Skip to content

Latest commit

 

History

History
107 lines (78 loc) · 2.79 KB

tutorial_5min.md

File metadata and controls

107 lines (78 loc) · 2.79 KB
Raw

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) )

However, we still try to keep most of the associated ANTsR functions which are stand-alone, e.g:

ants.get_spacing(img) # versus the pythonic `img.spacing`
ants.set_spacing(img, (2.,2.)) # versus `img.set_spacing`

imgclone = ants.image_clone(img) # versus img.clone()

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)

Indexing

Images can be indexed (getting and setting) exactly as if they were arrays.

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

vals = img[200,:,:] # get a slice

img[100,:,:] = 1 # set a slice

Operator Overloading

All common mathematical operators are overloaded to work directly on ANTsImages:

import ants
import numpy as np
img = ants.image_read( ants.get_ants_data('mni') )
img2 = img.clone()
img3 = img + img2
print(np.allclose(img.numpy()+img2.numpy(), img3.numpy())) # same as if done in numpy

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 )