retuve.hip_us.handlers.segs

Handles Segmentaitions that are not valid for analysis.

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 1# Copyright 2024 Adam McArthur
 2#
 3# Licensed under the Apache License, Version 2.0 (the "License");
 4# you may not use this file except in compliance with the License.
 5# You may obtain a copy of the License at
 6#
 7#     http://www.apache.org/licenses/LICENSE-2.0
 8#
 9# Unless required by applicable law or agreed to in writing, software
10# distributed under the License is distributed on an "AS IS" BASIS,
11# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12# See the License for the specific language governing permissions and
13# limitations under the License.
14
15"""
16Handles Segmentaitions that are not valid for analysis.
17"""
18
19from typing import Dict, List
20
21from PIL import Image
22
23from retuve.classes.seg import SegObject
24from retuve.hip_us.classes.enums import HipLabelsUS
25
26
27def remove_bad_objs(
28    hip_objs: Dict[HipLabelsUS, List[SegObject]], img: Image.Image
29) -> Dict[HipLabelsUS, SegObject]:
30    """
31    Remove bad segmentation objects from the Hip Objects.
32
33    For example, if there are multiple segmentations for the Illium and Acetabulum,
34    only keep the one that is the most left of the image.
35
36    :param hip_objs: Dict of Hip Objects.
37    :param img: Image object.
38
39    """
40
41    rejection_reasons = []
42
43    fem_head_ilium_wrong_way_round = False
44    if len(hip_objs[HipLabelsUS.IlliumAndAcetabulum]) > 1:
45        hip_objs[HipLabelsUS.IlliumAndAcetabulum] = [
46            sorted(
47                hip_objs[HipLabelsUS.IlliumAndAcetabulum],
48                key=lambda seg_obj: seg_obj.box[0],
49            )[0]
50        ]
51
52    # replace each value with the largest object
53    for k, v in hip_objs.items():
54        if len(v) != 0:
55            hip_objs[k] = max(v, key=lambda seg_obj: seg_obj.area())
56        else:
57            hip_objs[k] = SegObject(empty=True)
58
59    fem_head = hip_objs.get(HipLabelsUS.FemoralHead, None)
60
61    illium = hip_objs.get(HipLabelsUS.IlliumAndAcetabulum, None)
62    if illium and illium.box is not None and illium.box[0] > img.shape[1] / 2:
63        # check if the femoral head box is left of the illium box
64        if (
65            fem_head
66            and fem_head.box is not None
67            and illium.box[0] > fem_head.box[0]
68        ):
69            fem_head_ilium_wrong_way_round = True
70
71    # Femoral Heads should be at least 2.5%
72    expected_min_fem_size = img.shape[0] * img.shape[1] * 0.025
73    if fem_head and fem_head.area() < expected_min_fem_size:
74        hip_objs[HipLabelsUS.FemoralHead] = SegObject(empty=True)
75        rejection_reasons.append("Femoral Head too small")
76
77    return hip_objs, fem_head_ilium_wrong_way_round, rejection_reasons

def remove_bad_objs( hip_objs: Dict[retuve.hip_us.classes.enums.HipLabelsUS, List[retuve.classes.seg.SegObject]], img: PIL.Image.Image) -> Dict[retuve.hip_us.classes.enums.HipLabelsUS, retuve.classes.seg.SegObject]: View Source

28def remove_bad_objs(
29    hip_objs: Dict[HipLabelsUS, List[SegObject]], img: Image.Image
30) -> Dict[HipLabelsUS, SegObject]:
31    """
32    Remove bad segmentation objects from the Hip Objects.
33
34    For example, if there are multiple segmentations for the Illium and Acetabulum,
35    only keep the one that is the most left of the image.
36
37    :param hip_objs: Dict of Hip Objects.
38    :param img: Image object.
39
40    """
41
42    rejection_reasons = []
43
44    fem_head_ilium_wrong_way_round = False
45    if len(hip_objs[HipLabelsUS.IlliumAndAcetabulum]) > 1:
46        hip_objs[HipLabelsUS.IlliumAndAcetabulum] = [
47            sorted(
48                hip_objs[HipLabelsUS.IlliumAndAcetabulum],
49                key=lambda seg_obj: seg_obj.box[0],
50            )[0]
51        ]
52
53    # replace each value with the largest object
54    for k, v in hip_objs.items():
55        if len(v) != 0:
56            hip_objs[k] = max(v, key=lambda seg_obj: seg_obj.area())
57        else:
58            hip_objs[k] = SegObject(empty=True)
59
60    fem_head = hip_objs.get(HipLabelsUS.FemoralHead, None)
61
62    illium = hip_objs.get(HipLabelsUS.IlliumAndAcetabulum, None)
63    if illium and illium.box is not None and illium.box[0] > img.shape[1] / 2:
64        # check if the femoral head box is left of the illium box
65        if (
66            fem_head
67            and fem_head.box is not None
68            and illium.box[0] > fem_head.box[0]
69        ):
70            fem_head_ilium_wrong_way_round = True
71
72    # Femoral Heads should be at least 2.5%
73    expected_min_fem_size = img.shape[0] * img.shape[1] * 0.025
74    if fem_head and fem_head.area() < expected_min_fem_size:
75        hip_objs[HipLabelsUS.FemoralHead] = SegObject(empty=True)
76        rejection_reasons.append("Femoral Head too small")
77
78    return hip_objs, fem_head_ilium_wrong_way_round, rejection_reasons

Remove bad segmentation objects from the Hip Objects.

For example, if there are multiple segmentations for the Illium and Acetabulum, only keep the one that is the most left of the image.

Parameters

hip_objs: Dict of Hip Objects.
img: Image object.