Mercurial > hg > orthanc-book
annotate Sphinx/source/users/anonymization.rst @ 291:829ce317d215
added sample for /modify for sequences and binary fields
| author | Alain Mazy <alain@mazy.be> |
|---|---|
| date | Thu, 14 Nov 2019 10:28:31 +0100 |
| parents | 02399e86f046 |
| children | 22d567933381 |
| rev | line source |
|---|---|
| 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 | |
|
112
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
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. | |
|
112
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
34 * The DICOM tags can be specified either by their name |
|
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
35 (``PatientName``) or by their hexadecimal identifier (in the example |
|
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
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 | |
|
291
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
40 are applied after all the tags to anonymize have been removed. |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
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. | |
|
112
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
44 * If ``KeepPrivateTags`` is set to ``true`` in the JSON request, |
|
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
45 private tags (i.e. manufacturer-specific tags) are not removed by |
|
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
46 the anonymization process. The default behavior consists in removing |
|
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
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 | |
|
112
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
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). | |
|
112
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
68 * If ``RemovePrivateTags`` is set to ``true``, the private tags |
|
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
69 (i.e. manufacturer-specific tags) are removed. |
|
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
70 * The ``Force`` option must be set to ``true``, in order to allow the |
|
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
71 modification of the ``PatientID``, as such a modification of the |
|
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
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 |
|
291
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
78 .. highlight:: json |
| 0 | 79 |
|
291
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
80 * To replace a sequence of tags, you may use this syntax:: |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
81 |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
82 |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
83 { |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
84 "Replace" : { |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
85 "ProcedureCodeSequence" : [ |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
86 { |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
87 "CodeValue" : "2", |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
88 "CodingSchemeDesignator" : "1", |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
89 "CodeMeaning": "1" |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
90 } |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
91 ] |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
92 } |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
93 } |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
94 |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
95 * To replace a binary tag, you should encode it in base64 and use:: |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
96 |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
97 { |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
98 "Replace" : { |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
99 "EncryptedAttributesSequence" : [ |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
100 { |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
101 "EncryptedContentTransferSyntaxUID" : "1.2.840.10008.1.2", |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
102 "EncryptedContent" : "data:application/octet-stream;base64,SSB3YXMgaGVyZSBpbiAyMDE5LiAgTWFydHkgTWNGbHku" |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
103 } |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
104 ] |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
105 } |
|
829ce317d215
added sample for /modify for sequences and binary fields
Alain Mazy <alain@mazy.be>
parents:
224
diff
changeset
|
106 } |
| 0 | 107 Modification of Studies or Series |
| 108 --------------------------------- | |
| 109 | |
| 110 .. highlight:: bash | |
| 111 | |
| 112 It is possible to modify all the instances from a study or from a | |
| 113 series in a single request. In this case, the modified instances are | |
| 114 stored back into the Orthanc store. Here is how to modify a series:: | |
| 115 | |
| 116 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
| 117 | |
| 118 | |
| 119 .. highlight:: json | |
| 120 | |
| 121 The parameters are identical to those used to modify a single | |
| 122 instance. Orthanc will answer a JSON message that tells where the | |
| 123 modified series has been stored:: | |
| 124 | |
| 125 { | |
| 126 "ID" : "3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce", | |
| 127 "Path" : "/series/3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce" | |
| 128 } | |
| 129 | |
| 130 | |
| 131 .. highlight:: bash | |
| 132 | |
| 133 Similarly, here is an interaction to modify a study:: | |
| 134 | |
| 135 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
| 136 | |
| 137 .. highlight:: json | |
| 138 | |
| 139 :: | |
| 140 | |
| 141 { | |
| 142 "ID" : "1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28", | |
| 143 "Path" : "/studies/1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28" | |
| 144 } | |
| 145 | |
| 146 | |
| 147 Modification of Patients | |
| 148 ------------------------ | |
| 149 | |
| 150 .. highlight:: bash | |
| 151 | |
| 152 Starting with Orthanc 0.7.5, Orthanc can also modify all the instances | |
| 153 of a patient with a single REST call. Here is a sample:: | |
| 154 | |
|
112
6d357adfd892
updates for the new 1.3.0 API
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
111
diff
changeset
|
155 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/modify -X POST -d '{"Replace":{"PatientID":"Hello","PatientName":"Sample patient name"},"Force":true}' |
| 0 | 156 |
| 157 .. highlight:: json | |
| 158 | |
| 159 :: | |
| 160 | |
| 161 { | |
| 162 "ID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
| 163 "Path" : "/patients/f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
| 164 "PatientID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
| 165 "Type" : "Patient" | |
| 166 } | |
| 167 | |
| 168 Please note that, in this case, you have to set the value of the | |
| 169 ``PatientID (0010,0020)`` tag for Orthanc to accept this modification: | |
| 170 This is a security to prevent the merging of patient data before and | |
| 171 after anonymization, if the user does not explicitly tell Orthanc to | |
| 172 do so. | |
| 173 | |
| 174 | |
| 175 Anonymization of Patients, Studies or Series | |
| 176 -------------------------------------------- | |
| 177 | |
| 178 .. highlight:: bash | |
| 179 | |
| 180 Study and series can be anonymized the same way as they are modified:: | |
| 181 | |
| 182 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/anonymize -X POST -d '{}' | |
| 183 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/anonymize -X POST -d '{}' | |
| 184 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/anonymize -X POST -d '{}' | |
| 185 | |
| 186 As written above, the anonymization process can be fine-tuned by using | |
| 187 a JSON body. | |
| 167 | 188 |
| 189 | |
|
224
02399e86f046
starting documentation of jobs
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
178
diff
changeset
|
190 .. _split-merge: |
|
02399e86f046
starting documentation of jobs
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
178
diff
changeset
|
191 |
| 167 | 192 Split/merge of DICOM studies |
| 193 ---------------------------- | |
| 194 | |
| 178 | 195 Starting with Orthanc 1.5.0, Orthanc supports splitting and merging |
| 167 | 196 DICOM studies through its REST API. |
| 197 | |
|
224
02399e86f046
starting documentation of jobs
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
178
diff
changeset
|
198 .. _split: |
|
02399e86f046
starting documentation of jobs
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
178
diff
changeset
|
199 |
| 167 | 200 Splitting |
| 201 ^^^^^^^^^ | |
| 202 | |
| 203 Here is the syntax to **split** a DICOM study:: | |
| 204 | |
| 205 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/split -d \ | |
| 206 '{"Series":["6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"],"Replace":{"PatientName":"HELLO"},"Remove":["AccessionNumber"]}' | |
| 207 | |
| 208 By issuing this command, the series whose :ref:`Orthanc identifier | |
| 209 <dicom-identifiers>` is | |
| 210 ``6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228``, and that is part of | |
| 211 the source study with identifier | |
| 212 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``, will be removed from | |
| 213 the source study, and will be moved to a brand new study. | |
| 214 | |
| 215 This is done by generating a new value for all the following DICOM | |
| 216 tags in the DICOM instances of the series of interest: | |
| 217 ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID (0x0020, | |
| 218 0x000e)``, and ``SOPInstanceUID (0x0008, 0x0018)``. Here are the | |
| 219 arguments of this ``/studies/{study}/split`` URI: | |
| 220 | |
| 221 * ``Series`` gives the list of series to be separated from the parent | |
| 222 study (mandatory option). These series must all be children of the | |
| 223 same source study, that is specified in the URI. | |
| 224 * ``Replace`` allows to overwrite the DICOM tags that are part of the | |
| 225 "Patient Module Attributes" and the "General Study Module | |
| 226 Attributes", as specified by the DICOM 2011 standard in Tables C.7-1 | |
| 227 and C.7-3. | |
| 228 * ``Remove`` allows to remove DICOM tags from the same modules as in | |
| 229 the ``Replace`` options. | |
| 230 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
| 231 Orthanc to keep a copy of the original series in the source study. | |
| 232 By default, the original series are deleted from Orthanc. | |
| 233 | |
|
224
02399e86f046
starting documentation of jobs
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
178
diff
changeset
|
234 .. _merge: |
| 167 | 235 |
| 236 Merging | |
| 237 ^^^^^^^ | |
| 238 | |
| 239 Here is the syntax to **merge** DICOM series, into another DICOM study:: | |
| 240 | |
| 241 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/merge -d \ | |
| 242 '{"Resources":["ef2ce55f-9342856a-aee23907-2667e859-9f3b734d"]}' | |
| 243 | |
| 244 By issuing this command, the DICOM series whose :ref:`Orthanc | |
| 245 identifier <dicom-identifiers>` is | |
| 246 ``ef2ce55f-9342856a-aee23907-2667e859-9f3b734d``, will be merged into | |
| 247 target study with identifier | |
| 248 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``. | |
| 249 | |
| 250 As in the case of splitting, this is done by updating the following | |
| 251 DICOM tags: ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID | |
| 252 (0x0020, 0x000e)``, and ``SOPInstanceUID (0x0008, | |
| 253 0x0018)``. Furthermore, all the DICOM tags that are part of the | |
| 254 "Patient Module Attributes" and the "General Study Module Attributes" | |
| 255 (as specified by the DICOM 2011 standard in Tables C.7-1 and C.7-3), | |
| 256 are modified to match the target study. Here are the | |
| 257 arguments of this ``/studies/{study}/merge`` URI: | |
| 258 | |
| 259 * ``Resources`` gives the list of source studies or source series | |
| 260 that are to be merged into the target study. | |
| 261 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
| 262 Orthanc to keep the source studies and series. By default, the | |
| 263 original resources are deleted from Orthanc. |