chsasank / pypx

Python wrapper to interact with a PACS (based off DCMTK and PyDicom)

PyPx - 0.13

Table of Contents

• 1. Overview
• 2. Installation
• 3. Usage
  • px-echo
    • about px-echo
    • px-echo script
    • px-echo module
  • px-find
    • about px-find
    • px-find script
    • px-find module
  • px-move
    • about px-move
    • px-move script
    • px-move module
  • px-listen
    • about px-listen
    • px-listen script
• 4. Local testing
• 5. Credits

1. Overview

Pypx is a simple Python wrapper around DCMTK and PyDicom. It provides 4 simple way to interact with the PACS:

• px-echo: Ping the PACS to make sure it is online (echoscu).
• px-find: Find data on the PACS (findscu).
• px-move: Move data from the PACS (movescu).
• px-listen: Listen for incoming data from the PACS (storescp).

2. Installation

apt-get update \
&& apt-get install -y dcmtk \
&& apt-get install -y python3-pip python3-dev \
&& pip3 install --upgrade pip \
&& pip install pypx

3. Usage

px-echo

about px-echo

px-echo is a wrapper around dcmtk echoscu.

It sends a DICOM C-ECHO message to a Service Class Provider (SCP) and waits for a response.
The application can be used to verify basic DICOM connectivity.
-- DCMTK, about echoscu.

px-echo script

# need some help?
px-echo --help


# ping Orthanc PACS server
# calling aet: CHIPS
# called aet: ORTHANC
# Orthanc PACS server IP: 127.0.0.1
# Orthanc PACS server port: 4242
# echoscu executable: /usr/local/bin/echoscu
px-echo --aet CHIPS --aec ORTHANC --serverIP 127.0.0.1 --serverPort 4242 --executable /usr/local/bin/echoscu

# output
#   { 'status': 'success',
#     'command': '/usr/local/bin/echoscu --timeout 5  -aec ORTHANC -aet CHIPS 127.0.0.1 4242',
#     'data': ''}

px-echo module

# in yourscript.py
import pypx

pacs_settings = {
  'executable': '/usr/local/bin/echoscu',
  'aec': 'ORTHANC',
  'aet': 'CHIPS',
  'server_ip': '127.0.0.1',
  'server_port': '4242',
}

output = pypx.echo(pacs_settings)
print(output)

# output:
# {
#   'command': '/bin/echoscu --timeout 5  -aec MY-AEC -aet MY-AET 192.168.1.110 4242',
#   'data': '',
#   'status': 'success'
# }

px-find

about px-find

px-find is a wrapper around dcmtk findscu.

Find series on a PACS server given a vast array of parameters. See px-find --help for the full list.

It sends query keys to an SCP and awaits responses.
The application can be used to test SCPs of the Query/Retrieve and Basic Worklist Management Service Classes.
-- DCMTK, about findscu.

px-find script

# need some help?
px-find --help


# find data in Orthanc PACS server
# calling aet: CHIPS
# called aet: ORTHANC
# Orthanc PACS server IP: 127.0.0.1
# Orthanc PACS server port: 4242
# findscu executable: /usr/local/bin/findscu
px-find --aet CHIPS --aec ORTHANC --serverIP 127.0.0.1 --serverPort 4242 --executable /usr/local/bin/findscu \
  --patientID 32124

# output
#   {'status': 'success',
#    'command': '/usr/local/bin/findscu -xi -S
#      -k InstanceNumber
#      -k ModalitiesInStudy
#      -k NumberOfSeriesRelatedInstances
#      -k PatientBirthDate
#      -k "PatientID=32124"
#      -k PatientName
#      -k PatientSex
#      -k PerformedStationAETitle
#      -k "QueryRetrieveLevel=SERIES"
#      -k SeriesDate
#      -k SeriesDescription
#      -k SeriesInstanceUID
#      -k StudyDate
#      -k StudyDescription
#      -k StudyInstanceUID
#      -aec ORTHANC -aet CHIPS 127.0.0.1 4242',
#    'data': [lot of stuff if a match] # [] if no results
#    }

px-find module

# in yourscript.py
import pypx

pacs_settings = {
  'executable': '/usr/local/bin/findscu',
  'aec': 'ORTHANC',
  'aet': 'CHIPS',
  'server_ip': '127.0.0.1',
  'server_port': '4242',
}

# query parameters
query_settings = {
    'PatientID': 32124,
 }

# python 3.5 ** syntax
output = pypx.find({**pacs_settings, **query_settings})
print(output)

# output
#   {'status': 'success',
#    'command': '/usr/local/bin/findscu -xi -S
#      -k InstanceNumber
#      -k ModalitiesInStudy
#      -k NumberOfSeriesRelatedInstances
#      -k PatientBirthDate
#      -k "PatientID=32124"
#      -k PatientName
#      -k PatientSex
#      -k PerformedStationAETitle
#      -k "QueryRetrieveLevel=SERIES"
#      -k SeriesDate
#      -k SeriesDescription
#      -k SeriesInstanceUID
#      -k StudyDate
#      -k StudyDescription
#      -k StudyInstanceUID
#      -aec ORTHANC -aet CHIPS 127.0.0.1 4242',
#    'data': [lot of stuff if a match] # [] if no results
#    }

px-move

about px-move

px-move is a wrapper around dcmtk movescu.

Move series given its SeriesUID. SeriesUID can be retrieved with px-find.

It sends query keys to an SCP and awaits responses.
The application can be used to test SCPs of the Query/Retrieve Service Class. The movescu application can initiate the transfer of images to a third party or can retrieve images to itself.
-- DCMTK, about movescu.

px-move script

px-move --help

# move data from Orthanc PACS server to AETL
# calling aet: CHIPS
# calling aet that will receive the data: CHIPS
# called aet: ORTHANC
# Orthanc PACS server IP: 127.0.0.1
# Orthanc PACS server port: 4242
# movescu executable: /usr/local/bin/movescu
px-move --aet CHIPS --aetl CHIPS --aec ORTHANC --serverIP 127.0.0.1 --serverPort 4242 --executable /usr/local/bin/movescu \
  --seriesUID 1.3.12.2.1107.5.2.32.35235.2012041417312491079284166.0.0.0

# output
#   {'status': 'success',
#    'command': '/usr/local/bin/movescu --move CHIPS --timeout 5
#      -k QueryRetrieveLevel=SERIES
#      -k SeriesInstanceUID=1.3.12.2.1107.5.2.32.35235.2012041417312491079284166.0.0.0
#      -aec ORTHANC -aet CHIPS 127.0.0.1 4242',
#    'data': ''
#    }

px-move module

# in yourscript.py
import pypx

pacs_settings = {
  'executable': '/usr/local/bin/findscu',
  'aec': 'ORTHANC',
  'aet': 'CHIPS',
  'server_ip': '127.0.0.1',
  'server_port': '4242',
}

# query parameters
query_settings = {
    'SeriesInstanceUID': '1.3.12.2.1107.5.2.32.35235.2012041417312491079284166.0.0.0',
 }

# python 3.5 ** syntax
output = pypx.move({**pacs_settings, **query_settings})
print(output)

# output
#   {'status': 'success',
#    'command': '/usr/local/bin/movescu --move CHIPS --timeout 5
#      -k QueryRetrieveLevel=SERIES
#      -k SeriesInstanceUID=1.3.12.2.1107.5.2.32.35235.2012041417312491079284166.0.0.0
#      -aec ORTHANC -aet CHIPS 127.0.0.1 4242',
#    'data': ''
#    }

px-listen

about px-listen

px-listen is a wrapper around dcmtk storescp.

It should be connected to a daemon/service in order to act as a DICOM_Listener.

 It listens on a specific TCP/IP port for incoming association requests from a Storage Service Class User (SCU).
 It can receive both DICOM images and other DICOM composite objects.
-- DCMTK, about storescp.

px-listen script

px-listen --help

# receive DICOM data Orthanc PACS server
# tmp directory to store the data before ordering: /tmp
# log directory to log all incoming/processing data : /incoming/log
# data directory to store ordered data : /incoming/data
# storescp executable: /usr/local/bin/storescp
px-listen -t /tmp -l /incoming/log -d /incoming/data --executable /usr/local/bin/storescp

4. Local testing

Uncomment first 2 imports in the binary command to test then run is a below.

python3 bin/px-find --aet CHIPS --aec CHIPS --serverIP 192.168.0.1 --serverPort 4242

5. Credits

PyDicom

• Author(s): darcymason

DCMTK

• Author(s): Dicom @ OFFIS Team