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SynchronousCMove: Synchronous vs. asynchronous C-MOVE SCP
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 03 May 2021 14:31:42 +0200
parents 36bf58dfb7f7
children 9c23356b9464
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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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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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79 Compression is controlled by the ``StorageCompression`` option in the
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80 :ref:`Orthanc configuration file <configuration>`.
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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 using the DICOM protocol.
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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. This information is :ref:`not always
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137 available <series-completion>`.
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138 * Starting with Orthanc 1.2.0, ``TransferSyntax`` and ``SopClassUid``
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139 respectively stores the transfer syntax UID and the SOP class UID of
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140 DICOM instances, in order to speed up the access to this
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141 information.
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142 * ``RemoteIP`` (new in Orthanc 1.4.0): The IP address of the remote
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143 SCU (for REST API and DICOM protocol).
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144 * ``CalledAET`` (new in Orthanc 1.4.0): The AET that was called by the
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145 SCU, which normally matches the AET of Orthanc (for DICOM protocol).
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146 * ``HttpUsername`` (new in Orthanc 1.4.0): The username that created
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147 the instance (for REST API).
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148 * ``PixelDataOffset`` (new in Orthanc 1.9.1): Offset (in bytes) of the
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149 Pixel Data DICOM tag in the DICOM file, if available.
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150
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151
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152 Metadata listed above are set privately by the Orthanc core. They are
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153 **read-only** from the perspective of the end user, as Orthanc
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154 internally relies on them.
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155
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156
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157 User-defined metadata
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158 ^^^^^^^^^^^^^^^^^^^^^
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159
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160 The metadata described above where handled by the core of Orthanc.
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161 Orthanc users are however allowed to define their own **user-defined
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162 metadata**. Such metadata are associated with an integer key that is
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163 greater or equal to 1024 (whereas keys below 1023 are reserved for
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164 core metadata).
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165
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166 You can associate a symbolic name to user-defined metadata using the
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167 ``UserMetadata`` option inside the :ref:`configuration of Orthanc
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168 <configuration>`::
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169
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170 "UserMetadata" : {
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171 "SampleMetaData1" : 1024,
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172 "SampleMetaData2" : 1025
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173 }
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174
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175
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176 Accessing metadata
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177 ^^^^^^^^^^^^^^^^^^
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178
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179 .. highlight:: bash
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180
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181 Metadata associated with one DICOM resource can be accessed through
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182 the :ref:`REST API <rest>`, for instance::
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183
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184 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata
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185 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/RemoteAet
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186 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/SampleMetaData1
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187
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188 User-defined metadata can be modified by issuing a HTTP PUT against
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189 the REST API::
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190
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191 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024 -X PUT -d 'hello'
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192 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/metadata/1024
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193 hello
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194
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195
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196
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197 .. _attachments:
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198
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199 User-defined attachments
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200 ^^^^^^^^^^^^^^^^^^^^^^^^
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201
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202 Orthanc users are allowed to define their own **user-defined attachments**.
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203 Such attachments are associated with an integer key that is
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204 greater or equal to 1024 (whereas keys below 1023 are reserved for
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205 core attachments).
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206
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207 You can associate a symbolic name to user-defined attachments using the
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208 ``UserContentType`` option inside the :ref:`configuration of Orthanc
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209 <configuration>`. Optionally, the user may specify a MIME content type
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210 for the attachment::
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211
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212 "UserContentType" : {
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213 "samplePdf" : [1024, "application/pdf"],
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214 "sampleJson" : [1025, "application/json"],
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215 "sampleRaw" : 1026
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216 }
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217
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218 Accessing attachments
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219 ^^^^^^^^^^^^^^^^^^^^^
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220
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221 .. highlight:: bash
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222
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223 Attachments associated with one DICOM resource can be accessed through
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224 the :ref:`REST API <rest>`, for instance::
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225
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226 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf/data
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227 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleJson/data
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228
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229 User-defined attachments can be modified by issuing a HTTP PUT against
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230 the REST API::
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231
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232 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/samplePdf -X PUT --data-binary @sample.pdf
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233 $ curl http://localhost:8042/instances/cb855110-5f4da420-ec9dc9cb-2af6a9bb-dcbd180e/attachments/sampleRaw -X PUT -d 'raw data'
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234
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235
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236 DICOM-as-JSON attachments
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237 ^^^^^^^^^^^^^^^^^^^^^^^^^
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238
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239 In the version of Orthanc <= 1.9.0, whenever Orthanc receives a DICOM
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240 file, it pre-computes a JSON summary of its DICOM tags, and caches
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241 this JSON file as an attachment to the DICOM instance (accessible at
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242 the ``/instances/{...}/attachments/dicom-as-json/`` URI). This
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243 attachment is used as a cache to seep up future accesses to
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244 ``/instances/.../tags``, lookups using ``/tools/find`` or C-FIND
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245 queries.
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246
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247 This caching might cause issues if the dictionary of DICOM tags is
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248 subsequently modified, which implies that the cached JSON file does
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249 not perfectly match the new dictionary.
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250
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251 .. highlight:: bash
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252
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253 Since Orthanc 1.2.0, you can force the re-generation of the cached
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254 JSON file by DELETE-ing it, for instance::
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255
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256 $ curl -X DELETE http://localhost:8042/instances/301896f2-1416807b-3e05dcce-ff4ce9bb-a6138832/attachments/dicom-as-json
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257
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258 .. highlight:: text
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259
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260 The next time you open this particular instance with Orthanc Explorer,
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261 you will see messages in the Orthanc logs (in verbose mode) stating
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262 that the Orthanc server has reconstructed the JSON summary, which will
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263 match the new content of the dictionary::
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264
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265 I0222 08:56:00.923070 FilesystemStorage.cpp:155] Reading attachment "2309c47b-1cbd-4601-89b5-1be1ad80382c" of "DICOM" content type
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266 I0222 08:56:00.923394 ServerContext.cpp:401] Reconstructing the missing DICOM-as-JSON summary for instance: 301896f2-1416807b-3e05dcce-ff4ce9bb-a6138832
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267 I0222 08:56:00.929117 ServerContext.cpp:540] Adding attachment dicom-as-json to resource 301896f2-1416807b-3e05dcce-ff4ce9bb-a6138832
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268 I0222 08:56:00.929425 FilesystemStorage.cpp:118] Creating attachment "3c830b66-8a00-42f0-aa3a-5e37b4a8b5a4" of "JSON summary of DICOM" type (size: 1MB)
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269
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270 These DICOM-as-JSON attachments are not automatically generated
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271 anymore starting with Orthanc 1.9.1.
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272
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273
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274 .. _registry:
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275
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276 Central registry of metadata and attachments
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277 --------------------------------------------
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278
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279 Obviously, one must pay attention to the fact that different
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280 applications might use the same key to store different user-defined
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281 :ref:`metadata <metadata>`, which might result in incompatibilities
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282 between such applications. Similarly, incompatibilities might show up
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283 for user-defined :ref:`attachments <orthanc-storage>`.
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284
601
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285 Developers of applications/plugins that use user-defined metadata,
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286 attachments or global properties (using
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287 ``OrthancPluginSetGlobalProperty()``) are therefore kindly invited to
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288 complete the **central registry** below:
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289
622
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290 * ``Attachment 1`` is used by the core of Orthanc to store the DICOM
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291 file associated with one instance.
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292 * ``Attachment 2`` was used by Orthanc <= 1.9.0 to cache the so-called
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293 ``DICOM-as-JSON`` information (as returned by the
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294 ``/instances/.../tags`` URI in the :ref:`REST API <rest>`) in order
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295 to speed up subsequent requests to the same URI. This attachment is
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296 not automatically generated anymore starting with Orthanc 1.9.1, in
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297 order to improve performance (creating two files for each DICOM
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298 instance has a cost) and consistency (if the DICOM dictionary gets
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299 modified in the future).
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300 * ``Attachment 3`` is used since Orthanc 1.9.1 to store the DICOM
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301 instance until the ``Pixel Data (7fe0,0010)`` tag, if the global
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302 configuration option ``StorageCompression`` is ``true``, or if the
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303 storage area plugin doesn't support range reads. This allows to
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304 avoid downloading the full DICOM instance if not necessary.
359
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305 * ``Attachment 9997`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store series information.
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306 * ``Attachment 9998`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store instance information.
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307 * ``Attachment 9999`` is used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store annotations.
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308 * ``Attachments 10000-13999`` are used by the :ref:`Osimis WebViewer plugin <osimis_webviewer>` to store reduced quality images.
601
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309 * ``Global property 5467`` is used by the Osimis Cloud plugin.
602
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310 * ``Global property 5468`` is used by the :ref:`DICOMweb plugin <dicomweb>` to store the DICOMweb servers into the Orthanc database.
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311 * ``Metadata 4200`` is used by the plugin for :ref:`whole-slide imaging <wsi>` with version <= 0.7.
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312 * ``Metadata 4201`` is used by the plugin for :ref:`whole-slide imaging <wsi>` with version >= 1.0.
224
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313
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314
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315 Jobs
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316 ----
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317
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318 Check out the :ref:`advanced features of the REST API <jobs>`.
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319
642
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320
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321
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322 .. _stable-resources:
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323
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324 Stable resources
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325 ----------------
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326
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327 A DICOM resource (patient, study or series) is referred to as
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328 **stable** if it has not received any new instance for a certain
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329 amount of time.
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330
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331 This amount of time is configured by the the option ``StableAge`` in
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332 the :ref:`configuration file <configuration>`.
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333
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334 When some resource becomes stable, an event is generated as a log
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335 entry in the ``/changes`` :ref:`URI in the REST API <changes>`, a
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336 :ref:`Lua callback <lua-callbacks>` is invoked, the callback function
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337 registered by ``OrthancPluginRegisterOnChangeCallback()`` in
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338 :ref:`C/C++ plugins <creating-plugins>` is executed, as well as the
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339 :ref:`Python callback <python-changes>` registered by
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340 ``orthanc.RegisterOnChangeCallback()``.
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341
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342 The ``IsStable`` field is also available to get the status of an
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343 individual patient/study/series using the REST API of Orthanc.
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344
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345 In the multiple readers/writers scenario enabled since Orthanc 1.9.2,
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346 each Orthanc server is considered separately: The "stable" information
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347 is monitored by threads inside the Orthanc process, and is **not**
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348 shared in the database. In other words, the "stable" information is
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349 local to the Orthanc server that is queried. Synchronization between
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350 multiple readers/writers must be implemented at a higher level
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351 (e.g. using a distributed `message-broker system
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352 <https://en.wikipedia.org/wiki/Message_broker>`__ such as RabbitMQ
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diff changeset
353 that is fed by an Orthanc plugin).
643
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354
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355
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356 .. _revisions:
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357
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358 Revisions
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359 ---------
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360
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361 .. highlight:: bash
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362
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363 Higher-level applications built on the top of Orthanc might have to
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364 modify metadata and/or attachments. This can cause concurrency
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365 problems if multiple clients modify the same metadata/attachment
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366 simultaneously. To avoid such problems, Orthanc implements a so-called
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367 **revision mechanism** to protect from concurrent modifications.
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368
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369 The revision mechanism is optional, was introduced in **Orthanc
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370 1.9.2** and must be enabled by setting :ref:`configuration option
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371 <configuration>` ``CheckRevision`` to ``true``. It is strongly
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372 inspired by the `CouchDB API
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373 <https://docs.couchdb.org/en/stable/api/document/common.html>`__.
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374
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375 When the revision mechanism is enabled, each metadata and attachment
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376 is associated with a **revision number**. Whenever one sets a metadata
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377 for the first time using a ``PUT`` query, this revision number can be
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378 found in the HTTP header ``ETag`` that is reported by Orthanc::
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379
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380 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X PUT -d 'Hello'
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381 [...]
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382 < ETag: "0"
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383
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384 Any ``GET`` query will also return the current value of ``ETag``::
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385
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386 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024
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387 [...]
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388 < ETag: "0"
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389
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390 If one needs to subsequently modify or delete this metadata, the HTTP
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391 client must set this value of ``ETag`` into the ``If-Match`` HTTP
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392 header::
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393
645
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394 $ 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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395 [...]
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396 < ETag: "1"
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397
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398 Note how this second call has incremented the value of ``ETag``: This
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399 is the new revision number to be used in future updates. If a bad
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400 revision number is provided, the HTTP error ``409 Conflict`` is
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401 generated::
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402
645
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403 $ 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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404 [...]
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405 < HTTP/1.1 409 Conflict
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406
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diff changeset
407 Such a ``409`` error must be handled by the higher-level
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diff changeset
408 application. The revision number must similarly be given if deleting a
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409 metadata/attachment::
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diff changeset
410
645
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411 $ curl -v http://localhost:8042/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/metadata/1024 -X DELETE -H 'If-Match: "1"'
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412 [...]
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diff changeset
413 < HTTP/1.1 200 OK
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414
645
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415 Check out the `OpenAPI reference <https://api.orthanc-server.com/>`__
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416 of the REST API of Orthanc for more information.
643
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417
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418 **Warning:** The database index back-end must support revisions. As of
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419 writing, only the **PostgreSQL plugin** in versions above 4.0
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420 implement support for revisions.
672
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421
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422
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423 Synchronous vs. asynchronous C-MOVE SCP
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424 ---------------------------------------
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425
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426 The :ref:`C-MOVE SCP <dicom-move>` of Orthanc (i.e. the component of
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parents: 661
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427 the Orthanc server that is responsible for routing DICOM instances
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428 from Orthanc to other modalities) can be configured to run either in
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429 synchronous or in asynchronous mode, depending on the value of the
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430 ``SynchronousCMove`` :ref:`configuration option <configuration>`:
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parents: 661
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431
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432 * In **synchronous mode** (if ``SynchronousCMove`` is ``true``),
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433 Orthanc will interleave its C-STORE SCU commands with the C-MOVE
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parents: 661
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434 instructions received from the remote modality. In other words,
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parents: 661
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435 Orthanc immediately sends the DICOM instances while it handles the
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parents: 661
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436 C-MOVE command from the remote modality. This mode is for
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parents: 661
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437 compatibility with simple DICOM client software that considers that
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parents: 661
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438 when its C-MOVE SCU is over, it should have received all the
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parents: 661
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439 instructed DICOM instances. This is the default behavior of Orthanc.
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parents: 661
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440
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441 * In **asynchronous mode** (if ``SynchronousCMove`` is ``false``),
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parents: 661
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442 Orthanc will queue the C-MOVE instructions and :ref:`creates a job
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443 <jobs-synchronicity>` that will issue the C-STORE SCU commands
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parents: 661
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444 afterward. This behavior is typically encountered in hospital-wide
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parents: 661
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445 PACS systems, but requires the client software to be more complex as
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parents: 661
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446 it must be handle the delay between its C-MOVE queries and the
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parents: 661
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447 actual reception of the DICOM instances through C-STORE.
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parents: 661
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448
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449 As a consequence, by setting ``SynchronousCMove`` to ``true``, Orthanc
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parents: 661
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450 can be used as a buffer that enables communications between a simple
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451 C-MOVE client and a hospital-wide PACS. This can be interesting to
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parents: 661
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452 introduce compatibility with specialized image processing
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453 applications.