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annotate Sphinx/source/users/anonymization.rst @ 712:6c4fcd1ad337
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 16 Jun 2021 18:04:04 +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 |
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43 **Explanations:** |
| 0 | 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 * ``Remove`` can also be used to provide a list of tags to be manually |
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69 deleted. |
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70 |
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71 **Important:** Starting with Orthanc 1.9.4, the ``Replace``, ``Keep`` |
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72 and ``Remove`` fields can also specify sequences, using the same |
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73 syntax as the ``dcmodify`` command-line tool (wildcards are supported |
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74 as well). Earlier versions were limited to top-level tags in the DICOM |
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75 dataset. Check out the integration test ``test_modify_subsequences`` |
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76 for `examples |
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77 <https://hg.orthanc-server.com/orthanc-tests/file/default/Tests/Tests.py>`__. |
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78 |
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79 **Implementation:** Internally, the setup of the anonymization |
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80 profiles can be found in the methods ``SetupAnonymizationXXX()`` of |
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81 the class ``Orthanc::DicomModification`` (cf. `source code |
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82 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.9.3/OrthancFramework/Sources/DicomParsing/DicomModification.cpp>`__). |
| 0 | 83 |
| 84 | |
| 85 Modification of a Single Instance | |
| 86 --------------------------------- | |
| 87 | |
| 88 Orthanc allows to modify a set of specified tags in a single DICOM | |
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89 instance and to download the resulting modified DICOM |
| 0 | 90 file. Example:: |
| 91 | |
| 444 | 92 $ curl -X POST http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/modify \ |
| 93 --data '{ | |
| 94 "Replace": { | |
| 95 "PatientName":"hello", | |
| 96 "PatientID":"world" | |
| 97 }, | |
| 98 "Remove":[ | |
| 99 "InstitutionName" | |
| 100 ], | |
| 101 "RemovePrivateTags": true, | |
| 102 "Force": true, | |
| 103 "Transcode": "1.2.840.10008.1.2.4.70" | |
| 104 }' > Modified.dcm | |
| 0 | 105 |
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106 **Remarks:** |
| 0 | 107 |
| 108 * The ``Remove`` array specifies the list of the tags to remove. | |
| 109 * The ``Replace`` associative array specifies the substitions to be applied (cf. anonymization). | |
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110 * If ``RemovePrivateTags`` is set to ``true``, the private tags |
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111 (i.e. manufacturer-specific tags) are removed. |
| 444 | 112 * The ``Transcode`` option allows you to define the TransferSyntax |
| 113 of the modified file. | |
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114 * The ``Force`` option must be set to ``true``, in order to allow the |
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115 modification of the ``PatientID``, as such a modification of the |
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116 :ref:`DICOM identifiers <dicom-identifiers>` might lead to breaking |
| 113 | 117 the DICOM model of the real-world. In general, any explicit |
| 118 modification to one of the ``PatientID``, ``StudyInstanceUID``, | |
| 119 ``SeriesInstanceUID``, and ``SOPInstanceUID`` requires ``Force`` to | |
| 120 be set to ``true``, in order to prevent any unwanted side effect. | |
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121 |
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122 .. highlight:: json |
| 0 | 123 |
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124 * To replace a sequence of tags, you may use this syntax:: |
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125 |
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126 |
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127 { |
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128 "Replace" : { |
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129 "ProcedureCodeSequence" : [ |
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130 { |
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131 "CodeValue" : "2", |
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132 "CodingSchemeDesignator" : "1", |
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133 "CodeMeaning": "1" |
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134 } |
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135 ] |
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136 } |
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137 } |
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138 |
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139 * To replace a binary tag, you should encode it in base64 and use:: |
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140 |
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141 { |
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142 "Replace" : { |
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143 "EncryptedAttributesSequence" : [ |
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144 { |
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145 "EncryptedContentTransferSyntaxUID" : "1.2.840.10008.1.2", |
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146 "EncryptedContent" : "data:application/octet-stream;base64,SSB3YXMgaGVyZSBpbiAyMDE5LiAgTWFydHkgTWNGbHku" |
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147 } |
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148 ] |
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149 } |
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150 } |
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151 |
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152 |
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153 **Important:** Similarly to anonymization, starting with Orthanc |
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154 1.9.4, the ``Replace``, ``Keep`` and ``Remove`` fields can also |
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155 specify sequences, using the same syntax as the ``dcmodify`` |
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156 command-line tool (wildcards are supported as well). Earlier versions |
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157 were limited to top-level tags in the DICOM dataset. Check out the |
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158 integration test ``test_modify_subsequences`` for `examples |
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159 <https://hg.orthanc-server.com/orthanc-tests/file/default/Tests/Tests.py>`__. |
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160 |
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161 |
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162 .. _study-modification: |
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163 |
| 0 | 164 Modification of Studies or Series |
| 165 --------------------------------- | |
| 166 | |
| 167 .. highlight:: bash | |
| 168 | |
| 169 It is possible to modify all the instances from a study or from a | |
| 170 series in a single request. In this case, the modified instances are | |
| 171 stored back into the Orthanc store. Here is how to modify a series:: | |
| 172 | |
| 173 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
| 174 | |
| 175 | |
| 176 .. highlight:: json | |
| 177 | |
| 178 The parameters are identical to those used to modify a single | |
| 179 instance. Orthanc will answer a JSON message that tells where the | |
| 180 modified series has been stored:: | |
| 181 | |
| 182 { | |
| 183 "ID" : "3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce", | |
| 184 "Path" : "/series/3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce" | |
| 185 } | |
| 186 | |
| 187 | |
| 188 .. highlight:: bash | |
| 189 | |
| 190 Similarly, here is an interaction to modify a study:: | |
| 191 | |
| 192 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
| 193 | |
| 194 .. highlight:: json | |
| 195 | |
| 196 :: | |
| 197 | |
| 198 { | |
| 199 "ID" : "1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28", | |
| 200 "Path" : "/studies/1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28" | |
| 201 } | |
| 202 | |
| 203 | |
| 204 Modification of Patients | |
| 205 ------------------------ | |
| 206 | |
| 207 .. highlight:: bash | |
| 208 | |
| 209 Starting with Orthanc 0.7.5, Orthanc can also modify all the instances | |
| 210 of a patient with a single REST call. Here is a sample:: | |
| 211 | |
|
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212 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/modify -X POST -d '{"Replace":{"PatientID":"Hello","PatientName":"Sample patient name"},"Force":true}' |
| 0 | 213 |
| 214 .. highlight:: json | |
| 215 | |
| 216 :: | |
| 217 | |
| 218 { | |
| 219 "ID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
| 220 "Path" : "/patients/f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
| 221 "PatientID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
| 222 "Type" : "Patient" | |
| 223 } | |
| 224 | |
| 225 Please note that, in this case, you have to set the value of the | |
| 226 ``PatientID (0010,0020)`` tag for Orthanc to accept this modification: | |
| 227 This is a security to prevent the merging of patient data before and | |
| 228 after anonymization, if the user does not explicitly tell Orthanc to | |
| 229 do so. | |
| 230 | |
| 231 | |
| 232 Anonymization of Patients, Studies or Series | |
| 233 -------------------------------------------- | |
| 234 | |
| 235 .. highlight:: bash | |
| 236 | |
| 237 Study and series can be anonymized the same way as they are modified:: | |
| 238 | |
| 239 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/anonymize -X POST -d '{}' | |
| 240 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/anonymize -X POST -d '{}' | |
| 241 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/anonymize -X POST -d '{}' | |
| 242 | |
| 243 As written above, the anonymization process can be fine-tuned by using | |
| 244 a JSON body. | |
| 167 | 245 |
| 246 | |
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247 .. _bulk-modification: |
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248 |
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249 Bulk modification or anonymization |
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250 ---------------------------------- |
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251 |
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252 Starting with Orthanc 1.9.4, it is possible to use the new routes |
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253 ``/tools/bulk-modify`` and ``/tools/bulk-anonymize`` to respectively |
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254 modify or anonymize a set of multiple DICOM resources that are not |
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255 related (i.e. that don't share any parent DICOM resource). A typical |
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256 use case is to modify/anonymize a list of DICOM instances that don't |
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257 belong to the same parent patient/study/series. |
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258 |
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259 .. highlight:: bash |
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260 |
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261 These two routes accept the same arguments as described above, but |
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262 must also be provided with an additional argument ``Resources`` that |
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263 lists the :ref:`Orthanc identifiers <orthanc-ids>` of the resources of |
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264 interest (that may indifferently correspond to patients, studies, |
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265 series or instances). Here are two sample calls:: |
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266 |
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267 $ curl http://localhost:8042/tools/bulk-modify -d '{"Replace":{"SeriesDescription":"HELLO"},"Resources":["b6da0b16-a25ae9e7-1a80fc33-20df01a9-a6f7a1b0","d6634d97-24379e4a-1e68d3af-e6d0451f-e7bcd3d1"]}' |
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268 $ curl http://localhost:8042/tools/bulk-anonymize -d '{"Resources":["b6da0b16-a25ae9e7-1a80fc33-20df01a9-a6f7a1b0","d6634d97-24379e4a-1e68d3af-e6d0451f-e7bcd3d1"]}' |
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269 |
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270 .. highlight:: json |
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271 |
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272 The output of the modification/anonymization lists all the resources |
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273 that have been altered by the call (including their parents). Here is |
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274 the output of the second sample above:: |
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275 |
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276 { |
| 712 | 277 "Description" : "REST API", |
| 278 "FailedInstancesCount" : 0, | |
| 279 "InstancesCount" : 2, | |
| 280 "IsAnonymization" : true, | |
| 281 "Resources" : [ | |
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282 { |
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283 "ID" : "04c04806-27b01a5a-08ea66cb-cb36c8b9-ebe62fe3", |
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284 "Path" : "/instances/04c04806-27b01a5a-08ea66cb-cb36c8b9-ebe62fe3", |
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285 "Type" : "Instance" |
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286 }, |
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287 { |
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288 "ID" : "4e37fce9-6b33b8ba-7bb378e1-abc7e2c4-fca4ade3", |
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289 "Path" : "/instances/4e37fce9-6b33b8ba-7bb378e1-abc7e2c4-fca4ade3", |
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290 "Type" : "Instance" |
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291 }, |
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292 { |
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293 "ID" : "6438ee62-b58a4788-517931b3-e10321eb-d1ab2613", |
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294 "Path" : "/series/6438ee62-b58a4788-517931b3-e10321eb-d1ab2613", |
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295 "Type" : "Series" |
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296 }, |
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297 { |
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298 "ID" : "660494fd-1ddd661b-4358d996-ba600e5a-066d94cc", |
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299 "Path" : "/studies/660494fd-1ddd661b-4358d996-ba600e5a-066d94cc", |
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300 "Type" : "Study" |
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301 }, |
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302 { |
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303 "ID" : "5faa0bf8-8a45520b-3a07e536-fc24f241-f59ae3e1", |
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304 "Path" : "/patients/5faa0bf8-8a45520b-3a07e536-fc24f241-f59ae3e1", |
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305 "Type" : "Patient" |
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306 } |
| 712 | 307 ] |
| 308 } | |
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309 |
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310 |
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311 |
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312 .. _split-merge: |
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313 |
| 167 | 314 Split/merge of DICOM studies |
| 315 ---------------------------- | |
| 316 | |
| 178 | 317 Starting with Orthanc 1.5.0, Orthanc supports splitting and merging |
| 167 | 318 DICOM studies through its REST API. |
| 319 | |
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320 .. _split: |
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321 |
| 167 | 322 Splitting |
| 323 ^^^^^^^^^ | |
| 324 | |
| 325 Here is the syntax to **split** a DICOM study:: | |
| 326 | |
| 327 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/split -d \ | |
| 328 '{"Series":["6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"],"Replace":{"PatientName":"HELLO"},"Remove":["AccessionNumber"]}' | |
| 329 | |
| 330 By issuing this command, the series whose :ref:`Orthanc identifier | |
| 331 <dicom-identifiers>` is | |
| 332 ``6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228``, and that is part of | |
| 333 the source study with identifier | |
| 334 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``, will be removed from | |
| 335 the source study, and will be moved to a brand new study. | |
| 336 | |
| 337 This is done by generating a new value for all the following DICOM | |
| 338 tags in the DICOM instances of the series of interest: | |
| 339 ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID (0x0020, | |
| 340 0x000e)``, and ``SOPInstanceUID (0x0008, 0x0018)``. Here are the | |
| 341 arguments of this ``/studies/{study}/split`` URI: | |
| 342 | |
| 343 * ``Series`` gives the list of series to be separated from the parent | |
| 344 study (mandatory option). These series must all be children of the | |
| 345 same source study, that is specified in the URI. | |
| 346 * ``Replace`` allows to overwrite the DICOM tags that are part of the | |
| 347 "Patient Module Attributes" and the "General Study Module | |
| 348 Attributes", as specified by the DICOM 2011 standard in Tables C.7-1 | |
| 349 and C.7-3. | |
| 350 * ``Remove`` allows to remove DICOM tags from the same modules as in | |
| 351 the ``Replace`` options. | |
| 352 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
| 353 Orthanc to keep a copy of the original series in the source study. | |
| 354 By default, the original series are deleted from Orthanc. | |
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355 |
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356 .. _merge: |
| 167 | 357 |
| 358 Merging | |
| 359 ^^^^^^^ | |
| 360 | |
| 361 Here is the syntax to **merge** DICOM series, into another DICOM study:: | |
| 362 | |
| 363 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/merge -d \ | |
| 364 '{"Resources":["ef2ce55f-9342856a-aee23907-2667e859-9f3b734d"]}' | |
| 365 | |
| 366 By issuing this command, the DICOM series whose :ref:`Orthanc | |
| 367 identifier <dicom-identifiers>` is | |
| 368 ``ef2ce55f-9342856a-aee23907-2667e859-9f3b734d``, will be merged into | |
| 369 target study with identifier | |
| 370 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``. | |
| 371 | |
| 372 As in the case of splitting, this is done by updating the following | |
| 373 DICOM tags: ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID | |
| 374 (0x0020, 0x000e)``, and ``SOPInstanceUID (0x0008, | |
| 375 0x0018)``. Furthermore, all the DICOM tags that are part of the | |
| 376 "Patient Module Attributes" and the "General Study Module Attributes" | |
| 377 (as specified by the DICOM 2011 standard in Tables C.7-1 and C.7-3), | |
| 378 are modified to match the target study. Here are the | |
| 379 arguments of this ``/studies/{study}/merge`` URI: | |
| 380 | |
| 381 * ``Resources`` gives the list of source studies or source series | |
| 382 that are to be merged into the target study. | |
| 383 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
| 384 Orthanc to keep the source studies and series. By default, the | |
| 385 original resources are deleted from Orthanc. |