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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 17 Aug 2020 20:13:51 +0200 |
parents | 03dfb896ca4b |
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.. _python-plugin: Python plugin for Orthanc ========================= .. contents:: Overview -------- This plugin can be used to write :ref:`Orthanc plugins <creating-plugins>` using the `Python programming language <https://en.wikipedia.org/wiki/Python_(programming_language)>`__ instead of the more complex C/C++ programming languages. Python plugins have access to more features and a more consistent SDK than :ref:`Lua scripts <lua>`. The Python API is automatically generated from the `Orthanc plugin SDK in C <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.7.2/OrthancServer/Plugins/Include/orthanc/OrthancCPlugin.h>`__ using the `Clang <https://en.wikipedia.org/wiki/Clang>`__ compiler front-end. As of release 2.0 of the plugin, the coverage of the C SDK is about 75% (119 functions are automatically wrapped in Python out of a total of 157 functions in the Orthanc SDK 1.7.2). Source code ----------- * Link to the `official releases of this plugin <https://www.orthanc-server.com/browse.php?path=/plugin-python>`__. * Link to the `code repository <https://hg.orthanc-server.com/orthanc-python/>`__. Licensing --------- Pay attention to the fact that this plugin is licensed under the terms of the `AGPL license <https://en.wikipedia.org/wiki/GNU_Affero_General_Public_License>`__. This has an important consequence: If you distribute Orthanc to clients together with one Python script, or if you put an Orthanc server equipped with one Python script on a Web portal, you **must** disclose the source code of your Python script to the Orthanc community under the terms of the AGPL license. We suggest you to put the source code of your Python scripts on the dedicated `"OrthancContributed" repository on GitHub <https://github.com/jodogne/OrthancContributed/tree/master/Plugins>`__, and/or to send it to the `Orthanc Users <https://groups.google.com/forum/#!forum/orthanc-users>`__ discussion group. Check out the :ref:`FAQ about licensing <licensing>` for more context. Usage ----- Docker ...... .. highlight:: json The most direct way of starting Orthanc together with the Python plugin is through :ref:`Docker <docker>`. Let's create the file ``/tmp/hello.py`` that contains the following basic Python script:: print('Hello world!') .. highlight:: json Let's also create the file ``/tmp/orthanc.json`` that contains the following minimal :ref:`configuration for Orthanc <configuration>`:: { "StorageDirectory" : "/var/lib/orthanc/db", "RemoteAccessAllowed" : true, "Plugins" : [ "/usr/local/share/orthanc/plugins" ], "PythonScript" : "/etc/orthanc/hello.py" } .. highlight:: bash Given these two files, Orthanc can be started as follows:: $ docker run -p 4242:4242 -p 8042:8042 --rm \ -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro \ -v /tmp/hello.py:/etc/orthanc/hello.py:ro \ jodogne/orthanc-python .. highlight:: text You'll see the following excerpt in the log, which indicates that the Python plugin is properly loaded:: W0331 15:48:12.990661 PluginsManager.cpp:269] Registering plugin 'python' (version mainline) W0331 15:48:12.990691 PluginsManager.cpp:168] Python plugin is initializing W0331 15:48:12.990743 PluginsManager.cpp:168] Using Python script "hello.py" from directory: /etc/orthanc W0331 15:48:12.990819 PluginsManager.cpp:168] Program name: /usr/local/sbin/Orthanc Hello world! `Here <https://bitbucket.org/osimis/orthanc-setup-samples/src/master/docker/python/>`__ is a full example of a more complex setup using the :ref:`osimis/orthanc <docker-osimis>` images. Compiling from source ..................... .. highlight:: bash The procedure to compile this plugin from source is similar to that for the :ref:`core of Orthanc <compiling>`. The following commands should work for most UNIX-like distribution (including GNU/Linux):: $ mkdir Build $ cd Build $ cmake .. -DPYTHON_VERSION=3.7 -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release $ make Before running CMake, make sure that the Python interpreter and its associated development library are installed. On Ubuntu 18.04 LTS, you would for instance install packages ``libpython3.7-dev`` and ``python3.7``. The compilation will produce the shared library ``OrthancPython``, that can be loaded by properly setting the ``Plugins`` :ref:`configuration option <configuration>` of Orthanc. **Warning:** The shared library is only compatible with the Python interpreter whose version corresponds to the value of the ``PYTHON_VERSION`` argument that was given to CMake. Microsoft Windows ................. Pre-compiled binaries for Microsoft Windows `are also available <https://www.orthanc-server.com/browse.php?path=/plugin-python>`__. Beware that one version of the Python plugin can only be run against one version of the Python interpreter. This version is clearly indicated in the filename of the precompiled binaries. .. highlight:: text You are of course free to compile the plugin from sources. You'll have to explicitly specify the path to your Python installation while invoking CMake. For instance:: C:\orthanc-python\Build> cmake .. -DPYTHON_VERSION=2.7 -DPYTHON_WINDOWS_ROOT=C:/Python27 \ -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release -G "Visual Studio 15 2017" **Note about debug builds**: Usually, building Python modules such as the Python plugin for Orthanc in debug mode (where ``_DEBUG`` is defined) leads to a module (``.exe`` or ``.dll``) that requires a debug build of Python, and debug versions of all the Python libraries. This is quite cumbersome, for it requires building Python on your own or downloading additional debug files. Since using a debug build of Python is only necessary in very specific cases (such as the debugging of code at the boundary between Python and an extension), we have changed the default behavior to use the release Python library by default. This means that you are able to build this plugin in debug mode with the standard Python distribution. In case you need to use the Python debug libraries, you can instruct the build system to do so by setting the ``PYTHON_WINDOWS_USE_RELEASE_LIBS`` CMake option, that is ``ON`` by default, to ``OFF``. The previous build example would then be, should you require a full debug build:: C:\orthanc-python\Build> cmake .. -DPYTHON_VERSION=2.7 -DPYTHON_WINDOWS_ROOT=C:/Python27 \ -DSTATIC_BUILD=ON -DPYTHON_WINDOWS_USE_RELEASE_LIBS=OFF \ -DCMAKE_BUILD_TYPE=Debug -G "Visual Studio 15 2017" Please note that this CMake option only impacts **debug** builds under Windows, when using (any version of) the Microsoft Visual Studio compiler. The precompiled binaries all use release (i.e. non-debug) versions of Python. Configuration options --------------------- The only two configuration options that are available for this plugin are the following: * ``PythonScript`` indicates where the Python script is located. If this configuration option is not provided, the Python plugin is not started. * ``PythonVerbose`` is a Boolean value to make the Python interpreter verbose. Samples ------- Extending the REST API ...................... .. highlight:: python Here is a basic Python script that registers two new routes in the REST API:: import orthanc import pprint def OnRest(output, uri, **request): pprint.pprint(request) print('Accessing uri: %s' % uri) output.AnswerBuffer('ok\n', 'text/plain') orthanc.RegisterRestCallback('/(to)(t)o', OnRest) orthanc.RegisterRestCallback('/tata', OnRest) .. highlight:: json Here is the associated minimal configuration file for Orthanc (provided the Python script is saved as ``rest.py``):: { "Plugins" : [ "." ], "PythonScript" : "rest.py", "PythonVerbose" : false } .. highlight:: bash The route can then be accessed as:: $ curl http://localhost:8042/toto ok .. _python-changes: Listening to changes .................... .. highlight:: python This sample uploads a DICOM file as soon as Orthanc is started:: import orthanc def OnChange(changeType, level, resource): if changeType == orthanc.ChangeType.ORTHANC_STARTED: print('Started') with open('/tmp/sample.dcm', 'rb') as f: orthanc.RestApiPost('/instances', f.read()) elif changeType == orthanc.ChangeType.ORTHANC_STOPPED: print('Stopped') elif changeType == orthanc.ChangeType.NEW_INSTANCE: print('A new instance was uploaded: %s' % resource) orthanc.RegisterOnChangeCallback(OnChange) Accessing the content of a new instance ....................................... .. highlight:: python :: import orthanc import json import pprint def OnStoredInstance(dicom, instanceId): print('Received instance %s of size %d (transfer syntax %s, SOP class UID %s)' % ( instanceId, dicom.GetInstanceSize(), dicom.GetInstanceMetadata('TransferSyntax'), dicom.GetInstanceMetadata('SopClassUid'))) # Print the origin information if dicom.GetInstanceOrigin() == orthanc.InstanceOrigin.DICOM_PROTOCOL: print('This instance was received through the DICOM protocol') elif dicom.GetInstanceOrigin() == orthanc.InstanceOrigin.REST_API: print('This instance was received through the REST API') # Print the DICOM tags pprint.pprint(json.loads(dicom.GetInstanceSimplifiedJson())) orthanc.RegisterOnStoredInstanceCallback(OnStoredInstance) Calling pydicom ............... .. highlight:: python Here is a sample Python plugin that registers a REST callback to dump the content of the dataset of one given DICOM instance stored in Orthanc, using `pydicom <https://pydicom.github.io/>`__:: import io import orthanc import pydicom def DecodeInstance(output, uri, **request): if request['method'] == 'GET': # Retrieve the instance ID from the regular expression (*) instanceId = request['groups'][0] # Get the content of the DICOM file f = orthanc.GetDicomForInstance(instanceId) # Parse it using pydicom dicom = pydicom.dcmread(io.BytesIO(f)) # Return a string representation the dataset to the caller output.AnswerBuffer(str(dicom), 'text/plain') else: output.SendMethodNotAllowed('GET') orthanc.RegisterRestCallback('/pydicom/(.*)', DecodeInstance) # (*) .. highlight:: bash This can be called as follows:: $ curl http://localhost:8042/pydicom/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5 Auto-routing studies .................... .. highlight:: python Here is a sample Python plugin that routes any :ref:`stable study <lua-callbacks>` to a modality named ``samples`` (as declared in the ``DicomModalities`` configuration option):: import orthanc def OnChange(changeType, level, resourceId): if changeType == orthanc.ChangeType.STABLE_STUDY: print('Stable study: %s' % resourceId) orthanc.RestApiPost('/modalities/sample/store', resourceId) orthanc.RegisterOnChangeCallback(OnChange) Rendering a thumbnail using PIL/Pillow ...................................... .. highlight:: python :: from PIL import Image import io import orthanc def DecodeInstance(output, uri, **request): if request['method'] == 'GET': # Retrieve the instance ID from the regular expression (*) instanceId = request['groups'][0] # Render the instance, then open it in Python using PIL/Pillow png = orthanc.RestApiGet('/instances/%s/rendered' % instanceId) image = Image.open(io.BytesIO(png)) # Downsize the image as a 64x64 thumbnail image.thumbnail((64, 64), Image.ANTIALIAS) # Save the thumbnail as JPEG, then send the buffer to the caller jpeg = io.BytesIO() image.save(jpeg, format = "JPEG", quality = 80) jpeg.seek(0) output.AnswerBuffer(jpeg.read(), 'text/plain') else: output.SendMethodNotAllowed('GET') orthanc.RegisterRestCallback('/pydicom/(.*)', DecodeInstance) # (*) .. _python-introspection: Inspecting the available API ............................ .. highlight:: python Thanks to Python's introspection primitives, it is possible to inspect the API of the ``orthanc`` module in order to dump all the available features:: import inspect import numbers import orthanc # Loop over the members of the "orthanc" module for (name, obj) in inspect.getmembers(orthanc): if inspect.isroutine(obj): print('Function %s():\n Documentation: %s\n' % (name, inspect.getdoc(obj))) elif inspect.isclass(obj): print('Class %s:\n Documentation: %s' % (name, inspect.getdoc(obj))) # Loop over the members of the class for (subname, subobj) in inspect.getmembers(obj): if isinstance(subobj, numbers.Number): print(' - Enumeration value %s: %s' % (subname, subobj)) elif (not subname.startswith('_') and inspect.ismethoddescriptor(subobj)): print(' - Method %s(): %s' % (subname, inspect.getdoc(subobj))) print('') .. _python-scheduler: Scheduling a task for periodic execution ........................................ .. highlight:: python The following Python script will periodically (every second) run the function ``Hello()`` thanks to the ``threading`` module:: import orthanc import threading TIMER = None def Hello(): global TIMER TIMER = None orthanc.LogWarning("In Hello()") # Do stuff... TIMER = threading.Timer(1, Hello) # Re-schedule after 1 second TIMER.start() def OnChange(changeType, level, resource): if changeType == orthanc.ChangeType.ORTHANC_STARTED: orthanc.LogWarning("Starting the scheduler") Hello() elif changeType == orthanc.ChangeType.ORTHANC_STOPPED: if TIMER != None: orthanc.LogWarning("Stopping the scheduler") TIMER.cancel() orthanc.RegisterOnChangeCallback(OnChange) .. _python-metadata: Filtering and returning metadata ................................ Besides the main DICOM tags, Orthanc associates some metadata to each resource it stores (this includes the date of last update, the transfer syntax, the remote AET...). People are often interested in getting such metadata while calling the ``/tools/find`` route in the :ref:`REST API <rest-find>`, or even in filtering this metadata the same way they look for DICOM tags. This feature is not built in the core of Orthanc, as metadata is not indexed in the Orthanc database, contrarily to the main DICOM tags. Filtering metadata requires a linear search over all the matching resources, which induces a cost in the performance. .. highlight:: python Nevertheless, here is a full sample Python script that overwrites the ``/tools/find`` route in order to give access to metadata:: import json import orthanc import re # Get the path in the REST API to the given resource that was returned # by a call to "/tools/find" def GetPath(resource): if resource['Type'] == 'Patient': return '/patients/%s' % resource['ID'] elif resource['Type'] == 'Study': return '/studies/%s' % resource['ID'] elif resource['Type'] == 'Series': return '/series/%s' % resource['ID'] elif resource['Type'] == 'Instance': return '/instances/%s' % resource['ID'] else: raise Exception('Unknown resource level') def FindWithMetadata(output, uri, **request): # The "/tools/find" route expects a POST method if request['method'] != 'POST': output.SendMethodNotAllowed('POST') else: # Parse the query provided by the user, and backup the "Expand" field query = json.loads(request['body']) if 'Expand' in query: originalExpand = query['Expand'] else: originalExpand = False # Call the core "/tools/find" route query['Expand'] = True answers = orthanc.RestApiPost('/tools/find', json.dumps(query)) # Loop over the matching resources filteredAnswers = [] for answer in json.loads(answers): try: # Read the metadata that is associated with the resource metadata = json.loads(orthanc.RestApiGet('%s/metadata?expand' % GetPath(answer))) # Check whether the metadata matches the regular expressions # that were provided in the "Metadata" field of the user request isMetadataMatch = True if 'Metadata' in query: for (name, pattern) in query['Metadata'].items(): if name in metadata: value = metadata[name] else: value = '' if re.match(pattern, value) == None: isMetadataMatch = False break # If all the metadata matches the provided regular # expressions, add the resource to the filtered answers if isMetadataMatch: if originalExpand: answer['Metadata'] = metadata filteredAnswers.append(answer) else: filteredAnswers.append(answer['ID']) except: # The resource was deleted since the call to "/tools/find" pass # Return the filtered answers in the JSON format output.AnswerBuffer(json.dumps(filteredAnswers, indent = 3), 'application/json') orthanc.RegisterRestCallback('/tools/find', FindWithMetadata) **Warning:** In the sample above, the filtering of the metadata is done using Python's `library for regular expressions <https://docs.python.org/3/library/re.html>`__. It is evidently possible to adapt this script in order to use the DICOM conventions about `attribute matching <http://dicom.nema.org/medical/dicom/2019e/output/chtml/part04/sect_C.2.2.2.html>`__. .. highlight:: bash Here is a sample call to retrieve all the studies that were last updated in 2019 thanks to this Python script:: $ curl http://localhost:8042/tools/find -d '{"Level":"Study","Query":{},"Expand":true,"Metadata":{"LastUpdate":"^2019.*$"}}' .. _python-paging: Implementing basic paging ......................... .. highlight:: python As explained in the FAQ, the :ref:`Orthanc Explorer interface is low-level <improving-interface>`, and is not adapted for end-users. One common need is to implement paging of studies, which calls for server-side sorting of studies. This can be done using the following sample Python plugin that registers a new route ``/sort-studies`` in the REST API of Orthanc:: import json import orthanc def GetStudyDate(study): if 'StudyDate' in study['MainDicomTags']: return study['MainDicomTags']['StudyDate'] else: return '' def SortStudiesByDate(output, uri, **request): if request['method'] == 'GET': # Retrieve all the studies studies = json.loads(orthanc.RestApiGet('/studies?expand')) # Sort the studies according to the "StudyDate" DICOM tag studies = sorted(studies, key = GetStudyDate) # Read the limit/offset arguments provided by the user offset = 0 if 'offset' in request['get']: offset = int(request['get']['offset']) limit = 0 if 'limit' in request['get']: limit = int(request['get']['limit']) # Truncate the list of studies if limit == 0: studies = studies[offset : ] else: studies = studies[offset : offset + limit] # Return the truncated list of studies output.AnswerBuffer(json.dumps(studies), 'application/json') else: output.SendMethodNotAllowed('GET') orthanc.RegisterRestCallback('/sort-studies', SortStudiesByDate) .. highlight:: bash Here is a sample call to this new REST route, that could be issued by any JavaScript framework (the ``json_pp`` command-line pretty-prints a JSON file):: $ curl http://localhost:8042/sort-studies | json_pp This route also implement paging (i.e. it can limit and offset the returned studies):: $ curl 'http://localhost:8042/sort-studies?offset=2&limit=2' | json_pp Obviously, this basic sample can be improved in many ways. To improve performance, one could for instance cache the result of ``/studies?expand`` in memory by :ref:`listening to changes <python-changes>` in the list of studies (cf. ``orthanc.ChangeType.NEW_STUDY`` and ``orthanc.ChangeType.DELETED``). Performance and concurrency --------------------------- **Important:** This section only applies to UNIX-like systems. The ``multiprocessing`` package will not work on Microsoft Windows as the latter OS has a different model for `forking processes <https://en.wikipedia.org/wiki/Fork_(system_call)>`__. .. highlight:: python Let us consider the following sample Python script that makes a CPU-intensive computation on a REST callback:: import math import orthanc import time # CPU-intensive computation taking about 4 seconds def SlowComputation(): start = time.time() for i in range(1000): for j in range(30000): math.sqrt(float(j)) end = time.time() duration = (end - start) return 'computation done in %.03f seconds\n' % duration def OnRest(output, uri, **request): answer = SlowComputation() output.AnswerBuffer(answer, 'text/plain') orthanc.RegisterRestCallback('/computation', OnRest) .. highlight:: text Calling this REST route from the command-line returns the time that is needed to compute 30 million times a squared root on your CPU:: $ curl http://localhost:8042/computation computation done in 4.208 seconds Now, let us call this route three times concurrently (we use bash):: $ (curl http://localhost:8042/computation & curl http://localhost:8042/computation & curl http://localhost:8042/computation ) computation done in 11.262 seconds computation done in 12.457 seconds computation done in 13.360 seconds As can be seen, the computation time has tripled. This means that the computations were not distributed across the available CPU cores. This might seem surprising, as Orthanc is a threaded server (in Orthanc, a pool of C++ threads serves concurrent requests). The explanation is that the Python interpreter (`CPython <https://en.wikipedia.org/wiki/CPython>`__ actually) is built on the top of a so-called `Global Interpreter Lock (GIL) <https://en.wikipedia.org/wiki/Global_interpreter_lock>`__. The GIL is basically a mutex that protects all the calls to the Python interpreter. If multiple C++ threads from Orthanc call a Python callback, only one can proceed at any given time. Note however that the GIL only applies to the Python script: The baseline REST API of Orthanc is not affected by the GIL. .. highlight:: python The solution is to use the `multiprocessing primitives <https://docs.python.org/3/library/multiprocessing.html>`__ of Python. The "master" Python interpreter that is initially started by the Orthanc plugin, can start several `children processes <https://en.wikipedia.org/wiki/Process_(computing)>`__, each of these processes running a separate Python interpreter. This allows to offload intensive computations from the "master" Python interpreter of Orthanc onto those "slave" interpreters. The ``multiprocessing`` library is actually quite straightforward to use:: import math import multiprocessing import orthanc import signal import time # CPU-intensive computation taking about 4 seconds # (same code as above) def SlowComputation(): start = time.time() for i in range(1000): for j in range(30000): math.sqrt(float(j)) end = time.time() duration = (end - start) return 'computation done in %.03f seconds\n' % duration # Ignore CTRL+C in the slave processes def Initializer(): signal.signal(signal.SIGINT, signal.SIG_IGN) # Create a pool of 4 slave Python interpreters POOL = multiprocessing.Pool(4, initializer = Initializer) def OnRest(output, uri, **request): # Offload the call to "SlowComputation" onto one slave process. # The GIL is unlocked until the slave sends its answer back. answer = POOL.apply(SlowComputation) output.AnswerBuffer(answer, 'text/plain') orthanc.RegisterRestCallback('/computation', OnRest) .. highlight:: text Here is now the result of calling this route three times concurrently:: $ (curl http://localhost:8042/computation & curl http://localhost:8042/computation & curl http://localhost:8042/computation ) computation done in 4.211 seconds computation done in 4.215 seconds computation done in 4.225 seconds As can be seen, the calls to the Python computation now fully run in parallel (the time is cut down from 12 seconds to 4 seconds, the same as for one isolated request). Note also how the ``multiprocessing`` library allows to make a fine control over the computational resources that are available to the Python script: The number of "slave" interpreters can be easily changed in the constructor of the ``multiprocessing.Pool`` object, and are fully independent of the threads used by the Orthanc server. .. highlight:: python Very importantly, pay attention to the fact that only the "master" Python interpreter has access to the Orthanc SDK. For instance, here is how you would parse a DICOM file in a slave process:: import pydicom import io def OffloadedDicomParsing(dicom): # No access to the "orthanc" library here, as we are in the slave process dataset = pydicom.dcmread(io.BytesIO(dicom)) return str(dataset) def OnRest(output, uri, **request): # The call to "orthanc.RestApiGet()" is only possible in the master process dicom = orthanc.RestApiGet('/instances/19816330-cb02e1cf-df3a8fe8-bf510623-ccefe9f5/file') answer = POOL.apply(OffloadedDicomParsing, args = (dicom, )) output.AnswerBuffer(answer, 'text/plain') Communication primitives such as ``multiprocessing.Queue`` are available to exchange messages from the "slave" Python interpreters to the "master" Python interpreter if further calls to the Orthanc SDK are required. Obviously, an in-depth discussion about the ``multiprocessing`` library is out of the scope of this document. There are many references available on Internet. Also, note that ``threading`` is not useful here, as Python multithreading is also limited by the GIL, and is more targeted at dealing with costly I/O operations or with the :ref:`scheduling of commands <python-scheduler>`.