dicom4ortho 0.2.2

A DICOM Implementation for Orthodontic Images

dicom4ortho 0.2.2

A Python library to create fully defined orthodontic photographs in DICOM.
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• About The Project
  • Built With
• Getting Started
  • Prerequisites
  • Installation
  • Validation with dicom3tools
• Usage
  • CSV Image file format
    • patient_firstname
    • patient_lastname
    • patient_id
    • patient_sex
    • patient_birthdate
    • dental_provider_firstname
    • dental_provider_lastname
    • image_type
    • manufacturer
    • input_image_filename
    • study_instance_uid
    • study_description
    • series_instance_uid
    • series_description
• Known Issues
• Roadmap
• Contributing
• License
• Contact
• Acknowledgements

About The Project

The DICOM standard is ready for any developer in the orthodontic community to implement. However, it can be complicated and implementation can be time consuming. We want to create a proof of concept to demonstrate how to properly store orthodontic visible light images (aka photographs) using DICOM, while ensuring all codes (necessary to uniquely identify each image type) are in the proper place.

Here's why:

• Your time should be focused on creating something amazing.
• Being able to import and export DICOM images to and from your orthodontic software will open doors to you and the orthodontic provider.
• No one software will serve all orthodontic providers completely. Adding interoperability will allow your product to integrate with others, giving additional value to your solution.

You may suggest changes by forking this repo and creating a pull request or opening an issue. Thanks to all the people have have contributed to this project!

A list of commonly used resources that we find helpful are listed in the acknowledgements.

Built With

• pydicom
• pillow
• dicom3tools

Getting Started

Like any other Python module, install the module than use it. There is a CLI interface as well.

Prerequisites

• An installation of Python 3+.
• optional: dicom3tools

Installation

Install unsing pipenv by running

$ pipenv install dicom4ortho

Install using pip by running

$ pip install dicom4ortho

Only Python 3+ is supported

Validation with dicom3tools

The dicom3tools are used to validate and is only used when the --validate option is used. This is just a conveninece wrapper for debugging, and it's installation is not necessary for normal operation.

The dicom3tools can be installed from compiled binaries, which are available for macOS and Windows.

Once installed, point DICOM3TOOLS_PATH in defaults.py to the installation of the dicom3tools.

Usage

The official documentation of this project is available on line here. Source code for the documentation is in this repository under the gh-pages branch.

The DICOM images require a lot of information which is not contained in a flat PNG or JPEG image. This information would, in a production environment, usually come from the practice management software, or photo management software.

The easiest way to feed this information to dicom4ortho's CLI is using a CSV file. You can find an example CSV file here

Once installed, if necessary, start the virtual environment:

pipenv shell

then use dicom4ortho like this:

$ dicom4ortho <filename>

Where filename should be a .csv file. Passing a single image file with metadata through arguments is planned for future implementations.

CSV Image file format

The CSV file should be:

• with , as separator
• UTF-8 encoded

Each CSV file should containt the following columns (header)

patient_firstname

Patient first name. First part of DICOM tag (0010, 0010) Patient's Name.

patient_lastname

Patient last name. Second part of DICOM tag (0010, 0010) Patient's Name.

patient_id

Patient ID. DICOM (0010, 0020) Patient ID tag.

patient_sex

Patient's gender. DICOM (0010, 0040) Patient's Sex tag.

patient_birthdate

Patient's date of birth in YYYY-MM-DD format. DICOM (0010, 0030) Patient's Birth Date tag.

dental_provider_firstname

First name of orthodontic (or dental) provider. First part of DICOM (0008, 0090) Referring Physician's Name tag.

dental_provider_lastname

Last name of orthodontic (or dental) provider. Second part of DICOM (0008, 0090) Referring Physician's Name tag.

image_type

Image type as defined by ADA SCDI WP-1100. Type

dicom4ortho list-image-types

for a list of allowed image types.

manufacturer

Manufacturer of Camera. For example, when using an iPhone, use Apple here. Overrides input file's EXIF metadata.

input_image_filename

Full path of flat JPG/PNG/TIFF image file to use as input.

study_instance_uid

The unique identifier that distinguishes this study from any other study. For orthodontic purposes, all images taken during the same patient visit, should go under the same study, thus have the same study UID.

This is a DICOM UID object and goes into the DICOM (0020, 000d) Study Instance UID tag. The exact format is defined in DICOM Part 5 Data Structures and Encoding - Value Encoding - Value Representation

study_description

A description for this specific study. For orthodontic purposes, this value could be something like 'Initial Visit'.

This is a DICOM UID object and goes into the DICOM (0008, 1030) Study Description. Maximum 64 characters are allowed, as defined the DICOM LO VR

series_instance_uid

The unique identifier that distinguishes this series from any other series. For orthodontic purposes, all images taken with the same imaging device (for photographs, this would be the camera) and during the same study (hence appointment visit) should be part of the same series, thus have the same series UID.

This is a DICOM UID object and goest into the DICOM (0020, 000e) Series Instance UID tag. The exact format is defined in DICOM Part 5 Data Structures and Encoding - Value Encoding - Value Representation

series_description

A description for this specific series. For orthodontic purposes, this value could be something like 'Orthodontic Intraoral Series'.

This is a DICOM UID object and goes into the DICOM (0008, 103e) Series Description. Maximum 64 characters are allowed, as defined the DICOM LO VR

Known Issues

Please check the Implementation Status document.

Roadmap

See the open issues for a list of proposed features (and known issues).

Contributing

Contributions are what make the open source community such an amazing place to be learn, inspire, and create. Any contributions you make are greatly appreciated.

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

License

Distributed under the MIT License. See LICENSE for more information.

Contact

Toni Magni- @zgypa - [e-mail]

Project Link: https://github.com/open-ortho/dicom4ortho

Acknowledgements

• DICOM
• American Dental Association Standards Committee for Dental Informatics