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annotate Sphinx/source/users/rest.rst @ 933:a5e7e7001316 Orthanc-1.12.0
Orthanc 1.12.0
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Sat, 15 Apr 2023 10:44:42 +0200 |
| parents | 6474e299918b |
| children | 5491953f7492 |
| rev | line source |
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| 0 | 1 .. _rest: |
| 2 | |
| 3 REST API of Orthanc | |
| 4 =================== | |
| 5 | |
| 6 .. contents:: | |
| 7 :depth: 3 | |
| 8 | |
| 9 One of the major strengths of Orthanc lies in its built-in `RESTful | |
| 10 API | |
| 11 <https://en.wikipedia.org/wiki/Representational_state_transfer>`__, | |
| 12 that can be used to drive Orthanc from external applications, | |
| 13 independently of the programming language that is used to develop | |
| 14 these applications. The REST API of Orthanc gives a full programmatic | |
| 15 access to all the core features of Orthanc. | |
| 16 | |
| 17 Importantly, Orthanc Explorer (the embedded administrative interface | |
| 18 of Orthanc) entirely resorts to this REST API for all its features. | |
| 19 This implies that anything that can be done through Orthanc Explorer, | |
| 20 can also be done through REST queries. | |
| 21 | |
| 22 *Note:* All the examples are illustrated with the `cURL command-line | |
| 25 | 23 tool <https://curl.haxx.se/>`__, but equivalent calls can be readily |
| 0 | 24 transposed to any programming language that supports both HTTP and |
| 25 JSON. | |
| 26 | |
| 27 | |
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28 .. _curl-windows: |
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29 |
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30 Warning about using cURL from the Windows prompt |
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31 ------------------------------------------------ |
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32 |
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33 The examples on this page assume that the user is running a bash shell |
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34 on some GNU/Linux distribution. Such a shell has the major advantage |
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35 of having the possibility to use either single-quote or double-quotes |
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36 characters in order to group a set of characters (including spaces) as |
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37 a whole string. |
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38 |
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39 .. highlight:: bash |
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40 |
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41 Unfortunately, the default command-line prompt of Microsoft Windows |
| 675 | 42 **doesn't support single-quote characters**. If you copy/paste a cURL |
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43 command-line from this page that mixes single-quote and double-quotes, |
| 676 | 44 it won't work as such, and you'll have to replace single-quotes by |
| 45 double-quotes, and prefix the double-quotes by a backslash | |
| 46 character. For instance, consider the following command line that | |
| 47 works fine on GNU/Linux:: | |
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48 |
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49 $ curl -v -X PUT http://localhost:8042/modalities/sample \ |
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50 -d '{"AET" : "ORTHANCC", "Host": "127.0.0.1", "Port": 2002}' |
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51 |
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52 This call will **not** work on the Microsoft Windows prompt as it |
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53 contains single-quotes. You should adapt this command line as follows |
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54 to run it on Windows:: |
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55 |
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56 $ curl -v -X PUT http://localhost:8042/modalities/sample \ |
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57 -d "{\"AET\" : \"ORTHANCC\", \"Host\": \"127.0.0.1\", \"Port\": 2002}" |
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58 |
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59 As an alternative, consider using a different Windows shell, for |
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60 instance `Windows PowerShell |
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61 <https://fr.wikipedia.org/wiki/Windows_PowerShell>`__ (some examples |
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62 of PowerShell can be found below on this page). |
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63 |
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64 |
| 114 | 65 .. _sending-dicom-images: |
| 66 | |
| 0 | 67 Sending DICOM images |
| 68 -------------------- | |
| 69 | |
| 70 .. highlight:: bash | |
| 71 | |
| 72 The upload of DICOM files is possible by querying the REST API using | |
| 73 the following syntax:: | |
| 74 | |
| 75 $ curl -X POST http://localhost:8042/instances --data-binary @CT.X.1.2.276.0.7230010.dcm | |
| 868 | 76 $ curl -X POST http://localhost:8042/instances --data-binary @multiple-files.zip |
| 0 | 77 |
| 78 .. highlight:: json | |
| 79 | |
| 80 Orthanc will respond with a JSON file that contain information about | |
| 81 the location of the stored instance, such as:: | |
| 82 | |
| 83 { | |
| 868 | 84 "ID" : "5d4a3991-8a265cb2-da669bea-d8c761af-4a77113a", |
| 85 "ParentPatient" : "69a957ab-57545037-ce9a492a-d0bd89c1-d7e2220d", | |
| 86 "ParentSeries" : "87c81b2c-e9f92adf-2dc11d37-399b5214-37275cdb", | |
| 87 "ParentStudy" : "1b1cc0c9-c0377071-78e8cd3a-2e382948-a243db42", | |
| 88 "Path" : "/instances/5d4a3991-8a265cb2-da669bea-d8c761af-4a77113a", | |
| 0 | 89 "Status" : "Success" |
| 90 } | |
| 91 | |
| 92 .. highlight:: bash | |
| 93 | |
| 94 Note that in the case of curl, setting the ``Expect`` HTTP Header will | |
| 95 significantly `reduce the execution time of POST requests | |
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96 <https://stackoverflow.com/questions/463144/php-http-post-fails-when-curl-data-1024/463277#463277>`__:: |
| 0 | 97 |
| 98 $ curl -X POST -H "Expect:" http://localhost:8042/instances --data-binary @CT.X.1.2.276.0.7230010.dcm | |
| 99 | |
| 100 The code distribution of Orthanc contains a `sample Python script | |
| 933 | 101 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.12.0/OrthancServer/Resources/Samples/ImportDicomFiles/ImportDicomFiles.py>`__ |
| 0 | 102 that recursively upload the content of some folder into Orthanc using |
| 103 the REST API:: | |
| 104 | |
| 105 $ python ImportDicomFiles.py localhost 8042 ~/DICOM/ | |
| 106 | |
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107 Starting with Orthanc 1.8.1, the source distribution of Orthanc |
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108 includes another Python script named ``OrthancImport.py`` that |
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109 provides more features than ``ImportDicomFiles.py``. It can notably |
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110 import the content of ``.zip``, ``.tar.gz`` or ``.tar.bz2`` archives |
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111 without having to uncompress them first. It also provides more |
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112 comprehensive command-line options. `Check this script out |
| 933 | 113 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.12.0/OrthancServer/Resources/Samples/ImportDicomFiles/OrthancImport.py>`__. |
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114 |
| 0 | 115 |
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116 .. highlight:: perl |
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117 |
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118 If you are using Powershell (>= 3.0), you can use the following to send a single |
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119 Dicom instance to Orthanc:: |
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120 |
| 376 | 121 # disabling the progress bar makes the Invoke-RestMethod call MUCH faster |
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122 $ProgressPreference = 'SilentlyContinue' |
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123 |
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124 # upload it to Orthanc |
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125 $reply = Invoke-RestMethod http://localhost:8042/instances -Method POST -InFile CT.X.1.2.276.0.7230010.dcm |
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126 |
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127 # display the result |
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128 Write-Host "The instance can be retrieved at http://localhost:8042$($reply.Path)" |
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129 |
| 0 | 130 .. _rest-access: |
| 131 | |
| 132 Accessing the content of Orthanc | |
| 133 -------------------------------- | |
| 134 | |
| 135 Orthanc structures the stored DICOM resources using the "Patient, | |
| 136 Study, Series, Instance" model of the DICOM standard. Each DICOM | |
| 137 resource is associated with an :ref:`unique identifier <orthanc-ids>`. | |
| 138 | |
| 139 List all the DICOM resources | |
| 140 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 141 | |
| 142 Here is how you would list all the DICOM resources that are stored in | |
| 143 your local Orthanc instance:: | |
| 144 | |
| 145 $ curl http://localhost:8042/patients | |
| 146 $ curl http://localhost:8042/studies | |
| 147 $ curl http://localhost:8042/series | |
| 148 $ curl http://localhost:8042/instances | |
| 149 | |
| 150 Note that the result of this command is a `JSON file | |
| 25 | 151 <https://en.wikipedia.org/wiki/Json>`__ that contains an array of |
| 0 | 152 resource identifiers. The JSON file format is lightweight and can be |
| 153 parsed from almost any computer language. | |
| 154 | |
| 155 Accessing a patient | |
| 156 ^^^^^^^^^^^^^^^^^^^ | |
| 157 | |
| 158 .. highlight:: bash | |
| 159 | |
| 160 To access a single resource, add its identifier to the `URI | |
| 25 | 161 <https://en.wikipedia.org/wiki/Uniform_resource_identifier>`__. You |
| 0 | 162 would for instance retrieve the main information about one patient as |
| 163 follows:: | |
| 164 | |
| 165 $ curl http://localhost:8042/patients/dc65762c-f476e8b9-898834f4-2f8a5014-2599bc94 | |
| 166 | |
| 167 .. highlight:: json | |
| 168 | |
| 169 Here is a possible answer from Orthanc:: | |
| 170 | |
| 171 { | |
| 172 "ID" : "07a6ec1c-1be5920b-18ef5358-d24441f3-10e926ea", | |
| 173 "MainDicomTags" : { | |
| 174 "OtherPatientIDs" : "(null)", | |
| 175 "PatientBirthDate" : "0", | |
| 176 "PatientID" : "000000185", | |
| 177 "PatientName" : "Anonymous^Unknown", | |
| 178 "PatientSex" : "O" | |
| 179 }, | |
| 180 "Studies" : [ "9ad2b0da-a406c43c-6e0df76d-1204b86f-78d12c15" ], | |
| 181 "Type" : "Patient" | |
| 182 } | |
| 183 | |
| 184 This is once again a JSON file. Note how Orthanc gives you a summary | |
| 185 of the main DICOM tags that correspond to the patient level. | |
| 186 | |
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187 |
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188 .. _browsing-hierarchy: |
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189 |
| 0 | 190 Browsing from the patient down to the instance |
| 191 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 192 | |
| 193 .. highlight:: bash | |
| 194 | |
| 195 The field ``Studies`` list all the DICOM studies that are associated | |
| 196 with the patient. So, considering the patient above, we would go down | |
| 197 in her DICOM hierarchy as follows:: | |
| 198 | |
| 199 $ curl http://localhost:8042/studies/9ad2b0da-a406c43c-6e0df76d-1204b86f-78d12c15 | |
| 200 | |
| 201 .. highlight:: json | |
| 202 | |
| 203 And Orthanc could answer:: | |
| 204 | |
| 205 { | |
| 206 "ID" : "9ad2b0da-a406c43c-6e0df76d-1204b86f-78d12c15", | |
| 207 "MainDicomTags" : { | |
| 208 "AccessionNumber" : "(null)", | |
| 209 "StudyDate" : "20120716", | |
| 210 "StudyDescription" : "TestSUVce-TF", | |
| 211 "StudyID" : "23848", | |
| 212 "StudyInstanceUID" : "1.2.840.113704.1.111.7016.1342451220.40", | |
| 213 "StudyTime" : "170728" | |
| 214 }, | |
| 215 "ParentPatient" : "07a6ec1c-1be5920b-18ef5358-d24441f3-10e926ea", | |
| 216 "Series" : [ | |
| 217 "6821d761-31fb55a9-031ebecb-ba7f9aae-ffe4ddc0", | |
| 218 "2cc6336f-2d4ae733-537b3ca3-e98184b1-ba494b35", | |
| 219 "7384c47e-6398f2a8-901846ef-da1e2e0b-6c50d598" | |
| 220 ], | |
| 221 "Type" : "Study" | |
| 222 } | |
| 223 | |
| 224 .. highlight:: bash | |
| 225 | |
| 226 The main DICOM tags are now those that are related to the study | |
| 227 level. It is possible to retrieve the identifier of the patient in the | |
| 228 ``ParentPatient`` field, which can be used to go upward the DICOM | |
| 229 hierarchy. But let us rather go down to the series level by using the | |
| 230 ``Series`` array. The next command would return information about one | |
| 231 of the three series that have just been reported:: | |
| 232 | |
| 233 $ curl http://localhost:8042/series/2cc6336f-2d4ae733-537b3ca3-e98184b1-ba494b35 | |
| 234 | |
| 235 .. highlight:: json | |
| 236 | |
| 237 Here is a possible answer:: | |
| 238 | |
| 239 { | |
| 240 "ExpectedNumberOfInstances" : 45, | |
| 241 "ID" : "2cc6336f-2d4ae733-537b3ca3-e98184b1-ba494b35", | |
| 242 "Instances" : [ | |
| 243 "41bc3f74-360f9d10-6ae9ffa4-01ea2045-cbd457dd", | |
| 244 "1d3de868-6c4f0494-709fd140-7ccc4c94-a6daa3a8", | |
| 245 <...> | |
| 246 "1010f80b-161b71c0-897ec01b-c85cd206-e669a3ea", | |
| 247 "e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4" | |
| 248 ], | |
| 249 "MainDicomTags" : { | |
| 250 "Manufacturer" : "Philips Medical Systems", | |
| 251 "Modality" : "PT", | |
| 252 "NumberOfSlices" : "45", | |
| 253 "ProtocolName" : "CHU/Body_PET/CT___50", | |
| 254 "SeriesDate" : "20120716", | |
| 255 "SeriesDescription" : "[WB_CTAC] Body", | |
| 256 "SeriesInstanceUID" : "1.3.46.670589.28.2.12.30.26407.37145.2.2516.0.1342458737", | |
| 257 "SeriesNumber" : "587370", | |
| 258 "SeriesTime" : "171121", | |
| 259 "StationName" : "r054-svr" | |
| 260 }, | |
| 261 "ParentStudy" : "9ad2b0da-a406c43c-6e0df76d-1204b86f-78d12c15", | |
| 262 "Status" : "Complete", | |
| 263 "Type" : "Series" | |
| 264 } | |
| 265 | |
| 266 It can be seen that this series comes from a PET modality. Orthanc has | |
| 267 computed that this series should contain 45 instances. | |
| 268 | |
| 269 .. highlight:: bash | |
| 270 | |
| 271 So far, we have navigated from the patient level, to the study level, | |
| 272 and finally to the series level. There only remains the instance | |
| 273 level. Let us dump the content of one of the instances:: | |
| 274 | |
| 275 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4 | |
| 276 | |
| 277 .. highlight:: json | |
| 278 | |
| 279 The instance contains the following information:: | |
| 280 | |
| 281 { | |
| 282 "FileSize" : 70356, | |
| 283 "FileUuid" : "3fd265f0-c2b6-41a2-ace8-ae332db63e06", | |
| 284 "ID" : "e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4", | |
| 285 "IndexInSeries" : 6, | |
| 286 "MainDicomTags" : { | |
| 287 "ImageIndex" : "6", | |
| 288 "InstanceCreationDate" : "20120716", | |
| 289 "InstanceCreationTime" : "171344", | |
| 290 "InstanceNumber" : "6", | |
| 291 "SOPInstanceUID" : "1.3.46.670589.28.2.15.30.26407.37145.3.2116.39.1342458737" | |
| 292 }, | |
| 293 "ParentSeries" : "2cc6336f-2d4ae733-537b3ca3-e98184b1-ba494b35", | |
| 294 "Type" : "Instance" | |
| 295 } | |
| 296 | |
| 297 .. highlight:: bash | |
| 298 | |
| 299 The instance has the index 6 in the parent series. The instance is | |
| 300 stored as a raw DICOM file of 70356 bytes. You would download this | |
| 301 DICOM file using the following command:: | |
| 302 | |
| 303 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/file > Instance.dcm | |
| 304 | |
| 305 | |
| 306 Accessing the DICOM fields of an instance as a JSON file | |
| 307 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 308 | |
| 309 .. highlight:: bash | |
| 310 | |
| 311 When one gets to the instance level, you can retrieve the hierarchy of | |
| 312 all the DICOM tags of this instance as a JSON file:: | |
| 313 | |
| 314 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/simplified-tags | |
| 315 | |
| 316 .. highlight:: json | |
| 317 | |
| 318 Here is a excerpt of the Orthanc answer:: | |
| 319 | |
| 320 { | |
| 321 "ACR_NEMA_2C_VariablePixelDataGroupLength" : "57130", | |
| 322 "AccessionNumber" : null, | |
| 323 "AcquisitionDate" : "20120716", | |
| 324 "AcquisitionDateTime" : "20120716171219", | |
| 325 "AcquisitionTime" : "171219", | |
| 326 "ActualFrameDuration" : "3597793", | |
| 327 "AttenuationCorrectionMethod" : "CTAC-SG", | |
| 328 <...> | |
| 329 "PatientID" : "000000185", | |
| 330 "PatientName" : "Anonymous^Unknown", | |
| 331 "PatientOrientationCodeSequence" : [ | |
| 332 { | |
| 333 "CodeMeaning" : "recumbent", | |
| 334 "CodeValue" : "F-10450", | |
| 335 "CodingSchemeDesignator" : "99SDM", | |
| 336 "PatientOrientationModifierCodeSequence" : [ | |
| 337 { | |
| 338 "CodeMeaning" : "supine", | |
| 339 "CodeValue" : "F-10340", | |
| 340 "CodingSchemeDesignator" : "99SDM" | |
| 341 } | |
| 342 ] | |
| 343 } | |
| 344 ], | |
| 345 <...> | |
| 346 "StudyDescription" : "TestSUVce-TF", | |
| 347 "StudyID" : "23848", | |
| 348 "StudyInstanceUID" : "1.2.840.113704.1.111.7016.1342451220.40", | |
| 349 "StudyTime" : "171117", | |
| 350 "TypeOfDetectorMotion" : "NONE", | |
| 351 "Units" : "BQML", | |
| 352 "Unknown" : null, | |
| 353 "WindowCenter" : "1.496995e+04", | |
| 354 "WindowWidth" : "2.993990e+04" | |
| 355 } | |
| 356 | |
| 357 .. highlight:: bash | |
| 358 | |
| 359 If you need more detailed information about the type of the variables | |
| 360 or if you wish to use the hexadecimal indexes of DICOM tags, you are | |
| 361 free to use the following URL:: | |
| 362 | |
| 363 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/tags | |
| 364 | |
| 365 Accessing the raw DICOM fields of an instance | |
| 366 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 367 | |
| 368 .. highlight:: bash | |
| 369 | |
| 370 You also have the opportunity to access the raw value of the DICOM | |
| 371 tags of an instance, without going through a JSON file. Here is how | |
| 372 you would find the Patient Name of the instance:: | |
| 373 | |
| 374 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/content/0010-0010 | |
|
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375 Anonymous^Unknown |
| 0 | 376 |
| 377 The list of all the available tags for this instance can also be retrieved easily:: | |
| 378 | |
| 379 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/content | |
| 380 | |
| 381 It is also possible to recursively explore the sequences of tags:: | |
| 382 | |
| 383 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/content/0008-1250/0/0040-a170/0/0008-0104 | |
| 384 For Attenuation Correction | |
| 385 | |
| 386 The command above has opened the "0008-1250" tag that is a DICOM | |
| 387 sequence, taken its first child, opened its "0040-a170" tag that is | |
| 388 also a sequence, taken the first child of this child, and returned the | |
| 389 "0008-0104" DICOM tag. | |
| 390 | |
| 391 Downloading images | |
| 392 ^^^^^^^^^^^^^^^^^^ | |
| 393 | |
| 394 .. highlight:: bash | |
| 395 | |
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396 As :ref:`explained above <browsing-hierarchy>`, the raw DICOM file |
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397 corresponding to a single instance can be retrieved as follows:: |
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398 |
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399 $ curl http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/file > Instance.dcm |
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400 |
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401 It is also possible to download a preview PNG image that corresponds |
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402 to some DICOM instance:: |
| 0 | 403 |
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404 $ curl http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/preview > Preview.png |
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405 |
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406 The resulting image will be a standard graylevel PNG image (with 8 |
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407 bits per pixel) that can be opened by any painting software. The |
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408 dynamic range of the pixel data is stretched to the [0..255] range. |
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409 An equivalent JPEG image can be downloaded by setting the `HTTP header |
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410 <https://en.wikipedia.org/wiki/List_of_HTTP_header_fields>`__ |
| 910 | 411 ``Accept`` to ``image/jpeg``. By default, the jpeg quality is set to |
| 412 90% but this can be specified in the url:: | |
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413 |
| 169 | 414 $ curl -H 'Accept: image/jpeg' http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/preview > Preview.jpg |
| 910 | 415 $ curl -H 'Accept: image/jpeg' http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/preview?quality=80 > Preview80.jpg |
| 0 | 416 |
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417 If you don't want to stretch the dynamic range, and create a 8bpp or |
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418 16bpp PNG image, you can use the following URIs:: |
| 0 | 419 |
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420 $ curl http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/image-uint8 > full-8.png |
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421 $ curl http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/image-uint16 > full-16.png |
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422 |
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423 In these images, the values are cropped to the maximal value that can |
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424 be encoded by the target image format. The |
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425 ``/instances/{...}/image-int16`` is available as well to download |
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426 signed DICOM pixel data. |
| 0 | 427 |
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428 Since Orthanc 1.4.2, it is also possible to download such images in |
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429 the generic `PAM format |
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430 <https://en.wikipedia.org/wiki/Netpbm#PAM_graphics_format>`__:: |
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431 |
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432 $ curl -H 'Accept: image/x-portable-arbitrarymap' http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/image-uint16 > full-16.pam |
| 0 | 433 |
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434 Users of Matlab or Octave can find related information :ref:`in the |
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435 dedicated section <matlab>`. |
| 0 | 436 |
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437 |
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438 .. _download_numpy: |
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439 |
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440 Downloading decoded images from Python |
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441 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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442 |
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443 .. highlight:: python |
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444 |
| 839 | 445 Starting with Orthanc 1.11.0, it is possible to immediately download |
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446 DICOM instances and DICOM series as numpy arrays (even if they use a |
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447 compressed transfer syntax). This is especially useful for the |
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448 integration within AI (artificial intelligence) pipelines. Here is a |
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449 sample call:: |
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450 |
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451 import io |
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452 import numpy |
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453 import requests |
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454 |
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455 r = requests.get('https://demo.orthanc-server.com/instances/6582b1c0-292ad5ab-ba0f088f-f7a1766f-9a29a54f/numpy') |
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456 r.raise_for_status() |
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457 |
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458 image = numpy.load(io.BytesIO(r.content)) |
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459 print(image.shape) # (1, 358, 512, 1) |
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460 |
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461 The downloaded numpy array for one single DICOM instance contains |
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462 floating-point values, and has a shape of ``(1, height, width, 1)`` if |
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463 the corresponding instance is grayscale, or ``(1, height, width, 3)`` |
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464 if the instance has colors (e.g. in ultrasound images). If applicable, |
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465 the ``Rescale Slope (0028,1053)`` and ``Rescale Intercept |
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466 (0028,1052)`` DICOM tags are applied to the floating-point values. |
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467 |
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468 Similarly, this feature is available at the series level:: |
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469 |
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470 import io |
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471 import numpy |
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472 import requests |
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473 |
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474 r = requests.get('https://demo.orthanc-server.com/series/dc0216d2-a406a5ad-31ef7a78-113ae9d9-29939f9e/numpy') |
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475 r.raise_for_status() |
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476 |
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477 image = numpy.load(io.BytesIO(r.content)) |
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478 print(image.shape) # (100, 256, 256, 1) |
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479 |
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480 As can be seen, in the case of a DICOM series, the first dimension of |
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481 the resulting numpy array corresponds to the depth of the series |
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482 (i.e. to its number of 2D slices). |
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483 |
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484 Some options are available for these ``/instances/.../numpy`` and |
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485 ``/series/.../numpy`` routes: |
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486 |
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487 * ``?compress=1`` will return a ``.npz`` compressed numpy archive |
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488 instead of a plain ``.npy`` numpy array. This can be used to reduce |
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489 the network bandwidth. In such a case, the array of interest is |
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490 named ``arr_0`` in the ``.npz`` archive, e.g.:: |
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491 |
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492 print(image['arr_0'].shape) |
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493 |
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494 * ``?rescale=0`` will skip the conversion to floating-point values, |
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495 and will not apply the rescale slope/intercept. This can be useful |
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496 to reduce the network bandwidth or to receive the original integer |
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497 values of the voxels. |
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498 |
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499 |
| 380 | 500 Downloading studies |
| 411 | 501 ^^^^^^^^^^^^^^^^^^^ |
| 380 | 502 |
| 503 .. highlight:: bash | |
| 504 | |
| 505 All instances of a study can be retrieved as a zip file as follows:: | |
| 506 | |
| 507 $ curl http://localhost:8042/studies/6b9e19d9-62094390-5f9ddb01-4a191ae7-9766b715/archive > Study.zip | |
| 508 | |
| 509 It is also possible to download a zipped DICOMDIR through:: | |
| 510 | |
| 381 | 511 $ curl http://localhost:8042/studies/6b9e19d9-62094390-5f9ddb01-4a191ae7-9766b715/media > Study.zip |
| 380 | 512 |
| 218 | 513 |
|
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514 .. _download-pdf-videos: |
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515 |
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516 Downloading PDF or videos |
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517 ^^^^^^^^^^^^^^^^^^^^^^^^^ |
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518 |
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519 .. highlight:: bash |
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520 |
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521 Given a DICOM instance that embeds a PDF file (typically, one instance |
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522 whose SOP Class UID is ``1.2.840.10008.5.1.4.1.1.104.1`` - |
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523 Encapsulated PDF Storage), the PDF content can be downloaded as |
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524 follows:: |
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525 |
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526 $ curl http://localhost:8042/instances/1915e0cc-c2c1a0fc-12cdd7f5-3ba32114-a97c2c9b/content/0042,0011 > sample.pdf |
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527 |
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528 This corresponds to downloading the raw DICOM tag "Encapsulated |
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529 Document" (0042,0011). Beware that the last byte of the downloaded |
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530 file might correspond to one padding byte, if the source PDF had an |
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531 odd number of bytes. |
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532 |
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533 Similarly, if you know that a DICOM instance :ref:`embeds a video |
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534 <videos>` (which can be tested by checking the :ref:`value of the |
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535 metadata <metadata-core>` corresponding to its transfer syntax UID), |
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536 the raw video can be downloaded as follows:: |
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537 |
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538 $ curl http://localhost:8042/instances/e465dd27-83c96343-96848735-7035a133-1facf1a0/frames/0/raw > sample.mp4 |
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539 |
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540 |
| 218 | 541 .. _peering: |
| 542 | |
| 216 | 543 Sending resources to remote Orthanc over HTTP/HTTPS (through Orthanc peering) |
|
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544 ----------------------------------------------------------------------------- |
| 216 | 545 |
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546 Orthanc can send its DICOM instances to remote Orthanc servers over |
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547 HTTP/HTTPS. Such servers are referred to as :ref:`Orthanc peers |
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548 <peers>`. This process can be triggered by the REST API, which is |
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549 described in this section. |
| 216 | 550 |
| 551 Configuration | |
| 552 ^^^^^^^^^^^^^ | |
| 553 | |
| 554 .. highlight:: json | |
| 555 | |
|
314
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556 You first have to declare the Url of the remote orthanc inside the |
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557 :ref:`configuration file <configuration>`. For instance, here is how |
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558 to declare a remote orthanc peer:: |
| 216 | 559 |
| 560 ... | |
| 494 | 561 "OrthancPeers" : { |
| 216 | 562 "sample" : [ "http://localhost:8043" ], // short version |
| 563 "sample2" : { // long version | |
| 564 "Url" : "http://localhost:8044", | |
| 565 "Username" : "alice", // optional | |
| 566 "Password" : "alicePassword", // optional | |
| 567 "HttpHeaders" : { "Token" : "Hello world" }, // optional | |
| 568 "CertificateFile" : "client.crt", // optional (only if using client certificate authentication) | |
| 569 "CertificateKeyFile" : "client.key", // optional (only if using client certificate authentication) | |
| 570 "CertificateKeyPassword" : "certpass" // optional (only if using client certificate authentication) | |
| 571 }, | |
| 572 ... | |
| 573 | |
| 574 .. highlight:: bash | |
| 575 | |
| 576 Such a configuration would enable Orthanc to connect to two other | |
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577 Orthanc instances that listens on the localhost on the ports 8043 |
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578 and 8044. The peers that are known to Orthanc can be queried:: |
| 216 | 579 |
| 580 $ curl http://localhost:8042/peers?expand | |
| 581 | |
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582 Instead of using the configuration file, peers can be created or |
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583 updated through the REST API using the ``PUT`` method of HTTP:: |
| 216 | 584 |
| 585 $ curl -v -X PUT http://localhost:8042/peers/sample -d '{"Url" : "http://127.0.0.1:8043"}' | |
| 586 | |
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587 One peer can also be removed using the ``DELETE`` method as follows:: |
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588 |
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589 $ curl -v -X DELETE http://localhost:8042/peers/sample |
| 216 | 590 |
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591 Note that, by default, peers are read from the Orthanc configuration |
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592 files and are updated in Orthanc memory only. If you want your |
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593 modifications to be persistent, you should configure Orthanc to store |
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594 its peers in the database. This is done through this configuration:: |
| 0 | 595 |
| 216 | 596 ... |
| 597 "OrthancPeersInDatabase" : true, | |
| 598 ... | |
| 599 | |
| 600 Sending One Resource | |
| 601 ^^^^^^^^^^^^^^^^^^^^ | |
| 602 | |
| 603 .. highlight:: bash | |
| 604 | |
| 605 Once you have identified the Orthanc identifier of the DICOM resource | |
| 606 that would like to send :ref:`as explained above <rest-access>`, you | |
| 607 would use the following command to send it:: | |
| 608 | |
| 609 $ curl -X POST http://localhost:8042/peers/sample/store -d c4ec7f68-9b162055-2c8c5888-5bf5752f-155ab19f | |
| 610 | |
| 611 The ``/sample/`` component of the URI corresponds to the identifier of | |
| 612 the remote modality, as specified above in the configuration file. | |
| 613 | |
| 614 Note that you can send isolated DICOM instances with this command, but | |
| 615 also entire patients, studies or series. It is possible to send multiple instances with a single POST | |
| 616 request:: | |
| 617 | |
| 618 $ curl -X POST http://localhost:8042/peers/sample/store -d '["d4b46c8e-74b16992-b0f5ca11-f04a60fa-8eb13a88","d5604121-7d613ce6-c315a5-a77b3cf3-9c253b23","cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e"]' | |
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619 |
| 216 | 620 Note that the list of resources to be sent can include the |
| 621 :ref:`Orthanc identifiers <orthanc-ids>` of entire patients, | |
| 622 studies or series as well. | |
| 623 | |
|
633
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624 **Important remark:** Neither the :ref:`metadata <metadata>`, nor the |
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625 :ref:`attachments <attachments>` are transferred between the Orthanc |
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626 peers. This is because metadata and attachments are considered as |
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627 local to one Orthanc server. |
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628 |
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629 |
| 294 | 630 Testing connectivity with a remote peer |
| 631 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 632 | |
| 633 .. highlight:: bash | |
| 634 | |
| 635 In version 1.5.9+, we have introduced a route to retrieve the ``/system`` info from | |
| 636 a remote peer. This route can also be used to test the connectivity with that peer | |
| 637 without actually sending a DICOM resource.:: | |
| 638 | |
| 639 $ curl http://localhost:8042/peers/sample/system | |
| 640 | |
| 641 | |
| 216 | 642 Using HTTPS |
| 643 ^^^^^^^^^^^ | |
| 644 | |
|
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645 If you're transfering medical data over internet, it is mandatory to |
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646 use HTTPS. |
| 216 | 647 |
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648 On the server side, we recommend to put Orthanc behind an :ref:`HTTPS |
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649 server that will take care of the TLS <https>`. |
| 216 | 650 |
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651 On the client side, in order for the client Orthanc to recognize the |
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652 server certificate, you'll have to provide a path to the CA |
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653 (certification authority) certificates. This is done in the |
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654 configuration file through this configurationg:: |
| 216 | 655 |
| 656 ... | |
| 657 "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt, | |
| 658 ... | |
| 659 | |
| 223 | 660 If you want your server to accept incoming connections for known hosts only, you can either: |
| 216 | 661 |
| 662 - configure a firewall to accept incoming connections from known IP addresses | |
| 663 - configure your client Orthanc to use a client certificate to authenticate at the Server. This is done through the ``CertificateFile``, ``CertificateKeyFile`` and ``CertificateKeyPassword`` entries in the configuration file. | |
| 664 | |
| 665 | |
| 666 | |
| 667 | |
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668 Sending resources to remote modalities (through DICOM C-Store) |
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669 -------------------------------------------------------------- |
| 0 | 670 |
| 671 Orthanc can send its DICOM instances to remote DICOM modalities (C-Store SCU). This process | |
| 672 can be triggered by the REST API. | |
| 673 | |
| 674 Configuration | |
| 675 ^^^^^^^^^^^^^ | |
| 676 | |
| 677 .. highlight:: json | |
| 678 | |
| 679 You first have to declare the AET, the IP address and the port number | |
| 680 of the remote modality inside the :ref:`configuration file | |
| 681 <configuration>`. For instance, here is how to declare a remote | |
| 682 modality:: | |
| 683 | |
| 684 ... | |
| 685 "DicomModalities" : { | |
| 212 | 686 "sample" : [ "ORTHANCA", "127.0.0.1", 2000 ], // short version |
| 687 "sample2" : { // long version | |
| 688 "AET" : "ORTHANCB", | |
| 689 "Port" : 2001, | |
| 690 "Host" : "127.0.0.1", | |
| 691 "Manufacturer" : "Generic", | |
| 692 "AllowEcho" : true, | |
| 693 "AllowFind" : true, | |
| 694 "AllowMove" : true, | |
| 695 "AllowStore" : true | |
| 696 } | |
| 0 | 697 }, |
| 698 ... | |
| 699 | |
| 700 .. highlight:: bash | |
| 701 | |
| 212 | 702 Such a configuration would enable Orthanc to connect to two DICOM |
| 703 stores (for instance, other Orthanc instances) that listens on the | |
| 704 localhost on the port 2000 & 2001. The modalities that are known to Orthanc | |
| 0 | 705 can be queried:: |
| 706 | |
| 212 | 707 $ curl http://localhost:8042/modalities?expand |
| 708 | |
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709 Instead of using the configuration file, modalities can be created or |
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710 updated through the REST API using the ``PUT`` method of HTTP:: |
| 212 | 711 |
| 712 $ curl -v -X PUT http://localhost:8042/modalities/sample -d '{"AET" : "ORTHANCC", "Host": "127.0.0.1", "Port": 2002}' | |
| 713 | |
|
667
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714 One modality can also be removed using the ``DELETE`` method as follows:: |
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715 |
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716 $ curl -v -X DELETE http://localhost:8042/modalities/sample |
| 0 | 717 |
|
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718 Note that, by default, modalities are read from the Orthanc |
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719 configuration files and are updated in Orthanc memory only. If you |
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720 want your modifications to be persistent, you should configure Orthanc |
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721 to store the modalities in the database. This is done through this |
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722 configuration:: |
| 212 | 723 |
| 724 ... | |
| 725 "DicomModalitiesInDatabase" : true, | |
| 726 ... | |
| 0 | 727 |
|
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728 |
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729 .. _rest-store-scu: |
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730 |
| 0 | 731 Sending One Resource |
| 732 ^^^^^^^^^^^^^^^^^^^^ | |
| 733 | |
| 734 .. highlight:: bash | |
| 735 | |
| 736 Once you have identified the Orthanc identifier of the DICOM resource | |
| 737 that would like to send :ref:`as explained above <rest-access>`, you | |
| 738 would use the following command to send it:: | |
| 739 | |
| 740 $ curl -X POST http://localhost:8042/modalities/sample/store -d c4ec7f68-9b162055-2c8c5888-5bf5752f-155ab19f | |
| 741 | |
| 742 The ``/sample/`` component of the URI corresponds to the identifier of | |
| 743 the remote modality, as specified above in the configuration file. | |
| 744 | |
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745 Note that you can send isolated DICOM instances with this command, but |
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746 also entire patients, studies or series. |
| 0 | 747 |
| 407 | 748 Various optional fields are also available. i.e, if you need to |
| 749 monitor the state of a transfer, you can start the transfer in :ref:`asynchronous mode | |
| 750 <jobs>`, which will provide you with the identifier of the Orthanc job:: | |
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751 |
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752 $ curl -X POST http://localhost:8042/modalities/sample/store \ |
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753 --data '{ |
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754 "Resources" : ["d4b46c8e-74b16992-b0f5ca11-f04a60fa-8eb13a88"], |
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755 "Synchronous" : false, |
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756 "LocalAet" : "ORTHANC", |
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757 "MoveOriginatorAet": "ORTHANC", |
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758 "MoveOriginatorID": 1234, |
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759 "Timeout": 10, |
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760 "StorageCommitment": false |
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761 }' |
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762 |
| 403 | 763 |
| 0 | 764 Bulk Store SCU |
| 765 ^^^^^^^^^^^^^^ | |
| 766 | |
| 767 .. highlight:: bash | |
| 768 | |
| 769 Each time a POST request is made to ``/modalities/.../store``, a new | |
|
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770 DICOM association is possibly established. This may lead to a large |
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771 communication overhead if sending multiple isolated instances by |
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772 making one REST call for each of these instances. |
| 0 | 773 |
| 774 To circumvent this problem, you have 2 possibilities: | |
| 775 | |
| 776 1. Set the ``DicomAssociationCloseDelay`` option in the | |
| 777 :ref:`configuration file <configuration>` to a non-zero value. This | |
| 778 will keep the DICOM connection open for a certain amount of time, | |
|
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779 waiting for new instances to be routed. This is useful if |
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780 autorouting images :ref:`using Lua <lua-auto-routing>`. |
| 0 | 781 |
|
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782 2. It is possible to send multiple instances with a single POST |
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783 request (so-called "Bulk Store SCU", available from Orthanc |
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784 0.5.2):: |
| 0 | 785 |
| 786 $ curl -X POST http://localhost:8042/modalities/sample/store -d '["d4b46c8e-74b16992-b0f5ca11-f04a60fa-8eb13a88","d5604121-7d613ce6-c315a5-a77b3cf3-9c253b23","cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e"]' | |
| 787 | |
| 788 The list of the resources to be sent are given as a JSON array. In | |
| 789 this case, a single DICOM connection is used. `Sample code is | |
| 790 available | |
| 449 | 791 <https://hg.orthanc-server.com/orthanc/file/default/OrthancServer/Resources/Samples/Python/HighPerformanceAutoRouting.py>`__. |
| 0 | 792 |
|
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793 Note that the list of resources to be sent can include the |
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794 :ref:`Orthanc identifiers <orthanc-ids>` of entire patients, |
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795 studies or series as well. |
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796 |
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797 |
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798 Performing C-Echo |
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799 ----------------- |
| 0 | 800 |
|
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801 To validate the DICOM connectivity between Orthanc and a remote modality, |
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802 you can perform a C-ECHO:: |
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803 |
|
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804 $ curl -X POST http://localhost:8042/modalities/sample/echo -d '{}' |
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805 |
|
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806 From Orthanc 1.7.0, you can include an extra ``Timeout`` field:: |
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807 |
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808 $ curl -X POST http://localhost:8042/modalities/sample/echo -d '{ "Timeout": 10 }' |
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809 |
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810 If no ``Timeout`` parameter is specified, the value of the ``DicomScuTimeout`` |
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811 configuration is used as a default. If ``Timeout`` is set to zero, this means |
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812 no timeout. |
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813 |
|
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814 NB: A body containing a valid JSON object is needed by |
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815 ``/modalities/{id}/echo`` since Orthanc 1.7.0. |
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816 |
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817 |
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818 Performing C-Move |
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819 ----------------- |
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820 |
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821 .. highlight:: bash |
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822 |
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823 You can perform a DICOM C-Move to move a specific study from one modality |
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824 to another (including Orthanc itself if you don't specify the ``TargetAet`` |
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825 field). |
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826 |
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827 I.e. to move a study whose you know the ``StudyInstanceUID`` from |
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828 the modality ``sample`` to another Orthanc whose AET is ``ORTHANCB``:: |
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829 |
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830 $ curl --request POST --url http://localhost:8042/modalities/samples/move \ |
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831 --data '{ |
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832 "Level" : "Study", |
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833 "Resources" : [ |
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834 { |
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835 "StudyInstanceUID": "1.2.840.113543.6.6.4.7.64067529866380271256212683512383713111129" |
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836 } |
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837 ], |
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838 "TargetAet": "ORTHANCB", |
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839 "Timeout": 60 |
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840 }' |
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841 |
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842 |
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843 Performing Query/Retrieve (C-Find) and Find with REST |
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844 ----------------------------------------------------- |
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845 |
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846 *Section contributed by Bryan Dearlove* |
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847 |
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848 Orthanc can be used to perform queries on the local Orthanc instance, |
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849 or on remote modalities through the REST API. |
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850 |
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851 To perform a query of a remote modality you must define the modality |
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852 within the :ref:`configuration file <configuration>` (See |
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853 Configuration section under Sending resources to remote modalities). |
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854 |
| 698 | 855 .. _rest-find-scu: |
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856 |
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857 Performing Queries on Modalities |
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858 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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859 |
| 138 | 860 .. highlight:: bash |
| 861 | |
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862 To initiate a query you perform a POST command against the Modality |
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863 with the identifiers you are looking for. The the example below we are |
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864 performing a study level query against the modality sample for any |
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865 study descriptions with the word chest within it. This search is case |
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866 insensitive unless configured otherwise within the Orthanc |
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867 configuration file:: |
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868 |
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869 $ curl --request POST \ |
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870 --url http://localhost:8042/modalities/sample/query \ |
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871 --data '{ |
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872 "Level" : "Study", |
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873 "Query" : { |
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874 "PatientID" : "", |
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875 "StudyDescription" : "*Chest*", |
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876 "PatientName" : "" |
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877 } |
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878 }' |
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879 |
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880 You might be interested in including the ``Normalize`` option to bypass |
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881 the normalization of the outgoing C-FIND queries. For instance, for |
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882 the ``InstitutionName`` to be included at the ``Study`` level, one would |
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883 run:: |
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884 |
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885 $ curl -v http://localhost:8042/modalities/sample/query -X POST -d \ |
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886 '{"Level":"Study","Query":{"InstitutionName":"a"},"Normalize":false}' |
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887 |
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888 .. highlight:: json |
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889 |
| 138 | 890 You will receive back an ID which can be used to retrieve more |
| 891 information with GET commands or C-Move requests with a POST Command:: | |
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892 |
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893 { |
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894 "ID": "5af318ac-78fb-47ff-b0b0-0df18b0588e0", |
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895 "Path": "/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0" |
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896 } |
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897 |
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898 |
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899 Additional Options |
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900 ^^^^^^^^^^^^^^^^^^ |
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901 |
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902 .. highlight:: json |
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903 |
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904 You can use patient identifiers by including the ``*`` within your |
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905 search. For example if you were searching for a name beginning with |
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906 ``Jones`` you can do:: |
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907 |
| 139 | 908 "PatientName":"Jones*" |
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909 |
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910 If you wanted to search for a name with the words ``Jo`` anywhere |
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911 within it you can do:: |
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912 |
| 139 | 913 "PatientName":"*Jo*" |
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914 |
| 138 | 915 To perform date searches you can specify within StudyDate a starting |
| 916 date and/or a before date. For example ``"StudyDate":"20180323-"`` | |
| 917 would search for all study dates after the specified date to | |
| 918 now. Doing ``"StudyDate":"20180323-20180325"`` would search for all | |
| 919 study dates between the specified date. | |
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920 |
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921 |
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922 Reviewing Level |
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923 ^^^^^^^^^^^^^^^ |
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924 |
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925 .. highlight:: bash |
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926 |
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927 :: |
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928 |
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929 $ curl --request GET --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/level |
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930 |
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931 Will retrieve the level with which the query was performed, Study, |
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932 Series or Instance. |
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933 |
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934 |
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935 Reviewing Modality |
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936 ^^^^^^^^^^^^^^^^^^ |
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937 |
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938 .. highlight:: bash |
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939 |
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940 :: |
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941 |
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942 $ curl --request GET --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/modality |
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943 |
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944 Will provide the modality name which the original query was performed against. |
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945 |
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946 |
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947 Reviewing Query |
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948 ^^^^^^^^^^^^^^^ |
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949 |
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950 .. highlight:: bash |
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951 |
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952 To retrieve information on what identifiers the query was originally |
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953 performed using you can use the query filter:: |
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954 |
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955 $ curl --request GET --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/query |
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956 |
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957 |
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958 Reviewing Query Answers |
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959 ^^^^^^^^^^^^^^^^^^^^^^^ |
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960 |
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961 .. highlight:: bash |
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962 |
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963 You are able to individually review each answer returned by performing |
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964 a GET with the answers parameter:: |
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965 |
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966 $ curl --request GET --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/answers |
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967 |
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968 You will get a JSON back with numbered identifiers for each answer you |
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969 received back. For example because we performed a Study level query we |
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970 received back 5 studies answers back. We are able to query each answer |
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971 for content details:: |
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972 |
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973 $ curl --request GET --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/answers/0/content |
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974 |
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975 If there are content items missing, you may add them by adding that |
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976 identifier to the original query. For example if we wanted Modalities |
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977 listed in this JSON answer in the initial query we would add to the |
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978 POST body: ``"ModalitiesInStudy":""`` |
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979 |
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980 |
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981 Performing Retrieve (C-Move) |
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982 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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983 |
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984 .. highlight:: bash |
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985 |
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986 You can perform a C-Move to retrieve all studies within the original |
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987 query using a post command and identifying the Modality (named in this |
| 207 | 988 example ``Orthanc``), to be one to in the POST contents:: |
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989 |
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990 $ curl --request POST --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/retrieve --data Orthanc |
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991 |
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992 You are also able to perform individual C-Moves for a content item by |
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993 specifying that individual content item:: |
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994 |
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995 $ curl --request POST --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/answers/0/retrieve --data Orthanc |
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996 |
| 207 | 997 If C-Moves take too long (for example, performing a C-Move of a big |
|
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998 study), you may run the request in :ref:`asynchronous mode <jobs>`, |
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999 which will create a job in Orthanc:: |
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1000 |
| 207 | 1001 $ curl --request POST --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/retrieve \ |
| 1002 --data '{"TargetAet":"Orthanc","Synchronous":false}' | |
| 1003 | |
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1004 |
| 207 | 1005 .. highlight:: bash |
| 1006 | |
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1007 The answer of this POST request is the job ID taking care of the |
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1008 C-Move command, :ref:`whose status can be monitored <jobs-monitoring>` |
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1009 in order to detect failure or completion:: |
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1010 |
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1011 { |
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1012 "ID" : "11541b16-e368-41cf-a8e9-3acf4061d238", |
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1013 "Path" : "/jobs/11541b16-e368-41cf-a8e9-3acf4061d238" |
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1014 } |
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1015 |
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1016 |
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1017 |
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1018 .. _rest-find: |
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1019 |
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1020 Performing Finds within Orthanc |
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1021 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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1022 .. highlight:: bash |
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1023 |
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1024 Performing a find within the local database of Orthanc is very similar |
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1025 to using Queries against DICOM modalities and the additional options |
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1026 listed above work with find also. When performing a find, you will |
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1027 receive the Orthanc ID's of all the matched items within your |
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1028 find. For example if you perform a study level find and 5 Studies |
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1029 match you will receive 5 study level Orthanc ID's in JSON format as a |
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1030 response:: |
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1031 |
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1032 $ curl --request POST --url http://localhost:8042/tools/find \ |
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1033 --data '{ |
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1034 "Level" : "Instance", |
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1035 "Query" : { |
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1036 "Modality" : "CR", |
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1037 "StudyDate" : "20180323-", |
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1038 "PatientID" : "*" |
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1039 } |
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1040 }' |
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1041 |
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1042 Setting the ``Expand`` field to ``true`` in the POST body of the |
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1043 query will automatically report details about each study:: |
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1044 |
| 313 | 1045 $ curl https://demo.orthanc-server.com/tools/find -d '{"Level":"Study","Query":{"PatientName":"KNIX"}}' |
| 1046 [ | |
| 1047 "b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0" | |
| 1048 ] | |
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1049 $ curl https://demo.orthanc-server.com/tools/find -d '{"Level":"Study","Query":{"PatientName":"KNIX"},"Expand":true}' |
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1050 [ |
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1051 { |
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1052 "ID" : "b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0", |
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1053 "IsStable" : true, |
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1054 "LastUpdate" : "20180414T091528", |
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1055 "MainDicomTags" : { |
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1056 "InstitutionName" : "0ECJ52puWpVIjTuhnBA0um", |
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1057 "ReferringPhysicianName" : "1", |
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1058 "StudyDate" : "20070101", |
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1059 "StudyDescription" : "Knee (R)", |
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1060 "StudyID" : "1", |
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1061 "StudyInstanceUID" : "1.2.840.113619.2.176.2025.1499492.7391.1171285944.390", |
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1062 "StudyTime" : "120000.000000" |
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1063 }, |
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1064 "ParentPatient" : "6816cb19-844d5aee-85245eba-28e841e6-2414fae2", |
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1065 "PatientMainDicomTags" : { |
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1066 "PatientID" : "ozp00SjY2xG", |
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1067 "PatientName" : "KNIX" |
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1068 }, |
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1069 "Series" : [ |
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1070 "20b9d0c2-97d85e07-f4dbf4d2-f09e7e6a-0c19062e", |
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1071 "edbfa0a9-fa2641d7-29514b1c-45881d0b-46c374bd", |
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1072 "f2635388-f01d497a-15f7c06b-ad7dba06-c4c599fe", |
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1073 "4d04593b-953ced51-87e93f11-ae4cf03c-25defdcd", |
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1074 "5e343c3e-3633c396-03aefde8-ba0e08c7-9c8208d3", |
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1075 "8ea120d7-5057d919-837dfbcc-ccd04e0f-7f3a94aa" |
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1076 ], |
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1077 "Type" : "Study" |
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1078 } |
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1079 ] |
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1080 |
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1081 Here is a sample REST API call to find the Orthanc identifiers of all |
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1082 the DICOM series generated by an imaging modality whose "Device Serial |
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1083 Number (0018,1000)" DICOM tag is equal to "123":: |
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1084 |
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1085 $ curl -X POST http://localhost:8042/tools/find -d '{"Level":"Series","Query":{"DeviceSerialNumber":"123"},"Expand":true}' |
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1086 |
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1087 If you are interested by a **list of several items** (in this case, in |
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1088 a list of serial numbers), just separate them with backslashes as |
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1089 would do with DICOM C-FIND:: |
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1090 |
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1091 $ curl -X POST http://localhost:8042/tools/find -d '{"Level":"Series","Query":{"DeviceSerialNumber":"123\\abc"},"Expand":true}' |
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1092 |
|
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1093 |
| 138 | 1094 |
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1095 Additional Options |
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1096 ^^^^^^^^^^^^^^^^^^ |
| 138 | 1097 .. highlight:: json |
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1098 |
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1099 You also have the ability to limit the responses by specifying a limit within the body of the POST message. For example:: |
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1100 |
| 138 | 1101 "Limit":4 |
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1102 |
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1103 .. highlight:: bash |
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1104 |
| 839 | 1105 Since Orthanc 1.11.0, you may also request a specific list of tags in the response (like in a C-FIND) even if these |
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1106 tags are not stored in the MainDicomTags or if the tags needs to be computed (like ``ModalitiesInStudy``). This ``RequestedTags`` option is |
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1107 available only if you specify ``"Expand": true``:: |
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1108 |
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1109 $ curl -X POST http://localhost:8042/tools/find -d ' |
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1110 { |
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1111 "Level": "Studies", |
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1112 "Expand": true, |
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1113 "Query": { |
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1114 "StudyDate": "20220502" |
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1115 }, |
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1116 "RequestedTags": ["PatientName", "PatientID", "StudyDescription", "StudyDate", "StudyInstanceUID", "ModalitiesInStudy", "NumberOfStudyRelatedSeries"] |
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1117 }' |
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1118 |
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1119 .. highlight:: json |
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1120 |
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1121 This query will return a response like this one:: |
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1122 |
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1123 [ |
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1124 { |
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1125 "ID" : "8a8cf898-ca27c490-d0c7058c-929d0581-2bbf104d", |
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1126 "IsStable" : true, |
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1127 "LastUpdate" : "20220428T074549", |
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1128 "MainDicomTags" : { |
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1129 "...":"..." |
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1130 }, |
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1131 "..." : "...", |
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1132 "RequestedTags" : { |
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1133 "PatientName" : "Patient", |
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1134 "PatientID" : "1", |
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1135 "StudyDescription" : "Description", |
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1136 "StudyDate" : "20220502", |
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1137 "StudyInstanceUID" : "1.2.3", |
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1138 "ModalitiesInStudy" : "CT\\SEG\\SR", |
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1139 "NumberOfStudyRelatedSeries" : "3" |
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1140 }, |
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1141 "Series" : [ "93034833-163e42c3-bc9a428b-194620cf-2c5799e5" ], |
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1142 "Type" : "Study" |
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1143 } |
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1144 ] |
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1145 |
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1146 |
| 216 | 1147 .. _changes: |
| 1148 | |
| 0 | 1149 Tracking changes |
| 1150 ---------------- | |
| 1151 | |
| 1152 .. highlight:: bash | |
| 1153 | |
| 1154 Whenever Orthanc receives a new DICOM instance, this event is recorded | |
| 1155 in the so-called "Changes Log". This enables remote scripts to react | |
| 1156 to the arrival of new DICOM resources. A typical application is | |
| 1157 **auto-routing**, where an external script waits for a new DICOM | |
| 1158 instance to arrive into Orthanc, then forward this instance to another | |
| 1159 modality. | |
| 1160 | |
| 1161 The Changes Log can be accessed by the following command:: | |
| 1162 | |
| 1163 $ curl http://localhost:8042/changes | |
| 1164 | |
| 1165 .. highlight:: json | |
| 1166 | |
| 1167 Here is a typical output:: | |
| 1168 | |
| 1169 { | |
| 1170 "Changes" : [ | |
| 1171 { | |
| 1172 "ChangeType" : "NewInstance", | |
| 1173 "Date" : "20130507T143902", | |
| 1174 "ID" : "8e289db9-0e1437e1-3ecf395f-d8aae463-f4bb49fe", | |
| 1175 "Path" : "/instances/8e289db9-0e1437e1-3ecf395f-d8aae463-f4bb49fe", | |
| 1176 "ResourceType" : "Instance", | |
| 1177 "Seq" : 921 | |
| 1178 }, | |
| 1179 { | |
| 1180 "ChangeType" : "NewSeries", | |
| 1181 "Date" : "20130507T143902", | |
| 1182 "ID" : "cceb768f-e0f8df71-511b0277-07e55743-9ef8890d", | |
| 1183 "Path" : "/series/cceb768f-e0f8df71-511b0277-07e55743-9ef8890d", | |
| 1184 "ResourceType" : "Series", | |
| 1185 "Seq" : 922 | |
| 1186 }, | |
| 1187 { | |
| 1188 "ChangeType" : "NewStudy", | |
| 1189 "Date" : "20130507T143902", | |
| 1190 "ID" : "c4ec7f68-9b162055-2c8c5888-5bf5752f-155ab19f", | |
| 1191 "Path" : "/studies/c4ec7f68-9b162055-2c8c5888-5bf5752f-155ab19f", | |
| 1192 "ResourceType" : "Study", | |
| 1193 "Seq" : 923 | |
| 1194 }, | |
| 1195 { | |
| 1196 "ChangeType" : "NewPatient", | |
| 1197 "Date" : "20130507T143902", | |
| 1198 "ID" : "dc65762c-f476e8b9-898834f4-2f8a5014-2599bc94", | |
| 1199 "Path" : "/patients/dc65762c-f476e8b9-898834f4-2f8a5014-2599bc94", | |
| 1200 "ResourceType" : "Patient", | |
| 1201 "Seq" : 924 | |
| 1202 } | |
| 1203 ], | |
| 1204 "Done" : true, | |
| 1205 "Last" : 924 | |
| 1206 } | |
| 1207 | |
| 1208 This output corresponds to the receiving of one single DICOM instance | |
| 1209 by Orthanc. It records that a new instance, a new series, a new study | |
| 1210 and a new patient has been created inside Orthanc. Note that each | |
| 1211 changes is labeled by a ``ChangeType``, a ``Date`` (in the `ISO format | |
| 25 | 1212 <https://en.wikipedia.org/wiki/ISO_8601>`__), the location of the |
| 0 | 1213 resource inside Orthanc, and a sequence number (``Seq``). |
| 1214 | |
| 1215 Note that this call is non-blocking. It is up to the calling program | |
| 1216 to wait for the occurrence of a new event (by implementing a polling | |
| 1217 loop). | |
| 1218 | |
| 1219 .. highlight:: bash | |
| 1220 | |
| 1221 This call only returns a fixed number of events, that can be changed | |
| 1222 by using the ``limit`` option:: | |
| 1223 | |
| 1224 $ curl http://localhost:8042/changes?limit=100 | |
| 1225 | |
| 1226 The flag ``Last`` records the sequence number of the lastly returned | |
| 1227 event. The flag ``Done`` is set to ``true`` if no further event has | |
| 1228 occurred after this lastly returned event. If ``Done`` is set to | |
| 1229 ``false``, further events are available and can be retrieved. This is | |
| 1230 done by setting the ``since`` option that specifies from which | |
| 1231 sequence number the changes must be returned:: | |
| 1232 | |
| 1233 $ curl 'http://localhost:8042/changes?limit=100&since=922' | |
| 1234 | |
| 1235 A `sample code in the source distribution | |
| 449 | 1236 <https://hg.orthanc-server.com/orthanc/file/default/OrthancServer/Resources/Samples/Python/ChangesLoop.py>`__ |
| 0 | 1237 shows how to use this Changes API to implement a polling loop. |
| 1238 | |
| 1239 | |
| 1240 Deleting resources from Orthanc | |
| 1241 ------------------------------- | |
| 1242 | |
| 1243 .. highlight:: bash | |
| 1244 | |
| 1245 Deleting patients, studies, series or instances | |
| 1246 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 1247 | |
| 1248 Deleting DICOM resources (i.e. patients, studies, series or instances) | |
| 1249 from Orthanc is as simple as using a HTTP DELETE on the URI of this | |
| 1250 resource. | |
| 1251 | |
| 1252 Concretely, you would first explore the resources that are stored in | |
| 1253 Orthanc :ref:`as explained above <rest-access>`:: | |
| 1254 | |
| 1255 $ curl http://localhost:8042/patients | |
| 1256 $ curl http://localhost:8042/studies | |
| 1257 $ curl http://localhost:8042/series | |
| 1258 $ curl http://localhost:8042/instances | |
| 1259 | |
| 1260 Secondly, once you have spotted the resources to be removed, you would | |
| 1261 use the following command-line syntax to delete them:: | |
| 1262 | |
| 1263 $ curl -X DELETE http://localhost:8042/patients/dc65762c-f476e8b9-898834f4-2f8a5014-2599bc94 | |
| 1264 $ curl -X DELETE http://localhost:8042/studies/c4ec7f68-9b162055-2c8c5888-5bf5752f-155ab19f | |
| 1265 $ curl -X DELETE http://localhost:8042/series/cceb768f-e0f8df71-511b0277-07e55743-9ef8890d | |
| 1266 $ curl -X DELETE http://localhost:8042/instances/8e289db9-0e1437e1-3ecf395f-d8aae463-f4bb49fe | |
| 1267 | |
| 1268 | |
| 712 | 1269 Starting with Orthanc 1.9.4, it is also possible to ``POST`` on the |
| 1270 new route ``/tools/bulk-delete`` to delete at once a set of multiple | |
| 1271 DICOM resources that are not related (i.e. that don't share any parent | |
| 1272 DICOM resource). A typical use case is to delete a list of DICOM | |
| 1273 instances that don't belong to the same parent patient/study/series. | |
| 1274 The list of the :ref:`Orthanc identifiers <orthanc-ids>` of the | |
| 1275 resources to be deleted (that may indifferently correspond to | |
| 1276 patients, studies, series or instances) must be provided in an | |
| 1277 argument ``Resources`` in the body of the request. Here is a sample | |
| 1278 call:: | |
| 1279 | |
| 1280 $ curl http://localhost:8042/tools/bulk-delete -d '{"Resources":["b6da0b16-a25ae9e7-1a80fc33-20df01a9-a6f7a1b0","d6634d97-24379e4a-1e68d3af-e6d0451f-e7bcd3d1"]}' | |
| 1281 | |
| 1282 | |
| 0 | 1283 Clearing log of changes |
| 1284 ^^^^^^^^^^^^^^^^^^^^^^^ | |
| 1285 | |
| 1286 :ref:`As described above <changes>`, Orthanc keeps track of all the | |
| 1287 changes that occur in the DICOM store. This so-called "Changes Log" | |
| 1288 is accessible at the following URI:: | |
| 1289 | |
| 1290 $ curl http://localhost:8042/changes | |
| 1291 | |
| 1292 To clear the content of the Changes Log, simply DELETE this URI:: | |
| 1293 | |
| 1294 $ curl -X DELETE http://localhost:8042/changes | |
| 1295 | |
| 1296 | |
| 155 | 1297 Log of exported resources |
| 1298 ^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 1299 | |
| 1300 For medical traceability, Orthanc can be configured to store a log of | |
| 1301 all the resources that have been exported to remote modalities:: | |
| 0 | 1302 |
| 1303 $ curl http://localhost:8042/exports | |
| 1304 | |
| 1305 In auto-routing scenarios, it is important to prevent this log to grow | |
| 1306 indefinitely as incoming instances are routed. You can either disable | |
| 1307 this logging by setting the option ``LogExportedResources`` to ``false`` | |
| 1308 in the :ref:`configuration file <configuration>`, or periodically | |
| 1309 clear this log by DELETE-ing this URI:: | |
| 1310 | |
| 1311 $ curl -X DELETE http://localhost:8042/exports | |
| 1312 | |
| 155 | 1313 NB: Starting with Orthanc 1.4.0, the ``LogExportedResources`` is set |
| 1314 to ``false`` by default. If the logging is desired, set this option to | |
| 1315 ``true``. | |
| 1316 | |
| 0 | 1317 |
| 1318 Anonymization and modification | |
| 1319 ------------------------------ | |
| 1320 | |
| 1321 The process of anonymizing and modifying DICOM resources is | |
| 1322 :ref:`documented in a separate page <anonymization>`. | |
| 1323 | |
| 1324 | |
| 1325 Further reading | |
| 1326 --------------- | |
| 1327 | |
| 1328 The examples above have shown you the basic principles for driving an | |
| 1329 instance of Orthanc through its REST API. All the possibilities of the | |
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1330 API have not been described: |
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1331 |
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1332 * Advanced features of the REST API can be found on :ref:`another page |
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1333 <rest-advanced>`. |
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1334 * A :ref:`FAQ entry <rest-samples>` lists where you can find more |
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1335 advanced samples of the REST API of Orthanc. |
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1336 * A :ref:`short reference of the REST API of Orthanc <cheatsheet>` is |
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1337 part of the Orthanc Book. |
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1338 * The full documentation of the REST API in the OpenAPI/Swagger format |
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1339 is `available online <https://api.orthanc-server.com/>`__. This |
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1340 reference is automatically generated from the source code of |
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1341 Orthanc. |