#========================================================================== # # 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()