__all__ = ['crop_image',
'crop_indices',
'decrop_image']
import ants
from ants.decorators import image_method
from ants.internal import get_lib_fn
@image_method
def crop_image(image, label_image=None, label=1):
"""
Use a label image to crop a smaller ANTsImage from within a larger ANTsImage
ANTsR function: `cropImage`
Arguments
---------
image : ANTsImage
image to crop
label_image : ANTsImage
image with label values. If not supplied, estimated from data.
label : integer
the label value to use
Returns
-------
ANTsImage
Example
-------
>>> import ants
>>> fi = ants.image_read( ants.get_ants_data('r16') )
>>> cropped = ants.crop_image(fi)
>>> fi2 = ants.merge_channels([fi,fi])
>>> cropped2 = ants.crop_image(fi2)
>>> cropped = ants.crop_image(fi, fi, 100 )
"""
if image.has_components:
return ants.merge_channels([crop_image(img, label_image, label) for img in ants.split_channels(image)],
channels_first=image.channels_first)
inpixeltype = image.pixeltype
ndim = image.dimension
if image.pixeltype != 'float':
image = image.clone('float')
if label_image is None:
label_image = ants.get_mask(image)
if label_image.pixeltype != 'float':
label_image = label_image.clone('float')
libfn = get_lib_fn('cropImage')
itkimage = libfn(image.pointer, label_image.pointer, label, 0, [], [])
return ants.from_pointer(itkimage).clone(inpixeltype)
@image_method
def crop_indices(image, lowerind, upperind):
"""
Create a proper ANTsImage sub-image by indexing the image with indices.
This is similar to but different from array sub-setting in that
the resulting sub-image can be decropped back into its place without
having to store its original index locations explicitly.
ANTsR function: `cropIndices`
Arguments
---------
image : ANTsImage
image to crop
lowerind : list/tuple of integers
vector of lower index, should be length image dimensionality
upperind : list/tuple of integers
vector of upper index, should be length image dimensionality
Returns
-------
ANTsImage
Example
-------
>>> import ants
>>> fi = ants.image_read( ants.get_ants_data("r16"))
>>> cropped = ants.crop_indices( fi, (10,10), (100,100) )
>>> cropped = ants.smooth_image( cropped, 5 )
>>> decropped = ants.decrop_image( cropped, fi )
"""
if image.has_components:
return ants.merge_channels([crop_indices(img, lowerind, upperind) for img in ants.split_channels(image)],
channels_first=image.channels_first)
inpixeltype = 'float'
if image.pixeltype != 'float':
inpixeltype = image.pixeltype
image = image.clone('float')
if (image.dimension != len(lowerind)) or (image.dimension != len(upperind)):
raise ValueError('image dimensionality and index length must match')
libfn = get_lib_fn('cropImage')
itkimage = libfn(image.pointer, image.pointer, 1, 2, lowerind, upperind)
ants_image = ants.from_pointer(itkimage)
if inpixeltype != 'float':
ants_image = ants_image.clone(inpixeltype)
return ants_image
@image_method
def decrop_image(cropped_image, full_image):
"""
The inverse function for `ants.crop_image`
ANTsR function: `decropImage`
Arguments
---------
cropped_image : ANTsImage
cropped image
full_image : ANTsImage
image in which the cropped image will be put back
Returns
-------
ANTsImage
Example
-------
>>> import ants
>>> fi = ants.image_read(ants.get_ants_data('r16'))
>>> mask = ants.get_mask(fi)
>>> cropped = ants.crop_image(fi, mask, 1)
>>> cropped = ants.smooth_image(cropped, 1)
>>> decropped = ants.decrop_image(cropped, fi)
"""
inpixeltype = 'float'
if cropped_image.pixeltype != 'float':
inpixeltype= cropped_image.pixeltype
cropped_image = cropped_image.clone('float')
if full_image.pixeltype != 'float':
full_image = full_image.clone('float')
libfn = get_lib_fn('cropImage')
itkimage = libfn(cropped_image.pointer, full_image.pointer, 1, 1, [], [])
ants_image = ants.from_pointer(itkimage)
if inpixeltype != 'float':
ants_image = ants_image.clone(inpixeltype)
return ants_image
