from unittest import TestCase
import nibabel as nib
import numpy as np
from fetal_net.utils.utils import resize
from fetal_net.utils.sitk_utils import resample_to_spacing
class TestUtils(TestCase):
def _resize_image_test(self, image, target_shape):
original_image_shape = image.shape
new_image = resize(image, target_shape)
self.assertEqual(new_image.shape, target_shape)
new_image = resize(new_image, original_image_shape, interpolation="linear")
self.assertEqual(new_image.shape, original_image_shape)
def _create_image(self, image_shape):
data = np.asarray(np.arange(np.prod(image_shape)).reshape(image_shape), dtype=np.float)
affine = np.zeros((4, 4))
np.fill_diagonal(affine, 1)
return nib.Nifti1Image(data, affine)
def test_resize_image_1(self):
image_shape = (4, 4, 4)
image = self._create_image(image_shape)
new_size = (2, 2, 2)
self._resize_image_test(image, new_size)
def test_resize_image_2(self):
self._resize_image_test(self._create_image((12, 10, 8)), (8, 8, 8))
def test_resize_image_2d(self):
data = np.arange(1, 5).reshape((2, 2))
new_data = resample_to_spacing(data, (2, 2), (1, 1), interpolation="nearest")
self.assertTrue(np.all(new_data == np.asarray([[1, 1, 2, 2],
[1, 1, 2, 2],
[3, 3, 4, 4],
[3, 3, 4, 4]])))
orig_data = resample_to_spacing(new_data, (1, 1), (2, 2), interpolation="linear")
self.assertTrue(np.all(data == orig_data))
def test_resize_image_3(self):
self._resize_image_test(self._create_image((2, 5, 3)), (7, 5, 11))
def test_resize_image_3d(self):
data = np.arange(1, 9).reshape((2, 2, 2))
new_data = resample_to_spacing(data, (2, 2, 2), (1, 1, 1), interpolation="nearest")
self.assertTrue(np.all(new_data[0] == np.asarray([[1, 1, 2, 2],
[1, 1, 2, 2],
[3, 3, 4, 4],
[3, 3, 4, 4]])))
orig_data = resample_to_spacing(new_data, (1, 1, 1), (2, 2, 2), interpolation="linear")
self.assertTrue(np.all(data == orig_data))
def test_images_align(self):
data = np.arange(1, 9).reshape((2, 2, 2))
affine = np.diag(np.ones(4) * 2)
affine[3, 3] = 1
image_nib = nib.Nifti1Image(data, affine=affine)
new_image_nib = resize(image_nib, (4, 4, 4), interpolation="nearest")
self.assertTrue(np.all(new_image_nib.get_data()[0] == np.asarray([[1, 1, 2, 2],
[1, 1, 2, 2],
[3, 3, 4, 4],
[3, 3, 4, 4]])))
self.assertTrue(np.all(new_image_nib.affine == np.asarray([[1., 0., 0., -0.5],
[0., 1., 0., -0.5],
[0., 0., 1., -0.5],
[0., 0., 0., 1.]])))
