Better matching module, remove generic from classification evaluations

src/batdetect2/evaluate/__init__.py

@@ -1,11 +1,6 @@
-from batdetect2.evaluate.config import (
+from batdetect2.evaluate.config import EvaluationConfig, load_evaluation_config
-    EvaluationConfig,
-    load_evaluation_config,
-)
-from batdetect2.evaluate.match import match_predictions_and_annotations
 
 __all__ = [
     "EvaluationConfig",
     "load_evaluation_config",
-    "match_predictions_and_annotations",
 ]

src/batdetect2/evaluate/config.py

@@ -4,7 +4,7 @@ from pydantic import Field
 from soundevent import data
 
 from batdetect2.configs import BaseConfig, load_config
-from batdetect2.evaluate.match import MatchConfig
+from batdetect2.evaluate.match import MatchConfig, StartTimeMatchConfig
 
 __all__ = [
     "EvaluationConfig",
@@ -13,7 +13,7 @@ __all__ = [
 
 
 class EvaluationConfig(BaseConfig):
-    match: MatchConfig = Field(default_factory=MatchConfig)
+    match: MatchConfig = Field(default_factory=StartTimeMatchConfig)
 
 
 def load_evaluation_config(

src/batdetect2/evaluate/evaluate.py

@@ -4,9 +4,8 @@ import pandas as pd
 from soundevent import data
 
 from batdetect2.evaluate.dataframe import extract_matches_dataframe
-from batdetect2.evaluate.match import match_all_predictions
+from batdetect2.evaluate.match import build_matcher, match_all_predictions
 from batdetect2.evaluate.metrics import (
-    ClassificationAccuracy,
     ClassificationMeanAveragePrecision,
     DetectionAveragePrecision,
 )
@@ -77,11 +76,13 @@ def evaluate(
         clip_annotations.extend(clip_annotations)
         predictions.extend(predictions)
 
+    matcher = build_matcher(config.evaluation.match)
+
     matches = match_all_predictions(
         clip_annotations,
         predictions,
         targets=targets,
-        config=config.evaluation.match,
+        matcher=matcher,
     )
 
     df = extract_matches_dataframe(matches)
@@ -89,7 +90,6 @@ def evaluate(
     metrics = [
         DetectionAveragePrecision(),
         ClassificationMeanAveragePrecision(class_names=targets.class_names),
-        ClassificationAccuracy(class_names=targets.class_names),
     ]
 
     results = {

src/batdetect2/evaluate/match.py

@@ -1,63 +1,120 @@
 from collections.abc import Callable, Iterable, Mapping
 from dataclasses import dataclass, field
-from typing import List, Literal, Optional, Protocol, Tuple
+from typing import Annotated, List, Literal, Optional, Sequence, Tuple, Union
 
 import numpy as np
 from loguru import logger
+from pydantic import Field
 from soundevent import data
 from soundevent.evaluation import compute_affinity
 from soundevent.evaluation import match_geometries as optimal_match
 from soundevent.geometry import compute_bounds
 
 from batdetect2.configs import BaseConfig
+from batdetect2.data._core import Registry
+from batdetect2.targets import build_targets
 from batdetect2.typing import (
     MatchEvaluation,
     TargetProtocol,
 )
+from batdetect2.typing.evaluate import AffinityFunction, MatcherProtocol
 from batdetect2.typing.postprocess import RawPrediction
 
-MatchingStrategy = Literal["greedy", "optimal"]
-"""The type of matching algorithm to use: 'greedy' or 'optimal'."""
-
-
 MatchingGeometry = Literal["bbox", "interval", "timestamp"]
 """The geometry representation to use for matching."""
 
+matching_strategy = Registry("matching_strategy")
+
+
+class StartTimeMatchConfig(BaseConfig):
+    name: Literal["start_time"] = "start_time"
+    distance_threshold: float = 0.01
+
+
+@matching_strategy.register(StartTimeMatchConfig)
+class StartTimeMatcher(MatcherProtocol):
+    def __init__(self, distance_threshold: float):
+        self.distance_threshold = distance_threshold
 
-class AffinityFunction(Protocol):
     def __call__(
         self,
-        geometry1: data.Geometry,
+        ground_truth: Sequence[data.Geometry],
-        geometry2: data.Geometry,
+        predictions: Sequence[data.Geometry],
-        time_buffer: float = 0.01,
+        scores: Sequence[float],
-        freq_buffer: float = 1000,
+    ):
-    ) -> float: ...
+        return match_start_times(
+            ground_truth,
+            predictions,
+            scores,
+            distance_threshold=self.distance_threshold,
+        )
+
+    @classmethod
+    def from_config(cls, config: StartTimeMatchConfig) -> "StartTimeMatcher":
+        return cls(distance_threshold=config.distance_threshold)
 
 
-class MatchConfig(BaseConfig):
+def match_start_times(
-    """Configuration for matching geometries.
+    ground_truth: Sequence[data.Geometry],
+    predictions: Sequence[data.Geometry],
+    scores: Sequence[float],
+    distance_threshold: float = 0.01,
+) -> Iterable[Tuple[Optional[int], Optional[int], float]]:
+    if not ground_truth:
+        for index in range(len(predictions)):
+            yield index, None, 0
 
-    Attributes
+        return
-    ----------
-    strategy : MatchingStrategy, default="greedy"
-        The matching algorithm to use. 'greedy' prioritizes high-confidence
-        predictions, while 'optimal' finds the globally best set of matches.
-    geometry : MatchingGeometry, default="timestamp"
-        The geometric representation to use when computing affinity.
-    affinity_threshold : float, default=0.0
-        The minimum affinity score (e.g., IoU) required for a valid match.
-    time_buffer : float, default=0.005
-        Time tolerance in seconds used in affinity calculations.
-    frequency_buffer : float, default=1000
-        Frequency tolerance in Hertz used in affinity calculations.
-    """
 
-    strategy: MatchingStrategy = "greedy"
+    if not predictions:
-    geometry: MatchingGeometry = "timestamp"
+        for index in range(len(ground_truth)):
-    affinity_threshold: float = 0.0
+            yield None, index, 0
-    time_buffer: float = 0.005
+
-    frequency_buffer: float = 1_000
+        return
-    ignore_start_end: float = 0.01
+
+    gt_times = np.array([compute_bounds(geom)[0] for geom in ground_truth])
+    pred_times = np.array([compute_bounds(geom)[0] for geom in predictions])
+    scores = np.array(scores)
+
+    sort_args = np.argsort(scores)[::-1]
+
+    distances = np.abs(gt_times[None, :] - pred_times[:, None])
+    closests = np.argmin(distances, axis=-1)
+
+    unmatched_gt = set(range(len(gt_times)))
+
+    for pred_index in sort_args:
+        # Get the closest ground truth
+        gt_closest_index = closests[pred_index]
+
+        if gt_closest_index not in unmatched_gt:
+            # Does not match if closest has been assigned
+            yield pred_index, None, 0
+            continue
+
+        # Get the actual distance
+        distance = distances[pred_index, gt_closest_index]
+
+        if distance > distance_threshold:
+            # Does not match if too far from closest
+            yield pred_index, None, 0
+            continue
+
+        # Return affinity value: linear interpolation between 0 to 1, where a
+        # distance at the threshold maps to 0 affinity and a zero distance maps
+        # to 1.
+        affinity = np.interp(
+            distance,
+            [0, distance_threshold],
+            [1, 0],
+            left=1,
+            right=0,
+        )
+        unmatched_gt.remove(gt_closest_index)
+        yield pred_index, gt_closest_index, affinity
+
+    for missing_index in unmatched_gt:
+        yield None, missing_index, 0
 
 
 def _to_bbox(geometry: data.Geometry) -> data.BoundingBox:
@@ -142,50 +199,65 @@ def _interval_affinity(
 _affinity_functions: Mapping[MatchingGeometry, AffinityFunction] = {
     "timestamp": _timestamp_affinity,
     "interval": _interval_affinity,
+    "bbox": compute_affinity,
 }
 
 
-def match_geometries(
+class GreedyMatchConfig(BaseConfig):
-    source: List[data.Geometry],
+    name: Literal["greedy_match"] = "greedy_match"
-    target: List[data.Geometry],
+    geometry: MatchingGeometry = "timestamp"
-    config: MatchConfig,
+    affinity_threshold: float = 0.0
-    scores: Optional[List[float]] = None,
+    time_buffer: float = 0.005
-) -> Iterable[Tuple[Optional[int], Optional[int], float]]:
+    frequency_buffer: float = 1_000
-    geometry_cast = _geometry_cast_functions[config.geometry]
-    affinity_function = _affinity_functions.get(
-        config.geometry,
-        compute_affinity,
-    )
 
-    if config.strategy == "optimal":
-        return optimal_match(
-            source=[geometry_cast(geom) for geom in source],
-            target=[geometry_cast(geom) for geom in target],
-            time_buffer=config.time_buffer,
-            freq_buffer=config.frequency_buffer,
-            affinity_threshold=config.affinity_threshold,
-        )
 
-    if config.strategy == "greedy":
+@matching_strategy.register(GreedyMatchConfig)
+class GreedyMatcher(MatcherProtocol):
+    def __init__(
+        self,
+        geometry: MatchingGeometry,
+        affinity_threshold: float,
+        time_buffer: float,
+        frequency_buffer: float,
+    ):
+        self.geometry = geometry
+        self.affinity_threshold = affinity_threshold
+        self.time_buffer = time_buffer
+        self.frequency_buffer = frequency_buffer
+
+        self.affinity_function = _affinity_functions[self.geometry]
+        self.cast_geometry = _geometry_cast_functions[self.geometry]
+
+    def __call__(
+        self,
+        ground_truth: Sequence[data.Geometry],
+        predictions: Sequence[data.Geometry],
+        scores: Sequence[float],
+    ):
         return greedy_match(
-            source=[geometry_cast(geom) for geom in source],
+            ground_truth=[self.cast_geometry(geom) for geom in ground_truth],
-            target=[geometry_cast(geom) for geom in target],
+            predictions=[self.cast_geometry(geom) for geom in predictions],
-            time_buffer=config.time_buffer,
-            freq_buffer=config.frequency_buffer,
-            affinity_threshold=config.affinity_threshold,
-            affinity_function=affinity_function,
             scores=scores,
+            affinity_function=self.affinity_function,
+            affinity_threshold=self.affinity_threshold,
+            time_buffer=self.time_buffer,
+            freq_buffer=self.frequency_buffer,
         )
 
-    raise NotImplementedError(
+    @classmethod
-        f"Matching strategy not implemented {config.strategy}"
+    def from_config(cls, config: GreedyMatchConfig):
-    )
+        return cls(
+            geometry=config.geometry,
+            affinity_threshold=config.affinity_threshold,
+            time_buffer=config.time_buffer,
+            frequency_buffer=config.frequency_buffer,
+        )
 
 
 def greedy_match(
-    source: List[data.Geometry],
+    ground_truth: Sequence[data.Geometry],
-    target: List[data.Geometry],
+    predictions: Sequence[data.Geometry],
-    scores: Optional[List[float]] = None,
+    scores: Sequence[float],
     affinity_threshold: float = 0.5,
     affinity_function: AffinityFunction = compute_affinity,
     time_buffer: float = 0.001,
@@ -221,27 +293,24 @@ def greedy_match(
         - Unmatched Source (False Positive): `(source_idx, None, 0)`
         - Unmatched Target (False Negative): `(None, target_idx, 0)`
     """
-    assigned = set()
+    unassigned_gt = set(range(len(ground_truth)))
 
-    if not source:
+    if not predictions:
-        for target_idx in range(len(target)):
+        for target_idx in range(len(ground_truth)):
             yield None, target_idx, 0
 
         return
 
-    if not target:
+    if not ground_truth:
-        for source_idx in range(len(source)):
+        for source_idx in range(len(predictions)):
             yield source_idx, None, 0
 
         return
 
-    if scores is None:
+    indices = np.argsort(scores)[::-1]
-        indices = np.arange(len(source))
-    else:
-        indices = np.argsort(scores)[::-1]
 
     for source_idx in indices:
-        source_geometry = source[source_idx]
+        source_geometry = predictions[source_idx]
 
         affinities = np.array(
             [
@@ -251,7 +320,7 @@ def greedy_match(
                     time_buffer=time_buffer,
                     freq_buffer=freq_buffer,
                 )
-                for target_geometry in target
+                for target_geometry in ground_truth
             ]
         )
 
@@ -262,18 +331,74 @@ def greedy_match(
             yield source_idx, None, 0
             continue
 
-        if closest_target in assigned:
+        if closest_target not in unassigned_gt:
             yield source_idx, None, 0
             continue
 
-        assigned.add(closest_target)
+        unassigned_gt.remove(closest_target)
         yield source_idx, closest_target, affinity
 
-    missed_ground_truth = set(range(len(target))) - assigned
+    for target_idx in unassigned_gt:
-    for target_idx in missed_ground_truth:
         yield None, target_idx, 0
 
 
+class OptimalMatchConfig(BaseConfig):
+    name: Literal["optimal_match"] = "optimal_match"
+    affinity_threshold: float = 0.0
+    time_buffer: float = 0.005
+    frequency_buffer: float = 1_000
+
+
+@matching_strategy.register(OptimalMatchConfig)
+class OptimalMatcher(MatcherProtocol):
+    def __init__(
+        self,
+        affinity_threshold: float,
+        time_buffer: float,
+        frequency_buffer: float,
+    ):
+        self.affinity_threshold = affinity_threshold
+        self.time_buffer = time_buffer
+        self.frequency_buffer = frequency_buffer
+
+    def __call__(
+        self,
+        ground_truth: Sequence[data.Geometry],
+        predictions: Sequence[data.Geometry],
+        scores: Sequence[float],
+    ):
+        return optimal_match(
+            source=predictions,
+            target=ground_truth,
+            time_buffer=self.time_buffer,
+            freq_buffer=self.frequency_buffer,
+            affinity_threshold=self.affinity_threshold,
+        )
+
+    @classmethod
+    def from_config(cls, config: OptimalMatchConfig):
+        return cls(
+            affinity_threshold=config.affinity_threshold,
+            time_buffer=config.time_buffer,
+            frequency_buffer=config.frequency_buffer,
+        )
+
+
+MatchConfig = Annotated[
+    Union[
+        GreedyMatchConfig,
+        StartTimeMatchConfig,
+        OptimalMatchConfig,
+    ],
+    Field(discriminator="name"),
+]
+
+
+def build_matcher(config: Optional[MatchConfig] = None) -> MatcherProtocol:
+    config = config or StartTimeMatchConfig()
+    return matching_strategy.build(config)
+
+
 def _is_in_bounds(
     geometry: data.Geometry,
     clip: data.Clip,
@@ -285,13 +410,18 @@ def _is_in_bounds(
     )
 
 
-def match_sound_events_and_raw_predictions(
+def match_sound_events_and_predictions(
     clip_annotation: data.ClipAnnotation,
     raw_predictions: List[RawPrediction],
-    targets: TargetProtocol,
+    targets: Optional[TargetProtocol] = None,
-    config: Optional[MatchConfig] = None,
+    matcher: Optional[MatcherProtocol] = None,
+    ignore_start_end: float = 0.01,
 ) -> List[MatchEvaluation]:
-    config = config or MatchConfig()
+    if matcher is None:
+        matcher = build_matcher()
+
+    if targets is None:
+        targets = build_targets()
 
     target_sound_events = [
         sound_event_annotation
@@ -301,7 +431,7 @@ def match_sound_events_and_raw_predictions(
         and _is_in_bounds(
             sound_event_annotation.sound_event.geometry,
             clip=clip_annotation.clip,
-            buffer=config.ignore_start_end,
+            buffer=ignore_start_end,
         )
     ]
 
@@ -317,7 +447,7 @@ def match_sound_events_and_raw_predictions(
         if _is_in_bounds(
             raw_prediction.geometry,
             clip=clip_annotation.clip,
-            buffer=config.ignore_start_end,
+            buffer=ignore_start_end,
         )
     ]
 
@@ -331,10 +461,9 @@ def match_sound_events_and_raw_predictions(
 
     matches = []
 
-    for source_idx, target_idx, affinity in match_geometries(
+    for source_idx, target_idx, affinity in matcher(
-        source=predicted_geometries,
+        ground_truth=target_geometries,
-        target=target_geometries,
+        predictions=predicted_geometries,
-        config=config,
         scores=scores,
     ):
         target = (
@@ -344,7 +473,7 @@ def match_sound_events_and_raw_predictions(
             raw_predictions[source_idx] if source_idx is not None else None
         )
 
-        gt_det = target is not None
+        gt_det = target_idx is not None
         gt_class = targets.encode_class(target) if target is not None else None
 
         pred_score = float(prediction.detection_score) if prediction else 0
@@ -383,76 +512,12 @@ def match_sound_events_and_raw_predictions(
     return matches
 
 
-def match_predictions_and_annotations(
-    clip_annotation: data.ClipAnnotation,
-    clip_prediction: data.ClipPrediction,
-    config: Optional[MatchConfig] = None,
-) -> List[data.Match]:
-    config = config or MatchConfig()
-
-    annotated_sound_events = [
-        sound_event_annotation
-        for sound_event_annotation in clip_annotation.sound_events
-        if sound_event_annotation.sound_event.geometry is not None
-    ]
-
-    predicted_sound_events = [
-        sound_event_prediction
-        for sound_event_prediction in clip_prediction.sound_events
-        if sound_event_prediction.sound_event.geometry is not None
-    ]
-
-    annotated_geometries: List[data.Geometry] = [
-        sound_event.sound_event.geometry
-        for sound_event in annotated_sound_events
-        if sound_event.sound_event.geometry is not None
-    ]
-
-    predicted_geometries: List[data.Geometry] = [
-        sound_event.sound_event.geometry
-        for sound_event in predicted_sound_events
-        if sound_event.sound_event.geometry is not None
-    ]
-
-    scores = [
-        sound_event.score
-        for sound_event in predicted_sound_events
-        if sound_event.sound_event.geometry is not None
-    ]
-
-    matches = []
-    for source_idx, target_idx, affinity in match_geometries(
-        source=predicted_geometries,
-        target=annotated_geometries,
-        config=config,
-        scores=scores,
-    ):
-        target = (
-            annotated_sound_events[target_idx]
-            if target_idx is not None
-            else None
-        )
-        source = (
-            predicted_sound_events[source_idx]
-            if source_idx is not None
-            else None
-        )
-        matches.append(
-            data.Match(
-                source=source,
-                target=target,
-                affinity=affinity,
-            )
-        )
-
-    return matches
-
-
 def match_all_predictions(
     clip_annotations: List[data.ClipAnnotation],
     predictions: List[List[RawPrediction]],
-    targets: TargetProtocol,
+    targets: Optional[TargetProtocol] = None,
-    config: Optional[MatchConfig] = None,
+    matcher: Optional[MatcherProtocol] = None,
+    ignore_start_end: float = 0.01,
 ) -> List[MatchEvaluation]:
     logger.info("Matching all annotations and predictions...")
     return [
@@ -461,11 +526,12 @@ def match_all_predictions(
             clip_annotations,
             predictions,
         )
-        for match in match_sound_events_and_raw_predictions(
+        for match in match_sound_events_and_predictions(
             clip_annotation,
             raw_predictions,
             targets=targets,
-            config=config,
+            matcher=matcher,
+            ignore_start_end=ignore_start_end,
         )
     ]
 

src/batdetect2/evaluate/metrics.py

@@ -24,10 +24,12 @@ class ClassificationMeanAveragePrecision(MetricsProtocol):
         self.class_names = class_names
 
     def __call__(self, matches: List[MatchEvaluation]) -> Dict[str, float]:
+        # NOTE: Need to exclude generic but unclassified targets
         y_true = label_binarize(
             [
                 match.gt_class if match.gt_class is not None else "__NONE__"
                 for match in matches
+                if not (match.gt_det and match.gt_class is None)
             ],
             classes=self.class_names,
         )
@@ -38,11 +40,11 @@ class ClassificationMeanAveragePrecision(MetricsProtocol):
                     for name in self.class_names
                 }
                 for match in matches
+                if not (match.gt_det and match.gt_class is None)
             ]
         ).fillna(0)
 
         ret = {}
-
         for class_index, class_name in enumerate(self.class_names):
             y_true_class = y_true[:, class_index]
             y_pred_class = y_pred[class_name]
@@ -57,39 +59,3 @@ class ClassificationMeanAveragePrecision(MetricsProtocol):
         )
 
         return ret
-
-
-class ClassificationAccuracy(MetricsProtocol):
-    def __init__(self, class_names: List[str]):
-        self.class_names = class_names
-
-    def __call__(self, matches: List[MatchEvaluation]) -> Dict[str, float]:
-        y_true = [
-            match.gt_class if match.gt_class is not None else "__NONE__"
-            for match in matches
-        ]
-
-        y_pred = pd.DataFrame(
-            [
-                {
-                    name: match.pred_class_scores.get(name, 0)
-                    for name in self.class_names
-                }
-                for match in matches
-            ]
-        ).fillna(0)
-        y_pred = y_pred.apply(
-            lambda row: row.idxmax()
-            if row.max() >= (1 - row.sum())
-            else "__NONE__",
-            axis=1,
-        )
-
-        accuracy = metrics.balanced_accuracy_score(
-            y_true,
-            y_pred,
-        )
-
-        return {
-            "classification_acc": float(accuracy),
-        }

src/batdetect2/targets/__init__.py

@@ -8,13 +8,10 @@ from pydantic import Field, field_validator
 from soundevent import data
 
 from batdetect2.configs import BaseConfig, load_config
-from batdetect2.data.conditions import (
+from batdetect2.data.conditions import build_sound_event_condition
-    SoundEventCondition,
-    build_sound_event_condition,
-)
 from batdetect2.targets.classes import (
     DEFAULT_CLASSES,
-    DEFAULT_GENERIC_CLASS,
+    DEFAULT_DETECTION_CLASS,
     SoundEventDecoder,
     SoundEventEncoder,
     TargetClassConfig,
@@ -58,7 +55,9 @@ __all__ = [
 
 
 class TargetConfig(BaseConfig):
-    detection_target: TargetClassConfig = Field(default=DEFAULT_GENERIC_CLASS)
+    detection_target: TargetClassConfig = Field(
+        default=DEFAULT_DETECTION_CLASS
+    )
 
     classification_targets: List[TargetClassConfig] = Field(
         default_factory=lambda: DEFAULT_CLASSES
@@ -151,49 +150,36 @@ class Targets(TargetProtocol):
     dimension_names: List[str]
     detection_class_name: str
 
-    def __init__(
+    def __init__(self, config: TargetConfig):
-        self,
+        """Initialize the Targets object."""
-        detection_class_name: str,
+        self.config = config
-        encode_fn: SoundEventEncoder,
-        decode_fn: SoundEventDecoder,
-        roi_mapper: ROITargetMapper,
-        class_names: list[str],
-        detection_class_tags: List[data.Tag],
-        filter_fn: Optional[SoundEventCondition] = None,
-        roi_mapper_overrides: Optional[dict[str, ROITargetMapper]] = None,
-    ):
-        """Initialize the Targets object.
 
-        Note: This constructor is typically called internally by the
+        self._filter_fn = build_sound_event_condition(
-        `build_targets` factory function.
+            config.detection_target.match_if
+        )
+        self._encode_fn = build_sound_event_encoder(
+            config.classification_targets
+        )
+        self._decode_fn = build_sound_event_decoder(
+            config.classification_targets
+        )
 
-        Parameters
+        self._roi_mapper = build_roi_mapper(config.roi)
-        ----------
-        encode_fn : SoundEventEncoder
-            Configured function to encode annotations to class names.
-        decode_fn : SoundEventDecoder
-            Configured function to decode class names to tags.
-        roi_mapper : ROITargetMapper
-            Configured object for mapping geometry to/from position/size.
-        class_names : list[str]
-            Ordered list of specific target class names.
-        generic_class_tags : List[data.Tag]
-            List of tags representing the generic class.
-        filter_fn : SoundEventFilter, optional
-            Configured function to filter annotations. Defaults to None.
-        transform_fn : SoundEventTransformation, optional
-            Configured function to transform annotation tags. Defaults to None.
-        """
-        self.detection_class_name = detection_class_name
-        self.class_names = class_names
-        self.detection_class_tags = detection_class_tags
-        self.dimension_names = roi_mapper.dimension_names
 
-        self._roi_mapper = roi_mapper
+        self.dimension_names = self._roi_mapper.dimension_names
-        self._filter_fn = filter_fn
+
-        self._encode_fn = encode_fn
+        self.class_names = get_class_names_from_config(
-        self._decode_fn = decode_fn
+            config.classification_targets
-        self._roi_mapper_overrides = roi_mapper_overrides or {}
+        )
+
+        self.detection_class_name = config.detection_target.name
+        self.detection_class_tags = config.detection_target.assign_tags
+
+        self._roi_mapper_overrides = {
+            class_config.name: build_roi_mapper(class_config.roi)
+            for class_config in config.classification_targets
+            if class_config.roi is not None
+        }
 
         for class_name in self._roi_mapper_overrides:
             if class_name not in self.class_names:
@@ -218,8 +204,6 @@ class Targets(TargetProtocol):
             True if the annotation should be kept (passes the filter),
             False otherwise. If no filter was configured, always returns True.
         """
-        if not self._filter_fn:
-            return True
         return self._filter_fn(sound_event)
 
     def encode_class(
@@ -331,7 +315,7 @@ class Targets(TargetProtocol):
 
 DEFAULT_TARGET_CONFIG: TargetConfig = TargetConfig(
     classification_targets=DEFAULT_CLASSES,
-    detection_target=DEFAULT_GENERIC_CLASS,
+    detection_target=DEFAULT_DETECTION_CLASS,
     roi=AnchorBBoxMapperConfig(),
 )
 
@@ -339,13 +323,6 @@ DEFAULT_TARGET_CONFIG: TargetConfig = TargetConfig(
 def build_targets(config: Optional[TargetConfig] = None) -> Targets:
     """Build a Targets object from a loaded TargetConfig.
 
-    This factory function takes the unified `TargetConfig` and constructs all
-    necessary functional components (filter, transform, encoder,
-    decoder, ROI mapper) by calling their respective builder functions. It also
-    extracts metadata (class names, generic tags, dimension names) to create
-    and return a fully initialized `Targets` instance, ready to process
-    annotations.
-
     Parameters
     ----------
     config : TargetConfig
@@ -370,31 +347,7 @@ def build_targets(config: Optional[TargetConfig] = None) -> Targets:
         lambda: config.to_yaml_string(),
     )
 
-    filter_fn = build_sound_event_condition(config.detection_target.match_if)
+    return Targets(config=config)
-    encode_fn = build_sound_event_encoder(config.classification_targets)
-    decode_fn = build_sound_event_decoder(config.classification_targets)
-
-    roi_mapper = build_roi_mapper(config.roi)
-    class_names = get_class_names_from_config(config.classification_targets)
-
-    generic_class_tags = config.detection_target.assign_tags
-
-    roi_overrides = {
-        class_config.name: build_roi_mapper(class_config.roi)
-        for class_config in config.classification_targets
-        if class_config.roi is not None
-    }
-
-    return Targets(
-        filter_fn=filter_fn,
-        encode_fn=encode_fn,
-        decode_fn=decode_fn,
-        class_names=class_names,
-        roi_mapper=roi_mapper,
-        detection_class_name=config.detection_target.name,
-        detection_class_tags=generic_class_tags,
-        roi_mapper_overrides=roi_overrides,
-    )
 
 
 def load_targets(

src/batdetect2/targets/classes.py

@@ -15,6 +15,7 @@ from batdetect2.data.conditions import (
     build_sound_event_condition,
 )
 from batdetect2.targets.rois import ROIMapperConfig
+from batdetect2.targets.terms import call_type, generic_class
 from batdetect2.typing.targets import SoundEventDecoder, SoundEventEncoder
 
 __all__ = [
@@ -69,24 +70,27 @@ class TargetClassConfig(BaseConfig):
         return self._match_if
 
 
-DEFAULT_GENERIC_CLASS = TargetClassConfig(
+DEFAULT_DETECTION_CLASS = TargetClassConfig(
     name="bat",
     match_if=AllOfConfig(
         conditions=[
-            HasTagConfig(tag=data.Tag(key="event", value="Echolocation")),
+            HasTagConfig(tag=data.Tag(term=call_type, value="Echolocation")),
             NotConfig(
                 condition=HasAnyTagConfig(
                     tags=[
-                        data.Tag(key="event", value="Feeding"),
+                        data.Tag(term=call_type, value="Feeding"),
-                        data.Tag(key="event", value="Unknown"),
+                        data.Tag(term=call_type, value="Social"),
-                        data.Tag(key="event", value="Not Bat"),
+                        data.Tag(term=call_type, value="Unknown"),
+                        data.Tag(term=generic_class, value="Unknown"),
+                        data.Tag(term=generic_class, value="Not Bat"),
+                        data.Tag(term=call_type, value="Not Bat"),
                     ]
                 )
             ),
         ]
     ),
     assign_tags=[
-        data.Tag(key="call_type", value="Echolocation"),
+        data.Tag(term=call_type, value="Echolocation"),
         data.Tag(key="order", value="Chiroptera"),
     ],
 )
@@ -94,73 +98,73 @@ DEFAULT_GENERIC_CLASS = TargetClassConfig(
 
 DEFAULT_CLASSES = [
     TargetClassConfig(
-        name="myomys",
+        name="barbar",
-        tags=[data.Tag(key="class", value="Myotis mystacinus")],
+        tags=[data.Tag(key="class", value="Barbastellus barbastellus")],
-    ),
-    TargetClassConfig(
-        name="myoalc",
-        tags=[data.Tag(key="class", value="Myotis alcathoe")],
     ),
     TargetClassConfig(
         name="eptser",
         tags=[data.Tag(key="class", value="Eptesicus serotinus")],
     ),
     TargetClassConfig(
-        name="pipnat",
+        name="myoalc",
-        tags=[data.Tag(key="class", value="Pipistrellus nathusii")],
+        tags=[data.Tag(key="class", value="Myotis alcathoe")],
-    ),
-    TargetClassConfig(
-        name="barbar",
-        tags=[data.Tag(key="class", value="Barbastellus barbastellus")],
-    ),
-    TargetClassConfig(
-        name="myonat",
-        tags=[data.Tag(key="class", value="Myotis nattereri")],
-    ),
-    TargetClassConfig(
-        name="myodau",
-        tags=[data.Tag(key="class", value="Myotis daubentonii")],
-    ),
-    TargetClassConfig(
-        name="myobra",
-        tags=[data.Tag(key="class", value="Myotis brandtii")],
-    ),
-    TargetClassConfig(
-        name="pippip",
-        tags=[data.Tag(key="class", value="Pipistrellus pipistrellus")],
     ),
     TargetClassConfig(
         name="myobec",
         tags=[data.Tag(key="class", value="Myotis bechsteinii")],
     ),
     TargetClassConfig(
-        name="pippyg",
+        name="myobra",
-        tags=[data.Tag(key="class", value="Pipistrellus pygmaeus")],
+        tags=[data.Tag(key="class", value="Myotis brandtii")],
     ),
     TargetClassConfig(
-        name="rhihip",
+        name="myodau",
-        tags=[data.Tag(key="class", value="Rhinolophus hipposideros")],
+        tags=[data.Tag(key="class", value="Myotis daubentonii")],
+    ),
+    TargetClassConfig(
+        name="myomys",
+        tags=[data.Tag(key="class", value="Myotis mystacinus")],
+    ),
+    TargetClassConfig(
+        name="myonat",
+        tags=[data.Tag(key="class", value="Myotis nattereri")],
     ),
     TargetClassConfig(
         name="nyclei",
         tags=[data.Tag(key="class", value="Nyctalus leisleri")],
     ),
     TargetClassConfig(
-        name="rhifer",
+        name="nycnoc",
-        tags=[data.Tag(key="class", value="Rhinolophus ferrumequinum")],
+        tags=[data.Tag(key="class", value="Nyctalus noctula")],
+    ),
+    TargetClassConfig(
+        name="pipnat",
+        tags=[data.Tag(key="class", value="Pipistrellus nathusii")],
+    ),
+    TargetClassConfig(
+        name="pippip",
+        tags=[data.Tag(key="class", value="Pipistrellus pipistrellus")],
+    ),
+    TargetClassConfig(
+        name="pippyg",
+        tags=[data.Tag(key="class", value="Pipistrellus pygmaeus")],
     ),
     TargetClassConfig(
         name="pleaur",
         tags=[data.Tag(key="class", value="Plecotus auritus")],
     ),
-    TargetClassConfig(
-        name="nycnoc",
-        tags=[data.Tag(key="class", value="Nyctalus noctula")],
-    ),
     TargetClassConfig(
         name="pleaus",
         tags=[data.Tag(key="class", value="Plecotus austriacus")],
     ),
+    TargetClassConfig(
+        name="rhifer",
+        tags=[data.Tag(key="class", value="Rhinolophus ferrumequinum")],
+    ),
+    TargetClassConfig(
+        name="rhihip",
+        tags=[data.Tag(key="class", value="Rhinolophus hipposideros")],
+    ),
 ]
 
 

src/batdetect2/train/callbacks.py

@@ -7,6 +7,7 @@ from torch.utils.data import DataLoader
 
 from batdetect2.evaluate.match import (
     MatchConfig,
+    build_matcher,
     match_all_predictions,
 )
 from batdetect2.plotting.clips import PreprocessorProtocol
@@ -42,6 +43,8 @@ class ValidationMetrics(Callback):
         self.preprocessor = preprocessor
         self.plot = plot
 
+        self.matcher = build_matcher(config=match_config)
+
         self._clip_annotations: List[data.ClipAnnotation] = []
         self._predictions: List[List[RawPrediction]] = []
 
@@ -93,7 +96,7 @@ class ValidationMetrics(Callback):
             self._clip_annotations,
             self._predictions,
             targets=pl_module.model.targets,
-            config=self.match_config,
+            matcher=self.matcher,
         )
 
         self.log_metrics(pl_module, matches)

src/batdetect2/train/train.py

@@ -11,7 +11,6 @@ from torch.utils.data import DataLoader
 
 from batdetect2.evaluate.config import EvaluationConfig
 from batdetect2.evaluate.metrics import (
-    ClassificationAccuracy,
     ClassificationMeanAveragePrecision,
     DetectionAveragePrecision,
 )
@@ -175,7 +174,6 @@ def build_trainer_callbacks(
                 ClassificationMeanAveragePrecision(
                     class_names=targets.class_names
                 ),
-                ClassificationAccuracy(class_names=targets.class_names),
             ],
             preprocessor=preprocessor,
             match_config=config.match,

src/batdetect2/typing/evaluate.py

@@ -1,5 +1,15 @@
 from dataclasses import dataclass
-from typing import Dict, List, Optional, Protocol
+from typing import (
+    Dict,
+    Generic,
+    Iterable,
+    List,
+    Optional,
+    Protocol,
+    Sequence,
+    Tuple,
+    TypeVar,
+)
 
 from soundevent import data
 
@@ -40,5 +50,27 @@ class MatchEvaluation:
         return self.pred_class_scores[pred_class]
 
 
+class MatcherProtocol(Protocol):
+    def __call__(
+        self,
+        ground_truth: Sequence[data.Geometry],
+        predictions: Sequence[data.Geometry],
+        scores: Sequence[float],
+    ) -> Iterable[Tuple[Optional[int], Optional[int], float]]: ...
+
+
+Geom = TypeVar("Geom", bound=data.Geometry, contravariant=True)
+
+
+class AffinityFunction(Protocol, Generic[Geom]):
+    def __call__(
+        self,
+        geometry1: Geom,
+        geometry2: Geom,
+        time_buffer: float = 0.01,
+        freq_buffer: float = 1000,
+    ) -> float: ...
+
+
 class MetricsProtocol(Protocol):
     def __call__(self, matches: List[MatchEvaluation]) -> Dict[str, float]: ...