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

annotate Sphinx/source/plugins/python.rst @ 702:6e02cd89eb6a

moving python samples in separate files

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Fri, 11 Jun 2021 09:38:15 +0200
parents	f093160dd7f4
children	a589668768d7

rev	line source
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	1 .. _python-plugin:
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	2
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	3
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	4 Python plugin for Orthanc
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	5 =========================
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	6
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	7 .. contents::
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	8
371 5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	9
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	10 Overview
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	11 --------
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	12
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	13 This plugin can be used to write :ref:`Orthanc plugins
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	14 <creating-plugins>` using the `Python programming language
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	15 <https://en.wikipedia.org/wiki/Python_(programming_language)>`__
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	16 instead of the more complex C/C++ programming languages.
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	17
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	18 Python plugins have access to more features and a more consistent SDK
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	19 than :ref:`Lua scripts <lua>`. The Python API is automatically
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	20 generated from the `Orthanc plugin SDK in C
678 17c1ff4e6ae4 Orthanc 1.9.3 Sebastien Jodogne <s.jodogne@gmail.com> parents: 642 diff changeset	21 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.9.3/OrthancServer/Plugins/Include/orthanc/OrthancCPlugin.h>`__
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	22 using the `Clang <https://en.wikipedia.org/wiki/Clang>`__ compiler
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	23 front-end.
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	24
462 fcc352fd4283 upgrade python Sebastien Jodogne <s.jodogne@gmail.com> parents: 442 diff changeset	25 As of release 2.0 of the plugin, the coverage of the C SDK is about
fcc352fd4283 upgrade python Sebastien Jodogne <s.jodogne@gmail.com> parents: 442 diff changeset	26 75% (119 functions are automatically wrapped in Python out of a total
fcc352fd4283 upgrade python Sebastien Jodogne <s.jodogne@gmail.com> parents: 442 diff changeset	27 of 157 functions in the Orthanc SDK 1.7.2).
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	28
371 5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	29
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	30 Source code
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	31 -----------
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	32
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	33 * Link to the `official releases of this plugin
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	34 <https://www.orthanc-server.com/browse.php?path=/plugin-python>`__.
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	35
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	36 * Link to the `code repository
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	37 <https://hg.orthanc-server.com/orthanc-python/>`__.
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	38
5cb37e6b014b explicit links to the source code of python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	39
353 0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	40 Licensing
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	41 ---------
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	42
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	43 Pay attention to the fact that this plugin is licensed under the terms
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	44 of the `AGPL license
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	45 <https://en.wikipedia.org/wiki/GNU_Affero_General_Public_License>`__.
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	46
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	47 This has an important consequence: If you distribute Orthanc to
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	48 clients together with one Python script, or if you put an Orthanc
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	49 server equipped with one Python script on a Web portal, you must
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	50 disclose the source code of your Python script to the Orthanc
354 1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	51 community under the terms of the AGPL license.
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	52
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	53 We suggest you to put the source code of your Python scripts on the
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	54 dedicated `"OrthancContributed" repository on GitHub
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	55 <https://github.com/jodogne/OrthancContributed/tree/master/Plugins>`__,
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	56 and/or to send it to the `Orthanc Users
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	57 <https://groups.google.com/forum/#!forum/orthanc-users>`__ discussion
1ba75bac55fd cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 353 diff changeset	58 group.
353 0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	59
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	60 Check out the :ref:`FAQ about licensing <licensing>` for more context.
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	61
0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	62
364 234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	63 Usage
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	64 -----
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	65
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	66 Docker
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	67 ......
234de55ed125 usage of the python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 354 diff changeset	68
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 .. highlight:: python
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	219
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	220 Here is a basic Python script that registers two new routes in the
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	221 REST API::
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	222
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	223 import orthanc
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	224 import pprint
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	225
343 fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	226 def OnRest(output, uri, **request):
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	227 pprint.pprint(request)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	228 print('Accessing uri: %s' % uri)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	229 output.AnswerBuffer('ok\n', 'text/plain')
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	230
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	231 orthanc.RegisterRestCallback('/(to)(t)o', OnRest)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	232 orthanc.RegisterRestCallback('/tata', OnRest)
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	233
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	234 .. highlight:: json
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	235
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	236 Here is the associated minimal configuration file for Orthanc
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	237 (provided the Python script is saved as ``rest.py``)::
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	238
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	239 {
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	240 "Plugins" : [ "." ],
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	241 "PythonScript" : "rest.py",
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	242 "PythonVerbose" : false
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	243 }
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	244
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	245 .. highlight:: bash
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	246
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	247 The route can then be accessed as::
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	248
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	249 $ curl http://localhost:8042/toto
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	250 ok
fff45618262d creating the documentation of the Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	251
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	252
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	253 .. _python-changes:
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	254
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	255 Listening to changes
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	256 ....................
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	257
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	258 .. highlight:: python
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	259
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	260 This sample uploads a DICOM file as soon as Orthanc is started::
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	261
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	262 import orthanc
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	263
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	264 def OnChange(changeType, level, resource):
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	265 if changeType == orthanc.ChangeType.ORTHANC_STARTED:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	266 print('Started')
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	267
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	268 with open('/tmp/sample.dcm', 'rb') as f:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	269 orthanc.RestApiPost('/instances', f.read())
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	270
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	271 elif changeType == orthanc.ChangeType.ORTHANC_STOPPED:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	272 print('Stopped')
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	273
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	274 elif changeType == orthanc.ChangeType.NEW_INSTANCE:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	275 print('A new instance was uploaded: %s' % resource)
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	276
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	277 orthanc.RegisterOnChangeCallback(OnChange)
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	278
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	279
590 404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	280
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	281 .. warning::
600 4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	282 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	283 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	284 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	285 <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	286
600 4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	287 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	288 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	289 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	290 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	291 solution to postpone such deadlocks as much as possible by relying on
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	292 the multithreading primitives of Python::
591 2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	293
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	294 import orthanc
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	295 import threading
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	296
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	297 def OnChange(changeType, level, resource):
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	298 # One can safely invoke the "orthanc" module in this function
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	299 orthanc.LogWarning("Hello world")
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	300
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	301 def _OnChange(changeType, level, resource):
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	302 # Invoke the actual "OnChange()" function in a separate thread
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	303 t = threading.Timer(0, function = OnChange, args = (changeType, level, resource))
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	304 t.start()
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	305
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	306 orthanc.RegisterOnChangeCallback(_OnChange)
2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	307
600 4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	308
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	309 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	310 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	311 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	312 in releases >= 3.1 of the plugin.
4038ae299b18 note about deadlocks in python plugins Sebastien Jodogne <s.jodogne@gmail.com> parents: 591 diff changeset	313
591 2397b0e12bc8 solution to avoid deadlock in Python OnChange() Sebastien Jodogne <s.jodogne@gmail.com> parents: 590 diff changeset	314
590 404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	315
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	316 Accessing the content of a new instance
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	317 .......................................
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	318
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	319 .. highlight:: python
345 f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	320
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	321 ::
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	322
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	323 import orthanc
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	324 import json
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	325 import pprint
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	326
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	327 def OnStoredInstance(dicom, instanceId):
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	328 print('Received instance %s of size %d (transfer syntax %s, SOP class UID %s)' % (
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	329 instanceId, dicom.GetInstanceSize(),
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	330 dicom.GetInstanceMetadata('TransferSyntax'),
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	331 dicom.GetInstanceMetadata('SopClassUid')))
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	332
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	333 # Print the origin information
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	334 if dicom.GetInstanceOrigin() == orthanc.InstanceOrigin.DICOM_PROTOCOL:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	335 print('This instance was received through the DICOM protocol')
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	336 elif dicom.GetInstanceOrigin() == orthanc.InstanceOrigin.REST_API:
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	337 print('This instance was received through the REST API')
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	338
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	339 # Print the DICOM tags
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	340 pprint.pprint(json.loads(dicom.GetInstanceSimplifiedJson()))
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	341
f81b533a0fd0 python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 343 diff changeset	342 orthanc.RegisterOnStoredInstanceCallback(OnStoredInstance)
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	343
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	344
590 404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	345 .. warning::
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	346 Your callback function will be called synchronously with
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	347 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	348 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	349 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	350 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	351 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	352 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	353 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	354 message queue.
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	355
404aca6160f0 warning about deadlock in python Sebastien Jodogne <s.jodogne@gmail.com> parents: 568 diff changeset	356
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	357 Calling pydicom
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	358 ...............
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	359
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	360 .. highlight:: python
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	361
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	362 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	363 the content of the dataset of one given DICOM instance stored in
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	364 Orthanc, using `pydicom <https://pydicom.github.io/>`__::
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	365
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	366 import io
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	367 import orthanc
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	368 import pydicom
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	369
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	370 def DecodeInstance(output, uri, **request):
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	371 if request['method'] == 'GET':
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	372 # Retrieve the instance ID from the regular expression (*)
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	373 instanceId = request['groups'][0]
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	374 # Get the content of the DICOM file
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	375 f = orthanc.GetDicomForInstance(instanceId)
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	376 # Parse it using pydicom
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	377 dicom = pydicom.dcmread(io.BytesIO(f))
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	378 # Return a string representation the dataset to the caller
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	379 output.AnswerBuffer(str(dicom), 'text/plain')
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	380 else:
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	381 output.SendMethodNotAllowed('GET')
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	382
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	383 orthanc.RegisterRestCallback('/pydicom/(.)', DecodeInstance) # ()
346 bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	384
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	385 .. highlight:: bash
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	386
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	387 This can be called as follows::
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	388
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	389 $ curl http://localhost:8042/pydicom/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5
bdf8757449e3 more python samples Sebastien Jodogne <s.jodogne@gmail.com> parents: 345 diff changeset	390
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	391
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	392 Auto-routing studies
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	393 ....................
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	394
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	395 .. highlight:: python
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	396
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	397 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	398 <stable-resources>` to a modality named ``samples`` (as declared in the
347 04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	399 ``DicomModalities`` configuration option)::
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	400
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	401 import orthanc
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	402
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	403 def OnChange(changeType, level, resourceId):
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	404 if changeType == orthanc.ChangeType.STABLE_STUDY:
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	405 print('Stable study: %s' % resourceId)
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	406 orthanc.RestApiPost('/modalities/sample/store', resourceId)
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	407
04fae9d4b65f auto-routing Sebastien Jodogne <s.jodogne@gmail.com> parents: 346 diff changeset	408 orthanc.RegisterOnChangeCallback(OnChange)
348 d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	409
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	410
539 fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	411 Note that, if you want to use an orthanc plugin to transfer the study,
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	412 you should use the ``RestApiPostAfterPlugins()`` method::
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	413
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	414 import orthanc
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	415
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	416 def OnChange(changeType, level, resourceId):
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	417 if changeType == orthanc.ChangeType.STABLE_STUDY:
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	418 print('Stable study: %s' % resourceId)
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	419 orthanc.RestApiPostAfterPlugins('/dicom-web/servers/sample/store', resourceId)
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	420
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	421 orthanc.RegisterOnChangeCallback(OnChange)
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	422
fd5c1410db5b doc for RestApiPostAfterPlugins Alain Mazy <alain@mazy.be> parents: 528 diff changeset	423
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	424 Rendering a thumbnail using PIL/Pillow
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	425 ......................................
348 d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	426
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	427 .. highlight:: python
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	428
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	429 ::
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	430
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	431 from PIL import Image
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	432 import io
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	433 import orthanc
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	434
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	435 def DecodeInstance(output, uri, **request):
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	436 if request['method'] == 'GET':
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	437 # Retrieve the instance ID from the regular expression (*)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	438 instanceId = request['groups'][0]
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	439
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	440 # Render the instance, then open it in Python using PIL/Pillow
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	441 png = orthanc.RestApiGet('/instances/%s/rendered' % instanceId)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	442 image = Image.open(io.BytesIO(png))
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	443
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	444 # Downsize the image as a 64x64 thumbnail
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	445 image.thumbnail((64, 64), Image.ANTIALIAS)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	446
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	447 # Save the thumbnail as JPEG, then send the buffer to the caller
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	448 jpeg = io.BytesIO()
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	449 image.save(jpeg, format = "JPEG", quality = 80)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	450 jpeg.seek(0)
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	451 output.AnswerBuffer(jpeg.read(), 'text/plain')
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	452
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	453 else:
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	454 output.SendMethodNotAllowed('GET')
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	455
d8359cecdc89 pillow sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 347 diff changeset	456 orthanc.RegisterRestCallback('/pydicom/(.)', DecodeInstance) # ()
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	457
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	458
369 181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	459 .. _python-introspection:
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	460
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	461 Inspecting the available API
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	462 ............................
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	463
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	464 .. highlight:: python
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	465
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	466 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	467 the API of the ``orthanc`` module in order to dump all the available
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	468 features::
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	469
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	470 import inspect
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	471 import numbers
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	472 import orthanc
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	473
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	474 # Loop over the members of the "orthanc" module
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	475 for (name, obj) in inspect.getmembers(orthanc):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	476 if inspect.isroutine(obj):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	477 print('Function %s():\n Documentation: %s\n' % (name, inspect.getdoc(obj)))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	478
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	479 elif inspect.isclass(obj):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	480 print('Class %s:\n Documentation: %s' % (name, inspect.getdoc(obj)))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	481
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	482 # Loop over the members of the class
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	483 for (subname, subobj) in inspect.getmembers(obj):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	484 if isinstance(subobj, numbers.Number):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	485 print(' - Enumeration value %s: %s' % (subname, subobj))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	486 elif (not subname.startswith('_') and
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	487 inspect.ismethoddescriptor(subobj)):
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	488 print(' - Method %s(): %s' % (subname, inspect.getdoc(subobj)))
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	489 print('')
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	490
373 847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	491
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	492 .. _python-scheduler:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	493
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	494 Scheduling a task for periodic execution
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	495 ........................................
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	496
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	497 .. highlight:: python
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	498
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	499 The following Python script will periodically (every second) run the
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	500 function ``Hello()`` thanks to the ``threading`` module::
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	501
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	502 import orthanc
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	503 import threading
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	504
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	505 TIMER = None
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	506
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	507 def Hello():
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	508 global TIMER
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	509 TIMER = None
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	510 orthanc.LogWarning("In Hello()")
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	511 # Do stuff...
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	512 TIMER = threading.Timer(1, Hello) # Re-schedule after 1 second
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	513 TIMER.start()
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	514
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	515 def OnChange(changeType, level, resource):
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	516 if changeType == orthanc.ChangeType.ORTHANC_STARTED:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	517 orthanc.LogWarning("Starting the scheduler")
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	518 Hello()
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	519
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	520 elif changeType == orthanc.ChangeType.ORTHANC_STOPPED:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	521 if TIMER != None:
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	522 orthanc.LogWarning("Stopping the scheduler")
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	523 TIMER.cancel()
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	524
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	525 orthanc.RegisterOnChangeCallback(OnChange)
847996394688 Scheduling a task for periodic execution Sebastien Jodogne <s.jodogne@gmail.com> parents: 369 diff changeset	526
378 16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	527
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	528 .. _python-metadata:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	529
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	530 Filtering and returning metadata
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	531 ................................
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	532
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	533 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	534 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	535 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	536 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	537 :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	538 same way they look for DICOM tags.
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	539
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	540 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	541 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	542 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	543 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	544
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	545 .. highlight:: python
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	546
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	547 Nevertheless, here is a full sample Python script that overwrites the
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	548 ``/tools/find`` route in order to give access to metadata::
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	549
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	550 import json
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	551 import orthanc
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	552 import re
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	553
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	554 # Get the path in the REST API to the given resource that was returned
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	555 # by a call to "/tools/find"
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	556 def GetPath(resource):
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	557 if resource['Type'] == 'Patient':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	558 return '/patients/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	559 elif resource['Type'] == 'Study':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	560 return '/studies/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	561 elif resource['Type'] == 'Series':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	562 return '/series/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	563 elif resource['Type'] == 'Instance':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	564 return '/instances/%s' % resource['ID']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	565 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	566 raise Exception('Unknown resource level')
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	567
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	568 def FindWithMetadata(output, uri, **request):
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	569 # The "/tools/find" route expects a POST method
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	570 if request['method'] != 'POST':
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	571 output.SendMethodNotAllowed('POST')
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	572 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	573 # Parse the query provided by the user, and backup the "Expand" field
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	574 query = json.loads(request['body'])
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	575
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	576 if 'Expand' in query:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	577 originalExpand = query['Expand']
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	578 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	579 originalExpand = False
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	580
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	581 # Call the core "/tools/find" route
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	582 query['Expand'] = True
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	583 answers = orthanc.RestApiPost('/tools/find', json.dumps(query))
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	584
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	585 # Loop over the matching resources
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	586 filteredAnswers = []
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	587 for answer in json.loads(answers):
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	588 try:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	589 # Read the metadata that is associated with the resource
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	590 metadata = json.loads(orthanc.RestApiGet('%s/metadata?expand' % GetPath(answer)))
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	591
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	592 # Check whether the metadata matches the regular expressions
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	593 # that were provided in the "Metadata" field of the user request
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	594 isMetadataMatch = True
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	595 if 'Metadata' in query:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	596 for (name, pattern) in query['Metadata'].items():
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	597 if name in metadata:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	598 value = metadata[name]
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	599 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	600 value = ''
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	601
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	602 if re.match(pattern, value) == None:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	603 isMetadataMatch = False
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	604 break
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	605
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	606 # If all the metadata matches the provided regular
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	607 # expressions, add the resource to the filtered answers
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	608 if isMetadataMatch:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	609 if originalExpand:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	610 answer['Metadata'] = metadata
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	611 filteredAnswers.append(answer)
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	612 else:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	613 filteredAnswers.append(answer['ID'])
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	614 except:
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	615 # The resource was deleted since the call to "/tools/find"
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	616 pass
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	617
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	618 # Return the filtered answers in the JSON format
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	619 output.AnswerBuffer(json.dumps(filteredAnswers, indent = 3), 'application/json')
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	620
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	621 orthanc.RegisterRestCallback('/tools/find', FindWithMetadata)
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	622
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	623
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	624 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	625 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	626 <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	627 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	628 about `attribute matching
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	629 <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	630
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	631 .. highlight:: bash
378 16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	632
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	633 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	634 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	635
16dc3561b41e Filtering and returning metadata using Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 375 diff changeset	636 $ 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	637
181b02cea7ab inspecting Python API Sebastien Jodogne <s.jodogne@gmail.com> parents: 364 diff changeset	638
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	639 .. _python-paging:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	640
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	641 Implementing basic paging
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	642 .........................
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	643
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	644 .. highlight:: python
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	645
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	646 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	647 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	648 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	649 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	650 following sample Python plugin that registers a new route
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	651 ``/sort-studies`` in the REST API of Orthanc::
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	652
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	653 import json
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	654 import orthanc
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	655
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	656 def GetStudyDate(study):
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	657 if 'StudyDate' in study['MainDicomTags']:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	658 return study['MainDicomTags']['StudyDate']
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	659 else:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	660 return ''
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	661
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	662 def SortStudiesByDate(output, uri, **request):
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	663 if request['method'] == 'GET':
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	664 # Retrieve all the studies
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	665 studies = json.loads(orthanc.RestApiGet('/studies?expand'))
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	666
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	667 # Sort the studies according to the "StudyDate" DICOM tag
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	668 studies = sorted(studies, key = GetStudyDate)
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	669
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	670 # Read the limit/offset arguments provided by the user
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	671 offset = 0
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	672 if 'offset' in request['get']:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	673 offset = int(request['get']['offset'])
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	674
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	675 limit = 0
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	676 if 'limit' in request['get']:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	677 limit = int(request['get']['limit'])
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	678
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	679 # Truncate the list of studies
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	680 if limit == 0:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	681 studies = studies[offset : ]
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	682 else:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	683 studies = studies[offset : offset + limit]
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	684
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	685 # Return the truncated list of studies
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	686 output.AnswerBuffer(json.dumps(studies), 'application/json')
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	687 else:
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	688 output.SendMethodNotAllowed('GET')
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	689
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	690 orthanc.RegisterRestCallback('/sort-studies', SortStudiesByDate)
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	691
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	692
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	693 .. highlight:: bash
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	694
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	695 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	696 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	697 JSON file)::
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	698
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	699 $ 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	700
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	701 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	702 returned studies)::
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	703
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	704 $ 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	705
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	706 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	707 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	708 ``/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	709 <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	710 (cf. ``orthanc.ChangeType.NEW_STUDY`` and
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	711 ``orthanc.ChangeType.DELETED``).
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	712
46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	713
551 d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	714 .. _python_excel:
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	715
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	716 Creating a Microsoft Excel report
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	717 .................................
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	718
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	719 .. highlight:: python
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	720
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	721 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	722 very easy to implement a server-side plugin that generates a report in
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	723 the Microsoft Excel ``.xls`` format. Here is a working example::
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	724
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	725 import StringIO
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	726 import json
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	727 import orthanc
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	728 import xlwt
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	729
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	730 def CreateExcelReport(output, uri, **request):
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	731 if request['method'] != 'GET' :
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	732 output.SendMethodNotAllowed('GET')
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	733 else:
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	734 # Create an Excel writer
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	735 excel = xlwt.Workbook()
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	736 sheet = excel.add_sheet('Studies')
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	737
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	738 # Loop over the studies stored in Orthanc
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	739 row = 0
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	740 studies = orthanc.RestApiGet('/studies?expand')
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	741 for study in json.loads(studies):
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	742 sheet.write(row, 0, study['PatientMainDicomTags'].get('PatientID'))
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	743 sheet.write(row, 1, study['PatientMainDicomTags'].get('PatientName'))
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	744 sheet.write(row, 2, study['MainDicomTags'].get('StudyDescription'))
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	745 row += 1
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	746
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	747 # Serialize the Excel workbook to a string, and return it to the caller
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	748 # https://stackoverflow.com/a/15649139/881731
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	749 b = StringIO.StringIO()
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	750 excel.save(b)
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	751 output.AnswerBuffer(b.getvalue(), 'application/vnd.ms-excel')
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	752
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	753 orthanc.RegisterRestCallback('/report.xls', CreateExcelReport)
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	754
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	755 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	756 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	757 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	758 description.
d0332c5a2cb8 Python plugin: excel generation example Sebastien Jodogne <s.jodogne@gmail.com> parents: 539 diff changeset	759
469 46949efa5818 Implementing basic paging using a Python script Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	760
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	761 .. _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	762
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	763 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	764 ....................................................................
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	765
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	766 .. highlight:: python
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	767
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	768 The following Python script installs a callback that is triggered
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	769 whenever the HTTP server of Orthanc is accessed::
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	770
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	771 import orthanc
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	772 import pprint
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	773
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	774 def Filter(uri, **request):
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	775 print('User trying to access URI: %s' % uri)
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	776 pprint.pprint(request)
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	777 return True # False to forbid access
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	778
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	779 orthanc.RegisterIncomingHttpRequestFilter(Filter)
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	780
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	781 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	782 ``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	783 ``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	784 ``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	785 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	786 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	787
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	788 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	789 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	790
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	791 Thanks to Python, it is extremely easy to call remote Web services for
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	792 authorization. Here is an example using the ``requests`` library::
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	793
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	794 import json
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	795 import orthanc
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	796 import requests
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	797
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	798 def Filter(uri, **request):
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	799 body = {
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	800 'uri' : uri,
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	801 'headers' : request['headers']
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	802 }
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	803 r = requests.post('http://localhost:8000/authorize',
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	804 data = json.dumps(body))
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	805 return r.json() ['granted'] # Must be a Boolean
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	806
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	807 orthanc.RegisterIncomingHttpRequestFilter(Filter)
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	808
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	809 .. highlight:: javascript
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	810
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	811 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	812 implemented using `Node.js
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	813 <https://en.wikipedia.org/wiki/Node.js>`__::
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	814
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	815 const http = require('http');
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	816
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	817 const requestListener = function(req, res) {
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	818 let body = '';
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	819 req.on('data', function(chunk) {
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	820 body += chunk;
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	821 });
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	822 req.on('end', function() {
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	823 console.log(JSON.parse(body));
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	824 var answer = {
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	825 'granted' : false // Forbid access
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	826 };
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	827 res.writeHead(200);
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	828 res.end(JSON.stringify(answer));
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	829 });
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	830 }
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	831
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	832 http.createServer(requestListener).listen(8000);
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	833
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	834
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	835 .. _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	836
696 29e49f03dc27 fix Sebastien Jodogne <s.jodogne@gmail.com> parents: 695 diff changeset	837 Creating DICOM instances (new in 3.2)
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	838 .....................................
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	839
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	840 .. highlight:: python
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	841
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	842 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	843 instance including the traditional Lena sample image, and will decode
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	844 the single frame of this DICOM instance::
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	845
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	846 import json
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	847 import orthanc
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	848
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	849 def OnChange(changeType, level, resource):
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	850 if changeType == orthanc.ChangeType.ORTHANC_STARTED:
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	851 tags = {
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	852 'SOPClassUID' : '1.2.840.10008.5.1.4.1.1.1',
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	853 'PatientID' : 'HELLO',
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	854 'PatientName' : 'WORLD',
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	855 }
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	856
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	857 with open('Lena.png', 'rb') as f:
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	858 img = orthanc.UncompressImage(f.read(), orthanc.ImageFormat.PNG)
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	859
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	860 s = orthanc.CreateDicom(json.dumps(tags), img, orthanc.CreateDicomFlags.GENERATE_IDENTIFIERS)
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	861
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	862 with open('/tmp/sample.dcm', 'wb') as f:
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	863 f.write(s)
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	864
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	865 dicom = orthanc.CreateDicomInstance(s)
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	866 frame = dicom.GetInstanceDecodedFrame(0)
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	867 print('Size of the frame: %dx%d' % (frame.GetImageWidth(), frame.GetImageHeight()))
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	868
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	869 orthanc.RegisterOnChangeCallback(OnChange)
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	870
f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	871
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	872 .. _python_dicom_scp:
695 f4fc12ed00ee creating dicom instances in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 678 diff changeset	873
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	874 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	875 ........................................
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	876
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	877 .. highlight:: python
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	878
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	879 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	880 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	881 script. This feature can notably be used to create a custom DICOM
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	882 proxy. Here is a minimal example::
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	883
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	884 import json
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	885 import orthanc
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	886 import pprint
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	887
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	888 def OnFind(answers, query, issuerAet, calledAet):
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	889 print('Received incoming C-FIND request from %s:' % issuerAet)
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	890
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	891 answer = {}
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	892 for i in range(query.GetFindQuerySize()):
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	893 print(' %s (%04x,%04x) = [%s]' % (query.GetFindQueryTagName(i),
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	894 query.GetFindQueryTagGroup(i),
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	895 query.GetFindQueryTagElement(i),
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	896 query.GetFindQueryValue(i)))
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	897 answer[query.GetFindQueryTagName(i)] = ('HELLO%d-%s' % (i, query.GetFindQueryValue(i)))
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	898
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	899 answers.FindAddAnswer(orthanc.CreateDicom(
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	900 json.dumps(answer), None, orthanc.CreateDicomFlags.NONE))
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	901
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	902 def OnMove(**request):
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	903 orthanc.LogWarning('C-MOVE request to be handled in Python: %s' %
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	904 json.dumps(request, indent = 4, sort_keys = True))
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	905
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	906 orthanc.RegisterFindCallback(OnFind)
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	907 orthanc.RegisterMoveCallback(OnMove)
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	908
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	909 .. highlight:: text
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	910
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	911 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	912 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	913
699 a777b9e6ef70 clarifying sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 698 diff changeset	914 $ 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	915 I: ---------------------------
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	916 I: Find Response: 1 (Pending)
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	917 I:
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	918 I: # Dicom-Data-Set
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	919 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	920 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	921 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	922 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	923 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	924 I:
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	925
698 b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	926 A more realistic Python script could for instance call the route
b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	927 ``/modalities/{...}/query`` in the :ref:`REST API <rest-find-scu>` of
b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	928 Orthanc using ``orthanc.RestApiPost()``, in order to query the content
b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	929 a remote modality through a second C-FIND SCU request (this time
b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	930 issued by Orthanc as a SCU).
b931786385e6 note Sebastien Jodogne <s.jodogne@gmail.com> parents: 697 diff changeset	931
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	932 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	933
699 a777b9e6ef70 clarifying sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 698 diff changeset	934 $ 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	935
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	936 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	937 Orthanc logs::
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	938
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	939 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	940 "AccessionNumber": "",
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	941 "Level": "INSTANCE",
699 a777b9e6ef70 clarifying sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 698 diff changeset	942 "OriginatorAET": "MOVESCU",
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	943 "OriginatorID": 1,
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	944 "PatientID": "",
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	945 "SOPInstanceUID": "",
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	946 "SeriesInstanceUID": "",
699 a777b9e6ef70 clarifying sample Sebastien Jodogne <s.jodogne@gmail.com> parents: 698 diff changeset	947 "SourceAET": "SOURCE",
697 7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	948 "StudyInstanceUID": "1.2.3.4",
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	949 "TargetAET": "TARGET"
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	950 }
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	951
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	952 It is now up to your Python callback to proces the C-MOVE SCU request,
7581dc208323 Handling DICOM SCP requests using a Python plugin Sebastien Jodogne <s.jodogne@gmail.com> parents: 696 diff changeset	953 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	954 :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	955 ``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	956 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	957 much as possible.
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	958
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	959
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	960 .. _python_worklists:
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	961
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	962 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	963 ...........................................
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	964
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	965 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	966 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	967 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	968 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	969 to handle HL7 such as `python-hl7 library
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	970 <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	971
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	972 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	973 :ref:`sample modality worklists plugin <worklists-plugin>`:
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	974
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	975 .. literalinclude:: python/worklist.py
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	976 :language: python
56a06ca9ec20 Handling worklist SCP requests in Python Sebastien Jodogne <s.jodogne@gmail.com> parents: 699 diff changeset	977
701 f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	978 .. highlight:: text
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	979
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	980 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	981
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	982 $ 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	983 I: ---------------------------
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	984 I: Find Response: 1 (Pending)
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	985 I:
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	986 I: # Dicom-Data-Set
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	987 I: # Used TransferSyntax: Little Endian Explicit
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	988 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	989 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	990 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	991 I: (0008,0060) CS [MR] # 2, 1 Modality
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	992 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	993 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	994 I:
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	995 I: ---------------------------
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	996 I: Find Response: 2 (Pending)
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	997 I:
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	998 I: # Dicom-Data-Set
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	999 I: # Used TransferSyntax: Little Endian Explicit
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	1000 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	1001 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	1002 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	1003 I: (0008,0060) CS [MR] # 2, 1 Modality
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	1004 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	1005 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	1006 I:
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	1007
f093160dd7f4 cross-references regarding worklists Sebastien Jodogne <s.jodogne@gmail.com> parents: 700 diff changeset	1008
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	1009
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1010 Performance and concurrency
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1011 ---------------------------
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1012
471 a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	1013 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	1014 ``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	1015 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	1016 <https://en.wikipedia.org/wiki/Fork_(system_call)>`__.
a735476a0e6e note about fork on windows Sebastien Jodogne <s.jodogne@gmail.com> parents: 462 diff changeset	1017
555 6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1018 Using slave processes
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1019 .....................
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1020
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1021 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	1022 CPU-intensive computation on a REST callback:
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1023
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	1024 .. literalinclude:: python/multiprocessing-1.py
6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	1025 :language: python
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1026
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1027 .. highlight:: text
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1028
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1029 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	1030 needed to compute 30 million times a squared root on your CPU::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1031
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1032 $ curl http://localhost:8042/computation
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1033 computation done in 4.208 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1034
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1035 Now, let us call this route three times concurrently (we use bash)::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1036
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1037 $ (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	1038 computation done in 11.262 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1039 computation done in 12.457 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1040 computation done in 13.360 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1041
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1042 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	1043 computations were not distributed across the available CPU cores.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1044 This might seem surprising, as Orthanc is a threaded server (in
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1045 Orthanc, a pool of C++ threads serves concurrent requests).
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1046
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1047 The explanation is that the Python interpreter (`CPython
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1048 <https://en.wikipedia.org/wiki/CPython>`__ actually) is built on the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1049 top of a so-called `Global Interpreter Lock (GIL)
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1050 <https://en.wikipedia.org/wiki/Global_interpreter_lock>`__. The GIL is
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1051 basically a mutex that protects all the calls to the Python
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1052 interpreter. If multiple C++ threads from Orthanc call a Python
353 0122c668f4ec python licensing Sebastien Jodogne <s.jodogne@gmail.com> parents: 352 diff changeset	1053 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	1054 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	1055 Orthanc is not affected by the GIL.
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1056
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1057 The solution is to use the `multiprocessing primitives
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1058 <https://docs.python.org/3/library/multiprocessing.html>`__ of Python.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1059 The "master" Python interpreter that is initially started by the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1060 Orthanc plugin, can start several `children processes
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1061 <https://en.wikipedia.org/wiki/Process_(computing)>`__, each of these
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1062 processes running a separate Python interpreter. This allows to
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1063 offload intensive computations from the "master" Python interpreter of
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1064 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	1065 library is actually quite straightforward to use:
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1066
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	1067 .. literalinclude:: python/multiprocessing-2.py
6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	1068 :language: python
351 e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1069
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1070 .. highlight:: text
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1071
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1072 Here is now the result of calling this route three times concurrently::
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1073
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1074 $ (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	1075 computation done in 4.211 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1076 computation done in 4.215 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1077 computation done in 4.225 seconds
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1078
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1079 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	1080 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	1081 as for one isolated request).
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1082
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1083 Note also how the ``multiprocessing`` library allows to make a fine
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1084 control over the computational resources that are available to the
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1085 Python script: The number of "slave" interpreters can be easily
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1086 changed in the constructor of the ``multiprocessing.Pool`` object, and
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1087 are fully independent of the threads used by the Orthanc server.
e2863083fa30 multiprocessing Sebastien Jodogne <s.jodogne@gmail.com> parents: 350 diff changeset	1088
555 6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1089 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	1090 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	1091 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	1092 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	1093 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	1094 :ref:`scheduling of commands <python-scheduler>`.
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1095
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1096
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1097 Slave processes and the "orthanc" module
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1098 ........................................
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1099
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	1100 .. highlight:: python
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	1101
555 6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1102 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	1103 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	1104 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	1105
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1106 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	1107 ``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	1108 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	1109 slave process:
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	1110
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	1111 .. literalinclude:: python/multiprocessing-3.py
6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	1112 :language: python
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	1113
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	1114 Communication primitives such as ``multiprocessing.Queue`` are
6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	1115 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	1116 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	1117
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1118 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	1119 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	1120 way. The function ``orthanc.GenerateRestApiAuthorizationToken()`` can
6fb469a3c382 Python plugin: documentation of orthanc.GenerateRestApiAuthorizationToken() Sebastien Jodogne <s.jodogne@gmail.com> parents: 554 diff changeset	1121 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	1122 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	1123 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	1124 <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	1125 access the REST API of Orthanc. Here is a minimal example:
352 6258b2c14e56 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 351 diff changeset	1126
702 6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	1127 .. literalinclude:: python/multiprocessing-4.py
6e02cd89eb6a moving python samples in separate files Sebastien Jodogne <s.jodogne@gmail.com> parents: 701 diff changeset	1128 :language: python

Mercurial > hg > orthanc-book

annotate Sphinx/source/plugins/python.rst @ 702:6e02cd89eb6a