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# ==========================================================================
#
# Copyright NumFOCUS
#
# 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
#
# https://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.
#
# ==========================================================================*/
import sys
import unittest
import datetime as dt
import itk
import numpy as np
class TestNumpyITKMemoryviewInterface(unittest.TestCase):
"""This tests numpy array <-> ITK Scalar Image conversion."""
def setUp(self):
pass
def test_NDArrayITKBase_pickle(self):
"""
Test the serialization of itk.NDArrayITKBase
"""
Dimension = 3
ScalarImageType = itk.Image[itk.UC, Dimension]
RegionType = itk.ImageRegion[Dimension]
region = RegionType()
region.SetSize(0, 6)
region.SetSize(1, 6)
region.SetSize(2, 6)
scalarImage = ScalarImageType.New()
scalarImage.SetRegions(region)
scalarImage.Allocate(True)
scalarImage.SetPixel([0, 0, 0], 5)
scalarImage.SetPixel([0, 0, 1], 3)
scalarImage.SetPixel([5, 5, 5], 8)
ndarray_itk_base = itk.array_view_from_image(scalarImage)
import pickle
## test serialization of itk ndarray itk base
pickled = pickle.dumps(ndarray_itk_base)
reloaded = pickle.loads(pickled)
equal = (reloaded == ndarray_itk_base).all()
assert equal, "Different results before and after pickle"
try:
import dask
from distributed.protocol.serialize import dask_dumps, dask_loads
except (ImportError, RuntimeError):
pass
else:
header, frames = dask_dumps(ndarray_itk_base)
recon_obj = dask_loads(header, frames)
equal = (recon_obj == ndarray_itk_base).all()
assert equal, "Different results before and after pickle"
def test_EmptyImage_pickle(self):
"""
Test the serialization of an empty itk.Image
"""
Dimension = 3
ImageType = itk.Image[itk.UC, Dimension]
RegionType = itk.ImageRegion[Dimension]
region = RegionType()
region.SetSize(0, 6)
region.SetSize(1, 6)
region.SetSize(2, 6)
image = ImageType.New()
image.SetRegions(region)
spacing = [3.0, 4.0, 5.0]
image.SetSpacing(spacing)
# Before allocation
# scalarImage.Allocate(True)
import pickle
pickled = pickle.dumps(image)
reloaded = pickle.loads(pickled)
reloaded_spacing = reloaded.GetSpacing()
spacing = reloaded.GetSpacing()
assert spacing[0] == reloaded_spacing[0]
assert spacing[1] == reloaded_spacing[1]
assert spacing[2] == reloaded_spacing[2]
ndarray_itk_base = itk.array_view_from_image(image)
assert ndarray_itk_base == None
def test_NumPyBridge_itkScalarImage(self):
"Try to convert all pixel types to NumPy array view"
Dimension = 3
ScalarImageType = itk.Image[itk.UC, Dimension]
RegionType = itk.ImageRegion[Dimension]
region = RegionType()
region.SetSize(0, 30)
region.SetSize(1, 20)
region.SetSize(2, 10)
scalarImage = ScalarImageType.New()
scalarImage.SetRegions(region)
scalarImage.Allocate()
scalarndarr = itk.PyBuffer[ScalarImageType].GetArrayViewFromImage(scalarImage)
self.assertTrue(hasattr(scalarndarr, "itk_base"))
self.assertTrue(scalarndarr.itk_base, scalarImage)
self.assertTrue(isinstance(scalarndarr, np.ndarray))
convertedscalarImage = itk.PyBuffer[ScalarImageType].GetImageViewFromArray(
scalarndarr
)
ScalarDiffFilterType = itk.ComparisonImageFilter[
ScalarImageType, ScalarImageType
]
ScalarDiffFilter = ScalarDiffFilterType.New()
ScalarDiffFilter.SetValidInput(scalarImage)
ScalarDiffFilter.SetTestInput(convertedscalarImage)
ScalarDiffFilter.Update()
diff = ScalarDiffFilter.GetTotalDifference()
self.assertEqual(0, diff)
assert hasattr(convertedscalarImage, "base")
self.assertEqual(scalarndarr.ndim, convertedscalarImage.ndim)
self.assertEqual(scalarndarr.dtype, convertedscalarImage.dtype)
self.assertTupleEqual(scalarndarr.shape, convertedscalarImage.shape)
def test_NumPyBridge_itkScalarImageDeepCopy(self):
"Try to convert all pixel types to NumPy array view with a deep copy"
Dimension = 3
ScalarImageType = itk.Image[itk.UC, Dimension]
RegionType = itk.ImageRegion[Dimension]
region = RegionType()
region.SetSize(0, 30)
region.SetSize(1, 20)
region.SetSize(2, 10)
scalarImage = ScalarImageType.New()
scalarImage.SetRegions(region)
scalarImage.Allocate()
scalarImage.FillBuffer(0)
# Check that scalarndarr is not a view, but a deep copy
scalarndarr = itk.PyBuffer[ScalarImageType].GetArrayFromImage(scalarImage)
scalarImage.SetPixel([0, 0, 0], 1)
self.assertNotEqual(scalarImage.GetPixel([0, 0, 0]), scalarndarr[0, 0, 0])
convertedscalarImage = itk.PyBuffer[ScalarImageType].GetImageFromArray(
scalarndarr
)
scalarndarr[0, 0, 0] = 2
self.assertNotEqual(
convertedscalarImage.GetPixel([0, 0, 0]), scalarndarr[0, 0, 0]
)
def test_NumPyBridge_itkVectorImage(self):
"Try to convert all pixel types to NumPy array view"
Dimension = 3
VectorImageType = itk.VectorImage[itk.UC, Dimension]
RegionType = itk.ImageRegion[Dimension]
region = RegionType()
region.SetSize(0, 30)
region.SetSize(1, 20)
region.SetSize(2, 10)
vectorImage = VectorImageType.New()
vectorImage.SetRegions(region)
vectorImage.SetNumberOfComponentsPerPixel(3)
vectorImage.Allocate()
vectorndarr = itk.PyBuffer[VectorImageType].GetArrayViewFromImage(vectorImage)
convertedvectorImage = itk.PyBuffer[VectorImageType].GetImageViewFromArray(
vectorndarr, is_vector=True
)
self.assertEqual(vectorndarr.ndim, convertedvectorImage.ndim)
self.assertEqual(vectorndarr.dtype, convertedvectorImage.dtype)
self.assertTupleEqual(vectorndarr.shape, convertedvectorImage.shape)
vectorImage = VectorImageType.New()
vectorImage.SetRegions(region)
vectorImage.SetNumberOfComponentsPerPixel(1)
vectorImage.Allocate()
vectorndarr = itk.PyBuffer[VectorImageType].GetArrayViewFromImage(vectorImage)
convertedvectorImage = itk.PyBuffer[VectorImageType].GetImageViewFromArray(
vectorndarr, is_vector=True
)
self.assertEqual(vectorndarr.ndim, convertedvectorImage.ndim)
self.assertEqual(vectorndarr.dtype, convertedvectorImage.dtype)
self.assertTupleEqual(vectorndarr.shape, convertedvectorImage.shape)
def test_NumPyBridge_itkRGBImage(self):
"Try to convert an RGB ITK image to NumPy array view"
Dimension = 3
PixelType = itk.RGBPixel[itk.UC]
RGBImageType = itk.Image[PixelType, Dimension]
RegionType = itk.ImageRegion[Dimension]
region = RegionType()
region.SetSize(0, 30)
region.SetSize(1, 20)
region.SetSize(2, 10)
rgbImage = RGBImageType.New()
rgbImage.SetRegions(region)
rgbImage.Allocate()
rgbndarr = itk.PyBuffer[RGBImageType].GetArrayViewFromImage(rgbImage)
convertedRGBImage = itk.PyBuffer[RGBImageType].GetImageViewFromArray(
rgbndarr, is_vector=True
)
self.assertEqual(rgbndarr.ndim, convertedRGBImage.ndim)
self.assertEqual(rgbndarr.dtype, convertedRGBImage.dtype)
self.assertTupleEqual(rgbndarr.shape, convertedRGBImage.shape)
def test_NumPyBridge_itkRGBAImage(self):
"Try to convert an RGBA ITK image to NumPy array view"
Dimension = 3
PixelType = itk.RGBAPixel[itk.UC]
RGBAImageType = itk.Image[PixelType, Dimension]
RegionType = itk.ImageRegion[Dimension]
region = RegionType()
region.SetSize(0, 30)
region.SetSize(1, 20)
region.SetSize(2, 10)
rgbaImage = RGBAImageType.New()
rgbaImage.SetRegions(region)
rgbaImage.Allocate()
rgbandarr = itk.PyBuffer[RGBAImageType].GetArrayViewFromImage(rgbaImage)
convertedRGBAImage = itk.PyBuffer[RGBAImageType].GetImageViewFromArray(
rgbandarr, is_vector=True
)
self.assertEqual(rgbandarr.ndim, convertedRGBAImage.ndim)
self.assertEqual(rgbandarr.dtype, convertedRGBAImage.dtype)
self.assertTupleEqual(rgbandarr.shape, convertedRGBAImage.shape)
def test_NumPyBridge_itkVectorPixelImage(self):
"Try to convert an ITK image with vector pixels to NumPy array view"
Dimension = 3
PixelType = itk.Vector[itk.F, Dimension]
VectorImageType = itk.Image[PixelType, Dimension]
RegionType = itk.ImageRegion[Dimension]
region = RegionType()
region.SetSize(0, 30)
region.SetSize(1, 20)
region.SetSize(2, 10)
vectorImage = VectorImageType.New()
vectorImage.SetRegions(region)
vectorImage.Allocate()
vectorndarr = itk.PyBuffer[VectorImageType].GetArrayViewFromImage(vectorImage)
convertedVectorImage = itk.PyBuffer[VectorImageType].GetImageViewFromArray(
vectorndarr, is_vector=True
)
self.assertEqual(vectorndarr.ndim, convertedVectorImage.ndim)
self.assertEqual(vectorndarr.dtype, convertedVectorImage.dtype)
self.assertTupleEqual(vectorndarr.shape, convertedVectorImage.shape)
def test_NumPyBridge_FortranOrder(self):
"Try to convert an ITK image to / from a NumPy array with Fortran order"
Dimension = 2
PixelType = itk.ctype("signed short")
ImageType = itk.Image[PixelType, Dimension]
dtype = np.int16
arr = np.arange(6, dtype=dtype)
arrC = np.reshape(arr, (2, 3), order="C")
assert arrC.flags.c_contiguous
image = itk.PyBuffer[ImageType].GetImageViewFromArray(arrC)
index = itk.Index[Dimension]()
index[0] = 0
index[1] = 0
assert image.GetPixel(index) == 0
index[0] = 1
index[1] = 0
assert image.GetPixel(index) == 1
index[0] = 0
index[1] = 1
assert image.GetPixel(index) == 3
arrFortran = np.reshape(arr, (3, 2), order="F")
assert arrFortran.flags.f_contiguous
image = itk.PyBuffer[ImageType].GetImageViewFromArray(arrFortran)
index[0] = 0
index[1] = 0
assert image.GetPixel(index) == 0
index[0] = 1
index[1] = 0
assert image.GetPixel(index) == 1
index[0] = 0
index[1] = 1
assert image.GetPixel(index) == 3
def test_NumPyBridge_ImageFromBuffer(self):
"Create an image with image_from_array with a non-writeable input"
data = b"hello world "
array = np.frombuffer(data, dtype=np.uint8)
array = array.reshape((2, 6))
image = itk.image_from_array(array)
def test_non_contiguous_array(self):
"Check that a non-contiguous array can be converted to an itk.Image without issue"
data = np.random.random((10, 10, 10))
data = data[..., 0] # slicing the array makes it non-contiguous
assert not data.flags["C_CONTIGUOUS"]
assert not data.flags["F_CONTIGUOUS"]
image = itk.image_from_array(data)
if __name__ == "__main__":
unittest.main(verbosity=2)
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