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Remove remove_border and update testcases to use ITKReader
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Signed-off-by: Felix Schnabel <[email protected]>
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@Shadow-Devil
Shadow-Devil committed Jan 29, 2023
1 parent 9a8cc8d commit ce4fef5
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Showing 2 changed files with 39 additions and 74 deletions.
20 changes: 0 additions & 20 deletions monai/data/itk_torch_affine_matrix_bridge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,6 @@
__all__ = [
"metatensor_to_array",
"image_to_metatensor",
"remove_border",
"itk_to_monai_affine",
"monai_to_itk_affine",
"create_itk_affine_from_parameters",
Expand Down Expand Up @@ -67,25 +66,6 @@ def image_to_metatensor(image):
return metatensor


def remove_border(image):
"""
MONAI seems to have different behavior in the borders of the image than ITK.
This helper function sets the border of the ITK image as 0 (padding but keeping
the same image size) in order to allow numerical comparison between the
result from resampling with ITK/Elastix and resampling with MONAI.
To use: image[:] = remove_border(image)
Args:
image: The ITK image to be padded.
Returns:
The padded array of data.
"""
# TODO rewrite documentation
return np.pad(image[1:-1, 1:-1, 1:-1] if image.ndim == 3 else image[1:-1, 1:-1], pad_width=1)


def _compute_offset_matrix(image, center_of_rotation) -> tuple[torch.Tensor, torch.Tensor]:
ndim = image.ndim
offset = np.asarray(_get_itk_image_center(image)) - np.asarray(center_of_rotation)
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93 changes: 39 additions & 54 deletions tests/test_itk_torch_affine_matrix_bridge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,8 @@

from parameterized import parameterized

from monai.apps import download_and_extract
from monai.data import ITKReader
from monai.utils import optional_import
from tests.utils import skip_if_downloading_fails, testing_data_config

itk, has_itk = optional_import("itk")
import numpy as np
Expand All @@ -32,39 +31,42 @@
metatensor_to_array,
monai_affine_resample,
monai_to_itk_affine,
remove_border,
)

TEST_CASE_2D = {"filepath": "CT_2D_head_fixed.mha"}
TEST_CASES = [
"CT_2D_head_fixed.mha",
"CT_2D_head_moving.mha",
#"copd1_highres_INSP_STD_COPD_img.nii.gz"
]
# Download URL: https://data.kitware.com/api/v1/file/62a0f067bddec9d0c4175c5a/download
# SHA-521: 60193cd6ef0cf055c623046446b74f969a2be838444801bd32ad5bedc8a7eeecb343e8a1208769c9c7a711e101c806a3133eccdda7790c551a69a64b9b3701e9
TEST_CASE_3D = {"filepath": "copd1_highres_INSP_STD_COPD_img.nii.gz"}
#TEST_CASE_3D = {"filepath": "copd1_highres_INSP_STD_COPD_img.nii.gz"}


@unittest.skipUnless(has_itk, "Requires `itk` package.")
class TestITKTorchAffineMatrixBridge(unittest.TestCase):
def setUp(self):
# TODO: which data should be used
self.data_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "testing_data")
data_dir = os.path.join(self.data_dir, "MedNIST")
dataset_file = os.path.join(self.data_dir, "MedNIST.tar.gz")

if not os.path.exists(data_dir):
with skip_if_downloading_fails():
data_spec = testing_data_config("images", "mednist")
download_and_extract(
data_spec["url"],
dataset_file,
self.data_dir,
hash_val=data_spec["hash_val"],
hash_type=data_spec["hash_type"],
)

@parameterized.expand([TEST_CASE_2D, TEST_CASE_3D])
self.reader = ITKReader(pixel_type=itk.F)
#data_dir = os.path.join(self.data_dir, "MedNIST")
#dataset_file = os.path.join(self.data_dir, "MedNIST.tar.gz")
#
#if not os.path.exists(data_dir):
# with skip_if_downloading_fails():
# data_spec = testing_data_config("images", "mednist")
# download_and_extract(
# data_spec["url"],
# dataset_file,
# self.data_dir,
# hash_val=data_spec["hash_val"],
# hash_type=data_spec["hash_type"],
# )

@parameterized.expand(TEST_CASES)
def test_setting_affine_parameters(self, filepath):
# Read image
image = itk.imread(filepath, itk.F)
image[:] = remove_border(image)
image = self.reader.read(os.path.join(self.data_dir, filepath))
ndim = image.ndim

# Affine parameters
Expand All @@ -78,14 +80,12 @@ def test_setting_affine_parameters(self, filepath):
image.SetSpacing(spacing)

# ITK
matrix, translation = create_itk_affine_from_parameters(
image, translation=translation, rotation=rotation, scale=scale, shear=shear
)
matrix, translation = create_itk_affine_from_parameters(image, translation, rotation, scale, shear)
output_array_itk = itk_affine_resample(image, matrix=matrix, translation=translation)

# MONAI
metatensor = image_to_metatensor(image)
affine_matrix_for_monai = itk_to_monai_affine(image, matrix=matrix, translation=translation)
affine_matrix_for_monai = itk_to_monai_affine(image, matrix, translation)
output_array_monai = monai_affine_resample(metatensor, affine_matrix=affine_matrix_for_monai)

###########################################################################
Expand All @@ -107,11 +107,10 @@ def test_setting_affine_parameters(self, filepath):
# itk.imwrite(itk.GetImageFromArray(output_array_itk), "./output/output_itk.tif")
###########################################################################

@parameterized.expand([TEST_CASE_2D, TEST_CASE_3D])
@parameterized.expand(TEST_CASES)
def test_arbitary_center_of_rotation(self, filepath):
# Read image
image = itk.imread(filepath, itk.F)
image[:] = remove_border(image)
image = self.reader.read(os.path.join(self.data_dir, filepath))
ndim = image.ndim

# ITK matrix (3x3 affine matrix)
Expand All @@ -133,15 +132,11 @@ def test_arbitary_center_of_rotation(self, filepath):
image.SetOrigin(origin)

# ITK
output_array_itk = itk_affine_resample(
image, matrix=matrix, translation=translation, center_of_rotation=center_of_rotation
)
output_array_itk = itk_affine_resample(image, matrix, translation, center_of_rotation)

# MONAI
metatensor = image_to_metatensor(image)
affine_matrix_for_monai = itk_to_monai_affine(
image, matrix=matrix, translation=translation, center_of_rotation=center_of_rotation
)
affine_matrix_for_monai = itk_to_monai_affine(image, matrix, translation, center_of_rotation)
output_array_monai = monai_affine_resample(metatensor, affine_matrix=affine_matrix_for_monai)

# Make sure that the array conversion of the inputs is the same
Expand All @@ -158,13 +153,12 @@ def test_arbitary_center_of_rotation(self, filepath):
print(f"[Min, Max] diff: [{diff_output.min()}, {diff_output.max()}]")
###########################################################################

@parameterized.expand([TEST_CASE_2D, TEST_CASE_3D])
@parameterized.expand(TEST_CASES)
def test_monai_to_itk(self, filepath):
print("\nTEST: MONAI affine matrix -> ITK matrix + translation vector -> transform")
# Read image
image = itk.imread(filepath, itk.F)
image = self.reader.read(os.path.join(self.data_dir, filepath))

image[:] = remove_border(image)
ndim = image.ndim

# MONAI affine matrix
Expand All @@ -189,16 +183,12 @@ def test_monai_to_itk(self, filepath):
image.SetOrigin(origin)

# ITK
matrix, translation = monai_to_itk_affine(
image, affine_matrix=affine_matrix, center_of_rotation=center_of_rotation
)
output_array_itk = itk_affine_resample(
image, matrix=matrix, translation=translation, center_of_rotation=center_of_rotation
)
matrix, translation = monai_to_itk_affine(image, affine_matrix, center_of_rotation)
output_array_itk = itk_affine_resample(image, matrix, translation, center_of_rotation)

# MONAI
metatensor = image_to_metatensor(image)
output_array_monai = monai_affine_resample(metatensor, affine_matrix=affine_matrix)
output_array_monai = monai_affine_resample(metatensor, affine_matrix)

# Make sure that the array conversion of the inputs is the same
input_array_monai = metatensor_to_array(metatensor)
Expand All @@ -214,10 +204,9 @@ def test_monai_to_itk(self, filepath):
print(f"[Min, Max] diff: [{diff_output.min()}, {diff_output.max()}]")
###########################################################################

@parameterized.expand([TEST_CASE_2D, TEST_CASE_3D])
@parameterized.expand(TEST_CASES)
def test_cyclic_conversion(self, filepath):
image = itk.imread(filepath, itk.F)
image[:] = remove_border(image)
image = self.reader.read(os.path.join(self.data_dir, filepath))
ndim = image.ndim

# ITK matrix (3x3 affine matrix)
Expand All @@ -239,13 +228,9 @@ def test_cyclic_conversion(self, filepath):
image.SetSpacing(spacing)
image.SetOrigin(origin)

affine_matrix = itk_to_monai_affine(
image, matrix=matrix, translation=translation, center_of_rotation=center_of_rotation
)
affine_matrix = itk_to_monai_affine(image, matrix, translation, center_of_rotation)

matrix_result, translation_result = monai_to_itk_affine(
image, affine_matrix=affine_matrix, center_of_rotation=center_of_rotation
)
matrix_result, translation_result = monai_to_itk_affine(image, affine_matrix, center_of_rotation)

print("Matrix cyclic conversion: ", np.allclose(matrix, matrix_result))
print("Translation cyclic conversion: ", np.allclose(translation, translation_result))
Expand Down

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