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

annotate Sphinx/source/plugins/python.rst @ 747:56d48f6e52cc

catching exceptions in python plugins

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Mon, 09 Aug 2021 18:29:38 +0200
parents	97e6a0431c5e
children	a296fe06fd86

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
709 9d5e17100a8d update statistics from 2.0 to 3.2 Sebastien Jodogne <s.jodogne@gmail.com> parents: 708 diff changeset	19 than :ref:`Lua scripts <lua>`. The largest part of the Python API is
9d5e17100a8d update statistics from 2.0 to 3.2 Sebastien Jodogne <s.jodogne@gmail.com> parents: 708 diff changeset	20 automatically generated from the `Orthanc plugin SDK in C
741 97e6a0431c5e Orthanc 1.9.6 Sebastien Jodogne <s.jodogne@gmail.com> parents: 735 diff changeset	21 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.9.6/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
709 9d5e17100a8d update statistics from 2.0 to 3.2 Sebastien Jodogne <s.jodogne@gmail.com> parents: 708 diff changeset	25 As of release 3.2 of the plugin, the coverage of the C SDK is about
9d5e17100a8d update statistics from 2.0 to 3.2 Sebastien Jodogne <s.jodogne@gmail.com> parents: 708 diff changeset	26 87% (138 functions are automatically wrapped in Python out of a total
9d5e17100a8d update statistics from 2.0 to 3.2 Sebastien Jodogne <s.jodogne@gmail.com> parents: 708 diff changeset	27 of 158 functions from the Orthanc SDK 1.8.1).
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
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	69 .. highlight:: python
364 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 Here is a basic Python script that registers two new routes in the
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	219 REST API:
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	220
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	221 .. literalinclude:: python/extending-rest-api.py
a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	222 :language: python
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	223
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	224 .. highlight:: json
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 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	227 (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	228
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	229 {
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	230 "Plugins" : [ "." ],
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	231 "PythonScript" : "rest.py",
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	232 "PythonVerbose" : false
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
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	235 .. highlight:: bash
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	236
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	237 The route can then be accessed as::
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 $ curl http://localhost:8042/toto
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	240 ok
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	241
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	242
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	243 .. _python-changes:
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	244
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	245 Listening to changes
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	246 ....................
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	247
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	248 This sample uploads a DICOM file as soon as Orthanc is started:
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	249
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	250 .. literalinclude:: python/listening-changes.py
a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	251 :language: python
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	252
590 404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	253
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	254 .. warning::
600 4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	255 In releases <= 3.0 of the Python plugin, deadlocks might emerge if
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	256 you call other core primitives of Orthanc (such as the REST API) in
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	257 your callback function. This issue has been `fixed in release 3.1
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	258 <https://hg.orthanc-server.com/orthanc-python/rev/46fe70776d61>`__.
590 404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	259
600 4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	260 As a temporary workaround against such deadlocks in releases <=
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	261 3.0, if you have to call other primitives of Orthanc, you should make
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	262 these calls in a separate thread, passing the pending events to be
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	263 processed through a message queue. Here is the template of a possible
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	264 solution to postpone such deadlocks as much as possible by relying on
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	265 the multithreading primitives of Python:
591 2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	266
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	267 .. literalinclude:: python/changes-deadlock-3.0.py
a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	268 :language: python
600 4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	269
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	270 Beware that this workaround is imperfect and deadlocks have been
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	271 observed even if using it! Make sure to upgrade your plugin to solve
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	272 this issue for good. Note that this temporary workaround is not needed
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	273 in releases >= 3.1 of the plugin.
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	274
591 2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	275
590 404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	276
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	277 Accessing the content of a new instance
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	278 .......................................
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	279
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	280 .. literalinclude:: python/accessing-new-instance.py
a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	281 :language: python
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	282
590 404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	283 .. warning::
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	284 Your callback function will be called synchronously with
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	285 the core of Orthanc. This implies that deadlocks might emerge if
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	286 you call other core primitives of Orthanc in your callback (such
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	287 deadlocks are particular visible in the presence of other plugins
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	288 or Lua scripts). It is thus strongly advised to avoid any call to
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	289 the REST API of Orthanc in the callback. If you have to call other
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	290 primitives of Orthanc, you should make these calls in a separate
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	291 thread, passing the pending events to be processed through a
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	292 message queue.
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	293
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	294
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	295 Calling pydicom
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	296 ...............
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	297
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	298 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	299 the content of the dataset of one given DICOM instance stored in
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	300 Orthanc, using `pydicom <https://pydicom.github.io/>`__:
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	301
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	302 .. literalinclude:: python/pydicom.py
a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	303 :language: python
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	304
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	305 .. highlight:: bash
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	306
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	307 This callback can be called as follows::
346 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 $ curl http://localhost:8042/pydicom/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	310
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	311
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	312 Auto-routing studies
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	313 ....................
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	314
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	315 Here is a sample Python plugin that routes any :ref:`stable study
642 a76d83a00c68 definition of stable resources Sebastien Jodogne <s.jodogne@gmail.com> parents: 638 diff changeset	316 <stable-resources>` to a modality named ``samples`` (as declared in the
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	317 ``DicomModalities`` configuration option):
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	318
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	319 .. literalinclude:: python/autorouting-1.py
a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	320 :language: python
348 d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	321
539 fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	322 Note that, if you want to use an orthanc plugin to transfer the study,
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	323 you should use the ``RestApiPostAfterPlugins()`` method:
539 fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	324
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	325 .. literalinclude:: python/autorouting-2.py
a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	326 :language: python
a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	327
539 fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	328
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	329 Rendering a thumbnail using PIL/Pillow
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	330 ......................................
348 d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	331
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	332 .. literalinclude:: python/pil.py
a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	333 :language: python
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	334
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	335
369 181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	336 .. _python-introspection:
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	337
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	338 Inspecting the available API
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	339 ............................
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	340
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	341 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	342 the API of the ``orthanc`` module in order to dump all the available
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	343 features:
369 181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	344
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	345 .. literalinclude:: python/inspect-api.py
a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	346 :language: python
369 181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	347
703 a589668768d7 moving python samples in separate files (2) Sebastien Jodogne <s.jodogne@gmail.com> parents: 702 diff changeset	348
373 847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	349 .. _python-scheduler:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	350
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	351 Scheduling a task for periodic execution
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	352 ........................................
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	353
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	354 The following Python script will periodically (every second) run the
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	355 function ``Hello()`` thanks to the ``threading`` module:
373 847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	356
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	357 .. literalinclude:: python/periodic-execution.py
ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	358 :language: python
373 847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	359
378 16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	360
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	361 .. _python-metadata:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	362
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	363 Filtering and returning metadata
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	364 ................................
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	365
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	366 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	367 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	368 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	369 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	370 :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	371 same way they look for DICOM tags.
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	372
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	373 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	374 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	375 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	376 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	377
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	378 Nevertheless, here is a full sample Python script that overwrites the
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	379 ``/tools/find`` route in order to give access to metadata:
378 16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	380
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	381 .. literalinclude:: python/filtering-metadata.py
ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	382 :language: python
378 16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	383
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	384
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	385 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	386 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	387 <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	388 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	389 about `attribute matching
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	390 <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	391
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	392 .. highlight:: bash
378 16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	393
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	394 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	395 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	396
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	397 $ 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	398
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	399
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	400 .. _python-paging:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	401
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	402 Implementing basic paging
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	403 .........................
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	404
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	405 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	406 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	407 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	408 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	409 following sample Python plugin that registers a new route
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	410 ``/sort-studies`` in the REST API of Orthanc:
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	411
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	412 .. literalinclude:: python/paging.py
ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	413 :language: python
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	414
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	415 .. highlight:: bash
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	416
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	417 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	418 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	419 JSON file)::
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	420
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	421 $ 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	422
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	423 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	424 returned studies)::
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	425
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	426 $ 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	427
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	428 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	429 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	430 ``/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	431 <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	432 (cf. ``orthanc.ChangeType.NEW_STUDY`` and
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	433 ``orthanc.ChangeType.DELETED``).
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	434
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	435
551 d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	436 .. _python_excel:
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	437
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	438 Creating a Microsoft Excel report
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	439 .................................
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	440
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	441 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	442 very easy to implement a server-side plugin that generates a report in
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	443 the Microsoft Excel ``.xls`` format. Here is a working example:
551 d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	444
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	445 .. literalinclude:: python/excel.py
ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	446 :language: python
551 d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	447
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	448 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	449 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	450 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	451 description.
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	452
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	453
556 6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	454 .. _python_authorization:
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	455
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	456 Forbid or allow access to REST resources (authorization, new in 3.0)
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	457 ....................................................................
556 6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	458
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	459 The following Python script installs a callback that is triggered
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	460 whenever the HTTP server of Orthanc is accessed:
556 6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	461
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	462 .. literalinclude:: python/authorization-1.py
ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	463 :language: python
556 6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	464
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	465
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	466 If access is not granted, the ``Filter`` callback must return
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	467 ``False``. As a consequence, the HTTP status code would be set to
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	468 ``403 Forbidden``. If access is granted, the ``Filter`` must return
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	469 ``true``. The ``request`` argument contains more information about the
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	470 request (such as the HTTP headers, the IP address of the caller and
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	471 the GET arguments).
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	472
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	473 Note that this is similar to the ``IncomingHttpRequestFilter()``
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	474 callback that is available in :ref:`Lua scripts <lua-filter-rest>`.
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	475
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	476 Thanks to Python, it is extremely easy to call remote Web services for
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	477 authorization. Here is an example using the ``requests`` library:
556 6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	478
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	479 .. literalinclude:: python/authorization-2.py
ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	480 :language: python
556 6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	481
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	482 This filter could be used together with the following Web service
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	483 implemented using `Node.js
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	484 <https://en.wikipedia.org/wiki/Node.js>`__:
556 6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	485
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	486 .. literalinclude:: python/authorization-node-service.js
ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	487 :language: javascript
556 6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	488
6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	489
708 cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	490 .. _python_lookup_dictionary:
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	491
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	492 Lookup DICOM dictionary (new in 3.2)
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	493 ....................................
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	494
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	495 Python plugins can access the dictionary of the DICOM tags that are
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	496 handled by Orthanc:
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	497
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	498 .. literalinclude:: python/lookup-dictionary.py
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	499 :language: python
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	500
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	501 .. highlight:: text
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	502
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	503 Note how Python introspection is used in order to map the values in
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	504 enumeration ``orthanc.ValueRepresentation`` to a string description of
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	505 the value representation. If started, the plugin above would output
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	506 the following information in the Orthanc logs::
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	507
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	508 W0611 14:04:08.563957 PluginsManager.cpp:168] Entry in the dictionary: {
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	509 "Element": 32,
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	510 "Group": 16,
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	511 "MaxMultiplicity": 1,
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	512 "MinMultiplicity": 1,
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	513 "ValueRepresentation": 11
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	514 }
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	515 W0611 14:04:08.563975 PluginsManager.cpp:168] Name of the value representation: LO
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	516
cd70d23f34bc Lookup DICOM dictionary in Python scripts Sebastien Jodogne <s.jodogne@gmail.com> parents: 707 diff changeset	517
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	518 .. _python_create_dicom:
556 6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	519
696 29e49f03dc27 fix Sebastien Jodogne <s.jodogne@gmail.com> parents: 695 diff changeset	520 Creating DICOM instances (new in 3.2)
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	521 .....................................
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	522
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	523 The following sample Python script will write on the disk a new DICOM
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	524 instance including the traditional Lena sample image, and will decode
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	525 the single frame of this DICOM instance:
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	526
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	527 .. literalinclude:: python/create-dicom.py
ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	528 :language: python
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	529
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	530
706 c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	531 .. _python_pil_conversions:
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	532
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	533 Conversions between Orthanc and Python images (new in 3.2)
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	534 ..........................................................
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	535
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	536 The Python method ``orthanc.Image.GetImageBuffer()`` returns a copy of
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	537 the memory buffer of an image that is handled Orthanc. Conversely, the
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	538 Python function ``orthanc.CreateImageFromBuffer()`` can be used to
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	539 create an Orthanc image from a Python buffer. Taken together, these
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	540 two functions can be used to do bidirectional conversions between
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	541 Orthanc images and Python images.
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	542
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	543 Here is a full working example using PIL/Pillow that shows how to
707 daf07750e901 typo Sebastien Jodogne <s.jodogne@gmail.com> parents: 706 diff changeset	544 decode one frame of a DICOM instance using Orthanc, then to modify
daf07750e901 typo Sebastien Jodogne <s.jodogne@gmail.com> parents: 706 diff changeset	545 this image using PIL, and finally to upload the modified image as a
daf07750e901 typo Sebastien Jodogne <s.jodogne@gmail.com> parents: 706 diff changeset	546 new DICOM instance:
706 c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	547
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	548 .. literalinclude:: python/pil-conversions.py
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	549 :language: python
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	550
c62539d00251 Conversions between Orthanc and Python images Sebastien Jodogne <s.jodogne@gmail.com> parents: 704 diff changeset	551
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	552 .. _python_dicom_scp:
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	553
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	554 Handling DICOM SCP requests (new in 3.2)
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	555 ........................................
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	556
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	557 Starting with release 3.2 of the Python plugin, it is possible to
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	558 replace the C-FIND SCP and C-MOVE SCP of Orthanc by a Python
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	559 script. This feature can notably be used to create a custom DICOM
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	560 proxy. Here is a minimal example:
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	561
704 ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	562 .. literalinclude:: python/dicom-find-move-scp.py
ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	563 :language: python
ba2403ebd4b7 moving python samples in separate files (3) Sebastien Jodogne <s.jodogne@gmail.com> parents: 703 diff changeset	564
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	565
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	566 .. highlight:: text
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	567
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	568 In this sample, the C-FIND SCP will send one single answer that
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	569 reproduces the values provided by the SCU::
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	570
699 a777b9e6ef70 clarifying sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 698 diff changeset	571 $ findscu localhost 4242 -S -k QueryRetrieveLevel=STUDY -k PatientName=TEST -k SeriesDescription=
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	572 I: ---------------------------
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	573 I: Find Response: 1 (Pending)
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	574 I:
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	575 I: # Dicom-Data-Set
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	576 I: # Used TransferSyntax: Little Endian Explicit
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	577 I: (0008,0005) CS [ISO_IR 100] # 10, 1 SpecificCharacterSet
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	578 I: (0008,0052) CS [HELLO0-STUDY] # 12, 1 QueryRetrieveLevel
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	579 I: (0008,103e) LO [HELLO1- ] # 8, 1 SeriesDescription
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	580 I: (0010,0010) PN [HELLO2-TEST ] # 12, 1 PatientName
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	581 I:
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	582
698 b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	583 A more realistic Python script could for instance call the route
b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	584 ``/modalities/{...}/query`` in the :ref:`REST API <rest-find-scu>` of
b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	585 Orthanc using ``orthanc.RestApiPost()``, in order to query the content
b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	586 a remote modality through a second C-FIND SCU request (this time
b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	587 issued by Orthanc as a SCU).
b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	588
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	589 The C-MOVE SCP can be invoked as follows::
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	590
699 a777b9e6ef70 clarifying sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 698 diff changeset	591 $ movescu localhost 4242 -aem TARGET -aec SOURCE -aet MOVESCU -S -k QueryRetrieveLevel=IMAGE -k StudyInstanceUID=1.2.3.4
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	592
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	593 The C-MOVE request above would print the following information in the
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	594 Orthanc logs::
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	595
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	596 W0610 18:30:36.840865 PluginsManager.cpp:168] C-MOVE request to be handled in Python: {
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	597 "AccessionNumber": "",
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	598 "Level": "INSTANCE",
699 a777b9e6ef70 clarifying sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 698 diff changeset	599 "OriginatorAET": "MOVESCU",
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	600 "OriginatorID": 1,
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	601 "PatientID": "",
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	602 "SOPInstanceUID": "",
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	603 "SeriesInstanceUID": "",
699 a777b9e6ef70 clarifying sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 698 diff changeset	604 "SourceAET": "SOURCE",
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	605 "StudyInstanceUID": "1.2.3.4",
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	606 "TargetAET": "TARGET"
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	607 }
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	608
710 41e450b5ac2e typo Sebastien Jodogne <s.jodogne@gmail.com> parents: 709 diff changeset	609 It is now up to your Python callback to process the C-MOVE SCU request,
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	610 for instance by calling the route ``/modalities/{...}/store`` in the
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	611 :ref:`REST API <rest-store-scu>` of Orthanc using
700 56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	612 ``orthanc.RestApiPost()``. It is highly advised to create a Python
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	613 thread to handle the request, in order to avoid blocking Orthanc as
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	614 much as possible.
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	615
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	616
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	617 .. _python_worklists:
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	618
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	619 Handling worklist SCP requests (new in 3.2)
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	620 ...........................................
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	621
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	622 Starting with release 3.2 of the Python plugin, it is possible to
701 f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	623 answer :ref:`worklist queries <worklist>` using a Python script. This
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	624 is especially useful to easily create a bridge between Orthanc,
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	625 HL7/FHIR messages and RIS systems. Indeed, Python provides many tools
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	626 to handle HL7 such as `python-hl7 library
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	627 <https://python-hl7.readthedocs.io/en/latest/>`__.
700 56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	628
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	629 The following Python script reproduces features similar to the
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	630 :ref:`sample modality worklists plugin <worklists-plugin>`:
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	631
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	632 .. literalinclude:: python/worklist.py
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	633 :language: python
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	634
701 f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	635 .. highlight:: text
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	636
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	637 Here is the result of this plugin on a sample call::
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	638
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	639 $ findscu -W -k "ScheduledProcedureStepSequence[0].Modality=MR" 127.0.0.1 4242
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	640 I: ---------------------------
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	641 I: Find Response: 1 (Pending)
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	642 I:
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	643 I: # Dicom-Data-Set
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	644 I: # Used TransferSyntax: Little Endian Explicit
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	645 I: (0008,0005) CS [ISO_IR 100] # 10, 1 SpecificCharacterSet
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	646 I: (0040,0100) SQ (Sequence with explicit length #=1) # 18, 1 ScheduledProcedureStepSequence
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	647 I: (fffe,e000) na (Item with explicit length #=1) # 10, 1 Item
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	648 I: (0008,0060) CS [MR] # 2, 1 Modality
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	649 I: (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	650 I: (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	651 I:
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	652 I: ---------------------------
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	653 I: Find Response: 2 (Pending)
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	654 I:
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	655 I: # Dicom-Data-Set
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	656 I: # Used TransferSyntax: Little Endian Explicit
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	657 I: (0008,0005) CS [ISO_IR 100] # 10, 1 SpecificCharacterSet
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	658 I: (0040,0100) SQ (Sequence with explicit length #=1) # 18, 1 ScheduledProcedureStepSequence
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	659 I: (fffe,e000) na (Item with explicit length #=1) # 10, 1 Item
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	660 I: (0008,0060) CS [MR] # 2, 1 Modality
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	661 I: (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	662 I: (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	663 I:
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	664
727 698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	665
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	666 .. _pynetdicom:
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	667
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	668 Replacing DICOM SCP of Orthanc by pynetdicom
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	669 ............................................
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	670
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	671 .. highlight:: json
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	672
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	673 Thanks to Python plugins, it is also possible to replace the built-in
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	674 DICOM SCP of Orthanc by `pynetdicom
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	675 <https://pydicom.github.io/pynetdicom/stable/examples/storage.html>`__
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	676 so as to customize how the DICOM protocol is handled. Firstly, in the
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	677 configuration file, make sure to disable the Orthanc SCP by setting
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	678 ``DicomServerEnabled`` to ``false``::
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	679
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	680 {
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	681 "Plugins" : [ "." ],
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	682 "PythonScript" : "pynetdicom.py",
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	683 "DicomServerEnabled" : false
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	684 }
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	685
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	686 Secondly, here a basic plugin illustrating how to start and stop the
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	687 pynetdicom server, and handle incoming C-STORE requests:
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	688
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	689 .. literalinclude:: python/pynetdicom.py
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	690 :language: python
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	691
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	692 As can be seen in this listing, whenever the pynetdicom receives an
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	693 incoming C-STORE request, it makes a POST call to the URI
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	694 ``/instances`` in the REST API of Orthanc in order to store the
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	695 embedded DICOM dataset into Orthanc. Obviously, one can build more
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	696 complex DICOM servers by handling more messages than C-STORE alone.
698eb280060a pynetdicom sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 719 diff changeset	697
747 56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	698
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	699 .. _python_exception:
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	700
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	701 Catching exceptions
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	702 ...................
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	703
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	704 Starting with release 3.3 of the Python plugin, the plugin generates a
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	705 Python exception derived from class ``orthanc.OrthancException`` if an
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	706 error is encountered. This exception contains a tuple that provides
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	707 the error code and its textual description.
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	708
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	709 In releases <= 3.2, the Python plugin raised the `built-in exception
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	710 <https://docs.python.org/3/library/exceptions.html>`__ ``ValueError``.
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	711
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	712 Here is an example showing how to catch exceptions:
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	713
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	714 .. literalinclude:: python/exception.py
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	715 :language: python
56d48f6e52cc catching exceptions in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 741 diff changeset	716
556 6a3d48510b0b Python sample: "Forbid or allow access to REST resources (authorization)", deprecating advanced authorization plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 555 diff changeset	717
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	718 Performance and concurrency
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	719 ---------------------------
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	720
471 a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	721 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	722 ``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	723 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	724 <https://en.wikipedia.org/wiki/Fork_(system_call)>`__.
a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	725
555 6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	726 Using slave processes
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	727 .....................
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	728
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	729 Let us consider the following sample Python script that makes a
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	730 CPU-intensive computation on a REST callback:
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	731
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	732 .. literalinclude:: python/multiprocessing-1.py
6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	733 :language: python
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	734
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	735 .. highlight:: text
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	736
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	737 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	738 needed to compute 30 million times a squared root on your CPU::
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 $ curl http://localhost:8042/computation
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	741 computation done in 4.208 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	742
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	743 Now, let us call this route three times concurrently (we use bash)::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	744
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	745 $ (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	746 computation done in 11.262 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	747 computation done in 12.457 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	748 computation done in 13.360 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	749
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	750 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	751 computations were not distributed across the available CPU cores.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	752 This might seem surprising, as Orthanc is a threaded server (in
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	753 Orthanc, a pool of C++ threads serves concurrent requests).
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 The explanation is that the Python interpreter (`CPython
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	756 <https://en.wikipedia.org/wiki/CPython>`__ actually) is built on the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	757 top of a so-called `Global Interpreter Lock (GIL)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	758 <https://en.wikipedia.org/wiki/Global_interpreter_lock>`__. The GIL is
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	759 basically a mutex that protects all the calls to the Python
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	760 interpreter. If multiple C++ threads from Orthanc call a Python
353 0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	761 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	762 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	763 Orthanc is not affected by the GIL.
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	764
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	765 The solution is to use the `multiprocessing primitives
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	766 <https://docs.python.org/3/library/multiprocessing.html>`__ of Python.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	767 The "master" Python interpreter that is initially started by the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	768 Orthanc plugin, can start several `children processes
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	769 <https://en.wikipedia.org/wiki/Process_(computing)>`__, each of these
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	770 processes running a separate Python interpreter. This allows to
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	771 offload intensive computations from the "master" Python interpreter of
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	772 Orthanc onto those "slave" interpreters. The ``multiprocessing``
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	773 library is actually quite straightforward to use:
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	774
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	775 .. literalinclude:: python/multiprocessing-2.py
6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	776 :language: python
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	777
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	778 .. highlight:: text
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	779
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	780 Here is now the result of calling this route three times concurrently::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	781
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	782 $ (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	783 computation done in 4.211 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	784 computation done in 4.215 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	785 computation done in 4.225 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	786
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	787 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	788 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	789 as for one isolated request).
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	790
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	791 Note also how the ``multiprocessing`` library allows to make a fine
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	792 control over the computational resources that are available to the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	793 Python script: The number of "slave" interpreters can be easily
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	794 changed in the constructor of the ``multiprocessing.Pool`` object, and
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	795 are fully independent of the threads used by the Orthanc server.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	796
555 6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	797 Obviously, an in-depth discussion about the ``multiprocessing``
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	798 library is out of the scope of this document. There are many
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	799 references available on Internet. Also, note that ``threading`` is not
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	800 useful here, as Python multithreading is also limited by the GIL, and
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	801 is more targeted at dealing with costly I/O operations or with the
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	802 :ref:`scheduling of commands <python-scheduler>`.
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	803
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	804
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	805 Slave processes and the "orthanc" module
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	806 ........................................
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	807
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	808 Very importantly, pay attention to the fact that **only the "master"
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	809 Python interpreter has access to the Orthanc SDK**. The "slave"
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	810 processes have no access to the ``orthanc`` module.
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	811
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	812 You must write your Python plugin so as that all the calls to
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	813 ``orthanc`` are moved from the slaves process to the master
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	814 process. For instance, here is how you would parse a DICOM file in a
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	815 slave process:
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	816
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	817 .. literalinclude:: python/multiprocessing-3.py
6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	818 :language: python
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	819
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	820 Communication primitives such as ``multiprocessing.Queue`` are
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	821 available to exchange messages from the "slave" Python interpreters to
555 6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	822 the "master" Python interpreter for more advanced scenarios.
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	823
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	824 NB: Starting with release 3.0 of the Python plugin, it is possible to
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	825 call the REST API of Orthanc from a slave process in a more direct
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	826 way. The function ``orthanc.GenerateRestApiAuthorizationToken()`` can
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	827 be used to create an authorization token that provides full access to
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	828 the REST API of Orthanc (without have to set credentials in your
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	829 plugin). Any HTTP client library for Python, such as `requests
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	830 <https://requests.readthedocs.io/en/master/>`__, can then be used to
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	831 access the REST API of Orthanc. Here is a minimal example:
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	832
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	833 .. literalinclude:: python/multiprocessing-4.py
6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	834 :language: python

Mercurial > hg > orthanc-book

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