pyconquest 0.0.3

Python code which partly mimics the conquest pacs

PyConquest

Introduction

Python code to partly mimic the functionality of the Conquest Pacs system ( http://www.natura-ingenium.nl/dicom.html ). No (source) code of Conquest was used to write this python code. Program was optimised to be partly compatible (files and database), so queries etc. can be re-used.

Description:

Class is used to organise and index sets of dicom files. The dicom files are stored in a directory (default name : data), with the files of each patient stored in a subdirectory with the patientid as the name. The class will index all files in the directory and store information (tag information of the dicom files) in a sqlite database (default name : conquest.db). Which tags are stored in the database can be defined by the dicom.sql file, this file is optional, a standard set is used when not present.

Standard file/directory layout is :

conquest.db                       database file
data                              data_directory
    1                             subdirectory with name of PatientID
      file1_of_pat1.dcm           files of patient1
      file2_of_pat1.dcm
      ..
      ..
    2                             subdirectory with name of PatientID
      file1_of_pat2               files of patient2
      file2_of_pat2
      ..
      ..
[dicom.sql]                       optional definition of the database

Implemented features :

• indexer properties : read a dicom tree and build a sqlite database from this which conforms to the Conquest standard.
• use the conquest style dicom.sql file to define the columns
• add some special columns,with for instance the roinames in a RTSTRUCT file
• provide low level procedures to write and read to the database and helper files to create queries
• provide basic SCU and SCP functionality
• basic printing of data properties

What it is not and when you should use Conquest

• no attempt made to mimic full dicom functionality (this is no PACS)
• lua scripting
• image visualisation

Examples

(Re)create database and rebuild database

from pyconquest import pyconquest

c=pyconquest()
c.create_standard_dicom_tables()
nr_files=c.rebuild_database_from_dicom()

Basic database summary

from pyconquest import pyconquest

c=pyconquest()
c.dicom_series_summary()

Using non standard names and directories

from pyconquest import pyconquest

c=pyconquest(
    data_directory='data2',
    sql_inifile_name='dicom2.sql',
    database_filename='test.db',
    connect_and_read_sql=True)
    
nr_files=c.rebuild_database_from_dicom()   
c.dicom_series_summary()

Adding files to the database

Adding a single file specified by name (optionally remove original)

from pyconquest import pyconquest

c=pyconquest()
c.store_dicom_file('1.2.840.113704.1.111....931a31.dcm')
c.store_dicom_file('1.2.840.113704.1.111....931a31.dcm', remove_after_store=True)

to enter all dicom files in a directory into the database

from pyconquest import pyconquest

c=pyconquest()
c.store_dicom_files_from_directory('input_directory_name')
c.store_dicom_files_from_directory('input_directory_name', remove_after_store=True)

Sending and receiving files via dicom connectivity

Send dicom files via dicom protocol, by patientid, seriesuid or query

from pyconquest import pyconquest

c=pyconquest()
c.connect_db()
c.send_dicom(addres='127.0.0.1',port=5678,patientid='1234567')
c.send_dicom(seriesuid='2.16.840.1.113669.2.931128.880152.20190524082318.537836')

RTPLAN_query="select seriesinst from dicomseries where modality=\'RTPLAN\'"
c.send_dicom(query=RTPLAN_query)

Start receiver (received files are stored in data directory and database is updated )

from pyconquest import pyconquest

c=pyconquest(data_directory='data2')
c.start_dicom_listener(port=5678)

Copying files of a series on the disk to another directory

by seriesuid or list of seriesuids

from pyconquest import pyconquest

c.copy_dicom_files_to_dest(seriesuid='1.2...8024597.12',destination='out', UseSubDirectories=True)
c.copy_dicom_files_to_dest(seriesuid=['1.2.84..97.12','2.16.840....33'],destination='data2')

Or by query (query should return seriesinst)

from pyconquest import pyconquest

c=pyconquest()
CTquery="select seriesinst from dicomseries where modality=\'CT\'"
c.copy_dicom_files_to_dest(query=CTquery, destination='CTdata',UseSubDirectories=True)

Definition of the database structure

The database can be defined using various ways

• If a file dicom.sql exist that file is used
• If an alternative file is specified on creation of the instance, that file is used
  • use sql_infilename='filename.sql' when creating
• If no file is found, a hardcoded definition is taken
  • You can add columns to this definition as illustrated below:

from pyconquest import pyconquest

c=pyconquest(sql_inifile_name='dicom.sql',loglevel='INFO')
c.add_column_to_database(tablename='DICOMpatients',column_definition=['0x0020', '0x000d', 'StudyInst'])
c.create_standard_dicom_tables()

the .sql files are compatible with the original Conquest file format

To install and upload to PyPi:

python setup.py sdist
twine upload dist/*