dicom 0.7 → 0.8

data/lib/dicom/DServer.rb

@@ -1,304 +0,0 @@
-#    Copyright 2009-2010 Christoffer Lervag
-
-module DICOM
-
-  # This class contains code for setting up a Service Class Provider (SCP),
-  # which will act as a simple storage node (a server that receives images).
-  class DServer
-
-
-    # Run the server and take a block for initializing.
-    def self.run(port=104, path='./received/', &block)
-      server = DServer.new(port)
-      server.instance_eval(&block)
-      server.start_scp(path)
-    end
-
-    # Accessible attributes:
-    attr_accessor :host_ae, :max_package_size, :port, :timeout, :verbose, :file_handler
-    attr_reader :errors, :notices
-
-    # Initialize the instance with a host adress and a port number.
-    def initialize(port=104, options={})
-      require 'socket'
-      # Required parameters:
-      @port = port
-      # Optional parameters (and default values):
-      @file_handler = options[:file_handler] || FileHandler
-      @host_ae =  options[:host_ae]  || "RUBY_DICOM"
-      @max_package_size = options[:max_package_size] || 32768 # 16384
-      @timeout = options[:timeout] || 10 # seconds
-      @min_length = 12 # minimum number of bytes to expect in an incoming transmission
-      @verbose = options[:verbose]
-      @verbose = true if @verbose == nil # Default verbosity is 'on'.
-      # Other instance variables:
-      @errors = Array.new # errors and warnings are put in this array
-      @notices = Array.new # information on successful transmissions are put in this array
-      # Variables used for monitoring state of transmission:
-      @connection = nil # TCP connection status
-      @association = nil # DICOM Association status
-      @request_approved = nil # Status of our DICOM request
-      @release = nil # Status of received, valid release response
-      set_valid_abstract_syntaxes
-    end
-
-
-    # Add a specified abstract syntax to the list of syntaxes that the server instance will accept.
-    def add_abstract_syntax(value)
-      if value.is_a?(String)
-        @valid_abstract_syntaxes << value
-        @valid_abstract_syntaxes.sort!
-      else
-        add_error("Error: The specified abstract syntax is not a string!")
-      end
-    end
-
-
-    # Print the list of valid abstract syntaxes to the screen.
-    def print_syntaxes
-      puts "Abstract syntaxes accepted by this SCP:"
-      @valid_abstract_syntaxes.each do |syntax|
-        puts syntax
-      end
-    end
-
-
-    # Remove a specific abstract syntax from the list of syntaxes that the server instance will accept.
-    def remove_abstract_syntax(value)
-      if value.is_a?(String)
-        # Remove it:
-        @valid_abstract_syntaxes.delete(value)
-      else
-        add_error("Error: The specified abstract syntax is not a string!")
-      end
-    end
-
-
-    # Completely clear the list of syntaxes that the server instance will accept.
-    def remove_all_abstract_syntaxes
-      @valid_abstract_syntaxes = Array.new
-    end
-
-    # Start a Service Class Provider (SCP).
-    # This service will receive and store DICOM files in a specified folder.
-    def start_scp(path='./received/')
-      add_notice("Starting SCP server...")
-      add_notice("*********************************")
-      # Initiate server:
-      @scp = TCPServer.new(@port)
-      # Use a loop to listen for incoming messages:
-      loop do
-        Thread.start(@scp.accept) do |session|
-          # Initialize the network package handler for this session:
-          link = Link.new(:host_ae => @host_ae, :max_package_size => @max_package_size, :timeout => @timeout, :verbose => @verbose, :file_handler => @file_handler)
-          add_notice("Connection established (name: #{session.peeraddr[2]}, ip: #{session.peeraddr[3]})")
-          # Receive an incoming message:
-          #segments = link.receive_single_transmission(session)
-          segments = link.receive_multiple_transmissions(session)
-          info = segments.first
-          # Interpret the received message:
-          if info[:valid]
-            association_error = check_association_request(info)
-            unless association_error
-              syntax_result = check_syntax_requests(link, info)
-              link.handle_association_accept(session, info, syntax_result)
-              if syntax_result == "00" # Normal (no error)
-                add_notice("An incoming association request and its abstract syntax has been accepted.")
-                if info[:abstract_syntax] == "1.2.840.10008.1.1"
-                  # Verification SOP Class (used for testing connections):
-                  link.handle_release(session)
-                else
-                  # Process the incoming data:
-                  success, message = link.handle_incoming_data(session, path)
-                  if success
-                    add_notice(message)
-                    # Send a receipt for received data:
-                    link.handle_response(session)
-                  else
-                    # Something has gone wrong:
-                    add_error(message)
-                  end
-                  # Release the connection:
-                  link.handle_release(session)
-                end
-              else
-                # Abstract syntax in the incoming request was not accepted:
-                add_notice("An incoming association request was accepted, but it's abstract syntax was rejected. (#{abstract_syntax})")
-                # Since the requested abstract syntax was not accepted, the association must be released.
-                link.handle_release(session)
-              end
-            else
-              # The incoming association was not formally correct.
-              link.handle_rejection(session)
-            end
-          else
-            # The incoming message was not recognised as a valid DICOM message. Abort:
-            link.handle_abort(session)
-          end
-          # Terminate the connection:
-          session.close unless session.closed?
-          add_notice("Connection closed.")
-          add_notice("*********************************")
-        end
-      end
-    end
-
-
-    # Following methods are private:
-    private
-
-
-    # Adds a warning or error message to the instance array holding messages, and if verbose variable is true, prints the message as well.
-    def add_error(error)
-      if @verbose
-        puts error
-      end
-      @errors << error
-    end
-
-
-    # Adds a notice (information regarding progress or successful communications) to the instance array,
-    # and if verbosity is set for these kinds of messages, prints it to the screen as well.
-    def add_notice(notice)
-      if @verbose
-        puts notice
-      end
-      @notices << notice
-    end
-
-
-    # Check if the association request is formally correct.
-    # Things that can be checked here, are:
-    # Application context name, calling AE title, called AE title
-    # Error codes are given in the official dicom document, part 08_08, page 41
-    def check_association_request(info)
-      error = nil
-      # For the moment there is no control on AE titles.
-      # Check that Application context name is as expected:
-      if info[:application_context] != "1.2.840.10008.3.1.1.1"
-        error = "02" # application context name not supported
-        add_error("Warning: Application context not recognised in the incoming association request. (#{info[:application_context]})")
-      end
-      return error
-    end
-
-
-    # Check if the requested abstract syntax & transfer syntax are supported:
-    # Error codes are given in the official dicom document, part 08_08, page 39
-    def check_syntax_requests(link, info)
-      result = "00" # (no error)
-      # We will accept any transfer syntax (as long as it is recognized in the library):
-      # (Weakness: Only checking the first occuring transfer syntax for now)
-      transfer_syntax = link.extract_transfer_syntax(info)
-      unless LIBRARY.check_ts_validity(transfer_syntax)
-        result = "04" # transfer syntax not supported
-        add_error("Warning: Unsupported transfer syntax received in incoming association request. (#{transfer_syntax})")
-      end
-      # Check that abstract syntax is among the ones that have been set as valid for this server instance:
-      abstract_syntax = link.extract_abstract_syntax(info)
-      unless @valid_abstract_syntaxes.include?(abstract_syntax)
-        result = "03" # abstract syntax not supported
-      end
-      return result
-    end
-
-
-    # Set the default valid abstract syntaxes for our SCP.
-    def set_valid_abstract_syntaxes
-      @valid_abstract_syntaxes = [
-        "1.2.840.10008.1.1", # "Verification SOP Class"
-        "1.2.840.10008.5.1.4.1.1.1", # "Computed Radiography Image Storage"
-        "1.2.840.10008.5.1.4.1.1.1.1", # "Digital X-Ray Image Storage - For Presentation"
-        "1.2.840.10008.5.1.4.1.1.1.1.1", # "Digital X-Ray Image Storage - For Processing"
-        "1.2.840.10008.5.1.4.1.1.1.2", # "Digital Mammography X-Ray Image Storage - For Presentation"
-        "1.2.840.10008.5.1.4.1.1.1.2.1", # "Digital Mammography X-Ray Image Storage - For Processing"
-        "1.2.840.10008.5.1.4.1.1.1.3", # "Digital Intra-oral X-Ray Image Storage - For Presentation"
-        "1.2.840.10008.5.1.4.1.1.1.3.1", # "Digital Intra-oral X-Ray Image Storage - For Processing"
-        "1.2.840.10008.5.1.4.1.1.2", # "CT Image Storage"
-        "1.2.840.10008.5.1.4.1.1.2.1", # "Enhanced CT Image Storage"
-        "1.2.840.10008.5.1.4.1.1.3", # "Ultrasound Multi-frame Image Storage" # RET
-        "1.2.840.10008.5.1.4.1.1.3.1", # "Ultrasound Multi-frame Image Storage"
-        "1.2.840.10008.5.1.4.1.1.4", # "MR Image Storage"
-        "1.2.840.10008.5.1.4.1.1.4.1", # "Enhanced MR Image Storage"
-        "1.2.840.10008.5.1.4.1.1.4.2", # "MR Spectroscopy Storage"
-        "1.2.840.10008.5.1.4.1.1.5", # "Nuclear Medicine Image Storage"
-        "1.2.840.10008.5.1.4.1.1.6", # "Ultrasound Image Storage"
-        "1.2.840.10008.5.1.4.1.1.6.1", # "Ultrasound Image Storage"
-        "1.2.840.10008.5.1.4.1.1.7", # "Secondary Capture Image Storage"
-        "1.2.840.10008.5.1.4.1.1.7.1", # "Multi-frame Single Bit Secondary Capture Image Storage"
-        "1.2.840.10008.5.1.4.1.1.7.2", # "Multi-frame Grayscale Byte Secondary Capture Image Storage"
-        "1.2.840.10008.5.1.4.1.1.7.3", # "Multi-frame Grayscale Word Secondary Capture Image Storage"
-        "1.2.840.10008.5.1.4.1.1.7.4", # "Multi-frame True Color Secondary Capture Image Storage"
-        "1.2.840.10008.5.1.4.1.1.8", # "Standalone Overlay Storage" # RET
-        "1.2.840.10008.5.1.4.1.1.9", # "Standalone Curve Storage" # RET
-        "1.2.840.10008.5.1.4.1.1.9.1", # "Waveform Storage - Trial" # RET
-        "1.2.840.10008.5.1.4.1.1.9.1.1", # "12-lead ECG Waveform Storage"
-        "1.2.840.10008.5.1.4.1.1.9.1.2", # "General ECG Waveform Storage"
-        "1.2.840.10008.5.1.4.1.1.9.1.3", # "Ambulatory ECG Waveform Storage"
-        "1.2.840.10008.5.1.4.1.1.9.2.1", # "Hemodynamic Waveform Storage"
-        "1.2.840.10008.5.1.4.1.1.9.3.1", # "Cardiac Electrophysiology Waveform Storage"
-        "1.2.840.10008.5.1.4.1.1.9.4.1", # "Basic Voice Audio Waveform Storage"
-        "1.2.840.10008.5.1.4.1.1.10", # "Standalone Modality LUT Storage" # RET
-        "1.2.840.10008.5.1.4.1.1.11", # "Standalone VOI LUT Storage" # RET
-        "1.2.840.10008.5.1.4.1.1.11.1", # "Grayscale Softcopy Presentation State Storage SOP Class"
-        "1.2.840.10008.5.1.4.1.1.11.2", # "Color Softcopy Presentation State Storage SOP Class"
-        "1.2.840.10008.5.1.4.1.1.11.3", # "Pseudo-Color Softcopy Presentation State Storage SOP Class"
-        "1.2.840.10008.5.1.4.1.1.11.4", # "Blending Softcopy Presentation State Storage SOP Class"
-        "1.2.840.10008.5.1.4.1.1.12.1", # "X-Ray Angiographic Image Storage"
-        "1.2.840.10008.5.1.4.1.1.12.1.1", # "Enhanced XA Image Storage"
-        "1.2.840.10008.5.1.4.1.1.12.2", # "X-Ray Radiofluoroscopic Image Storage"
-        "1.2.840.10008.5.1.4.1.1.12.2.1", # "Enhanced XRF Image Storage"
-        "1.2.840.10008.5.1.4.1.1.13.1.1", # "X-Ray 3D Angiographic Image Storage"
-        "1.2.840.10008.5.1.4.1.1.13.1.2", # "X-Ray 3D Craniofacial Image Storage"
-        "1.2.840.10008.5.1.4.1.1.12.3", # "X-Ray Angiographic Bi-Plane Image Storage" # RET
-        "1.2.840.10008.5.1.4.1.1.20", # "Nuclear Medicine Image Storage"
-        "1.2.840.10008.5.1.4.1.1.66", # "Raw Data Storage"
-        "1.2.840.10008.5.1.4.1.1.66.1", # "Spatial Registration Storage"
-        "1.2.840.10008.5.1.4.1.1.66.2", # "Spatial Fiducials Storage"
-        "1.2.840.10008.5.1.4.1.1.66.3", # "Deformable Spatial Registration Storage"
-        "1.2.840.10008.5.1.4.1.1.66.4", # "Segmentation Storage"
-        "1.2.840.10008.5.1.4.1.1.67", # "Real World Value Mapping Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1", # "VL Image Storage - Trial" # RET
-        "1.2.840.10008.5.1.4.1.1.77.2", # "VL Multi-frame Image Storage - Trial" # RET
-        "1.2.840.10008.5.1.4.1.1.77.1.1", # "VL Endoscopic Image Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1.1.1", # "Video Endoscopic Image Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1.2", # "VL Microscopic Image Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1.2.1", # "Video Microscopic Image Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1.3", # "VL Slide-Coordinates Microscopic Image Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1.4", # "VL Photographic Image Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1.4.1", # "Video Photographic Image Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1.5.1", # "Ophthalmic Photography 8 Bit Image Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1.5.2", # "Ophthalmic Photography 16 Bit Image Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1.5.3", # "Stereometric Relationship Storage"
-        "1.2.840.10008.5.1.4.1.1.77.1.5.4", # "Ophthalmic Tomography Image Storage"
-        "1.2.840.10008.5.1.4.1.1.88.1", # "Text SR Storage - Trial" # RET
-        "1.2.840.10008.5.1.4.1.1.88.2", # "Audio SR Storage - Trial" # RET
-        "1.2.840.10008.5.1.4.1.1.88.3", # "Detail SR Storage - Trial" # RET
-        "1.2.840.10008.5.1.4.1.1.88.4", # "Comprehensive SR Storage - Trial" # RET
-        "1.2.840.10008.5.1.4.1.1.88.11", # "Basic Text SR Storage"
-        "1.2.840.10008.5.1.4.1.1.88.22", # "Enhanced SR Storage"
-        "1.2.840.10008.5.1.4.1.1.88.33", # "Comprehensive SR Storage"
-        "1.2.840.10008.5.1.4.1.1.88.40", # "Procedure Log Storage"
-        "1.2.840.10008.5.1.4.1.1.88.50", # "Mammography CAD SR Storage"
-        "1.2.840.10008.5.1.4.1.1.88.59", # "Key Object Selection Document Storage"
-        "1.2.840.10008.5.1.4.1.1.88.65", # "Chest CAD SR Storage"
-        "1.2.840.10008.5.1.4.1.1.88.67", # "X-Ray Radiation Dose SR Storage"
-        "1.2.840.10008.5.1.4.1.1.104.1", # "Encapsulated PDF Storage"
-        "1.2.840.10008.5.1.4.1.1.104.2", # "Encapsulated CDA Storage"
-        "1.2.840.10008.5.1.4.1.1.128", # "Positron Emission Tomography Image Storage"
-        "1.2.840.10008.5.1.4.1.1.129", # "Standalone PET Curve Storage" # RET
-        "1.2.840.10008.5.1.4.1.1.481.1", # "RT Image Storage"
-        "1.2.840.10008.5.1.4.1.1.481.2", # "RT Dose Storage"
-        "1.2.840.10008.5.1.4.1.1.481.3", # "RT Structure Set Storage"
-        "1.2.840.10008.5.1.4.1.1.481.4", # "RT Beams Treatment Record Storage"
-        "1.2.840.10008.5.1.4.1.1.481.5", # "RT Plan Storage"
-        "1.2.840.10008.5.1.4.1.1.481.6", # "RT Brachy Treatment Record Storage"
-        "1.2.840.10008.5.1.4.1.1.481.7", # "RT Treatment Summary Record Storage"
-        "1.2.840.10008.5.1.4.1.1.481.8", # "RT Ion Plan Storage"
-        "1.2.840.10008.5.1.4.1.1.481.9" # "RT Ion Beams Treatment Record Storage"
-      ]
-    end
-
-
-  end # of class
-end # of module

data/lib/dicom/DWrite.rb

@@ -1,410 +0,0 @@
-#    Copyright 2008-2010 Christoffer Lervag
-
-# Some notes about this DICOM file writing class:
-# In its current state, this class will always try to write the file such that it is compliant to the
-# official standard (DICOM 3 Part 10), containing header and meta information (group 0002).
-# If this is unwanted behaviour, it is easy to modify the source code here to avoid this.
-#
-# It is important to note, that while the goal is to be fully DICOM compliant, no guarantees are given
-# that this is actually achieved. You are encouraged to thouroughly test your files for compatibility after creation.
-# Please contact the author if you discover any issues with file creation.
-
-module DICOM
-
-  # Class for writing the data from a DObject to a valid DICOM file.
-  class DWrite
-
-    attr_writer :tags, :vr, :lengths, :bin, :rest_endian, :rest_explicit
-    attr_reader :success, :msg
-
-    # Initialize the DWrite instance.
-    def initialize(file_name=nil, options={})
-      # Process option values, setting defaults for the ones that are not specified:
-      @sys_endian = options[:sys_endian] || false
-      @file_name = file_name
-      @transfer_syntax = options[:transfer_syntax] || "1.2.840.10008.1.2" # Implicit, little endian
-
-      # Create arrays used for storing data element information:
-      @tags = Array.new
-      @vr = Array.new
-      @lengths = Array.new
-      @bin = Array.new
-      # Array for storing error/warning messages:
-      @msg = Array.new
-      # Default values that may be overwritten by the user:
-      # Explicitness of the remaining groups after the initial 0002 group:
-      @rest_explicit = false
-      # Endianness of the remaining groups after the first group:
-      @rest_endian = false
-    end
-
-
-    # Writes the DICOM information to file.
-    def write(body = nil)
-      # Check if we are able to create given file:
-      open_file(@file_name)
-      # Go ahead and write if the file was opened successfully:
-      if @file != nil
-        # Initiate necessary variables:
-        init_variables
-        # Create a Stream instance to handle the encoding of content to
-        # the binary string that will eventually be saved to file:
-        @stream = Stream.new(nil, @file_endian, @explicit)
-        # Tell the Stream instance which file to write to:
-        @stream.set_file(@file)
-        # Write header:
-        write_header
-        # Meta information:
-        # A simple check to determine whether we need to write meta information to the DICOM object:
-        if @tags.length > 0
-          write_meta unless @tags[0].include?("0002")
-        else
-          write_meta
-        end
-        # Write either body or data elements:
-        if body
-          @stream.add_last(body)
-        else
-          @tags.each_index do |i|
-            write_data_element(i)
-          end
-        end
-        # As file has been written successfully, it can be closed.
-        @file.close
-        # Mark this write session as successful:
-        @success = true
-      end
-    end
-
-
-    # Write DICOM content to a series of size-limited binary strings
-    # (typically used when transmitting DICOM objects through network connections)
-    # The method returns an array of binary strings.
-    def encode_segments(size)
-      # Initiate necessary variables:
-      init_variables
-      # When sending a DICOM file across the network, no header or meta information is needed.
-      # We must therefore find the position of the first tag which is not a meta information tag.
-      first_pos = first_non_meta
-      last_pos = @tags.length - 1
-      # Create a Stream instance to handle the encoding of content to
-      # the binary string that will eventually be saved to file:
-      @stream = Stream.new(nil, @file_endian, @explicit)
-      # Start encoding data elements, and start on a new string when the size limit is reached:
-      segments = Array.new
-      (first_pos..last_pos).each do |i|
-        value_length = @lengths[i].to_i
-        # Test the length of the upcoming data element against our size limitation:
-        if value_length > size
-          # Start writing content from this data element,
-          # then continue writing its content in the next segments.
-          # Write tag & vr/length:
-          write_tag(i)
-          write_vr_length(i)
-          # Find out how much of this element's value we can write, then add it:
-          available = size - @stream.length
-          value_first_part = @bin[i].slice(0, available)
-          @stream.add_last(value_first_part)
-          # Add segment and reset:
-          segments << @stream.string
-          @stream.reset
-          # Find out how many more segments our data element value will fill:
-          remaining_segments = ((value_length - available).to_f / size.to_f).ceil
-          index = available
-          # Iterate through the data element's value until we have added it entirely:
-          remaining_segments.times do
-            value = @bin[i].slice(index, size)
-            index = index + size
-            @stream.add_last(value)
-            # Add segment and reset:
-            segments << @stream.string
-            @stream.reset
-          end
-        elsif (10 + value_length + @stream.length) >= size
-          # End the current segment, and start on a new segment for the next data element.
-          segments << @stream.string
-          @stream.reset
-          write_data_element(i)
-        else
-          # Write the next data element to the current segment:
-          write_data_element(i)
-        end
-      end
-      # Mark this write session as successful:
-      @success = true
-      return segments
-    end
-
-
-    # Following methods are private:
-    private
-
-
-    # Add a binary string to (the end of) either file or string.
-    def add(string)
-      if @file
-        @stream.write(string)
-      else
-        @stream.add_last(string)
-      end
-    end
-
-
-    # Writes the official DICOM header:
-    def write_header
-      # Write the string "DICM" which along with the empty bytes that
-      # will be put before it, identifies this as a valid DICOM file:
-      identifier = @stream.encode("DICM", "STR")
-      # Fill in 128 empty bytes:
-      filler = @stream.encode("00"*128, "HEX")
-      @stream.write(filler)
-      @stream.write(identifier)
-    end
-
-
-    # Inserts group 0002 data elements.
-    def write_meta
-      # File Meta Information Version:
-      tag = @stream.encode_tag("0002,0001")
-      @stream.add_last(tag)
-      @stream.encode_last("OB", "STR")
-      @stream.encode_last("0000", "HEX") # (2 reserved bytes)
-      @stream.encode_last(2, "UL")
-      @stream.encode_last("0001", "HEX") # (Value)
-      # Transfer Syntax UID:
-      tag = @stream.encode_tag("0002,0010")
-      @stream.add_last(tag)
-      @stream.encode_last("UI", "STR")
-      value = @stream.encode_value(@transfer_syntax, "STR")
-      @stream.encode_last(value.length, "US")
-      @stream.add_last(value)
-      # Implementation Class UID:
-      tag = @stream.encode_tag("0002,0012")
-      @stream.add_last(tag)
-      @stream.encode_last("UI", "STR")
-      value = @stream.encode_value(UID, "STR")
-      @stream.encode_last(value.length, "US")
-      @stream.add_last(value)
-      # Implementation Version Name:
-      tag = @stream.encode_tag("0002,0013")
-      @stream.add_last(tag)
-      @stream.encode_last("SH", "STR")
-      value = @stream.encode_value(NAME, "STR")
-      @stream.encode_last(value.length, "US")
-      @stream.add_last(value)
-      # Group length:
-      # This data element will be put first in the binary string, and built 'backwards'.
-      # Value:
-      value = @stream.encode(@stream.length, "UL")
-      @stream.add_first(value)
-      # Length:
-      length = @stream.encode(4, "US")
-      @stream.add_first(length)
-      # VR:
-      vr = @stream.encode("UL", "STR")
-      @stream.add_first(vr)
-      # Tag:
-      tag = @stream.encode_tag("0002,0000")
-      @stream.add_first(tag)
-      # Write the meta information to file:
-      @stream.write(@stream.string)
-    end
-
-
-    # Writes each data element to file:
-    def write_data_element(i)
-      # Step 1: Write tag:
-      write_tag(i)
-      # Step 2: Write [vr] and value length:
-      write_vr_length(i)
-      # Step 3: Write value:
-      write_value(i)
-      # If DICOM object contains encapsulated pixel data, we need some special handling for its items:
-      if @tags[i] == "7FE0,0010"
-        @enc_image = true if @lengths[i].to_i == 0
-      end
-    end
-
-
-    # Writes the tag (first part of the data element):
-    def write_tag(i)
-      # Extract current tag:
-      tag = @tags[i]
-      # Group 0002 is always little endian, but the rest of the file may be little or big endian.
-      # When we shift from group 0002 to another group we need to update our endian/explicitness variables:
-      if tag[0..3] != "0002" and @switched == false
-        switch_syntax
-      end
-      # Write to binary string:
-      bin_tag = @stream.encode_tag(tag)
-      add(bin_tag)
-    end
-
-
-    # Writes the VR (if it is to be written) and length value
-    # (these two are the middle part of the data element):
-    def write_vr_length(i)
-      # First some preprocessing:
-      # Set length value:
-      if @lengths[i] == nil
-        # Set length value to 0:
-        length4 = @stream.encode(0, "UL")
-        length2 = @stream.encode(0, "US")
-      elsif @lengths[i] == "UNDEFINED"
-        # Set length to 'ff ff ff ff':
-        length4 = @stream.encode(4294967295, "UL")
-        # No length2 necessary for this case.
-      else
-        # Pick length value from array:
-        length4 = @stream.encode(@lengths[i], "UL")
-        length2 = @stream.encode(@lengths[i], "US")
-      end
-      # Structure will differ, dependent on whether we have explicit or implicit encoding:
-      # *****EXPLICIT*****:
-      if @explicit == true
-        # Step 1: Write VR (if it is to be written)
-        unless @tags[i] == "FFFE,E000" or @tags[i] == "FFFE,E00D" or @tags[i] == "FFFE,E0DD"
-          # Write data element VR (2 bytes - since we are not dealing with an item related element):
-          vr = @stream.encode(@vr[i], "STR")
-          add(vr)
-        end
-        # Step 2: Write length
-        # Three possible structures for value length here, dependent on data element vr:
-        case @vr[i]
-          when "OB","OW","SQ","UN","UT"
-            if @enc_image
-              # Item under an encapsulated Pixel Data (7FE0,0010):
-              # 4 bytes:
-              add(length4)
-            else
-              # 6 bytes total:
-              # Two empty first:
-              empty = @stream.encode("00"*2, "HEX")
-              add(empty)
-              # Value length (4 bytes):
-              add(length4)
-            end
-          when "()"
-            # 4 bytes:
-            # For tags "FFFE,E000", "FFFE,E00D" and "FFFE,E0DD"
-            add(length4)
-          else
-            # 2 bytes:
-            # For all the other data element vr, value length is 2 bytes:
-            add(length2)
-        end
-      else
-        # *****IMPLICIT*****:
-        # No VR written.
-        # Writing value length (4 bytes):
-        add(length4)
-      end
-    end # of write_vr_length
-
-
-    # Writes the value (last part of the data element):
-    def write_value(i)
-      # This is pretty straightforward, just dump the binary data to the file/string:
-      add(@bin[i])
-    end
-
-
-    # Tests if the file/path is writable, creates any folders
-    # if necessary, and opens the file for writing.
-    def open_file(file)
-      # Two cases: File already exists or it does not.
-      # Check if file exists:
-      if File.exist?(file)
-        # Is it writable?
-        if File.writable?(file)
-          @file = File.new(file, "wb")
-        else
-          # Existing file is not writable:
-          @msg << "Error! The program does not have permission or resources to create the file you specified. Returning. (#{file})"
-        end
-      else
-        # File does not exist.
-        # Check if this file's path contains a folder that does not exist, and therefore needs to be created:
-        folders = file.split(File::SEPARATOR)
-        if folders.length > 1
-          # Remove last element (which should be the file string):
-          folders.pop
-          path = folders.join(File::SEPARATOR)
-          # Check if this path exists:
-          unless File.directory?(path)
-            # We need to create (parts of) this path:
-            require 'fileutils'
-            FileUtils.mkdir_p path
-          end
-        end
-        # The path to this non-existing file should now be prepared, and we proceed to creating the file:
-        @file = File.new(file, "wb")
-      end
-    end
-
-
-    # Changes encoding variables as the file writing proceeds past the initial 0002 group of the DICOM file.
-    def switch_syntax
-      # The information from the Transfer syntax element (if present), needs to be processed:
-      result = LIBRARY.process_transfer_syntax(@transfer_syntax.rstrip)
-      # Result is a 3-element array: [Validity of ts, explicitness, endianness]
-      unless result[0]
-        @msg << "Warning: Invalid/unknown transfer syntax! Will still write the file, but you should give this a closer look."
-      end
-      @rest_explicit = result[1]
-      @rest_endian = result[2]
-      # We only plan to run this method once:
-      @switched = true
-      # Update explicitness and endianness (pack/unpack variables):
-      @file_endian = @rest_endian
-      @stream.set_endian(@rest_endian)
-      @explicit = @rest_explicit
-      @stream.explicit = @rest_explicit
-      if @sys_endian == @file_endian
-        @endian = true
-      else
-        @endian = false
-      end
-    end
-
-
-    # Find the position of the first tag which is not a group "0002" tag:
-    def first_non_meta
-      i = 0
-      go = true
-      while go == true and i < @tags.length do
-        tag = @tags[i]
-        if tag[0..3] == "0002"
-          i += 1
-        else
-          go = false
-        end
-      end
-      return i
-    end
-
-
-    # Initializes the variables used when executing this program.
-    def init_variables
-      # Variables that are accesible from outside:
-      # Until a DICOM write has completed successfully the status is 'unsuccessful':
-      @success = false
-      # Variables used internally:
-      # Default explicitness of start of DICOM file:
-      @explicit = true
-      # Default endianness of start of DICOM files is little endian:
-      @file_endian = false
-      # When the file switch from group 0002 to a later group we will update encoding values, and this switch will keep track of that:
-      @switched = false
-      # Use a "relationship endian" variable to guide writing of file:
-      if @sys_endian == @file_endian
-        @endian = true
-      else
-        @endian = false
-      end
-      # Items contained under the Pixel Data element needs some special attention to write correctly:
-      @enc_image = false
-    end
-
-  end # of class
-end # of module