orthanc-book: Sphinx/source/plugins/python.rst annotate

annotate Sphinx/source/plugins/python.rst @ 471:a735476a0e6e

note about fork on windows

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Tue, 04 Aug 2020 20:53:18 +0200
parents	fcc352fd4283
children	03dfb896ca4b

rev	line source
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	1 .. _python-plugin:
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	2
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	3
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	4 Python plugin for Orthanc
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	5 =========================
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	6
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	7 .. contents::
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	8
371 5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	9
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	10 Overview
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	11 --------
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	12
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	13 This plugin can be used to write :ref:`Orthanc plugins
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	14 <creating-plugins>` using the `Python programming language
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	15 <https://en.wikipedia.org/wiki/Python_(programming_language)>`__
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	16 instead of the more complex C/C++ programming languages.
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	17
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	18 Python plugins have access to more features and a more consistent SDK
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	19 than :ref:`Lua scripts <lua>`. The Python API is automatically
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	20 generated from the `Orthanc plugin SDK in C
462 fcc352fd4283 upgrade python Sebastien Jodogne <s.jodogne@gmail.com> parents: 442 diff changeset	21 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.7.2/OrthancServer/Plugins/Include/orthanc/OrthancCPlugin.h>`__
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	22 using the `Clang <https://en.wikipedia.org/wiki/Clang>`__ compiler
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	23 front-end.
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	24
462 fcc352fd4283 upgrade python Sebastien Jodogne <s.jodogne@gmail.com> parents: 442 diff changeset	25 As of release 2.0 of the plugin, the coverage of the C SDK is about
fcc352fd4283 upgrade python Sebastien Jodogne <s.jodogne@gmail.com> parents: 442 diff changeset	26 75% (119 functions are automatically wrapped in Python out of a total
fcc352fd4283 upgrade python Sebastien Jodogne <s.jodogne@gmail.com> parents: 442 diff changeset	27 of 157 functions in the Orthanc SDK 1.7.2).
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	28
371 5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	29
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	30 Source code
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	31 -----------
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	32
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	33 * Link to the `official releases of this plugin
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	34 <https://www.orthanc-server.com/browse.php?path=/plugin-python>`__.
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	35
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	36 * Link to the `code repository
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	37 <https://hg.orthanc-server.com/orthanc-python/>`__.
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	38
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	39
353 0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	40 Licensing
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	41 ---------
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	42
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	43 Pay attention to the fact that this plugin is licensed under the terms
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	44 of the `AGPL license
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	45 <https://en.wikipedia.org/wiki/GNU_Affero_General_Public_License>`__.
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	46
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	47 This has an important consequence: If you distribute Orthanc to
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	48 clients together with one Python script, or if you put an Orthanc
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	49 server equipped with one Python script on a Web portal, you must
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	50 disclose the source code of your Python script to the Orthanc
354 1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	51 community under the terms of the AGPL license.
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	52
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	53 We suggest you to put the source code of your Python scripts on the
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	54 dedicated `"OrthancContributed" repository on GitHub
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	55 <https://github.com/jodogne/OrthancContributed/tree/master/Plugins>`__,
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	56 and/or to send it to the `Orthanc Users
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	57 <https://groups.google.com/forum/#!forum/orthanc-users>`__ discussion
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	58 group.
353 0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	59
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	60 Check out the :ref:`FAQ about licensing <licensing>` for more context.
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	61
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	62
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	63 Usage
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	64 -----
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	65
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	66 Docker
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	67 ......
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	68
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	69 .. highlight:: json
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	70
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	71 The most direct way of starting Orthanc together with the Python
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	72 plugin is through :ref:`Docker <docker>`. Let's create the file
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	73 ``/tmp/hello.py`` that contains the following basic Python script::
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	74
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	75 print('Hello world!')
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	76
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	77 .. highlight:: json
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	78
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	79 Let's also create the file ``/tmp/orthanc.json`` that contains the
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	80 following minimal :ref:`configuration for Orthanc <configuration>`::
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	81
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	82 {
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	83 "StorageDirectory" : "/var/lib/orthanc/db",
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	84 "RemoteAccessAllowed" : true,
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	85 "Plugins" : [
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	86 "/usr/local/share/orthanc/plugins"
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	87 ],
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	88 "PythonScript" : "/etc/orthanc/hello.py"
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	89 }
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	90
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	91 .. highlight:: bash
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	92
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	93 Given these two files, Orthanc can be started as follows::
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	94
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	95 $ docker run -p 4242:4242 -p 8042:8042 --rm \
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	96 -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro \
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	97 -v /tmp/hello.py:/etc/orthanc/hello.py:ro \
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	98 jodogne/orthanc-python
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	99
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	100 .. highlight:: text
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	101
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	102 You'll see the following excerpt in the log, which indicates that the Python plugin is properly loaded::
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	103
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	104 W0331 15:48:12.990661 PluginsManager.cpp:269] Registering plugin 'python' (version mainline)
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	105 W0331 15:48:12.990691 PluginsManager.cpp:168] Python plugin is initializing
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	106 W0331 15:48:12.990743 PluginsManager.cpp:168] Using Python script "hello.py" from directory: /etc/orthanc
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	107 W0331 15:48:12.990819 PluginsManager.cpp:168] Program name: /usr/local/sbin/Orthanc
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	108 Hello world!
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	109
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	110
405 ba486cac480a link to python sample Alain Mazy <alain@mazy.be> parents: 379 diff changeset	111 `Here <https://bitbucket.org/osimis/orthanc-setup-samples/src/master/docker/python/>`__ is a full example
ba486cac480a link to python sample Alain Mazy <alain@mazy.be> parents: 379 diff changeset	112 of a more complex setup using the :ref:`osimis/orthanc <docker-osimis>` images.
ba486cac480a link to python sample Alain Mazy <alain@mazy.be> parents: 379 diff changeset	113
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	114 Compiling from source
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	115 .....................
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	116
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	117 .. highlight:: bash
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	118
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	119 The procedure to compile this plugin from source is similar to that
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	120 for the :ref:`core of Orthanc <compiling>`. The following commands
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	121 should work for most UNIX-like distribution (including GNU/Linux)::
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	122
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	123 $ mkdir Build
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	124 $ cd Build
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	125 $ cmake .. -DPYTHON_VERSION=3.7 -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	126 $ make
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	127
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	128 Before running CMake, make sure that the Python interpreter and its
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	129 associated development library are installed. On Ubuntu 18.04 LTS, you
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	130 would for instance install packages ``libpython3.7-dev`` and
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	131 ``python3.7``.
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	132
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	133 The compilation will produce the shared library ``OrthancPython``,
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	134 that can be loaded by properly setting the ``Plugins``
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	135 :ref:`configuration option <configuration>` of Orthanc.
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	136
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	137 Warning: The shared library is only compatible with the Python
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	138 interpreter whose version corresponds to the value of the
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	139 ``PYTHON_VERSION`` argument that was given to CMake.
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	140
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	141
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	142 Microsoft Windows
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	143 .................
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	144
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	145 Pre-compiled binaries for Microsoft Windows `are also available
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	146 <https://www.orthanc-server.com/browse.php?path=/plugin-python>`__.
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	147
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	148 Beware that one version of the Python plugin can only be run against
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	149 one version of the Python interpreter. This version is clearly
442 8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	150 indicated in the filename of the precompiled binaries.
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	151
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	152 .. highlight:: text
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	153
442 8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	154 You are of course free to compile the plugin from sources. You'll have
8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	155 to explicitly specify the path to your Python installation while
8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	156 invoking CMake. For instance::
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	157
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	158 C:\orthanc-python\Build> cmake .. -DPYTHON_VERSION=2.7 -DPYTHON_WINDOWS_ROOT=C:/Python27 \
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	159 -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release -G "Visual Studio 15 2017"
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	160
442 8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	161 Note about debug builds: Usually, building Python modules such as the Python
377 ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	162 plugin for Orthanc in debug mode (where ``_DEBUG`` is defined) leads to a module
442 8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	163 (``.exe`` or ``.dll``) that requires a debug build of Python, and debug versions of all
377 ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	164 the Python libraries. This is quite cumbersome, for it requires building Python
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	165 on your own or downloading additional debug files.
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	166
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	167 Since using a debug build of Python is only necessary in very specific cases
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	168 (such as the debugging of code at the boundary between Python and an extension),
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	169 we have changed the default behavior to use the release Python library by default.
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	170
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	171 This means that you are able to build this plugin in debug mode with the
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	172 standard Python distribution.
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	173
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	174 In case you need to use the Python debug libraries, you can instruct the build
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	175 system to do so by setting the ``PYTHON_WINDOWS_USE_RELEASE_LIBS`` CMake option,
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	176 that is ``ON`` by default, to ``OFF``. The previous build example would then be,
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	177 should you require a full debug build::
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	178
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	179 C:\orthanc-python\Build> cmake .. -DPYTHON_VERSION=2.7 -DPYTHON_WINDOWS_ROOT=C:/Python27 \
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	180 -DSTATIC_BUILD=ON -DPYTHON_WINDOWS_USE_RELEASE_LIBS=OFF \
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	181 -DCMAKE_BUILD_TYPE=Debug -G "Visual Studio 15 2017"
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	182
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	183 Please note that this CMake option only impacts debug builds under Windows,
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	184 when using (any version of) the Microsoft Visual Studio compiler.
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	185
442 8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	186 The precompiled binaries all use release (i.e. non-debug) versions of Python.
8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	187
8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	188
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	189 Configuration options
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	190 ---------------------
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	191
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	192 The only two configuration options that are available for this plugin
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	193 are the following:
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	194
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	195 * ``PythonScript`` indicates where the Python script is located. If
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	196 this configuration option is not provided, the Python plugin is not
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	197 started.
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	198
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	199 * ``PythonVerbose`` is a Boolean value to make the Python interpreter
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	200 verbose.
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	201
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	202
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	203 Samples
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	204 -------
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	205
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	206 Extending the REST API
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	207 ......................
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	208
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	209 .. highlight:: python
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	210
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	211 Here is a basic Python script that registers two new routes in the
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	212 REST API::
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	213
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	214 import orthanc
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	215 import pprint
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	216
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	217 def OnRest(output, uri, **request):
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	218 pprint.pprint(request)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	219 print('Accessing uri: %s' % uri)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	220 output.AnswerBuffer('ok\n', 'text/plain')
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	221
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	222 orthanc.RegisterRestCallback('/(to)(t)o', OnRest)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	223 orthanc.RegisterRestCallback('/tata', OnRest)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	224
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	225 .. highlight:: json
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	226
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	227 Here is the associated minimal configuration file for Orthanc
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	228 (provided the Python script is saved as ``rest.py``)::
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	229
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	230 {
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	231 "Plugins" : [ "." ],
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	232 "PythonScript" : "rest.py",
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	233 "PythonVerbose" : false
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	234 }
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	235
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	236 .. highlight:: bash
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	237
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	238 The route can then be accessed as::
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	239
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	240 $ curl http://localhost:8042/toto
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	241 ok
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	242
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	243
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	244 Listening to changes
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	245 ....................
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	246
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	247 .. highlight:: python
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	248
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	249 This sample uploads a DICOM file as soon as Orthanc is started::
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	250
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	251 import orthanc
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	252
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	253 def OnChange(changeType, level, resource):
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	254 if changeType == orthanc.ChangeType.ORTHANC_STARTED:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	255 print('Started')
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	256
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	257 with open('/tmp/sample.dcm', 'rb') as f:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	258 orthanc.RestApiPost('/instances', f.read())
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	259
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	260 elif changeType == orthanc.ChangeType.ORTHANC_STOPPED:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	261 print('Stopped')
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	262
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	263 elif changeType == orthanc.ChangeType.NEW_INSTANCE:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	264 print('A new instance was uploaded: %s' % resource)
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	265
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	266 orthanc.RegisterOnChangeCallback(OnChange)
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	267
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	268
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	269 Accessing the content of a new instance
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	270 .......................................
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	271
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	272 .. highlight:: python
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	273
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	274 ::
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	275
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	276 import orthanc
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	277 import json
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	278 import pprint
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	279
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	280 def OnStoredInstance(dicom, instanceId):
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	281 print('Received instance %s of size %d (transfer syntax %s, SOP class UID %s)' % (
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	282 instanceId, dicom.GetInstanceSize(),
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	283 dicom.GetInstanceMetadata('TransferSyntax'),
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	284 dicom.GetInstanceMetadata('SopClassUid')))
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	285
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	286 # Print the origin information
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	287 if dicom.GetInstanceOrigin() == orthanc.InstanceOrigin.DICOM_PROTOCOL:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	288 print('This instance was received through the DICOM protocol')
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	289 elif dicom.GetInstanceOrigin() == orthanc.InstanceOrigin.REST_API:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	290 print('This instance was received through the REST API')
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	291
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	292 # Print the DICOM tags
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	293 pprint.pprint(json.loads(dicom.GetInstanceSimplifiedJson()))
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	294
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	295 orthanc.RegisterOnStoredInstanceCallback(OnStoredInstance)
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	296
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	297
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	298 Calling pydicom
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	299 ...............
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	300
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	301 .. highlight:: python
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	302
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	303 Here is a sample Python plugin that registers a REST callback to dump
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	304 the content of the dataset of one given DICOM instance stored in
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	305 Orthanc, using `pydicom <https://pydicom.github.io/>`__::
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	306
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	307 import io
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	308 import orthanc
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	309 import pydicom
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	310
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	311 def DecodeInstance(output, uri, **request):
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	312 if request['method'] == 'GET':
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	313 # Retrieve the instance ID from the regular expression (*)
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	314 instanceId = request['groups'][0]
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	315 # Get the content of the DICOM file
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	316 f = orthanc.GetDicomForInstance(instanceId)
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	317 # Parse it using pydicom
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	318 dicom = pydicom.dcmread(io.BytesIO(f))
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	319 # Return a string representation the dataset to the caller
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	320 output.AnswerBuffer(str(dicom), 'text/plain')
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	321 else:
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	322 output.SendMethodNotAllowed('GET')
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	323
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	324 orthanc.RegisterRestCallback('/pydicom/(.)', DecodeInstance) # ()
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	325
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	326 .. highlight:: bash
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	327
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	328 This can be called as follows::
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	329
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	330 $ curl http://localhost:8042/pydicom/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	331
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	332
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	333 Auto-routing studies
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	334 ....................
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	335
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	336 .. highlight:: python
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	337
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	338 Here is a sample Python plugin that routes any :ref:`stable study
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	339 <lua-callbacks>` to a modality named ``samples`` (as declared in the
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	340 ``DicomModalities`` configuration option)::
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	341
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	342 import orthanc
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	343
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	344 def OnChange(changeType, level, resourceId):
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	345 if changeType == orthanc.ChangeType.STABLE_STUDY:
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	346 print('Stable study: %s' % resourceId)
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	347 orthanc.RestApiPost('/modalities/sample/store', resourceId)
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	348
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	349 orthanc.RegisterOnChangeCallback(OnChange)
348 d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	350
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	351
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	352 Rendering a thumbnail using PIL/Pillow
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	353 ......................................
348 d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	354
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	355 .. highlight:: python
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	356
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	357 ::
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	358
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	359 from PIL import Image
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	360 import io
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	361 import orthanc
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	362
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	363 def DecodeInstance(output, uri, **request):
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	364 if request['method'] == 'GET':
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	365 # Retrieve the instance ID from the regular expression (*)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	366 instanceId = request['groups'][0]
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	367
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	368 # Render the instance, then open it in Python using PIL/Pillow
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	369 png = orthanc.RestApiGet('/instances/%s/rendered' % instanceId)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	370 image = Image.open(io.BytesIO(png))
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	371
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	372 # Downsize the image as a 64x64 thumbnail
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	373 image.thumbnail((64, 64), Image.ANTIALIAS)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	374
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	375 # Save the thumbnail as JPEG, then send the buffer to the caller
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	376 jpeg = io.BytesIO()
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	377 image.save(jpeg, format = "JPEG", quality = 80)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	378 jpeg.seek(0)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	379 output.AnswerBuffer(jpeg.read(), 'text/plain')
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	380
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	381 else:
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	382 output.SendMethodNotAllowed('GET')
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	383
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	384 orthanc.RegisterRestCallback('/pydicom/(.)', DecodeInstance) # ()
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	385
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	386
369 181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	387 .. _python-introspection:
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	388
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	389 Inspecting the available API
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	390 ............................
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	391
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	392 .. highlight:: python
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	393
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	394 Thanks to Python's introspection primitives, it is possible to inspect
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	395 the API of the ``orthanc`` module in order to dump all the available
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	396 features::
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	397
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	398 import inspect
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	399 import numbers
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	400 import orthanc
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	401
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	402 # Loop over the members of the "orthanc" module
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	403 for (name, obj) in inspect.getmembers(orthanc):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	404 if inspect.isroutine(obj):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	405 print('Function %s():\n Documentation: %s\n' % (name, inspect.getdoc(obj)))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	406
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	407 elif inspect.isclass(obj):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	408 print('Class %s:\n Documentation: %s' % (name, inspect.getdoc(obj)))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	409
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	410 # Loop over the members of the class
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	411 for (subname, subobj) in inspect.getmembers(obj):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	412 if isinstance(subobj, numbers.Number):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	413 print(' - Enumeration value %s: %s' % (subname, subobj))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	414 elif (not subname.startswith('_') and
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	415 inspect.ismethoddescriptor(subobj)):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	416 print(' - Method %s(): %s' % (subname, inspect.getdoc(subobj)))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	417 print('')
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	418
373 847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	419
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	420 .. _python-scheduler:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	421
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	422 Scheduling a task for periodic execution
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	423 ........................................
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	424
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	425 .. highlight:: python
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	426
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	427 The following Python script will periodically (every second) run the
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	428 function ``Hello()`` thanks to the ``threading`` module::
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	429
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	430 import orthanc
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	431 import threading
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	432
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	433 TIMER = None
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	434
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	435 def Hello():
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	436 global TIMER
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	437 TIMER = None
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	438 orthanc.LogWarning("In Hello()")
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	439 # Do stuff...
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	440 TIMER = threading.Timer(1, Hello) # Re-schedule after 1 second
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	441 TIMER.start()
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	442
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	443 def OnChange(changeType, level, resource):
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	444 if changeType == orthanc.ChangeType.ORTHANC_STARTED:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	445 orthanc.LogWarning("Starting the scheduler")
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	446 Hello()
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	447
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	448 elif changeType == orthanc.ChangeType.ORTHANC_STOPPED:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	449 if TIMER != None:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	450 orthanc.LogWarning("Stopping the scheduler")
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	451 TIMER.cancel()
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	452
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	453 orthanc.RegisterOnChangeCallback(OnChange)
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	454
378 16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	455
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	456 .. _python-metadata:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	457
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	458 Filtering and returning metadata
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	459 ................................
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	460
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	461 Besides the main DICOM tags, Orthanc associates some metadata to each
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	462 resource it stores (this includes the date of last update, the
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	463 transfer syntax, the remote AET...). People are often interested in
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	464 getting such metadata while calling the ``/tools/find`` route in the
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	465 :ref:`REST API <rest-find>`, or even in filtering this metadata the
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	466 same way they look for DICOM tags.
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	467
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	468 This feature is not built in the core of Orthanc, as metadata is not
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	469 indexed in the Orthanc database, contrarily to the main DICOM
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	470 tags. Filtering metadata requires a linear search over all the
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	471 matching resources, which induces a cost in the performance.
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	472
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	473 .. highlight:: python
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	474
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	475 Nevertheless, here is a full sample Python script that overwrites the
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	476 ``/tools/find`` route in order to give access to metadata::
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	477
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	478 import json
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	479 import orthanc
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	480 import re
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	481
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	482 # Get the path in the REST API to the given resource that was returned
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	483 # by a call to "/tools/find"
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	484 def GetPath(resource):
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	485 if resource['Type'] == 'Patient':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	486 return '/patients/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	487 elif resource['Type'] == 'Study':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	488 return '/studies/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	489 elif resource['Type'] == 'Series':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	490 return '/series/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	491 elif resource['Type'] == 'Instance':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	492 return '/instances/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	493 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	494 raise Exception('Unknown resource level')
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	495
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	496 def FindWithMetadata(output, uri, **request):
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	497 # The "/tools/find" route expects a POST method
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	498 if request['method'] != 'POST':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	499 output.SendMethodNotAllowed('POST')
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	500 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	501 # Parse the query provided by the user, and backup the "Expand" field
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	502 query = json.loads(request['body'])
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	503
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	504 if 'Expand' in query:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	505 originalExpand = query['Expand']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	506 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	507 originalExpand = False
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	508
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	509 # Call the core "/tools/find" route
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	510 query['Expand'] = True
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	511 answers = orthanc.RestApiPost('/tools/find', json.dumps(query))
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	512
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	513 # Loop over the matching resources
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	514 filteredAnswers = []
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	515 for answer in json.loads(answers):
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	516 try:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	517 # Read the metadata that is associated with the resource
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	518 metadata = json.loads(orthanc.RestApiGet('%s/metadata?expand' % GetPath(answer)))
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	519
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	520 # Check whether the metadata matches the regular expressions
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	521 # that were provided in the "Metadata" field of the user request
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	522 isMetadataMatch = True
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	523 if 'Metadata' in query:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	524 for (name, pattern) in query['Metadata'].items():
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	525 if name in metadata:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	526 value = metadata[name]
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	527 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	528 value = ''
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	529
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	530 if re.match(pattern, value) == None:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	531 isMetadataMatch = False
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	532 break
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	533
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	534 # If all the metadata matches the provided regular
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	535 # expressions, add the resource to the filtered answers
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	536 if isMetadataMatch:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	537 if originalExpand:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	538 answer['Metadata'] = metadata
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	539 filteredAnswers.append(answer)
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	540 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	541 filteredAnswers.append(answer['ID'])
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	542 except:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	543 # The resource was deleted since the call to "/tools/find"
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	544 pass
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	545
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	546 # Return the filtered answers in the JSON format
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	547 output.AnswerBuffer(json.dumps(filteredAnswers, indent = 3), 'application/json')
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	548
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	549 orthanc.RegisterRestCallback('/tools/find', FindWithMetadata)
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	550
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	551
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	552 Warning: In the sample above, the filtering of the metadata is
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	553 done using Python's `library for regular expressions
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	554 <https://docs.python.org/3/library/re.html>`__. It is evidently
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	555 possible to adapt this script in order to use the DICOM conventions
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	556 about `attribute matching
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	557 <http://dicom.nema.org/medical/dicom/2019e/output/chtml/part04/sect_C.2.2.2.html>`__.
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	558
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	559 .. highlight:: python
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	560
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	561 Here is a sample call to retrieve all the studies that were last
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	562 updated in 2019 thanks to this Python script::
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	563
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	564 $ curl http://localhost:8042/tools/find -d '{"Level":"Study","Query":{},"Expand":true,"Metadata":{"LastUpdate":"^2019.*$"}}'
369 181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	565
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	566
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	567 Performance and concurrency
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	568 ---------------------------
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	569
471 a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	570 Important: This section only applies to UNIX-like systems. The
a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	571 ``multiprocessing`` package will not work on Microsoft Windows as the
a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	572 latter OS has a different model for `forking processes
a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	573 <https://en.wikipedia.org/wiki/Fork_(system_call)>`__.
a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	574
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	575 .. highlight:: python
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	576
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	577 Let us consider the following sample Python script that makes a
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	578 CPU-intensive computation on a REST callback::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	579
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	580 import math
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	581 import orthanc
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	582 import time
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	583
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	584 # CPU-intensive computation taking about 4 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	585 def SlowComputation():
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	586 start = time.time()
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	587 for i in range(1000):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	588 for j in range(30000):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	589 math.sqrt(float(j))
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	590 end = time.time()
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	591 duration = (end - start)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	592 return 'computation done in %.03f seconds\n' % duration
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	593
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	594 def OnRest(output, uri, **request):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	595 answer = SlowComputation()
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	596 output.AnswerBuffer(answer, 'text/plain')
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	597
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	598 orthanc.RegisterRestCallback('/computation', OnRest)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	599
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	600
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	601 .. highlight:: text
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	602
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	603 Calling this REST route from the command-line returns the time that is
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	604 needed to compute 30 million times a squared root on your CPU::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	605
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	606 $ curl http://localhost:8042/computation
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	607 computation done in 4.208 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	608
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	609 Now, let us call this route three times concurrently (we use bash)::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	610
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	611 $ (curl http://localhost:8042/computation & curl http://localhost:8042/computation & curl http://localhost:8042/computation )
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	612 computation done in 11.262 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	613 computation done in 12.457 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	614 computation done in 13.360 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	615
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	616 As can be seen, the computation time has tripled. This means that the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	617 computations were not distributed across the available CPU cores.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	618 This might seem surprising, as Orthanc is a threaded server (in
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	619 Orthanc, a pool of C++ threads serves concurrent requests).
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	620
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	621 The explanation is that the Python interpreter (`CPython
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	622 <https://en.wikipedia.org/wiki/CPython>`__ actually) is built on the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	623 top of a so-called `Global Interpreter Lock (GIL)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	624 <https://en.wikipedia.org/wiki/Global_interpreter_lock>`__. The GIL is
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	625 basically a mutex that protects all the calls to the Python
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	626 interpreter. If multiple C++ threads from Orthanc call a Python
353 0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	627 callback, only one can proceed at any given time. Note however that
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	628 the GIL only applies to the Python script: The baseline REST API of
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	629 Orthanc is not affected by the GIL.
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	630
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	631 .. highlight:: python
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	632
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	633 The solution is to use the `multiprocessing primitives
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	634 <https://docs.python.org/3/library/multiprocessing.html>`__ of Python.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	635 The "master" Python interpreter that is initially started by the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	636 Orthanc plugin, can start several `children processes
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	637 <https://en.wikipedia.org/wiki/Process_(computing)>`__, each of these
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	638 processes running a separate Python interpreter. This allows to
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	639 offload intensive computations from the "master" Python interpreter of
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	640 Orthanc onto those "slave" interpreters. The ``multiprocessing``
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	641 library is actually quite straightforward to use::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	642
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	643 import math
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	644 import multiprocessing
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	645 import orthanc
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	646 import signal
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	647 import time
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	648
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	649 # CPU-intensive computation taking about 4 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	650 # (same code as above)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	651 def SlowComputation():
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	652 start = time.time()
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	653 for i in range(1000):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	654 for j in range(30000):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	655 math.sqrt(float(j))
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	656 end = time.time()
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	657 duration = (end - start)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	658 return 'computation done in %.03f seconds\n' % duration
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	659
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	660 # Ignore CTRL+C in the slave processes
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	661 def Initializer():
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	662 signal.signal(signal.SIGINT, signal.SIG_IGN)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	663
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	664 # Create a pool of 4 slave Python interpreters
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	665 POOL = multiprocessing.Pool(4, initializer = Initializer)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	666
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	667 def OnRest(output, uri, **request):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	668 # Offload the call to "SlowComputation" onto one slave process.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	669 # The GIL is unlocked until the slave sends its answer back.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	670 answer = POOL.apply(SlowComputation)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	671 output.AnswerBuffer(answer, 'text/plain')
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	672
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	673 orthanc.RegisterRestCallback('/computation', OnRest)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	674
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	675 .. highlight:: text
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	676
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	677 Here is now the result of calling this route three times concurrently::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	678
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	679 $ (curl http://localhost:8042/computation & curl http://localhost:8042/computation & curl http://localhost:8042/computation )
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	680 computation done in 4.211 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	681 computation done in 4.215 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	682 computation done in 4.225 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	683
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	684 As can be seen, the calls to the Python computation now fully run in
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	685 parallel (the time is cut down from 12 seconds to 4 seconds, the same
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	686 as for one isolated request).
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	687
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	688 Note also how the ``multiprocessing`` library allows to make a fine
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	689 control over the computational resources that are available to the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	690 Python script: The number of "slave" interpreters can be easily
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	691 changed in the constructor of the ``multiprocessing.Pool`` object, and
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	692 are fully independent of the threads used by the Orthanc server.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	693
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	694 .. highlight:: python
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	695
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	696 Very importantly, pay attention to the fact that only the "master"
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	697 Python interpreter has access to the Orthanc SDK. For instance, here
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	698 is how you would parse a DICOM file in a slave process::
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	699
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	700 import pydicom
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	701 import io
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	702
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	703 def OffloadedDicomParsing(dicom):
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	704 # No access to the "orthanc" library here, as we are in the slave process
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	705 dataset = pydicom.dcmread(io.BytesIO(dicom))
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	706 return str(dataset)
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	707
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	708 def OnRest(output, uri, **request):
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	709 # The call to "orthanc.RestApiGet()" is only possible in the master process
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	710 dicom = orthanc.RestApiGet('/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/file')
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	711 answer = POOL.apply(OffloadedDicomParsing, args = (dicom, ))
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	712 output.AnswerBuffer(answer, 'text/plain')
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	713
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	714 Communication primitives such as ``multiprocessing.Queue`` are
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	715 available to exchange messages from the "slave" Python interpreters to
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	716 the "master" Python interpreter if further calls to the Orthanc SDK
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	717 are required.
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	718
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	719 Obviously, an in-depth discussion about the ``multiprocessing``
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	720 library is out of the scope of this document. There are many
375 766fe39fdf35 typo Sebastien Jodogne <s.jodogne@gmail.com> parents: 374 diff changeset	721 references available on Internet. Also, note that ``threading`` is not
766fe39fdf35 typo Sebastien Jodogne <s.jodogne@gmail.com> parents: 374 diff changeset	722 useful here, as Python multithreading is also limited by the GIL, and
766fe39fdf35 typo Sebastien Jodogne <s.jodogne@gmail.com> parents: 374 diff changeset	723 is more targeted at dealing with costly I/O operations or with the
766fe39fdf35 typo Sebastien Jodogne <s.jodogne@gmail.com> parents: 374 diff changeset	724 :ref:`scheduling of commands <python-scheduler>`.

Mercurial > hg > orthanc-book

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