Source code for dosma.msk.knee

"""
Command line interface declaration for knee-related analyses

@author: Arjun Desai
        (C) Stanford University, 2019
"""

import logging
import uuid

from dosma.defaults import preferences
from dosma.quant_vals import QuantitativeValueType as QV
from dosma.tissues import FemoralCartilage, Meniscus, PatellarCartilage, TibialCartilage

KNEE_KEY = "knee"
MEDIAL_TO_LATERAL_KEY = "ml"
TISSUES_KEY = "tissues"
LOAD_KEY = "load"
SAVE_KEY = "save"
PID_KEY = "pid"

SUPPORTED_TISSUES = [FemoralCartilage, Meniscus, TibialCartilage, PatellarCartilage]
SUPPORTED_QUANTITATIVE_VALUES = [QV.T2, QV.T1_RHO, QV.T2_STAR]


def knee_parser(base_parser):
    """Parse command line input related to knee

    :param base_parser: the base parser to add knee subcommand to
    """
    parser_tissue = base_parser.add_parser(
        KNEE_KEY, help="calculate/analyze quantitative data for knee"
    )

    parser_tissue.add_argument(
        "--%s" % MEDIAL_TO_LATERAL_KEY,
        action="store_const",
        const=True,
        default=False,
        help="defines slices in sagittal direction going from medial -> lateral",
    )

    parser_tissue.add_argument(
        "--%s" % PID_KEY, nargs="?", default=str(uuid.uuid4()), help="specify pid"
    )

    for tissue in SUPPORTED_TISSUES:
        parser_tissue.add_argument(
            "--%s" % tissue.STR_ID,
            action="store_const",
            default=False,
            const=True,
            help="analyze %s" % tissue.FULL_NAME,
        )

    qvs_dict = dict()
    for qv in SUPPORTED_QUANTITATIVE_VALUES:
        qv_name = qv.name.lower()
        qvs_dict[qv_name] = qv
        parser_tissue.add_argument(
            "--%s" % qv_name,
            action="store_const",
            const=True,
            default=False,
            help="quantify %s" % qv_name,
        )

    parser_tissue.set_defaults(func=handle_knee)


def handle_knee(vargin):
    """Handle parsing command-line input for knee subcommand
    :param vargin:
    :return:
    """
    tissues = vargin[TISSUES_KEY]
    load_path = vargin[LOAD_KEY]
    medial_to_lateral = vargin[MEDIAL_TO_LATERAL_KEY]
    pid = vargin[PID_KEY]

    if tissues is None or len(tissues) == 0:
        logging.info("Computing for all supported knee tissues...")
        tissues = []
        for t in SUPPORTED_TISSUES:
            tissues.append(t())

    # Get all supported quantitative values
    qvs = []
    for qv in SUPPORTED_QUANTITATIVE_VALUES:
        if vargin[qv.name.lower()]:
            qvs.append(qv)

    if len(qvs) == 0:
        logging.info("Computing for all supported quantitative values...")
        qvs = SUPPORTED_QUANTITATIVE_VALUES

    for tissue in tissues:
        tissue.pid = pid
        tissue.medial_to_lateral = medial_to_lateral
        tissue.load_data(load_path)

        logging.info("")
        logging.info("==" * 40)
        logging.info(tissue.FULL_NAME)
        logging.info("==" * 40)

        for qv in qvs:
            # load file
            logging.info("Analyzing %s" % qv.name.lower())
            tissue.calc_quant_vals()

    for tissue in tissues:
        tissue.save_data(vargin[SAVE_KEY], data_format=preferences.image_data_format)

    return tissues