xenon-oscillation-imaging-python/script_process_batch.py at main · junlanlu/xenon-oscillation-imaging-python · GitHub

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
"""Scripts to run oscillation mapping pipeline in batches."""
import glob
import importlib
import logging
import os
import pdb

from absl import app, flags

from main import oscillation_mapping_readin, oscillation_mapping_reconstruction

FLAGS = flags.FLAGS

flags.DEFINE_string("cohort", "healthy", "cohort folder name in config folder")

CONFIG_PATH = "config/"


def main(argv):
    """Run the oscillation imaging pipeline in multiple subjects.

    Import the config file and run the oscillation imaging pipeline on all
    subjects specified in by the cohort flag.
    """
    if FLAGS.cohort == "healthy":
        subjects = glob.glob(os.path.join(CONFIG_PATH, "healthy", "*py"))
    elif FLAGS.cohort == "cteph":
        subjects = glob.glob(os.path.join(CONFIG_PATH, "cteph", "*py"))
    elif FLAGS.cohort == "ild":
        subjects = glob.glob(os.path.join(CONFIG_PATH, "ild", "*py"))
    elif FLAGS.cohort == "tyvaso":
        subjects = glob.glob(os.path.join(CONFIG_PATH, "tyvaso", "*py"))
    elif FLAGS.cohort == "jupiter":
        subjects = glob.glob(os.path.join(CONFIG_PATH, "jupiter", "*py"))
    elif FLAGS.cohort == "all":
        subjects = glob.glob(os.path.join(CONFIG_PATH, "healthy", "*py"))
        subjects += glob.glob(os.path.join(CONFIG_PATH, "cteph", "*py"))
        subjects += glob.glob(os.path.join(CONFIG_PATH, "ild", "*py"))
        subjects += glob.glob(os.path.join(CONFIG_PATH, "tyvaso", "*py"))
    elif "-" in FLAGS.cohort:
        cohorts = FLAGS.cohort.split("-")
        subjects = []
        for cohort in cohorts:
            if cohort == "healthy":
                subjects += glob.glob(os.path.join(CONFIG_PATH, "healthy", "*py"))
            elif cohort == "cteph":
                subjects += glob.glob(os.path.join(CONFIG_PATH, "cteph", "*py"))
            elif cohort == "ild":
                subjects += glob.glob(os.path.join(CONFIG_PATH, "ild", "*py"))
            elif cohort == "tyvaso":
                subjects += glob.glob(os.path.join(CONFIG_PATH, "tyvaso", "*py"))
            else:
                raise ValueError("Invalid cohort name")
    else:
        raise ValueError("Invalid cohort name")

    for subject in subjects:
        config_obj = importlib.import_module(
            name=subject[:-3].replace("/", "."), package=None
        )
        config = config_obj.get_config()
        logging.info("Processing subject: %s", config.subject_id)
        if FLAGS.force_recon:
            oscillation_mapping_reconstruction(config)
        elif FLAGS.force_readin:
            oscillation_mapping_readin(config)
        elif config.processes.oscillation_mapping_reconstruction:
            oscillation_mapping_reconstruction(config)
        elif config.processes.oscillation_mapping_readin:
            oscillation_mapping_readin(config)
        else:
            pass


if __name__ == "__main__":
    app.run(main)