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remove some v1 class map from map_to_binary
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@wasserth
wasserth committed Sep 21, 2023
1 parent 8e1706c commit d0eb302
Showing 1 changed file with 110 additions and 268 deletions.
378 changes: 110 additions & 268 deletions totalsegmentator/map_to_binary.py
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Original file line number Diff line number Diff line change
@@ -1,110 +1,114 @@
class_map = {
"total_v1": {
1: "spleen",
2: "kidney_right",
3: "kidney_left",
4: "gallbladder",
5: "liver",
6: "stomach",
7: "aorta",
8: "inferior_vena_cava",
9: "portal_vein_and_splenic_vein",
10: "pancreas",
11: "adrenal_gland_right",
12: "adrenal_gland_left",
13: "lung_upper_lobe_left",
14: "lung_lower_lobe_left",
15: "lung_upper_lobe_right",
16: "lung_middle_lobe_right",
17: "lung_lower_lobe_right",
18: "vertebrae_L5",
19: "vertebrae_L4",
20: "vertebrae_L3",
21: "vertebrae_L2",
22: "vertebrae_L1",
23: "vertebrae_T12",
24: "vertebrae_T11",
25: "vertebrae_T10",
26: "vertebrae_T9",
27: "vertebrae_T8",
28: "vertebrae_T7",
29: "vertebrae_T6",
30: "vertebrae_T5",
31: "vertebrae_T4",
32: "vertebrae_T3",
33: "vertebrae_T2",
34: "vertebrae_T1",
35: "vertebrae_C7",
36: "vertebrae_C6",
37: "vertebrae_C5",
38: "vertebrae_C4",
39: "vertebrae_C3",
40: "vertebrae_C2",
41: "vertebrae_C1",
42: "esophagus",
43: "trachea",
44: "heart_myocardium",
45: "heart_atrium_left",
46: "heart_ventricle_left",
47: "heart_atrium_right",
48: "heart_ventricle_right",
49: "pulmonary_artery",
50: "brain",
51: "iliac_artery_left",
52: "iliac_artery_right",
53: "iliac_vena_left",
54: "iliac_vena_right",
55: "small_bowel",
56: "duodenum",
57: "colon",
58: "rib_left_1",
59: "rib_left_2",
60: "rib_left_3",
61: "rib_left_4",
62: "rib_left_5",
63: "rib_left_6",
64: "rib_left_7",
65: "rib_left_8",
66: "rib_left_9",
67: "rib_left_10",
68: "rib_left_11",
69: "rib_left_12",
70: "rib_right_1",
71: "rib_right_2",
72: "rib_right_3",
73: "rib_right_4",
74: "rib_right_5",
75: "rib_right_6",
76: "rib_right_7",
77: "rib_right_8",
78: "rib_right_9",
79: "rib_right_10",
80: "rib_right_11",
81: "rib_right_12",
82: "humerus_left",
83: "humerus_right",
84: "scapula_left",
85: "scapula_right",
86: "clavicula_left",
87: "clavicula_right",
88: "femur_left",
89: "femur_right",
90: "hip_left",
91: "hip_right",
92: "sacrum",
93: "face",
94: "gluteus_maximus_left",
95: "gluteus_maximus_right",
96: "gluteus_medius_left",
97: "gluteus_medius_right",
98: "gluteus_minimus_left",
99: "gluteus_minimus_right",
100: "autochthon_left",
101: "autochthon_right",
102: "iliopsoas_left",
103: "iliopsoas_right",
104: "urinary_bladder"
},

# classes of old TotalSegmentator v1
# "total_v1": {
# 1: "spleen",
# 2: "kidney_right",
# 3: "kidney_left",
# 4: "gallbladder",
# 5: "liver",
# 6: "stomach",
# 7: "aorta",
# 8: "inferior_vena_cava",
# 9: "portal_vein_and_splenic_vein",
# 10: "pancreas",
# 11: "adrenal_gland_right",
# 12: "adrenal_gland_left",
# 13: "lung_upper_lobe_left",
# 14: "lung_lower_lobe_left",
# 15: "lung_upper_lobe_right",
# 16: "lung_middle_lobe_right",
# 17: "lung_lower_lobe_right",
# 18: "vertebrae_L5",
# 19: "vertebrae_L4",
# 20: "vertebrae_L3",
# 21: "vertebrae_L2",
# 22: "vertebrae_L1",
# 23: "vertebrae_T12",
# 24: "vertebrae_T11",
# 25: "vertebrae_T10",
# 26: "vertebrae_T9",
# 27: "vertebrae_T8",
# 28: "vertebrae_T7",
# 29: "vertebrae_T6",
# 30: "vertebrae_T5",
# 31: "vertebrae_T4",
# 32: "vertebrae_T3",
# 33: "vertebrae_T2",
# 34: "vertebrae_T1",
# 35: "vertebrae_C7",
# 36: "vertebrae_C6",
# 37: "vertebrae_C5",
# 38: "vertebrae_C4",
# 39: "vertebrae_C3",
# 40: "vertebrae_C2",
# 41: "vertebrae_C1",
# 42: "esophagus",
# 43: "trachea",
# 44: "heart_myocardium",
# 45: "heart_atrium_left",
# 46: "heart_ventricle_left",
# 47: "heart_atrium_right",
# 48: "heart_ventricle_right",
# 49: "pulmonary_artery",
# 50: "brain",
# 51: "iliac_artery_left",
# 52: "iliac_artery_right",
# 53: "iliac_vena_left",
# 54: "iliac_vena_right",
# 55: "small_bowel",
# 56: "duodenum",
# 57: "colon",
# 58: "rib_left_1",
# 59: "rib_left_2",
# 60: "rib_left_3",
# 61: "rib_left_4",
# 62: "rib_left_5",
# 63: "rib_left_6",
# 64: "rib_left_7",
# 65: "rib_left_8",
# 66: "rib_left_9",
# 67: "rib_left_10",
# 68: "rib_left_11",
# 69: "rib_left_12",
# 70: "rib_right_1",
# 71: "rib_right_2",
# 72: "rib_right_3",
# 73: "rib_right_4",
# 74: "rib_right_5",
# 75: "rib_right_6",
# 76: "rib_right_7",
# 77: "rib_right_8",
# 78: "rib_right_9",
# 79: "rib_right_10",
# 80: "rib_right_11",
# 81: "rib_right_12",
# 82: "humerus_left",
# 83: "humerus_right",
# 84: "scapula_left",
# 85: "scapula_right",
# 86: "clavicula_left",
# 87: "clavicula_right",
# 88: "femur_left",
# 89: "femur_right",
# 90: "hip_left",
# 91: "hip_right",
# 92: "sacrum",
# 93: "face",
# 94: "gluteus_maximus_left",
# 95: "gluteus_maximus_right",
# 96: "gluteus_medius_left",
# 97: "gluteus_medius_right",
# 98: "gluteus_minimus_left",
# 99: "gluteus_minimus_right",
# 100: "autochthon_left",
# 101: "autochthon_right",
# 102: "iliopsoas_left",
# 103: "iliopsoas_right",
# 104: "urinary_bladder"
# },

# classes of new TotalSegmentator v2
"total": {
1: "spleen",
2: "kidney_right",
@@ -312,168 +316,6 @@
# - everything highres?


class_map_5_parts_v1 = {

# 17 classes
"class_map_part_organs": {
1: "spleen",
2: "kidney_right",
3: "kidney_left",
4: "gallbladder",
5: "liver",
6: "stomach",
7: "aorta",
8: "inferior_vena_cava",
9: "portal_vein_and_splenic_vein",
10: "pancreas",
11: "adrenal_gland_right",
12: "adrenal_gland_left",
13: "lung_upper_lobe_left",
14: "lung_lower_lobe_left",
15: "lung_upper_lobe_right",
16: "lung_middle_lobe_right",
17: "lung_lower_lobe_right"
},

# 24 classes
"class_map_part_vertebrae": {
1: "vertebrae_L5",
2: "vertebrae_L4",
3: "vertebrae_L3",
4: "vertebrae_L2",
5: "vertebrae_L1",
6: "vertebrae_T12",
7: "vertebrae_T11",
8: "vertebrae_T10",
9: "vertebrae_T9",
10: "vertebrae_T8",
11: "vertebrae_T7",
12: "vertebrae_T6",
13: "vertebrae_T5",
14: "vertebrae_T4",
15: "vertebrae_T3",
16: "vertebrae_T2",
17: "vertebrae_T1",
18: "vertebrae_C7",
19: "vertebrae_C6",
20: "vertebrae_C5",
21: "vertebrae_C4",
22: "vertebrae_C3",
23: "vertebrae_C2",
24: "vertebrae_C1"
},

# 18
"class_map_part_cardiac": {
1: "esophagus",
2: "trachea",
3: "heart_myocardium",
4: "heart_atrium_left",
5: "heart_ventricle_left",
6: "heart_atrium_right",
7: "heart_ventricle_right",
8: "pulmonary_artery",
9: "brain",
10: "iliac_artery_left",
11: "iliac_artery_right",
12: "iliac_vena_left",
13: "iliac_vena_right",
14: "small_bowel",
15: "duodenum",
16: "colon",
17: "urinary_bladder",
18: "face"
},

# 21
"class_map_part_muscles": {
1: "humerus_left",
2: "humerus_right",
3: "scapula_left",
4: "scapula_right",
5: "clavicula_left",
6: "clavicula_right",
7: "femur_left",
8: "femur_right",
9: "hip_left",
10: "hip_right",
11: "sacrum",
12: "gluteus_maximus_left",
13: "gluteus_maximus_right",
14: "gluteus_medius_left",
15: "gluteus_medius_right",
16: "gluteus_minimus_left",
17: "gluteus_minimus_right",
18: "autochthon_left",
19: "autochthon_right",
20: "iliopsoas_left",
21: "iliopsoas_right"
},

# --roi_subset does not work anymore with this
# without humerus and femur
# "class_map_part_muscles_v2": {
# 1: "scapula_left",
# 2: "scapula_right",
# 3: "clavicula_left",
# 4: "clavicula_right",
# 5: "hip_left",
# 6: "hip_right",
# 7: "sacrum",
# 8: "gluteus_maximus_left",
# 9: "gluteus_maximus_right",
# 10: "gluteus_medius_left",
# 11: "gluteus_medius_right",
# 12: "gluteus_minimus_left",
# 13: "gluteus_minimus_right",
# 14: "autochthon_left",
# 15: "autochthon_right",
# 16: "iliopsoas_left",
# 17: "iliopsoas_right"
# },

# 24 classes
# 12. ribs start from vertebrae T12
# Small subset of population (roughly 8%) have 13. rib below 12. rib
# (would start from L1 then)
# -> this has label rib_12
# Even smaller subset (roughly 1%) has extra rib above 1. rib ("Halsrippe")
# (the extra rib would start from C7)
# -> this has label rib_1
#
# Quite often only 11 ribs (12. ribs probably so small that not found). Those
# cases often wrongly segmented.
"class_map_part_ribs": {
1: "rib_left_1",
2: "rib_left_2",
3: "rib_left_3",
4: "rib_left_4",
5: "rib_left_5",
6: "rib_left_6",
7: "rib_left_7",
8: "rib_left_8",
9: "rib_left_9",
10: "rib_left_10",
11: "rib_left_11",
12: "rib_left_12",
13: "rib_right_1",
14: "rib_right_2",
15: "rib_right_3",
16: "rib_right_4",
17: "rib_right_5",
18: "rib_right_6",
19: "rib_right_7",
20: "rib_right_8",
21: "rib_right_9",
22: "rib_right_10",
23: "rib_right_11",
24: "rib_right_12"
},

"test": class_map["test"]
}


class_map_5_parts = {

# 24 classes

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