rtp-connect 1.2 → 1.3

data/CHANGELOG.rdoc

@@ -1,3 +1,12 @@
+= 1.3
+
+=== 12th October, 2012
+
+* Added support for the updated ExtendedField record values introduced in Mosaiq 2.4.
+* Simply log a warning instead of raising an exception when reading a record with more values than excpected.
+* Allow reading (incomplete) records that contain the required values but not all the optional ones (instead of raising an exception).
+
+
 = 1.2
 
 === 13th July, 2012

data/lib/rtp-connect/control_point.rb

@@ -58,7 +58,10 @@ module RTP
     def self.load(string, parent)
       # Get the quote-less values:
       values = string.to_s.values
-      raise ArgumentError, "Invalid argument 'string': Expected exactly 233 elements, got #{values.length}." unless values.length == 233
+      low_limit = 233
+      high_limit = 233
+      raise ArgumentError, "Invalid argument 'string': Expected at least #{low_limit} elements, got #{values.length}." if values.length < low_limit
+      RTP.logger.warn "The number of elements (#{values.length}) for this ControlPoint record exceeds the known number of data items for this record (#{high_limit}). This may indicate an invalid record or that the RTP format has recently been expanded with new items." if values.length > high_limit
       cp = self.new(parent)
       # Assign the values to attributes:
       cp.keyword = values[0]
@@ -95,7 +98,7 @@ module RTP
       cp.couch_ped_dir = values[31]
       cp.mlc_lp_a = [*values[32..131]]
       cp.mlc_lp_b = [*values[132..231]]
-      cp.crc = values[232]
+      cp.crc = values[-1]
       return cp
     end
 

data/lib/rtp-connect/dose_tracking.rb

@@ -31,7 +31,10 @@ module RTP
     def self.load(string, parent)
       # Get the quote-less values:
       values = string.to_s.values
-      raise ArgumentError, "Invalid argument 'string': Expected exactly 26 elements, got #{values.length}." unless values.length == 26
+      low_limit = 24
+      high_limit = 26
+      raise ArgumentError, "Invalid argument 'string': Expected at least #{low_limit} elements, got #{values.length}." if values.length < low_limit
+      RTP.logger.warn "The number of elements (#{values.length}) for this DoseTracking record exceeds the known number of data items for this record (#{high_limit}). This may indicate an invalid record or that the RTP format has recently been expanded with new items." if values.length > high_limit
       d = self.new(parent)
       # Assign the values to attributes:
       d.keyword = values[0]
@@ -41,7 +44,7 @@ module RTP
       d.region_coeffs = values.values_at(4, 6, 8, 10, 12, 14, 16, 18, 20, 22)
       d.actual_dose = values[23]
       d.actual_fractions = values[24]
-      d.crc = values[25]
+      d.crc = values[-1]
       return d
     end
 

data/lib/rtp-connect/extended_field.rb

@@ -14,6 +14,10 @@ module RTP
     attr_reader :original_plan_uid
     attr_reader :original_beam_number
     attr_reader :original_beam_name
+    attr_reader :is_fff
+    attr_reader :accessory_code
+    attr_reader :accessory_type
+    attr_reader :high_dose_authorization
 
     # Creates a new (treatment) ExtendedField by parsing a RTPConnect string line.
     #
@@ -25,15 +29,23 @@ module RTP
     def self.load(string, parent)
       # Get the quote-less values:
       values = string.to_s.values
-      raise ArgumentError, "Invalid argument 'string': Expected exactly 6 elements, got #{values.length}." unless values.length == 6
+      low_limit = 4
+      high_limit = 10
+      raise ArgumentError, "Invalid argument 'string': Expected at least #{low_limit} elements, got #{values.length}." if values.length < low_limit
+      RTP.logger.warn "The number of elements (#{values.length}) for this ExtendedField record exceeds the known number of data items for this record (#{high_limit}). This may indicate an invalid record or that the RTP format has recently been expanded with new items." if values.length > high_limit
       ef = self.new(parent)
-      # Assign the values to attributes:
+      # Mandatory attributes:
       ef.keyword = values[0]
       ef.field_id = values[1]
       ef.original_plan_uid = values[2]
+      # Optional attributes:
       ef.original_beam_number = values[3]
       ef.original_beam_name = values[4]
-      ef.crc = values[5]
+      ef.is_fff = values[5] if values[5]
+      ef.accessory_code = values[6]
+      ef.accessory_type = values[7]
+      ef.high_dose_authorization = values[8]
+      ef.crc = values[-1]
       return ef
     end
 
@@ -93,7 +105,11 @@ module RTP
         @field_id,
         @original_plan_uid,
         @original_beam_number,
-        @original_beam_name
+        @original_beam_name,
+        @is_fff,
+        @accessory_code,
+        @accessory_type,
+        @high_dose_authorization
       ]
     end
 
@@ -166,6 +182,38 @@ module RTP
       @original_beam_name = value && value.to_s
     end
 
+    # Sets the is_fff attribute.
+    #
+    # @param [nil, #to_s] value the new attribute value
+    #
+    def is_fff=(value)
+      @is_fff = value && value.to_s
+    end
+
+    # Sets the accessory_code attribute.
+    #
+    # @param [nil, #to_s] value the new attribute value
+    #
+    def accessory_code=(value)
+      @accessory_code = value && value.to_s
+    end
+
+    # Sets the accessory_type attribute.
+    #
+    # @param [nil, #to_s] value the new attribute value
+    #
+    def accessory_type=(value)
+      @accessory_type = value && value.to_s
+    end
+
+    # Sets the high_dose_authorization attribute.
+    #
+    # @param [nil, #to_s] value the new attribute value
+    #
+    def high_dose_authorization=(value)
+      @high_dose_authorization = value && value.to_s
+    end
+
 
     private
 

data/lib/rtp-connect/field.rb

@@ -72,7 +72,10 @@ module RTP
     def self.load(string, parent)
       # Get the quote-less values:
       values = string.to_s.values
-      raise ArgumentError, "Invalid argument 'string': Expected exactly 49 elements, got #{values.length}." unless values.length == 49
+      low_limit = 27
+      high_limit = 49
+      raise ArgumentError, "Invalid argument 'string': Expected at least #{low_limit} elements, got #{values.length}." if values.length < low_limit
+      RTP.logger.warn "The number of elements (#{values.length}) for this Field record exceeds the known number of data items for this record (#{high_limit}). This may indicate an invalid record or that the RTP format has recently been expanded with new items." if values.length > high_limit
       f = self.new(parent)
       # Assign the values to attributes:
       f.keyword = values[0]
@@ -123,7 +126,7 @@ module RTP
       f.portfilm_delta_open = values[45]
       f.portfilm_mu_treat = values[46]
       f.portfilm_coeff_treat = values[47]
-      f.crc = values[48]
+      f.crc = values[-1]
       return f
     end
 

data/lib/rtp-connect/plan.rb

@@ -69,7 +69,10 @@ module RTP
     def self.load(string)
       # Get the quote-less values:
       values = string.to_s.values
-      raise ArgumentError, "Invalid argument 'string': Expected exactly 28 elements, got #{values.length}." unless values.length == 28
+      low_limit = 10
+      high_limit = 28
+      raise ArgumentError, "Invalid argument 'string': Expected at least #{low_limit} elements, got #{values.length}." if values.length < low_limit
+      RTP.logger.warn "The number of elements (#{values.length}) for this Plan record exceeds the known number of data items for this record (#{high_limit}). This may indicate an invalid record or that the RTP format has recently been expanded with new items." if values.length > high_limit
       rtp = self.new
       # Assign the values to attributes:
       rtp.keyword = values[0]
@@ -99,7 +102,7 @@ module RTP
       rtp.rtp_version = values[24]
       rtp.rtp_if_protocol = values[25]
       rtp.rtp_if_version = values[26]
-      rtp.crc = values[27]
+      rtp.crc = values[-1]
       return rtp
     end
 
@@ -151,6 +154,7 @@ module RTP
               logger.error("This file is too small to contain valid RTP information: #{file}.")
             else
               str = File.open(file, "rb") { |f| f.read }
+              #str = File.open(file, "r:UTF-8") { |f| f.read }
             end
           end
         end

data/lib/rtp-connect/plan_to_dcm.rb

@@ -5,6 +5,12 @@ module RTP
     # Converts the Plan (and child) records to a
     # DICOM::DObject of modality RTPLAN.
     #
+    # @note Only static photon plans have been tested.
+    #   Electron beams or dynamic photon beams may give an invalid DICOM file.
+    #   Also note that, due to limitations in the RTP file format, some original
+    #   values can not be recreated, like e.g. Study UID or Series UID.
+    # @return [DICOM::DObject] the converted DICOM object
+    #
     def to_dcm
       #
       # FIXME: This method is rather big, with a few sections of somewhat similar, repeating code.

data/lib/rtp-connect/prescription.rb

@@ -36,7 +36,10 @@ module RTP
     def self.load(string, parent)
       # Get the quote-less values:
       values = string.to_s.values
-      raise ArgumentError, "Invalid argument 'string': Expected exactly 13 elements, got #{values.length}." unless values.length == 13
+      low_limit = 4
+      high_limit = 13
+      raise ArgumentError, "Invalid argument 'string': Expected at least #{low_limit} elements, got #{values.length}." if values.length < low_limit
+      RTP.logger.warn "The number of elements (#{values.length}) for this Prescription record exceeds the known number of data items for this record (#{high_limit}). This may indicate an invalid record or that the RTP format has recently been expanded with new items." if values.length > high_limit
       p = self.new(parent)
       # Assign the values to attributes:
       p.keyword = values[0]
@@ -51,7 +54,7 @@ module RTP
       p.pattern = values[9]
       p.rx_note = values[10]
       p.number_of_fields = values[11]
-      p.crc = values[12]
+      p.crc = values[-1]
       return p
     end
 

data/lib/rtp-connect/site_setup.rb

@@ -35,7 +35,10 @@ module RTP
     def self.load(string, parent)
       # Get the quote-less values:
       values = string.to_s.values
-      raise ArgumentError, "Invalid argument 'string': Expected exactly 16 elements, got #{values.length}." unless values.length == 16
+      low_limit = 5
+      high_limit = 16
+      raise ArgumentError, "Invalid argument 'string': Expected at least #{low_limit} elements, got #{values.length}." if values.length < low_limit
+      RTP.logger.warn "The number of elements (#{values.length}) for this SiteSetup record exceeds the known number of data items for this record (#{high_limit}). This may indicate an invalid record or that the RTP format has recently been expanded with new items." if values.length > high_limit
       s = self.new(parent)
       # Assign the values to attributes:
       s.keyword = values[0]
@@ -53,7 +56,7 @@ module RTP
       s.couch_longitudinal = values[12]
       s.couch_angle = values[13]
       s.couch_pedestal = values[14]
-      s.crc = values[15]
+      s.crc = values[-1]
       return s
     end
 

data/lib/rtp-connect/version.rb

@@ -1,6 +1,6 @@
 module RTP
 
   # The RTPConnect library version string.
-  VERSION = "1.2"
+  VERSION = "1.3"
 
 end

data/rakefile.rb

@@ -1,8 +1,10 @@
 # Available commands:
 # Testing the specification:
 #   bundle exec rake spec
-# Building a gem package from source:
+# Building a gem from source with rake:
 #   bundle exec rake package
+# Building a gem from source with rubygems:
+#   bundle exec gem build rtp-connect.gemspec
 # Create html documentation files:
 #   bundle exec rake yard
 

data/rtp-connect.gemspec

@@ -18,12 +18,11 @@ Gem::Specification.new do |s|
   s.rubyforge_project = 'rtp-connect'
 
   s.required_ruby_version = '>= 1.9.2'
-  s.required_rubygems_version = '>= 1.8.6'
 
-  s.add_development_dependency('bundler', '>= 1.0.0')
-  s.add_development_dependency('dicom', '>= 0.9.3')
-  s.add_development_dependency('rake', '>= 0.9.2.2')
-  s.add_development_dependency('rspec', '>= 2.9.0')
-  s.add_development_dependency('mocha', '>= 0.10.5')
-  s.add_development_dependency('yard', '>= 0.8.2')
+  s.add_development_dependency('bundler', '~> 1.2')
+  s.add_development_dependency('dicom', '0.9.3')
+  s.add_development_dependency('mocha', '~> 0.12')
+  s.add_development_dependency('rake', '~> 0.9.2')
+  s.add_development_dependency('rspec', '~> 2.11')
+  s.add_development_dependency('yard', '~> 0.8.2')
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rtp-connect
 version: !ruby/object:Gem::Version
-  version: '1.2'
+  version: '1.3'
   prerelease: 
 platform: ruby
 authors:
@@ -9,30 +9,30 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-13 00:00:00.000000000 Z
+date: 2012-10-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '1.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '1.2'
 - !ruby/object:Gem::Dependency
   name: dicom
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
         version: 0.9.3
   type: :development
@@ -40,63 +40,63 @@ dependencies:
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
         version: 0.9.3
 - !ruby/object:Gem::Dependency
-  name: rake
+  name: mocha
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.2.2
+        version: '0.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.2.2
+        version: '0.12'
 - !ruby/object:Gem::Dependency
-  name: rspec
+  name: rake
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 2.9.0
+        version: 0.9.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 2.9.0
+        version: 0.9.2
 - !ruby/object:Gem::Dependency
-  name: mocha
+  name: rspec
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.10.5
+        version: '2.11'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.10.5
+        version: '2.11'
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
         version: 0.8.2
   type: :development
@@ -104,7 +104,7 @@ dependencies:
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
         version: 0.8.2
 description: RTPConnect is a file format used in radiotherapy for export & import
@@ -133,7 +133,6 @@ files:
 - CHANGELOG.rdoc
 - COPYING
 - Gemfile
-- Gemfile.lock
 - rakefile.rb
 - README.rdoc
 - rtp-connect.gemspec
@@ -155,7 +154,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
-      version: 1.8.6
+      version: '0'
 requirements: []
 rubyforge_project: rtp-connect
 rubygems_version: 1.8.24
@@ -163,3 +162,4 @@ signing_key:
 specification_version: 3
 summary: Library for handling RTPConnect files.
 test_files: []
+has_rdoc: 

data/Gemfile.lock

@@ -1,35 +0,0 @@
-PATH
-  remote: .
-  specs:
-    rtp-connect (1.1)
-
-GEM
-  remote: http://www.rubygems.org/
-  specs:
-    dicom (0.9.3)
-    diff-lcs (1.1.3)
-    metaclass (0.0.1)
-    mocha (0.12.0)
-      metaclass (~> 0.0.1)
-    rake (0.9.2.2)
-    rspec (2.11.0)
-      rspec-core (~> 2.11.0)
-      rspec-expectations (~> 2.11.0)
-      rspec-mocks (~> 2.11.0)
-    rspec-core (2.11.0)
-    rspec-expectations (2.11.1)
-      diff-lcs (~> 1.1.3)
-    rspec-mocks (2.11.1)
-    yard (0.8.2.1)
-
-PLATFORMS
-  x86-mingw32
-
-DEPENDENCIES
-  bundler (>= 1.0.0)
-  dicom (>= 0.9.3)
-  mocha (>= 0.10.5)
-  rake (>= 0.9.2.2)
-  rspec (>= 2.9.0)
-  rtp-connect!
-  yard (>= 0.8.2)