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annotate Sphinx/source/users/anonymization.rst @ 817:01fa632daae9 Orthanc-1.10.0

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Orthanc 1.10.0
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 23 Feb 2022 15:03:44 +0100
parents 4e9dc26a5cb9
children e95713f90614
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1 .. highlight:: bash
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2 .. _anonymization:
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3
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4 Anonymization and modification
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5 ==============================
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6
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7 .. contents::
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8 :depth: 2
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9
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10 Orthanc 0.5.0 introduces the anonymization of DICOM resources
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11 (i.e. patients, studies, series or instances). This page summarizes
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12 how to use this feature.
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14
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15 Anonymization of a Single Instance
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16 ----------------------------------
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18 Orthanc allows to anonymize a single DICOM instance and to download
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19 the resulting anonymized DICOM file (without storing the anonymized
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20 DICOM instance into Orthanc). Anonymization consists in erasing all
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21 the tags that are specified in `Table E.1-1 from PS 3.15
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22 <http://dicom.nema.org/medical/dicom/current/output/chtml/part15/chapter_E.html#table_E.1-1>`__
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23 of the DICOM standard 2008, 2017c or 2021b (default). Example::
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25 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{}' > Anonymized.dcm
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26
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27 It is possible to control how anonymization is achieved by specifying
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28 a JSON body::
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29
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30 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST \
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31 --data '{
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32 "Replace": {
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33 "PatientName": "Hello",
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34 "0010-1001": "World"
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35 },
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36 "Keep": [
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37 "StudyDescription",
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38 "SeriesDescription"
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39 ],
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40 "KeepPrivateTags": true,
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41 "DicomVersion" : "2017c"
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42 }' > Anonymized.dcm
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43
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44 **Explanations:**
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45
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46 * New UUIDs are automatically generated for the study, the series and
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47 the instance.
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48 * The DICOM tags can be specified either by their name
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49 (``PatientName``) or by their hexadecimal identifier (in the example
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50 above, ``0010-1001`` corresponds to ``Other Patient Names``).
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51 * ``Replace`` is an associative array that associates a DICOM tag with its
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52 new string value. The value is dynamically cast to the proper DICOM
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53 data type (an HTTP error will occur if the cast fails). Replacements
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54 are applied after all the tags to anonymize have been removed.
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55 You may also use the ``Replace`` field to add new tags to the file.
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56 * ``Keep`` specifies a list of tags that should be preserved from full
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57 anonymization.
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58 * If ``KeepPrivateTags`` is set to ``true`` in the JSON request,
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59 private tags (i.e. manufacturer-specific tags) are not removed by
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60 the anonymization process. The default behavior consists in removing
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61 the private tags, as such tags can contain patient-specific
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62 information.
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63 * ``DicomVersion`` specifies which version of the DICOM standard shall
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64 be used for anonymization. Allowed values are ``2008``, ``2017c``,
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65 or ``2021b`` (new in Orthanc 1.9.4). This parameter has been
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66 introduced in Orthanc 1.3.0. In earlier version, the ``2008``
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67 standard was used. If the parameter is absent, the highest version
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68 that is supported by Orthanc is used.
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69 * ``Remove`` can also be used to provide a list of tags to be manually
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70 deleted.
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71
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72 **Important:** Starting with Orthanc 1.9.4, the ``Replace``, ``Keep``
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73 and ``Remove`` fields can also specify sequences, using the same
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74 syntax as the ``dcmodify`` command-line tool (wildcards are supported
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75 as well). Earlier versions were limited to top-level tags in the DICOM
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76 dataset. Check out the integration test ``test_modify_subsequences``
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77 for `examples
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78 <https://hg.orthanc-server.com/orthanc-tests/file/default/Tests/Tests.py>`__.
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79
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80 **Implementation:** Internally, the setup of the anonymization
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81 profiles can be found in the methods ``SetupAnonymizationXXX()`` of
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82 the class ``Orthanc::DicomModification`` (cf. `source code
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83 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.10.0/OrthancFramework/Sources/DicomParsing/DicomModification.cpp>`__).
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86 Modification of a Single Instance
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87 ---------------------------------
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89 Orthanc allows to modify a set of specified tags in a single DICOM
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90 instance and to download the resulting modified DICOM file (without
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91 storing the modified DICOM instance into Orthanc). Example::
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92
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93 $ curl -X POST http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/modify \
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94 --data '{
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95 "Replace": {
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96 "PatientName":"hello",
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97 "PatientID":"world"
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98 },
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99 "Remove":[
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100 "InstitutionName"
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101 ],
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102 "RemovePrivateTags": true,
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103 "Force": true,
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104 "Transcode": "1.2.840.10008.1.2.4.70"
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105 }' > Modified.dcm
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106
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107 **Remarks:**
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108
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109 * The ``Remove`` array specifies the list of the tags to remove.
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110 * The ``Replace`` associative array specifies the substitions to be applied (cf. anonymization).
112
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111 * If ``RemovePrivateTags`` is set to ``true``, the private tags
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112 (i.e. manufacturer-specific tags) are removed.
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113 * The ``Transcode`` option allows you to define the TransferSyntax
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114 of the modified file.
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115 * The ``Force`` option must be set to ``true``, in order to allow the
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116 modification of the ``PatientID``, as such a modification of the
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117 :ref:`DICOM identifiers <dicom-identifiers>` might lead to breaking
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118 the DICOM model of the real-world. In general, any explicit
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119 modification to one of the ``PatientID``, ``StudyInstanceUID``,
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120 ``SeriesInstanceUID``, and ``SOPInstanceUID`` requires ``Force`` to
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121 be set to ``true``, in order to prevent any unwanted side effect.
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122
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123 .. highlight:: json
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124
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125 * To replace a sequence of tags, you may use this syntax::
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126
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127
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128 {
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129 "Replace" : {
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130 "ProcedureCodeSequence" : [
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131 {
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132 "CodeValue" : "2",
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133 "CodingSchemeDesignator" : "1",
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134 "CodeMeaning": "1"
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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
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140 * To replace a binary tag, you should encode it in base64 and use::
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141
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142 {
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143 "Replace" : {
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144 "EncryptedAttributesSequence" : [
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145 {
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146 "EncryptedContentTransferSyntaxUID" : "1.2.840.10008.1.2",
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147 "EncryptedContent" : "data:application/octet-stream;base64,SSB3YXMgaGVyZSBpbiAyMDE5LiAgTWFydHkgTWNGbHku"
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148 }
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149 ]
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150 }
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151 }
300
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152
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153
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154 **Important:** Similarly to anonymization, starting with Orthanc
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155 1.9.4, the ``Replace``, ``Keep`` and ``Remove`` fields can also
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156 specify sequences, using the same syntax as the ``dcmodify``
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157 command-line tool (wildcards are supported as well). Earlier versions
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158 were limited to top-level tags in the DICOM dataset. Check out the
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159 integration test ``test_modify_subsequences`` for `examples
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160 <https://hg.orthanc-server.com/orthanc-tests/file/default/Tests/Tests.py>`__.
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161
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162
331
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163 .. _study-modification:
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164
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165 Modification of Studies or Series
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166 ---------------------------------
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167
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168 .. highlight:: bash
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169
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170 It is possible to modify all the instances from a study or from a
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171 series in a single request. In this case, the modified instances are
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172 stored back into the Orthanc store. Here is how to modify a series::
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173
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174 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}'
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175
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176
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177 .. highlight:: json
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178
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179 The parameters are identical to those used to modify a single
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180 instance. Orthanc will answer a JSON message that tells where the
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181 modified series has been stored::
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182
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183 {
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184 "ID" : "3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce",
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185 "Path" : "/series/3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce"
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186 }
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187
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188
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189 .. highlight:: bash
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190
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191 Similarly, here is an interaction to modify a study::
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192
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193 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}'
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194
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195 .. highlight:: json
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196
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197 ::
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198
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199 {
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200 "ID" : "1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28",
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201 "Path" : "/studies/1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28"
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202 }
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203
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204 Pay attention to the fact that Orthanc implements safety checks to
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205 preserve the :ref:`DICOM model of the real world <model-world>`. These
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206 checks prevent the modification of some tags that are known to belong
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207 to a level in the patient/study/series/instance hierarchy that is
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208 higher than the level that corresponds to the REST API call. For
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209 instance, the tag ``PatientID`` cannot be modified if using the
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210 ``/studies/{id}/modify`` route (in the latter case, the
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211 ``/patients/{id}/modify`` route must be used, cf. next section). You
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212 also have to set the ``Force`` argument to ``true`` if modifying one
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213 of the :ref:`DICOM identifiers tags <orthanc-ids>`
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214 (i.e. ``PatientID``, ``StudyInstanceUID``, ``SeriesInstanceUID`` and
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215 ``SOPInstanceUID``).
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216
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217
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218 Modification of Patients
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219 ------------------------
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220
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221 .. highlight:: bash
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222
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223 Starting with Orthanc 0.7.5, Orthanc can also modify all the instances
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224 of a patient with a single REST call. Here is a sample::
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225
112
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226 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/modify -X POST -d '{"Replace":{"PatientID":"Hello","PatientName":"Sample patient name"},"Force":true}'
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227
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228 .. highlight:: json
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229
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230 ::
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231
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232 {
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233 "ID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0",
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234 "Path" : "/patients/f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0",
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235 "PatientID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0",
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236 "Type" : "Patient"
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237 }
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238
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239 Please note that, in this case, you have to set the value of the
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240 ``PatientID (0010,0020)`` tag for Orthanc to accept this modification:
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241 This is a security to prevent the merging of patient data before and
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242 after anonymization, if the user does not explicitly tell Orthanc to
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243 do so.
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244
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245
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246 Anonymization of Patients, Studies or Series
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247 --------------------------------------------
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248
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249 .. highlight:: bash
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250
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251 Study and series can be anonymized the same way as they are modified::
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252
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253 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/anonymize -X POST -d '{}'
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254 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/anonymize -X POST -d '{}'
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255 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/anonymize -X POST -d '{}'
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256
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257 As written above, the anonymization process can be fine-tuned by using
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258 a JSON body.
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259
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260
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261 .. _bulk-modification:
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262
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263 Bulk modification or anonymization
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264 ----------------------------------
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265
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266 Starting with Orthanc 1.9.4, it is possible to use the new routes
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267 ``/tools/bulk-modify`` and ``/tools/bulk-anonymize`` to respectively
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268 modify or anonymize a set of multiple DICOM resources that are not
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269 related (i.e. that don't share any parent DICOM resource). A typical
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270 use case is to modify/anonymize a list of DICOM instances that don't
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271 belong to the same parent patient/study/series.
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272
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273 .. highlight:: bash
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274
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275 These two routes accept the same arguments as described above, but
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276 must also be provided with an additional argument ``Resources`` that
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277 lists the :ref:`Orthanc identifiers <orthanc-ids>` of the resources of
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278 interest (that may indifferently correspond to patients, studies,
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279 series or instances). Here are two sample calls::
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280
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281 $ 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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282 $ curl http://localhost:8042/tools/bulk-anonymize -d '{"Resources":["b6da0b16-a25ae9e7-1a80fc33-20df01a9-a6f7a1b0","d6634d97-24379e4a-1e68d3af-e6d0451f-e7bcd3d1"]}'
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283
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284 .. highlight:: json
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285
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286 The output of the modification/anonymization lists all the resources
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287 that have been altered by the call (including their parents). Here is
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288 the output of the second sample above::
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289
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290 {
712
6c4fcd1ad337 bulk deletion
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291 "Description" : "REST API",
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292 "FailedInstancesCount" : 0,
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293 "InstancesCount" : 2,
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294 "IsAnonymization" : true,
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295 "Resources" : [
711
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296 {
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297 "ID" : "04c04806-27b01a5a-08ea66cb-cb36c8b9-ebe62fe3",
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298 "Path" : "/instances/04c04806-27b01a5a-08ea66cb-cb36c8b9-ebe62fe3",
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299 "Type" : "Instance"
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300 },
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301 {
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302 "ID" : "4e37fce9-6b33b8ba-7bb378e1-abc7e2c4-fca4ade3",
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303 "Path" : "/instances/4e37fce9-6b33b8ba-7bb378e1-abc7e2c4-fca4ade3",
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304 "Type" : "Instance"
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305 },
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306 {
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307 "ID" : "6438ee62-b58a4788-517931b3-e10321eb-d1ab2613",
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308 "Path" : "/series/6438ee62-b58a4788-517931b3-e10321eb-d1ab2613",
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309 "Type" : "Series"
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310 },
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311 {
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312 "ID" : "660494fd-1ddd661b-4358d996-ba600e5a-066d94cc",
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313 "Path" : "/studies/660494fd-1ddd661b-4358d996-ba600e5a-066d94cc",
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314 "Type" : "Study"
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315 },
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316 {
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317 "ID" : "5faa0bf8-8a45520b-3a07e536-fc24f241-f59ae3e1",
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318 "Path" : "/patients/5faa0bf8-8a45520b-3a07e536-fc24f241-f59ae3e1",
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319 "Type" : "Patient"
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320 }
712
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321 ]
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322 }
711
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323
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324
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325
224
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326 .. _split-merge:
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327
167
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328 Split/merge of DICOM studies
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329 ----------------------------
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330
178
981e5a996b11 Orthanc 1.5.0
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331 Starting with Orthanc 1.5.0, Orthanc supports splitting and merging
167
7ba16d90ed93 split/merge
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332 DICOM studies through its REST API.
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333
224
02399e86f046 starting documentation of jobs
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334 .. _split:
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335
167
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336 Splitting
7ba16d90ed93 split/merge
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337 ^^^^^^^^^
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338
7ba16d90ed93 split/merge
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339 Here is the syntax to **split** a DICOM study::
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340
7ba16d90ed93 split/merge
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341 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/split -d \
7ba16d90ed93 split/merge
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342 '{"Series":["6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"],"Replace":{"PatientName":"HELLO"},"Remove":["AccessionNumber"]}'
7ba16d90ed93 split/merge
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diff changeset
343
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diff changeset
344 By issuing this command, the series whose :ref:`Orthanc identifier
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345 <dicom-identifiers>` is
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346 ``6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228``, and that is part of
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diff changeset
347 the source study with identifier
7ba16d90ed93 split/merge
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348 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``, will be removed from
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diff changeset
349 the source study, and will be moved to a brand new study.
7ba16d90ed93 split/merge
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diff changeset
350
7ba16d90ed93 split/merge
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351 This is done by generating a new value for all the following DICOM
7ba16d90ed93 split/merge
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diff changeset
352 tags in the DICOM instances of the series of interest:
7ba16d90ed93 split/merge
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diff changeset
353 ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID (0x0020,
7ba16d90ed93 split/merge
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diff changeset
354 0x000e)``, and ``SOPInstanceUID (0x0008, 0x0018)``. Here are the
7ba16d90ed93 split/merge
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355 arguments of this ``/studies/{study}/split`` URI:
7ba16d90ed93 split/merge
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diff changeset
356
7ba16d90ed93 split/merge
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357 * ``Series`` gives the list of series to be separated from the parent
7ba16d90ed93 split/merge
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358 study (mandatory option). These series must all be children of the
7ba16d90ed93 split/merge
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diff changeset
359 same source study, that is specified in the URI.
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diff changeset
360 * ``Replace`` allows to overwrite the DICOM tags that are part of the
7ba16d90ed93 split/merge
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diff changeset
361 "Patient Module Attributes" and the "General Study Module
7ba16d90ed93 split/merge
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diff changeset
362 Attributes", as specified by the DICOM 2011 standard in Tables C.7-1
7ba16d90ed93 split/merge
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diff changeset
363 and C.7-3.
7ba16d90ed93 split/merge
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364 * ``Remove`` allows to remove DICOM tags from the same modules as in
7ba16d90ed93 split/merge
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diff changeset
365 the ``Replace`` options.
7ba16d90ed93 split/merge
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diff changeset
366 * ``KeepSource`` (Boolean value), if set to ``true``, instructs
7ba16d90ed93 split/merge
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diff changeset
367 Orthanc to keep a copy of the original series in the source study.
7ba16d90ed93 split/merge
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diff changeset
368 By default, the original series are deleted from Orthanc.
691
b8a744941e58 DicomVersion 2021b for anonymization
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parents: 648
diff changeset
369
224
02399e86f046 starting documentation of jobs
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diff changeset
370 .. _merge:
167
7ba16d90ed93 split/merge
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diff changeset
371
7ba16d90ed93 split/merge
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diff changeset
372 Merging
7ba16d90ed93 split/merge
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
373 ^^^^^^^
7ba16d90ed93 split/merge
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diff changeset
374
7ba16d90ed93 split/merge
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diff changeset
375 Here is the syntax to **merge** DICOM series, into another DICOM study::
7ba16d90ed93 split/merge
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diff changeset
376
7ba16d90ed93 split/merge
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diff changeset
377 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/merge -d \
7ba16d90ed93 split/merge
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diff changeset
378 '{"Resources":["ef2ce55f-9342856a-aee23907-2667e859-9f3b734d"]}'
7ba16d90ed93 split/merge
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parents: 113
diff changeset
379
7ba16d90ed93 split/merge
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diff changeset
380 By issuing this command, the DICOM series whose :ref:`Orthanc
7ba16d90ed93 split/merge
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diff changeset
381 identifier <dicom-identifiers>` is
7ba16d90ed93 split/merge
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diff changeset
382 ``ef2ce55f-9342856a-aee23907-2667e859-9f3b734d``, will be merged into
7ba16d90ed93 split/merge
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diff changeset
383 target study with identifier
7ba16d90ed93 split/merge
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diff changeset
384 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``.
7ba16d90ed93 split/merge
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parents: 113
diff changeset
385
7ba16d90ed93 split/merge
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diff changeset
386 As in the case of splitting, this is done by updating the following
7ba16d90ed93 split/merge
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diff changeset
387 DICOM tags: ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID
7ba16d90ed93 split/merge
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diff changeset
388 (0x0020, 0x000e)``, and ``SOPInstanceUID (0x0008,
7ba16d90ed93 split/merge
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parents: 113
diff changeset
389 0x0018)``. Furthermore, all the DICOM tags that are part of the
7ba16d90ed93 split/merge
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parents: 113
diff changeset
390 "Patient Module Attributes" and the "General Study Module Attributes"
7ba16d90ed93 split/merge
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parents: 113
diff changeset
391 (as specified by the DICOM 2011 standard in Tables C.7-1 and C.7-3),
7ba16d90ed93 split/merge
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diff changeset
392 are modified to match the target study. Here are the
7ba16d90ed93 split/merge
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diff changeset
393 arguments of this ``/studies/{study}/merge`` URI:
7ba16d90ed93 split/merge
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diff changeset
394
7ba16d90ed93 split/merge
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diff changeset
395 * ``Resources`` gives the list of source studies or source series
7ba16d90ed93 split/merge
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diff changeset
396 that are to be merged into the target study.
7ba16d90ed93 split/merge
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diff changeset
397 * ``KeepSource`` (Boolean value), if set to ``true``, instructs
7ba16d90ed93 split/merge
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diff changeset
398 Orthanc to keep the source studies and series. By default, the
7ba16d90ed93 split/merge
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diff changeset
399 original resources are deleted from Orthanc.