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author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 24 Apr 2021 10:45:36 +0200
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1 Terminology of advanced features
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2 ================================
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3
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4 .. contents::
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5 :depth: 3
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6
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7 .. _peers:
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8
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9 Peers
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10 -----
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11
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12 An "Orthanc peer" is another instance of Orthanc, possibly running on
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13 a remote computer.
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14
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15 Contrarily to a "modality", it is possible to communicate with a peer
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16 through the **HTTP/HTTPS protocol** (i.e. through the REST API of
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17 Orthanc), and not through the DICOM protocol. This implies a much
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18 easier configuration: It is only required to know the URL, the
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19 username and the password to communicate with an Orthanc peer. This
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20 contrasts with DICOM query/retrieve, that is quite complex and that
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21 involves a lot of pitfalls (cf. the FAQ entry about :ref:`troubleshooting
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22 DICOM communications <dicom>`) that can be bypassed if using HTTP.
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23
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24 Furthermore, as HTTP(S) communications are generally not blocked by
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25 firewalls (contrarily to the DICOM protocol that is inherently an
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26 Intranet protocol and that often requires the setup of VPN tunnels),
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27 it is much easier to setup communications of medical images through
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28 the Internet with :ref:`Orthanc peers <peering>`.
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31 .. _recycling:
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33 Recycling/Protection
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34 --------------------
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35
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36 Because of its focus on low-end computers, Orthanc implements **disk
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37 space recycling**: The patient that has been stored for the longest
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38 time inside Orthanc can be automatically deleted when the disk space
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39 used by Orthanc grows above a threshold, or when the number of stored
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40 patients grows above a threshold. This feature enables the automated
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41 control of the disk space dedicated to Orthanc. Note that each time
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42 a new instance is received for an existing patient, the patient will
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43 be marked as the most recent one in the recycling order.
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45 Recycling is controlled by the ``MaximumStorageSize`` and the
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46 ``MaximumPatientCount`` options in the :ref:`Orthanc configuration
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47 file <configuration>`. Setting both these values to 0 will disable
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48 recycling.
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50 It is possible to prevent important data from being automatically
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51 recycled. This mechanism is called **protection**. Each patient can be
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52 individually protected against recycling by using the
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53 ``Unprotected/Protected`` switch that is available from Orthanc
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54 Explorer.
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55
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56 Note that protection is only available at the patient level. It
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57 protects all the studies/series/instances of the patient against
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58 recycling. The rationale is that we think it is important to keep
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59 available all the data related to one patient. Unwillingly losing a
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60 study/series that is part of the same patient might lead to a loss in
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61 consistency with respect to the medical history of this patient.
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63 .. _compression:
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64
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65 Compression
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66 -----------
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67
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68 If your disk space is limited, besides :ref:`recycling`, you should
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69 also consider using **disk space compression**. When compression is
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70 enabled, Orthanc compresses the incoming DICOM instances on-the-fly
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71 before writing them to the filesystem, using `zlib
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72 <https://en.wikipedia.org/wiki/Zlib>`_. This is useful, because the
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73 images are often stored as raw, uncompressed arrays in DICOM
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74 instances: The size of a typical DICOM instance can hopefully be
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75 divided by a factor 2 through lossless compression. This compression
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76 process is transparent to the user, as Orthanc automatically
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77 decompresses the file before sending it back to the external world.
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78
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79 Compression is controlled by the ``StorageCompression`` option in the
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80 :ref:`Orthanc configuration file <configuration>`.
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81
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82
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83 .. _metadata:
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84
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85 Metadata & attachments
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86 ----------------------
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87
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88 Metadata consists in an **associative key-value array** (mapping a
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89 integer key in the range [0,65535] to a string value) that is
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90 associated with each :ref:`DICOM resource <orthanc-ids>` stored inside
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91 Orthanc (may it be a patient, a study, a series or a DICOM
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92 instance). Metadata can be either referred to using the integer key,
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93 or using a symbolic name (if configured). Metadata records
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94 information that is not readily available in the DICOM tags.
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95
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96 In spirit, the metadata mechanism is similar to the :ref:`attachment
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97 mechanism <orthanc-storage>`. However, metadata is stored directly
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98 inside the database, whereas attachments are stored as separate files
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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>`__.
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109
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110 Also note that metadata and attachments are only available for
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111 resources stored inside Orthanc. Once one DICOM instance leaves the
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112 Orthanc ecosystem, its associated metadata and attachments are lost.
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113
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114
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115 Core metadata
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116 ^^^^^^^^^^^^^
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117
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118 Here are the main metadata handled by the Orthanc core:
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119
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120 * ``ReceptionDate`` records when a DICOM instance was received by
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121 Orthanc. Similarly, ``LastUpdate`` records, for each
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122 patient/study/series, the last time a DICOM instance was added to
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123 this resource.
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124 * ``RemoteAet`` records the AET of the modality that has sent some
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125 DICOM instance to Orthanc.
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126 * ``ModifiedFrom`` and ``AnonymizedFrom`` hold from which original
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127 resource, a resource was modified or anonymized. The presence of
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128 this metadata indicates that the resource is the result of a
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129 modification or anonymization that was carried on by Orthanc.
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130 * ``Origin`` records through which mechanism the instance was received
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131 by Orthanc (may be ``Unknown``, ``DicomProtocol``, ``RestApi``,
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132 ``Plugins``, or ``Lua``).
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133 * ``IndexInSeries`` records the expected index of a DICOM instance
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134 inside its parent series. Conversely, ``ExpectedNumberOfInstances``
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135 associates to each series, the number of DICOM instances this series
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136 is expected to contain.
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137 * Starting with Orthanc 1.2.0, ``TransferSyntax`` and ``SopClassUid``
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138 respectively stores the transfer syntax UID and the SOP class UID of
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139 DICOM instances, in order to speed up the access to this
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140 information.
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141
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142 Metadata listed above are set privately by the Orthanc core. They are
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143 **read-only** from the perspective of the end user, as Orthanc
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144 internally relies on them.
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145
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146
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147 User-defined metadata
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148 ^^^^^^^^^^^^^^^^^^^^^
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149
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150 The metadata described above where handled by the core of Orthanc.
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151 Orthanc users are however allowed to define their own **user-defined
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152 metadata**. Such metadata are associated with an integer key that is
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153 greater or equal to 1024 (whereas keys below 1023 are reserved for
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154 core metadata).
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155
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156 You can associate a symbolic name to user-defined metadata using the
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157 ``UserMetadata`` option inside the :ref:`configuration of Orthanc
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158 <configuration>`::
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159
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160 "UserMetadata" : {
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161 "SampleMetaData1" : 1024,
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162 "SampleMetaData2" : 1025
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163 }
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164
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165
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166 Accessing metadata
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167 ^^^^^^^^^^^^^^^^^^
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168
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169 .. highlight:: bash
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170
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171 Metadata associated with one DICOM resource can be accessed through
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172 the :ref:`REST API <rest>`, for instance::
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173
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174 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata
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175 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/RemoteAet
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176 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/SampleMetaData1
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177
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178 User-defined metadata can be modified by issuing a HTTP PUT against
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179 the REST API::
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180
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181 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024 -X PUT -d 'hello'
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182 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024
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183 hello
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184
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185
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186
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187 .. _attachments:
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188
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189 User-defined attachments
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190 ^^^^^^^^^^^^^^^^^^^^^^^^
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191
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192 Orthanc users are allowed to define their own **user-defined attachments**.
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193 Such attachments are associated with an integer key that is
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194 greater or equal to 1024 (whereas keys below 1023 are reserved for
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195 core attachments).
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196
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197 You can associate a symbolic name to user-defined attachments using the
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198 ``UserContentType`` option inside the :ref:`configuration of Orthanc
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199 <configuration>`. Optionally, the user may specify a MIME content type
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200 for the attachment::
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201
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202 "UserContentType" : {
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203 "samplePdf" : [1024, "application/pdf"],
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204 "sampleJson" : [1025, "application/json"],
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205 "sampleRaw" : 1026
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206 }
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207
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208 Accessing attachments
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209 ^^^^^^^^^^^^^^^^^^^^^
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210
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211 .. highlight:: bash
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212
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213 Attachments associated with one DICOM resource can be accessed through
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214 the :ref:`REST API <rest>`, for instance::
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215
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216 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf/data
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217 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleJson/data
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218
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219 User-defined attachments can be modified by issuing a HTTP PUT against
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220 the REST API::
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221
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222 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf -X PUT --data-binary @sample.pdf
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223 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleRaw -X PUT -d 'raw data'
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224
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225
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226 .. _registry:
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227
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228 Central registry of metadata and attachments
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229 --------------------------------------------
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230
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231 Obviously, one must pay attention to the fact that different
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232 applications might use the same key to store different user-defined
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233 :ref:`metadata <metadata>`, which might result in incompatibilities
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234 between such applications. Similarly, incompatibilities might show up
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235 for user-defined :ref:`attachments <orthanc-storage>`.
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236
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237 Developers of applications/plugins that use user-defined metadata,
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238 attachments or global properties (using
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239 ``OrthancPluginSetGlobalProperty()``) are therefore kindly invited to
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240 complete the **central registry** below:
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241
622
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242 * ``Attachment 1`` is used by the core of Orthanc to store the DICOM
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243 file associated with one instance.
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244 * ``Attachment 2`` was used by Orthanc <= 1.9.0 to cache the so-called
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245 ``DICOM-as-JSON`` information (as returned by the
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246 ``/instances/.../tags`` URI in the :ref:`REST API <rest>`) in order
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247 to speed up subsequent requests to the same URI. This attachment is
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248 not automatically generated anymore starting with Orthanc 1.9.1, in
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249 order to improve performance (creating two files for each DICOM
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250 instance has a cost) and consistency (if the DICOM dictionary gets
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251 modified in the future).
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252 * ``Attachment 3`` is used since Orthanc 1.9.1 to store the DICOM
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253 instance until the ``Pixel Data (7fe0,0010)`` tag, if the global
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254 configuration option ``StorageCompression`` is ``true``, or if the
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255 storage area plugin doesn't support range reads. This allows to
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256 avoid downloading the full DICOM instance if not necessary.
359
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257 * ``Attachment 9997`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store series information.
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258 * ``Attachment 9998`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store instance information.
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259 * ``Attachment 9999`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store annotations.
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260 * ``Attachments 10000-13999`` are used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store reduced quality images.
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261 * ``Global property 5467`` is used by the Osimis Cloud plugin.
602
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262 * ``Global property 5468`` is used by the :ref:`DICOMweb plugin <dicomweb>` to store the DICOMweb servers into the Orthanc database.
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263 * ``Metadata 4200`` is used by the plugin for :ref:`whole-slide imaging <wsi>` with version <= 0.7.
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264 * ``Metadata 4201`` is used by the plugin for :ref:`whole-slide imaging <wsi>` with version >= 1.0.
224
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265
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266
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267 Jobs
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268 ----
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269
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270 Check out the :ref:`advanced features of the REST API <jobs>`.
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271
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272
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273
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274 .. _stable-resources:
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275
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276 Stable resources
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277 ----------------
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278
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279 A DICOM resource (patient, study or series) is referred to as
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280 **stable** if it has not received any new instance for a certain
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281 amount of time.
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282
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283 This amount of time is configured by the the option ``StableAge`` in
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284 the :ref:`configuration file <configuration>`.
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285
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286 When some resource becomes stable, an event is generated as a log
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287 entry in the ``/changes`` :ref:`URI in the REST API <changes>`, a
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288 :ref:`Lua callback <lua-callbacks>` is invoked, the callback function
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289 registered by ``OrthancPluginRegisterOnChangeCallback()`` in
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290 :ref:`C/C++ plugins <creating-plugins>` is executed, as well as the
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291 :ref:`Python callback <python-changes>` registered by
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292 ``orthanc.RegisterOnChangeCallback()``.
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293
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294 The ``IsStable`` field is also available to get the status of an
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295 individual patient/study/series using the REST API of Orthanc.
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296
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297 In the multiple readers/writers scenario enabled since Orthanc 1.9.2,
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298 each Orthanc server is considered separately: The "stable" information
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299 is monitored by threads inside the Orthanc process, and is **not**
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300 shared in the database. In other words, the "stable" information is
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301 local to the Orthanc server that is queried. Synchronization between
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302 multiple readers/writers must be implemented at a higher level
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303 (e.g. using a distributed `message-broker system
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304 <https://en.wikipedia.org/wiki/Message_broker>`__ such as RabbitMQ
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305 that is fed by an Orthanc plugin).
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306
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307
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308 .. _revisions:
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309
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310 Revisions
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311 ---------
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312
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313 .. highlight:: bash
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314
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315 Higher-level applications built on the top of Orthanc might have to
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316 modify metadata and/or attachments. This can cause concurrency
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317 problems if multiple clients modify the same metadata/attachment
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318 simultaneously. To avoid such problems, Orthanc implements a so-called
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319 **revision mechanism** to protect from concurrent modifications.
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320
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321 The revision mechanism is optional, was introduced in **Orthanc
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322 1.9.2** and must be enabled by setting :ref:`configuration option
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323 <configuration>` ``CheckRevision`` to ``true``. It is strongly
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324 inspired by the `CouchDB API
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325 <https://docs.couchdb.org/en/stable/api/document/common.html>`__.
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326
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327 When the revision mechanism is enabled, each metadata and attachment
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328 is associated with a **revision number**. Whenever one sets a metadata
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329 for the first time using a ``PUT`` query, this revision number can be
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330 found in the HTTP header ``ETag`` that is reported by Orthanc::
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331
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332 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X PUT -d 'Hello'
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333 [...]
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334 < ETag: "0"
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335
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336 Any ``GET`` query will also return the current value of ``ETag``::
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337
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338 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024
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339 [...]
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340 < ETag: "0"
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341
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342 If one needs to subsequently modify or delete this metadata, the HTTP
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343 client must set this value of ``ETag`` into the ``If-Match`` HTTP
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344 header::
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345
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346 $ 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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347 [...]
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348 < ETag: "1"
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349
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350 Note how this second call has incremented the value of ``ETag``: This
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351 is the new revision number to be used in future updates. If a bad
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352 revision number is provided, the HTTP error ``409 Conflict`` is
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353 generated::
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354
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355 $ 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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356 [...]
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357 < HTTP/1.1 409 Conflict
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358
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359 Such a ``409`` error must be handled by the higher-level
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360 application. The revision number must similarly be given if deleting a
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361 metadata/attachment::
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362
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363 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X DELETE -H 'If-Match: "1"'
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364 [...]
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365 < HTTP/1.1 200 OK
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366
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367 Check out the `OpenAPI reference <https://api.orthanc-server.com/>`__
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368 of the REST API of Orthanc for more information.
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369
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370 **Warning:** The database index back-end must support revisions. As of
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371 writing, only the **PostgreSQL plugin** in versions above 4.0
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372 implement support for revisions.