1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
|
#==========================================================================
#
# Copyright Insight Software Consortium
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0.txt
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
#==========================================================================*/
from __future__ import print_function
import sys
import unittest
import SimpleITK as sitk
import numpy as np
sizeX = 4
sizeY = 5
sizeZ = 3
class TestNumpySimpleITKInterface(unittest.TestCase):
""" This tests numpy array <-> SimpleITK Image conversion. """
def setUp(self):
pass
def _helper_check_sitk_to_numpy_type(self, sitkType, numpyType):
image = sitk.Image( (9, 10), sitkType, 1 )
a = sitk.GetArrayFromImage( image )
self.assertEqual( numpyType, a.dtype )
self.assertEqual( (10, 9), a.shape )
def test_type_to_numpy(self):
"try all sitk pixel type to convert to numpy"
self._helper_check_sitk_to_numpy_type(sitk.sitkUInt8, np.uint8)
self._helper_check_sitk_to_numpy_type(sitk.sitkUInt16, np.uint16)
self._helper_check_sitk_to_numpy_type(sitk.sitkUInt32, np.uint32)
if sitk.sitkUInt64 != sitk.sitkUnknown:
self._helper_check_sitk_to_numpy_type(sitk.sitkUInt64, np.uint64)
self._helper_check_sitk_to_numpy_type(sitk.sitkInt8, np.int8)
self._helper_check_sitk_to_numpy_type(sitk.sitkInt16, np.int16)
self._helper_check_sitk_to_numpy_type(sitk.sitkInt32, np.int32)
if sitk.sitkInt64 != sitk.sitkUnknown:
self._helper_check_sitk_to_numpy_type(sitk.sitkInt64, np.int64)
self._helper_check_sitk_to_numpy_type(sitk.sitkFloat32, np.float32)
self._helper_check_sitk_to_numpy_type(sitk.sitkFloat64, np.float64)
#self._helper_check_sitk_to_numpy_type(sitk.sitkComplexFloat32, np.complex64)
#self._helper_check_sitk_to_numpy_type(sitk.sitkComplexFloat64, np.complex128)
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorUInt8, np.uint8)
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorInt8, np.int8)
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorUInt16, np.uint16)
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorInt16, np.int16)
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorUInt32, np.uint32)
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorInt32, np.int32)
if sitk.sitkVectorUInt64 != sitk.sitkUnknown:
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorUInt64, np.uint64)
if sitk.sitkVectorInt64 != sitk.sitkUnknown:
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorInt64, np.int64)
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorFloat32, np.float32)
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorFloat64, np.float64)
#self._helper_check_sitk_to_numpy_type(sitk.sitkLabelUInt8, np.uint8)
#self._helper_check_sitk_to_numpy_type(sitk.sitkLabelUInt16, np.uint16)
#self._helper_check_sitk_to_numpy_type(sitk.sitkLabelUInt32, np.uint32)
#self._helper_check_sitk_to_numpy_type(sitk.sitkLabelUInt64, np.uint64)
def test_to_numpy_and_back(self):
"""Test converting an image to numpy and back"""
img = sitk.GaussianSource( sitk.sitkFloat32, [100,100], sigma=[10]*3, mean = [50,50] )
h = sitk.Hash( img )
# convert the image to and fro a numpy array
img = sitk.GetImageFromArray( sitk.GetArrayFromImage( img ) )
self.assertEqual( h, sitk.Hash( img ))
def test_vector_image_to_numpy(self):
"""Test converting back and forth between numpy and SimpleITK
images were the SimpleITK image has multiple componets and
stored as a VectorImage."""
# Check 2D
img = sitk.PhysicalPointSource(sitk.sitkVectorFloat32, [3,4])
h = sitk.Hash( img )
nda = sitk.GetArrayFromImage(img)
self.assertEqual(nda.shape, (4,3,2))
self.assertEqual(nda[0,0].tolist(), [0,0])
self.assertEqual(nda[2,1].tolist(), [1,2])
self.assertEqual(nda[0,:,0].tolist(), [0,1,2])
img2 = sitk.GetImageFromArray( nda, isVector=True)
self.assertEqual( h, sitk.Hash(img2) )
# check 3D
img = sitk.PhysicalPointSource(sitk.sitkVectorFloat32, [3,4,5])
h = sitk.Hash( img )
nda = sitk.GetArrayFromImage(img)
self.assertEqual(nda.shape, (5,4,3,3))
self.assertEqual(nda[0,0,0].tolist(), [0,0,0])
self.assertEqual(nda[0,0,:,0].tolist(), [0,1,2])
self.assertEqual(nda[0,:,1,1].tolist(), [0,1,2,3])
img2 = sitk.GetImageFromArray(nda)
self.assertEqual(img2.GetSize(), img.GetSize())
self.assertEqual(img2.GetNumberOfComponentsPerPixel(), img.GetNumberOfComponentsPerPixel())
self.assertEqual(h, sitk.Hash(img2))
def test_legacy(self):
"""Test SimpleITK Image to numpy array."""
# self.assertRaises(TypeError, sitk.GetArrayFromImage, 3)
# 2D image
image = sitk.Image(sizeX, sizeY, sitk.sitkInt32)
for j in range(sizeY):
for i in range(sizeX):
image[i, j] = j*sizeX + i
print(sitk.GetArrayFromImage(image))
self.assertEqual( type (sitk.GetArrayFromImage(image)), np.ndarray )
# 3D image
image = sitk.Image(sizeX, sizeY, sizeZ, sitk.sitkFloat32)
for k in range(sizeZ):
for j in range(sizeY):
for i in range(sizeX):
image[i, j, k] = (sizeY*k +j)*sizeX + i
print(sitk.GetArrayFromImage(image))
self.assertEqual( type (sitk.GetArrayFromImage(image)), np.ndarray )
def test_legacy_array2sitk(self):
"""Test numpy array to SimpleITK Image."""
arr = np.arange(20, dtype=np.float64)
arr.shape = (sizeY, sizeX)
image = sitk.GetImageFromArray(arr)
self.assertEqual(image.GetSize(), (sizeX, sizeY))
self.assertEqual(image[0,0], 0.0)
self.assertEqual(image[1,1], 5.0)
self.assertEqual(image[2,2], 10.0)
arr = np.arange(60, dtype=np.int16)
arr.shape = (sizeZ, sizeY, sizeX)
image = sitk.GetImageFromArray(arr)
self.assertEqual(image.GetSize(), (sizeX, sizeY, sizeZ))
self.assertEqual(image[0,0,0], 0)
self.assertEqual(image[1,1,1], 25)
self.assertEqual(image[2,2,2], 50)
if __name__ == '__main__':
unittest.main()
|
