Source code for clinicadl.metrics.config.segmentation

from typing import Optional, Tuple

import monai
import monai.metrics
from pydantic import NonNegativeFloat, PositiveInt, field_validator

from clinicadl.losses.config.enum import Reduction
from clinicadl.utils.doc import add_suffix_to_doc
from clinicadl.utils.factories import get_defaults_from

from ..enum import Optimum
from .base import (
    DOCUMENT_EXTRA_PARAMETERS,
    MetricConfig,
    _GetNotNansConfig,
)
from .enum import (
    DistanceMetric,
    WeightType,
)

__all__ = [
    "DiceMetricConfig",
    "MeanIoUConfig",
    "GeneralizedDiceScoreConfig",
    "SurfaceDistanceMetricConfig",
    "HausdorffDistanceMetricConfig",
    "SurfaceDiceMetricConfig",
]

DICE_MONAI_DEFAULTS = get_defaults_from(monai.metrics.DiceMetric)
MEAN_IOU_MONAI_DEFAULTS = get_defaults_from(monai.metrics.MeanIoU)
GENERALIZED_DICE_SCORE_MONAI_DEFAULTS = get_defaults_from(
    monai.metrics.GeneralizedDiceScore
)
SURFACE_DISTANCE_METRIC_MONAI_DEFAULTS = get_defaults_from(
    monai.metrics.SurfaceDistanceMetric
)
HAUSDORFF_DISTANCE_METRIC_MONAI_DEFAULTS = get_defaults_from(
    monai.metrics.HausdorffDistanceMetric
)
SURFACE_DICE_METRIC_MONAI_DEFAULTS = get_defaults_from(monai.metrics.SurfaceDiceMetric)



[docs]
@add_suffix_to_doc(DOCUMENT_EXTRA_PARAMETERS)
class DiceMetricConfig(MetricConfig, _GetNotNansConfig):
    """
    Config class for :py:class:`monai.metrics.DiceMetric`.

    ``get_not_nans`` is not supported currently.
    """

    include_background: bool = DICE_MONAI_DEFAULTS["include_background"]
    reduction: Reduction = DICE_MONAI_DEFAULTS["reduction"]
    ignore_empty: bool = DICE_MONAI_DEFAULTS["ignore_empty"]
    num_classes: Optional[PositiveInt] = DICE_MONAI_DEFAULTS["num_classes"]
    return_with_label: bool = DICE_MONAI_DEFAULTS["return_with_label"]

    @staticmethod
    def optimum() -> Optimum:
        """The optimum of the metric."""
        return Optimum.MAX

    @field_validator("return_with_label", mode="after")
    @classmethod
    def validator_return_with_label(cls, v):
        assert (
            not v
        ), "'return_with_label' not supported in ClinicaDL. Please leave to False."

        return v




[docs]
@add_suffix_to_doc(DOCUMENT_EXTRA_PARAMETERS)
class MeanIoUConfig(MetricConfig, _GetNotNansConfig):
    """
    Config class for :py:class:`monai.metrics.MeanIoU`.

    ``get_not_nans`` is not supported currently.
    """

    include_background: bool = MEAN_IOU_MONAI_DEFAULTS["include_background"]
    reduction: Reduction = MEAN_IOU_MONAI_DEFAULTS["reduction"]
    ignore_empty: bool = MEAN_IOU_MONAI_DEFAULTS["ignore_empty"]

    @staticmethod
    def optimum() -> Optimum:
        """The optimum of the metric."""
        return Optimum.MAX




[docs]
@add_suffix_to_doc(DOCUMENT_EXTRA_PARAMETERS)
class GeneralizedDiceScoreConfig(MetricConfig):
    """
    Config class for :py:class:`monai.metrics.GeneralizedDiceScore`.
    """

    include_background: bool = GENERALIZED_DICE_SCORE_MONAI_DEFAULTS[
        "include_background"
    ]
    reduction: Reduction = GENERALIZED_DICE_SCORE_MONAI_DEFAULTS["reduction"]
    weight_type: WeightType = GENERALIZED_DICE_SCORE_MONAI_DEFAULTS["weight_type"]

    @staticmethod
    def optimum() -> Optimum:
        """The optimum of the metric."""
        return Optimum.MAX




[docs]
@add_suffix_to_doc(DOCUMENT_EXTRA_PARAMETERS)
class SurfaceDistanceMetricConfig(MetricConfig, _GetNotNansConfig):
    """
    Config class for :py:class:`monai.metrics.SurfaceDistanceMetric`.

    ``get_not_nans`` is not supported currently.
    """

    include_background: bool = SURFACE_DISTANCE_METRIC_MONAI_DEFAULTS[
        "include_background"
    ]
    symmetric: bool = SURFACE_DISTANCE_METRIC_MONAI_DEFAULTS["symmetric"]
    distance_metric: DistanceMetric = SURFACE_DISTANCE_METRIC_MONAI_DEFAULTS[
        "distance_metric"
    ]
    reduction: Reduction = SURFACE_DISTANCE_METRIC_MONAI_DEFAULTS["reduction"]

    @staticmethod
    def optimum() -> Optimum:
        """The optimum of the metric."""
        return Optimum.MIN




[docs]
@add_suffix_to_doc(DOCUMENT_EXTRA_PARAMETERS)
class HausdorffDistanceMetricConfig(MetricConfig, _GetNotNansConfig):
    """
    Config class for :py:class:`monai.metrics.HausdorffDistanceMetric`.

    ``get_not_nans`` is not supported currently.
    """

    include_background: bool = HAUSDORFF_DISTANCE_METRIC_MONAI_DEFAULTS[
        "include_background"
    ]
    distance_metric: DistanceMetric = HAUSDORFF_DISTANCE_METRIC_MONAI_DEFAULTS[
        "distance_metric"
    ]
    percentile: Optional[NonNegativeFloat] = HAUSDORFF_DISTANCE_METRIC_MONAI_DEFAULTS[
        "percentile"
    ]
    directed: bool = HAUSDORFF_DISTANCE_METRIC_MONAI_DEFAULTS["directed"]
    reduction: Reduction = HAUSDORFF_DISTANCE_METRIC_MONAI_DEFAULTS["reduction"]

    @staticmethod
    def optimum() -> Optimum:
        """The optimum of the metric."""
        return Optimum.MIN

    @field_validator("percentile", mode="after")
    @classmethod
    def validator_percentile(cls, v):
        if isinstance(v, float):
            assert (
                0 <= v <= 100
            ), f"percentile must be between 0 and 100. You passed: {v}."

        return v




[docs]
@add_suffix_to_doc(DOCUMENT_EXTRA_PARAMETERS)
class SurfaceDiceMetricConfig(MetricConfig, _GetNotNansConfig):
    """
    Config class for :py:class:`monai.metrics.SurfaceDiceMetric`.

    ``get_not_nans`` is not supported currently.
    """

    class_thresholds: Tuple[NonNegativeFloat, ...]
    include_background: bool = SURFACE_DICE_METRIC_MONAI_DEFAULTS["include_background"]
    distance_metric: DistanceMetric = SURFACE_DICE_METRIC_MONAI_DEFAULTS[
        "distance_metric"
    ]
    reduction: Reduction = SURFACE_DICE_METRIC_MONAI_DEFAULTS["reduction"]
    use_subvoxels: bool = SURFACE_DICE_METRIC_MONAI_DEFAULTS["use_subvoxels"]

    @staticmethod
    def optimum() -> Optimum:
        """The optimum of the metric."""
        return Optimum.MAX