corrct

Physically corrected projectors for X-ray induced emission CT.

https://github.com/cicwi/pycorrectedemissionct

Science Score: 49.0%

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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DOI references
Found 4 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Scientific vocabulary similarity
Low similarity (13.2%) to scientific vocabulary

Keywords

diffraction fluorescence tomography xrd-ct xrf-ct

Last synced: 6 months ago · JSON representation

Repository

Physically corrected projectors for X-ray induced emission CT.

Basic Info

Host: GitHub
Owner: cicwi
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://cicwi.github.io/PyCorrectedEmissionCT/
Size: 15.5 MB

Statistics

Stars: 7
Watchers: 2
Forks: 3
Open Issues: 3
Releases: 23

Topics

diffraction fluorescence tomography xrd-ct xrf-ct

Created over 6 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog Contributing License Codemeta

PyCorrectedEmissionCT (corrct)

GitHub tag (latest by date) License

Physically corrected projectors for X-ray induced emission CT. PyCorrectedEmissionCT is usually abbreviated to its python module name: corrct (either pronounced "corr-C-T" or "correct").

This package provides the following functionality:

Support for attenuation correction of the forward-projection and back-projection.
Various solvers (reconstruction algorithms):
- Simultaneous Iterative Reconstruction Technique (SIRT).
- Maximum Likelihood Estimation Maximisation (MLEM).
- Simultaneous Algebraic Reconstruction Technique (SART).
- Primal-dual optimization from Chambolle-Pock (Primal-Dual Hybrid Gradient - PDHG), with:
- Various data fitting terms, including Gaussian and Poisson noise modelling.
- Various optional regularization terms, including: TV-min, l1-min, laplacian, and wavelet l1-min.
- Multi-channel (collaborative) regularization terms, like: TNV (Total Nuclear Variation).
- Filtered Back-Projection (FBP), and its data-dependent filter learning variant (PyMR-FBP).
Two projector backends, based on: astra-toolbox and scikit-image.
Guided regularization parameter selection, through cross-validation and elbow method.
Projection alignment routines.

It contains the code used for the following paper, which also provides a mathematical description of the attenuation correction concepts and algorithms used here:

N. Viganò and V. A. Solé, "Physically corrected forward operators for induced emission tomography: a simulation study," Meas. Sci. Technol., no. Advanced X-Ray Tomography, pp. 1–26, Nov. 2017.
https://doi.org/10.1088/1361-6501/aa9d54

Other useful information:

Free software: BSD 3-Clause license
Documentation: https://cicwi.github.io/PyCorrectedEmissionCT/

Getting Started

It takes a few steps to setup PyCorrectedEmissionCT on your machine. We recommend installing Anaconda package manager for Python 3.

Installing with conda

Simply install with: conda install -c n-vigano corrct

If you want fast tomographic projectors using the astra-toolbox: conda install -c astra-toolbox astra-toolbox

Installing from PyPI

Simply install with: pip install corrct

If you are on jupyter, and don't have the rights to install packages system-wide (e.g. on jupyter-slurm at ESRF), then you can install with: ! pip install --user corrct

Installing from source

To install PyCorrectedEmissionCT, simply clone this GitHub project. Go to the cloned directory and run PIP installer: git clone https://github.com/cicwi/PyCorrectedEmissionCT.git corrct cd corrct pip install -e .

Running the examples

To learn more about the functionality of the package check out our examples folder.

Authors and contributors

Nicola VIGANÒ - Main developer
Jerome LESAINT - Contributor
Patrick HARRISON - Contributor

See also the list of contributors who participated in this project.

How to contribute

Contributions are always welcome. Please submit pull requests against the main branch.

If you have any issues, questions, or remarks, then please open an issue on GitHub.

License

This project is licensed under the BSD license - see the LICENSE.md file for details.

Owner

Name: Computational Imaging, CWI
Login: cicwi
Kind: organization

Repositories: 14
Profile: https://github.com/cicwi

CodeMeta (codemeta.json)

{
  "@context": "https://w3id.org/codemeta/3.0",
  "type": "SoftwareSourceCode",
  "applicationCategory": "Computed Tomography",
  "author": [
    {
      "id": "https://orcid.org/0000-0003-1704-5574",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "CEA-IRIG, UGA, MEM, Grenoble, France"
      },
      "email": "nicola.vigano@cea.fr",
      "familyName": "Vigan",
      "givenName": "Nicola"
    },
    {
      "id": "_:author_2",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "ESRF - The European Synchrotron"
      },
      "email": "jerome.lesaint@esrf.fr",
      "familyName": "Lesaint",
      "givenName": "Jerome"
    },
    {
      "id": "https://orcid.org/0000-0001-9798-8710",
      "type": "Person",
      "familyName": "Harrison",
      "givenName": "Patrick"
    }
  ],
  "codeRepository": "github.com:cicwi/PyCorrectedEmissionCT.git",
  "description": "Physically corrected projectors for X-ray-induced emission CT. PyCorrectedEmissionCT is usually abbreviated to its Python module name: corrct (either pronounced \"corr-C-T\" or \"correct\").",
  "identifier": "10.5281/zenodo.3569684",
  "keywords": [
    "xrf-ct",
    "X-ray",
    "self-attenuation",
    "attenuation correction",
    "tomography"
  ],
  "license": "https://spdx.org/licenses/BSD-3-Clause",
  "name": "PyCorrectedEmissionCT",
  "operatingSystem": [
    "Linux",
    "Windows",
    "macOS"
  ],
  "programmingLanguage": "Python",
  "issueTracker": "https://github.com/cicwi/PyCorrectedEmissionCT/issues"
}

GitHub Events

Total

Create event: 4
Issues event: 1
Release event: 1
Watch event: 2
Push event: 21
Pull request event: 1

Last Year

Create event: 4
Issues event: 1
Release event: 1
Watch event: 2
Push event: 21
Pull request event: 1

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 462
Total Committers: 4
Avg Commits per committer: 115.5
Development Distribution Score (DDS): 0.048

Top Committers

Name	Email	Commits
Nicola VIGANO	n**o@e**r	440
Nicola Viganò	O**n@u**m	9
Nicola Viganò	b**y@g**m	8
Nicola VIGANÒ	N**o@c**l	5

Committer Domains (Top 20 + Academic)

cwi.nl: 1 esrf.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 12
Total pull requests: 12
Average time to close issues: 6 months
Average time to close pull requests: 5 months
Total issue authors: 2
Total pull request authors: 3
Average comments per issue: 0.75
Average comments per pull request: 0.83
Merged pull requests: 10
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 7 days
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

Obi-Wan (11)
harripj (1)

Pull Request Authors

Obi-Wan (12)
lesaintjerome (1)
harripj (1)

Top Labels

Issue Labels

enhancement (6)

Pull Request Labels

enhancement (11)

Packages

Total packages: 1
Total downloads:
- pypi 49 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 19
Total maintainers: 1

pypi.org: corrct

Physically corrected projectors for X-ray induced emission CT.

Homepage: https://github.com/cicwi/PyCorrectedEmissionCT
Documentation: https://cicwi.github.io/PyCorrectedEmissionCT
License: bsd-3-clause
Latest release: 1.0.0
published 11 months ago

Versions: 19
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 49 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 19.1%

Average: 20.8%

Dependent repos count: 21.6%

Downloads: 25.5%

Stargazers count: 27.8%

Maintainers (1)

nicolavigano

Last synced: 6 months ago

corrct

Science Score: 49.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

PyCorrectedEmissionCT (corrct)

Getting Started

Installing with conda

Installing from PyPI

Installing from source

Running the examples

Authors and contributors

How to contribute

License

Owner

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: corrct

Rankings

Maintainers (1)