From d61c5f9172489c47c0d85b956a3301f7224bf012 Mon Sep 17 00:00:00 2001 From: ncullen93 Date: Thu, 15 Feb 2024 21:50:12 +0100 Subject: [PATCH] update readme --- README.md | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index a5b330a1..27a99472 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,3 @@ - - # Advanced Normalization Tools in Python ![img](https://media0.giphy.com/media/OCMGLUo7d5jJ6/200_s.gif) @@ -7,7 +5,7 @@ Coverage Status - Documentation Status +Documentation Status ![Downloads](https://img.shields.io/github/downloads/antsx/antspy/total) ![PyPI - Downloads](https://img.shields.io/pypi/dm/antspyx?label=pypi%20downloads) @@ -18,7 +16,6 @@ [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/stnava/ANTsPyDocker/master) [![PubMed](https://img.shields.io/badge/ANTsX_paper-Open_Access-8DABFF?logo=pubmed)](https://pubmed.ncbi.nlm.nih.gov/33907199/) - ## About ANTsPy Search [ANTsPy documentation at read the docs.](https://antspyx.readthedocs.io/en/latest/?badge=latest) @@ -38,19 +35,20 @@ scratch - see [C++ Wrap Guide](tutorials/UsingITK.md) for a succinct tutorial. If you want to contribute to ANTsPy or simply want to learn about the package architecture and wrapping process, please read the extensive [contributors guide](CONTRIBUTING.md). -If you have any questions or feature requests, feel free to open an issue or email Nick (ncullen at pennmedicine dot upenn dot edu). +If you have any questions or feature requests, feel free to open an issue. ## Installation ### NOTE: old pip wheels will be deleted!!! -we dont have the quota on pypi to support more than one or two prior releases. if you care about this: (1) open a pypi issue requesting more quota for this project; (2) propose another alternative. +we dont have the quota on pypi to support more than one or two prior releases. if you care about this: (1) open a pypi issue requesting more quota for this project; (2) propose another alternative. We recommend that users install the latest pre-compiled binaries, which takes ~1 minute. Note that ANTsPy is not currently tested for Python 2.7 support. Copy the following command and paste it into your bash terminal: For MacOS and Linux: + ```bash pip install antspyx ``` @@ -64,34 +62,34 @@ git clone https://github.com/ANTsX/ANTsPy cd ANTsPy python3 setup.py install ``` + or see below for an alternative strategy using `pip`. If you want more detailed instructions on compiling ANTsPy from source, you can read the [installation tutorial](https://github.com/ANTsX/ANTsPy/blob/master/tutorials/InstallingANTsPy.md). - ### Installing older versions We cannot store the entire history of releases because storage space on `pip` is limited. if you need an older release, you can check the [Github Releases page](https://github.com/ANTsX/ANTsPy/releases) or -build from source. +build from source. Try something like: ```bash pip install 'antspyx @ git+https://github.com/ANTsX/ANTsPy@v0.3.2' ``` -which will attempt to build from source (requires a machine with developer tools). - +which will attempt to build from source (requires a machine with developer tools). ### Recent wheels Non-release commits have wheels built automatically, which are available for download for a limited period. -Look under the [Actions tab](https://github.com/ANTsX/ANTsPy/actions). Then click on the commit for the software version you want. +Look under the [Actions tab](https://github.com/ANTsX/ANTsPy/actions). Then click on the commit for the software version you want. Recent commits will have wheels stored as "artifacts". we build wheels locally like this: + ``` rm -r -f build/ antspymm.egg-info/ dist/ python3 setup.py sdist bdist_wheel @@ -103,13 +101,14 @@ pipx run twine upload dist/* Available on [Docker Hub](https://hub.docker.com/repository/docker/antsx/antspy). To build ANTsPy docker images, see the (installation tutorial)(https://github.com/ANTsX/ANTsPy/blob/master/tutorials/InstallingANTsPy.md#docker-installation). ------------------------------------------------------------------------------- +--- ## ANTsR Comparison Here is a quick example to show the similarity with ANTsR: ANTsR code: + ```R library(ANTsR) img <- antsImageRead(getANTsRData("r16")) @@ -119,6 +118,7 @@ segs1 <- atropos(a=img, m='[0.2,1x1]', c='[2,0]', i='kmeans[3]', x=mask ) ``` ANTsPy code: + ```python from ants import atropos, get_ants_data, image_read, resample_image, get_mask img = image_read(get_ants_data("r16"))