɣ", "I_ɣ", "ΔI_ɣ", "e", "Δe"].join("\t")
 		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")
+			puts [ p[:energy].nio_write, p[:energy].delta, p[:intensity].nio_write, p[:intensity].delta, p[:efficiency].nio_write, "%.0E" % p[:efficiency].delta ].join("\t")
 		end
 	end
 

data/lib/radiation/resource/iaea.rb

@@ -10,7 +10,7 @@ module Radiation::Resource
 		def fetch(nuclide)
 			@nuclide = nuclide
 			begin
-				@data = load_data(@nuclide)
+				@data = load_data.select{|n| n[:nuclide] == nuclide}.first
 				# 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
@@ -19,9 +19,13 @@ module Radiation::Resource
 			self
 		end
 
+		def list
+			load_data.collect{|n| n[:nuclide]}
+		end
+
 		private
-		def load_data(nuclide)
-			JSON.parse( IO.read("#{PATH}/#{FILENAME}"), {:symbolize_names => true} ).select{|n| n[:nuclide] == nuclide}.first
+		def load_data
+			JSON.parse( IO.read("#{PATH}/#{FILENAME}"), {:symbolize_names => true} )
 		end
 
 	end

data/lib/radiation/resource/nucleideorg.rb

@@ -7,7 +7,8 @@ require 'tmpdir'
 
 module Radiation::Resource
 	class Nucleideorg < Base
-		
+		OpenURI::Cache.cache_path = "#{Dir.tmpdir}/radiation/"
+
 		def fetch(nuclide)
 			@nuclide = nuclide
 			@nuclide = "Ra-226D" if @nuclide == "Ra-226" #Ra-226 in equilibrium with daughters
@@ -16,7 +17,6 @@ module Radiation::Resource
 
 				@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|
@@ -40,5 +40,9 @@ module Radiation::Resource
 			self
 		end
 
+		def list
+			open("http://www.nucleide.org/DDEP_WG/DDEPdata.htm").read.scan(/Nuclides\/(.*).lara.txt/).flatten
+		end
+
 	end
-end
+end 

data/lib/radiation/version.rb

@@ -1,3 +1,3 @@
 module Radiation
-  VERSION = "0.1.3"
+  VERSION = "0.1.4"
 end

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