Module: DICOM

Includes:
Logging
Defined in:
lib/dicom/d_object.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/logging.rb,
lib/dicom/version.rb,
lib/dicom/d_client.rb,
lib/dicom/d_server.rb,
lib/dicom/sequence.rb,
lib/dicom/constants.rb,
lib/dicom/d_library.rb,
lib/dicom/elemental.rb,
lib/dicom/variables.rb,
lib/dicom/anonymizer.rb,
lib/dicom/deprecated.rb,
lib/dicom/image_item.rb,
lib/dicom/audit_trail.rb,
lib/dicom/file_handler.rb,
lib/dicom/image_processor.rb,
lib/dicom/dictionary_element.rb,
lib/dicom/image_processor_r_magick.rb,
lib/dicom/image_processor_mini_magick.rb

Overview

Copyright 2008-2013 Christoffer Lervag

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

Constant Summary collapse

VERSION =

The ruby-dicom version string.

'0.9.5'
ROOT_DIR =

Defines the gem root directory in the file system.

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

0
ACCEPTANCE =

Network proposition accepted.

0
ABSTRACT_SYNTAX_REJECTED =

Presentation context rejected by abstract syntax.

3
TRANSFER_SYNTAX_REJECTED =

Presentation context rejected by transfer syntax.

4
C_STORE_RQ =

Some network command element codes:

1
C_GET_RQ =

(encodes to 0001H as US)

16
C_FIND_RQ =

(encodes to 0010H as US)

32
C_MOVE_RQ =

(encodes to 0020H as US)

33
C_ECHO_RQ =

(encodes to 0021H as US)

48
C_CANCEL_RQ =

(encodes to 0030 as US)

4095
C_STORE_RSP =

(encodes to 0FFFH as US)

32769
C_GET_RSP =

(encodes to 8001H as US)

32784
C_FIND_RSP =

(encodes to 8010H as US)

32800
C_MOVE_RSP =

(encodes to 8020H as US)

32801
C_ECHO_RSP =

(encodes to 8021H as US)

32816
NO_DATA_SET_PRESENT =

(encodes to 8030H as US)

257
DATA_SET_PRESENT =

(encodes to 0101H as US)

1
DEFAULT_MESSAGE_ID = 
1
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.


      
        
CUSTOM_SS =
          

  

    

Custom string used for (un)packing big endian signed short.



  





  



        

        
"k*"

      
        
CUSTOM_SL =
          

  

    

Custom string used for (un)packing big endian signed long.



  





  



        

        
"r*"

      
        
LIBRARY =
          

  

    

ruby-dicom’s library instance (data dictionary).



  





  



        

        
DICOM::DLibrary.new

      
        
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'  => 'JIS_X0201',
  '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

  




  
    

      Class Method Summary
      collapse
    


    
  


  
  
  
  
  
  
  
  
  
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/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/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/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
    

    
      
    
    • 
  





  

    
      


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# File 'lib/dicom/variables.rb', line 30

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/variables.rb', line 88

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/variables.rb', line 82

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/variables.rb', line 76

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:




Returns:


    
  
    
  • 
      
      
        (Array<DObject>)
      
      
      
        —
        
    

    an array of successfully loaded DICOM objects
    

    
      
    
    • 
  





  

    
      


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# File 'lib/dicom/variables.rb', line 46

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