def test_pad_nd_image_and_seg_2D(self):
input_shape = (5, 5, 30, 30)
data = np.random.random(input_shape)
seg = np.random.random(data.shape)
new_shape = (15, 15, 50, 50)
new_shape2 = (4, 2, 10, 10)
d, s = pad_nd_image_and_seg(data, seg, new_shape=new_shape)
d2, s2 = pad_nd_image_and_seg(data, seg, new_shape=new_shape2)
self.assertTrue(all(i == j for i, j in zip(new_shape, d.shape)), "data has unexpected shape")
self.assertTrue(all(i == j for i, j in zip(new_shape, s.shape)), "seg has unexpected shape")
np.testing.assert_array_equal(d[5:10, 5:10, 10:40, 10:40], data, err_msg="data wrongly padded")
np.testing.assert_array_equal(s[5:10, 5:10, 10:40, 10:40], seg, err_msg="seg wrongly padded")
self.assertAlmostEqual(np.sum(d.flatten()), np.sum(data.flatten()), msg="Padding of data is not zero")
self.assertAlmostEqual(np.sum(s.flatten()), np.sum(seg.flatten()), msg="Padding of data is not zero")
self.assertTrue(all(i == j for i, j in zip(input_shape, d2.shape)), "data has unexpected shape")
self.assertTrue(all(i == j for i, j in zip(input_shape, s2.shape)), "seg has unexpected shape")
np.testing.assert_array_equal(d2, data, err_msg="data wrongly padded for smaller output shape than input shape")
np.testing.assert_array_equal(s2, seg, err_msg="seg wrongly padded for smaller output shape than input shape")
def __call__(self, **data_dict):
data = data_dict.get(self.data_key)
seg = data_dict.get(self.label_key)
assert len(self.new_size) + 2 == len(data.shape), "new size must be a tuple/list/np.ndarray with shape " \
"(x, y(, z))"
data, seg = pad_nd_image_and_seg(data, seg, self.new_size, None,
np_pad_kwargs_data=self.np_pad_kwargs_data,
np_pad_kwargs_seg=self.np_pad_kwargs_seg,
pad_mode_data=self.pad_mode_data,
pad_mode_seg=self.pad_mode_seg)
data_dict[self.data_key] = data
if seg is not None:
data_dict[self.label_key] = seg
return data_dict
def test_pad_nd_image_and_seg_3D(self):
print('Test test_pad_nd_image_and_seg_3D. [START]')
input_shape = (5, 5, 30, 30, 30)
data = np.random.random(input_shape)
seg = np.random.random(data.shape)
new_shape = (15, 15, 50, 50, 50)
new_shape2 = (4, 2, 10, 10, 10)
new_shape3 = (4, 2, 50, 50, 50)
new_shape4 = (5, 5, 51, 51, 49)
new_shape5 = (50, 50)
new_shape6 = (2, 5, 5, 50, 50, 50)
new_shape7 = (5, 5, 30, 30, 50)
expected_shape3 = (5, 5, 50, 50, 50)
expected_shape5 = (5, 5, 30, 50, 50)
number_of_padded_ones7 = np.prod(new_shape7) - np.prod(input_shape)
data_padded, seg_padded = pad_nd_image_and_seg(data,
seg,
new_shape=new_shape)
data_padded2, seg_padded2 = pad_nd_image_and_seg(data,
seg,
new_shape=new_shape2)
data_padded3, seg_padded3 = pad_nd_image_and_seg(data,
seg,
new_shape=new_shape3)
data_padded4, seg_padded4 = pad_nd_image_and_seg(data,
seg,
new_shape=new_shape4)
data_padded5, seg_padded5 = pad_nd_image_and_seg(data,
seg,
new_shape=new_shape5)
data_padded7, seg_padded7 = pad_nd_image_and_seg(
data,
seg,
new_shape=new_shape7,
np_pad_kwargs_data={'constant_values': 1},
np_pad_kwargs_seg={'constant_values': 1})
print('Zero padding to bigger output shape in all dimensions. [START]')
self.assertTrue(
all(i == j for i, j in zip(new_shape, data_padded.shape)),
"padded data has unexpected shape")
self.assertTrue(
all(i == j for i, j in zip(new_shape, seg_padded.shape)),
"padded seg has unexpected shape")
np.testing.assert_array_equal(data_padded[5:10, 5:10, 10:40, 10:40,
10:40],
data,
err_msg="data wrongly padded")
np.testing.assert_array_equal(seg_padded[5:10, 5:10, 10:40, 10:40,
10:40],
seg,
err_msg="seg wrongly padded")
self.assertAlmostEqual(np.sum(data_padded.flatten()),
np.sum(data.flatten()),
msg="Padding of data is not zero")
self.assertAlmostEqual(np.sum(seg_padded.flatten()),
np.sum(seg.flatten()),
msg="Padding of data is not zero")
print('Zero padding to bigger output shape in all dimensions. [DONE]')
print(
'Zero padding to smaller output shape in all dimensions. [START]')
self.assertTrue(
all(i == j for i, j in zip(input_shape, data_padded2.shape)),
"padded data has unexpected shape")
self.assertTrue(
all(i == j for i, j in zip(input_shape, seg_padded2.shape)),
"padded seg has unexpected shape")
np.testing.assert_array_equal(
data_padded2,
data,
err_msg=
"data wrongly padded for smaller output shape than input shape")
np.testing.assert_array_equal(
seg_padded2,
seg,
err_msg=
"seg wrongly padded for smaller output shape than input shape")
print('Zero padding to smaller output shape in all dimensions. [DONE]')
print(
'Zero padding to smaller output shape in first two dimensions and bigger output shape in last two dimensions. [START]'
)
self.assertTrue(
all(i == j for i, j in zip(expected_shape3, data_padded3.shape)),
"padded data has unexpected shape")
self.assertTrue(
all(i == j for i, j in zip(expected_shape3, seg_padded3.shape)),
"padded seg has unexpected shape")
np.testing.assert_array_equal(data_padded3[:, :, 10:40, 10:40, 10:40],
data,
err_msg="data wrongly padded")
np.testing.assert_array_equal(seg_padded3[:, :, 10:40, 10:40, 10:40],
seg,
err_msg="seg wrongly padded")
self.assertAlmostEqual(np.sum(data_padded3.flatten()),
np.sum(data.flatten()),
msg="Padding of data is not zero")
self.assertAlmostEqual(np.sum(seg_padded3.flatten()),
np.sum(seg.flatten()),
msg="Padding of data is not zero")
print(
'Zero padding to smaller output shape in first two dimensions and bigger output shape in last two dimensions. [DONE]'
)
print('Zero padding to odd padding dimensions. [START]')
self.assertTrue(
all(i == j for i, j in zip(new_shape4, data_padded4.shape)),
"padded data has unexpected shape")
self.assertTrue(
all(i == j for i, j in zip(new_shape4, seg_padded4.shape)),
"padded seg has unexpected shape")
np.testing.assert_array_equal(data_padded4[:, :, 10:40, 10:40, 9:39],
data,
err_msg="data wrongly padded")
np.testing.assert_array_equal(seg_padded4[:, :, 10:40, 10:40, 9:39],
seg,
err_msg="seg wrongly padded")
self.assertAlmostEqual(np.sum(data_padded4.flatten()),
np.sum(data.flatten()),
msg="Padding of data is not zero")
self.assertAlmostEqual(np.sum(seg_padded4.flatten()),
np.sum(seg.flatten()),
msg="Padding of data is not zero")
print('Zero padding to odd padding dimensions. [DONE]')
print(
'Zero padding with new_shape.shape smaller than data.shape. [START]'
)
self.assertTrue(
all(i == j for i, j in zip(expected_shape5, data_padded5.shape)),
"data has unexpected shape")
self.assertTrue(
all(i == j for i, j in zip(expected_shape5, seg_padded5.shape)),
"seg has unexpected shape")
np.testing.assert_array_equal(data_padded5[:, :, :, 10:40, 10:40],
data,
err_msg="data wrongly padded")
np.testing.assert_array_equal(seg_padded5[:, :, :, 10:40, 10:40],
seg,
err_msg="seg wrongly padded")
self.assertAlmostEqual(np.sum(data_padded5.flatten()),
np.sum(data.flatten()),
msg="Padding of data is not zero")
self.assertAlmostEqual(np.sum(seg_padded5.flatten()),
np.sum(seg.flatten()),
msg="Padding of data is not zero")
print(
'Zero padding with new_shape.shape smaller than data.shape. [DONE]'
)
print(
'Zero padding with new_shape.shape bigger than data.shape. [START]'
)
self.assertRaises(IndexError,
pad_nd_image_and_seg,
data,
seg,
new_shape=new_shape6)
print(
'Zero padding with new_shape.shape bigger than data.shape. [DONE]')
print(
'Padding to bigger output shape in all dimensions with constant_value=1 for segmentation padding . [START]'
)
self.assertTrue(
all(i == j for i, j in zip(new_shape, data_padded.shape)),
"padded data has unexpected shape")
self.assertTrue(
all(i == j for i, j in zip(new_shape, seg_padded.shape)),
"padded seg has unexpected shape")
np.testing.assert_array_equal(data_padded7[:, :, :, :, 10:40],
data,
err_msg="data wrongly padded")
np.testing.assert_array_equal(seg_padded7[:, :, :, :, 10:40],
seg,
err_msg="seg wrongly padded")
self.assertAlmostEqual(np.sum(data_padded7.flatten()),
np.sum(data.flatten()) + number_of_padded_ones7,
msg="Padding of data is not one")
self.assertAlmostEqual(np.sum(seg_padded7.flatten()),
np.sum(seg.flatten()) + number_of_padded_ones7,
msg="Padding of data is not one")
print(
'Padding to bigger output shape in all dimensions with constant_value=1 for segmentation padding . [DONE]'
)
print('Test test_pad_nd_image_and_seg_3D. [DONE]')