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
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
import os
import pydicom as dicomio
import numpy as np
import argparse
import json
from do_elastix import do_elastix
from matched_pairs import matched_pairs
def elastix_processing(args):
# 创建工作目录
save_root = os.path.join(args.job_data_root, 'output/elastix')
if not os.path.exists(save_root):
os.makedirs(save_root)
# 根据patientid筛选可以进行配准的uid
dcm_root = os.path.join(args.job_data_root, 'output/tmp')
uids = [uid for uid in os.listdir(dcm_root) if 'rpns' not in uid]
patient_infos = {}
for uid in uids:
dcms = os.listdir(os.path.join(dcm_root, uid))
dcm_meta = dicomio.read_file(os.path.join(dcm_root, uid, dcms[0]), force=True)
patientid = dcm_meta.get('PatientID', '')
acq_time = dcm_meta.get('AcquisitionDateTime', '')
if patientid:
if patientid not in patient_infos.keys():
patient_infos[patientid] = [[],[]]
patient_infos[patientid][0].append(os.path.join(dcm_root, uid))
patient_infos[patientid][1].append(acq_time)
else:
patient_infos[patientid][0].append(os.path.join(dcm_root, uid))
patient_infos[patientid][1].append(acq_time)
## 删除不符合要求的patient
for key in list(patient_infos.keys()):
if len(patient_infos[key][0]) < 2:
del patient_infos[key]
## 根据拍摄时间进行排序
for key in list(patient_infos.keys()):
temp = []
time_list = patient_infos[key][1]
sort_idx = np.argsort(time_list)
for idx in sort_idx:
temp.append([patient_infos[key][0][idx], time_list[idx]])
patient_infos[key] = temp
# 开始处理每一个病人数据
for key in list(patient_infos.keys()):
uids = patient_infos[key]
for start_id in range(len(uids) - 1):
fixed_path, fixed_time = uids[start_id]
moving_path, moving_time = uids[start_id + 1]
save_path = os.path.join(save_root, 'pid-{}_elastix_step-{}'.format(key, start_id + 1))
if not os.path.exists(save_path):
os.makedirs(save_path)
# 解析json文件得到target_points
target_path = os.path.join(args.job_data_root, 'output/eval/eval_file_details')
fixed_json_path = os.path.join(target_path, fixed_path.split('/')[-1] + '.json')
json_info = json.load(open(fixed_json_path, 'r'))
points = json_info['annotationSessions'][0]['annotationSet']
point_list = []
for point in points:
left_point, right_point = point['coordinates'][0], point['coordinates'][1]
center_point = [(left_point['x'] + right_point['x']) / 2.0,
(left_point['y'] + right_point['y']) / 2.0,
(left_point['z'] + right_point['z']) / 2.0]
point_list.append(center_point)
target_point_path = os.path.join(save_path, 'target_points.txt')
with open(target_point_path, 'w+') as file:
file.write('point')
file.write('\n')
file.write(str(len(point_list)))
file.write('\n')
for info in point_list:
file.write(str(round(info[0], 6)))
file.write(' ')
file.write(str(round(info[1], 6)))
file.write(' ')
file.write(str(round(info[2], 6)))
file.write('\n')
# 开始配准，从moving到fixed, 并且可以将fixed上的target_points映射到moving上。
do_elastix(fixed_path=fixed_path,
moving_path=moving_path,
affine_param=args.elastix_params_affine,
bspline_param=args.elastix_param_bspline,
save_path=save_path,
target_points=target_point_path)
if os.path.exists(os.path.join(save_path, 'outputpoints.txt')):
print('Finished elastix, and obtain in outputpoints-{}'.format(os.path.join(save_path,'outputpoints.txt')))
# 开始匹配, 返回字典 key：matched， missing， new
moving_json_path = os.path.join(target_path, moving_path.split('/')[-1] + '.json')
match_results = matched_pairs(fixed_json_path, moving_json_path, save_path)
match_results['info'] = [fixed_path.split('/')[-1], fixed_time, moving_path.split('/')[-1], moving_time]
with open(os.path.join(save_path, 'match_results.json'), 'w+') as file:
json.dump(match_results, file, indent=4)
print('Finished all work !!!')
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='elastix processing')
parser.add_argument('--job_data_root', default='/data/job_715/job_data_preprocess', type=str, help='model')
parser.add_argument('--elastix_params_affine', default='/shared/lung_cancer_registration/my_elastix_params/configuration_pulmonary_registration_param_parameters_Affine.txt', type=str)
parser.add_argument('--elastix_param_bspline', default='/shared/lung_cancer_registration/my_elastix_params/configuration_pulmonary_registration_param_parameters_Bspline.txt', type=str)
args = parser.parse_args()
elastix_processing(args)