Mercurial > hg > orthanc-book
annotate Sphinx/source/faq/features.rst @ 622:debcf6b6d070
dicom-as-json is now deprecated
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
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| date | Fri, 26 Feb 2021 10:03:21 +0100 |
| parents | 05a5a7369126 |
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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 | |
| 100 attachments). Choosing between metadata and attachments is a matter of | |
| 101 trade-off: Metadata must be kept small (as a rule of thumb, under 1KB) | |
| 102 and used if fast access is needed, whereas attachments can be used to | |
| 103 store arbitrarily large piece of data. | |
| 104 | |
| 79 | 105 Also note that metadata and attachments are only available for |
| 106 resources stored inside Orthanc. Once one DICOM instance leaves the | |
| 107 Orthanc ecosystem, its associated metadata and attachments are lost. | |
| 108 | |
| 78 | 109 |
| 110 Core metadata | |
| 111 ^^^^^^^^^^^^^ | |
| 112 | |
| 113 Here are the main metadata handled by the Orthanc core: | |
| 114 | |
| 115 * ``ReceptionDate`` records when a DICOM instance was received by | |
| 116 Orthanc. Similarly, ``LastUpdate`` records, for each | |
| 117 patient/study/series, the last time a DICOM instance was added to | |
| 118 this resource. | |
| 119 * ``RemoteAet`` records the AET of the modality that has sent some | |
| 120 DICOM instance to Orthanc. | |
| 121 * ``ModifiedFrom`` and ``AnonymizedFrom`` hold from which original | |
| 122 resource, a resource was modified or anonymized. The presence of | |
| 123 this metadata indicates that the resource is the result of a | |
| 124 modification or anonymization that was carried on by Orthanc. | |
| 125 * ``Origin`` records through which mechanism the instance was received | |
| 126 by Orthanc (may be ``Unknown``, ``DicomProtocol``, ``RestApi``, | |
| 127 ``Plugins``, or ``Lua``). | |
| 128 * ``IndexInSeries`` records the expected index of a DICOM instance | |
| 129 inside its parent series. Conversely, ``ExpectedNumberOfInstances`` | |
| 130 associates to each series, the number of DICOM instances this series | |
| 131 is expected to contain. | |
| 132 * Starting with Orthanc 1.2.0, ``TransferSyntax`` and ``SopClassUid`` | |
| 133 respectively stores the transfer syntax UID and the SOP class UID of | |
| 134 DICOM instances, in order to speed up the access to this | |
| 135 information. | |
| 136 | |
| 137 Metadata listed above are set privately by the Orthanc core. They are | |
| 138 **read-only** from the perspective of the end user, as Orthanc | |
| 139 internally relies on them. | |
| 140 | |
| 141 | |
| 142 User-defined metadata | |
| 143 ^^^^^^^^^^^^^^^^^^^^^ | |
| 144 | |
| 145 The metadata described above where handled by the core of Orthanc. | |
| 146 Orthanc users are however allowed to define their own **user-defined | |
| 147 metadata**. Such metadata are associated with an integer key that is | |
| 148 greater or equal to 1024 (whereas keys below 1023 are reserved for | |
| 149 core metadata). | |
| 150 | |
| 151 You can associate a symbolic name to user-defined metadata using the | |
| 152 ``UserMetadata`` option inside the :ref:`configuration of Orthanc | |
| 92 | 153 <configuration>`:: |
| 154 | |
| 155 "UserMetadata" : { | |
| 156 "SampleMetaData1" : 1024, | |
| 157 "SampleMetaData2" : 1025 | |
| 158 } | |
| 78 | 159 |
| 160 | |
| 161 Accessing metadata | |
| 162 ^^^^^^^^^^^^^^^^^^ | |
| 163 | |
| 164 .. highlight:: bash | |
| 165 | |
| 166 Metadata associated with one DICOM resource can be accessed through | |
| 80 | 167 the :ref:`REST API <rest>`, for instance:: |
| 78 | 168 |
| 169 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata | |
| 170 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/RemoteAet | |
| 92 | 171 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/SampleMetaData1 |
| 78 | 172 |
| 173 User-defined metadata can be modified by issuing a HTTP PUT against | |
| 174 the REST API:: | |
| 175 | |
| 176 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024 -X PUT -d 'hello' | |
| 177 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024 | |
| 178 hello | |
| 179 | |
| 180 | |
| 181 | |
| 92 | 182 .. _attachments: |
| 183 | |
| 184 User-defined attachments | |
| 185 ^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 186 | |
| 187 Orthanc users are allowed to define their own **user-defined attachments**. | |
| 188 Such attachments are associated with an integer key that is | |
| 189 greater or equal to 1024 (whereas keys below 1023 are reserved for | |
| 190 core attachments). | |
| 191 | |
| 192 You can associate a symbolic name to user-defined attachments using the | |
| 193 ``UserContentType`` option inside the :ref:`configuration of Orthanc | |
| 194 <configuration>`. Optionally, the user may specify a MIME content type | |
| 195 for the attachment:: | |
| 196 | |
| 197 "UserContentType" : { | |
| 198 "samplePdf" : [1024, "application/pdf"], | |
| 199 "sampleJson" : [1025, "application/json"], | |
| 200 "sampleRaw" : 1026 | |
| 201 } | |
| 202 | |
| 203 Accessing attachments | |
| 204 ^^^^^^^^^^^^^^^^^^^^^ | |
| 205 | |
| 206 .. highlight:: bash | |
| 207 | |
| 208 Attachments associated with one DICOM resource can be accessed through | |
| 209 the :ref:`REST API <rest>`, for instance:: | |
| 210 | |
| 211 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf/data | |
| 212 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleJson/data | |
| 213 | |
| 214 User-defined attachments can be modified by issuing a HTTP PUT against | |
| 215 the REST API:: | |
| 216 | |
| 217 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf -X PUT --data-binary @sample.pdf | |
| 218 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleRaw -X PUT -d 'raw data' | |
| 219 | |
| 220 | |
| 78 | 221 .. _registry: |
| 222 | |
| 223 Central registry of metadata and attachments | |
| 224 -------------------------------------------- | |
| 225 | |
| 226 Obviously, one must pay attention to the fact that different | |
| 227 applications might use the same key to store different user-defined | |
| 228 :ref:`metadata <metadata>`, which might result in incompatibilities | |
| 229 between such applications. Similarly, incompatibilities might show up | |
| 230 for user-defined :ref:`attachments <orthanc-storage>`. | |
| 231 | |
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232 Developers of applications/plugins that use user-defined metadata, |
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233 attachments or global properties (using |
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234 ``OrthancPluginSetGlobalProperty()``) are therefore kindly invited to |
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235 complete the **central registry** below: |
| 78 | 236 |
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237 * ``Attachment 1`` is used by the core of Orthanc to store the DICOM |
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238 file associated with one instance. |
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239 * ``Attachment 2`` was used by Orthanc <= 1.9.0 to cache the so-called |
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240 ``DICOM-as-JSON`` information (as returned by the |
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241 ``/instances/.../tags`` URI in the :ref:`REST API <rest>`) in order |
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242 to speed up subsequent requests to the same URI. This attachment is |
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243 not automatically generated anymore starting with Orthanc 1.9.1, in |
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244 order to improve performance (creating two files for each DICOM |
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245 instance has a cost) and consistency (if the DICOM dictionary gets |
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246 modified in the future). |
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247 * ``Attachment 3`` is used since Orthanc 1.9.1 to store the DICOM |
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248 instance until the ``Pixel Data (7fe0,0010)`` tag, if the global |
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249 configuration option ``StorageCompression`` is ``true``, or if the |
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250 storage area plugin doesn't support range reads. This allows to |
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251 avoid downloading the full DICOM instance if not necessary. |
| 359 | 252 * ``Attachment 9997`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store series information. |
| 253 * ``Attachment 9998`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store instance information. | |
| 254 * ``Attachment 9999`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store annotations. | |
| 255 * ``Attachments 10000-13999`` are used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store reduced quality images. | |
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256 * ``Global property 5467`` is used by the Osimis Cloud plugin. |
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257 * ``Global property 5468`` is used by the :ref:`DICOMweb plugin <dicomweb>` to store the DICOMweb servers into the Orthanc database. |
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258 * ``Metadata 4200`` is used by the plugin for :ref:`whole-slide imaging <wsi>` with version <= 0.7. |
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259 * ``Metadata 4201`` is used by the plugin for :ref:`whole-slide imaging <wsi>` with version >= 1.0. |
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260 |
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261 |
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262 Jobs |
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263 ---- |
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264 |
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265 Check out the :ref:`advanced features of the REST API <jobs>`. |
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266 |