diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 766d4bd2..d8008360 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,10 +2,15 @@ If you have ideas or code to contribute, please first open an [issue](https://github.com/oncoray/mirp/issues). We will then discuss your ideas and create an implementation roadmap. -Please keep the following in mind when contributiing: +Please keep the following in mind when contributing: -- The main branch of `mirp` is protected. You can therefore make a pull request for your contribution to a development branch of the intended future version. -- If you introduce new functionality, this functionality should be tested as part of the tests in `test`. -- Code is styled according to [PEP8](https://peps.python.org/pep-0008/). +- The main branch of `mirp` is protected. You can therefore make a pull request for your contribution to a + development branch of the intended future version. +- If you introduce new functionality, this functionality should be tested as part of the tests in the `test`directory. + After implementation, please ensure that all tests complete without errors by running `pytest` from your IDE or + console using `python -m pytest test` from the mirp main directory. +- Code is styled according to [PEP8](https://peps.python.org/pep-0008/). Using a linter or IDE with automated linter + is recommended. - Function, class and method documentation is done using Numpy-flavoured [docstrings](https://numpydoc.readthedocs.io/en/latest/format.html). - [Long-form documentation](https://oncoray.github.io/mirp/) is partially created from function, class and method documention, embedded in restructured text files in `docs_source`. + [Long-form documentation](https://oncoray.github.io/mirp/) is partially created from function, class and method + documentation, embedded in restructured text files in `docs_source`. diff --git a/NEWS.md b/NEWS.md index 4ff7c1d9..a2b465cc 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,29 @@ +# Version 2.2.0 + +## Major changes + +- Added support for intensity scaling using the `intensity_scaling` parameter. Intensity scaling multiplies + intensities by a scalar value. Intensity scaling occurs after intensity normalisation (if any) and prior to adding + noise (if any). For example, intensity scaling can be used after intensity normalisation to scale intensities to a + different range. `intensity_normalisation = "range"` with `intensity_scaling = 1000.0` maps image intensities to + [1000.0, 0.0] instead of [1.0, 0.0]. + +- Added support for intensity transformation filters: square root (`"pyradiomics_square_root"`), square + (`"pyradiomics_square"`), logarithm (`"pyradiomics_logarithm"`) and exponential (`"pyradiomics_exponential"`). + These implementations are based on the definitions in the `pyradiomics` + [documentation](https://pyradiomics.readthedocs.io/en/latest/radiomics.html#module-radiomics.imageoperations). + Since these filters do not currently have an IBSI reference standard, these are mostly intended for reproducing + and validating radiomics models based on features extracted from pyradiomics. + +- Modules were renamed according to the PEP8 standard. This does not affect the documented public interface, but may + affect external extensions. Public and private parts of the API are now indicated. + +## Minor changes + +- Added support for Python version 3.10 using `typing-extensions`. +- Several changes were made to ensure proper functioning of MIRP with future versions of `pandas`. +- Some changes were made prevent deprecation warnings in future version of `numpy`. + # Version 2.1.1 ## Fixes diff --git a/README.md b/README.md index 416719d2..c123f899 100644 --- a/README.md +++ b/README.md @@ -159,6 +159,9 @@ mask_labels = extract_mask_labels( A publication for MIRP is forthcoming. For now, please cite the following work: ```Zwanenburg A, Leger S, Agolli L, Pilz K, Troost EG, Richter C, Löck S. Assessing robustness of radiomic features by image perturbation. Scientific reports. 2019 Jan 24;9(1):614.``` +# Contributing +If you have ideas for improving MIRP, please read the short [contribution guide](./CONTRIBUTING.md). + # Developers and contributors MIRP is developed by: diff --git a/docs/.buildinfo b/docs/.buildinfo index 3f2ece84..4c4a3fe0 100644 --- a/docs/.buildinfo +++ b/docs/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: ab60819b912204cb527868dbfe8edebc +config: 17cbf7e65c49e001bf222ac3d01664cc tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_modules/index.html b/docs/_modules/index.html index e03387bd..eb1b87f0 100644 --- a/docs/_modules/index.html +++ b/docs/_modules/index.html @@ -1,22 +1,22 @@ - + - Overview: module code — mirp 2.1.1 documentation - - + Overview: module code — mirp 2.2.0 documentation + + - - - - - + + + + + @@ -75,19 +75,19 @@

All modules for which code is available

-