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| a | b/ants/contrib/sampling/affine3d.py | ||
|---|---|---|---|
| 1 | """ |
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| 2 | Affine transforms |
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| 3 | |||
| 4 | See http://www.cs.cornell.edu/courses/cs4620/2010fa/lectures/03transforms3d.pdf |
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| 5 | """ |
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| 6 | |||
| 7 | __all__ = [ |
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| 8 | "Zoom3D", |
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| 9 | "RandomZoom3D", |
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| 10 | "Rotate3D", |
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| 11 | "RandomRotate3D", |
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| 12 | "Shear3D", |
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| 13 | "RandomShear3D", |
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| 14 | "Translate3D", |
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| 15 | "RandomTranslate3D", |
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| 16 | "Affine3D", |
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| 17 | ] |
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| 18 | |||
| 19 | import random |
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| 20 | import math |
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| 21 | import numpy as np |
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| 22 | |||
| 23 | from ...core import ants_transform as tio |
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| 24 | |||
| 25 | class Affine3D(object): |
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| 26 | """ |
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| 27 | Create a specified ANTs Affine Transform |
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| 28 | """ |
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| 29 | |||
| 30 | def __init__(self, transformation, reference=None, lazy=False): |
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| 31 | """ |
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| 32 | Initialize a Affine object |
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| 33 | |||
| 34 | Arguments |
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| 35 | --------- |
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| 36 | transformation : array |
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| 37 | affine transformation array (3x4) |
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| 38 | |||
| 39 | reference : ANTsImage (optional but recommended) |
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| 40 | image providing the reference space for the transform. |
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| 41 | this will also set the transform fixed parameters. |
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| 42 | |||
| 43 | lazy : boolean (default = False) |
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| 44 | if True, calling the `transform` method only returns |
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| 45 | the randomly generated transform and does not actually |
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| 46 | transform the image |
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| 47 | """ |
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| 48 | if (not isinstance(transformation, np.ndarray) or transformation.shape != (3,4)): |
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| 49 | raise ValueError( |
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| 50 | "transformation argument must be 3x4 Numpy array!" |
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| 51 | ) |
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| 52 | |||
| 53 | self.transformation = transformation |
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| 54 | self.lazy = lazy |
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| 55 | self.reference = reference |
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| 56 | |||
| 57 | self.tx = tio.ANTsTransform( |
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| 58 | precision="float", dimension=3, transform_type="AffineTransform" |
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| 59 | ) |
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| 60 | if self.reference is not None: |
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| 61 | self.tx.set_fixed_parameters(self.reference.get_center_of_mass()) |
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| 62 | |||
| 63 | def transform(self, X=None, y=None): |
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| 64 | """ |
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| 65 | Transform an image using an Affine transform with the given |
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| 66 | translation parameters. Return the transform if X=None. |
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| 67 | |||
| 68 | Arguments |
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| 69 | --------- |
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| 70 | X : ANTsImage |
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| 71 | Image to transform |
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| 72 | |||
| 73 | y : ANTsImage (optional) |
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| 74 | Another image to transform |
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| 75 | |||
| 76 | Returns |
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| 77 | ------- |
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| 78 | ANTsImage if y is None, else a tuple of ANTsImage types |
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| 79 | |||
| 80 | Examples |
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| 81 | -------- |
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| 82 | >>> import ants |
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| 83 | >>> img = ants.image_read(ants.get_data('ch2')) |
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| 84 | >>> tx = ants.contrib.Affine3D(transformation=np.array([[1, 0, 0, dx], [0, 1, 0, dy],[0, 0, 1, dz]]) |
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| 85 | >>> img2_x = tx.transform(img)# image translated by (dx, dy, dz) |
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| 86 | """ |
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| 87 | # unpack |
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| 88 | |||
| 89 | transformation_matrix = self.transformation |
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| 90 | |||
| 91 | |||
| 92 | self.tx.set_parameters(transformation_matrix) |
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| 93 | if self.lazy or X is None: |
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| 94 | return self.tx |
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| 95 | else: |
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| 96 | if y is None: |
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| 97 | return self.tx.apply_to_image(X, reference=self.reference) |
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| 98 | else: |
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| 99 | return ( |
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| 100 | self.tx.apply_to_image(X, reference=self.reference), |
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| 101 | self.tx.apply_to_image(y, reference=self.reference), |
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| 102 | ) |
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| 103 | |||
| 104 | |||
| 105 | class Translate3D(object): |
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| 106 | """ |
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| 107 | Create an ANTs Affine Transform with a specified translation. |
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| 108 | """ |
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| 109 | |||
| 110 | def __init__(self, translation, reference=None, lazy=False): |
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| 111 | """ |
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| 112 | Initialize a Translate3D object |
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| 113 | |||
| 114 | Arguments |
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| 115 | --------- |
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| 116 | translation : list or tuple |
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| 117 | translation values for each axis, in degrees. |
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| 118 | Negative values can be used for translation in the |
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| 119 | other direction |
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| 120 | |||
| 121 | reference : ANTsImage (optional but recommended) |
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| 122 | image providing the reference space for the transform. |
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| 123 | this will also set the transform fixed parameters. |
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| 124 | |||
| 125 | lazy : boolean (default = False) |
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| 126 | if True, calling the `transform` method only returns |
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| 127 | the randomly generated transform and does not actually |
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| 128 | transform the image |
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| 129 | """ |
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| 130 | if (not isinstance(translation, (list, tuple))) or (len(translation) != 3): |
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| 131 | raise ValueError( |
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| 132 | "translation argument must be list/tuple with three values!" |
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| 133 | ) |
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| 134 | |||
| 135 | self.translation = translation |
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| 136 | self.lazy = lazy |
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| 137 | self.reference = reference |
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| 138 | |||
| 139 | self.tx = tio.ANTsTransform( |
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| 140 | precision="float", dimension=3, transform_type="AffineTransform" |
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| 141 | ) |
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| 142 | if self.reference is not None: |
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| 143 | self.tx.set_fixed_parameters(self.reference.get_center_of_mass()) |
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| 144 | |||
| 145 | def transform(self, X=None, y=None): |
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| 146 | """ |
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| 147 | Transform an image using an Affine transform with the given |
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| 148 | translation parameters. Return the transform if X=None. |
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| 149 | |||
| 150 | Arguments |
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| 151 | --------- |
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| 152 | X : ANTsImage |
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| 153 | Image to transform |
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| 154 | |||
| 155 | y : ANTsImage (optional) |
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| 156 | Another image to transform |
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| 157 | |||
| 158 | Returns |
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| 159 | ------- |
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| 160 | ANTsImage if y is None, else a tuple of ANTsImage types |
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| 161 | |||
| 162 | Examples |
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| 163 | -------- |
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| 164 | >>> import ants |
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| 165 | >>> img = ants.image_read(ants.get_data('ch2')) |
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| 166 | >>> tx = ants.contrib.Translate3D(translation=(10,0,0)) |
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| 167 | >>> img2_x = tx.transform(img)# x axis stays same |
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| 168 | >>> tx = ants.contrib.Translate3D(translation=(-10,0,0)) # other direction |
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| 169 | >>> img2_x = tx.transform(img)# x axis stays same |
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| 170 | >>> tx = ants.contrib.Translate3D(translation=(0,10,0)) |
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| 171 | >>> img2_y = tx.transform(img) # y axis stays same |
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| 172 | >>> tx = ants.contrib.Translate3D(translation=(0,0,10)) |
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| 173 | >>> img2_z = tx.transform(img) # z axis stays same |
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| 174 | >>> tx = ants.contrib.Translate3D(translation=(10,10,10)) |
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| 175 | >>> img2 = tx.transform(img) |
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| 176 | """ |
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| 177 | # unpack |
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| 178 | translation_x, translation_y, translation_z = self.translation |
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| 179 | |||
| 180 | translation_matrix = np.array( |
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| 181 | [ |
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| 182 | [1, 0, 0, translation_x], |
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| 183 | [0, 1, 0, translation_y], |
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| 184 | [0, 0, 1, translation_z], |
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| 185 | ] |
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| 186 | ) |
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| 187 | self.tx.set_parameters(translation_matrix) |
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| 188 | if self.lazy or X is None: |
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| 189 | return self.tx |
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| 190 | else: |
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| 191 | if y is None: |
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| 192 | return self.tx.apply_to_image(X, reference=self.reference) |
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| 193 | else: |
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| 194 | return ( |
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| 195 | self.tx.apply_to_image(X, reference=self.reference), |
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| 196 | self.tx.apply_to_image(y, reference=self.reference), |
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| 197 | ) |
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| 198 | |||
| 199 | |||
| 200 | class RandomTranslate3D(object): |
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| 201 | """ |
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| 202 | Apply a Translate3D transform to an image, but with the shear |
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| 203 | parameters randomly generated from a user-specified range. |
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| 204 | The range is determined by a mean (first parameter) and standard deviation |
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| 205 | (second parameter) via calls to random.gauss. |
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| 206 | """ |
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| 207 | |||
| 208 | def __init__(self, translation_range, reference=None, lazy=False): |
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| 209 | """ |
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| 210 | Initialize a RandomTranslate3D object |
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| 211 | |||
| 212 | Arguments |
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| 213 | --------- |
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| 214 | translation_range : list or tuple |
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| 215 | Lower and Upper bounds on rotation parameter, in degrees. |
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| 216 | e.g. translation_range = (-10,10) will result in a random |
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| 217 | draw of the rotation parameters between -10 and 10 degrees |
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| 218 | |||
| 219 | reference : ANTsImage (optional but recommended) |
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| 220 | image providing the reference space for the transform. |
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| 221 | this will also set the transform fixed parameters. |
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| 222 | |||
| 223 | lazy : boolean (default = False) |
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| 224 | if True, calling the `transform` method only returns |
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| 225 | the randomly generated transform and does not actually |
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| 226 | transform the image |
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| 227 | """ |
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| 228 | if (not isinstance(translation_range, (list, tuple))) or ( |
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| 229 | len(translation_range) != 2 |
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| 230 | ): |
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| 231 | raise ValueError("shear_range argument must be list/tuple with two values!") |
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| 232 | |||
| 233 | self.translation_range = translation_range |
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| 234 | self.reference = reference |
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| 235 | self.lazy = lazy |
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| 236 | |||
| 237 | def transform(self, X=None, y=None): |
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| 238 | """ |
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| 239 | Transform an image using an Affine transform with |
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| 240 | translation parameters randomly generated from the user-specified |
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| 241 | range. Return the transform if X=None. |
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| 242 | |||
| 243 | Arguments |
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| 244 | --------- |
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| 245 | X : ANTsImage |
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| 246 | Image to transform |
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| 247 | |||
| 248 | y : ANTsImage (optional) |
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| 249 | Another image to transform |
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| 250 | |||
| 251 | Returns |
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| 252 | ------- |
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| 253 | ANTsImage if y is None, else a tuple of ANTsImage types |
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| 254 | |||
| 255 | Examples |
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| 256 | -------- |
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| 257 | >>> import ants |
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| 258 | >>> img = ants.image_read(ants.get_data('ch2')) |
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| 259 | >>> tx = ants.contrib.RandomShear3D(translation_range=(-10,10)) |
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| 260 | >>> img2 = tx.transform(img) |
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| 261 | """ |
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| 262 | # random draw in translation range |
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| 263 | translation_x = random.gauss( |
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| 264 | self.translation_range[0], self.translation_range[1] |
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| 265 | ) |
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| 266 | translation_y = random.gauss( |
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| 267 | self.translation_range[0], self.translation_range[1] |
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| 268 | ) |
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| 269 | translation_z = random.gauss( |
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| 270 | self.translation_range[0], self.translation_range[1] |
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| 271 | ) |
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| 272 | self.params = (translation_x, translation_y, translation_z) |
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| 273 | |||
| 274 | tx = Translate3D( |
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| 275 | (translation_x, translation_y, translation_z), |
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| 276 | reference=self.reference, |
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| 277 | lazy=self.lazy, |
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| 278 | ) |
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| 279 | |||
| 280 | return tx.transform(X, y) |
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| 281 | |||
| 282 | |||
| 283 | class Shear3D(object): |
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| 284 | """ |
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| 285 | Create an ANTs Affine Transform with a specified shear. |
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| 286 | """ |
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| 287 | |||
| 288 | def __init__(self, shear, reference=None, lazy=False): |
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| 289 | """ |
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| 290 | Initialize a Shear3D object |
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| 291 | |||
| 292 | Arguments |
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| 293 | --------- |
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| 294 | shear : list or tuple |
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| 295 | shear values for each axis, in degrees. |
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| 296 | Negative values can be used for shear in the |
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| 297 | other direction |
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| 298 | |||
| 299 | reference : ANTsImage (optional but recommended) |
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| 300 | image providing the reference space for the transform. |
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| 301 | this will also set the transform fixed parameters. |
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| 302 | |||
| 303 | lazy : boolean (default = False) |
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| 304 | if True, calling the `transform` method only returns |
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| 305 | the randomly generated transform and does not actually |
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| 306 | transform the image |
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| 307 | """ |
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| 308 | if (not isinstance(shear, (list, tuple))) or (len(shear) != 3): |
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| 309 | raise ValueError("shear argument must be list/tuple with three values!") |
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| 310 | |||
| 311 | self.shear = shear |
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| 312 | self.lazy = lazy |
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| 313 | self.reference = reference |
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| 314 | |||
| 315 | self.tx = tio.ANTsTransform( |
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| 316 | precision="float", dimension=3, transform_type="AffineTransform" |
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| 317 | ) |
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| 318 | if self.reference is not None: |
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| 319 | self.tx.set_fixed_parameters(self.reference.get_center_of_mass()) |
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| 320 | |||
| 321 | def transform(self, X=None, y=None): |
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| 322 | """ |
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| 323 | Transform an image using an Affine transform with the given |
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| 324 | shear parameters. Return the transform if X=None. |
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| 325 | |||
| 326 | Arguments |
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| 327 | --------- |
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| 328 | X : ANTsImage |
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| 329 | Image to transform |
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| 330 | |||
| 331 | y : ANTsImage (optional) |
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| 332 | Another image to transform |
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| 333 | |||
| 334 | Returns |
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| 335 | ------- |
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| 336 | ANTsImage if y is None, else a tuple of ANTsImage types |
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| 337 | |||
| 338 | Examples |
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| 339 | -------- |
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| 340 | >>> import ants |
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| 341 | >>> img = ants.image_read(ants.get_data('ch2')) |
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| 342 | >>> tx = ants.contrib.Shear3D(shear=(10,0,0)) |
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| 343 | >>> img2_x = tx.transform(img)# x axis stays same |
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| 344 | >>> tx = ants.contrib.Shear3D(shear=(-10,0,0)) # other direction |
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| 345 | >>> img2_x = tx.transform(img)# x axis stays same |
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| 346 | >>> tx = ants.contrib.Shear3D(shear=(0,10,0)) |
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| 347 | >>> img2_y = tx.transform(img) # y axis stays same |
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| 348 | >>> tx = ants.contrib.Shear3D(shear=(0,0,10)) |
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| 349 | >>> img2_z = tx.transform(img) # z axis stays same |
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| 350 | >>> tx = ants.contrib.Shear3D(shear=(10,10,10)) |
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| 351 | >>> img2 = tx.transform(img) |
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| 352 | """ |
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| 353 | # convert to radians and unpack |
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| 354 | shear = [math.pi / 180 * s for s in self.shear] |
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| 355 | shear_x, shear_y, shear_z = shear |
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| 356 | |||
| 357 | shear_matrix = np.array( |
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| 358 | [ |
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| 359 | [1, shear_x, shear_x, 0], |
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| 360 | [shear_y, 1, shear_y, 0], |
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| 361 | [shear_z, shear_z, 1, 0], |
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| 362 | ] |
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| 363 | ) |
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| 364 | self.tx.set_parameters(shear_matrix) |
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| 365 | if self.lazy or X is None: |
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| 366 | return self.tx |
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| 367 | else: |
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| 368 | if y is None: |
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| 369 | return self.tx.apply_to_image(X, reference=self.reference) |
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| 370 | else: |
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| 371 | return ( |
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| 372 | self.tx.apply_to_image(X, reference=self.reference), |
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| 373 | self.tx.apply_to_image(y, reference=self.reference), |
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| 374 | ) |
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| 375 | |||
| 376 | |||
| 377 | class RandomShear3D(object): |
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| 378 | """ |
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| 379 | Apply a Shear3D transform to an image, but with the shear |
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| 380 | parameters randomly generated from a user-specified range. |
||
| 381 | The range is determined by a mean (first parameter) and standard deviation |
||
| 382 | (second parameter) via calls to random.gauss. |
||
| 383 | """ |
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| 384 | |||
| 385 | def __init__(self, shear_range, reference=None, lazy=False): |
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| 386 | """ |
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| 387 | Initialize a RandomShear3D object |
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| 388 | |||
| 389 | Arguments |
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| 390 | --------- |
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| 391 | shear_range : list or tuple |
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| 392 | Lower and Upper bounds on rotation parameter, in degrees. |
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| 393 | e.g. shear_range = (-10,10) will result in a random |
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| 394 | draw of the rotation parameters between -10 and 10 degrees |
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| 395 | |||
| 396 | reference : ANTsImage (optional but recommended) |
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| 397 | image providing the reference space for the transform. |
||
| 398 | this will also set the transform fixed parameters. |
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| 399 | |||
| 400 | lazy : boolean (default = False) |
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| 401 | if True, calling the `transform` method only returns |
||
| 402 | the randomly generated transform and does not actually |
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| 403 | transform the image |
||
| 404 | """ |
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| 405 | if (not isinstance(shear_range, (list, tuple))) or (len(shear_range) != 2): |
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| 406 | raise ValueError("shear_range argument must be list/tuple with two values!") |
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| 407 | |||
| 408 | self.shear_range = shear_range |
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| 409 | self.reference = reference |
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| 410 | self.lazy = lazy |
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| 411 | |||
| 412 | def transform(self, X=None, y=None): |
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| 413 | """ |
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| 414 | Transform an image using an Affine transform with |
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| 415 | shear parameters randomly generated from the user-specified |
||
| 416 | range. Return the transform if X=None. |
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| 417 | |||
| 418 | Arguments |
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| 419 | --------- |
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| 420 | X : ANTsImage |
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| 421 | Image to transform |
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| 422 | |||
| 423 | y : ANTsImage (optional) |
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| 424 | Another image to transform |
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| 425 | |||
| 426 | Returns |
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| 427 | ------- |
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| 428 | ANTsImage if y is None, else a tuple of ANTsImage types |
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| 429 | |||
| 430 | Examples |
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| 431 | -------- |
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| 432 | >>> import ants |
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| 433 | >>> img = ants.image_read(ants.get_data('ch2')) |
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| 434 | >>> tx = ants.contrib.RandomShear3D(shear_range=(-10,10)) |
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| 435 | >>> img2 = tx.transform(img) |
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| 436 | """ |
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| 437 | # random draw in shear range |
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| 438 | shear_x = random.gauss(self.shear_range[0], self.shear_range[1]) |
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| 439 | shear_y = random.gauss(self.shear_range[0], self.shear_range[1]) |
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| 440 | shear_z = random.gauss(self.shear_range[0], self.shear_range[1]) |
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| 441 | self.params = (shear_x, shear_y, shear_z) |
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| 442 | |||
| 443 | tx = Shear3D( |
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| 444 | (shear_x, shear_y, shear_z), reference=self.reference, lazy=self.lazy |
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| 445 | ) |
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| 446 | |||
| 447 | return tx.transform(X, y) |
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| 448 | |||
| 449 | |||
| 450 | class Rotate3D(object): |
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| 451 | """ |
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| 452 | Create an ANTs Affine Transform with a specified level |
||
| 453 | of rotation. |
||
| 454 | """ |
||
| 455 | |||
| 456 | def __init__(self, rotation, reference=None, lazy=False): |
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| 457 | """ |
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| 458 | Initialize a Rotate3D object |
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| 459 | |||
| 460 | Arguments |
||
| 461 | --------- |
||
| 462 | rotation : list or tuple |
||
| 463 | rotation values for each axis, in degrees. |
||
| 464 | Negative values can be used for rotation in the |
||
| 465 | other direction |
||
| 466 | |||
| 467 | reference : ANTsImage (optional but recommended) |
||
| 468 | image providing the reference space for the transform. |
||
| 469 | this will also set the transform fixed parameters. |
||
| 470 | |||
| 471 | lazy : boolean (default = False) |
||
| 472 | if True, calling the `transform` method only returns |
||
| 473 | the randomly generated transform and does not actually |
||
| 474 | transform the image |
||
| 475 | """ |
||
| 476 | if (not isinstance(rotation, (list, tuple))) or (len(rotation) != 3): |
||
| 477 | raise ValueError("rotation argument must be list/tuple with three values!") |
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| 478 | |||
| 479 | self.rotation = rotation |
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| 480 | self.lazy = lazy |
||
| 481 | self.reference = reference |
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| 482 | |||
| 483 | self.tx = tio.ANTsTransform( |
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| 484 | precision="float", dimension=3, transform_type="AffineTransform" |
||
| 485 | ) |
||
| 486 | if self.reference is not None: |
||
| 487 | self.tx.set_fixed_parameters(self.reference.get_center_of_mass()) |
||
| 488 | |||
| 489 | def transform(self, X=None, y=None): |
||
| 490 | """ |
||
| 491 | Transform an image using an Affine transform with the given |
||
| 492 | rotation parameters. Return the transform if X=None. |
||
| 493 | |||
| 494 | Arguments |
||
| 495 | --------- |
||
| 496 | X : ANTsImage |
||
| 497 | Image to transform |
||
| 498 | |||
| 499 | y : ANTsImage (optional) |
||
| 500 | Another image to transform |
||
| 501 | |||
| 502 | Returns |
||
| 503 | ------- |
||
| 504 | ANTsImage if y is None, else a tuple of ANTsImage types |
||
| 505 | |||
| 506 | Examples |
||
| 507 | -------- |
||
| 508 | >>> import ants |
||
| 509 | >>> img = ants.image_read(ants.get_data('ch2')) |
||
| 510 | >>> tx = ants.contrib.Rotate3D(rotation=(10,-5,12)) |
||
| 511 | >>> img2 = tx.transform(img) |
||
| 512 | """ |
||
| 513 | # unpack zoom range |
||
| 514 | rotation_x, rotation_y, rotation_z = self.rotation |
||
| 515 | |||
| 516 | # Rotation about X axis |
||
| 517 | theta_x = math.pi / 180 * rotation_x |
||
| 518 | rotate_matrix_x = np.array( |
||
| 519 | [ |
||
| 520 | [1, 0, 0, 0], |
||
| 521 | [0, math.cos(theta_x), -math.sin(theta_x), 0], |
||
| 522 | [0, math.sin(theta_x), math.cos(theta_x), 0], |
||
| 523 | [0, 0, 0, 1], |
||
| 524 | ] |
||
| 525 | ) |
||
| 526 | |||
| 527 | # Rotation about Y axis |
||
| 528 | theta_y = math.pi / 180 * rotation_y |
||
| 529 | rotate_matrix_y = np.array( |
||
| 530 | [ |
||
| 531 | [math.cos(theta_y), 0, math.sin(theta_y), 0], |
||
| 532 | [0, 1, 0, 0], |
||
| 533 | [-math.sin(theta_y), 0, math.cos(theta_y), 0], |
||
| 534 | [0, 0, 0, 1], |
||
| 535 | ] |
||
| 536 | ) |
||
| 537 | |||
| 538 | # Rotation about Z axis |
||
| 539 | theta_z = math.pi / 180 * rotation_z |
||
| 540 | rotate_matrix_z = np.array( |
||
| 541 | [ |
||
| 542 | [math.cos(theta_z), -math.sin(theta_z), 0, 0], |
||
| 543 | [math.sin(theta_z), math.cos(theta_z), 0, 0], |
||
| 544 | [0, 0, 1, 0], |
||
| 545 | [0, 0, 0, 1], |
||
| 546 | ] |
||
| 547 | ) |
||
| 548 | rotate_matrix = rotate_matrix_x.dot(rotate_matrix_y).dot(rotate_matrix_z)[:3, :] |
||
| 549 | |||
| 550 | self.tx.set_parameters(rotate_matrix) |
||
| 551 | if self.lazy or X is None: |
||
| 552 | return self.tx |
||
| 553 | else: |
||
| 554 | if y is None: |
||
| 555 | return self.tx.apply_to_image(X, reference=self.reference) |
||
| 556 | else: |
||
| 557 | return ( |
||
| 558 | self.tx.apply_to_image(X, reference=self.reference), |
||
| 559 | self.tx.apply_to_image(y, reference=self.reference), |
||
| 560 | ) |
||
| 561 | |||
| 562 | |||
| 563 | class RandomRotate3D(object): |
||
| 564 | """ |
||
| 565 | Apply a Rotate3D transform to an image, but with the zoom |
||
| 566 | parameters randomly generated from a user-specified range. |
||
| 567 | The range is determined by a mean (first parameter) and standard deviation |
||
| 568 | (second parameter) via calls to random.gauss. |
||
| 569 | """ |
||
| 570 | |||
| 571 | def __init__(self, rotation_range, reference=None, lazy=False): |
||
| 572 | """ |
||
| 573 | Initialize a RandomRotate3D object |
||
| 574 | |||
| 575 | Arguments |
||
| 576 | --------- |
||
| 577 | rotation_range : list or tuple |
||
| 578 | Lower and Upper bounds on rotation parameter, in degrees. |
||
| 579 | e.g. rotation_range = (-10,10) will result in a random |
||
| 580 | draw of the rotation parameters between -10 and 10 degrees |
||
| 581 | |||
| 582 | reference : ANTsImage (optional but recommended) |
||
| 583 | image providing the reference space for the transform. |
||
| 584 | this will also set the transform fixed parameters. |
||
| 585 | |||
| 586 | lazy : boolean (default = False) |
||
| 587 | if True, calling the `transform` method only returns |
||
| 588 | the randomly generated transform and does not actually |
||
| 589 | transform the image |
||
| 590 | """ |
||
| 591 | if (not isinstance(rotation_range, (list, tuple))) or ( |
||
| 592 | len(rotation_range) != 2 |
||
| 593 | ): |
||
| 594 | raise ValueError( |
||
| 595 | "rotation_range argument must be list/tuple with two values!" |
||
| 596 | ) |
||
| 597 | |||
| 598 | self.rotation_range = rotation_range |
||
| 599 | self.reference = reference |
||
| 600 | self.lazy = lazy |
||
| 601 | |||
| 602 | def transform(self, X=None, y=None): |
||
| 603 | """ |
||
| 604 | Transform an image using an Affine transform with |
||
| 605 | rotation parameters randomly generated from the user-specified |
||
| 606 | range. Return the transform if X=None. |
||
| 607 | |||
| 608 | Arguments |
||
| 609 | --------- |
||
| 610 | X : ANTsImage |
||
| 611 | Image to transform |
||
| 612 | |||
| 613 | y : ANTsImage (optional) |
||
| 614 | Another image to transform |
||
| 615 | |||
| 616 | Returns |
||
| 617 | ------- |
||
| 618 | ANTsImage if y is None, else a tuple of ANTsImage types |
||
| 619 | |||
| 620 | Examples |
||
| 621 | -------- |
||
| 622 | >>> import ants |
||
| 623 | >>> img = ants.image_read(ants.get_data('ch2')) |
||
| 624 | >>> tx = ants.contrib.RandomRotate3D(rotation_range=(-10,10)) |
||
| 625 | >>> img2 = tx.transform(img) |
||
| 626 | """ |
||
| 627 | # random draw in rotation range |
||
| 628 | rotation_x = random.gauss(self.rotation_range[0], self.rotation_range[1]) |
||
| 629 | rotation_y = random.gauss(self.rotation_range[0], self.rotation_range[1]) |
||
| 630 | rotation_z = random.gauss(self.rotation_range[0], self.rotation_range[1]) |
||
| 631 | self.params = (rotation_x, rotation_y, rotation_z) |
||
| 632 | |||
| 633 | tx = Rotate3D( |
||
| 634 | (rotation_x, rotation_y, rotation_z), |
||
| 635 | reference=self.reference, |
||
| 636 | lazy=self.lazy, |
||
| 637 | ) |
||
| 638 | |||
| 639 | return tx.transform(X, y) |
||
| 640 | |||
| 641 | |||
| 642 | class Zoom3D(object): |
||
| 643 | """ |
||
| 644 | Create an ANTs Affine Transform with a specified level |
||
| 645 | of zoom. Any value greater than 1 implies a "zoom-out" and anything |
||
| 646 | less than 1 implies a "zoom-in". |
||
| 647 | """ |
||
| 648 | |||
| 649 | def __init__(self, zoom, reference=None, lazy=False): |
||
| 650 | """ |
||
| 651 | Initialize a Zoom3D object |
||
| 652 | |||
| 653 | Arguments |
||
| 654 | --------- |
||
| 655 | zoom_range : list or tuple |
||
| 656 | Lower and Upper bounds on zoom parameter. |
||
| 657 | e.g. zoom_range = (0.7,0.9) will result in a random |
||
| 658 | draw of the zoom parameters between 0.7 and 0.9 |
||
| 659 | |||
| 660 | reference : ANTsImage (optional but recommended) |
||
| 661 | image providing the reference space for the transform. |
||
| 662 | this will also set the transform fixed parameters. |
||
| 663 | |||
| 664 | lazy : boolean (default = False) |
||
| 665 | if True, calling the `transform` method only returns |
||
| 666 | the randomly generated transform and does not actually |
||
| 667 | transform the image |
||
| 668 | """ |
||
| 669 | if (not isinstance(zoom, (list, tuple))) or (len(zoom) != 3): |
||
| 670 | raise ValueError( |
||
| 671 | "zoom_range argument must be list/tuple with three values!" |
||
| 672 | ) |
||
| 673 | |||
| 674 | self.zoom = zoom |
||
| 675 | self.lazy = lazy |
||
| 676 | self.reference = reference |
||
| 677 | |||
| 678 | self.tx = tio.ANTsTransform( |
||
| 679 | precision="float", dimension=3, transform_type="AffineTransform" |
||
| 680 | ) |
||
| 681 | if self.reference is not None: |
||
| 682 | self.tx.set_fixed_parameters(self.reference.get_center_of_mass()) |
||
| 683 | |||
| 684 | def transform(self, X=None, y=None): |
||
| 685 | """ |
||
| 686 | Transform an image using an Affine transform with the given |
||
| 687 | zoom parameters. Return the transform if X=None. |
||
| 688 | |||
| 689 | Arguments |
||
| 690 | --------- |
||
| 691 | X : ANTsImage |
||
| 692 | Image to transform |
||
| 693 | |||
| 694 | y : ANTsImage (optional) |
||
| 695 | Another image to transform |
||
| 696 | |||
| 697 | Returns |
||
| 698 | ------- |
||
| 699 | ANTsImage if y is None, else a tuple of ANTsImage types |
||
| 700 | |||
| 701 | Examples |
||
| 702 | -------- |
||
| 703 | >>> import ants |
||
| 704 | >>> img = ants.image_read(ants.get_data('ch2')) |
||
| 705 | >>> tx = ants.contrib.Zoom3D(zoom=(0.8,0.8,0.8)) |
||
| 706 | >>> img2 = tx.transform(img) |
||
| 707 | """ |
||
| 708 | # unpack zoom range |
||
| 709 | zoom_x, zoom_y, zoom_z = self.zoom |
||
| 710 | |||
| 711 | self.params = (zoom_x, zoom_y, zoom_z) |
||
| 712 | zoom_matrix = np.array( |
||
| 713 | [[zoom_x, 0, 0, 0], [0, zoom_y, 0, 0], [0, 0, zoom_z, 0]] |
||
| 714 | ) |
||
| 715 | self.tx.set_parameters(zoom_matrix) |
||
| 716 | if self.lazy or X is None: |
||
| 717 | return self.tx |
||
| 718 | else: |
||
| 719 | if y is None: |
||
| 720 | return self.tx.apply_to_image(X, reference=self.reference) |
||
| 721 | else: |
||
| 722 | return ( |
||
| 723 | self.tx.apply_to_image(X, reference=self.reference), |
||
| 724 | self.tx.apply_to_image(y, reference=self.reference), |
||
| 725 | ) |
||
| 726 | |||
| 727 | |||
| 728 | class RandomZoom3D(object): |
||
| 729 | """ |
||
| 730 | Apply a Zoom3D transform to an image, but with the zoom |
||
| 731 | parameters randomly generated from a user-specified range. |
||
| 732 | The range is determined by a mean (first parameter) and standard deviation |
||
| 733 | (second parameter) via calls to random.gauss. |
||
| 734 | """ |
||
| 735 | |||
| 736 | def __init__(self, zoom_range, reference=None, lazy=False): |
||
| 737 | """ |
||
| 738 | Initialize a RandomZoom3D object |
||
| 739 | |||
| 740 | Arguments |
||
| 741 | --------- |
||
| 742 | zoom_range : list or tuple |
||
| 743 | Lower and Upper bounds on zoom parameter. |
||
| 744 | e.g. zoom_range = (0.7,0.9) will result in a random |
||
| 745 | draw of the zoom parameters between 0.7 and 0.9 |
||
| 746 | |||
| 747 | reference : ANTsImage (optional but recommended) |
||
| 748 | image providing the reference space for the transform |
||
| 749 | this will also set the transform fixed parameters. |
||
| 750 | |||
| 751 | lazy : boolean (default = False) |
||
| 752 | if True, calling the `transform` method only returns |
||
| 753 | the randomly generated transform and does not actually |
||
| 754 | transform the image |
||
| 755 | """ |
||
| 756 | if (not isinstance(zoom_range, (list, tuple))) or (len(zoom_range) != 2): |
||
| 757 | raise ValueError("zoom_range argument must be list/tuple with two values!") |
||
| 758 | |||
| 759 | self.zoom_range = zoom_range |
||
| 760 | self.reference = reference |
||
| 761 | self.lazy = lazy |
||
| 762 | |||
| 763 | def transform(self, X=None, y=None): |
||
| 764 | """ |
||
| 765 | Transform an image using an Affine transform with |
||
| 766 | zoom parameters randomly generated from the user-specified |
||
| 767 | range. Return the transform if X=None. |
||
| 768 | |||
| 769 | Arguments |
||
| 770 | --------- |
||
| 771 | X : ANTsImage |
||
| 772 | Image to transform |
||
| 773 | |||
| 774 | y : ANTsImage (optional) |
||
| 775 | Another image to transform |
||
| 776 | |||
| 777 | Returns |
||
| 778 | ------- |
||
| 779 | ANTsImage if y is None, else a tuple of ANTsImage types |
||
| 780 | |||
| 781 | Examples |
||
| 782 | -------- |
||
| 783 | >>> import ants |
||
| 784 | >>> img = ants.image_read(ants.get_data('ch2')) |
||
| 785 | >>> tx = ants.contrib.RandomZoom3D(zoom_range=(0.8,0.9)) |
||
| 786 | >>> img2 = tx.transform(img) |
||
| 787 | """ |
||
| 788 | # random draw in zoom range |
||
| 789 | zoom_x = np.exp( |
||
| 790 | random.gauss(np.log(self.zoom_range[0]), np.log(self.zoom_range[1])) |
||
| 791 | ) |
||
| 792 | zoom_y = np.exp( |
||
| 793 | random.gauss(np.log(self.zoom_range[0]), np.log(self.zoom_range[1])) |
||
| 794 | ) |
||
| 795 | zoom_z = np.exp( |
||
| 796 | random.gauss(np.log(self.zoom_range[0]), np.log(self.zoom_range[1])) |
||
| 797 | ) |
||
| 798 | self.params = (zoom_x, zoom_y, zoom_z) |
||
| 799 | |||
| 800 | tx = Zoom3D((zoom_x, zoom_y, zoom_z), reference=self.reference, lazy=self.lazy) |
||
| 801 | |||
| 802 | return tx.transform(X, y) |