pdf2dcm 0.5.0

Description:

pdf2dcm 0.5.0

pdf2dcm


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.