diff --git a/CHANGELOG.md b/CHANGELOG.md index 8d1aee1..d24a653 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,12 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](http://semver.org/). -## [0.5.0] - 20222-02-23 +## [0.6.0] - 2022-02-25 + +### Changed +* The type for the `-peak-to-tail` option in the CLI was changed from int to float. + +## [0.5.0] - 2022-02-23 ### Added * `threshold_noise` option to the command line script and as keyword argument to the fit function defined in DiffusionFitBase. diff --git a/README.md b/README.md index 2b25670..5976df5 100644 --- a/README.md +++ b/README.md @@ -11,8 +11,8 @@ Additionally, we have extended the framework to provide a model for fitting data ### What's new in -#### version 0.5.0 - * New option to specify how the noise is estimated from the tail signal when applying the thresholding for images to determine whether to terminate the fitting early: the `-threshold_noise` option from the command line. +#### version 0.6.0 + * The command line interface now accepts float values for the `-peak-to-tail` input option instead of just integers. See the [CHANGELOG](CHANGELOG.md) for additional details. @@ -53,16 +53,25 @@ Note that `diffusion-fit` has the following core dependencies: * [Numba](https://numba.pydata.org/) ### pip install -You can install `diffusionfit` version 0.5.0 with `pip` sourced from the GitHub repo: +You can install `diffusionfit` version 0.6.0 with `pip` sourced from the GitHub repo: ##### with git installed: +Fresh install: ``` -pip install git+https://github.com/NTBEL/diffusion-fit@v0.5.0 +pip install git+https://github.com/NTBEL/diffusion-fit@v0.6.0 +``` +Or to upgrade from an older version: +``` +pip install --upgrade git+https://github.com/NTBEL/diffusion-fit@v0.6.0 ``` - ##### without git installed: +Fresh install: +``` +pip install https://github.com/NTBEL/diffusion-fit/archive/refs/tags/v0.6.0.zip +``` +Or to upgrade from an older version: ``` -pip install https://github.com/NTBEL/diffusion-fit/archive/refs/tags/v0.5.0.zip +pip install --upgrade https://github.com/NTBEL/diffusion-fit/archive/refs/tags/v0.6.0.zip ``` ### Manual install First, download the repository. Then from the `diffusion-fit` folder/directory run diff --git a/diffusionfit/__main__.py b/diffusionfit/__main__.py index fbaa2df..5a88625 100644 --- a/diffusionfit/__main__.py +++ b/diffusionfit/__main__.py @@ -57,7 +57,7 @@ def tqdm(iterator, **kwargs): "-peak-to-tail", nargs="?", metavar="peak_to_tail", - type=int, + type=float, default=3, help="Set the peak/tail threshold during step 1 fitting for terminating the fitting analysis.", ) diff --git a/diffusionfit/dfbase.py b/diffusionfit/dfbase.py index 9232b11..aea6fc8 100644 --- a/diffusionfit/dfbase.py +++ b/diffusionfit/dfbase.py @@ -236,7 +236,7 @@ def fit( if threshold_noise == "std_error": tail_std /= np.sqrt(n_tail) - print(peak, tail_mean, tail_std, step1_threshold) + # print(peak, tail_mean, tail_std, step1_threshold) if apply_step1_threshold and ( peak < tail_mean + step1_threshold * tail_std ): diff --git a/setup.py b/setup.py index 943adc4..68cc759 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setuptools.setup( name="diffusionfit", - version="0.5.0", + version="0.6.0", python_requires=">=3.9", install_requires=[ "numpy",