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https://github.com/a-parida12/pdf2dcm

Python Package for PDF to DICOM Conversion
https://github.com/a-parida12/pdf2dcm

dicom hacktoberfest pdf pdf2dcm pdf2dicom pydicom python

Last synced: 4 days ago
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Python Package for PDF to DICOM Conversion

Host: GitHub
URL: https://github.com/a-parida12/pdf2dcm
Owner: a-parida12
License: mit
Created: 2022-01-23T23:14:44.000Z (almost 3 years ago)
Default Branch: main
Last Pushed: 2024-12-26T14:20:43.000Z (6 days ago)
Last Synced: 2024-12-26T15:24:58.173Z (6 days ago)
Topics: dicom, hacktoberfest, pdf, pdf2dcm, pdf2dicom, pydicom, python
Language: Python
Homepage: https://a-parida12.github.io/pdf2dcm
Size: 1.29 MB
Stars: 22
Watchers: 3
Forks: 4
Open Issues: 4
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Security: SECURITY.md

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README

        # pdf2dcm

[![PyPI version](https://img.shields.io/pypi/v/pdf2dcm.svg?logo=pypi&logoColor=FFE873)](https://pypi.org/project/pdf2dcm/) [![Supported Python versions](https://img.shields.io/pypi/pyversions/pdf2dcm.svg?logo=python&logoColor=FFE873)](https://pypi.org/project/pdf2dcm)[![Downloads](https://static.pepy.tech/personalized-badge/pdf2dcm?period=month&units=abbreviation&left_color=brightgreen&right_color=blue&left_text=PyPi%20Velocity)](https://pepy.tech/project/pdf2dcm) [![Downloads](https://static.pepy.tech/personalized-badge/pdf2dcm?period=total&units=abbreviation&left_color=brightgreen&right_color=blue&left_text=PyPi%20Downloads)](https://pepy.tech/project/pdf2dcm)

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)[![codecov](https://codecov.io/gh/a-parida12/pdf2dcm/branch/main/graph/badge.svg?token=MGY9MHRP46)](https://codecov.io/gh/a-parida12/pdf2dcm)[![Test Pipeline](https://github.com/a-parida12/pdf2dcm/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/a-parida12/pdf2dcm/actions/workflows/test.yml)[![Release Pipeline](https://github.com/a-parida12/pdf2dcm/actions/workflows/release.yml/badge.svg?branch=main)](https://github.com/a-parida12/pdf2dcm/actions/workflows/release.yml)

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

```bash

pip install pdf2dcm

```

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

```bash

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

```bash

conda install -c conda-forge poppler

```

Ubuntu

```bash

sudo apt-get install poppler-utils

```

MacOS

```bash

brew install poppler

```

## PDF to Encapsulated DCM

### Usage

```python

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

```python

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:

```python

fields = [

    "PatientName",

    "PatientID",

    "PatientSex",

    "StudyInstanceUID",

    "AccessionNumber"

]

converter = Pdf2RgbSC(repersonalisation_fields=fields)

```

note: this will overwrite the default fields.