dcm_dict 0.1.0

data/LICENSE

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+DcmDict is a Ruby gem (dcm_dict) to handle
+in a simple way the Data defined within the DICOM Standard.
+
+Copyright (C) 2014  Enrico Rivarola
+
+DcmDict 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.
+
+DcmDict 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 DcmDict (file 'COPYING').  If not, see <http://www.gnu.org/licenses/>.
+
+This software has neither been tested nor approved for clinical use
+or for incorporation in a medical device.
+It is the redistributor's or user's responsibility to comply with any
+applicable local, state, national or international regulations.

data/README.md

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+# What's *DcmDict*
+**DcmDict** is a Ruby gem (*dcm\_dict*) to handle in a simple way the Data defined within the [DICOM(r)][1] Standard such as DICOM Data Elements or DICOM Unique Identifiers.
+
+# Why *DcmDict*
+With the latest releases in this year (2014) DICOM documents are available in different format including one particularly interesting, the *DocBook* XML version.
+As written by D. Clunie on [its web site][2]:
+> "... other formats (such as DocBook, HTML, Word and ODT) are also made available for the convenience of implementors who may need to extract machine-readable content, ..."
+
+This is great news for anyone involved in the study of the standard !
+
+Starting from this thing was born the idea of trying to automate the extraction of data from XML documents to make available the information in a simple way that simplifies the study of the DICOM standard, in the hope this idea will be useful and inspiration.
+
+# *DcmDict* features
+The library involve *String*, *Array* and *Symbol* class as *refinements* to access to DICOM information. In this way is possible to *play* with the 'Patient's Birth Date' tag defined as (0010,0030) by:
+```ruby
+> "(0010,0030)".tag_name
+ => "Patient's Birth Date"
+> 'PatientBirthDate'.tag_vr
+ => [:DA]
+> "Patient's Birth Date".tag_vm
+ => ["1"]
+> :patient_birth_date.tag
+ => [16, 48]
+> [16,48].tag_key
+ => "PatientBirthDate"
+> [16, 48].tag_group
+ => 16
+> '00100030'.tag_element
+ => 48
+> :patient_birth_date.tag_group
+ => 16
+> "Patient's Birth Date".tag_element
+ => 48
+```
+as well for UIDs
+```ruby
+> '1.2.840.10008.1.2'.uid_name
+ => "Implicit VR Little Endian: Default Transfer Syntax for DICOM"
+> '1.2.840.10008.1.2'.uid_type
+ => :transfer_syntax
+> "Implicit VR Little Endian: Default Transfer Syntax for DICOM".uid_value
+ => "1.2.840.10008.1.2"
+```
+
+let see all features in detail:
+
+## Library usage
+The library involve **Ruby Refinements** so use it is simple, it is necessary to include the specific *using directive*:
+
+```ruby
+using DcmDict::Refine::StringRefine
+```
+for the String object,
+```ruby
+using DcmDict::Refine::ArrayRefine
+```
+for the Array object and
+
+```ruby
+using DcmDict::Refine::SymbolRefine
+```
+for the Symbol object.
+
+That's it.
+
+**Note**: It is possible to use also the the *monkey patching* way, this is a *deprecated* utilization but possible, and, may be, useful technique in certain contexts or for some particular test. For the *monkey patching* is possible to include some specific *common modules* into the class you want to use as "keyword": there are two base modules *DcmDict::Refine::DataElementRefine* and *DcmDict::Refine::UidRefine*.
+
+For example in the String class will have the code:
+```ruby
+class String
+  include DcmDict::Refine::DataElementRefine
+  include DcmDict::Refine::UidRefine
+end
+```
+*The main way remains **Ruby Refinements***.
+
+**Rubies compatibility**: at this moment the other considered rubies is only [Rubinius][4] (v2.2.10). In order to try to ensure a minimum compatibility there is a file under *lib/dcm_dict/rubies/* called *rb_ext.rb* able to *mask*/*simulates* the refinements through [refine gem][5] and add the required *bit_length* method to *Fixnum* class through [backports gem][6].
+This sort of extension is not loaded by default but only into *spec files* for the *'rbx' Ruby Engine*. See *spec_helper.rb* and *rb_ext.rb* for details.
+
+## Data Element data in detail
+Any Data Element features can be accessed from a *String*, *Array* or *Symbol* objects.
+
+For these objects is possible to access to Tag (group/element), Name, Keyword, Value Representation (VR) and Value Multiplicity (VM) for any single Data Element.
+
+The main methods supported are:
+
+|Method  | Note| Type||
+|:------|:------------:|:---:|:---:|
+|**tag**     | tag as Array| Array of two Fixnum|(alias of *tag_ary*)|
+|**tag_name**    | name of tag| String|
+|**tag_keyword** | keyword| String|
+|**tag_key** | keyword| String|
+|**tag_vr**      | Value Representation| Array of Symbol|
+|**tag_vm**      | Value Multiplicity| Array of Symbol|
+|**tag_ps**  | tag as string (as standard doc)| String|
+|**tag_ary** | tag as Array|Array of two Fixnum|
+|**tag_sym** | tag as Symbol|Symbol|
+|**tag_ndm** | tag as in Native DICOM Model|String|
+|**tag_str** | tag as string (similar to tag_ps)|String|
+|**tag_note** | tag note|String|
+|**tag_multiple?** | is a multiple tag ? |boolean|
+||useful for 'multi tag' attribute|
+
+each data element is indexed by these fields:
+
+|Field|Type|
+|:----|:-----:|
+|**tag_key** | String|
+|**tag_ps**  | String|
+|**tag_ary** | Array|
+|**tag_sym** | Symbol|
+|**tag_ndm** | String|
+|**tag_str** | String|
+|**tag_name** | String|
+
+Through these fields is possible to access to data element informations.
+Consider the case of the tag (0010,1005) (*Patient's Birth Name*), the primary fields are:
+**'(0010,1005)'**, **"Patient's Birth Name"**, **'PatientBirthName'**, **:patient_birth_name**, **'00101005'** and **[0x0010,0x1005]**
+
+- As String key you may use the standard tag format **'(0010,1005)'**, the tag name **'Patient's Birth Name'**, the tag keyword **'PatientBirthName'** or the Native DICOM Format tag **'00101005'**
+- As Array key you may use the numeric array **[0x0010,0x1005]**
+- As Symbol key you may use **:patient_birth_name**
+
+### example:
+Consider the previous case of tag (0010,1005), the code:
+
+```ruby
+puts "Patient's Birth Name".tag_ps.inspect
+puts [0x0010,0x1005].tag_name.inspect
+puts '(0010,1005)'.tag_key.inspect
+puts :patient_birth_name.tag_vr.inspect
+puts 'PatientBirthName'.tag_vm.inspect
+puts '00101005'.tag.inspect
+puts '(0010,1005)'.tag_ary.inspect
+puts '00101005'.tag_sym.inspect
+puts 'PatientBirthName'.tag_ndm.inspect
+puts "Patient's Birth Name".tag_str.inspect
+puts [0x0010,0x1005].tag_note.inspect
+puts [0x0010,0x1005].tag_group.inspect
+puts :patient_birth_name.tag_element.inspect
+```
+
+will produce
+
+
+```ruby
+"(0010,1005)"
+"Patient's Birth Name"
+"PatientBirthName"
+[:PN]
+["1"]
+[16, 4101]
+[16, 4101]
+:patient_birth_name
+"00101005"
+"(0010,1005)"
+""
+16
+4101
+```
+
+### Multiple Tag
+The library also manage 'multiple tags' such as *(0020,31XX)* (*Source Image IDs*).
+As an example for this data element the default tag in array form is [0x0020,0x3122] and all fields are expressed as:
+
+|Method/field  | Value|
+|:------|:------------:|
+|**tag**     | [0x0020,0x3122]|
+|**tag_name**    | "Source Image IDs"|
+|**tag_keyword** | 'SourceImageIDs'|
+|**tag_key** | 'SourceImageIDs'|
+|**tag_vr**      |  [:CS]|
+|**tag_vm**      |  ["1-n"]|
+|**tag_ps**  | '(0020,31XX)'|
+|**tag_ary** | [0x0020,0x3122]|
+|**tag_sym** | :source_image_ids|
+|**tag_ndm** | '00203122'
+|**tag_str** | '(0020,3122)'|
+|**tag_note** |  'RET'|
+|**tag_multiple?** | true|
+
+[0x0020,0x3122] is the default value for group/element pair (*[32, 12578]*), but any valid pair of numbers for this tag will be refers that information:
+
+```ruby
+> '(0020,31XX)'.tag_name
+ => "Source Image IDs"
+> '(0020,31XX)'.tag_ndm
+ => "00203122"
+> "SourceImageIDs".tag_ary
+ => [32, 12578]
+> '(0020,3178)'.tag_name
+ => "Source Image IDs"
+[0x0020,0x3146].tag_sym
+ => :source_image_ids
+> '00203120'.tag_key
+ => "SourceImageIDs"
+ > [0x0020,0x3138].tag_vr
+ => [:CS]
+ > '(0020,3144)'.tag_note
+ => "RET"
+```
+and so on.
+
+## UID data in detail
+Any UID features can be accessed from a *String* object.
+
+### UID Values
+For these objects is possible to access to value, name and type values for any single uid.
+Main methods supported are:
+
+|Method  | Note| Type||
+|:------|:------------:|:---:|:---:|
+|**uid**     | value of uid| String|(alias of *uid_value*)|
+|**uid_value**     | value of uid| String|
+|**uid_name**    | name of uid| String|
+|**uid_type** | type of uid| Symbol|
+
+each uid is indexed by:
+
+|Field|Type|
+|:----|:-----|
+|**uid_value** | String|
+|**uid_name**  | String|
+
+From these fields is possible to access to all uid informations.
+Consider the case of the uid *1.2.840.10008.1.1* (*Verification SOP Class*), the primary fields are the strings **'1.2.840.10008.1.1'** and **"Verification SOP Class"**.
+- As String key you may use the standard value **'1.2.840.10008.1.1'** and the uid name **"Verification SOP Class"**
+
+For this uid all fields are expressed as:
+
+|Method/field  | Value|
+|:------|:------------:|
+|**uid** | '1.2.840.10008.1.1'|
+|**uid_value** | '1.2.840.10008.1.1'|
+|**uid_name**  | "Verification SOP Class"|
+|**uid_type**  | :sop_class|
+
+### example:
+```ruby
+> "Verification SOP Class".uid_value
+ => "1.2.840.10008.1.1"
+> "1.2.840.10008.1.1".uid_type
+ => :sop_class
+> "1.2.840.10008.1.1".uid_name
+ => "Verification SOP Class"
+> "Verification SOP Class".uid
+ => "1.2.840.10008.1.1"
+```
+
+## How data is extracted
+The library also contains a script (*dcm_dict_converter.rb* into *bin* folder) able to download the xml documents and extracts the source data in a *Ruby compatible format*.
+The script produces the conversion in the *stdout* so for example is possible to extract the Tag Values by:
+
+```ruby
+dcm_dict_converter.rb tag > /tmp/tag-dict.rb
+```
+
+Note: the script use the [Nokogiri][3] as XML parser if installed as gem, otherwise the standard *REXML*.
+
+Check the file for other details.
+
+## Install
+
+    $ gem install dcm_dict
+
+*Note for Windows users*: may be that it is installed a previous version of Ruby 2.1, at the moment [RubyInstaller][7] does not provide the official release for this version. It is still possible to make it manually by clone/download the ['git' version of RubyInstaller][8] and execute the rake command ```rake ruby21``` (see RubyInstaller doc for details).
+
+## What's next
+The main idea is that *dictionary* should include only fixed data defined in the DICOM standard to encode and then make it available in easy way.
+There are many possible *candidates* for inclusion in the *dictionary*, here are some *"ideas"*:
+- Directory Record type data
+- Well-known Frames of Reference UID Values
+- Context Group UID Values
+- Standard Color Palettes UID Values
+- IOD definition data
+- ...
+
+## Contributing
+TBD
+
+## License
+Copyright (C) 2014  Enrico Rivarola.
+See the `LICENSE` and `COPYING` files for license details.
+
+## Source Code
+Main source code repository on github at [henrythebuilder/dcm_dict](https://github.com/henrythebuilder/dcm_dict)
+
+
+[1]: http://medical.nema.org/dicom/ "DICOM Homepage"
+[2]: http://www.dclunie.com/dicom-status/status.html "DICOM Standard Status"
+[3]: http://nokogiri.org/ "Nokogiri"
+[4]: http://rubini.us/ "Rubinius"
+[5]: https://rubygems.org/gems/refine "Refine gem at RubyGems.org"
+[6]: https://rubygems.org/gems/backports "Backports gem at RubyGems.org"
+[7]: http://rubyinstaller.org/ "The easy way to install Ruby on Windows"
+[8]: https://github.com/oneclick/rubyinstaller "RubyInstaller for Windows"

data/Rakefile

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+$:.push File.expand_path("../lib", __FILE__)
+require "dcm_dict/version"
+require 'rake'
+require 'rspec/core/rake_task'
+
+desc "Check all spec"
+RSpec::Core::RakeTask.new(:spec) do |t|
+  t.pattern = 'spec/**/*_spec.rb'
+  t.ruby_opts = "-w"
+  t.rspec_opts = '--color --format documentation'
+end
+
+desc "Check all spec with code coverage"
+task :coverage do
+  ENV['COVERAGE'] = "true"
+  Rake::Task["spec"].execute
+end
+
+desc(task(:coverage).comment)
+task :default => :coverage
+
+desc "Build dcm_dict v#{DcmDict::VERSION} gem"
+task :build do
+  system "gem build dcm_dict.gemspec"
+  FileUtils.mkdir_p "pkg"
+  FileUtils.mv "dcm_dict-#{DcmDict::VERSION}.gem", "pkg"
+end
+
+desc "Open IRB with DcmDict support"
+task :console do
+  require 'irb'
+  require 'irb/completion'
+  require 'dcm_dict'
+  ARGV.clear
+  IRB.start
+end

data/bin/dcm_dict_converter.rb

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+#!/usr/bin/env ruby
+# -*- ruby -*-
+#
+#  Copyright (C) 2014  Enrico Rivarola
+#
+#  This file is part of DcmDict gem (dcm_dict).
+#
+#  DcmDict 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.
+#
+#  DcmDict 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 DcmDict.  If not, see <http://www.gnu.org/licenses/>.
+#
+#  This software has neither been tested nor approved for clinical use
+#  or for incorporation in a medical device.
+#  It is the redistributor's or user's responsibility to comply with any
+#  applicable local, state, national or international regulations.
+#
+require 'open-uri'
+require 'tempfile'
+require 'dcm_dict'
+require 'dcm_dict/xml/xml_tool'
+
+LICENSE_TEXT=<<END_LICENSE
+  Copyright (C) 2014  Enrico Rivarola
+
+  This file is part of DcmDict gem (dcm_dict).
+
+  DcmDict 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.
+
+  DcmDict 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 DcmDict.  If not, see <http://www.gnu.org/licenses/>.
+
+  This software has neither been tested nor approved for clinical use
+  or for incorporation in a medical device.
+  It is the redistributor's or user's responsibility to comply with any
+  applicable local, state, national or international regulations
+
+END_LICENSE
+
+class DcmDictConverter
+  Part6XmlUrl="http://dicom.nema.org/medical/dicom/2014a/source/docbook/part06/part06.xml"
+  Part7XmlUrl="http://dicom.nema.org/medical/dicom/2014a/source/docbook/part07/part07.xml"
+  DataElementSource={
+    Part7XmlUrl => ["table_E.1-1", "table_E.2-1"],
+    Part6XmlUrl => ["table_7-1", "table_8-1", "table_6-1"]
+  }
+
+  UidSource={
+    Part6XmlUrl => ["table_A-1"]
+  }
+
+  DataElementFix = {
+    "table_E.2-1" => {:tag_note => 'RET'}
+  }
+
+  def initialize
+
+  end
+
+  def print_out_tag
+    trace("Print out data to stdout\n")
+    print_out_data_elements()
+    trace("Print out done.\n")
+  end
+
+  def print_out_uid
+    trace("Print out data to stdout\n")
+    print_out_uid_data()
+    trace("Print out done.\n")
+  end
+
+  private
+  def pull_standard_draft(url, output)
+    buffer_size = 256 * 1_024
+    trace("Downloading #{url}\n")
+    open(url, "r",
+         :content_length_proc => lambda {|content_length| trace("Content Length: #{content_length} bytes\n.") },
+         :progress_proc => lambda { |size| trace(".") }) do |src|
+      while (buffer = src.read(buffer_size))
+        output.write(buffer)
+      end
+    end
+    trace("Done.\n")
+    output.flush
+    output.rewind
+  end
+
+  def extract_node_set(xml_file, table_to_map)
+    xml_doc = DcmDict::XML::XmlTool.create_xml_doc(File.read(xml_file))
+    table_to_map.each do |table|
+      trace("Extracting data from '#{table}':")
+      xpath="//xmlns:table[@xml:id=\"#{table}\"]//xmlns:tbody/xmlns:tr"
+      DcmDict::XML::XmlTool.each_tr_set(xml_doc, xpath) do |tdset|
+        yield(table, tdset)
+      end
+      trace("Done.\n")
+    end
+  end
+
+  def extract_data_element(xml_file, table_to_map)
+    extract_node_set(xml_file, table_to_map) do |table, td|
+      data = DcmDict::XML::XmlTool.extract_data_element_field_from_tr_set(td)
+      check_data_element_data(data, table)
+      yield(data) if block_given?
+    end
+  end
+
+  def check_data_element_data(data, table)
+    if (DataElementFix.has_key?(table))
+      DataElementFix[table].each{|key, val| data[key]=val if data[key].empty?}
+    end
+  end
+
+  def print_out_data_elements()
+    print_out(DcmDict::Encoder::DataToCode.data_element_header)
+    DataElementSource.each do |url, table_to_map|
+      Tempfile.create('dcmps') do |xml_file|
+        pull_standard_draft(url, xml_file)
+        extract_data_element(xml_file, table_to_map) do |data|
+          print_out(DcmDict::Encoder::DataToCode.data_element_data_to_code(data, 6))
+          print_out("\r\n")
+          trace('.')
+        end
+      end
+    end
+    print_out(DcmDict::Encoder::DataToCode.data_element_footer)
+  end
+
+  def extract_uid(xml_file, table_to_map)
+    extract_node_set(xml_file, table_to_map) do |table, td|
+      data = DcmDict::XML::XmlTool.extract_uid_field_from_tr_set(td)
+      yield(data) if block_given?
+    end
+  end
+
+  def print_out_uid_data()
+    print_out(DcmDict::Encoder::DataToCode.uid_header)
+    UidSource.each do |url, table_to_map|
+      Tempfile.create('dcmps') do |xml_file|
+        pull_standard_draft(url, xml_file)
+        extract_uid(xml_file, table_to_map) do |data|
+          print_out(DcmDict::Encoder::DataToCode.uid_data_to_code(data, 6))
+          print_out("\r\n")
+          trace('.')
+        end
+      end
+    end
+    print_out(DcmDict::Encoder::DataToCode.uid_footer)
+  end
+
+  def print_out(string)
+    $stdout.print(string)
+  end
+
+  def trace(msg)
+    $stderr.print(msg)
+  end
+
+end
+
+STDERR << LICENSE_TEXT
+STDERR << "\nAny key to continue or Ctrl-C to break.\n"
+STDIN.getc
+
+if (DcmDict::XML.nokogiri_enable?)
+  STDERR << "Parsing XML data with Nokogiri.\n\n"
+else
+  STDERR << "Parsing XML data with REXML.\n\n"
+end
+
+case ARGV[0]
+when "tag"
+  DcmDictConverter.new.print_out_tag
+when "uid"
+  DcmDictConverter.new.print_out_uid
+else
+  STDERR << "\nwrong option: use 'tag' or 'uid' (ie dcm_dict_converter.rb tag > uid_values.rb)\n"
+end