Updating to new Augmentation object

batdetect2/cli/train.py

@@ -5,16 +5,10 @@ import click
 
 from batdetect2.cli.base import cli
 from batdetect2.data import load_dataset_from_config
-from batdetect2.preprocess import (
-    load_preprocessing_config,
-)
-from batdetect2.targets import (
-    load_label_config,
-    load_target_config,
-)
-from batdetect2.train import (
-    preprocess_annotations,
-)
+from batdetect2.preprocess import build_preprocessor, load_preprocessing_config
+from batdetect2.targets import build_targets, load_target_config
+from batdetect2.train import load_label_config, preprocess_annotations
+from batdetect2.train.labels import build_clip_labeler
 
 __all__ = ["train"]
 
@@ -129,9 +123,9 @@ def train(): ...
 def preprocess(
     dataset_config: Path,
     output: Path,
+    target_config: Path,
     base_dir: Optional[Path] = None,
     preprocess_config: Optional[Path] = None,
-    target_config: Optional[Path] = None,
     label_config: Optional[Path] = None,
     force: bool = False,
     num_workers: Optional[int] = None,
@@ -152,13 +146,9 @@ def preprocess(
         else None
     )
 
-    target = (
-        load_target_config(
-            target_config,
-            field=target_config_field,
-        )
-        if target_config
-        else None
+    target = load_target_config(
+        target_config,
+        field=target_config_field,
     )
 
     label = (
@@ -176,15 +166,18 @@ def preprocess(
         base_dir=base_dir,
     )
 
+    targets = build_targets(config=target)
+    preprocessor = build_preprocessor(config=preprocess)
+    labeller = build_clip_labeler(targets, config=label)
+
     if not output.exists():
         output.mkdir(parents=True)
 
     preprocess_annotations(
-        dataset.clip_annotations,
+        dataset,
         output_dir=output,
+        preprocessor=preprocessor,
+        labeller=labeller,
         replace=force,
-        preprocessing_config=preprocess,
-        label_config=label,
-        target_config=target,
         max_workers=num_workers,
     )

batdetect2/postprocess/extraction.py

@@ -63,7 +63,7 @@ def extract_values_at_positions(
             ],
             Dimensions.time.value: positions.coords[Dimensions.time.value],
         }
-    )
+    ).T
 
 
 def extract_detection_xr_dataset(
@@ -109,9 +109,9 @@ def extract_detection_xr_dataset(
           DataArrays share the 'detection' dimension and associated
           time/frequency coordinates.
     """
-    sizes = extract_values_at_positions(sizes, positions).T
-    classes = extract_values_at_positions(classes, positions).T
-    features = extract_values_at_positions(features, positions).T
+    sizes = extract_values_at_positions(sizes, positions)
+    classes = extract_values_at_positions(classes, positions)
+    features = extract_values_at_positions(features, positions)
     return xr.Dataset(
         {
             "scores": positions,

batdetect2/train/__init__.py

@@ -1,8 +1,12 @@
 from batdetect2.train.augmentations import (
     AugmentationsConfig,
+    EchoAugmentationConfig,
+    FrequencyMaskAugmentationConfig,
+    TimeMaskAugmentationConfig,
+    VolumeAugmentationConfig,
+    WarpAugmentationConfig,
     add_echo,
-    augment_example,
-    load_agumentation_config,
+    build_augmentations,
     mask_frequency,
     mask_time,
     mix_examples,
@@ -17,6 +21,7 @@ from batdetect2.train.dataset import (
     TrainExample,
     get_preprocessed_files,
 )
+from batdetect2.train.labels import load_label_config
 from batdetect2.train.losses import compute_loss
 from batdetect2.train.preprocess import (
     generate_train_example,
@@ -26,17 +31,21 @@ from batdetect2.train.train import TrainerConfig, load_trainer_config, train
 
 __all__ = [
     "AugmentationsConfig",
+    "EchoAugmentationConfig",
+    "FrequencyMaskAugmentationConfig",
     "LabeledDataset",
     "SubclipConfig",
+    "TimeMaskAugmentationConfig",
     "TrainExample",
     "TrainerConfig",
     "TrainingConfig",
+    "VolumeAugmentationConfig",
+    "WarpAugmentationConfig",
     "add_echo",
-    "augment_example",
+    "build_augmentations",
     "compute_loss",
     "generate_train_example",
     "get_preprocessed_files",
-    "load_agumentation_config",
     "load_train_config",
     "load_trainer_config",
     "mask_frequency",
@@ -47,4 +56,5 @@ __all__ = [
     "select_subclip",
     "train",
     "warp_spectrogram",
+    "load_label_config",
 ]

batdetect2/train/dataset.py

@@ -11,8 +11,8 @@ from torch.utils.data import Dataset
 
 from batdetect2.configs import BaseConfig
 from batdetect2.train.augmentations import (
+    Augmentation,
     AugmentationsConfig,
-    augment_example,
     select_subclip,
 )
 from batdetect2.train.preprocess import PreprocessorProtocol
@@ -54,7 +54,7 @@ class LabeledDataset(Dataset):
         preprocessor: PreprocessorProtocol,
         filenames: Sequence[PathLike],
         subclip: Optional[SubclipConfig] = None,
-        augmentation: Optional[AugmentationsConfig] = None,
+        augmentation: Optional[Augmentation] = None,
     ):
         self.preprocessor = preprocessor
         self.filenames = filenames
@@ -76,12 +76,7 @@ class LabeledDataset(Dataset):
             )
 
         if self.augmentation:
-            dataset = augment_example(
-                dataset,
-                self.augmentation,
-                preprocessor=self.preprocessor,
-                others=self.get_random_example,
-            )
+            dataset = self.augmentation(dataset)
 
         return TrainExample(
             spec=self.to_tensor(dataset["spectrogram"]).unsqueeze(0),
@@ -98,7 +93,7 @@ class LabeledDataset(Dataset):
         preprocessor: PreprocessorProtocol,
         extension: str = ".nc",
         subclip: Optional[SubclipConfig] = None,
-        augmentation: Optional[AugmentationsConfig] = None,
+        augmentation: Optional[Augmentation] = None,
     ):
         return cls(
             preprocessor=preprocessor,

batdetect2/train/labels.py

@@ -71,7 +71,7 @@ class LabelConfig(BaseConfig):
 
 def build_clip_labeler(
     targets: TargetProtocol,
-    config: LabelConfig,
+    config: Optional[LabelConfig] = None,
 ) -> ClipLabeller:
     """Construct the final clip labelling function.
 
@@ -98,7 +98,7 @@ def build_clip_labeler(
     return partial(
         generate_clip_label,
         targets=targets,
-        config=config,
+        config=config or LabelConfig(),
     )