Mercurial > hg > orthanc-book
annotate Sphinx/source/faq/features.rst @ 838:6afc236cd60a
dicom-web & main-dicom-tags
author | Alain Mazy <am@osimis.io> |
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date | Thu, 05 May 2022 12:27:09 +0200 |
parents | 66ff2f30afcc |
children | c29ac12e3160 |
rev | line source |
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0 | 1 Terminology of advanced features |
2 ================================ | |
3 | |
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4 .. contents:: |
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5 :depth: 3 |
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6 |
0 | 7 .. _peers: |
8 | |
9 Peers | |
10 ----- | |
11 | |
12 An "Orthanc peer" is another instance of Orthanc, possibly running on | |
13 a remote computer. | |
14 | |
15 Contrarily to a "modality", it is possible to communicate with a peer | |
16 through the **HTTP/HTTPS protocol** (i.e. through the REST API of | |
17 Orthanc), and not through the DICOM protocol. This implies a much | |
18 easier configuration: It is only required to know the URL, the | |
19 username and the password to communicate with an Orthanc peer. This | |
20 contrasts with DICOM query/retrieve, that is quite complex and that | |
21 involves a lot of pitfalls (cf. the FAQ entry about :ref:`troubleshooting | |
22 DICOM communications <dicom>`) that can be bypassed if using HTTP. | |
23 | |
24 Furthermore, as HTTP(S) communications are generally not blocked by | |
25 firewalls (contrarily to the DICOM protocol that is inherently an | |
26 Intranet protocol and that often requires the setup of VPN tunnels), | |
27 it is much easier to setup communications of medical images through | |
218 | 28 the Internet with :ref:`Orthanc peers <peering>`. |
0 | 29 |
30 | |
31 .. _recycling: | |
32 | |
33 Recycling/Protection | |
34 -------------------- | |
35 | |
36 Because of its focus on low-end computers, Orthanc implements **disk | |
37 space recycling**: The patient that has been stored for the longest | |
38 time inside Orthanc can be automatically deleted when the disk space | |
39 used by Orthanc grows above a threshold, or when the number of stored | |
40 patients grows above a threshold. This feature enables the automated | |
278 | 41 control of the disk space dedicated to Orthanc. Note that each time |
42 a new instance is received for an existing patient, the patient will | |
43 be marked as the most recent one in the recycling order. | |
0 | 44 |
45 Recycling is controlled by the ``MaximumStorageSize`` and the | |
46 ``MaximumPatientCount`` options in the :ref:`Orthanc configuration | |
106 | 47 file <configuration>`. Setting both these values to 0 will disable |
48 recycling. | |
0 | 49 |
50 It is possible to prevent important data from being automatically | |
51 recycled. This mechanism is called **protection**. Each patient can be | |
52 individually protected against recycling by using the | |
53 ``Unprotected/Protected`` switch that is available from Orthanc | |
54 Explorer. | |
55 | |
56 Note that protection is only available at the patient level. It | |
57 protects all the studies/series/instances of the patient against | |
58 recycling. The rationale is that we think it is important to keep | |
59 available all the data related to one patient. Unwillingly losing a | |
60 study/series that is part of the same patient might lead to a loss in | |
61 consistency with respect to the medical history of this patient. | |
62 | |
63 .. _compression: | |
64 | |
65 Compression | |
66 ----------- | |
67 | |
68 If your disk space is limited, besides :ref:`recycling`, you should | |
69 also consider using **disk space compression**. When compression is | |
70 enabled, Orthanc compresses the incoming DICOM instances on-the-fly | |
71 before writing them to the filesystem, using `zlib | |
25 | 72 <https://en.wikipedia.org/wiki/Zlib>`_. This is useful, because the |
0 | 73 images are often stored as raw, uncompressed arrays in DICOM |
74 instances: The size of a typical DICOM instance can hopefully be | |
75 divided by a factor 2 through lossless compression. This compression | |
76 process is transparent to the user, as Orthanc automatically | |
77 decompresses the file before sending it back to the external world. | |
78 | |
79 Compression is controlled by the ``StorageCompression`` option in the | |
80 :ref:`Orthanc configuration file <configuration>`. | |
78 | 81 |
82 | |
83 .. _metadata: | |
84 | |
92 | 85 Metadata & attachments |
86 ---------------------- | |
78 | 87 |
88 Metadata consists in an **associative key-value array** (mapping a | |
89 integer key in the range [0,65535] to a string value) that is | |
90 associated with each :ref:`DICOM resource <orthanc-ids>` stored inside | |
91 Orthanc (may it be a patient, a study, a series or a DICOM | |
92 instance). Metadata can be either referred to using the integer key, | |
93 or using a symbolic name (if configured). Metadata records | |
94 information that is not readily available in the DICOM tags. | |
95 | |
96 In spirit, the metadata mechanism is similar to the :ref:`attachment | |
97 mechanism <orthanc-storage>`. However, metadata is stored directly | |
98 inside the database, whereas attachments are stored as separate files | |
99 on the filesystem (the database only stores a reference to the | |
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100 attachments). Choosing between metadata and attachments is most often |
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101 a matter of trade-off: Metadata must be kept small (as a rule of |
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102 thumb, under 1KB) and used if fast access is needed, whereas |
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103 attachments can be used to store arbitrarily large piece of data. |
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104 |
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105 However, pay attention to the fact that metadata must be UTF-8 strings |
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106 terminated by the ``\0`` character. If you need to store arbitrary |
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107 binary objects, use an attachment or use `Base64 encoding |
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108 <https://en.wikipedia.org/wiki/Base64>`__. |
78 | 109 |
79 | 110 Also note that metadata and attachments are only available for |
111 resources stored inside Orthanc. Once one DICOM instance leaves the | |
112 Orthanc ecosystem, its associated metadata and attachments are lost. | |
113 | |
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114 .. _metadata-core: |
78 | 115 |
116 Core metadata | |
117 ^^^^^^^^^^^^^ | |
118 | |
119 Here are the main metadata handled by the Orthanc core: | |
120 | |
121 * ``ReceptionDate`` records when a DICOM instance was received by | |
122 Orthanc. Similarly, ``LastUpdate`` records, for each | |
123 patient/study/series, the last time a DICOM instance was added to | |
124 this resource. | |
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125 * ``RemoteAET`` records the AET of the modality that has sent some |
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126 DICOM instance to Orthanc using the DICOM protocol. |
78 | 127 * ``ModifiedFrom`` and ``AnonymizedFrom`` hold from which original |
128 resource, a resource was modified or anonymized. The presence of | |
129 this metadata indicates that the resource is the result of a | |
130 modification or anonymization that was carried on by Orthanc. | |
131 * ``Origin`` records through which mechanism the instance was received | |
132 by Orthanc (may be ``Unknown``, ``DicomProtocol``, ``RestApi``, | |
133 ``Plugins``, or ``Lua``). | |
134 * ``IndexInSeries`` records the expected index of a DICOM instance | |
135 inside its parent series. Conversely, ``ExpectedNumberOfInstances`` | |
136 associates to each series, the number of DICOM instances this series | |
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137 is expected to contain. This information is :ref:`not always |
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138 available <series-completion>`. |
78 | 139 * Starting with Orthanc 1.2.0, ``TransferSyntax`` and ``SopClassUid`` |
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140 respectively stores the `transfer syntax UID |
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141 <http://dicom.nema.org/medical/dicom/current/output/html/part05.html#chapter_10>`__ |
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142 and the `SOP class UID |
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143 <http://dicom.nema.org/medical/dicom/current/output/chtml/part02/sect_A.1.html>`__ |
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144 of DICOM instances, in order to speed up the access to this |
78 | 145 information. |
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146 * ``RemoteIP`` (new in Orthanc 1.4.0): The IP address of the remote |
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147 SCU (for REST API and DICOM protocol). |
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148 * ``CalledAET`` (new in Orthanc 1.4.0): The AET that was called by the |
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149 SCU, which normally matches the AET of Orthanc (for DICOM protocol). |
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150 * ``HttpUsername`` (new in Orthanc 1.4.0): The username that created |
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151 the instance (for REST API). |
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152 * ``PixelDataOffset`` (new in Orthanc 1.9.1): Offset (in bytes) of the |
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153 Pixel Data DICOM tag in the DICOM file, if available. |
838 | 154 * ``MainDicomTagsSignature`` (new in Orthanc 1.11.0 - not released yet): |
155 The list of :ref:`MainDicomTags <main-dicom-tags>` that have been | |
156 saved in DB for this resource. | |
78 | 157 |
158 Metadata listed above are set privately by the Orthanc core. They are | |
159 **read-only** from the perspective of the end user, as Orthanc | |
160 internally relies on them. | |
161 | |
162 | |
163 User-defined metadata | |
164 ^^^^^^^^^^^^^^^^^^^^^ | |
165 | |
166 The metadata described above where handled by the core of Orthanc. | |
167 Orthanc users are however allowed to define their own **user-defined | |
168 metadata**. Such metadata are associated with an integer key that is | |
169 greater or equal to 1024 (whereas keys below 1023 are reserved for | |
170 core metadata). | |
171 | |
172 You can associate a symbolic name to user-defined metadata using the | |
173 ``UserMetadata`` option inside the :ref:`configuration of Orthanc | |
92 | 174 <configuration>`:: |
175 | |
176 "UserMetadata" : { | |
177 "SampleMetaData1" : 1024, | |
178 "SampleMetaData2" : 1025 | |
179 } | |
78 | 180 |
181 | |
182 Accessing metadata | |
183 ^^^^^^^^^^^^^^^^^^ | |
184 | |
185 .. highlight:: bash | |
186 | |
187 Metadata associated with one DICOM resource can be accessed through | |
80 | 188 the :ref:`REST API <rest>`, for instance:: |
78 | 189 |
190 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata | |
838 | 191 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata?expand |
78 | 192 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/RemoteAet |
92 | 193 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/SampleMetaData1 |
78 | 194 |
195 User-defined metadata can be modified by issuing a HTTP PUT against | |
196 the REST API:: | |
197 | |
198 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024 -X PUT -d 'hello' | |
199 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024 | |
200 hello | |
201 | |
202 | |
203 | |
92 | 204 .. _attachments: |
205 | |
206 User-defined attachments | |
207 ^^^^^^^^^^^^^^^^^^^^^^^^ | |
208 | |
209 Orthanc users are allowed to define their own **user-defined attachments**. | |
210 Such attachments are associated with an integer key that is | |
211 greater or equal to 1024 (whereas keys below 1023 are reserved for | |
212 core attachments). | |
213 | |
214 You can associate a symbolic name to user-defined attachments using the | |
215 ``UserContentType`` option inside the :ref:`configuration of Orthanc | |
216 <configuration>`. Optionally, the user may specify a MIME content type | |
217 for the attachment:: | |
218 | |
219 "UserContentType" : { | |
220 "samplePdf" : [1024, "application/pdf"], | |
221 "sampleJson" : [1025, "application/json"], | |
222 "sampleRaw" : 1026 | |
223 } | |
224 | |
225 Accessing attachments | |
226 ^^^^^^^^^^^^^^^^^^^^^ | |
227 | |
228 .. highlight:: bash | |
229 | |
230 Attachments associated with one DICOM resource can be accessed through | |
231 the :ref:`REST API <rest>`, for instance:: | |
232 | |
233 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf/data | |
234 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleJson/data | |
235 | |
236 User-defined attachments can be modified by issuing a HTTP PUT against | |
237 the REST API:: | |
238 | |
239 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf -X PUT --data-binary @sample.pdf | |
240 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleRaw -X PUT -d 'raw data' | |
660 | 241 |
242 | |
243 DICOM-as-JSON attachments | |
244 ^^^^^^^^^^^^^^^^^^^^^^^^^ | |
245 | |
246 In the version of Orthanc <= 1.9.0, whenever Orthanc receives a DICOM | |
247 file, it pre-computes a JSON summary of its DICOM tags, and caches | |
248 this JSON file as an attachment to the DICOM instance (accessible at | |
249 the ``/instances/{...}/attachments/dicom-as-json/`` URI). This | |
250 attachment is used as a cache to seep up future accesses to | |
251 ``/instances/.../tags``, lookups using ``/tools/find`` or C-FIND | |
252 queries. | |
253 | |
254 This caching might cause issues if the dictionary of DICOM tags is | |
255 subsequently modified, which implies that the cached JSON file does | |
256 not perfectly match the new dictionary. | |
257 | |
258 .. highlight:: bash | |
259 | |
260 Since Orthanc 1.2.0, you can force the re-generation of the cached | |
261 JSON file by DELETE-ing it, for instance:: | |
262 | |
263 $ curl -X DELETE http://localhost:8042/instances/301896f2-1416807b-3e05dcce-ff4ce9bb-a6138832/attachments/dicom-as-json | |
264 | |
265 .. highlight:: text | |
266 | |
267 The next time you open this particular instance with Orthanc Explorer, | |
268 you will see messages in the Orthanc logs (in verbose mode) stating | |
269 that the Orthanc server has reconstructed the JSON summary, which will | |
270 match the new content of the dictionary:: | |
271 | |
272 I0222 08:56:00.923070 FilesystemStorage.cpp:155] Reading attachment "2309c47b-1cbd-4601-89b5-1be1ad80382c" of "DICOM" content type | |
273 I0222 08:56:00.923394 ServerContext.cpp:401] Reconstructing the missing DICOM-as-JSON summary for instance: 301896f2-1416807b-3e05dcce-ff4ce9bb-a6138832 | |
274 I0222 08:56:00.929117 ServerContext.cpp:540] Adding attachment dicom-as-json to resource 301896f2-1416807b-3e05dcce-ff4ce9bb-a6138832 | |
275 I0222 08:56:00.929425 FilesystemStorage.cpp:118] Creating attachment "3c830b66-8a00-42f0-aa3a-5e37b4a8b5a4" of "JSON summary of DICOM" type (size: 1MB) | |
276 | |
277 These DICOM-as-JSON attachments are not automatically generated | |
278 anymore starting with Orthanc 1.9.1. | |
279 | |
92 | 280 |
78 | 281 .. _registry: |
282 | |
283 Central registry of metadata and attachments | |
284 -------------------------------------------- | |
285 | |
286 Obviously, one must pay attention to the fact that different | |
287 applications might use the same key to store different user-defined | |
288 :ref:`metadata <metadata>`, which might result in incompatibilities | |
289 between such applications. Similarly, incompatibilities might show up | |
290 for user-defined :ref:`attachments <orthanc-storage>`. | |
291 | |
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292 Developers of applications/plugins that use user-defined metadata, |
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293 attachments or global properties (using |
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294 ``OrthancPluginSetGlobalProperty()``) are therefore kindly invited to |
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295 complete the **central registry** below: |
78 | 296 |
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297 * ``Attachment 1`` is used by the core of Orthanc to store the DICOM |
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298 file associated with one instance. |
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299 * ``Attachment 2`` was used by Orthanc <= 1.9.0 to cache the so-called |
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300 ``DICOM-as-JSON`` information (as returned by the |
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301 ``/instances/.../tags`` URI in the :ref:`REST API <rest>`) in order |
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302 to speed up subsequent requests to the same URI. This attachment is |
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303 not automatically generated anymore starting with Orthanc 1.9.1, in |
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304 order to improve performance (creating two files for each DICOM |
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305 instance has a cost) and consistency (if the DICOM dictionary gets |
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306 modified in the future). |
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307 * ``Attachment 3`` is used since Orthanc 1.9.1 to store the DICOM |
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308 instance until the ``Pixel Data (7fe0,0010)`` tag, if the global |
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309 configuration option ``StorageCompression`` is ``true``, or if the |
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310 storage area plugin doesn't support range reads. This allows to |
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311 avoid downloading the full DICOM instance if not necessary. |
359 | 312 * ``Attachment 9997`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store series information. |
313 * ``Attachment 9998`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store instance information. | |
314 * ``Attachment 9999`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store annotations. | |
315 * ``Attachments 10000-13999`` are used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store reduced quality images. | |
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316 * ``Global property 1025`` is used by default by the Housekeeper plugin. |
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317 * ``Global property 5467`` is used by the Osimis Cloud plugin. |
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318 * ``Global property 5468`` is used by the :ref:`DICOMweb plugin <dicomweb>` to store the DICOMweb servers into the Orthanc database. |
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319 * ``Metadata 4200`` is used by the plugin for :ref:`whole-slide imaging <wsi>` with version <= 0.7. |
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320 * ``Metadata 4201`` is used by the plugin for :ref:`whole-slide imaging <wsi>` with version >= 1.0. |
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321 |
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322 |
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323 Jobs |
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324 ---- |
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325 |
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326 Check out the :ref:`advanced features of the REST API <jobs>`. |
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327 |
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328 |
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329 |
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330 .. _stable-resources: |
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331 |
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332 Stable resources |
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333 ---------------- |
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334 |
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335 A DICOM resource (patient, study or series) is referred to as |
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336 **stable** if it has not received any new instance for a certain |
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337 amount of time. |
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338 |
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339 This amount of time is configured by the the option ``StableAge`` in |
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340 the :ref:`configuration file <configuration>`. |
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341 |
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342 When some resource becomes stable, an event is generated as a log |
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343 entry in the ``/changes`` :ref:`URI in the REST API <changes>`, a |
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344 :ref:`Lua callback <lua-callbacks>` is invoked, the callback function |
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345 registered by ``OrthancPluginRegisterOnChangeCallback()`` in |
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346 :ref:`C/C++ plugins <creating-plugins>` is executed, as well as the |
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347 :ref:`Python callback <python-changes>` registered by |
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348 ``orthanc.RegisterOnChangeCallback()``. |
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349 |
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350 The ``IsStable`` field is also available to get the status of an |
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351 individual patient/study/series using the REST API of Orthanc. |
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352 |
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353 In the multiple readers/writers scenario enabled since Orthanc 1.9.2, |
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354 each Orthanc server is considered separately: The "stable" information |
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355 is monitored by threads inside the Orthanc process, and is **not** |
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356 shared in the database. In other words, the "stable" information is |
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357 local to the Orthanc server that is queried. Synchronization between |
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358 multiple readers/writers must be implemented at a higher level |
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359 (e.g. using a distributed `message-broker system |
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360 <https://en.wikipedia.org/wiki/Message_broker>`__ such as RabbitMQ |
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361 that is fed by an Orthanc plugin). |
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362 |
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363 |
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364 .. _revisions: |
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365 |
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366 Revisions |
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367 --------- |
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368 |
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369 .. highlight:: bash |
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370 |
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371 Higher-level applications built on the top of Orthanc might have to |
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372 modify metadata and/or attachments. This can cause concurrency |
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373 problems if multiple clients modify the same metadata/attachment |
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374 simultaneously. To avoid such problems, Orthanc implements a so-called |
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375 **revision mechanism** to protect from concurrent modifications. |
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376 |
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377 The revision mechanism is optional, was introduced in **Orthanc |
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378 1.9.2** and must be enabled by setting :ref:`configuration option |
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379 <configuration>` ``CheckRevisions`` to ``true``. It is strongly |
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380 inspired by the `CouchDB API |
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381 <https://docs.couchdb.org/en/stable/api/document/common.html>`__. |
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382 |
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383 When the revision mechanism is enabled, each metadata and attachment |
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384 is associated with a **revision number**. Whenever one sets a metadata |
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385 for the first time using a ``PUT`` query, this revision number can be |
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386 found in the HTTP header ``ETag`` that is reported by Orthanc:: |
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387 |
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388 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X PUT -d 'Hello' |
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389 [...] |
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390 < ETag: "0" |
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391 |
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392 Any ``GET`` query will also return the current value of ``ETag``:: |
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393 |
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394 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 |
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395 [...] |
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396 < ETag: "0" |
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397 |
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398 If one needs to subsequently modify or delete this metadata, the HTTP |
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399 client must set this value of ``ETag`` into the ``If-Match`` HTTP |
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400 header:: |
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401 |
645 | 402 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X PUT -d 'Hello 2' -H 'If-Match: "0"' |
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403 [...] |
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404 < ETag: "1" |
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405 |
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406 Note how this second call has incremented the value of ``ETag``: This |
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407 is the new revision number to be used in future updates. If a bad |
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408 revision number is provided, the HTTP error ``409 Conflict`` is |
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409 generated:: |
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410 |
645 | 411 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X PUT -d 'Hello 3' -H 'If-Match: "0"' |
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412 [...] |
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413 < HTTP/1.1 409 Conflict |
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414 |
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415 Such a ``409`` error must be handled by the higher-level |
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416 application. The revision number must similarly be given if deleting a |
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417 metadata/attachment:: |
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418 |
645 | 419 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X DELETE -H 'If-Match: "1"' |
643
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420 [...] |
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421 < HTTP/1.1 200 OK |
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422 |
645 | 423 Check out the `OpenAPI reference <https://api.orthanc-server.com/>`__ |
424 of the REST API of Orthanc for more information. | |
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425 |
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426 **Warning:** The database index back-end must support revisions. As of |
750 | 427 writing, only the **PostgreSQL plugins** in versions above 4.0 and the |
428 **ODBC plugins** implement support for revisions. | |
672
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429 |
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430 |
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431 Synchronous vs. asynchronous C-MOVE SCP |
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432 --------------------------------------- |
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433 |
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434 The :ref:`C-MOVE SCP <dicom-move>` of Orthanc (i.e. the component of |
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435 the Orthanc server that is responsible for routing DICOM instances |
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436 from Orthanc to other modalities) can be configured to run either in |
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437 synchronous or in asynchronous mode, depending on the value of the |
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438 ``SynchronousCMove`` :ref:`configuration option <configuration>`: |
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439 |
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440 * In **synchronous mode** (if ``SynchronousCMove`` is ``true``), |
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441 Orthanc will interleave its C-STORE SCU commands with the C-MOVE |
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442 instructions received from the remote modality. In other words, |
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443 Orthanc immediately sends the DICOM instances while it handles the |
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444 C-MOVE command from the remote modality. This mode is for |
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445 compatibility with simple DICOM client software that considers that |
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446 when its C-MOVE SCU is over, it should have received all the |
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447 instructed DICOM instances. This is the default behavior of Orthanc. |
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448 |
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449 * In **asynchronous mode** (if ``SynchronousCMove`` is ``false``), |
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450 Orthanc will queue the C-MOVE instructions and :ref:`creates a job |
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451 <jobs-synchronicity>` that will issue the C-STORE SCU commands |
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452 afterward. This behavior is typically encountered in hospital-wide |
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453 PACS systems, but requires the client software to be more complex as |
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454 it must be handle the delay between its C-MOVE queries and the |
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455 actual reception of the DICOM instances through C-STORE. |
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456 |
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457 As a consequence, by setting ``SynchronousCMove`` to ``true``, Orthanc |
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458 can be used as a buffer that enables communications between a simple |
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459 C-MOVE client and a hospital-wide PACS. This can be interesting to |
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460 introduce compatibility with specialized image processing |
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461 applications. |