Handle case of empty preds or gt

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 DEFAULT_MATCH_CONFIG, MatchConfig
+from batdetect2.evaluate.match import MatchConfig
 
 __all__ = [
     "EvaluationConfig",
@@ -13,9 +13,7 @@ __all__ = [
 
 
 class EvaluationConfig(BaseConfig):
-    match: MatchConfig = Field(
-        default_factory=lambda: DEFAULT_MATCH_CONFIG.model_copy(),
-    )
+    match: MatchConfig = Field(default_factory=MatchConfig)
 
 
 def load_evaluation_config(

src/batdetect2/evaluate/match.py

@@ -1,8 +1,12 @@
-from typing import Annotated, List, Literal, Optional, Union
+from collections.abc import Callable, Iterable, Mapping
+from typing import List, Literal, Optional, Tuple
 
-from pydantic import Field
+import numpy as np
 from soundevent import data
-from soundevent.evaluation import match_geometries
+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
@@ -10,70 +14,186 @@ from batdetect2.evaluate.types import MatchEvaluation
 from batdetect2.postprocess.types import BatDetect2Prediction
 from batdetect2.targets.types import TargetProtocol
 
+MatchingStrategy = Literal["greedy", "optimal"]
+"""The type of matching algorithm to use: 'greedy' or 'optimal'."""
 
-class BBoxMatchConfig(BaseConfig):
-    match_method: Literal["BBoxIOU"] = "BBoxIOU"
-    affinity_threshold: float = 0.5
-    time_buffer: float = 0.01
+
+MatchingGeometry = Literal["bbox", "interval", "timestamp"]
+"""The geometry representation to use for matching."""
+
+
+class MatchConfig(BaseConfig):
+    """Configuration for matching geometries.
+
+    Attributes
+    ----------
+    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"
+    geometry: MatchingGeometry = "timestamp"
+    affinity_threshold: float = 0.0
+    time_buffer: float = 0.005
     frequency_buffer: float = 1_000
 
 
-class IntervalMatchConfig(BaseConfig):
-    match_method: Literal["IntervalIOU"] = "IntervalIOU"
-    affinity_threshold: float = 0.5
-    time_buffer: float = 0.01
-
-
-class StartTimeMatchConfig(BaseConfig):
-    match_method: Literal["StartTime"] = "StartTime"
-    time_buffer: float = 0.01
-
-
-MatchConfig = Annotated[
-    Union[BBoxMatchConfig, IntervalMatchConfig, StartTimeMatchConfig],
-    Field(discriminator="match_method"),
-]
-
-
-DEFAULT_MATCH_CONFIG = BBoxMatchConfig()
-
-
-def prepare_geometry(
-    geometry: data.Geometry, config: MatchConfig
-) -> data.Geometry:
+def _to_bbox(geometry: data.Geometry) -> data.BoundingBox:
     start_time, low_freq, end_time, high_freq = compute_bounds(geometry)
-
-    if config.match_method == "BBoxIOU":
     return data.BoundingBox(
         coordinates=[start_time, low_freq, end_time, high_freq]
     )
 
-    if config.match_method == "IntervalIOU":
+
+def _to_interval(geometry: data.Geometry) -> data.TimeInterval:
+    start_time, _, end_time, _ = compute_bounds(geometry)
     return data.TimeInterval(coordinates=[start_time, end_time])
 
-    if config.match_method == "StartTime":
+
+def _to_timestamp(geometry: data.Geometry) -> data.TimeStamp:
+    start_time = compute_bounds(geometry)[0]
     return data.TimeStamp(coordinates=start_time)
 
+
+_geometry_cast_functions: Mapping[
+    MatchingGeometry, Callable[[data.Geometry], data.Geometry]
+] = {
+    "bbox": _to_bbox,
+    "interval": _to_interval,
+    "timestamp": _to_timestamp,
+}
+
+
+def match_geometries(
+    source: List[data.Geometry],
+    target: List[data.Geometry],
+    config: MatchConfig,
+    scores: Optional[List[float]] = None,
+) -> Iterable[Tuple[Optional[int], Optional[int], float]]:
+    geometry_cast = _geometry_cast_functions[config.geometry]
+
+    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":
+        return greedy_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,
+            scores=scores,
+        )
+
     raise NotImplementedError(
-        f"Invalid matching configuration. Unknown match method: {config.match_method}"
+        f"Matching strategy not implemented {config.strategy}"
     )
 
 
-def _get_frequency_buffer(config: MatchConfig) -> float:
-    if config.match_method == "BBoxIOU":
-        return config.frequency_buffer
+def greedy_match(
+    source: List[data.Geometry],
+    target: List[data.Geometry],
+    scores: Optional[List[float]] = None,
+    affinity_threshold: float = 0.5,
+    time_buffer: float = 0.001,
+    freq_buffer: float = 1000,
+) -> Iterable[Tuple[Optional[int], Optional[int], float]]:
+    """Performs a greedy, one-to-one matching of source to target geometries.
 
-    return 0
+    Iterates through source geometries, prioritizing by score if provided. Each
+    source is matched to the best available target, provided the affinity
+    exceeds the threshold and the target has not already been assigned.
 
+    Parameters
+    ----------
+    source
+        A list of source geometries (e.g., predictions).
+    target
+        A list of target geometries (e.g., ground truths).
+    scores
+        Confidence scores for each source geometry for prioritization.
+    affinity_threshold
+        The minimum affinity score required for a valid match.
+    time_buffer
+        Time tolerance in seconds for affinity calculation.
+    freq_buffer
+        Frequency tolerance in Hertz for affinity calculation.
 
-def _get_affinity_threshold(config: MatchConfig) -> float:
-    if (
-        config.match_method == "BBoxIOU"
-        or config.match_method == "IntervalIOU"
-    ):
-        return config.affinity_threshold
+    Yields
+    ------
+    Tuple[Optional[int], Optional[int], float]
+        A 3-element tuple describing a match or a miss. There are three
+        possible formats:
+        - Successful Match: `(source_idx, target_idx, affinity)`
+        - Unmatched Source (False Positive): `(source_idx, None, 0)`
+        - Unmatched Target (False Negative): `(None, target_idx, 0)`
+    """
+    assigned = set()
 
-    return 0
+    if not source:
+        for target_idx in range(len(target)):
+            yield None, target_idx, 0
+
+        return
+
+    if not target:
+        for source_idx in range(len(source)):
+            yield source_idx, None, 0
+
+        return
+
+    if scores is None:
+        indices = np.arange(len(source))
+    else:
+        indices = np.argsort(scores)[::-1]
+
+    for source_idx in indices:
+        source_geometry = source[source_idx]
+
+        affinities = np.array(
+            [
+                compute_affinity(
+                    source_geometry,
+                    target_geometry,
+                    time_buffer=time_buffer,
+                    freq_buffer=freq_buffer,
+                )
+                for target_geometry in target
+            ]
+        )
+
+        closest_target = int(np.argmax(affinities))
+        affinity = affinities[closest_target]
+
+        if affinities[closest_target] <= affinity_threshold:
+            yield source_idx, None, 0
+            continue
+
+        if closest_target in assigned:
+            yield source_idx, None, 0
+            continue
+
+        assigned.add(closest_target)
+        yield source_idx, closest_target, affinity
+
+    missed_ground_truth = set(range(len(target))) - assigned
+    for target_idx in missed_ground_truth:
+        yield None, target_idx, 0
 
 
 def match_sound_events_and_raw_predictions(
@@ -82,7 +202,7 @@ def match_sound_events_and_raw_predictions(
     targets: TargetProtocol,
     config: Optional[MatchConfig] = None,
 ) -> List[MatchEvaluation]:
-    config = config or DEFAULT_MATCH_CONFIG
+    config = config or MatchConfig()
 
     target_sound_events = [
         targets.transform(sound_event_annotation)
@@ -92,30 +212,34 @@ def match_sound_events_and_raw_predictions(
     ]
 
     target_geometries: List[data.Geometry] = [  # type: ignore
-        prepare_geometry(
-            sound_event_annotation.sound_event.geometry,
-            config=config,
-        )
+        sound_event_annotation.sound_event.geometry
         for sound_event_annotation in target_sound_events
         if sound_event_annotation.sound_event.geometry is not None
     ]
 
     predicted_geometries = [
-        prepare_geometry(raw_prediction.raw.geometry, config=config)
+        raw_prediction.raw.geometry for raw_prediction in raw_predictions
+    ]
+
+    scores = [
+        raw_prediction.raw.detection_score
         for raw_prediction in raw_predictions
     ]
 
     matches = []
 
-    for id1, id2, affinity in match_geometries(
-        target_geometries,
-        predicted_geometries,
-        time_buffer=config.time_buffer,
-        freq_buffer=_get_frequency_buffer(config),
-        affinity_threshold=_get_affinity_threshold(config),
+    for source_idx, target_idx, affinity in match_geometries(
+        source=predicted_geometries,
+        target=target_geometries,
+        config=config,
+        scores=scores,
     ):
-        target = target_sound_events[id1] if id1 is not None else None
-        prediction = raw_predictions[id2] if id2 is not None else None
+        target = (
+            target_sound_events[target_idx] if target_idx is not None else None
+        )
+        prediction = (
+            raw_predictions[source_idx] if source_idx is not None else None
+        )
 
         gt_det = target is not None
         gt_class = targets.encode_class(target) if target is not None else None
@@ -158,7 +282,7 @@ def match_predictions_and_annotations(
     clip_prediction: data.ClipPrediction,
     config: Optional[MatchConfig] = None,
 ) -> List[data.Match]:
-    config = config or DEFAULT_MATCH_CONFIG
+    config = config or MatchConfig()
 
     annotated_sound_events = [
         sound_event_annotation
@@ -173,29 +297,46 @@ def match_predictions_and_annotations(
     ]
 
     annotated_geometries: List[data.Geometry] = [
-        prepare_geometry(sound_event.sound_event.geometry, config=config)
+        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] = [
-        prepare_geometry(sound_event.sound_event.geometry, config=config)
+        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 id1, id2, affinity in match_geometries(
-        annotated_geometries,
-        predicted_geometries,
-        time_buffer=config.time_buffer,
-        freq_buffer=_get_frequency_buffer(config),
-        affinity_threshold=_get_affinity_threshold(config),
+    for source_idx, target_idx, affinity in match_geometries(
+        source=predicted_geometries,
+        target=annotated_geometries,
+        config=config,
+        scores=scores,
     ):
-        target = annotated_sound_events[id1] if id1 is not None else None
-        source = predicted_sound_events[id2] if id2 is not None else None
+        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)
+            data.Match(
+                source=source,
+                target=target,
+                affinity=affinity,
+            )
         )
 
     return matches

src/batdetect2/train/callbacks.py

@@ -177,7 +177,10 @@ def _match_all_collected_examples(
         match
         for clip_annotation, raw_predictions in pre_matches
         for match in match_sound_events_and_raw_predictions(
-            clip_annotation, raw_predictions, targets=targets, config=config
+            clip_annotation,
+            raw_predictions,
+            targets=targets,
+            config=config,
         )
     ]