dicom 0.9.5 → 0.9.6

data/dicom.gemspec

@@ -1,6 +1,6 @@
 # encoding: UTF-8
 
-require File.expand_path('../lib/dicom/version', __FILE__)
+require File.expand_path('../lib/dicom/general/version', __FILE__)
 
 Gem::Specification.new do |s|
   s.platform = Gem::Platform::RUBY
@@ -17,14 +17,15 @@ Gem::Specification.new do |s|
   s.files = Dir["{lib}/**/*", "[A-Z]*"]
   s.rubyforge_project = 'dicom'
 
-  s.required_ruby_version = '>= 1.9.2'
+  s.required_ruby_version = '>= 1.9.3'
 
-  s.add_development_dependency('bundler', '~> 1.3')
-  s.add_development_dependency('mocha', '~> 0.13')
-  s.add_development_dependency('mini_magick', '~> 3.5')
-  s.add_development_dependency('narray', '~> 0.6.0.8')
-  s.add_development_dependency('rake', '~> 0.9.6')
-  s.add_development_dependency('rmagick', '~> 2.13.2')
-  s.add_development_dependency('rspec', '~> 2.13')
-  s.add_development_dependency('yard', '~> 0.8.5')
+  s.add_development_dependency('bundler', '~> 1.6')
+  s.add_development_dependency('mini_magick', '~> 3.7')
+  s.add_development_dependency('mocha', '~> 1.1')
+  s.add_development_dependency('narray', '~> 0.6', '>= 0.6.0.8')
+  s.add_development_dependency('rake', '~> 10.3')
+  s.add_development_dependency('redcarpet', '~> 3.1')
+  s.add_development_dependency('rmagick', '~> 2.13', '>= 2.13.2')
+  s.add_development_dependency('rspec', '~> 3.0')
+  s.add_development_dependency('yard', '~> 0.8', '>= 0.8.7')
 end

data/lib/dicom.rb

@@ -12,14 +12,30 @@
 # The rest of the classes visible in the documentation generated by YARD are
 # in principle 'private' classes, which are mainly of interest to developers.
 
-# Logging:
-require_relative 'dicom/logging'
+# Standard library dependencies:
+require 'json'
+require 'yaml'
+
+# Gem specific extensions:
+require_relative 'dicom/extensions/array'
+require_relative 'dicom/extensions/hash'
+require_relative 'dicom/extensions/string'
+
+# General module features/settings:
+require_relative 'dicom/general/version'
+require_relative 'dicom/general/constants'
+require_relative 'dicom/general/variables'
+require_relative 'dicom/general/methods'
+require_relative 'dicom/general/logging'
+require_relative 'dicom/general/deprecated'
+
 # Core library:
 # Super classes/modules:
 require_relative 'dicom/image_processor'
 require_relative 'dicom/parent'
 require_relative 'dicom/image_item'
 require_relative 'dicom/elemental'
+require_relative 'dicom/elemental_parent'
 # Subclasses and independent classes:
 require_relative 'dicom/d_client'
 require_relative 'dicom/d_object'
@@ -36,18 +52,21 @@ require_relative 'dicom/stream'
 require_relative 'dicom/d_library'
 require_relative 'dicom/dictionary_element'
 require_relative 'dicom/uid'
-# Extensions to the Ruby library:
-require_relative 'dicom/ruby_extensions'
-# Module settings:
-require_relative 'dicom/version'
-require_relative 'dicom/constants'
-require_relative 'dicom/variables'
 # Image processors:
 require_relative 'dicom/image_processor_mini_magick'
 require_relative 'dicom/image_processor_r_magick'
-# Deprecated methods:
-require_relative 'dicom/deprecated'
 
 # Extensions (non-core functionality):
 require_relative 'dicom/anonymizer'
-require_relative 'dicom/audit_trail'
+require_relative 'dicom/audit_trail'
+
+
+module DICOM
+
+  # Defines the gem root directory in the file system.
+  ROOT_DIR = "#{File.dirname(__FILE__)}/dicom"
+
+  # The library instance (data dictionary) of the DICOM module.
+  LIBRARY =  DICOM::DLibrary.new
+
+end

data/lib/dicom/anonymizer.rb

@@ -1,649 +1,654 @@
-module DICOM
-
-  # This is a convenience class for handling the anonymization
-  # (de-identification) of DICOM files.
-  #
-  # @note
-  #   For a thorough introduction to the concept of DICOM anonymization,
-  #   please refer to The DICOM Standard, Part 15: Security and System
-  #   Management Profiles, Annex E: Attribute Confidentiality Profiles.
-  #   For guidance on settings for individual data elements, please
-  #   refer to DICOM PS 3.15, Annex E, Table E.1-1: Application Level
-  #   Confidentiality Profile Attributes.
-  #
-  class Anonymizer
-    include Logging
-
-    # An AuditTrail instance used for this anonymization (if specified).
-    attr_reader :audit_trail
-    # The file name used for the AuditTrail serialization (if specified).
-    attr_reader :audit_trail_file
-    # A boolean that if set as true will cause all anonymized tags to be blank instead of get some generic value.
-    attr_accessor :blank
-    # An hash of elements (represented by tag keys) that will be deleted from the DICOM objects on anonymization.
-    attr_reader :delete
-    # A boolean that if set as true, will make the anonymization delete all private tags.
-    attr_accessor :delete_private
-    # The cryptographic hash function to be used for encrypting DICOM values recorded in an audit trail file.
-    attr_reader :encryption
-    # A boolean that if set as true will cause all anonymized tags to be get enumerated values, to enable post-anonymization re-identification by the user.
-    attr_accessor :enumeration
-    # The logger level which is applied to DObject operations during anonymization (defaults to Logger::FATAL).
-    attr_reader :logger_level
-    # A boolean that if set as true will cause all anonymized files to be written with random file names (if write_path has been specified).
-    attr_accessor :random_file_name
-    # A boolean that if set as true, will cause the anonymization to run on all levels of the DICOM file tag hierarchy.
-    attr_accessor :recursive
-    # A boolean indicating whether or not UIDs shall be replaced when executing the anonymization.
-    attr_accessor :uid
-    # The DICOM UID root to use when generating new UIDs.
-    attr_accessor :uid_root
-    # The path where the anonymized files will be saved. If this value is not set, the original DICOM files will be overwritten.
-    attr_accessor :write_path
-
-    # Creates an Anonymizer instance.
-    #
-    # @note To customize logging behaviour, refer to the Logging module documentation.
-    # @param [Hash] options the options to create an anonymizer instance with
-    # @option options [String] :audit_trail a file name path (if the file contains old audit data, these are loaded and used in the current anonymization)
-    # @option options [Boolean] :blank toggles whether to set the values of anonymized elements as empty instead of some generic value
-    # @option options [Boolean] :delete_private toggles whether private elements are to be deleted
-    # @option options [TrueClass, Digest::Class] :encryption if set as true, the default hash function (MD5) will be used for representing DICOM values in an audit file. Otherwise a Digest class can be given, e.g. Digest::SHA256
-    # @option options [Boolean] :enumeration toggles whether (some) elements get enumerated values (to enable post-anonymization re-identification)
-    # @option options [Fixnum] :logger_level the logger level which is applied to DObject operations during anonymization (defaults to Logger::FATAL)
-    # @option options [Boolean] :random_file_name toggles whether anonymized files will be given random file names when rewritten (in combination with the :write_path option)
-    # @option options [Boolean] :recursive toggles whether to anonymize on all sub-levels of the DICOM object tag hierarchies
-    # @option options [Boolean] :uid toggles whether UIDs will be replaced with custom generated UIDs (beware that to preserve UID relations in studies/series, the audit_trail feature must be used)
-    # @option options [String] :uid_root an organization (or custom) UID root to use when replacing UIDs
-    # @option options [String] :write_path a directory where the anonymized files are re-written (if not specified, files are overwritten)
-    # @example Create an Anonymizer instance and increase the log output
-    #   a = Anonymizer.new
-    #   a.logger.level = Logger::INFO
-    # @example Perform anonymization using the audit trail feature
-    #   a = Anonymizer.new(:audit_trail => 'trail.json')
-    #   a.enumeration = true
-    #   a.write_path = '//anonymized/'
-    #   a.anonymize('//dicom/today/')
-    #
-    def initialize(options={})
-      # Transfer options to attributes:
-      @blank = options[:blank]
-      @delete_private = options[:delete_private]
-      @enumeration = options[:enumeration]
-      @logger_level = options[:logger_level] || Logger::FATAL
-      @random_file_name = options[:random_file_name]
-      @recursive = options[:recursive]
-      @uid = options[:uid]
-      @uid_root = options[:uid_root] ? options[:uid_root] : UID_ROOT
-      @write_path = options[:write_path]
-      # Array of folders to be processed for anonymization:
-      @folders = Array.new
-      # Folders that will be skipped:
-      @exceptions = Array.new
-      # Data elements which will be anonymized (the array will hold a list of tag strings):
-      @tags = Array.new
-      # Default values to use on anonymized data elements:
-      @values = Array.new
-      # Which data elements will have enumeration applied, if requested by the user:
-      @enumerations = Array.new
-      # We use a Hash to store information from DICOM files if enumeration is desired:
-      @enum_old_hash = Hash.new
-      @enum_new_hash = Hash.new
-      # All the files to be anonymized will be put in this array:
-      @files = Array.new
-      @prefixes = Hash.new
-      # Setup audit trail if requested:
-      if options[:audit_trail]
-        @audit_trail_file = options[:audit_trail]
-        if File.exists?(@audit_trail_file) && File.size(@audit_trail_file) > 2
-          # Load the pre-existing audit trail from file:
-          @audit_trail = AuditTrail.read(@audit_trail_file)
-        else
-          # Start from scratch with an empty audit trail:
-          @audit_trail = AuditTrail.new
-        end
-        # Set up encryption if indicated:
-        if options[:encryption]
-          require 'digest'
-          if options[:encryption].respond_to?(:hexdigest)
-            @encryption = options[:encryption]
-          else
-            @encryption = Digest::MD5
-          end
-        end
-      end
-      # Set the default data elements to be anonymized:
-      set_defaults
-    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_anonymizer)
-        other.send(:state) == state
-      end
-    end
-
-    alias_method :eql?, :==
-
-    # Anonymizes the given DICOM data with the settings of this Anonymizer instance.
-    #
-    # @param [String, DObject, Array<String, DObject>] data single or multiple DICOM data (directories, file paths, binary strings, DICOM objects)
-    # @return [Array<DObject>] an array of the anonymized DICOM objects
-    #
-    def anonymize(data)
-      dicom = prepare(data)
-      if @tags.length > 0
-        dicom.each do |dcm|
-          anonymize_dcm(dcm)
-          # Write DICOM object to file unless it was passed to the anonymizer as an object:
-          write(dcm) unless dcm.was_dcm_on_input
-        end
-      else
-        logger.warn("No tags have been selected for anonymization. Aborting anonymization.")
-      end
-      # Reset the ruby-dicom log threshold to its original level:
-      logger.level = @original_level
-      # Save the audit trail (if used):
-      @audit_trail.write(@audit_trail_file) if @audit_trail
-      logger.info("Anonymization complete.")
-      dicom
-    end
-
-    # Specifies that the given tag is to be completely deleted
-    # from the anonymized DICOM objects.
-    #
-    # @param [String] tag a data element tag
-    # @example Completely delete the Patient's Name tag from the DICOM files
-    #   a.delete_tag('0010,0010')
-    #
-    def delete_tag(tag)
-      raise ArgumentError, "Expected String, got #{tag.class}." unless tag.is_a?(String)
-      raise ArgumentError, "Expected a valid tag of format 'GGGG,EEEE', got #{tag}." unless tag.tag?
-      @delete[tag] = true
-    end
-
-    # Checks the enumeration status of this tag.
-    #
-    # @param [String] tag a data element tag
-    # @return [Boolean, NilClass] the enumeration status of the tag, or nil if the tag has no match
-    #
-    def enum(tag)
-      raise ArgumentError, "Expected String, got #{tag.class}." unless tag.is_a?(String)
-      raise ArgumentError, "Expected a valid tag of format 'GGGG,EEEE', got #{tag}." unless tag.tag?
-      pos = @tags.index(tag)
-      if pos
-        return @enumerations[pos]
-      else
-        logger.warn("The specified tag (#{tag}) was not found in the list of tags to be anonymized.")
-        return nil
-      end
-    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
-
-    # Removes a tag from the list of tags that will be anonymized.
-    #
-    # @param [String] tag a data element tag
-    # @example Do not anonymize the Patient's Name tag
-    #   a.remove_tag('0010,0010')
-    #
-    def remove_tag(tag)
-      raise ArgumentError, "Expected String, got #{tag.class}." unless tag.is_a?(String)
-      raise ArgumentError, "Expected a valid tag of format 'GGGG,EEEE', got #{tag}." unless tag.tag?
-      pos = @tags.index(tag)
-      if pos
-        @tags.delete_at(pos)
-        @values.delete_at(pos)
-        @enumerations.delete_at(pos)
-      end
-    end
-
-    # Sets the anonymization settings for the specified tag. If the tag is already present in the list
-    # of tags to be anonymized, its settings are updated, and if not, a new tag entry is created.
-    #
-    # @param [String] tag a data element tag
-    # @param [Hash] options the anonymization settings for the specified tag
-    # @option options [String, Integer, Float] :value the replacement value to be used when anonymizing this data element. Defaults to the pre-existing value and '' for new tags.
-    # @option options [String, Integer, Float] :enum specifies if enumeration is to be used for this tag. Defaults to the pre-existing value and false for new tags.
-    # @example Set the anonymization settings of the Patient's Name tag
-    #   a.set_tag('0010,0010', :value => 'MrAnonymous', :enum => true)
-    #
-    def set_tag(tag, options={})
-      raise ArgumentError, "Expected String, got #{tag.class}." unless tag.is_a?(String)
-      raise ArgumentError, "Expected a valid tag of format 'GGGG,EEEE', got #{tag}." unless tag.tag?
-      pos = @tags.index(tag)
-      if pos
-        # Update existing values:
-        @values[pos] = options[:value] if options[:value]
-        @enumerations[pos] = options[:enum] if options[:enum] != nil
-      else
-        # Add new elements:
-        @tags << tag
-        @values << (options[:value] ? options[:value] : default_value(tag))
-        @enumerations << (options[:enum] ? options[:enum] : false)
-      end
-    end
-
-    # Returns self.
-    #
-    # @return [Anonymizer] self
-    #
-    def to_anonymizer
-      self
-    end
-
-    # Gives the value which will be used when anonymizing this tag.
-    #
-    # @note If enumeration is selected for a string type tag, a number will be
-    #   appended in addition to the string that is returned here.
-    #
-    # @param [String] tag a data element tag
-    # @return [String, Integer, Float, NilClass] the replacement value for the specified tag, or nil if the tag is not matched
-    #
-    def value(tag)
-      raise ArgumentError, "Expected String, got #{tag.class}." unless tag.is_a?(String)
-      raise ArgumentError, "Expected a valid tag of format 'GGGG,EEEE', got #{tag}." unless tag.tag?
-      pos = @tags.index(tag)
-      if pos
-        return @values[pos]
-      else
-        logger.warn("The specified tag (#{tag}) was not found in the list of tags to be anonymized.")
-        return nil
-      end
-    end
-
-
-    private
-
-
-    # Performs anonymization on a DICOM object.
-    #
-    # @param [DObject] dcm a DICOM object
-    #
-    def anonymize_dcm(dcm)
-      # Extract the data element parents to investigate:
-      parents = element_parents(dcm)
-      parents.each do |parent|
-        # Anonymize the desired tags:
-        @tags.each_index do |j|
-          if parent.exists?(@tags[j])
-            element = parent[@tags[j]]
-            if element.is_a?(Element)
-              if @blank
-                value = ''
-              elsif @enumeration
-                old_value = element.value
-                # Only launch enumeration logic if there is an actual value to the data element:
-                if old_value
-                  value = enumerated_value(old_value, j)
-                else
-                  value = ''
-                end
-              else
-                # Use the value that has been set for this tag:
-                value = @values[j]
-              end
-              element.value = value
-            end
-          end
-        end
-        # Delete elements marked for deletion:
-        @delete.each_key do |tag|
-          parent.delete(tag) if parent.exists?(tag)
-        end
-      end
-      # General DICOM object manipulation:
-      # Add a Patient Identity Removed attribute (as per
-      # DICOM PS 3.15, Annex E, E.1.1 De-Identifier, point 6):
-      dcm.add(Element.new('0012,0062', 'YES'))
-      # Add a De-Identification Method Code Sequence Item:
-      dcm.add(Sequence.new('0012,0064')) unless dcm.exists?('0012,0064')
-      i = dcm['0012,0064'].add_item
-      i.add(Element.new('0012,0063', 'De-identified by the ruby-dicom Anonymizer'))
-      # FIXME: At some point we should add a set of de-indentification method codes, as per
-      #   DICOM PS 3.16 CID 7050 which corresponds to the settings chosen for the anonymizer.
-      # Delete the old File Meta Information group (as per
-      # DICOM PS 3.15, Annex E, E.1.1 De-Identifier, point 7):
-      dcm.delete_group('0002')
-      # Handle UIDs if requested:
-      replace_uids(parents) if @uid
-      # Delete private tags if indicated:
-      dcm.delete_private if @delete_private
-    end
-
-    # Gives the value to be used for the audit trail, which is either
-    # the original value itself, or an encrypted string based on it.
-    #
-    # @param [String, Integer, Float] original the original value of the tag to be anonymized
-    # @return [String, Integer, Float] with encryption, a hash string is returned, otherwise the original value
-    #
-    def at_value(original)
-      @encryption ? @encryption.hexdigest(original) : original
-    end
-
-    # Creates a hash that is used for storing information that is used when enumeration is selected.
-    #
-    def create_enum_hash
-      @enumerations.each_index do |i|
-        @enum_old_hash[@tags[i]] = Array.new
-        @enum_new_hash[@tags[i]] = Array.new
-      end
-    end
-
-    # Determines a default value to use for anonymizing the given tag.
-    #
-    # @param [String] tag a data element tag
-    # @return [String, Integer, Float] the default replacement value for a given tag
-    #
-    def default_value(tag)
-      name, vr = LIBRARY.name_and_vr(tag)
-      conversion = VALUE_CONVERSION[vr] || :to_s
-      case conversion
-      when :to_i then return 0
-      when :to_f then return 0.0
-      else
-        # Assume type is string and return an empty string:
-        return ''
-      end
-    end
-
-    # Creates a write path for the given DICOM object, based on the object's
-    # original file path and the write_path attribute.
-    #
-    # @param [DObject] dcm a DICOM object
-    # @return [String] the destination directory path
-    #
-    def destination(dcm)
-      # Split the source path into dir and file:
-      source_dir = File.dirname(dcm.source)
-      source_folders = source_dir.split(File::SEPARATOR)
-      target_folders = @write_path.split(File::SEPARATOR)
-      # If the first element is the current dir symbol, get rid of it:
-      source_folders.delete('.')
-      # Check for equalness of folder names in a range limited by the shortest array:
-      common_length = [source_folders.length, target_folders.length].min
-      uncommon_index = nil
-      common_length.times do |i|
-        if target_folders[i] != source_folders[i]
-          uncommon_index = i
-          break
-        end
-      end
-      # Create the output path by joining the two paths together using the determined index:
-      append_path = uncommon_index ? source_folders[uncommon_index..-1] : nil
-      [target_folders, append_path].compact.join(File::SEPARATOR)
-    end
-
-    # Extracts all parents from a DObject instance which potentially
-    # have child (data) elements. This typically means the DObject
-    # instance itself as well as items (i.e. not sequences).
-    # Note that unless the @recursive attribute has been set,
-    # this method will only return the DObject (placed inside an array).
-    #
-    # @param [DObject] dcm a DICOM object
-    # @return [Array<DObject, Item>] an array containing either just a DObject or also all parental child items within the tag hierarchy
-    #
-    def element_parents(dcm)
-      parents = Array.new
-      parents << dcm
-      if @recursive
-        dcm.sequences.each do |s|
-          parents += element_parents_recursive(s)
-        end
-      end
-      parents
-    end
-
-    # Recursively extracts all item parents from a sequence instance (including
-    # any sub-sequences) which actually contain child (data) elements.
-    #
-    # @param [Sequence] sequence a Sequence instance
-    # @return [Array<Item>] an array containing items within the tag hierarchy that contains child elements
-    #
-    def element_parents_recursive(sequence)
-      parents = Array.new
-      sequence.items.each do |i|
-        parents << i if i.elements?
-        i.sequences.each do |s|
-          parents += element_parents_recursive(s)
-        end
-      end
-      parents
-    end
-
-    # Handles the enumeration for the given data element tag.
-    # If its value has been encountered before, its corresponding enumerated
-    # replacement value is retrieved, and if a new original value is encountered,
-    # a new enumerated replacement value is found by increasing an index by 1.
-    #
-    # @param [String, Integer, Float] original the original value of the tag to be anonymized
-    # @param [Fixnum] j the index of this tag in the tag-related instance arrays
-    # @return [String, Integer, Float] the replacement value which is used for the anonymization of the tag
-    #
-    def enumerated_value(original, j)
-      # Is enumeration requested for this tag?
-      if @enumerations[j]
-        if @audit_trail
-          # Check if the UID has been encountered already:
-          replacement = @audit_trail.replacement(@tags[j], at_value(original))
-          unless replacement
-            # This original value has not been encountered yet. Determine the index to use.
-            index = @audit_trail.records(@tags[j]).length + 1
-            # Create the replacement value:
-            if @values[j].is_a?(String)
-              replacement = @values[j] + index.to_s
-            else
-              replacement = @values[j] + index
-            end
-            # Add this tag record to the audit trail:
-            @audit_trail.add_record(@tags[j], at_value(original), replacement)
-          end
-        else
-          # Retrieve earlier used anonymization values:
-          previous_old = @enum_old_hash[@tags[j]]
-          previous_new = @enum_new_hash[@tags[j]]
-          p_index = previous_old.length
-          if previous_old.index(original) == nil
-            # Current value has not been encountered before:
-            replacement = @values[j]+(p_index + 1).to_s
-            # Store value in array (and hash):
-            previous_old << original
-            previous_new << replacement
-            @enum_old_hash[@tags[j]] = previous_old
-            @enum_new_hash[@tags[j]] = previous_new
-          else
-            # Current value has been observed before:
-            replacement = previous_new[previous_old.index(original)]
-          end
-        end
-      else
-        replacement = @values[j]
-      end
-      return replacement
-    end
-
-    # Establishes a prefix for a given UID tag.
-    # This makes it somewhat easier to distinguish
-    # between different types of random generated UIDs.
-    #
-    # @param [String] tag a data element string tag
-    #
-    def prefix(tag)
-      if @prefixes[tag]
-        @prefixes[tag]
-      else
-        @prefixes[tag] = @prefixes.length + 1
-        @prefixes[tag]
-      end
-    end
-
-    # Prepares the data for anonymization.
-    #
-    # @param [String, DObject, Array<String, DObject>] data single or multiple DICOM data (directories, file paths, binary strings, DICOM objects)
-    # @return [Array] the original data (wrapped in an array) as well as an array of loaded DObject instances
-    #
-    def prepare(data)
-      logger.info("Loading DICOM data.")
-      # Temporarily adjust the ruby-dicom log threshold (usually to suppress messages from the DObject class):
-      @original_level = logger.level
-      logger.level = @logger_level
-      dicom = DICOM.load(data)
-      logger.level = @original_level
-      logger.info("#{dicom.length} DICOM objects have been prepared for anonymization.")
-      logger.level = @logger_level
-      # Set up enumeration if requested:
-      create_enum_hash if @enumeration
-      require 'securerandom' if @random_file_name
-      dicom
-    end
-
-    # Replaces the UIDs of the given DICOM object.
-    #
-    # @note Empty UIDs are ignored (we don't generate new UIDs for these).
-    # @note If AuditTrail is set, the relationship between old and new UIDs are preserved,
-    #   and the relations between files in a study/series should remain valid.
-    # @param [Array<DObject, Item>] parents dicom parent objects who's child elements will be investigated
-    #
-    def replace_uids(parents)
-      parents.each do |parent|
-        parent.each_element do |element|
-          if element.vr == ('UI') and !@static_uids[element.tag]
-            original = element.value
-            if original && original.length > 0
-              # We have a UID value, go ahead and replace it:
-              if @audit_trail
-                # Check if the UID has been encountered already:
-                replacement = @audit_trail.replacement('uids', original)
-                unless replacement
-                  # The UID has not been stored previously. Generate a new one:
-                  replacement = DICOM.generate_uid(@uid_root, prefix(element.tag))
-                  # Add this tag record to the audit trail:
-                  @audit_trail.add_record('uids', original, replacement)
-                end
-                # Replace the UID in the DICOM object:
-                element.value = replacement
-              else
-                # We don't care about preserving UID relations. Just insert a custom UID:
-                element.value = DICOM.generate_uid(@uid_root, prefix(element.tag))
-              end
-            end
-          end
-        end
-      end
-    end
-
-    # Sets up some default information variables that are used by the Anonymizer.
-    #
-    def set_defaults
-      # Some UIDs should not be remapped even if uid anonymization has been requested:
-      @static_uids = {
-        # Private related:
-        '0002,0100' => true,
-        '0004,1432' => true,
-        # Coding scheme related:
-        '0008,010C' => true,
-        '0008,010D' => true,
-        # Transfer syntax related:
-        '0002,0010' => true,
-        '0400,0010' => true,
-        '0400,0510' => true,
-        '0004,1512' => true,
-        # SOP class related:
-        '0000,0002' => true,
-        '0000,0003' => true,
-        '0002,0002' => true,
-        '0004,1510' => true,
-        '0004,151A' => true,
-        '0008,0016' => true,
-        '0008,001A' => true,
-        '0008,001B' => true,
-        '0008,0062' => true,
-        '0008,1150' => true,
-        '0008,115A' => true
-      }
-      # Sets up default tags that will be anonymized, along with default replacement values and enumeration settings.
-      # This data is stored in 3 separate instance arrays for tags, values and enumeration.
-      data = [
-        ['0008,0012', '20000101', false], # Instance Creation Date
-        ['0008,0013', '000000.00', false], # Instance Creation Time
-        ['0008,0020', '20000101', false], # Study Date
-        ['0008,0021', '20000101', false], # Series Date
-        ['0008,0022', '20000101', false], # Acquisition Date
-        ['0008,0023', '20000101', false], # Image Date
-        ['0008,0030', '000000.00', false], # Study Time
-        ['0008,0031', '000000.00', false], # Series Time
-        ['0008,0032', '000000.00', false], # Acquisition Time
-        ['0008,0033', '000000.00', false], # Image Time
-        ['0008,0050', '', true], # Accession Number
-        ['0008,0080', 'Institution', true], # Institution name
-        ['0008,0081', 'Address', true], # Institution Address
-        ['0008,0090', 'Physician', true], # Referring Physician's name
-        ['0008,1010', 'Station', true], # Station name
-        ['0008,1040', 'Department', true], # Institutional Department name
-        ['0008,1070', 'Operator', true], # Operator's Name
-        ['0010,0010', 'Patient', true], # Patient's name
-        ['0010,0020', 'ID', true], # Patient's ID
-        ['0010,0030', '20000101', false], # Patient's Birth Date
-        ['0010,0040', 'O', false], # Patient's Sex
-        ['0010,1010', '', false], # Patient's Age
-        ['0020,4000', '', false], # Image Comments
-      ].transpose
-      @tags = data[0]
-      @values = data[1]
-      @enumerations = data[2]
-      # Tags to be deleted completely during anonymization:
-      @delete = Hash.new
-    end
-
-    # Collects the attributes of this instance.
-    #
-    # @return [Array] an array of attributes
-    #
-    def state
-       [
-        @tags, @values, @enumerations, @delete, @blank,
-        @delete_private, @enumeration, @logger_level,
-        @random_file_name, @recursive, @uid, @uid_root, @write_path
-       ]
-    end
-
-    # Writes a DICOM object to file.
-    #
-    # @param [DObject] dcm a DICOM object
-    #
-    def write(dcm)
-      if @write_path
-        # The DICOM object is to be written to a separate directory. If the
-        # original and the new directories have a common root, this is taken into
-        # consideration when determining the object's write path:
-        path = destination(dcm)
-        if @random_file_name
-          file_name = "#{SecureRandom.hex(16)}.dcm"
-        else
-          file_name = File.basename(dcm.source)
-        end
-        dcm.write(File.join(path, file_name))
-      else
-        # The original DICOM file is overwritten with the anonymized DICOM object:
-        dcm.write(dcm.source)
-      end
-    end
-
-  end
-
-end
+module DICOM
+
+  # This is a convenience class for handling the anonymization
+  # (de-identification) of DICOM files.
+  #
+  # @note
+  #   For a thorough introduction to the concept of DICOM anonymization,
+  #   please refer to The DICOM Standard, Part 15: Security and System
+  #   Management Profiles, Annex E: Attribute Confidentiality Profiles.
+  #   For guidance on settings for individual data elements, please
+  #   refer to DICOM PS 3.15, Annex E, Table E.1-1: Application Level
+  #   Confidentiality Profile Attributes.
+  #
+  class Anonymizer
+    include Logging
+
+    # An AuditTrail instance used for this anonymization (if specified).
+    attr_reader :audit_trail
+    # The file name used for the AuditTrail serialization (if specified).
+    attr_reader :audit_trail_file
+    # A boolean that if set as true will cause all anonymized tags to be blank instead of get some generic value.
+    attr_accessor :blank
+    # An hash of elements (represented by tag keys) that will be deleted from the DICOM objects on anonymization.
+    attr_reader :delete
+    # A boolean that if set as true, will make the anonymization delete all private tags.
+    attr_accessor :delete_private
+    # The cryptographic hash function to be used for encrypting DICOM values recorded in an audit trail file.
+    attr_reader :encryption
+    # A boolean that if set as true will cause all anonymized tags to be get enumerated values, to enable post-anonymization re-identification by the user.
+    attr_accessor :enumeration
+    # The logger level which is applied to DObject operations during anonymization (defaults to Logger::FATAL).
+    attr_reader :logger_level
+    # A boolean that if set as true will cause all anonymized files to be written with random file names (if write_path has been specified).
+    attr_accessor :random_file_name
+    # A boolean that if set as true, will cause the anonymization to run on all levels of the DICOM file tag hierarchy.
+    attr_accessor :recursive
+    # A boolean indicating whether or not UIDs shall be replaced when executing the anonymization.
+    attr_accessor :uid
+    # The DICOM UID root to use when generating new UIDs.
+    attr_accessor :uid_root
+    # The path where the anonymized files will be saved. If this value is not set, the original DICOM files will be overwritten.
+    attr_accessor :write_path
+
+    # Creates an Anonymizer instance.
+    #
+    # @note To customize logging behaviour, refer to the Logging module documentation.
+    # @param [Hash] options the options to create an anonymizer instance with
+    # @option options [String] :audit_trail a file name path (if the file contains old audit data, these are loaded and used in the current anonymization)
+    # @option options [Boolean] :blank toggles whether to set the values of anonymized elements as empty instead of some generic value
+    # @option options [Boolean] :delete_private toggles whether private elements are to be deleted
+    # @option options [TrueClass, Digest::Class] :encryption if set as true, the default hash function (MD5) will be used for representing DICOM values in an audit file. Otherwise a Digest class can be given, e.g. Digest::SHA256
+    # @option options [Boolean] :enumeration toggles whether (some) elements get enumerated values (to enable post-anonymization re-identification)
+    # @option options [Fixnum] :logger_level the logger level which is applied to DObject operations during anonymization (defaults to Logger::FATAL)
+    # @option options [Boolean] :random_file_name toggles whether anonymized files will be given random file names when rewritten (in combination with the :write_path option)
+    # @option options [Boolean] :recursive toggles whether to anonymize on all sub-levels of the DICOM object tag hierarchies
+    # @option options [Boolean] :uid toggles whether UIDs will be replaced with custom generated UIDs (beware that to preserve UID relations in studies/series, the audit_trail feature must be used)
+    # @option options [String] :uid_root an organization (or custom) UID root to use when replacing UIDs
+    # @option options [String] :write_path a directory where the anonymized files are re-written (if not specified, files are overwritten)
+    # @example Create an Anonymizer instance and increase the log output
+    #   a = Anonymizer.new
+    #   a.logger.level = Logger::INFO
+    # @example Perform anonymization using the audit trail feature
+    #   a = Anonymizer.new(:audit_trail => 'trail.json')
+    #   a.enumeration = true
+    #   a.write_path = '//anonymized/'
+    #   a.anonymize('//dicom/today/')
+    #
+    def initialize(options={})
+      # Transfer options to attributes:
+      @blank = options[:blank]
+      @delete_private = options[:delete_private]
+      @enumeration = options[:enumeration]
+      @logger_level = options[:logger_level] || Logger::FATAL
+      @random_file_name = options[:random_file_name]
+      @recursive = options[:recursive]
+      @uid = options[:uid]
+      @uid_root = options[:uid_root] ? options[:uid_root] : UID_ROOT
+      @write_path = options[:write_path]
+      # Array of folders to be processed for anonymization:
+      @folders = Array.new
+      # Folders that will be skipped:
+      @exceptions = Array.new
+      # Data elements which will be anonymized (the array will hold a list of tag strings):
+      @tags = Array.new
+      # Default values to use on anonymized data elements:
+      @values = Array.new
+      # Which data elements will have enumeration applied, if requested by the user:
+      @enumerations = Array.new
+      # We use a Hash to store information from DICOM files if enumeration is desired:
+      @enum_old_hash = Hash.new
+      @enum_new_hash = Hash.new
+      # All the files to be anonymized will be put in this array:
+      @files = Array.new
+      @prefixes = Hash.new
+      # Setup audit trail if requested:
+      if options[:audit_trail]
+        @audit_trail_file = options[:audit_trail]
+        if File.exists?(@audit_trail_file) && File.size(@audit_trail_file) > 2
+          # Load the pre-existing audit trail from file:
+          @audit_trail = AuditTrail.read(@audit_trail_file)
+        else
+          # Start from scratch with an empty audit trail:
+          @audit_trail = AuditTrail.new
+        end
+        # Set up encryption if indicated:
+        if options[:encryption]
+          require 'digest'
+          if options[:encryption].respond_to?(:hexdigest)
+            @encryption = options[:encryption]
+          else
+            @encryption = Digest::MD5
+          end
+        end
+      end
+      # Set the default data elements to be anonymized:
+      set_defaults
+    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_anonymizer)
+        other.send(:state) == state
+      end
+    end
+
+    alias_method :eql?, :==
+
+    # Anonymizes the given DICOM data with the settings of this Anonymizer instance.
+    #
+    # @param [String, DObject, Array<String, DObject>] data single or multiple DICOM data (directories, file paths, binary strings, DICOM objects)
+    # @return [Array<DObject>] an array of the anonymized DICOM objects
+    #
+    def anonymize(data)
+      dicom = prepare(data)
+      if @tags.length > 0
+        dicom.each do |dcm|
+          anonymize_dcm(dcm)
+          # Write DICOM object to file unless it was passed to the anonymizer as an object:
+          write(dcm) unless dcm.was_dcm_on_input
+        end
+      else
+        logger.warn("No tags have been selected for anonymization. Aborting anonymization.")
+      end
+      # Reset the ruby-dicom log threshold to its original level:
+      logger.level = @original_level
+      # Save the audit trail (if used):
+      @audit_trail.write(@audit_trail_file) if @audit_trail
+      logger.info("Anonymization complete.")
+      dicom
+    end
+
+    # Specifies that the given tag is to be completely deleted
+    # from the anonymized DICOM objects.
+    #
+    # @param [String] tag a data element tag
+    # @example Completely delete the Patient's Name tag from the DICOM files
+    #   a.delete_tag('0010,0010')
+    #
+    def delete_tag(tag)
+      raise ArgumentError, "Expected String, got #{tag.class}." unless tag.is_a?(String)
+      raise ArgumentError, "Expected a valid tag of format 'GGGG,EEEE', got #{tag}." unless tag.tag?
+      @delete[tag] = true
+    end
+
+    # Checks the enumeration status of this tag.
+    #
+    # @param [String] tag a data element tag
+    # @return [Boolean, NilClass] the enumeration status of the tag, or nil if the tag has no match
+    #
+    def enum(tag)
+      raise ArgumentError, "Expected String, got #{tag.class}." unless tag.is_a?(String)
+      raise ArgumentError, "Expected a valid tag of format 'GGGG,EEEE', got #{tag}." unless tag.tag?
+      pos = @tags.index(tag)
+      if pos
+        return @enumerations[pos]
+      else
+        logger.warn("The specified tag (#{tag}) was not found in the list of tags to be anonymized.")
+        return nil
+      end
+    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
+
+    # Removes a tag from the list of tags that will be anonymized.
+    #
+    # @param [String] tag a data element tag
+    # @example Do not anonymize the Patient's Name tag
+    #   a.remove_tag('0010,0010')
+    #
+    def remove_tag(tag)
+      raise ArgumentError, "Expected String, got #{tag.class}." unless tag.is_a?(String)
+      raise ArgumentError, "Expected a valid tag of format 'GGGG,EEEE', got #{tag}." unless tag.tag?
+      pos = @tags.index(tag)
+      if pos
+        @tags.delete_at(pos)
+        @values.delete_at(pos)
+        @enumerations.delete_at(pos)
+      end
+    end
+
+    # Sets the anonymization settings for the specified tag. If the tag is already present in the list
+    # of tags to be anonymized, its settings are updated, and if not, a new tag entry is created.
+    #
+    # @param [String] tag a data element tag
+    # @param [Hash] options the anonymization settings for the specified tag
+    # @option options [String, Integer, Float] :value the replacement value to be used when anonymizing this data element. Defaults to the pre-existing value and '' for new tags.
+    # @option options [String, Integer, Float] :enum specifies if enumeration is to be used for this tag. Defaults to the pre-existing value and false for new tags.
+    # @example Set the anonymization settings of the Patient's Name tag
+    #   a.set_tag('0010,0010', :value => 'MrAnonymous', :enum => true)
+    #
+    def set_tag(tag, options={})
+      raise ArgumentError, "Expected String, got #{tag.class}." unless tag.is_a?(String)
+      raise ArgumentError, "Expected a valid tag of format 'GGGG,EEEE', got #{tag}." unless tag.tag?
+      pos = @tags.index(tag)
+      if pos
+        # Update existing values:
+        @values[pos] = options[:value] if options[:value]
+        @enumerations[pos] = options[:enum] if options[:enum] != nil
+      else
+        # Add new elements:
+        @tags << tag
+        @values << (options[:value] ? options[:value] : default_value(tag))
+        @enumerations << (options[:enum] ? options[:enum] : false)
+      end
+    end
+
+    # Returns self.
+    #
+    # @return [Anonymizer] self
+    #
+    def to_anonymizer
+      self
+    end
+
+    # Gives the value which will be used when anonymizing this tag.
+    #
+    # @note If enumeration is selected for a string type tag, a number will be
+    #   appended in addition to the string that is returned here.
+    #
+    # @param [String] tag a data element tag
+    # @return [String, Integer, Float, NilClass] the replacement value for the specified tag, or nil if the tag is not matched
+    #
+    def value(tag)
+      raise ArgumentError, "Expected String, got #{tag.class}." unless tag.is_a?(String)
+      raise ArgumentError, "Expected a valid tag of format 'GGGG,EEEE', got #{tag}." unless tag.tag?
+      pos = @tags.index(tag)
+      if pos
+        return @values[pos]
+      else
+        logger.warn("The specified tag (#{tag}) was not found in the list of tags to be anonymized.")
+        return nil
+      end
+    end
+
+
+    private
+
+
+    # Performs anonymization on a DICOM object.
+    #
+    # @param [DObject] dcm a DICOM object
+    #
+    def anonymize_dcm(dcm)
+      # Extract the data element parents to investigate:
+      parents = element_parents(dcm)
+      parents.each do |parent|
+        # Anonymize the desired tags:
+        @tags.each_index do |j|
+          if parent.exists?(@tags[j])
+            element = parent[@tags[j]]
+            if element.is_a?(Element)
+              if @blank
+                value = ''
+              elsif @enumeration
+                old_value = element.value
+                # Only launch enumeration logic if there is an actual value to the data element:
+                if old_value
+                  value = enumerated_value(old_value, j)
+                else
+                  value = ''
+                end
+              else
+                # Use the value that has been set for this tag:
+                value = @values[j]
+              end
+              element.value = value
+            end
+          end
+        end
+        # Delete elements marked for deletion:
+        @delete.each_key do |tag|
+          parent.delete(tag) if parent.exists?(tag)
+        end
+      end
+      # General DICOM object manipulation:
+      # Add a Patient Identity Removed attribute (as per
+      # DICOM PS 3.15, Annex E, E.1.1 De-Identifier, point 6):
+      dcm.add(Element.new('0012,0062', 'YES'))
+      # Add a De-Identification Method Code Sequence Item:
+      dcm.add(Sequence.new('0012,0064')) unless dcm.exists?('0012,0064')
+      i = dcm['0012,0064'].add_item
+      i.add(Element.new('0012,0063', 'De-identified by the ruby-dicom Anonymizer'))
+      # FIXME: At some point we should add a set of de-indentification method codes, as per
+      #   DICOM PS 3.16 CID 7050 which corresponds to the settings chosen for the anonymizer.
+      # Delete the old File Meta Information group (as per
+      # DICOM PS 3.15, Annex E, E.1.1 De-Identifier, point 7):
+      dcm.delete_group('0002')
+      # Handle UIDs if requested:
+      replace_uids(parents) if @uid
+      # Delete private tags if indicated:
+      dcm.delete_private if @delete_private
+    end
+
+    # Gives the value to be used for the audit trail, which is either
+    # the original value itself, or an encrypted string based on it.
+    #
+    # @param [String, Integer, Float] original the original value of the tag to be anonymized
+    # @return [String, Integer, Float] with encryption, a hash string is returned, otherwise the original value
+    #
+    def at_value(original)
+      @encryption ? @encryption.hexdigest(original) : original
+    end
+
+    # Creates a hash that is used for storing information that is used when enumeration is selected.
+    #
+    def create_enum_hash
+      @enumerations.each_index do |i|
+        @enum_old_hash[@tags[i]] = Array.new
+        @enum_new_hash[@tags[i]] = Array.new
+      end
+    end
+
+    # Determines a default value to use for anonymizing the given tag.
+    #
+    # @param [String] tag a data element tag
+    # @return [String, Integer, Float] the default replacement value for a given tag
+    #
+    def default_value(tag)
+      name, vr = LIBRARY.name_and_vr(tag)
+      conversion = VALUE_CONVERSION[vr]
+      case conversion
+      when :to_i then return 0
+      when :to_f then return 0.0
+      else
+        # Assume type is string and return an empty string:
+        return ''
+      end
+    end
+
+    # Creates a write path for the given DICOM object, based on the object's
+    # original file path and the write_path attribute.
+    #
+    # @param [DObject] dcm a DICOM object
+    # @return [String] the destination directory path
+    #
+    def destination(dcm)
+      # Separate the path from the source file string:
+      file_start = dcm.source.rindex(File.basename(dcm.source))
+      if file_start == 0
+        source_dir = "."
+      else
+        source_dir = dcm.source[0..(file_start-1)]
+      end
+      source_folders = source_dir.split(File::SEPARATOR)
+      target_folders = @write_path.split(File::SEPARATOR)
+      # If the first element is the current dir symbol, get rid of it:
+      source_folders.delete('.')
+      # Check for equalness of folder names in a range limited by the shortest array:
+      common_length = [source_folders.length, target_folders.length].min
+      uncommon_index = nil
+      common_length.times do |i|
+        if target_folders[i] != source_folders[i]
+          uncommon_index = i
+          break
+        end
+      end
+      # Create the output path by joining the two paths together using the determined index:
+      append_path = uncommon_index ? source_folders[uncommon_index..-1] : nil
+      [target_folders, append_path].compact.join(File::SEPARATOR)
+    end
+
+    # Extracts all parents from a DObject instance which potentially
+    # have child (data) elements. This typically means the DObject
+    # instance itself as well as items (i.e. not sequences).
+    # Note that unless the @recursive attribute has been set,
+    # this method will only return the DObject (placed inside an array).
+    #
+    # @param [DObject] dcm a DICOM object
+    # @return [Array<DObject, Item>] an array containing either just a DObject or also all parental child items within the tag hierarchy
+    #
+    def element_parents(dcm)
+      parents = Array.new
+      parents << dcm
+      if @recursive
+        dcm.sequences.each do |s|
+          parents += element_parents_recursive(s)
+        end
+      end
+      parents
+    end
+
+    # Recursively extracts all item parents from a sequence instance (including
+    # any sub-sequences) which actually contain child (data) elements.
+    #
+    # @param [Sequence] sequence a Sequence instance
+    # @return [Array<Item>] an array containing items within the tag hierarchy that contains child elements
+    #
+    def element_parents_recursive(sequence)
+      parents = Array.new
+      sequence.items.each do |i|
+        parents << i if i.elements?
+        i.sequences.each do |s|
+          parents += element_parents_recursive(s)
+        end
+      end
+      parents
+    end
+
+    # Handles the enumeration for the given data element tag.
+    # If its value has been encountered before, its corresponding enumerated
+    # replacement value is retrieved, and if a new original value is encountered,
+    # a new enumerated replacement value is found by increasing an index by 1.
+    #
+    # @param [String, Integer, Float] original the original value of the tag to be anonymized
+    # @param [Fixnum] j the index of this tag in the tag-related instance arrays
+    # @return [String, Integer, Float] the replacement value which is used for the anonymization of the tag
+    #
+    def enumerated_value(original, j)
+      # Is enumeration requested for this tag?
+      if @enumerations[j]
+        if @audit_trail
+          # Check if the UID has been encountered already:
+          replacement = @audit_trail.replacement(@tags[j], at_value(original))
+          unless replacement
+            # This original value has not been encountered yet. Determine the index to use.
+            index = @audit_trail.records(@tags[j]).length + 1
+            # Create the replacement value:
+            if @values[j].is_a?(String)
+              replacement = @values[j] + index.to_s
+            else
+              replacement = @values[j] + index
+            end
+            # Add this tag record to the audit trail:
+            @audit_trail.add_record(@tags[j], at_value(original), replacement)
+          end
+        else
+          # Retrieve earlier used anonymization values:
+          previous_old = @enum_old_hash[@tags[j]]
+          previous_new = @enum_new_hash[@tags[j]]
+          p_index = previous_old.length
+          if previous_old.index(original) == nil
+            # Current value has not been encountered before:
+            replacement = @values[j]+(p_index + 1).to_s
+            # Store value in array (and hash):
+            previous_old << original
+            previous_new << replacement
+            @enum_old_hash[@tags[j]] = previous_old
+            @enum_new_hash[@tags[j]] = previous_new
+          else
+            # Current value has been observed before:
+            replacement = previous_new[previous_old.index(original)]
+          end
+        end
+      else
+        replacement = @values[j]
+      end
+      return replacement
+    end
+
+    # Establishes a prefix for a given UID tag.
+    # This makes it somewhat easier to distinguish
+    # between different types of random generated UIDs.
+    #
+    # @param [String] tag a data element string tag
+    #
+    def prefix(tag)
+      if @prefixes[tag]
+        @prefixes[tag]
+      else
+        @prefixes[tag] = @prefixes.length + 1
+        @prefixes[tag]
+      end
+    end
+
+    # Prepares the data for anonymization.
+    #
+    # @param [String, DObject, Array<String, DObject>] data single or multiple DICOM data (directories, file paths, binary strings, DICOM objects)
+    # @return [Array] the original data (wrapped in an array) as well as an array of loaded DObject instances
+    #
+    def prepare(data)
+      logger.info("Loading DICOM data.")
+      # Temporarily adjust the ruby-dicom log threshold (usually to suppress messages from the DObject class):
+      @original_level = logger.level
+      logger.level = @logger_level
+      dicom = DICOM.load(data)
+      logger.level = @original_level
+      logger.info("#{dicom.length} DICOM objects have been prepared for anonymization.")
+      logger.level = @logger_level
+      # Set up enumeration if requested:
+      create_enum_hash if @enumeration
+      require 'securerandom' if @random_file_name
+      dicom
+    end
+
+    # Replaces the UIDs of the given DICOM object.
+    #
+    # @note Empty UIDs are ignored (we don't generate new UIDs for these).
+    # @note If AuditTrail is set, the relationship between old and new UIDs are preserved,
+    #   and the relations between files in a study/series should remain valid.
+    # @param [Array<DObject, Item>] parents dicom parent objects who's child elements will be investigated
+    #
+    def replace_uids(parents)
+      parents.each do |parent|
+        parent.each_element do |element|
+          if element.vr == ('UI') and !@static_uids[element.tag]
+            original = element.value
+            if original && original.length > 0
+              # We have a UID value, go ahead and replace it:
+              if @audit_trail
+                # Check if the UID has been encountered already:
+                replacement = @audit_trail.replacement('uids', original)
+                unless replacement
+                  # The UID has not been stored previously. Generate a new one:
+                  replacement = DICOM.generate_uid(@uid_root, prefix(element.tag))
+                  # Add this tag record to the audit trail:
+                  @audit_trail.add_record('uids', original, replacement)
+                end
+                # Replace the UID in the DICOM object:
+                element.value = replacement
+              else
+                # We don't care about preserving UID relations. Just insert a custom UID:
+                element.value = DICOM.generate_uid(@uid_root, prefix(element.tag))
+              end
+            end
+          end
+        end
+      end
+    end
+
+    # Sets up some default information variables that are used by the Anonymizer.
+    #
+    def set_defaults
+      # Some UIDs should not be remapped even if uid anonymization has been requested:
+      @static_uids = {
+        # Private related:
+        '0002,0100' => true,
+        '0004,1432' => true,
+        # Coding scheme related:
+        '0008,010C' => true,
+        '0008,010D' => true,
+        # Transfer syntax related:
+        '0002,0010' => true,
+        '0400,0010' => true,
+        '0400,0510' => true,
+        '0004,1512' => true,
+        # SOP class related:
+        '0000,0002' => true,
+        '0000,0003' => true,
+        '0002,0002' => true,
+        '0004,1510' => true,
+        '0004,151A' => true,
+        '0008,0016' => true,
+        '0008,001A' => true,
+        '0008,001B' => true,
+        '0008,0062' => true,
+        '0008,1150' => true,
+        '0008,115A' => true
+      }
+      # Sets up default tags that will be anonymized, along with default replacement values and enumeration settings.
+      # This data is stored in 3 separate instance arrays for tags, values and enumeration.
+      data = [
+        ['0008,0012', '20000101', false], # Instance Creation Date
+        ['0008,0013', '000000.00', false], # Instance Creation Time
+        ['0008,0020', '20000101', false], # Study Date
+        ['0008,0021', '20000101', false], # Series Date
+        ['0008,0022', '20000101', false], # Acquisition Date
+        ['0008,0023', '20000101', false], # Image Date
+        ['0008,0030', '000000.00', false], # Study Time
+        ['0008,0031', '000000.00', false], # Series Time
+        ['0008,0032', '000000.00', false], # Acquisition Time
+        ['0008,0033', '000000.00', false], # Image Time
+        ['0008,0050', '', true], # Accession Number
+        ['0008,0080', 'Institution', true], # Institution name
+        ['0008,0081', 'Address', true], # Institution Address
+        ['0008,0090', 'Physician', true], # Referring Physician's name
+        ['0008,1010', 'Station', true], # Station name
+        ['0008,1040', 'Department', true], # Institutional Department name
+        ['0008,1070', 'Operator', true], # Operator's Name
+        ['0010,0010', 'Patient', true], # Patient's name
+        ['0010,0020', 'ID', true], # Patient's ID
+        ['0010,0030', '20000101', false], # Patient's Birth Date
+        ['0010,0040', 'O', false], # Patient's Sex
+        ['0010,1010', '', false], # Patient's Age
+        ['0020,4000', '', false], # Image Comments
+      ].transpose
+      @tags = data[0]
+      @values = data[1]
+      @enumerations = data[2]
+      # Tags to be deleted completely during anonymization:
+      @delete = Hash.new
+    end
+
+    # Collects the attributes of this instance.
+    #
+    # @return [Array] an array of attributes
+    #
+    def state
+       [
+        @tags, @values, @enumerations, @delete, @blank,
+        @delete_private, @enumeration, @logger_level,
+        @random_file_name, @recursive, @uid, @uid_root, @write_path
+       ]
+    end
+
+    # Writes a DICOM object to file.
+    #
+    # @param [DObject] dcm a DICOM object
+    #
+    def write(dcm)
+      if @write_path
+        # The DICOM object is to be written to a separate directory. If the
+        # original and the new directories have a common root, this is taken into
+        # consideration when determining the object's write path:
+        path = destination(dcm)
+        if @random_file_name
+          file_name = "#{SecureRandom.hex(16)}.dcm"
+        else
+          file_name = File.basename(dcm.source)
+        end
+        dcm.write(File.join(path, file_name))
+      else
+        # The original DICOM file is overwritten with the anonymized DICOM object:
+        dcm.write(dcm.source)
+      end
+    end
+
+  end
+
+end