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01bd570 | 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 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 | # Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from __future__ import annotations
from collections.abc import Callable
from monai.handlers.ignite_metric import IgniteMetricHandler
from monai.metrics import MetricsReloadedBinary, MetricsReloadedCategorical
from monai.utils.enums import MetricReduction
class MetricsReloadedBinaryHandler(IgniteMetricHandler):
"""
Handler of MetricsReloadedBinary, which wraps the binary pairwise metrics of MetricsReloaded.
"""
def __init__(
self,
metric_name: str,
include_background: bool = True,
reduction: MetricReduction | str = MetricReduction.MEAN,
get_not_nans: bool = False,
output_transform: Callable = lambda x: x,
save_details: bool = True,
) -> None:
"""
Args:
metric_name: Name of a binary metric from the MetricsReloaded package.
include_background: whether to include computation on the first channel of
the predicted output. Defaults to ``True``.
reduction: define mode of reduction to the metrics, will only apply reduction on `not-nan` values,
available reduction modes: {``"none"``, ``"mean"``, ``"sum"``, ``"mean_batch"``, ``"sum_batch"``,
``"mean_channel"``, ``"sum_channel"``}, default to ``"mean"``. if "none", will not do reduction.
get_not_nans: whether to return the `not_nans` count, if True, aggregate() returns (metric, not_nans).
Here `not_nans` count the number of not nans for the metric,
thus its shape equals to the shape of the metric.
output_transform: callable to extract `y_pred` and `y` from `ignite.engine.state.output` then
construct `(y_pred, y)` pair, where `y_pred` and `y` can be `batch-first` Tensors or
lists of `channel-first` Tensors. the form of `(y_pred, y)` is required by the `update()`.
`engine.state` and `output_transform` inherit from the ignite concept:
https://pytorch.org/ignite/concepts.html#state, explanation and usage example are in the tutorial:
https://github.com/Project-MONAI/tutorials/blob/master/modules/batch_output_transform.ipynb.
save_details: whether to save metric computation details per image, for example: TP/TN/FP/FN of every image.
default to True, will save to `engine.state.metric_details` dict with the metric name as key.
See also:
:py:meth:`monai.metrics.wrapper`
"""
metric_fn = MetricsReloadedBinary(
metric_name=metric_name,
include_background=include_background,
reduction=reduction,
get_not_nans=get_not_nans,
)
super().__init__(metric_fn=metric_fn, output_transform=output_transform, save_details=save_details)
class MetricsReloadedCategoricalHandler(IgniteMetricHandler):
"""
Handler of MetricsReloadedCategorical, which wraps the categorical pairwise metrics of MetricsReloaded.
"""
def __init__(
self,
metric_name: str,
include_background: bool = True,
reduction: MetricReduction | str = MetricReduction.MEAN,
get_not_nans: bool = False,
smooth_dr: float = 1e-5,
output_transform: Callable = lambda x: x,
save_details: bool = True,
) -> None:
"""
Args:
metric_name: Name of a categorical metric from the MetricsReloaded package.
include_background: whether to include computation on the first channel of
the predicted output. Defaults to ``True``.
reduction: define mode of reduction to the metrics, will only apply reduction on `not-nan` values,
available reduction modes: {``"none"``, ``"mean"``, ``"sum"``, ``"mean_batch"``, ``"sum_batch"``,
``"mean_channel"``, ``"sum_channel"``}, default to ``"mean"``. if "none", will not do reduction.
get_not_nans: whether to return the `not_nans` count, if True, aggregate() returns (metric, not_nans).
Here `not_nans` count the number of not nans for the metric,
thus its shape equals to the shape of the metric.
smooth_dr: a small constant added to the denominator to avoid nan. OBS: should be greater than zero.
output_transform: callable to extract `y_pred` and `y` from `ignite.engine.state.output` then
construct `(y_pred, y)` pair, where `y_pred` and `y` can be `batch-first` Tensors or
lists of `channel-first` Tensors. the form of `(y_pred, y)` is required by the `update()`.
`engine.state` and `output_transform` inherit from the ignite concept:
https://pytorch.org/ignite/concepts.html#state, explanation and usage example are in the tutorial:
https://github.com/Project-MONAI/tutorials/blob/master/modules/batch_output_transform.ipynb.
save_details: whether to save metric computation details per image, for example: TP/TN/FP/FN of every image.
default to True, will save to `engine.state.metric_details` dict with the metric name as key.
See also:
:py:meth:`monai.metrics.wrapper`
"""
metric_fn = MetricsReloadedCategorical(
metric_name=metric_name,
include_background=include_background,
reduction=reduction,
get_not_nans=get_not_nans,
smooth_dr=smooth_dr,
)
super().__init__(metric_fn=metric_fn, output_transform=output_transform, save_details=save_details)
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