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About Pynetdicom

Pynetdicom is an MCP server in the Healthcare category: a Python implementation of the DICOM networking protocol.

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pynetdicom

A Python implementation of the DICOM <https://www.dicomstandard.org>_ networking protocol, originally based on (legacy) pynetdicom <https://github.com/patmun/pynetdicom_legacy>_.

Description

DICOM <https://www.dicomstandard.org>_ is the international standard for medical images and related information. It defines the formats and communication protocols for media exchange in radiology, cardiology, radiotherapy and other medical domains.

pynetdicom is a pure Python package that implements the DICOM networking protocol. Working with pydicom <https://github.com/pydicom/pydicom>_, it allows the easy creation of DICOM Service Class Users (SCUs) and Service Class Providers (SCPs).

pynetdicom's main user class is AE <https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.ae.ApplicationEntity.html>_ and is used to represent a DICOM Application Entity. With it you can:

Start the application as an SCP by specifying the supported presentation contexts then calling AE.start_server() <https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.ae.ApplicationEntity.html#pynetdicom.ae.ApplicationEntity.start_server>_ and waiting for incoming association requests
Use the application as an SCU by specifying the presentation contexts you want the peer SCP to support, then requesting an association via the AE.associate() <https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.ae.ApplicationEntity.html#pynetdicom.ae.ApplicationEntity.associate>_ method, which returns an Association <https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association>_ thread.

Once associated, the services available to the association can be used by sending DIMSE-C <https://dicom.nema.org/medical/dicom/current/output/html/part07.html#chapter_9>_ and DIMSE-N <https://dicom.nema.org/medical/dicom/current/output/html/part07.html#chapter_10>_ messages.

Documentation

The pynetdicom tutorials <https://pydicom.github.io/pynetdicom/stable/tutorials/index.html>, user guide <https://pydicom.github.io/pynetdicom/stable/user/index.html>, code examples <https://pydicom.github.io/pynetdicom/stable/examples/index.html>, application <https://pydicom.github.io/pynetdicom/stable/apps/index.html> and API reference <https://pydicom.github.io/pynetdicom/stable/reference/index.html>_ documentation is available for the current release <https://pydicom.github.io/pynetdicom/>_ as well as the development version <https://pydicom.github.io/pynetdicom/dev>_.

Installation

Dependencies

`pydicom <https://github.com/pydicom/pydicom>`_

Installing current release

Using pip:

.. code-block:: sh

pip install -U pynetdicom

Using conda:

.. code-block:: sh

conda install -c conda-forge pynetdicom

For more detailed instructions, including how to install the current development version, please see the installation guide <https://pydicom.github.io/pynetdicom/stable/tutorials/installation.html>_.

Supported DIMSE Services

SCU Services


When the AE is acting as an SCU and an association has been established with a peer
SCP, the following DIMSE-C and -N services are available:

.. _assoc: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html
.. _echo: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_c_echo
.. _find: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_c_find
.. _c_get: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_c_get
.. _move: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_c_move
.. _store: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_c_store
.. _action: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_n_action
.. _create: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_n_create
.. _delete: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_n_delete
.. _er: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_n_event_report
.. _n_get: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_n_get
.. _set: https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html#pynetdicom.association.Association.send_n_set


+----------------+----------------------------------------------------------------------------------------+
| DIMSE service  | `Association <assoc_>`_ method                                                         |
+================+========================================================================================+
| C-ECHO         | `Association.send_c_echo() <echo_>`_                                                   |
+----------------+----------------------------------------------------------------------------------------+
| C-FIND         | `Association.send_c_find(dataset, query_model) <find_>`_                               |
+----------------+----------------------------------------------------------------------------------------+
| C-GET          | `Association.send_c_get(dataset, query_model) <c_get_>`_                               |
+----------------+----------------------------------------------------------------------------------------+
| C-MOVE         | `Association.send_c_move(dataset, move_aet, query_model) <move_>`_                     |
+----------------+----------------------------------------------------------------------------------------+
| C-STORE        | `Association.send_c_store(dataset) <store_>`_                                          |
+----------------+----------------------------------------------------------------------------------------+
| N-ACTION       | `Association.send_n_action(dataset, action_type, class_uid, instance_uid) <action_>`_  |
+----------------+----------------------------------------------------------------------------------------+
| N-CREATE       | `Association.send_n_create(dataset, class_uid, instance_uid) <create_>`_               |
+----------------+----------------------------------------------------------------------------------------+
| N-DELETE       | `Association.send_n_delete(class_uid, instance_uid) <delete_>`_                        |
+----------------+----------------------------------------------------------------------------------------+
| N-EVENT-REPORT | `Association.send_n_event_report(dataset, event_type, class_uid, instance_uid) <er_>`_ |
+----------------+----------------------------------------------------------------------------------------+
| N-GET          | `Association.send_n_get(identifier_list, class_uid, instance_uid) <n_get_>`_           |
+----------------+----------------------------------------------------------------------------------------+
| N-SET          | `Association.send_n_set(dataset, class_uid, instance_uid) <set_>`_                     |
+----------------+----------------------------------------------------------------------------------------+

Where *dataset* is a pydicom
`Dataset <https://pydicom.github.io/pydicom/stable/ref_guide.html#dataset>`_
object, *query_model* is a UID string, *identifier_list* is a list of pydicom
`Tag <https://pydicom.github.io/pydicom/stable/api_ref.html#pydicom.tag.Tag>`_
objects, *event_type* and *action_type* are ints and *class_uid* and
*instance_uid* are UID strings. See the
`Association documentation <https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.association.Association.html>`_
for more information.


SCP Services

When the AE is acting as an SCP the following DIMSE-C and -N services are available to the peer once an association has been established:

With the exception of the C-ECHO service, a user-defined callable function, handler, must be bound to the corresponding intervention event <https://pydicom.github.io/pynetdicom/stable/user/events#intervention-events>_ in order to complete a DIMSE service request. Events can be imported with from pynetdicom import evt and a handler can be bound to an event prior to starting an association through the evt_handlers keyword arguments in AE.start_server() <https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.ae.ApplicationEntity.html#pynetdicom.ae.ApplicationEntity.start_server>_ and AE.associate() <https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.ae.ApplicationEntity.html#pynetdicom.ae.ApplicationEntity.associate>_.

When an event occurs the handler function is called and passed a single parameter, event, which is an Event <https://pydicom.github.io/pynetdicom/stable/reference/generated/pynetdicom.events.Event.html>_ object whose specific attributes are dependent on the type of event that occurred. Handlers bound to intervention events must return or yield certain values. See the handler documentation <https://pydicom.github.io/pynetdicom/stable/reference/events>_ for information on what attributes and properties are available in Event for each event type and the expected returns/yields for the corresponding handlers.

Applications

Some basic DICOM applications are included with pynetdicom:

echoscp <https://pydicom.github.io/pynetdicom/stable/apps/echoscp.html>_
echoscu <https://pydicom.github.io/pynetdicom/stable/apps/echoscu.html>_
findscu <https://pydicom.github.io/pynetdicom/stable/apps/findscu.html>_
getscu <https://pydicom.github.io/pynetdicom/stable/apps/getscu.html>_
qrscp <https://pydicom.github.io/pynetdicom/stable/apps/qrscp.html>_ (requires sqlalchemy <https://www.sqlalchemy.org/>_)
movescu <https://pydicom.github.io/pynetdicom/stable/apps/movescu.html>_
storescp <https://pydicom.github.io/pynetdicom/stable/apps/storescp.html>_
storescu <https://pydicom.github.io/pynetdicom/stable/apps/storescu.html>_

Code Examples

More code examples <https://pydicom.github.io/pynetdicom/stable/examples/index.html>_ are available in the documentation.

Echo SCU

Send a C-ECHO request to a Verification SCP (at TCP/IP address *addr*, listen port
number *port*):

.. code-block:: python

        from pynetdicom import AE

        ae = AE(ae_title='MY_ECHO_SCU')
        # Verification SOP Class has a UID of 1.2.840.10008.1.1
        #   we can use the UID str directly when adding the requested
        #   presentation context
        ae.add_requested_context('1.2.840.10008.1.1')

        # Associate with a peer AE
        assoc = ae.associate(addr, port)

        if assoc.is_established:
            # Send a DIMSE C-ECHO request to the peer
            status = assoc.send_c_echo()

            # Print the response from the peer
            if status:
                print('C-ECHO Response: 0x{0:04x}'.format(status.Status))

            # Release the association
            assoc.release()

Echo SCP

Create a blocking Echo SCP on port 11112 (you may optionally bind a handler to the evt.EVT_C_ECHO event if you want to return something other than an 0x0000 Success status):

.. code-block:: python

    from pynetdicom import AE, VerificationPresentationContexts

    ae = AE(ae_title='MY_ECHO_SCP')
    # Or we can use the inbuilt VerificationPresentationContexts list,
    #   there's one for each of the supported Service Classes
    # In this case, we are supporting any requests to use Verification SOP
    #   Class in the association
    ae.supported_contexts = VerificationPresentationContexts

    # Start the SCP on (host, port) in blocking mode
    ae.start_server(("localhost", 11112), block=True)

Alternatively, you can start the SCP in non-blocking mode, which returns the running server instance. This can be useful when you want to run a Storage SCP and make C-MOVE requests within the same AE.

In the next example we'll create a non-blocking Verification SCP and bind a handler for the C-ECHO service request event evt.EVT_C_ECHO that logs the requestor's address and port number and the timestamp for the event.

.. code-block:: python

    import logging

    from pynetdicom import AE, evt, debug_logger
    from pynetdicom.sop_class import Verification

    # Setup logging to use the StreamHandler at the debug level
    debug_logger()

    ae = AE(ae_title='MY_ECHO_SCP')
    ae.add_supported_context(Verification)

    # Implement the EVT_C_ECHO handler
    def handle_echo(event, logger):
        """Handle a C-ECHO service request.

        Parameters
        ----------
        event : evt.Event
            The C-ECHO service request event, this parameter is always
            present.
        logger : logging.Logger
            The logger to use, this parameter is only present because we
            bound ``evt.EVT_C_ECHO`` using a 3-tuple.

        Returns
        -------
        int or pydicom.dataset.Dataset
            The status returned to the peer AE in the C-ECHO response.
            Must be a valid C-ECHO status value as either an ``int`` or a
            ``Dataset`` object containing an (0000,0900) *Status* element.
        """
        # Every *Event* includes `assoc` and `timestamp` attributes
        #   which are the *Association* instance the event occurred in
        #   and the *datetime.datetime* the event occurred at
        requestor = event.assoc.requestor
        timestamp = event.timestamp.strftime("%Y-%m-%d %H:%M:%S")
        msg = (
            "Received C-ECHO service request from "
            f"({requestor.address}, {requestor.port}) at {timestamp}"
        )
        logger.info(msg)

        # Return a *Success* status
        return 0x0000

    # By binding using a 3-tuple we can pass extra arguments to
    #   the handler
    handlers = [(evt.EVT_C_ECHO, handle_echo, [logging.getLogger('pynetdicom')])]

    # Start the SCP in non-blocking mode
    scp = ae.start_server(("localhost", 11112), block=False, evt_handlers=handlers)

    # Associate and send a C-ECHO request to our own Verification SCP
    ae.add_requested_context(Verification)
    assoc = ae.associate('localhost', 11112)
    if assoc.is_established:
        status = assoc.send_c_echo()
        assoc.release()

    # Shutdown the SCP
    scp.shutdown()

Storage SCU

Send the DICOM *CT Image Storage* dataset in *file-in.dcm* to a peer Storage
SCP (at TCP/IP address *addr*, listen port number *port*):

.. code-block:: python

        from pydicom import dcmread
        from pydicom.uid import ImplicitVRLittleEndian

        from pynetdicom import AE, VerificationPresentationContexts
        from pynetdicom.sop_class import CTImageStorage, MRImageStorage

        ae = AE(ae_title='MY_STORAGE_SCU')
        # We can also do the same thing with the requested contexts
        ae.requested_contexts = VerificationPresentationContexts
        # Or we can use inbuilt objects like CTImageStorage.
        # The requested presentation context's transfer syntaxes can also
        #   be specified using a str/UID or list of str/UIDs
        ae.add_requested_context(
            CTImageStorage,
            transfer_syntax=ImplicitVRLittleEndian,
        )
        # Adding a presentation context with multiple transfer syntaxes
        ae.add_requested_context(
            MRImageStorage,
            transfer_syntax=[ImplicitVRLittleEndian, '1.2.840.10008.1.2.1'],
        )

        assoc = ae.associate(addr, port)
        if assoc.is_established:
            dataset = dcmread('file-in.dcm')
            # `status` is the response from the peer to the store request
            # but may be an empty pydicom Dataset if the peer timed out or
            # sent an invalid dataset.
            status = assoc.send_c_store(dataset)

            assoc.release()

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