LR Scheduler takes num of total batches

example_data/config.yaml

@@ -1,14 +1,3 @@
-datasets:
-  train:
-    name: example dataset
-    description: Only for demonstration purposes
-    sources:
-      - format: batdetect2
-        name: Example Data
-        description: Examples included for testing batdetect2
-        annotations_dir: example_data/anns
-        audio_dir: example_data/audio
-
 targets:
   classes:
     classes:
@@ -99,7 +88,9 @@ model:
             out_channels: 256
   bottleneck:
     channels: 256
-    self_attention: true
+    layers:
+      - block_type: SelfAttention
+        attention_channels: 256
   decoder:
     layers:
       - block_type: FreqCoordConvUp
@@ -114,9 +105,19 @@ model:
             out_channels: 32
 
 train:
-  batch_size: 8
   learning_rate: 0.001
   t_max: 100
+
+  dataloaders:
+    train:
+      batch_size: 8
+      num_workers: 2
+      shuffle: True
+
+    val:
+      batch_size: 8
+      num_workers: 2
+
   loss:
     detection:
       weight: 1.0
@@ -130,14 +131,12 @@ train:
         alpha: 2
     size:
       weight: 0.1
+
   logger:
-    logger_type: mlflow
-    experiment_name: batdetect2
-    tracking_uri: http://localhost:5000
-    log_model: true
+    logger_type: csv
     save_dir: outputs/log/
-    artifact_location: outputs/artifacts/
-    checkpoint_path_prefix: outputs/checkpoints/
+    name: logs
+
   augmentations:
     steps:
       - augmentation_type: mix_audio

example_data/dataset.yaml

@@ -0,0 +1,8 @@
+name: example dataset
+description: Only for demonstration purposes
+sources:
+  - format: batdetect2
+    name: Example Data
+    description: Examples included for testing batdetect2
+    annotations_dir: example_data/anns
+    audio_dir: example_data/audio

src/batdetect2/evaluate/match.py

@@ -1,6 +1,6 @@
 from collections.abc import Callable, Iterable, Mapping
 from dataclasses import dataclass, field
-from typing import List, Literal, Optional, Tuple
+from typing import List, Literal, Optional, Protocol, Tuple
 
 import numpy as np
 from soundevent import data
@@ -23,6 +23,16 @@ MatchingGeometry = Literal["bbox", "interval", "timestamp"]
 """The geometry representation to use for matching."""
 
 
+class AffinityFunction(Protocol):
+    def __call__(
+        self,
+        geometry1: data.Geometry,
+        geometry2: data.Geometry,
+        time_buffer: float = 0.01,
+        freq_buffer: float = 1000,
+    ) -> float: ...
+
+
 class MatchConfig(BaseConfig):
     """Configuration for matching geometries.
 
@@ -74,6 +84,65 @@ _geometry_cast_functions: Mapping[
 }
 
 
+def _timestamp_affinity(
+    geometry1: data.Geometry,
+    geometry2: data.Geometry,
+    time_buffer: float = 0.01,
+    freq_buffer: float = 1000,
+) -> float:
+    assert isinstance(geometry1, data.TimeStamp)
+    assert isinstance(geometry2, data.TimeStamp)
+
+    start_time1 = geometry1.coordinates
+    start_time2 = geometry2.coordinates
+
+    a = min(start_time1, start_time2)
+    b = max(start_time1, start_time2)
+
+    if b - a >= 2 * time_buffer:
+        return 0
+
+    intersection = a - b + 2 * time_buffer
+    union = b - a + 2 * time_buffer
+    return intersection / union
+
+
+def _interval_affinity(
+    geometry1: data.Geometry,
+    geometry2: data.Geometry,
+    time_buffer: float = 0.01,
+    freq_buffer: float = 1000,
+) -> float:
+    assert isinstance(geometry1, data.TimeInterval)
+    assert isinstance(geometry2, data.TimeInterval)
+
+    start_time1, end_time1 = geometry1.coordinates
+    start_time2, end_time2 = geometry1.coordinates
+
+    start_time1 -= time_buffer
+    start_time2 -= time_buffer
+    end_time1 += time_buffer
+    end_time2 += time_buffer
+
+    intersection = max(
+        0, min(end_time1, end_time2) - max(start_time1, start_time2)
+    )
+    union = (
+        (end_time1 - start_time1) + (end_time2 - start_time2) - intersection
+    )
+
+    if union == 0:
+        return 0
+
+    return intersection / union
+
+
+_affinity_functions: Mapping[MatchingGeometry, AffinityFunction] = {
+    "timestamp": _timestamp_affinity,
+    "interval": _interval_affinity,
+}
+
+
 def match_geometries(
     source: List[data.Geometry],
     target: List[data.Geometry],
@@ -81,6 +150,10 @@ def match_geometries(
     scores: Optional[List[float]] = None,
 ) -> Iterable[Tuple[Optional[int], Optional[int], float]]:
     geometry_cast = _geometry_cast_functions[config.geometry]
+    affinity_function = _affinity_functions.get(
+        config.geometry,
+        compute_affinity,
+    )
 
     if config.strategy == "optimal":
         return optimal_match(
@@ -98,6 +171,7 @@ def match_geometries(
             time_buffer=config.time_buffer,
             freq_buffer=config.frequency_buffer,
             affinity_threshold=config.affinity_threshold,
+            affinity_function=affinity_function,
             scores=scores,
         )
 
@@ -111,6 +185,7 @@ def greedy_match(
     target: List[data.Geometry],
     scores: Optional[List[float]] = None,
     affinity_threshold: float = 0.5,
+    affinity_function: AffinityFunction = compute_affinity,
     time_buffer: float = 0.001,
     freq_buffer: float = 1000,
 ) -> Iterable[Tuple[Optional[int], Optional[int], float]]:
@@ -168,7 +243,7 @@ def greedy_match(
 
         affinities = np.array(
             [
-                compute_affinity(
+                affinity_function(
                     source_geometry,
                     target_geometry,
                     time_buffer=time_buffer,

src/batdetect2/models/__init__.py

@@ -26,13 +26,14 @@ for creating a standard BatDetect2 model instance is the `build_model` function
 provided here.
 """
 
-from typing import Optional
+from typing import List, Optional
 
 import torch
 from lightning import LightningModule
 from pydantic import Field
+from soundevent.data import PathLike
 
-from batdetect2.configs import BaseConfig
+from batdetect2.configs import BaseConfig, load_config
 from batdetect2.models.backbones import (
     Backbone,
     BackboneConfig,
@@ -66,8 +67,8 @@ from batdetect2.models.heads import BBoxHead, ClassifierHead, DetectorHead
 from batdetect2.postprocess import PostprocessConfig, build_postprocessor
 from batdetect2.preprocess import PreprocessingConfig, build_preprocessor
 from batdetect2.targets import TargetConfig, build_targets
-from batdetect2.typing.models import DetectionModel, ModelOutput
-from batdetect2.typing.postprocess import PostprocessorProtocol
+from batdetect2.typing.models import DetectionModel
+from batdetect2.typing.postprocess import Detections, PostprocessorProtocol
 from batdetect2.typing.preprocess import PreprocessorProtocol
 from batdetect2.typing.targets import TargetProtocol
 
@@ -119,9 +120,12 @@ class Model(LightningModule):
         self.preprocessor = preprocessor
         self.postprocessor = postprocessor
         self.targets = targets
+        self.save_hyperparameters()
 
-    def forward(self, spec: torch.Tensor) -> ModelOutput:
-        return self.detector(spec)
+    def forward(self, wav: torch.Tensor) -> List[Detections]:
+        spec = self.preprocessor(wav)
+        outputs = self.detector(spec)
+        return self.postprocessor(outputs)
 
 
 class ModelConfig(BaseConfig):
@@ -139,7 +143,6 @@ def build_model(config: Optional[ModelConfig] = None):
     targets = build_targets(config=config.targets)
     preprocessor = build_preprocessor(config=config.preprocess)
     postprocessor = build_postprocessor(
-        targets=targets,
         preprocessor=preprocessor,
         config=config.postprocess,
     )
@@ -153,3 +156,9 @@ def build_model(config: Optional[ModelConfig] = None):
         preprocessor=preprocessor,
         targets=targets,
     )
+
+
+def load_model_config(
+    path: PathLike, field: Optional[str] = None
+) -> ModelConfig:
+    return load_config(path, schema=ModelConfig, field=field)

src/batdetect2/models/blocks.py

@@ -55,6 +55,12 @@ __all__ = [
 ]
 
 
+class SelfAttentionConfig(BaseConfig):
+    block_type: Literal["SelfAttention"] = "SelfAttention"
+    attention_channels: int
+    temperature: float = 1
+
+
 class SelfAttention(nn.Module):
     """Self-Attention mechanism operating along the time dimension.
 
@@ -115,6 +121,7 @@ class SelfAttention(nn.Module):
         # Note, does not encode position information (absolute or relative)
         self.temperature = temperature
         self.att_dim = attention_channels
+
         self.key_fun = nn.Linear(in_channels, attention_channels)
         self.value_fun = nn.Linear(in_channels, attention_channels)
         self.query_fun = nn.Linear(in_channels, attention_channels)
@@ -654,6 +661,7 @@ LayerConfig = Annotated[
         StandardConvDownConfig,
         FreqCoordConvUpConfig,
         StandardConvUpConfig,
+        SelfAttentionConfig,
         "LayerGroupConfig",
     ],
     Field(discriminator="block_type"),
@@ -769,6 +777,17 @@ def build_layer_from_config(
             input_height * 2,
         )
 
+    if config.block_type == "SelfAttention":
+        return (
+            SelfAttention(
+                in_channels=in_channels,
+                attention_channels=config.attention_channels,
+                temperature=config.temperature,
+            ),
+            config.attention_channels,
+            input_height,
+        )
+
     if config.block_type == "LayerGroup":
         current_channels = in_channels
         current_height = input_height

src/batdetect2/models/bottleneck.py

@@ -14,47 +14,27 @@ A factory function `build_bottleneck` constructs the appropriate bottleneck
 module based on the provided configuration.
 """
 
-from typing import Optional
+from typing import Annotated, List, Optional, Union
 
 import torch
+from pydantic import Field
 from torch import nn
 
 from batdetect2.configs import BaseConfig
-from batdetect2.models.blocks import SelfAttention, VerticalConv
+from batdetect2.models.blocks import (
+    LayerConfig,
+    SelfAttentionConfig,
+    VerticalConv,
+    build_layer_from_config,
+)
 
 __all__ = [
     "BottleneckConfig",
     "Bottleneck",
-    "BottleneckAttn",
     "build_bottleneck",
 ]
 
 
-class BottleneckConfig(BaseConfig):
-    """Configuration for the bottleneck layer(s).
-
-    Defines the number of channels within the bottleneck and whether to include
-    a self-attention mechanism.
-
-    Attributes
-    ----------
-    channels : int
-        The number of output channels produced by the main convolutional layer
-        within the bottleneck. This often matches the number of channels coming
-        from the last encoder stage, but can be different. Must be positive.
-        This also defines the channel dimensions used within the optional
-        `SelfAttention` layer.
-    self_attention : bool
-        If True, includes a `SelfAttention` layer operating on the time
-        dimension after an initial `VerticalConv` layer within the bottleneck.
-        If False, only the initial `VerticalConv` (and height repetition) is
-        performed.
-    """
-
-    channels: int
-    self_attention: bool
-
-
 class Bottleneck(nn.Module):
     """Base Bottleneck module for Encoder-Decoder architectures.
 
@@ -99,16 +79,24 @@ class Bottleneck(nn.Module):
         input_height: int,
         in_channels: int,
         out_channels: int,
+        bottleneck_channels: Optional[int] = None,
+        layers: Optional[List[torch.nn.Module]] = None,
     ) -> None:
         """Initialize the base Bottleneck layer."""
         super().__init__()
         self.in_channels = in_channels
         self.input_height = input_height
         self.out_channels = out_channels
+        self.bottleneck_channels = (
+            bottleneck_channels
+            if bottleneck_channels is not None
+            else out_channels
+        )
+        self.layers = nn.ModuleList(layers or [])
 
         self.conv_vert = VerticalConv(
             in_channels=in_channels,
-            out_channels=out_channels,
+            out_channels=self.bottleneck_channels,
             input_height=input_height,
         )
 
@@ -132,73 +120,52 @@ class Bottleneck(nn.Module):
             convolution.
         """
         x = self.conv_vert(x)
+
+        for layer in self.layers:
+            x = layer(x)
+
         return x.repeat([1, 1, self.input_height, 1])
 
 
-class BottleneckAttn(Bottleneck):
-    """Bottleneck module including a Self-Attention layer.
+BottleneckLayerConfig = Annotated[
+    Union[SelfAttentionConfig,],
+    Field(discriminator="block_type"),
+]
+"""Type alias for the discriminated union of block configs usable in Decoder."""
 
-    Extends the base `Bottleneck` by inserting a `SelfAttention` layer after
-    the initial `VerticalConv`. This allows the bottleneck to capture global
-    temporal dependencies in the summarized frequency features before passing
-    them to the decoder.
 
-    Sequence: VerticalConv -> SelfAttention -> Repeat Height.
+class BottleneckConfig(BaseConfig):
+    """Configuration for the bottleneck layer(s).
 
-    Parameters
+    Defines the number of channels within the bottleneck and whether to include
+    a self-attention mechanism.
+
+    Attributes
     ----------
-    input_height : int
-        Height (frequency bins) of the input tensor from the encoder.
-    in_channels : int
-        Number of channels in the input tensor from the encoder.
-    out_channels : int
-        Number of output channels produced by the `VerticalConv` and
-        subsequently processed and output by this bottleneck. Also determines
-        the input/output channels of the internal `SelfAttention` layer.
-    attention : nn.Module
-        An initialized `SelfAttention` module instance.
-
-    Raises
-    ------
-    ValueError
-        If `input_height`, `in_channels`, or `out_channels` are not positive.
+    channels : int
+        The number of output channels produced by the main convolutional layer
+        within the bottleneck. This often matches the number of channels coming
+        from the last encoder stage, but can be different. Must be positive.
+        This also defines the channel dimensions used within the optional
+        `SelfAttention` layer.
+    self_attention : bool
+        If True, includes a `SelfAttention` layer operating on the time
+        dimension after an initial `VerticalConv` layer within the bottleneck.
+        If False, only the initial `VerticalConv` (and height repetition) is
+        performed.
     """
 
-    def __init__(
-        self,
-        input_height: int,
-        in_channels: int,
-        out_channels: int,
-        attention: nn.Module,
-    ) -> None:
-        """Initialize the Bottleneck with Self-Attention."""
-        super().__init__(input_height, in_channels, out_channels)
-        self.attention = attention
-
-    def forward(self, x: torch.Tensor) -> torch.Tensor:
-        """Process input tensor.
-
-        Parameters
-        ----------
-        x : torch.Tensor
-            Input tensor from the encoder bottleneck, shape
-            `(B, C_in, H_in, W)`. `C_in` must match `self.in_channels`,
-            `H_in` must match `self.input_height`.
-
-        Returns
-        -------
-        torch.Tensor
-            Output tensor, shape `(B, C_out, H_in, W)`, after applying attention
-            and repeating the height dimension.
-        """
-        x = self.conv_vert(x)
-        x = self.attention(x)
-        return x.repeat([1, 1, self.input_height, 1])
+    channels: int
+    layers: List[BottleneckLayerConfig] = Field(
+        default_factory=list,
+    )
 
 
 DEFAULT_BOTTLENECK_CONFIG: BottleneckConfig = BottleneckConfig(
     channels=256,
-    self_attention=True,
+    layers=[
+        SelfAttentionConfig(attention_channels=256),
+    ],
 )
 
 
@@ -234,21 +201,25 @@ def build_bottleneck(
     """
     config = config or DEFAULT_BOTTLENECK_CONFIG
 
-    if config.self_attention:
-        attention = SelfAttention(
-            in_channels=config.channels,
-            attention_channels=config.channels,
-        )
+    current_channels = in_channels
+    current_height = input_height
 
-        return BottleneckAttn(
-            input_height=input_height,
-            in_channels=in_channels,
-            out_channels=config.channels,
-            attention=attention,
+    layers = []
+
+    for layer_config in config.layers:
+        layer, current_channels, current_height = build_layer_from_config(
+            input_height=current_height,
+            in_channels=current_channels,
+            config=layer_config,
         )
+        assert current_height == input_height, (
+            "Bottleneck layers should not change the spectrogram height"
+        )
+        layers.append(layer)
 
     return Bottleneck(
         input_height=input_height,
         in_channels=in_channels,
         out_channels=config.channels,
+        layers=layers,
     )

src/batdetect2/plotting/common.py

@@ -26,19 +26,32 @@ def create_ax(
 
 def plot_spectrogram(
     spec: Union[torch.Tensor, np.ndarray],
-    start_time: float,
-    end_time: float,
-    min_freq: float,
-    max_freq: float,
+    start_time: Optional[float] = None,
+    end_time: Optional[float] = None,
+    min_freq: Optional[float] = None,
+    max_freq: Optional[float] = None,
     ax: Optional[axes.Axes] = None,
     figsize: Optional[Tuple[int, int]] = None,
     cmap="gray",
 ) -> axes.Axes:
+
     if isinstance(spec, torch.Tensor):
         spec = spec.numpy()
 
     ax = create_ax(ax=ax, figsize=figsize)
 
+    if start_time is None:
+        start_time = 0
+
+    if end_time is None:
+        end_time = spec.shape[-1]
+
+    if min_freq is None:
+        min_freq = 0
+
+    if max_freq is None:
+        max_freq = spec.shape[-2]
+
     ax.pcolormesh(
         np.linspace(start_time, end_time, spec.shape[-1] + 1, endpoint=True),
         np.linspace(min_freq, max_freq, spec.shape[-2] + 1, endpoint=True),

src/batdetect2/postprocess/__init__.py

@@ -2,6 +2,7 @@
 
 from typing import List, Optional
 
+import torch
 from loguru import logger
 from pydantic import Field
 from soundevent import data
@@ -20,13 +21,15 @@ from batdetect2.postprocess.nms import (
 )
 from batdetect2.postprocess.remapping import map_detection_to_clip
 from batdetect2.preprocess import MAX_FREQ, MIN_FREQ
-from batdetect2.typing import ModelOutput, PreprocessorProtocol, TargetProtocol
+from batdetect2.typing import ModelOutput
 from batdetect2.typing.postprocess import (
     BatDetect2Prediction,
     Detections,
     PostprocessorProtocol,
     RawPrediction,
 )
+from batdetect2.typing.preprocess import PreprocessorProtocol
+from batdetect2.typing.targets import TargetProtocol
 
 __all__ = [
     "DEFAULT_CLASSIFICATION_THRESHOLD",
@@ -128,7 +131,6 @@ def load_postprocess_config(
 
 
 def build_postprocessor(
-    targets: TargetProtocol,
     preprocessor: PreprocessorProtocol,
     config: Optional[PostprocessConfig] = None,
 ) -> PostprocessorProtocol:
@@ -139,29 +141,52 @@ def build_postprocessor(
         lambda: config.to_yaml_string(),
     )
     return Postprocessor(
-        targets=targets,
-        preprocessor=preprocessor,
-        config=config,
+        samplerate=preprocessor.output_samplerate,
+        min_freq=preprocessor.min_freq,
+        max_freq=preprocessor.max_freq,
+        top_k_per_sec=config.top_k_per_sec,
+        detection_threshold=config.detection_threshold,
     )
 
 
-class Postprocessor(PostprocessorProtocol):
+class Postprocessor(torch.nn.Module, PostprocessorProtocol):
     """Standard implementation of the postprocessing pipeline."""
 
-    targets: TargetProtocol
-
-    preprocessor: PreprocessorProtocol
-
     def __init__(
         self,
-        targets: TargetProtocol,
-        preprocessor: PreprocessorProtocol,
-        config: PostprocessConfig,
+        samplerate: float,
+        min_freq: float,
+        max_freq: float,
+        top_k_per_sec: int = 200,
+        detection_threshold: float = 0.01,
     ):
         """Initialize the Postprocessor."""
-        self.targets = targets
-        self.preprocessor = preprocessor
-        self.config = config
+        super().__init__()
+        self.samplerate = samplerate
+        self.min_freq = min_freq
+        self.max_freq = max_freq
+        self.top_k_per_sec = top_k_per_sec
+        self.detection_threshold = detection_threshold
+
+    def forward(self, output: ModelOutput) -> List[Detections]:
+        width = output.detection_probs.shape[-1]
+        duration = width / self.samplerate
+        max_detections = int(self.top_k_per_sec * duration)
+        detections = extract_prediction_tensor(
+            output,
+            max_detections=max_detections,
+            threshold=self.detection_threshold,
+        )
+        return [
+            map_detection_to_clip(
+                detection,
+                start_time=0,
+                end_time=duration,
+                min_freq=self.min_freq,
+                max_freq=self.max_freq,
+            )
+            for detection in detections
+        ]
 
     def get_detections(
         self,
@@ -169,13 +194,13 @@ class Postprocessor(PostprocessorProtocol):
         clips: Optional[List[data.Clip]] = None,
     ) -> List[Detections]:
         width = output.detection_probs.shape[-1]
-        duration = width / self.preprocessor.output_samplerate
-        max_detections = int(self.config.top_k_per_sec * duration)
+        duration = width / self.samplerate
+        max_detections = int(self.top_k_per_sec * duration)
 
         detections = extract_prediction_tensor(
             output,
             max_detections=max_detections,
-            threshold=self.config.detection_threshold,
+            threshold=self.detection_threshold,
         )
 
         if clips is None:
@@ -186,17 +211,19 @@ class Postprocessor(PostprocessorProtocol):
                 detection,
                 start_time=clip.start_time,
                 end_time=clip.end_time,
-                min_freq=self.preprocessor.min_freq,
-                max_freq=self.preprocessor.max_freq,
+                min_freq=self.min_freq,
+                max_freq=self.max_freq,
             )
             for detection, clip in zip(detections, clips)
         ]
 
-    def get_raw_predictions(
-        self,
+
+def get_raw_predictions(
     output: ModelOutput,
     clips: List[data.Clip],
-    ) -> List[List[RawPrediction]]:
+    targets: TargetProtocol,
+    postprocessor: PostprocessorProtocol,
+) -> List[List[RawPrediction]]:
     """Extract intermediate RawPrediction objects for a batch.
 
     Processes raw model output through remapping, NMS, detection, data
@@ -216,21 +243,29 @@ class Postprocessor(PostprocessorProtocol):
         List of lists (one inner list per input clip). Each inner list
         contains `RawPrediction` objects for detections in that clip.
     """
-        detections = self.get_detections(output, clips)
+    detections = postprocessor.get_detections(output, clips)
     return [
         convert_detections_to_raw_predictions(
             dataset,
-                targets=self.targets,
+            targets=targets,
         )
         for dataset in detections
     ]
 
-    def get_sound_event_predictions(
-        self,
+
+def get_sound_event_predictions(
     output: ModelOutput,
     clips: List[data.Clip],
-    ) -> List[List[BatDetect2Prediction]]:
-        raw_predictions = self.get_raw_predictions(output, clips)
+    targets: TargetProtocol,
+    postprocessor: PostprocessorProtocol,
+    classification_threshold: float = DEFAULT_CLASSIFICATION_THRESHOLD,
+) -> List[List[BatDetect2Prediction]]:
+    raw_predictions = get_raw_predictions(
+        output,
+        clips,
+        targets=targets,
+        postprocessor=postprocessor,
+    )
     return [
         [
             BatDetect2Prediction(
@@ -238,8 +273,8 @@ class Postprocessor(PostprocessorProtocol):
                 sound_event_prediction=convert_raw_prediction_to_sound_event_prediction(
                     raw,
                     recording=clip.recording,
-                        targets=self.targets,
-                        classification_threshold=self.config.classification_threshold,
+                    targets=targets,
+                    classification_threshold=classification_threshold,
                 ),
             )
             for raw in predictions
@@ -247,9 +282,14 @@ class Postprocessor(PostprocessorProtocol):
         for predictions, clip in zip(raw_predictions, clips)
     ]
 
-    def get_predictions(
-        self, output: ModelOutput, clips: List[data.Clip]
-    ) -> List[data.ClipPrediction]:
+
+def get_predictions(
+    output: ModelOutput,
+    clips: List[data.Clip],
+    targets: TargetProtocol,
+    postprocessor: PostprocessorProtocol,
+    classification_threshold: float = DEFAULT_CLASSIFICATION_THRESHOLD,
+) -> List[data.ClipPrediction]:
     """Perform the full postprocessing pipeline for a batch.
 
     Takes raw model output and corresponding clips, applies the entire
@@ -269,13 +309,18 @@ class Postprocessor(PostprocessorProtocol):
         List containing one `ClipPrediction` object for each input clip,
         populated with `SoundEventPrediction` objects.
     """
-        raw_predictions = self.get_raw_predictions(output, clips)
+    raw_predictions = get_raw_predictions(
+        output,
+        clips,
+        targets=targets,
+        postprocessor=postprocessor,
+    )
     return [
         convert_raw_predictions_to_clip_prediction(
             prediction,
             clip,
-                targets=self.targets,
-                classification_threshold=self.config.classification_threshold,
+            targets=targets,
+            classification_threshold=classification_threshold,
         )
         for prediction, clip in zip(raw_predictions, clips)
     ]

src/batdetect2/preprocess/spectrogram.py

@@ -139,7 +139,21 @@ class FrequencyClip(torch.nn.Module):
         self.high_index = high_index
 
     def forward(self, spec: torch.Tensor) -> torch.Tensor:
-        return spec[self.low_index : self.high_index]
+        low_index = self.low_index
+        if low_index is None:
+            low_index = 0
+
+        if self.high_index is None:
+            length = spec.shape[-2] - low_index
+        else:
+            length = self.high_index - low_index
+
+        return torch.narrow(
+            spec,
+            dim=-2,
+            start=low_index,
+            length=length,
+        )
 
 
 class PcenConfig(BaseConfig):
@@ -256,15 +270,21 @@ class ResizeSpec(torch.nn.Module):
     def forward(self, spec: torch.Tensor) -> torch.Tensor:
         current_length = spec.shape[-1]
         target_length = int(self.time_factor * current_length)
-        return (
-            torch.nn.functional.interpolate(
-                spec.unsqueeze(0).unsqueeze(0),
+
+        original_ndim = spec.ndim
+        while spec.ndim < 4:
+            spec = spec.unsqueeze(0)
+
+        resized = torch.nn.functional.interpolate(
+            spec,
             size=(self.height, target_length),
             mode="bilinear",
         )
-            .squeeze(0)
-            .squeeze(0)
-        )
+
+        while resized.ndim != original_ndim:
+            resized = resized.squeeze(0)
+
+        return resized
 
 
 class PeakNormalizeConfig(BaseConfig):

src/batdetect2/train/__init__.py

@@ -2,6 +2,7 @@ from batdetect2.train.augmentations import (
     AugmentationsConfig,
     EchoAugmentationConfig,
     FrequencyMaskAugmentationConfig,
+    RandomExampleSource,
     TimeMaskAugmentationConfig,
     VolumeAugmentationConfig,
     WarpAugmentationConfig,
@@ -23,7 +24,6 @@ from batdetect2.train.config import (
 )
 from batdetect2.train.dataset import (
     LabeledDataset,
-    RandomExampleSource,
     list_preprocessed_files,
 )
 from batdetect2.train.labels import build_clip_labeler, load_label_config

src/batdetect2/train/augmentations.py

@@ -1,6 +1,7 @@
 """Applies data augmentation techniques to BatDetect2 training examples."""
 
 import warnings
+from collections.abc import Sequence
 from typing import Annotated, Callable, List, Literal, Optional, Tuple, Union
 
 import numpy as np
@@ -10,8 +11,12 @@ from pydantic import Field
 from soundevent import data
 
 from batdetect2.configs import BaseConfig, load_config
+from batdetect2.train.preprocess import (
+    list_preprocessed_files,
+    load_preprocessed_example,
+)
 from batdetect2.typing import Augmentation, PreprocessorProtocol
-from batdetect2.typing.train import PreprocessedExample
+from batdetect2.typing.train import ClipperProtocol, PreprocessedExample
 from batdetect2.utils.arrays import adjust_width
 
 __all__ = [
@@ -39,21 +44,6 @@ ExampleSource = Callable[[], PreprocessedExample]
 """Type alias for a function that returns a training example"""
 
 
-class MixAugmentationConfig(BaseConfig):
-    """Configuration for MixUp augmentation (mixing two examples)."""
-
-    augmentation_type: Literal["mix_audio"] = "mix_audio"
-
-    probability: float = 0.2
-    """Probability of applying this augmentation to an example."""
-
-    min_weight: float = 0.3
-    """Minimum mixing weight (lambda) applied to the primary example."""
-
-    max_weight: float = 0.7
-    """Maximum mixing weight (lambda) applied to the primary example."""
-
-
 def mix_examples(
     example: PreprocessedExample,
     other: PreprocessedExample,
@@ -149,7 +139,12 @@ def add_echo(
 
     audio = example.audio
     delay_steps = int(preprocessor.input_samplerate * delay)
-    audio_delay = adjust_width(audio[delay_steps:], audio.shape[-1])
+
+    slices = [slice(None)] * audio.ndim
+    slices[-1] = slice(None, -delay_steps)
+    audio_delay = adjust_width(audio[tuple(slices)], audio.shape[-1]).roll(
+        delay_steps, dims=-1
+    )
 
     audio = audio + weight * audio_delay
     spectrogram = preprocessor(audio)
@@ -184,7 +179,7 @@ class VolumeAugmentationConfig(BaseConfig):
 
 
 class ScaleVolume(torch.nn.Module):
-    def __init__(self, min_scaling: float, max_scaling: float):
+    def __init__(self, min_scaling: float = 0.0, max_scaling: float = 2.0):
         super().__init__()
         self.min_scaling = min_scaling
         self.max_scaling = max_scaling
@@ -228,32 +223,22 @@ def warp_spectrogram(
     example: PreprocessedExample, factor: float
 ) -> PreprocessedExample:
     """Apply time warping by resampling the time axis."""
-    target_shape = example.spectrogram.shape
+    width = example.spectrogram.shape[-1]
+    height = example.spectrogram.shape[-2]
+    target_shape = [height, width]
     new_width = int(target_shape[-1] * factor)
 
-    spectrogram = (
-        torch.nn.functional.interpolate(
-            adjust_width(example.spectrogram, new_width)
-            .unsqueeze(0)
-            .unsqueeze(0),
+    spectrogram = torch.nn.functional.interpolate(
+        adjust_width(example.spectrogram, new_width).unsqueeze(0),
         size=target_shape,
         mode="bilinear",
-        )
-        .squeeze(0)
-        .squeeze(0)
-    )
+    ).squeeze(0)
 
-    detection = (
-        torch.nn.functional.interpolate(
-            adjust_width(example.detection_heatmap, new_width)
-            .unsqueeze(0)
-            .unsqueeze(0),
+    detection = torch.nn.functional.interpolate(
+        adjust_width(example.detection_heatmap, new_width).unsqueeze(0),
         size=target_shape,
         mode="nearest",
-        )
-        .squeeze(0)
-        .squeeze(0)
-    )
+    ).squeeze(0)
 
     classification = torch.nn.functional.interpolate(
         adjust_width(example.class_heatmap, new_width).unsqueeze(1),
@@ -284,10 +269,16 @@ class TimeMaskAugmentationConfig(BaseConfig):
 
 
 class MaskTime(torch.nn.Module):
-    def __init__(self, max_perc: float = 0.05, max_masks: int = 3) -> None:
+    def __init__(
+        self,
+        max_perc: float = 0.05,
+        max_masks: int = 3,
+        mask_heatmaps: bool = False,
+    ) -> None:
         super().__init__()
         self.max_perc = max_perc
         self.max_masks = max_masks
+        self.mask_heatmaps = mask_heatmaps
 
     def forward(self, example: PreprocessedExample) -> PreprocessedExample:
         num_masks = np.random.randint(1, self.max_masks + 1)
@@ -306,20 +297,28 @@ class MaskTime(torch.nn.Module):
         masks = [
             (start, start + size) for start, size in zip(mask_start, mask_size)
         ]
-        return mask_time(example, masks)
+        return mask_time(example, masks, mask_heatmaps=self.mask_heatmaps)
 
 
 def mask_time(
     example: PreprocessedExample,
     masks: List[Tuple[int, int]],
+    mask_heatmaps: bool = False,
 ) -> PreprocessedExample:
     """Apply time masking to the spectrogram."""
 
     for start, end in masks:
-        example.spectrogram[:, start:end] = example.spectrogram.mean()
-        example.class_heatmap[:, :, start:end] = 0
-        example.size_heatmap[:, :, start:end] = 0
-        example.detection_heatmap[:, start:end] = 0
+        slices = [slice(None)] * example.spectrogram.ndim
+        slices[-1] = slice(start, end)
+
+        example.spectrogram[tuple(slices)] = 0
+
+        if not mask_heatmaps:
+            continue
+
+        example.class_heatmap[tuple(slices)] = 0
+        example.size_heatmap[tuple(slices)] = 0
+        example.detection_heatmap[tuple(slices)] = 0
 
     return PreprocessedExample(
         audio=example.audio,
@@ -335,13 +334,20 @@ class FrequencyMaskAugmentationConfig(BaseConfig):
     probability: float = 0.2
     max_perc: float = 0.10
     max_masks: int = 3
+    mask_heatmaps: bool = False
 
 
 class MaskFrequency(torch.nn.Module):
-    def __init__(self, max_perc: float = 0.10, max_masks: int = 3) -> None:
+    def __init__(
+        self,
+        max_perc: float = 0.10,
+        max_masks: int = 3,
+        mask_heatmaps: bool = False,
+    ) -> None:
         super().__init__()
         self.max_perc = max_perc
         self.max_masks = max_masks
+        self.mask_heatmaps = mask_heatmaps
 
     def forward(self, example: PreprocessedExample) -> PreprocessedExample:
         num_masks = np.random.randint(1, self.max_masks + 1)
@@ -360,19 +366,26 @@ class MaskFrequency(torch.nn.Module):
         masks = [
             (start, start + size) for start, size in zip(mask_start, mask_size)
         ]
-        return mask_frequency(example, masks)
+        return mask_frequency(example, masks, mask_heatmaps=self.mask_heatmaps)
 
 
 def mask_frequency(
     example: PreprocessedExample,
     masks: List[Tuple[int, int]],
+    mask_heatmaps: bool = False,
 ) -> PreprocessedExample:
     """Apply frequency masking to the spectrogram."""
     for start, end in masks:
-        example.spectrogram[start:end, :] = example.spectrogram.mean()
-        example.class_heatmap[:, start:end, :] = 0
-        example.size_heatmap[:, start:end, :] = 0
-        example.detection_heatmap[start:end, :] = 0
+        slices = [slice(None)] * example.spectrogram.ndim
+        slices[-2] = slice(start, end)
+        example.spectrogram[tuple(slices)] = 0
+
+        if not mask_heatmaps:
+            continue
+
+        example.class_heatmap[tuple(slices)] = 0
+        example.size_heatmap[tuple(slices)] = 0
+        example.detection_heatmap[tuple(slices)] = 0
 
     return PreprocessedExample(
         audio=example.audio,
@@ -383,6 +396,50 @@ def mask_frequency(
     )
 
 
+class MixAugmentationConfig(BaseConfig):
+    """Configuration for MixUp augmentation (mixing two examples)."""
+
+    augmentation_type: Literal["mix_audio"] = "mix_audio"
+
+    probability: float = 0.2
+    """Probability of applying this augmentation to an example."""
+
+    min_weight: float = 0.3
+    """Minimum mixing weight (lambda) applied to the primary example."""
+
+    max_weight: float = 0.7
+    """Maximum mixing weight (lambda) applied to the primary example."""
+
+
+class MixAudio(torch.nn.Module):
+    """Callable class for MixUp augmentation, handling example fetching."""
+
+    def __init__(
+        self,
+        example_source: ExampleSource,
+        preprocessor: PreprocessorProtocol,
+        min_weight: float = 0.3,
+        max_weight: float = 0.7,
+    ):
+        """Initialize the AudioMixer."""
+        super().__init__()
+        self.min_weight = min_weight
+        self.example_source = example_source
+        self.max_weight = max_weight
+        self.preprocessor = preprocessor
+
+    def __call__(self, example: PreprocessedExample) -> PreprocessedExample:
+        """Fetch another example and perform mixup."""
+        other = self.example_source()
+        weight = np.random.uniform(self.min_weight, self.max_weight)
+        return mix_examples(
+            example,
+            other,
+            self.preprocessor,
+            weight=weight,
+        )
+
+
 AugmentationConfig = Annotated[
     Union[
         MixAugmentationConfig,
@@ -445,35 +502,6 @@ class MaybeApply(torch.nn.Module):
         return self.augmentation(example)
 
 
-class AudioMixer(torch.nn.Module):
-    """Callable class for MixUp augmentation, handling example fetching."""
-
-    def __init__(
-        self,
-        min_weight: float,
-        max_weight: float,
-        example_source: ExampleSource,
-        preprocessor: PreprocessorProtocol,
-    ):
-        """Initialize the AudioMixer."""
-        super().__init__()
-        self.min_weight = min_weight
-        self.example_source = example_source
-        self.max_weight = max_weight
-        self.preprocessor = preprocessor
-
-    def __call__(self, example: PreprocessedExample) -> PreprocessedExample:
-        """Fetch another example and perform mixup."""
-        other = self.example_source()
-        weight = np.random.uniform(self.min_weight, self.max_weight)
-        return mix_examples(
-            example,
-            other,
-            self.preprocessor,
-            weight=weight,
-        )
-
-
 def build_augmentation_from_config(
     config: AugmentationConfig,
     preprocessor: PreprocessorProtocol,
@@ -489,7 +517,7 @@ def build_augmentation_from_config(
             )
             return None
 
-        return AudioMixer(
+        return MixAudio(
             example_source=example_source,
             preprocessor=preprocessor,
             min_weight=config.min_weight,
@@ -585,3 +613,25 @@ def load_augmentation_config(
 ) -> AugmentationsConfig:
     """Load the augmentations configuration from a file."""
     return load_config(path, schema=AugmentationsConfig, field=field)
+
+
+class RandomExampleSource:
+    def __init__(
+        self,
+        filenames: Sequence[data.PathLike],
+        clipper: ClipperProtocol,
+    ):
+        self.filenames = filenames
+        self.clipper = clipper
+
+    def __call__(self) -> PreprocessedExample:
+        index = int(np.random.randint(len(self.filenames)))
+        filename = self.filenames[index]
+        example = load_preprocessed_example(filename)
+        example, _, _ = self.clipper(example)
+        return example
+
+    @classmethod
+    def from_directory(cls, path: data.PathLike, clipper: ClipperProtocol):
+        filenames = list_preprocessed_files(path)
+        return cls(filenames, clipper=clipper)

src/batdetect2/train/callbacks.py

@@ -14,7 +14,9 @@ from batdetect2.evaluate.match import (
     MatchConfig,
     match_sound_events_and_raw_predictions,
 )
+from batdetect2.models import Model
 from batdetect2.plotting.evaluation import plot_example_gallery
+from batdetect2.postprocess import get_sound_event_predictions
 from batdetect2.train.dataset import LabeledDataset
 from batdetect2.train.lightning import TrainingModule
 from batdetect2.typing import (
@@ -22,7 +24,6 @@ from batdetect2.typing import (
     MatchEvaluation,
     MetricsProtocol,
     ModelOutput,
-    PostprocessorProtocol,
     TargetProtocol,
     TrainExample,
 )
@@ -127,8 +128,7 @@ class ValidationMetrics(Callback):
                 batch,
                 outputs,
                 dataset=self.get_dataset(trainer),
-                postprocessor=pl_module.model.postprocessor,
-                targets=pl_module.model.targets,
+                model=pl_module.model,
             )
         )
 
@@ -137,15 +137,14 @@ def _get_batch_clips_and_predictions(
     batch: TrainExample,
     outputs: ModelOutput,
     dataset: LabeledDataset,
-    postprocessor: PostprocessorProtocol,
-    targets: TargetProtocol,
+    model: Model,
 ) -> List[Tuple[data.ClipAnnotation, List[BatDetect2Prediction]]]:
     clip_annotations = [
         _get_subclip(
             dataset.get_clip_annotation(example_id),
             start_time=start_time.item(),
             end_time=end_time.item(),
-            targets=targets,
+            targets=model.targets,
         )
         for example_id, start_time, end_time in zip(
             batch.idx,
@@ -156,9 +155,11 @@ def _get_batch_clips_and_predictions(
 
     clips = [clip_annotation.clip for clip_annotation in clip_annotations]
 
-    raw_predictions = postprocessor.get_sound_event_predictions(
+    raw_predictions = get_sound_event_predictions(
         outputs,
         clips,
+        targets=model.targets,
+        postprocessor=model.postprocessor
     )
 
     return [

src/batdetect2/train/clips.py

@@ -8,7 +8,7 @@ from batdetect2.configs import BaseConfig
 from batdetect2.typing import ClipperProtocol
 from batdetect2.typing.preprocess import PreprocessorProtocol
 from batdetect2.typing.train import PreprocessedExample
-from batdetect2.utils.arrays import adjust_width
+from batdetect2.utils.arrays import adjust_width, slice_tensor
 
 DEFAULT_TRAIN_CLIP_DURATION = 0.512
 DEFAULT_MAX_EMPTY_CLIP = 0.1
@@ -90,7 +90,12 @@ def select_subclip(
     audio_start = int(np.floor(start * input_samplerate))
 
     audio = adjust_width(
-        example.audio[audio_start : audio_start + audio_width],
+        slice_tensor(
+            example.audio,
+            start=audio_start,
+            end=audio_start + audio_width,
+            dim=-1,
+        ),
         audio_width,
         value=fill_value,
     )
@@ -100,19 +105,39 @@ def select_subclip(
     return PreprocessedExample(
         audio=audio,
         spectrogram=adjust_width(
-            example.spectrogram[:, spec_start : spec_start + spec_width],
+            slice_tensor(
+                example.spectrogram,
+                start=spec_start,
+                end=spec_start + spec_width,
+                dim=-1,
+            ),
             spec_width,
         ),
         class_heatmap=adjust_width(
-            example.class_heatmap[:, :, spec_start : spec_start + spec_width],
+            slice_tensor(
+                example.class_heatmap,
+                start=spec_start,
+                end=spec_start + spec_width,
+                dim=-1,
+            ),
             spec_width,
         ),
         detection_heatmap=adjust_width(
-            example.detection_heatmap[:, spec_start : spec_start + spec_width],
+            slice_tensor(
+                example.detection_heatmap,
+                start=spec_start,
+                end=spec_start + spec_width,
+                dim=-1,
+            ),
             spec_width,
         ),
         size_heatmap=adjust_width(
-            example.size_heatmap[:, :, spec_start : spec_start + spec_width],
+            slice_tensor(
+                example.size_heatmap,
+                start=spec_start,
+                end=spec_start + spec_width,
+                dim=-1,
+            ),
             spec_width,
         ),
     )

src/batdetect2/train/config.py

@@ -44,8 +44,8 @@ class PLTrainerConfig(BaseConfig):
 
 
 class DataLoaderConfig(BaseConfig):
-    batch_size: int
-    shuffle: bool
+    batch_size: int = 8
+    shuffle: bool = False
     num_workers: int = 0
 
 

src/batdetect2/train/dataset.py

@@ -1,5 +1,4 @@
-from pathlib import Path
-from typing import List, Optional, Sequence, Tuple
+from typing import Optional, Sequence, Tuple
 
 import numpy as np
 import torch
@@ -7,6 +6,10 @@ from soundevent import data
 from torch.utils.data import Dataset
 
 from batdetect2.train.augmentations import Augmentation
+from batdetect2.train.preprocess import (
+    list_preprocessed_files,
+    load_preprocessed_example,
+)
 from batdetect2.typing import ClipperProtocol, TrainExample
 from batdetect2.typing.train import PreprocessedExample
 
@@ -38,8 +41,8 @@ class LabeledDataset(Dataset):
             example = self.augmentation(example)
 
         return TrainExample(
-            spec=example.spectrogram.unsqueeze(0),
-            detection_heatmap=example.detection_heatmap.unsqueeze(0),
+            spec=example.spectrogram,
+            detection_heatmap=example.detection_heatmap,
             class_heatmap=example.class_heatmap,
             size_heatmap=example.size_heatmap,
             idx=torch.tensor(idx),
@@ -73,37 +76,3 @@ class LabeledDataset(Dataset):
     def get_clip_annotation(self, idx) -> data.ClipAnnotation:
         item = np.load(self.filenames[idx], allow_pickle=True, mmap_mode="r+")
         return item["clip_annotation"].tolist()
-
-
-def load_preprocessed_example(path: data.PathLike) -> PreprocessedExample:
-    item = np.load(path, mmap_mode="r+")
-    return PreprocessedExample(
-        audio=torch.tensor(item["audio"]),
-        spectrogram=torch.tensor(item["spectrogram"]),
-        size_heatmap=torch.tensor(item["size_heatmap"]),
-        detection_heatmap=torch.tensor(item["detection_heatmap"]),
-        class_heatmap=torch.tensor(item["class_heatmap"]),
-    )
-
-
-def list_preprocessed_files(
-    directory: data.PathLike, extension: str = ".npz"
-) -> List[Path]:
-    return list(Path(directory).glob(f"*{extension}"))
-
-
-class RandomExampleSource:
-    def __init__(
-        self,
-        filenames: List[data.PathLike],
-        clipper: ClipperProtocol,
-    ):
-        self.filenames = filenames
-        self.clipper = clipper
-
-    def __call__(self) -> PreprocessedExample:
-        index = int(np.random.randint(len(self.filenames)))
-        filename = self.filenames[index]
-        example = load_preprocessed_example(filename)
-        example, _, _ = self.clipper(example)
-        return example

src/batdetect2/train/labels.py

@@ -41,7 +41,6 @@ from batdetect2.typing import (
 __all__ = [
     "LabelConfig",
     "build_clip_labeler",
-    "generate_clip_label",
     "generate_heatmaps",
     "load_label_config",
 ]
@@ -99,21 +98,26 @@ def build_clip_labeler(
         lambda: config.to_yaml_string(),
     )
     return partial(
-        generate_clip_label,
+        generate_heatmaps,
         targets=targets,
-        config=config,
         min_freq=min_freq,
         max_freq=max_freq,
+        target_sigma=config.sigma,
     )
 
 
-def generate_clip_label(
+def map_to_pixels(x, size, min_val, max_val) -> int:
+    return int(np.interp(x, [min_val, max_val], [0, size]))
+
+
+def generate_heatmaps(
     clip_annotation: data.ClipAnnotation,
     spec: torch.Tensor,
     targets: TargetProtocol,
-    config: LabelConfig,
     min_freq: float,
     max_freq: float,
+    target_sigma: float = 3.0,
+    dtype=torch.float32,
 ) -> Heatmaps:
     """Generate training heatmaps for a single annotated clip.
 
@@ -150,57 +154,14 @@ def generate_clip_label(
         num=len(clip_annotation.sound_events),
     )
 
-    sound_events = []
-
-    for sound_event_annotation in clip_annotation.sound_events:
-        if not targets.filter(sound_event_annotation):
-            logger.debug(
-                "Sound event {sound_event} did not pass the filter. Tags: {tags}",
-                sound_event=sound_event_annotation,
-                tags=sound_event_annotation.tags,
-            )
-            continue
-
-        sound_events.append(targets.transform(sound_event_annotation))
-
-    return generate_heatmaps(
-        clip_annotation.model_copy(update=dict(sound_events=sound_events)),
-        spec=spec,
-        targets=targets,
-        target_sigma=config.sigma,
-        min_freq=min_freq,
-        max_freq=max_freq,
-    )
-
-
-def map_to_pixels(x, size, min_val, max_val) -> int:
-    return int(np.interp(x, [min_val, max_val], [0, size]))
-
-
-def generate_heatmaps(
-    clip_annotation: data.ClipAnnotation,
-    spec: torch.Tensor,
-    targets: TargetProtocol,
-    min_freq: float,
-    max_freq: float,
-    target_sigma: float = 3.0,
-    dtype=torch.float32,
-) -> Heatmaps:
-    if not spec.ndim == 2:
-        raise ValueError(
-            "Expecting a 2-dimensional tensor of shape (H, W), "
-            "H is the height of the spectrogram "
-            "(frequency bins), and W is the width of the spectrogram "
-            f"(temporal bins). Instead got: {spec.shape}"
-        )
-
-    height, width = spec.shape
+    height = spec.shape[-2]
+    width = spec.shape[-1]
     num_classes = len(targets.class_names)
     num_dims = len(targets.dimension_names)
     clip = clip_annotation.clip
 
     # Initialize heatmaps
-    detection_heatmap = torch.zeros([height, width], dtype=dtype)
+    detection_heatmap = torch.zeros([1, height, width], dtype=dtype)
     class_heatmap = torch.zeros([num_classes, height, width], dtype=dtype)
     size_heatmap = torch.zeros([num_dims, height, width], dtype=dtype)
 
@@ -214,6 +175,16 @@ def generate_heatmaps(
     times = times.to(spec.device)
 
     for sound_event_annotation in clip_annotation.sound_events:
+        if not targets.filter(sound_event_annotation):
+            logger.debug(
+                "Sound event {sound_event} did not pass the filter. Tags: {tags}",
+                sound_event=sound_event_annotation,
+                tags=sound_event_annotation.tags,
+            )
+            continue
+
+        sound_event_annotation = targets.transform(sound_event_annotation)
+
         geom = sound_event_annotation.sound_event.geometry
         if geom is None:
             logger.debug(
@@ -245,7 +216,10 @@ def generate_heatmaps(
         distance = (times - time_index) ** 2 + (freqs - freq_index) ** 2
         gaussian_blob = torch.exp(-distance / (2 * target_sigma**2))
 
-        detection_heatmap = torch.maximum(detection_heatmap, gaussian_blob)
+        detection_heatmap[0] = torch.maximum(
+            detection_heatmap[0],
+            gaussian_blob,
+        )
         size_heatmap[:, freq_index, time_index] = torch.tensor(size[:])
 
         # Get the class name of the sound event

src/batdetect2/train/lightning.py

@@ -34,7 +34,7 @@ class TrainingModule(L.LightningModule):
         return self.model(spec)
 
     def training_step(self, batch: TrainExample):
-        outputs = self.model(batch.spec)
+        outputs = self.model.detector(batch.spec)
         losses = self.loss(outputs, batch)
         self.log("total_loss/train", losses.total, prog_bar=True, logger=True)
         self.log("detection_loss/train", losses.total, logger=True)
@@ -47,7 +47,7 @@ class TrainingModule(L.LightningModule):
         batch: TrainExample,
         batch_idx: int,
     ) -> ModelOutput:
-        outputs = self.model(batch.spec)
+        outputs = self.model.detector(batch.spec)
         losses = self.loss(outputs, batch)
         self.log("total_loss/val", losses.total, prog_bar=True, logger=True)
         self.log("detection_loss/val", losses.total, logger=True)

src/batdetect2/train/preprocess.py

@@ -2,7 +2,7 @@
 
 import os
 from pathlib import Path
-from typing import Callable, Optional, Sequence, TypedDict
+from typing import Callable, List, Optional, Sequence, TypedDict
 
 import numpy as np
 import torch
@@ -28,6 +28,8 @@ __all__ = [
     "preprocess_dataset",
     "TrainPreprocessConfig",
     "load_train_preprocessing_config",
+    "save_preprocessed_example",
+    "load_preprocessed_example",
 ]
 
 FilenameFn = Callable[[data.ClipAnnotation], str]
@@ -94,8 +96,10 @@ def generate_train_example(
     labeller: ClipLabeller,
 ) -> PreprocessedExample:
     """Generate a complete training example for one annotation."""
-    wave = torch.tensor(audio_loader.load_clip(clip_annotation.clip))
-    spectrogram = preprocessor(wave)
+    wave = torch.tensor(
+        audio_loader.load_clip(clip_annotation.clip)
+    ).unsqueeze(0)
+    spectrogram = preprocessor(wave.unsqueeze(0)).squeeze(0)
     heatmaps = labeller(clip_annotation, spectrogram)
     return PreprocessedExample(
         audio=wave,
@@ -145,7 +149,7 @@ class PreprocessingDataset(torch.utils.data.Dataset):
             labeller=self.labeller,
         )
 
-        save_example_to_file(example, clip_annotation, path)
+        save_preprocessed_example(example, clip_annotation, path)
 
         return idx
 
@@ -153,7 +157,7 @@ class PreprocessingDataset(torch.utils.data.Dataset):
         return len(self.clips)
 
 
-def save_example_to_file(
+def save_preprocessed_example(
     example: PreprocessedExample,
     clip_annotation: data.ClipAnnotation,
     path: data.PathLike,
@@ -169,6 +173,23 @@ def save_example_to_file(
     )
 
 
+def load_preprocessed_example(path: data.PathLike) -> PreprocessedExample:
+    item = np.load(path, mmap_mode="r+")
+    return PreprocessedExample(
+        audio=torch.tensor(item["audio"]),
+        spectrogram=torch.tensor(item["spectrogram"]),
+        size_heatmap=torch.tensor(item["size_heatmap"]),
+        detection_heatmap=torch.tensor(item["detection_heatmap"]),
+        class_heatmap=torch.tensor(item["class_heatmap"]),
+    )
+
+
+def list_preprocessed_files(
+    directory: data.PathLike, extension: str = ".npz"
+) -> List[Path]:
+    return list(Path(directory).glob(f"*{extension}"))
+
+
 def _get_filename(clip_annotation: data.ClipAnnotation) -> str:
     """Generate a default output filename based on the annotation UUID."""
     return f"{clip_annotation.uuid}"

src/batdetect2/train/train.py

@@ -14,14 +14,16 @@ from batdetect2.evaluate.metrics import (
     ClassificationMeanAveragePrecision,
     DetectionAveragePrecision,
 )
-from batdetect2.models import build_model
-from batdetect2.train.augmentations import build_augmentations
+from batdetect2.models import Model, build_model
+from batdetect2.train.augmentations import (
+    RandomExampleSource,
+    build_augmentations,
+)
 from batdetect2.train.callbacks import ValidationMetrics
 from batdetect2.train.clips import build_clipper
 from batdetect2.train.config import FullTrainingConfig, TrainingConfig
 from batdetect2.train.dataset import (
     LabeledDataset,
-    RandomExampleSource,
 )
 from batdetect2.train.lightning import TrainingModule
 from batdetect2.train.logging import build_logger
@@ -53,17 +55,13 @@ def train(
 ):
     config = config or FullTrainingConfig()
 
-    if model_path is not None:
-        logger.debug("Loading model from: {path}", path=model_path)
-        module = TrainingModule.load_from_checkpoint(model_path)  # type: ignore
-    else:
-        module = build_training_module(config)
+    model = build_model(config=config)
 
-    trainer = build_trainer(config, targets=module.model.targets)
+    trainer = build_trainer(config, targets=model.targets)
 
     train_dataloader = build_train_loader(
         train_examples,
-        preprocessor=module.model.preprocessor,
+        preprocessor=model.preprocessor,
         config=config.train,
         num_workers=train_workers,
     )
@@ -71,7 +69,7 @@ def train(
     val_dataloader = (
         build_val_loader(
             val_examples,
-            preprocessor=module.model.preprocessor,
+            preprocessor=model.preprocessor,
             config=config.train,
             num_workers=val_workers,
         )
@@ -79,6 +77,16 @@ def train(
         else None
     )
 
+    if model_path is not None:
+        logger.debug("Loading model from: {path}", path=model_path)
+        module = TrainingModule.load_from_checkpoint(model_path)  # type: ignore
+    else:
+        module = build_training_module(
+            model,
+            config,
+            batches_per_epoch=len(train_dataloader),
+        )
+
     logger.info("Starting main training loop...")
     trainer.fit(
         module,
@@ -88,14 +96,17 @@ def train(
     logger.info("Training complete.")
 
 
-def build_training_module(config: FullTrainingConfig) -> TrainingModule:
-    model = build_model(config=config)
+def build_training_module(
+    model: Model,
+    config: FullTrainingConfig,
+    batches_per_epoch: int,
+) -> TrainingModule:
     loss = build_loss(config=config.train.loss)
     return TrainingModule(
         model=model,
         loss=loss,
         learning_rate=config.train.learning_rate,
-        t_max=config.train.t_max,
+        t_max=config.train.t_max * batches_per_epoch,
     )
 
 

src/batdetect2/typing/postprocess.py

@@ -95,69 +95,10 @@ class BatDetect2Prediction:
 class PostprocessorProtocol(Protocol):
     """Protocol defining the interface for the full postprocessing pipeline."""
 
+    def __call__(self, output: ModelOutput) -> List[Detections]: ...
+
     def get_detections(
         self,
         output: ModelOutput,
         clips: Optional[List[data.Clip]] = None,
     ) -> List[Detections]: ...
-
-    def get_raw_predictions(
-        self,
-        output: ModelOutput,
-        clips: List[data.Clip],
-    ) -> List[List[RawPrediction]]:
-        """Extract intermediate RawPrediction objects for a batch.
-
-        Processes the raw model output for a batch through remapping, NMS,
-        detection, data extraction, and geometry recovery to produce a list of
-        `RawPrediction` objects for each corresponding input clip. This provides
-        a simplified, intermediate representation before final tag decoding.
-
-        Parameters
-        ----------
-        output : ModelOutput
-            The raw output from the neural network model for a batch.
-        clips : List[data.Clip]
-            A list of `soundevent.data.Clip` objects corresponding to the batch
-            items, providing context. Must match the batch size of `output`.
-
-        Returns
-        -------
-        List[List[RawPrediction]]
-            A list of lists (one inner list per input clip, in order). Each
-            inner list contains the `RawPrediction` objects extracted for the
-            corresponding input clip.
-        """
-        ...
-
-    def get_sound_event_predictions(
-        self, output: ModelOutput, clips: List[data.Clip]
-    ) -> List[List[BatDetect2Prediction]]: ...
-
-    def get_predictions(
-        self,
-        output: ModelOutput,
-        clips: List[data.Clip],
-    ) -> List[data.ClipPrediction]:
-        """Perform the full postprocessing pipeline for a batch.
-
-        Takes raw model output for a batch and corresponding clips, applies the
-        entire postprocessing chain, and returns the final, interpretable
-        predictions as a list of `soundevent.data.ClipPrediction` objects.
-
-        Parameters
-        ----------
-        output : ModelOutput
-            The raw output from the neural network model for a batch.
-        clips : List[data.Clip]
-            A list of `soundevent.data.Clip` objects corresponding to the batch
-            items, providing context. Must match the batch size of `output`.
-
-        Returns
-        -------
-        List[data.ClipPrediction]
-            A list containing one `ClipPrediction` object for each input clip
-            (in the same order), populated with `SoundEventPrediction` objects
-            representing the final detections with decoded tags and geometry.
-        """
-        ...

src/batdetect2/typing/targets.py

@@ -12,8 +12,8 @@ that components responsible for these tasks can be interacted with consistently
 throughout BatDetect2.
 """
 
-from collections.abc import Callable
-from typing import List, Optional, Protocol
+from collections.abc import Callable, Iterable
+from typing import List, Optional, Protocol, Tuple
 
 import numpy as np
 from soundevent import data

src/batdetect2/utils/arrays.py

@@ -1,3 +1,5 @@
+from typing import Optional
+
 import numpy as np
 import torch
 import xarray as xr
@@ -80,3 +82,14 @@ def adjust_width(
         for index in range(dims)
     ]
     return tensor[tuple(slices)]
+
+
+def slice_tensor(
+    tensor: torch.Tensor,
+    start: Optional[int] = None,
+    end: Optional[int] = None,
+    dim: int = -1,
+) -> torch.Tensor:
+    slices = [slice(None)] * tensor.ndim
+    slices[dim] = slice(start, end)
+    return tensor[tuple(slices)]

tests/test_train/test_preprocessing.py

@@ -38,7 +38,6 @@ def build_from_config(
             max_freq=preprocessor.max_freq,
         )
         postprocessor = build_postprocessor(
-            targets,
             preprocessor=preprocessor,
             config=postprocessing_config,
         )