Module: DICOM

Includes:: Logging

Defined in:: lib/dicom/d_object.rb,
lib/dicom.rb,
lib/dicom/uid.rb,
lib/dicom/item.rb,
lib/dicom/link.rb,
lib/dicom/d_read.rb,
lib/dicom/parent.rb,
lib/dicom/stream.rb,
lib/dicom/d_write.rb,
lib/dicom/element.rb,
lib/dicom/d_client.rb,
lib/dicom/d_server.rb,
lib/dicom/sequence.rb,
lib/dicom/d_library.rb,
lib/dicom/elemental.rb,
lib/dicom/anonymizer.rb,
lib/dicom/image_item.rb,
lib/dicom/audit_trail.rb,
lib/dicom/file_handler.rb,
lib/dicom/general/logging.rb,
lib/dicom/general/methods.rb,
lib/dicom/general/version.rb,
lib/dicom/image_processor.rb,
lib/dicom/elemental_parent.rb,
lib/dicom/general/constants.rb,
lib/dicom/general/variables.rb,
lib/dicom/dictionary_element.rb,
lib/dicom/image_processor_r_magick.rb,
lib/dicom/image_processor_mini_magick.rb

Overview

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

Defined Under Namespace

Modules: Elemental, ElementalParent, ImageProcessor, Logging Classes: Anonymizer, AuditTrail, DClient, DLibrary, DObject, DServer, DictionaryElement, Element, FileHandler, ImageItem, Item, Link, Parent, Sequence, Stream, UID

Constant Summary collapse

ROOT_DIR = Defines the gem root directory in the file system.

"#{File.dirname(__FILE__)}/dicom"

LIBRARY = The library instance (data dictionary) of the DICOM module.

DICOM::DLibrary.new

VERSION = The ruby-dicom version string.

'0.9.8'

UID_ROOT = Ruby DICOM’s registered DICOM UID root (Implementation Class UID).

"1.2.826.0.1.3680043.8.641"

NAME = Ruby DICOM name & version (max 16 characters).

"RUBY-DCM_" + DICOM::VERSION

ITEM_TAG = Item tag.

"FFFE,E000"

ITEM_TAGS = All Item related tags (includes both types of delimitation items).

["FFFE,E000", "FFFE,E00D", "FFFE,E0DD"]

ITEM_DELIMITER = Item delimiter tag.

"FFFE,E00D"

SEQUENCE_DELIMITER = Sequence delimiter tag.

"FFFE,E0DD"

DELIMITER_TAGS = All delimiter tags.

["FFFE,E00D", "FFFE,E0DD"]

ITEM_VR = The VR used for the item elements.

"  "

PIXEL_TAG = Pixel tag.

"7FE0,0010"

ENCAPSULATED_PIXEL_NAME = Name of the pixel tag when holding encapsulated data.

"Encapsulated Pixel Data"

PIXEL_ITEM_NAME = Name of encapsulated items.

"Pixel Data Item"

META_GROUP = File meta group.

"0002"

GROUP_LENGTH = Group length element.

"0000"

IMPLICIT_LITTLE_ENDIAN = Implicit, little endian (the default transfer syntax).

"1.2.840.10008.1.2"

EXPLICIT_LITTLE_ENDIAN = Explicit, little endian transfer syntax.

"1.2.840.10008.1.2.1"

EXPLICIT_BIG_ENDIAN = Explicit, big endian transfer syntax.

"1.2.840.10008.1.2.2"

VERIFICATION_SOP = Verification SOP class UID.

"1.2.840.10008.1.1"

APPLICATION_CONTEXT = Application context SOP class UID.

"1.2.840.10008.3.1.1.1"

SUCCESS = Network transmission successful.

ACCEPTANCE = Network proposition accepted.

ABSTRACT_SYNTAX_REJECTED = Presentation context rejected by abstract syntax.

TRANSFER_SYNTAX_REJECTED = Presentation context rejected by transfer syntax.

C_STORE_RQ = Some network command element codes:

C_GET_RQ = (encodes to 0001H as US)

C_FIND_RQ = (encodes to 0010H as US)

C_MOVE_RQ = (encodes to 0020H as US)

C_ECHO_RQ = (encodes to 0021H as US)

C_CANCEL_RQ = (encodes to 0030 as US)

C_STORE_RSP = (encodes to 0FFFH as US)

C_GET_RSP = (encodes to 8001H as US)

C_FIND_RSP = (encodes to 8010H as US)

C_MOVE_RSP = (encodes to 8020H as US)

C_ECHO_RSP = (encodes to 8021H as US)

NO_DATA_SET_PRESENT = (encodes to 8030H as US)

DATA_SET_PRESENT = (encodes to 0101H as US)

DEFAULT_MESSAGE_ID =

DATA_MORE_FRAGMENTS = The network communication flags:

"00"

COMMAND_MORE_FRAGMENTS =

"01"

DATA_LAST_FRAGMENT =

"02"

COMMAND_LAST_FRAGMENT =

"03"

PDU_ASSOCIATION_REQUEST = Network communication PDU types:

"01"

PDU_ASSOCIATION_ACCEPT =

"02"

PDU_ASSOCIATION_REJECT =

"03"

PDU_DATA =

"04"

PDU_RELEASE_REQUEST =

"05"

PDU_RELEASE_RESPONSE =

"06"

PDU_ABORT =

"07"

ITEM_APPLICATION_CONTEXT = Network communication item types:

"10"

ITEM_PRESENTATION_CONTEXT_REQUEST =

"20"

ITEM_PRESENTATION_CONTEXT_RESPONSE =

"21"

ITEM_ABSTRACT_SYNTAX =

"30"

ITEM_TRANSFER_SYNTAX =

"40"

ITEM_USER_INFORMATION =

"50"

ITEM_MAX_LENGTH =

"51"

ITEM_IMPLEMENTATION_UID =

"52"

ITEM_MAX_OPERATIONS_INVOKED =

"53"

ITEM_ROLE_NEGOTIATION =

"54"

ITEM_IMPLEMENTATION_VERSION =

"55"

CPU_ENDIAN = System (CPU) Endianness.

TXS_IMPLICIT_LITTLE_ENDIAN = General

'1.2.840.10008.1.2'

TXS_EXPLICIT_LITTLE_ENDIAN = also defined as IMPLICIT_LITTLE_ENDIAN, default transfer syntax

'1.2.840.10008.1.2.1'

TXS_EXPLICIT_BIG_ENDIAN = also defined as EXPLICIT_LITTLE_ENDIAN

'1.2.840.10008.1.2.2'

TXS_JPEG_BASELINE = TRANSFER SYNTAXES FOR ENCAPSULATION OF ENCODED PIXEL DATA

'1.2.840.10008.1.2.4.50'

TXS_JPEG_EXTENDED =

'1.2.840.10008.1.2.4.51'

TXS_JPEG_LOSSLESS_NH = NH: non-hirarchical

'1.2.840.10008.1.2.4.57'

TXS_JPEG_LOSSLESS_NH_FOP = NH: non-hirarchical, FOP: first-order prediction

'1.2.840.10008.1.2.4.70'

TXS_JPEG_LS_LOSSLESS =

'1.2.840.10008.1.2.4.80'

TXS_JPEG_LS_NEAR_LOSSLESS =

'1.2.840.10008.1.2.4.81'

TXS_JPEG_2000_PART1_LOSSLESS =

'1.2.840.10008.1.2.4.90'

TXS_JPEG_2000_PART1_LOSSLESS_OR_LOSSY =

'1.2.840.10008.1.2.4.91'

TXS_JPEG_2000_PART2_LOSSLESS =

'1.2.840.10008.1.2.4.92'

TXS_JPEG_2000_PART2_LOSSLESS_OR_LOSSY =

'1.2.840.10008.1.2.4.93'

TXS_MPEG2_MP_ML =

'1.2.840.10008.1.2.4.100'

TXS_MPEG2_MP_HL =

'1.2.840.10008.1.2.4.101'

TXS_DEFLATED_LITTLE_ENDIAN = ZIP Compression

'1.2.840.10008.1.2.1.99'

TXS_JPIP =

'1.2.840.10008.1.2.4.94'

TXS_JPIP_DEFLATE =

'1.2.840.10008.1.2.4.95'

TXS_RLE =

'1.2.840.10008.1.2.5'

PI_MONOCHROME1 = Photometric Interpretations Taken from DICOM Specification PS 3.3 C.7.6.3.1.2 Photometric Interpretation

'MONOCHROME1'

PI_MONOCHROME2 =

'MONOCHROME2'

PI_PALETTE_COLOR =

'PALETTE COLOR'

PI_RGB =

'RGB'

PI_YBR_FULL =

'YBR_FULL'

PI_YBR_FULL_422 =

'YBR_FULL_422 '

PI_YBR_PARTIAL_422 =

'YBR_PARTIAL_422'

PI_YBR_PARTIAL_420 =

'YBR_PARTIAL_420'

PI_YBR_ICT =

'YBR_ICT'

PI_YBR_RCT =

'YBR_RCT'

PI_HSV = Retired Photometric Interpretations, are those needed to be supported?

'HSV'

PI_ARGB =

'ARGB'

PI_CMYK =

'CMYK'

ENCODING_NAME = The relationship between DICOM Character Set and Encoding name.

{
  'ISO_IR 100' => 'ISO-8859-1',
  'ISO_IR 101' => 'ISO-8859-2',
  'ISO_IR 109' => 'ISO-8859-3',
  'ISO_IR 110' => 'ISO-8859-4',
  'ISO_IR 144' => 'ISO-8859-5',
  'ISO_IR 127' => 'ISO-8859-6',
  'ISO_IR 126' => 'ISO-8859-7',
  'ISO_IR 138' => 'ISO-8859-8',
  'ISO_IR 148' => 'ISO-8859-9',
  'ISO_IR 13'  => 'Shift_JIS',
  'ISO 2022 IR 13' => 'Shift_JIS',
  'ISO 2022 IR 13\\ISO 2022 IR 87' => 'Shift_JIS',
  'ISO 2022 IR 87' => 'ISO-2022-JP',
  'ISO_IR 166' => 'ISO-8859-11',
  'GB18030'    => 'GB18030',
  'ISO_IR 192' => 'UTF-8'
}

VALUE_CONVERSION = The type conversion (method) used for the various value representations.

{
  'BY' => :to_i,
  'US' => :to_i,
  'SS' => :to_i,
  'UL' => :to_i,
  'SL' => :to_i,
  'OB' => :to_i,
  'OW' => :to_i,
  'OF' => :to_f,
  'FL' => :to_f,
  'FD' => :to_f,
  'AT' => :to_s,
  'AE' => :to_s,
  'AS' => :to_s,
  'CS' => :to_s,
  'DA' => :to_s,
  'DS' => :to_s,
  'DT' => :to_s,
  'IS' => :to_s,
  'LO' => :to_s,
  'LT' => :to_s,
  'PN' => :to_s,
  'SH' => :to_s,
  'ST' => :to_s,
  'TM' => :to_s,
  'UI' => :to_s,
  'UT' => :to_s
}

Class Attribute Summary collapse

.image_processor ⇒ Object

The ruby-dicom image processor to be used.
.key_representation ⇒ Object

The key representation for hashes, json, yaml.
.source_app_title ⇒ Object

Source Application Entity Title (gets written to the DICOM header in files where it is undefined).

Class Method Summary collapse

.generate_uid(root = UID_ROOT, prefix = 1) ⇒ String

Generates a unique identifier string.
.key_use_method_names ⇒ Object

Use method names as key.
.key_use_names ⇒ Object

Use names as key.
.key_use_tags ⇒ Object

Use tags as key.
.load(data) ⇒ Array<DObject>

Loads DICOM data to DObject instances and returns them in an array.
.load_files(path) ⇒ Array<String>

Loads DICOM files from a given path (which points to either a directory or a file).

Methods included from Logging

included, #logger

Class Attribute Details

.image_processor ⇒ `Object`

The ruby-dicom image processor to be used.



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# File 'lib/dicom/general/variables.rb', line 10

def image_processor
  @image_processor
end

.key_representation ⇒ `Object`

The key representation for hashes, json, yaml.



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# File 'lib/dicom/general/variables.rb', line 12

def key_representation
  @key_representation
end

.source_app_title ⇒ `Object`

Source Application Entity Title (gets written to the DICOM header in files where it is undefined).



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# File 'lib/dicom/general/variables.rb', line 14

def source_app_title
  @source_app_title
end

Class Method Details

.generate_uid(root = UID_ROOT, prefix = 1) ⇒ `String`

Generates a unique identifier string. The UID is composed of a DICOM root UID, a type prefix, a datetime part and a random number part.

Examples:

Create a random UID with specified root and prefix

uid = DICOM.generate_uid('1.2.840.999', '5')

Parameters:

root (String) (defaults to: UID_ROOT) —

the DICOM root UID to be used for generating the UID string
prefix (String) (defaults to: 1) —

an integer string which is placed between the dicom root and the time/random part of the UID

Returns:

(String) —

the generated unique identifier

# File 'lib/dicom/general/methods.rb', line 19

def generate_uid(root=UID_ROOT, prefix=1)
  # NB! For UIDs, leading zeroes immediately after a dot is not allowed.
  date = Time.now.strftime("%Y%m%d").to_i.to_s
  time = Time.now.strftime("%H%M%S").to_i.to_s
  random = rand(99999) + 1 # (Minimum 1, max. 99999)
  uid = [root, prefix, date, time, random].join('.')
  return uid
end

.key_use_method_names ⇒ `Object`

Use method names as key. Example: :patients_name



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# File 'lib/dicom/general/methods.rb', line 93

def key_use_method_names
  @key_representation = :name_as_method
end

.key_use_names ⇒ `Object`

Use names as key. Example: “Patient’s Name”



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# File 'lib/dicom/general/methods.rb', line 87

def key_use_names
  @key_representation = :name
end

.key_use_tags ⇒ `Object`

Use tags as key. Example: ‘0010,0010’



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# File 'lib/dicom/general/methods.rb', line 81

def key_use_tags
  @key_representation = :tag
end

.load(data) ⇒ `Array<DObject>`

Loads DICOM data to DObject instances and returns them in an array. Invalid DICOM sources (files) are ignored. If no valid DICOM source is given, an empty array is returned.

Parameters:

data (String, DObject, Array<String, DObject>) —

single or multiple DICOM data (directories, file paths, binary strings, DICOM objects)

Returns:

(Array<DObject>) —

an array of successfully loaded DICOM objects

# File 'lib/dicom/general/methods.rb', line 35

def load(data)
  data = Array[data] unless data.respond_to?(:to_ary)
  ary = Array.new
  data.each do |element|
    if element.is_a?(String)
      begin
        if File.directory?(element)
          files = Dir[File.join(element, '**/*')].reject {|f| File.directory?(f) }
          dcms = files.collect {|f| DObject.read(f)}
        elsif File.file?(element)
          dcms = [DObject.read(element)]
        else
          dcms = [DObject.parse(element)]
        end
      rescue
        dcms = [DObject.parse(element)]
      end
      ary += dcms.keep_if {|dcm| dcm.read?}
    else
      # The element was not a string, and the only remaining valid element type is a DICOM object:
      raise ArgumentError, "Invalid element (#{element.class}) given. Expected string or DObject." unless element.respond_to?(:to_dcm)
      element.was_dcm_on_input = true
      ary << element.to_dcm
    end
  end
  ary
end

.load_files(path) ⇒ `Array<String>`

Loads DICOM files from a given path (which points to either a directory or a file).

Parameters:

path (String) —

a file or directory path

Returns:

(Array<String>) —

an array of individual file paths

# File 'lib/dicom/general/methods.rb', line 68

def load_files(path)
  files = Array.new
  if File.directory?(path)
    files = Dir[File.join(path, '**/*')].reject {|f| File.directory?(f) }
  else
    # This path is presumably a file.
    files << path
  end
  files
end

Module: DICOM

Overview

Defined Under Namespace

Constant Summary collapse

Class Attribute Summary collapse

Class Method Summary collapse

Methods included from Logging

Class Attribute Details

.image_processor ⇒ Object

.key_representation ⇒ Object

.source_app_title ⇒ Object

Class Method Details

.generate_uid(root = UID_ROOT, prefix = 1) ⇒ String

.key_use_method_names ⇒ Object

.key_use_names ⇒ Object

.key_use_tags ⇒ Object

.load(data) ⇒ Array<DObject>

.load_files(path) ⇒ Array<String>

.image_processor ⇒ `Object`

.key_representation ⇒ `Object`

.source_app_title ⇒ `Object`

.generate_uid(root = UID_ROOT, prefix = 1) ⇒ `String`

.key_use_method_names ⇒ `Object`

.key_use_names ⇒ `Object`

.key_use_tags ⇒ `Object`

.load(data) ⇒ `Array<DObject>`

.load_files(path) ⇒ `Array<String>`