radiation 0.0.3 → 0.0.4

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data/README.md

@@ -9,15 +9,20 @@ by [Laboratoire National Henri Becquerel](http://www.nucleide.org/DDEP_WG/DDEPda
 
 ## 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
-* CLI
 * Better access to resources
 
 

data/bin/radiation

@@ -0,0 +1,11 @@
+#!/usr/bin/env ruby
+
+# Trap interrupts to quit cleanly. See
+# https://twitter.com/mitchellh/status/283014103189053442
+Signal.trap("INT") { exit 1 }
+
+require 'radiation/cli'
+# Set debug flag so we can rescue Thor::error's
+# and set the correct exit code.
+ENV["THOR_DEBUG"] = "1"
+Radiation::CLI.start(ARGV)

data/lib/radiation/cli.rb

@@ -0,0 +1,38 @@
+# encoding: utf-8
+require "radiation"
+require "thor"
+
+module Radiation
+class CLI < Thor
+
+	desc "version", "Prints version information"
+	def version
+		puts "radiation version #{Radiation::VERSION}"
+	end
+	map %w(-v --version) => :version
+
+	option :resource
+	desc "source NUCLIDE", "decay radiation data"
+	def source(nuclide)
+		resource = options[:resource] ? options[:resource] : "internal"
+		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") }
+	end
+
+	option :resource
+	desc "calibrate NUCLIDE SPECTRUM.xml", "calibrate a spectrum"
+	long_desc <<-LONGDESC
+	Calibrates a decay radiation spectrum that has been analysed with HDTV. Stored peak fits in HDTV can be stored with hdtv>fit write filname.xml
+	Example: \n
+	$>radiation calibrate Ra-226 Ge00.xml
+	With --resource=nucleide.org more decay radiation sources are available.
+	LONGDESC
+	def calibrate(nuclide, file)
+		resource = options[:resource] ? options[:resource] : "internal"
+		source   = Radiation::Source.new(nuclide: nuclide, resource: resource)
+		spectrum = Radiation::Spectrum.new(source: source ).parse_hdtv(file)
+		spectrum.calibrate.calibration.each{|c| puts c}
+	end
+
+end
+end

data/lib/radiation/source/resource.rb

@@ -2,7 +2,8 @@
 require 'radiation/source/resource/internal'
 require 'radiation/source/resource/nucleideorg'
 
-class Radiation::Source
+module Radiation
+class Source
 	class Resource
 		
 		def initialize(resource)
@@ -21,3 +22,4 @@ class Radiation::Source
 
 	end
 end
+end

data/lib/radiation/source.rb

@@ -3,7 +3,8 @@ require 'radiation/source/resource'
 require 'combinatorics'
 
 
-class Radiation::Source
+module Radiation
+class Source
 	attr_reader :data
 
 	def initialize(options={})
@@ -32,4 +33,5 @@ class Radiation::Source
 		!!(nuclide =~ /\A[a-zA-Z]{1,2}-\d{1,3}\z/)
 	end
 
+end
 end

data/lib/radiation/spectrum.rb

@@ -3,7 +3,8 @@ require "linefit"
 require "plusminus"
 require "xmlsimple"
 
-class Radiation::Spectrum
+module Radiation
+class Spectrum
 	attr_accessor :peaks, :source, :calibration
 
 	def initialize(options={})
@@ -46,7 +47,7 @@ class Radiation::Spectrum
 		return self
 	end
 
-	def guess_calibration(energies=@source.energies, rounding=3)
+	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 $a \approx 0$
@@ -69,7 +70,7 @@ class Radiation::Spectrum
 	end
 
 end
-
+end
 
 
 class Float

data/lib/radiation/version.rb

@@ -1,3 +1,3 @@
 module Radiation
-  VERSION = "0.0.3"
+  VERSION = "0.0.4"
 end

data/radiation.gemspec

@@ -23,6 +23,7 @@ Gem::Specification.new do |spec|
   spec.add_dependency "combinatorics"
   spec.add_dependency "linefit"
   spec.add_dependency "xml-simple"
+  spec.add_dependency "thor"
 
   
   spec.add_development_dependency "bundler", "~> 1.3"

data/spec/radiation_spec.rb

@@ -49,7 +49,7 @@ describe Radiation do
 		source = Radiation::Source.new(nuclide: "Ra-226")
 
 		it "can guess a inital energy calibration based on adc values" do
-			Radiation::Spectrum.new(peaks: peaks, source: source).guess_calibration.calibration.should be == [0, 0.36]
+			Radiation::Spectrum.new(peaks: peaks, source: source).guess_calibration.calibration.should be == [0, 0.3597]
 		end
 
 		it "can match channels to given energies by using a calibration" do
@@ -63,7 +63,7 @@ describe Radiation do
 
 		it "can read peaks from hdtv xml data" do
 			expect { Radiation::Spectrum.new(source: source ).parse_hdtv("./samples/B0-Ra226.xml") }.to_not raise_error
-			Radiation::Spectrum.new(source: source ).parse_hdtv("./samples/B0-Ra226.xml").calibrate.calibration.should be == [0.311879195357135.pm(0.002317818766849388), 0.10022085942781585.pm(4.767016096075808e-07)]
+			Radiation::Spectrum.new(source: source ).parse_hdtv("./samples/B0-Ra226.xml").calibrate.calibration[1].round(3).should be == 0.100
 		end
 
 	end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: radiation
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors:
 - Jan Mayer
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-18 00:00:00.000000000 Z
+date: 2013-06-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: plusminus
@@ -80,6 +80,20 @@ dependencies:
     - - ! '>='
       - !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
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -125,7 +139,8 @@ dependencies:
 description: Decay Radiation
 email:
 - jan.mayer@ikp.uni-koeln.de
-executables: []
+executables:
+- radiation
 extensions: []
 extra_rdoc_files: []
 files:
@@ -137,11 +152,13 @@ files:
 - LICENSE.txt
 - README.md
 - Rakefile
+- bin/radiation
 - data/Eu-152.bib
 - data/Eu-152.csv
 - data/Ra-226.bib
 - data/Ra-226.csv
 - lib/radiation.rb
+- lib/radiation/cli.rb
 - lib/radiation/source.rb
 - lib/radiation/source/resource.rb
 - lib/radiation/source/resource/internal.rb