Advanced Normalization Tools in Python

What is ANTsPy?

ANTsPy -- pronounced "ant-spy" like an ant who is a secret agent -- is a Python library which wraps much of the medical image processing functionality of ANTs, provides much of the statistical capabilities of ANTsR, and allows seemless integration with Numpy and the greater Python community.

The engine underlying AntsPy and ANTsR is the same, so you can generally expect exactly the same results between the two packages given that the algorithm in question is itself deterministic.

Installation

To install, run the following:

git clone https://github.com/ANTsConsortium/ANTsPy.git
cd ANTsPy
python setup.py develop # note `develop` instead of `install` here.. IMPORTANT!

By default, ANTsPy will search for an existing ITK build by checking if the ITK_DIR environment variable is set. If that is not found, it will build it for you. It does NOT require the Python wrappings for ITK. If you want to use 3D visualization tools such as ants.Surf or ants.Vol, you need to build VTK on your own right now.

ANTsPy is known to install on MacOS and Ubuntu, both with Python3.6. It's unlikely that it will work with Python2.7.

ANTsR Comparison

Here are a few example to get you up-and-running if coming from ANTsR:

Example 1

ANTsR code:

library(ANTsR)
img <- antsImageRead( getANTsRData("r16") , 2 )
img <- resampleImage( img, c(64,64), 1, 0 )
mask <- getMask(img)
segs1 <- atropos( a = img, m = '[0.2,1x1]', c = '[2,0]',  i = 'kmeans[3]', x = mask )

ANTsPy code:

import ants
img = ants.image_read(ants.get_ants_data('r16'))
img = ants.resample_image(img, (64,64), 1, 0)
mask = ants.get_mask(img)
seg1 = ants.atropos(a = img, m = '[0.2,1x1]', c = '[2,0]',  i = 'kmeans[3]', x = mask )

Quick Tutorial

ANTsPy functions and classes are generally faithful to the respective ANTsR versions, with the following consistent changes in naming convention:

• camel case in ANTsR is underscore case in ANTsPy
  • e.g. resampleImage -> resample_image
• anything preceeded by ants or antsr in ANTsR is removed since ANTsPy uses namespaces already
  • e.g. antsImageRead -> ants.image_read

Read an Image

import ants
img = ants.image_read( ants.get_ants_data('r16') )
print(img)

Image Properties

Image properties are pythonic and easy to get/set:

import ants
img = ants.image_read( ants.get_ants_data('r16') )

print(img.spacing)
img.set_spacing( (2., 2.) )

print(img.origin)
img.set_origin( (100,100) )

Converting to Numpy

ANTsPy provides seamless conversions to Numpy arrays. Through the use of memory buffers directly in the C++ api, these calls are instantaneous and essentially free.

import ants
img = ants.image_read( ants.get_ants_data('mni') )
img_array = img.numpy()

Do operations directly in numpy if you want, then simply make an ANTsImage right back from the numpy array (again instantaneous and "free"):

import ants
img = ants.image_read( ants.get_ants_data('mni') )
img_array = img.numpy()

img_array += 5

# copies image information and just changes the data
new_img1 = img.new_image_like(img_array)

# doesnt copy any information
new_img2 = ants.from_numpy(img_array)

# verbose way to copy information
new_img3 = ants.from_numpy(img_array, spacing=img.spacing,
                           origin=img.origin, direction=img.direction)

Chaining Commands

In ANTsR you can use the %>% command to chain operations. That's real nice. In ANTsPy, you can do this automatically on ANTsImages. Amazing stuff..

import ants
img = ants.image_read(ants.get_ants_data('r16'))
img = img.resample_image((64,64), 1, 0).get_mask().atropos(m = '[0.2,1x1]', c = '[2,0]',  i = 'kmeans[3]', x = mask )

Frequently Asked Questions

• How long does ANTsPy take to install?
  • 15-20 minutes if you don't have a local ITK build
• What are the chances this project builds and installs correctly on the first try?
  • 83%