Skip to main content

Classes for representing various medical imaging file formats in Python classes for use in type hinting in data workflows

Project description

https://github.com/ArcanaFramework/fileformats-medimage/actions/workflows/ci-cd.yml/badge.svg https://codecov.io/gh/ArcanaFramework/fileformats-medimage/branch/main/graph/badge.svg?token=UIS0OGPST7 Supported Python versions Latest Version

This is an extension module to the fileformats package, which that adds support for commonly used medical imaging formats, such as DICOM (sets/directories), NIfTI, and MRtrix Image Format, etc…

Quick Installation

This extension can be installed for Python 3 using pip:

$ pip3 install fileformats-medimage

This will install the core package and any other dependencies to validate the file formats.

To use converters and metadata reading methods that depend on third-party packages, also install the associated extras package:

$ pip3 install fileformats-medimage-extras

For most of the converters to work, you will need to install the Dcm2NiiX and MRtrix software packages. There are various ways to do this, but on Ubuntu you can install Dcm2NiiX with:

$ sudo apt install libopenjp2-7
$ curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip
$ unzip dcm2niix_lnx.zip
$ mv dcm2niix /usr/local/bin

(on Mac you can use Homebrew instead of apt to install libopenjp2-7). MRtrix can be installed with miniconda:

$ conda install -c mrtrix3 mrtrix3

License

This work is licensed under a Creative Commons Attribution 4.0 International License

Creative Commons Attribution 4.0 International License

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

fileformats_medimage-0.9.4.tar.gz (35.3 kB view details)

Uploaded Source

Built Distribution

fileformats_medimage-0.9.4-py3-none-any.whl (31.0 kB view details)

Uploaded Python 3

File details

Details for the file fileformats_medimage-0.9.4.tar.gz.

File metadata

  • Download URL: fileformats_medimage-0.9.4.tar.gz
  • Upload date:
  • Size: 35.3 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.1.1 CPython/3.12.6

File hashes

Hashes for fileformats_medimage-0.9.4.tar.gz
Algorithm Hash digest
SHA256 0d64a2756cb301ec93f24453b0463153523cd5192456f42115a73ed52df61e51
MD5 56cb124faf515168e9404b2a78086c30
BLAKE2b-256 2cf514c9a111b65bb5da78f1b793f9d8782c97179781f34fcf00d450b12270e2

See more details on using hashes here.

File details

Details for the file fileformats_medimage-0.9.4-py3-none-any.whl.

File metadata

File hashes

Hashes for fileformats_medimage-0.9.4-py3-none-any.whl
Algorithm Hash digest
SHA256 4b4a69f2a02ba61e41c4ebff4bd1c9dab409a5a4af71aefa670bfa43a1a81267
MD5 905b478a3f763def16235b26f844991e
BLAKE2b-256 d10bfbeca27d24e8c52dc39a9da0aeb8a5c96ce849a0c19cad281a3e8ddcc07a

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page