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annotate Sphinx/source/users/anonymization.rst @ 404:7469b6c5618b
DICOM commands: Timeout + improved existing doc
author | Alain Mazy <alain@mazy.be> |
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date | Wed, 29 Apr 2020 12:59:34 +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 | |
20 all the tags that are specified in Table E.1-1 from PS 3.15 of the | |
111 | 21 DICOM standard 2008 or 2017c (default). Example:: |
0 | 22 |
23 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{}' > Anonymized.dcm | |
24 | |
25 It is possible to control how anonymization is achieved by specifying | |
26 a JSON body:: | |
27 | |
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28 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{"Replace":{"PatientName":"Hello","0010-1001":"World"},"Keep":["StudyDescription", "SeriesDescription"],"KeepPrivateTags": true, "DicomVersion" : "2017c"}' > Anonymized.dcm |
0 | 29 |
30 Explanations: | |
31 | |
32 * New UUIDs are automatically generated for the study, the series and | |
33 the instance. | |
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34 * The DICOM tags can be specified either by their name |
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35 (``PatientName``) or by their hexadecimal identifier (in the example |
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36 above, ``0010-1001`` corresponds to ``Other Patient Names``). |
0 | 37 * ``Replace`` is an associative array that associates a DICOM tag with its |
38 new string value. The value is dynamically cast to the proper DICOM | |
39 data type (an HTTP error will occur if the cast fails). Replacements | |
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40 are applied after all the tags to anonymize have been removed. |
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41 You may also use the ``Replace`` field to add new tags to the file. |
0 | 42 * ``Keep`` specifies a list of tags that should be preserved from full |
43 anonymization. | |
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44 * If ``KeepPrivateTags`` is set to ``true`` in the JSON request, |
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45 private tags (i.e. manufacturer-specific tags) are not removed by |
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46 the anonymization process. The default behavior consists in removing |
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47 the private tags, as such tags can contain patient-specific |
0 | 48 information. |
111 | 49 * ``DicomVersion`` specifies which version of the DICOM standard shall be used |
50 for anonymization. Allowed values are ``2008`` and ``2017c`` (default value | |
51 if the parameter is absent). This parameter has been introduced in Orthanc | |
52 1.3.0. In earlier version, the ``2008`` standard was used. | |
0 | 53 |
54 | |
55 Modification of a Single Instance | |
56 --------------------------------- | |
57 | |
58 Orthanc allows to modify a set of specified tags in a single DICOM | |
59 instance and to download the resulting anonymized DICOM | |
60 file. Example:: | |
61 | |
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62 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/modify -X POST -d '{"Replace":{"PatientName":"hello","PatientID":"world"},"Remove":["InstitutionName"],"RemovePrivateTags": true, "Force": true}' > Modified.dcm |
0 | 63 |
64 Remarks: | |
65 | |
66 * The ``Remove`` array specifies the list of the tags to remove. | |
67 * The ``Replace`` associative array specifies the substitions to be applied (cf. anonymization). | |
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68 * If ``RemovePrivateTags`` is set to ``true``, the private tags |
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69 (i.e. manufacturer-specific tags) are removed. |
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70 * The ``Force`` option must be set to ``true``, in order to allow the |
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71 modification of the ``PatientID``, as such a modification of the |
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72 :ref:`DICOM identifiers <dicom-identifiers>` might lead to breaking |
113 | 73 the DICOM model of the real-world. In general, any explicit |
74 modification to one of the ``PatientID``, ``StudyInstanceUID``, | |
75 ``SeriesInstanceUID``, and ``SOPInstanceUID`` requires ``Force`` to | |
76 be set to ``true``, in order to prevent any unwanted side effect. | |
0 | 77 |
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78 .. highlight:: json |
0 | 79 |
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80 * To replace a sequence of tags, you may use this syntax:: |
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81 |
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82 |
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83 { |
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84 "Replace" : { |
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85 "ProcedureCodeSequence" : [ |
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86 { |
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87 "CodeValue" : "2", |
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88 "CodingSchemeDesignator" : "1", |
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89 "CodeMeaning": "1" |
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90 } |
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91 ] |
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92 } |
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93 } |
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94 |
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95 * To replace a binary tag, you should encode it in base64 and use:: |
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96 |
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97 { |
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98 "Replace" : { |
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99 "EncryptedAttributesSequence" : [ |
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100 { |
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101 "EncryptedContentTransferSyntaxUID" : "1.2.840.10008.1.2", |
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102 "EncryptedContent" : "data:application/octet-stream;base64,SSB3YXMgaGVyZSBpbiAyMDE5LiAgTWFydHkgTWNGbHku" |
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103 } |
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104 ] |
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105 } |
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106 } |
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107 |
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108 .. _study-modification: |
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109 |
0 | 110 Modification of Studies or Series |
111 --------------------------------- | |
112 | |
113 .. highlight:: bash | |
114 | |
115 It is possible to modify all the instances from a study or from a | |
116 series in a single request. In this case, the modified instances are | |
117 stored back into the Orthanc store. Here is how to modify a series:: | |
118 | |
119 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
120 | |
121 | |
122 .. highlight:: json | |
123 | |
124 The parameters are identical to those used to modify a single | |
125 instance. Orthanc will answer a JSON message that tells where the | |
126 modified series has been stored:: | |
127 | |
128 { | |
129 "ID" : "3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce", | |
130 "Path" : "/series/3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce" | |
131 } | |
132 | |
133 | |
134 .. highlight:: bash | |
135 | |
136 Similarly, here is an interaction to modify a study:: | |
137 | |
138 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
139 | |
140 .. highlight:: json | |
141 | |
142 :: | |
143 | |
144 { | |
145 "ID" : "1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28", | |
146 "Path" : "/studies/1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28" | |
147 } | |
148 | |
149 | |
150 Modification of Patients | |
151 ------------------------ | |
152 | |
153 .. highlight:: bash | |
154 | |
155 Starting with Orthanc 0.7.5, Orthanc can also modify all the instances | |
156 of a patient with a single REST call. Here is a sample:: | |
157 | |
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158 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/modify -X POST -d '{"Replace":{"PatientID":"Hello","PatientName":"Sample patient name"},"Force":true}' |
0 | 159 |
160 .. highlight:: json | |
161 | |
162 :: | |
163 | |
164 { | |
165 "ID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
166 "Path" : "/patients/f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
167 "PatientID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
168 "Type" : "Patient" | |
169 } | |
170 | |
171 Please note that, in this case, you have to set the value of the | |
172 ``PatientID (0010,0020)`` tag for Orthanc to accept this modification: | |
173 This is a security to prevent the merging of patient data before and | |
174 after anonymization, if the user does not explicitly tell Orthanc to | |
175 do so. | |
176 | |
177 | |
178 Anonymization of Patients, Studies or Series | |
179 -------------------------------------------- | |
180 | |
181 .. highlight:: bash | |
182 | |
183 Study and series can be anonymized the same way as they are modified:: | |
184 | |
185 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/anonymize -X POST -d '{}' | |
186 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/anonymize -X POST -d '{}' | |
187 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/anonymize -X POST -d '{}' | |
188 | |
189 As written above, the anonymization process can be fine-tuned by using | |
190 a JSON body. | |
167 | 191 |
192 | |
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193 .. _split-merge: |
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194 |
167 | 195 Split/merge of DICOM studies |
196 ---------------------------- | |
197 | |
178 | 198 Starting with Orthanc 1.5.0, Orthanc supports splitting and merging |
167 | 199 DICOM studies through its REST API. |
200 | |
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201 .. _split: |
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202 |
167 | 203 Splitting |
204 ^^^^^^^^^ | |
205 | |
206 Here is the syntax to **split** a DICOM study:: | |
207 | |
208 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/split -d \ | |
209 '{"Series":["6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"],"Replace":{"PatientName":"HELLO"},"Remove":["AccessionNumber"]}' | |
210 | |
211 By issuing this command, the series whose :ref:`Orthanc identifier | |
212 <dicom-identifiers>` is | |
213 ``6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228``, and that is part of | |
214 the source study with identifier | |
215 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``, will be removed from | |
216 the source study, and will be moved to a brand new study. | |
217 | |
218 This is done by generating a new value for all the following DICOM | |
219 tags in the DICOM instances of the series of interest: | |
220 ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID (0x0020, | |
221 0x000e)``, and ``SOPInstanceUID (0x0008, 0x0018)``. Here are the | |
222 arguments of this ``/studies/{study}/split`` URI: | |
223 | |
224 * ``Series`` gives the list of series to be separated from the parent | |
225 study (mandatory option). These series must all be children of the | |
226 same source study, that is specified in the URI. | |
227 * ``Replace`` allows to overwrite the DICOM tags that are part of the | |
228 "Patient Module Attributes" and the "General Study Module | |
229 Attributes", as specified by the DICOM 2011 standard in Tables C.7-1 | |
230 and C.7-3. | |
231 * ``Remove`` allows to remove DICOM tags from the same modules as in | |
232 the ``Replace`` options. | |
233 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
234 Orthanc to keep a copy of the original series in the source study. | |
235 By default, the original series are deleted from Orthanc. | |
236 | |
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237 .. _merge: |
167 | 238 |
239 Merging | |
240 ^^^^^^^ | |
241 | |
242 Here is the syntax to **merge** DICOM series, into another DICOM study:: | |
243 | |
244 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/merge -d \ | |
245 '{"Resources":["ef2ce55f-9342856a-aee23907-2667e859-9f3b734d"]}' | |
246 | |
247 By issuing this command, the DICOM series whose :ref:`Orthanc | |
248 identifier <dicom-identifiers>` is | |
249 ``ef2ce55f-9342856a-aee23907-2667e859-9f3b734d``, will be merged into | |
250 target study with identifier | |
251 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``. | |
252 | |
253 As in the case of splitting, this is done by updating the following | |
254 DICOM tags: ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID | |
255 (0x0020, 0x000e)``, and ``SOPInstanceUID (0x0008, | |
256 0x0018)``. Furthermore, all the DICOM tags that are part of the | |
257 "Patient Module Attributes" and the "General Study Module Attributes" | |
258 (as specified by the DICOM 2011 standard in Tables C.7-1 and C.7-3), | |
259 are modified to match the target study. Here are the | |
260 arguments of this ``/studies/{study}/merge`` URI: | |
261 | |
262 * ``Resources`` gives the list of source studies or source series | |
263 that are to be merged into the target study. | |
264 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
265 Orthanc to keep the source studies and series. By default, the | |
266 original resources are deleted from Orthanc. |