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
An attribute set as nil. This attribute is included to provide consistency with the other element types which usually have a parent defined.
A boolean which is set as true if a DICOM
file has been successfully read & parsed from a file (or binary string).
A boolean which is set as true if a DICOM
file has been successfully read & parsed from a file (or binary string).
The source of the DObject
(nil, :str or file name string).
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).
A boolean which is set as true if a DObject
instance has been successfully written to file (or successfully encoded).
A boolean which is set as true if a DObject
instance has been successfully written to file (or successfully encoded).
Public Class Methods
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
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
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
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
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
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
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
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
Prints information of interest related to the DICOM
object. Calls the Parent#print
method as well as DObject#summary
.
# File lib/dicom/d_object.rb, line 250 def print_all puts "" print(:value_max => 30) summary end
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
Returns self.
@return [DObject] self
# File lib/dicom/d_object.rb, line 342 def to_dcm self end
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
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
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
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
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
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