radiation 0.1.4 → 0.1.5

checksums.yaml

@@ -1,15 +1,7 @@
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data/.coveralls.yml

@@ -0,0 +1 @@
+service_name: travis-ci

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

@@ -4,4 +4,4 @@ rvm:
   - "1.9.3"
   - "2.0.0"
   - jruby-19mode # JRuby in 1.9 mode
-  - rbx-19mode
+#  - rbx-19mode

data/CHANGELOG.md

@@ -1,42 +1,42 @@
-## 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
+## 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

@@ -1,6 +1,6 @@
-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
+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

@@ -1,52 +1,53 @@
-# 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
-
+# 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)
+[![Coverage Status](https://coveralls.io/repos/janmayer/radiation/badge.png)](https://coveralls.io/r/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/spectrum.rb

@@ -6,21 +6,22 @@ require "xmlsimple"
 
 module Radiation
 	class Spectrum
-		attr_accessor :peaks, :source, :calibration, :livetime, :activity
-	
+		attr_accessor :peaks, :source, :calibration, :livetime, :activity, :count_correction
+
 		def initialize(options={})
 			@peaks		= options.key?(:peaks) ? options[:peaks] : []
 			@source		= options.key?(:source) ? options[:source] : nil
 			@calibration= options.key?(:calibration) ? options[:calibration] : [0, 1]
 			@livetime	= options.key?(:livetime) ? options[:livetime] : 1
 			@activity	= options.key?(:activity) ? options[:activity] : 1
+			@count_correction = options.key?(:count_correction) ? options[:count_correction] : 1
 		end
-	
+
 		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 preliminary calibration to improve"
@@ -33,7 +34,7 @@ module Radiation
 			@calibration = apply_linefit(@peaks)
 			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
@@ -42,20 +43,20 @@ module Radiation
 			@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) } 
+		 		:counts => p["vol"].first["value"].first.to_f.pm(p["vol"].first["error"].first.to_f) }
 			end
 			return self
 		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)}
@@ -76,7 +77,7 @@ module Radiation
 
 
 		def channel_efficiency(peak)
-			peak[:counts]/(peak[:intensity]*@livetime*@activity)
+			peak[:counts]*@count_correction/(peak[:intensity]*@livetime*@activity)
 		end
 
 	private
@@ -94,7 +95,7 @@ module Radiation
 			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))]
@@ -102,8 +103,8 @@ module Radiation
 
 	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 = "0.1.4"
+  VERSION = "0.1.5"
 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

data/spec/spec_helper.rb

@@ -1,5 +1,5 @@
+require 'coveralls'
+Coveralls.wear!
+
 require 'radiation'
 require 'plusminus'
-
-require 'coveralls'
-Coveralls.wear!

metadata

@@ -1,97 +1,97 @@
 --- !ruby/object:Gem::Specification
 name: radiation
 version: !ruby/object:Gem::Version
-  version: 0.1.4
+  version: 0.1.5
 platform: ruby
 authors:
 - Jan Mayer
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-03 00:00:00.000000000 Z
+date: 2013-11-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: plusminus
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: open-uri-cached
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: combinatorics
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: linefit
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: xml-simple
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: thor
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
@@ -112,28 +112,28 @@ dependencies:
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 description: Decay Radiation
@@ -144,6 +144,7 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
+- .coveralls.yml
 - .gitignore
 - .rspec
 - .travis.yml
@@ -184,17 +185,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.6
+rubygems_version: 2.0.3
 signing_key: 
 specification_version: 4
 summary: This gem provides easy access to energies and intensities from the decay