Authors	Project	Build Status	License	Code Quality	Documentation
R. Biondi	IPT	Windows : Ubuntu :		codebeat codacy

Image Processing Tools

A more or less organized collection of script and functions of medical image analysis tools.

What is IPT

IPT is a repository that collects all those function, scripts, etc that I am implementing during my journey in medical image analysis

What is not IPT

IPT is not an organic library for image processing like ITK, PIL or OpenCV.

1. Contents
2. Prerequisites
3. Installation
4. Usage
5. Contribute
6. License
7. Authors
8. References
9. Acknowledgments
10. Citation

Contents

Module Name	Description
io	Functions to read and write medical images
itk_wrapping	Functional Wrapping of itk filters
decorators	collection of useful decoratos
visualization	inline plotting and rendering of medical image volumes

Prerequisites

Supported python versions: . Also vesion 3.6 and 3.7 are supperted but not tested.

To run the tests you need to install PyTest and Hypothesis. Installation instructions are available at: PyTest, Hypothesis

Installation

Download the project or the latest release:

git clone https://github.com/RiccardoBiondi/segmentation

Now build and activate the conda environment

conda env create -f environment.yaml
conda env activate ipt

Or, if you are using pip, install the required packages:

python -m pip install -r requirements.txt

Now you are ready to build the package:

python setup.py develop --user

Testing

We have provide a test routine in test directory. This routine use:

• pytest >= 3.0.7

• hypothesis >= 4.13.0

Please install these packages to perform the test. You can run the full set of test with:

  python -m pytest

Usage

import itk
import IPT.io as io
import IPT.itk_wrapping as itkf

# Load a volume
image = io.itk_image_file_reader('/path/to/image.nrrd', itk.Image[itk.F, 3])

# apply a median filter
median = itkf.itk_median(image.GetOutput(), radius=2)

# and save the image
_ = io.itk_image_file_writer('/path/to/output.nii', median.GetOutput())

Contribute

Any contribution is welcome. You can fill a issue or a pull request!

License

Any contribution is more than welcome. Just fill an issue or a pull request and we will check ASAP!

See here for further information about how to contribute with this project.

Authors

• Riccardo Biondi git, unibo

References

1- McCormick M, Liu X, Jomier J, Marion C, Ibanez L. ITK: enabling reproducible research and open science. Front Neuroinform. 2014;8:13. Published 2014 Feb 20. doi:10.3389/fninf.2014.00013

2- Yoo TS, Ackerman MJ, Lorensen WE, Schroeder W, Chalana V, Aylward S, Metaxas D, Whitaker R. Engineering and Algorithm Design for an Image Processing API: A Technical Report on ITK – The Insight Toolkit. In Proc. of Medicine Meets Virtual Reality, J. Westwood, ed., IOS Press Amsterdam pp 586-592 (2002).

Citation

If you have found Image Processing Tools helpful in your research, please consider citing the project

@misc{IPT_2022,
  author = {Biondi, Riccardo},
  title = {Image Processing Tools},
  year = {2022},
  publisher = {GitHub},
  howpublished = {\url{https://github.com/RiccardoBiondi/ImageProcessingTools}},
}