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

annotate Sphinx/source/plugins/python.rst @ 551:d0332c5a2cb8

Python plugin: excel generation example

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Sat, 05 Dec 2020 10:48:08 +0100
parents	fd5c1410db5b
children	4f3a6145ae34

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
528 50bdd7c7e9b9 Orthanc 1.8.0 Sebastien Jodogne <s.jodogne@gmail.com> parents: 513 diff changeset	21 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.8.0/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.
501 98592b9e7ad5 force version of python on os x Sebastien Jodogne <s.jodogne@gmail.com> parents: 490 diff changeset	140
98592b9e7ad5 force version of python on os x Sebastien Jodogne <s.jodogne@gmail.com> parents: 490 diff changeset	141 Note for OS X: As indicated by `Stephen Douglas Scotti
98592b9e7ad5 force version of python on os x Sebastien Jodogne <s.jodogne@gmail.com> parents: 490 diff changeset	142 <https://groups.google.com/g/orthanc-users/c/RnmZKFv8FaY/m/HhvOD2A2CAAJ>`__,
98592b9e7ad5 force version of python on os x Sebastien Jodogne <s.jodogne@gmail.com> parents: 490 diff changeset	143 here is a sample invocation of CMake to force the version of Python to
98592b9e7ad5 force version of python on os x Sebastien Jodogne <s.jodogne@gmail.com> parents: 490 diff changeset	144 be used on OS X::
98592b9e7ad5 force version of python on os x Sebastien Jodogne <s.jodogne@gmail.com> parents: 490 diff changeset	145
98592b9e7ad5 force version of python on os x Sebastien Jodogne <s.jodogne@gmail.com> parents: 490 diff changeset	146 $ cmake .. -DPYTHON_VERSION=3.8 -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release \
98592b9e7ad5 force version of python on os x Sebastien Jodogne <s.jodogne@gmail.com> parents: 490 diff changeset	147 -DPYTHON_LIBRARY=/usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/libpython3.8.dylib \
98592b9e7ad5 force version of python on os x Sebastien Jodogne <s.jodogne@gmail.com> parents: 490 diff changeset	148 -DPYTHON_INCLUDE_DIR=/usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/include/python3.8/
98592b9e7ad5 force version of python on os x Sebastien Jodogne <s.jodogne@gmail.com> parents: 490 diff changeset	149
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	150
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	151 Microsoft Windows
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	152 .................
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	153
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	154 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	155 <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	156
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	157 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	158 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	159 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	160
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	161 .. highlight:: text
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	162
442 8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	163 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	164 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	165 invoking CMake. For instance::
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	166
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	167 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	168 -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	169
442 8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	170 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	171 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	172 (``.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	173 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	174 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	175
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 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	177 (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	178 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	179
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 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	181 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	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 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	184 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	185 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	186 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	187
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	188 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	189 -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	190 -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	191
ffe62e6c086f Added a note about the debug libraries when building under Windows with Visual Studio. Benjamin Golinvaux <bgo@osimis.io> parents: 375 diff changeset	192 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	193 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	194
442 8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	195 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	196
8b2c648c0f46 clarifications about windows precompiled binaries Sebastien Jodogne <s.jodogne@gmail.com> parents: 405 diff changeset	197
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	198 Configuration options
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	199 ---------------------
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	200
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	201 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	202 are the following:
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	203
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	204 * ``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	205 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	206 started.
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	207
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	208 * ``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	209 verbose.
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	210
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	211
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	212 Samples
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
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	215 Extending the REST API
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
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	218 .. highlight:: python
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	219
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	220 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	221 REST API::
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	222
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	223 import orthanc
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	224 import pprint
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	225
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	226 def OnRest(output, uri, **request):
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	227 pprint.pprint(request)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	228 print('Accessing uri: %s' % uri)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	229 output.AnswerBuffer('ok\n', 'text/plain')
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 orthanc.RegisterRestCallback('/(to)(t)o', OnRest)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	232 orthanc.RegisterRestCallback('/tata', OnRest)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	233
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	234 .. highlight:: json
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 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	237 (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	238
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 "Plugins" : [ "." ],
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	241 "PythonScript" : "rest.py",
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	242 "PythonVerbose" : false
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	243 }
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	244
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	245 .. highlight:: bash
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	246
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	247 The route can then be accessed as::
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	248
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	249 $ curl http://localhost:8042/toto
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	250 ok
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	251
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	252
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	253 .. _python-changes:
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	254
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	255 Listening to changes
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
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	258 .. highlight:: python
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	259
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	260 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	261
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	262 import orthanc
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	263
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	264 def OnChange(changeType, level, resource):
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	265 if changeType == orthanc.ChangeType.ORTHANC_STARTED:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	266 print('Started')
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 with open('/tmp/sample.dcm', 'rb') as f:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	269 orthanc.RestApiPost('/instances', f.read())
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	270
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	271 elif changeType == orthanc.ChangeType.ORTHANC_STOPPED:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	272 print('Stopped')
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 elif changeType == orthanc.ChangeType.NEW_INSTANCE:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	275 print('A new instance was uploaded: %s' % resource)
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	276
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	277 orthanc.RegisterOnChangeCallback(OnChange)
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	278
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 Accessing the content of a new instance
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	281 .......................................
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	282
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	283 .. highlight:: python
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	284
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
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	287 import orthanc
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	288 import json
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	289 import pprint
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	290
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	291 def OnStoredInstance(dicom, instanceId):
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	292 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	293 instanceId, dicom.GetInstanceSize(),
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	294 dicom.GetInstanceMetadata('TransferSyntax'),
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	295 dicom.GetInstanceMetadata('SopClassUid')))
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	296
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	297 # Print the origin information
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	298 if dicom.GetInstanceOrigin() == orthanc.InstanceOrigin.DICOM_PROTOCOL:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	299 print('This instance was received through the DICOM protocol')
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	300 elif dicom.GetInstanceOrigin() == orthanc.InstanceOrigin.REST_API:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	301 print('This instance was received through the REST API')
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	302
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	303 # Print the DICOM tags
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	304 pprint.pprint(json.loads(dicom.GetInstanceSimplifiedJson()))
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	305
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	306 orthanc.RegisterOnStoredInstanceCallback(OnStoredInstance)
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	307
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	308
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	309 Calling 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
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	312 .. highlight:: python
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	313
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	314 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	315 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	316 Orthanc, using `pydicom <https://pydicom.github.io/>`__::
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	317
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	318 import io
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	319 import orthanc
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	320 import pydicom
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	321
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	322 def DecodeInstance(output, uri, **request):
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	323 if request['method'] == 'GET':
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	324 # Retrieve the instance ID from the regular expression (*)
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	325 instanceId = request['groups'][0]
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	326 # Get the content of the DICOM file
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	327 f = orthanc.GetDicomForInstance(instanceId)
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	328 # Parse it using pydicom
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	329 dicom = pydicom.dcmread(io.BytesIO(f))
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	330 # Return a string representation the dataset to the caller
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	331 output.AnswerBuffer(str(dicom), 'text/plain')
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	332 else:
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	333 output.SendMethodNotAllowed('GET')
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	334
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	335 orthanc.RegisterRestCallback('/pydicom/(.)', DecodeInstance) # ()
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	336
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	337 .. highlight:: bash
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	338
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	339 This can be called as follows::
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	340
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	341 $ curl http://localhost:8042/pydicom/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	342
347 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 Auto-routing studies
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	345 ....................
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	346
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	347 .. highlight:: python
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 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	350 <lua-callbacks>` to a modality named ``samples`` (as declared in the
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	351 ``DicomModalities`` configuration option)::
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	352
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	353 import orthanc
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	354
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	355 def OnChange(changeType, level, resourceId):
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	356 if changeType == orthanc.ChangeType.STABLE_STUDY:
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	357 print('Stable study: %s' % resourceId)
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	358 orthanc.RestApiPost('/modalities/sample/store', resourceId)
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	359
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	360 orthanc.RegisterOnChangeCallback(OnChange)
348 d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	361
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	362
539 fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	363 Note that, if you want to use an orthanc plugin to transfer the study,
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	364 you should use the ``RestApiPostAfterPlugins()`` method::
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	365
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	366 import orthanc
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	367
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	368 def OnChange(changeType, level, resourceId):
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	369 if changeType == orthanc.ChangeType.STABLE_STUDY:
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	370 print('Stable study: %s' % resourceId)
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	371 orthanc.RestApiPostAfterPlugins('/dicom-web/servers/sample/store', resourceId)
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	372
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	373 orthanc.RegisterOnChangeCallback(OnChange)
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	374
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	375
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	376 Rendering a thumbnail using PIL/Pillow
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	377 ......................................
348 d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	378
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	379 .. highlight:: python
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 ::
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	382
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	383 from PIL import Image
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	384 import io
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	385 import orthanc
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	386
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	387 def DecodeInstance(output, uri, **request):
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	388 if request['method'] == 'GET':
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	389 # Retrieve the instance ID from the regular expression (*)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	390 instanceId = request['groups'][0]
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	391
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	392 # Render the instance, then open it in Python using PIL/Pillow
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	393 png = orthanc.RestApiGet('/instances/%s/rendered' % instanceId)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	394 image = Image.open(io.BytesIO(png))
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	395
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	396 # Downsize the image as a 64x64 thumbnail
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	397 image.thumbnail((64, 64), Image.ANTIALIAS)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	398
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	399 # 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	400 jpeg = io.BytesIO()
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	401 image.save(jpeg, format = "JPEG", quality = 80)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	402 jpeg.seek(0)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	403 output.AnswerBuffer(jpeg.read(), 'text/plain')
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	404
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	405 else:
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	406 output.SendMethodNotAllowed('GET')
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	407
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	408 orthanc.RegisterRestCallback('/pydicom/(.)', DecodeInstance) # ()
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	409
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	410
369 181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	411 .. _python-introspection:
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	412
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	413 Inspecting the available API
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	414 ............................
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	415
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	416 .. highlight:: python
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	417
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	418 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	419 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	420 features::
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	421
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	422 import inspect
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	423 import numbers
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	424 import orthanc
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	425
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	426 # Loop over the members of the "orthanc" module
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	427 for (name, obj) in inspect.getmembers(orthanc):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	428 if inspect.isroutine(obj):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	429 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	430
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	431 elif inspect.isclass(obj):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	432 print('Class %s:\n Documentation: %s' % (name, inspect.getdoc(obj)))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	433
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	434 # Loop over the members of the class
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	435 for (subname, subobj) in inspect.getmembers(obj):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	436 if isinstance(subobj, numbers.Number):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	437 print(' - Enumeration value %s: %s' % (subname, subobj))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	438 elif (not subname.startswith('_') and
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	439 inspect.ismethoddescriptor(subobj)):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	440 print(' - Method %s(): %s' % (subname, inspect.getdoc(subobj)))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	441 print('')
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	442
373 847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	443
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	444 .. _python-scheduler:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	445
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	446 Scheduling a task for periodic execution
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
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	449 .. highlight:: python
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	450
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	451 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	452 function ``Hello()`` thanks to the ``threading`` module::
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	453
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	454 import orthanc
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	455 import threading
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	456
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	457 TIMER = None
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	458
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	459 def Hello():
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	460 global TIMER
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	461 TIMER = None
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	462 orthanc.LogWarning("In Hello()")
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	463 # Do stuff...
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	464 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	465 TIMER.start()
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	466
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	467 def OnChange(changeType, level, resource):
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	468 if changeType == orthanc.ChangeType.ORTHANC_STARTED:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	469 orthanc.LogWarning("Starting the scheduler")
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	470 Hello()
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	471
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	472 elif changeType == orthanc.ChangeType.ORTHANC_STOPPED:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	473 if TIMER != None:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	474 orthanc.LogWarning("Stopping the scheduler")
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	475 TIMER.cancel()
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	476
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	477 orthanc.RegisterOnChangeCallback(OnChange)
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	478
378 16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	479
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	480 .. _python-metadata:
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 Filtering and returning metadata
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	483 ................................
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	484
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	485 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	486 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	487 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	488 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	489 :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	490 same way they look for DICOM tags.
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	491
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	492 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	493 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	494 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	495 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	496
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	497 .. highlight:: python
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	498
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	499 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	500 ``/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	501
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	502 import json
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	503 import orthanc
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	504 import re
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	505
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	506 # 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	507 # by a call to "/tools/find"
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	508 def GetPath(resource):
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	509 if resource['Type'] == 'Patient':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	510 return '/patients/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	511 elif resource['Type'] == 'Study':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	512 return '/studies/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	513 elif resource['Type'] == 'Series':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	514 return '/series/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	515 elif resource['Type'] == 'Instance':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	516 return '/instances/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	517 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	518 raise Exception('Unknown resource level')
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 def FindWithMetadata(output, uri, **request):
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	521 # 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	522 if request['method'] != 'POST':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	523 output.SendMethodNotAllowed('POST')
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	524 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	525 # 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	526 query = json.loads(request['body'])
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	527
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	528 if 'Expand' in query:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	529 originalExpand = query['Expand']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	530 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	531 originalExpand = False
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	532
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	533 # Call the core "/tools/find" route
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	534 query['Expand'] = True
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	535 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	536
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	537 # Loop over the matching resources
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	538 filteredAnswers = []
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	539 for answer in json.loads(answers):
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	540 try:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	541 # 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	542 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	543
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	544 # 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	545 # 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	546 isMetadataMatch = True
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	547 if 'Metadata' in query:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	548 for (name, pattern) in query['Metadata'].items():
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	549 if name in metadata:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	550 value = metadata[name]
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	551 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	552 value = ''
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	553
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	554 if re.match(pattern, value) == None:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	555 isMetadataMatch = False
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	556 break
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	557
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	558 # 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	559 # 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	560 if isMetadataMatch:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	561 if originalExpand:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	562 answer['Metadata'] = metadata
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	563 filteredAnswers.append(answer)
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	564 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	565 filteredAnswers.append(answer['ID'])
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	566 except:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	567 # 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	568 pass
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	569
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	570 # 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	571 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	572
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	573 orthanc.RegisterRestCallback('/tools/find', FindWithMetadata)
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	574
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	575
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	576 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	577 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	578 <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	579 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	580 about `attribute matching
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	581 <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	582
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	583 .. highlight:: bash
378 16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	584
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	585 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	586 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	587
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	588 $ 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	589
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	590
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	591 .. _python-paging:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	592
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	593 Implementing basic paging
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	594 .........................
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	595
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	596 .. highlight:: python
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	597
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	598 As explained in the FAQ, the :ref:`Orthanc Explorer interface is
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	599 low-level <improving-interface>`, and is not adapted for
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	600 end-users. One common need is to implement paging of studies, which
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	601 calls for server-side sorting of studies. This can be done using the
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	602 following sample Python plugin that registers a new route
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	603 ``/sort-studies`` in the REST API of Orthanc::
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	604
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	605 import json
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	606 import orthanc
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	607
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	608 def GetStudyDate(study):
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	609 if 'StudyDate' in study['MainDicomTags']:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	610 return study['MainDicomTags']['StudyDate']
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	611 else:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	612 return ''
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	613
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	614 def SortStudiesByDate(output, uri, **request):
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	615 if request['method'] == 'GET':
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	616 # Retrieve all the studies
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	617 studies = json.loads(orthanc.RestApiGet('/studies?expand'))
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	618
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	619 # Sort the studies according to the "StudyDate" DICOM tag
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	620 studies = sorted(studies, key = GetStudyDate)
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	621
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	622 # Read the limit/offset arguments provided by the user
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	623 offset = 0
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	624 if 'offset' in request['get']:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	625 offset = int(request['get']['offset'])
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	626
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	627 limit = 0
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	628 if 'limit' in request['get']:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	629 limit = int(request['get']['limit'])
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	630
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	631 # Truncate the list of studies
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	632 if limit == 0:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	633 studies = studies[offset : ]
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	634 else:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	635 studies = studies[offset : offset + limit]
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	636
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	637 # Return the truncated list of studies
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	638 output.AnswerBuffer(json.dumps(studies), 'application/json')
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	639 else:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	640 output.SendMethodNotAllowed('GET')
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	641
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	642 orthanc.RegisterRestCallback('/sort-studies', SortStudiesByDate)
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	643
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	644
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	645 .. highlight:: bash
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	646
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	647 Here is a sample call to this new REST route, that could be issued by
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	648 any JavaScript framework (the ``json_pp`` command-line pretty-prints a
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	649 JSON file)::
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	650
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	651 $ curl http://localhost:8042/sort-studies \| json_pp
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	652
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	653 This route also implement paging (i.e. it can limit and offset the
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	654 returned studies)::
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	655
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	656 $ curl 'http://localhost:8042/sort-studies?offset=2&limit=2' \| json_pp
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	657
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	658 Obviously, this basic sample can be improved in many ways. To improve
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	659 performance, one could for instance cache the result of
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	660 ``/studies?expand`` in memory by :ref:`listening to changes
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	661 <python-changes>` in the list of studies
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	662 (cf. ``orthanc.ChangeType.NEW_STUDY`` and
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	663 ``orthanc.ChangeType.DELETED``).
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	664
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	665
551 d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	666 .. _python_excel:
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	667
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	668 Creating a Microsoft Excel report
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	669 .................................
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	670
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	671 .. highlight:: python
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	672
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	673 As Orthanc plugins have access to any installed Python module, it is
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	674 very easy to implement a server-side plugin that generates a report in
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	675 the Microsoft Excel ``.xls`` format. Here is a working example::
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	676
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	677 import StringIO
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	678 import json
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	679 import orthanc
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	680 import xlwt
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	681
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	682 def CreateExcelReport(output, uri, **request):
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	683 if request['method'] != 'GET' :
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	684 output.SendMethodNotAllowed('GET')
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	685 else:
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	686 # Create an Excel writer
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	687 excel = xlwt.Workbook()
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	688 sheet = excel.add_sheet('Studies')
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	689
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	690 # Loop over the studies stored in Orthanc
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	691 row = 0
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	692 studies = orthanc.RestApiGet('/studies?expand')
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	693 for study in json.loads(studies):
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	694 sheet.write(row, 0, study['PatientMainDicomTags'].get('PatientID'))
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	695 sheet.write(row, 1, study['PatientMainDicomTags'].get('PatientName'))
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	696 sheet.write(row, 2, study['MainDicomTags'].get('StudyDescription'))
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	697 row += 1
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	698
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	699 # Serialize the Excel workbook to a string, and return it to the caller
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	700 # https://stackoverflow.com/a/15649139/881731
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	701 b = StringIO.StringIO()
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	702 excel.save(b)
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	703 output.AnswerBuffer(b.getvalue(), 'application/vnd.ms-excel')
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	704
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	705 orthanc.RegisterRestCallback('/report.xls', CreateExcelReport)
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	706
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	707 If opening the ``http://localhost:8042/report.xls`` URI, this Python
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	708 will generate a workbook with one sheet that contains the list of
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	709 studies, with the patient ID, the patient name and the study
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	710 description.
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	711
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	712
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	713 Performance and concurrency
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	714 ---------------------------
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	715
471 a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	716 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	717 ``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	718 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	719 <https://en.wikipedia.org/wiki/Fork_(system_call)>`__.
a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	720
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	721 .. highlight:: python
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	722
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	723 Let us consider the following sample Python script that makes a
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	724 CPU-intensive computation on a REST callback::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	725
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	726 import math
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	727 import orthanc
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	728 import time
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	729
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	730 # CPU-intensive computation taking about 4 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	731 def SlowComputation():
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	732 start = time.time()
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	733 for i in range(1000):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	734 for j in range(30000):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	735 math.sqrt(float(j))
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	736 end = time.time()
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	737 duration = (end - start)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	738 return 'computation done in %.03f seconds\n' % duration
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	739
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	740 def OnRest(output, uri, **request):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	741 answer = SlowComputation()
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	742 output.AnswerBuffer(answer, 'text/plain')
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	743
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	744 orthanc.RegisterRestCallback('/computation', OnRest)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	745
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	746
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	747 .. highlight:: text
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	748
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	749 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	750 needed to compute 30 million times a squared root on your CPU::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	751
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	752 $ curl http://localhost:8042/computation
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	753 computation done in 4.208 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	754
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	755 Now, let us call this route three times concurrently (we use bash)::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	756
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	757 $ (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	758 computation done in 11.262 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	759 computation done in 12.457 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	760 computation done in 13.360 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	761
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	762 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	763 computations were not distributed across the available CPU cores.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	764 This might seem surprising, as Orthanc is a threaded server (in
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	765 Orthanc, a pool of C++ threads serves concurrent requests).
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	766
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	767 The explanation is that the Python interpreter (`CPython
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	768 <https://en.wikipedia.org/wiki/CPython>`__ actually) is built on the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	769 top of a so-called `Global Interpreter Lock (GIL)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	770 <https://en.wikipedia.org/wiki/Global_interpreter_lock>`__. The GIL is
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	771 basically a mutex that protects all the calls to the Python
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	772 interpreter. If multiple C++ threads from Orthanc call a Python
353 0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	773 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	774 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	775 Orthanc is not affected by the GIL.
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	776
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	777 .. highlight:: python
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	778
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	779 The solution is to use the `multiprocessing primitives
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	780 <https://docs.python.org/3/library/multiprocessing.html>`__ of Python.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	781 The "master" Python interpreter that is initially started by the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	782 Orthanc plugin, can start several `children processes
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	783 <https://en.wikipedia.org/wiki/Process_(computing)>`__, each of these
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	784 processes running a separate Python interpreter. This allows to
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	785 offload intensive computations from the "master" Python interpreter of
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	786 Orthanc onto those "slave" interpreters. The ``multiprocessing``
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	787 library is actually quite straightforward to use::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	788
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	789 import math
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	790 import multiprocessing
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	791 import orthanc
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	792 import signal
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	793 import time
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	794
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	795 # CPU-intensive computation taking about 4 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	796 # (same code as above)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	797 def SlowComputation():
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	798 start = time.time()
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	799 for i in range(1000):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	800 for j in range(30000):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	801 math.sqrt(float(j))
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	802 end = time.time()
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	803 duration = (end - start)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	804 return 'computation done in %.03f seconds\n' % duration
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	805
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	806 # Ignore CTRL+C in the slave processes
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	807 def Initializer():
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	808 signal.signal(signal.SIGINT, signal.SIG_IGN)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	809
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	810 # Create a pool of 4 slave Python interpreters
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	811 POOL = multiprocessing.Pool(4, initializer = Initializer)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	812
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	813 def OnRest(output, uri, **request):
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	814 # Offload the call to "SlowComputation" onto one slave process.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	815 # The GIL is unlocked until the slave sends its answer back.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	816 answer = POOL.apply(SlowComputation)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	817 output.AnswerBuffer(answer, 'text/plain')
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	818
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	819 orthanc.RegisterRestCallback('/computation', OnRest)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	820
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	821 .. highlight:: text
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	822
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	823 Here is now the result of calling this route three times concurrently::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	824
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	825 $ (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	826 computation done in 4.211 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	827 computation done in 4.215 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	828 computation done in 4.225 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	829
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	830 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	831 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	832 as for one isolated request).
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	833
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	834 Note also how the ``multiprocessing`` library allows to make a fine
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	835 control over the computational resources that are available to the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	836 Python script: The number of "slave" interpreters can be easily
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	837 changed in the constructor of the ``multiprocessing.Pool`` object, and
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	838 are fully independent of the threads used by the Orthanc server.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	839
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	840 .. highlight:: python
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	841
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	842 Very importantly, pay attention to the fact that only the "master"
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	843 Python interpreter has access to the Orthanc SDK. For instance, here
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	844 is how you would parse a DICOM file in a slave process::
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	845
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	846 import pydicom
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	847 import io
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	848
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	849 def OffloadedDicomParsing(dicom):
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	850 # 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	851 dataset = pydicom.dcmread(io.BytesIO(dicom))
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	852 return str(dataset)
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	853
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	854 def OnRest(output, uri, **request):
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	855 # The call to "orthanc.RestApiGet()" is only possible in the master process
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	856 dicom = orthanc.RestApiGet('/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/file')
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	857 answer = POOL.apply(OffloadedDicomParsing, args = (dicom, ))
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	858 output.AnswerBuffer(answer, 'text/plain')
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	859
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	860 Communication primitives such as ``multiprocessing.Queue`` are
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	861 available to exchange messages from the "slave" Python interpreters to
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	862 the "master" Python interpreter if further calls to the Orthanc SDK
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	863 are required.
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	864
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	865 Obviously, an in-depth discussion about the ``multiprocessing``
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	866 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	867 references available on Internet. Also, note that ``threading`` is not
766fe39fdf35 typo Sebastien Jodogne <s.jodogne@gmail.com> parents: 374 diff changeset	868 useful here, as Python multithreading is also limited by the GIL, and
766fe39fdf35 typo Sebastien Jodogne <s.jodogne@gmail.com> parents: 374 diff changeset	869 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	870 :ref:`scheduling of commands <python-scheduler>`.

Mercurial > hg > orthanc-book

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