Exported types at module level

src/batdetect2/api_v2.py

@@ -7,35 +7,35 @@ import torch
 from soundevent import data
 from soundevent.audio.files import get_audio_files
 
-from batdetect2.audio import build_audio_loader
-from batdetect2.audio.types import AudioLoader
+from batdetect2.audio import AudioLoader, build_audio_loader
 from batdetect2.config import BatDetect2Config
 from batdetect2.core import merge_configs
-from batdetect2.data import load_dataset_from_config
-from batdetect2.data.datasets import Dataset
-from batdetect2.evaluate import DEFAULT_EVAL_DIR, build_evaluator, run_evaluate
-from batdetect2.evaluate.types import EvaluatorProtocol
+from batdetect2.data import Dataset, load_dataset_from_config
+from batdetect2.evaluate import (
+    DEFAULT_EVAL_DIR,
+    EvaluatorProtocol,
+    build_evaluator,
+    run_evaluate,
+)
 from batdetect2.inference import process_file_list, run_batch_inference
 from batdetect2.logging import DEFAULT_LOGS_DIR
 from batdetect2.models import Model, build_model
 from batdetect2.outputs import (
     OutputFormatConfig,
+    OutputFormatterProtocol,
     OutputTransformProtocol,
     build_output_formatter,
     build_output_transform,
     get_output_formatter,
 )
-from batdetect2.outputs.types import OutputFormatterProtocol
-from batdetect2.postprocess import build_postprocessor
-from batdetect2.postprocess.types import (
+from batdetect2.postprocess import (
     ClipDetections,
     Detection,
     PostprocessorProtocol,
+    build_postprocessor,
 )
-from batdetect2.preprocess import build_preprocessor
-from batdetect2.preprocess.types import PreprocessorProtocol
-from batdetect2.targets import build_targets
-from batdetect2.targets.types import TargetProtocol
+from batdetect2.preprocess import PreprocessorProtocol, build_preprocessor
+from batdetect2.targets import TargetProtocol, build_targets
 from batdetect2.train import (
     DEFAULT_CHECKPOINT_DIR,
     load_model_from_checkpoint,
@@ -168,6 +168,9 @@ class BatDetect2API:
     def load_audio(self, path: data.PathLike) -> np.ndarray:
         return self.audio_loader.load_file(path)
 
+    def load_recording(self, recording: data.Recording) -> np.ndarray:
+        return self.audio_loader.load_recording(recording)
+
     def load_clip(self, clip: data.Clip) -> np.ndarray:
         return self.audio_loader.load_clip(clip)
 
@@ -178,7 +181,7 @@ class BatDetect2API:
         tensor = torch.tensor(audio).unsqueeze(0)
         return self.preprocessor(tensor)
 
-    def process_file(self, audio_file: str) -> ClipDetections:
+    def process_file(self, audio_file: data.PathLike) -> ClipDetections:
         recording = data.Recording.from_file(audio_file, compute_hash=False)
         wav = self.audio_loader.load_recording(recording)
         detections = self.process_audio(wav)
@@ -230,6 +233,7 @@ class BatDetect2API:
     def process_files(
         self,
         audio_files: Sequence[data.PathLike],
+        batch_size: int | None = None,
         num_workers: int = 0,
     ) -> list[ClipDetections]:
         return process_file_list(

src/batdetect2/audio/__init__.py

@@ -5,8 +5,11 @@ from batdetect2.audio.loader import (
     SoundEventAudioLoader,
     build_audio_loader,
 )
+from batdetect2.audio.types import AudioLoader, ClipperProtocol
 
 __all__ = [
+    "AudioLoader",
+    "ClipperProtocol",
     "TARGET_SAMPLERATE_HZ",
     "AudioConfig",
     "SoundEventAudioLoader",

src/batdetect2/data/__init__.py

@@ -7,6 +7,7 @@ from batdetect2.data.annotations import (
     load_annotated_dataset,
 )
 from batdetect2.data.datasets import (
+    Dataset,
     DatasetConfig,
     load_dataset,
     load_dataset_config,
@@ -19,6 +20,7 @@ from batdetect2.data.summary import (
 )
 
 __all__ = [
+    "Dataset",
     "AOEFAnnotations",
     "AnnotatedDataset",
     "AnnotationFormats",

src/batdetect2/evaluate/__init__.py

@@ -2,14 +2,30 @@ from batdetect2.evaluate.config import EvaluationConfig, load_evaluation_config
 from batdetect2.evaluate.evaluate import DEFAULT_EVAL_DIR, run_evaluate
 from batdetect2.evaluate.evaluator import Evaluator, build_evaluator
 from batdetect2.evaluate.tasks import TaskConfig, build_task
+from batdetect2.evaluate.types import (
+    AffinityFunction,
+    ClipMatches,
+    EvaluationTaskProtocol,
+    EvaluatorProtocol,
+    MetricsProtocol,
+    PlotterProtocol,
+)
 
 __all__ = [
+    "AffinityFunction",
+    "ClipMatches",
+    "DEFAULT_EVAL_DIR",
     "EvaluationConfig",
+    "EvaluationTaskProtocol",
     "Evaluator",
+    "EvaluatorProtocol",
+    "MatchEvaluation",
+    "MatcherProtocol",
+    "MetricsProtocol",
+    "PlotterProtocol",
     "TaskConfig",
     "build_evaluator",
     "build_task",
-    "run_evaluate",
     "load_evaluation_config",
-    "DEFAULT_EVAL_DIR",
+    "run_evaluate",
 ]

src/batdetect2/inference/batch.py

@@ -1,49 +1,52 @@
-from typing import TYPE_CHECKING, List, Optional, Sequence
+from typing import Sequence
 
 from lightning import Trainer
 from soundevent import data
 
+from batdetect2.audio import AudioConfig
 from batdetect2.audio.loader import build_audio_loader
 from batdetect2.audio.types import AudioLoader
+from batdetect2.inference import InferenceConfig
 from batdetect2.inference.clips import get_clips_from_files
 from batdetect2.inference.dataset import build_inference_loader
 from batdetect2.inference.lightning import InferenceModule
 from batdetect2.models import Model
-from batdetect2.outputs import OutputTransformProtocol, build_output_transform
+from batdetect2.outputs import (
+    OutputsConfig,
+    OutputTransformProtocol,
+    build_output_transform,
+)
 from batdetect2.postprocess.types import ClipDetections
-from batdetect2.preprocess.preprocessor import build_preprocessor
 from batdetect2.preprocess.types import PreprocessorProtocol
-from batdetect2.targets.targets import build_targets
 from batdetect2.targets.types import TargetProtocol
 
-if TYPE_CHECKING:
-    from batdetect2.config import BatDetect2Config
-
 
 def run_batch_inference(
-    model,
+    model: Model,
     clips: Sequence[data.Clip],
-    targets: Optional["TargetProtocol"] = None,
-    audio_loader: Optional["AudioLoader"] = None,
-    preprocessor: Optional["PreprocessorProtocol"] = None,
-    config: Optional["BatDetect2Config"] = None,
-    output_transform: Optional[OutputTransformProtocol] = None,
+    targets: TargetProtocol | None = None,
+    audio_loader: AudioLoader | None = None,
+    preprocessor: PreprocessorProtocol | None = None,
+    audio_config: AudioConfig | None = None,
+    output_transform: OutputTransformProtocol | None = None,
+    output_config: OutputsConfig | None = None,
+    inference_config: InferenceConfig | None = None,
     num_workers: int = 1,
     batch_size: int | None = None,
-) -> List[ClipDetections]:
-    from batdetect2.config import BatDetect2Config
-
-    config = config or BatDetect2Config()
-
-    audio_loader = audio_loader or build_audio_loader()
-
-    preprocessor = preprocessor or build_preprocessor(
-        input_samplerate=audio_loader.samplerate,
+) -> list[ClipDetections]:
+    audio_config = audio_config or AudioConfig(
+        samplerate=model.preprocessor.input_samplerate,
     )
+    output_config = output_config or OutputsConfig()
+    inference_config = inference_config or InferenceConfig()
+
+    audio_loader = audio_loader or build_audio_loader(config=audio_config)
+
+    preprocessor = preprocessor or model.preprocessor
+    targets = targets or model.targets
 
-    targets = targets or build_targets()
     output_transform = output_transform or build_output_transform(
-        config=config.outputs.transform,
+        config=output_config.transform,
         targets=targets,
     )
 
@@ -51,7 +54,7 @@ def run_batch_inference(
         clips,
         audio_loader=audio_loader,
         preprocessor=preprocessor,
-        config=config.inference.loader,
+        config=inference_config.loader,
         num_workers=num_workers,
         batch_size=batch_size,
     )
@@ -72,13 +75,18 @@ def run_batch_inference(
 def process_file_list(
     model: Model,
     paths: Sequence[data.PathLike],
-    config: "BatDetect2Config",
-    targets: Optional["TargetProtocol"] = None,
-    audio_loader: Optional["AudioLoader"] = None,
-    preprocessor: Optional["PreprocessorProtocol"] = None,
+    targets: TargetProtocol | None = None,
+    audio_loader: AudioLoader | None = None,
+    audio_config: AudioConfig | None = None,
+    preprocessor: PreprocessorProtocol | None = None,
+    inference_config: InferenceConfig | None = None,
+    output_config: OutputsConfig | None = None,
+    output_transform: OutputTransformProtocol | None = None,
+    batch_size: int | None = None,
     num_workers: int = 0,
-) -> List[ClipDetections]:
-    clip_config = config.inference.clipping
+) -> list[ClipDetections]:
+    inference_config = inference_config or InferenceConfig()
+    clip_config = inference_config.clipping
     clips = get_clips_from_files(
         paths,
         duration=clip_config.duration,
@@ -92,6 +100,10 @@ def process_file_list(
         targets=targets,
         audio_loader=audio_loader,
         preprocessor=preprocessor,
-        config=config,
+        batch_size=batch_size,
         num_workers=num_workers,
+        output_config=output_config,
+        audio_config=audio_config,
+        output_transform=output_transform,
+        inference_config=inference_config,
     )

src/batdetect2/outputs/__init__.py

@@ -13,11 +13,15 @@ from batdetect2.outputs.transforms import (
     OutputTransformConfig,
     build_output_transform,
 )
-from batdetect2.outputs.types import OutputTransformProtocol
+from batdetect2.outputs.types import (
+    OutputFormatterProtocol,
+    OutputTransformProtocol,
+)
 
 __all__ = [
     "BatDetect2OutputConfig",
     "OutputFormatConfig",
+    "OutputFormatterProtocol",
     "OutputTransformConfig",
     "OutputTransformProtocol",
     "OutputsConfig",

src/batdetect2/postprocess/__init__.py

@@ -9,10 +9,26 @@ from batdetect2.postprocess.postprocessor import (
     Postprocessor,
     build_postprocessor,
 )
+from batdetect2.postprocess.types import (
+    ClipDetections,
+    ClipDetectionsArray,
+    ClipDetectionsTensor,
+    ClipPrediction,
+    Detection,
+    GeometryDecoder,
+    PostprocessorProtocol,
+)
 
 __all__ = [
+    "ClipDetections",
+    "ClipDetectionsArray",
+    "ClipDetectionsTensor",
+    "ClipPrediction",
+    "Detection",
+    "GeometryDecoder",
     "PostprocessConfig",
     "Postprocessor",
+    "PostprocessorProtocol",
     "build_postprocessor",
     "load_postprocess_config",
     "non_max_suppression",

src/batdetect2/preprocess/__init__.py

@@ -7,8 +7,10 @@ from batdetect2.preprocess.config import (
 )
 from batdetect2.preprocess.preprocessor import Preprocessor, build_preprocessor
 from batdetect2.preprocess.spectrogram import MAX_FREQ, MIN_FREQ
+from batdetect2.preprocess.types import PreprocessorProtocol
 
 __all__ = [
+    "PreprocessorProtocol",
     "MAX_FREQ",
     "MIN_FREQ",
     "PreprocessingConfig",

src/batdetect2/targets/__init__.py

@@ -1,8 +1,6 @@
 """BatDetect2 Target Definition system."""
 
 from batdetect2.targets.classes import (
-    SoundEventDecoder,
-    SoundEventEncoder,
     TargetClassConfig,
     build_sound_event_decoder,
     build_sound_event_encoder,
@@ -12,7 +10,6 @@ from batdetect2.targets.config import TargetConfig, load_target_config
 from batdetect2.targets.rois import (
     AnchorBBoxMapperConfig,
     ROIMapperConfig,
-    ROITargetMapper,
     build_roi_mapper,
 )
 from batdetect2.targets.targets import (
@@ -27,15 +24,27 @@ from batdetect2.targets.terms import (
     generic_class,
     individual,
 )
+from batdetect2.targets.types import (
+    Position,
+    ROITargetMapper,
+    Size,
+    SoundEventDecoder,
+    SoundEventEncoder,
+    TargetProtocol,
+)
 
 __all__ = [
     "AnchorBBoxMapperConfig",
+    "Position",
     "ROIMapperConfig",
     "ROITargetMapper",
+    "Size",
     "SoundEventDecoder",
     "SoundEventEncoder",
+    "SoundEventFilter",
     "TargetClassConfig",
     "TargetConfig",
+    "TargetProtocol",
     "Targets",
     "build_roi_mapper",
     "build_sound_event_decoder",