Mercurial > hg > orthanc-book
annotate Sphinx/source/faq/features.rst @ 218:8bb11cd0f20f
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| author | amazy |
|---|---|
| date | Mon, 25 Feb 2019 19:01:45 +0100 |
| parents | a577963a2176 |
| children | 02399e86f046 |
| rev | line source |
|---|---|
| 0 | 1 Terminology of advanced features |
| 2 ================================ | |
| 3 | |
| 4 .. _peers: | |
| 5 | |
| 6 Peers | |
| 7 ----- | |
| 8 | |
| 9 An "Orthanc peer" is another instance of Orthanc, possibly running on | |
| 10 a remote computer. | |
| 11 | |
| 12 Contrarily to a "modality", it is possible to communicate with a peer | |
| 13 through the **HTTP/HTTPS protocol** (i.e. through the REST API of | |
| 14 Orthanc), and not through the DICOM protocol. This implies a much | |
| 15 easier configuration: It is only required to know the URL, the | |
| 16 username and the password to communicate with an Orthanc peer. This | |
| 17 contrasts with DICOM query/retrieve, that is quite complex and that | |
| 18 involves a lot of pitfalls (cf. the FAQ entry about :ref:`troubleshooting | |
| 19 DICOM communications <dicom>`) that can be bypassed if using HTTP. | |
| 20 | |
| 21 Furthermore, as HTTP(S) communications are generally not blocked by | |
| 22 firewalls (contrarily to the DICOM protocol that is inherently an | |
| 23 Intranet protocol and that often requires the setup of VPN tunnels), | |
| 24 it is much easier to setup communications of medical images through | |
| 218 | 25 the Internet with :ref:`Orthanc peers <peering>`. |
| 0 | 26 |
| 27 | |
| 28 .. _recycling: | |
| 29 | |
| 30 Recycling/Protection | |
| 31 -------------------- | |
| 32 | |
| 33 Because of its focus on low-end computers, Orthanc implements **disk | |
| 34 space recycling**: The patient that has been stored for the longest | |
| 35 time inside Orthanc can be automatically deleted when the disk space | |
| 36 used by Orthanc grows above a threshold, or when the number of stored | |
| 37 patients grows above a threshold. This feature enables the automated | |
| 106 | 38 control of the disk space dedicated to Orthanc. Note that pushing a |
| 39 new study for an existing patient will not change its position in the | |
| 40 recycling order. | |
| 0 | 41 |
| 42 Recycling is controlled by the ``MaximumStorageSize`` and the | |
| 43 ``MaximumPatientCount`` options in the :ref:`Orthanc configuration | |
| 106 | 44 file <configuration>`. Setting both these values to 0 will disable |
| 45 recycling. | |
| 0 | 46 |
| 47 It is possible to prevent important data from being automatically | |
| 48 recycled. This mechanism is called **protection**. Each patient can be | |
| 49 individually protected against recycling by using the | |
| 50 ``Unprotected/Protected`` switch that is available from Orthanc | |
| 51 Explorer. | |
| 52 | |
| 53 Note that protection is only available at the patient level. It | |
| 54 protects all the studies/series/instances of the patient against | |
| 55 recycling. The rationale is that we think it is important to keep | |
| 56 available all the data related to one patient. Unwillingly losing a | |
| 57 study/series that is part of the same patient might lead to a loss in | |
| 58 consistency with respect to the medical history of this patient. | |
| 59 | |
| 60 .. _compression: | |
| 61 | |
| 62 Compression | |
| 63 ----------- | |
| 64 | |
| 65 If your disk space is limited, besides :ref:`recycling`, you should | |
| 66 also consider using **disk space compression**. When compression is | |
| 67 enabled, Orthanc compresses the incoming DICOM instances on-the-fly | |
| 68 before writing them to the filesystem, using `zlib | |
| 25 | 69 <https://en.wikipedia.org/wiki/Zlib>`_. This is useful, because the |
| 0 | 70 images are often stored as raw, uncompressed arrays in DICOM |
| 71 instances: The size of a typical DICOM instance can hopefully be | |
| 72 divided by a factor 2 through lossless compression. This compression | |
| 73 process is transparent to the user, as Orthanc automatically | |
| 74 decompresses the file before sending it back to the external world. | |
| 75 | |
| 76 Compression is controlled by the ``StorageCompression`` option in the | |
| 77 :ref:`Orthanc configuration file <configuration>`. | |
| 78 | 78 |
| 79 | |
| 80 .. _metadata: | |
| 81 | |
| 92 | 82 Metadata & attachments |
| 83 ---------------------- | |
| 78 | 84 |
| 85 Metadata consists in an **associative key-value array** (mapping a | |
| 86 integer key in the range [0,65535] to a string value) that is | |
| 87 associated with each :ref:`DICOM resource <orthanc-ids>` stored inside | |
| 88 Orthanc (may it be a patient, a study, a series or a DICOM | |
| 89 instance). Metadata can be either referred to using the integer key, | |
| 90 or using a symbolic name (if configured). Metadata records | |
| 91 information that is not readily available in the DICOM tags. | |
| 92 | |
| 93 In spirit, the metadata mechanism is similar to the :ref:`attachment | |
| 94 mechanism <orthanc-storage>`. However, metadata is stored directly | |
| 95 inside the database, whereas attachments are stored as separate files | |
| 96 on the filesystem (the database only stores a reference to the | |
| 97 attachments). Choosing between metadata and attachments is a matter of | |
| 98 trade-off: Metadata must be kept small (as a rule of thumb, under 1KB) | |
| 99 and used if fast access is needed, whereas attachments can be used to | |
| 100 store arbitrarily large piece of data. | |
| 101 | |
| 79 | 102 Also note that metadata and attachments are only available for |
| 103 resources stored inside Orthanc. Once one DICOM instance leaves the | |
| 104 Orthanc ecosystem, its associated metadata and attachments are lost. | |
| 105 | |
| 78 | 106 |
| 107 Core metadata | |
| 108 ^^^^^^^^^^^^^ | |
| 109 | |
| 110 Here are the main metadata handled by the Orthanc core: | |
| 111 | |
| 112 * ``ReceptionDate`` records when a DICOM instance was received by | |
| 113 Orthanc. Similarly, ``LastUpdate`` records, for each | |
| 114 patient/study/series, the last time a DICOM instance was added to | |
| 115 this resource. | |
| 116 * ``RemoteAet`` records the AET of the modality that has sent some | |
| 117 DICOM instance to Orthanc. | |
| 118 * ``ModifiedFrom`` and ``AnonymizedFrom`` hold from which original | |
| 119 resource, a resource was modified or anonymized. The presence of | |
| 120 this metadata indicates that the resource is the result of a | |
| 121 modification or anonymization that was carried on by Orthanc. | |
| 122 * ``Origin`` records through which mechanism the instance was received | |
| 123 by Orthanc (may be ``Unknown``, ``DicomProtocol``, ``RestApi``, | |
| 124 ``Plugins``, or ``Lua``). | |
| 125 * ``IndexInSeries`` records the expected index of a DICOM instance | |
| 126 inside its parent series. Conversely, ``ExpectedNumberOfInstances`` | |
| 127 associates to each series, the number of DICOM instances this series | |
| 128 is expected to contain. | |
| 129 * Starting with Orthanc 1.2.0, ``TransferSyntax`` and ``SopClassUid`` | |
| 130 respectively stores the transfer syntax UID and the SOP class UID of | |
| 131 DICOM instances, in order to speed up the access to this | |
| 132 information. | |
| 133 | |
| 134 Metadata listed above are set privately by the Orthanc core. They are | |
| 135 **read-only** from the perspective of the end user, as Orthanc | |
| 136 internally relies on them. | |
| 137 | |
| 138 | |
| 139 User-defined metadata | |
| 140 ^^^^^^^^^^^^^^^^^^^^^ | |
| 141 | |
| 142 The metadata described above where handled by the core of Orthanc. | |
| 143 Orthanc users are however allowed to define their own **user-defined | |
| 144 metadata**. Such metadata are associated with an integer key that is | |
| 145 greater or equal to 1024 (whereas keys below 1023 are reserved for | |
| 146 core metadata). | |
| 147 | |
| 148 You can associate a symbolic name to user-defined metadata using the | |
| 149 ``UserMetadata`` option inside the :ref:`configuration of Orthanc | |
| 92 | 150 <configuration>`:: |
| 151 | |
| 152 "UserMetadata" : { | |
| 153 "SampleMetaData1" : 1024, | |
| 154 "SampleMetaData2" : 1025 | |
| 155 } | |
| 78 | 156 |
| 157 | |
| 158 Accessing metadata | |
| 159 ^^^^^^^^^^^^^^^^^^ | |
| 160 | |
| 161 .. highlight:: bash | |
| 162 | |
| 163 Metadata associated with one DICOM resource can be accessed through | |
| 80 | 164 the :ref:`REST API <rest>`, for instance:: |
| 78 | 165 |
| 166 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata | |
| 167 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/RemoteAet | |
| 92 | 168 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/SampleMetaData1 |
| 78 | 169 |
| 170 User-defined metadata can be modified by issuing a HTTP PUT against | |
| 171 the REST API:: | |
| 172 | |
| 173 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024 -X PUT -d 'hello' | |
| 174 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024 | |
| 175 hello | |
| 176 | |
| 177 | |
| 178 | |
| 92 | 179 .. _attachments: |
| 180 | |
| 181 User-defined attachments | |
| 182 ^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 183 | |
| 184 Orthanc users are allowed to define their own **user-defined attachments**. | |
| 185 Such attachments are associated with an integer key that is | |
| 186 greater or equal to 1024 (whereas keys below 1023 are reserved for | |
| 187 core attachments). | |
| 188 | |
| 189 You can associate a symbolic name to user-defined attachments using the | |
| 190 ``UserContentType`` option inside the :ref:`configuration of Orthanc | |
| 191 <configuration>`. Optionally, the user may specify a MIME content type | |
| 192 for the attachment:: | |
| 193 | |
| 194 "UserContentType" : { | |
| 195 "samplePdf" : [1024, "application/pdf"], | |
| 196 "sampleJson" : [1025, "application/json"], | |
| 197 "sampleRaw" : 1026 | |
| 198 } | |
| 199 | |
| 200 Accessing attachments | |
| 201 ^^^^^^^^^^^^^^^^^^^^^ | |
| 202 | |
| 203 .. highlight:: bash | |
| 204 | |
| 205 Attachments associated with one DICOM resource can be accessed through | |
| 206 the :ref:`REST API <rest>`, for instance:: | |
| 207 | |
| 208 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf/data | |
| 209 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleJson/data | |
| 210 | |
| 211 User-defined attachments can be modified by issuing a HTTP PUT against | |
| 212 the REST API:: | |
| 213 | |
| 214 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf -X PUT --data-binary @sample.pdf | |
| 215 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleRaw -X PUT -d 'raw data' | |
| 216 | |
| 217 | |
| 78 | 218 .. _registry: |
| 219 | |
| 220 Central registry of metadata and attachments | |
| 221 -------------------------------------------- | |
| 222 | |
| 223 Obviously, one must pay attention to the fact that different | |
| 224 applications might use the same key to store different user-defined | |
| 225 :ref:`metadata <metadata>`, which might result in incompatibilities | |
| 226 between such applications. Similarly, incompatibilities might show up | |
| 227 for user-defined :ref:`attachments <orthanc-storage>`. | |
| 228 | |
| 229 Developers of applications/plugins that use user-defined metadata or | |
| 230 attachments are therefore kindly invited to complete the **central | |
| 231 registry** below: | |
| 232 | |
| 233 * ``Metadata 4200`` is used by the plugin for :ref:`whole-slide imaging <wsi>`. | |
| 170 | 234 * ``Attachment 9997`` is used by the `Osimis WebViewer plugin <https://bitbucket.org/osimis/osimis-webviewer-plugin>`__ to store series information. |
| 131 | 235 * ``Attachment 9998`` is used by the `Osimis WebViewer plugin <https://bitbucket.org/osimis/osimis-webviewer-plugin>`__ to store instance information. |
|
95
065350232191
added reference to attachment ids used by the Osimis Web Viewer
amazy
parents:
92
diff
changeset
|
236 * ``Attachment 9999`` is used by the `Osimis WebViewer plugin <https://bitbucket.org/osimis/osimis-webviewer-plugin>`__ to store annotations. |
|
065350232191
added reference to attachment ids used by the Osimis Web Viewer
amazy
parents:
92
diff
changeset
|
237 * ``Attachments 10000-13999`` are used by the `Osimis WebViewer plugin <https://bitbucket.org/osimis/osimis-webviewer-plugin>`__ to store reduced quality images. |