Mercurial > hg > orthanc-book
annotate Sphinx/source/users/rest.rst @ 380:06ab5ab05a2d
API doc: download study
author | Alain Mazy <alain@mazy.be> |
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date | Wed, 08 Apr 2020 12:20:46 +0200 |
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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 | |
114 | 28 .. _sending-dicom-images: |
29 | |
0 | 30 Sending DICOM images |
31 -------------------- | |
32 | |
33 .. highlight:: bash | |
34 | |
35 The upload of DICOM files is possible by querying the REST API using | |
36 the following syntax:: | |
37 | |
38 $ curl -X POST http://localhost:8042/instances --data-binary @CT.X.1.2.276.0.7230010.dcm | |
39 | |
40 .. highlight:: json | |
41 | |
42 Orthanc will respond with a JSON file that contain information about | |
43 the location of the stored instance, such as:: | |
44 | |
45 { | |
46 "ID" : "e87da270-c52b-4f2a-b8c6-bae25928d0b0", | |
47 "Path" : "/instances/e87da270-c52b-4f2a-b8c6-bae25928d0b0", | |
48 "Status" : "Success" | |
49 } | |
50 | |
51 .. highlight:: bash | |
52 | |
53 Note that in the case of curl, setting the ``Expect`` HTTP Header will | |
54 significantly `reduce the execution time of POST requests | |
358
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55 <https://stackoverflow.com/questions/463144/php-http-post-fails-when-curl-data-1024/463277#463277>`__:: |
0 | 56 |
57 $ curl -X POST -H "Expect:" http://localhost:8042/instances --data-binary @CT.X.1.2.276.0.7230010.dcm | |
58 | |
59 The code distribution of Orthanc contains a `sample Python script | |
360 | 60 <https://hg.orthanc-server.com/orthanc/file/default/Resources/Samples/ImportDicomFiles/ImportDicomFiles.py>`__ |
0 | 61 that recursively upload the content of some folder into Orthanc using |
62 the REST API:: | |
63 | |
64 $ python ImportDicomFiles.py localhost 8042 ~/DICOM/ | |
65 | |
66 | |
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67 .. highlight:: perl |
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68 |
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69 If you are using Powershell (>= 3.0), you can use the following to send a single |
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70 Dicom instance to Orthanc:: |
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71 |
376 | 72 # disabling the progress bar makes the Invoke-RestMethod call MUCH faster |
297
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73 $ProgressPreference = 'SilentlyContinue' |
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74 |
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75 # upload it to Orthanc |
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76 $reply = Invoke-RestMethod http://localhost:8042/instances -Method POST -InFile CT.X.1.2.276.0.7230010.dcm |
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77 |
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78 # display the result |
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79 Write-Host "The instance can be retrieved at http://localhost:8042$($reply.Path)" |
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80 |
0 | 81 .. _rest-access: |
82 | |
83 Accessing the content of Orthanc | |
84 -------------------------------- | |
85 | |
86 Orthanc structures the stored DICOM resources using the "Patient, | |
87 Study, Series, Instance" model of the DICOM standard. Each DICOM | |
88 resource is associated with an :ref:`unique identifier <orthanc-ids>`. | |
89 | |
90 List all the DICOM resources | |
91 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
92 | |
93 Here is how you would list all the DICOM resources that are stored in | |
94 your local Orthanc instance:: | |
95 | |
96 $ curl http://localhost:8042/patients | |
97 $ curl http://localhost:8042/studies | |
98 $ curl http://localhost:8042/series | |
99 $ curl http://localhost:8042/instances | |
100 | |
101 Note that the result of this command is a `JSON file | |
25 | 102 <https://en.wikipedia.org/wiki/Json>`__ that contains an array of |
0 | 103 resource identifiers. The JSON file format is lightweight and can be |
104 parsed from almost any computer language. | |
105 | |
106 Accessing a patient | |
107 ^^^^^^^^^^^^^^^^^^^ | |
108 | |
109 .. highlight:: bash | |
110 | |
111 To access a single resource, add its identifier to the `URI | |
25 | 112 <https://en.wikipedia.org/wiki/Uniform_resource_identifier>`__. You |
0 | 113 would for instance retrieve the main information about one patient as |
114 follows:: | |
115 | |
116 $ curl http://localhost:8042/patients/dc65762c-f476e8b9-898834f4-2f8a5014-2599bc94 | |
117 | |
118 .. highlight:: json | |
119 | |
120 Here is a possible answer from Orthanc:: | |
121 | |
122 { | |
123 "ID" : "07a6ec1c-1be5920b-18ef5358-d24441f3-10e926ea", | |
124 "MainDicomTags" : { | |
125 "OtherPatientIDs" : "(null)", | |
126 "PatientBirthDate" : "0", | |
127 "PatientID" : "000000185", | |
128 "PatientName" : "Anonymous^Unknown", | |
129 "PatientSex" : "O" | |
130 }, | |
131 "Studies" : [ "9ad2b0da-a406c43c-6e0df76d-1204b86f-78d12c15" ], | |
132 "Type" : "Patient" | |
133 } | |
134 | |
135 This is once again a JSON file. Note how Orthanc gives you a summary | |
136 of the main DICOM tags that correspond to the patient level. | |
137 | |
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138 |
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139 .. _browsing-hierarchy: |
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140 |
0 | 141 Browsing from the patient down to the instance |
142 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
143 | |
144 .. highlight:: bash | |
145 | |
146 The field ``Studies`` list all the DICOM studies that are associated | |
147 with the patient. So, considering the patient above, we would go down | |
148 in her DICOM hierarchy as follows:: | |
149 | |
150 $ curl http://localhost:8042/studies/9ad2b0da-a406c43c-6e0df76d-1204b86f-78d12c15 | |
151 | |
152 .. highlight:: json | |
153 | |
154 And Orthanc could answer:: | |
155 | |
156 { | |
157 "ID" : "9ad2b0da-a406c43c-6e0df76d-1204b86f-78d12c15", | |
158 "MainDicomTags" : { | |
159 "AccessionNumber" : "(null)", | |
160 "StudyDate" : "20120716", | |
161 "StudyDescription" : "TestSUVce-TF", | |
162 "StudyID" : "23848", | |
163 "StudyInstanceUID" : "1.2.840.113704.1.111.7016.1342451220.40", | |
164 "StudyTime" : "170728" | |
165 }, | |
166 "ParentPatient" : "07a6ec1c-1be5920b-18ef5358-d24441f3-10e926ea", | |
167 "Series" : [ | |
168 "6821d761-31fb55a9-031ebecb-ba7f9aae-ffe4ddc0", | |
169 "2cc6336f-2d4ae733-537b3ca3-e98184b1-ba494b35", | |
170 "7384c47e-6398f2a8-901846ef-da1e2e0b-6c50d598" | |
171 ], | |
172 "Type" : "Study" | |
173 } | |
174 | |
175 .. highlight:: bash | |
176 | |
177 The main DICOM tags are now those that are related to the study | |
178 level. It is possible to retrieve the identifier of the patient in the | |
179 ``ParentPatient`` field, which can be used to go upward the DICOM | |
180 hierarchy. But let us rather go down to the series level by using the | |
181 ``Series`` array. The next command would return information about one | |
182 of the three series that have just been reported:: | |
183 | |
184 $ curl http://localhost:8042/series/2cc6336f-2d4ae733-537b3ca3-e98184b1-ba494b35 | |
185 | |
186 .. highlight:: json | |
187 | |
188 Here is a possible answer:: | |
189 | |
190 { | |
191 "ExpectedNumberOfInstances" : 45, | |
192 "ID" : "2cc6336f-2d4ae733-537b3ca3-e98184b1-ba494b35", | |
193 "Instances" : [ | |
194 "41bc3f74-360f9d10-6ae9ffa4-01ea2045-cbd457dd", | |
195 "1d3de868-6c4f0494-709fd140-7ccc4c94-a6daa3a8", | |
196 <...> | |
197 "1010f80b-161b71c0-897ec01b-c85cd206-e669a3ea", | |
198 "e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4" | |
199 ], | |
200 "MainDicomTags" : { | |
201 "Manufacturer" : "Philips Medical Systems", | |
202 "Modality" : "PT", | |
203 "NumberOfSlices" : "45", | |
204 "ProtocolName" : "CHU/Body_PET/CT___50", | |
205 "SeriesDate" : "20120716", | |
206 "SeriesDescription" : "[WB_CTAC] Body", | |
207 "SeriesInstanceUID" : "1.3.46.670589.28.2.12.30.26407.37145.2.2516.0.1342458737", | |
208 "SeriesNumber" : "587370", | |
209 "SeriesTime" : "171121", | |
210 "StationName" : "r054-svr" | |
211 }, | |
212 "ParentStudy" : "9ad2b0da-a406c43c-6e0df76d-1204b86f-78d12c15", | |
213 "Status" : "Complete", | |
214 "Type" : "Series" | |
215 } | |
216 | |
217 It can be seen that this series comes from a PET modality. Orthanc has | |
218 computed that this series should contain 45 instances. | |
219 | |
220 .. highlight:: bash | |
221 | |
222 So far, we have navigated from the patient level, to the study level, | |
223 and finally to the series level. There only remains the instance | |
224 level. Let us dump the content of one of the instances:: | |
225 | |
226 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4 | |
227 | |
228 .. highlight:: json | |
229 | |
230 The instance contains the following information:: | |
231 | |
232 { | |
233 "FileSize" : 70356, | |
234 "FileUuid" : "3fd265f0-c2b6-41a2-ace8-ae332db63e06", | |
235 "ID" : "e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4", | |
236 "IndexInSeries" : 6, | |
237 "MainDicomTags" : { | |
238 "ImageIndex" : "6", | |
239 "InstanceCreationDate" : "20120716", | |
240 "InstanceCreationTime" : "171344", | |
241 "InstanceNumber" : "6", | |
242 "SOPInstanceUID" : "1.3.46.670589.28.2.15.30.26407.37145.3.2116.39.1342458737" | |
243 }, | |
244 "ParentSeries" : "2cc6336f-2d4ae733-537b3ca3-e98184b1-ba494b35", | |
245 "Type" : "Instance" | |
246 } | |
247 | |
248 .. highlight:: bash | |
249 | |
250 The instance has the index 6 in the parent series. The instance is | |
251 stored as a raw DICOM file of 70356 bytes. You would download this | |
252 DICOM file using the following command:: | |
253 | |
254 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/file > Instance.dcm | |
255 | |
256 | |
257 Accessing the DICOM fields of an instance as a JSON file | |
258 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
259 | |
260 .. highlight:: bash | |
261 | |
262 When one gets to the instance level, you can retrieve the hierarchy of | |
263 all the DICOM tags of this instance as a JSON file:: | |
264 | |
265 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/simplified-tags | |
266 | |
267 .. highlight:: json | |
268 | |
269 Here is a excerpt of the Orthanc answer:: | |
270 | |
271 { | |
272 "ACR_NEMA_2C_VariablePixelDataGroupLength" : "57130", | |
273 "AccessionNumber" : null, | |
274 "AcquisitionDate" : "20120716", | |
275 "AcquisitionDateTime" : "20120716171219", | |
276 "AcquisitionTime" : "171219", | |
277 "ActualFrameDuration" : "3597793", | |
278 "AttenuationCorrectionMethod" : "CTAC-SG", | |
279 <...> | |
280 "PatientID" : "000000185", | |
281 "PatientName" : "Anonymous^Unknown", | |
282 "PatientOrientationCodeSequence" : [ | |
283 { | |
284 "CodeMeaning" : "recumbent", | |
285 "CodeValue" : "F-10450", | |
286 "CodingSchemeDesignator" : "99SDM", | |
287 "PatientOrientationModifierCodeSequence" : [ | |
288 { | |
289 "CodeMeaning" : "supine", | |
290 "CodeValue" : "F-10340", | |
291 "CodingSchemeDesignator" : "99SDM" | |
292 } | |
293 ] | |
294 } | |
295 ], | |
296 <...> | |
297 "StudyDescription" : "TestSUVce-TF", | |
298 "StudyID" : "23848", | |
299 "StudyInstanceUID" : "1.2.840.113704.1.111.7016.1342451220.40", | |
300 "StudyTime" : "171117", | |
301 "TypeOfDetectorMotion" : "NONE", | |
302 "Units" : "BQML", | |
303 "Unknown" : null, | |
304 "WindowCenter" : "1.496995e+04", | |
305 "WindowWidth" : "2.993990e+04" | |
306 } | |
307 | |
308 .. highlight:: bash | |
309 | |
310 If you need more detailed information about the type of the variables | |
311 or if you wish to use the hexadecimal indexes of DICOM tags, you are | |
312 free to use the following URL:: | |
313 | |
314 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/tags | |
315 | |
316 Accessing the raw DICOM fields of an instance | |
317 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
318 | |
319 .. highlight:: bash | |
320 | |
321 You also have the opportunity to access the raw value of the DICOM | |
322 tags of an instance, without going through a JSON file. Here is how | |
323 you would find the Patient Name of the instance:: | |
324 | |
325 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/content/0010-0010 | |
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326 Anonymous^Unknown |
0 | 327 |
328 The list of all the available tags for this instance can also be retrieved easily:: | |
329 | |
330 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/content | |
331 | |
332 It is also possible to recursively explore the sequences of tags:: | |
333 | |
334 $ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/content/0008-1250/0/0040-a170/0/0008-0104 | |
335 For Attenuation Correction | |
336 | |
337 The command above has opened the "0008-1250" tag that is a DICOM | |
338 sequence, taken its first child, opened its "0040-a170" tag that is | |
339 also a sequence, taken the first child of this child, and returned the | |
340 "0008-0104" DICOM tag. | |
341 | |
342 Downloading images | |
343 ^^^^^^^^^^^^^^^^^^ | |
344 | |
345 .. highlight:: bash | |
346 | |
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347 As :ref:`explained above <browsing-hierarchy>`, the raw DICOM file |
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348 corresponding to a single instance can be retrieved as follows:: |
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349 |
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350 $ curl http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/file > Instance.dcm |
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351 |
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352 It is also possible to download a preview PNG image that corresponds |
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353 to some DICOM instance:: |
0 | 354 |
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355 $ curl http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/preview > Preview.png |
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356 |
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357 The resulting image will be a standard graylevel PNG image (with 8 |
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358 bits per pixel) that can be opened by any painting software. The |
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359 dynamic range of the pixel data is stretched to the [0..255] range. |
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360 An equivalent JPEG image can be downloaded by setting the `HTTP header |
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361 <https://en.wikipedia.org/wiki/List_of_HTTP_header_fields>`__ |
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362 ``Accept`` to ``image/jpeg``:: |
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363 |
169 | 364 $ curl -H 'Accept: image/jpeg' http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/preview > Preview.jpg |
0 | 365 |
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366 If you don't want to stretch the dynamic range, and create a 8bpp or |
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367 16bpp PNG image, you can use the following URIs:: |
0 | 368 |
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369 $ curl http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/image-uint8 > full-8.png |
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370 $ curl http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/image-uint16 > full-16.png |
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371 |
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372 In these images, the values are cropped to the maximal value that can |
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373 be encoded by the target image format. The |
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374 ``/instances/{...}/image-int16`` is available as well to download |
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375 signed DICOM pixel data. |
0 | 376 |
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377 Since Orthanc 1.4.2, it is also possible to download such images in |
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378 the generic `PAM format |
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379 <https://en.wikipedia.org/wiki/Netpbm#PAM_graphics_format>`__:: |
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380 |
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381 $ curl -H 'Accept: image/x-portable-arbitrarymap' http://localhost:8042/instances/609665c0-c5198aa2-8632476b-a00e0de0-e9075d94/image-uint16 > full-16.pam |
0 | 382 |
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383 Users of Matlab or Octave can find related information :ref:`in the |
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384 dedicated section <matlab>`. |
0 | 385 |
380 | 386 Downloading studies |
387 ^^^^^^^^^^^^^^^^^^ | |
388 | |
389 .. highlight:: bash | |
390 | |
391 All instances of a study can be retrieved as a zip file as follows:: | |
392 | |
393 $ curl http://localhost:8042/studies/6b9e19d9-62094390-5f9ddb01-4a191ae7-9766b715/archive > Study.zip | |
394 | |
395 It is also possible to download a zipped DICOMDIR through:: | |
396 | |
397 $ curl http://localhost:8042/instances/6b9e19d9-62094390-5f9ddb01-4a191ae7-9766b715/media > Study.zip | |
398 | |
218 | 399 |
400 .. _peering: | |
401 | |
216 | 402 Sending resources to remote Orthanc over HTTP/HTTPS (through Orthanc peering) |
224
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403 ----------------------------------------------------------------------------- |
216 | 404 |
405 Orthanc can send its DICOM instances to remote Orthanc over HTTP/HTTPS through its Rest API. | |
406 This process can be triggered by the REST API. | |
407 | |
408 Configuration | |
409 ^^^^^^^^^^^^^ | |
410 | |
411 .. highlight:: json | |
412 | |
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413 You first have to declare the Url of the remote orthanc inside the |
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414 :ref:`configuration file <configuration>`. For instance, here is how |
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415 to declare a remote orthanc peer:: |
216 | 416 |
417 ... | |
418 "Peers" : { | |
419 "sample" : [ "http://localhost:8043" ], // short version | |
420 "sample2" : { // long version | |
421 "Url" : "http://localhost:8044", | |
422 "Username" : "alice", // optional | |
423 "Password" : "alicePassword", // optional | |
424 "HttpHeaders" : { "Token" : "Hello world" }, // optional | |
425 "CertificateFile" : "client.crt", // optional (only if using client certificate authentication) | |
426 "CertificateKeyFile" : "client.key", // optional (only if using client certificate authentication) | |
427 "CertificateKeyPassword" : "certpass" // optional (only if using client certificate authentication) | |
428 }, | |
429 ... | |
430 | |
431 .. highlight:: bash | |
432 | |
433 Such a configuration would enable Orthanc to connect to two other | |
434 Orthanc instances that listens on the | |
435 localhost on the port 8043 & 8044. The peers that are known to Orthanc | |
436 can be queried:: | |
437 | |
438 $ curl http://localhost:8042/peers?expand | |
439 | |
440 The peers can then be updated through the API too:: | |
441 | |
442 $ curl -v -X PUT http://localhost:8042/peers/sample -d '{"Url" : "http://127.0.0.1:8043"}' | |
443 | |
444 | |
445 Note that, by default, peers are stored in Orthanc configuration files | |
446 and are updated in Orthanc memory only. If you want your modifications | |
447 to be persistent, you should configure Orthanc to store its peers | |
448 in the database. This is done through this configuration:: | |
0 | 449 |
216 | 450 ... |
451 "OrthancPeersInDatabase" : true, | |
452 ... | |
453 | |
454 Sending One Resource | |
455 ^^^^^^^^^^^^^^^^^^^^ | |
456 | |
457 .. highlight:: bash | |
458 | |
459 Once you have identified the Orthanc identifier of the DICOM resource | |
460 that would like to send :ref:`as explained above <rest-access>`, you | |
461 would use the following command to send it:: | |
462 | |
463 $ curl -X POST http://localhost:8042/peers/sample/store -d c4ec7f68-9b162055-2c8c5888-5bf5752f-155ab19f | |
464 | |
465 The ``/sample/`` component of the URI corresponds to the identifier of | |
466 the remote modality, as specified above in the configuration file. | |
467 | |
468 Note that you can send isolated DICOM instances with this command, but | |
469 also entire patients, studies or series. It is possible to send multiple instances with a single POST | |
470 request:: | |
471 | |
472 $ 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"]' | |
473 | |
474 Note that the list of resources to be sent can include the | |
475 :ref:`Orthanc identifiers <orthanc-ids>` of entire patients, | |
476 studies or series as well. | |
477 | |
294 | 478 Testing connectivity with a remote peer |
479 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
480 | |
481 .. highlight:: bash | |
482 | |
483 In version 1.5.9+, we have introduced a route to retrieve the ``/system`` info from | |
484 a remote peer. This route can also be used to test the connectivity with that peer | |
485 without actually sending a DICOM resource.:: | |
486 | |
487 $ curl http://localhost:8042/peers/sample/system | |
488 | |
489 | |
216 | 490 Using HTTPS |
491 ^^^^^^^^^^^ | |
492 | |
493 If you're transfering medical data over internet, it is mandatory to use HTTPS. | |
494 | |
495 On the server side, we recommend to put Orthanc behing an :ref:`HTTPS server that will take care of the TLS <https>`. | |
496 | |
497 On the client side, in order for the client Orthanc to recognize the server certificate, you'll have to provide a path | |
498 to the CA (certification authority) certificates. This is done in the configuration file through this configurationg:: | |
499 | |
500 ... | |
501 "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt, | |
502 ... | |
503 | |
223 | 504 If you want your server to accept incoming connections for known hosts only, you can either: |
216 | 505 |
506 - configure a firewall to accept incoming connections from known IP addresses | |
507 - 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. | |
508 | |
509 | |
510 | |
511 | |
512 Sending resources to remote modalities (through DICOM) | |
513 ------------------------------------------------------ | |
0 | 514 |
515 Orthanc can send its DICOM instances to remote DICOM modalities (C-Store SCU). This process | |
516 can be triggered by the REST API. | |
517 | |
518 Configuration | |
519 ^^^^^^^^^^^^^ | |
520 | |
521 .. highlight:: json | |
522 | |
523 You first have to declare the AET, the IP address and the port number | |
524 of the remote modality inside the :ref:`configuration file | |
525 <configuration>`. For instance, here is how to declare a remote | |
526 modality:: | |
527 | |
528 ... | |
529 "DicomModalities" : { | |
212 | 530 "sample" : [ "ORTHANCA", "127.0.0.1", 2000 ], // short version |
531 "sample2" : { // long version | |
532 "AET" : "ORTHANCB", | |
533 "Port" : 2001, | |
534 "Host" : "127.0.0.1", | |
535 "Manufacturer" : "Generic", | |
536 "AllowEcho" : true, | |
537 "AllowFind" : true, | |
538 "AllowMove" : true, | |
539 "AllowStore" : true | |
540 } | |
0 | 541 }, |
542 ... | |
543 | |
544 .. highlight:: bash | |
545 | |
212 | 546 Such a configuration would enable Orthanc to connect to two DICOM |
547 stores (for instance, other Orthanc instances) that listens on the | |
548 localhost on the port 2000 & 2001. The modalities that are known to Orthanc | |
0 | 549 can be queried:: |
550 | |
212 | 551 $ curl http://localhost:8042/modalities?expand |
552 | |
553 The modalities can then be updated through the API too:: | |
554 | |
555 $ curl -v -X PUT http://localhost:8042/modalities/sample -d '{"AET" : "ORTHANCC", "Host": "127.0.0.1", "Port": 2002}' | |
556 | |
0 | 557 |
212 | 558 Note that, by default, modalities are stored in Orthanc configuration files |
559 and are updated in Orthanc memory only. If you want your modifications | |
560 to be persistent, you should configure Orthanc to store its modalities | |
561 in the database. This is done through this configuration:: | |
562 | |
563 ... | |
564 "DicomModalitiesInDatabase" : true, | |
565 ... | |
0 | 566 |
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567 |
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568 .. _rest-store-scu: |
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569 |
0 | 570 Sending One Resource |
571 ^^^^^^^^^^^^^^^^^^^^ | |
572 | |
573 .. highlight:: bash | |
574 | |
575 Once you have identified the Orthanc identifier of the DICOM resource | |
576 that would like to send :ref:`as explained above <rest-access>`, you | |
577 would use the following command to send it:: | |
578 | |
579 $ curl -X POST http://localhost:8042/modalities/sample/store -d c4ec7f68-9b162055-2c8c5888-5bf5752f-155ab19f | |
580 | |
581 The ``/sample/`` component of the URI corresponds to the identifier of | |
582 the remote modality, as specified above in the configuration file. | |
583 | |
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584 Note that you can send isolated DICOM instances with this command, but |
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585 also entire patients, studies or series. |
0 | 586 |
587 Bulk Store SCU | |
588 ^^^^^^^^^^^^^^ | |
589 | |
590 .. highlight:: bash | |
591 | |
592 Each time a POST request is made to ``/modalities/.../store``, a new | |
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593 DICOM association is possibly established. This may lead to a large |
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594 communication overhead if sending multiple isolated instances by |
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595 making one REST call for each of these instances. |
0 | 596 |
597 To circumvent this problem, you have 2 possibilities: | |
598 | |
599 1. Set the ``DicomAssociationCloseDelay`` option in the | |
600 :ref:`configuration file <configuration>` to a non-zero value. This | |
601 will keep the DICOM connection open for a certain amount of time, | |
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602 waiting for new instances to be routed. This is useful if |
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603 autorouting images :ref:`using Lua <lua-auto-routing>`. |
0 | 604 |
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605 2. It is possible to send multiple instances with a single POST |
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606 request (so-called "Bulk Store SCU", available from Orthanc |
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607 0.5.2):: |
0 | 608 |
609 $ 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"]' | |
610 | |
611 The list of the resources to be sent are given as a JSON array. In | |
612 this case, a single DICOM connection is used. `Sample code is | |
613 available | |
360 | 614 <https://hg.orthanc-server.com/orthanc/file/default/Resources/Samples/Python/HighPerformanceAutoRouting.py>`__. |
0 | 615 |
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616 Note that the list of resources to be sent can include the |
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617 :ref:`Orthanc identifiers <orthanc-ids>` of entire patients, |
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618 studies or series as well. |
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619 |
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620 |
0 | 621 |
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622 Performing Query/Retrieve and Find with REST |
138 | 623 -------------------------------------------- |
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624 |
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625 *Section contributed by Bryan Dearlove* |
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626 |
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627 Orthanc can be used to perform queries on the local Orthanc instance, |
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628 or on remote modalities through the REST API. |
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629 |
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630 To perform a query of a remote modality you must define the modality |
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631 within the :ref:`configuration file <configuration>` (See |
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632 Configuration section under Sending resources to remote modalities). |
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633 |
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634 |
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635 Performing Queries on Modalities |
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636 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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637 |
138 | 638 .. highlight:: bash |
639 | |
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640 To initiate a query you perform a POST command against the Modality |
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641 with the identifiers you are looking for. The the example below we are |
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642 performing a study level query against the modality sample for any |
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643 study descriptions with the word chest within it. This search is case |
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644 insensitive unless configured otherwise within the Orthanc |
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645 configuration file:: |
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646 |
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647 $ curl --request POST \ |
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648 --url http://localhost:8042/modalities/sample/query \ |
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649 --data '{"Level":"Study","Query": {"PatientID":"","StudyDescription":"*Chest*","PatientName":""}}' |
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650 |
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651 You might be interested in including the ``Normalize`` option to bypass |
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652 the normalization of the outgoing C-FIND queries. For instance, for |
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653 the ``InstitutionName`` to be included at the ``Study`` level, one would |
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654 run:: |
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655 |
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656 $ curl -v http://localhost:8042/modalities/sample/query -X POST -d \ |
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657 '{"Level":"Study","Query":{"InstitutionName":"a"},"Normalize":false}' |
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658 |
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659 .. highlight:: json |
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660 |
138 | 661 You will receive back an ID which can be used to retrieve more |
662 information with GET commands or C-Move requests with a POST Command:: | |
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663 |
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664 { |
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665 "ID": "5af318ac-78fb-47ff-b0b0-0df18b0588e0", |
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666 "Path": "/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0" |
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667 } |
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668 |
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669 |
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670 Additional Options |
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671 ^^^^^^^^^^^^^^^^^^ |
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672 |
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673 .. highlight:: json |
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674 |
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675 You can use patient identifiers by including the ``*`` within your |
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676 search. For example if you were searching for a name beginning with |
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677 ``Jones`` you can do:: |
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678 |
139 | 679 "PatientName":"Jones*" |
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680 |
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681 If you wanted to search for a name with the words ``Jo`` anywhere |
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682 within it you can do:: |
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683 |
139 | 684 "PatientName":"*Jo*" |
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685 |
138 | 686 To perform date searches you can specify within StudyDate a starting |
687 date and/or a before date. For example ``"StudyDate":"20180323-"`` | |
688 would search for all study dates after the specified date to | |
689 now. Doing ``"StudyDate":"20180323-20180325"`` would search for all | |
690 study dates between the specified date. | |
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691 |
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692 |
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693 Reviewing Level |
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694 ^^^^^^^^^^^^^^^ |
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695 |
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696 .. highlight:: bash |
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697 |
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698 :: |
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699 |
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700 $ curl --request GET --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/level |
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701 |
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702 Will retrieve the level with which the query was performed, Study, |
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703 Series or Instance. |
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704 |
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705 |
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706 Reviewing Modality |
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707 ^^^^^^^^^^^^^^^^^^ |
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708 |
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709 .. highlight:: bash |
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710 |
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711 :: |
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712 |
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713 $ curl --request GET --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/modality |
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714 |
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715 Will provide the modality name which the original query was performed against. |
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716 |
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717 |
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718 Reviewing Query |
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719 ^^^^^^^^^^^^^^^ |
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720 |
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721 .. highlight:: bash |
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722 |
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723 To retrieve information on what identifiers the query was originally |
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724 performed using you can use the query filter:: |
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725 |
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726 $ curl --request GET --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/query |
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727 |
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728 |
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729 Reviewing Query Answers |
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730 ^^^^^^^^^^^^^^^^^^^^^^^ |
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731 |
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732 .. highlight:: bash |
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733 |
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734 You are able to individually review each answer returned by performing |
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735 a GET with the answers parameter:: |
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736 |
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737 $ curl --request GET --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/answers |
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738 |
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739 You will get a JSON back with numbered identifiers for each answer you |
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740 received back. For example because we performed a Study level query we |
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741 received back 5 studies answers back. We are able to query each answer |
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742 for content details:: |
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743 |
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744 $ curl --request GET --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/answers/0/content |
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745 |
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746 If there are content items missing, you may add them by adding that |
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747 identifier to the original query. For example if we wanted Modalities |
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748 listed in this JSON answer in the initial query we would add to the |
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749 POST body: ``"ModalitiesInStudy":""`` |
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750 |
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751 |
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752 Performing Retrieve (C-Move) |
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753 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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754 |
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755 .. highlight:: bash |
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756 |
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757 You can perform a C-Move to retrieve all studies within the original |
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758 query using a post command and identifying the Modality (named in this |
207 | 759 example ``Orthanc``), to be one to in the POST contents:: |
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760 |
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761 $ curl --request POST --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/retrieve --data Orthanc |
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762 |
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763 You are also able to perform individual C-Moves for a content item by |
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764 specifying that individual content item:: |
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765 |
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766 $ curl --request POST --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/answers/0/retrieve --data Orthanc |
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767 |
207 | 768 If C-Moves take too long (for example, performing a C-Move of a big |
769 study), you may run the request in asynchronous fashion, which will | |
770 create a job in Orthanc:: | |
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771 |
207 | 772 $ curl --request POST --url http://localhost:8042/queries/5af318ac-78fb-47ff-b0b0-0df18b0588e0/retrieve \ |
773 --data '{"TargetAet":"Orthanc","Synchronous":false}' | |
774 | |
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775 |
207 | 776 .. highlight:: bash |
777 | |
778 The answer of this POST request is the job ID taking care of the C-Move:: | |
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779 |
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780 { |
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781 "ID" : "11541b16-e368-41cf-a8e9-3acf4061d238", |
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782 "Path" : "/jobs/11541b16-e368-41cf-a8e9-3acf4061d238" |
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783 } |
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784 |
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785 |
378
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786 .. _rest-find: |
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787 |
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788 Performing Finds within Orthanc |
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789 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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790 .. highlight:: bash |
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791 |
138 | 792 Performing a find within Orthanc is very similar to using Queries |
793 against DICOM modalities and the additional options listed above work | |
794 with find also. When performing a find, you will receive the Orthanc | |
795 ID's of all the matched items within your find. For example if you | |
796 perform a study level find and 5 Studies match you will receive 5 | |
797 study level Orthanc ID's in JSON format as a response:: | |
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798 |
138 | 799 $ curl --request POST --url http://localhost:8042/tools/find --data '{"Level":"Instance","Query":{"Modality":"CR","StudyDate":"20180323-","PatientID":"*"}}' |
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800 |
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801 Setting the ``Expand`` field to ``true`` in the POST body of the |
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802 query will automatically report details about each study:: |
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803 |
313 | 804 $ curl https://demo.orthanc-server.com/tools/find -d '{"Level":"Study","Query":{"PatientName":"KNIX"}}' |
805 [ | |
806 "b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0" | |
807 ] | |
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808 $ curl https://demo.orthanc-server.com/tools/find -d '{"Level":"Study","Query":{"PatientName":"KNIX"},"Expand":true}' |
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809 [ |
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810 { |
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811 "ID" : "b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0", |
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812 "IsStable" : true, |
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813 "LastUpdate" : "20180414T091528", |
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814 "MainDicomTags" : { |
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815 "InstitutionName" : "0ECJ52puWpVIjTuhnBA0um", |
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816 "ReferringPhysicianName" : "1", |
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817 "StudyDate" : "20070101", |
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818 "StudyDescription" : "Knee (R)", |
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819 "StudyID" : "1", |
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820 "StudyInstanceUID" : "1.2.840.113619.2.176.2025.1499492.7391.1171285944.390", |
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821 "StudyTime" : "120000.000000" |
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822 }, |
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823 "ParentPatient" : "6816cb19-844d5aee-85245eba-28e841e6-2414fae2", |
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824 "PatientMainDicomTags" : { |
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825 "PatientID" : "ozp00SjY2xG", |
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826 "PatientName" : "KNIX" |
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827 }, |
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828 "Series" : [ |
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829 "20b9d0c2-97d85e07-f4dbf4d2-f09e7e6a-0c19062e", |
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830 "edbfa0a9-fa2641d7-29514b1c-45881d0b-46c374bd", |
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831 "f2635388-f01d497a-15f7c06b-ad7dba06-c4c599fe", |
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832 "4d04593b-953ced51-87e93f11-ae4cf03c-25defdcd", |
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833 "5e343c3e-3633c396-03aefde8-ba0e08c7-9c8208d3", |
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834 "8ea120d7-5057d919-837dfbcc-ccd04e0f-7f3a94aa" |
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835 ], |
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836 "Type" : "Study" |
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837 } |
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838 ] |
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839 |
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840 |
138 | 841 |
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842 Additional Options |
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843 ^^^^^^^^^^^^^^^^^^ |
138 | 844 .. highlight:: json |
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845 |
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846 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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847 |
138 | 848 "Limit":4 |
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850 |
216 | 851 .. _changes: |
852 | |
0 | 853 Tracking changes |
854 ---------------- | |
855 | |
856 .. highlight:: bash | |
857 | |
858 Whenever Orthanc receives a new DICOM instance, this event is recorded | |
859 in the so-called "Changes Log". This enables remote scripts to react | |
860 to the arrival of new DICOM resources. A typical application is | |
861 **auto-routing**, where an external script waits for a new DICOM | |
862 instance to arrive into Orthanc, then forward this instance to another | |
863 modality. | |
864 | |
865 The Changes Log can be accessed by the following command:: | |
866 | |
867 $ curl http://localhost:8042/changes | |
868 | |
869 .. highlight:: json | |
870 | |
871 Here is a typical output:: | |
872 | |
873 { | |
874 "Changes" : [ | |
875 { | |
876 "ChangeType" : "NewInstance", | |
877 "Date" : "20130507T143902", | |
878 "ID" : "8e289db9-0e1437e1-3ecf395f-d8aae463-f4bb49fe", | |
879 "Path" : "/instances/8e289db9-0e1437e1-3ecf395f-d8aae463-f4bb49fe", | |
880 "ResourceType" : "Instance", | |
881 "Seq" : 921 | |
882 }, | |
883 { | |
884 "ChangeType" : "NewSeries", | |
885 "Date" : "20130507T143902", | |
886 "ID" : "cceb768f-e0f8df71-511b0277-07e55743-9ef8890d", | |
887 "Path" : "/series/cceb768f-e0f8df71-511b0277-07e55743-9ef8890d", | |
888 "ResourceType" : "Series", | |
889 "Seq" : 922 | |
890 }, | |
891 { | |
892 "ChangeType" : "NewStudy", | |
893 "Date" : "20130507T143902", | |
894 "ID" : "c4ec7f68-9b162055-2c8c5888-5bf5752f-155ab19f", | |
895 "Path" : "/studies/c4ec7f68-9b162055-2c8c5888-5bf5752f-155ab19f", | |
896 "ResourceType" : "Study", | |
897 "Seq" : 923 | |
898 }, | |
899 { | |
900 "ChangeType" : "NewPatient", | |
901 "Date" : "20130507T143902", | |
902 "ID" : "dc65762c-f476e8b9-898834f4-2f8a5014-2599bc94", | |
903 "Path" : "/patients/dc65762c-f476e8b9-898834f4-2f8a5014-2599bc94", | |
904 "ResourceType" : "Patient", | |
905 "Seq" : 924 | |
906 } | |
907 ], | |
908 "Done" : true, | |
909 "Last" : 924 | |
910 } | |
911 | |
912 This output corresponds to the receiving of one single DICOM instance | |
913 by Orthanc. It records that a new instance, a new series, a new study | |
914 and a new patient has been created inside Orthanc. Note that each | |
915 changes is labeled by a ``ChangeType``, a ``Date`` (in the `ISO format | |
25 | 916 <https://en.wikipedia.org/wiki/ISO_8601>`__), the location of the |
0 | 917 resource inside Orthanc, and a sequence number (``Seq``). |
918 | |
919 Note that this call is non-blocking. It is up to the calling program | |
920 to wait for the occurrence of a new event (by implementing a polling | |
921 loop). | |
922 | |
923 .. highlight:: bash | |
924 | |
925 This call only returns a fixed number of events, that can be changed | |
926 by using the ``limit`` option:: | |
927 | |
928 $ curl http://localhost:8042/changes?limit=100 | |
929 | |
930 The flag ``Last`` records the sequence number of the lastly returned | |
931 event. The flag ``Done`` is set to ``true`` if no further event has | |
932 occurred after this lastly returned event. If ``Done`` is set to | |
933 ``false``, further events are available and can be retrieved. This is | |
934 done by setting the ``since`` option that specifies from which | |
935 sequence number the changes must be returned:: | |
936 | |
937 $ curl 'http://localhost:8042/changes?limit=100&since=922' | |
938 | |
939 A `sample code in the source distribution | |
360 | 940 <https://hg.orthanc-server.com/orthanc/file/default/Resources/Samples/Python/ChangesLoop.py>`__ |
0 | 941 shows how to use this Changes API to implement a polling loop. |
942 | |
943 | |
944 Deleting resources from Orthanc | |
945 ------------------------------- | |
946 | |
947 .. highlight:: bash | |
948 | |
949 Deleting patients, studies, series or instances | |
950 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
951 | |
952 Deleting DICOM resources (i.e. patients, studies, series or instances) | |
953 from Orthanc is as simple as using a HTTP DELETE on the URI of this | |
954 resource. | |
955 | |
956 Concretely, you would first explore the resources that are stored in | |
957 Orthanc :ref:`as explained above <rest-access>`:: | |
958 | |
959 $ curl http://localhost:8042/patients | |
960 $ curl http://localhost:8042/studies | |
961 $ curl http://localhost:8042/series | |
962 $ curl http://localhost:8042/instances | |
963 | |
964 Secondly, once you have spotted the resources to be removed, you would | |
965 use the following command-line syntax to delete them:: | |
966 | |
967 $ curl -X DELETE http://localhost:8042/patients/dc65762c-f476e8b9-898834f4-2f8a5014-2599bc94 | |
968 $ curl -X DELETE http://localhost:8042/studies/c4ec7f68-9b162055-2c8c5888-5bf5752f-155ab19f | |
969 $ curl -X DELETE http://localhost:8042/series/cceb768f-e0f8df71-511b0277-07e55743-9ef8890d | |
970 $ curl -X DELETE http://localhost:8042/instances/8e289db9-0e1437e1-3ecf395f-d8aae463-f4bb49fe | |
971 | |
972 | |
973 Clearing log of changes | |
974 ^^^^^^^^^^^^^^^^^^^^^^^ | |
975 | |
976 :ref:`As described above <changes>`, Orthanc keeps track of all the | |
977 changes that occur in the DICOM store. This so-called "Changes Log" | |
978 is accessible at the following URI:: | |
979 | |
980 $ curl http://localhost:8042/changes | |
981 | |
982 To clear the content of the Changes Log, simply DELETE this URI:: | |
983 | |
984 $ curl -X DELETE http://localhost:8042/changes | |
985 | |
986 | |
155 | 987 Log of exported resources |
988 ^^^^^^^^^^^^^^^^^^^^^^^^^ | |
989 | |
990 For medical traceability, Orthanc can be configured to store a log of | |
991 all the resources that have been exported to remote modalities:: | |
0 | 992 |
993 $ curl http://localhost:8042/exports | |
994 | |
995 In auto-routing scenarios, it is important to prevent this log to grow | |
996 indefinitely as incoming instances are routed. You can either disable | |
997 this logging by setting the option ``LogExportedResources`` to ``false`` | |
998 in the :ref:`configuration file <configuration>`, or periodically | |
999 clear this log by DELETE-ing this URI:: | |
1000 | |
1001 $ curl -X DELETE http://localhost:8042/exports | |
1002 | |
155 | 1003 NB: Starting with Orthanc 1.4.0, the ``LogExportedResources`` is set |
1004 to ``false`` by default. If the logging is desired, set this option to | |
1005 ``true``. | |
1006 | |
0 | 1007 |
1008 Anonymization and modification | |
1009 ------------------------------ | |
1010 | |
1011 The process of anonymizing and modifying DICOM resources is | |
1012 :ref:`documented in a separate page <anonymization>`. | |
1013 | |
1014 | |
1015 Further reading | |
1016 --------------- | |
1017 | |
1018 The examples above have shown you the basic principles for driving an | |
1019 instance of Orthanc through its REST API. All the possibilities of the | |
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1020 API have not been described: |
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1021 |
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1022 * Advanced features of the REST API can be found on :ref:`another page |
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1023 <rest-advanced>`. |
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1024 * A :ref:`FAQ entry <rest-samples>` lists where you can find more |
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1025 advanced samples of the REST API of Orthanc. |
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1026 * The full documentation of the REST API is maintained as an online |
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1027 spreadsheet accessible from the `documentation part of the official |
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1028 Web site |
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1029 <https://www.orthanc-server.com/static.php?page=documentation>`__ |
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1030 (click on the *Reference of the REST API* button). |
275 | 1031 * A documentation of the REST API in the OpenAPI/Swagger format is |
1032 `available as work-in-progress <https://api.orthanc-server.com/>`__. |