Update example config

example_data/config.yaml

@@ -138,27 +138,49 @@ train:
     name: csv
 
   validation:
-    metrics:
+    tasks:
-      - name: detection_ap
+      - name: sound_event_detection
-      - name: detection_roc_auc
+        metrics:
-      - name: classification_ap
+          - name: average_precision
-      - name: classification_roc_auc
+      - name: sound_event_classification
-      - name: top_class_ap
+        metrics:
-      - name: classification_balanced_accuracy
+          - name: average_precision
-      - name: clip_ap
-      - name: clip_roc_auc
 
 evaluation:
-  match_strategy:
+  tasks:
-    name: start_time_match
+    - name: sound_event_detection
-    distance_threshold: 0.01
+      metrics:
-  metrics:
+        - name: average_precision
-    - name: classification_ap
+        - name: roc_auc
-    - name: detection_ap
+      plots:
-  plots:
+        - name: pr_curve
-    - name: example_gallery
+        - name: score_distribution
-    - name: example_clip
+        - name: example_detection
-    - name: detection_pr_curve
+    - name: sound_event_classification
-    - name: classification_pr_curves
+      metrics:
-    - name: detection_roc_curve
+        - name: average_precision
-    - name: classification_roc_curves
+        - name: roc_auc
+      plots:
+        - name: pr_curve
+    - name: top_class_detection
+      metrics:
+        - name: average_precision
+      plots:
+        - name: pr_curve
+        - name: confusion_matrix
+        - name: example_classification
+    - name: clip_detection
+      metrics:
+        - name: average_precision
+        - name: roc_auc
+      plots:
+        - name: pr_curve
+        - name: roc_curve
+        - name: score_distribution
+    - name: clip_classification
+      metrics:
+        - name: average_precision
+        - name: roc_auc
+      plots:
+        - name: pr_curve
+        - name: roc_curve

src/batdetect2/api/base.py

@@ -1,6 +1,7 @@
 from pathlib import Path
-from typing import Optional, Sequence
+from typing import List, Optional, Sequence
 
+import torch
 from soundevent import data
 
 from batdetect2.audio import build_audio_loader
@@ -8,6 +9,7 @@ from batdetect2.config import BatDetect2Config
 from batdetect2.evaluate import build_evaluator, evaluate
 from batdetect2.models import Model, build_model
 from batdetect2.postprocess import build_postprocessor
+from batdetect2.postprocess.decoding import to_raw_predictions
 from batdetect2.preprocess import build_preprocessor
 from batdetect2.targets.targets import build_targets
 from batdetect2.train import train
@@ -19,6 +21,7 @@ from batdetect2.typing import (
     PreprocessorProtocol,
     TargetProtocol,
 )
+from batdetect2.typing.postprocess import RawPrediction
 
 
 class BatDetect2API:
@@ -92,6 +95,18 @@ class BatDetect2API:
             run_name=run_name,
         )
 
+    def process_spectrogram(
+        self,
+        spec: torch.Tensor,
+        start_times: Optional[Sequence[float]] = None,
+    ) -> List[List[RawPrediction]]:
+        outputs = self.model.detector(spec)
+        clip_detections = self.postprocessor(outputs, start_times=start_times)
+        return [
+            to_raw_predictions(clip_dets.numpy(), self.targets)
+            for clip_dets in clip_detections
+        ]
+
     @classmethod
     def from_config(cls, config: BatDetect2Config):
         targets = build_targets(config=config.targets)
@@ -108,10 +123,7 @@ class BatDetect2API:
             config=config.postprocess,
         )
 
-        evaluator = build_evaluator(
+        evaluator = build_evaluator(config=config.evaluation, targets=targets)
-            config=config.evaluation,
-            targets=targets,
-        )
 
         # NOTE: Better to have a separate instance of
         # preprocessor and postprocessor as these may be moved
@@ -163,10 +175,7 @@ class BatDetect2API:
             config=config.postprocess,
         )
 
-        evaluator = build_evaluator(
+        evaluator = build_evaluator(config=config.evaluation, targets=targets)
-            config=config.evaluation,
-            targets=targets,
-        )
 
         return cls(
             config=config,

src/batdetect2/audio/clips.py

@@ -56,18 +56,16 @@ class RandomClip:
             min_sound_event_overlap=self.min_sound_event_overlap,
         )
 
-    @classmethod
+    @clipper_registry.register(RandomClipConfig)
-    def from_config(cls, config: RandomClipConfig):
+    @staticmethod
-        return cls(
+    def from_config(config: RandomClipConfig):
+        return RandomClip(
             duration=config.duration,
             max_empty=config.max_empty,
             min_sound_event_overlap=config.min_sound_event_overlap,
         )
 
 
-clipper_registry.register(RandomClipConfig, RandomClip)
-
-
 def get_subclip_annotation(
     clip_annotation: data.ClipAnnotation,
     random: bool = True,
@@ -184,13 +182,12 @@ class PaddedClip:
         )
         return clip_annotation.model_copy(update=dict(clip=clip))
 
-    @classmethod
+    @clipper_registry.register(PaddedClipConfig)
-    def from_config(cls, config: PaddedClipConfig):
+    @staticmethod
-        return cls(chunk_size=config.chunk_size)
+    def from_config(config: PaddedClipConfig):
+        return PaddedClip(chunk_size=config.chunk_size)
 
 
-clipper_registry.register(PaddedClipConfig, PaddedClip)
-
 ClipConfig = Annotated[
     Union[RandomClipConfig, PaddedClipConfig], Field(discriminator="name")
 ]

src/batdetect2/core/configs.py

@@ -53,6 +53,7 @@ class BaseConfig(BaseModel):
         """
         return yaml.dump(
             self.model_dump(
+                mode="json",
                 exclude_none=exclude_none,
                 exclude_unset=exclude_unset,
                 exclude_defaults=exclude_defaults,

src/batdetect2/core/registries.py

@@ -1,16 +1,16 @@
 import sys
-from typing import Generic, Protocol, Type, TypeVar
+from typing import Callable, Dict, Generic, Tuple, Type, TypeVar
 
 from pydantic import BaseModel
-from typing_extensions import assert_type
 
 if sys.version_info >= (3, 10):
-    from typing import ParamSpec
+    from typing import Concatenate, ParamSpec
 else:
-    from typing_extensions import ParamSpec
+    from typing_extensions import Concatenate, ParamSpec
 
 __all__ = [
     "Registry",
+    "SimpleRegistry",
 ]
 
 T_Config = TypeVar("T_Config", bound=BaseModel, contravariant=True)
@@ -18,19 +18,26 @@ T_Type = TypeVar("T_Type", covariant=True)
 P_Type = ParamSpec("P_Type")
 
 
-class LogicProtocol(Generic[T_Config, T_Type, P_Type], Protocol):
+T = TypeVar("T")
-    """A generic protocol for the logic classes."""
-
-    @classmethod
-    def from_config(
-        cls,
-        config: T_Config,
-        *args: P_Type.args,
-        **kwargs: P_Type.kwargs,
-    ) -> T_Type: ...
 
 
-T_Proto = TypeVar("T_Proto", bound=LogicProtocol)
+class SimpleRegistry(Generic[T]):
+    def __init__(self, name: str):
+        self._name = name
+        self._registry = {}
+
+    def register(self, name: str):
+        def decorator(obj: T) -> T:
+            self._registry[name] = obj
+            return obj
+
+        return decorator
+
+    def get(self, name: str) -> T:
+        return self._registry[name]
+
+    def has(self, name: str) -> bool:
+        return name in self._registry
 
 
 class Registry(Generic[T_Type, P_Type]):
@@ -38,13 +45,15 @@ class Registry(Generic[T_Type, P_Type]):
 
     def __init__(self, name: str):
         self._name = name
-        self._registry = {}
+        self._registry: Dict[
+            str, Callable[Concatenate[..., P_Type], T_Type]
+        ] = {}
+        self._config_types: Dict[str, Type[BaseModel]] = {}
 
     def register(
         self,
         config_cls: Type[T_Config],
-        logic_cls: LogicProtocol[T_Config, T_Type, P_Type],
+    ):
-    ) -> None:
         fields = config_cls.model_fields
 
         if "name" not in fields:
@@ -52,10 +61,21 @@ class Registry(Generic[T_Type, P_Type]):
 
         name = fields["name"].default
 
+        self._config_types[name] = config_cls
+
         if not isinstance(name, str):
             raise ValueError("'name' field must be a string literal.")
 
-        self._registry[name] = logic_cls
+        def decorator(
+            func: Callable[Concatenate[T_Config, P_Type], T_Type],
+        ):
+            self._registry[name] = func
+            return func
+
+        return decorator
+
+    def get_config_types(self) -> Tuple[Type[BaseModel], ...]:
+        return tuple(self._config_types.values())
 
     def build(
         self,
@@ -75,4 +95,4 @@ class Registry(Generic[T_Type, P_Type]):
                 f"No {self._name} with name '{name}' is registered."
             )
 
-        return self._registry[name].from_config(config, *args, **kwargs)
+        return self._registry[name](config, *args, **kwargs)

src/batdetect2/data/conditions.py

@@ -10,7 +10,7 @@ from batdetect2.core.registries import Registry
 
 SoundEventCondition = Callable[[data.SoundEventAnnotation], bool]
 
-condition_registry: Registry[SoundEventCondition, []] = Registry("condition")
+conditions: Registry[SoundEventCondition, []] = Registry("condition")
 
 
 class HasTagConfig(BaseConfig):
@@ -27,12 +27,10 @@ class HasTag:
     ) -> bool:
         return self.tag in sound_event_annotation.tags
 
-    @classmethod
+    @conditions.register(HasTagConfig)
-    def from_config(cls, config: HasTagConfig):
+    @staticmethod
-        return cls(tag=config.tag)
+    def from_config(config: HasTagConfig):
-
+        return HasTag(tag=config.tag)
-
-condition_registry.register(HasTagConfig, HasTag)
 
 
 class HasAllTagsConfig(BaseConfig):
@@ -52,12 +50,10 @@ class HasAllTags:
     ) -> bool:
         return self.tags.issubset(sound_event_annotation.tags)
 
-    @classmethod
+    @conditions.register(HasAllTagsConfig)
-    def from_config(cls, config: HasAllTagsConfig):
+    @staticmethod
-        return cls(tags=config.tags)
+    def from_config(config: HasAllTagsConfig):
-
+        return HasAllTags(tags=config.tags)
-
-condition_registry.register(HasAllTagsConfig, HasAllTags)
 
 
 class HasAnyTagConfig(BaseConfig):
@@ -77,13 +73,12 @@ class HasAnyTag:
     ) -> bool:
         return bool(self.tags.intersection(sound_event_annotation.tags))
 
-    @classmethod
+    @conditions.register(HasAnyTagConfig)
-    def from_config(cls, config: HasAnyTagConfig):
+    @staticmethod
-        return cls(tags=config.tags)
+    def from_config(config: HasAnyTagConfig):
+        return HasAnyTag(tags=config.tags)
 
 
-condition_registry.register(HasAnyTagConfig, HasAnyTag)
-
 Operator = Literal["gt", "gte", "lt", "lte", "eq"]
 
 
@@ -134,12 +129,10 @@ class Duration:
 
         return self._comparator(duration)
 
-    @classmethod
+    @conditions.register(DurationConfig)
-    def from_config(cls, config: DurationConfig):
+    @staticmethod
-        return cls(operator=config.operator, seconds=config.seconds)
+    def from_config(config: DurationConfig):
-
+        return Duration(operator=config.operator, seconds=config.seconds)
-
-condition_registry.register(DurationConfig, Duration)
 
 
 class FrequencyConfig(BaseConfig):
@@ -181,18 +174,16 @@ class Frequency:
 
         return self._comparator(high_freq)
 
-    @classmethod
+    @conditions.register(FrequencyConfig)
-    def from_config(cls, config: FrequencyConfig):
+    @staticmethod
-        return cls(
+    def from_config(config: FrequencyConfig):
+        return Frequency(
             operator=config.operator,
             boundary=config.boundary,
             hertz=config.hertz,
         )
 
 
-condition_registry.register(FrequencyConfig, Frequency)
-
-
 class AllOfConfig(BaseConfig):
     name: Literal["all_of"] = "all_of"
     conditions: Sequence["SoundEventConditionConfig"]
@@ -207,15 +198,13 @@ class AllOf:
     ) -> bool:
         return all(c(sound_event_annotation) for c in self.conditions)
 
-    @classmethod
+    @conditions.register(AllOfConfig)
-    def from_config(cls, config: AllOfConfig):
+    @staticmethod
+    def from_config(config: AllOfConfig):
         conditions = [
             build_sound_event_condition(cond) for cond in config.conditions
         ]
-        return cls(conditions)
+        return AllOf(conditions)
-
-
-condition_registry.register(AllOfConfig, AllOf)
 
 
 class AnyOfConfig(BaseConfig):
@@ -232,15 +221,13 @@ class AnyOf:
     ) -> bool:
         return any(c(sound_event_annotation) for c in self.conditions)
 
-    @classmethod
+    @conditions.register(AnyOfConfig)
-    def from_config(cls, config: AnyOfConfig):
+    @staticmethod
+    def from_config(config: AnyOfConfig):
         conditions = [
             build_sound_event_condition(cond) for cond in config.conditions
         ]
-        return cls(conditions)
+        return AnyOf(conditions)
-
-
-condition_registry.register(AnyOfConfig, AnyOf)
 
 
 class NotConfig(BaseConfig):
@@ -257,14 +244,13 @@ class Not:
     ) -> bool:
         return not self.condition(sound_event_annotation)
 
-    @classmethod
+    @conditions.register(NotConfig)
-    def from_config(cls, config: NotConfig):
+    @staticmethod
+    def from_config(config: NotConfig):
         condition = build_sound_event_condition(config.condition)
-        return cls(condition)
+        return Not(condition)
 
 
-condition_registry.register(NotConfig, Not)
-
 SoundEventConditionConfig = Annotated[
     Union[
         HasTagConfig,
@@ -283,7 +269,7 @@ SoundEventConditionConfig = Annotated[
 def build_sound_event_condition(
     config: SoundEventConditionConfig,
 ) -> SoundEventCondition:
-    return condition_registry.build(config)
+    return conditions.build(config)
 
 
 def filter_clip_annotation(

src/batdetect2/data/transforms.py

@@ -17,7 +17,7 @@ SoundEventTransform = Callable[
     data.SoundEventAnnotation,
 ]
 
-transform_registry: Registry[SoundEventTransform, []] = Registry("transform")
+transforms: Registry[SoundEventTransform, []] = Registry("transform")
 
 
 class SetFrequencyBoundConfig(BaseConfig):
@@ -63,12 +63,10 @@ class SetFrequencyBound:
             update=dict(sound_event=sound_event)
         )
 
-    @classmethod
+    @transforms.register(SetFrequencyBoundConfig)
-    def from_config(cls, config: SetFrequencyBoundConfig):
+    @staticmethod
-        return cls(hertz=config.hertz, boundary=config.boundary)
+    def from_config(config: SetFrequencyBoundConfig):
-
+        return SetFrequencyBound(hertz=config.hertz, boundary=config.boundary)
-
-transform_registry.register(SetFrequencyBoundConfig, SetFrequencyBound)
 
 
 class ApplyIfConfig(BaseConfig):
@@ -95,14 +93,12 @@ class ApplyIf:
 
         return self.transform(sound_event_annotation)
 
-    @classmethod
+    @transforms.register(ApplyIfConfig)
-    def from_config(cls, config: ApplyIfConfig):
+    @staticmethod
+    def from_config(config: ApplyIfConfig):
         transform = build_sound_event_transform(config.transform)
         condition = build_sound_event_condition(config.condition)
-        return cls(condition=condition, transform=transform)
+        return ApplyIf(condition=condition, transform=transform)
-
-
-transform_registry.register(ApplyIfConfig, ApplyIf)
 
 
 class ReplaceTagConfig(BaseConfig):
@@ -134,12 +130,12 @@ class ReplaceTag:
 
         return sound_event_annotation.model_copy(update=dict(tags=tags))
 
-    @classmethod
+    @transforms.register(ReplaceTagConfig)
-    def from_config(cls, config: ReplaceTagConfig):
+    @staticmethod
-        return cls(original=config.original, replacement=config.replacement)
+    def from_config(config: ReplaceTagConfig):
-
+        return ReplaceTag(
-
+            original=config.original, replacement=config.replacement
-transform_registry.register(ReplaceTagConfig, ReplaceTag)
+        )
 
 
 class MapTagValueConfig(BaseConfig):
@@ -189,18 +185,16 @@ class MapTagValue:
 
         return sound_event_annotation.model_copy(update=dict(tags=tags))
 
-    @classmethod
+    @transforms.register(MapTagValueConfig)
-    def from_config(cls, config: MapTagValueConfig):
+    @staticmethod
-        return cls(
+    def from_config(config: MapTagValueConfig):
+        return MapTagValue(
             tag_key=config.tag_key,
             value_mapping=config.value_mapping,
             target_key=config.target_key,
         )
 
 
-transform_registry.register(MapTagValueConfig, MapTagValue)
-
-
 class ApplyAllConfig(BaseConfig):
     name: Literal["apply_all"] = "apply_all"
     steps: List["SoundEventTransformConfig"] = Field(default_factory=list)
@@ -219,14 +213,13 @@ class ApplyAll:
 
         return sound_event_annotation
 
-    @classmethod
+    @transforms.register(ApplyAllConfig)
-    def from_config(cls, config: ApplyAllConfig):
+    @staticmethod
+    def from_config(config: ApplyAllConfig):
         steps = [build_sound_event_transform(step) for step in config.steps]
-        return cls(steps)
+        return ApplyAll(steps)
 
 
-transform_registry.register(ApplyAllConfig, ApplyAll)
-
 SoundEventTransformConfig = Annotated[
     Union[
         SetFrequencyBoundConfig,
@@ -242,7 +235,7 @@ SoundEventTransformConfig = Annotated[
 def build_sound_event_transform(
     config: SoundEventTransformConfig,
 ) -> SoundEventTransform:
-    return transform_registry.build(config)
+    return transforms.build(config)
 
 
 def transform_clip_annotation(

src/batdetect2/evaluate/__init__.py

@@ -1,11 +1,14 @@
 from batdetect2.evaluate.config import EvaluationConfig, load_evaluation_config
 from batdetect2.evaluate.evaluate import evaluate
 from batdetect2.evaluate.evaluator import Evaluator, build_evaluator
+from batdetect2.evaluate.tasks import TaskConfig, build_task
 
 __all__ = [
     "EvaluationConfig",
-    "load_evaluation_config",
-    "evaluate",
     "Evaluator",
+    "TaskConfig",
     "build_evaluator",
+    "build_task",
+    "evaluate",
+    "load_evaluation_config",
 ]

src/batdetect2/evaluate/affinity.py

@@ -3,6 +3,7 @@ from typing import Annotated, Literal, Optional, Union
 from pydantic import Field
 from soundevent import data
 from soundevent.evaluation import compute_affinity
+from soundevent.geometry import compute_interval_overlap
 
 from batdetect2.core.configs import BaseConfig
 from batdetect2.core.registries import Registry
@@ -27,12 +28,10 @@ class TimeAffinity(AffinityFunction):
             geometry1, geometry2, time_buffer=self.time_buffer
         )
 
-    @classmethod
+    @affinity_functions.register(TimeAffinityConfig)
-    def from_config(cls, config: TimeAffinityConfig):
+    @staticmethod
-        return cls(time_buffer=config.time_buffer)
+    def from_config(config: TimeAffinityConfig):
-
+        return TimeAffinity(time_buffer=config.time_buffer)
-
-affinity_functions.register(TimeAffinityConfig, TimeAffinity)
 
 
 def compute_timestamp_affinity(
@@ -73,12 +72,10 @@ class IntervalIOU(AffinityFunction):
             time_buffer=self.time_buffer,
         )
 
-    @classmethod
+    @affinity_functions.register(IntervalIOUConfig)
-    def from_config(cls, config: IntervalIOUConfig):
+    @staticmethod
-        return cls(time_buffer=config.time_buffer)
+    def from_config(config: IntervalIOUConfig):
-
+        return IntervalIOU(time_buffer=config.time_buffer)
-
-affinity_functions.register(IntervalIOUConfig, IntervalIOU)
 
 
 def compute_interval_iou(
@@ -97,9 +94,11 @@ def compute_interval_iou(
     end_time1 += time_buffer
     end_time2 += time_buffer
 
-    intersection = max(
+    intersection = compute_interval_overlap(
-        0, min(end_time1, end_time2) - max(start_time1, start_time2)
+        (start_time1, end_time1),
+        (start_time2, end_time2),
     )
+
     union = (
         (end_time1 - start_time1) + (end_time2 - start_time2) - intersection
     )
@@ -110,6 +109,86 @@ def compute_interval_iou(
     return intersection / union
 
 
+class BBoxIOUConfig(BaseConfig):
+    name: Literal["bbox_iou"] = "bbox_iou"
+    time_buffer: float = 0.01
+    freq_buffer: float = 1000
+
+
+class BBoxIOU(AffinityFunction):
+    def __init__(self, time_buffer: float, freq_buffer: float):
+        self.time_buffer = time_buffer
+        self.freq_buffer = freq_buffer
+
+    def __call__(self, geometry1: data.Geometry, geometry2: data.Geometry):
+        if not isinstance(geometry1, data.BoundingBox):
+            raise TypeError(
+                f"Expected geometry1 to be a BoundingBox, got {type(geometry1)}"
+            )
+
+        if not isinstance(geometry2, data.BoundingBox):
+            raise TypeError(
+                f"Expected geometry2 to be a BoundingBox, got {type(geometry2)}"
+            )
+        return bbox_iou(
+            geometry1,
+            geometry2,
+            time_buffer=self.time_buffer,
+            freq_buffer=self.freq_buffer,
+        )
+
+    @affinity_functions.register(BBoxIOUConfig)
+    @staticmethod
+    def from_config(config: BBoxIOUConfig):
+        return BBoxIOU(
+            time_buffer=config.time_buffer,
+            freq_buffer=config.freq_buffer,
+        )
+
+
+def bbox_iou(
+    geometry1: data.BoundingBox,
+    geometry2: data.BoundingBox,
+    time_buffer: float = 0.01,
+    freq_buffer: float = 1000,
+) -> float:
+    start_time1, low_freq1, end_time1, high_freq1 = geometry1.coordinates
+    start_time2, low_freq2, end_time2, high_freq2 = geometry2.coordinates
+
+    start_time1 -= time_buffer
+    start_time2 -= time_buffer
+    end_time1 += time_buffer
+    end_time2 += time_buffer
+
+    low_freq1 -= freq_buffer
+    low_freq2 -= freq_buffer
+    high_freq1 += freq_buffer
+    high_freq2 += freq_buffer
+
+    time_intersection = compute_interval_overlap(
+        (start_time1, end_time1),
+        (start_time2, end_time2),
+    )
+
+    freq_intersection = max(
+        0,
+        min(high_freq1, high_freq2) - max(low_freq1, low_freq2),
+    )
+
+    intersection = time_intersection * freq_intersection
+
+    if intersection == 0:
+        return 0
+
+    union = (
+        (end_time1 - start_time1) * (high_freq1 - low_freq1)
+        + (end_time2 - start_time2) * (high_freq2 - low_freq2)
+        - intersection
+    )
+
+    return intersection / union
+
+
 class GeometricIOUConfig(BaseConfig):
     name: Literal["geometric_iou"] = "geometric_iou"
     time_buffer: float = 0.01
@@ -127,17 +206,17 @@ class GeometricIOU(AffinityFunction):
             time_buffer=self.time_buffer,
         )
 
-    @classmethod
+    @affinity_functions.register(GeometricIOUConfig)
-    def from_config(cls, config: GeometricIOUConfig):
+    @staticmethod
-        return cls(time_buffer=config.time_buffer)
+    def from_config(config: GeometricIOUConfig):
+        return GeometricIOU(time_buffer=config.time_buffer)
 
 
-affinity_functions.register(GeometricIOUConfig, GeometricIOU)
-
 AffinityConfig = Annotated[
     Union[
         TimeAffinityConfig,
         IntervalIOUConfig,
+        BBoxIOUConfig,
         GeometricIOUConfig,
     ],
     Field(discriminator="name"),

src/batdetect2/evaluate/config.py

@@ -4,13 +4,11 @@ from pydantic import Field
 from soundevent import data
 
 from batdetect2.core.configs import BaseConfig, load_config
-from batdetect2.evaluate.match import MatchConfig, StartTimeMatchConfig
+from batdetect2.evaluate.tasks import (
-from batdetect2.evaluate.metrics import (
+    TaskConfig,
-    ClassificationAPConfig,
-    DetectionAPConfig,
-    MetricConfig,
 )
-from batdetect2.evaluate.plots import PlotConfig
+from batdetect2.evaluate.tasks.classification import ClassificationTaskConfig
+from batdetect2.evaluate.tasks.detection import DetectionTaskConfig
 from batdetect2.logging import CSVLoggerConfig, LoggerConfig
 
 __all__ = [
@@ -20,15 +18,12 @@ __all__ = [
 
 
 class EvaluationConfig(BaseConfig):
-    ignore_start_end: float = 0.01
+    tasks: List[TaskConfig] = Field(
-    match_strategy: MatchConfig = Field(default_factory=StartTimeMatchConfig)
-    metrics: List[MetricConfig] = Field(
         default_factory=lambda: [
-            DetectionAPConfig(),
+            DetectionTaskConfig(),
-            ClassificationAPConfig(),
+            ClassificationTaskConfig(),
         ]
     )
-    plots: List[PlotConfig] = Field(default_factory=list)
     logger: LoggerConfig = Field(default_factory=CSVLoggerConfig)
 
 

src/batdetect2/evaluate/evaluator.py

@@ -1,23 +1,12 @@
-from typing import Dict, Iterable, List, Optional, Sequence, Tuple
+from typing import Any, Dict, Iterable, List, Optional, Sequence, Tuple, Union
 
 from matplotlib.figure import Figure
 from soundevent import data
-from soundevent.geometry import compute_bounds
 
 from batdetect2.evaluate.config import EvaluationConfig
-from batdetect2.evaluate.match import build_matcher, match
+from batdetect2.evaluate.tasks import build_task
-from batdetect2.evaluate.metrics import build_metric
-from batdetect2.evaluate.plots import build_plotter
 from batdetect2.targets import build_targets
-from batdetect2.typing.evaluate import (
+from batdetect2.typing import EvaluatorProtocol, RawPrediction, TargetProtocol
-    ClipEvaluation,
-    EvaluatorProtocol,
-    MatcherProtocol,
-    MetricsProtocol,
-    PlotterProtocol,
-)
-from batdetect2.typing.postprocess import RawPrediction
-from batdetect2.typing.targets import TargetProtocol
 
 __all__ = [
     "Evaluator",
@@ -28,146 +17,51 @@ __all__ = [
 class Evaluator:
     def __init__(
         self,
-        config: EvaluationConfig,
         targets: TargetProtocol,
-        matcher: MatcherProtocol,
+        tasks: Sequence[EvaluatorProtocol],
-        metrics: List[MetricsProtocol],
-        plots: List[PlotterProtocol],
     ):
-        self.config = config
         self.targets = targets
-        self.matcher = matcher
+        self.tasks = tasks
-        self.metrics = metrics
-        self.plots = plots
-
-    def match(
-        self,
-        clip_annotation: data.ClipAnnotation,
-        predictions: Sequence[RawPrediction],
-    ) -> ClipEvaluation:
-        clip = clip_annotation.clip
-        ground_truth = [
-            sound_event
-            for sound_event in clip_annotation.sound_events
-            if self.filter_sound_event_annotations(sound_event, clip)
-        ]
-        predictions = [
-            prediction
-            for prediction in predictions
-            if self.filter_predictions(prediction, clip)
-        ]
-        return ClipEvaluation(
-            clip=clip_annotation.clip,
-            matches=match(
-                ground_truth,
-                predictions,
-                clip=clip,
-                targets=self.targets,
-                matcher=self.matcher,
-            ),
-        )
-
-    def filter_sound_event_annotations(
-        self,
-        sound_event_annotation: data.SoundEventAnnotation,
-        clip: data.Clip,
-    ) -> bool:
-        if not self.targets.filter(sound_event_annotation):
-            return False
-
-        geometry = sound_event_annotation.sound_event.geometry
-        if geometry is None:
-            return False
-
-        return is_in_bounds(
-            geometry,
-            clip,
-            self.config.ignore_start_end,
-        )
-
-    def filter_predictions(
-        self,
-        prediction: RawPrediction,
-        clip: data.Clip,
-    ) -> bool:
-        return is_in_bounds(
-            prediction.geometry,
-            clip,
-            self.config.ignore_start_end,
-        )
 
     def evaluate(
         self,
         clip_annotations: Sequence[data.ClipAnnotation],
         predictions: Sequence[Sequence[RawPrediction]],
-    ) -> List[ClipEvaluation]:
+    ) -> List[Any]:
-        if len(clip_annotations) != len(predictions):
-            raise ValueError(
-                "Number of annotated clips and sets of predictions do not match"
-            )
-
         return [
-            self.match(clip_annotation, preds)
+            task.evaluate(clip_annotations, predictions) for task in self.tasks
-            for clip_annotation, preds in zip(clip_annotations, predictions)
         ]
 
-    def compute_metrics(
+    def compute_metrics(self, eval_outputs: List[Any]) -> Dict[str, float]:
-        self,
-        clip_evaluations: Sequence[ClipEvaluation],
-    ) -> Dict[str, float]:
         results = {}
 
-        for metric in self.metrics:
+        for task, outputs in zip(self.tasks, eval_outputs):
-            results.update(metric(clip_evaluations))
+            results.update(task.compute_metrics(outputs))
 
         return results
 
     def generate_plots(
-        self, clip_evaluations: Sequence[ClipEvaluation]
+        self,
+        eval_outputs: List[Any],
     ) -> Iterable[Tuple[str, Figure]]:
-        for plotter in self.plots:
+        for task, outputs in zip(self.tasks, eval_outputs):
-            for name, fig in plotter(clip_evaluations):
+            for name, fig in task.generate_plots(outputs):
                 yield name, fig
 
 
 def build_evaluator(
-    config: Optional[EvaluationConfig] = None,
+    config: Optional[Union[EvaluationConfig, dict]] = None,
     targets: Optional[TargetProtocol] = None,
-    matcher: Optional[MatcherProtocol] = None,
-    plots: Optional[List[PlotterProtocol]] = None,
-    metrics: Optional[List[MetricsProtocol]] = None,
 ) -> EvaluatorProtocol:
-    config = config or EvaluationConfig()
     targets = targets or build_targets()
-    matcher = matcher or build_matcher(config.match_strategy)
 
-    if metrics is None:
+    if config is None:
-        metrics = [
+        config = EvaluationConfig()
-            build_metric(config, targets.class_names)
-            for config in config.metrics
-        ]
 
-    if plots is None:
+    if not isinstance(config, EvaluationConfig):
-        plots = [
+        config = EvaluationConfig.model_validate(config)
-            build_plotter(config, targets.class_names)
-            for config in config.plots
-        ]
 
     return Evaluator(
-        config=config,
         targets=targets,
-        matcher=matcher,
+        tasks=[build_task(task, targets=targets) for task in config.tasks],
-        metrics=metrics,
-        plots=plots,
-    )
-
-
-def is_in_bounds(
-    geometry: data.Geometry,
-    clip: data.Clip,
-    buffer: float,
-) -> bool:
-    start_time = compute_bounds(geometry)[0]
-    return (start_time >= clip.start_time + buffer) and (
-        start_time <= clip.end_time - buffer
     )

src/batdetect2/evaluate/lightning.py

@@ -4,11 +4,10 @@ from lightning import LightningModule
 from torch.utils.data import DataLoader
 
 from batdetect2.evaluate.dataset import TestDataset, TestExample
-from batdetect2.evaluate.tables import FullEvaluationTable
+from batdetect2.logging import get_image_logger
-from batdetect2.logging import get_image_logger, get_table_logger
 from batdetect2.models import Model
 from batdetect2.postprocess import to_raw_predictions
-from batdetect2.typing import ClipEvaluation, EvaluatorProtocol
+from batdetect2.typing import ClipMatches, EvaluatorProtocol
 
 
 class EvaluationModule(LightningModule):
@@ -54,18 +53,8 @@ class EvaluationModule(LightningModule):
     def on_test_epoch_end(self):
         self.log_metrics(self.clip_evaluations)
         self.plot_examples(self.clip_evaluations)
-        self.log_table(self.clip_evaluations)
 
-    def log_table(self, evaluated_clips: Sequence[ClipEvaluation]):
+    def plot_examples(self, evaluated_clips: Sequence[ClipMatches]):
-        table_logger = get_table_logger(self.logger)  # type: ignore
-
-        if table_logger is None:
-            return
-
-        df = FullEvaluationTable()(evaluated_clips)
-        table_logger("full_evaluation", df, 0)
-
-    def plot_examples(self, evaluated_clips: Sequence[ClipEvaluation]):
         plotter = get_image_logger(self.logger)  # type: ignore
 
         if plotter is None:
@@ -74,7 +63,7 @@ class EvaluationModule(LightningModule):
         for figure_name, fig in self.evaluator.generate_plots(evaluated_clips):
             plotter(figure_name, fig, self.global_step)
 
-    def log_metrics(self, evaluated_clips: Sequence[ClipEvaluation]):
+    def log_metrics(self, evaluated_clips: Sequence[ClipMatches]):
         metrics = self.evaluator.compute_metrics(evaluated_clips)
         self.log_dict(metrics)
 

src/batdetect2/evaluate/match.py

@@ -8,8 +8,7 @@ from soundevent.evaluation import compute_affinity
 from soundevent.evaluation import match_geometries as optimal_match
 from soundevent.geometry import compute_bounds
 
-from batdetect2.core.configs import BaseConfig
+from batdetect2.core import BaseConfig, Registry
-from batdetect2.core.registries import Registry
 from batdetect2.evaluate.affinity import (
     AffinityConfig,
     GeometricIOUConfig,
@@ -17,11 +16,13 @@ from batdetect2.evaluate.affinity import (
 )
 from batdetect2.targets import build_targets
 from batdetect2.typing import (
+    AffinityFunction,
+    MatcherProtocol,
     MatchEvaluation,
+    RawPrediction,
     TargetProtocol,
 )
-from batdetect2.typing.evaluate import AffinityFunction, MatcherProtocol
+from batdetect2.typing.evaluate import ClipMatches
-from batdetect2.typing.postprocess import RawPrediction
 
 MatchingGeometry = Literal["bbox", "interval", "timestamp"]
 """The geometry representation to use for matching."""
@@ -33,9 +34,10 @@ def match(
     sound_event_annotations: Sequence[data.SoundEventAnnotation],
     raw_predictions: Sequence[RawPrediction],
     clip: data.Clip,
+    scores: Optional[Sequence[float]] = None,
     targets: Optional[TargetProtocol] = None,
     matcher: Optional[MatcherProtocol] = None,
-) -> List[MatchEvaluation]:
+) -> ClipMatches:
     if matcher is None:
         matcher = build_matcher()
 
@@ -51,9 +53,11 @@ def match(
         raw_prediction.geometry for raw_prediction in raw_predictions
     ]
 
-    scores = [
+    if scores is None:
-        raw_prediction.detection_score for raw_prediction in raw_predictions
+        scores = [
-    ]
+            raw_prediction.detection_score
+            for raw_prediction in raw_predictions
+        ]
 
     matches = []
 
@@ -73,9 +77,11 @@ def match(
 
         gt_det = target_idx is not None
         gt_class = targets.encode_class(target) if target is not None else None
+        gt_geometry = (
+            target_geometries[target_idx] if target_idx is not None else None
+        )
 
         pred_score = float(prediction.detection_score) if prediction else 0
-
         pred_geometry = (
             predicted_geometries[source_idx]
             if source_idx is not None
@@ -84,7 +90,7 @@ def match(
 
         class_scores = (
             {
-                str(class_name): float(score)
+                class_name: score
                 for class_name, score in zip(
                     targets.class_names,
                     prediction.class_scores,
@@ -100,6 +106,7 @@ def match(
                 sound_event_annotation=target,
                 gt_det=gt_det,
                 gt_class=gt_class,
+                gt_geometry=gt_geometry,
                 pred_score=pred_score,
                 pred_class_scores=class_scores,
                 pred_geometry=pred_geometry,
@@ -107,7 +114,7 @@ def match(
             )
         )
 
-    return matches
+    return ClipMatches(clip=clip, matches=matches)
 
 
 class StartTimeMatchConfig(BaseConfig):
@@ -132,12 +139,10 @@ class StartTimeMatcher(MatcherProtocol):
             distance_threshold=self.distance_threshold,
         )
 
-    @classmethod
+    @matching_strategies.register(StartTimeMatchConfig)
-    def from_config(cls, config: StartTimeMatchConfig) -> "StartTimeMatcher":
+    @staticmethod
-        return cls(distance_threshold=config.distance_threshold)
+    def from_config(config: StartTimeMatchConfig):
-
+        return StartTimeMatcher(distance_threshold=config.distance_threshold)
-
-matching_strategies.register(StartTimeMatchConfig, StartTimeMatcher)
 
 
 def match_start_times(
@@ -264,19 +269,17 @@ class GreedyMatcher(MatcherProtocol):
             affinity_threshold=self.affinity_threshold,
         )
 
-    @classmethod
+    @matching_strategies.register(GreedyMatchConfig)
-    def from_config(cls, config: GreedyMatchConfig):
+    @staticmethod
+    def from_config(config: GreedyMatchConfig):
         affinity_function = build_affinity_function(config.affinity_function)
-        return cls(
+        return GreedyMatcher(
             geometry=config.geometry,
             affinity_threshold=config.affinity_threshold,
             affinity_function=affinity_function,
         )
 
 
-matching_strategies.register(GreedyMatchConfig, GreedyMatcher)
-
-
 def greedy_match(
     ground_truth: Sequence[data.Geometry],
     predictions: Sequence[data.Geometry],
@@ -313,21 +316,21 @@ def greedy_match(
     unassigned_gt = set(range(len(ground_truth)))
 
     if not predictions:
-        for target_idx in range(len(ground_truth)):
+        for gt_idx in range(len(ground_truth)):
-            yield None, target_idx, 0
+            yield None, gt_idx, 0
 
         return
 
     if not ground_truth:
-        for source_idx in range(len(predictions)):
+        for pred_idx in range(len(predictions)):
-            yield source_idx, None, 0
+            yield pred_idx, None, 0
 
         return
 
     indices = np.argsort(scores)[::-1]
 
-    for source_idx in indices:
+    for pred_idx in indices:
-        source_geometry = predictions[source_idx]
+        source_geometry = predictions[pred_idx]
 
         affinities = np.array(
             [
@@ -340,18 +343,18 @@ def greedy_match(
         affinity = affinities[closest_target]
 
         if affinities[closest_target] <= affinity_threshold:
-            yield source_idx, None, 0
+            yield pred_idx, None, 0
             continue
 
         if closest_target not in unassigned_gt:
-            yield source_idx, None, 0
+            yield pred_idx, None, 0
             continue
 
         unassigned_gt.remove(closest_target)
-        yield source_idx, closest_target, affinity
+        yield pred_idx, closest_target, affinity
 
-    for target_idx in unassigned_gt:
+    for gt_idx in unassigned_gt:
-        yield None, target_idx, 0
+        yield None, gt_idx, 0
 
 
 class OptimalMatchConfig(BaseConfig):
@@ -386,17 +389,16 @@ class OptimalMatcher(MatcherProtocol):
             affinity_threshold=self.affinity_threshold,
         )
 
-    @classmethod
+    @matching_strategies.register(OptimalMatchConfig)
-    def from_config(cls, config: OptimalMatchConfig):
+    @staticmethod
-        return cls(
+    def from_config(config: OptimalMatchConfig):
+        return OptimalMatcher(
             affinity_threshold=config.affinity_threshold,
             time_buffer=config.time_buffer,
             frequency_buffer=config.frequency_buffer,
         )
 
 
-matching_strategies.register(OptimalMatchConfig, OptimalMatcher)
-
 MatchConfig = Annotated[
     Union[
         GreedyMatchConfig,

src/batdetect2/evaluate/metrics.py

@@ -1,712 +0,0 @@
-from collections import defaultdict
-from collections.abc import Callable, Mapping
-from typing import (
-    Annotated,
-    Any,
-    Dict,
-    List,
-    Literal,
-    Optional,
-    Sequence,
-    Union,
-)
-
-import numpy as np
-from pydantic import Field
-from sklearn import metrics, preprocessing
-
-from batdetect2.core import BaseConfig, Registry
-from batdetect2.typing import ClipEvaluation, MetricsProtocol
-
-__all__ = ["DetectionAP", "ClassificationAP"]
-
-
-metrics_registry: Registry[MetricsProtocol, [List[str]]] = Registry("metric")
-
-
-APImplementation = Literal["sklearn", "pascal_voc"]
-
-
-class DetectionAPConfig(BaseConfig):
-    name: Literal["detection_ap"] = "detection_ap"
-    ap_implementation: APImplementation = "pascal_voc"
-
-
-class DetectionAP(MetricsProtocol):
-    def __init__(
-        self,
-        implementation: APImplementation = "pascal_voc",
-    ):
-        self.implementation = implementation
-        self.metric = _ap_impl_mapping[self.implementation]
-
-    def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
-    ) -> Dict[str, float]:
-        y_true, y_score = zip(
-            *[
-                (match.gt_det, match.pred_score)
-                for clip_eval in clip_evaluations
-                for match in clip_eval.matches
-            ]
-        )
-        score = float(self.metric(y_true, y_score))
-        return {"detection_AP": score}
-
-    @classmethod
-    def from_config(cls, config: DetectionAPConfig, class_names: List[str]):
-        return cls(implementation=config.ap_implementation)
-
-
-metrics_registry.register(DetectionAPConfig, DetectionAP)
-
-
-class DetectionROCAUCConfig(BaseConfig):
-    name: Literal["detection_roc_auc"] = "detection_roc_auc"
-
-
-class DetectionROCAUC(MetricsProtocol):
-    def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
-    ) -> Dict[str, float]:
-        y_true, y_score = zip(
-            *[
-                (match.gt_det, match.pred_score)
-                for clip_eval in clip_evaluations
-                for match in clip_eval.matches
-            ]
-        )
-        score = float(metrics.roc_auc_score(y_true, y_score))
-        return {"detection_ROC_AUC": score}
-
-    @classmethod
-    def from_config(
-        cls, config: DetectionROCAUCConfig, class_names: List[str]
-    ):
-        return cls()
-
-
-metrics_registry.register(DetectionROCAUCConfig, DetectionROCAUC)
-
-
-class ClassificationAPConfig(BaseConfig):
-    name: Literal["classification_ap"] = "classification_ap"
-    ap_implementation: APImplementation = "pascal_voc"
-    include: Optional[List[str]] = None
-    exclude: Optional[List[str]] = None
-
-
-class ClassificationAP(MetricsProtocol):
-    def __init__(
-        self,
-        class_names: List[str],
-        implementation: APImplementation = "pascal_voc",
-        include: Optional[List[str]] = None,
-        exclude: Optional[List[str]] = None,
-    ):
-        self.implementation = implementation
-        self.metric = _ap_impl_mapping[self.implementation]
-        self.class_names = class_names
-
-        self.selected = class_names
-
-        if include is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name in include
-            ]
-
-        if exclude is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name not in exclude
-            ]
-
-    def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
-    ) -> Dict[str, float]:
-        y_true = []
-        y_pred = []
-
-        for clip_eval in clip_evaluations:
-            for match in clip_eval.matches:
-                # Ignore generic unclassified targets
-                if match.gt_det and match.gt_class is None:
-                    continue
-
-                y_true.append(
-                    match.gt_class
-                    if match.gt_class is not None
-                    else "__NONE__"
-                )
-
-                y_pred.append(
-                    np.array(
-                        [
-                            match.pred_class_scores.get(name, 0)
-                            for name in self.class_names
-                        ]
-                    )
-                )
-
-        y_true = preprocessing.label_binarize(y_true, classes=self.class_names)
-        y_pred = np.stack(y_pred)
-
-        class_scores = {}
-        for class_index, class_name in enumerate(self.class_names):
-            y_true_class = y_true[:, class_index]
-            y_pred_class = y_pred[:, class_index]
-            class_ap = self.metric(y_true_class, y_pred_class)
-            class_scores[class_name] = float(class_ap)
-
-        mean_ap = np.mean(
-            [value for value in class_scores.values() if value != 0]
-        )
-
-        return {
-            "classification_mAP": float(mean_ap),
-            **{
-                f"classification_AP/{class_name}": class_scores[class_name]
-                for class_name in self.selected
-            },
-        }
-
-    @classmethod
-    def from_config(
-        cls,
-        config: ClassificationAPConfig,
-        class_names: List[str],
-    ):
-        return cls(
-            class_names,
-            implementation=config.ap_implementation,
-            include=config.include,
-            exclude=config.exclude,
-        )
-
-
-metrics_registry.register(ClassificationAPConfig, ClassificationAP)
-
-
-class ClassificationROCAUCConfig(BaseConfig):
-    name: Literal["classification_roc_auc"] = "classification_roc_auc"
-    include: Optional[List[str]] = None
-    exclude: Optional[List[str]] = None
-
-
-class ClassificationROCAUC(MetricsProtocol):
-    def __init__(
-        self,
-        class_names: List[str],
-        include: Optional[List[str]] = None,
-        exclude: Optional[List[str]] = None,
-    ):
-        self.class_names = class_names
-        self.selected = class_names
-
-        if include is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name in include
-            ]
-
-        if exclude is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name not in exclude
-            ]
-
-    def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
-    ) -> Dict[str, float]:
-        y_true = []
-        y_pred = []
-
-        for clip_eval in clip_evaluations:
-            for match in clip_eval.matches:
-                # Ignore generic unclassified targets
-                if match.gt_det and match.gt_class is None:
-                    continue
-
-                y_true.append(
-                    match.gt_class
-                    if match.gt_class is not None
-                    else "__NONE__"
-                )
-
-                y_pred.append(
-                    np.array(
-                        [
-                            match.pred_class_scores.get(name, 0)
-                            for name in self.class_names
-                        ]
-                    )
-                )
-
-        y_true = preprocessing.label_binarize(y_true, classes=self.class_names)
-        y_pred = np.stack(y_pred)
-
-        class_scores = {}
-        for class_index, class_name in enumerate(self.class_names):
-            y_true_class = y_true[:, class_index]
-            y_pred_class = y_pred[:, class_index]
-            class_roc_auc = metrics.roc_auc_score(y_true_class, y_pred_class)
-            class_scores[class_name] = float(class_roc_auc)
-
-        mean_roc_auc = np.mean(
-            [value for value in class_scores.values() if value != 0]
-        )
-
-        return {
-            "classification_macro_average_ROC_AUC": float(mean_roc_auc),
-            **{
-                f"classification_ROC_AUC/{class_name}": class_scores[
-                    class_name
-                ]
-                for class_name in self.selected
-            },
-        }
-
-    @classmethod
-    def from_config(
-        cls,
-        config: ClassificationROCAUCConfig,
-        class_names: List[str],
-    ):
-        return cls(
-            class_names,
-            include=config.include,
-            exclude=config.exclude,
-        )
-
-
-metrics_registry.register(ClassificationROCAUCConfig, ClassificationROCAUC)
-
-
-class TopClassAPConfig(BaseConfig):
-    name: Literal["top_class_ap"] = "top_class_ap"
-    ap_implementation: APImplementation = "pascal_voc"
-
-
-class TopClassAP(MetricsProtocol):
-    def __init__(
-        self,
-        implementation: APImplementation = "pascal_voc",
-    ):
-        self.implementation = implementation
-        self.metric = _ap_impl_mapping[self.implementation]
-
-    def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
-    ) -> Dict[str, float]:
-        y_true = []
-        y_score = []
-
-        for clip_eval in clip_evaluations:
-            for match in clip_eval.matches:
-                # Ignore generic unclassified targets
-                if match.gt_det and match.gt_class is None:
-                    continue
-
-                top_class = match.pred_class
-
-                y_true.append(top_class == match.gt_class)
-                y_score.append(match.pred_class_score)
-
-        score = float(self.metric(y_true, y_score))
-        return {"top_class_AP": score}
-
-    @classmethod
-    def from_config(cls, config: TopClassAPConfig, class_names: List[str]):
-        return cls(implementation=config.ap_implementation)
-
-
-metrics_registry.register(TopClassAPConfig, TopClassAP)
-
-
-class ClassificationBalancedAccuracyConfig(BaseConfig):
-    name: Literal["classification_balanced_accuracy"] = (
-        "classification_balanced_accuracy"
-    )
-
-
-class ClassificationBalancedAccuracy(MetricsProtocol):
-    def __init__(self, class_names: List[str]):
-        self.class_names = class_names
-
-    def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
-    ) -> Dict[str, float]:
-        y_true = []
-        y_pred = []
-
-        for clip_eval in clip_evaluations:
-            for match in clip_eval.matches:
-                top_class = match.pred_class
-
-                # Focus on matches
-                if match.gt_class is None or top_class is None:
-                    continue
-
-                y_true.append(self.class_names.index(match.gt_class))
-                y_pred.append(self.class_names.index(top_class))
-
-        score = float(metrics.balanced_accuracy_score(y_true, y_pred))
-        return {"classification_balanced_accuracy": score}
-
-    @classmethod
-    def from_config(
-        cls,
-        config: ClassificationBalancedAccuracyConfig,
-        class_names: List[str],
-    ):
-        return cls(class_names)
-
-
-metrics_registry.register(
-    ClassificationBalancedAccuracyConfig,
-    ClassificationBalancedAccuracy,
-)
-
-
-class ClipDetectionAPConfig(BaseConfig):
-    name: Literal["clip_detection_ap"] = "clip_detection_ap"
-    ap_implementation: APImplementation = "pascal_voc"
-
-
-class ClipDetectionAP(MetricsProtocol):
-    def __init__(
-        self,
-        implementation: APImplementation,
-    ):
-        self.implementation = implementation
-        self.metric = _ap_impl_mapping[self.implementation]
-
-    def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
-    ) -> Dict[str, float]:
-        y_true = []
-        y_score = []
-
-        for clip_eval in clip_evaluations:
-            clip_det = []
-            clip_scores = []
-
-            for match in clip_eval.matches:
-                clip_det.append(match.gt_det)
-                clip_scores.append(match.pred_score)
-
-            y_true.append(any(clip_det))
-            y_score.append(max(clip_scores or [0]))
-
-        return {"clip_detection_ap": self.metric(y_true, y_score)}
-
-    @classmethod
-    def from_config(
-        cls,
-        config: ClipDetectionAPConfig,
-        class_names: List[str],
-    ):
-        return cls(implementation=config.ap_implementation)
-
-
-metrics_registry.register(ClipDetectionAPConfig, ClipDetectionAP)
-
-
-class ClipDetectionROCAUCConfig(BaseConfig):
-    name: Literal["clip_detection_roc_auc"] = "clip_detection_roc_auc"
-
-
-class ClipDetectionROCAUC(MetricsProtocol):
-    def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
-    ) -> Dict[str, float]:
-        y_true = []
-        y_score = []
-
-        for clip_eval in clip_evaluations:
-            clip_det = []
-            clip_scores = []
-
-            for match in clip_eval.matches:
-                clip_det.append(match.gt_det)
-                clip_scores.append(match.pred_score)
-
-            y_true.append(any(clip_det))
-            y_score.append(max(clip_scores or [0]))
-
-        return {
-            "clip_detection_ap": float(metrics.roc_auc_score(y_true, y_score))
-        }
-
-    @classmethod
-    def from_config(
-        cls,
-        config: ClipDetectionROCAUCConfig,
-        class_names: List[str],
-    ):
-        return cls()
-
-
-metrics_registry.register(ClipDetectionROCAUCConfig, ClipDetectionROCAUC)
-
-
-class ClipMulticlassAPConfig(BaseConfig):
-    name: Literal["clip_multiclass_ap"] = "clip_multiclass_ap"
-    ap_implementation: APImplementation = "pascal_voc"
-    include: Optional[List[str]] = None
-    exclude: Optional[List[str]] = None
-
-
-class ClipMulticlassAP(MetricsProtocol):
-    def __init__(
-        self,
-        class_names: List[str],
-        implementation: APImplementation,
-        include: Optional[Sequence[str]] = None,
-        exclude: Optional[Sequence[str]] = None,
-    ):
-        self.implementation = implementation
-        self.metric = _ap_impl_mapping[self.implementation]
-        self.class_names = class_names
-
-        self.selected = class_names
-
-        if include is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name in include
-            ]
-
-        if exclude is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name not in exclude
-            ]
-
-    def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
-    ) -> Dict[str, float]:
-        y_true = []
-        y_pred = []
-
-        for clip_eval in clip_evaluations:
-            clip_classes = set()
-            clip_scores = defaultdict(list)
-
-            for match in clip_eval.matches:
-                if match.gt_class is not None:
-                    clip_classes.add(match.gt_class)
-
-                for class_name, score in match.pred_class_scores.items():
-                    clip_scores[class_name].append(score)
-
-            y_true.append(clip_classes)
-            y_pred.append(
-                np.array(
-                    [
-                        # Get max score for each class
-                        max(clip_scores.get(class_name, [0]))
-                        for class_name in self.class_names
-                    ]
-                )
-            )
-
-        y_true = preprocessing.MultiLabelBinarizer(
-            classes=self.class_names
-        ).fit_transform(y_true)
-        y_pred = np.stack(y_pred)
-
-        class_scores = {}
-        for class_index, class_name in enumerate(self.class_names):
-            y_true_class = y_true[:, class_index]
-            y_pred_class = y_pred[:, class_index]
-            class_ap = self.metric(y_true_class, y_pred_class)
-            class_scores[class_name] = float(class_ap)
-
-        mean_ap = np.mean(
-            [value for value in class_scores.values() if value != 0]
-        )
-        return {
-            "clip_multiclass_mAP": float(mean_ap),
-            **{
-                f"clip_multiclass_AP/{class_name}": class_scores[class_name]
-                for class_name in self.selected
-            },
-        }
-
-    @classmethod
-    def from_config(
-        cls, config: ClipMulticlassAPConfig, class_names: List[str]
-    ):
-        return cls(
-            implementation=config.ap_implementation,
-            include=config.include,
-            exclude=config.exclude,
-            class_names=class_names,
-        )
-
-
-metrics_registry.register(ClipMulticlassAPConfig, ClipMulticlassAP)
-
-
-class ClipMulticlassROCAUCConfig(BaseConfig):
-    name: Literal["clip_multiclass_roc_auc"] = "clip_multiclass_roc_auc"
-    include: Optional[List[str]] = None
-    exclude: Optional[List[str]] = None
-
-
-class ClipMulticlassROCAUC(MetricsProtocol):
-    def __init__(
-        self,
-        class_names: List[str],
-        include: Optional[Sequence[str]] = None,
-        exclude: Optional[Sequence[str]] = None,
-    ):
-        self.class_names = class_names
-        self.selected = class_names
-
-        if include is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name in include
-            ]
-
-        if exclude is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name not in exclude
-            ]
-
-    def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
-    ) -> Dict[str, float]:
-        y_true = []
-        y_pred = []
-
-        for clip_eval in clip_evaluations:
-            clip_classes = set()
-            clip_scores = defaultdict(list)
-
-            for match in clip_eval.matches:
-                if match.gt_class is not None:
-                    clip_classes.add(match.gt_class)
-
-                for class_name, score in match.pred_class_scores.items():
-                    clip_scores[class_name].append(score)
-
-            y_true.append(clip_classes)
-            y_pred.append(
-                np.array(
-                    [
-                        # Get maximum score for each class
-                        max(clip_scores.get(class_name, [0]))
-                        for class_name in self.class_names
-                    ]
-                )
-            )
-
-        y_true = preprocessing.MultiLabelBinarizer(
-            classes=self.class_names
-        ).fit_transform(y_true)
-        y_pred = np.stack(y_pred)
-
-        class_scores = {}
-        for class_index, class_name in enumerate(self.class_names):
-            y_true_class = y_true[:, class_index]
-            y_pred_class = y_pred[:, class_index]
-            class_roc_auc = metrics.roc_auc_score(y_true_class, y_pred_class)
-            class_scores[class_name] = float(class_roc_auc)
-
-        mean_roc_auc = np.mean(
-            [value for value in class_scores.values() if value != 0]
-        )
-        return {
-            "clip_multiclass_macro_ROC_AUC": float(mean_roc_auc),
-            **{
-                f"clip_multiclass_ROC_AUC/{class_name}": class_scores[
-                    class_name
-                ]
-                for class_name in self.selected
-            },
-        }
-
-    @classmethod
-    def from_config(
-        cls,
-        config: ClipMulticlassROCAUCConfig,
-        class_names: List[str],
-    ):
-        return cls(
-            include=config.include,
-            exclude=config.exclude,
-            class_names=class_names,
-        )
-
-
-metrics_registry.register(ClipMulticlassROCAUCConfig, ClipMulticlassROCAUC)
-
-MetricConfig = Annotated[
-    Union[
-        DetectionAPConfig,
-        DetectionROCAUCConfig,
-        ClassificationAPConfig,
-        ClassificationROCAUCConfig,
-        TopClassAPConfig,
-        ClassificationBalancedAccuracyConfig,
-        ClipDetectionAPConfig,
-        ClipDetectionROCAUCConfig,
-        ClipMulticlassAPConfig,
-        ClipMulticlassROCAUCConfig,
-    ],
-    Field(discriminator="name"),
-]
-
-
-def build_metric(config: MetricConfig, class_names: List[str]):
-    return metrics_registry.build(config, class_names)
-
-
-def pascal_voc_average_precision(y_true, y_score) -> float:
-    y_true = np.array(y_true)
-    y_score = np.array(y_score)
-
-    sort_ind = np.argsort(y_score)[::-1]
-    y_true_sorted = y_true[sort_ind]
-
-    num_positives = y_true.sum()
-    false_pos_c = np.cumsum(1 - y_true_sorted)
-    true_pos_c = np.cumsum(y_true_sorted)
-
-    recall = true_pos_c / num_positives
-    precision = true_pos_c / np.maximum(
-        true_pos_c + false_pos_c,
-        np.finfo(np.float64).eps,
-    )
-
-    precision[np.isnan(precision)] = 0
-    recall[np.isnan(recall)] = 0
-
-    # pascal 12 way
-    mprec = np.hstack((0, precision, 0))
-    mrec = np.hstack((0, recall, 1))
-    for ii in range(mprec.shape[0] - 2, -1, -1):
-        mprec[ii] = np.maximum(mprec[ii], mprec[ii + 1])
-    inds = np.where(np.not_equal(mrec[1:], mrec[:-1]))[0] + 1
-    ave_prec = ((mrec[inds] - mrec[inds - 1]) * mprec[inds]).sum()
-
-    return ave_prec
-
-
-_ap_impl_mapping: Mapping[APImplementation, Callable[[Any, Any], float]] = {
-    "sklearn": metrics.average_precision_score,
-    "pascal_voc": pascal_voc_average_precision,
-}

src/batdetect2/evaluate/metrics/classification.py

@@ -0,0 +1,267 @@
+from collections import defaultdict
+from dataclasses import dataclass
+from typing import (
+    Annotated,
+    Callable,
+    Dict,
+    List,
+    Literal,
+    Mapping,
+    Optional,
+    Sequence,
+    Union,
+)
+
+import numpy as np
+from pydantic import Field
+from sklearn import metrics
+from soundevent import data
+
+from batdetect2.core import BaseConfig, Registry
+from batdetect2.evaluate.metrics.common import average_precision
+from batdetect2.typing import RawPrediction, TargetProtocol
+
+__all__ = [
+    "ClassificationMetric",
+    "ClassificationMetricConfig",
+    "build_classification_metric",
+]
+
+
+@dataclass
+class MatchEval:
+    clip: data.Clip
+    gt: Optional[data.SoundEventAnnotation]
+    pred: Optional[RawPrediction]
+
+    is_prediction: bool
+    is_ground_truth: bool
+    is_generic: bool
+    true_class: Optional[str]
+    score: float
+
+
+@dataclass
+class ClipEval:
+    clip: data.Clip
+    matches: Mapping[str, List[MatchEval]]
+
+
+ClassificationMetric = Callable[[Sequence[ClipEval]], Dict[str, float]]
+
+
+classification_metrics: Registry[ClassificationMetric, [TargetProtocol]] = (
+    Registry("classification_metric")
+)
+
+
+class BaseClassificationConfig(BaseConfig):
+    include: Optional[List[str]] = None
+    exclude: Optional[List[str]] = None
+
+
+class BaseClassificationMetric:
+    def __init__(
+        self,
+        targets: TargetProtocol,
+        include: Optional[List[str]] = None,
+        exclude: Optional[List[str]] = None,
+    ):
+        self.targets = targets
+        self.include = include
+        self.exclude = exclude
+
+    def include_class(self, class_name: str) -> bool:
+        if self.include is not None:
+            return class_name in self.include
+
+        if self.exclude is not None:
+            return class_name not in self.exclude
+
+        return True
+
+
+class ClassificationAveragePrecisionConfig(BaseClassificationConfig):
+    name: Literal["average_precision"] = "average_precision"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+    label: str = "average_precision"
+
+
+class ClassificationAveragePrecision(BaseClassificationMetric):
+    def __init__(
+        self,
+        targets: TargetProtocol,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        label: str = "average_precision",
+        include: Optional[List[str]] = None,
+        exclude: Optional[List[str]] = None,
+    ):
+        super().__init__(include=include, exclude=exclude, targets=targets)
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+        self.label = label
+
+    def __call__(
+        self, clip_evaluations: Sequence[ClipEval]
+    ) -> Dict[str, float]:
+        y_true, y_score, num_positives = _extract_per_class_metric_data(
+            clip_evaluations,
+            ignore_non_predictions=self.ignore_non_predictions,
+            ignore_generic=self.ignore_generic,
+        )
+
+        class_scores = {
+            class_name: average_precision(
+                y_true[class_name],
+                y_score[class_name],
+                num_positives=num_positives[class_name],
+            )
+            for class_name in self.targets.class_names
+        }
+
+        mean_score = float(
+            np.mean([v for v in class_scores.values() if v != np.nan])
+        )
+
+        return {
+            f"mean_{self.label}": mean_score,
+            **{
+                f"{self.label}/{class_name}": score
+                for class_name, score in class_scores.items()
+                if self.include_class(class_name)
+            },
+        }
+
+    @classification_metrics.register(ClassificationAveragePrecisionConfig)
+    @staticmethod
+    def from_config(
+        config: ClassificationAveragePrecisionConfig,
+        targets: TargetProtocol,
+    ):
+        return ClassificationAveragePrecision(
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+            label=config.label,
+            include=config.include,
+            exclude=config.exclude,
+        )
+
+
+class ClassificationROCAUCConfig(BaseClassificationConfig):
+    name: Literal["roc_auc"] = "roc_auc"
+    label: str = "roc_auc"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+
+
+class ClassificationROCAUC(BaseClassificationMetric):
+    def __init__(
+        self,
+        targets: TargetProtocol,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        label: str = "roc_auc",
+        include: Optional[List[str]] = None,
+        exclude: Optional[List[str]] = None,
+    ):
+        self.targets = targets
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+        self.label = label
+        self.include = include
+        self.exclude = exclude
+
+    def __call__(
+        self, clip_evaluations: Sequence[ClipEval]
+    ) -> Dict[str, float]:
+        y_true, y_score, _ = _extract_per_class_metric_data(
+            clip_evaluations,
+            ignore_non_predictions=self.ignore_non_predictions,
+            ignore_generic=self.ignore_generic,
+        )
+
+        class_scores = {
+            class_name: float(
+                metrics.roc_auc_score(
+                    y_true[class_name],
+                    y_score[class_name],
+                )
+            )
+            for class_name in self.targets.class_names
+        }
+
+        mean_score = float(
+            np.mean([v for v in class_scores.values() if v != np.nan])
+        )
+
+        return {
+            f"mean_{self.label}": mean_score,
+            **{
+                f"{self.label}/{class_name}": score
+                for class_name, score in class_scores.items()
+                if self.include_class(class_name)
+            },
+        }
+
+    @classification_metrics.register(ClassificationROCAUCConfig)
+    @staticmethod
+    def from_config(
+        config: ClassificationROCAUCConfig, targets: TargetProtocol
+    ):
+        return ClassificationROCAUC(
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+            label=config.label,
+        )
+
+
+ClassificationMetricConfig = Annotated[
+    Union[
+        ClassificationAveragePrecisionConfig,
+        ClassificationROCAUCConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_classification_metric(
+    config: ClassificationMetricConfig,
+    targets: TargetProtocol,
+) -> ClassificationMetric:
+    return classification_metrics.build(config, targets)
+
+
+def _extract_per_class_metric_data(
+    clip_evaluations: Sequence[ClipEval],
+    ignore_non_predictions: bool = True,
+    ignore_generic: bool = True,
+):
+    y_true = defaultdict(list)
+    y_score = defaultdict(list)
+    num_positives = defaultdict(lambda: 0)
+
+    for clip_eval in clip_evaluations:
+        for class_name, matches in clip_eval.matches.items():
+            for m in matches:
+                # Exclude matches with ground truth sounds where the class
+                # is unknown
+                if m.is_generic and ignore_generic:
+                    continue
+
+                is_class = m.true_class == class_name
+
+                if is_class:
+                    num_positives[class_name] += 1
+
+                # Ignore matches that don't correspond to a prediction
+                if not m.is_prediction and ignore_non_predictions:
+                    continue
+
+                y_true[class_name].append(is_class)
+                y_score[class_name].append(m.score)
+
+    return y_true, y_score, num_positives

src/batdetect2/evaluate/metrics/clip_classification.py

@@ -0,0 +1,135 @@
+from collections import defaultdict
+from dataclasses import dataclass
+from typing import Annotated, Callable, Dict, Literal, Sequence, Set, Union
+
+import numpy as np
+from pydantic import Field
+from sklearn import metrics
+
+from batdetect2.core.configs import BaseConfig
+from batdetect2.core.registries import Registry
+from batdetect2.evaluate.metrics.common import average_precision
+
+
+@dataclass
+class ClipEval:
+    true_classes: Set[str]
+    class_scores: Dict[str, float]
+
+
+ClipClassificationMetric = Callable[[Sequence[ClipEval]], Dict[str, float]]
+
+clip_classification_metrics: Registry[ClipClassificationMetric, []] = Registry(
+    "clip_classification_metric"
+)
+
+
+class ClipClassificationAveragePrecisionConfig(BaseConfig):
+    name: Literal["average_precision"] = "average_precision"
+    label: str = "average_precision"
+
+
+class ClipClassificationAveragePrecision:
+    def __init__(self, label: str = "average_precision"):
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        y_true = defaultdict(list)
+        y_score = defaultdict(list)
+
+        for clip_eval in clip_evaluations:
+            for class_name, score in clip_eval.class_scores.items():
+                y_true[class_name].append(class_name in clip_eval.true_classes)
+                y_score[class_name].append(score)
+
+        class_scores = {
+            class_name: float(
+                average_precision(
+                    y_true=y_true[class_name],
+                    y_score=y_score[class_name],
+                )
+            )
+            for class_name in y_true
+        }
+
+        mean = np.mean([v for v in class_scores.values() if not np.isnan(v)])
+
+        return {
+            f"mean_{self.label}": float(mean),
+            **{
+                f"{self.label}/{class_name}": score
+                for class_name, score in class_scores.items()
+                if not np.isnan(score)
+            },
+        }
+
+    @clip_classification_metrics.register(
+        ClipClassificationAveragePrecisionConfig
+    )
+    @staticmethod
+    def from_config(config: ClipClassificationAveragePrecisionConfig):
+        return ClipClassificationAveragePrecision(label=config.label)
+
+
+class ClipClassificationROCAUCConfig(BaseConfig):
+    name: Literal["roc_auc"] = "roc_auc"
+    label: str = "roc_auc"
+
+
+class ClipClassificationROCAUC:
+    def __init__(self, label: str = "roc_auc"):
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        y_true = defaultdict(list)
+        y_score = defaultdict(list)
+
+        for clip_eval in clip_evaluations:
+            for class_name, score in clip_eval.class_scores.items():
+                y_true[class_name].append(class_name in clip_eval.true_classes)
+                y_score[class_name].append(score)
+
+        class_scores = {
+            class_name: float(
+                metrics.roc_auc_score(
+                    y_true=y_true[class_name],
+                    y_score=y_score[class_name],
+                )
+            )
+            for class_name in y_true
+        }
+
+        mean = np.mean([v for v in class_scores.values() if not np.isnan(v)])
+
+        return {
+            f"mean_{self.label}": float(mean),
+            **{
+                f"{self.label}/{class_name}": score
+                for class_name, score in class_scores.items()
+                if not np.isnan(score)
+            },
+        }
+
+    @clip_classification_metrics.register(ClipClassificationROCAUCConfig)
+    @staticmethod
+    def from_config(config: ClipClassificationROCAUCConfig):
+        return ClipClassificationROCAUC(label=config.label)
+
+
+ClipClassificationMetricConfig = Annotated[
+    Union[
+        ClipClassificationAveragePrecisionConfig,
+        ClipClassificationROCAUCConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_clip_metric(config: ClipClassificationMetricConfig):
+    return clip_classification_metrics.build(config)

src/batdetect2/evaluate/metrics/clip_detection.py

@@ -0,0 +1,173 @@
+from dataclasses import dataclass
+from typing import Annotated, Callable, Dict, Literal, Sequence, Union
+
+import numpy as np
+from pydantic import Field
+from sklearn import metrics
+
+from batdetect2.core.configs import BaseConfig
+from batdetect2.core.registries import Registry
+from batdetect2.evaluate.metrics.common import average_precision
+
+
+@dataclass
+class ClipEval:
+    gt_det: bool
+    score: float
+
+
+ClipDetectionMetric = Callable[[Sequence[ClipEval]], Dict[str, float]]
+
+clip_detection_metrics: Registry[ClipDetectionMetric, []] = Registry(
+    "clip_detection_metric"
+)
+
+
+class ClipDetectionAveragePrecisionConfig(BaseConfig):
+    name: Literal["average_precision"] = "average_precision"
+    label: str = "average_precision"
+
+
+class ClipDetectionAveragePrecision:
+    def __init__(self, label: str = "average_precision"):
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        y_true = []
+        y_score = []
+
+        for clip_eval in clip_evaluations:
+            y_true.append(clip_eval.gt_det)
+            y_score.append(clip_eval.score)
+
+        score = average_precision(y_true=y_true, y_score=y_score)
+        return {self.label: score}
+
+    @clip_detection_metrics.register(ClipDetectionAveragePrecisionConfig)
+    @staticmethod
+    def from_config(config: ClipDetectionAveragePrecisionConfig):
+        return ClipDetectionAveragePrecision(label=config.label)
+
+
+class ClipDetectionROCAUCConfig(BaseConfig):
+    name: Literal["roc_auc"] = "roc_auc"
+    label: str = "roc_auc"
+
+
+class ClipDetectionROCAUC:
+    def __init__(self, label: str = "roc_auc"):
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        y_true = []
+        y_score = []
+
+        for clip_eval in clip_evaluations:
+            y_true.append(clip_eval.gt_det)
+            y_score.append(clip_eval.score)
+
+        score = float(metrics.roc_auc_score(y_true=y_true, y_score=y_score))
+        return {self.label: score}
+
+    @clip_detection_metrics.register(ClipDetectionROCAUCConfig)
+    @staticmethod
+    def from_config(config: ClipDetectionROCAUCConfig):
+        return ClipDetectionROCAUC(label=config.label)
+
+
+class ClipDetectionRecallConfig(BaseConfig):
+    name: Literal["recall"] = "recall"
+    threshold: float = 0.5
+    label: str = "recall"
+
+
+class ClipDetectionRecall:
+    def __init__(self, threshold: float, label: str = "recall"):
+        self.threshold = threshold
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        num_positives = 0
+        true_positives = 0
+
+        for clip_eval in clip_evaluations:
+            if clip_eval.gt_det:
+                num_positives += 1
+
+            if clip_eval.score >= self.threshold and clip_eval.gt_det:
+                true_positives += 1
+
+        if num_positives == 0:
+            return {self.label: np.nan}
+
+        score = true_positives / num_positives
+        return {self.label: score}
+
+    @clip_detection_metrics.register(ClipDetectionRecallConfig)
+    @staticmethod
+    def from_config(config: ClipDetectionRecallConfig):
+        return ClipDetectionRecall(
+            threshold=config.threshold, label=config.label
+        )
+
+
+class ClipDetectionPrecisionConfig(BaseConfig):
+    name: Literal["precision"] = "precision"
+    threshold: float = 0.5
+    label: str = "precision"
+
+
+class ClipDetectionPrecision:
+    def __init__(self, threshold: float, label: str = "precision"):
+        self.threshold = threshold
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        num_detections = 0
+        true_positives = 0
+        for clip_eval in clip_evaluations:
+            if clip_eval.score >= self.threshold:
+                num_detections += 1
+
+            if clip_eval.score >= self.threshold and clip_eval.gt_det:
+                true_positives += 1
+
+        if num_detections == 0:
+            return {self.label: np.nan}
+
+        score = true_positives / num_detections
+        return {self.label: score}
+
+    @clip_detection_metrics.register(ClipDetectionPrecisionConfig)
+    @staticmethod
+    def from_config(config: ClipDetectionPrecisionConfig):
+        return ClipDetectionPrecision(
+            threshold=config.threshold, label=config.label
+        )
+
+
+ClipDetectionMetricConfig = Annotated[
+    Union[
+        ClipDetectionAveragePrecisionConfig,
+        ClipDetectionROCAUCConfig,
+        ClipDetectionRecallConfig,
+        ClipDetectionPrecisionConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_clip_metric(config: ClipDetectionMetricConfig):
+    return clip_detection_metrics.build(config)

src/batdetect2/evaluate/metrics/common.py

@@ -0,0 +1,60 @@
+from typing import Optional, Tuple
+
+import numpy as np
+
+__all__ = [
+    "compute_precision_recall",
+    "average_precision",
+]
+
+
+def compute_precision_recall(
+    y_true,
+    y_score,
+    num_positives: Optional[int] = None,
+) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
+    y_true = np.array(y_true)
+    y_score = np.array(y_score)
+
+    if num_positives is None:
+        num_positives = y_true.sum()
+
+    # Sort by score
+    sort_ind = np.argsort(y_score)[::-1]
+    y_true_sorted = y_true[sort_ind]
+    y_score_sorted = y_score[sort_ind]
+
+    false_pos_c = np.cumsum(1 - y_true_sorted)
+    true_pos_c = np.cumsum(y_true_sorted)
+
+    recall = true_pos_c / num_positives
+    precision = true_pos_c / np.maximum(
+        true_pos_c + false_pos_c,
+        np.finfo(np.float64).eps,
+    )
+
+    precision[np.isnan(precision)] = 0
+    recall[np.isnan(recall)] = 0
+    return precision, recall, y_score_sorted
+
+
+def average_precision(
+    y_true,
+    y_score,
+    num_positives: Optional[int] = None,
+) -> float:
+    precision, recall, _ = compute_precision_recall(
+        y_true,
+        y_score,
+        num_positives=num_positives,
+    )
+
+    # pascal 12 way
+    mprec = np.hstack((0, precision, 0))
+    mrec = np.hstack((0, recall, 1))
+    for ii in range(mprec.shape[0] - 2, -1, -1):
+        mprec[ii] = np.maximum(mprec[ii], mprec[ii + 1])
+    inds = np.where(np.not_equal(mrec[1:], mrec[:-1]))[0] + 1
+    ave_prec = ((mrec[inds] - mrec[inds - 1]) * mprec[inds]).sum()
+
+    return ave_prec

src/batdetect2/evaluate/metrics/detection.py

@@ -0,0 +1,226 @@
+from dataclasses import dataclass
+from typing import (
+    Annotated,
+    Callable,
+    Dict,
+    List,
+    Literal,
+    Optional,
+    Sequence,
+    Union,
+)
+
+import numpy as np
+from pydantic import Field
+from sklearn import metrics
+from soundevent import data
+
+from batdetect2.core import BaseConfig, Registry
+from batdetect2.evaluate.metrics.common import average_precision
+from batdetect2.typing import RawPrediction
+
+__all__ = [
+    "DetectionMetricConfig",
+    "DetectionMetric",
+    "build_detection_metric",
+]
+
+
+@dataclass
+class MatchEval:
+    gt: Optional[data.SoundEventAnnotation]
+    pred: Optional[RawPrediction]
+
+    is_prediction: bool
+    is_ground_truth: bool
+    score: float
+
+
+@dataclass
+class ClipEval:
+    clip: data.Clip
+    matches: List[MatchEval]
+
+
+DetectionMetric = Callable[[Sequence[ClipEval]], Dict[str, float]]
+
+
+detection_metrics: Registry[DetectionMetric, []] = Registry("detection_metric")
+
+
+class DetectionAveragePrecisionConfig(BaseConfig):
+    name: Literal["average_precision"] = "average_precision"
+    label: str = "average_precision"
+    ignore_non_predictions: bool = True
+
+
+class DetectionAveragePrecision:
+    def __init__(self, label: str, ignore_non_predictions: bool = True):
+        self.ignore_non_predictions = ignore_non_predictions
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evals: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        y_true = []
+        y_score = []
+        num_positives = 0
+
+        for clip_eval in clip_evals:
+            for m in clip_eval.matches:
+                num_positives += int(m.is_ground_truth)
+
+                # Ignore matches that don't correspond to a prediction
+                if not m.is_prediction and self.ignore_non_predictions:
+                    continue
+
+                y_true.append(m.is_ground_truth)
+                y_score.append(m.score)
+
+        ap = average_precision(y_true, y_score, num_positives=num_positives)
+        return {self.label: ap}
+
+    @detection_metrics.register(DetectionAveragePrecisionConfig)
+    @staticmethod
+    def from_config(config: DetectionAveragePrecisionConfig):
+        return DetectionAveragePrecision(
+            label=config.label,
+            ignore_non_predictions=config.ignore_non_predictions,
+        )
+
+
+class DetectionROCAUCConfig(BaseConfig):
+    name: Literal["roc_auc"] = "roc_auc"
+    label: str = "roc_auc"
+    ignore_non_predictions: bool = True
+
+
+class DetectionROCAUC:
+    def __init__(
+        self,
+        label: str = "roc_auc",
+        ignore_non_predictions: bool = True,
+    ):
+        self.label = label
+        self.ignore_non_predictions = ignore_non_predictions
+
+    def __call__(self, clip_evals: Sequence[ClipEval]) -> Dict[str, float]:
+        y_true: List[bool] = []
+        y_score: List[float] = []
+
+        for clip_eval in clip_evals:
+            for m in clip_eval.matches:
+                if not m.is_prediction and self.ignore_non_predictions:
+                    # Ignore matches that don't correspond to a prediction
+                    continue
+
+                y_true.append(m.is_ground_truth)
+                y_score.append(m.score)
+
+        score = float(metrics.roc_auc_score(y_true, y_score))
+        return {self.label: score}
+
+    @detection_metrics.register(DetectionROCAUCConfig)
+    @staticmethod
+    def from_config(config: DetectionROCAUCConfig):
+        return DetectionROCAUC(
+            label=config.label,
+            ignore_non_predictions=config.ignore_non_predictions,
+        )
+
+
+class DetectionRecallConfig(BaseConfig):
+    name: Literal["recall"] = "recall"
+    label: str = "recall"
+    threshold: float = 0.5
+
+
+class DetectionRecall:
+    def __init__(self, threshold: float, label: str = "recall"):
+        self.label = label
+        self.threshold = threshold
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        num_positives = 0
+        true_positives = 0
+
+        for clip_eval in clip_evaluations:
+            for m in clip_eval.matches:
+                if m.is_ground_truth:
+                    num_positives += 1
+
+                if m.score >= self.threshold and m.is_ground_truth:
+                    true_positives += 1
+
+        if num_positives == 0:
+            return {self.label: np.nan}
+
+        score = true_positives / num_positives
+        return {self.label: score}
+
+    @detection_metrics.register(DetectionRecallConfig)
+    @staticmethod
+    def from_config(config: DetectionRecallConfig):
+        return DetectionRecall(threshold=config.threshold, label=config.label)
+
+
+class DetectionPrecisionConfig(BaseConfig):
+    name: Literal["precision"] = "precision"
+    label: str = "precision"
+    threshold: float = 0.5
+
+
+class DetectionPrecision:
+    def __init__(self, threshold: float, label: str = "precision"):
+        self.threshold = threshold
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        num_detections = 0
+        true_positives = 0
+
+        for clip_eval in clip_evaluations:
+            for m in clip_eval.matches:
+                is_detection = m.score >= self.threshold
+
+                if is_detection:
+                    num_detections += 1
+
+                if is_detection and m.is_ground_truth:
+                    true_positives += 1
+
+        if num_detections == 0:
+            return {self.label: np.nan}
+
+        score = true_positives / num_detections
+        return {self.label: score}
+
+    @detection_metrics.register(DetectionPrecisionConfig)
+    @staticmethod
+    def from_config(config: DetectionPrecisionConfig):
+        return DetectionPrecision(
+            threshold=config.threshold,
+            label=config.label,
+        )
+
+
+DetectionMetricConfig = Annotated[
+    Union[
+        DetectionAveragePrecisionConfig,
+        DetectionROCAUCConfig,
+        DetectionRecallConfig,
+        DetectionPrecisionConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_detection_metric(config: DetectionMetricConfig):
+    return detection_metrics.build(config)

src/batdetect2/evaluate/metrics/top_class.py

@@ -0,0 +1,314 @@
+from dataclasses import dataclass
+from typing import (
+    Annotated,
+    Callable,
+    Dict,
+    List,
+    Literal,
+    Optional,
+    Sequence,
+    Union,
+)
+
+import numpy as np
+from pydantic import Field
+from sklearn import metrics, preprocessing
+from soundevent import data
+
+from batdetect2.core import BaseConfig, Registry
+from batdetect2.evaluate.metrics.common import average_precision
+from batdetect2.typing import RawPrediction
+
+__all__ = [
+    "TopClassMetricConfig",
+    "TopClassMetric",
+    "build_top_class_metric",
+]
+
+
+@dataclass
+class MatchEval:
+    clip: data.Clip
+    gt: Optional[data.SoundEventAnnotation]
+    pred: Optional[RawPrediction]
+
+    is_ground_truth: bool
+    is_generic: bool
+    is_prediction: bool
+    pred_class: Optional[str]
+    true_class: Optional[str]
+    score: float
+
+
+@dataclass
+class ClipEval:
+    clip: data.Clip
+    matches: List[MatchEval]
+
+
+TopClassMetric = Callable[[Sequence[ClipEval]], Dict[str, float]]
+
+
+top_class_metrics: Registry[TopClassMetric, []] = Registry("top_class_metric")
+
+
+class TopClassAveragePrecisionConfig(BaseConfig):
+    name: Literal["average_precision"] = "average_precision"
+    label: str = "average_precision"
+    ignore_generic: bool = True
+    ignore_non_predictions: bool = True
+
+
+class TopClassAveragePrecision:
+    def __init__(
+        self,
+        ignore_generic: bool = True,
+        ignore_non_predictions: bool = True,
+        label: str = "average_precision",
+    ):
+        self.ignore_generic = ignore_generic
+        self.ignore_non_predictions = ignore_non_predictions
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evals: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        y_true = []
+        y_score = []
+        num_positives = 0
+
+        for clip_eval in clip_evals:
+            for m in clip_eval.matches:
+                if m.is_generic and self.ignore_generic:
+                    # Ignore gt sounds with unknown class
+                    continue
+
+                num_positives += int(m.is_ground_truth)
+
+                if not m.is_prediction and self.ignore_non_predictions:
+                    # Ignore non predictions
+                    continue
+
+                y_true.append(m.pred_class == m.true_class)
+                y_score.append(m.score)
+
+        score = average_precision(y_true, y_score, num_positives=num_positives)
+        return {self.label: score}
+
+    @top_class_metrics.register(TopClassAveragePrecisionConfig)
+    @staticmethod
+    def from_config(config: TopClassAveragePrecisionConfig):
+        return TopClassAveragePrecision(
+            ignore_generic=config.ignore_generic,
+            label=config.label,
+        )
+
+
+class TopClassROCAUCConfig(BaseConfig):
+    name: Literal["roc_auc"] = "roc_auc"
+    ignore_generic: bool = True
+    ignore_non_predictions: bool = True
+    label: str = "roc_auc"
+
+
+class TopClassROCAUC:
+    def __init__(
+        self,
+        ignore_generic: bool = True,
+        ignore_non_predictions: bool = True,
+        label: str = "roc_auc",
+    ):
+        self.ignore_generic = ignore_generic
+        self.ignore_non_predictions = ignore_non_predictions
+        self.label = label
+
+    def __call__(self, clip_evals: Sequence[ClipEval]) -> Dict[str, float]:
+        y_true: List[bool] = []
+        y_score: List[float] = []
+
+        for clip_eval in clip_evals:
+            for m in clip_eval.matches:
+                if m.is_generic and self.ignore_generic:
+                    # Ignore gt sounds with unknown class
+                    continue
+
+                if not m.is_prediction and self.ignore_non_predictions:
+                    # Ignore non predictions
+                    continue
+
+                y_true.append(m.pred_class == m.true_class)
+                y_score.append(m.score)
+
+        score = float(metrics.roc_auc_score(y_true, y_score))
+        return {self.label: score}
+
+    @top_class_metrics.register(TopClassROCAUCConfig)
+    @staticmethod
+    def from_config(config: TopClassROCAUCConfig):
+        return TopClassROCAUC(
+            ignore_generic=config.ignore_generic,
+            label=config.label,
+        )
+
+
+class TopClassRecallConfig(BaseConfig):
+    name: Literal["recall"] = "recall"
+    threshold: float = 0.5
+    label: str = "recall"
+
+
+class TopClassRecall:
+    def __init__(self, threshold: float, label: str = "recall"):
+        self.threshold = threshold
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        num_positives = 0
+        true_positives = 0
+
+        for clip_eval in clip_evaluations:
+            for m in clip_eval.matches:
+                if m.is_ground_truth:
+                    num_positives += 1
+
+                if m.score >= self.threshold and m.pred_class == m.true_class:
+                    true_positives += 1
+
+        if num_positives == 0:
+            return {self.label: np.nan}
+
+        score = true_positives / num_positives
+        return {self.label: score}
+
+    @top_class_metrics.register(TopClassRecallConfig)
+    @staticmethod
+    def from_config(config: TopClassRecallConfig):
+        return TopClassRecall(
+            threshold=config.threshold,
+            label=config.label,
+        )
+
+
+class TopClassPrecisionConfig(BaseConfig):
+    name: Literal["precision"] = "precision"
+    threshold: float = 0.5
+    label: str = "precision"
+
+
+class TopClassPrecision:
+    def __init__(self, threshold: float, label: str = "precision"):
+        self.threshold = threshold
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        num_detections = 0
+        true_positives = 0
+
+        for clip_eval in clip_evaluations:
+            for m in clip_eval.matches:
+                is_detection = m.score >= self.threshold
+
+                if is_detection:
+                    num_detections += 1
+
+                if is_detection and m.pred_class == m.true_class:
+                    true_positives += 1
+
+        if num_detections == 0:
+            return {self.label: np.nan}
+
+        score = true_positives / num_detections
+        return {self.label: score}
+
+    @top_class_metrics.register(TopClassPrecisionConfig)
+    @staticmethod
+    def from_config(config: TopClassPrecisionConfig):
+        return TopClassPrecision(
+            threshold=config.threshold,
+            label=config.label,
+        )
+
+
+class BalancedAccuracyConfig(BaseConfig):
+    name: Literal["balanced_accuracy"] = "balanced_accuracy"
+    label: str = "balanced_accuracy"
+    exclude_noise: bool = False
+    noise_class: str = "noise"
+
+
+class BalancedAccuracy:
+    def __init__(
+        self,
+        exclude_noise: bool = True,
+        noise_class: str = "noise",
+        label: str = "balanced_accuracy",
+    ):
+        self.exclude_noise = exclude_noise
+        self.noise_class = noise_class
+        self.label = label
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Dict[str, float]:
+        y_true: List[str] = []
+        y_pred: List[str] = []
+
+        for clip_eval in clip_evaluations:
+            for m in clip_eval.matches:
+                if m.is_generic:
+                    # Ignore matches that correspond to a sound event
+                    # with unknown class
+                    continue
+
+                if not m.is_ground_truth and self.exclude_noise:
+                    # Ignore predictions that were not matched to a
+                    # ground truth
+                    continue
+
+                if m.pred_class is None and self.exclude_noise:
+                    # Ignore non-predictions
+                    continue
+
+                y_true.append(m.true_class or self.noise_class)
+                y_pred.append(m.pred_class or self.noise_class)
+
+        encoder = preprocessing.LabelEncoder()
+        encoder.fit(list(set(y_true) | set(y_pred)))
+
+        y_true = encoder.transform(y_true)
+        y_pred = encoder.transform(y_pred)
+        score = metrics.balanced_accuracy_score(y_true, y_pred)
+        return {self.label: score}
+
+    @top_class_metrics.register(BalancedAccuracyConfig)
+    @staticmethod
+    def from_config(config: BalancedAccuracyConfig):
+        return BalancedAccuracy(
+            exclude_noise=config.exclude_noise,
+            noise_class=config.noise_class,
+            label=config.label,
+        )
+
+
+TopClassMetricConfig = Annotated[
+    Union[
+        TopClassAveragePrecisionConfig,
+        TopClassROCAUCConfig,
+        TopClassRecallConfig,
+        TopClassPrecisionConfig,
+        BalancedAccuracyConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_top_class_metric(config: TopClassMetricConfig):
+    return top_class_metrics.build(config)

src/batdetect2/evaluate/plots.py

@@ -1,560 +0,0 @@
-import random
-from collections import defaultdict
-from dataclasses import dataclass, field
-from typing import Annotated, Dict, List, Literal, Optional, Sequence, Union
-
-import matplotlib.pyplot as plt
-import numpy as np
-import pandas as pd
-from pydantic import Field
-from sklearn import metrics
-from sklearn.preprocessing import label_binarize
-
-from batdetect2.audio import AudioConfig, build_audio_loader
-from batdetect2.core import BaseConfig, Registry
-from batdetect2.plotting.gallery import plot_match_gallery
-from batdetect2.plotting.matches import plot_matches
-from batdetect2.preprocess import PreprocessingConfig, build_preprocessor
-from batdetect2.typing import (
-    AudioLoader,
-    ClipEvaluation,
-    MatchEvaluation,
-    PlotterProtocol,
-    PreprocessorProtocol,
-)
-
-__all__ = [
-    "build_plotter",
-    "ExampleGallery",
-    "ExampleGalleryConfig",
-]
-
-
-plots_registry: Registry[PlotterProtocol, [List[str]]] = Registry("plot")
-
-
-class ExampleGalleryConfig(BaseConfig):
-    name: Literal["example_gallery"] = "example_gallery"
-    examples_per_class: int = 5
-    audio: AudioConfig = Field(default_factory=AudioConfig)
-    preprocessing: PreprocessingConfig = Field(
-        default_factory=PreprocessingConfig
-    )
-
-
-class ExampleGallery(PlotterProtocol):
-    def __init__(
-        self,
-        examples_per_class: int,
-        preprocessor: Optional[PreprocessorProtocol] = None,
-        audio_loader: Optional[AudioLoader] = None,
-    ):
-        self.examples_per_class = examples_per_class
-        self.preprocessor = preprocessor or build_preprocessor()
-        self.audio_loader = audio_loader or build_audio_loader()
-
-    def __call__(self, clip_evaluations: Sequence[ClipEvaluation]):
-        per_class_matches = group_matches(clip_evaluations)
-
-        for class_name, matches in per_class_matches.items():
-            true_positives = get_binned_sample(
-                matches.true_positives,
-                n_examples=self.examples_per_class,
-            )
-
-            false_positives = get_binned_sample(
-                matches.false_positives,
-                n_examples=self.examples_per_class,
-            )
-
-            false_negatives = random.sample(
-                matches.false_negatives,
-                k=min(self.examples_per_class, len(matches.false_negatives)),
-            )
-
-            cross_triggers = get_binned_sample(
-                matches.cross_triggers,
-                n_examples=self.examples_per_class,
-            )
-
-            fig = plot_match_gallery(
-                true_positives,
-                false_positives,
-                false_negatives,
-                cross_triggers,
-                preprocessor=self.preprocessor,
-                audio_loader=self.audio_loader,
-                n_examples=self.examples_per_class,
-            )
-
-            yield f"example_gallery/{class_name}", fig
-
-            plt.close(fig)
-
-    @classmethod
-    def from_config(cls, config: ExampleGalleryConfig, class_names: List[str]):
-        audio_loader = build_audio_loader(config.audio)
-        preprocessor = build_preprocessor(
-            config.preprocessing,
-            input_samplerate=audio_loader.samplerate,
-        )
-        return cls(
-            examples_per_class=config.examples_per_class,
-            preprocessor=preprocessor,
-            audio_loader=audio_loader,
-        )
-
-
-plots_registry.register(ExampleGalleryConfig, ExampleGallery)
-
-
-class ClipEvaluationPlotConfig(BaseConfig):
-    name: Literal["example_clip"] = "example_clip"
-    num_plots: int = 5
-    audio: AudioConfig = Field(default_factory=AudioConfig)
-    preprocessing: PreprocessingConfig = Field(
-        default_factory=PreprocessingConfig
-    )
-
-
-class PlotClipEvaluation(PlotterProtocol):
-    def __init__(
-        self,
-        num_plots: int = 3,
-        preprocessor: Optional[PreprocessorProtocol] = None,
-        audio_loader: Optional[AudioLoader] = None,
-    ):
-        self.preprocessor = preprocessor
-        self.audio_loader = audio_loader
-        self.num_plots = num_plots
-
-    def __call__(self, clip_evaluations: Sequence[ClipEvaluation]):
-        examples = random.sample(
-            clip_evaluations,
-            k=min(self.num_plots, len(clip_evaluations)),
-        )
-
-        for index, clip_evaluation in enumerate(examples):
-            fig, ax = plt.subplots()
-            plot_matches(
-                clip_evaluation.matches,
-                clip=clip_evaluation.clip,
-                audio_loader=self.audio_loader,
-                ax=ax,
-            )
-            yield f"clip_evaluation/example_{index}", fig
-            plt.close(fig)
-
-    @classmethod
-    def from_config(
-        cls,
-        config: ClipEvaluationPlotConfig,
-        class_names: List[str],
-    ):
-        audio_loader = build_audio_loader(config.audio)
-        preprocessor = build_preprocessor(
-            config.preprocessing,
-            input_samplerate=audio_loader.samplerate,
-        )
-        return cls(
-            num_plots=config.num_plots,
-            preprocessor=preprocessor,
-            audio_loader=audio_loader,
-        )
-
-
-plots_registry.register(ClipEvaluationPlotConfig, PlotClipEvaluation)
-
-
-class DetectionPRCurveConfig(BaseConfig):
-    name: Literal["detection_pr_curve"] = "detection_pr_curve"
-
-
-class DetectionPRCurve(PlotterProtocol):
-    def __call__(self, clip_evaluations: Sequence[ClipEvaluation]):
-        y_true, y_score = zip(
-            *[
-                (match.gt_det, match.pred_score)
-                for clip_eval in clip_evaluations
-                for match in clip_eval.matches
-            ]
-        )
-        precision, recall, _ = metrics.precision_recall_curve(y_true, y_score)
-        fig, ax = plt.subplots()
-
-        ax.plot(recall, precision, label="Detector")
-        ax.set_xlabel("Recall")
-        ax.set_ylabel("Precision")
-        ax.legend()
-
-        yield "detection_pr_curve", fig
-
-    @classmethod
-    def from_config(
-        cls,
-        config: DetectionPRCurveConfig,
-        class_names: List[str],
-    ):
-        return cls()
-
-
-plots_registry.register(DetectionPRCurveConfig, DetectionPRCurve)
-
-
-class ClassificationPRCurvesConfig(BaseConfig):
-    name: Literal["classification_pr_curves"] = "classification_pr_curves"
-    include: Optional[List[str]] = None
-    exclude: Optional[List[str]] = None
-
-
-class ClassificationPRCurves(PlotterProtocol):
-    def __init__(
-        self,
-        class_names: List[str],
-        include: Optional[List[str]] = None,
-        exclude: Optional[List[str]] = None,
-    ):
-        self.class_names = class_names
-        self.selected = class_names
-
-        if include is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name in include
-            ]
-
-        if exclude is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name not in exclude
-            ]
-
-    def __call__(self, clip_evaluations: Sequence[ClipEvaluation]):
-        y_true = []
-        y_pred = []
-
-        for clip_eval in clip_evaluations:
-            for match in clip_eval.matches:
-                # Ignore generic unclassified targets
-                if match.gt_det and match.gt_class is None:
-                    continue
-
-                y_true.append(
-                    match.gt_class
-                    if match.gt_class is not None
-                    else "__NONE__"
-                )
-
-                y_pred.append(
-                    np.array(
-                        [
-                            match.pred_class_scores.get(name, 0)
-                            for name in self.class_names
-                        ]
-                    )
-                )
-
-        y_true = label_binarize(y_true, classes=self.class_names)
-        y_pred = np.stack(y_pred)
-
-        fig, ax = plt.subplots(figsize=(10, 10))
-        for class_index, class_name in enumerate(self.class_names):
-            if class_name not in self.selected:
-                continue
-
-            y_true_class = y_true[:, class_index]
-            y_pred_class = y_pred[:, class_index]
-            precision, recall, _ = metrics.precision_recall_curve(
-                y_true_class,
-                y_pred_class,
-            )
-            ax.plot(recall, precision, label=class_name)
-
-        ax.set_xlabel("Recall")
-        ax.set_ylabel("Precision")
-        ax.legend(
-            bbox_to_anchor=(1.05, 1),
-            loc="upper left",
-            borderaxespad=0.0,
-        )
-
-        yield "classification_pr_curve", fig
-
-    @classmethod
-    def from_config(
-        cls,
-        config: ClassificationPRCurvesConfig,
-        class_names: List[str],
-    ):
-        return cls(
-            class_names=class_names,
-            include=config.include,
-            exclude=config.exclude,
-        )
-
-
-plots_registry.register(ClassificationPRCurvesConfig, ClassificationPRCurves)
-
-
-class DetectionROCCurveConfig(BaseConfig):
-    name: Literal["detection_roc_curve"] = "detection_roc_curve"
-
-
-class DetectionROCCurve(PlotterProtocol):
-    def __call__(self, clip_evaluations: Sequence[ClipEvaluation]):
-        y_true, y_score = zip(
-            *[
-                (match.gt_det, match.pred_score)
-                for clip_eval in clip_evaluations
-                for match in clip_eval.matches
-            ]
-        )
-        fpr, tpr, _ = metrics.roc_curve(y_true, y_score)
-        fig, ax = plt.subplots()
-
-        ax.plot(fpr, tpr, label="Detection")
-        ax.set_xlabel("False Positive Rate")
-        ax.set_ylabel("True Positive Rate")
-        ax.legend()
-
-        yield "detection_roc_curve", fig
-
-    @classmethod
-    def from_config(
-        cls,
-        config: DetectionROCCurveConfig,
-        class_names: List[str],
-    ):
-        return cls()
-
-
-plots_registry.register(DetectionROCCurveConfig, DetectionROCCurve)
-
-
-class ClassificationROCCurvesConfig(BaseConfig):
-    name: Literal["classification_roc_curves"] = "classification_roc_curves"
-    include: Optional[List[str]] = None
-    exclude: Optional[List[str]] = None
-
-
-class ClassificationROCCurves(PlotterProtocol):
-    def __init__(
-        self,
-        class_names: List[str],
-        include: Optional[List[str]] = None,
-        exclude: Optional[List[str]] = None,
-    ):
-        self.class_names = class_names
-        self.selected = class_names
-
-        if include is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name in include
-            ]
-
-        if exclude is not None:
-            self.selected = [
-                class_name
-                for class_name in self.selected
-                if class_name not in exclude
-            ]
-
-    def __call__(self, clip_evaluations: Sequence[ClipEvaluation]):
-        y_true = []
-        y_pred = []
-
-        for clip_eval in clip_evaluations:
-            for match in clip_eval.matches:
-                # Ignore generic unclassified targets
-                if match.gt_det and match.gt_class is None:
-                    continue
-
-                y_true.append(
-                    match.gt_class
-                    if match.gt_class is not None
-                    else "__NONE__"
-                )
-
-                y_pred.append(
-                    np.array(
-                        [
-                            match.pred_class_scores.get(name, 0)
-                            for name in self.class_names
-                        ]
-                    )
-                )
-
-        y_true = label_binarize(y_true, classes=self.class_names)
-        y_pred = np.stack(y_pred)
-
-        fig, ax = plt.subplots(figsize=(10, 10))
-        for class_index, class_name in enumerate(self.class_names):
-            if class_name not in self.selected:
-                continue
-
-            y_true_class = y_true[:, class_index]
-            y_roced_class = y_pred[:, class_index]
-            fpr, tpr, _ = metrics.roc_curve(
-                y_true_class,
-                y_roced_class,
-            )
-            ax.plot(fpr, tpr, label=class_name)
-
-        ax.set_xlabel("False Positive Rate")
-        ax.set_ylabel("True Positive Rate")
-        ax.legend(
-            bbox_to_anchor=(1.05, 1),
-            loc="upper left",
-            borderaxespad=0.0,
-        )
-
-        yield "classification_roc_curve", fig
-
-    @classmethod
-    def from_config(
-        cls,
-        config: ClassificationROCCurvesConfig,
-        class_names: List[str],
-    ):
-        return cls(
-            class_names=class_names,
-            include=config.include,
-            exclude=config.exclude,
-        )
-
-
-plots_registry.register(ClassificationROCCurvesConfig, ClassificationROCCurves)
-
-
-class ConfusionMatrixConfig(BaseConfig):
-    name: Literal["confusion_matrix"] = "confusion_matrix"
-    background_class: str = "noise"
-
-
-class ConfusionMatrix(PlotterProtocol):
-    def __init__(self, background_class: str, class_names: List[str]):
-        self.background_class = background_class
-        self.class_names = class_names
-
-    def __call__(self, clip_evaluations: Sequence[ClipEvaluation]):
-        y_true = []
-        y_pred = []
-
-        for clip_eval in clip_evaluations:
-            for match in clip_eval.matches:
-                # Ignore generic unclassified targets
-                if match.gt_det and match.gt_class is None:
-                    continue
-
-                y_true.append(
-                    match.gt_class
-                    if match.gt_class is not None
-                    else self.background_class
-                )
-
-                top_class = match.pred_class
-                y_pred.append(
-                    top_class
-                    if top_class is not None
-                    else self.background_class
-                )
-
-        display = metrics.ConfusionMatrixDisplay.from_predictions(
-            y_true,
-            y_pred,
-            labels=[*self.class_names, self.background_class],
-        )
-
-        yield "confusion_matrix", display.figure_
-
-    @classmethod
-    def from_config(
-        cls,
-        config: ConfusionMatrixConfig,
-        class_names: List[str],
-    ):
-        return cls(
-            background_class=config.background_class,
-            class_names=class_names,
-        )
-
-
-plots_registry.register(ConfusionMatrixConfig, ConfusionMatrix)
-
-
-PlotConfig = Annotated[
-    Union[
-        ExampleGalleryConfig,
-        ClipEvaluationPlotConfig,
-        DetectionPRCurveConfig,
-        ClassificationPRCurvesConfig,
-        DetectionROCCurveConfig,
-        ClassificationROCCurvesConfig,
-        ConfusionMatrixConfig,
-    ],
-    Field(discriminator="name"),
-]
-
-
-def build_plotter(
-    config: PlotConfig, class_names: List[str]
-) -> PlotterProtocol:
-    return plots_registry.build(config, class_names)
-
-
-@dataclass
-class ClassMatches:
-    false_positives: List[MatchEvaluation] = field(default_factory=list)
-    false_negatives: List[MatchEvaluation] = field(default_factory=list)
-    true_positives: List[MatchEvaluation] = field(default_factory=list)
-    cross_triggers: List[MatchEvaluation] = field(default_factory=list)
-
-
-def group_matches(
-    clip_evaluations: Sequence[ClipEvaluation],
-) -> Dict[str, ClassMatches]:
-    class_examples = defaultdict(ClassMatches)
-
-    for clip_evaluation in clip_evaluations:
-        for match in clip_evaluation.matches:
-            gt_class = match.gt_class
-            pred_class = match.pred_class
-
-            if pred_class is None:
-                class_examples[gt_class].false_negatives.append(match)
-                continue
-
-            if gt_class is None:
-                class_examples[pred_class].false_positives.append(match)
-                continue
-
-            if gt_class != pred_class:
-                class_examples[gt_class].cross_triggers.append(match)
-                class_examples[pred_class].cross_triggers.append(match)
-                continue
-
-            class_examples[gt_class].true_positives.append(match)
-
-    return class_examples
-
-
-def get_binned_sample(matches: List[MatchEvaluation], n_examples: int = 5):
-    if len(matches) < n_examples:
-        return matches
-
-    indices, pred_scores = zip(
-        *[
-            (index, match.pred_class_scores[pred_class])
-            for index, match in enumerate(matches)
-            if (pred_class := match.pred_class) is not None
-        ]
-    )
-
-    bins = pd.qcut(pred_scores, q=n_examples, labels=False, duplicates="drop")
-    df = pd.DataFrame({"indices": indices, "bins": bins})
-    sample = df.groupby("bins").sample(1)
-    return [matches[ind] for ind in sample["indices"]]

src/batdetect2/evaluate/plots/base.py

@@ -0,0 +1,54 @@
+from typing import Optional
+
+import matplotlib.pyplot as plt
+from matplotlib.figure import Figure
+
+from batdetect2.core import BaseConfig
+from batdetect2.typing import TargetProtocol
+
+
+class BasePlotConfig(BaseConfig):
+    label: str = "plot"
+    theme: str = "default"
+    title: Optional[str] = None
+    figsize: tuple[int, int] = (10, 10)
+    dpi: int = 100
+
+
+class BasePlot:
+    def __init__(
+        self,
+        targets: TargetProtocol,
+        label: str = "plot",
+        figsize: tuple[int, int] = (10, 10),
+        title: Optional[str] = None,
+        dpi: int = 100,
+        theme: str = "default",
+    ):
+        self.targets = targets
+        self.label = label
+        self.figsize = figsize
+        self.dpi = dpi
+        self.theme = theme
+        self.title = title
+
+    def create_figure(self) -> Figure:
+        plt.style.use(self.theme)
+        fig = plt.figure(figsize=self.figsize, dpi=self.dpi)
+
+        if self.title is not None:
+            fig.suptitle(self.title)
+
+        return fig
+
+    @classmethod
+    def build(cls, config: BasePlotConfig, targets: TargetProtocol, **kwargs):
+        return cls(
+            targets=targets,
+            figsize=config.figsize,
+            dpi=config.dpi,
+            theme=config.theme,
+            label=config.label,
+            title=config.title,
+            **kwargs,
+        )

src/batdetect2/evaluate/plots/classification.py

@@ -0,0 +1,370 @@
+from typing import (
+    Annotated,
+    Callable,
+    Iterable,
+    Literal,
+    Optional,
+    Sequence,
+    Tuple,
+    Union,
+)
+
+import matplotlib.pyplot as plt
+from matplotlib.figure import Figure
+from pydantic import Field
+from sklearn import metrics
+
+from batdetect2.core import Registry
+from batdetect2.evaluate.metrics.classification import (
+    ClipEval,
+    _extract_per_class_metric_data,
+)
+from batdetect2.evaluate.metrics.common import compute_precision_recall
+from batdetect2.evaluate.plots.base import BasePlot, BasePlotConfig
+from batdetect2.plotting.metrics import (
+    plot_pr_curve,
+    plot_pr_curves,
+    plot_roc_curve,
+    plot_roc_curves,
+    plot_threshold_precision_curve,
+    plot_threshold_precision_curves,
+    plot_threshold_recall_curve,
+    plot_threshold_recall_curves,
+)
+from batdetect2.typing import TargetProtocol
+
+ClassificationPlotter = Callable[
+    [Sequence[ClipEval]], Iterable[Tuple[str, Figure]]
+]
+
+classification_plots: Registry[ClassificationPlotter, [TargetProtocol]] = (
+    Registry("classification_plot")
+)
+
+
+class PRCurveConfig(BasePlotConfig):
+    name: Literal["pr_curve"] = "pr_curve"
+    label: str = "pr_curve"
+    title: Optional[str] = "Classification Precision-Recall Curve"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+    separate_figures: bool = False
+
+
+class PRCurve(BasePlot):
+    def __init__(
+        self,
+        *args,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        separate_figures: bool = False,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+        self.separate_figures = separate_figures
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true, y_score, num_positives = _extract_per_class_metric_data(
+            clip_evaluations,
+            ignore_non_predictions=self.ignore_non_predictions,
+            ignore_generic=self.ignore_generic,
+        )
+
+        data = {
+            class_name: compute_precision_recall(
+                y_true[class_name],
+                y_score[class_name],
+                num_positives=num_positives[class_name],
+            )
+            for class_name in self.targets.class_names
+        }
+
+        if not self.separate_figures:
+            fig = self.create_figure()
+            ax = fig.subplots()
+            plot_pr_curves(data, ax=ax)
+            yield self.label, fig
+            return
+
+        for class_name, (precision, recall, thresholds) in data.items():
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            ax = plot_pr_curve(precision, recall, thresholds, ax=ax)
+            ax.set_title(class_name)
+
+            yield f"{self.label}/{class_name}", fig
+
+            plt.close(fig)
+
+    @classification_plots.register(PRCurveConfig)
+    @staticmethod
+    def from_config(config: PRCurveConfig, targets: TargetProtocol):
+        return PRCurve.build(
+            config=config,
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+            separate_figures=config.separate_figures,
+        )
+
+
+class ThresholdPrecisionCurveConfig(BasePlotConfig):
+    name: Literal["threshold_precision_curve"] = "threshold_precision_curve"
+    label: str = "threshold_precision_curve"
+    title: Optional[str] = "Classification Threshold-Precision Curve"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+    separate_figures: bool = False
+
+
+class ThresholdPrecisionCurve(BasePlot):
+    def __init__(
+        self,
+        *args,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        separate_figures: bool = False,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+        self.separate_figures = separate_figures
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true, y_score, num_positives = _extract_per_class_metric_data(
+            clip_evaluations,
+            ignore_non_predictions=self.ignore_non_predictions,
+            ignore_generic=self.ignore_generic,
+        )
+
+        data = {
+            class_name: compute_precision_recall(
+                y_true[class_name],
+                y_score[class_name],
+                num_positives[class_name],
+            )
+            for class_name in self.targets.class_names
+        }
+
+        if not self.separate_figures:
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            plot_threshold_precision_curves(data, ax=ax)
+
+            yield self.label, fig
+
+            return
+
+        for class_name, (precision, _, thresholds) in data.items():
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            ax = plot_threshold_precision_curve(
+                thresholds,
+                precision,
+                ax=ax,
+            )
+
+            ax.set_title(class_name)
+
+            yield f"{self.label}/{class_name}", fig
+
+            plt.close(fig)
+
+    @classification_plots.register(ThresholdPrecisionCurveConfig)
+    @staticmethod
+    def from_config(
+        config: ThresholdPrecisionCurveConfig, targets: TargetProtocol
+    ):
+        return ThresholdPrecisionCurve.build(
+            config=config,
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+            separate_figures=config.separate_figures,
+        )
+
+
+class ThresholdRecallCurveConfig(BasePlotConfig):
+    name: Literal["threshold_recall_curve"] = "threshold_recall_curve"
+    label: str = "threshold_recall_curve"
+    title: Optional[str] = "Classification Threshold-Recall Curve"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+    separate_figures: bool = False
+
+
+class ThresholdRecallCurve(BasePlot):
+    def __init__(
+        self,
+        *args,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        separate_figures: bool = False,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+        self.separate_figures = separate_figures
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true, y_score, num_positives = _extract_per_class_metric_data(
+            clip_evaluations,
+            ignore_non_predictions=self.ignore_non_predictions,
+            ignore_generic=self.ignore_generic,
+        )
+
+        data = {
+            class_name: compute_precision_recall(
+                y_true[class_name],
+                y_score[class_name],
+                num_positives[class_name],
+            )
+            for class_name in self.targets.class_names
+        }
+
+        if not self.separate_figures:
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            plot_threshold_recall_curves(data, ax=ax, add_legend=True)
+
+            yield self.label, fig
+
+            return
+
+        for class_name, (_, recall, thresholds) in data.items():
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            ax = plot_threshold_recall_curve(
+                thresholds,
+                recall,
+                ax=ax,
+            )
+
+            ax.set_title(class_name)
+
+            yield f"{self.label}/{class_name}", fig
+
+            plt.close(fig)
+
+    @classification_plots.register(ThresholdRecallCurveConfig)
+    @staticmethod
+    def from_config(
+        config: ThresholdRecallCurveConfig, targets: TargetProtocol
+    ):
+        return ThresholdRecallCurve.build(
+            config=config,
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+            separate_figures=config.separate_figures,
+        )
+
+
+class ROCCurveConfig(BasePlotConfig):
+    name: Literal["roc_curve"] = "roc_curve"
+    label: str = "roc_curve"
+    title: Optional[str] = "Classification ROC Curve"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+    separate_figures: bool = False
+
+
+class ROCCurve(BasePlot):
+    def __init__(
+        self,
+        *args,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        separate_figures: bool = False,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+        self.separate_figures = separate_figures
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true, y_score, _ = _extract_per_class_metric_data(
+            clip_evaluations,
+            ignore_non_predictions=self.ignore_non_predictions,
+            ignore_generic=self.ignore_generic,
+        )
+
+        data = {
+            class_name: metrics.roc_curve(
+                y_true[class_name],
+                y_score[class_name],
+            )
+            for class_name in self.targets.class_names
+        }
+
+        if not self.separate_figures:
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            plot_roc_curves(data, ax=ax)
+
+            yield self.label, fig
+
+            return
+
+        for class_name, (fpr, tpr, thresholds) in data.items():
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            ax = plot_roc_curve(fpr, tpr, thresholds, ax=ax)
+            ax.set_title(class_name)
+
+            yield f"{self.label}/{class_name}", fig
+
+            plt.close(fig)
+
+    @classification_plots.register(ROCCurveConfig)
+    @staticmethod
+    def from_config(config: ROCCurveConfig, targets: TargetProtocol):
+        return ROCCurve.build(
+            config=config,
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+            separate_figures=config.separate_figures,
+        )
+
+
+ClassificationPlotConfig = Annotated[
+    Union[
+        PRCurveConfig,
+        ROCCurveConfig,
+        ThresholdPrecisionCurveConfig,
+        ThresholdRecallCurveConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_classification_plotter(
+    config: ClassificationPlotConfig,
+    targets: TargetProtocol,
+) -> ClassificationPlotter:
+    return classification_plots.build(config, targets)

src/batdetect2/evaluate/plots/clip_classification.py

@@ -0,0 +1,189 @@
+from typing import (
+    Annotated,
+    Callable,
+    Iterable,
+    Literal,
+    Optional,
+    Sequence,
+    Tuple,
+    Union,
+)
+
+import matplotlib.pyplot as plt
+from matplotlib.figure import Figure
+from pydantic import Field
+from sklearn import metrics
+
+from batdetect2.core import Registry
+from batdetect2.evaluate.metrics.clip_classification import ClipEval
+from batdetect2.evaluate.metrics.common import compute_precision_recall
+from batdetect2.evaluate.plots.base import BasePlot, BasePlotConfig
+from batdetect2.plotting.metrics import (
+    plot_pr_curve,
+    plot_pr_curves,
+    plot_roc_curve,
+    plot_roc_curves,
+)
+from batdetect2.typing import TargetProtocol
+
+__all__ = [
+    "ClipClassificationPlotConfig",
+    "ClipClassificationPlotter",
+    "build_clip_classification_plotter",
+]
+
+ClipClassificationPlotter = Callable[
+    [Sequence[ClipEval]], Iterable[Tuple[str, Figure]]
+]
+
+clip_classification_plots: Registry[
+    ClipClassificationPlotter, [TargetProtocol]
+] = Registry("clip_classification_plot")
+
+
+class PRCurveConfig(BasePlotConfig):
+    name: Literal["pr_curve"] = "pr_curve"
+    label: str = "pr_curve"
+    title: Optional[str] = "Clip Classification Precision-Recall Curve"
+    separate_figures: bool = False
+
+
+class PRCurve(BasePlot):
+    def __init__(
+        self,
+        *args,
+        separate_figures: bool = False,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.separate_figures = separate_figures
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        data = {}
+
+        for class_name in self.targets.class_names:
+            y_true = [class_name in c.true_classes for c in clip_evaluations]
+            y_score = [
+                c.class_scores.get(class_name, 0) for c in clip_evaluations
+            ]
+
+            precision, recall, thresholds = compute_precision_recall(
+                y_true,
+                y_score,
+            )
+
+            data[class_name] = (precision, recall, thresholds)
+
+        if not self.separate_figures:
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            plot_pr_curves(data, ax=ax)
+
+            yield self.label, fig
+
+            return
+
+        for class_name, (precision, recall, thresholds) in data.items():
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            ax = plot_pr_curve(precision, recall, thresholds, ax=ax)
+            ax.set_title(class_name)
+
+            yield f"{self.label}/{class_name}", fig
+
+            plt.close(fig)
+
+    @clip_classification_plots.register(PRCurveConfig)
+    @staticmethod
+    def from_config(config: PRCurveConfig, targets: TargetProtocol):
+        return PRCurve.build(
+            config=config,
+            targets=targets,
+            separate_figures=config.separate_figures,
+        )
+
+
+class ROCCurveConfig(BasePlotConfig):
+    name: Literal["roc_curve"] = "roc_curve"
+    label: str = "roc_curve"
+    title: Optional[str] = "Clip Classification ROC Curve"
+    separate_figures: bool = False
+
+
+class ROCCurve(BasePlot):
+    def __init__(
+        self,
+        *args,
+        separate_figures: bool = False,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.separate_figures = separate_figures
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        data = {}
+
+        for class_name in self.targets.class_names:
+            y_true = [class_name in c.true_classes for c in clip_evaluations]
+            y_score = [
+                c.class_scores.get(class_name, 0) for c in clip_evaluations
+            ]
+
+            fpr, tpr, thresholds = metrics.roc_curve(
+                y_true,
+                y_score,
+            )
+
+            data[class_name] = (fpr, tpr, thresholds)
+
+        if not self.separate_figures:
+            fig = self.create_figure()
+            ax = fig.subplots()
+            plot_roc_curves(data, ax=ax)
+            yield self.label, fig
+
+            return
+
+        for class_name, (fpr, tpr, thresholds) in data.items():
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            ax = plot_roc_curve(fpr, tpr, thresholds, ax=ax)
+            ax.set_title(class_name)
+
+            yield f"{self.label}/{class_name}", fig
+
+            plt.close(fig)
+
+    @clip_classification_plots.register(ROCCurveConfig)
+    @staticmethod
+    def from_config(config: ROCCurveConfig, targets: TargetProtocol):
+        return ROCCurve.build(
+            config=config,
+            targets=targets,
+            separate_figures=config.separate_figures,
+        )
+
+
+ClipClassificationPlotConfig = Annotated[
+    Union[
+        PRCurveConfig,
+        ROCCurveConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_clip_classification_plotter(
+    config: ClipClassificationPlotConfig,
+    targets: TargetProtocol,
+) -> ClipClassificationPlotter:
+    return clip_classification_plots.build(config, targets)

src/batdetect2/evaluate/plots/clip_detection.py

@@ -0,0 +1,163 @@
+from typing import (
+    Annotated,
+    Callable,
+    Iterable,
+    Literal,
+    Optional,
+    Sequence,
+    Tuple,
+    Union,
+)
+
+import pandas as pd
+import seaborn as sns
+from matplotlib.figure import Figure
+from pydantic import Field
+from sklearn import metrics
+
+from batdetect2.core import Registry
+from batdetect2.evaluate.metrics.clip_detection import ClipEval
+from batdetect2.evaluate.metrics.common import compute_precision_recall
+from batdetect2.evaluate.plots.base import BasePlot, BasePlotConfig
+from batdetect2.plotting.metrics import plot_pr_curve, plot_roc_curve
+from batdetect2.typing import TargetProtocol
+
+__all__ = [
+    "ClipDetectionPlotConfig",
+    "ClipDetectionPlotter",
+    "build_clip_detection_plotter",
+]
+
+ClipDetectionPlotter = Callable[
+    [Sequence[ClipEval]], Iterable[Tuple[str, Figure]]
+]
+
+
+clip_detection_plots: Registry[ClipDetectionPlotter, [TargetProtocol]] = (
+    Registry("clip_detection_plot")
+)
+
+
+class PRCurveConfig(BasePlotConfig):
+    name: Literal["pr_curve"] = "pr_curve"
+    label: str = "pr_curve"
+    title: Optional[str] = "Clip Detection Precision-Recall Curve"
+
+
+class PRCurve(BasePlot):
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true = [c.gt_det for c in clip_evaluations]
+        y_score = [c.score for c in clip_evaluations]
+
+        precision, recall, thresholds = compute_precision_recall(
+            y_true,
+            y_score,
+        )
+
+        fig = self.create_figure()
+        ax = fig.subplots()
+        plot_pr_curve(precision, recall, thresholds, ax=ax)
+        yield self.label, fig
+
+    @clip_detection_plots.register(PRCurveConfig)
+    @staticmethod
+    def from_config(config: PRCurveConfig, targets: TargetProtocol):
+        return PRCurve.build(
+            config=config,
+            targets=targets,
+        )
+
+
+class ROCCurveConfig(BasePlotConfig):
+    name: Literal["roc_curve"] = "roc_curve"
+    label: str = "roc_curve"
+    title: Optional[str] = "Clip Detection ROC Curve"
+
+
+class ROCCurve(BasePlot):
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true = [c.gt_det for c in clip_evaluations]
+        y_score = [c.score for c in clip_evaluations]
+
+        fpr, tpr, thresholds = metrics.roc_curve(
+            y_true,
+            y_score,
+        )
+
+        fig = self.create_figure()
+        ax = fig.subplots()
+        plot_roc_curve(fpr, tpr, thresholds, ax=ax)
+        yield self.label, fig
+
+    @clip_detection_plots.register(ROCCurveConfig)
+    @staticmethod
+    def from_config(config: ROCCurveConfig, targets: TargetProtocol):
+        return ROCCurve.build(
+            config=config,
+            targets=targets,
+        )
+
+
+class ScoreDistributionPlotConfig(BasePlotConfig):
+    name: Literal["score_distribution"] = "score_distribution"
+    label: str = "score_distribution"
+    title: Optional[str] = "Clip Detection Score Distribution"
+
+
+class ScoreDistributionPlot(BasePlot):
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true = [c.gt_det for c in clip_evaluations]
+        y_score = [c.score for c in clip_evaluations]
+
+        fig = self.create_figure()
+        ax = fig.subplots()
+
+        df = pd.DataFrame({"is_true": y_true, "score": y_score})
+        sns.histplot(
+            data=df,
+            x="score",
+            binwidth=0.025,
+            binrange=(0, 1),
+            hue="is_true",
+            ax=ax,
+            stat="probability",
+            common_norm=False,
+        )
+
+        yield self.label, fig
+
+    @clip_detection_plots.register(ScoreDistributionPlotConfig)
+    @staticmethod
+    def from_config(
+        config: ScoreDistributionPlotConfig, targets: TargetProtocol
+    ):
+        return ScoreDistributionPlot.build(
+            config=config,
+            targets=targets,
+        )
+
+
+ClipDetectionPlotConfig = Annotated[
+    Union[
+        PRCurveConfig,
+        ROCCurveConfig,
+        ScoreDistributionPlotConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_clip_detection_plotter(
+    config: ClipDetectionPlotConfig,
+    targets: TargetProtocol,
+) -> ClipDetectionPlotter:
+    return clip_detection_plots.build(config, targets)

src/batdetect2/evaluate/plots/detection.py

@@ -0,0 +1,309 @@
+import random
+from typing import (
+    Annotated,
+    Callable,
+    Iterable,
+    Literal,
+    Optional,
+    Sequence,
+    Tuple,
+    Union,
+)
+
+import matplotlib.pyplot as plt
+import pandas as pd
+import seaborn as sns
+from matplotlib.figure import Figure
+from pydantic import Field
+from sklearn import metrics
+
+from batdetect2.audio import AudioConfig, build_audio_loader
+from batdetect2.core import Registry
+from batdetect2.evaluate.metrics.common import compute_precision_recall
+from batdetect2.evaluate.metrics.detection import ClipEval
+from batdetect2.evaluate.plots.base import BasePlot, BasePlotConfig
+from batdetect2.plotting.detections import plot_clip_detections
+from batdetect2.plotting.metrics import plot_pr_curve, plot_roc_curve
+from batdetect2.preprocess import PreprocessingConfig, build_preprocessor
+from batdetect2.typing import AudioLoader, PreprocessorProtocol, TargetProtocol
+
+DetectionPlotter = Callable[[Sequence[ClipEval]], Iterable[Tuple[str, Figure]]]
+
+detection_plots: Registry[DetectionPlotter, [TargetProtocol]] = Registry(
+    name="detection_plot"
+)
+
+
+class PRCurveConfig(BasePlotConfig):
+    name: Literal["pr_curve"] = "pr_curve"
+    label: str = "pr_curve"
+    title: Optional[str] = "Detection Precision-Recall Curve"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+
+
+class PRCurve(BasePlot):
+    def __init__(
+        self,
+        *args,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+
+    def __call__(
+        self,
+        clip_evals: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true = []
+        y_score = []
+        num_positives = 0
+
+        for clip_eval in clip_evals:
+            for m in clip_eval.matches:
+                num_positives += int(m.is_ground_truth)
+
+                # Ignore matches that don't correspond to a prediction
+                if not m.is_prediction and self.ignore_non_predictions:
+                    continue
+
+                y_true.append(m.is_ground_truth)
+                y_score.append(m.score)
+
+        precision, recall, thresholds = compute_precision_recall(
+            y_true,
+            y_score,
+            num_positives=num_positives,
+        )
+
+        fig = self.create_figure()
+        ax = fig.subplots()
+
+        plot_pr_curve(precision, recall, thresholds, ax=ax)
+
+        yield self.label, fig
+
+    @detection_plots.register(PRCurveConfig)
+    @staticmethod
+    def from_config(config: PRCurveConfig, targets: TargetProtocol):
+        return PRCurve.build(
+            config=config,
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+        )
+
+
+class ROCCurveConfig(BasePlotConfig):
+    name: Literal["roc_curve"] = "roc_curve"
+    label: str = "roc_curve"
+    title: Optional[str] = "Detection ROC Curve"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+
+
+class ROCCurve(BasePlot):
+    def __init__(
+        self,
+        *args,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true = []
+        y_score = []
+
+        for clip_eval in clip_evaluations:
+            for m in clip_eval.matches:
+                if not m.is_prediction and self.ignore_non_predictions:
+                    # Ignore matches that don't correspond to a prediction
+                    continue
+
+                y_true.append(m.is_ground_truth)
+                y_score.append(m.score)
+
+        fpr, tpr, thresholds = metrics.roc_curve(
+            y_true,
+            y_score,
+        )
+
+        fig = self.create_figure()
+        ax = fig.subplots()
+
+        plot_roc_curve(fpr, tpr, thresholds, ax=ax)
+
+        yield self.label, fig
+
+    @detection_plots.register(ROCCurveConfig)
+    @staticmethod
+    def from_config(config: ROCCurveConfig, targets: TargetProtocol):
+        return ROCCurve.build(
+            config=config,
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+        )
+
+
+class ScoreDistributionPlotConfig(BasePlotConfig):
+    name: Literal["score_distribution"] = "score_distribution"
+    label: str = "score_distribution"
+    title: Optional[str] = "Detection Score Distribution"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+
+
+class ScoreDistributionPlot(BasePlot):
+    def __init__(
+        self,
+        *args,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true = []
+        y_score = []
+
+        for clip_eval in clip_evaluations:
+            for m in clip_eval.matches:
+                if not m.is_prediction and self.ignore_non_predictions:
+                    # Ignore matches that don't correspond to a prediction
+                    continue
+
+                y_true.append(m.is_ground_truth)
+                y_score.append(m.score)
+
+        df = pd.DataFrame({"is_true": y_true, "score": y_score})
+
+        fig = self.create_figure()
+        ax = fig.subplots()
+
+        sns.histplot(
+            data=df,
+            x="score",
+            binwidth=0.025,
+            binrange=(0, 1),
+            hue="is_true",
+            ax=ax,
+            stat="probability",
+            common_norm=False,
+        )
+
+        yield self.label, fig
+
+    @detection_plots.register(ScoreDistributionPlotConfig)
+    @staticmethod
+    def from_config(
+        config: ScoreDistributionPlotConfig, targets: TargetProtocol
+    ):
+        return ScoreDistributionPlot.build(
+            config=config,
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+        )
+
+
+class ExampleDetectionPlotConfig(BasePlotConfig):
+    name: Literal["example_detection"] = "example_detection"
+    label: str = "example_detection"
+    title: Optional[str] = "Example Detection"
+    figsize: tuple[int, int] = (10, 4)
+    num_examples: int = 5
+    threshold: float = 0.2
+    audio: AudioConfig = Field(default_factory=AudioConfig)
+    preprocessing: PreprocessingConfig = Field(
+        default_factory=PreprocessingConfig
+    )
+
+
+class ExampleDetectionPlot(BasePlot):
+    def __init__(
+        self,
+        *args,
+        num_examples: int = 5,
+        threshold: float = 0.2,
+        audio_loader: AudioLoader,
+        preprocessor: PreprocessorProtocol,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.num_examples = num_examples
+        self.audio_loader = audio_loader
+        self.threshold = threshold
+        self.preprocessor = preprocessor
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        sample = clip_evaluations
+
+        if self.num_examples < len(sample):
+            sample = random.sample(sample, self.num_examples)
+
+        for num_example, clip_eval in enumerate(sample):
+            fig = self.create_figure()
+            ax = fig.subplots()
+
+            plot_clip_detections(
+                clip_eval,
+                ax=ax,
+                audio_loader=self.audio_loader,
+                preprocessor=self.preprocessor,
+            )
+
+            yield f"{self.label}/example_{num_example}", fig
+
+            plt.close(fig)
+
+    @detection_plots.register(ExampleDetectionPlotConfig)
+    @staticmethod
+    def from_config(
+        config: ExampleDetectionPlotConfig,
+        targets: TargetProtocol,
+    ):
+        return ExampleDetectionPlot.build(
+            config=config,
+            targets=targets,
+            num_examples=config.num_examples,
+            audio_loader=build_audio_loader(config.audio),
+            preprocessor=build_preprocessor(config.preprocessing),
+        )
+
+
+DetectionPlotConfig = Annotated[
+    Union[
+        PRCurveConfig,
+        ROCCurveConfig,
+        ScoreDistributionPlotConfig,
+        ExampleDetectionPlotConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_detection_plotter(
+    config: DetectionPlotConfig,
+    targets: TargetProtocol,
+) -> DetectionPlotter:
+    return detection_plots.build(config, targets)

src/batdetect2/evaluate/plots/top_class.py

@@ -0,0 +1,444 @@
+import random
+from collections import defaultdict
+from dataclasses import dataclass, field
+from typing import (
+    Annotated,
+    Callable,
+    Dict,
+    Iterable,
+    List,
+    Literal,
+    Optional,
+    Sequence,
+    Tuple,
+    Union,
+)
+
+import matplotlib.pyplot as plt
+import pandas as pd
+from matplotlib.figure import Figure
+from pydantic import Field
+from sklearn import metrics
+
+from batdetect2.audio import AudioConfig, build_audio_loader
+from batdetect2.core import Registry
+from batdetect2.evaluate.metrics.common import compute_precision_recall
+from batdetect2.evaluate.metrics.top_class import ClipEval, MatchEval
+from batdetect2.evaluate.plots.base import BasePlot, BasePlotConfig
+from batdetect2.plotting.gallery import plot_match_gallery
+from batdetect2.plotting.metrics import plot_pr_curve, plot_roc_curve
+from batdetect2.preprocess import PreprocessingConfig, build_preprocessor
+from batdetect2.typing import AudioLoader, PreprocessorProtocol, TargetProtocol
+
+TopClassPlotter = Callable[[Sequence[ClipEval]], Iterable[Tuple[str, Figure]]]
+
+top_class_plots: Registry[TopClassPlotter, [TargetProtocol]] = Registry(
+    name="top_class_plot"
+)
+
+
+class PRCurveConfig(BasePlotConfig):
+    name: Literal["pr_curve"] = "pr_curve"
+    label: str = "pr_curve"
+    title: Optional[str] = "Top Class Precision-Recall Curve"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+
+
+class PRCurve(BasePlot):
+    def __init__(
+        self,
+        *args,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true = []
+        y_score = []
+        num_positives = 0
+
+        for clip_eval in clip_evaluations:
+            for m in clip_eval.matches:
+                if m.is_generic and self.ignore_generic:
+                    # Ignore gt sounds with unknown class
+                    continue
+
+                num_positives += int(m.is_ground_truth)
+
+                if not m.is_prediction and self.ignore_non_predictions:
+                    # Ignore non predictions
+                    continue
+
+                y_true.append(m.pred_class == m.true_class)
+                y_score.append(m.score)
+
+        precision, recall, thresholds = compute_precision_recall(
+            y_true,
+            y_score,
+            num_positives=num_positives,
+        )
+
+        fig = self.create_figure()
+        ax = fig.subplots()
+
+        plot_pr_curve(precision, recall, thresholds, ax=ax)
+
+        yield self.label, fig
+
+    @top_class_plots.register(PRCurveConfig)
+    @staticmethod
+    def from_config(config: PRCurveConfig, targets: TargetProtocol):
+        return PRCurve.build(
+            config=config,
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+        )
+
+
+class ROCCurveConfig(BasePlotConfig):
+    name: Literal["roc_curve"] = "roc_curve"
+    label: str = "roc_curve"
+    title: Optional[str] = "Top Class ROC Curve"
+    ignore_non_predictions: bool = True
+    ignore_generic: bool = True
+
+
+class ROCCurve(BasePlot):
+    def __init__(
+        self,
+        *args,
+        ignore_non_predictions: bool = True,
+        ignore_generic: bool = True,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.ignore_non_predictions = ignore_non_predictions
+        self.ignore_generic = ignore_generic
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true = []
+        y_score = []
+
+        for clip_eval in clip_evaluations:
+            for m in clip_eval.matches:
+                if m.is_generic and self.ignore_generic:
+                    # Ignore gt sounds with unknown class
+                    continue
+
+                if not m.is_prediction and self.ignore_non_predictions:
+                    # Ignore non predictions
+                    continue
+
+                y_true.append(m.pred_class == m.true_class)
+                y_score.append(m.score)
+
+        fpr, tpr, thresholds = metrics.roc_curve(
+            y_true,
+            y_score,
+        )
+
+        fig = self.create_figure()
+        ax = fig.subplots()
+
+        plot_roc_curve(fpr, tpr, thresholds, ax=ax)
+
+        yield self.label, fig
+
+    @top_class_plots.register(ROCCurveConfig)
+    @staticmethod
+    def from_config(config: ROCCurveConfig, targets: TargetProtocol):
+        return ROCCurve.build(
+            config=config,
+            targets=targets,
+            ignore_non_predictions=config.ignore_non_predictions,
+            ignore_generic=config.ignore_generic,
+        )
+
+
+class ConfusionMatrixConfig(BasePlotConfig):
+    name: Literal["confusion_matrix"] = "confusion_matrix"
+    title: Optional[str] = "Top Class Confusion Matrix"
+    figsize: tuple[int, int] = (10, 10)
+    label: str = "confusion_matrix"
+    exclude_generic: bool = True
+    exclude_noise: bool = False
+    noise_class: str = "noise"
+    normalize: Literal["true", "pred", "all", "none"] = "true"
+    threshold: float = 0.2
+    add_colorbar: bool = True
+    cmap: str = "Blues"
+
+
+class ConfusionMatrix(BasePlot):
+    def __init__(
+        self,
+        *args,
+        exclude_generic: bool = True,
+        exclude_noise: bool = False,
+        noise_class: str = "noise",
+        add_colorbar: bool = True,
+        normalize: Literal["true", "pred", "all", "none"] = "true",
+        cmap: str = "Blues",
+        threshold: float = 0.2,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.exclude_generic = exclude_generic
+        self.exclude_noise = exclude_noise
+        self.noise_class = noise_class
+        self.normalize = normalize
+        self.add_colorbar = add_colorbar
+        self.threshold = threshold
+        self.cmap = cmap
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        y_true: List[str] = []
+        y_pred: List[str] = []
+
+        for clip_eval in clip_evaluations:
+            for m in clip_eval.matches:
+                true_class = m.true_class
+                pred_class = m.pred_class
+
+                if not m.is_prediction and self.exclude_noise:
+                    # Ignore matches that don't correspond to a prediction
+                    continue
+
+                if not m.is_ground_truth and self.exclude_noise:
+                    # Ignore matches that don't correspond to a ground truth
+                    continue
+
+                if m.score < self.threshold:
+                    if self.exclude_noise:
+                        continue
+
+                    pred_class = self.noise_class
+
+                if m.is_generic:
+                    if self.exclude_generic:
+                        # Ignore gt sounds with unknown class
+                        continue
+
+                    true_class = self.targets.detection_class_name
+
+                y_true.append(true_class or self.noise_class)
+                y_pred.append(pred_class or self.noise_class)
+
+        fig = self.create_figure()
+        ax = fig.subplots()
+
+        class_names = [*self.targets.class_names]
+
+        if not self.exclude_generic:
+            class_names.append(self.targets.detection_class_name)
+
+        if not self.exclude_noise:
+            class_names.append(self.noise_class)
+
+        metrics.ConfusionMatrixDisplay.from_predictions(
+            y_true,
+            y_pred,
+            labels=class_names,
+            ax=ax,
+            xticks_rotation="vertical",
+            cmap=self.cmap,
+            colorbar=self.add_colorbar,
+            normalize=self.normalize if self.normalize != "none" else None,
+            values_format=".2f",
+        )
+
+        yield self.label, fig
+
+    @top_class_plots.register(ConfusionMatrixConfig)
+    @staticmethod
+    def from_config(config: ConfusionMatrixConfig, targets: TargetProtocol):
+        return ConfusionMatrix.build(
+            config=config,
+            targets=targets,
+            exclude_generic=config.exclude_generic,
+            exclude_noise=config.exclude_noise,
+            noise_class=config.noise_class,
+            add_colorbar=config.add_colorbar,
+            normalize=config.normalize,
+            cmap=config.cmap,
+        )
+
+
+class ExampleClassificationPlotConfig(BasePlotConfig):
+    name: Literal["example_classification"] = "example_classification"
+    label: str = "example_classification"
+    title: Optional[str] = "Example Classification"
+    num_examples: int = 4
+    threshold: float = 0.2
+    audio: AudioConfig = Field(default_factory=AudioConfig)
+    preprocessing: PreprocessingConfig = Field(
+        default_factory=PreprocessingConfig
+    )
+
+
+class ExampleClassificationPlot(BasePlot):
+    def __init__(
+        self,
+        *args,
+        num_examples: int = 4,
+        threshold: float = 0.2,
+        audio_loader: AudioLoader,
+        preprocessor: PreprocessorProtocol,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.num_examples = num_examples
+        self.audio_loader = audio_loader
+        self.threshold = threshold
+        self.preprocessor = preprocessor
+        self.num_examples = num_examples
+
+    def __call__(
+        self,
+        clip_evaluations: Sequence[ClipEval],
+    ) -> Iterable[Tuple[str, Figure]]:
+        grouped = group_matches(clip_evaluations, threshold=self.threshold)
+
+        for class_name, matches in grouped.items():
+            true_positives: List[MatchEval] = get_binned_sample(
+                matches.true_positives,
+                n_examples=self.num_examples,
+            )
+
+            false_positives: List[MatchEval] = get_binned_sample(
+                matches.false_positives,
+                n_examples=self.num_examples,
+            )
+
+            false_negatives: List[MatchEval] = random.sample(
+                matches.false_negatives,
+                k=min(self.num_examples, len(matches.false_negatives)),
+            )
+
+            cross_triggers: List[MatchEval] = get_binned_sample(
+                matches.cross_triggers, n_examples=self.num_examples
+            )
+
+            fig = self.create_figure()
+
+            fig = plot_match_gallery(
+                true_positives,
+                false_positives,
+                false_negatives,
+                cross_triggers,
+                preprocessor=self.preprocessor,
+                audio_loader=self.audio_loader,
+                n_examples=self.num_examples,
+                fig=fig,
+            )
+
+            if self.title is not None:
+                fig.suptitle(f"{self.title}: {class_name}")
+            else:
+                fig.suptitle(class_name)
+
+            yield f"{self.label}/{class_name}", fig
+
+            plt.close(fig)
+
+    @top_class_plots.register(ExampleClassificationPlotConfig)
+    @staticmethod
+    def from_config(
+        config: ExampleClassificationPlotConfig,
+        targets: TargetProtocol,
+    ):
+        return ExampleClassificationPlot.build(
+            config=config,
+            targets=targets,
+            num_examples=config.num_examples,
+            threshold=config.threshold,
+            audio_loader=build_audio_loader(config.audio),
+            preprocessor=build_preprocessor(config.preprocessing),
+        )
+
+
+TopClassPlotConfig = Annotated[
+    Union[
+        PRCurveConfig,
+        ROCCurveConfig,
+        ConfusionMatrixConfig,
+        ExampleClassificationPlotConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_top_class_plotter(
+    config: TopClassPlotConfig,
+    targets: TargetProtocol,
+) -> TopClassPlotter:
+    return top_class_plots.build(config, targets)
+
+
+@dataclass
+class ClassMatches:
+    false_positives: List[MatchEval] = field(default_factory=list)
+    false_negatives: List[MatchEval] = field(default_factory=list)
+    true_positives: List[MatchEval] = field(default_factory=list)
+    cross_triggers: List[MatchEval] = field(default_factory=list)
+
+
+def group_matches(
+    clip_evals: Sequence[ClipEval],
+    threshold: float = 0.2,
+) -> Dict[str, ClassMatches]:
+    class_examples = defaultdict(ClassMatches)
+
+    for clip_eval in clip_evals:
+        for match in clip_eval.matches:
+            gt_class = match.true_class
+            pred_class = match.pred_class
+            is_pred = match.score >= threshold
+
+            if not is_pred and gt_class is not None:
+                class_examples[gt_class].false_negatives.append(match)
+                continue
+
+            if not is_pred:
+                continue
+
+            if gt_class is None:
+                class_examples[pred_class].false_positives.append(match)
+                continue
+
+            if gt_class != pred_class:
+                class_examples[pred_class].cross_triggers.append(match)
+                continue
+
+            class_examples[gt_class].true_positives.append(match)
+
+    return class_examples
+
+
+def get_binned_sample(matches: List[MatchEval], n_examples: int = 5):
+    if len(matches) < n_examples:
+        return matches
+
+    indices, pred_scores = zip(
+        *[(index, match.score) for index, match in enumerate(matches)]
+    )
+
+    bins = pd.qcut(pred_scores, q=n_examples, labels=False, duplicates="drop")
+    df = pd.DataFrame({"indices": indices, "bins": bins})
+    sample = df.groupby("bins").sample(1)
+    return [matches[ind] for ind in sample["indices"]]

src/batdetect2/evaluate/tables.py

@@ -5,9 +5,9 @@ from pydantic import Field
 from soundevent.geometry import compute_bounds
 
 from batdetect2.core import BaseConfig, Registry
-from batdetect2.typing import ClipEvaluation
+from batdetect2.typing import ClipMatches
 
-EvaluationTableGenerator = Callable[[Sequence[ClipEvaluation]], pd.DataFrame]
+EvaluationTableGenerator = Callable[[Sequence[ClipMatches]], pd.DataFrame]
 
 
 tables_registry: Registry[EvaluationTableGenerator, []] = Registry(
@@ -21,20 +21,18 @@ class FullEvaluationTableConfig(BaseConfig):
 
 class FullEvaluationTable:
     def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
+        self, clip_evaluations: Sequence[ClipMatches]
     ) -> pd.DataFrame:
         return extract_matches_dataframe(clip_evaluations)
 
-    @classmethod
+    @tables_registry.register(FullEvaluationTableConfig)
-    def from_config(cls, config: FullEvaluationTableConfig):
+    @staticmethod
-        return cls()
+    def from_config(config: FullEvaluationTableConfig):
-
+        return FullEvaluationTable()
-
-tables_registry.register(FullEvaluationTableConfig, FullEvaluationTable)
 
 
 def extract_matches_dataframe(
-    clip_evaluations: Sequence[ClipEvaluation],
+    clip_evaluations: Sequence[ClipMatches],
 ) -> pd.DataFrame:
     data = []
 
@@ -78,8 +76,8 @@ def extract_matches_dataframe(
                     ("gt", "low_freq"): gt_low_freq,
                     ("gt", "high_freq"): gt_high_freq,
                     ("pred", "score"): match.pred_score,
-                    ("pred", "class"): match.pred_class,
+                    ("pred", "class"): match.top_class,
-                    ("pred", "class_score"): match.pred_class_score,
+                    ("pred", "class_score"): match.top_class_score,
                     ("pred", "start_time"): pred_start_time,
                     ("pred", "end_time"): pred_end_time,
                     ("pred", "low_freq"): pred_low_freq,

src/batdetect2/evaluate/tasks/__init__.py

@@ -0,0 +1,39 @@
+from typing import Annotated, Optional, Union
+
+from pydantic import Field
+
+from batdetect2.evaluate.tasks.base import tasks_registry
+from batdetect2.evaluate.tasks.classification import ClassificationTaskConfig
+from batdetect2.evaluate.tasks.clip_classification import (
+    ClipClassificationTaskConfig,
+)
+from batdetect2.evaluate.tasks.clip_detection import ClipDetectionTaskConfig
+from batdetect2.evaluate.tasks.detection import DetectionTaskConfig
+from batdetect2.evaluate.tasks.top_class import TopClassDetectionTaskConfig
+from batdetect2.targets import build_targets
+from batdetect2.typing import EvaluatorProtocol, TargetProtocol
+
+__all__ = [
+    "TaskConfig",
+    "build_task",
+]
+
+
+TaskConfig = Annotated[
+    Union[
+        ClassificationTaskConfig,
+        DetectionTaskConfig,
+        ClipDetectionTaskConfig,
+        ClipClassificationTaskConfig,
+        TopClassDetectionTaskConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_task(
+    config: TaskConfig,
+    targets: Optional[TargetProtocol] = None,
+) -> EvaluatorProtocol:
+    targets = targets or build_targets()
+    return tasks_registry.build(config, targets)

src/batdetect2/evaluate/tasks/base.py

@@ -0,0 +1,175 @@
+from typing import (
+    Callable,
+    Dict,
+    Generic,
+    Iterable,
+    List,
+    Optional,
+    Sequence,
+    Tuple,
+    TypeVar,
+)
+
+from matplotlib.figure import Figure
+from pydantic import Field
+from soundevent import data
+from soundevent.geometry import compute_bounds
+
+from batdetect2.core import BaseConfig
+from batdetect2.core.registries import Registry
+from batdetect2.evaluate.match import (
+    MatchConfig,
+    StartTimeMatchConfig,
+    build_matcher,
+)
+from batdetect2.typing.evaluate import EvaluatorProtocol, MatcherProtocol
+from batdetect2.typing.postprocess import RawPrediction
+from batdetect2.typing.targets import TargetProtocol
+
+__all__ = [
+    "BaseTaskConfig",
+    "BaseTask",
+]
+
+tasks_registry: Registry[EvaluatorProtocol, [TargetProtocol]] = Registry(
+    "tasks"
+)
+
+
+T_Output = TypeVar("T_Output")
+
+
+class BaseTaskConfig(BaseConfig):
+    prefix: str
+    ignore_start_end: float = 0.01
+    matching_strategy: MatchConfig = Field(
+        default_factory=StartTimeMatchConfig
+    )
+
+
+class BaseTask(EvaluatorProtocol, Generic[T_Output]):
+    targets: TargetProtocol
+
+    matcher: MatcherProtocol
+
+    metrics: List[Callable[[Sequence[T_Output]], Dict[str, float]]]
+
+    plots: List[Callable[[Sequence[T_Output]], Iterable[Tuple[str, Figure]]]]
+
+    ignore_start_end: float
+
+    prefix: str
+
+    def __init__(
+        self,
+        matcher: MatcherProtocol,
+        targets: TargetProtocol,
+        metrics: List[Callable[[Sequence[T_Output]], Dict[str, float]]],
+        prefix: str,
+        ignore_start_end: float = 0.01,
+        plots: Optional[
+            List[Callable[[Sequence[T_Output]], Iterable[Tuple[str, Figure]]]]
+        ] = None,
+    ):
+        self.matcher = matcher
+        self.metrics = metrics
+        self.plots = plots or []
+        self.targets = targets
+        self.prefix = prefix
+        self.ignore_start_end = ignore_start_end
+
+    def compute_metrics(
+        self,
+        eval_outputs: List[T_Output],
+    ) -> Dict[str, float]:
+        scores = [metric(eval_outputs) for metric in self.metrics]
+        return {
+            f"{self.prefix}/{name}": score
+            for metric_output in scores
+            for name, score in metric_output.items()
+        }
+
+    def generate_plots(
+        self, eval_outputs: List[T_Output]
+    ) -> Iterable[Tuple[str, Figure]]:
+        for plot in self.plots:
+            for name, fig in plot(eval_outputs):
+                yield f"{self.prefix}/{name}", fig
+
+    def evaluate(
+        self,
+        clip_annotations: Sequence[data.ClipAnnotation],
+        predictions: Sequence[Sequence[RawPrediction]],
+    ) -> List[T_Output]:
+        return [
+            self.evaluate_clip(clip_annotation, preds)
+            for clip_annotation, preds in zip(clip_annotations, predictions)
+        ]
+
+    def evaluate_clip(
+        self,
+        clip_annotation: data.ClipAnnotation,
+        predictions: Sequence[RawPrediction],
+    ) -> T_Output: ...
+
+    def include_sound_event_annotation(
+        self,
+        sound_event_annotation: data.SoundEventAnnotation,
+        clip: data.Clip,
+    ) -> bool:
+        if not self.targets.filter(sound_event_annotation):
+            return False
+
+        geometry = sound_event_annotation.sound_event.geometry
+        if geometry is None:
+            return False
+
+        return is_in_bounds(
+            geometry,
+            clip,
+            self.ignore_start_end,
+        )
+
+    def include_prediction(
+        self,
+        prediction: RawPrediction,
+        clip: data.Clip,
+    ) -> bool:
+        return is_in_bounds(
+            prediction.geometry,
+            clip,
+            self.ignore_start_end,
+        )
+
+    @classmethod
+    def build(
+        cls,
+        config: BaseTaskConfig,
+        targets: TargetProtocol,
+        metrics: List[Callable[[Sequence[T_Output]], Dict[str, float]]],
+        plots: Optional[
+            List[Callable[[Sequence[T_Output]], Iterable[Tuple[str, Figure]]]]
+        ] = None,
+        **kwargs,
+    ):
+        matcher = build_matcher(config.matching_strategy)
+        return cls(
+            matcher=matcher,
+            targets=targets,
+            metrics=metrics,
+            plots=plots,
+            prefix=config.prefix,
+            ignore_start_end=config.ignore_start_end,
+            **kwargs,
+        )
+
+
+def is_in_bounds(
+    geometry: data.Geometry,
+    clip: data.Clip,
+    buffer: float,
+) -> bool:
+    start_time = compute_bounds(geometry)[0]
+    return (start_time >= clip.start_time + buffer) and (
+        start_time <= clip.end_time - buffer
+    )

src/batdetect2/evaluate/tasks/classification.py

@@ -0,0 +1,149 @@
+from typing import (
+    List,
+    Literal,
+    Sequence,
+)
+
+from pydantic import Field
+from soundevent import data
+
+from batdetect2.evaluate.metrics.classification import (
+    ClassificationAveragePrecisionConfig,
+    ClassificationMetricConfig,
+    ClipEval,
+    MatchEval,
+    build_classification_metric,
+)
+from batdetect2.evaluate.plots.classification import (
+    ClassificationPlotConfig,
+    build_classification_plotter,
+)
+from batdetect2.evaluate.tasks.base import (
+    BaseTask,
+    BaseTaskConfig,
+    tasks_registry,
+)
+from batdetect2.typing import RawPrediction, TargetProtocol
+
+
+class ClassificationTaskConfig(BaseTaskConfig):
+    name: Literal["sound_event_classification"] = "sound_event_classification"
+    prefix: str = "classification"
+    metrics: List[ClassificationMetricConfig] = Field(
+        default_factory=lambda: [ClassificationAveragePrecisionConfig()]
+    )
+    plots: List[ClassificationPlotConfig] = Field(default_factory=list)
+    include_generics: bool = True
+
+
+class ClassificationTask(BaseTask[ClipEval]):
+    def __init__(
+        self,
+        *args,
+        include_generics: bool = True,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.include_generics = include_generics
+
+    def evaluate_clip(
+        self,
+        clip_annotation: data.ClipAnnotation,
+        predictions: Sequence[RawPrediction],
+    ) -> ClipEval:
+        clip = clip_annotation.clip
+
+        preds = [
+            pred for pred in predictions if self.include_prediction(pred, clip)
+        ]
+
+        all_gts = [
+            sound_event
+            for sound_event in clip_annotation.sound_events
+            if self.include_sound_event_annotation(sound_event, clip)
+        ]
+
+        per_class_matches = {}
+
+        for class_name in self.targets.class_names:
+            class_idx = self.targets.class_names.index(class_name)
+
+            # Only match to targets of the given class
+            gts = [
+                sound_event
+                for sound_event in all_gts
+                if self.is_class(sound_event, class_name)
+            ]
+            scores = [float(pred.class_scores[class_idx]) for pred in preds]
+
+            matches = []
+
+            for pred_idx, gt_idx, _ in self.matcher(
+                ground_truth=[se.sound_event.geometry for se in gts],  # type: ignore
+                predictions=[pred.geometry for pred in preds],
+                scores=scores,
+            ):
+                gt = gts[gt_idx] if gt_idx is not None else None
+                pred = preds[pred_idx] if pred_idx is not None else None
+
+                true_class = (
+                    self.targets.encode_class(gt) if gt is not None else None
+                )
+
+                score = (
+                    float(pred.class_scores[class_idx])
+                    if pred is not None
+                    else 0
+                )
+
+                matches.append(
+                    MatchEval(
+                        clip=clip,
+                        gt=gt,
+                        pred=pred,
+                        is_prediction=pred is not None,
+                        is_ground_truth=gt is not None,
+                        is_generic=gt is not None and true_class is None,
+                        true_class=true_class,
+                        score=score,
+                    )
+                )
+
+            per_class_matches[class_name] = matches
+
+        return ClipEval(clip=clip, matches=per_class_matches)
+
+    def is_class(
+        self,
+        sound_event: data.SoundEventAnnotation,
+        class_name: str,
+    ) -> bool:
+        sound_event_class = self.targets.encode_class(sound_event)
+
+        if sound_event_class is None and self.include_generics:
+            # Sound events that are generic could be of the given
+            # class
+            return True
+
+        return sound_event_class == class_name
+
+    @tasks_registry.register(ClassificationTaskConfig)
+    @staticmethod
+    def from_config(
+        config: ClassificationTaskConfig,
+        targets: TargetProtocol,
+    ):
+        metrics = [
+            build_classification_metric(metric, targets)
+            for metric in config.metrics
+        ]
+        plots = [
+            build_classification_plotter(plot, targets)
+            for plot in config.plots
+        ]
+        return ClassificationTask.build(
+            config=config,
+            plots=plots,
+            targets=targets,
+            metrics=metrics,
+        )

src/batdetect2/evaluate/tasks/clip_classification.py

@@ -0,0 +1,85 @@
+from collections import defaultdict
+from typing import List, Literal, Sequence
+
+from pydantic import Field
+from soundevent import data
+
+from batdetect2.evaluate.metrics.clip_classification import (
+    ClipClassificationAveragePrecisionConfig,
+    ClipClassificationMetricConfig,
+    ClipEval,
+    build_clip_metric,
+)
+from batdetect2.evaluate.plots.clip_classification import (
+    ClipClassificationPlotConfig,
+    build_clip_classification_plotter,
+)
+from batdetect2.evaluate.tasks.base import (
+    BaseTask,
+    BaseTaskConfig,
+    tasks_registry,
+)
+from batdetect2.typing import RawPrediction, TargetProtocol
+
+
+class ClipClassificationTaskConfig(BaseTaskConfig):
+    name: Literal["clip_classification"] = "clip_classification"
+    prefix: str = "clip_classification"
+    metrics: List[ClipClassificationMetricConfig] = Field(
+        default_factory=lambda: [
+            ClipClassificationAveragePrecisionConfig(),
+        ]
+    )
+    plots: List[ClipClassificationPlotConfig] = Field(default_factory=list)
+
+
+class ClipClassificationTask(BaseTask[ClipEval]):
+    def evaluate_clip(
+        self,
+        clip_annotation: data.ClipAnnotation,
+        predictions: Sequence[RawPrediction],
+    ) -> ClipEval:
+        clip = clip_annotation.clip
+
+        gt_classes = set()
+        for sound_event in clip_annotation.sound_events:
+            if not self.include_sound_event_annotation(sound_event, clip):
+                continue
+
+            class_name = self.targets.encode_class(sound_event)
+
+            if class_name is None:
+                continue
+
+            gt_classes.add(class_name)
+
+        pred_scores = defaultdict(float)
+        for pred in predictions:
+            if not self.include_prediction(pred, clip):
+                continue
+
+            for class_idx, class_name in enumerate(self.targets.class_names):
+                pred_scores[class_name] = max(
+                    float(pred.class_scores[class_idx]),
+                    pred_scores[class_name],
+                )
+
+        return ClipEval(true_classes=gt_classes, class_scores=pred_scores)
+
+    @tasks_registry.register(ClipClassificationTaskConfig)
+    @staticmethod
+    def from_config(
+        config: ClipClassificationTaskConfig,
+        targets: TargetProtocol,
+    ):
+        metrics = [build_clip_metric(metric) for metric in config.metrics]
+        plots = [
+            build_clip_classification_plotter(plot, targets)
+            for plot in config.plots
+        ]
+        return ClipClassificationTask.build(
+            config=config,
+            plots=plots,
+            metrics=metrics,
+            targets=targets,
+        )

src/batdetect2/evaluate/tasks/clip_detection.py

@@ -0,0 +1,76 @@
+from typing import List, Literal, Sequence
+
+from pydantic import Field
+from soundevent import data
+
+from batdetect2.evaluate.metrics.clip_detection import (
+    ClipDetectionAveragePrecisionConfig,
+    ClipDetectionMetricConfig,
+    ClipEval,
+    build_clip_metric,
+)
+from batdetect2.evaluate.plots.clip_detection import (
+    ClipDetectionPlotConfig,
+    build_clip_detection_plotter,
+)
+from batdetect2.evaluate.tasks.base import (
+    BaseTask,
+    BaseTaskConfig,
+    tasks_registry,
+)
+from batdetect2.typing import RawPrediction, TargetProtocol
+
+
+class ClipDetectionTaskConfig(BaseTaskConfig):
+    name: Literal["clip_detection"] = "clip_detection"
+    prefix: str = "clip_detection"
+    metrics: List[ClipDetectionMetricConfig] = Field(
+        default_factory=lambda: [
+            ClipDetectionAveragePrecisionConfig(),
+        ]
+    )
+    plots: List[ClipDetectionPlotConfig] = Field(default_factory=list)
+
+
+class ClipDetectionTask(BaseTask[ClipEval]):
+    def evaluate_clip(
+        self,
+        clip_annotation: data.ClipAnnotation,
+        predictions: Sequence[RawPrediction],
+    ) -> ClipEval:
+        clip = clip_annotation.clip
+
+        gt_det = any(
+            self.include_sound_event_annotation(sound_event, clip)
+            for sound_event in clip_annotation.sound_events
+        )
+
+        pred_score = 0
+        for pred in predictions:
+            if not self.include_prediction(pred, clip):
+                continue
+
+            pred_score = max(pred_score, pred.detection_score)
+
+        return ClipEval(
+            gt_det=gt_det,
+            score=pred_score,
+        )
+
+    @tasks_registry.register(ClipDetectionTaskConfig)
+    @staticmethod
+    def from_config(
+        config: ClipDetectionTaskConfig,
+        targets: TargetProtocol,
+    ):
+        metrics = [build_clip_metric(metric) for metric in config.metrics]
+        plots = [
+            build_clip_detection_plotter(plot, targets)
+            for plot in config.plots
+        ]
+        return ClipDetectionTask.build(
+            config=config,
+            metrics=metrics,
+            targets=targets,
+            plots=plots,
+        )

src/batdetect2/evaluate/tasks/detection.py

@@ -0,0 +1,88 @@
+from typing import List, Literal, Sequence
+
+from pydantic import Field
+from soundevent import data
+
+from batdetect2.evaluate.metrics.detection import (
+    ClipEval,
+    DetectionAveragePrecisionConfig,
+    DetectionMetricConfig,
+    MatchEval,
+    build_detection_metric,
+)
+from batdetect2.evaluate.plots.detection import (
+    DetectionPlotConfig,
+    build_detection_plotter,
+)
+from batdetect2.evaluate.tasks.base import (
+    BaseTask,
+    BaseTaskConfig,
+    tasks_registry,
+)
+from batdetect2.typing import RawPrediction, TargetProtocol
+
+
+class DetectionTaskConfig(BaseTaskConfig):
+    name: Literal["sound_event_detection"] = "sound_event_detection"
+    prefix: str = "detection"
+    metrics: List[DetectionMetricConfig] = Field(
+        default_factory=lambda: [DetectionAveragePrecisionConfig()]
+    )
+    plots: List[DetectionPlotConfig] = Field(default_factory=list)
+
+
+class DetectionTask(BaseTask[ClipEval]):
+    def evaluate_clip(
+        self,
+        clip_annotation: data.ClipAnnotation,
+        predictions: Sequence[RawPrediction],
+    ) -> ClipEval:
+        clip = clip_annotation.clip
+
+        gts = [
+            sound_event
+            for sound_event in clip_annotation.sound_events
+            if self.include_sound_event_annotation(sound_event, clip)
+        ]
+        preds = [
+            pred for pred in predictions if self.include_prediction(pred, clip)
+        ]
+        scores = [pred.detection_score for pred in preds]
+
+        matches = []
+        for pred_idx, gt_idx, _ in self.matcher(
+            ground_truth=[se.sound_event.geometry for se in gts],  # type: ignore
+            predictions=[pred.geometry for pred in preds],
+            scores=scores,
+        ):
+            gt = gts[gt_idx] if gt_idx is not None else None
+            pred = preds[pred_idx] if pred_idx is not None else None
+
+            matches.append(
+                MatchEval(
+                    gt=gt,
+                    pred=pred,
+                    is_prediction=pred is not None,
+                    is_ground_truth=gt is not None,
+                    score=pred.detection_score if pred is not None else 0,
+                )
+            )
+
+        return ClipEval(clip=clip, matches=matches)
+
+    @tasks_registry.register(DetectionTaskConfig)
+    @staticmethod
+    def from_config(
+        config: DetectionTaskConfig,
+        targets: TargetProtocol,
+    ):
+        metrics = [build_detection_metric(metric) for metric in config.metrics]
+        plots = [
+            build_detection_plotter(plot, targets) for plot in config.plots
+        ]
+        return DetectionTask.build(
+            config=config,
+            metrics=metrics,
+            targets=targets,
+            plots=plots,
+        )

src/batdetect2/evaluate/tasks/top_class.py

@@ -0,0 +1,111 @@
+from typing import List, Literal, Sequence
+
+from pydantic import Field
+from soundevent import data
+
+from batdetect2.evaluate.metrics.top_class import (
+    ClipEval,
+    MatchEval,
+    TopClassAveragePrecisionConfig,
+    TopClassMetricConfig,
+    build_top_class_metric,
+)
+from batdetect2.evaluate.plots.top_class import (
+    TopClassPlotConfig,
+    build_top_class_plotter,
+)
+from batdetect2.evaluate.tasks.base import (
+    BaseTask,
+    BaseTaskConfig,
+    tasks_registry,
+)
+from batdetect2.typing import RawPrediction, TargetProtocol
+
+
+class TopClassDetectionTaskConfig(BaseTaskConfig):
+    name: Literal["top_class_detection"] = "top_class_detection"
+    prefix: str = "top_class"
+    metrics: List[TopClassMetricConfig] = Field(
+        default_factory=lambda: [TopClassAveragePrecisionConfig()]
+    )
+    plots: List[TopClassPlotConfig] = Field(default_factory=list)
+
+
+class TopClassDetectionTask(BaseTask[ClipEval]):
+    def evaluate_clip(
+        self,
+        clip_annotation: data.ClipAnnotation,
+        predictions: Sequence[RawPrediction],
+    ) -> ClipEval:
+        clip = clip_annotation.clip
+
+        gts = [
+            sound_event
+            for sound_event in clip_annotation.sound_events
+            if self.include_sound_event_annotation(sound_event, clip)
+        ]
+        preds = [
+            pred for pred in predictions if self.include_prediction(pred, clip)
+        ]
+        # Take the highest score for each prediction
+        scores = [pred.class_scores.max() for pred in preds]
+
+        matches = []
+        for pred_idx, gt_idx, _ in self.matcher(
+            ground_truth=[se.sound_event.geometry for se in gts],  # type: ignore
+            predictions=[pred.geometry for pred in preds],
+            scores=scores,
+        ):
+            gt = gts[gt_idx] if gt_idx is not None else None
+            pred = preds[pred_idx] if pred_idx is not None else None
+
+            true_class = (
+                self.targets.encode_class(gt) if gt is not None else None
+            )
+
+            class_idx = (
+                pred.class_scores.argmax() if pred is not None else None
+            )
+
+            score = (
+                float(pred.class_scores[class_idx]) if pred is not None else 0
+            )
+
+            pred_class = (
+                self.targets.class_names[class_idx]
+                if class_idx is not None
+                else None
+            )
+
+            matches.append(
+                MatchEval(
+                    clip=clip,
+                    gt=gt,
+                    pred=pred,
+                    is_ground_truth=gt is not None,
+                    is_prediction=pred is not None,
+                    true_class=true_class,
+                    is_generic=gt is not None and true_class is None,
+                    pred_class=pred_class,
+                    score=score,
+                )
+            )
+
+        return ClipEval(clip=clip, matches=matches)
+
+    @tasks_registry.register(TopClassDetectionTaskConfig)
+    @staticmethod
+    def from_config(
+        config: TopClassDetectionTaskConfig,
+        targets: TargetProtocol,
+    ):
+        metrics = [build_top_class_metric(metric) for metric in config.metrics]
+        plots = [
+            build_top_class_plotter(plot, targets) for plot in config.plots
+        ]
+        return TopClassDetectionTask.build(
+            config=config,
+            plots=plots,
+            metrics=metrics,
+            targets=targets,
+        )

src/batdetect2/plotting/__init__.py

@@ -11,7 +11,6 @@ from batdetect2.plotting.matches import (
     plot_cross_trigger_match,
     plot_false_negative_match,
     plot_false_positive_match,
-    plot_matches,
     plot_true_positive_match,
 )
 
@@ -22,7 +21,6 @@ __all__ = [
     "plot_cross_trigger_match",
     "plot_false_negative_match",
     "plot_false_positive_match",
-    "plot_matches",
     "plot_spectrogram",
     "plot_true_positive_match",
     "plot_detection_heatmap",

src/batdetect2/plotting/clip_annotations.py

@@ -65,8 +65,6 @@ def plot_anchor_points(
         if not targets.filter(sound_event):
             continue
 
-        sound_event = targets.transform(sound_event)
-
         position, _ = targets.encode_roi(sound_event)
         positions.append(position)
 

src/batdetect2/plotting/common.py

@@ -19,7 +19,7 @@ def create_ax(
 ) -> axes.Axes:
     """Create a new axis if none is provided"""
     if ax is None:
-        _, ax = plt.subplots(figsize=figsize, **kwargs)  # type: ignore
+        _, ax = plt.subplots(figsize=figsize, nrows=1, ncols=1, **kwargs)  # type: ignore
 
     return ax  # type: ignore
 
@@ -66,6 +66,9 @@ def plot_spectrogram(
         vmax=vmax,
     )
 
+    ax.set_xlim(start_time, end_time)
+    ax.set_ylim(min_freq, max_freq)
+
     if add_colorbar:
         plt.colorbar(mappable, ax=ax, **(colorbar_kwargs or {}))
 

src/batdetect2/plotting/detections.py

@@ -0,0 +1,113 @@
+from typing import Optional
+
+from matplotlib import axes, patches
+from soundevent.plot import plot_geometry
+
+from batdetect2.evaluate.metrics.detection import ClipEval
+from batdetect2.plotting.clips import (
+    AudioLoader,
+    PreprocessorProtocol,
+    plot_clip,
+)
+from batdetect2.plotting.common import create_ax
+
+__all__ = [
+    "plot_clip_detections",
+]
+
+
+def plot_clip_detections(
+    clip_eval: ClipEval,
+    figsize: tuple[int, int] = (10, 10),
+    ax: Optional[axes.Axes] = None,
+    audio_loader: Optional[AudioLoader] = None,
+    preprocessor: Optional[PreprocessorProtocol] = None,
+    threshold: float = 0.2,
+    add_legend: bool = True,
+    add_title: bool = True,
+    fill: bool = False,
+    linewidth: float = 1.0,
+    gt_color: str = "green",
+    gt_linestyle: str = "-",
+    true_pred_color: str = "yellow",
+    true_pred_linestyle: str = "--",
+    false_pred_color: str = "blue",
+    false_pred_linestyle: str = "-",
+    missed_gt_color: str = "red",
+    missed_gt_linestyle: str = "-",
+) -> axes.Axes:
+    ax = create_ax(figsize=figsize, ax=ax)
+
+    plot_clip(
+        clip_eval.clip,
+        audio_loader=audio_loader,
+        preprocessor=preprocessor,
+        ax=ax,
+    )
+
+    for m in clip_eval.matches:
+        is_match = (
+            m.pred is not None and m.gt is not None and m.score >= threshold
+        )
+
+        if m.pred is not None:
+            color = true_pred_color if is_match else false_pred_color
+            plot_geometry(
+                m.pred.geometry,
+                ax=ax,
+                add_points=False,
+                facecolor="none" if not fill else color,
+                alpha=m.pred.detection_score,
+                linewidth=linewidth,
+                linestyle=true_pred_linestyle
+                if is_match
+                else missed_gt_linestyle,
+                color=color,
+            )
+
+        if m.gt is not None:
+            color = gt_color if is_match else missed_gt_color
+            plot_geometry(
+                m.gt.sound_event.geometry,  # type: ignore
+                ax=ax,
+                add_points=False,
+                linewidth=linewidth,
+                facecolor="none" if not fill else color,
+                linestyle=gt_linestyle if is_match else false_pred_linestyle,
+                color=color,
+            )
+
+    if add_title:
+        ax.set_title(clip_eval.clip.recording.path.name)
+
+    if add_legend:
+        ax.legend(
+            handles=[
+                patches.Patch(
+                    label="found GT",
+                    edgecolor=gt_color,
+                    facecolor="none" if not fill else gt_color,
+                    linestyle=gt_linestyle,
+                ),
+                patches.Patch(
+                    label="missed GT",
+                    edgecolor=missed_gt_color,
+                    facecolor="none" if not fill else missed_gt_color,
+                    linestyle=missed_gt_linestyle,
+                ),
+                patches.Patch(
+                    label="true Det",
+                    edgecolor=true_pred_color,
+                    facecolor="none" if not fill else true_pred_color,
+                    linestyle=true_pred_linestyle,
+                ),
+                patches.Patch(
+                    label="false Det",
+                    edgecolor=false_pred_color,
+                    facecolor="none" if not fill else false_pred_color,
+                    linestyle=false_pred_linestyle,
+                ),
+            ]
+        )
+
+    return ax

src/batdetect2/plotting/gallery.py

@@ -1,81 +1,109 @@
-from typing import List, Optional
+from typing import Optional, Sequence
 
 import matplotlib.pyplot as plt
+from matplotlib.figure import Figure
 
 from batdetect2.plotting.matches import (
+    MatchProtocol,
     plot_cross_trigger_match,
     plot_false_negative_match,
     plot_false_positive_match,
     plot_true_positive_match,
 )
-from batdetect2.typing.evaluate import MatchEvaluation
 from batdetect2.typing.preprocess import AudioLoader, PreprocessorProtocol
 
 __all__ = ["plot_match_gallery"]
 
 
 def plot_match_gallery(
-    true_positives: List[MatchEvaluation],
+    true_positives: Sequence[MatchProtocol],
-    false_positives: List[MatchEvaluation],
+    false_positives: Sequence[MatchProtocol],
-    false_negatives: List[MatchEvaluation],
+    false_negatives: Sequence[MatchProtocol],
-    cross_triggers: List[MatchEvaluation],
+    cross_triggers: Sequence[MatchProtocol],
     audio_loader: Optional[AudioLoader] = None,
     preprocessor: Optional[PreprocessorProtocol] = None,
     n_examples: int = 5,
     duration: float = 0.1,
+    fig: Optional[Figure] = None,
 ):
-    fig = plt.figure(figsize=(20, 20))
+    if fig is None:
+        fig = plt.figure(figsize=(20, 20))
 
-    for index, match in enumerate(true_positives[:n_examples]):
+    axes = fig.subplots(
-        ax = plt.subplot(4, n_examples, index + 1)
+        nrows=4,
+        ncols=n_examples,
+        sharex="none",
+        sharey="row",
+    )
+
+    for tp_ax, tp_match in zip(axes[0], true_positives[:n_examples]):
         try:
             plot_true_positive_match(
-                match,
+                tp_match,
-                ax=ax,
+                ax=tp_ax,
                 audio_loader=audio_loader,
                 preprocessor=preprocessor,
                 duration=duration,
             )
-        except (ValueError, AssertionError, RuntimeError, FileNotFoundError):
+        except (
+            ValueError,
+            AssertionError,
+            RuntimeError,
+            FileNotFoundError,
+        ):
             continue
 
-    for index, match in enumerate(false_positives[:n_examples]):
+    for fp_ax, fp_match in zip(axes[1], false_positives[:n_examples]):
-        ax = plt.subplot(4, n_examples, n_examples + index + 1)
         try:
             plot_false_positive_match(
-                match,
+                fp_match,
-                ax=ax,
+                ax=fp_ax,
                 audio_loader=audio_loader,
                 preprocessor=preprocessor,
                 duration=duration,
             )
-        except (ValueError, AssertionError, RuntimeError, FileNotFoundError):
+        except (
+            ValueError,
+            AssertionError,
+            RuntimeError,
+            FileNotFoundError,
+        ):
             continue
 
-    for index, match in enumerate(false_negatives[:n_examples]):
+    for fn_ax, fn_match in zip(axes[2], false_negatives[:n_examples]):
-        ax = plt.subplot(4, n_examples, 2 * n_examples + index + 1)
         try:
             plot_false_negative_match(
-                match,
+                fn_match,
-                ax=ax,
+                ax=fn_ax,
                 audio_loader=audio_loader,
                 preprocessor=preprocessor,
                 duration=duration,
             )
-        except (ValueError, AssertionError, RuntimeError, FileNotFoundError):
+        except (
+            ValueError,
+            AssertionError,
+            RuntimeError,
+            FileNotFoundError,
+        ):
             continue
 
-    for index, match in enumerate(cross_triggers[:n_examples]):
+    for ct_ax, ct_match in zip(axes[3], cross_triggers[:n_examples]):
-        ax = plt.subplot(4, n_examples, 3 * n_examples + index + 1)
         try:
             plot_cross_trigger_match(
-                match,
+                ct_match,
-                ax=ax,
+                ax=ct_ax,
                 audio_loader=audio_loader,
                 preprocessor=preprocessor,
                 duration=duration,
             )
-        except (ValueError, AssertionError, RuntimeError, FileNotFoundError):
+        except (
+            ValueError,
+            AssertionError,
+            RuntimeError,
+            FileNotFoundError,
+        ):
             continue
 
+    fig.tight_layout()
+
     return fig

src/batdetect2/plotting/matches.py

@@ -1,16 +1,17 @@
-from typing import List, Optional, Tuple, Union
+from typing import Optional, Protocol, Tuple, Union
 
-import matplotlib.pyplot as plt
 from matplotlib.axes import Axes
 from soundevent import data, plot
 from soundevent.geometry import compute_bounds
-from soundevent.plot.tags import TagColorMapper
 
-from batdetect2.plotting.clips import AudioLoader, plot_clip
+from batdetect2.plotting.clips import plot_clip
-from batdetect2.typing import MatchEvaluation, PreprocessorProtocol
+from batdetect2.typing import (
+    AudioLoader,
+    PreprocessorProtocol,
+    RawPrediction,
+)
 
 __all__ = [
-    "plot_matches",
     "plot_false_positive_match",
     "plot_true_positive_match",
     "plot_false_negative_match",
@@ -18,6 +19,14 @@ __all__ = [
 ]
 
 
+class MatchProtocol(Protocol):
+    clip: data.Clip
+    gt: Optional[data.SoundEventAnnotation]
+    pred: Optional[RawPrediction]
+    score: float
+    true_class: Optional[str]
+
+
 DEFAULT_DURATION = 0.05
 DEFAULT_FALSE_POSITIVE_COLOR = "orange"
 DEFAULT_FALSE_NEGATIVE_COLOR = "red"
@@ -27,88 +36,8 @@ DEFAULT_ANNOTATION_LINE_STYLE = "-"
 DEFAULT_PREDICTION_LINE_STYLE = "--"
 
 
-def plot_matches(
-    matches: List[MatchEvaluation],
-    clip: data.Clip,
-    audio_loader: Optional[AudioLoader] = None,
-    preprocessor: Optional[PreprocessorProtocol] = None,
-    figsize: Optional[Tuple[int, int]] = None,
-    ax: Optional[Axes] = None,
-    audio_dir: Optional[data.PathLike] = None,
-    color_mapper: Optional[TagColorMapper] = None,
-    add_points: bool = False,
-    fill: bool = False,
-    spec_cmap: str = "gray",
-    false_positive_color: str = DEFAULT_FALSE_POSITIVE_COLOR,
-    false_negative_color: str = DEFAULT_FALSE_NEGATIVE_COLOR,
-    true_positive_color: str = DEFAULT_TRUE_POSITIVE_COLOR,
-    cross_trigger_color: str = DEFAULT_CROSS_TRIGGER_COLOR,
-) -> Axes:
-    ax = plot_clip(
-        clip,
-        ax=ax,
-        audio_loader=audio_loader,
-        preprocessor=preprocessor,
-        figsize=figsize,
-        audio_dir=audio_dir,
-        spec_cmap=spec_cmap,
-    )
-
-    if color_mapper is None:
-        color_mapper = TagColorMapper()
-
-    for match in matches:
-        if match.is_cross_trigger():
-            plot_cross_trigger_match(
-                match,
-                ax=ax,
-                fill=fill,
-                add_points=add_points,
-                add_spectrogram=False,
-                use_score=True,
-                color=cross_trigger_color,
-                add_text=False,
-            )
-        elif match.is_true_positive():
-            plot_true_positive_match(
-                match,
-                ax=ax,
-                fill=fill,
-                add_spectrogram=False,
-                use_score=True,
-                add_points=add_points,
-                color=true_positive_color,
-                add_text=False,
-            )
-        elif match.is_false_negative():
-            plot_false_negative_match(
-                match,
-                ax=ax,
-                fill=fill,
-                add_spectrogram=False,
-                add_points=add_points,
-                color=false_negative_color,
-                add_text=False,
-            )
-        elif match.is_false_positive:
-            plot_false_positive_match(
-                match,
-                ax=ax,
-                fill=fill,
-                add_spectrogram=False,
-                use_score=True,
-                add_points=add_points,
-                color=false_positive_color,
-                add_text=False,
-            )
-        else:
-            continue
-
-    return ax
-
-
 def plot_false_positive_match(
-    match: MatchEvaluation,
+    match: MatchProtocol,
     audio_loader: Optional[AudioLoader] = None,
     preprocessor: Optional[PreprocessorProtocol] = None,
     figsize: Optional[Tuple[int, int]] = None,
@@ -119,21 +48,24 @@ def plot_false_positive_match(
     add_spectrogram: bool = True,
     add_text: bool = True,
     add_points: bool = False,
+    add_title: bool = True,
     fill: bool = False,
     spec_cmap: str = "gray",
     color: str = DEFAULT_FALSE_POSITIVE_COLOR,
     fontsize: Union[float, str] = "small",
 ) -> Axes:
-    assert match.pred_geometry is not None
+    assert match.pred is not None
-    assert match.sound_event_annotation is None
 
-    start_time, _, _, high_freq = compute_bounds(match.pred_geometry)
+    start_time, _, _, high_freq = compute_bounds(match.pred.geometry)
 
     clip = data.Clip(
-        start_time=max(start_time - duration / 2, 0),
+        start_time=max(
+            start_time - duration / 2,
+            0,
+        ),
         end_time=min(
             start_time + duration / 2,
-            match.clip.end_time,
+            match.clip.recording.duration,
         ),
         recording=match.clip.recording,
     )
@@ -150,30 +82,33 @@ def plot_false_positive_match(
         )
 
     ax = plot.plot_geometry(
-        match.pred_geometry,
+        match.pred.geometry,
         ax=ax,
         add_points=add_points,
         facecolor="none" if not fill else None,
-        alpha=match.pred_score if use_score else 1,
+        alpha=match.score if use_score else 1,
         color=color,
     )
 
     if add_text:
-        plt.text(
+        ax.text(
             start_time,
             high_freq,
-            f"False Positive \nScore: {match.pred_score:.2f} \nTop Class: {match.pred_class} \nTop Class Score: {match.pred_class_score:.2f} ",
+            f"score={match.score:.2f}",
             va="top",
             ha="right",
             color=color,
             fontsize=fontsize,
         )
 
+    if add_title:
+        ax.set_title("False Positive")
+
     return ax
 
 
 def plot_false_negative_match(
-    match: MatchEvaluation,
+    match: MatchProtocol,
     audio_loader: Optional[AudioLoader] = None,
     preprocessor: Optional[PreprocessorProtocol] = None,
     figsize: Optional[Tuple[int, int]] = None,
@@ -182,26 +117,28 @@ def plot_false_negative_match(
     duration: float = DEFAULT_DURATION,
     add_spectrogram: bool = True,
     add_points: bool = False,
-    add_text: bool = True,
+    add_title: bool = True,
     fill: bool = False,
     spec_cmap: str = "gray",
     color: str = DEFAULT_FALSE_NEGATIVE_COLOR,
-    fontsize: Union[float, str] = "small",
 ) -> Axes:
-    assert match.pred_geometry is None
+    assert match.gt is not None
-    assert match.sound_event_annotation is not None
+
-    sound_event = match.sound_event_annotation.sound_event
+    geometry = match.gt.sound_event.geometry
-    geometry = sound_event.geometry
     assert geometry is not None
 
-    start_time, _, _, high_freq = compute_bounds(geometry)
+    start_time = compute_bounds(geometry)[0]
 
     clip = data.Clip(
-        start_time=max(start_time - duration / 2, 0),
+        start_time=max(
-        end_time=min(
+            start_time - duration / 2,
-            start_time + duration / 2, sound_event.recording.duration
+            0,
         ),
-        recording=sound_event.recording,
+        end_time=min(
+            start_time + duration / 2,
+            match.clip.recording.duration,
+        ),
+        recording=match.clip.recording,
     )
 
     if add_spectrogram:
@@ -215,33 +152,23 @@ def plot_false_negative_match(
             spec_cmap=spec_cmap,
         )
 
-    ax = plot.plot_annotation(
+    ax = plot.plot_geometry(
-        match.sound_event_annotation,
+        geometry,
         ax=ax,
-        time_offset=0.001,
-        freq_offset=2_000,
         add_points=add_points,
         facecolor="none" if not fill else None,
         alpha=1,
         color=color,
     )
 
-    if add_text:
+    if add_title:
-        plt.text(
+        ax.set_title("False Negative")
-            start_time,
-            high_freq,
-            f"False Negative \nClass: {match.gt_class} ",
-            va="top",
-            ha="right",
-            color=color,
-            fontsize=fontsize,
-        )
 
     return ax
 
 
 def plot_true_positive_match(
-    match: MatchEvaluation,
+    match: MatchProtocol,
     preprocessor: Optional[PreprocessorProtocol] = None,
     audio_loader: Optional[AudioLoader] = None,
     figsize: Optional[Tuple[int, int]] = None,
@@ -258,39 +185,42 @@ def plot_true_positive_match(
     fontsize: Union[float, str] = "small",
     annotation_linestyle: str = DEFAULT_ANNOTATION_LINE_STYLE,
     prediction_linestyle: str = DEFAULT_PREDICTION_LINE_STYLE,
+    add_title: bool = True,
 ) -> Axes:
-    assert match.sound_event_annotation is not None
+    assert match.gt is not None
-    assert match.pred_geometry is not None
+    assert match.pred is not None
-    sound_event = match.sound_event_annotation.sound_event
+
-    geometry = sound_event.geometry
+    geometry = match.gt.sound_event.geometry
     assert geometry is not None
 
     start_time, _, _, high_freq = compute_bounds(geometry)
 
     clip = data.Clip(
-        start_time=max(start_time - duration / 2, 0),
+        start_time=max(
-        end_time=min(
+            start_time - duration / 2,
-            start_time + duration / 2, sound_event.recording.duration
+            0,
         ),
-        recording=sound_event.recording,
+        end_time=min(
+            start_time + duration / 2,
+            match.clip.recording.duration,
+        ),
+        recording=match.clip.recording,
     )
 
     if add_spectrogram:
         ax = plot_clip(
             clip,
+            ax=ax,
             audio_loader=audio_loader,
             preprocessor=preprocessor,
             figsize=figsize,
-            ax=ax,
             audio_dir=audio_dir,
             spec_cmap=spec_cmap,
         )
 
-    ax = plot.plot_annotation(
+    ax = plot.plot_geometry(
-        match.sound_event_annotation,
+        geometry,
         ax=ax,
-        time_offset=0.001,
-        freq_offset=2_000,
         add_points=add_points,
         facecolor="none" if not fill else None,
         alpha=1,
@@ -299,31 +229,34 @@ def plot_true_positive_match(
     )
 
     plot.plot_geometry(
-        match.pred_geometry,
+        match.pred.geometry,
         ax=ax,
         add_points=add_points,
         facecolor="none" if not fill else None,
-        alpha=match.pred_score if use_score else 1,
+        alpha=match.score if use_score else 1,
         color=color,
         linestyle=prediction_linestyle,
     )
 
     if add_text:
-        plt.text(
+        ax.text(
             start_time,
             high_freq,
-            f"True Positive \nClass: {match.gt_class} \nDet Score: {match.pred_score:.2f} \nTop Class Score: {match.pred_class_score:.2f} ",
+            f"score={match.score:.2f}",
             va="top",
             ha="right",
             color=color,
             fontsize=fontsize,
         )
 
+    if add_title:
+        ax.set_title("True Positive")
+
     return ax
 
 
 def plot_cross_trigger_match(
-    match: MatchEvaluation,
+    match: MatchProtocol,
     preprocessor: Optional[PreprocessorProtocol] = None,
     audio_loader: Optional[AudioLoader] = None,
     figsize: Optional[Tuple[int, int]] = None,
@@ -334,6 +267,7 @@ def plot_cross_trigger_match(
     add_spectrogram: bool = True,
     add_points: bool = False,
     add_text: bool = True,
+    add_title: bool = True,
     fill: bool = False,
     spec_cmap: str = "gray",
     color: str = DEFAULT_CROSS_TRIGGER_COLOR,
@@ -341,20 +275,24 @@ def plot_cross_trigger_match(
     annotation_linestyle: str = DEFAULT_ANNOTATION_LINE_STYLE,
     prediction_linestyle: str = DEFAULT_PREDICTION_LINE_STYLE,
 ) -> Axes:
-    assert match.sound_event_annotation is not None
+    assert match.gt is not None
-    assert match.pred_geometry is not None
+    assert match.pred is not None
-    sound_event = match.sound_event_annotation.sound_event
+
-    geometry = sound_event.geometry
+    geometry = match.gt.sound_event.geometry
     assert geometry is not None
 
     start_time, _, _, high_freq = compute_bounds(geometry)
 
     clip = data.Clip(
-        start_time=max(start_time - duration / 2, 0),
+        start_time=max(
-        end_time=min(
+            start_time - duration / 2,
-            start_time + duration / 2, sound_event.recording.duration
+            0,
         ),
-        recording=sound_event.recording,
+        end_time=min(
+            start_time + duration / 2,
+            match.clip.recording.duration,
+        ),
+        recording=match.clip.recording,
     )
 
     if add_spectrogram:
@@ -368,11 +306,9 @@ def plot_cross_trigger_match(
             spec_cmap=spec_cmap,
         )
 
-    ax = plot.plot_annotation(
+    ax = plot.plot_geometry(
-        match.sound_event_annotation,
+        geometry,
         ax=ax,
-        time_offset=0.001,
-        freq_offset=2_000,
         add_points=add_points,
         facecolor="none" if not fill else None,
         alpha=1,
@@ -381,24 +317,28 @@ def plot_cross_trigger_match(
     )
 
     ax = plot.plot_geometry(
-        match.pred_geometry,
+        match.pred.geometry,
         ax=ax,
         add_points=add_points,
         facecolor="none" if not fill else None,
-        alpha=match.pred_score if use_score else 1,
+        alpha=match.score if use_score else 1,
         color=color,
         linestyle=prediction_linestyle,
     )
 
     if add_text:
-        plt.text(
+        ax.text(
             start_time,
             high_freq,
-            f"Cross Trigger \nTrue Class: {match.gt_class} \nPred Class: {match.pred_class} \nDet Score: {match.pred_score:.2f} \nTop Class Score: {match.pred_class_score:.2f} ",
+            f"score={match.score:.2f}\nclass={match.true_class}",
             va="top",
             ha="right",
             color=color,
             fontsize=fontsize,
         )
 
+    if add_title:
+        ax.set_title("Cross Trigger")
+
     return ax
+

src/batdetect2/plotting/metrics.py

@@ -0,0 +1,286 @@
+from typing import Dict, Optional, Tuple
+
+import numpy as np
+import seaborn as sns
+from cycler import cycler
+from matplotlib import axes
+
+from batdetect2.plotting.common import create_ax
+
+
+def set_default_styler(ax: axes.Axes) -> axes.Axes:
+    color_cycler = cycler(color=sns.color_palette("muted"))
+    style_cycler = cycler(linestyle=["-", "--", ":"]) * cycler(
+        marker=["o", "s", "^"]
+    )
+    custom_cycler = color_cycler * len(style_cycler) + style_cycler * len(
+        color_cycler
+    )
+
+    ax.set_prop_cycle(custom_cycler)
+    return ax
+
+
+def set_default_style(ax: axes.Axes) -> axes.Axes:
+    ax = set_default_styler(ax)
+    ax.spines.right.set_visible(False)
+    ax.spines.top.set_visible(False)
+    return ax
+
+
+def plot_pr_curve(
+    precision: np.ndarray,
+    recall: np.ndarray,
+    thresholds: np.ndarray,
+    ax: Optional[axes.Axes] = None,
+    figsize: Optional[Tuple[int, int]] = None,
+    add_labels: bool = True,
+    add_legend: bool = False,
+    label: str = "PR Curve",
+) -> axes.Axes:
+    ax = create_ax(ax=ax, figsize=figsize)
+
+    ax = set_default_style(ax)
+
+    ax.plot(
+        recall,
+        precision,
+        label=label,
+        marker="o",
+        markevery=_get_marker_positions(thresholds),
+    )
+
+    ax.set_xlim(0, 1.05)
+    ax.set_ylim(0, 1.05)
+
+    if add_legend:
+        ax.legend()
+
+    if add_labels:
+        ax.set_xlabel("Recall")
+        ax.set_ylabel("Precision")
+
+    return ax
+
+
+def plot_pr_curves(
+    data: Dict[str, Tuple[np.ndarray, np.ndarray, np.ndarray]],
+    ax: Optional[axes.Axes] = None,
+    figsize: Optional[Tuple[int, int]] = None,
+    add_legend: bool = True,
+    add_labels: bool = True,
+) -> axes.Axes:
+    ax = create_ax(ax=ax, figsize=figsize)
+    ax = set_default_style(ax)
+
+    for name, (precision, recall, thresholds) in data.items():
+        ax.plot(
+            recall,
+            precision,
+            label=name,
+            markevery=_get_marker_positions(thresholds),
+        )
+
+    ax.set_xlim(0, 1.05)
+    ax.set_ylim(0, 1.05)
+
+    if add_labels:
+        ax.set_xlabel("Recall")
+        ax.set_ylabel("Precision")
+
+    if add_legend:
+        ax.legend(
+            bbox_to_anchor=(1.05, 1),
+            loc="upper left",
+            borderaxespad=0.0,
+        )
+    return ax
+
+
+def plot_threshold_precision_curve(
+    threshold: np.ndarray,
+    precision: np.ndarray,
+    ax: Optional[axes.Axes] = None,
+    figsize: Optional[Tuple[int, int]] = None,
+    add_labels: bool = True,
+):
+    ax = create_ax(ax=ax, figsize=figsize)
+
+    ax = set_default_style(ax)
+
+    ax.plot(threshold, precision, markevery=_get_marker_positions(threshold))
+
+    ax.set_xlim(0, 1.05)
+    ax.set_ylim(0, 1.05)
+
+    if add_labels:
+        ax.set_xlabel("Threshold")
+        ax.set_ylabel("Precision")
+
+    return ax
+
+
+def plot_threshold_precision_curves(
+    data: Dict[str, Tuple[np.ndarray, np.ndarray, np.ndarray]],
+    ax: Optional[axes.Axes] = None,
+    figsize: Optional[Tuple[int, int]] = None,
+    add_legend: bool = True,
+    add_labels: bool = True,
+):
+    ax = create_ax(ax=ax, figsize=figsize)
+    ax = set_default_style(ax)
+
+    for name, (precision, _, thresholds) in data.items():
+        ax.plot(
+            thresholds,
+            precision,
+            label=name,
+            markevery=_get_marker_positions(thresholds),
+        )
+
+    if add_legend:
+        ax.legend(
+            bbox_to_anchor=(1.05, 1),
+            loc="upper left",
+            borderaxespad=0.0,
+        )
+
+    ax.set_xlim(0, 1.05)
+    ax.set_ylim(0, 1.05)
+
+    if add_labels:
+        ax.set_xlabel("Threshold")
+        ax.set_ylabel("Precision")
+
+    return ax
+
+
+def plot_threshold_recall_curve(
+    threshold: np.ndarray,
+    recall: np.ndarray,
+    ax: Optional[axes.Axes] = None,
+    figsize: Optional[Tuple[int, int]] = None,
+    add_labels: bool = True,
+):
+    ax = create_ax(ax=ax, figsize=figsize)
+
+    ax = set_default_style(ax)
+
+    ax.plot(threshold, recall, markevery=_get_marker_positions(threshold))
+
+    ax.set_xlim(0, 1.05)
+    ax.set_ylim(0, 1.05)
+
+    if add_labels:
+        ax.set_xlabel("Threshold")
+        ax.set_ylabel("Recall")
+
+    return ax
+
+
+def plot_threshold_recall_curves(
+    data: Dict[str, Tuple[np.ndarray, np.ndarray, np.ndarray]],
+    ax: Optional[axes.Axes] = None,
+    figsize: Optional[Tuple[int, int]] = None,
+    add_legend: bool = True,
+    add_labels: bool = True,
+):
+    ax = create_ax(ax=ax, figsize=figsize)
+    ax = set_default_style(ax)
+
+    for name, (_, recall, thresholds) in data.items():
+        ax.plot(
+            thresholds,
+            recall,
+            label=name,
+            markevery=_get_marker_positions(thresholds),
+        )
+
+    if add_legend:
+        ax.legend(
+            bbox_to_anchor=(1.05, 1),
+            loc="upper left",
+            borderaxespad=0.0,
+        )
+
+    ax.set_xlim(0, 1.05)
+    ax.set_ylim(0, 1.05)
+
+    if add_labels:
+        ax.set_xlabel("Threshold")
+        ax.set_ylabel("Recall")
+
+    return ax
+
+
+def plot_roc_curve(
+    fpr: np.ndarray,
+    tpr: np.ndarray,
+    thresholds: np.ndarray,
+    ax: Optional[axes.Axes] = None,
+    figsize: Optional[Tuple[int, int]] = None,
+    add_labels: bool = True,
+) -> axes.Axes:
+    ax = create_ax(ax=ax, figsize=figsize)
+
+    ax = set_default_style(ax)
+
+    ax.plot(
+        fpr,
+        tpr,
+        markevery=_get_marker_positions(thresholds),
+    )
+
+    ax.set_xlim(0, 1.05)
+    ax.set_ylim(0, 1.05)
+
+    if add_labels:
+        ax.set_xlabel("False Positive Rate")
+        ax.set_ylabel("True Positive Rate")
+
+    return ax
+
+
+def plot_roc_curves(
+    data: Dict[str, Tuple[np.ndarray, np.ndarray, np.ndarray]],
+    ax: Optional[axes.Axes] = None,
+    figsize: Optional[Tuple[int, int]] = None,
+    add_legend: bool = True,
+    add_labels: bool = True,
+) -> axes.Axes:
+    ax = create_ax(ax=ax, figsize=figsize)
+    ax = set_default_style(ax)
+
+    for name, (fpr, tpr, thresholds) in data.items():
+        ax.plot(
+            fpr,
+            tpr,
+            label=name,
+            markevery=_get_marker_positions(thresholds),
+        )
+
+    if add_legend:
+        ax.legend(
+            bbox_to_anchor=(1.05, 1),
+            loc="upper left",
+            borderaxespad=0.0,
+        )
+
+    ax.set_xlim(0, 1.05)
+    ax.set_ylim(0, 1.05)
+
+    if add_labels:
+        ax.set_xlabel("False Positive Rate")
+        ax.set_ylabel("True Positive Rate")
+
+    return ax
+
+
+def _get_marker_positions(
+    thresholds: np.ndarray,
+    n_points: int = 11,
+) -> np.ndarray:
+    size = len(thresholds)
+    cut_points = np.linspace(0, 1, n_points)
+    indices = np.searchsorted(thresholds[::-1], cut_points)
+    return np.clip(size - indices, 0, size - 1)  # type: ignore

src/batdetect2/preprocess/audio.py

@@ -28,12 +28,10 @@ class CenterAudio(torch.nn.Module):
     def forward(self, wav: torch.Tensor) -> torch.Tensor:
         return center_tensor(wav)
 
-    @classmethod
+    @audio_transforms.register(CenterAudioConfig)
-    def from_config(cls, config: CenterAudioConfig, samplerate: int):
+    @staticmethod
-        return cls()
+    def from_config(config: CenterAudioConfig, samplerate: int):
-
+        return CenterAudio()
-
-audio_transforms.register(CenterAudioConfig, CenterAudio)
 
 
 class ScaleAudioConfig(BaseConfig):
@@ -44,12 +42,10 @@ class ScaleAudio(torch.nn.Module):
     def forward(self, wav: torch.Tensor) -> torch.Tensor:
         return peak_normalize(wav)
 
-    @classmethod
+    @audio_transforms.register(ScaleAudioConfig)
-    def from_config(cls, config: ScaleAudioConfig, samplerate: int):
+    @staticmethod
-        return cls()
+    def from_config(config: ScaleAudioConfig, samplerate: int):
-
+        return ScaleAudio()
-
-audio_transforms.register(ScaleAudioConfig, ScaleAudio)
 
 
 class FixDurationConfig(BaseConfig):
@@ -75,13 +71,12 @@ class FixDuration(torch.nn.Module):
 
         return torch.nn.functional.pad(wav, (0, self.length - length))
 
-    @classmethod
+    @audio_transforms.register(FixDurationConfig)
-    def from_config(cls, config: FixDurationConfig, samplerate: int):
+    @staticmethod
-        return cls(samplerate=samplerate, duration=config.duration)
+    def from_config(config: FixDurationConfig, samplerate: int):
+        return FixDuration(samplerate=samplerate, duration=config.duration)
 
 
-audio_transforms.register(FixDurationConfig, FixDuration)
-
 AudioTransform = Annotated[
     Union[
         FixDurationConfig,

src/batdetect2/preprocess/spectrogram.py

@@ -285,10 +285,11 @@ class PCEN(torch.nn.Module):
             * torch.expm1(self.power * torch.log1p(S * smooth / self.bias))
         ).to(spec.dtype)
 
-    @classmethod
+    @spectrogram_transforms.register(PcenConfig)
-    def from_config(cls, config: PcenConfig, samplerate: int):
+    @staticmethod
+    def from_config(config: PcenConfig, samplerate: int):
         smooth = _compute_smoothing_constant(samplerate, config.time_constant)
-        return cls(
+        return PCEN(
             smoothing_constant=smooth,
             gain=config.gain,
             bias=config.bias,
@@ -296,9 +297,6 @@ class PCEN(torch.nn.Module):
         )
 
 
-spectrogram_transforms.register(PcenConfig, PCEN)
-
-
 def _compute_smoothing_constant(
     samplerate: int,
     time_constant: float,
@@ -335,12 +333,10 @@ class ScaleAmplitude(torch.nn.Module):
     def forward(self, spec: torch.Tensor) -> torch.Tensor:
         return self.scaler(spec)
 
-    @classmethod
+    @spectrogram_transforms.register(ScaleAmplitudeConfig)
-    def from_config(cls, config: ScaleAmplitudeConfig, samplerate: int):
+    @staticmethod
-        return cls(scale=config.scale)
+    def from_config(config: ScaleAmplitudeConfig, samplerate: int):
-
+        return ScaleAmplitude(scale=config.scale)
-
-spectrogram_transforms.register(ScaleAmplitudeConfig, ScaleAmplitude)
 
 
 class SpectralMeanSubstractionConfig(BaseConfig):
@@ -352,19 +348,13 @@ class SpectralMeanSubstraction(torch.nn.Module):
         mean = spec.mean(-1, keepdim=True)
         return (spec - mean).clamp(min=0)
 
-    @classmethod
+    @spectrogram_transforms.register(SpectralMeanSubstractionConfig)
+    @staticmethod
     def from_config(
-        cls,
         config: SpectralMeanSubstractionConfig,
         samplerate: int,
     ):
-        return cls()
+        return SpectralMeanSubstraction()
-
-
-spectrogram_transforms.register(
-    SpectralMeanSubstractionConfig,
-    SpectralMeanSubstraction,
-)
 
 
 class PeakNormalizeConfig(BaseConfig):
@@ -375,13 +365,12 @@ class PeakNormalize(torch.nn.Module):
     def forward(self, spec: torch.Tensor) -> torch.Tensor:
         return peak_normalize(spec)
 
-    @classmethod
+    @spectrogram_transforms.register(PeakNormalizeConfig)
-    def from_config(cls, config: PeakNormalizeConfig, samplerate: int):
+    @staticmethod
-        return cls()
+    def from_config(config: PeakNormalizeConfig, samplerate: int):
+        return PeakNormalize()
 
 
-spectrogram_transforms.register(PeakNormalizeConfig, PeakNormalize)
-
 SpectrogramTransform = Annotated[
     Union[
         PcenConfig,

src/batdetect2/targets/classes.py

@@ -99,7 +99,7 @@ DEFAULT_DETECTION_CLASS = TargetClassConfig(
 DEFAULT_CLASSES = [
     TargetClassConfig(
         name="barbar",
-        tags=[data.Tag(key="class", value="Barbastellus barbastellus")],
+        tags=[data.Tag(key="class", value="Barbastella barbastellus")],
     ),
     TargetClassConfig(
         name="eptser",

src/batdetect2/train/__init__.py

@@ -1,11 +1,11 @@
 from batdetect2.train.augmentations import (
     AugmentationsConfig,
-    EchoAugmentationConfig,
+    AddEchoConfig,
-    FrequencyMaskAugmentationConfig,
+    MaskFrequencyConfig,
     RandomAudioSource,
-    TimeMaskAugmentationConfig,
+    MaskTimeConfig,
-    VolumeAugmentationConfig,
+    ScaleVolumeConfig,
-    WarpAugmentationConfig,
+    WarpConfig,
     add_echo,
     build_augmentations,
     mask_frequency,
@@ -43,20 +43,20 @@ __all__ = [
     "AugmentationsConfig",
     "ClassificationLossConfig",
     "DetectionLossConfig",
-    "EchoAugmentationConfig",
+    "AddEchoConfig",
-    "FrequencyMaskAugmentationConfig",
+    "MaskFrequencyConfig",
     "LossConfig",
     "LossFunction",
     "PLTrainerConfig",
     "RandomAudioSource",
     "SizeLossConfig",
-    "TimeMaskAugmentationConfig",
+    "MaskTimeConfig",
     "TrainingConfig",
     "TrainingDataset",
     "TrainingModule",
     "ValidationDataset",
-    "VolumeAugmentationConfig",
+    "ScaleVolumeConfig",
-    "WarpAugmentationConfig",
+    "WarpConfig",
     "add_echo",
     "build_augmentations",
     "build_clip_labeler",

src/batdetect2/train/augmentations.py

@@ -12,21 +12,23 @@ from soundevent import data
 from soundevent.geometry import scale_geometry, shift_geometry
 
 from batdetect2.audio.clips import get_subclip_annotation
+from batdetect2.audio.loader import TARGET_SAMPLERATE_HZ
 from batdetect2.core.arrays import adjust_width
 from batdetect2.core.configs import BaseConfig, load_config
+from batdetect2.core.registries import Registry
 from batdetect2.typing import AudioLoader, Augmentation
 
 __all__ = [
     "AugmentationConfig",
     "AugmentationsConfig",
     "DEFAULT_AUGMENTATION_CONFIG",
-    "EchoAugmentationConfig",
+    "AddEchoConfig",
     "AudioSource",
-    "FrequencyMaskAugmentationConfig",
+    "MaskFrequencyConfig",
-    "MixAugmentationConfig",
+    "MixAudioConfig",
-    "TimeMaskAugmentationConfig",
+    "MaskTimeConfig",
-    "VolumeAugmentationConfig",
+    "ScaleVolumeConfig",
-    "WarpAugmentationConfig",
+    "WarpConfig",
     "add_echo",
     "build_augmentations",
     "load_augmentation_config",
@@ -37,10 +39,19 @@ __all__ = [
     "warp_spectrogram",
 ]
 
+
 AudioSource = Callable[[float], tuple[torch.Tensor, data.ClipAnnotation]]
 
+audio_augmentations: Registry[Augmentation, [int, Optional[AudioSource]]] = (
+    Registry(name="audio_augmentation")
+)
 
-class MixAugmentationConfig(BaseConfig):
+spec_augmentations: Registry[Augmentation, []] = Registry(
+    name="spec_augmentation"
+)
+
+
+class MixAudioConfig(BaseConfig):
     """Configuration for MixUp augmentation (mixing two examples)."""
 
     name: Literal["mix_audio"] = "mix_audio"
@@ -87,6 +98,27 @@ class MixAudio(torch.nn.Module):
         )
         return mixed_audio, mixed_annotations
 
+    @audio_augmentations.register(MixAudioConfig)
+    @staticmethod
+    def from_config(
+        config: MixAudioConfig,
+        samplerate: int,
+        source: Optional[AudioSource],
+    ):
+        if source is None:
+            warnings.warn(
+                "Mix audio augmentation ('mix_audio') requires an "
+                "'example_source' callable to be provided.",
+                stacklevel=2,
+            )
+            return lambda wav, clip_annotation: (wav, clip_annotation)
+
+        return MixAudio(
+            example_source=source,
+            min_weight=config.min_weight,
+            max_weight=config.max_weight,
+        )
+
 
 def mix_audio(
     wav1: torch.Tensor,
@@ -136,7 +168,7 @@ def combine_clip_annotations(
     )
 
 
-class EchoAugmentationConfig(BaseConfig):
+class AddEchoConfig(BaseConfig):
     """Configuration for adding synthetic echo/reverb."""
 
     name: Literal["add_echo"] = "add_echo"
@@ -149,14 +181,17 @@ class EchoAugmentationConfig(BaseConfig):
 class AddEcho(torch.nn.Module):
     def __init__(
         self,
+        samplerate: int = TARGET_SAMPLERATE_HZ,
         min_weight: float = 0.1,
         max_weight: float = 1.0,
-        max_delay: int = 2560,
+        max_delay: float = 0.005,
     ):
         super().__init__()
+        self.samplerate = samplerate
         self.min_weight = min_weight
         self.max_weight = max_weight
-        self.max_delay = max_delay
+        self.max_delay_s = max_delay
+        self.max_delay = int(max_delay * samplerate)
 
     def forward(
         self,
@@ -167,6 +202,20 @@ class AddEcho(torch.nn.Module):
         weight = np.random.uniform(self.min_weight, self.max_weight)
         return add_echo(wav, delay=delay, weight=weight), clip_annotation
 
+    @audio_augmentations.register(AddEchoConfig)
+    @staticmethod
+    def from_config(
+        config: AddEchoConfig,
+        samplerate: int,
+        source: Optional[AudioSource],
+    ):
+        return AddEcho(
+            samplerate=samplerate,
+            min_weight=config.min_weight,
+            max_weight=config.max_weight,
+            max_delay=config.max_delay,
+        )
+
 
 def add_echo(
     wav: torch.Tensor,
@@ -183,7 +232,7 @@ def add_echo(
     return mix_audio(wav, audio_delay, weight)
 
 
-class VolumeAugmentationConfig(BaseConfig):
+class ScaleVolumeConfig(BaseConfig):
     """Configuration for random volume scaling of the spectrogram."""
 
     name: Literal["scale_volume"] = "scale_volume"
@@ -206,19 +255,27 @@ class ScaleVolume(torch.nn.Module):
         factor = np.random.uniform(self.min_scaling, self.max_scaling)
         return scale_volume(spec, factor=factor), clip_annotation
 
+    @spec_augmentations.register(ScaleVolumeConfig)
+    @staticmethod
+    def from_config(config: ScaleVolumeConfig):
+        return ScaleVolume(
+            min_scaling=config.min_scaling,
+            max_scaling=config.max_scaling,
+        )
+
 
 def scale_volume(spec: torch.Tensor, factor: float) -> torch.Tensor:
     """Scale the amplitude of the spectrogram by a factor."""
     return spec * factor
 
 
-class WarpAugmentationConfig(BaseConfig):
+class WarpConfig(BaseConfig):
     name: Literal["warp"] = "warp"
     probability: float = 0.2
     delta: float = 0.04
 
 
-class WarpSpectrogram(torch.nn.Module):
+class Warp(torch.nn.Module):
     def __init__(self, delta: float = 0.04) -> None:
         super().__init__()
         self.delta = delta
@@ -234,6 +291,11 @@ class WarpSpectrogram(torch.nn.Module):
             warp_clip_annotation(clip_annotation, factor=factor),
         )
 
+    @spec_augmentations.register(WarpConfig)
+    @staticmethod
+    def from_config(config: WarpConfig):
+        return Warp(delta=config.delta)
+
 
 def warp_sound_event_annotation(
     sound_event_annotation: data.SoundEventAnnotation,
@@ -294,7 +356,7 @@ def warp_spectrogram(
     ).squeeze(0)
 
 
-class TimeMaskAugmentationConfig(BaseConfig):
+class MaskTimeConfig(BaseConfig):
     name: Literal["mask_time"] = "mask_time"
     probability: float = 0.2
     max_perc: float = 0.05
@@ -336,6 +398,14 @@ class MaskTime(torch.nn.Module):
         ]
         return mask_time(spec, masks), clip_annotation
 
+    @spec_augmentations.register(MaskTimeConfig)
+    @staticmethod
+    def from_config(config: MaskTimeConfig):
+        return MaskTime(
+            max_perc=config.max_perc,
+            max_masks=config.max_masks,
+        )
+
 
 def mask_time(
     spec: torch.Tensor,
@@ -351,7 +421,7 @@ def mask_time(
     return spec
 
 
-class FrequencyMaskAugmentationConfig(BaseConfig):
+class MaskFrequencyConfig(BaseConfig):
     name: Literal["mask_freq"] = "mask_freq"
     probability: float = 0.2
     max_perc: float = 0.10
@@ -394,6 +464,14 @@ class MaskFrequency(torch.nn.Module):
         ]
         return mask_frequency(spec, masks), clip_annotation
 
+    @spec_augmentations.register(MaskFrequencyConfig)
+    @staticmethod
+    def from_config(config: MaskFrequencyConfig):
+        return MaskFrequency(
+            max_perc=config.max_perc,
+            max_masks=config.max_masks,
+        )
+
 
 def mask_frequency(
     spec: torch.Tensor,
@@ -410,8 +488,8 @@ def mask_frequency(
 
 AudioAugmentationConfig = Annotated[
     Union[
-        MixAugmentationConfig,
+        MixAudioConfig,
-        EchoAugmentationConfig,
+        AddEchoConfig,
     ],
     Field(discriminator="name"),
 ]
@@ -419,22 +497,22 @@ AudioAugmentationConfig = Annotated[
 
 SpectrogramAugmentationConfig = Annotated[
     Union[
-        VolumeAugmentationConfig,
+        ScaleVolumeConfig,
-        WarpAugmentationConfig,
+        WarpConfig,
-        FrequencyMaskAugmentationConfig,
+        MaskFrequencyConfig,
-        TimeMaskAugmentationConfig,
+        MaskTimeConfig,
     ],
     Field(discriminator="name"),
 ]
 
 AugmentationConfig = Annotated[
     Union[
-        MixAugmentationConfig,
+        MixAudioConfig,
-        EchoAugmentationConfig,
+        AddEchoConfig,
-        VolumeAugmentationConfig,
+        ScaleVolumeConfig,
-        WarpAugmentationConfig,
+        WarpConfig,
-        FrequencyMaskAugmentationConfig,
+        MaskFrequencyConfig,
-        TimeMaskAugmentationConfig,
+        MaskTimeConfig,
     ],
     Field(discriminator="name"),
 ]
@@ -513,7 +591,7 @@ def build_augmentation_from_config(
         )
 
     if config.name == "warp":
-        return WarpSpectrogram(
+        return Warp(
             delta=config.delta,
         )
 
@@ -538,14 +616,14 @@ def build_augmentation_from_config(
 DEFAULT_AUGMENTATION_CONFIG: AugmentationsConfig = AugmentationsConfig(
     enabled=True,
     audio=[
-        MixAugmentationConfig(),
+        MixAudioConfig(),
-        EchoAugmentationConfig(),
+        AddEchoConfig(),
     ],
     spectrogram=[
-        VolumeAugmentationConfig(),
+        ScaleVolumeConfig(),
-        WarpAugmentationConfig(),
+        WarpConfig(),
-        TimeMaskAugmentationConfig(),
+        MaskTimeConfig(),
-        FrequencyMaskAugmentationConfig(),
+        MaskFrequencyConfig(),
     ],
 )
 
@@ -566,9 +644,9 @@ class AugmentationSequence(torch.nn.Module):
         return tensor, clip_annotation
 
 
-def build_augmentation_sequence(
+def build_audio_augmentations(
-    samplerate: int,
+    steps: Optional[Sequence[AudioAugmentationConfig]] = None,
-    steps: Optional[Sequence[AugmentationConfig]] = None,
+    samplerate: int = TARGET_SAMPLERATE_HZ,
     audio_source: Optional[AudioSource] = None,
 ) -> Optional[Augmentation]:
     if not steps:
@@ -577,10 +655,8 @@ def build_augmentation_sequence(
     augmentations = []
 
     for step_config in steps:
-        augmentation = build_augmentation_from_config(
+        augmentation = audio_augmentations.build(
-            step_config,
+            step_config, samplerate, audio_source
-            samplerate=samplerate,
-            audio_source=audio_source,
         )
 
         if augmentation is None:
@@ -596,6 +672,30 @@ def build_augmentation_sequence(
     return AugmentationSequence(augmentations)
 
 
+def build_spectrogram_augmentations(
+    steps: Optional[Sequence[SpectrogramAugmentationConfig]] = None,
+) -> Optional[Augmentation]:
+    if not steps:
+        return None
+
+    augmentations = []
+
+    for step_config in steps:
+        augmentation = spec_augmentations.build(step_config)
+
+        if augmentation is None:
+            continue
+
+        augmentations.append(
+            MaybeApply(
+                augmentation=augmentation,
+                probability=step_config.probability,
+            )
+        )
+
+    return AugmentationSequence(augmentations)
+
+
 def build_augmentations(
     samplerate: int,
     config: Optional[AugmentationsConfig] = None,
@@ -609,16 +709,14 @@ def build_augmentations(
         lambda: config.to_yaml_string(),
     )
 
-    audio_augmentation = build_augmentation_sequence(
+    audio_augmentation = build_audio_augmentations(
-        samplerate,
         steps=config.audio,
+        samplerate=samplerate,
         audio_source=audio_source,
     )
 
-    spectrogram_augmentation = build_augmentation_sequence(
+    spectrogram_augmentation = build_spectrogram_augmentations(
-        samplerate,
+        steps=config.spectrogram,
-        steps=config.audio,
-        audio_source=audio_source,
     )
 
     return audio_augmentation, spectrogram_augmentation

src/batdetect2/train/callbacks.py

@@ -1,4 +1,4 @@
-from typing import List
+from typing import Any, List
 
 from lightning import LightningModule, Trainer
 from lightning.pytorch.callbacks import Callback
@@ -10,7 +10,6 @@ from batdetect2.postprocess import to_raw_predictions
 from batdetect2.train.dataset import ValidationDataset
 from batdetect2.train.lightning import TrainingModule
 from batdetect2.typing import (
-    ClipEvaluation,
     EvaluatorProtocol,
     ModelOutput,
     RawPrediction,
@@ -36,23 +35,23 @@ class ValidationMetrics(Callback):
 
     def generate_plots(
         self,
+        eval_outputs: Any,
         pl_module: LightningModule,
-        evaluated_clips: List[ClipEvaluation],
     ):
         plotter = get_image_logger(pl_module.logger)  # type: ignore
 
         if plotter is None:
             return
 
-        for figure_name, fig in self.evaluator.generate_plots(evaluated_clips):
+        for figure_name, fig in self.evaluator.generate_plots(eval_outputs):
             plotter(figure_name, fig, pl_module.global_step)
 
     def log_metrics(
         self,
+        eval_outputs: Any,
         pl_module: LightningModule,
-        evaluated_clips: List[ClipEvaluation],
     ):
-        metrics = self.evaluator.compute_metrics(evaluated_clips)
+        metrics = self.evaluator.compute_metrics(eval_outputs)
         pl_module.log_dict(metrics)
 
     def on_validation_epoch_end(
@@ -60,13 +59,13 @@ class ValidationMetrics(Callback):
         trainer: Trainer,
         pl_module: LightningModule,
     ) -> None:
-        clip_evaluations = self.evaluator.evaluate(
+        eval_outputs = self.evaluator.evaluate(
             self._clip_annotations,
             self._predictions,
         )
 
-        self.log_metrics(pl_module, clip_evaluations)
+        self.log_metrics(eval_outputs, pl_module)
-        self.generate_plots(pl_module, clip_evaluations)
+        self.generate_plots(eval_outputs, pl_module)
 
         return super().on_validation_epoch_end(trainer, pl_module)
 

src/batdetect2/train/train.py

@@ -8,7 +8,7 @@ from loguru import logger
 from soundevent import data
 
 from batdetect2.audio import build_audio_loader
-from batdetect2.evaluate.evaluator import build_evaluator
+from batdetect2.evaluate import build_evaluator
 from batdetect2.logging import build_logger
 from batdetect2.preprocess import build_preprocessor
 from batdetect2.targets import build_targets
@@ -105,7 +105,10 @@ def train(
     trainer = trainer or build_trainer(
         config,
         targets=targets,
-        evaluator=build_evaluator(config.train.validation, targets=targets),
+        evaluator=build_evaluator(
+            config.train.validation,
+            targets=targets,
+        ),
         checkpoint_dir=checkpoint_dir,
         log_dir=log_dir,
         experiment_name=experiment_name,
@@ -143,7 +146,7 @@ def build_trainer_callbacks(
         ModelCheckpoint(
             dirpath=str(checkpoint_dir),
             save_top_k=1,
-            monitor="total_loss/val",
+            monitor="classification/mean_average_precision",
         ),
         ValidationMetrics(evaluator),
     ]

src/batdetect2/typing/__init__.py

@@ -1,6 +1,8 @@
 from batdetect2.typing.evaluate import (
-    ClipEvaluation,
+    AffinityFunction,
+    ClipMatches,
     EvaluatorProtocol,
+    MatcherProtocol,
     MatchEvaluation,
     MetricsProtocol,
     PlotterProtocol,
@@ -36,19 +38,22 @@ from batdetect2.typing.train import (
 )
 
 __all__ = [
+    "AffinityFunction",
     "AudioLoader",
     "Augmentation",
     "BackboneModel",
     "BatDetect2Prediction",
-    "ClipEvaluation",
+    "ClipMatches",
     "ClipLabeller",
     "ClipperProtocol",
     "DetectionModel",
+    "EvaluatorProtocol",
     "GeometryDecoder",
     "Heatmaps",
     "LossProtocol",
     "Losses",
     "MatchEvaluation",
+    "MatcherProtocol",
     "MetricsProtocol",
     "ModelOutput",
     "PlotterProtocol",
@@ -63,5 +68,4 @@ __all__ = [
     "SoundEventFilter",
     "TargetProtocol",
     "TrainExample",
-    "EvaluatorProtocol",
 ]

src/batdetect2/typing/evaluate.py

@@ -31,6 +31,7 @@ class MatchEvaluation:
     sound_event_annotation: Optional[data.SoundEventAnnotation]
     gt_det: bool
     gt_class: Optional[str]
+    gt_geometry: Optional[data.Geometry]
 
     pred_score: float
     pred_class_scores: Dict[str, float]
@@ -39,44 +40,32 @@ class MatchEvaluation:
     affinity: float
 
     @property
-    def pred_class(self) -> Optional[str]:
+    def top_class(self) -> Optional[str]:
         if not self.pred_class_scores:
             return None
 
         return max(self.pred_class_scores, key=self.pred_class_scores.get)  # type: ignore
 
     @property
-    def pred_class_score(self) -> float:
+    def is_prediction(self) -> bool:
-        pred_class = self.pred_class
+        return self.pred_geometry is not None
+
+    @property
+    def is_generic(self) -> bool:
+        return self.gt_det and self.gt_class is None
+
+    @property
+    def top_class_score(self) -> float:
+        pred_class = self.top_class
 
         if pred_class is None:
             return 0
 
         return self.pred_class_scores[pred_class]
 
-    def is_true_positive(self, threshold: float = 0) -> bool:
-        return (
-            self.gt_det
-            and self.pred_score > threshold
-            and self.gt_class == self.pred_class
-        )
-
-    def is_false_positive(self, threshold: float = 0) -> bool:
-        return self.gt_det is None and self.pred_score > threshold
-
-    def is_false_negative(self, threshold: float = 0) -> bool:
-        return self.gt_det and self.pred_score <= threshold
-
-    def is_cross_trigger(self, threshold: float = 0) -> bool:
-        return (
-            self.gt_det
-            and self.pred_score > threshold
-            and self.gt_class != self.pred_class
-        )
-
 
 @dataclass
-class ClipEvaluation:
+class ClipMatches:
     clip: data.Clip
     matches: List[MatchEvaluation]
 
@@ -103,29 +92,36 @@ class AffinityFunction(Protocol, Generic[Geom]):
 
 class MetricsProtocol(Protocol):
     def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
+        self,
+        clip_annotations: Sequence[data.ClipAnnotation],
+        predictions: Sequence[Sequence[RawPrediction]],
     ) -> Dict[str, float]: ...
 
 
 class PlotterProtocol(Protocol):
     def __call__(
-        self, clip_evaluations: Sequence[ClipEvaluation]
+        self,
+        clip_annotations: Sequence[data.ClipAnnotation],
+        predictions: Sequence[Sequence[RawPrediction]],
     ) -> Iterable[Tuple[str, Figure]]: ...
 
 
-class EvaluatorProtocol(Protocol):
+EvaluationOutput = TypeVar("EvaluationOutput")
+
+
+class EvaluatorProtocol(Protocol, Generic[EvaluationOutput]):
     targets: TargetProtocol
 
     def evaluate(
         self,
         clip_annotations: Sequence[data.ClipAnnotation],
         predictions: Sequence[Sequence[RawPrediction]],
-    ) -> List[ClipEvaluation]: ...
+    ) -> EvaluationOutput: ...
 
     def compute_metrics(
-        self, clip_evaluations: Sequence[ClipEvaluation]
+        self, eval_outputs: EvaluationOutput
     ) -> Dict[str, float]: ...
 
     def generate_plots(
-        self, clip_evaluations: Sequence[ClipEvaluation]
+        self, eval_outputs: EvaluationOutput
     ) -> Iterable[Tuple[str, Figure]]: ...