radiation 0.0.1 → 0.0.2

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data/.travis.yml

@@ -1,2 +1,9 @@
+language: ruby
 rvm:
-  - 1.9
+  #- "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

data/CHANGELOG.md

@@ -1,3 +1,7 @@
+## v0.0.2
+
+* Added spectrum class with energy calibration options
+
 ## v0.0.1
 
 * initial release

data/Gemfile

@@ -1,4 +1,5 @@
 source 'https://rubygems.org'
 
+gem "linefit", git: "https://github.com/janmayer/linefit.git"
 # Specify your gem's dependencies in radiation.gemspec
 gemspec

data/README.md

@@ -1,17 +1,21 @@
-# Radiation
+# Radiation [![Build Status](https://travis-ci.org/janmayer/radiation.png?branch=master)](https://travis-ci.org/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)
+by [Laboratoire National Henri Becquerel](http://www.nucleide.org/DDEP_WG/DDEPdata.htm).
 
 ## Example Usage
 
     Radiation::Source.new(nuclide: "Ra-226").energies.collect{|e| e.value}
 
+See also files in `./samples/`.
+
 
 ## Planned features
 
-Energy and efficiency calibration for given peaks or spectra.
+* Efficiency calibration for given peaks or spectra
+* CLI
+* Better access to resources
 
 
 ## Installation

data/lib/radiation/source/resource/nucleideorg.rb

@@ -11,7 +11,7 @@ class Radiation::Source
 
 		private
 		def datasource_nukleideorg(nuclide)
-			nuclide = "Ra-226D" if nuclide == "Ra-226" #Ra-226 in equlibrium with daughters
+			nuclide = "Ra-226D" if nuclide == "Ra-226" #Ra-226 in equilibrium with daughters
 			begin
 				@data[:nuclide] = nuclide.to_s
 				OpenURI::Cache.cache_path = "#{Dir.tmpdir}/radiation/"

data/lib/radiation/source.rb

@@ -1,5 +1,7 @@
 # encoding: utf-8
 require 'radiation/source/resource'
+require 'combinatorics'
+
 
 class Radiation::Source
 	attr_reader :data
@@ -29,4 +31,5 @@ class Radiation::Source
 	def is_nuclide?(nuclide)
 		!!(nuclide =~ /\A[a-zA-Z]{1,2}-\d{1,3}\z/)
 	end
+
 end

data/lib/radiation/spectrum.rb

@@ -0,0 +1,73 @@
+# encoding: utf-8
+require "linefit"
+require "plusminus"
+
+class Radiation::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"
+		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
+		#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]).approx_equal?(energy, rounding)
+			end
+		end
+		return self
+	end
+
+	def guess_calibration(energies=@source.energies, rounding=3)
+		# 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
+
+end
+
+
+
+class Float
+	def approx_equal?(other,threshold=0.5)
+		if (self-other).abs < threshold    # "<" not exact either
+			return true
+		else
+			return false
+		end
+	end
+end

data/lib/radiation/version.rb

@@ -1,3 +1,3 @@
 module Radiation
-  VERSION = "0.0.1"
+  VERSION = "0.0.2"
 end

data/lib/radiation.rb

@@ -1,5 +1,6 @@
 require "radiation/version"
 require "radiation/source"
+require "radiation/spectrum"
 
 module Radiation
   # Your code goes here...

data/radiation.gemspec

@@ -10,7 +10,7 @@ Gem::Specification.new do |spec|
   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      = ""
+  spec.homepage      = "https://github.com/janmayer/radiation"
   spec.license       = "MIT"
 
   spec.files         = `git ls-files`.split($/)
@@ -20,6 +20,9 @@ Gem::Specification.new do |spec|
 
   spec.add_dependency "plusminus"
   spec.add_dependency "open-uri-cached"
+  spec.add_dependency "combinatorics"
+  spec.add_dependency "linefit", "~> 0.3.1"
+
   
   spec.add_development_dependency "bundler", "~> 1.3"
   spec.add_development_dependency "rake"

data/samples/calibrate_a_spectrum.rb

@@ -0,0 +1,13 @@
+# encoding: utf-8
+require 'radiation'
+
+channels = [512.9592, 668.6611, 715.773, 759.483, 817.0175, 975.0220, 1075.977, 1124.82, 1261.666, 1281.123, 1333.194, 1351.650, 1417.69, 1481.380, 1610.736, 1691.9637, 1848.412, 1953.350, 2000.193, 2135.6125, 2184.578, 2241.203, 2332.889, 2595.4352, 2678.202, 3112.7327, 3209.900, 3440.820, 3560.182, 3829.513, 3850.791, 3895.915, 3913.953, 4196.125, 4621.221, 4811.183, 4908.2438, 5139.402, 5895.042, 6133.533, 6811.046]
+peaks    = channels.collect{|a| {channel: a} }
+source   = Radiation::Source.new(nuclide: "Ra-226")
+spectrum = Radiation::Spectrum.new(peaks: peaks, source: source )
+
+puts spectrum.calibrate.calibration.to_s
+
+puts "\n"
+
+puts spectrum.peaks.collect{|p| [ p[:channel], p[:energy] ].join("\t") }

data/spec/radiation_spec.rb

@@ -3,54 +3,64 @@ require 'spec_helper'
 
 describe Radiation do
 	describe Radiation::Source do
+		name = "Ra-226"
+		source = Radiation::Source.new(nuclide: name)
 
-		describe "Features" do
-			name = "Ra-226"
-			source = Radiation::Source.new(nuclide: name)
-	
-	
-			it "provides information about itself" do
-				source.nuclide.should eq(name)
-				#source.reference.should be_a_kind_of(String)
-				#source.halflive.should be_a_kind_of(Plusminus::PlusminusFloat)
-			end
-	
-			it "returns an array with gamma-ray energies for a given source" do
-				source.energies.should be_a_kind_of(Array)
-				source.energies.length.should be > 0
-				source.energies[0].should be_a_kind_of(Plusminus::PlusminusFloat)
-			end
-	
-			it "returns intensities for energies" do
-				source.intensities.should be_a_kind_of(Array)
-				source.intensities.first.should be_a_kind_of(Hash)
-				source.intensities.length.should be > 0
-			end
-
-			it "can access different data resources" do
-				expect { Radiation::Source.new(nuclide: "Ra-226") }.to_not raise_error
-				expect { Radiation::Source.new(nuclide: "Ra-226", resource: "nucleide.org") }.to_not raise_error
-			end
-	
-		end
-
-		describe "Errors" do
-			it "cheks for valid nuclei" do
-				Radiation::Source.new.is_nuclide?("Nukular9000").should be false
-				Radiation::Source.new.is_nuclide?("226Ra-226").should be false
-				Radiation::Source.new.is_nuclide?("Ra-226").should be true
-				Radiation::Source.new.is_nuclide?("C-14").should be true
-				Radiation::Source.new.is_nuclide?("H-1").should be true
-				expect { Radiation::Source.new(nuclide: "Nukular9000") }.to raise_error
-				expect { Radiation::Source.new(nuclide: "Ra-226") }.to_not raise_error
-			end
-
-			it "gives an error if no record is found" do
-				expect { Radiation::Source.new(nuclide: "Ra-15") }.to raise_error
-				expect { Radiation::Source.new(nuclide: "Ra-15", resource: "nucleide.org") }.to raise_error
-			end
+		it "provides information about itself" do
+			source.nuclide.should eq(name)
+			#source.reference.should be_a_kind_of(String)
+			#source.halflive.should be_a_kind_of(Plusminus::PlusminusFloat)
+		end
+
+		it "returns an array with gamma-ray energies for a given source" do
+			source.energies.should be_a_kind_of(Array)
+			source.energies.length.should be > 0
+			source.energies[0].should be_a_kind_of(Plusminus::PlusminusFloat)
+		end
+
+		it "returns intensities for energies" do
+			source.intensities.should be_a_kind_of(Array)
+			source.intensities.first.should be_a_kind_of(Hash)
+			source.intensities.length.should be > 0
+		end
+		it "can access different data resources" do
+			expect { Radiation::Source.new(nuclide: "Ra-226") }.to_not raise_error
+			expect { Radiation::Source.new(nuclide: "Ra-226", resource: "nucleide.org") }.to_not raise_error
+		end
+
+		it "cheks for valid nuclei" do
+			Radiation::Source.new.is_nuclide?("Nukular9000").should be false
+			Radiation::Source.new.is_nuclide?("226Ra-226").should be false
+			Radiation::Source.new.is_nuclide?("Ra-226").should be true
+			Radiation::Source.new.is_nuclide?("C-14").should be true
+			Radiation::Source.new.is_nuclide?("H-1").should be true
+			expect { Radiation::Source.new(nuclide: "Nukular9000") }.to raise_error
+			expect { Radiation::Source.new(nuclide: "Ra-226") }.to_not raise_error
+		end
+		it "gives an error if no record is found" do
+			expect { Radiation::Source.new(nuclide: "Ra-15") }.to raise_error
+			expect { Radiation::Source.new(nuclide: "Ra-15", resource: "nucleide.org") }.to raise_error
+		end
+	end
+
+	describe Radiation::Spectrum do
+		channels = [512.9592, 668.6611, 715.773, 759.483, 817.0175, 975.0220, 1075.977, 1124.82, 1261.666, 1281.123, 1333.194, 1351.650, 1417.69, 1481.380, 1610.736, 1691.9637, 1848.412, 1953.350, 2000.193, 2135.6125, 2184.578, 2241.203, 2332.889, 2595.4352, 2678.202, 3112.7327, 3209.900, 3440.820, 3560.182, 3829.513, 3850.791, 3895.915, 3913.953, 4196.125, 4621.221, 4811.183, 4908.2438, 5139.402, 5895.042, 6133.533, 6811.046]
+		peaks = channels.collect{|a| {channel: a} }
+		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]
+		end
+
+		it "can match channels to given energies by using a calibration" do
+			Radiation::Spectrum.new(peaks: peaks, source: source ).guess_calibration.match_channels.peaks[0][:energy].should be == 186.2
+		end
 
+		it "can calibrate a spectrum" do
+			expect { Radiation::Spectrum.new(peaks: peaks, source: source ).calibrate }.to_not raise_error
+			Radiation::Spectrum.new(peaks: peaks, source: source ).calibrate.calibration[0].should be_a_kind_of(Plusminus::PlusminusFloat)
 		end
 
 	end
+
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: radiation
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - Jan Mayer
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-03 00:00:00.000000000 Z
+date: 2013-06-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: plusminus
@@ -38,6 +38,34 @@ dependencies:
     - - ! '>='
       - !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: 0.3.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.3.1
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -104,12 +132,14 @@ files:
 - lib/radiation/source/resource.rb
 - lib/radiation/source/resource/internal.rb
 - lib/radiation/source/resource/nucleideorg.rb
+- lib/radiation/spectrum.rb
 - lib/radiation/version.rb
 - radiation.gemspec
+- samples/calibrate_a_spectrum.rb
 - samples/get_some_data.rb
 - spec/radiation_spec.rb
 - spec/spec_helper.rb
-homepage: ''
+homepage: https://github.com/janmayer/radiation
 licenses:
 - MIT
 metadata: {}