"""

Command line interface declaration for knee-related analyses

@author: Arjun Desai

        (C) Stanford University, 2019

"""

import logging

import uuid

from dosma.core.quant_vals import QuantitativeValueType as QV

from dosma.defaults import preferences

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]

_logger = logging.getLogger(__name__)

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 = {}

    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:

        _logger.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:

        _logger.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)

        _logger.info("")

        _logger.info("==" * 40)

        _logger.info(tissue.FULL_NAME)

        _logger.info("==" * 40)

        for qv in qvs:

            # load file

            _logger.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