spydcmtk

Simple PYthon DiCoM Tool Kit

Dicom organisational, querying and conversion toolkit

spydcmtk is a pure Python package built on top of pydicom.

This package extends pydicom with a class structure based upon the Patient-Study-Series-Image hierarchy. In addition, it provides a number of built in routines for common actions when working with dicom files, such as human readable renaming, anonymisation, searching and summarising.

Version

Current is VERSION 1.1.9 Release.

• 1.2.0: Improved stability of VTK conversion. Bug fixes. Add basic interactive functionality. Add functionality to construct 4D-flow datasets. Add reliance on external library ngawari for basic IO operations, format conversion and vtk filter actions.
• 1.1.9: Permit user naming of series directory when writing at series level. Assistance for modifying tag values.
• 1.1.8: Added improved functionality for dicom to: VTK image data; and VTK structured grid data conversion
• 1.1.7: Add basic DCM-SEG read/write/conversion functionality. Rewrote dcm2vtk routines for improved consistency in some edge cases.
• 1.1.5: Add option to retrieve tag value from commandline. Small bug fix on safe naming.
• 1.1.4: Additional configuration moved to config file. DCM2VTI active.
• 1.1.1: Add option to keep private tags when running anonymisation. Dcm2nii path configurable from config file.
• 1.1.0: Some bug fixes and restrict the use of dicom to vti (WIP)
• 1.0.0: Initial Release

Installation

Using pip:

pip install spydcmtk

Quick start

If you installed via pip then spydcmtk console script will be exposed in your python environment.

Access via:

spydcmtk -h

to see the commandline usage available to you.

If you would like to incorporate spydcmtk into your python project, then import as:

import spydcmtk

listOfStudies = spydcmtk.dcmTK.ListOfDicomStudies.setFromDirectory(MY_DICOM_DIRECTORY)
# Example filtering
dcmStudy = listOfStudies.getStudyByDate('20230429') # Dates in dicom standard string format: YYYYMMDD
dcmSeries = dcmStudy.getSeriesBySeriesNumber(1)
# Example writing new dicom files with anonymisation
dcmStudy.writeToOrganisedFileStructure(tmpDir, anonName='Not A Name')

Configuration

spydcmtk uses a spydcmtk.conf file for configuration.

By default spydcmtk.conf files are search for in the following locations:

1. source_code_directory/spydcmtk.conf (file with default settings)
2. $HOME/spydcmtk.conf
3. $HOME/.spydcmtk.conf
4. $HOME/.config/spydcmtk.conf
5. Full file path defined at environment variable: "SPYDCMTK_CONF"
6. Full path passed as commandline argument to spydcmtk

Files are read in the above order with each subsequent variable present over writing any previously defined. For information on files found and variables used run:

spydcmtk -INFO

Documentation

Clear documentation of basic features can be seen by running the "spycmtk -h" command as referenced above. For detailed documentation please see spydcmtk-documnetation

Works in progress

Basic handling of DicomSegmentation images is added :

• writing a label map to dicom segmentation
• basic reading a dicom segmentation and writing to vti/vts
• handling multi label dicom segmentations
• improved, explicit handling of data orientation for
  • multi-volume dicom images
  • multi-label dicom seg images