Patch Denoising Methods
This repository implements patch-denoising methods, with a particular focus on local-low rank methods.
The target application is functional MRI thermal noise removal, but this methods can be applied to a wide range of image modalities.
It includes several local-low-rank based denoising methods (see the documentation for more details):
MP-PCA
Hybrid-PCA
NORDIC
Optimal Thresholding
Raw Singular Value Thresholding
A mathematical description of these methods is available in the documentation.
Installation
$ pip install patch-denoisepatch-denoise requires Python>=3.9
Quickstart
After installing you can use the patch-denoise command-line.
$ patch-denoise input_file.nii output_file.nii --mask="auto"See patch-denoise --help for detailed options.
Documentation and Examples
Documentation and examples are available at https://paquiteau.github.io/patch-denoising/
Development version
$ git clone https://github.com/paquiteau/patch-denoising
$ pip install -e patch-denoising[optional] --group devCitation
If you use this package for academic work, please cite the associated publication, available on HAL
@inproceedings{comby2023,
TITLE = {{Denoising of fMRI volumes using local low rank methods}},
AUTHOR = {Pierre-Antoine, Comby and Zaineb, Amor and Alexandre, Vignaud and Philippe, Ciuciu},
URL = {https://hal.science/hal-03895194},
BOOKTITLE = {{ISBI 2023 - International Symposium on Biomedical Imaging 2023}},
ADDRESS = {Carthagena de India, Colombia},
YEAR = {2023},
MONTH = Apr,
KEYWORDS = {functional MRI ; patch denoising ; singular value thresholding ; functional MRI patch denoising singular value thresholding},
PDF = {https://hal.science/hal-03895194/file/isbi2023_denoise.pdf},
HAL_ID = {hal-03895194},
HAL_VERSION = {v1},
}
1 maintainer
Metadata
1 maintainer
Release files for patch-denoise 2.3.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| patch_denoise-2.3.0.tar.gz | 75.7 kB | Without provenance | Details for patch_denoise-2.3.0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| patch_denoise-2.3.0-py3-none-any.whl | Python 3 | none | any | Details for patch_denoise-2.3.0-py3-none-any.whl |
Total release size: 135.1 kB
Release files / patch_denoise-2.3.0.tar.gz
| Download URL | patch_denoise-2.3.0.tar.gz |
|---|---|
| Size | 75.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
135874dc9a8892dc8cf3761ba0ef672170ad826c874c5114b2dafc23313d483d
|
|
BLAKE2b-256 checksum How to use checksums |
238d1c962e3cd0e8a80a3d7326dbdb50aa39514fe3818a367692e37e83f269c1
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / patch_denoise-2.3.0-py3-none-any.whl
| Download URL | patch_denoise-2.3.0-py3-none-any.whl |
|---|---|
| Size | 59.4 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
0b179de5821c513e655cb2746ff5bc91ba7f5ea6dc3904e81055f80cc09df2d2
|
|
BLAKE2b-256 checksum How to use checksums |
a7d1a69b4b064ed594108b12bb99929e6b906249a9a1b0a01cb3c541a0a03376
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Security for patch-denoise 2.3.0
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
