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
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171 | # -*- coding: utf-8 -*-
"""
Converts DICOM files to NIfTI files including their JSON sidecars in a
temporary directory which can be inspected to make a dc2mbids config file.
"""
import argparse
import logging
import platform
import sys
import os
from pathlib import Path
from datetime import datetime
from dcm2bids.dcm2niix_gen import Dcm2niixGen
from dcm2bids.utils.utils import DEFAULT
from dcm2bids.utils.tools import dcm2niix_version, check_latest
from dcm2bids.utils.logger import setup_logging
from dcm2bids.utils.args import assert_dirs_empty
from dcm2bids.version import __version__
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.doc,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument("-d", "--dicom_dir",
required=True, nargs="+",
help="DICOM files directory.")
p.add_argument("-o", "--output_dir",
required=False,
default=Path(DEFAULT.output_dir) / DEFAULT.tmp_dir_name /
DEFAULT.helper_dir,
help="Output directory. (Default: [%(default)s]")
p.add_argument("-n", "--nest",
nargs="?", const=True, default=False, required=False,
help="Nest a directory in <output_dir>. Useful if many helper "
"runs are needed\nto make a config file due to slight "
"variations in MRI acquisitions.\n"
"Defaults to DICOM_DIR if no name is provided.\n"
"(Default: [%(default)s])")
p.add_argument('--force', '--force_dcm2bids',
dest='overwrite', action='store_true',
help='Force command to overwrite existing output files.')
p.add_argument("-l", "--log_level",
required=False,
default=DEFAULT.cli_log_level,
choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
help="Set logging level to the console. [%(default)s]")
return p
def main():
"""Let's go"""
parser = _build_arg_parser()
args = parser.parse_args()
out_dir = Path(args.output_dir)
log_file = (Path(DEFAULT.output_dir)
/ DEFAULT.tmp_dir_name
/ "log"
/ f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")
if args.nest:
if isinstance(args.nest, str):
log_file = Path(
str(log_file).replace("helper_",
f"helper_{args.nest.replace(os.path.sep, '-')}_"))
out_dir = out_dir / args.nest
else:
log_file = Path(str(log_file).replace(
"helper_", f"helper_{args.dicom_dir[0].replace(os.path.sep, '-')}_")
)
out_dir = out_dir / args.dicom_dir[0]
log_file.parent.mkdir(parents=True, exist_ok=True)
setup_logging(args.log_level, log_file)
logger = logging.getLogger(__name__)
logger.info("--- dcm2bids_helper start ---")
logger.info("Running the following command: " + " ".join(sys.argv))
logger.info("OS version: %s", platform.platform())
logger.info("Python version: %s", sys.version.replace("\n", ""))
logger.info(f"dcm2bids version: { __version__}")
logger.info(f"dcm2niix version: {dcm2niix_version()}")
logger.info("Checking for software update")
check_latest("dcm2bids")
check_latest("dcm2niix")
assert_dirs_empty(parser, args, out_dir)
app = Dcm2niixGen(dicom_dirs=args.dicom_dir, bids_dir=out_dir, helper=True)
rsl = app.run(force=args.overwrite)
logger.info(f"Helper files in: {out_dir}\n")
logger.info(f"Log file saved at {log_file}")
logger.info("--- dcm2bids_helper end ---")
return rsl
if __name__ == "__main__":
main()
|