dcm_dict 0.26.0 → 0.31.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/CHANGELOG.md +38 -0
- data/LICENSE +1 -1
- data/README.md +80 -65
- data/bin/dcm_dict_converter.rb +3 -3
- data/lib/dcm_dict.rb +1 -1
- data/lib/dcm_dict/dictionary/base_dictionary.rb +1 -1
- data/lib/dcm_dict/dictionary/base_record.rb +1 -1
- data/lib/dcm_dict/dictionary/data_element_dictionary.rb +1 -1
- data/lib/dcm_dict/dictionary/data_element_record.rb +1 -1
- data/lib/dcm_dict/dictionary/uid_dictionary.rb +2 -4
- data/lib/dcm_dict/dictionary/uid_record.rb +6 -1
- data/lib/dcm_dict/encoder/data_to_code.rb +2 -2
- data/lib/dcm_dict/error/dictionary_error.rb +1 -1
- data/lib/dcm_dict/ext/object_extension.rb +1 -1
- data/lib/dcm_dict/refine/array_refine.rb +1 -1
- data/lib/dcm_dict/refine/data_element_refine.rb +1 -1
- data/lib/dcm_dict/refine/internal/array_refine_internal.rb +1 -1
- data/lib/dcm_dict/refine/internal/hash_refine_internal.rb +14 -1
- data/lib/dcm_dict/refine/internal/string_refine_internal.rb +1 -1
- data/lib/dcm_dict/refine/string_refine.rb +1 -1
- data/lib/dcm_dict/refine/symbol_refine.rb +2 -1
- data/lib/dcm_dict/refine/uid_refine.rb +1 -1
- data/lib/dcm_dict/rubies/rb_ext.rb +1 -1
- data/lib/dcm_dict/source_data/data_elements_data.rb +84 -3
- data/lib/dcm_dict/source_data/detached_data.rb +1 -1
- data/lib/dcm_dict/source_data/uid_values_data.rb +445 -421
- data/lib/dcm_dict/version.rb +3 -3
- data/lib/dcm_dict/xml/constant.rb +3 -2
- data/lib/dcm_dict/xml/field_data.rb +1 -1
- data/lib/dcm_dict/xml/nokogiri_tool.rb +1 -1
- data/lib/dcm_dict/xml/rexml_tool.rb +1 -1
- data/lib/dcm_dict/xml/tag_field_data.rb +1 -1
- data/lib/dcm_dict/xml/uid_field_data.rb +14 -4
- data/lib/dcm_dict/xml/xml_tool.rb +1 -1
- data/spec/data_element_sample_spec_helper.rb +12 -2
- data/spec/data_element_shared_example_spec_helper.rb +1 -1
- data/spec/dcm_dict/dictionary/data_element_dictionary_spec.rb +1 -1
- data/spec/dcm_dict/dictionary/data_element_record_spec.rb +1 -1
- data/spec/dcm_dict/dictionary/uid_dictionary_spec.rb +62 -17
- data/spec/dcm_dict/dictionary/uid_record_spec.rb +8 -4
- data/spec/dcm_dict/encoder/data_to_code_spec.rb +2 -2
- data/spec/dcm_dict/ext/object_extension_spec.rb +1 -1
- data/spec/dcm_dict/refine/array_refine_spec.rb +1 -1
- data/spec/dcm_dict/refine/internal/array_refine_internal_spec.rb +1 -1
- data/spec/dcm_dict/refine/internal/hash_refine_internal_spec.rb +19 -1
- data/spec/dcm_dict/refine/internal/string_refine_internal_spec.rb +1 -1
- data/spec/dcm_dict/refine/string_refine_spec.rb +4 -4
- data/spec/dcm_dict/refine/symbol_refine_spec.rb +26 -1
- data/spec/dcm_dict/rubies/rb_ext_spec.rb +1 -1
- data/spec/dcm_dict/source_data/data_elements_data_spec.rb +1 -1
- data/spec/dcm_dict/source_data/detached_data_spec.rb +1 -1
- data/spec/dcm_dict/source_data/uid_values_data_spec.rb +1 -1
- data/spec/dcm_dict/version_spec.rb +1 -1
- data/spec/dcm_dict/xml/tag_field_data_spec.rb +1 -1
- data/spec/dcm_dict/xml/uid_field_data_spec.rb +1 -1
- data/spec/dictionary_shared_example_spec_helper.rb +3 -3
- data/spec/refine_shared_example_spec_helper.rb +1 -1
- data/spec/spec_helper.rb +1 -1
- data/spec/xml_sample_spec_helper.rb +80 -32
- metadata +18 -18
checksums.yaml
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metadata.gz: e2d0df30790bfcb71c48d0fbf9b674a8b1a6150ec77db1148280126ec7a0dd558be0c5d960670497a6491fd29431470cf21389dff424d157174c3b169f4f8f2f
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data.tar.gz: 00a86d7fbb1bd1e932df26a139642e7d83336969db99d6ce4828bf9cc85e981c89c8210391e7c05811fdf481c65befff566d4e4469405d052f68a8edefae0ba2
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data/CHANGELOG.md
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# DcmDict project Changelog
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## v0.31.0 (2020-12-07)
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* Update to 2020e Base Standard
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___
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## v0.30.0 (2020-10-03)
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* Update to 2020d Base Standard
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* Add keywords support for standard UIDs
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___
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## v0.29.0 (2020-07-21)
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* Update to 2020c Base Standard
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___
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## v0.28.1 (2020-03-18)
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* Updated dcm_dict.gemspec due to a security vulnerabilities into the Rake gem as defined into gemspec (>=10.3 to >=12.3.3)
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#### Note for gemspec security report:
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>rake vulnerability found in dcm_dict.gemspec:
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>CVE-2020-8130 (moderate severity)
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>Vulnerable versions: <= 12.3.2
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>Patched version: 12.3.3
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>There is an OS command injection vulnerability in Ruby Rake before 12.3.3 in Rake::FileList when supplying a filename that begins with the pipe character |.
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>
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>Remediation:
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>Upgrade rake to version 12.3.3 or later.
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>
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>["OS Command Injection in Rake"](https://github.com/advisories/GHSA-jppv-gw3r-w3q8)
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>["CVE-2020-8130 Detail"](https://nvd.nist.gov/vuln/detail/CVE-2020-8130)
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___
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## v0.28.0 (2020-03-18)
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* Update to 2020b Base Standard
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* Remove warning for deprecated method 'Kernel#open'
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___
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## v0.27.0 (2020-02-05)
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* Update to 2020a Base Standard
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___
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## v0.26.2 (2020-02-05)
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* Update copyright year
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___
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## v0.26.1 (2020-01-03)
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* Fix test to be compatible with ruby 2.7
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* (No Dictionary Change from 2019e)
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___
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## v0.26.0 (2019-11-20)
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* Update to 2019e Base Standard
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data/LICENSE
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DcmDict is a Ruby gem (dcm_dict) to handle
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in a simple way the Data defined within the DICOM Standard.
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Copyright (C) 2014-
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Copyright (C) 2014-2020 Enrico Rivarola
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DcmDict is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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data/README.md
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# Why *DcmDict*
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With the new releases from year 2014 DICOM documents are available in different format including one particularly interesting, the *DocBook* XML version.
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This is confirmed in the DICOM<sup>®</sup> Standard [web site][10] where each part is published in [multiple formats][11] and the XML format is defined:
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>"... good for machine readability, e.g. self-updating validators ..."
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As confirmed in the DICOM<sup>®</sup> Standard [web site][10] where each part is published in [multiple formats][11] and XML format is defined by:
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>"... XML – good for machine readability, e.g. self-updating validators ..."
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This is great news for anyone involved in the study of the standard !
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=> :transfer_syntax
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> "Implicit VR Little Endian: Default Transfer Syntax for DICOM".uid_value
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=> "1.2.840.10008.1.2"
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> "Verification SOP Class".uid_value
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=> "1.2.840.10008.1.1"
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> "1.2.840.10008.1.1".uid_type
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=> :sop_class
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> "Verification".uid
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=> "1.2.840.10008.1.1"
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> :verification.uid
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=> "1.2.840.10008.1.1"
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```
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let see all features in detail:
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The main methods supported are:
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| Method | Note | Type | |
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|:------------------|:---------------------------------:|:-------------------:|:----------------------------------:|
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| **tag** | tag as Array | Array of two Fixnum | (alias of *tag_ary*) |
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| **tag_name** | name of tag | String | |
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| **tag_keyword** | keyword | String | |
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| **tag_key** | keyword | String | |
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| **tag_vr** | Value Representation | Array of Symbol | |
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| **tag_vm** | Value Multiplicity | Array of Symbol | |
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| **tag_ps** | tag as string (as standard doc) | String | |
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| **tag_ary** | tag as Array | Array of two Fixnum | |
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| **tag_sym** | tag as Symbol | Symbol | |
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| **tag_ndm** | tag as in Native DICOM Model | String | |
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| **tag_str** | tag as string (similar to tag_ps) | String | |
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| **tag_note** | tag note | String | |
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| **tag_multiple?** | is a multiple tag ? | boolean | (useful for 'multi tag' attribute) |
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each data element is indexed by these fields:
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| **tag_key** | String |
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| **tag_ps** | String |
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| **tag_ary** | Array |
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| **tag_sym** | Symbol |
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| **tag_ndm** | String |
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| **tag_str** | String |
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| **tag_name** | String |
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By these fields is possible to access to data element informations.
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Consider the case of the tag (0010,1005) (*Patient's Birth Name*), the primary fields are:
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The library also manage 'multiple tags' such as *(0020,31XX)* (*Source Image IDs*).
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As an example for this data element the default tag in array form is [0x0020,0x3122] and all fields are expressed as:
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| **tag** | [0x0020,0x3122] |
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| **tag_name** | "Source Image IDs" |
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| **tag_keyword** | 'SourceImageIDs' |
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| **tag_key** | 'SourceImageIDs' |
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| **tag_vr** | [:CS] |
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| **tag_vm** | ["1-n"] |
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| **tag_ps** | '(0020,31XX)' |
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| **tag_ary** | [0x0020,0x3122] |
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| **tag_sym** | :source_image_ids |
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| **tag_ndm** | '00203122' |
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| **tag_str** | '(0020,3122)' |
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| **tag_note** | 'RET' |
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| **tag_multiple?** | true |
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[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:
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and so on.
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## UID data in detail
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Any UID features can be accessed from a *String* or a *Symbol* object.
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### UID Values
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For these objects is possible to access to value, name and type values for any single uid.
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Main methods supported are:
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| **uid** | value of uid | String | (alias of *uid_value*) |
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| **uid_value** | value of uid | String | |
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| **uid_name** | name of uid | String | |
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| **uid_key** | keyword of uid | String | |
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| **uid_sym** | keyword as symbol of uid | Symbol | |
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| **uid_type** | type of uid | Symbol | |
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From these fields is possible to access to all uid informations.
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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'**, **"Verification SOP Class"**, **"Verification"**.
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- As key you may use the standard value **'1.2.840.10008.1.1'**, the uid name **"Verification SOP Class"**, the uid keyword **"Verification"** and the symbol **:verification**
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For this uid all fields are expressed as:
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| **uid** | '1.2.840.10008.1.1' |
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| **uid_value** | '1.2.840.10008.1.1' |
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### example:
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257
268
|
=> "Verification SOP Class"
|
|
258
269
|
> "Verification SOP Class".uid
|
|
259
270
|
=> "1.2.840.10008.1.1"
|
|
271
|
+
> "Verification".uid
|
|
272
|
+
=> "1.2.840.10008.1.1"
|
|
273
|
+
> :verification.uid
|
|
274
|
+
=> "1.2.840.10008.1.1"
|
|
260
275
|
```
|
|
261
276
|
|
|
262
277
|
## How data is extracted
|
|
@@ -272,7 +287,7 @@ Note: the script use the [Nokogiri][3] as XML parser if installed as gem, otherw
|
|
|
272
287
|
Check the file for other details.
|
|
273
288
|
|
|
274
289
|
## Note
|
|
275
|
-
Current library version is aligned to *DICOM Base Standard* **
|
|
290
|
+
Current library version is aligned to *DICOM Base Standard* **2020e**
|
|
276
291
|
|
|
277
292
|
## Install
|
|
278
293
|
|
|
@@ -295,7 +310,7 @@ There are many possible *candidates* for inclusion in the *dictionary*, here are
|
|
|
295
310
|
TBD
|
|
296
311
|
|
|
297
312
|
## License
|
|
298
|
-
Copyright (C) 2014-
|
|
313
|
+
Copyright (C) 2014-2020 Enrico Rivarola.
|
|
299
314
|
See the `LICENSE` and `COPYING` files for license details.
|
|
300
315
|
|
|
301
316
|
## Ruby Gem
|
data/bin/dcm_dict_converter.rb
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
#!/usr/bin/env ruby
|
|
2
2
|
# -*- ruby -*-
|
|
3
3
|
#
|
|
4
|
-
# Copyright (C) 2014-
|
|
4
|
+
# Copyright (C) 2014-2020 Enrico Rivarola
|
|
5
5
|
#
|
|
6
6
|
# This file is part of DcmDict gem (dcm_dict).
|
|
7
7
|
#
|
|
@@ -29,7 +29,7 @@ require 'dcm_dict'
|
|
|
29
29
|
require 'dcm_dict/xml/xml_tool'
|
|
30
30
|
|
|
31
31
|
LICENSE_TEXT=<<END_LICENSE
|
|
32
|
-
Copyright (C) 2014-
|
|
32
|
+
Copyright (C) 2014-2020 Enrico Rivarola
|
|
33
33
|
|
|
34
34
|
This file is part of DcmDict gem (dcm_dict).
|
|
35
35
|
|
|
@@ -89,7 +89,7 @@ class DcmDictConverter
|
|
|
89
89
|
def pull_standard_draft(url, output)
|
|
90
90
|
buffer_size = 256 * 1_024
|
|
91
91
|
trace("Downloading #{url}\n")
|
|
92
|
-
open(url, "r",
|
|
92
|
+
URI.open(url, "r",
|
|
93
93
|
:content_length_proc => lambda {|content_length| trace("Content Length: #{content_length} bytes\n.") },
|
|
94
94
|
:progress_proc => lambda { |size| trace(".") }) do |src|
|
|
95
95
|
while (buffer = src.read(buffer_size))
|
data/lib/dcm_dict.rb
CHANGED
|
@@ -25,7 +25,7 @@ module DcmDict
|
|
|
25
25
|
module Dictionary
|
|
26
26
|
using DcmDict::Refine::Internal::StringRefineInternal
|
|
27
27
|
|
|
28
|
-
UidIndexKey = [:uid_value, :uid_name]
|
|
28
|
+
UidIndexKey = [:uid_value, :uid_name, :uid_key, :uid_sym]
|
|
29
29
|
|
|
30
30
|
# Main class to handle uid data as dictionary
|
|
31
31
|
class UidDictionary < BaseDictionary
|
|
@@ -70,9 +70,7 @@ module DcmDict
|
|
|
70
70
|
|
|
71
71
|
def try_to_find_unknown_uid(uid)
|
|
72
72
|
raise "Unknown UID value" unless uid.uid_value?
|
|
73
|
-
UidRecord.new({ uid_value: uid
|
|
74
|
-
uid_name: 'Unknown UID',
|
|
75
|
-
uid_type: :unknown })
|
|
73
|
+
UidRecord.new({ uid_value: uid })
|
|
76
74
|
end
|
|
77
75
|
end
|
|
78
76
|
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
#
|
|
2
|
-
# Copyright (C) 2014-
|
|
2
|
+
# Copyright (C) 2014-2020 Enrico Rivarola
|
|
3
3
|
#
|
|
4
4
|
# This file is part of DcmDict gem (dcm_dict).
|
|
5
5
|
#
|
|
@@ -25,8 +25,12 @@ require_relative 'base_record'
|
|
|
25
25
|
|
|
26
26
|
module DcmDict
|
|
27
27
|
module Dictionary
|
|
28
|
+
using DcmDict::Refine::Internal::HashRefineInternal
|
|
29
|
+
|
|
28
30
|
UidMethodMap = {uid_value: :uid_value,
|
|
29
31
|
uid: :uid_value,
|
|
32
|
+
uid_key: :uid_key,
|
|
33
|
+
uid_sym: :uid_sym,
|
|
30
34
|
uid_name: :uid_name,
|
|
31
35
|
uid_type: :uid_type }.freeze
|
|
32
36
|
|
|
@@ -35,6 +39,7 @@ module DcmDict
|
|
|
35
39
|
# Class to handle uid record from source dictionary data
|
|
36
40
|
class UidRecord < BaseRecord
|
|
37
41
|
def initialize(data)
|
|
42
|
+
data.check_base_data_uid_field!
|
|
38
43
|
super
|
|
39
44
|
end
|
|
40
45
|
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
#
|
|
2
|
-
# Copyright (C) 2014-
|
|
2
|
+
# Copyright (C) 2014-2020 Enrico Rivarola
|
|
3
3
|
#
|
|
4
4
|
# This file is part of DcmDict gem (dcm_dict).
|
|
5
5
|
#
|
|
@@ -72,7 +72,7 @@ END
|
|
|
72
72
|
# Convert uid +data+ to Ruby code using +indent+ spaces indentation
|
|
73
73
|
def self.uid_data_to_code(data, indent=4)
|
|
74
74
|
indent = 4 unless indent
|
|
75
|
-
"#{' '*indent}{ uid_value: '#{data[:uid_value]}', uid_name:
|
|
75
|
+
"#{' '*indent}{ uid_value: '#{data[:uid_value]}', uid_name: '#{data[:uid_name]}', uid_key: '#{data[:uid_key]}', uid_sym: #{data[:uid_sym].inspect}, uid_type: #{data[:uid_type].inspect}},"
|
|
76
76
|
end
|
|
77
77
|
end
|
|
78
78
|
end
|