pymedphys_tool

#!/usr/bin/env python3

"""
The script exports of Pinnacle data from the given Patient sources.
It takes 2 arguments:

    :input_path: (str) - The path to folder of Patient source files;
    :output_directory: (str) - The output files of this tool for Patient;

Settings:

   ERROR_LOG_FILE_LOCATION - location of errors log file;

Usage:

    $ python pymedphys_tool.py Patient_15000/ results_for_patient_15000/

    On any error appear, it will quietly finish without interrupting. Output
    directory will be renamed to `results_for_patient_15000_failed_20221006_032145`
    and there will be added a proper record in your error log file.
    Both success and failure cases are accompanied by information in output.
    This info does not track.


Built & tested on Macos in python3.10 environment.
"""
import datetime
import logging
import os
import sys
import traceback

from pymedphys._experimental.pinnacle.pinnacle_cli import export_cli


ERROR_LOG_FILE_LOCATION: str = "errors.log"


class Args:
    """
    Mock arguments required by the lib
    """

    def __init__(self, input_path, output_path):
        self.input_path = input_path
        self.output_directory = output_path
        self.modality = ["CT", "RTSTRUCT", "RTDOSE", "RTPLAN"]
        self.plan = None
        self.trial = None
        self.list = []
        self.image = None
        self.uid_prefix = None
        self.roiskip = None
        self.mrn = None
        self.verbose = False


def run_tool(args):
    logger = logging.getLogger(__name__)
    fh = logging.FileHandler(ERROR_LOG_FILE_LOCATION)
    fh.setLevel(logging.DEBUG)
    err_string = (f"%(asctime)s\t%(levelname)s\tinput_path={args.input_path}\t"
                  f"output_directory={args.output_directory}\t%(message)s")
    fh.setFormatter(logging.Formatter(err_string))
    logger.addHandler(fh)

    try:
        export_cli(args)
    except Exception:  # catch any error
        timestamp = datetime.datetime.now().strftime("%Y%m%d_%H%M%S")
        logger.error(traceback.format_exc())

        failed_folder_name = f"{args.output_directory}_failed_{timestamp}"
        os.rename(args.output_directory, failed_folder_name)


if __name__ == "__main__":
    run_tool(Args(input_path=sys.argv[1], output_path=sys.argv[2]))