diff --git a/totalsegmentator/map_to_binary.py b/totalsegmentator/map_to_binary.py index afae0798b..d5f659cc6 100644 --- a/totalsegmentator/map_to_binary.py +++ b/totalsegmentator/map_to_binary.py @@ -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