dicom 0.9.5 → 0.9.6

data/lib/dicom/sequence.rb

@@ -4,8 +4,8 @@ module DICOM
   #
   class Sequence < Parent
 
-    # Include the Elemental mix-in module:
     include Elemental
+    include ElementalParent
 
     # Creates a Sequence instance.
     #
@@ -74,18 +74,6 @@ module DICOM
       state.hash
     end
 
-    # Loads data from an encoded DICOM string and creates
-    # items and elements which are linked to this instance.
-    #
-    # @param [String] bin an encoded binary string containing DICOM information
-    # @param [String] syntax the transfer syntax to use when decoding the DICOM string
-    #
-    def parse(bin, syntax)
-      raise ArgumentError, "Invalid argument 'bin'. Expected String, got #{bin.class}." unless bin.is_a?(String)
-      raise ArgumentError, "Invalid argument 'syntax'. Expected String, got #{syntax.class}." unless syntax.is_a?(String)
-      read(bin, signature=false, :syntax => syntax)
-    end
-
     # Returns self.
     #
     # @return [Sequence] self

data/lib/dicom/stream.rb

@@ -41,7 +41,7 @@ module DICOM
     # @param [String] binary a binary string
     #
     def add_first(binary)
-      @string = binary + @string if binary
+      @string = "#{binary}#{@string}" if binary
     end
 
     # Appends a pre-encoded string to the instance string (inserts at the end).
@@ -49,7 +49,7 @@ module DICOM
     # @param [String] binary a binary string
     #
     def add_last(binary)
-      @string = @string + binary if binary
+      @string = "#{@string}#{binary}" if binary
     end
 
     # Decodes a section of the instance string.
@@ -63,12 +63,9 @@ module DICOM
     def decode(length, type)
       raise ArgumentError, "Invalid argument length. Expected Fixnum, got #{length.class}" unless length.is_a?(Fixnum)
       raise ArgumentError, "Invalid argument type. Expected string, got #{type.class}" unless type.is_a?(String)
-      # Check if values are valid:
-      if (@index + length) > @string.length
-        # The index number is bigger then the length of the binary string.
-        # We have reached the end and will return nil.
-        value = nil
-      else
+      value = nil
+      if (@index + length) <= @string.length
+        # There are sufficient bytes remaining to extract the value:
         if type == 'AT'
           # We need to guard ourselves against the case where a string contains an invalid 'AT' value:
           if length == 4
@@ -76,7 +73,6 @@ module DICOM
           else
             # Invalid. Just return nil.
             skip(length)
-            value = nil
           end
         else
           # Decode the binary string and return value:
@@ -92,7 +88,7 @@ module DICOM
           skip(length)
         end
       end
-      return value
+      value
     end
 
     # Decodes the entire instance string (typically used for decoding image data).
@@ -114,23 +110,19 @@ module DICOM
     #
     def decode_tag
       length = 4
-      # Check if values are valid:
-      if (@index + length) > @string.length
-        # The index number is bigger then the length of the binary string.
-        # We have reached the end and will return nil.
-        tag = nil
-      else
-        # Decode and process:
-        string = @string.slice(@index, length).unpack(@hex)[0].upcase
+      tag = nil
+      if (@index + length) <= @string.length
+        # There are sufficient bytes remaining to extract a full tag:
+        str = @string.slice(@index, length).unpack(@hex)[0].upcase
         if @equal_endian
-          tag = string[2..3] + string[0..1] + ',' + string[6..7] + string[4..5]
+          tag = "#{str[2..3]}#{str[0..1]},#{str[6..7]}#{str[4..5]}"
         else
-          tag = string[0..3] + ',' + string[4..7]
+          tag = "#{str[0..3]},#{str[4..7]}"
         end
         # Update our position in the string:
         skip(length)
       end
-      return tag
+      tag
     end
 
     # Encodes a given value to a binary string.
@@ -152,8 +144,7 @@ module DICOM
     #
     def encode_first(value, type)
       value = [value] unless value.is_a?(Array)
-      bin = value.pack(vr_to_str(type))
-      @string = bin + @string
+      @string = "#{value.pack(vr_to_str(type))}#{@string}"
     end
 
     # Encodes a value to a binary string and appends it to the instance string.
@@ -163,8 +154,7 @@ module DICOM
     #
     def encode_last(value, type)
       value = [value] unless value.is_a?(Array)
-      bin = value.pack(vr_to_str(type))
-      @string = @string + bin
+      @string = "#{@string}#{value.pack(vr_to_str(type))}"
     end
 
     # Appends a string with trailling spaces to achieve a target length, and encodes it to a binary string.
@@ -176,7 +166,7 @@ module DICOM
     def encode_string_with_trailing_spaces(string, target_length)
       length = string.length
       if length < target_length
-        return [string].pack(@str)+['20'*(target_length-length)].pack(@hex)
+        return "#{[string].pack(@str)}#{['20'*(target_length-length)].pack(@hex)}"
       elsif length == target_length
         return [string].pack(@str)
       else
@@ -190,12 +180,9 @@ module DICOM
     # @return [String] an encoded binary string
     #
     def encode_tag(tag)
-      if @equal_endian
-        clean_tag = tag[2..3] + tag[0..1] + tag[7..8] + tag[5..6]
-      else
-        clean_tag = tag[0..3] + tag[5..8]
-      end
-      return [clean_tag].pack(@hex)
+      [
+        @equal_endian ? "#{tag[2..3]}#{tag[0..1]}#{tag[7..8]}#{tag[5..6]}" : "#{tag[0..3]}#{tag[5..8]}"
+      ].pack(@hex)
     end
 
     # Encodes a value, and if the the resulting binary string has an
@@ -216,7 +203,7 @@ module DICOM
         # Encode:
         bin = value.pack(type)
         # Add an empty byte if the resulting binary has an odd length:
-        bin = bin + @pad_byte[vr] if bin.length.odd?
+        bin = "#{bin}#{@pad_byte[vr]}" if bin.length.odd?
       end
       return bin
     end
@@ -372,36 +359,36 @@ module DICOM
     #
     def set_format_hash
       @format = {
-        "BY" => @by, # Byte/Character (1-byte integers)
-        "US" => @us, # Unsigned short (2 bytes)
-        "SS" => @ss, # Signed short (2 bytes)
-        "UL" => @ul, # Unsigned long (4 bytes)
-        "SL" => @sl, # Signed long (4 bytes)
-        "FL" => @fs, # Floating point single (4 bytes)
-        "FD" => @fd, # Floating point double (8 bytes)
-        "OB" => @by, # Other byte string (1-byte integers)
-        "OF" => @fs, # Other float string (4-byte floating point numbers)
-        "OW" => @us, # Other word string (2-byte integers)
-        "AT" => @hex, # Tag reference (4 bytes) NB: For tags the spesialized encode_tag/decode_tag methods are used instead of this lookup table.
-        "UN" => @hex, # Unknown information (header element is not recognized from local database)
-        "HEX" => @hex, # HEX
+        'BY' => @by, # Byte/Character (1-byte integers)
+        'US' => @us, # Unsigned short (2 bytes)
+        'SS' => @ss, # Signed short (2 bytes)
+        'UL' => @ul, # Unsigned long (4 bytes)
+        'SL' => @sl, # Signed long (4 bytes)
+        'FL' => @fs, # Floating point single (4 bytes)
+        'FD' => @fd, # Floating point double (8 bytes)
+        'OB' => @by, # Other byte string (1-byte integers)
+        'OF' => @fs, # Other float string (4-byte floating point numbers)
+        'OW' => @us, # Other word string (2-byte integers)
+        'AT' => @hex, # Tag reference (4 bytes) NB: For tags the spesialized encode_tag/decode_tag methods are used instead of this lookup table.
+        'UN' => @hex, # Unknown information (header element is not recognized from local database)
+        'HEX' => @hex, # HEX
         # We have a number of VRs that are decoded as string:
-        "AE" => @str,
-        "AS" => @str,
-        "CS" => @str,
-        "DA" => @str,
-        "DS" => @str,
-        "DT" => @str,
-        "IS" => @str,
-        "LO" => @str,
-        "LT" => @str,
-        "PN" => @str,
-        "SH" => @str,
-        "ST" => @str,
-        "TM" => @str,
-        "UI" => @str,
-        "UT" => @str,
-        "STR" => @str
+        'AE' => @str,
+        'AS' => @str,
+        'CS' => @str,
+        'DA' => @str,
+        'DS' => @str,
+        'DT' => @str,
+        'IS' => @str,
+        'LO' => @str,
+        'LT' => @str,
+        'PN' => @str,
+        'SH' => @str,
+        'ST' => @str,
+        'TM' => @str,
+        'UI' => @str,
+        'UT' => @str,
+        'STR' => @str
       }
     end
 
@@ -411,35 +398,35 @@ module DICOM
     def set_pad_byte
       @pad_byte = {
         # Space character:
-        "AE" => "\x20",
-        "AS" => "\x20",
-        "CS" => "\x20",
-        "DA" => "\x20",
-        "DS" => "\x20",
-        "DT" => "\x20",
-        "IS" => "\x20",
-        "LO" => "\x20",
-        "LT" => "\x20",
-        "PN" => "\x20",
-        "SH" => "\x20",
-        "ST" => "\x20",
-        "TM" => "\x20",
-        "UT" => "\x20",
+        'AE' => "\x20",
+        'AS' => "\x20",
+        'CS' => "\x20",
+        'DA' => "\x20",
+        'DS' => "\x20",
+        'DT' => "\x20",
+        'IS' => "\x20",
+        'LO' => "\x20",
+        'LT' => "\x20",
+        'PN' => "\x20",
+        'SH' => "\x20",
+        'ST' => "\x20",
+        'TM' => "\x20",
+        'UT' => "\x20",
         # Zero byte:
-        "AT" => "\x00",
-        "BY" => "\x00",
-        "FL" => "\x00",
-        "FD" => "\x00",
-        "OB" => "\x00",
-        "OF" => "\x00",
-        "OW" => "\x00",
-        "SL" => "\x00",
-        "SQ" => "\x00",
-        "SS" => "\x00",
-        "UI" => "\x00",
-        "UL" => "\x00",
-        "UN" => "\x00",
-        "US" => "\x00"
+        'AT' => "\x00",
+        'BY' => "\x00",
+        'FL' => "\x00",
+        'FD' => "\x00",
+        'OB' => "\x00",
+        'OF' => "\x00",
+        'OW' => "\x00",
+        'SL' => "\x00",
+        'SQ' => "\x00",
+        'SS' => "\x00",
+        'UI' => "\x00",
+        'UL' => "\x00",
+        'UN' => "\x00",
+        'US' => "\x00"
       }
     end
 
@@ -447,34 +434,27 @@ module DICOM
     # Some of these depends on the endianness of the system and the encoded string.
     #
     def set_string_formats
-      # FIXME:
-      # Surprisingly the Ruby pack/unpack methods lack a format for signed short
-      # and signed long in the network byte order. A hack has been implemented to to ensure
-      # correct behaviour in this case, but it is slower (~4 times slower than a normal pack/unpack).
-      # Update: This seems to have been fixed in Ruby 1.9.3, so when we are able to bump the Ruby
-      # dependency eventually, this situation can finally be cleaned up.
-      #
       if @equal_endian
-        # Native byte order:
-        @us = "S*" # Unsigned short (2 bytes)
-        @ss = "s*" # Signed short (2 bytes)
-        @ul = "I*" # Unsigned long (4 bytes)
-        @sl = "l*" # Signed long (4 bytes)
-        @fs = "e*" # Floating point single (4 bytes)
-        @fd = "E*" # Floating point double ( 8 bytes)
+        # Little endian byte order:
+        @us = 'S<*' # Unsigned short (2 bytes)
+        @ss = 's<*' # Signed short (2 bytes)
+        @ul = 'L<*' # Unsigned long (4 bytes)
+        @sl = 'l<*' # Signed long (4 bytes)
+        @fs = 'e*' # Floating point single (4 bytes)
+        @fd = 'E*' # Floating point double ( 8 bytes)
       else
-        # Network byte order:
-        @us = "n*"
-        @ss = CUSTOM_SS # Custom string for our redefined pack/unpack.
-        @ul = "N*"
-        @sl = CUSTOM_SL # Custom string for our redefined pack/unpack.
-        @fs = "g*"
-        @fd = "G*"
+        # Network (big endian) byte order:
+        @us = 'S>*'
+        @ss = 's>*'
+        @ul = 'L>*'
+        @sl = 'l>'
+        @fs = 'g*'
+        @fd = 'G*'
       end
       # Format strings that are not dependent on endianness:
-      @by = "C*" # Unsigned char (1 byte)
-      @str = "a*"
-      @hex = "H*" # (this may be dependent on endianness(?))
+      @by = 'C*' # Unsigned char (1 byte)
+      @str = 'a*'
+      @hex = 'H*' # (this may be dependent on endianness(?))
     end
 
   end

data/rakefile.rb

@@ -19,7 +19,7 @@ Gem::PackageTask.new(gem_spec) do |pkg|
   pkg.need_tar = true
 end
 
-# RSpec 2:
+# RSpec:
 RSpec::Core::RakeTask.new do |t|
   t.rspec_opts = ["-c", "-f progress", "-r ./spec/spec_helper.rb"]
   t.pattern = 'spec/**/*_spec.rb'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: dicom
 version: !ruby/object:Gem::Version
-  version: 0.9.5
+  version: 0.9.6
 platform: ruby
 authors:
 - Christoffer Lervag
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-03-26 00:00:00.000000000 Z
+date: 2014-06-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -16,47 +16,50 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '1.6'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '1.6'
 - !ruby/object:Gem::Dependency
-  name: mocha
+  name: mini_magick
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.13'
+        version: '3.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.13'
+        version: '3.7'
 - !ruby/object:Gem::Dependency
-  name: mini_magick
+  name: mocha
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '3.5'
+        version: '1.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '3.5'
+        version: '1.1'
 - !ruby/object:Gem::Dependency
   name: narray
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.6'
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.6.0.8
   type: :development
@@ -64,6 +67,9 @@ dependencies:
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.6'
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.6.0.8
 - !ruby/object:Gem::Dependency
@@ -72,19 +78,36 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.6
+        version: '10.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '10.3'
+- !ruby/object:Gem::Dependency
+  name: redcarpet
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.6
+        version: '3.1'
 - !ruby/object:Gem::Dependency
   name: rmagick
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.13'
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 2.13.2
   type: :development
@@ -92,6 +115,9 @@ dependencies:
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.13'
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 2.13.2
 - !ruby/object:Gem::Dependency
@@ -100,28 +126,34 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '2.13'
+        version: '3.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '2.13'
+        version: '3.0'
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.8.5
+        version: '0.8'
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.8.7
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.8.5
+        version: '0.8'
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.8.7
 description: DICOM is a standard widely used throughout the world to store and transfer
   medical image data. This library enables efficient and powerful handling of DICOM
   in Ruby, to the benefit of any student or professional who would like to use their
@@ -131,44 +163,49 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- CHANGELOG.md
+- CONTRIBUTING.md
+- COPYING
+- Gemfile
+- Gemfile.lock
+- README.md
+- dicom.gemspec
+- lib/dicom.rb
 - lib/dicom/anonymizer.rb
 - lib/dicom/audit_trail.rb
-- lib/dicom/constants.rb
-- lib/dicom/deprecated.rb
-- lib/dicom/dictionary/elements.txt
-- lib/dicom/dictionary/uids.txt
-- lib/dicom/dictionary_element.rb
 - lib/dicom/d_client.rb
 - lib/dicom/d_library.rb
 - lib/dicom/d_object.rb
 - lib/dicom/d_read.rb
 - lib/dicom/d_server.rb
 - lib/dicom/d_write.rb
+- lib/dicom/dictionary/elements.tsv
+- lib/dicom/dictionary/uids.tsv
+- lib/dicom/dictionary_element.rb
 - lib/dicom/element.rb
 - lib/dicom/elemental.rb
+- lib/dicom/elemental_parent.rb
+- lib/dicom/extensions/array.rb
+- lib/dicom/extensions/hash.rb
+- lib/dicom/extensions/string.rb
 - lib/dicom/file_handler.rb
+- lib/dicom/general/constants.rb
+- lib/dicom/general/deprecated.rb
+- lib/dicom/general/logging.rb
+- lib/dicom/general/methods.rb
+- lib/dicom/general/variables.rb
+- lib/dicom/general/version.rb
 - lib/dicom/image_item.rb
 - lib/dicom/image_processor.rb
 - lib/dicom/image_processor_mini_magick.rb
 - lib/dicom/image_processor_r_magick.rb
 - lib/dicom/item.rb
 - lib/dicom/link.rb
-- lib/dicom/logging.rb
 - lib/dicom/parent.rb
-- lib/dicom/ruby_extensions.rb
 - lib/dicom/sequence.rb
 - lib/dicom/stream.rb
 - lib/dicom/uid.rb
-- lib/dicom/variables.rb
-- lib/dicom/version.rb
-- lib/dicom.rb
-- CHANGELOG.rdoc
-- CONTRIBUTING.rdoc
-- COPYING
-- dicom.gemspec
-- Gemfile
 - rakefile.rb
-- README.rdoc
 homepage: http://dicom.rubyforge.org/
 licenses:
 - GPLv3
@@ -179,17 +216,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ! '>='
     - !ruby/object:Gem::Version
-      version: 1.9.2
+      version: 1.9.3
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: dicom
-rubygems_version: 2.0.0
+rubygems_version: 2.2.1
 signing_key: 
 specification_version: 4
 summary: Library for handling DICOM files and DICOM network communication.