class DICOM::DObject

The DObject class is the main class for interacting with the DICOM object. Reading from and writing to files is executed from instances of this class.

Inheritance

As the DObject class inherits from the ImageItem class, which itself inherits from the Parent class, all ImageItem and Parent methods are also available to instances of DObject.

Attributes

parent[R]

An attribute set as nil. This attribute is included to provide consistency with the other element types which usually have a parent defined.

read?[RW]

A boolean which is set as true if a DICOM file has been successfully read & parsed from a file (or binary string).

read_success[RW]

A boolean which is set as true if a DICOM file has been successfully read & parsed from a file (or binary string).

source[RW]

The source of the DObject (nil, :str or file name string).

stream[R]

The Stream instance associated with this DObject instance (this attribute is mostly used internally).

was_dcm_on_input[RW]

An attribute (used by e.g. DICOM.load) to indicate that a DObject-type instance was given to the load method (instead of e.g. a file).

write_success[R]

A boolean which is set as true if a DObject instance has been successfully written to file (or successfully encoded).

written?[R]

A boolean which is set as true if a DObject instance has been successfully written to file (or successfully encoded).

Public Class Methods

get(link) click to toggle source

Creates a DObject instance by downloading a DICOM file specified by a hyperlink, and parsing the retrieved file.

@note Highly experimental and un-tested! @note Designed for the HTTP protocol only. @note Whether this method should be included or removed from ruby-dicom is up for debate.

@param [String] link a hyperlink string which specifies remote location of the DICOM file to be loaded @return [DObject] the created DObject instance

# File lib/dicom/d_object.rb, line 55
def self.get(link)
  raise ArgumentError, "Invalid argument 'link'. Expected String, got #{link.class}." unless link.is_a?(String)
  raise ArgumentError, "Invalid argument 'link'. Expected a string starting with 'http', got #{link}." unless link.index('http') == 0
  require 'open-uri'
  bin = nil
  file = nil
  # Try to open the remote file using open-uri:
  retrials = 0
  begin
    file = open(link, 'rb') # binary encoding (ASCII-8BIT)
  rescue Exception => e
    if retrials > 3
      retrials = 0
      raise "Unable to retrieve the file. File does not exist?"
    else
      logger.warn("Exception in ruby-dicom when loading a dicom file from: #{file}")
      logger.debug("Retrying... #{retrials}")
      retrials += 1
      retry
    end
  end
  bin = File.open(file, "rb") { |f| f.read }
  # Parse the file contents and create the DICOM object:
  if bin
    dcm = self.parse(bin)
  else
    dcm = self.new
    dcm.read_success = false
  end
  dcm.source = link
  return dcm
end
new() click to toggle source

Creates a DObject instance (DObject is an abbreviation for “DICOM object”).

The DObject instance holds references to the different types of objects (Element, Item, Sequence) that makes up a DICOM object. A DObject is typically buildt by reading and parsing a file or a binary string (with DObject::read or ::parse), but can also be buildt from an empty state by this method.

To customize logging behaviour, refer to the Logging module documentation.

@example Create an empty DICOM object

require 'dicom'
dcm = DICOM::DObject.new

@example Increasing the log message threshold (default level is INFO)

DICOM.logger.level = Logger::ERROR
# File lib/dicom/d_object.rb, line 182
def initialize
  # Initialization of variables that DObject share with other parent elements:
  initialize_parent
  # Structural information (default values):
  @explicit = true
  @str_endian = false
  # Control variables:
  @read_success = nil
  # Initialize a Stream instance which is used for encoding/decoding:
  @stream = Stream.new(nil, @str_endian)
  # The DObject instance is the top of the hierarchy and unlike other elements it has no parent:
  @parent = nil
end
parse(string, options={}) click to toggle source

Creates a DObject instance by parsing an encoded binary DICOM string.

@param [String] string an encoded binary string containing DICOM information @param [Hash] options the options to use for parsing the DICOM string @option options [Boolean] :overwrite for the rare case of a DICOM file containing duplicate elements, setting this as true instructs the parsing algorithm to overwrite the original element with duplicates @option options [Boolean] :signature if set as false, the parsing algorithm will not be looking for the DICOM header signature (defaults to true) @option options [String] :syntax if a syntax string is specified, the parsing algorithm will be forced to use this transfer syntax when decoding the binary string @example Parse a DICOM file that has already been loaded to a binary string

require 'dicom'
dcm = DICOM::DObject.parse(str)

@example Parse a header-less DICOM string with explicit little endian transfer syntax

dcm = DICOM::DObject.parse(str, :syntax => '1.2.840.10008.1.2.1')
# File lib/dicom/d_object.rb, line 101
def self.parse(string, options={})
  raise ArgumentError, "Invalid argument 'string'. Expected String, got #{string.class}." unless string.is_a?(String)
  raise ArgumentError, "Invalid option :syntax. Expected String, got #{options[:syntax].class}." if options[:syntax] && !options[:syntax].is_a?(String)
  signature = options[:signature].nil? ? true : options[:signature]
  dcm = self.new
  dcm.send(:read, string, signature, :overwrite => options[:overwrite], :syntax => options[:syntax])
  if dcm.read?
    logger.debug("DICOM string successfully parsed.")
  else
    logger.warn("Failed to parse this string as DICOM.")
  end
  dcm.source = :str
  return dcm
end
read(file, options={}) click to toggle source

Creates a DObject instance by reading and parsing a DICOM file.

@param [String] file a string which specifies the path of the DICOM file to be loaded @param [Hash] options the options to use for reading the DICOM file @option options [Boolean] :overwrite for the rare case of a DICOM file containing duplicate elements, setting this as true instructs the parsing algorithm to overwrite the original element with duplicates @example Load a DICOM file

require 'dicom'
dcm = DICOM::DObject.read('test.dcm')
# File lib/dicom/d_object.rb, line 125
def self.read(file, options={})
  raise ArgumentError, "Invalid argument 'file'. Expected String, got #{file.class}." unless file.is_a?(String)
  # Read the file content:
  bin = nil
  unless File.exist?(file)
    logger.error("Invalid (non-existing) file: #{file}")
  else
    unless File.readable?(file)
      logger.error("File exists but I don't have permission to read it: #{file}")
    else
      if File.directory?(file)
        logger.error("Expected a file, got a directory: #{file}")
      else
        if File.size(file) < 8
          logger.error("This file is too small to contain any DICOM information: #{file}.")
        else
          bin = File.open(file, "rb") { |f| f.read }
        end
      end
    end
  end
  # Parse the file contents and create the DICOM object:
  if bin
    dcm = self.parse(bin, options)
    # If reading failed, and no transfer syntax was detected, we will make another attempt at reading the file while forcing explicit (little endian) decoding.
    # This will help for some rare cases where the DICOM file is saved (erroneously, Im sure) with explicit encoding without specifying the transfer syntax tag.
    if !dcm.read? and !dcm.exists?("0002,0010")
      logger.info("Attempting a second decode pass (assuming Explicit Little Endian transfer syntax).")
      options[:syntax] = EXPLICIT_LITTLE_ENDIAN
      dcm = self.parse(bin, options)
    end
  else
    dcm = self.new
  end
  if dcm.read?
    logger.info("DICOM file successfully read: #{file}")
  else
    logger.warn("Reading DICOM file failed: #{file}")
  end
  dcm.source = file
  return dcm
end

Public Instance Methods

==(other) click to toggle source

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

# File lib/dicom/d_object.rb, line 204
def ==(other)
  if other.respond_to?(:to_dcm)
    other.send(:state) == state
  end
end
Also aliased as: eql?
anonymize(a=Anonymizer.new) click to toggle source

Performs de-identification (anonymization) on the DICOM object.

@param [Anonymizer] a an Anonymizer instance to use for the anonymization

# File lib/dicom/d_object.rb, line 216
def anonymize(a=Anonymizer.new)
  a.to_anonymizer.anonymize(self)
end
encode_segments(max_size, transfer_syntax=IMPLICIT_LITTLE_ENDIAN) click to toggle source

Encodes the DICOM object into a series of binary string segments with a specified maximum length.

Returns the encoded binary strings in an array.

@param [Integer] max_size the maximum allowed size of the binary data strings to be encoded @param [String] transfer_syntax the transfer syntax string to be used when encoding the DICOM object to string segments. When this method is used for making network packets, the transfer_syntax is not part of the object, and thus needs to be specified. @return [Array<String>] the encoded DICOM strings @example Encode the DObject to strings of max length 2^14 bytes

encoded_strings = dcm.encode_segments(16384)
# File lib/dicom/d_object.rb, line 230
def encode_segments(max_size, transfer_syntax=IMPLICIT_LITTLE_ENDIAN)
  raise ArgumentError, "Invalid argument. Expected an Integer, got #{max_size.class}." unless max_size.is_a?(Integer)
  raise ArgumentError, "Argument too low (#{max_size}), please specify a bigger Integer." unless max_size > 16
  raise "Can not encode binary segments for an empty DICOM object." if children.length == 0
  encode_in_segments(max_size, :syntax => transfer_syntax)
end
eql?(other)
Alias for: ==
hash() click to toggle source

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

# File lib/dicom/d_object.rb, line 243
def hash
  state.hash
end
print_all() click to toggle source

Prints information of interest related to the DICOM object. Calls the Parent#print method as well as DObject#summary.

summary() click to toggle source

Gathers key information about the DObject as well as some system data, and prints this information to the screen. This information includes properties like encoding, byte order, modality and various image properties.

@return [Array<String>] strings describing the properties of the DICOM object

# File lib/dicom/d_object.rb, line 261
def summary
  # FIXME: Perhaps this method should be split up in one or two separate methods
  # which just builds the information arrays, and a third method for printing this to the screen.
  sys_info = Array.new
  info = Array.new
  # Version of Ruby DICOM used:
  sys_info << "Ruby DICOM version:   #{VERSION}"
  # System endian:
  cpu = (CPU_ENDIAN ? "Big Endian" : "Little Endian")
  sys_info << "Byte Order (CPU):     #{cpu}"
  # Source (file name):
  if @source
    if @source == :str
      source = "Binary string #{@read_success ? '(successfully parsed)' : '(failed to parse)'}"
    else
      source = "File #{@read_success ? '(successfully read)' : '(failed to read)'}: #{@source}"
    end
  else
    source = 'Created from scratch'
  end
  info << "Source:               #{source}"
  # Modality:
  modality = (LIBRARY.uid(value('0008,0016')) ? LIBRARY.uid(value('0008,0016')).name : "SOP Class unknown or not specified!")
  info << "Modality:             #{modality}"
  # Meta header presence (Simply check for the presence of the transfer syntax data element), VR and byte order:
  ts_status = self['0002,0010'] ? '' : ' (Assumed)'
  ts = LIBRARY.uid(transfer_syntax)
  explicit = ts ? ts.explicit? : true
  endian = ts ? ts.big_endian? : false
  meta_comment = ts ? "" : " (But unknown/invalid transfer syntax: #{transfer_syntax})"
  info << "Meta Header:          #{self['0002,0010'] ? 'Yes' : 'No'}#{meta_comment}"
  info << "Value Representation: #{explicit ? 'Explicit' : 'Implicit'}#{ts_status}"
  info << "Byte Order (File):    #{endian ? 'Big Endian' : 'Little Endian'}#{ts_status}"
  # Pixel data:
  pixels = self[PIXEL_TAG]
  unless pixels
    info << "Pixel Data:           No"
  else
    info << "Pixel Data:           Yes"
    # Image size:
    cols = (exists?("0028,0011") ? self["0028,0011"].value : "Columns missing")
    rows = (exists?("0028,0010") ? self["0028,0010"].value : "Rows missing")
    info << "Image Size:           #{cols}*#{rows}"
    # Frames:
    frames = value("0028,0008") || "1"
    unless frames == "1" or frames == 1
      # Encapsulated or 3D pixel data:
      if pixels.is_a?(Element)
        frames = frames.to_s + " (3D Pixel Data)"
      else
        frames = frames.to_s + " (Encapsulated Multiframe Image)"
      end
    end
    info << "Number of frames:     #{frames}"
    # Color:
    colors = (exists?("0028,0004") ? self["0028,0004"].value : "Not specified")
    info << "Photometry:           #{colors}"
    # Compression:
    compression = (ts ? (ts.compressed_pixels? ? ts.name : 'No') : 'No' )
    info << "Compression:          #{compression}#{ts_status}"
    # Pixel bits (allocated):
    bits = (exists?("0028,0100") ? self["0028,0100"].value : "Not specified")
    info << "Bits per Pixel:       #{bits}"
  end
  # Print the DICOM object's key properties:
  separator = "-------------------------------------------"
  puts "System Properties:"
  puts separator + "\n"
  puts sys_info
  puts "\n"
  puts "DICOM Object Properties:"
  puts separator
  puts info
  puts separator
  return info
end
to_dcm() click to toggle source

Returns self.

@return [DObject] self

# File lib/dicom/d_object.rb, line 342
def to_dcm
  self
end
transfer_syntax() click to toggle source

Gives the transfer syntax string of the DObject.

If a transfer syntax has not been defined in the DObject, a default tansfer syntax is assumed and returned.

@return [String] the DObject's transfer syntax

# File lib/dicom/d_object.rb, line 352
def transfer_syntax
  return value("0002,0010") || IMPLICIT_LITTLE_ENDIAN
end
transfer_syntax=(new_syntax) click to toggle source

Changes the transfer syntax Element of the DObject instance, and performs re-encoding of all numerical values if a switch of endianness is implied.

@note This method does not change the compressed state of the pixel data element. Changing the transfer syntax between an uncompressed and compressed state will NOT change the pixel data accordingly (this must be taken care of manually).

@param [String] new_syntax the new transfer syntax string to be applied to the DObject

# File lib/dicom/d_object.rb, line 365
def transfer_syntax=(new_syntax)
  # Verify old and new transfer syntax:
  new_uid = LIBRARY.uid(new_syntax)
  old_uid = LIBRARY.uid(transfer_syntax)
  raise ArgumentError, "Invalid/unknown transfer syntax specified: #{new_syntax}" unless new_uid && new_uid.transfer_syntax?
  raise ArgumentError, "Invalid/unknown existing transfer syntax: #{new_syntax} Unable to reliably handle byte order encoding. Modify the transfer syntax element directly instead." unless old_uid && old_uid.transfer_syntax?
  # Set the new transfer syntax:
  if exists?("0002,0010")
    self["0002,0010"].value = new_syntax
  else
    add(Element.new("0002,0010", new_syntax))
  end
  # Update our Stream instance with the new encoding:
  @stream.endian = new_uid.big_endian?
  # If endianness is changed, re-encode elements (only elements depending on endianness will actually be re-encoded):
  encode_children(old_uid.big_endian?) if old_uid.big_endian? != new_uid.big_endian?
end
write(file_name, options={}) click to toggle source

Writes the DICOM object to file.

@note The goal of the Ruby DICOM library is to yield maximum conformance with the DICOM standard when outputting DICOM files. Therefore, when encoding the DICOM file, manipulation of items such as the meta group, group lengths and header signature may occur. Therefore, the file that is written may not be an exact bitwise copy of the file that was read, even if no DObject manipulation has been done by the user.

@param [String] file_name the path of the DICOM file which is to be written to disk @param [Hash] options the options to use for writing the DICOM file @option options [Boolean] :ignore_meta if true, no manipulation of the DICOM object's meta group will be performed before the DObject is written to file @option options [Boolean] :include_empty_parents if true, childless parents (sequences & items) are written to the DICOM file @example Encode a DICOM file from a DObject

dcm.write('C:/dicom/test.dcm')
# File lib/dicom/d_object.rb, line 398
def write(file_name, options={})
  raise ArgumentError, "Invalid file_name. Expected String, got #{file_name.class}." unless file_name.is_a?(String)
  @include_empty_parents = options[:include_empty_parents]
  insert_missing_meta unless options[:ignore_meta]
  write_elements(:file_name => file_name, :signature => true, :syntax => transfer_syntax)
end

Private Instance Methods

insert_missing_meta() click to toggle source

Adds any missing meta group (0002,xxxx) data elements to the DICOM object, to ensure that a valid DICOM object is encoded.

# File lib/dicom/d_object.rb, line 412
def insert_missing_meta
  {
    '0002,0001' => [0,1], # File Meta Information Version
    '0002,0002' => value('0008,0016'), # Media Storage SOP Class UID
    '0002,0003' => value('0008,0018'), # Media Storage SOP Instance UID
    '0002,0010' => transfer_syntax, # Transfer Syntax UID
    '0002,0016' => DICOM.source_app_title, # Source Application Entity Title
  }.each_pair do |tag, value|
    add_element(tag, value) unless exists?(tag)
  end
  if !exists?("0002,0012") && !exists?("0002,0013")
    # Implementation Class UID:
    add_element("0002,0012", UID_ROOT)
    # Implementation Version Name:
    add_element("0002,0013", NAME)
  end
  # Delete the old group length first (if it exists) to avoid a miscount
  # in the coming group length determination.
  delete("0002,0000")
  add_element("0002,0000", meta_group_length)
end
meta_group_length() click to toggle source

Determines the length of the meta group in the DObject instance.

@return [Integer] the length of the file meta group string

# File lib/dicom/d_object.rb, line 438
def meta_group_length
  group_length = 0
  meta_elements = group(META_GROUP)
  tag = 4
  vr = 2
  meta_elements.each do |element|
    case element.vr
      when "OB","OW","OF","SQ","UN","UT"
        length = 6
      else
        length = 2
    end
    group_length += tag + vr + length + element.bin.length
  end
  group_length
end
state() click to toggle source

Collects the attributes of this instance.

@return [Array<Element, Sequence>] an array of elements and sequences

# File lib/dicom/d_object.rb, line 459
def state
  @tags
end