Source code for ants.contrib.sampling.transforms
"""
Various data augmentation transforms for ANTsImage types
List of Transformations:
======================
- CastIntensity
- BlurIntensity
- NormalizeIntensity
- RescaleIntensity
- ShiftScaleIntensity
- SigmoidIntensity
======================
- FlipImage
- TranslateImage
TODO
----
- RotateImage
- ShearImage
- ScaleImage
- DeformImage
- PadImage
- HistogramEqualizeIntensity
- TruncateIntensity
- SharpenIntensity
- MorpholigicalIntensity
- MD
- ME
- MO
- MC
- GD
- GE
- GO
- GC
"""
__all__ = ['CastIntensity',
'BlurIntensity',
'LocallyBlurIntensity',
'NormalizeIntensity',
'RescaleIntensity',
'ShiftScaleIntensity',
'SigmoidIntensity',
'FlipImage',
'ScaleImage',
'TranslateImage',
'MultiResolutionImage']
from ... import utils
from ...core import ants_image as iio
[docs]class MultiResolutionImage(object):
"""
Generate a set of images at multiple resolutions from an original image
"""
def __init__(self, levels=4, keep_shape=False):
self.levels = levels
self.keep_shape = keep_shape
[docs] def transform(self, X, y=None):
"""
Generate a set of multi-resolution ANTsImage types
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform
Example
-------
>>> import ants
>>> multires = ants.contrib.MultiResolutionImage(levels=4)
>>> img = ants.image_read(ants.get_data('r16'))
>>> imgs = multires.transform(img)
"""
insuffix = X._libsuffix
multires_fn = utils.get_lib_fn('multiResolutionAntsImage%s' % (insuffix))
casted_ptrs = multires_fn(X.pointer, self.levels)
imgs = []
for casted_ptr in casted_ptrs:
img = iio.ANTsImage(pixeltype=X.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr)
if self.keep_shape:
img = img.resample_image_to_target(X)
imgs.append(img)
return imgs
## Intensity Transforms ##
[docs]class CastIntensity(object):
"""
Cast the pixeltype of an ANTsImage to a given type.
This code uses the C++ ITK library directly, so it is fast.
NOTE: This offers a ~2.5x speedup over using img.clone(pixeltype):
Timings vs Cloning
------------------
>>> import ants
>>> import time
>>> caster = ants.contrib.CastIntensity('float')
>>> img = ants.image_read(ants.get_data('mni')).clone('unsigned int')
>>> s = time.time()
>>> for i in range(1000):
... img_float = caster.transform(img)
>>> e = time.time()
>>> print(e - s) # 9.6s
>>> s = time.time()
>>> for i in range(1000):
... img_float = img.clone('float')
>>> e = time.time()
>>> print(e - s) # 25.3s
"""
def __init__(self, pixeltype):
"""
Initialize a CastIntensity transform
Arguments
---------
pixeltype : string
pixeltype to which images will be casted
Example
-------
>>> import ants
>>> caster = ants.contrib.CastIntensity('float')
"""
self.pixeltype = pixeltype
[docs] def transform(self, X, y=None):
"""
Transform an image by casting its type
Arguments
---------
X : ANTsImage
image to cast
y : ANTsImage (optional)
another image to cast.
Example
-------
>>> import ants
>>> caster = ants.contrib.CastIntensity('float')
>>> img2d = ants.image_read(ants.get_data('r16')).clone('unsigned int')
>>> img2d_float = caster.transform(img2d)
>>> print(img2d.pixeltype, '- ', img2d_float.pixeltype)
>>> img3d = ants.image_read(ants.get_data('mni')).clone('unsigned int')
>>> img3d_float = caster.transform(img3d)
>>> print(img3d.pixeltype, ' - ' , img3d_float.pixeltype)
"""
insuffix = X._libsuffix
outsuffix = '%s%i' % (utils.short_ptype(self.pixeltype), X.dimension)
cast_fn = utils.get_lib_fn('castAntsImage%s%s' % (insuffix, outsuffix))
casted_ptr = cast_fn(X.pointer)
return iio.ANTsImage(pixeltype=self.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr)
[docs]class BlurIntensity(object):
"""
Transform for blurring the intensity of an ANTsImage
using a Gaussian Filter
"""
def __init__(self, sigma, width):
"""
Initialize a BlurIntensity transform
Arguments
---------
sigma : float
variance of gaussian kernel intensity
increasing this value increasing the amount
of blur
width : int
width of gaussian kernel shape
increasing this value increase the number of
neighboring voxels which are used for blurring
Example
-------
>>> import ants
>>> blur = ants.contrib.BlurIntensity(2,3)
"""
self.sigma = sigma
self.width = width
[docs] def transform(self, X, y=None):
"""
Blur an image by applying a gaussian filter.
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform.
Example
-------
>>> import ants
>>> blur = ants.contrib.BlurIntensity(2,3)
>>> img2d = ants.image_read(ants.get_data('r16'))
>>> img2d_b = blur.transform(img2d)
>>> ants.plot(img2d)
>>> ants.plot(img2d_b)
>>> img3d = ants.image_read(ants.get_data('mni'))
>>> img3d_b = blur.transform(img3d)
>>> ants.plot(img3d)
>>> ants.plot(img3d_b)
"""
if X.pixeltype != 'float':
raise ValueError('image.pixeltype must be float ... use TypeCast transform or clone to float')
insuffix = X._libsuffix
cast_fn = utils.get_lib_fn('blurAntsImage%s' % (insuffix))
casted_ptr = cast_fn(X.pointer, self.sigma, self.width)
return iio.ANTsImage(pixeltype=X.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr,
origin=X.origin)
[docs]class LocallyBlurIntensity(object):
"""
Blur an ANTsImage locally using a gradient anisotropic
diffusion filter, thereby preserving the sharpeness of edges as best
as possible.
"""
def __init__(self, conductance=1, iters=5):
self.conductance = conductance
self.iters = iters
[docs] def transform(self, X, y=None):
"""
Locally blur an image by applying a gradient anisotropic diffusion filter.
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform.
Example
-------
>>> import ants
>>> blur = ants.contrib.LocallyBlurIntensity(1,5)
>>> img2d = ants.image_read(ants.get_data('r16'))
>>> img2d_b = blur.transform(img2d)
>>> ants.plot(img2d)
>>> ants.plot(img2d_b)
>>> img3d = ants.image_read(ants.get_data('mni'))
>>> img3d_b = blur.transform(img3d)
>>> ants.plot(img3d)
>>> ants.plot(img3d_b)
"""
#if X.pixeltype != 'float':
# raise ValueError('image.pixeltype must be float ... use TypeCast transform or clone to float')
insuffix = X._libsuffix
cast_fn = utils.get_lib_fn('locallyBlurAntsImage%s' % (insuffix))
casted_ptr = cast_fn(X.pointer, self.iters, self.conductance)
return iio.ANTsImage(pixeltype=X.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr)
[docs]class NormalizeIntensity(object):
"""
Normalize the intensity values of an ANTsImage to have
zero mean and unit variance
NOTE: this transform is more-or-less the same in speed
as an equivalent numpy+scikit-learn solution.
Timing vs Numpy+Scikit-Learn
----------------------------
>>> import ants
>>> import numpy as np
>>> from sklearn.preprocessing import StandardScaler
>>> import time
>>> img = ants.image_read(ants.get_data('mni'))
>>> arr = img.numpy().reshape(1,-1)
>>> normalizer = ants.contrib.NormalizeIntensity()
>>> normalizer2 = StandardScaler()
>>> s = time.time()
>>> for i in range(100):
... img_scaled = normalizer.transform(img)
>>> e = time.time()
>>> print(e - s) # 3.3s
>>> s = time.time()
>>> for i in range(100):
... arr_scaled = normalizer2.fit_transform(arr)
>>> e = time.time()
>>> print(e - s) # 3.5s
"""
def __init__(self):
"""
Initialize a NormalizeIntensity transform
"""
pass
[docs] def transform(self, X, y=None):
"""
Transform an image by normalizing its intensity values to
have zero mean and unit variance.
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform.
Example
-------
>>> import ants
>>> normalizer = ants.contrib.NormalizeIntensity()
>>> img2d = ants.image_read(ants.get_data('r16'))
>>> img2d_r = normalizer.transform(img2d)
>>> print(img2d.mean(), ',', img2d.std(), ' -> ', img2d_r.mean(), ',', img2d_r.std())
>>> img3d = ants.image_read(ants.get_data('mni'))
>>> img3d_r = normalizer.transform(img3d)
>>> print(img3d.mean(), ',' , img3d.std(), ',', ' -> ', img3d_r.mean(), ',' , img3d_r.std())
"""
if X.pixeltype != 'float':
raise ValueError('image.pixeltype must be float ... use TypeCast transform or clone to float')
insuffix = X._libsuffix
cast_fn = utils.get_lib_fn('normalizeAntsImage%s' % (insuffix))
casted_ptr = cast_fn(X.pointer)
return iio.ANTsImage(pixeltype=X.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr)
[docs]class RescaleIntensity(object):
"""
Rescale the pixeltype of an ANTsImage linearly to be between a given
minimum and maximum value.
This code uses the C++ ITK library directly, so it is fast.
NOTE: this offered a ~5x speedup over using built-in arithmetic operations in ANTs.
It is also more-or-less the same in speed as an equivalent numpy+scikit-learn
solution.
Timing vs Built-in Operations
-----------------------------
>>> import ants
>>> import time
>>> rescaler = ants.contrib.RescaleIntensity(0,1)
>>> img = ants.image_read(ants.get_data('mni'))
>>> s = time.time()
>>> for i in range(100):
... img_float = rescaler.transform(img)
>>> e = time.time()
>>> print(e - s) # 2.8s
>>> s = time.time()
>>> for i in range(100):
... maxval = img.max()
... img_float = (img - maxval) / (maxval - img.min())
>>> e = time.time()
>>> print(e - s) # 13.9s
Timing vs Numpy+Scikit-Learn
----------------------------
>>> import ants
>>> import numpy as np
>>> from sklearn.preprocessing import MinMaxScaler
>>> import time
>>> img = ants.image_read(ants.get_data('mni'))
>>> arr = img.numpy().reshape(1,-1)
>>> rescaler = ants.contrib.RescaleIntensity(-1,1)
>>> rescaler2 = MinMaxScaler((-1,1)).fit(arr)
>>> s = time.time()
>>> for i in range(100):
... img_scaled = rescaler.transform(img)
>>> e = time.time()
>>> print(e - s) # 2.8s
>>> s = time.time()
>>> for i in range(100):
... arr_scaled = rescaler2.transform(arr)
>>> e = time.time()
>>> print(e - s) # 3s
"""
def __init__(self, min_val, max_val):
"""
Initialize a RescaleIntensity transform.
Arguments
---------
min_val : float
minimum value to which image(s) will be rescaled
max_val : float
maximum value to which image(s) will be rescaled
Example
-------
>>> import ants
>>> rescaler = ants.contrib.RescaleIntensity(0,1)
"""
self.min_val = min_val
self.max_val = max_val
[docs] def transform(self, X, y=None):
"""
Transform an image by linearly rescaling its intensity to
be between a minimum and maximum value
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform.
Example
-------
>>> import ants
>>> rescaler = ants.contrib.RescaleIntensity(0,1)
>>> img2d = ants.image_read(ants.get_data('r16'))
>>> img2d_r = rescaler.transform(img2d)
>>> print(img2d.min(), ',', img2d.max(), ' -> ', img2d_r.min(), ',', img2d_r.max())
>>> img3d = ants.image_read(ants.get_data('mni'))
>>> img3d_r = rescaler.transform(img3d)
>>> print(img3d.min(), ',' , img3d.max(), ' -> ', img3d_r.min(), ',' , img3d_r.max())
"""
if X.pixeltype != 'float':
raise ValueError('image.pixeltype must be float ... use TypeCast transform or clone to float')
insuffix = X._libsuffix
cast_fn = utils.get_lib_fn('rescaleAntsImage%s' % (insuffix))
casted_ptr = cast_fn(X.pointer, self.min_val, self.max_val)
return iio.ANTsImage(pixeltype=X.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr)
[docs]class ShiftScaleIntensity(object):
"""
Shift and scale the intensity of an ANTsImage
"""
def __init__(self, shift, scale):
"""
Initialize a ShiftScaleIntensity transform
Arguments
---------
shift : float
shift all of the intensity values by the given amount through addition.
For example, if the minimum image value is 0.0 and the shift
is 10.0, then the new minimum value (before scaling) will be 10.0
scale : float
scale all the intensity values by the given amount through multiplication.
For example, if the min/max image values are 10/20 and the scale
is 2.0, then then new min/max values will be 20/40
Example
-------
>>> import ants
>>> shiftscaler = ants.contrib.ShiftScaleIntensity(shift=10, scale=2)
"""
self.shift = shift
self.scale = scale
[docs] def transform(self, X, y=None):
"""
Transform an image by shifting and scaling its intensity values.
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform.
Example
-------
>>> import ants
>>> shiftscaler = ants.contrib.ShiftScaleIntensity(10,2.)
>>> img2d = ants.image_read(ants.get_data('r16'))
>>> img2d_r = shiftscaler.transform(img2d)
>>> print(img2d.min(), ',', img2d.max(), ' -> ', img2d_r.min(), ',', img2d_r.max())
>>> img3d = ants.image_read(ants.get_data('mni'))
>>> img3d_r = shiftscaler.transform(img3d)
>>> print(img3d.min(), ',' , img3d.max(), ',', ' -> ', img3d_r.min(), ',' , img3d_r.max())
"""
if X.pixeltype != 'float':
raise ValueError('image.pixeltype must be float ... use TypeCast transform or clone to float')
insuffix = X._libsuffix
cast_fn = utils.get_lib_fn('shiftScaleAntsImage%s' % (insuffix))
casted_ptr = cast_fn(X.pointer, self.scale, self.shift)
return iio.ANTsImage(pixeltype=X.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr)
[docs]class SigmoidIntensity(object):
"""
Transform an image using a sigmoid function
"""
def __init__(self, min_val, max_val, alpha, beta):
"""
Initialize a SigmoidIntensity transform
Arguments
---------
min_val : float
minimum value
max_val : float
maximum value
alpha : float
alpha value for sigmoid
beta : flaot
beta value for sigmoid
Example
-------
>>> import ants
>>> sigscaler = ants.contrib.SigmoidIntensity(0,1,1,1)
"""
self.min_val = min_val
self.max_val = max_val
self.alpha = alpha
self.beta = beta
[docs] def transform(self, X, y=None):
"""
Transform an image by applying a sigmoid function.
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform.
Example
-------
>>> import ants
>>> sigscaler = ants.contrib.SigmoidIntensity(0,1,1,1)
>>> img2d = ants.image_read(ants.get_data('r16'))
>>> img2d_r = sigscaler.transform(img2d)
>>> img3d = ants.image_read(ants.get_data('mni'))
>>> img3d_r = sigscaler.transform(img3d)
"""
if X.pixeltype != 'float':
raise ValueError('image.pixeltype must be float ... use TypeCast transform or clone to float')
insuffix = X._libsuffix
cast_fn = utils.get_lib_fn('sigmoidAntsImage%s' % (insuffix))
casted_ptr = cast_fn(X.pointer, self.min_val, self.max_val, self.alpha, self.beta)
return iio.ANTsImage(pixeltype=X.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr)
## Physical Transforms ##
[docs]class FlipImage(object):
"""
Transform an image by flipping two axes.
"""
def __init__(self, axis1, axis2):
"""
Initialize a SigmoidIntensity transform
Arguments
---------
axis1 : int
axis to flip
axis2 : int
other axis to flip
Example
-------
>>> import ants
>>> flipper = ants.contrib.FlipImage(0,1)
"""
self.axis1 = axis1
self.axis2 = axis2
[docs] def transform(self, X, y=None):
"""
Transform an image by applying a sigmoid function.
Arguments
---------
X : ANTsImage
image to transform
y : ANTsImage (optional)
another image to transform.
Example
-------
>>> import ants
>>> flipper = ants.contrib.FlipImage(0,1)
>>> img2d = ants.image_read(ants.get_data('r16'))
>>> img2d_r = flipper.transform(img2d)
>>> ants.plot(img2d)
>>> ants.plot(img2d_r)
>>> flipper2 = ants.contrib.FlipImage(1,0)
>>> img2d = ants.image_read(ants.get_data('r16'))
>>> img2d_r = flipper2.transform(img2d)
>>> ants.plot(img2d)
>>> ants.plot(img2d_r)
"""
if X.pixeltype != 'float':
raise ValueError('image.pixeltype must be float ... use TypeCast transform or clone to float')
insuffix = X._libsuffix
cast_fn = utils.get_lib_fn('flipAntsImage%s' % (insuffix))
casted_ptr = cast_fn(X.pointer, self.axis1, self.axis2)
return iio.ANTsImage(pixeltype=X.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr,
origin=X.origin)
[docs]class TranslateImage(object):
"""
Translate an image in physical space. This function calls
highly optimized ITK/C++ code.
"""
def __init__(self, translation, reference=None, interp='linear'):
"""
Initialize a TranslateImage transform
Arguments
---------
translation : list, tuple, or numpy.ndarray
absolute pixel transformation in each axis
reference : ANTsImage (optional)
image which provides the reference physical space in which
to perform the transform
interp : string
type of interpolation to use
options: linear, nearest
Example
-------
>>> import ants
>>> translater = ants.contrib.TranslateImage((10,10), interp='linear')
"""
if interp not in {'linear', 'nearest'}:
raise ValueError('interp must be one of {linear, nearest}')
self.translation = list(translation)
self.reference = reference
self.interp = interp
[docs] def transform(self, X, y=None):
"""
Example
-------
>>> import ants
>>> translater = ants.contrib.TranslateImage((40,0))
>>> img2d = ants.image_read(ants.get_data('r16'))
>>> img2d_r = translater.transform(img2d)
>>> ants.plot(img2d, img2d_r)
>>> translater = ants.contrib.TranslateImage((40,0,0))
>>> img3d = ants.image_read(ants.get_data('mni'))
>>> img3d_r = translater.transform(img3d)
>>> ants.plot(img3d, img3d_r, axis=2)
"""
if X.pixeltype != 'float':
raise ValueError('image.pixeltype must be float ... use TypeCast transform or clone to float')
if len(self.translation) != X.dimension:
raise ValueError('must give a translation value for each image dimension')
if self.reference is None:
reference = X
else:
reference = self.reference
insuffix = X._libsuffix
cast_fn = utils.get_lib_fn('translateAntsImage%s_%s' % (insuffix, self.interp))
casted_ptr = cast_fn(X.pointer, reference.pointer, self.translation)
return iio.ANTsImage(pixeltype=X.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr)
[docs]class ScaleImage(object):
"""
Scale an image in physical space. This function calls
highly optimized ITK/C++ code.
"""
def __init__(self, scale, reference=None, interp='linear'):
"""
Initialize a TranslateImage transform
Arguments
---------
scale : list, tuple, or numpy.ndarray
relative scaling along each axis
reference : ANTsImage (optional)
image which provides the reference physical space in which
to perform the transform
interp : string
type of interpolation to use
options: linear, nearest
Example
-------
>>> import ants
>>> translater = ants.contrib.TranslateImage((10,10), interp='linear')
"""
if interp not in {'linear', 'nearest'}:
raise ValueError('interp must be one of {linear, nearest}')
self.scale = list(scale)
self.reference = reference
self.interp = interp
[docs] def transform(self, X, y=None):
"""
Example
-------
>>> import ants
>>> scaler = ants.contrib.ScaleImage((1.2,1.2))
>>> img2d = ants.image_read(ants.get_data('r16'))
>>> img2d_r = scaler.transform(img2d)
>>> ants.plot(img2d, img2d_r)
>>> scaler = ants.contrib.ScaleImage((1.2,1.2,1.2))
>>> img3d = ants.image_read(ants.get_data('mni'))
>>> img3d_r = scaler.transform(img3d)
>>> ants.plot(img3d, img3d_r)
"""
if X.pixeltype != 'float':
raise ValueError('image.pixeltype must be float ... use TypeCast transform or clone to float')
if len(self.scale) != X.dimension:
raise ValueError('must give a scale value for each image dimension')
if self.reference is None:
reference = X
else:
reference = self.reference
insuffix = X._libsuffix
cast_fn = utils.get_lib_fn('scaleAntsImage%s_%s' % (insuffix, self.interp))
casted_ptr = cast_fn(X.pointer, reference.pointer, self.scale)
return iio.ANTsImage(pixeltype=X.pixeltype, dimension=X.dimension,
components=X.components, pointer=casted_ptr)
