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spyrit

A Python toolbox for deep image reconstruction, with emphasis on single-pixel imaging.

https://github.com/openspyrit/spyrit

Science Score: 49.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
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    Committers with academic emails
    2 of 10 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (15.9%) to scientific vocabulary

Keywords

deep-learning image-reconstruction medical-imaging pypi python single-pixel-camera torch
Last synced: 4 months ago · JSON representation

Repository

A Python toolbox for deep image reconstruction, with emphasis on single-pixel imaging.

Basic Info
Statistics
  • Stars: 58
  • Watchers: 5
  • Forks: 15
  • Open Issues: 21
  • Releases: 6
Topics
deep-learning image-reconstruction medical-imaging pypi python single-pixel-camera torch
Created almost 5 years ago · Last pushed 5 months ago
Metadata Files
Readme Changelog License Authors Codemeta

README.md

GitHub tag (latest by date) GitHub PyPI pyversions Docs

SPyRiT

SPyRiT is a PyTorch-based deep image reconstruction package primarily designed for single-pixel imaging.

Installation

The spyrit package is available for Linux, MacOs and Windows. We recommend to use a virtual environment.

Linux and MacOs

(user mode) pip install spyrit (developper mode) git clone https://github.com/openspyrit/spyrit.git cd spyrit pip install -e .

Windows

On Windows you may need to install PyTorch first. It may also be necessary to run the following commands using administrator rights (e.g., starting your Python environment with administrator rights).

Adapt the two examples below to your configuration (see here for the latest instructions)

(CPU version using pip)

pip3 install torch torchvision torchaudio

(GPU version using conda)

shell conda install pytorch torchvision torchaudio pytorch-cuda=12.4 -c pytorch -c nvidia

Then, install SPyRiT using pip:

(user mode) pip install spyrit (developper mode) git clone https://github.com/openspyrit/spyrit.git cd spyrit pip install -e .

Test

To check the installation, run in your python terminal: import spyrit

Get started - Examples

To start, check the documentation tutorials. These tutorials must be runned from tutorial folder (they load image samples from spyrit/images/): cd spyrit/tutorial/

More advanced reconstruction examples can be found in spyrit-examples/tutorial. Run advanced tutorial in colab: Open In Colab

API Documentation

https://spyrit.readthedocs.io/

Contributors (alphabetical order)

  • Juan Abascal - Website
  • Thomas Baudier
  • Sebastien Crombez
  • Nicolas Ducros - Website
  • Antonio Tomas Lorente Mur - Website
  • Romain Phan
  • Fadoua Taia-Alaoui

How to cite?

When using SPyRiT in scientific publications, please cite the following paper:

  • G. Beneti-Martin, L Mahieu-Williame, T Baudier, N Ducros, "OpenSpyrit: an Ecosystem for Reproducible Single-Pixel Hyperspectral Imaging," Optics Express, Vol. 31, No. 10, (2023). https://doi.org/10.1364/OE.483937.

When using SPyRiT specifically for the denoised completion network, please cite the following paper:

  • A Lorente Mur, P Leclerc, F Peyrin, and N Ducros, "Single-pixel image reconstruction from experimental data using neural networks," Opt. Express 29, 17097-17110 (2021). https://doi.org/10.1364/OE.424228.

License

This project is licensed under the LGPL-3.0 license - see the LICENSE.md file for details

Acknowledgments

  • Jin LI for his implementation of Convolutional Gated Recurrent Units for PyTorch
  • Erik Lindernoren for his processing of the UCF-101 Dataset.

Owner

  • Name: openspyrit
  • Login: openspyrit
  • Kind: organization

CodeMeta (Codemeta.json) 

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "type": "SoftwareSourceCode",
  "applicationCategory": "Single-pixel imaging",
  "codeRepository": "https://github.com/openspyrit/spyrit",
  "dateCreated": "2020-12-10",
  "datePublished": "2021-03-11",
  "description": "SPyRiT is a PyTorch-based deep image reconstruction package primarily designed for single-pixel imaging.",
  "keywords": [
    "Single-pixel imaging",
    "pytorch"
  ],
  "license": "https://spdx.org/licenses/LGPL-3.0",
  "name": "SPyRiT",
  "operatingSystem": [
    "Linux",
    "Windows",
    "MacOS"
  ],
  "programmingLanguage": "Python 3",
  "contIntegration": "https://github.com/openspyrit/spyrit/actions",
  "codemeta:continuousIntegration": {
    "id": "https://github.com/openspyrit/spyrit/actions"
  },
  "issueTracker": "https://github.com/openspyrit/spyrit/issues"
}

GitHub Events

Total
  • Create event: 28
  • Release event: 4
  • Issues event: 58
  • Watch event: 22
  • Delete event: 25
  • Member event: 2
  • Issue comment event: 68
  • Push event: 318
  • Gollum event: 9
  • Pull request review event: 1
  • Pull request event: 46
Last Year
  • Create event: 28
  • Release event: 4
  • Issues event: 58
  • Watch event: 22
  • Delete event: 25
  • Member event: 2
  • Issue comment event: 68
  • Push event: 318
  • Gollum event: 9
  • Pull request review event: 1
  • Pull request event: 46

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 155
  • Total Committers: 10
  • Avg Commits per committer: 15.5
  • Development Distribution Score (DDS): 0.729
Top Committers
Name Email Commits
Thomas BAUDIER t****r@c****r 42
cmouton c****n@c****r 36
Sebastien Crombez s****z@u****r 32
ducros n****s@i****r 30
Antonio Tomas Lorente Mur a****r@i****r 6
AMADOR ARAYA LUIS p1926613 l****a@e****r 3
Guilherme Beneti b****i@c****r 2
guilhermebene g****n@h****m 2
Guilherme Beneti Martins g****s@g****m 1
Guilherme Beneti Martins g****s@u****r 1
Committer Domains (Top 20 + Academic)
creatis.insa-lyon.fr: 3 insa-lyon.fr: 2 usp.br: 1 etu.univ-lyon1.fr: 1 univ-lyon1.fr: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 106
  • Total pull requests: 198
  • Average time to close issues: 9 months
  • Average time to close pull requests: 20 days
  • Total issue authors: 8
  • Total pull request authors: 11
  • Average comments per issue: 1.37
  • Average comments per pull request: 0.8
  • Merged pull requests: 157
  • Bot issues: 0
  • Bot pull requests: 9
Past Year
  • Issues: 35
  • Pull requests: 40
  • Average time to close issues: 3 months
  • Average time to close pull requests: 10 days
  • Issue authors: 4
  • Pull request authors: 5
  • Average comments per issue: 0.71
  • Average comments per pull request: 0.95
  • Merged pull requests: 35
  • Bot issues: 0
  • Bot pull requests: 3
View more stats
Top Authors
Issue Authors
  • nducros (56)
  • romainphan (28)
  • tbaudier (6)
  • guilhermebene (5)
  • cmouton (4)
  • WH-CSU (3)
  • jabascal (3)
  • Tommte (1)
  • pre-commit-ci[bot] (1)
Pull Request Authors
  • romainphan (117)
  • nducros (54)
  • tbaudier (39)
  • jabascal (25)
  • pre-commit-ci[bot] (13)
  • TALAOUI (7)
  • lucxt18 (3)
  • guilhermebene (3)
  • Tommte (2)
  • sebcrom (1)
  • cmouton (1)
Top Labels
Issue Labels
enhancement (36) documentation (23) bug (14) old (10) question (4)
Pull Request Labels
enhancement (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 218 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 20
  • Total maintainers: 2
pypi.org: spyrit

Toolbox for deep image reconstruction

  • Documentation: https://spyrit.readthedocs.io/
  • License: GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below. 0. Additional Definitions. As used herein, "this License" refers to version 3 of the GNU Lesser General Public License, and the "GNU GPL" refers to version 3 of the GNU General Public License. "The Library" refers to a covered work governed by this License, other than an Application or a Combined Work as defined below. An "Application" is any work that makes use of an interface provided by the Library, but which is not otherwise based on the Library. Defining a subclass of a class defined by the Library is deemed a mode of using an interface provided by the Library. A "Combined Work" is a work produced by combining or linking an Application with the Library. The particular version of the Library with which the Combined Work was made is also called the "Linked Version". The "Minimal Corresponding Source" for a Combined Work means the Corresponding Source for the Combined Work, excluding any source code for portions of the Combined Work that, considered in isolation, are based on the Application, and not on the Linked Version. The "Corresponding Application Code" for a Combined Work means the object code and/or source code for the Application, including any data and utility programs needed for reproducing the Combined Work from the Application, but excluding the System Libraries of the Combined Work. 1. Exception to Section 3 of the GNU GPL. You may convey a covered work under sections 3 and 4 of this License without being bound by section 3 of the GNU GPL. 2. Conveying Modified Versions. If you modify a copy of the Library, and, in your modifications, a facility refers to a function or data to be supplied by an Application that uses the facility (other than as an argument passed when the facility is invoked), then you may convey a copy of the modified version: a) under this License, provided that you make a good faith effort to ensure that, in the event an Application does not supply the function or data, the facility still operates, and performs whatever part of its purpose remains meaningful, or b) under the GNU GPL, with none of the additional permissions of this License applicable to that copy. 3. Object Code Incorporating Material from Library Header Files. The object code form of an Application may incorporate material from a header file that is part of the Library. You may convey such object code under terms of your choice, provided that, if the incorporated material is not limited to numerical parameters, data structure layouts and accessors, or small macros, inline functions and templates (ten or fewer lines in length), you do both of the following: a) Give prominent notice with each copy of the object code that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the object code with a copy of the GNU GPL and this license document. 4. Combined Works. You may convey a Combined Work under terms of your choice that, taken together, effectively do not restrict modification of the portions of the Library contained in the Combined Work and reverse engineering for debugging such modifications, if you also do each of the following: a) Give prominent notice with each copy of the Combined Work that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the Combined Work with a copy of the GNU GPL and this license document. c) For a Combined Work that displays copyright notices during execution, include the copyright notice for the Library among these notices, as well as a reference directing the user to the copies of the GNU GPL and this license document. d) Do one of the following: 0) Convey the Minimal Corresponding Source under the terms of this License, and the Corresponding Application Code in a form suitable for, and under terms that permit, the user to recombine or relink the Application with a modified version of the Linked Version to produce a modified Combined Work, in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source. 1) Use a suitable shared library mechanism for linking with the Library. A suitable mechanism is one that (a) uses at run time a copy of the Library already present on the user's computer system, and (b) will operate properly with a modified version of the Library that is interface-compatible with the Linked Version. e) Provide Installation Information, but only if you would otherwise be required to provide such information under section 6 of the GNU GPL, and only to the extent that such information is necessary to install and execute a modified version of the Combined Work produced by recombining or relinking the Application with a modified version of the Linked Version. (If you use option 4d0, the Installation Information must accompany the Minimal Corresponding Source and Corresponding Application Code. If you use option 4d1, you must provide the Installation Information in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source.) 5. Combined Libraries. You may place library facilities that are a work based on the Library side by side in a single library together with other library facilities that are not Applications and are not covered by this License, and convey such a combined library under terms of your choice, if you do both of the following: a) Accompany the combined library with a copy of the same work based on the Library, uncombined with any other library facilities, conveyed under the terms of this License. b) Give prominent notice with the combined library that part of it is a work based on the Library, and explaining where to find the accompanying uncombined form of the same work. 6. Revised Versions of the GNU Lesser General Public License. The Free Software Foundation may publish revised and/or new versions of the GNU Lesser General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library.
  • Latest release: 3.0.2
    published 6 months ago
  • Versions: 20
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 218 Last month
Rankings
Forks count: 9.8%
Dependent packages count: 10.0%
Stargazers count: 12.4%
Average: 15.7%
Dependent repos count: 21.7%
Downloads: 24.4%
Maintainers (2)
tbaudier mouton
Last synced: 5 months ago

Dependencies

requirements.txt pypi
  • Pillow *
  • PyWavelets *
  • astropy *
  • imageio *
  • imutils *
  • matplotlib *
  • numpy *
  • opencv-python *
  • scipy *
  • sympy *
  • torch *
  • torchvision *
  • wget *
setup.py pypi
  • Pillow *
  • PyWavelets *
  • astropy *
  • imageio *
  • imutils *
  • matplotlib *
  • numpy *
  • opencv-python *
  • scipy *
  • sympy *
  • torch *
  • torchvision *
  • wget *
.github/workflows/main.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/download-artifact v2 composite
  • actions/download-artifact v1 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v1 composite
  • pypa/gh-action-pypi-publish master composite