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906fcb9 1baebae 906fcb9 1baebae caf6ee7 906fcb9 caf6ee7 906fcb9 caf6ee7 906fcb9 caf6ee7 906fcb9 caf6ee7 906fcb9 1baebae 906fcb9 caf6ee7 906fcb9 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 | # Copyright 2020 - 2022 MONAI 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
# 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.
# python scripts/center_crop.py --file_name path/to/t2_image --out_name cropped_t2
# import argparse
from typing import Union, cast
import SimpleITK as sitk # noqa N813
def _flatten(t):
return [item for sublist in t for item in sublist]
def crop(
image: sitk.Image,
margin_: Union[int, float, list[Union[int, float]]],
interpolator=sitk.sitkLinear,
):
"""
Crops a sitk.Image while retaining correct spacing. Negative margins will lead to zero padding
Args:
image: a sitk.Image
margin: margins to crop. Single integer or float (percentage crop),
lists of int/float or nestes lists are supported.
"""
if isinstance(margin_, (list, tuple)):
margin_temp = margin_
assert len(margin_) == 3, "expected margin to be of length 3"
else:
assert isinstance(margin_, (int, float)), "expected margin to be a float value"
margin_temp = [margin_, margin_, margin_]
margin = [m if isinstance(m, (tuple, list)) else [m, m] for m in margin_temp]
old_size = image.GetSize()
# calculate new origin and new image size
if all([isinstance(m, float) for m in _flatten(margin)]):
assert all([m >= 0 and m < 0.5 for m in _flatten(margin)]), (
"margins must be between 0 and 0.5"
)
to_crop = [[int(sz * _m) for _m in m] for sz, m in zip(old_size, margin)]
elif all([isinstance(m, int) for m in _flatten(margin)]):
to_crop = cast(list[list[int]], margin)
else:
raise ValueError("Wrong format of margins.")
new_size = [sz - sum(c) for sz, c in zip(old_size, to_crop)]
# origin has Index (0,0,0)
# new origin has Index (to_crop[0][0], to_crop[2][0], to_crop[2][0])
new_origin = image.TransformIndexToPhysicalPoint([c[0] for c in to_crop])
# create reference plane to resample image
ref_image = sitk.Image(new_size, image.GetPixelIDValue())
ref_image.SetSpacing(image.GetSpacing())
ref_image.SetOrigin(new_origin)
ref_image.SetDirection(image.GetDirection())
return sitk.Resample(image, ref_image, interpolator=interpolator)
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