dicom 0.9.7 → 0.9.8

data/lib/dicom/elemental.rb

@@ -1,121 +1,121 @@
-module DICOM
-
-  # The Elemental mix-in module contains methods that
-  # are common among the various element type classes:
-  # * Element
-  # * Item
-  # * Sequence
-  #
-  module Elemental
-
-    # The encoded, binary value of the elemental (String).
-    attr_reader :bin
-    # The elemental's length (Fixnum).
-    attr_reader :length
-    # The elemental's name (String).
-    attr_reader :name
-    # The parent of this elemental (which may be an Item, Sequence or DObject).
-    attr_reader :parent
-    # The elemental's tag (String).
-    attr_reader :tag
-    # The elemental's value representation (String).
-    attr_reader :vr
-
-    # Gives the method (symbol) corresponding to the name string of this element.
-    #
-    # @return [Symbol, NilClass] the matched element method (or nil, if no match is made)
-    #
-    def name_as_method
-      LIBRARY.as_method(@name)
-    end
-
-    # Retrieves the entire chain of parents connected to this elemental
-    # (or an empty array, if the element is parent-less).
-    #
-    # @return [Array] array of parents (immediate parent first, top parent last)
-    #
-    def parents
-      all_parents = Array.new
-      # Extract all parents and add to array recursively:
-      if parent
-        all_parents = parent.parents if parent.parent
-        all_parents.insert(0, parent)
-      end
-      return all_parents
-    end
-
-    # Sets a specified parent instance as this elemental's parent, while taking
-    # care to delete this elemental from any previous parent, as well as adding
-    # itself to the new parent (unless new parent is nil).
-    #
-    # @param [DObject, Item, Sequence, NilClass] new_parent the new parent object for this elemental
-    # @example Create a new Sequence and connect it to a DObject instance
-    #   structure_set_roi = Sequence.new("3006,0020")
-    #   structure_set_roi.parent = dcm
-    #
-    def parent=(new_parent)
-      # First take care of 'dependencies':
-      if self.parent
-        # Remove ourselves from the previous parent:
-        if self.is_a?(Item)
-          self.parent.delete(self.index, :no_follow => true)
-        else
-          self.parent.delete(self.tag, :no_follow => true)
-        end
-      end
-      if new_parent
-        # Add ourselves to the new parent:
-        if self.is_a?(Item)
-          new_parent.add_item(self, :no_follow => true)
-        else
-          new_parent.add(self, :no_follow => true)
-        end
-      end
-      # Set the new parent (should we bother to test for parent validity here?):
-      @parent = new_parent
-    end
-
-    # Sets a specified parent instance as this elemental's parent, without doing any other updates,
-    # like removing the elemental from any previous parent or adding itself to the new parent.
-    #
-    # @param [DObject, Item, Sequence, NilClass] new_parent the new parent object for this elemental
-    #
-    def set_parent(new_parent)
-      # Set the new parent (should we bother to test for parent validity here?):
-      @parent = new_parent
-    end
-
-    # Returns a Stream instance which can be used for encoding a value to binary.
-    #
-    # @note Retrieves the Stream instance of the top parent DObject instance.
-    #   If this fails, a new Stream instance is created (with little endian encoding assumed).
-    #
-    def stream
-      if top_parent.is_a?(DObject)
-        return top_parent.stream
-      else
-        return Stream.new(nil, file_endian=false)
-      end
-    end
-
-    # Returns the top parent of a particular elemental.
-    #
-    # @note Unless the elemental, or one of its parent instances, are independent,
-    #   the top parent will be a DObject instance.
-    #
-    def top_parent
-      # The top parent is determined recursively:
-      if parent
-        if parent.is_a?(DObject)
-          return parent
-        else
-          return parent.top_parent
-        end
-      else
-        return self
-      end
-    end
-
-  end
-
-end
+module DICOM
+
+  # The Elemental mix-in module contains methods that
+  # are common among the various element type classes:
+  # * Element
+  # * Item
+  # * Sequence
+  #
+  module Elemental
+
+    # The encoded, binary value of the elemental (String).
+    attr_reader :bin
+    # The elemental's length (Integer).
+    attr_reader :length
+    # The elemental's name (String).
+    attr_reader :name
+    # The parent of this elemental (which may be an Item, Sequence or DObject).
+    attr_reader :parent
+    # The elemental's tag (String).
+    attr_reader :tag
+    # The elemental's value representation (String).
+    attr_reader :vr
+
+    # Gives the method (symbol) corresponding to the name string of this element.
+    #
+    # @return [Symbol, NilClass] the matched element method (or nil, if no match is made)
+    #
+    def name_as_method
+      LIBRARY.as_method(@name)
+    end
+
+    # Retrieves the entire chain of parents connected to this elemental
+    # (or an empty array, if the element is parent-less).
+    #
+    # @return [Array] array of parents (immediate parent first, top parent last)
+    #
+    def parents
+      all_parents = Array.new
+      # Extract all parents and add to array recursively:
+      if parent
+        all_parents = parent.parents if parent.parent
+        all_parents.insert(0, parent)
+      end
+      return all_parents
+    end
+
+    # Sets a specified parent instance as this elemental's parent, while taking
+    # care to delete this elemental from any previous parent, as well as adding
+    # itself to the new parent (unless new parent is nil).
+    #
+    # @param [DObject, Item, Sequence, NilClass] new_parent the new parent object for this elemental
+    # @example Create a new Sequence and connect it to a DObject instance
+    #   structure_set_roi = Sequence.new("3006,0020")
+    #   structure_set_roi.parent = dcm
+    #
+    def parent=(new_parent)
+      # First take care of 'dependencies':
+      if self.parent
+        # Remove ourselves from the previous parent:
+        if self.is_a?(Item)
+          self.parent.delete(self.index, :no_follow => true)
+        else
+          self.parent.delete(self.tag, :no_follow => true)
+        end
+      end
+      if new_parent
+        # Add ourselves to the new parent:
+        if self.is_a?(Item)
+          new_parent.add_item(self, :no_follow => true)
+        else
+          new_parent.add(self, :no_follow => true)
+        end
+      end
+      # Set the new parent (should we bother to test for parent validity here?):
+      @parent = new_parent
+    end
+
+    # Sets a specified parent instance as this elemental's parent, without doing any other updates,
+    # like removing the elemental from any previous parent or adding itself to the new parent.
+    #
+    # @param [DObject, Item, Sequence, NilClass] new_parent the new parent object for this elemental
+    #
+    def set_parent(new_parent)
+      # Set the new parent (should we bother to test for parent validity here?):
+      @parent = new_parent
+    end
+
+    # Returns a Stream instance which can be used for encoding a value to binary.
+    #
+    # @note Retrieves the Stream instance of the top parent DObject instance.
+    #   If this fails, a new Stream instance is created (with little endian encoding assumed).
+    #
+    def stream
+      if top_parent.is_a?(DObject)
+        return top_parent.stream
+      else
+        return Stream.new(nil, file_endian=false)
+      end
+    end
+
+    # Returns the top parent of a particular elemental.
+    #
+    # @note Unless the elemental, or one of its parent instances, are independent,
+    #   the top parent will be a DObject instance.
+    #
+    def top_parent
+      # The top parent is determined recursively:
+      if parent
+        if parent.is_a?(DObject)
+          return parent
+        else
+          return parent.top_parent
+        end
+      else
+        return self
+      end
+    end
+
+  end
+
+end

data/lib/dicom/general/constants.rb

@@ -168,7 +168,10 @@ module DICOM
     'ISO_IR 126' => 'ISO-8859-7',
     'ISO_IR 138' => 'ISO-8859-8',
     'ISO_IR 148' => 'ISO-8859-9',
-    'ISO_IR 13'  => 'JIS_X0201',
+    'ISO_IR 13'  => 'Shift_JIS',
+    'ISO 2022 IR 13' => 'Shift_JIS',
+    'ISO 2022 IR 13\\ISO 2022 IR 87' => 'Shift_JIS',
+    'ISO 2022 IR 87' => 'ISO-2022-JP',
     'ISO_IR 166' => 'ISO-8859-11',
     'GB18030'    => 'GB18030',
     'ISO_IR 192' => 'UTF-8'

data/lib/dicom/general/version.rb

@@ -1,6 +1,6 @@
 module DICOM
 
   # The ruby-dicom version string.
-  VERSION = '0.9.7'
+  VERSION = '0.9.8'
 
 end

data/lib/dicom/image_item.rb

@@ -349,13 +349,13 @@ module DICOM
             raise "Missing Rows and/or Columns Element. Unable to construct pixel data array." unless num_rows and num_cols
             if num_frames > 1 or options[:volume]
               # Create an empty 3D NArray. fill it with pixels frame by frame, then reassign the pixels variable to it:
-              narr = NArray.int(num_frames, num_cols, num_rows)
+              narr = Numo::Int16.zeros(num_frames, num_cols, num_rows)
               num_frames.times do |i|
-                narr[i, true, true] = NArray.to_na(pixels[(i * num_cols * num_rows)..((i + 1) * num_cols * num_rows - 1)]).reshape!(num_cols, num_rows)
+                narr[i, true, true] = Numo::NArray[*pixels[(i * num_cols * num_rows)..((i + 1) * num_cols * num_rows - 1)]].reshape!(num_cols, num_rows)
               end
               pixels = narr
             else
-              pixels = NArray.to_na(pixels).reshape!(num_cols, num_rows)
+              pixels = Numo::NArray[*pixels].reshape!(num_cols, num_rows)
             end
             # Remap the image from pixel values to presentation values if the user has requested this:
             pixels = process_presentation_values_narray(pixels, -65535, 65535, options[:level]) if options[:remap] or options[:level]
@@ -680,7 +680,7 @@ module DICOM
       end
       # Need to convert to NArray?
       if pixel_data.is_a?(Array)
-        n_arr = NArray.to_na(pixel_data)
+        n_arr = Numo::NArray[*pixel_data]
       else
         n_arr = pixel_data
       end
@@ -779,7 +779,7 @@ module DICOM
       # Number of bytes used per pixel will determine how to unpack this:
       case depth
       when 8 # (1 byte)
-        template = 'BY' # Byte/Character/Fixnum
+        template = 'BY' # Byte/Character/Integer
       when 16 # (2 bytes)
         if pixel_representation == 1
          template = 'SS' # Signed short
@@ -834,4 +834,4 @@ module DICOM
     end
 
   end
-end
+end

data/lib/dicom/item.rb

@@ -1,122 +1,122 @@
-module DICOM
-
-  # The Item class handles information related to items - the elements contained in sequences.
-  #
-  # === Inheritance
-  #
-  # As the Item class inherits from the ImageItem class, which itself inherits from the Parent class,
-  # all ImageItem and Parent methods are also available to instances of Item.
-  #
-  class Item < ImageItem
-
-    include Elemental
-    include ElementalParent
-
-    # The index of this Item in the group of items belonging to its parent. If the Item is without parent, index is nil.
-    attr_accessor :index
-
-    # Creates an Item instance.
-    #
-    # Normally, an Item contains data elements and/or sequences. However,
-    # in some cases, an Item will instead/also carry binary string data,
-    # like the pixel data of an encapsulated image fragment.
-    #
-    # @param [Hash] options the options to use for creating the item
-    # @option options [String] :bin a binary string to be carried by the item
-    # @option options [String] :indexif the item is to be inserted at a specific index (Item number), this option parameter needs to set
-    # @option options [String] :length theiItem length (which either refers to the length of the encoded string of children of this item, or the length of its binary data)
-    # @option options [String] :name the name of the item may be specified upon creation  (if not, a default name is used)
-    # @option options [String] :parent a Sequence or DObject instance which the item instance shall belong to
-    # @option options [String] :vr the value representation of the item may be specified upon creation (if not, a default vr is used)
-    #
-    # @example Create an empty Item and connect it to the "Structure Set ROI Sequence"
-    #   item = Item.new(:parent => dcm["3006,0020"])
-    # @example Create a "Pixel Data Item" which carries an encapsulated image frame (a pre-encoded binary)
-    #   pixel_item = Item.new(:bin => processed_pixel_data, :parent => dcm["7FE0,0010"][1])
-    #
-    def initialize(options={})
-      # Set common parent variables:
-      initialize_parent
-      # Set instance variables:
-      @tag = ITEM_TAG
-      @value = nil
-      @name = options[:name] || "Item"
-      @vr = options[:vr] || ITEM_VR
-      if options[:bin]
-        self.bin = options[:bin]
-      else
-        @length = options[:length] || -1
-      end
-      if options[:parent]
-        @parent = options[:parent]
-        @index = options[:index] if options[:index]
-        @parent.add_item(self, :index => options[:index], :no_follow => true)
-      end
-    end
-
-    # Checks for equality.
-    #
-    # Other and self are considered equivalent if they are
-    # of compatible types and their attributes are equivalent.
-    #
-    # @param other an object to be compared with self.
-    # @return [Boolean] true if self and other are considered equivalent
-    #
-    def ==(other)
-      if other.respond_to?(:to_item)
-        other.send(:state) == state
-      end
-    end
-
-    alias_method :eql?, :==
-
-    # Sets the binary string that the Item will contain.
-    #
-    # @param [String] new_bin a binary string of encoded data
-    # @example Insert a custom jpeg in the (encapsulated) pixel data element (in it's first pixel data item)
-    #   dcm['7FE0,0010'][1].children.first.bin = jpeg_binary_string
-    #
-    def bin=(new_bin)
-      raise ArgumentError, "Invalid parameter type. String was expected, got #{new_bin.class}." unless new_bin.is_a?(String)
-      # Add an empty byte at the end if the length of the binary is odd:
-      if new_bin.length.odd?
-        @bin = new_bin + "\x00"
-      else
-        @bin = new_bin
-      end
-      @value = nil
-      @length = @bin.length
-    end
-
-    # Computes a hash code for this object.
-    #
-    # @note Two objects with the same attributes will have the same hash code.
-    #
-    # @return [Fixnum] the object's hash code
-    #
-    def hash
-      state.hash
-    end
-
-    # Returns self.
-    #
-    # @return [Item] self
-    #
-    def to_item
-      self
-    end
-
-
-    private
-
-
-    # Collects the attributes of this instance.
-    #
-    # @return [Array<String, Sequence, Element>] an array of attributes
-    #
-    def state
-      [@vr, @name, @tags]
-    end
-
-  end
-end
+module DICOM
+
+  # The Item class handles information related to items - the elements contained in sequences.
+  #
+  # === Inheritance
+  #
+  # As the Item class inherits from the ImageItem class, which itself inherits from the Parent class,
+  # all ImageItem and Parent methods are also available to instances of Item.
+  #
+  class Item < ImageItem
+
+    include Elemental
+    include ElementalParent
+
+    # The index of this Item in the group of items belonging to its parent. If the Item is without parent, index is nil.
+    attr_accessor :index
+
+    # Creates an Item instance.
+    #
+    # Normally, an Item contains data elements and/or sequences. However,
+    # in some cases, an Item will instead/also carry binary string data,
+    # like the pixel data of an encapsulated image fragment.
+    #
+    # @param [Hash] options the options to use for creating the item
+    # @option options [String] :bin a binary string to be carried by the item
+    # @option options [String] :indexif the item is to be inserted at a specific index (Item number), this option parameter needs to set
+    # @option options [String] :length theiItem length (which either refers to the length of the encoded string of children of this item, or the length of its binary data)
+    # @option options [String] :name the name of the item may be specified upon creation  (if not, a default name is used)
+    # @option options [String] :parent a Sequence or DObject instance which the item instance shall belong to
+    # @option options [String] :vr the value representation of the item may be specified upon creation (if not, a default vr is used)
+    #
+    # @example Create an empty Item and connect it to the "Structure Set ROI Sequence"
+    #   item = Item.new(:parent => dcm["3006,0020"])
+    # @example Create a "Pixel Data Item" which carries an encapsulated image frame (a pre-encoded binary)
+    #   pixel_item = Item.new(:bin => processed_pixel_data, :parent => dcm["7FE0,0010"][1])
+    #
+    def initialize(options={})
+      # Set common parent variables:
+      initialize_parent
+      # Set instance variables:
+      @tag = ITEM_TAG
+      @value = nil
+      @name = options[:name] || "Item"
+      @vr = options[:vr] || ITEM_VR
+      if options[:bin]
+        self.bin = options[:bin]
+      else
+        @length = options[:length] || -1
+      end
+      if options[:parent]
+        @parent = options[:parent]
+        @index = options[:index] if options[:index]
+        @parent.add_item(self, :index => options[:index], :no_follow => true)
+      end
+    end
+
+    # Checks for equality.
+    #
+    # Other and self are considered equivalent if they are
+    # of compatible types and their attributes are equivalent.
+    #
+    # @param other an object to be compared with self.
+    # @return [Boolean] true if self and other are considered equivalent
+    #
+    def ==(other)
+      if other.respond_to?(:to_item)
+        other.send(:state) == state
+      end
+    end
+
+    alias_method :eql?, :==
+
+    # Sets the binary string that the Item will contain.
+    #
+    # @param [String] new_bin a binary string of encoded data
+    # @example Insert a custom jpeg in the (encapsulated) pixel data element (in it's first pixel data item)
+    #   dcm['7FE0,0010'][1].children.first.bin = jpeg_binary_string
+    #
+    def bin=(new_bin)
+      raise ArgumentError, "Invalid parameter type. String was expected, got #{new_bin.class}." unless new_bin.is_a?(String)
+      # Add an empty byte at the end if the length of the binary is odd:
+      if new_bin.length.odd?
+        @bin = new_bin + "\x00"
+      else
+        @bin = new_bin
+      end
+      @value = nil
+      @length = @bin.length
+    end
+
+    # Computes a hash code for this object.
+    #
+    # @note Two objects with the same attributes will have the same hash code.
+    #
+    # @return [Integer] the object's hash code
+    #
+    def hash
+      state.hash
+    end
+
+    # Returns self.
+    #
+    # @return [Item] self
+    #
+    def to_item
+      self
+    end
+
+
+    private
+
+
+    # Collects the attributes of this instance.
+    #
+    # @return [Array<String, Sequence, Element>] an array of attributes
+    #
+    def state
+      [@vr, @name, @tags]
+    end
+
+  end
+end