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annotate Sphinx/source/users/anonymization.rst @ 692:549824ebdf5a
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 03 Jun 2021 21:22:20 +0200 |
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0 | 1 .. highlight:: bash |
2 .. _anonymization: | |
3 | |
4 Anonymization and modification | |
5 ============================== | |
6 | |
7 .. contents:: | |
8 :depth: 2 | |
9 | |
10 Orthanc 0.5.0 introduces the anonymization of DICOM resources | |
11 (i.e. patients, studies, series or instances). This page summarizes | |
12 how to use this feature. | |
13 | |
14 | |
15 Anonymization of a Single Instance | |
16 ---------------------------------- | |
17 | |
18 Orthanc allows to anonymize a single DICOM instance and to download | |
19 the resulting anonymized DICOM file. Anonymization consists in erasing | |
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20 all the tags that are specified in `Table E.1-1 from PS 3.15 |
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21 <http://dicom.nema.org/medical/dicom/current/output/chtml/part15/chapter_E.html#table_E.1-1>`__ |
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22 of the DICOM standard 2008, 2017c or 2021b (default). Example:: |
0 | 23 |
24 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{}' > Anonymized.dcm | |
25 | |
26 It is possible to control how anonymization is achieved by specifying | |
27 a JSON body:: | |
28 | |
444 | 29 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST \ |
30 --data '{ | |
31 "Replace": { | |
32 "PatientName": "Hello", | |
33 "0010-1001": "World" | |
34 }, | |
35 "Keep": [ | |
36 "StudyDescription", | |
37 "SeriesDescription" | |
38 ], | |
39 "KeepPrivateTags": true, | |
40 "DicomVersion" : "2017c" | |
41 }' > Anonymized.dcm | |
0 | 42 |
43 Explanations: | |
44 | |
45 * New UUIDs are automatically generated for the study, the series and | |
46 the instance. | |
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47 * The DICOM tags can be specified either by their name |
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48 (``PatientName``) or by their hexadecimal identifier (in the example |
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49 above, ``0010-1001`` corresponds to ``Other Patient Names``). |
0 | 50 * ``Replace`` is an associative array that associates a DICOM tag with its |
51 new string value. The value is dynamically cast to the proper DICOM | |
52 data type (an HTTP error will occur if the cast fails). Replacements | |
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53 are applied after all the tags to anonymize have been removed. |
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54 You may also use the ``Replace`` field to add new tags to the file. |
0 | 55 * ``Keep`` specifies a list of tags that should be preserved from full |
56 anonymization. | |
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57 * If ``KeepPrivateTags`` is set to ``true`` in the JSON request, |
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58 private tags (i.e. manufacturer-specific tags) are not removed by |
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59 the anonymization process. The default behavior consists in removing |
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60 the private tags, as such tags can contain patient-specific |
0 | 61 information. |
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62 * ``DicomVersion`` specifies which version of the DICOM standard shall |
692 | 63 be used for anonymization. Allowed values are ``2008``, ``2017c``, |
64 or ``2021b`` (new in Orthanc 1.9.4). This parameter has been | |
65 introduced in Orthanc 1.3.0. In earlier version, the ``2008`` | |
66 standard was used. If the parameter is absent, the highest version | |
67 that is supported by Orthanc is used. | |
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68 |
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69 |
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70 **Implementation:** Internally, the setup of the anonymization |
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71 profiles can be found in the methods ``SetupAnonymizationXXX()`` of |
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72 the class ``Orthanc::DicomModification`` (cf. `source code |
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73 <https://hg.orthanc-server.com/orthanc/file/tip/OrthancFramework/Sources/DicomParsing/DicomModification.cpp>`__). |
0 | 74 |
75 | |
76 Modification of a Single Instance | |
77 --------------------------------- | |
78 | |
79 Orthanc allows to modify a set of specified tags in a single DICOM | |
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80 instance and to download the resulting modified DICOM |
0 | 81 file. Example:: |
82 | |
444 | 83 $ curl -X POST http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/modify \ |
84 --data '{ | |
85 "Replace": { | |
86 "PatientName":"hello", | |
87 "PatientID":"world" | |
88 }, | |
89 "Remove":[ | |
90 "InstitutionName" | |
91 ], | |
92 "RemovePrivateTags": true, | |
93 "Force": true, | |
94 "Transcode": "1.2.840.10008.1.2.4.70" | |
95 }' > Modified.dcm | |
0 | 96 |
97 Remarks: | |
98 | |
99 * The ``Remove`` array specifies the list of the tags to remove. | |
100 * The ``Replace`` associative array specifies the substitions to be applied (cf. anonymization). | |
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101 * If ``RemovePrivateTags`` is set to ``true``, the private tags |
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102 (i.e. manufacturer-specific tags) are removed. |
444 | 103 * The ``Transcode`` option allows you to define the TransferSyntax |
104 of the modified file. | |
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105 * The ``Force`` option must be set to ``true``, in order to allow the |
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106 modification of the ``PatientID``, as such a modification of the |
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107 :ref:`DICOM identifiers <dicom-identifiers>` might lead to breaking |
113 | 108 the DICOM model of the real-world. In general, any explicit |
109 modification to one of the ``PatientID``, ``StudyInstanceUID``, | |
110 ``SeriesInstanceUID``, and ``SOPInstanceUID`` requires ``Force`` to | |
111 be set to ``true``, in order to prevent any unwanted side effect. | |
0 | 112 |
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113 .. highlight:: json |
0 | 114 |
291
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115 * To replace a sequence of tags, you may use this syntax:: |
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116 |
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117 |
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118 { |
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119 "Replace" : { |
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120 "ProcedureCodeSequence" : [ |
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121 { |
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122 "CodeValue" : "2", |
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123 "CodingSchemeDesignator" : "1", |
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124 "CodeMeaning": "1" |
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125 } |
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126 ] |
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127 } |
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128 } |
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129 |
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130 * To replace a binary tag, you should encode it in base64 and use:: |
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131 |
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132 { |
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133 "Replace" : { |
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134 "EncryptedAttributesSequence" : [ |
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135 { |
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136 "EncryptedContentTransferSyntaxUID" : "1.2.840.10008.1.2", |
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137 "EncryptedContent" : "data:application/octet-stream;base64,SSB3YXMgaGVyZSBpbiAyMDE5LiAgTWFydHkgTWNGbHku" |
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138 } |
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139 ] |
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140 } |
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141 } |
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142 |
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143 .. _study-modification: |
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144 |
0 | 145 Modification of Studies or Series |
146 --------------------------------- | |
147 | |
148 .. highlight:: bash | |
149 | |
150 It is possible to modify all the instances from a study or from a | |
151 series in a single request. In this case, the modified instances are | |
152 stored back into the Orthanc store. Here is how to modify a series:: | |
153 | |
154 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
155 | |
156 | |
157 .. highlight:: json | |
158 | |
159 The parameters are identical to those used to modify a single | |
160 instance. Orthanc will answer a JSON message that tells where the | |
161 modified series has been stored:: | |
162 | |
163 { | |
164 "ID" : "3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce", | |
165 "Path" : "/series/3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce" | |
166 } | |
167 | |
168 | |
169 .. highlight:: bash | |
170 | |
171 Similarly, here is an interaction to modify a study:: | |
172 | |
173 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
174 | |
175 .. highlight:: json | |
176 | |
177 :: | |
178 | |
179 { | |
180 "ID" : "1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28", | |
181 "Path" : "/studies/1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28" | |
182 } | |
183 | |
184 | |
185 Modification of Patients | |
186 ------------------------ | |
187 | |
188 .. highlight:: bash | |
189 | |
190 Starting with Orthanc 0.7.5, Orthanc can also modify all the instances | |
191 of a patient with a single REST call. Here is a sample:: | |
192 | |
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193 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/modify -X POST -d '{"Replace":{"PatientID":"Hello","PatientName":"Sample patient name"},"Force":true}' |
0 | 194 |
195 .. highlight:: json | |
196 | |
197 :: | |
198 | |
199 { | |
200 "ID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
201 "Path" : "/patients/f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
202 "PatientID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
203 "Type" : "Patient" | |
204 } | |
205 | |
206 Please note that, in this case, you have to set the value of the | |
207 ``PatientID (0010,0020)`` tag for Orthanc to accept this modification: | |
208 This is a security to prevent the merging of patient data before and | |
209 after anonymization, if the user does not explicitly tell Orthanc to | |
210 do so. | |
211 | |
212 | |
213 Anonymization of Patients, Studies or Series | |
214 -------------------------------------------- | |
215 | |
216 .. highlight:: bash | |
217 | |
218 Study and series can be anonymized the same way as they are modified:: | |
219 | |
220 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/anonymize -X POST -d '{}' | |
221 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/anonymize -X POST -d '{}' | |
222 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/anonymize -X POST -d '{}' | |
223 | |
224 As written above, the anonymization process can be fine-tuned by using | |
225 a JSON body. | |
167 | 226 |
227 | |
224
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228 .. _split-merge: |
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229 |
167 | 230 Split/merge of DICOM studies |
231 ---------------------------- | |
232 | |
178 | 233 Starting with Orthanc 1.5.0, Orthanc supports splitting and merging |
167 | 234 DICOM studies through its REST API. |
235 | |
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236 .. _split: |
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237 |
167 | 238 Splitting |
239 ^^^^^^^^^ | |
240 | |
241 Here is the syntax to **split** a DICOM study:: | |
242 | |
243 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/split -d \ | |
244 '{"Series":["6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"],"Replace":{"PatientName":"HELLO"},"Remove":["AccessionNumber"]}' | |
245 | |
246 By issuing this command, the series whose :ref:`Orthanc identifier | |
247 <dicom-identifiers>` is | |
248 ``6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228``, and that is part of | |
249 the source study with identifier | |
250 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``, will be removed from | |
251 the source study, and will be moved to a brand new study. | |
252 | |
253 This is done by generating a new value for all the following DICOM | |
254 tags in the DICOM instances of the series of interest: | |
255 ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID (0x0020, | |
256 0x000e)``, and ``SOPInstanceUID (0x0008, 0x0018)``. Here are the | |
257 arguments of this ``/studies/{study}/split`` URI: | |
258 | |
259 * ``Series`` gives the list of series to be separated from the parent | |
260 study (mandatory option). These series must all be children of the | |
261 same source study, that is specified in the URI. | |
262 * ``Replace`` allows to overwrite the DICOM tags that are part of the | |
263 "Patient Module Attributes" and the "General Study Module | |
264 Attributes", as specified by the DICOM 2011 standard in Tables C.7-1 | |
265 and C.7-3. | |
266 * ``Remove`` allows to remove DICOM tags from the same modules as in | |
267 the ``Replace`` options. | |
268 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
269 Orthanc to keep a copy of the original series in the source study. | |
270 By default, the original series are deleted from Orthanc. | |
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271 |
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272 .. _merge: |
167 | 273 |
274 Merging | |
275 ^^^^^^^ | |
276 | |
277 Here is the syntax to **merge** DICOM series, into another DICOM study:: | |
278 | |
279 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/merge -d \ | |
280 '{"Resources":["ef2ce55f-9342856a-aee23907-2667e859-9f3b734d"]}' | |
281 | |
282 By issuing this command, the DICOM series whose :ref:`Orthanc | |
283 identifier <dicom-identifiers>` is | |
284 ``ef2ce55f-9342856a-aee23907-2667e859-9f3b734d``, will be merged into | |
285 target study with identifier | |
286 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``. | |
287 | |
288 As in the case of splitting, this is done by updating the following | |
289 DICOM tags: ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID | |
290 (0x0020, 0x000e)``, and ``SOPInstanceUID (0x0008, | |
291 0x0018)``. Furthermore, all the DICOM tags that are part of the | |
292 "Patient Module Attributes" and the "General Study Module Attributes" | |
293 (as specified by the DICOM 2011 standard in Tables C.7-1 and C.7-3), | |
294 are modified to match the target study. Here are the | |
295 arguments of this ``/studies/{study}/merge`` URI: | |
296 | |
297 * ``Resources`` gives the list of source studies or source series | |
298 that are to be merged into the target study. | |
299 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
300 Orthanc to keep the source studies and series. By default, the | |
301 original resources are deleted from Orthanc. |