Instantiate lightnign module from config

src/batdetect2/train/__init__.py

@@ -15,8 +15,10 @@ from batdetect2.train.augmentations import (
 )
 from batdetect2.train.clips import build_clipper, select_subclip
 from batdetect2.train.config import (
+    FullTrainingConfig,
     PLTrainerConfig,
     TrainingConfig,
+    load_full_training_config,
     load_train_config,
 )
 from batdetect2.train.dataset import (
@@ -26,6 +28,7 @@ from batdetect2.train.dataset import (
     list_preprocessed_files,
 )
 from batdetect2.train.labels import build_clip_labeler, load_label_config
+from batdetect2.train.lightning import TrainingModule
 from batdetect2.train.losses import (
     ClassificationLossConfig,
     DetectionLossConfig,
@@ -39,14 +42,11 @@ from batdetect2.train.preprocess import (
     preprocess_annotations,
 )
 from batdetect2.train.train import (
-    FullTrainingConfig,
     build_train_dataset,
     build_train_loader,
     build_trainer,
-    build_training_module,
     build_val_dataset,
     build_val_loader,
-    load_full_training_config,
     train,
 )
 
@@ -66,6 +66,7 @@ __all__ = [
     "TimeMaskAugmentationConfig",
     "TrainExample",
     "TrainingConfig",
+    "TrainingModule",
     "VolumeAugmentationConfig",
     "WarpAugmentationConfig",
     "add_echo",
@@ -76,7 +77,6 @@ __all__ = [
     "build_train_dataset",
     "build_train_loader",
     "build_trainer",
-    "build_training_module",
     "build_val_dataset",
     "build_val_loader",
     "generate_train_example",

src/batdetect2/train/config.py

@@ -4,6 +4,10 @@ from pydantic import Field
 from soundevent import data
 
 from batdetect2.configs import BaseConfig, load_config
+from batdetect2.models import BackboneConfig
+from batdetect2.postprocess import PostprocessConfig
+from batdetect2.preprocess import PreprocessingConfig
+from batdetect2.targets import TargetConfig
 from batdetect2.train.augmentations import (
     DEFAULT_AUGMENTATION_CONFIG,
     AugmentationsConfig,
@@ -15,6 +19,8 @@ from batdetect2.train.losses import LossConfig
 __all__ = [
     "TrainingConfig",
     "load_train_config",
+    "FullTrainingConfig",
+    "load_full_training_config",
 ]
 
 
@@ -57,3 +63,23 @@ def load_train_config(
     field: Optional[str] = None,
 ) -> TrainingConfig:
     return load_config(path, schema=TrainingConfig, field=field)
+
+
+class FullTrainingConfig(BaseConfig):
+    """Full training configuration."""
+
+    train: TrainingConfig = Field(default_factory=TrainingConfig)
+    targets: TargetConfig = Field(default_factory=TargetConfig)
+    model: BackboneConfig = Field(default_factory=BackboneConfig)
+    preprocess: PreprocessingConfig = Field(
+        default_factory=PreprocessingConfig
+    )
+    postprocess: PostprocessConfig = Field(default_factory=PostprocessConfig)
+
+
+def load_full_training_config(
+    path: data.PathLike,
+    field: Optional[str] = None,
+) -> FullTrainingConfig:
+    """Load the full training configuration."""
+    return load_config(path, schema=FullTrainingConfig, field=field)

src/batdetect2/train/lightning.py

@@ -3,15 +3,13 @@ import torch
 from torch.optim.adam import Adam
 from torch.optim.lr_scheduler import CosineAnnealingLR
 
-from batdetect2.models import (
+from batdetect2.models import ModelOutput, build_model
-    DetectionModel,
+from batdetect2.postprocess import build_postprocessor
-    ModelOutput,
+from batdetect2.preprocess import build_preprocessor
-)
+from batdetect2.targets import build_targets
-from batdetect2.postprocess.types import PostprocessorProtocol
-from batdetect2.preprocess.types import PreprocessorProtocol
-from batdetect2.targets.types import TargetProtocol
 from batdetect2.train import TrainExample
-from batdetect2.train.types import LossProtocol
+from batdetect2.train.config import FullTrainingConfig
+from batdetect2.train.losses import build_loss
 
 __all__ = [
     "TrainingModule",
@@ -19,26 +17,25 @@ __all__ = [
 
 
 class TrainingModule(L.LightningModule):
-    def __init__(
+    def __init__(self, config: FullTrainingConfig):
-        self,
-        detector: DetectionModel,
-        loss: LossProtocol,
-        targets: TargetProtocol,
-        preprocessor: PreprocessorProtocol,
-        postprocessor: PostprocessorProtocol,
-        learning_rate: float = 0.001,
-        t_max: int = 100,
-    ):
         super().__init__()
 
-        self.loss = loss
+        self.save_hyperparameters()
-        self.detector = detector
-        self.preprocessor = preprocessor
-        self.targets = targets
-        self.postprocessor = postprocessor
 
-        self.learning_rate = learning_rate
+        self.loss = build_loss(config.train.loss)
-        self.t_max = t_max
+        self.targets = build_targets(config.targets)
+        self.detector = build_model(
+            num_classes=len(self.targets.class_names),
+            config=config.model,
+        )
+        self.preprocessor = build_preprocessor(config.preprocess)
+        self.postprocessor = build_postprocessor(
+            self.targets,
+            min_freq=self.preprocessor.min_freq,
+            max_freq=self.preprocessor.max_freq,
+        )
+
+        self.config = config
 
     def forward(self, spec: torch.Tensor) -> ModelOutput:
         return self.detector(spec)
@@ -68,6 +65,6 @@ class TrainingModule(L.LightningModule):
         return outputs
 
     def configure_optimizers(self):
-        optimizer = Adam(self.parameters(), lr=self.learning_rate)
+        optimizer = Adam(self.parameters(), lr=self.config.train.learning_rate)
-        scheduler = CosineAnnealingLR(optimizer, T_max=self.t_max)
+        scheduler = CosineAnnealingLR(optimizer, T_max=self.config.train.t_max)
         return [optimizer], [scheduler]

src/batdetect2/train/train.py

@@ -3,28 +3,22 @@ from typing import List, Optional
 
 from lightning import Trainer
 from lightning.pytorch.callbacks import Callback
-from pydantic import Field
 from soundevent import data
 from torch.utils.data import DataLoader
 
-from batdetect2.configs import BaseConfig, load_config
 from batdetect2.evaluate.metrics import (
     ClassificationAccuracy,
     ClassificationMeanAveragePrecision,
     DetectionAveragePrecision,
 )
-from batdetect2.models import BackboneConfig, build_model
-from batdetect2.postprocess import PostprocessConfig, build_postprocessor
 from batdetect2.preprocess import (
-    PreprocessingConfig,
     PreprocessorProtocol,
-    build_preprocessor,
 )
-from batdetect2.targets import TargetConfig, TargetProtocol, build_targets
+from batdetect2.targets import TargetProtocol
 from batdetect2.train.augmentations import build_augmentations
 from batdetect2.train.callbacks import ValidationMetrics
 from batdetect2.train.clips import build_clipper
-from batdetect2.train.config import TrainingConfig
+from batdetect2.train.config import FullTrainingConfig, TrainingConfig
 from batdetect2.train.dataset import (
     LabeledDataset,
     RandomExampleSource,
@@ -32,41 +26,17 @@ from batdetect2.train.dataset import (
 )
 from batdetect2.train.lightning import TrainingModule
 from batdetect2.train.logging import build_logger
-from batdetect2.train.losses import build_loss
 
 __all__ = [
-    "FullTrainingConfig",
     "build_train_dataset",
     "build_train_loader",
     "build_trainer",
-    "build_training_module",
     "build_val_dataset",
     "build_val_loader",
-    "load_full_training_config",
     "train",
 ]
 
 
-class FullTrainingConfig(BaseConfig):
-    """Full training configuration."""
-
-    train: TrainingConfig = Field(default_factory=TrainingConfig)
-    targets: TargetConfig = Field(default_factory=TargetConfig)
-    model: BackboneConfig = Field(default_factory=BackboneConfig)
-    preprocess: PreprocessingConfig = Field(
-        default_factory=PreprocessingConfig
-    )
-    postprocess: PostprocessConfig = Field(default_factory=PostprocessConfig)
-
-
-def load_full_training_config(
-    path: data.PathLike,
-    field: Optional[str] = None,
-) -> FullTrainingConfig:
-    """Load the full training configuration."""
-    return load_config(path, schema=FullTrainingConfig, field=field)
-
-
 def train(
     train_examples: Sequence[data.PathLike],
     val_examples: Optional[Sequence[data.PathLike]] = None,
@@ -80,7 +50,7 @@ def train(
     if model_path is not None:
         module = TrainingModule.load_from_checkpoint(model_path)  # type: ignore
     else:
-        module = build_training_module(conf)
+        module = TrainingModule(conf)
 
     trainer = build_trainer(conf, targets=module.targets)
 
@@ -108,35 +78,6 @@ def train(
     )
 
 
-def build_training_module(conf: FullTrainingConfig) -> TrainingModule:
-    preprocessor = build_preprocessor(conf.preprocess)
-
-    targets = build_targets(conf.targets)
-
-    postprocessor = build_postprocessor(
-        targets,
-        min_freq=preprocessor.min_freq,
-        max_freq=preprocessor.max_freq,
-    )
-
-    model = build_model(
-        num_classes=len(targets.class_names),
-        config=conf.model,
-    )
-
-    loss = build_loss(conf.train.loss)
-
-    return TrainingModule(
-        detector=model,
-        loss=loss,
-        targets=targets,
-        preprocessor=preprocessor,
-        postprocessor=postprocessor,
-        learning_rate=conf.train.learning_rate,
-        t_max=conf.train.t_max,
-    )
-
-
 def build_trainer_callbacks(targets: TargetProtocol) -> List[Callback]:
     return [
         ValidationMetrics(

tests/test_train/test_lightning.py

@@ -1,31 +1,16 @@
 from pathlib import Path
 
 import lightning as L
+import pytest
 import torch
 import xarray as xr
 from soundevent import data
 
-from batdetect2.models import build_model
+from batdetect2.train import FullTrainingConfig, TrainingModule
-from batdetect2.postprocess import build_postprocessor
-from batdetect2.preprocess import build_preprocessor
-from batdetect2.targets import build_targets
-from batdetect2.train.lightning import TrainingModule
-from batdetect2.train.losses import build_loss
 
 
 def build_default_module():
-    loss = build_loss()
+    return TrainingModule(FullTrainingConfig())
-    targets = build_targets()
-    detector = build_model(num_classes=len(targets.class_names))
-    preprocessor = build_preprocessor()
-    postprocessor = build_postprocessor(targets)
-    return TrainingModule(
-        detector=detector,
-        loss=loss,
-        targets=targets,
-        preprocessor=preprocessor,
-        postprocessor=postprocessor,
-    )
 
 
 def test_can_initialize_default_module():