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#==========================================================================
#
# 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 datetime as dt
import timeit
import SimpleITK as sitk
import numpy as np
sizeX = 4
sizeY = 5
sizeZ = 3
newSimpleITKPixelValueInt32 = -3000
newNumPyElementValueInt32 = 200
class TestNumpySimpleITKMemoryviewInterface(unittest.TestCase):
""" This tests numpy array <-> SimpleITK Image conversion. """
def setUp(self):
pass
def _helper_check_sitk_to_numpy_type(self, sitkType, numpyType):
if sitkType == sitk.sitkUnknown:
return
image = sitk.Image((9, 10), sitkType, 1)
a = sitk.GetArrayViewFromImage(image)
self.assertEqual(numpyType, a.dtype)
self.assertEqual((10, 9), a.shape)
def test_type_to_numpy(self):
"try all sitk pixel types to convert to NumPy array view"
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)
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)
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.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)
self._helper_check_sitk_to_numpy_type(sitk.sitkVectorUInt64, np.uint64)
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)
def test_to_numpy_and_back(self):
"""Test converting an image to NumPy array view and back"""
img = sitk.GaussianSource( sitk.sitkFloat32, [100,100], sigma=[10]*3, mean=[50,50] )
h = sitk.Hash( img )
img2 = sitk.GetImageFromArray( sitk.GetArrayViewFromImage(img))
self.assertEqual( h, sitk.Hash( img2 ))
def test_vector_image_to_numpy(self):
"""Test converting back and forth between NumPy array view and SimpleITK
images where the SimpleITK image has multiple components and
stored as a VectorImage."""
# Check 2D
img = sitk.PhysicalPointSource(sitk.sitkVectorFloat32, [3,4])
h = sitk.Hash( img )
nda = sitk.GetArrayViewFromImage(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.GetArrayViewFromImage(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_arrayview_writable(self):
"""Test correct behavior of writablity to the returned array view."""
img = sitk.Image((9, 10), sitk.sitkFloat32, 1)
a = sitk.GetArrayViewFromImage(img)
with self.assertRaises(ValueError):
a.fill(0)
def test_processing_time(self):
"""Check the processing time the conversions from SimpleITK Image
to numpy array (GetArrayViewFromImage) and
numpy memoryview (GetArrayViewFromImage)."""
# Performance test for SimpleITK Image -> NumPy array
img = sitk.GaussianSource(sitk.sitkFloat32, [3000,3000], sigma=[10]*3, mean=[50,50])
print("\nGet NumPy array from 3000x3000 SimpleITK Image")
nparray_time_elapsed = min(timeit.repeat(lambda: sitk.GetArrayFromImage(img), repeat=5, number=1))
print ("Processing time of GetArrayFromImage (Copy operation) :: {0} (us)".format(nparray_time_elapsed*1e6))
npview_time_elapsed = min(timeit.repeat(lambda: sitk.GetArrayViewFromImage(img), repeat=5, number=1))
print ("Processing time of GetArrayViewFromImage (Array view) :: {0} (us)".format(npview_time_elapsed*1e6))
self.assertTrue( nparray_time_elapsed > npview_time_elapsed)
# Performance test for NumPy array -> SimpleITK Image
Big_nparray = np.zeros((3000,3000), dtype=np.int64);
if __name__ == '__main__':
unittest.main()
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