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pdf2dcm

PyPI version Supported Python versionsDownloads Downloads License: MITcodecovTest PipelineRelease Pipeline

PDF to DICOM Converter

A python package for PDF to Encapsulated DCM and PDF to DICOM RGB converter

SETUP

Python Package Setup

The python package is available for use on PyPI. It can be setup simply via pip

pip install pdf2dcm

To the check the setup, simply check the version number of the pdf2dcm package by

python -c 'import pdf2dcm; print(pdf2dcm.__version__)'

Poppler Setup

Poppler is a popular project that is used for the creation of Dicom RGB Secondary Capture. You can check if you already have it installed by calling pdftoppm -h in your terminal/cmd. To install poppler these are some of the recommended ways-

Conda

conda install -c conda-forge poppler

Ubuntu

sudo apt-get install poppler-utils

MacOS

brew install poppler

PDF to Encapsulated DCM

Usage

from pdf2dcm import Pdf2EncapsDCM

converter = Pdf2EncapsDCM()
converted_dcm = converter.run(path_pdf='tests/test_data/test_file.pdf', path_template_dcm='tests/test_data/CT_small.dcm', suffix =".dcm")
print(converted_dcm)
# [ 'tests/test_data/test_file.dcm' ]

Parameters converter.run:

  • path_pdf (str): path of the pdf that needs to be encapsulated
  • path_template_dcm (str, optional): path to template for getting the repersonalisation of data.
  • suffix (str, optional): suffix of the dicom files. Defaults to ".dcm".

Returns:

  • List[Path]: list of path of the stored encapsulated dcm

PDF to RGB Secondary Capture DCM

Usage

from pdf2dcm import Pdf2RgbSC

converter = Pdf2RgbSC()
converted_dcm = converter.run(path_pdf='tests/test_data/test_file.pdf', path_template_dcm='tests/test_data/CT_small.dcm', suffix =".dcm")
print(converted_dcm)
# [ 'tests/test_data/test_file_0.dcm', 'tests/test_data/test_file_1.dcm' ]

Parameters converter.run:

  • path_pdf (str): path of the pdf that needs to be converted
  • path_template_dcm (str, optional): path to template for getting the repersonalisation of data.
  • suffix (str, optional): suffix of the dicom files. Defaults to ".dcm".

Returns:

  • List[Path]: list of paths of the stored secondary capture dcm

Notes

  • The name of the output dicom is same as the name of the input pdf
  • If no template is provided no repersonalisation takes place
  • It is possible to produce dicoms without a suffix by simply passing suffix="" to the converter.run()

Repersonalisation

It is the process of copying over data regarding the identity of the encapsualted pdf from a template dicom. Currently, the fields that are repersonalised by default are-

  • PatientName
  • PatientID
  • PatientSex
  • StudyInstanceUID
  • SeriesInstanceUID
  • SOPInstanceUID

The fields SeriesInstanceUID and SOPInstanceUID have been removed from the repersonalization by copying as it violates the DICOM standards.

You can set the fields to repersonalize by passing repersonalisation_fields into Pdf2EncapsDCM(), or Pdf2RgbSC()

Example:

fields = [
    "PatientName",
    "PatientID",
    "PatientSex",
    "StudyInstanceUID",
    "AccessionNumber"
]
converter = Pdf2RgbSC(repersonalisation_fields=fields)

note: this will overwrite the default fields.