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# Advanced Normalization Tools in Python

![img](https://media0.giphy.com/media/OCMGLUo7d5jJ6/200_s.gif)
<br>

<a href='https://coveralls.io/github/ANTsX/ANTsPy?branch=master'><img src='https://coveralls.io/repos/github/ANTsX/ANTsPy/badge.svg?branch=master' alt='Coverage Status' /></a>
<a href='http://antspyx.readthedocs.io/en/latest/?badge=latest'>
<img src='https://readthedocs.org/projects/antspyx/badge/?version=latest' alt='Documentation Status' />
<img src='https://readthedocs.org/projects/antspyx/badge/?version=latest' alt='Documentation Status' />
</a>
![Downloads](https://img.shields.io/github/downloads/antsx/antspy/total)
![PyPI - Downloads](https://img.shields.io/pypi/dm/antspyx?label=pypi%20downloads)
Expand All @@ -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)
Expand All @@ -38,19 +35,20 @@ scratch - see [C++ Wrap Guide](tutorials/UsingITK.md) for a succinct tutorial.
If you want to contribute to <i>ANTsPy</i> 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 <i>ANTsPy</i> 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
```
Expand All @@ -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 <i>ANTsPy</i> 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/[email protected]'
```
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
Expand All @@ -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 <i>ANTsR</i>:

<i>ANTsR</i> code:

```R
library(ANTsR)
img <- antsImageRead(getANTsRData("r16"))
Expand All @@ -119,6 +118,7 @@ segs1 <- atropos(a=img, m='[0.2,1x1]', c='[2,0]', i='kmeans[3]', x=mask )
```

<i>ANTsPy</i> code:

```python
from ants import atropos, get_ants_data, image_read, resample_image, get_mask
img = image_read(get_ants_data("r16"))
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