A DICOM Implementation for Orthodontic Images
Project description
dicom4ortho 0.2.2
A Python library to create fully defined orthodontic photographs in DICOM.
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- About The Project
- Getting Started
- Usage
- 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
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.
- Fork the Project
- Create your Feature Branch (
git checkout -b feature/AmazingFeature
) - Commit your Changes (
git commit -m 'Add some AmazingFeature'
) - Push to the Branch (
git push origin feature/AmazingFeature
) - Open a Pull Request
License
Distributed under the MIT License. See LICENSE for more information.
Contact
Toni Magni- @zgypa - open-ortho@afm.co
Project Link: https://github.com/open-ortho/dicom4ortho
Acknowledgements
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