.gitignore

@@ -107,7 +107,7 @@ experiments/*
 
 # DO Include
 !batdetect2_notebook.ipynb
-!src/batdetect2/models/checkpoints/*.pth.tar
+!batdetect2/models/checkpoints/*.pth.tar
 !tests/data/*.wav
 !notebooks/*.ipynb
 !tests/data/**/*.wav

Makefile

@@ -1,7 +1,7 @@
 # Variables
-SOURCE_DIR = src
+SOURCE_DIR = batdetect2
 TESTS_DIR = tests
-PYTHON_DIRS = src tests
+PYTHON_DIRS = batdetect2 tests
 DOCS_SOURCE = docs/source
 DOCS_BUILD = docs/build
 HTML_COVERAGE_DIR = htmlcov

batdetect2/cli/train.py

@@ -189,7 +189,8 @@ def train_command(
             config=postprocess_config_loaded,
         )
         logger.debug(
-            "Loaded postprocessor from file {path}", path=postprocess_config
+            "Loaded postprocessor from file {path}",
+            path=train_config,
         )
     except IOError:
         logger.debug(

batdetect2/configs.py

@@ -157,4 +157,4 @@ def load_config(
     if field:
         config = get_object_field(config, field)
 
-    return schema.model_validate(config or {})
+    return schema.model_validate(config)

batdetect2/data/__init__.py

@@ -8,7 +8,6 @@ from batdetect2.data.annotations import (
 from batdetect2.data.datasets import (
     DatasetConfig,
     load_dataset,
-    load_dataset_config,
     load_dataset_from_config,
 )
 
@@ -20,6 +19,5 @@ __all__ = [
     "DatasetConfig",
     "load_annotated_dataset",
     "load_dataset",
-    "load_dataset_config",
     "load_dataset_from_config",
 ]

batdetect2/data/datasets.py

@@ -161,11 +161,6 @@ def insert_source_tag(
     )
 
 
-# TODO: add documentation
-def load_dataset_config(path: data.PathLike, field: Optional[str] = None):
-    return load_config(path=path, schema=DatasetConfig, field=field)
-
-
 def load_dataset_from_config(
     path: data.PathLike,
     field: Optional[str] = None,

batdetect2/data/iterators.py

@@ -72,7 +72,7 @@ def iterate_over_sound_events(
                     sound_event_annotation
                 )
 
-            class_name = targets.encode_class(sound_event_annotation)
+            class_name = targets.encode(sound_event_annotation)
             if class_name is None and exclude_generic:
                 continue
 

batdetect2/evaluate/evaluate.py

@@ -1,3 +1,4 @@
+
 import numpy as np
 from sklearn.metrics import auc, roc_curve
 

batdetect2/evaluate/match.py

@@ -40,7 +40,7 @@ def match_sound_events_and_raw_predictions(
 
         gt_uuid = target.uuid if target is not None else None
         gt_det = target is not None
-        gt_class = targets.encode_class(target) if target is not None else None
+        gt_class = targets.encode(target) if target is not None else None
 
         pred_score = float(prediction.detection_score) if prediction else 0
 

batdetect2/postprocess/__init__.py

@@ -7,8 +7,8 @@ containing detected sound events with associated class tags and geometry.
 
 The pipeline involves several configurable steps, implemented in submodules:
 1.  Non-Maximum Suppression (`.nms`): Isolates distinct detection peaks.
-2.  Coordinate Remapping (`.remapping`): Adds time/frequency coordinates to raw
+2.  Coordinate Remapping (`.remapping`): Adds real-world time/frequency
-    model output arrays.
+    coordinates to raw model output arrays.
 3.  Detection Extraction (`.detection`): Identifies candidate detection points
     (location and score) based on thresholds and score ranking (top-k).
 4.  Data Extraction (`.extraction`): Gathers associated model outputs (size,
@@ -526,7 +526,7 @@ class Postprocessor(PostprocessorProtocol):
         return [
             convert_xr_dataset_to_raw_prediction(
                 dataset,
-                self.targets.decode_roi,
+                self.targets.recover_roi,
             )
             for dataset in detection_datasets
         ]
@@ -558,7 +558,7 @@ class Postprocessor(PostprocessorProtocol):
             convert_raw_predictions_to_clip_prediction(
                 prediction,
                 clip,
-                sound_event_decoder=self.targets.decode_class,
+                sound_event_decoder=self.targets.decode,
                 generic_class_tags=self.targets.generic_class_tags,
                 classification_threshold=self.config.classification_threshold,
             )

batdetect2/postprocess/decoding.py

@@ -4,7 +4,8 @@ This module handles the final stages of the BatDetect2 postprocessing pipeline.
 It takes the structured detection data extracted by the `extraction` module
 (typically an `xarray.Dataset` containing scores, positions, predicted sizes,
  class probabilities, and features for each detection point) and converts it
-into standardized prediction objects based on the `soundevent` data model.
+into meaningful, standardized prediction objects based on the `soundevent` data
+model.
 
 The process involves:
 1.  Converting the `xarray.Dataset` into a list of intermediate `RawPrediction`
@@ -32,7 +33,7 @@ import numpy as np
 import xarray as xr
 from soundevent import data
 
-from batdetect2.postprocess.types import GeometryDecoder, RawPrediction
+from batdetect2.postprocess.types import GeometryBuilder, RawPrediction
 from batdetect2.targets.classes import SoundEventDecoder
 from batdetect2.utils.arrays import iterate_over_array
 
@@ -54,7 +55,7 @@ decoding.
 
 def convert_xr_dataset_to_raw_prediction(
     detection_dataset: xr.Dataset,
-    geometry_decoder: GeometryDecoder,
+    geometry_builder: GeometryBuilder,
 ) -> List[RawPrediction]:
     """Convert an xarray.Dataset of detections to RawPrediction objects.
 
@@ -71,7 +72,7 @@ def convert_xr_dataset_to_raw_prediction(
         output by `extract_detection_xr_dataset`. Expected variables include
         'scores' (with time/freq coords), 'dimensions', 'classes', 'features'.
         Must have a 'detection' dimension.
-    geometry_decoder : GeometryDecoder
+    geometry_builder : GeometryBuilder
         A function that takes a position tuple `(time, freq)` and a NumPy array
         of dimensions, and returns the corresponding reconstructed
         `soundevent.data.Geometry`.
@@ -95,20 +96,14 @@ def convert_xr_dataset_to_raw_prediction(
     for det_num in range(detection_dataset.sizes["detection"]):
         det_info = detection_dataset.sel(detection=det_num)
 
-        # TODO: Maybe clean this up
+        geom = geometry_builder(
-        highest_scoring_class = det_info.coords["category"][
-            det_info["classes"].argmax()
-        ].item()
-
-        geom = geometry_decoder(
             (det_info.time, det_info.frequency),
             det_info.dimensions,
-            class_name=highest_scoring_class,
         )
 
         detections.append(
             RawPrediction(
-                detection_score=det_info.scores,
+                detection_score=det_info.score,
                 geometry=geom,
                 class_scores=det_info.classes,
                 features=det_info.features,

batdetect2/postprocess/detection.py

@@ -1,6 +1,6 @@
 """Extracts candidate detection points from a model output heatmap.
 
-This module implements Step 3 within the BatDetect2 postprocessing
+This module implements a specific step within the BatDetect2 postprocessing
 pipeline. Its primary function is to identify potential sound event locations
 by finding peaks (local maxima or high-scoring points) in the detection heatmap
 produced by the neural network (usually after Non-Maximum Suppression and

batdetect2/postprocess/extraction.py

@@ -1,9 +1,9 @@
 """Extracts associated data for detected points from model output arrays.
 
-This module implements a Step 4 in the BatDetect2 postprocessing pipeline.
+This module implements a key step (Step 4) in the BatDetect2 postprocessing
-After candidate detection points (time, frequency, score) have been identified,
+pipeline. After candidate detection points (time, frequency, score) have been
-this module extracts the corresponding values from other raw model output
+identified, this module extracts the corresponding values from other raw model
-arrays, such as:
+output arrays, such as:
 
 - Predicted bounding box sizes (width, height).
 - Class probability scores for each defined target class.

batdetect2/postprocess/types.py

@@ -11,37 +11,30 @@ modularity and consistent interaction between different parts of the BatDetect2
 system that deal with model predictions.
 """
 
-from typing import List, NamedTuple, Optional, Protocol
+from typing import Callable, List, NamedTuple, Protocol
 
+import numpy as np
 import xarray as xr
 from soundevent import data
 
 from batdetect2.models.types import ModelOutput
-from batdetect2.targets.types import Position, Size
 
 __all__ = [
     "RawPrediction",
     "PostprocessorProtocol",
-    "GeometryDecoder",
+    "GeometryBuilder",
 ]
 
 
-# TODO: update the docstring
+GeometryBuilder = Callable[[tuple[float, float], np.ndarray], data.Geometry]
-class GeometryDecoder(Protocol):
+"""Type alias for a function that recovers geometry from position and size.
-    """Type alias for a function that recovers geometry from position and size.
 
-    This callable takes:
+This callable takes:
-    1.  A position tuple `(time, frequency)`.
+1.  A position tuple `(time, frequency)`.
-    2.  A NumPy array of size dimensions (e.g., `[width, height]`).
+2.  A NumPy array of size dimensions (e.g., `[width, height]`).
-    3.  Optionally a class name of the highest scoring class. This is to accomodate
+It should return the reconstructed `soundevent.data.Geometry` (typically a
-        different ways of decoding geometry that depend on the predicted class.
+`BoundingBox`).
-    It should return the reconstructed `soundevent.data.Geometry` (typically a
+"""
-    `BoundingBox`).
-    """
-
-    def __call__(
-        self, position: Position, size: Size, class_name: Optional[str] = None
-    ) -> data.Geometry: ...
 
 
 class RawPrediction(NamedTuple):

batdetect2/targets/__init__.py

@@ -23,7 +23,7 @@ object is via the `build_targets` or `load_targets` functions.
 
 from typing import List, Optional
 
-from loguru import logger
+import numpy as np
 from pydantic import Field
 from soundevent import data
 
@@ -50,8 +50,7 @@ from batdetect2.targets.filtering import (
     load_filter_from_config,
 )
 from batdetect2.targets.rois import (
-    AnchorBBoxMapperConfig,
+    ROIConfig,
-    ROIMapperConfig,
     ROITargetMapper,
     build_roi_mapper,
 )
@@ -60,11 +59,11 @@ from batdetect2.targets.terms import (
     TermInfo,
     TermRegistry,
     call_type,
-    default_term_registry,
     get_tag_from_info,
     get_term_from_key,
     individual,
     register_term,
+    term_registry,
 )
 from batdetect2.targets.transform import (
     DerivationRegistry,
@@ -74,13 +73,13 @@ from batdetect2.targets.transform import (
     SoundEventTransformation,
     TransformConfig,
     build_transformation_from_config,
-    default_derivation_registry,
+    derivation_registry,
     get_derivation,
     load_transformation_config,
     load_transformation_from_config,
     register_derivation,
 )
-from batdetect2.targets.types import Position, Size, TargetProtocol
+from batdetect2.targets.types import TargetProtocol
 
 __all__ = [
     "ClassesConfig",
@@ -89,7 +88,7 @@ __all__ = [
     "FilterConfig",
     "FilterRule",
     "MapValueRule",
-    "AnchorBBoxMapperConfig",
+    "ROIConfig",
     "ROITargetMapper",
     "ReplaceRule",
     "SoundEventDecoder",
@@ -157,12 +156,12 @@ class TargetConfig(BaseConfig):
         omitted, default ROI mapping settings are used.
     """
 
-    filtering: FilterConfig = Field(default_factory=FilterConfig)
+    filtering: Optional[FilterConfig] = None
-    transforms: TransformConfig = Field(default_factory=TransformConfig)
+    transforms: Optional[TransformConfig] = None
     classes: ClassesConfig = Field(
         default_factory=lambda: DEFAULT_CLASSES_CONFIG
     )
-    roi: ROIMapperConfig = Field(default_factory=AnchorBBoxMapperConfig)
+    roi: Optional[ROIConfig] = None
 
 
 def load_target_config(
@@ -241,7 +240,6 @@ class Targets(TargetProtocol):
         generic_class_tags: List[data.Tag],
         filter_fn: Optional[SoundEventFilter] = None,
         transform_fn: Optional[SoundEventTransformation] = None,
-        roi_mapper_overrides: Optional[dict[str, ROITargetMapper]] = None,
     ):
         """Initialize the Targets object.
 
@@ -274,16 +272,6 @@ class Targets(TargetProtocol):
         self._encode_fn = encode_fn
         self._decode_fn = decode_fn
         self._transform_fn = transform_fn
-        self._roi_mapper_overrides = roi_mapper_overrides or {}
-
-        for class_name in self._roi_mapper_overrides:
-            if class_name not in self.class_names:
-                # TODO: improve this warning
-                logger.warning(
-                    "The ROI mapper overrides contains a class ({class_name}) "
-                    "not present in the class names.",
-                    class_name=class_name,
-                )
 
     def filter(self, sound_event: data.SoundEventAnnotation) -> bool:
         """Apply the configured filter to a sound event annotation.
@@ -303,9 +291,7 @@ class Targets(TargetProtocol):
             return True
         return self._filter_fn(sound_event)
 
-    def encode_class(
+    def encode(self, sound_event: data.SoundEventAnnotation) -> Optional[str]:
-        self, sound_event: data.SoundEventAnnotation
-    ) -> Optional[str]:
         """Encode a sound event annotation to its target class name.
 
         Applies the configured class definition rules (including priority)
@@ -326,7 +312,7 @@ class Targets(TargetProtocol):
         """
         return self._encode_fn(sound_event)
 
-    def decode_class(self, class_label: str) -> List[data.Tag]:
+    def decode(self, class_label: str) -> List[data.Tag]:
         """Decode a predicted class name back into representative tags.
 
         Uses the configured mapping (based on `TargetClass.output_tags` or
@@ -366,9 +352,9 @@ class Targets(TargetProtocol):
             return self._transform_fn(sound_event)
         return sound_event
 
-    def encode_roi(
+    def get_position(
         self, sound_event: data.SoundEventAnnotation
-    ) -> tuple[Position, Size]:
+    ) -> tuple[float, float]:
         """Extract the target reference position from the annotation's roi.
 
         Delegates to the internal ROI mapper's `get_roi_position` method.
@@ -388,20 +374,50 @@ class Targets(TargetProtocol):
         ValueError
             If the annotation lacks geometry.
         """
-        class_name = self.encode_class(sound_event)
+        geom = sound_event.sound_event.geometry
 
-        if class_name in self._roi_mapper_overrides:
+        if geom is None:
-            return self._roi_mapper_overrides[class_name].encode(
+            raise ValueError(
-                sound_event.sound_event
+                "Sound event has no geometry, cannot get its position."
             )
 
-        return self._roi_mapper.encode(sound_event.sound_event)
+        return self._roi_mapper.get_roi_position(geom)
 
-    def decode_roi(
+    def get_size(self, sound_event: data.SoundEventAnnotation) -> np.ndarray:
+        """Calculate the target size dimensions from the annotation's geometry.
+
+        Delegates to the internal ROI mapper's `get_roi_size` method, which
+        applies configured scaling factors.
+
+        Parameters
+        ----------
+        sound_event : data.SoundEventAnnotation
+            The annotation containing the geometry (ROI).
+
+        Returns
+        -------
+        np.ndarray
+            NumPy array containing the size dimensions, matching the
+            order in `self.dimension_names` (e.g., `[width, height]`).
+
+        Raises
+        ------
+        ValueError
+            If the annotation lacks geometry.
+        """
+        geom = sound_event.sound_event.geometry
+
+        if geom is None:
+            raise ValueError(
+                "Sound event has no geometry, cannot get its size."
+            )
+
+        return self._roi_mapper.get_roi_size(geom)
+
+    def recover_roi(
         self,
-        position: Position,
+        pos: tuple[float, float],
-        size: Size,
+        dims: np.ndarray,
-        class_name: Optional[str] = None,
     ) -> data.Geometry:
         """Recover an approximate geometric ROI from a position and dimensions.
 
@@ -422,13 +438,7 @@ class Targets(TargetProtocol):
         data.Geometry
             The reconstructed geometry (typically `BoundingBox`).
         """
-        if class_name in self._roi_mapper_overrides:
+        return self._roi_mapper.recover_roi(pos, dims)
-            return self._roi_mapper_overrides[class_name].decode(
-                position,
-                size,
-            )
-
-        return self._roi_mapper.decode(position, size)
 
 
 DEFAULT_CLASSES = [
@@ -483,12 +493,10 @@ DEFAULT_CLASSES = [
     TargetClass(
         tags=[TagInfo(value="Nyctalus leisleri")],
         name="nyclei",
-        roi=AnchorBBoxMapperConfig(anchor="top-left"),
     ),
     TargetClass(
         tags=[TagInfo(value="Rhinolophus ferrumequinum")],
         name="rhifer",
-        roi=AnchorBBoxMapperConfig(anchor="top-left"),
     ),
     TargetClass(
         tags=[TagInfo(value="Plecotus auritus")],
@@ -529,14 +537,13 @@ DEFAULT_TARGET_CONFIG: TargetConfig = TargetConfig(
         ]
     ),
     classes=DEFAULT_CLASSES_CONFIG,
-    roi=AnchorBBoxMapperConfig(),
 )
 
 
 def build_targets(
     config: Optional[TargetConfig] = None,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
-    derivation_registry: DerivationRegistry = default_derivation_registry,
+    derivation_registry: DerivationRegistry = derivation_registry,
 ) -> Targets:
     """Build a Targets object from a loaded TargetConfig.
 
@@ -599,17 +606,12 @@ def build_targets(
         if config.transforms
         else None
     )
-    roi_mapper = build_roi_mapper(config.roi)
+    roi_mapper = build_roi_mapper(config.roi or ROIConfig())
     class_names = get_class_names_from_config(config.classes)
     generic_class_tags = build_generic_class_tags(
         config.classes,
         term_registry=term_registry,
     )
-    roi_overrides = {
-        class_config.name: build_roi_mapper(class_config.roi)
-        for class_config in config.classes.classes
-        if class_config.roi is not None
-    }
 
     return Targets(
         filter_fn=filter_fn,
@@ -619,15 +621,14 @@ def build_targets(
         roi_mapper=roi_mapper,
         generic_class_tags=generic_class_tags,
         transform_fn=transform_fn,
-        roi_mapper_overrides=roi_overrides,
     )
 
 
 def load_targets(
     config_path: data.PathLike,
     field: Optional[str] = None,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
-    derivation_registry: DerivationRegistry = default_derivation_registry,
+    derivation_registry: DerivationRegistry = derivation_registry,
 ) -> Targets:
     """Load a Targets object directly from a configuration file.
 

batdetect2/targets/classes.py

@@ -6,27 +6,29 @@ from pydantic import Field, field_validator
 from soundevent import data
 
 from batdetect2.configs import BaseConfig, load_config
-from batdetect2.targets.rois import ROIMapperConfig
 from batdetect2.targets.terms import (
     GENERIC_CLASS_KEY,
     TagInfo,
     TermRegistry,
-    default_term_registry,
     get_tag_from_info,
+    term_registry,
 )
 
 __all__ = [
-    "DEFAULT_SPECIES_LIST",
+    "SoundEventEncoder",
-    "build_generic_class_tags",
+    "SoundEventDecoder",
-    "build_sound_event_decoder",
+    "TargetClass",
-    "build_sound_event_encoder",
+    "ClassesConfig",
-    "get_class_names_from_config",
     "load_classes_config",
-    "load_decoder_from_config",
     "load_encoder_from_config",
+    "load_decoder_from_config",
+    "build_sound_event_encoder",
+    "build_sound_event_decoder",
+    "build_generic_class_tags",
+    "get_class_names_from_config",
+    "DEFAULT_SPECIES_LIST",
 ]
 
-
 SoundEventEncoder = Callable[[data.SoundEventAnnotation], Optional[str]]
 """Type alias for a sound event class encoder function.
 
@@ -111,7 +113,6 @@ class TargetClass(BaseConfig):
     tags: List[TagInfo] = Field(min_length=1)
     match_type: Literal["all", "any"] = Field(default="all")
     output_tags: Optional[List[TagInfo]] = None
-    roi: Optional[ROIMapperConfig] = None
 
 
 def _get_default_classes() -> List[TargetClass]:
@@ -234,7 +235,7 @@ class ClassesConfig(BaseConfig):
         return v
 
 
-def is_target_class(
+def _is_target_class(
     sound_event_annotation: data.SoundEventAnnotation,
     tags: Set[data.Tag],
     match_all: bool = True,
@@ -315,7 +316,7 @@ def _encode_with_multiple_classifiers(
 
 def build_sound_event_encoder(
     config: ClassesConfig,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
 ) -> SoundEventEncoder:
     """Build a sound event encoder function from the classes configuration.
 
@@ -349,7 +350,7 @@ def build_sound_event_encoder(
         (
             class_info.name,
             partial(
-                is_target_class,
+                _is_target_class,
                 tags={
                     get_tag_from_info(tag_info, term_registry=term_registry)
                     for tag_info in class_info.tags
@@ -409,7 +410,7 @@ def _decode_class(
 
 def build_sound_event_decoder(
     config: ClassesConfig,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
     raise_on_unmapped: bool = False,
 ) -> SoundEventDecoder:
     """Build a sound event decoder function from the classes configuration.
@@ -464,7 +465,7 @@ def build_sound_event_decoder(
 
 def build_generic_class_tags(
     config: ClassesConfig,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
 ) -> List[data.Tag]:
     """Extract and build the list of tags for the generic class from config.
 
@@ -529,7 +530,7 @@ def load_classes_config(
 def load_encoder_from_config(
     path: data.PathLike,
     field: Optional[str] = None,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
 ) -> SoundEventEncoder:
     """Load a class encoder function directly from a configuration file.
 
@@ -570,7 +571,7 @@ def load_encoder_from_config(
 def load_decoder_from_config(
     path: data.PathLike,
     field: Optional[str] = None,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
     raise_on_unmapped: bool = False,
 ) -> SoundEventDecoder:
     """Load a class decoder function directly from a configuration file.

batdetect2/targets/filtering.py

@@ -10,7 +10,7 @@ from batdetect2.targets.terms import (
     TagInfo,
     TermRegistry,
     get_tag_from_info,
-    default_term_registry,
+    term_registry,
 )
 
 __all__ = [
@@ -156,7 +156,7 @@ def equal_tags(
 
 def build_filter_from_rule(
     rule: FilterRule,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
 ) -> SoundEventFilter:
     """Creates a callable filter function from a single FilterRule.
 
@@ -243,7 +243,7 @@ class FilterConfig(BaseConfig):
 
 def build_sound_event_filter(
     config: FilterConfig,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
 ) -> SoundEventFilter:
     """Builds a merged filter function from a FilterConfig object.
 
@@ -291,7 +291,7 @@ def load_filter_config(
 def load_filter_from_config(
     path: data.PathLike,
     field: Optional[str] = None,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
 ) -> SoundEventFilter:
     """Loads filter configuration from a file and builds the filter function.
 

batdetect2/targets/rois.py

@@ -0,0 +1,511 @@
+"""Handles mapping between geometric ROIs and target representations.
+
+This module defines the interface and provides implementation for converting
+a sound event's Region of Interest (ROI), typically represented by a
+`soundevent.data.Geometry` object like a `BoundingBox`, into a format
+suitable for use as a machine learning target. This usually involves:
+
+1.  Extracting a single reference point (time, frequency) from the geometry.
+2.  Calculating relevant size dimensions (e.g., duration/width,
+    bandwidth/height) and applying scaling factors.
+
+It also provides the inverse operation: recovering an approximate geometric ROI
+(like a `BoundingBox`) from a predicted reference point and predicted size
+dimensions.
+
+This logic is encapsulated within components adhering to the `ROITargetMapper`
+protocol. Configuration for this mapping (e.g., which reference point to use,
+scaling factors) is managed by the `ROIConfig`. This module separates the
+*geometric* aspect of target definition from the *semantic* classification
+handled in `batdetect2.targets.classes`.
+"""
+
+from typing import List, Literal, Optional, Protocol, Tuple
+
+import numpy as np
+from soundevent import data
+
+from batdetect2.configs import BaseConfig, load_config
+
+Positions = Literal[
+    "bottom-left",
+    "bottom-right",
+    "top-left",
+    "top-right",
+    "center-left",
+    "center-right",
+    "top-center",
+    "bottom-center",
+    "center",
+    "centroid",
+    "point_on_surface",
+]
+
+__all__ = [
+    "ROITargetMapper",
+    "ROIConfig",
+    "BBoxEncoder",
+    "build_roi_mapper",
+    "load_roi_mapper",
+    "DEFAULT_POSITION",
+    "SIZE_WIDTH",
+    "SIZE_HEIGHT",
+    "SIZE_ORDER",
+    "DEFAULT_TIME_SCALE",
+    "DEFAULT_FREQUENCY_SCALE",
+]
+
+SIZE_WIDTH = "width"
+"""Standard name for the width/time dimension component ('width')."""
+
+SIZE_HEIGHT = "height"
+"""Standard name for the height/frequency dimension component ('height')."""
+
+SIZE_ORDER = (SIZE_WIDTH, SIZE_HEIGHT)
+"""Standard order of dimensions for size arrays ([width, height])."""
+
+DEFAULT_TIME_SCALE = 1000.0
+"""Default scaling factor for time duration."""
+
+DEFAULT_FREQUENCY_SCALE = 1 / 859.375
+"""Default scaling factor for frequency bandwidth."""
+
+
+DEFAULT_POSITION = "bottom-left"
+"""Default reference position within the geometry ('bottom-left' corner)."""
+
+
+class ROITargetMapper(Protocol):
+    """Protocol defining the interface for ROI-to-target mapping.
+
+    Specifies the methods required for converting a geometric region of interest
+    (`soundevent.data.Geometry`) into a target representation (reference point
+    and scaled dimensions) and for recovering an approximate ROI from that
+    representation.
+
+    Attributes
+    ----------
+    dimension_names : List[str]
+        A list containing the names of the dimensions returned by
+        `get_roi_size` and expected by `recover_roi`
+        (e.g., ['width', 'height']).
+    """
+
+    dimension_names: List[str]
+
+    def get_roi_position(
+        self,
+        geom: data.Geometry,
+        position: Optional[Positions] = None,
+    ) -> tuple[float, float]:
+        """Extract the reference position from a geometry.
+
+        Parameters
+        ----------
+        geom : soundevent.data.Geometry
+            The input geometry (e.g., BoundingBox, Polygon).
+        position : Positions, optional
+            Overrides the default `position` configured for the mapper.
+            If provided, this position will be used instead of the mapper's
+            internal default.
+
+        Returns
+        -------
+        Tuple[float, float]
+            The calculated reference position as (time, frequency) coordinates,
+            based on the implementing class's configuration (e.g., "center",
+            "bottom-left").
+
+        Raises
+        ------
+        ValueError
+            If the position cannot be calculated for the given geometry type
+            or configured reference point.
+        """
+        ...
+
+    def get_roi_size(self, geom: data.Geometry) -> np.ndarray:
+        """Calculate the scaled target dimensions from a geometry.
+
+        Computes the relevant size measures.
+
+        Parameters
+        ----------
+        geom : soundevent.data.Geometry
+            The input geometry.
+
+        Returns
+        -------
+        np.ndarray
+            A NumPy array containing the scaled dimensions corresponding to
+            `dimension_names`. For bounding boxes, typically contains
+            `[scaled_width, scaled_height]`.
+
+        Raises
+        ------
+        TypeError, ValueError
+            If the size cannot be computed for the given geometry type.
+        """
+        ...
+
+    def recover_roi(
+        self,
+        pos: tuple[float, float],
+        dims: np.ndarray,
+        position: Optional[Positions] = None,
+    ) -> data.Geometry:
+        """Recover an approximate ROI from a position and target dimensions.
+
+        Performs the inverse mapping: takes a reference position and the
+        predicted dimensions and reconstructs a geometric representation.
+
+        Parameters
+        ----------
+        pos : Tuple[float, float]
+            The reference position (time, frequency).
+        dims : np.ndarray
+            NumPy array containing the dimensions, matching the order
+            specified by `dimension_names`.
+        position : Positions, optional
+            Overrides the default `position` configured for the mapper.
+            If provided, this position will be used instead of the mapper's
+            internal default when reconstructing the roi geometry.
+
+        Returns
+        -------
+        soundevent.data.Geometry
+            The reconstructed geometry.
+
+        Raises
+        ------
+        ValueError
+            If the number of provided dimensions `dims` does not match
+            `dimension_names` or if reconstruction fails.
+        """
+        ...
+
+
+class ROIConfig(BaseConfig):
+    """Configuration for mapping Regions of Interest (ROIs).
+
+    Defines parameters controlling how geometric ROIs are converted into
+    target representations (reference points and scaled sizes).
+
+    Attributes
+    ----------
+    position : Positions, default="bottom-left"
+        Specifies the reference point within the geometry (e.g., bounding box)
+        to use as the target location (e.g., "center", "bottom-left").
+        See `soundevent.geometry.operations.Positions`.
+    time_scale : float, default=1000.0
+        Scaling factor applied to the time duration (width) of the ROI
+        when calculating the target size representation. Must match model
+        expectations.
+    frequency_scale : float, default=1/859.375
+        Scaling factor applied to the frequency bandwidth (height) of the ROI
+        when calculating the target size representation. Must match model
+        expectations.
+    """
+
+    position: Positions = DEFAULT_POSITION
+    time_scale: float = DEFAULT_TIME_SCALE
+    frequency_scale: float = DEFAULT_FREQUENCY_SCALE
+
+
+class BBoxEncoder(ROITargetMapper):
+    """Concrete implementation of `ROITargetMapper` focused on Bounding Boxes.
+
+    This class implements the ROI mapping protocol primarily for
+    `soundevent.data.BoundingBox` geometry. It extracts reference points,
+    calculates scaled width/height, and recovers bounding boxes based on
+    configured position and scaling factors.
+
+    Attributes
+    ----------
+    dimension_names : List[str]
+        Specifies the output dimension names as ['width', 'height'].
+    position : Positions
+        The configured reference point type (e.g., "center", "bottom-left").
+    time_scale : float
+        The configured scaling factor for the time dimension (width).
+    frequency_scale : float
+        The configured scaling factor for the frequency dimension (height).
+    """
+
+    dimension_names = [SIZE_WIDTH, SIZE_HEIGHT]
+
+    def __init__(
+        self,
+        position: Positions = DEFAULT_POSITION,
+        time_scale: float = DEFAULT_TIME_SCALE,
+        frequency_scale: float = DEFAULT_FREQUENCY_SCALE,
+    ):
+        """Initialize the BBoxEncoder.
+
+        Parameters
+        ----------
+        position : Positions, default="bottom-left"
+            Reference point type within the bounding box.
+        time_scale : float, default=1000.0
+            Scaling factor for time duration (width).
+        frequency_scale : float, default=1/859.375
+            Scaling factor for frequency bandwidth (height).
+        """
+        self.position: Positions = position
+        self.time_scale = time_scale
+        self.frequency_scale = frequency_scale
+
+    def get_roi_position(
+        self,
+        geom: data.Geometry,
+        position: Optional[Positions] = None,
+    ) -> Tuple[float, float]:
+        """Extract the configured reference position from the geometry.
+
+        Uses `soundevent.geometry.get_geometry_point`.
+
+        Parameters
+        ----------
+        geom : soundevent.data.Geometry
+            Input geometry (e.g., BoundingBox).
+        position : Positions, optional
+            Overrides the default `position` configured for the encoder.
+            If provided, this position will be used instead of `self.position`.
+
+        Returns
+        -------
+        Tuple[float, float]
+            Reference position (time, frequency).
+        """
+        from soundevent import geometry
+
+        position = position or self.position
+        return geometry.get_geometry_point(geom, position=position)
+
+    def get_roi_size(self, geom: data.Geometry) -> np.ndarray:
+        """Calculate the scaled [width, height] from the geometry's bounds.
+
+        Computes the bounding box, extracts duration and bandwidth, and applies
+        the configured `time_scale` and `frequency_scale`.
+
+        Parameters
+        ----------
+        geom : soundevent.data.Geometry
+            Input geometry.
+
+        Returns
+        -------
+        np.ndarray
+            A 1D NumPy array: `[scaled_width, scaled_height]`.
+        """
+        from soundevent import geometry
+
+        start_time, low_freq, end_time, high_freq = geometry.compute_bounds(
+            geom
+        )
+        return np.array(
+            [
+                (end_time - start_time) * self.time_scale,
+                (high_freq - low_freq) * self.frequency_scale,
+            ]
+        )
+
+    def recover_roi(
+        self,
+        pos: tuple[float, float],
+        dims: np.ndarray,
+        position: Optional[Positions] = None,
+    ) -> data.Geometry:
+        """Recover a BoundingBox from a position and scaled dimensions.
+
+        Un-scales the input dimensions using the configured factors and
+        reconstructs a `soundevent.data.BoundingBox` centered or anchored at
+        the given reference `pos` according to the configured `position` type.
+
+        Parameters
+        ----------
+        pos : Tuple[float, float]
+            Reference position (time, frequency).
+        dims : np.ndarray
+            NumPy array containing the *scaled* dimensions, expected order is
+            [scaled_width, scaled_height].
+        position : Positions, optional
+            Overrides the default `position` configured for the encoder.
+            If provided, this position will be used instead of `self.position`
+            when reconstructing the bounding box.
+
+        Returns
+        -------
+        soundevent.data.BoundingBox
+            The reconstructed bounding box.
+
+        Raises
+        ------
+        ValueError
+            If `dims` does not have the expected shape (length 2).
+        """
+        position = position or self.position
+
+        if dims.ndim != 1 or dims.shape[0] != 2:
+            raise ValueError(
+                "Dimension array does not have the expected shape. "
+                f"({dims.shape = }) != ([2])"
+            )
+
+        width, height = dims
+        return _build_bounding_box(
+            pos,
+            duration=float(width) / self.time_scale,
+            bandwidth=float(height) / self.frequency_scale,
+            position=self.position,
+        )
+
+
+def build_roi_mapper(config: ROIConfig) -> ROITargetMapper:
+    """Factory function to create an ROITargetMapper from configuration.
+
+    Currently creates a `BBoxEncoder` instance based on the provided
+    `ROIConfig`.
+
+    Parameters
+    ----------
+    config : ROIConfig
+        Configuration object specifying ROI mapping parameters.
+
+    Returns
+    -------
+    ROITargetMapper
+        An initialized `BBoxEncoder` instance configured with the settings
+        from `config`.
+    """
+    return BBoxEncoder(
+        position=config.position,
+        time_scale=config.time_scale,
+        frequency_scale=config.frequency_scale,
+    )
+
+
+def load_roi_mapper(
+    path: data.PathLike, field: Optional[str] = None
+) -> ROITargetMapper:
+    """Load ROI mapping configuration from a file and build the mapper.
+
+    Convenience function that loads an `ROIConfig` from the specified file
+    (and optional field) and then uses `build_roi_mapper` to create the
+    corresponding `ROITargetMapper` instance.
+
+    Parameters
+    ----------
+    path : PathLike
+        Path to the configuration file (e.g., YAML).
+    field : str, optional
+        Dot-separated path to a nested section within the file containing the
+        ROI configuration. If None, the entire file content is used.
+
+    Returns
+    -------
+    ROITargetMapper
+        An initialized ROI mapper instance based on the configuration file.
+
+    Raises
+    ------
+    FileNotFoundError, yaml.YAMLError, pydantic.ValidationError, KeyError,
+    TypeError
+        If the configuration file cannot be found, parsed, validated, or if
+        the specified `field` is invalid.
+    """
+    config = load_config(path=path, schema=ROIConfig, field=field)
+    return build_roi_mapper(config)
+
+
+VALID_POSITIONS = [
+    "bottom-left",
+    "bottom-right",
+    "top-left",
+    "top-right",
+    "center-left",
+    "center-right",
+    "top-center",
+    "bottom-center",
+    "center",
+    "centroid",
+    "point_on_surface",
+]
+
+
+def _build_bounding_box(
+    pos: tuple[float, float],
+    duration: float,
+    bandwidth: float,
+    position: Positions = DEFAULT_POSITION,
+) -> data.BoundingBox:
+    """Construct a BoundingBox from a reference point, size, and position type.
+
+    Internal helper for `BBoxEncoder.recover_roi`. Calculates the box
+    coordinates [start_time, low_freq, end_time, high_freq] based on where
+    the input `pos` (time, freq) is located relative to the box (e.g.,
+    center, corner).
+
+    Parameters
+    ----------
+    pos : Tuple[float, float]
+        Reference position (time, frequency).
+    duration : float
+        The required *unscaled* duration (width) of the bounding box.
+    bandwidth : float
+        The required *unscaled* frequency bandwidth (height) of the bounding
+        box.
+    position : Positions, default="bottom-left"
+        Specifies which part of the bounding box the input `pos` corresponds to.
+
+    Returns
+    -------
+    data.BoundingBox
+        The constructed bounding box object.
+
+    Raises
+    ------
+    ValueError
+        If `position` is not a recognized value or format.
+    """
+    time, freq = map(float, pos)
+    duration = max(0, duration)
+    bandwidth = max(0, bandwidth)
+    if position in ["center", "centroid", "point_on_surface"]:
+        return data.BoundingBox(
+            coordinates=[
+                max(time - duration / 2, 0),
+                max(freq - bandwidth / 2, 0),
+                max(time + duration / 2, 0),
+                max(freq + bandwidth / 2, 0),
+            ]
+        )
+
+    if position not in VALID_POSITIONS:
+        raise ValueError(
+            f"Invalid position: {position}. "
+            f"Valid options are: {VALID_POSITIONS}"
+        )
+
+    y, x = position.split("-")
+
+    start_time = {
+        "left": time,
+        "center": time - duration / 2,
+        "right": time - duration,
+    }[x]
+
+    low_freq = {
+        "bottom": freq,
+        "center": freq - bandwidth / 2,
+        "top": freq - bandwidth,
+    }[y]
+
+    return data.BoundingBox(
+        coordinates=[
+            max(0, start_time),
+            max(0, low_freq),
+            max(0, start_time + duration),
+            max(0, low_freq + bandwidth),
+        ]
+    )

batdetect2/targets/terms.py

@@ -230,12 +230,11 @@ class TermRegistry(Mapping[str, data.Term]):
         del self._terms[key]
 
 
-default_term_registry = TermRegistry(
+term_registry = TermRegistry(
     terms=dict(
         [
             *getmembers(terms, lambda x: isinstance(x, data.Term)),
             ("event", call_type),
-            ("species", terms.scientific_name),
             ("individual", individual),
             ("data_source", data_source),
             (GENERIC_CLASS_KEY, generic_class),
@@ -253,7 +252,7 @@ is explicitly passed.
 
 def get_term_from_key(
     key: str,
-    term_registry: Optional[TermRegistry] = None,
+    term_registry: TermRegistry = term_registry,
 ) -> data.Term:
     """Convenience function to retrieve a term by key from a registry.
 
@@ -278,13 +277,10 @@ def get_term_from_key(
     KeyError
         If the key is not found in the specified registry.
     """
-    term_registry = term_registry or default_term_registry
     return term_registry.get_term(key)
 
 
-def get_term_keys(
+def get_term_keys(term_registry: TermRegistry = term_registry) -> List[str]:
-    term_registry: TermRegistry = default_term_registry,
-) -> List[str]:
     """Convenience function to get all registered keys from a registry.
 
     Uses the global default registry unless a specific `term_registry`
@@ -303,9 +299,7 @@ def get_term_keys(
     return term_registry.get_keys()
 
 
-def get_terms(
+def get_terms(term_registry: TermRegistry = term_registry) -> List[data.Term]:
-    term_registry: TermRegistry = default_term_registry,
-) -> List[data.Term]:
     """Convenience function to get all registered terms from a registry.
 
     Uses the global default registry unless a specific `term_registry`
@@ -348,7 +342,7 @@ class TagInfo(BaseModel):
 
 def get_tag_from_info(
     tag_info: TagInfo,
-    term_registry: Optional[TermRegistry] = None,
+    term_registry: TermRegistry = term_registry,
 ) -> data.Tag:
     """Creates a soundevent.data.Tag object from TagInfo data.
 
@@ -374,7 +368,6 @@ def get_tag_from_info(
         If the term key specified in `tag_info.key` is not found
         in the registry.
     """
-    term_registry = term_registry or default_term_registry
     term = get_term_from_key(tag_info.key, term_registry=term_registry)
     return data.Tag(term=term, value=tag_info.value)
 
@@ -446,7 +439,7 @@ class TermConfig(BaseModel):
 def load_terms_from_config(
     path: data.PathLike,
     field: Optional[str] = None,
-    term_registry: TermRegistry = default_term_registry,
+    term_registry: TermRegistry = term_registry,
 ) -> Dict[str, data.Term]:
     """Loads term definitions from a configuration file and registers them.
 
@@ -497,6 +490,6 @@ def load_terms_from_config(
 
 
 def register_term(
-    key: str, term: data.Term, registry: TermRegistry = default_term_registry
+    key: str, term: data.Term, registry: TermRegistry = term_registry
 ) -> None:
     registry.add_term(key, term)

batdetect2/targets/transform.py

@@ -21,6 +21,9 @@ from batdetect2.targets.terms import (
     get_tag_from_info,
     get_term_from_key,
 )
+from batdetect2.targets.terms import (
+    term_registry as default_term_registry,
+)
 
 __all__ = [
     "DerivationRegistry",
@@ -31,7 +34,7 @@ __all__ = [
     "TransformConfig",
     "build_transform_from_rule",
     "build_transformation_from_config",
-    "default_derivation_registry",
+    "derivation_registry",
     "get_derivation",
     "load_transformation_config",
     "load_transformation_from_config",
@@ -395,7 +398,7 @@ class DerivationRegistry(Mapping[str, Derivation]):
         return list(self._derivations.values())
 
 
-default_derivation_registry = DerivationRegistry()
+derivation_registry = DerivationRegistry()
 """Global instance of the DerivationRegistry.
 
 Register custom derivation functions here to make them available by key
@@ -406,7 +409,7 @@ in `DeriveTagRule` configuration.
 def get_derivation(
     key: str,
     import_derivation: bool = False,
-    registry: Optional[DerivationRegistry] = None,
+    registry: DerivationRegistry = derivation_registry,
 ):
     """Retrieve a derivation function by key, optionally importing it.
 
@@ -440,8 +443,6 @@ def get_derivation(
     AttributeError
         If dynamic import fails because the function name isn't in the module.
     """
-    registry = registry or default_derivation_registry
-
     if not import_derivation or key in registry:
         return registry.get_derivation(key)
 
@@ -457,16 +458,10 @@ def get_derivation(
         ) from err
 
 
-TranformationRule = Annotated[
-    Union[ReplaceRule, MapValueRule, DeriveTagRule],
-    Field(discriminator="rule_type"),
-]
-
-
 def build_transform_from_rule(
-    rule: TranformationRule,
+    rule: Union[ReplaceRule, MapValueRule, DeriveTagRule],
-    derivation_registry: Optional[DerivationRegistry] = None,
+    derivation_registry: DerivationRegistry = derivation_registry,
-    term_registry: Optional[TermRegistry] = None,
+    term_registry: TermRegistry = default_term_registry,
 ) -> SoundEventTransformation:
     """Build a specific SoundEventTransformation function from a rule config.
 
@@ -564,8 +559,8 @@ def build_transform_from_rule(
 
 def build_transformation_from_config(
     config: TransformConfig,
-    derivation_registry: Optional[DerivationRegistry] = None,
+    derivation_registry: DerivationRegistry = derivation_registry,
-    term_registry: Optional[TermRegistry] = None,
+    term_registry: TermRegistry = default_term_registry,
 ) -> SoundEventTransformation:
     """Build a composite transformation function from a TransformConfig.
 
@@ -586,7 +581,6 @@ def build_transformation_from_config(
     SoundEventTransformation
         A single function that applies all configured transformations in order.
     """
-
     transforms = [
         build_transform_from_rule(
             rule,
@@ -596,16 +590,14 @@ def build_transformation_from_config(
         for rule in config.rules
     ]
 
-    return partial(apply_sequence_of_transforms, transforms=transforms)
+    def transformation(
+        sound_event_annotation: data.SoundEventAnnotation,
+    ) -> data.SoundEventAnnotation:
+        for transform in transforms:
+            sound_event_annotation = transform(sound_event_annotation)
+        return sound_event_annotation
 
-
+    return transformation
-def apply_sequence_of_transforms(
-    sound_event_annotation: data.SoundEventAnnotation,
-    transforms: list[SoundEventTransformation],
-) -> data.SoundEventAnnotation:
-    for transform in transforms:
-        sound_event_annotation = transform(sound_event_annotation)
-    return sound_event_annotation
 
 
 def load_transformation_config(
@@ -639,8 +631,8 @@ def load_transformation_config(
 def load_transformation_from_config(
     path: data.PathLike,
     field: Optional[str] = None,
-    derivation_registry: Optional[DerivationRegistry] = None,
+    derivation_registry: DerivationRegistry = derivation_registry,
-    term_registry: Optional[TermRegistry] = None,
+    term_registry: TermRegistry = default_term_registry,
 ) -> SoundEventTransformation:
     """Load transformation config from a file and build the final function.
 
@@ -685,7 +677,7 @@ def load_transformation_from_config(
 def register_derivation(
     key: str,
     derivation: Derivation,
-    derivation_registry: Optional[DerivationRegistry] = None,
+    derivation_registry: DerivationRegistry = derivation_registry,
 ) -> None:
     """Register a new derivation function in the global registry.
 
@@ -704,5 +696,4 @@ def register_derivation(
     KeyError
         If a derivation function with the same key is already registered.
     """
-    derivation_registry = derivation_registry or default_derivation_registry
     derivation_registry.register(key, derivation)

batdetect2/targets/types.py

@@ -19,16 +19,8 @@ from soundevent import data
 
 __all__ = [
     "TargetProtocol",
-    "Position",
-    "Size",
 ]
 
-Position = tuple[float, float]
-"""A tuple representing (time, frequency) coordinates."""
-
-Size = np.ndarray
-"""A NumPy array representing the size dimensions of a target."""
-
 
 class TargetProtocol(Protocol):
     """Protocol defining the interface for the target definition pipeline.
@@ -110,7 +102,7 @@ class TargetProtocol(Protocol):
         """
         ...
 
-    def encode_class(
+    def encode(
         self,
         sound_event: data.SoundEventAnnotation,
     ) -> Optional[str]:
@@ -131,7 +123,7 @@ class TargetProtocol(Protocol):
         """
         ...
 
-    def decode_class(self, class_label: str) -> List[data.Tag]:
+    def decode(self, class_label: str) -> List[data.Tag]:
         """Decode a predicted class name back into representative tags.
 
         Parameters
@@ -155,9 +147,9 @@ class TargetProtocol(Protocol):
         """
         ...
 
-    def encode_roi(
+    def get_position(
         self, sound_event: data.SoundEventAnnotation
-    ) -> tuple[Position, Size]:
+    ) -> tuple[float, float]:
         """Extract the target reference position from the annotation's geometry.
 
         Calculates the `(time, frequency)` coordinate representing the primary
@@ -181,12 +173,36 @@ class TargetProtocol(Protocol):
         """
         ...
 
-    # TODO: Update docstrings
+    def get_size(self, sound_event: data.SoundEventAnnotation) -> np.ndarray:
-    def decode_roi(
+        """Calculate the target size dimensions from the annotation's geometry.
-        self,
+
-        position: Position,
+        Computes the relevant physical size (e.g., duration/width,
-        size: Size,
+        bandwidth/height from a bounding box) to produce
-        class_name: Optional[str] = None,
+        the numerical target values expected by the model.
+
+        Parameters
+        ----------
+        sound_event : data.SoundEventAnnotation
+            The annotation containing the geometry (ROI) to process.
+
+        Returns
+        -------
+        np.ndarray
+            A NumPy array containing the size dimensions, matching the
+            order specified by the `dimension_names` attribute (e.g.,
+            `[width, height]`).
+
+        Raises
+        ------
+        ValueError
+            If the annotation lacks geometry or if the size cannot be computed.
+        TypeError
+            If geometry type is unsupported.
+        """
+        ...
+
+    def recover_roi(
+        self, pos: tuple[float, float], dims: np.ndarray
     ) -> data.Geometry:
         """Recover the ROI geometry from a position and dimensions.
 
@@ -201,8 +217,6 @@ class TargetProtocol(Protocol):
         dims : np.ndarray
             The NumPy array containing the dimensions (e.g., predicted
             by the model), corresponding to the order in `dimension_names`.
-        class_name: str
-            class
 
         Returns
         -------

batdetect2/train/callbacks.py

@@ -97,7 +97,7 @@ def _is_in_subclip(
     start_time: float,
     end_time: float,
 ) -> bool:
-    (time, _), _ = targets.encode_roi(sound_event_annotation)
+    time, _ = targets.get_position(sound_event_annotation)
     return start_time <= time <= end_time
 
 

batdetect2/train/labels.py

@@ -138,7 +138,7 @@ def generate_clip_label(
     logger.debug(
         "Will generate heatmaps for clip annotation {uuid} with {num} annotated sound events",
         uuid=clip_annotation.uuid,
-        num=len(clip_annotation.sound_events),
+        num=len(clip_annotation.sound_events)
     )
 
     sound_events = []
@@ -260,7 +260,7 @@ def generate_heatmaps(
             continue
 
         # Get the position of the sound event
-        (time, frequency), size = targets.encode_roi(sound_event_annotation)
+        time, frequency = targets.get_position(sound_event_annotation)
 
         # Set 1.0 at the position of the sound event in the detection heatmap
         try:
@@ -280,6 +280,8 @@ def generate_heatmaps(
             )
             continue
 
+        size = targets.get_size(sound_event_annotation)
+
         size_heatmap = arrays.set_value_at_pos(
             size_heatmap,
             size,
@@ -289,7 +291,7 @@ def generate_heatmaps(
 
         # Get the class name of the sound event
         try:
-            class_name = targets.encode_class(sound_event_annotation)
+            class_name = targets.encode(sound_event_annotation)
         except ValueError as e:
             logger.warning(
                 "Skipping annotation %s: Unexpected error while encoding "

notebooks/signal_generation.py

@@ -1,19 +0,0 @@
-import marimo
-
-__generated_with = "0.13.15"
-app = marimo.App(width="medium")
-
-
-@app.cell
-def _():
-    from batdetect2.preprocess import build_preprocessor
-    return
-
-
-@app.cell
-def _():
-    return
-
-
-if __name__ == "__main__":
-    app.run()