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dcmrtstruct2nii

DICOM RT-Struct to mask

https://github.com/sikerdebaard/dcmrtstruct2nii

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.6%) to scientific vocabulary

Keywords from Contributors

interactive serializer packaging network-simulation shellcodes hacking autograding observability genomics embedded
Last synced: 10 months ago · JSON representation

Repository

DICOM RT-Struct to mask

Basic Info
  • Host: GitHub
  • Owner: Sikerdebaard
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 4.09 MB
Statistics
  • Stars: 101
  • Watchers: 1
  • Forks: 29
  • Open Issues: 8
  • Releases: 4
Created over 7 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

DOI unit tests

dcmrtstruct2nii

DICOM RT-Struct to nii-mask. This is a naïve approach to rasterizing rt-struct to masks in nii format. If there's holes in your RT-Struct then this approach will most likely not work. The RT-Struct needs to be within the bounds of the slices of the original DICOM. Rasterization is done on a slice-by-slice basis, interpolation between slices is currently unsupported.

Interpolation

Interpolation of the mask between slices is currently unsupported. Send us an algorithm or a pull requests and we'll happly add it.

Input file format

The DICOM and RT-Struct inputs need to be unzipped in a directory. Currently this is the only way to read the input files.

CLI Tool

```

install using pip and show tool help

pip install dcmrtstruct2nii dcmrtstruct2nii --help

list structures in DICOM RT Struct

dcmrtstruct2nii ls -r /path/to/rtstruct/file

convert help output

dcmrtstruct2nii convert --help

convert DICOM RT Structs to .nii.gz masks

dcmrtstruct2nii convert -r /path/to/rtstruct/file.dcm -d /path/to/original/extracted/dicom -o /output/path ```

Python API

```

install using pip and show tool help

pip install dcmrtstruct2nii ```

```

lets test it

from dcmrtstruct2nii import dcmrtstruct2nii, listrtstructs

print(listrtstructs('/path/to/dicom/rtstruct/file.dcm'))

dcmrtstruct2nii('/path/to/dicom/rtstruct/file.dcm', '/path/to/original/extracted/dicom/files', '/output/path') ```

License and academic use

The software is licensed MIT License.

For academic use, use a presistent copy from DOI.

Please cite:

Thomas Phil, Thomas Albrecht, Skylar Gay, & Mathis Ersted Rasmussen. (2023). Sikerdebaard/dcmrtstruct2nii: dcmrtstruct2nii v5 (Version v5). Zenodo. https://doi.org/10.5281/zenodo.4037864

Owner

  • Name: Thomas Phil
  • Login: Sikerdebaard
  • Kind: user
  • Location: Netherlands

PhD Student @ Erasmus MC Rotterdam, the Netherlands

GitHub Events

Total
  • Issues event: 1
  • Watch event: 7
  • Issue comment event: 2
  • Pull request event: 3
  • Fork event: 3
Last Year
  • Issues event: 1
  • Watch event: 7
  • Issue comment event: 2
  • Pull request event: 3
  • Fork event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 90
  • Total Committers: 7
  • Avg Commits per committer: 12.857
  • Development Distribution Score (DDS): 0.556
Past Year
  • Commits: 17
  • Committers: 2
  • Avg Commits per committer: 8.5
  • Development Distribution Score (DDS): 0.059
Top Committers
Name Email Commits
t.phil t****s@t****l 40
Thomas t****l@e****l 28
Thomas Phil S****d 11
dependabot[bot] 4****] 6
Thomas T****t@r****m 3
S. Gay s****7@g****m 1
Mathis Rasmussen m****s@o****k 1
Committer Domains (Top 20 + Academic)
oncology.au.dk: 1 roche.com: 1 erasmusmc.nl: 1 tphil.nl: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 28
  • Total pull requests: 25
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 23
  • Total pull request authors: 5
  • Average comments per issue: 1.61
  • Average comments per pull request: 1.16
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 18
Past Year
  • Issues: 2
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mathiser (3)
  • Karol-G (2)
  • wanderine (2)
  • xfuren (2)
  • wwq1204 (1)
  • fishdda (1)
  • jantunes14 (1)
  • Sikerdebaard (1)
  • 1413194910 (1)
  • monjoybme (1)
  • craigrusselltiu (1)
  • kundan1974 (1)
  • ff98li (1)
  • fcjxxl (1)
  • pierre-nedelec (1)
Pull Request Authors
  • dependabot[bot] (18)
  • mathiser (4)
  • StellarStorm (1)
  • sarthakpati (1)
  • thomas-albrecht (1)
  • pierre-nedelec (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (18)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 1,206 last-month
  • Total docker downloads: 24
  • Total dependent packages: 1
  • Total dependent repositories: 8
  • Total versions: 14
  • Total maintainers: 1
pypi.org: dcmrtstruct2nii

Convert DICOM RT-Struct to nii

  • Versions: 14
  • Dependent Packages: 1
  • Dependent Repositories: 8
  • Downloads: 1,206 Last month
  • Docker Downloads: 24
Rankings
Dependent packages count: 4.7%
Dependent repos count: 5.2%
Average: 6.6%
Downloads: 7.4%
Forks count: 7.8%
Stargazers count: 7.9%
Maintainers (1)
sikerdebaard
Last synced: 11 months ago

Dependencies

setup.py pypi
  • SimpleITK >=1.2.0
  • cleo >=0.7.2
  • numpy >=1.15.4
  • pydicom >=1.2.1
  • scikit-image >=0.17.1
  • scipy >=1.2.0
test_requirements.txt pypi
  • Babel ==2.9.0 test
  • Jinja2 ==2.11.3 test
  • MarkupSafe ==1.1.1 test
  • Pillow ==8.1.1 test
  • PyWavelets ==1.1.1 test
  • Pygments ==2.7.4 test
  • SecretStorage ==3.1.2 test
  • SimpleITK ==1.2.4 test
  • Sphinx ==3.4.3 test
  • alabaster ==0.7.12 test
  • attrs ==20.3.0 test
  • bleach ==3.3.0 test
  • certifi ==2020.6.20 test
  • cffi ==1.14.2 test
  • chardet ==3.0.4 test
  • cleo ==0.8.1 test
  • clikit ==0.6.2 test
  • colorama ==0.4.3 test
  • crashtest ==0.3.1 test
  • cryptography ==3.3.2 test
  • cycler ==0.10.0 test
  • decorator ==4.4.2 test
  • docutils ==0.16 test
  • filehash ==0.1.dev5 test
  • flake8 ==3.8.4 test
  • idna ==2.10 test
  • imageio ==2.9.0 test
  • imagesize ==1.2.0 test
  • importlib-metadata ==1.7.0 test
  • iniconfig ==1.1.1 test
  • isodate ==0.6.0 test
  • jeepney ==0.4.3 test
  • joblib ==1.0.0 test
  • keyring ==21.4.0 test
  • kiwisolver ==1.2.0 test
  • matplotlib ==3.3.2 test
  • mccabe ==0.6.1 test
  • networkx ==2.5 test
  • nibabel ==3.2.1 test
  • numpy ==1.19.2 test
  • packaging ==20.4 test
  • pastel ==0.2.1 test
  • pkginfo ==1.5.0.1 test
  • pluggy ==0.13.1 test
  • progressbar2 ==3.53.1 test
  • py ==1.10.0 test
  • pycodestyle ==2.6.0 test
  • pycparser ==2.20 test
  • pydicom ==2.0.0 test
  • pyflakes ==2.2.0 test
  • pylev ==1.3.0 test
  • pyparsing ==2.4.7 test
  • pytest ==6.2.1 test
  • python-dateutil ==2.8.1 test
  • python-utils ==2.5.2 test
  • pytz ==2020.5 test
  • readme-renderer ==26.0 test
  • requests ==2.24.0 test
  • requests-toolbelt ==0.9.1 test
  • rfc3986 ==1.4.0 test
  • scikit-image ==0.17.2 test
  • scipy ==1.5.2 test
  • six ==1.15.0 test
  • snowballstemmer ==2.1.0 test
  • sphinx-rtd-theme ==0.5.1 test
  • sphinxcontrib-applehelp ==1.0.2 test
  • sphinxcontrib-devhelp ==1.0.2 test
  • sphinxcontrib-htmlhelp ==1.0.3 test
  • sphinxcontrib-jsmath ==1.0.1 test
  • sphinxcontrib-qthelp ==1.0.3 test
  • sphinxcontrib-serializinghtml ==1.1.4 test
  • tifffile ==2020.9.3 test
  • toml ==0.10.2 test
  • tqdm ==4.49.0 test
  • twine ==3.2.0 test
  • urllib3 ==1.25.10 test
  • webencodings ==0.5.1 test
  • xnat ==0.3.25 test
  • zipp ==3.1.0 test
.github/workflows/python-package.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite